title: Plasmacytoid dendritic cells from healthy donor HD1

description:
HD1_dendP
mRNA-3' from plasmacytoid dendritic cells sorted from healthy donor

value: No

value: peripheral blood


title: auCC9, Whole mucosa (colon)

status: Public on May 03 2021

type: SRA

city: Kiel

first: Celia

last: Escudero-Hernández

state: Schleswig-Holstein

address: Institute of Clinical Molecular Biology (IKMB), Am Bota

department: Dep. Cell Biology

country: Germany

institute: University Hospital Schleswig-Holstein

description: paired with itCC9

library_source: transcriptomic

data_processing:
FASTQ files were generated using bcl2fastq software v2.18. Data was analyzed using the R Bioconductor software v3.5.1 (R Core Team 2018), including SARTools v1.6.6 and DESeq2 v1.22.1 packages
Differential gene expression (DGE) from RNA-seq data was determined with linear models using DESeq2 v1.22.1 and significance decided by Benjamini-Hochberg false discovery rate (FDR) adjusted p-values <0.05
Genome_build: Ensembl GRCh38 genome version, release 92
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: Whole mucosa (colon)

extract_protocol:
Biopsies were homogenized in RLT buffer from RNeasy Mini Kit (Qiagen, Hilden, Germany) supplemented with 1% 2-mercaptoethanol using a T10 Ultra Turrax homogenizer (IKA, ThermoFisher Scientific). Total RNA from homogenized biopsy samples was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions
RNA sequencing libraries were constructed with SENSE totalRNA with Ribo cop rRNA depletion (Lexogene GmbH, Vienna, Austria), and single-read sequenced for 75 cycles to a depth of 25 million base reads on a HiSeq4000 instrument (Illumina, San Diego, CA), according to the manufacturer’s recommendations

tag: tissue

value: colon

tag: disease activity

value: Active CC

tag: treatment

tag: gender

value: female

tag: age


title: Basophils from healthy donor HD1

city: New York

first: Juan-Jose

last: Garces

state: New York

address: 321 E 61st St

country: USA

institute: Memorial Sloan Kettering Cancer Center

description:
HD1_basos
mRNA-3' from basophils sorted from healthy donor

data_processing:
FASTQ polyA trimming
STAR alignment (version 2.7.3a): outFilterMismatchNmax 1, alignEndsType EndToEnd
Gene counts performed using quant3p
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix counts. Each column corresponds to gene counts for each generated BAM (after merging all resequenced samples and downsampled to 10 millions of reads for each one).

source_name: Basophils from peripheral blood

extract_protocol:
Cells were FACSorted in Lysis Binding Buffer and mRNA was extracted through Dynabeads polyT
RNA was sample-barcodad by a RT reaction. After, cDNA was purified with SPRIselect and amplified using the T7 promotor as template. RNA molecules were fragmented and purified again. Afterwards, a ssRNA adaptor was ligated to the 3’-end of the RNA fragments and, finally, cDNA was amplified.

tag: individual

value: healthy donor HD1

tag: covid status

value: Healthy donor

value: Female

tag: hospitalization

tag: exitus

tag: haematological tumor

tag: cell type

value: Basophils

tag: number of cells


title: Bulk_Mouse_038_Tfr_PBS

city: La Jolla

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Division of Vaccine Discovery

institute: La Jolla Institute for Allergy and Immunology

description: Whole Transcriptome Amplification (Smart-seq2 - Picelli et al.2014)

data_processing:
Bulk RNA–seq data were mapped against the mouse mm10 reference genome using TopHat (v2.0.9 , (--library-type fr-unstranded --no-coverage-search
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
Genome_build: mm10
Supplementary_files_format_and_content: Bulk_Mouse_RawCounts.txt contains raw counts of sequencing reads obtained with HTSeq-count
Supplementary_files_format_and_content: Bulk_Mouse_TPM.txt contains Transcript per Million normalized counts

molecule: polyA RNA

organism: Mus musculus

source_name: murine infection model

growth_protocol: Cell types were isolated from tissue samples and directly sorted by Flow cytometry into trizol or lysis buffer. No particular cell growth procedure was required.

extract_protocol:
RNA-seq was performed as described previously by Seumois et al 2016 and Ganesan et al 2017 using smart-seq2 method  with 0.5ng of total RNA. Total RNA was purified using a miRNAeasy kit (Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
Barcoded Illumina sequencing libraries were constructed as per the protocol described by illumina (Nextera XT library preparation kit, Illumina).
DNA sequencing - Libraries were sequenced on the NovaSeq6000 to obtain 50-bp paired end reads (barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina)).

treatment_protocol: Mice were immunzied with either mock PBS or 100ug Ovalbumin with either Complete Freund's adjuvant or MPLA.

tag: cell type surface markers

value: Tfr

tag: donor #

value: PBS


title: Bulk_Human_Donor006_Tfr

data_processing:
Bulk RNA–seq data were mapped against the human hg19 reference genome using TopHat (v2.0.9 , (--library-type fr-unstranded --no-coverage-search
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
Genome_build: hg19
Supplementary_files_format_and_content: Bulk_Human_RawCounts.txt contains raw counts of sequencing reads obtained with HTSeq-count
Supplementary_files_format_and_content: Bulk_Human_TPM.txt contains Transcript per Million normalized counts

source_name: Human cancer tissue

extract_protocol:
RNA-seq was performed as described previously by Seumois et al 2016 and Ganesan et al 2017 using smart-seq2 method  with 0.5ng of total RNA. Total RNA was purified using a miRNAeasy kit (Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
Barcoded Illumina sequencing libraries were constructed as per the protocol described by illumina (Nextera XT library preparation kit, Illumina).
DNA sequencing - Libraries were sequenced on the HiSeq2500 Illumina platform to obtain 50-bp single end reads and on the NovaSeq6000 to obtain 50-bp paired end reads (barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina)).


title: Bulk_Mouse_014_Treg_MPLA

value: Treg

value: MPLA


title: auCC7, Whole mucosa (colon)

description: paired with itCC7


title: Bulk_Human_Donor005_Tfr


title: Bulk_Mouse_040_Treg_PBS


title: Bulk_Mouse_006_Treg_MPLA


title: auCC8, Whole mucosa (colon)

description: paired with itCC8

value: male


title: Bulk_Mouse_032_Tfr_OC

value: OC


title: Plasmacytoid dendritic cells from healthy donor HD1 (resequenced)

description:
HD1_dendP_reseq420
mRNA-3' from plasmacytoid dendritic cells sorted from healthy donor

source_name: Plasmacytoid dendritic cells from peripheral blood

value: Plasmacytoid dendritic cells


title: Bulk_Mouse_035_Tfr_PBS


title: auCC6, Whole mucosa (colon)

description: paired with itCC6


title: Bulk_Mouse_028_Tfr_OC


title: Bulk_Human_Donor003_Tfr


title: auCC5, Whole mucosa (colon)

description: paired with itCC5


title: Bulk_Human_Donor002_Tfr


title: auCC4, Whole mucosa (colon)

description: paired with itCC4


title: Bulk_Mouse_020_Tfr_OC


title: Bulk_Mouse_012_Tfr_MPLA


title: Bulk_Mouse_016_Tfr_MPLA


title: ID_006553_FuP_S_tex_C

city: Würzburg

first: Falk

last: Ponath

address: Josef-Schneider-Straße 2

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

description: the bacterium was grown to stationary phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 3

data_processing:
Reads were trimmed for the NEBNext adapter sequence using Cutadapt version 2.5 with default parameters. In addition, Cutadapt was given the –nextseq-trim=20 switch to handle two colour sequencing chemistry. Reads that were trimmed to length=0 were discarded.The READemption pipeline version 4.5 (Förstner et al., 2014) with segemehl version 0.2 (Otto et al., 2014) was used for read mapping and calculation of read counts. Reads were mapped on CP010905.2 with additional annotations for ncRNAs, 3’UTRs and 5’UTRs. For the prediction of transcriptional start sites (TSS) and small regulatory RNAs (sRNA), we used the modular, command-line tool ANNOgesic (Yu et al., 2018). All parameters were kept at the default setting, unless stated otherwise.  Secondary TSSs were excluded if a primary TSS was within seven nucleotides distance. For annotation of 5’ untranslated regions (5’UTRs) the default settings for maximum length was corrected to 300 nt.  For the prediction of sRNA, we used the default settings, that is, the transcript must have a predicted TSS or PS at their 5’end, form a stable secondary structure (calculated with RNAfold from Vienna RNA package), and a length between 30 to 500 nt. For 5’UTR-derived sRNA the transcripts must have a processing site (PS) at their 3’end. For 3’UTR-derived sRNA the transcript can either have a TSS or PS at their 5’end and share its terminator with the parental gene.
Genome_build: NZ_CP007062.1 (FNA); NC_022196.1 (FNV); NZ_CP028108.1 (FuP)
Supplementary_files_format_and_content: wiggle

organism: Fusobacterium periodonticum 2_1_31

source_name: gift from Emma Allen-Vercoe (University of Guelph)

growth_protocol: Growth was performed in Columbia broth at 37°C inside an anaerobic chamber. Pre-cultures were inoculated with a signel colony. After 24h, the working cultures were inoculated at a dilution 1:50 and samples taken at the indicated growth stages.

extract_protocol:
Total RNA was extracted using the hot phenol protocol. Bacterial cultures were grown to the desired OD600, mixed with 0.2 volumes of STOP solution (95 % ethanol, 5 % phenol) and snap-frozen at – 80 °C if not directly processed. The bacterial solution was centrifuged for 20 min, 4500 rpm at 4 °C and the supernatant was completely discarded. Cells were suspended in 600 μl of 10 mg/ml lysozyme in TE buffer (pH 8.0) and incubated at 37 °C for 10 min. Next, 60 μl of 10 % w/v SDS was added and everything mixed by inversion. Samples were incubated in a water bath at 64 °C, 1-2 min before adding 66 μl 3 M NaOAc, pH 5.2. Next, 750 μl acid phenol (Roti-Aqua phenol) was added, followed by incubation for 5 min. at 64 °C. Samples were briefly placed on ice to cool before centrifugation for 15 min, 13,000 rpm at 4 °C. The aqueous layer was transferred into a 2 ml phase lock gel tube (Eppendorf), 750 μl chloroform (Roth, #Y015.2) was added, and everything centrifuged for 12 min, 13,000 rpm at room temperature. For ethanol precipitation, the aqueous layer was transferred to a fresh tube, 2 volumes of 30:1 mix (EtOH:3 M NaOAc, pH 6.5) was added and incubated overnight at -20 °C. Precipitated RNA was harvested by centrifugation, washed with cold 75 % v/v ethanol and air-dried. Purified RNA was resuspended in 50 µl RNase-free water and stored at -80 °C.
Library preparation for dRNA-seq was accomplished by Vertis Biotechnology AG. In brief, total RNA was analyzed on a Shimadzu MultiNA microchip electrophoresis system. 23S/16S ratio for all samples was 1.3. RNA was fragmented via ultrasound (4 pulses a 30 sec, 4 °C) and subsequently treated with T4 Polynucleotide Kinase (NEB). Half of the samples were then treated with terminator exonuclease (TEX) for dRNA-seq. For the cDNA synthesis, the RNA fragments were poly(A)-tailed and 5’PPP structures were removed with RNA 5’ Polyphosphatase (Epicentre). The RNA sequencing adapter with the barcodes were ligated to the 5’-monophosphate of the fragments. First strand cDNA was synthesized with an oligo(dT)-adapter primer and M-MLV reverse transcriptase. Amplification of cDNA was done via PCR to an approximate amount of 10 20 ng/µl. cDNA was purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed with Shimadzu MultiNA microchip electrophoresis. Equimolar amounts of the samples were pooled for sequencing. cDNAs had a size between 200 and 550 bp. The library pool was fractionated via differential clean-up with the Agencourt AMPure kit. The cDNA pool was checked with capillary electrophoresis as stated above. Libraries were sequenced on an Illumina NextSeq 500 system using 75 bp read length.

treatment_protocol: see description of samples

value: TEX treated


title: Bulk_Human_Donor004_Tfr


title: auCC3, Whole mucosa (colon)

description: paired with itCC3

value: No


title: ID_006551_FuP_S_tex_A

description: the bacterium was grown to stationary phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 1


title: ID_006550_FuP_M_tex_C

description: the bacterium was grown to mid-exponential phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 3


title: ID_006552_FuP_S_tex_B

description: the bacterium was grown to stationary phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 2


title: Hc13, Whole mucosa (colon)


title: Bulk_Mouse_008_Tfr_MPLA


title: ID_006549_FuP_M_tex_B

description: the bacterium was grown to mid-exponential phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 2


title: Bulk_Mouse_004_Tfr_MPLA


title: Hc12, Whole mucosa (colon)


title: ID_006548_FuP_M_tex_A

description: the bacterium was grown to mid-exponential phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 1


title: Bulk_Mouse_024_Tfr_OC


title: auCC2, Whole mucosa (colon)

description: paired with itCC2


title: ID_006547_FuP_E_tex_C

description: the bacterium was grown to early exponential phase and samples collected for RNA extraction; RNA was split for untreated and TEX treated libraries; bio. Replicate 3


title: Hc11, Whole mucosa (colon)


title: Bulk_Mouse_037_Tfh_PBS

value: Tfh


title: Bulk_Mouse_034_Tfh_PBS


title: ID_006545_FuP_E_tex_A

description: the bacterium was grown to early exponential phase and samples collected for RNA extraction; RNA was split for untreated and TEX treated libraries; bio. Replicate 1


title: auCC1, Whole mucosa (colon)

description: paired with itCC1

value: colon


title: ID_006544_FuP_S_notex_C

value: untreated


title: Bulk_Mouse_027_Tfh_OC


title: ID_006546_FuP_E_tex_B

description: the bacterium was grown to early exponential phase and samples collected for RNA extraction; RNA was split for untreated and TEX treated libraries; bio. Replicate 2


title: Hc6, Whole mucosa (colon)

value: female


title: Bulk_Mouse_031_Tfh_OC


title: Bulk_Mouse_023_Tfh_OC


title: Hc7, Whole mucosa (colon)


title: Hc9, Whole mucosa (colon)


title: ID_006543_FuP_S_notex_B


title: Hc10, Whole mucosa (colon)


title: ID_006542_FuP_S_notex_A


title: Hc8, Whole mucosa (colon)


title: Bulk_Mouse_015_Tfh_MPLA


title: ID_006541_FuP_M_notex_C


title: Bulk_Mouse_019_Tfh_OC


title: Hc5, Whole mucosa (colon)


title: Bulk_Mouse_041_Tfh_PBS


title: Hc3, Whole mucosa (colon)


title: ID_006540_FuP_M_notex_B


title: Hc4, Whole mucosa (colon)


title: ID_006539_FuP_M_notex_A


title: Hc2, Whole mucosa (colon)


title: Bulk_Mouse_007_Tfh_MPLA


title: Hc1, Whole mucosa (colon)


title: Bulk_Mouse_003_Tfh_MPLA


title: ID_006537_FuP_E_notex_B


title: Bulk_Mouse_025_Teff_OC

value: Teff


title: Bulk_Mouse_029_Teff_OC


title: Bulk_Mouse_039_Teff_PBS


title: ID_006588_FNA_S_tex_B

organism: Fusobacterium animalis 7_1


title: ID_006536_FuP_E_notex_A


title: Bulk_Mouse_017_Teff_OC


title: Bulk_Mouse_013_Teff_MPLA


title: ID_006585_FNA_M_tex_B


title: Bulk_Mouse_009_Teff_MPLA


title: aRCC5, Colonic IEC

source_name: Colonic IEC

extract_protocol:
RNA from laser capture microdissection (LCM) material was isolated with RNeasy FFPE kit (Qiagen, following the manufacturer's instructions)
RNA sequencing libraries were constructed with SENSE totalRNA with Ribo cop rRNA depletion (Lexogene GmbH, Vienna, Austria), and single-read sequenced for 75 cycles to a depth of 25 million base reads on a HiSeq4000 instrument (Illumina, San Diego, CA), according to the manufacturer’s recommendations

treatment_protocol: Colonic biopsy samples collected in PBS were fixed in paraformaldehyde and embedded in paraffin (FFPE samples). Samples were cut into 10 µm sections and mounted on RNase-free MMI Membrane Slides (Molecular Machines and Industry, MMI AG, Eching, Germany); afterwards, samples were stained with hematoxylin following standard protocols. The sections were dehydrated with 100% ethanol and xylene, followed by air-drying in a desiccator for at least 30 min. Intestinal epithelial cells (area of 106 µm2, corresponding to approx. 104 cells) were isolated from all samples with a UV-LCM MMI Cellcut device connected to an Olympus IX71 microscope, and collected in MMI isolation caps with diffuser (all from MMI AG), following the manufacturer’s recommendations. Isolated intestinal epithelial cells (IEC) were kept in PKD lysis buffer from RNeasy FFPE kit (Qiagen, Hilden, Germany) at -80ºC until RNA was isolated.

value: Active CC


title: aRCC8, Colonic IEC


title: aRCC7, Colonic IEC


title: aRCC6, Colonic IEC


title: ID_006586_FNA_M_tex_C


title: WT_cyclo_contra_rep3

city: Tucson

first: Danielle

last: Becktel

state: AZ

address: 1656 E Mabel Street, Rm 214

department: Immunobiology

institute: University of Arizona

data_processing:
Sequenced reads were demultiplexed using bcl2fastq v2.19 and trimmed of their indexing adaptors using Trimmomatic v0.32
Trimmed reads were aligned to GRCm38 reference genome using STAR v2.5.2b
Gene expression was calculated using htseq-count function in the HTSeq python tool
Genes were annotated using BioMart database
Differentially expressed genes (>2-fold and FDR-adjusted p-value <0.05) were identified by DESeq2
Genome_build: mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include counts for each gene

source_name: Brain

extract_protocol:
Fresh brain tissue dissected from WT mice was immersed in RNAlater (Invitrogen, Cat. No. AM7020). Samples were assessed for quality with an Advanced Analytics Fragment Analyzer (High Sensitivity RNA Analysis Kit, Cat. No. DNF-491/User Guide DNF-491-2014AUG13) and quantity with a Qubit RNA HS Assay Kit (Cat. No. Q32852).
Given satisfactory quality (RNA integrity number >8) and quantity, samples were used for library construction with the TruSeq Stranded mRNA Library Prep Kit from Illumina (Cat. No. 20020595), as well as the KAPA Dual-Indexed Adapter Kit from Roche (Cat. No. 8278555702).

treatment_protocol: We treated 18-month-old C57BL/6J mice with subcutaneous injections of either sterile PBS (vehicle control) or 4 g/kg HPBCD (treatment) three times per week for 6 weeks following DH stroke, beginning 1 week after stroke.

tag: background strain

tag: genotype

value: wild type

value: 18 months

value: Contralateral hemisphere

tag: time point

value: 7 weeks

tag: agent

value: HPBCD


title: WT_cyclo_contra_rep4

tag: tissue


title: aRCC4, Colonic IEC

tag: disease activity

tag: treatment


title: WT_cyclo_contra_rep5

tag: age


title: aRCC9, Colonic IEC

tag: gender


title: ID_006584_FNA_M_tex_A


title: aRCC3, Colonic IEC


title: Bulk_Mouse_021_Teff_OC


title: ID_006583_FNA_E_tex_C


title: aRCC2, Colonic IEC


title: Bulk_Mouse_001_Teff_MPLA

value: MPLA


title: WT_cyclo_contra_rep2


title: WT_cyclo_contra_rep1


title: ID_006582_FNA_E_tex_B


title: WT_cyclo_peri_infarct_rep5

value: Stroke peri-infarct region


title: aRCC1, Colonic IEC


title: itCC9, Colonic IEC

description: paired with auCC9

value: Inactive/Clinical remission CC

value: 6-9 mg/day budesonide


title: ID_006581_FNA_E_tex_A

value: TEX treated


title: WT_cyclo_peri_infarct_rep4


title: itCC8, Colonic IEC

description: paired with auCC8

value: male


title: ID_006580_FNA_S_notex_C


title: WT_cyclo_peri_infarct_rep3


title: ID_006579_FNA_S_notex_B


title: itCC5, Colonic IEC

description: paired with auCC5


title: ID_006578_FNA_S_notex_A


title: itCC4, Colonic IEC

description: paired with auCC4


title: ID_006577_FNA_M_notex_C


title: WT_cyclo_peri_infarct_rep1


title: WT_veh_contra_rep5

value: vehicle


title: adjacent non-tumor tissue, 32B [A9362]

type: RNA

city: chengdou

first: ji

middle: hong

last: jie

address: 37 Guoxue Road, Chengdu, China

country: China

institute: West China Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Expression Profiling Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: adjacent non-tumor tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Fresh tumor specimens were collected from HCC patients who underwent curative resection.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: Tissues were collected, flash frozen on dry ice

tag: subject status

value: Hepatocellular carcinoma (HCC) patient

tag: subject id

value: liver

tag: tissue subtype

value: adjacent non-tumor tissue


title: liver cancer tissue,32A [A9361]

source_name: HBV-associated HCC

value: liver cancer tissue


title: adjacent non-tumor tissue, 31B [A9360]


title: WT_veh_contra_rep4


title: WT_veh_contra_rep3


title: Bulk_Mouse_011_Tfh_MPLA

value: Tfh


title: liver cancer tissue,31A [A9359]


title: itCC2, Colonic IEC

description: paired with auCC2

value: colon

value: female


title: liver cancer tissue,30A [A9008]


title: itCC3, Colonic IEC

description: paired with auCC3


title: ID_006575_FNA_M_notex_A

value: untreated


title: adjacent non-tumor tissue, 30B [A9009]


title: ID_006574_FNA_E_notex_C


title: ID_006576_FNA_M_notex_B


title: auCC9, Colonic IEC

description: paired with itCC9

value: Active CC

value: No


title: ID_006573_FNA_E_notex_B


title: itCC1, Colonic IEC

description: paired with auCC1


title: WT_veh_contra_rep1

value: wild type

value: 18 months

value: Contralateral hemisphere

value: 7 weeks


title: WT_veh_contra_rep2


title: ID_006572_FNA_E_notex_A


title: auCC8, Colonic IEC

description: paired with itCC8


title: adjacent non-tumor tissue, 29B [A9007]


title: liver cancer tissue,28A [A9004]


title: auCC7, Colonic IEC

description: paired with itCC7


title: WT_veh_peri_infarct_rep4

value: Stroke peri-infarct region


title: auCC5, Colonic IEC

description: paired with itCC5


title: auCC4, Colonic IEC

description: paired with itCC4


title: ID-005345_FNN_S_tex_plus_repB

data_processing:
Reads were trimmed for the NEBNext adapter sequence using Cutadapt version 2.5 with default parameters. In addition, Cutadapt was given the –nextseq-trim=20 switch to handle two colour sequencing chemistry. Reads that were trimmed to length=0 were discarded.The READemption pipeline version 4.5 (Förstner et al., 2014) with segemehl version 0.2 (Otto et al., 2014) was used for read mapping and calculation of read counts. Reads were mapped on CP010905.2 with additional annotations for ncRNAs, 3’UTRs and 5’UTRs. For the prediction of transcriptional start sites (TSS) and small regulatory RNAs (sRNA), we used the modular, command-line tool ANNOgesic (Yu et al., 2018). All parameters were kept at the default setting, unless stated otherwise.  Secondary TSSs were excluded if a primary TSS was within seven nucleotides distance. For annotation of 5’ untranslated regions (5’UTRs) the default settings for maximum length was corrected to 300 nt.  For the prediction of sRNA, we used the default settings, that is, the transcript must have a predicted TSS or PS at their 5’end, form a stable secondary structure (calculated with RNAfold from Vienna RNA package), and a length between 30 to 500 nt. For 5’UTR-derived sRNA the transcripts must have a processing site (PS) at their 3’end. For 3’UTR-derived sRNA the transcript can either have a TSS or PS at their 5’end and share its terminator with the parental gene.
Genome_build: AE009951.2
Supplementary_files_format_and_content: wiggle

organism: Fusobacterium nucleatum subsp. nucleatum ATCC 25586

source_name: German Collection of Microorganisms and Cell Cultures GmbH

value: TEX treated


title: ID-005346_FNN_S_tex_plus_repC


title: liver cancer tissue,29A [A9006]


title: adjacent non-tumor tissue, 28B [A9005]


title: ID-005344_FNN_S_tex_plus_repA


title: auCC3, Colonic IEC

description: paired with itCC3

value: male


title: ID-005343_FNN_M_tex_plus_repC


title: WT_veh_peri_infarct_rep1

value: vehicle


title: adjacent non-tumor tissue, 27B [A9003]

value: Hepatocellular carcinoma (HCC) patient

value: liver


title: auCC2, Colonic IEC

description: paired with itCC2


title: ID-005342_FNN_M_tex_plus_repB


title: WT_veh_peri_infarct_rep5


title: adjacent non-tumor tissue, 26B [A9001]

value: adjacent non-tumor tissue


title: adjacent non-tumor tissue, 24B [A8997]


title: WT_veh_peri_infarct_rep2


title: auCC1, Colonic IEC

description: paired with itCC1


title: Hc9, Colonic IEC


title: WT_cyclo_infarct_rep4

value: WT

value: HPBCD

value: Stroke infarct


title: ID-005340_FNN_E_tex_plus_repC


title: WT_cyclo_infarct_rep3

tag: genotype:


title: liver cancer tissue,26A [A9000]

value: liver cancer tissue


title: ID-005341_FNN_M_tex_plus_repA


title: ID-005339_FNN_E_tex_plus_repB


title: liver cancer tissue,27A [A9002]


title: Hc7, Colonic IEC

value: colon


title: Hc8, Colonic IEC


title: WT_cyclo_infarct_rep2


title: adjacent non-tumor tissue, 21B [A8991]


title: WT_cyclo_infarct_rep1


title: Hc6, Colonic IEC

value: female


title: ID-005338_FNN_E_tex_plus_repA


title: WT_veh_infarct_rep4

value: wild type


title: liver cancer tissue,24A [A8996]


title: WT_veh_infarct_rep3

value: 18 months


title: liver cancer tissue,21A [A8990]


title: adjacent non-tumor tissue, 20B [A8989]


title: ID-005328_FNN_S_untreated_repC

value: untreated


title: WT_veh_infarct_rep2

value: 7 weeks


title: Hc4, Colonic IEC


title: ID-005327_FNN_S_untreated_repB


title: liver cancer tissue,20A [A8988]


title: ID-005326_FNN_S_untreated_repA


title: ID-005325_FNN_M_untreated_repC


title: Hc3, Colonic IEC


title: B_inf_3

city: Philadelphia

first: Boris

last: Striepen

state: Pennsylvania

address: 380 S University Ave, Room H344

department: Pathobiology

institute: University of Pennsylvania

data_processing:
fastq files were aligned to version 79 of mouse reference genome GRCm38 using kallisto
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (³1-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: version 79 of mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample

source_name: ileal intestinal epithelial cells

growth_protocol: intestinal segments were digested using DTT and EDTA with gentle agitation, then filtered; single-cell suspensions were sorted for CD45.2– EpCAM+ IECs on a FACS Jazz flow sorter

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

treatment_protocol: Mice were left uninfected or infected with Cryptosporidium tyzzeri for 3 (JG183)  or 5 (JG182) days

tag: cell type

value: ileal intestinal epithelial cells

value: wild-type

value: infected 3 days


title: Hc2, Colonic IEC

value: male


title: ID-005323_FNN_M_untreated_repA


title: Hc1, Colonic IEC


title: liver cancer tissue,18A [A8984]

value: Hepatocellular carcinoma (HCC) patient


title: adjacent non-tumor tissue, 18B [A8985]

value: liver


title: Hc5, Colonic IEC


title: adjacent non-tumor tissue, 19B [A8987]

value: adjacent non-tumor tissue


title: ID_006538_FuP_E_notex_C


title: ID-005322_FNN_E_untreated_repC


title: SGC7901_input

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Paired-end clean reads were aligned to the reference genome using Bowtie v2.2.6.
After mapping reads to the reference genome, we used the MACS2 version 2.1.0 (model-based analysis of ChIP-seq) peak finding algorithm to indentify regions of IP enrichment over background. A q value threshold of enrichment of 0.05 was used for all data sets. Then, the distribute of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited peak file include information about identified peaks

source_name: gastric cancer cell

growth_protocol: The human gastric cancer cell line SGC7901 was purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The gastric cancer cell line SGC7901 was cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
The immunoprecipitated RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
RNA samples were fragmented into fragments by RNA fragmentation buffer. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. 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-selected, adaptor-ligated cDNA at 37℃ for 15 min followed by 5 min at 95℃ 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.

treatment_protocol: After crosslinking with 0.5% formaldehyde for 10 min at room temperature, cells were harvested and lysed in RIP lysis buffer with RNasin (1000 U/ml), DNase I (50 U/ml) and protease inhibitor cocktail. After the genomic DNA was digested, lysates were further subjected to sonication. Supernatants cleared by centrifugation were incubated with the anti-ILF3 antibody or IgG overnight at 4 °C. Protein A/G beads were added for a further 4 h incubation at room temperature. After the beads were washed with wash buffer, immunocomplexes of proteins and RNAs were de-crosslinked at 95 °C for 15 min. The immunoprecipitated RNAs were then purified for RNA sequencing and qRT-PCR analysis.

tag: cell line

value: gastric cancer

tag: group

value: Input


title: liver cancer tissue,19A [A8986]


title: liver cancer tissue,16A [A8980]


title: B_uninf_2

value: uninfected


title: adjacent non-tumor tissue, 16B [A8981]


title: ID-005324_FNN_M_untreated_repB


title: SGC7901_miR-138_mimics

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/gencode.v26.annotation.gtf.gz.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include count and FPKM values for each Sample

growth_protocol: The human gastric cancer cell line SGC7901 were purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The gastric cancer cell lines were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
Gastric cancer cells were grown in 6-well plates and transfected with corresponding plasmids. After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. MRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

treatment_protocol: SGC7901 cells were seeded were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 20%-30%, GC cells were transfected with corresponding plasmids by Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. At 48 h post-transfection, cells were harvested for RNA sequencing.

tag: transfection

value: miR-138-5p mimics


title: WT_veh_peri_infarct_rep3

tag: background strain

value: Stroke peri-infarct region

value: vehicle


title: B_uninf_3

tag: genotype


title: ID-005321_FNN_E_untreated_repB


title: SGC7901_α-ILF3_target

value: Target (anti-ILF3)


title: blood_Transwomen_postreatment, rep1 [TV6-517]

type: genomic

city: A Coruña

first: Rosa

last: Fernandez

state: None / N/A

address: Campus Elviña

department: Psychology

country: Spain

institute: University of A Coruña

description:
IC204921840071_R06C01
TV6-517
Trans women
transgender

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation850 BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
DNA quality checks, data normalization, and statistical filters were performed with the Partek® Genomics Suite® v7.19.1018 Methylation Module.
Average Beta

molecule: genomic DNA

source_name: blood, trans, post-treatment

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNAs were extracted from peripheral blood samples using the DNeasy Blood & Tissue Kit from Qiagen.

value: blood

value: female

tag: birth sex

value: 50 years

tag: population

value: Caucasian

tag: ethnicity

value: Flemish Belgian

value: gender affirming hormone treatment (GAHT), 6 months


title: SGC7901_NC_miR-138

value: negative control siRNA


title: adjacent non-tumor tissue, 14B [A8977]

value: Hepatocellular carcinoma (HCC) patient

tag: tissue


title: liver cancer tissue,14A [A8976]

value: liver

value: liver cancer tissue


title: blood_Transwomen_postreatment, rep1 [TV6-533]

description:
IC204921840071_R07C01
TV6-533
Trans women
transgender

value: male

value: 47 years

tag: treatment


title: A_inf_2

value: ileal intestinal epithelial cells

value: wild-type

value: infected 5 days


title: blood_Transwomen_postreatment, rep1 [TV6-514]

description:
IC204921840071_R05C01
TV6-514
Trans women
transgender

tag: age

value: 31 years


title: liver cancer tissue,13A [A8974]


title: A_inf_3

description: JG182; removed from analysis due to poor sequencing depth


title: adjacent non-tumor tissue, 13B [A8975]

value: adjacent non-tumor tissue


title: blood_Transwomen_postreatment, rep1 [TV6-513]

description:
IC204921840071_R04C01
TV6-513
Trans women
transgender

value: blood

tag: gender

value: 27 years


title: ID-005320_FNN_E_untreated_repA

value: untreated


title: SGC7901_NC_IGFBP7

value: gastric cancer


title: WT_cyclo_peri_infarct_rep2

value: wild type

value: 18 months

value: Stroke peri-infarct region

tag: time point

value: 7 weeks

tag: agent

value: HPBCD


title: B_uninf_1

value: uninfected


title: A_inf_1


title: blood_Transwomen_postreatment, rep1 [TV6-502]

description:
IC204921840071_R03C01
TV6-502
Trans women
transgender

value: female

value: male

value: 28 years

value: Caucasian

value: Flemish Belgian

value: gender affirming hormone treatment (GAHT), 6 months


title: A_uninf_3

value: ileal intestinal epithelial cells

value: wild-type


title: SGC7901_IGFBP7#2


title: adjacent non-tumor tissue, 12B [A8973]

tag: subject status

value: Hepatocellular carcinoma (HCC) patient

tag: subject id

value: liver

tag: tissue subtype

value: adjacent non-tumor tissue


title: SGC7901_UBE2CP3_siRNA#5

tag: cell line

tag: cell type

value: gastric cancer


title: ID_006589_FNA_S_tex_C

value: TEX treated


title: blood_Transwomen_postreatment, rep1 [TV6-493]

description:
IC204921840071_R02C01
TV6-493
Trans women
transgender

value: blood

value: 36 years


title: A_uninf_2


title: SGC7901_IGFBP7#1

tag: transfection


title: SGC7901_UBE2CP3_siRNA#1


title: A_uninf_1

tag: background strain


title: blood_Transwomen_postreatment, rep1 [TV6-486]

description:
IC204921840071_R01C01
TV6-486
Trans women
transgender

value: 59 years


title: SGC7901_NC_rep2

value: negative control siRNA


title: liver cancer tissue,12A [A8972]

value: liver cancer tissue


title: liver cancer tissue,10A [A8968]


title: SGC7901_NC_rep1


title: blood_Transmen_postreatment, rep1 [TM6-535]

description:
IC204921840027_R02C01
TM6-535
Trans men
transgender

value: male

value: female

value: 21 years


title: blood_Transmen_postreatment, rep1 [TM6-534]

description:
IC204921840027_R01C01
TM6-534
Trans men
transgender

value: 19 years

value: Caucasian

value: Flemish Belgian


title: Inj cKO2

city: Creteil

first: Joana

last: Esteves de Lima

address: 8 rue du general sarrail

department: IMRB INSERM U955

country: France

institute: INSERM

data_processing:
FASTQ groomer tool  (https://usegalaxy.org)
BOWTIE2 v2.3.4.2  (https://usegalaxy.org)
featureCounts v1.6.3+galaxy2 (https://usegalaxy.org)
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 v2.11.40.6+galaxy1 (https://usegalaxy.org)

source_name: skeletal muscle

growth_protocol: 5 days post-injury satellite cells (control and deleted for Hira, cKO)  were cultured for 48h in high serum medium at low density

extract_protocol:
cultured satellite cells were collected for RNA extraction using Machery Nagel NucleoSpin RNA purification kit
Libraries were prepared with TruSeq Stranded Total Library preparation kit according to supplier recommendations. Briefly, the key stages of this protocol are successively, the removal of ribosomal RNA fraction from 400ng of total RNA using the Ribo-Zero Gold Kit; fragmentation using divalent cations under elevated temperature to obtain approximately 300bp pieces; double strand cDNA synthesis using reverse transcriptase and random primers, and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing. Sequencing was carried out on single-end 75bp of Illumina NextSeq500

tag: strain

tag: genotype

value: Hira cKO

value: satellite


title: CTRL_H3K27Me3_Rep2

city: Chicago

first: Megan

last: McNerney

state: IL

address: 900 E 57th St

department: Pathology

institute: The University of Chicago

library_source: genomic

data_processing:
RNAseq: FastQC was used for quality checking; the sequenced reads were aligned to the mouse genome (UCSC mm10) with STAR aligner (Dobin et al 2013), and alignments with a mapping quality <30 were removed.
RNAseq: Differential gene expression analysis was performed using DESeq2 (Love, Huber and Anders, 2014), and a negative binomial general linearized model fitting and Wald statistics were used to generate p values, with p values adjusted using the Benjamini Hochberg method
ChIP-seq: Sequencing reads were aligned to the human hg19 genome using BWA (version 0.7.12) (Li and Durbin, 2009) and low quality leads were removed using the SAMtools q30 filter (Li and Durbin, 2009)
ChIP-seq: Peaks were called using MACS2 (Zhang et al., 2008) with a q value threshold of 0.05
ChIP-seq: For differential peak calling, Diffbind (Stark and Brown, 2011) software was applied using an FDR cutoff of 0.10
ChIP-seq: The average read density from two biological replicates was normalized by RPKM in 50bp bins and visualized using the Deeptools software (Ramírez et al, 2016)
Genome_build: mm10, hg19
Supplementary_files_format_and_content: RNA-seq: DESeq2-generated rlog normalized read counts for each gene
Supplementary_files_format_and_content: CHIP-seq: bigWig files generated using bedGraphtoBigWig; peak text files

source_name: K562 cells

growth_protocol: K562 cells were single-cell cloned after knockdown of HPRT (control) or CUX1 as indicated, and CHIP-seq was performed. Mice were treated with doxycycline for five days, HSCs were sorted from the bone marrow and RNA was extracted.

extract_protocol:
RNA was isolated from bone marrow cells with Trizol and collected on RNeasy Micro columns
DNA after ChIP protocol was isolated using QIAquick PCR purification column (Qiagen)
RNA libraries were constructed using Illumina's TruSEQ kit; CHIP-seq libraries were constucted using Ovation Ultralow Library Kit (NuGEN)

treatment_protocol: Mice were treated for five days with doxycycline in vivo

tag: crispr guide

value: gHPRT

tag: shRNA

tag: chip antibody


title: Inj cKO3


title: Inj cKO1


title: blood_Transmen_postreatment, rep1 [TM6-531]

description:
IC204921840011_R08C01
TM6-531
Trans men
transgender

tag: tissue

tag: birth sex

value: 24 years

tag: population

tag: ethnicity

tag: treatment

value: gender affirming hormone treatment (GAHT), 6 months


title: adjacent non-tumor tissue, 10B [A8969]

tag: subject status

value: Hepatocellular carcinoma (HCC) patient

value: liver

value: adjacent non-tumor tissue


title: Inj C3

value: WT


title: CTRL_H3K27Me3_Rep1


title: blood_Transmen_postreatment, rep1 [TM6-501]

description:
IC204921840011_R06C01
TM6-501
Trans men
transgender

value: blood

tag: gender

tag: age

value: 65 years


title: liver cancer tissue,9A [A8966]

tag: subject id

tag: tissue subtype

value: liver cancer tissue


title: Inj C2

tag: cell type


title: blood_Transmen_postreatment, rep1 [TM6-499]

description:
IC204921840011_R05C01
TM6-499
Trans men
transgender

value: male

value: female

value: 42 years


title: adjacent non-tumor tissue, 9B [A8967]


title: CUX1_KD_H3K27Me3_Rep2


title: ID_006571_FNV_S_tex_C

description: the bacterium was grown to stationary phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 3

organism: Fusobacterium vincentii 3_1_36A2

value: TEX treated


title: Inj C1


title: blood_Transmen_postreatment, rep1 [TM6-497]

description:
IC204921840011_R03C01
TM6-497
Trans men
transgender

value: Caucasian

value: Flemish Belgian


title: CUX1_KD_H3K27Me3_Rep1


title: adjacent non-tumor tissue, 6B [A8963]


title: liver cancer tissue,6A [A8962]


title: blood_Transmen_postreatment, rep1 [TM6-491]

description:
IC204921840011_R02C01
TM6-491
Trans men
transgender


title: RNASeq.pDC4

first: Raul

last: Rabadan

state: NY

institute: Columbia University

description: RNASeq.rawcounts.txt

data_processing:
RNASeq: We mapped 9 BPDCN samples – 5 cases belonging to the discovery set and 4 cases belonging to the extended set- by means of STAR aligner (version 2.4.0)
on human reference genome hg19 and obtained an average of 70 million paired-end mapped reads per sample.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

source_name: pDC

extract_protocol:
Total RNA from the nine biopsies was extracted using TRIzol reagent (Invitrogen).
RNA libraries were prepared using TruSeq RNA sample preparation kit v2 protocol (Illumina, San Diego, USA).

value: pDCs isolated from blood

tag: sample type

value: normal

tag: tratment

value: Untreated


title: RNASeq.pDC3

description: RNASeq.rawcounts.txt


title: Pax7 KR FI-SC replicate 3

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Reads quantified against transcripts from the GENCODE vM25 assembly using salmon v1.3.0 (flags --gcBias --validateMappings; index includes genomic decoys)
Fold change analysis performed using DESeq2
Transcript quantification data read using the tximport library. Count matrix filtered to retain only genes with 5+ reads in at least two samples.
Differential expression computed with DESeq2 (v1.28.1) using the results() function to compare Pax7-KO vs WT conditions
Genome_build: GRCm38
Supplementary_files_format_and_content: Salmon transcript quantification: tab-delimited text
Supplementary_files_format_and_content: DESeq2 differential expression results: tab-delimited text

source_name: freshly isolated satellite cells

extract_protocol:
Freshly isolated satellite cells (α7-INTEGRIN+, CD34+, CD31-, CD11b-, SCA-1- and CD45-) were sorted from uninjured hindlimb muscles,  using a MoFlo XDP cell sorter (Beckman Coulter). Total RNA was purified using Arcturus PicoPure RNA Isolation Kit (Applied Biosystems) using the manufacturer’s instructions.
For each biological sample, 15ng of RNA was used as input for the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs).

tag: strain

value: freshly isolated satellite cells

tag: genotype

value: Pax7 KR


title: blood_Transmen_postreatment, rep1 [TM6-490]

description:
IC204921840011_R01C01
TM6-490
Trans men
transgender

value: 30 years

value: gender affirming hormone treatment (GAHT), 6 months


title: ID_006570_FNV_S_tex_B

description: the bacterium was grown to stationary phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 2


title: Pax7 KR FI-SC replicate 2


title: RNASeq.pDC2

description: RNASeq.rawcounts.txt


title: ID_006569_FNV_S_tex_A

description: the bacterium was grown to stationary phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 1


title: adjacent non-tumor tissue,1B [A8959]

value: Hepatocellular carcinoma (HCC) patient

value: liver

value: adjacent non-tumor tissue


title: liver cancer tissue,1A [A8958]

value: liver cancer tissue


title: blood_Transmen_postreatment, rep1 [TM6-484]

description:
IC204921840006_R08C01
TM6-484
Trans men
transgender

value: blood

value: male

value: 18 years


title: RNASeq.pDC1

description: RNASeq.rawcounts.txt


title: Pax7 KR FI-SC replicate 1


title: ID_006587_FNA_S_tex_A

value: TEX treated


title: RNASeq.BPDCN_43

description: RNASeq.rawcounts.txt

source_name: BPDCN

value: skin

value: tumor


title: Pax7 WT FI-SC replicate 3

value: Pax7 WT


title: itCC7, Colonic IEC

description: paired with auCC7

value: colon

tag: disease activity

value: Inactive/Clinical remission CC

value: 6-9 mg/day budesonide

value: female


title: ID_006568_FNV_M_tex_C

description: the bacterium was grown to mid-exponential phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 3


title: ID_006567_FNV_M_tex_B

description: the bacterium was grown to mid-exponential phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 2


title: blood_Transwomen_pretreatment, rep1 [TV533]

description:
204088100012_R07C01
TV533
Trans women
transgender

source_name: blood, trans, pre-treatment

value: 47 years

value: Caucasian

value: Flemish Belgian


title: blood_Transwomen_pretreatment, rep1 [TV517]

description:
204088100012_R05C01
TV517
Trans women
transgender

value: 50 years


title: Pax7 WT FI-SC replicate 2

value: freshly isolated satellite cells


title: RNASeq.BPDCN_37

description: RNASeq.rawcounts.txt

value: Untreated


title: ID_006566_FNV_M_tex_A

description: the bacterium was grown to mid-exponential phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 1


title: Pax7 WT FI-SC replicate 1


title: blood_Transwomen_pretreatment, rep1 [TV514]

description:
204088100012_R04C01
TV514
Trans women
transgender

value: blood

value: 31 years


title: RNASeq.BPDCN_25

description: RNASeq.rawcounts.txt


title: ID_006565_FNV_E_tex_C

description: the bacterium was grown to early exponential phase and samples collected for RNA extraction; RNA was split for untreated and TEX treated libraries; bio. Replicate 3


title: blood_Transwomen_pretreatment, rep1 [TV513]

description:
204088100012_R03C01
TV513
Trans women
transgender

value: male

value: 27 years


title: RNASeq.BPDCN_24

description: RNASeq.rawcounts.txt

value: skin


title: blood_Transwomen_pretreatment, rep1 [TV502]

description:
204088100012_R02C01
TV502
Trans women
transgender

value: 28 years


title: ID_006564_FNV_E_tex_B

description: the bacterium was grown to early exponential phase and samples collected for RNA extraction; RNA was split for untreated and TEX treated libraries; bio. Replicate 2

value: TEX treated


title: RNASeq.BPDCN_23

description: RNASeq.rawcounts.txt

value: tumor


title: F4L5.13 treated 24 hours Rep 1

city: Toronto

first: Graham

last: MacLeod

address: 144 College Street

department: Pharmaceutical Sciences

institute: University of Toronto

data_processing:
Illumina NextSeq-500 Instrument
fastq mapped to GRCm38.96 and quantified using Kallisto
Genome_build: GRCm38.96
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: cells were grown in 10% FBS DMEM

extract_protocol:
RNA extracted with Trizol reagent
TruSeq V2mRNA-enriched library kit

treatment_protocol: 30 nM NDP/F4L5.13 for indicated duration

tag: cell line

value: mouse brain-derived endothelial cell line

tag: duration

value: 24 hours


title: F4L5.13 treated 24 hours Rep 3


title: ID_006563_FNV_E_tex_A

description: the bacterium was grown to early exponential phase and samples collected for RNA extraction; RNA was split for untreated and TEX treated libraries; bio. Replicate 1


title: blood_Transwomen_pretreatment, rep1 [TV493]

description:
203717910113_R02C01
TV493
Trans women
transgender

tag: tissue

value: female

tag: birth sex

value: 36 years


title: RNASeq.BPDCN_22

description: RNASeq.rawcounts.txt


title: RNASeq.BPDCN_42

description: RNASeq.rawcounts.txt


title: F4L5.13 treated 8 hours Rep 3

value: 8 hours


title: blood_Transwomen_pretreatment, rep1 [TV486]

description:
204088100012_R01C01
TV486
Trans women
transgender

value: 59 years

tag: population

value: Caucasian

tag: ethnicity

value: Flemish Belgian


title: ID_006561_FNV_S_notex_B

tag: treatment

value: untreated


title: F4L5.13 treated 8 hours Rep 2


title: RNASeq.BPDCN_21

description: RNASeq.rawcounts.txt

value: Untreated


title: RNASeq.BPDCN_20

description: RNASeq.rawcounts.txt


title: F4L5.13 treated 8 hours Rep 1


title: ID_006560_FNV_S_notex_A


title: blood_Transmen_pretreatment, rep1 [TM534]

description:
204088090160_R05C01
TM534
Trans men
transgender

value: blood

tag: gender

value: 19 years


title: F4L5.13 treated 24 hours Rep 2


title: NDP treated 24 hours Rep3

value: NDP


title: B_inf_1

value: ileal intestinal epithelial cells

tag: background strain

value: wild-type

value: infected 3 days


title: novobiocin_3

city: Braunschweig

first: Raimo

last: Franke

state: Lower Saxony

address: Inhoffenstr. 7

department: Chemical Biology

institute: Helmholtz Centre for Infection Research

description: start OD600 of 0.05; treated with IC50 of novobiocin from OD600 of 0.05 to 0.6

data_processing:
Short reads were aligned to the UCBPP-PA14 reference genome NC_008463 using the subread algorithm implemented in R, Rsubread version 1.32.4.
Count estimation was performed using the featureCounts function as implemented in Rsubread.
Genome_build: NC_008463
Supplementary_files_format_and_content: rpg_matrix_PA14_gyr_inhibitors.csv, reads per gene counts for each sample as determined by the featureCounts function

organism: Pseudomonas aeruginosa UCBPP-PA14

source_name: RNASeq of planctonic culture of P. aeruginosa UCBPP-PA14 treated with IC50 of novobiocin from OD 0.05 to OD 0.6

growth_protocol: Bacterial subcultures were grown in liquid BM2, at 37 °C and 150 rpm shaking.

extract_protocol:
Bacterial cell pellets were resuspended in RNAprotect. RNA extraction was done as previously described (Schinner et al., 2020)
Libraries were generated according to Shishkin et al., 2015 and Bhattacharyya et al., 2019.

treatment_protocol: Cells were treated with the IC50 of the gyrase inhibitor at OD600 of 0.05 and harvested at OD600 of 0.6.

tag: strain/genotype

value: PA14 WT

tag: culture type

value: planctonic

tag: treatement


title: ID_006558_FNV_M_notex_B


title: novobiocin_2

value: IC50 of novobiocin from OD 0.05 to OD 0.6


title: NDP treated 24 hours Rep2

tag: cell type

value: mouse brain-derived endothelial cell line

value: 24 hours


title: Bulk_Mouse_005_Teff_MPLA

description: Whole Transcriptome Amplification (Smart-seq2 - Picelli et al.2014)

source_name: murine infection model

tag: cell type surface markers

value: Teff

tag: donor #

value: MPLA


title: ID_006562_FNV_S_notex_C

description: the bacterium was grown to stationary phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 3

source_name: gift from Emma Allen-Vercoe (University of Guelph)


title: ID_006557_FNV_M_notex_A


title: NDP treated 24 hours Rep1


title: novobiocin_1


title: ID_006556_FNV_E_notex_C


title: blood_Transmen_pretreatment, rep1 [TM499]

description:
203717910075_R07C01
TM499
Trans men
transgender

value: male

value: female

tag: age

value: 42 years

value: Caucasian


title: lomefloxacin_3

description: start OD600 of 0.05; treated with IC50 of lomefloxacin from OD600 of 0.05 to 0.6

source_name: RNASeq of planctonic culture of P. aeruginosa UCBPP-PA14 treated with IC50 of lomefloxacin from OD 0.05 to OD 0.6


title: blood_Transmen_pretreatment, rep1 [TM535]

description:
204088090160_R06C01
TM535
Trans men
transgender

value: blood

value: 21 years

value: Flemish Belgian


title: NDP treated 8 hours Rep3

value: NDP

value: 8 hours


title: blood_Transmen_pretreatment, rep1 [TM497]

description:
203717910075_R05C01
TM497
Trans men
transgender

value: 24 years


title: lomefloxacin_2

value: PA14 WT

value: IC50 of lomefloxacin from OD 0.05 to OD 0.6


title: B_inf_2

value: ileal intestinal epithelial cells

tag: genotype

value: wild-type

value: infected 3 days


title: lomefloxacin_1

value: planctonic


title: ID_006559_FNV_M_notex_C

description: the bacterium was grown to mid-exponential phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 3

value: untreated


title: NDP treated 8 hours Rep2

tag: cell line

value: mouse brain-derived endothelial cell line


title: blood_Transmen_pretreatment, rep1 [TM491]

description:
203717910075_R04C01
TM491
Trans men
transgender

value: male

value: female


title: ID_006555_FNV_E_notex_B


title: NDP treated 8 hours Rep1

tag: duration


title: ID_006554_FNV_E_notex_A


title: blood_Transmen_pretreatment, rep1 [TM490]

description:
203717910075_R03C01
TM490
Trans men
transgender

tag: tissue

value: 30 years

value: Caucasian


title: blood_Transmen_pretreatment, rep1 [TM531]

description:
204088090160_R04C01
TM531
Trans men
transgender

value: blood

tag: birth sex


title: ID-005379_FNP_S_tex_plus_repC

organism: Fusobacterium polymorphum ATCC 10953

value: TEX treated


title: blood_Transmen_pretreatment, rep1 [TM484]

description:
204088090160_R01C01
TM484
Trans men
transgender

value: 18 years

tag: population

value: Flemish Belgian


title: levofloxacin_3

description: start OD600 of 0.05; treated with IC50 of levofloxacin from OD600 of 0.05 to 0.6

source_name: RNASeq of planctonic culture of P. aeruginosa UCBPP-PA14 treated with IC50 of levofloxacin from OD 0.05 to OD 0.6


title: Untreated Rep 3


title: blood_Transmen_pretreatment, rep1 [TM501]

description:
203717910075_R08C01
TM501
Trans men
transgender

value: 65 years

tag: ethnicity


title: Untreated Rep 2

tag: treatment


title: levofloxacin_2

value: PA14 WT

value: IC50 of levofloxacin from OD 0.05 to OD 0.6


title: blood_Ciswomen_pretreatment, rep1 [CV7]

description:
203717910049_R01C01
CV7
Cis women
cisgender

source_name: blood, cis, pre-treatment

tag: gender

value: 22 years


title: levofloxacin_1


title: Untreated Rep 1


title: blood_Ciswomen_pretreatment, rep1 [CV6]

description:
203717910049_R02C01
CV6
Cis women
cisgender


title: coumermycin_3

description: start OD600 of 0.05; treated with IC50 of coumermycin from OD600 of 0.05 to 0.6

source_name: RNASeq of planctonic culture of P. aeruginosa UCBPP-PA14 treated with IC50 of coumermycin from OD 0.05 to OD 0.6


title: ID-005377_FNP_S_tex_plus_repA

description: the bacterium was grown to stationary phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 1

source_name: German Collection of Microorganisms and Cell Cultures GmbH


title: blood_Ciswomen_pretreatment, rep1 [CV51]

description:
203717910049_R07C01
CV51
Cis women
cisgender

value: 43 years


title: Hira_KO_ATAC_rep2

data_processing:
alignment: BWA algorithm (mem mode; default settings)
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file and with the –nomodel option
Genome_build: mm10
Supplementary_files_format_and_content: Signal maps and peak locations were used as input data to Active Motif’s proprietary analysis program

growth_protocol: C2C12 control and C2C12 Hira KO cell lines were collected when grown in high serum medium at low density (proliferating conditions)

extract_protocol:
C2C12 cells were harvested and cell pellets were resuspended in lysis buffer, pelleted and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina)
Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems)

tag: strain background

value: skeletal muscle cell line

value: Hira -/-


title: coumermycin_2

tag: strain/genotype

value: planctonic

value: IC50 of coumermycin from OD 0.05 to OD 0.6


title: Hira_KO_ATAC_rep1


title: coumermycin_1

tag: culture type


title: blood_Ciswomen_pretreatment, rep1 [CV26]

description:
203717910049_R05C01
CV26
Cis women
cisgender

value: 24 years


title: ID-005375_FNP_M_tex_plus_repB

description: the bacterium was grown to mid-exponential phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 2


title: C2C12_ATAC_rep2

value: WT


title: CN_DM_681_3

description: start OD600 of 0.05; treated with IC50 of cystobactamid CN-DM-861 from OD600 of 0.05 to 0.6

source_name: RNASeq of planctonic culture of P. aeruginosa UCBPP-PA14 treated with IC50 of cystobactamid CN-DM-681 from OD 0.05 to OD 0.6

tag: treatement


title: ID-005376_FNP_M_tex_plus_repC


title: ID-005373_FNP_E_tex_plus_repC

description: the bacterium was grown to early exponential phase and samples collected for RNA extraction; RNA was split for untreated and TEX treated libraries; bio. Replicate 3


title: ID-005374_FNP_M_tex_plus_repA

description: the bacterium was grown to mid-exponential phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 1


title: C2C12_ATAC_rep1

tag: cell type


title: ID-005378_FNP_S_tex_plus_repB

description: the bacterium was grown to stationary phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 2


title: CN_DM_681_2

value: IC50 of cystobactamid CN-DM-681 from OD 0.05 to OD 0.6


title: blood_Ciswomen_pretreatment, rep1 [CV23]

description:
203717910049_R04C01
CV23
Cis women
cisgender

value: female

value: 20 years

value: Caucasian


title: blood_Ciswomen_pretreatment, rep1 [CV16]

description:
203717910049_R06C01
CV16
Cis women
cisgender

value: blood


title: CN_DM_681_1


title: blood_Ciswomen_pretreatment, rep1 [CV14]

description:
203717910049_R08C01
CV14
Cis women
cisgender

value: 47 years

value: Flemish Belgian


title: ID-005370_FNP_S_untreated_repC

description: the bacterium was grown to stationary phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 3

value: untreated


title: ID-005372_FNP_E_tex_plus_repB

description: the bacterium was grown to early exponential phase and samples collected for RNA extraction; RNA was split for untreated and TEX treated libraries; bio. Replicate 2

value: TEX treated


title: ID-005371_FNP_E_tex_plus_repA

description: the bacterium was grown to early exponential phase and samples collected for RNA extraction; RNA was split for untreated and TEX treated libraries; bio. Replicate 1


title: ciprofloxacin_3

description: start OD600 of 0.05; treated with IC50 of ciprofloxacin from OD600 of 0.05 to 0.6

source_name: RNASeq of planctonic culture of P. aeruginosa UCBPP-PA14 treated with IC50 of ciprofloxacin from OD 0.05 to OD 0.6

value: PA14 WT


title: k4me2_CD4+_spl

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus Medical Center

data_processing:
Reads were aligned using bowtie 2with default parameters.
Sorted and indexed bam files were parsed to HOMER to creat tag directories without duplicates and bedgraphs for browser visualization.
HOMER was used to identify enriched regions ('peak calling') using findPeaks with -region -size 1000 -minDist 2500 options
Genome_build: mm10
Supplementary_files_format_and_content: HOMER peak calling files

source_name: spleen

extract_protocol:
Lymphocyte fractions were obtained from Gata3-YFP/YFP mice with airway inflammation. Cells were FACS-sorted using specific antibodies and YFP as described in detail in the manuscript.
Nextera DNA library construction (as described in Schmidl et al. Nature Methods 2015).

value: spleen

value: CD4+ lymphocytes

tag: antibody

value: anti-H3K4Me2, Abcam ab32356


title: IgG_CD4+_thy

source_name: thymus

value: thymus


title: k4me2_CD4+_thy


title: blood_Cismen_pretreatment, rep1 [CM45]

description:
203717910051_R07C01
CM45
Cis men
cisgender

value: male

value: 32 years


title: blood_Ciswomen_pretreatment, rep1 [CV28]

description:
203717910049_R03C01
CV28
Cis women
cisgender

value: 22 years


title: ID-005369_FNP_S_untreated_repB


title: blood_Cismen_pretreatment, rep1 [CM35]

description:
203717910051_R08C01
CM35
Cis men
cisgender

value: 27 years


title: ciprofloxacin_2

value: planctonic

value: IC50 of ciprofloxacin from OD 0.05 to OD 0.6


title: ID-005368_FNP_S_untreated_repA

description: the bacterium was grown to stationary phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 1


title: ciprofloxacin_1


title: IgG_CD4+_spl


title: k4me2_ILC2_2

source_name: mediastinal lymph node

value: mediastinal lymph node

value: group 2 innate lymphoid cells (ILC2s)


title: blood_Cismen_pretreatment, rep1 [CM25]

description:
203717910051_R04C01
CM25
Cis men
cisgender

value: blood

value: 21 years

value: Caucasian


title: WT_veh_infarct_rep1

source_name: Brain

tag: genotype:

tag: agent

value: vehicle

tag: background strain

value: wild type

value: 18 months

value: Stroke infarct

tag: time point

value: 7 weeks


title: blood_Cismen_pretreatment, rep1 [CM27]

description:
203717910051_R06C01
CM27
Cis men
cisgender

tag: age

value: 28 years

value: Flemish Belgian


title: AR351_3

description: start OD600 of 0.05; treated with IC50 of cystobactamid AR351 from OD600 of 0.05 to 0.6

source_name: RNASeq of planctonic culture of P. aeruginosa UCBPP-PA14 treated with IC50 of cystobactamid AR351 from OD 0.05 to OD 0.6

value: PA14 WT


title: AR351_2

value: IC50 of cystobactamid AR351 from OD 0.05 to OD 0.6


title: ID-005367_FNP_M_untreated_repC

description: the bacterium was grown to mid-exponential phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 3

value: untreated


title: ID-005366_FNP_M_untreated_repB

description: the bacterium was grown to mid-exponential phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 2


title: k4me2_ILC2_1

source_name: Bronchoalveolar lavage

tag: tissue

value: Bronchoalveolar lavage

value: anti-H3K4Me2, Abcam ab32356


title: k4me2_Th2_2

value: mediastinal lymph node

value: T helper-2 (Th2) cells


title: blood_Cismen_pretreatment, rep1 [CM21]

description:
203717910051_R03C01
CM21
Cis men
cisgender

value: blood

value: male

tag: birth sex


title: AR351_1

value: planctonic


title: ID-005365_FNP_M_untreated_repA

description: the bacterium was grown to mid-exponential phase and samples collected for RNA extraction;RNA was split for untreated and TEX treated libraries; bio. Replicate 1


title: blood_Cismen_pretreatment, rep1 [CM2]

description:
203717910051_R02C01
CM2
Cis men
cisgender

value: 27 years

tag: population

value: Caucasian


title: ID-005364_FNP_E_untreated_repC

description: the bacterium was grown to early exponential phase and samples collected for RNA extraction; RNA was split for untreated and TEX treated libraries; bio. Replicate 3


title: k4me2_Th2_1


title: untreated_3

description: start OD600 of 0.05; untreated control, harvested at OD600 of 0.6

source_name: RNASeq of planctonic culture of P. aeruginosa UCBPP-PA14  harvested at OD 0.6

value: none; harvested at OD 0.6


title: k4me2_naiveT_2

value: naive T cells


title: blood_Cismen_pretreatment, rep1 [CM17]

description:
203717910051_R05C01
CM17
Cis men
cisgender

value: 29 years

tag: ethnicity


title: untreated_1


title: ID-005362_FNP_E_untreated_repA

description: the bacterium was grown to early exponential phase and samples collected for RNA extraction; RNA was split for untreated and TEX treated libraries; bio. Replicate 1

tag: treatment


title: ID-005363_FNP_E_untreated_repB

description: the bacterium was grown to early exponential phase and samples collected for RNA extraction; RNA was split for untreated and TEX treated libraries; bio. Replicate 2


title: blood_Cismen_pretreatment, rep1 [CM11]

description:
203717910051_R01C01
CM11
Cis men
cisgender

tag: gender

value: 32 years


title: k4me2_naiveT_1


title: Lyn KO / Irf5 Het rep3

status: Public on May 02 2021

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

country: Japan

institute: Yokohama City University

data_processing:
Illumina Real-Time Analysis (RTA) v2 software was used for basecalling.
All sequenced reads were converted to FASTQ file using bcl2fastq, followed by mapping the mouse genome reference sequence mm10 using STAR.
Raw read counts were obtained using featureCounts.
After normalization to trimmed mean of M values (TMM) by calcNormFactors function using edgeR, final read counts were obtained by rpkm function.
Genome_build: mm10
Supplementary_files_format_and_content: EXCEL file include RPKM values for all samples

source_name: Peripheral blood

extract_protocol:
Total RNA from peripheral blood stabilized in RNAprotect Animal Blood Tubes (Qiagen) was purified using the RNeasy Protect Animal Blood Kit (Qiagen).
Libraries were prepared from 500 ng of total RNA using SureSelect Strand-Specific RNA Library Prep for Illumina Multiplexed Sequencing (Agilent Technologies). Pooled libraries were subjected to the sequencing using the Illumina NextSeq 500/550 High Output Kit v2 (75 cycles) and NextSeq 500 System.

tag: strain background

value: 22-23 weeks of age

tag: genotype

value: Lyn KO / Irf5 Het

value: Peripheral blood


title: Lyn KO / Irf5 Het rep4


title: Lyn KO / Irf5 KO rep3

tag: strain

value: Lyn KO / Irf5 KO


title: Lyn KO / Irf5 Het rep2


title: Lyn KO / Irf5 Het rep1


title: Lyn KO / Irf5 KO rep1


title: Lyn KO / Irf5 KO rep2


title: Lyn KO / Ifnar1 KO rep4

value: Lyn KO / Ifnar1 KO


title: Lyn KO / Ifnar1 KO rep2


title: Lyn KO / Ifnar1 KO rep3


title: Lyn KO rep4

value: Lyn KO


title: Lyn KO rep2


title: Lyn KO / Irf5 KO rep4


title: untreated_2

tag: strain/genotype

value: PA14 WT

tag: culture type

tag: treatement


title: HEK-293T CIRTS-hADAR biosensor - ABA

first: Bryan

middle: C

last: Dickinson

department: Chemistry

data_processing:
PCR duplicates were removed using clumpify.sh before raw reads were trimmed using cutadapt to omit the first 6 nucleotides.
Raw reads were aligned to the hg19 genome file downloaded from the UCSC database using hisat2.
A-to-G mutations were identified using bamtools readcount with a coverage cutoff > 5 and minimum mutation count =3 & mutation rate of 1%.
SNPs were excluded and RADAR-known sites annotated in R.
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing editing rates for firefly luciferase in the no ABA vs ABA samples.

source_name: HEK-293T cells

extract_protocol:
RNA samples were extracted from HEK-293T cells using RNeasy Mini kit with the standard protocol; mRNA was enriched and sequenecing libraries were prepared.
Libraries were constructed using a commercial KAPA mRNA HyperPrep Kit.

tag: cell line


title: Lyn KO rep3


title: Lyn KO rep1


title: cell_Salmonella_expressing_Rck_PagN_invalidated_T3SS1_5

city: Jouy-en-Josas

first: Marco

last: Moroldo

address: Domaine de Vilvert

department: Animal Genetics

institute: INRA

description:
STM-Z_5
Gene expression treatment 1

hyb_protocol: Subsequently, for each sample 600 ng of Cy3-labeled cRNA (specific activity > 9.0 pmol Cy3/µg of cRNA) were fragmented at 60°C for 30 minutes in a volume of 25 µl containing 25x of Agilent Fragmentation Buffer and 10x of Agilent Blocking Agent. Afterwards, 25 µl of 2x Agilent Hybridization Buffer were added to the fragmentation mixture and hybridized to the array following the recommended protocol. After hybridization, microarrays were washed 1 minute at room temperature with the GE Wash Buffer 1 (Agilent Technologies) and 1 minute at 37°C using the GE Wash Buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing using a G2565CA Scanner System (Agilent Technologies) using one color scan settings for 8X60K slides.

data_processing: The scanned images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09).

organism: Rattus norvegicus

label_protocol: Cyanine-3 (Cy3) labeled cRNAs were prepared using the One-Color Low Input Quick Amp Labeling kit (Agilent Technologies) and using 100 ng of total RNA. Specific activities and cRNA yields were measured using the NanoDrop ND-1000 (Thermo Fisher Scientific).

growth_protocol: The intestinal epithelial cell line IEC-6 (ATCC CRL-1592) was grown in DMEM (Dulbecco’s modified Eagle’s medium with glucose 4.5g/L) supplemented with 5% (v/v) fetal calf serum and 0.1 Unit/mL bovine insulin (Sigma). Cells were maintained in a humidified incubator (90% relative humidity) at 37°C under 5% (v/v) CO2.

extract_protocol: Total RNAs were extracted using the NucleoSpin RNA kit (Macherey Nagel, Duüren, Germany) according to the manufacturer’s recommendations. RNA yield and purity were measured using a NanoDrop 1000 (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

treatment_protocol: At confluence, cells were infected with a multiplicity of infection of 10 for 1h30. Subsequently, gentamicin (100µg/ml) was added before extraction for 1h30.

tag: cell type

value: intestinal epithelial cell line

tag: type of infection

value: Salmonella expressing Rck, PagN invalidated T3SS1


title: cell_Salmonella_expressing_Rck_PagN_T3SS1_6

description:
STM-ZT_6
Gene expression treatment 2

value: Salmonella expressing Rck, PagN, T3SS1


title: cell_Salmonella_expressing_Rck_PagN_invalidated_T3SS1_6

description:
STM-Z_6
Gene expression treatment 1


title: cell_Non_infected_5

description:
Cont_5
Gene expression control

source_name: cell culture, Non_infected

value: Non infected


title: WT rep4

value: Wild type


title: cell_Salmonella_invalidated_Rck_PagN_5

description:
STM-T_5
Gene expression treatment 3

value: Salmonella invalidated Rck, PagN


title: cell_Salmonella_expressing_Rck_PagN_T3SS1_5

description:
STM-ZT_5
Gene expression treatment 2


title: cell_Salmonella_expressing_Rck_PagN_T3SS1_4

description:
STM-ZT_4
Gene expression treatment 2


title: HEK-293T CIRTS-hADAR biosensor - no ABA


title: cell_Salmonella_expressing_Rck_PagN_invalidated_T3SS1_4

description:
STM-Z_4
Gene expression treatment 1


title: cell_Salmonella_invalidated_Rck_PagN_4

description:
STM-T_4
Gene expression treatment 3


title: WT rep3


title: DMSO treated K562 cells replicate 2

city: Ithaca

first: Yimon

last: Aye

address: 259 East Ave.

department: Department of Chemistry and Chemical Biology

institute: Cornell University

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.5 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0.13 (--no-novel-juncs --library-type fr-firststrand) was used to map reads to the Human hg19 reference genome (UCSC).
cuffquant (--no-novel-juncs --library-type fr-firststrand) was used to quantify transcripts based on the Human hg19 reference transcriptome (UCSC).
cuffdiff v2.2.1 (--library-type fr-firststrand) was used to call differentially expressed genes based on the Human hg19 reference transcriptome (UCSC).
Genome_build: Human hg19 (UCSC)
Supplementary_files_format_and_content: Tab delimited text files including counts, FPKM values, and p-values generated from Cuffdiff2 when corrected for multiple hypothesis testing

source_name: K562 cells

growth_protocol: K562 cells were grown and maintained in RPMI containing 10% FBS in a 5 %CO2 incubator at 37°C.

extract_protocol:
TRIzol LS was used for total RNA extraction.
Directional RNA-seq libraries were prepared from 1 ug total RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Clofarabine was dissolved in 100% DMSO and added to the media at final concentration 5uM (0.005% DMSO).

value: DMSO treated

tag: time point

value: 3 h


title: DMSO treated K562 cells replicate 1


title: cell_Non_infected_6

description:
Cont_6
Gene expression control


title: Lyn KO / Ifnar1 KO rep1

tag: age


title: cell_Salmonella_expressing_Rck_PagN_T3SS1_3

description:
STM-ZT_3
Gene expression treatment 2


title: cell_Salmonella_expressing_Rck_PagN_invalidated_T3SS1_3

description:
STM-Z_3
Gene expression treatment 1


title: WT rep2

tag: tissue


title: clofarabine treated K562 cells replicate 2

value: clofarabine treated


title: WT rep1


title: clofarabine treated K562 cells replicate 1


title: cell_Non_infected_4

description:
Cont_4
Gene expression control


title: cell_Salmonella_invalidated_Rck_PagN_2

description:
STM-T_2
Gene expression treatment 3


title: cell_Salmonella_invalidated_Rck_PagN_3

description:
STM-T_3
Gene expression treatment 3


title: cell_Salmonella_expressing_Rck_PagN_T3SS1_2

description:
STM-ZT_2
Gene expression treatment 2


title: cell_Salmonella_invalidated_Rck_PagN_1

description:
STM-T_1
Gene expression treatment 3


title: cell_Salmonella_expressing_Rck_PagN_T3SS1_1

description:
STM-ZT_1
Gene expression treatment 2


title: cell_Salmonella_expressing_Rck_PagN_invalidated_T3SS1_2

description:
STM-Z_2
Gene expression treatment 1


title: J_R_6h_rep1

status: Public on May 01 2021

city: Beijing

first: Wei

last: Wei

state: Beijing

address: Chaoyang District, Beichen West Road, Campus #1, No 2

institute: Institute of Genetics and Developmental Biology

description: JACK, treated with 150 mM NaCl for 6h

data_processing:
RNA-sequencing was performed using an Illumina instrument of NovaSeq 6000
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Glycine max whole genome using Hisat2
Reads counting was performed using featureCounts software.
Differential expressed genes were analyzed using DESeq2 software.

organism: Glycine max

source_name: root

extract_protocol:
TRIzol reagent method (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: root

value: 150 mM NaCl for 6h


title: N3_R_6h_rep3

description: GmNFYA, treated with 150 mM NaCl for 6h

value: Transgenic soybean


title: J_R_0h_rep1

description: JACK, untreated

value: untreated


title: J_R_6h_rep3

description: JACK, treated with 150 mM NaCl for 6h


title: J_R_0h_rep3

description: JACK, untreated


title: J_R_6h_rep2

description: JACK, treated with 150 mM NaCl for 6h


title: cell_Non_infected_2

description:
Cont_2
Gene expression control


title: N3_R_6h_rep1

description: GmNFYA, treated with 150 mM NaCl for 6h


title: N3_R_0h_rep1

description: GmNFYA, untreated


title: cell_Salmonella_expressing_Rck_PagN_invalidated_T3SS1_1

description:
STM-Z_1
Gene expression treatment 1


title: J_L_6h_rep1

description: JACK, treated with 150 mM NaCl for 6h

source_name: leaf

value: leaf


title: sRNA-seq_mantle

first: Xuejing

last: Zhu

address: Tsinghua University, Haidian District Beijing

department: School of Life Sciences

institute: Tsinghua University

description: RNA fragments of 18-30nt

data_processing:
Bcl2fastq（v2.17.1.14）software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Clean reads mapped to the P. fucata genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
FastQC（v0.10.1) software used for quality assessment
Genome_build: assembly GCA_002216045.1
Supplementary_files_format_and_content: tab-delimited text files include read counts…

organism: Pinctada fucata

source_name: mantle

growth_protocol: Live and healthy adult pearl oysters P. fucata (shell length 5-6cm and wet weight 30-40g) were cultured at controlled temperature 19 ℃, PH 8.1 and salinity 33‰ in tanks with aerated artificial seawater for 2 weeks.

extract_protocol:
mantles were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Library Preparation Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mantle

value: adult

tag: length


title: N3_R_0h_rep2

description: GmNFYA, untreated


title: J_R_0h_rep2

description: JACK, untreated


title: N3_R_6h_rep2

description: GmNFYA, treated with 150 mM NaCl for 6h


title: J_L_0h_rep3

description: JACK, untreated


title: J_L_6h_rep3

description: JACK, treated with 150 mM NaCl for 6h


title: cell_Non_infected_1

description:
Cont_1
Gene expression control


title: N3_L_6h_rep3

description: GmNFYA, treated with 150 mM NaCl for 6h


title: N3_R_0h_rep3

description: GmNFYA, untreated


title: N3_L_6h_rep2

description: GmNFYA, treated with 150 mM NaCl for 6h


title: N3_L_0h_rep3

description: GmNFYA, untreated


title: J_L_6h_rep2

description: JACK, treated with 150 mM NaCl for 6h


title: N3_L_0h_rep2

description: GmNFYA, untreated


title: N3_L_6h_rep1

description: GmNFYA, treated with 150 mM NaCl for 6h


title: N3_L_0h_rep1

description: GmNFYA, untreated


title: J_L_0h_rep1

description: JACK, untreated


title: J_L_0h_rep2

description: JACK, untreated


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 196

city: Berkeley

first: David

last: DeTomaso

state: CA

address: Stanley Hall

department: Computational Biology

institute: UC Berkeley

data_processing:
Sequencing reads were initially filtered with Trimmomatic 0.32 to remove low quality ends and adapter sequences
Bowtie2 v2.2.9  was used to align reads to a reference transcriptome derived from the GRCm38 Mus musculus genome (NCBI Refseq).
RSEM 1.2.31 was used to compile the transcriptome and estimate transcript abundance following read alignment.
Prior to alignment, the GRCm38 reference was augmented to include the modified eGFP+IL23R functional knockout transcript.
Genome_build: GRCm38
Supplementary_files_format_and_content: gene_expression_tpm.txt.gz: tab-delimited text table (genes x cells) of TPM-normalized gene expression values.  cell_metadata.txt: tab-delimited table which contains GFP label, genotype, and stimulation for each cell.

source_name: Th1 differentiated CD4 T Cell - eGFP_neg_IL23R Knockout

extract_protocol:
Spleen and lymph nodes were extracted and then a single-cell suspension was prepared by homogenization with a syringe plunger and debris was filtered with a 70um filter. Red blood cells were lysed with ACK lysis buffer from Lonza. CD4+ T cells were enriched using a bead protocol from Miltenyi Biotech (cat #. 130-117-043) and then stained with anti-CD44 (clone IM7), anti-CD62L (clone Mel14), anti-CD4 (clone RM4-5) and anti-CD25 (clone PC61) in preparation for FACS. Naive T cells were sorted based on CD44lowCD62LhiCD4+CD25-.
T cells were sorted into 96-well plates containing 5 μl TCL Buffer (QIAGEN) with 1% 2-mercaptoethanol, centrifuged and frozen at −80 °C.  Single-cell sequencing libraries were then created using the Smart-seq2 protocol (Picelli et al., Nature Methods 2014) and carried out as described in Singer et. al, Cell 2016.

treatment_protocol: 1x106/ml naive T cells were plated in 6 well dishes and incubated for 4 days with (1) IL-12+IL-21+IL-23 (Th1 cell condition) and (2) IL-1b+IL-6+IL-23 (pathogenic Th17 cell condition). Viable CD4+ T cells were sorted with FACS into eGFP+ (i.e. IL-23R+) and eGFP- (i.e. IL-23R-) population as single cells into 96 well plates pre-loaded with 5ul TCL buffer (containing b-mercaptoethanol according to the manufacturer's instructions, Qiagen). cDNA libraries were prepared as outlined in Pawlak M., DeTomaso, D. et al. 2021 and sequenced.

tag: differentiation

tag: gfp

value: IL23R Knockout

value: CD4 T Cells


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 90

source_name: Th1 differentiated CD4 T Cell - eGFP_neg_Control

value: Control


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 91


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 195


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 194


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 201


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 198


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 92


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 193


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 94


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 96


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 199


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 89


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 200


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 93


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 87


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 86


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 85


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 197


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 82


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 81


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 80


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 95


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 78


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 77


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 88


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 76


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 74


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 75


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 70


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 69


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 73


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 72


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 84


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 64


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 66


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 67


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 83


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 65


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 61


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 63


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 60


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 79


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 57


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 55


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 58


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 56


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 59


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 54


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 53


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 52


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 71


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 68


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 62


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 50


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 51


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 46


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 44


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 48


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 45


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 43


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 39


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 41


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 35


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 36


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 42


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 38


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 34


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 40


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 49


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 37


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 47


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 31


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 33


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 29


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 30


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 32


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 27


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 26


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 28


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 24


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 25


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 23


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 21


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 20


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 19


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 17


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 16


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 22


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 14


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 18


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 15


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 13


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 9


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 8


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 10


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 12


title: cell_Non_infected_3

description:
Cont_3
Gene expression control

value: intestinal epithelial cell line


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 6


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 4


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 2


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 1


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 3


title: Sham-WT

city: Dallas

first: Miao

last: Cui

state: Texas

address: UT Southwestern Medical Center Department of Molecular Biology 6000 Harry Hines Blvd.

institute: UTSW

description: single-nucleus RNAseq

data_processing:
The Cell Ranger Single-Cell Software Suit was used to perform sample demultiplexing, barcode processing and single-cell 3′ gene counting.
The cDNA reads were aligned to the mm10/GRCm38 premRNA reference genome.
Further analyses for quality filtering was performed using the Seurat R package
Doublets were identified using Scrublet and removed from downstream analysis
For quantity filtering, we removed cells that had more than 2500 or fewer than 200 detected genes. We then normalized the data by the total expression, multiplied by a scale factor of 10,000 and log-transformed the result. To account for variation in the number of genes and UMI detected in each cell, we normalized the scaled expression matrix using the ScaleData function and set the vars.to.regress to nUMI and nGenes.  IntegrateData function implemented in Seurat V3 was used to correct batch effects between samples and to merge samples into one Seurat object.
Genome_build: mm10
Supplementary_files_format_and_content: count matrix

source_name: cadiac nuclei

extract_protocol:
Hearts from wildtype and Nrf1 knockout mice were dissected in ice-cold PBS and a transverse cut on the ligation plane (for MI hearts) or similar level (for sham hearts) was made. Heart tissue below the ligation plane was collected and pooled from 4-6 hearts of the same genotype for nuclei isolation.  Cardiac nuclei isolation was performed as previously described (PMID:33111095)
Total cardiac nuclei were used to generate single nucleus RNA-seq libraries using Single Cell 3’ Reagent Kits v2 (10xGenomics) according to the manufacturer’s protocol
single-nucleus RNA-seq

treatment_protocol: Timed-pregnant Nrf1fl/fl:aMHC-Cre and Nrf1fl/fl mice in the C57BL/6 background were used to deliver pups for neonatal MI surgery at P3. Neonatal mice were anesthetized by hypothermia, and neonatal MI was performed as described previously. Briefly, neonatal mice were anesthetized by hypothermia on an ice bed. Lateral thoracotomy at the fourth intercostal space was performed by blunt dissection of the intercostal muscles after skin incision. A tapered needle attached to a non-absorbable 8-0 suture (PROLENE, Ethicon) was passed through the mid-ventricle below the origin of the left anterior descending artery (LAD) coronary artery and tied to induce infarction. The pericardial membrane remained intact after LAD ligation. Myocardial ischemia was indicated by the light pallor of the myocardium below the ligature after suturing. After LAD ligation, neonates were removed from the ice, thoracic wall incisions were sutured with a 7-0 non-absorbable suture, and the skin wound closed by using skin adhesive. Sham-operated mice underwent the same procedure involving thoracotomy without LAD ligation.

value: purified nuclei from heart

value: Wildtype


title: MI-KO

description: single-nucleus RNAseq

value: Nrf1 cardiomyocyte knockout


title: MI-WT

description: single-nucleus RNAseq


title: P1MID7

description: Visium spatial transcriptome  RNAseq

data_processing:
The Space Ranger Single-Cell Software Suit was used to perform sample demultiplexing, reads alignment, and to generate feature-spot matrices.
The cDNA reads were aligned to the mm10/GRCm38 mRNA reference genome. The H&E staining image was supplemented to Spatial Ranger for tissue detection, fiducial detection, and alignment of the spatial position of sequenced data points.
Genome_build: mm10
Supplementary_files_format_and_content: count matrix
Supplementary_files_format_and_content: H&E tissue staining image

source_name: heart transverse section

extract_protocol:
Hearts at 7-day post the surgery were dissected and immediately embedded in a tissue embedding mold filled with OCT and placed in a bath of isopentane and liquid nitrogen. OCT embedded heart tissue blocks were cryosectioned in a cryostat to generate appropriately sized sections for Visium Spatial slides. 10 um sections at 200 um below the ligation suture were collected and placed on the Visum Spatial slides capture areas.
Heart sections were permeabilized for 18 min followed by RNA reverse transcription. The optimized permeabilization time was determined using the Visum Spatial Tissue Optimization Kit (10xGenomics) according to the manufacturer’s protocol. Second strand cDNA was subsequently synthesized on tissue sections and was transferred to an Eppendorf tube after denaturation. The cDNA from the tissue slide that was spatially barcoded was next amplified via PCR and enzymatically fragmentated. P5, P7, i7 and i5 sample indexes are added via End Repair, A-tailing, Adaptor ligation and PCR to make the final sequencing library.
Visium Spatial Transcriptome RNAseq

treatment_protocol: Myocardial infarction surgery was performed on 1-day-old mice by ligating the  left anterior descending artery

tag: position

value: 200 um below ligation suture

tag: condition

value: Myocardial infarction

tag: Stage

value: day 7 post myocardial infarction performed at postnatal day 1


title: Nrf2-1

data_processing:
For data analysis, quality control of RNA-seq data was performed using FastQC Tool (Version 0.11.4).
Sequencing reads were aligned to rat Rnor 6.0 reference genome using HiSAT2 (Version 2.0.4) with default settings and --rna-strandness F. Duplicate reads using Samtools v0.1.18
Aligned reads were counted using featurecount (Version 1.6.0) per gene ID
Differential gene expression analysis was performed with the R package edgeR (Version 3.20.5).
Genome_build: Rnor 6.0
Supplementary_files_format_and_content: Gene expressin fold-change (output from edgeR)

source_name: Cardiomyocytes

growth_protocol: Primary cardomyocytes were isolated from 1- or 2-day-ols Sprague-Dawley rats with the Isolation System for Neonatal Rat/Mouse Cardiomyocytes (Cellutron, nc-6031) according to the manufacturer’s instructions. Cells were plated at a density of 3x105 cells/well to gelatin-coated 12-well plates and were maintained in DMEM/199 medium (3:1, 3% FBS) for 48 h before adenoviral infection.

extract_protocol:
RNA was harvested using Trizol reagent and ectracted using RNeasy Mini Kit (QIAGEN, 74104).
Libraries were prepared using KAPA mRNA HyperPrep Kits

treatment_protocol: Adenoviruses were diluted in DMEM/199 medium containing 3% FBS and were added to cells at an MOI of 50.

value: primary rat neonatal ventricular cardiomyocytes

value: Sprague Dawley

tag: gene overexpression


title: Nrf2-3

tag: strain


title: Nrf2-2


title: Nrf1-3


title: Th1 differentiated CD4 T Cell - eGFP_neg, Control, cell 7

tag: genotype


title: Nrf1-2