title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155(pMH94[Buttersgp57r]), 30 mins, bio rep3

description:
raw_counts
TPM_values


title: B cells; CpGA2

status: Public on Dec 24 2022

type: SRA

city: Changchun

first: Tete

last: Li

state: Jilin

address: Dongminzhu Street No.519

country: China

institute: Jilin University

library_source: transcriptomic

data_processing:
Basecalls performed using Zebracall
After reads filtering, sequenced reads were mapped to mm10 whole genome using HISAT and Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
Transcripts of each sample were reconstructed using StringTie, and the reconstructed information of all samples were combined using Cuffmerge. The integrated transcripts were compared with reference annotation information using Cuffcompare. Then new transcripts were selected, defined, and predicted using CPC.
SNP and INDEL variant of each sample were detected using GATK.
Fragments per kilobase of transcript per million mapped read (FPKM)  were calculated using RSEM v1.2.8
Genome_build: mm10
Supplementary_files_format_and_content: xls files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Spleen

growth_protocol: B cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin and 1 μM of three classes of CpG ODNs for 24 h.

extract_protocol:
B cells were collected, and RNA was extracted using the EasyPure® RNA Kit (ER101-01, TransGen Biotech)
RNA libraries were prepared for sequencing using DNBSEQ protocols

tag: cell type

value: B cells

tag: treatment

value: CpG-A

tag: strain

value: BALB/c

tag: tissue

value: Spleen

tag: age

value: post natal day 42-49


title: CpGB1

source_name: Bone marrow

growth_protocol: pDCs were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, 1% nonessential amino acids, 1% β-mercaptoethanol, and 0.5 μM of three classes of CpG ODNs for 24 h.

extract_protocol:
pDCs were sorted,  and RNA was extracted using Trizol reagent. Illumina HiSeq RNA Sample Prep Kit  was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: pDCs

value: CpG-B

value: Bone marrow

value: post natal day 56-63


title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155(pMH94[Buttersgp57r]), 30 mins, bio rep2

city: Bethlehem

first: Vassie

last: Ware

state: PA

address: 111 research drive

department: Biological Sciences

country: USA

institute: Lehigh University

description:
raw_counts
TPM_values

data_processing:
Azenta Life Sciences  Bioinformatics analysis workflow. (Differential Gene Expression and Gene Ontology Analysis)
Assembly: Mycolicibacterium smegmatis mc2155, Mycobacterium phage Island3, Mycobacterium phage Butters
Supplementary files format and content: Text document, raw_counts
Supplementary files format and content: Text document, normalized_counts
Supplementary files format and content: Excel comma separated value, DEGs

organism:
Mycolicibacterium smegmatis MC2 155
Mycobacterium phage Island3

source_name: Lehigh University

growth_protocol: Bacteria cells were grown to saturated phase and infected with Island3 at MOI of 1:1

extract_protocol:
Azenta Life Sciences
Azenta Life Sciences RNA-seq Library Preparation Workflow

treatment_protocol: Samples were taken at early (30 mins) and late (150 mins) of infection

tag: stage of_infection

value: early infection

tag: time

value: 30 mins

value: Lehigh University


title: TN_6

type: RNA

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: Hybridisation was performed by means of the Agilent Gene Expression Hybridization Kit on whole genome SurePrint G3 Human GE 8x60K V3 microarrays containing probes for 26,803 coding RNAs and 30,606 lncRNAs; slides were washed using the Gene Expression Wash Buffer Kit.

scan_protocol: Slides were then scanned with the Agilent scanner version C. All protocols and kits were purchased from Agilent Technologies.

data_processing: After scanning, array image analysis was carried out using the Agilent Feature Extraction Software v12.1, and then raw expression data was processed by background subtraction (normexp offset = 50) followed by within and between array normalisation, using the LIMMA (LInear Models for Microarray Analysis) package in R software. This dataset contains log normalised intensities.

organism: Homo sapiens

source_name: TNBC sample

label_protocol: cDNA was amplified and labelled with the Agilent SureTag DNA Labeling Kit.

extract_protocol: After tumour area selection, total RNA was isolated from macrodissected sections using the Agilent Absolutely RNA FFPE Kit; reverse-transcribed to corresponding cDNA and in vitro transcribed with the Sigma TransPlex Whole Transcriptome Amplification Kit.

tag: gender

value: female


title: CpGA3


title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155(pMH94[Buttersgp57r]), 30 mins, bio rep1

description:
raw_counts
TPM_values


title: CpGA2


title: CpGA1


title: TN_7


title: TN_5


title: TN_1


title: KO_LDL3

city: Wenzhou

first: Guang

last: Liang

address: Chashan

institute: Wenzhou Medical University

data_processing:
Illumina novaseq 6000 software used for basecalling.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Mouse primary peritoneal macrophages

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mouse primary peritoneal macrophages

tag: genotype

value: KO

value: oxLDL


title: KO_LDL2


title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155, 150 mins, bio rep3

description:
raw_counts
TPM_values

value: control

value: late infection

value: 150 mins


title: 2013/6402


title: 2013/7011


title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155, 150 mins, bio rep2

description:
raw_counts
TPM_values


title: WT_LDL3

value: WT


title: CpGB3

value: BALB/c


title: WT_LDL1


title: 2013/3076


title: KO_LDL1


title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155, 30 mins, bio rep3

description:
raw_counts
TPM_values


title: WT_LDL2


title: KO_Ang3

address: Chashan Street

data_processing:
Illumina novaseq 6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: aorta

value: aorta

value: Ang II


title: KO_Ang2


title: KO_Ang1


title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155, 30 mins, bio rep2

description:
raw_counts
TPM_values


title: Ang3


title: 2013/2443


title: 2014/6175


title: Ang2


title: Ang1


title: E10.5 mouse placenta, young female RNA-seq, litter 3 embryo 1

city: Calgary

first: Myriam

last: Hemberger

state: Alberta

address: 3330 Hospital Drive NW

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

data_processing:
Sequence reads were mapped to GRCm38/mm10 using  STAR aligner (sorted by coordinate) for the RNA-seq fastq files
Read count extraction and normalization were performed on the RNA-seq BAM files using htseq count (order=pos, mode=intersection-nonempty, stranded=reverse)
Assembly: mm10
Supplementary files format and content: tab-delimited text files with raw counts per gene

source_name: placenta

growth_protocol: Young female cohort mice were 7 - 13 weeks of age, and aged female cohort mice were 43 - 50 weeks of age

extract_protocol:
RNA was extracted from tissues using the Invitrogen™ mirVana™ miRNA Isolation Kit
RNA libraries for RNA-seq were prepared using Ultra II Directional RNA Library Prep kit.

value: placenta

tag: developmental stage

value: embryo

tag: maternal age

value: young female


title: YOY-CAF

city: Suwon, Korea

first: Jung Woo

last: Eun

state: Korea

address: Department of Gastroenterology

country: South Korea

institute: Ajou University of Korea

description:
cancer-associated fibroblasts from patient's tissue
YOY-CAF

data_processing:
Sanger / Illumina 1.9 software used for basecalling
Sequencing was performed on Illumina HiSeq2000 machines (Illumina) using the standard Illumina RNAseq protocol with a read length of 2 x 100 bases
All sequenced reads were quality checked using FastQC
featureCounts used for abundance measurement
count data with DESeq2 used for indentifying differentially expressed genes
Genome_build: Genome Research Consortium Human Build 38 [GRCh38], hg38
Supplementary_files_format_and_content: text files with Fastq_screen for each genome

source_name: Hepatocellular carcinoma

growth_protocol: HCC specimens were obtained from patients undergoing tumor resection surgery at the Ajou University Hospital (Suwon, Republic of Korea). Fibroblasts were isolated from their HCC tissues (CAFs), paired adjacent tissues (PAFs), and normal tissues (normal fibroblasts [NFs]). Fresh tissue samples were washed with phosphate-buffered saline (GenDEPOT, Barker, TX, USA) and finely minced into small pieces (<1 mm3). Then, tissues were incubated in fresh culture medium to promote attachment of fibroblasts to the culture dish. Isolated fibroblasts were maintained in Dulbecco’s modified Eagle’s medium (GenDEPOT) containing 10% FBS (Invitrogen, Waltham, MA, USA) and 100 units/mL penicillin-streptomycin (GenDEPOT), at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
For next generation sequencing RNA-seq analysis, total RNA was extracted from normal fibroblasts (NFs), para-cancer-associated fibroblasts (PAFs), and cancer-associated fibroblasts (CAFs) using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). RNA quality control was performed with the Agilent Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA). The sequencing library was prepared with Truseq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, CA, USA), followed with library quality check using Agilent Bioanalyzer system.
Sequencing was performed on Illumina HiSeq2000 machines (Illumina) using the standard Illumina RNAseq protocol with a read length of 2 x 100 bases. All sequenced reads were quality checked using FastQC followed by mapping to the human reference genome (Genome Research Consortium Human Build 38 [GRCh38], hg38) and the Ensembl release-102 version 73 gene annotation using HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts 2) (v2.2.1). To compare expression between genes within samples, gene expression was estimated using StringTie v2.1.4 (v2.1.4) from the “new Tuxedo” package. Gene abundances were normalized to library and gene length by calculating fragments per kilobase of exon per million mapped reads using featureCounts and differentially expressed genes were identified by count data with DESeq2.

tag: fibroblast type

value: cancer-associated fibroblasts

value: liver tissue

tag: diagnosis

value: HCC


title: 2015/5160

value: female


title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155, 150 mins, bio rep1

description:
raw_counts
TPM_values

value: Lehigh University


title: E10.5 mouse placenta, young female RNA-seq, litter 2 embryo 1


title: E10.5 mouse placenta, young female RNA-seq, litter 1 embryo 1


title: E10.5 mouse heart, young female RNA-seq, litter 2 embryo 1

source_name: heart

value: heart


title: SDH-CAF

description:
cancer-associated fibroblasts from patient's tissue
SDH-CAF


title: SMJ-CAF

description:
cancer-associated fibroblasts from patient's tissue
SMJ-CAF


title: 2015/4683


title: E10.5 mouse heart, young female RNA-seq, litter 1 embryo 1


title: PYS-CAF

description:
cancer-associated fibroblasts from patient's tissue
PYS-CAF


title: E10.5 mouse facial prominences, young female RNA-seq, litter 1 embryo 1

source_name: face

value: face


title: E10.5 mouse facial prominences, young female RNA-seq, litter 2 embryo 1


title: LKO-CAF

description:
cancer-associated fibroblasts from patient's tissue
LKO-CAF


title: E10.5 mouse facial prominences, young female RNA-seq, litter 3 embryo 1


title: E10.5 mouse brain, young female RNA-seq, litter 3 embryo 1

source_name: brain

value: brain


title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155, 30 mins, bio rep1

description:
raw_counts
TPM_values

value: control

value: early infection

value: 30 mins


title: KYS-CAF

description:
cancer-associated fibroblasts from patient's tissue
KYS-CAF


title: 2015/1022


title: 2016/8698


title: E10.5 mouse brain, young female RNA-seq, litter 1 embryo 1


title: 2016/763


title: E10.5 mouse heart, young female RNA-seq, litter 3 embryo 1


title: E10.5 mouse placenta, aged female RNA-seq, litter 3 embryo 2

value: aged female


title: 2016/3262


title: 2014/5721


title: 2015/2474


title: DHS-CAF

description:
cancer-associated fibroblasts from patient's tissue
DHS-CAF


title: E10.5 mouse placenta, aged female RNA-seq, litter 3 embryo 1


title: 2014/4762


title: E10.5 mouse placenta, aged female RNA-seq, litter 2 embryo 2


title: E10.5 mouse placenta, aged female RNA-seq, litter 2 embryo 1


title: CHI-CAF

description:
cancer-associated fibroblasts from patient's tissue
CHI-CAF


title: E10.5 mouse placenta, aged female RNA-seq, litter 1 embryo 2


title: ASY-CAF

description:
cancer-associated fibroblasts from patient's tissue
ASY-CAF


title: tMCAO8

city: New York

first: Teresa

last: Sanchez

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
Normalized cDNA libraries were pooled and sequenced on Illumina HiSeq4000 sequencer with pair-end 75 cycles
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing
Cutadapt was used to trim low quality bases and adapters
Raw read counts were calculated using HTseq-count
Differential expression analysis was performed using DEseq2 package
Assembly: STAR was used to align raw sequencing reads to the mouse GRCm38 - mm10 reference genome
Supplementary files format and content: Excel file of Log2FC analyses and Z-score calculation

extract_protocol:
RNA was isolated using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA integrity and other quality control measures were performed  along with ribosomal RNA depletion
RNA libraries for RNA-seq were prepared using Total RNA Library Prep Kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

tag: cell line

value: microvessel

value: wild type

value: tMCAO


title: E10.5 mouse brain, young female RNA-seq, litter 2 embryo 1

value: embryo


title: tMCAO7


title: E10.5 mouse heart, aged female RNA-seq, litter 3 embryo 2


title: tMCAO6


title: YOY-PAF

description:
para-cancer fibroblasts from patient's tissue
YOY-PAF

value: para-cancer fibroblasts


title: E10.5 mouse heart, aged female RNA-seq, litter 3 embryo 1


title: E10.5 mouse heart, aged female RNA-seq, litter 2 embryo 2


title: E10.5 mouse heart, aged female RNA-seq, litter 2 embryo 1


title: tMCAO5


title: SMJ-PAF

description:
para-cancer fibroblasts from patient's tissue
SMJ-PAF


title: 2013/843


title: SDH-PAF

description:
para-cancer fibroblasts from patient's tissue
SDH-PAF


title: E10.5 mouse heart, aged female RNA-seq, litter 1 embryo 2


title: E10.5 mouse placenta, aged female RNA-seq, litter 1 embryo 1

value: placenta


title: 2013/699


title: E10.5 mouse heart, aged female RNA-seq, litter 1 embryo 1


title: E10.5 mouse facial prominences, aged female RNA-seq, litter 3 embryo 1


title: PYS-PAF

description:
para-cancer fibroblasts from patient's tissue
PYS-PAF

value: liver tissue


title: E10.5 mouse facial prominences, aged female RNA-seq, litter 3 embryo 2


title: SHAM3

value: sham


title: E10.5 mouse facial prominences, aged female RNA-seq, litter 2 embryo 2


title: SHAM2


title: LKO-PAF

description:
para-cancer fibroblasts from patient's tissue
LKO-PAF

value: HCC


title: E10.5 mouse facial prominences, aged female RNA-seq, litter 2 embryo 1


title: E10.5 mouse facial prominences, aged female RNA-seq, litter 1 embryo 2


title: KYS-PAF

description:
para-cancer fibroblasts from patient's tissue
KYS-PAF


title: E10.5 mouse facial prominences, aged female RNA-seq, litter 1 embryo 1


title: DHS-PAF

description:
para-cancer fibroblasts from patient's tissue
DHS-PAF


title: SHAM1


title: TN_24

value: female


title: E10.5 mouse brain, aged female RNA-seq, litter 3 embryo 2


title: E10.5 mouse brain, aged female RNA-seq, litter 3 embryo 1


title: E10.5 mouse brain, aged female RNA-seq, litter 2 embryo 2


title: CHI-PAF

description:
para-cancer fibroblasts from patient's tissue
CHI-PAF


title: E10.5 mouse brain, aged female RNA-seq, litter 2 embryo 1


title: SHAM4


title: E10.5 mouse brain, aged female RNA-seq, litter 1 embryo 2


title: E10.5 mouse brain, aged female RNA-seq, litter 1 embryo 1


title: Oc2svz

city: Palo Alto

first: Ling

last: Liu

address: 300 Pasteur Drive

institute: Stanford University

data_processing:
Sequences were demultiplexed using CellRanger version 2.0 (10x Genomics) with default parameters.
Reads were aligned to the mm10plus genome using STAR.
Gene counts were produced using HTSEQ with default parameters except “stranded” was set to false and “mode” was set to intersection-nonempty.
Genome_build: mm10plus

source_name: brain subventricular zone

extract_protocol: 10x Genomics protocol using GenCode Single-Cell 3’ Gel Bead and Library V3 kit

value: male

value: 22 months


title: HWY-NF

description:
normal fibroblasts from patient's tissue
HWY-NF

value: Normal fibroblasts


title: Oc3svz

value: control


title: ASY-PAF

description:
para-cancer fibroblasts from patient's tissue
ASY-PAF


title: Oc4svz


title: WT-iEpiSC-rp3

city: Guangzhou

first: gibh

last: hpc

state: Guangdong

address: No. 190, Kaiyuan Avenue, Huangpu District,

department: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

institute: Biomedical Data & HPC

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
RNAseq reads were aligned to the mm10 genome assembly using rsem with options --bowtie2 --bowtie2-sensitivity-level very_sensitive
expected_count were extract from the sample_name.genes.results and merged together to get a big table
RNAseq data was normalized by EDAseq
Genome_build: mm10
Supplementary_files_format_and_content: tsv file was generated form normalized RNAseq data, it include all samples' RNAseq data

source_name: WT-iEpiSC

growth_protocol: ESCs cells cells were cultured in N2B27+2i+LIF medium, EpiSCs were maintained in FN medium which comprised F12 / Neurobasal (1:1) with N2, B27, NEAA, GlutaMAX, BSA, 100 mM 2-mercaptoethanol, 20 ng/ml ActivinA and 20 ng/ml bFGF

extract_protocol:
Total RNA was prepared with TRIzol. For quantitative PCR, cDNAs were synthesized with ReverTra Ace (Toyobo) and oligo-dT (Takara), and then analyzed by qPCR with Premix Ex Taq (Takara).
For RNA-seq, TruSeq RNA Sample Prep Kit (RS-122-2001, Illumina) was used for library construction and the sequencing was done using a NextSeq 500 High Output Kit v2 (75 cycles) (FC-404-1005, Illumina), according to the manufacturers instructions.

treatment_protocol: ESCs were digested to single cells and replanted in serum coated 6-well plate at a density of 1×10^4 per well. After 8 hours, the ESCs culture medium was removed, and cells were washed with DPBS twice carefully. FN medium plus XAV939 (2 μM) and IWR-1 (2.5 μM) was used to convert ESCs to iEpiSCs. FN+X/I medium were changed everyday, and EpiSC-like colonies were emerged at 4-5 days. iEpiSCs were cultured as EpiSCs

value: EpiSC


title: Oex4svz

value: 5-week voluntary wheel running


title: Oex3svz


title: Response regulator deletion mutant, replicate 2

city: Williamsburg

first: Madison

last: Allen

address: 540 Landrum Dr

department: Biology

institute: William & Mary

data_processing:
The raw data is filtered to remove low-quality reads as well as sequences that contain adapters using a software called HISAT2. Using Feature Counts the number of reads that map to a single location were summarized and from here, the reads are then assigned to a gene. The RNA-seq data was then  normalized to account for the total reads sequenced for each sample or the read depth.
To check for differentially expressed genes, a software called DESeq2 was used. This software used the raw data to calculate a group mean and a global mean. It then calculatesdthe deviations of the group mean from the global mean to determine if any changes in gene expression are significant. The output from this provided p-values to determine the significance as well as the gene name, location, and description of its function.
Assembly: H. pylori 26695 genome (GenBank accession no. CP003904.1).

organism: Helicobacter pylori 26695

growth_protocol: H. pylori cells were cultured in sulfite-free brucella broth with cholesterol for 6 h.

extract_protocol:
RNA was harvested using RNAzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols with 1ug of total RNA.
Libraries were sequenced on a NovaSeq 6000 with paired reads of 150-bp length, according to the manufacturer’s protocol.

value: Response regulator deletion mutant


title: Histidine kinase deletion mutant, replicate 2

value: Histidine kinase deletion mutant


title: Control mutant, replicate 1

value: Control mutant


title: Oex2svz


title: Response regulator deletion mutant, replicate 1


title: Histidine kinase deletion mutant, replicate 1


title: Jun-iEpiSC-rp3

source_name: Jun-iEpiSC

value: c-Jun-/-


title: Oex1svz


title: Jun-iEpiSC-rp2


title: Yc4svz

value: 4 months


title: Yc2svz


title: Yc3svz


title: Control mutant, replicate 2


title: LG255_biolrep_2

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

institute: University of British Columbia

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v2.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: http://gigadb.org/dataset/100246
Supplementary files format and content: Tab-separated values files and matrix files

organism: Eublepharis macularius

source_name: tissues enclosing oral mucosa, dental lamina and dental mesenchyme

extract_protocol:
Soft tissues from adult gecko jaws that included unerupted teeth and dental lamina were dissected and place in cold 1X HANKS solution without Calcium and Magnesium with 10% fetal bovine serum (FBS). The tissues were chopped into small segments. Animal LG252 pieces were placed in the dissection media with collagenase D (SIGMA, COLLD-RO; 1.5 U/ml)/ Dispase II (SIGMA, D4693; 2.4 U/ml) for 37°C for 4-5 hours in an orbital shaker. LG255 pieces were placed into Bacillus Licheniforms protease (SIGMA, 85380; 10 mg/ml) in dissection media on a shaker at 4 degrees for 6 hours.  Once the cells were mechanically dissociated, cells were spun down and counted. They were transferred into FACS buffer (2 ml EDTA, 2% FBS, 1X PBS) and resuspended in 2 ml final volume. Cells were passed through a 40 µm cell filter to remove clumps. Live versus dead cells were distinguished with propidium iodide exclusion (1:5000 in FACS buffer). Cells were fluorescence activated cell sorted in DMEM + 5% FBS media. Then, we collected cells at a final concentration of 50,000 cell/ml.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).


title: Yc1svz


title: Yex4svz


title: WT-iEpiSC-rp2

value: wild type


title: LG252_biolrep_2

description: 10x Genomics

value: tissues enclosing oral mucosa, dental lamina and dental mesenchyme


title: LG252_biolrep_1

description: 10x Genomics


title: SG200_12dpi_3

city: Cambridge

first: Clement

last: Pellegrin

address: Downing Site

department: Plant Sciences

country: United Kingdom

institute: University of Cambridge

description: Gene expression data

data_processing:
Reads were quality-filtered (PhredScores lower 20), trimmed for the TruSeq adapters and statically trimmed 12 nucleotides at the 5’ end. Reads smaller than 50 nucleotides were discarded. When the paired end reads did overlap with at least 10 nucleotides they were merged to single reads. All analysis was performed using the CLC Genomics Workbench v8.5 (CLC Bio-Qiagen).
For the U. maydis analysis, all reads were filtered against the maize genes (90% identity over 80% of the sequence) and only un-mapped reads were mapped against the U. maydis genes (80% identity over 60% of the sequence). Mapping was performed using the CLC Genomics Workbench v8.5 (CLC Bio-Qiagen).
For the U. maydis analysis, all unique exon read counts of the samples 1-9 were normalized using DESeq2 v1.10.
Genome_build: The U. maydis reference genome was from NCBI (http://www.ncbi.nlm.nih.gov/, accession numbers NC_026478.1 - NC_026500.1, NW_011929455.1 - NW_011929458.1, NC_008368.1).
Genome_build: The Z. mays reference genome was from Ensembl (http://plants.ensembl.org/info/website/ftp/index.html, Zea_mays.AGPv3.28.dna.toplevel).
Supplementary_files_format_and_content: Tab delimited text files containing total number of unique exon counts for each U. maydis gene (Counts_Um.txt), DESeq2-normalized counts for each U. maydis gene (NormCounts_Um.txt).

molecule: polyA RNA

organism: Mycosarcoma maydis

source_name: infected plant material

growth_protocol: Ustilago maydis strains SG200 was grown to OD600=1.0 in YEPSL, pelleted and resuspended in water. The compatible strains were mixed in equal quantities and injected into 7-day old maize seedlings

extract_protocol:
For each sample, leaf sections from 10 different plants infected with SG200 U. maydis were collected, pooled and frozen in liquid nitrogen. Samples were ground to a fine powder in liquid nitrogen and total RNAs were extracted using the TRIzol method (Invitrogen)
Sequencing libraries were prepared with the Illumina TruSeq stranded mRNA library Prep Kit starting from 2µg total RNA.

tag: fungal strain

tag: host plant

value: EGB

tag: Stage

value: 12 days post infection

tag: agent

value: Zea Mays


title: SG200_2dpi_3

description: Gene expression data

value: 2 days post infection


title: SG200_12dpi_2

description: Gene expression data


title: SG200_12dpi_1

description: Gene expression data


title: Yex3svz

value: male

tag: treatment


title: LG255_biolrep_1

description: 10x Genomics


title: Yex2svz

tag: strain


title: SG200_2dpi_2

description: Gene expression data


title: SG200_2dpi_1

description: Gene expression data


title: SG200_ax_3

description: Gene expression data

source_name: fungal axenic culture

value: yeast-like cells


title: Yex1svz


title: SG200_ax_2

description: Gene expression data


title: SG200_ax_1

description: Gene expression data


title: LPS4_NS

first: Yingzhou

last: Shi

address: 余杭塘路866号浙江大学紫金港校区白沙4舍111

institute: 浙江大学

description: CircRNA, lncRNA and mRNA expression in injured spinal cord in heart in mice at 6 hours after  intraperitoneal injection of LPS

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R

source_name: LPS, 6h replicate 4

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: tissue

value: heart


title: LPS2_NS

address: 余杭塘路866号浙江大学紫金港校区白沙4舍111

source_name: LPS, 6h replicate 2

tag: age


title: cfea_470d

status: Public on Dec 23 2022

type: genomic

city: Chicago

first: Emma

last: Thompson

state: IL

address: 920 E 58th St, CLSC Rm 501

department: Human Genetics

institute: The University of Chicago

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using standard Illumina scanner settings.

data_processing:
Probes located on the sex chromosomes and those with detection P values > 0.01 in 75% of samples were removed. Probes mapping to more than one genomic location or overlapping with known SNPs (MAF>5%) were also excluded. Data were processed using Minfi; Infinium type I and type II probe bias were corrected using ENmix. Please see https://github.com/hansenlab/IlluminaHumanMethylationAllergymanifest for annotation and manifest packages (use version 0.8.0).
ENmix normalized Beta values

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina protocol.

extract_protocol: Samples were spun through a Qiashredder column and then extracted using AllPrep DNA/RNA mini kits (Qiagen) following the manufacturer's protocol.

tag: Sex

value: Female

tag: percentciliatedepithelialcells

tag: proportionpositiveskinpricktests

tag: plate

tag: array


title: d902_4698

value: Male


title: 62c5_4d11


title: bf7c_4c07


title: b5bf_44ef


title: f66f_4cda


title: 0a13_43f4


title: d1b2_42f1


title: 81f8_457f


title: a2aa_4f37


title: 540b_41ce


title: LPS3_NS

address: 余杭塘路866号浙江大学紫金港校区白沙4舍111

source_name: LPS, 6h replicate 3

tag: gender


title: LPS1_NS

address: 余杭塘路866号浙江大学紫金港校区白沙4舍111

source_name: LPS, 6h replicate 1


title: cd72_4cbe


title: cont1_NS

address: 余杭塘路866号浙江大学紫金港校区白沙4舍111

description: CircRNA, lncRNA and mRNA expression in normal heart in mice

source_name: Control, replicate 1


title: cont3_NS

address: 余杭塘路866号浙江大学紫金港校区白沙4舍111

source_name: Control, replicate 3


title: cont2_NS

address: 余杭塘路866号浙江大学紫金港校区白沙4舍111

source_name: Control, replicate 2


title: b43a_4247


title: db7d_4d13


title: d4a8_4b32


title: 5498_40e4


title: a122_483d


title: antagomiR31 naive CD4+ T cells-large cells

city: Shanghai

first: Lingyan

last: Zhu

address: 2901 Caolang Road, Jin Shan District

institute: Shanghai Public Health Clinical Center, Fudan University

hyb_protocol: The microarray hybridization and washing were performed based on the manufacturer’s standard protocols.

scan_protocol: Slides were scanned immediately after washing by the Agilent Scanner G2505C(Agilent Technologies)

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data.

source_name: antagomiR31, naive CD4+ T cells, large cells

label_protocol: The sample labeling was performed based on the manufacturer’s standard protocols.

extract_protocol: Total RNA was prepared using Direct-zol RNA Mini Prep (ZYMO RESEARCH) following the manufacturer's recommendations.  Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies)

treatment_protocol: Naive CD4+ T cells were isolated from peripheral blood from healthy volunteers, then transfected with antagomiR-31 (120 pmol/1 × 106 cells) by Turbofect to inhibit endogenous miR-31, negative control was employed in parallelly.  Cells were cultured with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum, and incubated for 48 hours at 37 ºC in a humidified incubator with 5% CO2.

value: whole blood

tag: cell type

value: naive CD4+ T cell


title: antagoNC treated naive CD4+ T cells

source_name: antagoNC, naive CD4+ T cells


title: 2244_4759


title: Cont4_NS

address: 余杭塘路866号浙江大学紫金港校区白沙4舍111

source_name: Control, replicate 4


title: aacf_4181


title: antagomiR31 treated naive CD4+ T cells-small cells

source_name: antagomiR31, naive CD4+ T cells, small cells


title: e7cc_41d3


title: a567_4fc3


title: 3206_422c


title: 60c3_4cd8


title: eb8a_436e


title: c5dd_4ee6


title: 8af4_407f


title: d1e7_402b


title: 227d_4725


title: 8809_4320


title: 770d_4553


title: 10e7_4e7b


title: ed75_4417


title: d267_4880


title: fa79_4cc3


title: 192f_4945


title: b74e_49f1


title: 4680_4b7c


title: 4bcf_414d


title: 099a_4799


title: c005_446f


title: 4438_4db6


title: 9cb0_48bf


title: 7e48_44cb


title: 4193_4778


title: 4da9_4107


title: ecad_4437


title: 6979_489c


title: 83a6_464b


title: 365d_450b


title: 917d_4410


title: 8be9_46af


title: 3450_4e8e


title: 7622_45fe


title: 96f7_46dd


title: 65f1_447a


title: c851_439a


title: e7de_4d41


title: 73c8_4609


title: 219a_49ed


title: 6ace_4528


title: 03b3_4f8c


title: 3f3a_408c


title: e653_43c4


title: e3c7_4cdd


title: da4b_43af


title: 2a21_497b


title: a812_455a


title: 8d48_42c7


title: fbf2_4f46


title: 5340_4c6e


title: 1f68_4160


title: 85aa_4e0f


title: 1b47_432d


title: f70a_47b0


title: 55d2_4cce


title: b030_4319


title: 1796_4d1a


title: 5ece_44ed


title: 5831_458f


title: f972_4900


title: 4fe8_4e7f


title: c9f7_426d


title: 0276_4d38


title: a963_44d0


title: f4e1_42aa


title: 45a5_4e0f


title: f665_4e1b


title: 0235_44d9


title: 00d1_4cde


title: 4081_4b64


title: d18f_4008


title: a706_4f38


title: 7a6d_4bda


title: 1c92_4793


title: c18f_4818


title: 32fa_4a92


title: 5450_4370


title: 446a_413f


title: 1f03_445a


title: e0e9_4dc6


title: 06f1_4902


title: 83cf_4f30


title: 3e33_44a4


title: 504c_425c


title: 2a8d_46e8


title: 56bb_47e9


title: e47c_4e9b


title: 248d_4901


title: a55c_472f


title: a60f_493d


title: 9790_40b6


title: 628c_4467


title: 5ef4_459d


title: 85cd_4430


title: cc7c_421d


title: 99e1_4d92


title: 3867_4ee0


title: 294a_4d95


title: 5ac0_4c3e


title: 2c93_4702


title: 71e3_4eb8


title: 5aeb_466f


title: d9bd_448a


title: 5348_41b1


title: 7804_4bab


title: 1723_4ac8


title: 60aa_40f1


title: fda4_4c5e


title: 3cde_4458


title: d084_4cd9


title: 7131_4332


title: 4554_4bab


title: 9e45_40b0


title: 8e15_45ca


title: 3c61_4020


title: 8fc1_4c8c


title: 5a30_4238


title: 1455_4f52


title: 6a32_47fc


title: 68f8_4d10


title: e083_4c15


title: 3844_44af


title: 7a8b_490f


title: 303d_4f34


title: 2e3c_4388


title: 8941_454a


title: 9df6_44a2


title: c9c3_41ae


title: 7a79_4237


title: c21a_4a25


title: 7527_417c


title: ac8a_4da4


title: 204568250060_R08C01

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

hyb_protocol: Bisulfite-converted DNAs were used as a substrate for the Illumina EPIC BeadArrays, as recommended by the manufacturer and first described in Moran, 2016. Specifically, each sample was whole genome amplified (WGA) and enzymatically fragmented. Samples were then hybridized overnight to an 8-sample BeadArray, in which the WGA-DNA molecules annealed to locus-specific DNA oligomers linked to individual bead types. The oligomer probe designs follow the Infinium I and II chemistries, in which base extension follows hybridization to a locus-specific oligomer.

scan_protocol: After the chemistry steps, BeadArrays are scanned and data recorded as iDAT files

data_processing:
Statistical analysis was carried out in R version 4.2.1. For analysis of our novel cohort, probes were normalized using the preprocessQuantile() function of the minfi package, while specifying sample sex. Probes were removed from downstream analysis if: (i) they had a detection P-value>0.01; (ii) were cross-reactive; (iii) contained a SNP at the single base extension or CpG interrogation site at any MAF; (iv) were not present in a CpG context; and (v) were present on either sex chromosome. Additional probes were removed if they failed in at least one sample under default parameters of the openSesame() function.
Each "race" was analyzed individually and subjected to differing filtering levels, resulting in different files for detection P values and processed betas according to self-reported race.

label: Cy3, Cy5

label_protocol: Not provided

extract_protocol: Genomic DNA was isolated from rectal tissues using the Qiagen DNA Midi Kit (Qiagen, Valencia, CA). Genomic DNA was eluted in 50-100 µl elution buffer. It was then quantified using Nanodrop technology before bisulfite conversion using the Zymo EZ kit (Zymo Research, Irvine, CA) according to the manufacturer’s recommendations.

value: F

tag: bmi

tag: adenoma

value: No

tag: race

value: African American

value: Normal Rectum


title: 204568250060_R06C01

value: Yes


title: 204568250060_R07C01

value: M


title: 19c1_493c


title: ead4_485e


title: 1822_46c3


title: e32e_430b


title: 204367460146_R08C01


title: 204568250060_R05C01

value: European American


title: 204568250060_R03C01


title: 204568250060_R02C01


title: 204568250060_R01C01


title: 204568250060_R04C01


title: 204367460146_R06C01


title: 75a1_4e15


title: 9747_46ec


title: 204367460146_R05C01


title: c9ed_47e4


title: 204367460146_R03C01


title: 204367460146_R04C01


title: ce4e_4ee7


title: 204367460146_R02C01


title: 9ea6_469e


title: 45f8_4239


title: debb_4963


title: 204367460131_R08C01


title: 2ca0_46f0


title: cf5a_43e2


title: 204367460146_R01C01


title: 204367460131_R07C01


title: 12d8_4b2c


title: 4fd7_42e0


title: 204367460131_R06C01


title: 204367460131_R05C01


title: 56e0_4dbf


title: 204367460131_R02C01


title: 204367460131_R03C01


title: cb8c_4f8c


title: a102_4294


title: 94db_415e


title: 797f_4a4f


title: 204367460131_R01C01


title: 1644_43b3


title: eaa4_49a1


title: 78f3_41a8


title: 204367460076_R06C01


title: 204367460076_R08C01


title: 61ab_4b98


title: 204367460076_R07C01


title: 204367460076_R05C01


title: 204367460076_R04C01


title: 849c_424f


title: 204367460076_R03C01


title: c327_4fff


title: 204367460076_R01C01


title: 204367460131_R04C01


title: a894_4adc


title: 835d_496e


title: 4ca7_42b1


title: 204367460037_R07C01


title: 204367460037_R06C01


title: 204367460037_R08C01


title: 204367460037_R05C01


title: a768_4b98


title: 2bcd_4835


title: 91ff_4ca7


title: f1e1_45c6


title: 204367460037_R03C01


title: 61a2_48bb


title: 204367460037_R02C01


title: cfa6_4e5f


title: 56b6_49db


title: 204367460037_R01C01


title: e454_4e68


title: aae5_4276


title: 6a3c_49d4


title: 204367410057_R06C01


title: f5de_46e9


title: d7bb_48eb


title: 204367410057_R05C01


title: 204367410057_R04C01


title: 67a8_4cad


title: cc03_400c


title: 68ad_4244


title: 204367410057_R02C01


title: 204367410057_R03C01


title: b6f6_4619


title: 204367410009_R05C01


title: dc0b_4294


title: 204367410009_R08C01


title: 204367460037_R04C01


title: 204367410057_R01C01


title: 8dab_416d


title: 5b26_42a3


title: ca71_44ab


title: 204367410009_R07C01


title: 204367410009_R02C01


title: 975b_4857


title: 204367410057_R07C01


title: fae2_422f


title: 204367400133_R08C01


title: 180e_47a6


title: 204367410009_R03C01


title: 26f6_4a54


title: 204367400133_R05C01


title: 204367400133_R04C01


title: fb23_478a


title: 204367400133_R07C01


title: 9b22_452c


title: 204367410009_R04C01


title: 4781_40a3


title: 9854_46d3


title: 204367400133_R06C01


title: 204367400133_R01C01


title: e217_4562


title: 204367400133_R03C01


title: 204367400128_R08C01


title: 204367400128_R07C01


title: f947_445f


title: cdd3_4282


title: 204367400128_R06C01


title: 204367400128_R04C01


title: 204367400128_R02C01


title: 5f28_4154


title: e013_484e


title: 204367400128_R01C01


title: e3fe_4b4e


title: 204367400127_R08C01


title: f173_43c7


title: d3d0_4867


title: 80e0_4fa8


title: 204367400127_R07C01


title: 8207_47b9


title: 204367400128_R05C01


title: 204367400127_R04C01


title: 8fed_4797


title: 204367400127_R03C01


title: 204367400127_R01C01


title: baf5_4b60


title: 5a5e_4c64


title: 204367400127_R02C01


title: 42b8_4d34


title: 62a4_487e


title: ad65_430b


title: 204367400082_R08C01


title: 204367400082_R05C01


title: 87f4_4ec7


title: 204367400082_R06C01


title: 57aa_42ac


title: 204367400082_R07C01


title: 819d_425d


title: 204367400082_R04C01


title: 28f6_409a


title: 083e_47e3


title: 204367400082_R03C01


title: 204367400082_R02C01


title: 204367400031_R08C01


title: 6229_4f52


title: 204367400031_R07C01


title: b0f0_4248


title: 204367400031_R06C01


title: 4e16_40e8


title: 204367400127_R06C01


title: f408_46cc


title: 8b6b_436d


title: 65d9_411e


title: a280_4aa3


title: dc7f_4ede


title: 204367400025_R08C01


title: 204367400031_R03C01


title: 204367400031_R02C01


title: d251_4dd9


title: 204367400031_R01C01


title: e001_49ca


title: 6c79_4493


title: 204367400025_R04C01


title: 204367400025_R03C01


title: fd34_4c71


title: 11fb_4a49


title: 204367400025_R02C01


title: 925c_4863


title: 2ac4_41fa


title: 204367400025_R01C01


title: b563_48fa


title: 204367400018_R08C01


title: 204367400018_R07C01


title: f22c_4753


title: 204367400031_R05C01


title: 204367400031_R04C01


title: 204367400018_R06C01


title: 204367400025_R06C01


title: c513_4773


title: 204367400018_R05C01


title: c897_4012


title: d39c_4ee4


title: tail Fltp+

city: Munich

first: Karin

last: Hrovatin

address: Ingolstädter Landstraße 1

department: Institute of Computational Biology

country: Germany

institute: Helmholtz Munich

data_processing:
Cell Ranger
Assembly: Ensembl release 94 mm10 with custom genes for Fltp reporter
Supplementary files format and content: Raw UMI count matrix (feature x droplet barcode) from 10X Genomics single cell RNAseq experiments. Gzipped collection of count matrix in market matrix format, droplet barcodes as tab-delimited text file, and gene names as tab-delimited text file.

source_name: pancreas tail - islets of Langerhans

extract_protocol:
Pancreas head and tail were anatomically separated, followed by islet isolation with a standard protocol (Corbin et al., 2021; https://doi.org/10.1186/s12575-021-00143-x; D.-S. Li et al., 2009; https://doi.org/10.1038/nprot.2009.150). Islets from six FltpZV/+  mice were pooled. Fltp Venus reporter positive and negative cells were sorted.
Libraries of single cells were produced using the Chromium Single-Cell 3′ library and 10XGenomics gel bead kit v2 (PN #120237). Briefly, 10,000 cells were loaded per channel of a 10x chip to produce gel bead-in-emulsions (GEMs). Then the samples underwent reverse transcription to barcode RNA followed by cleanup, cDNA amplification, enzymatic fragmentation, 5′ adaptor, and sample index attachment. The samples were sequenced using a HiSeq4000 (Illumina) with 150 bp paired-end sequencing.

value: pancreas tail - islets of Langerhans

tag: genotype

value: Fltp ZV (Het)

tag: cell sorting

value: Fltp+

value: 4 months


title: 204367400025_R05C01


title: 204367400018_R04C01


title: 9681_4fc0


title: afd9_4a3c


title: 204367400018_R03C01


title: 204367400014_R08C01


title: 204367400018_R01C01


title: head Fltp+

source_name: pancreas head - islets of Langerhans

value: pancreas head - islets of Langerhans

value: male


title: 204367400018_R02C01


title: 99e1_41b9

value: Female


title: 204367400014_R06C01


title: 204367400014_R05C01


title: head Fltp-

value: Fltp-


title: 204367400014_R03C01


title: 4cb1_4368


title: a183_4278


title: 204367400014_R01C01


title: 204367400013_R08C01


title: 24

city: Seattle

first: Brennan

middle: H

last: Baker

state: WA

institute: Columbia University Mailman School of Public Health

data_processing:
FASTQ files were preprocessed with fastp using the default settings to filter bad reads, trim low quality bases, and cut adaptors.
Reads were mapped to the GRCM38(mm10) mouse genome using BWA-MEM
Mapped reads assigned to exons using featureCounts
Performed differential expression analysis using DESeq2.
Gene expression fold-changes compared acetaminophen treated to control offspring, accounting for sex.
Assembly: Grcm38(mm10)
Supplementary files format and content: Normalized counts from deseq2

source_name: Prefrontal cortex

extract_protocol:
Qiagen Rneasy
Library preparation, Illumina, RNA with PolyA selection

value: Acetaminophen

value: Prefrontal cortex


title: 23


title: 204367400013_R06C01


title: 55c8_4f16

value: Male


title: 22


title: 204367400013_R05C01

value: F

value: No


title: tail Fltp-


title: 21


title: 204367400014_R07C01

value: African American

value: Normal Rectum


title: 204367400013_R03C01

value: M


title: cbc2_4320


title: 30e4_4640


title: 20


title: 204367400013_R02C01


title: 204367400013_R01C01

value: Yes


title: 204367400012_R07C01


title: 204367400012_R08C01

value: European American


title: 204367400012_R06C01


title: 204367400012_R05C01


title: 18

value: female


title: cf68_4ec1


title: 204367400014_R02C01


title: 204367400012_R04C01


title: 17


title: 204367400012_R02C01


title: 204367400012_R03C01


title: 7f3a_4ad2


title: 16


title: 2794_48f9


title: 204367400013_R04C01


title: a666_4d31


title: 348c_4810


title: 15


title: 204367400012_R01C01


title: 204367400006_R07C01


title: 204367400006_R08C01


title: 19


title: 204367400006_R06C01


title: 14


title: 5636_4f30


title: 204367400006_R04C01


title: 204367400006_R05C01


title: 13


title: 204367400006_R03C01


title: 204367400006_R02C01


title: 12

value: Control


title: 204308910033_R08C01


title: 90d2_46cd


title: 204367400006_R01C01


title: 11


title: 459b_4030


title: 204308910033_R07C01


title: 204308910033_R06C01


title: cd06_4d2c


title: 204308910033_R04C01


title: 9


title: 204308910033_R03C01


title: 4c2b_4543


title: 204308910033_R01C01


title: 10


title: 8


title: 7a4b_4bc0


title: 7


title: 0229_43b6


title: 204308910033_R05C01


title: mpra_plasmid

city: Stanford

first: Margaret

last: Guo

state: CA

address: 269 Campus Dr. CCSR Room 2150

data_processing:
To count number of reads per unique barcode sequence, we took the read 1 sequence, extracted the 20bp region corresponding to the random barcode, and aligned the sequence to the reference MPRA library using bowtie212. Barcodes were allowed a maximum of one mismatch during alignment. The barcodes were counted to determine barcode-oligo frequencies in the plasmid library. Similar alignment was done with read 2 to align the sequence to the genomic instance of the variant to assess for template switching.
Assembly: hg19
Supplementary files format and content: tab-delimited files include barcode counts for each cell type for each repliccate
Library strategy: MPRA-seq

source_name: plasmid

extract_protocol:
To perform the MPRA in cell lines, an MPRA lentiviral library titration was performed to determine the volume of concentrated lentivirus needed to achieve a high infection rate without negatively affecting cell growth. Titration was also performed to test the optimal concentration of blastocidin S HCl needed for a 48 hour selection. For each sample, 10 million cells were transduced with 700µL of the MPRA lentiviral library and 5 µg/mL polybrene. Cells were plated into two 10cm plates (5 million cells/plate) and cultured overnight. Approximately 24 hours post transduction, cells were lifted and plated into two 15cm plates in media supplemented with blasticidin S HCl. Non-transduced cells were fully selected within 48 hours. After 72 hours of drug selection, cells were collected and lysed in Qiagen buffer RLT Plus containing 2-mercaptoethanol. Transductions were performed in triplicate. Lysates were frozen at -80°C prior to performing RNA isolation using a Qiagen RNeasy Plus Mini Kit (Qiagen cat. no. 74136).
Both the plasmid library and cDNA libraries were sequenced. The plasmid library was sequenced to assess oligo frequencies. Briefly, Illumina adaptors were PCRed onto the plasmid libraries, upstream and downstream of the oligo inserts. Final libraries concentrations were assessed by Kapa Library Quantification Kit (Roche) and sequenced on an Illumina MiSeq instrument using 30 cycles for read 1 (barcode) and 115 cycles for read 2 (genomic instance). Paired-end sequencing was used to assess template switching.  cDNA libraries were synthesized from total RNA.  Briefly, SuperScript IV was used to synthesize cDNA with a sample specific primer that annealed to the MPRA mRNA transcript. A 12 bp random sequence was included in the primer to serve as a transcript UMI. cDNA synthesis reactions were size selected using SPRIselect beads (Beckman) to remove the cDNA synthesis oligo. Partial Illumina sequencing adaptors were added using PrimeSTAR Max DNA Polymerase (Takara) in a PCR1 consisting of five cycles. Full adapters and sample indices were added in a PCR2 and monitored by qPCR on a Stratagene MX3005P machine. Amplification was terminated while qPCR curves were still in the linear phase to avoid library-over amplification and minimize library skew. The final library was gel purified in a 2% agarose gel. Library concentrations were determined using a Kapa Library Quantification Kit (Roche) and on an Agilent Bioanalyzer. Average molarity was used to equally mix a final cDNA library. Libraries were sequenced on an Illumina MiSeq instrument to ensure each sample had adequate coverage. Deeper sequencing runs were performed on an Illumina Novaseq 6000 SP flow cell (Novogene) with 50 read 1 cycles, 8 index 1 cycles, and 20 index 2 cycles.

value: plasmid

tag: cell line


title: 46fa_4aad


title: 5

tag: treatment


title: d45_WT fly muscle_3

first: Jingshu

last: Li

address: 100 Hai Ke Rd., Pudong

institute: Chinese Academy of Sciences

description: WT flies

data_processing:
Trim Galore (version 0.6.6) was used for quality control of fastq files with parameters ‘--nextseq 30 --paired’. Sequencing reads were mapped to the reference genome dmel_r6.36 with STAR-2.7.6a by default parameter. The read counts for each gene were calculated by featureCounts (version 2.0.1) with parameters ‘-p -B -C’. The count files were used as input to R package DESeq2 for normalization and the differential expression analysis. The criterion for differential expression genes was the absolute fold-change of counts between groups > 2 and adjusted p-value < 0.05.
Assembly: dmel_r6.36
Supplementary files format and content: DESeq2 was used for calling differential expression.tab-delimited text files include foldChange,pvalue

organism: Drosophila melanogaster

source_name: Fly muscle

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa, catalog: 9108)
RNA libraries were prepared according to instructions of Abclonal mRNA-seq Library Prep Kit for Illumina (RK20302)
RNA-Seq; Sample1-24: 100bp single-end; Sample25-39: 150bp paired-end

value: WT


title: 6

tag: strain


title: d30_WT fly muscle_3

description: WT flies


title: d45_WT fly muscle_2

description: WT flies


title: d45_WT fly muscle_1

description: WT flies


title: d30_WT fly muscle_1

description: WT flies


title: d30_WT fly muscle_2

description: WT flies


title: 4

tag: tissue


title: 29dc_4e34


title: d15_WT fly muscle_3

description: WT flies

tag: age


title: c003_4ac7

tag: Sex


title: 510c_4155

tag: percentciliatedepithelialcells


title: 204308910033_R02C01


title: d15_WT fly muscle_2

description: WT flies


title: d15_WT fly muscle_1

description: WT flies


title: 3


title: d3_WT fly muscle_3

description: WT flies


title: 2


title: d3_WT fly muscle_1

description: WT flies


title: 7fea_4d2a

tag: proportionpositiveskinpricktests


title: d3_WT fly muscle_2

description: WT flies


title: 747d_4031

tag: plate


title: f3e1_47fb

tag: array


title: d45_WT fly head_3

description: WT flies

source_name: Fly head


title: 1


title: e519_4818


title: d45_WT fly head_2

description: WT flies


title: d45_WT fly head_1

description: WT flies


title: p35S::AtH2B-GFP, Input, rep2

city: Erlangen

first: Benedikt

last: Kost

state: Bavaria

address: Staudtstraße 5

library_source: genomic

data_processing:
Bioinformatic analyses were performed by Novogene and comprised initial base calling, trimming and filtering of raw reads, mapping, peak calling, peak annotation and motif prediction.
Adapter removal and filtering of low quality reads was performed using skewer 0.1.126 (Jiang et al., 2014) with parameters -m pe -t 1 -l 18 -z -q 20 -Q 20 -k 6 -n -f sanger.
Reads were aligned to the reference genome (TAIR10) via BWA 0.7.12 (Li et al., 2009) using parameters: mem -k 18 -T 18 -t 1 -M.
MACS2 2.1.0 was used for peak calling with the significance cut-off q-value <= 0.05 (additional parameters: --nomodel --extsize --call-summits).
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: TAIR10
Supplementary files format and content: bigWig, narrowPeak (except for Input samples)

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: surface sterilized seeds were plated on 1/2MS supplemented with 2% sucrose, stratified at 4°C for 2 days and transferred to Long-Day conditions (16h Light/8h Dark, 22°C). Whole seedlings were harvested 7 days after germination.

extract_protocol:
Samples were prepared according to Chromotek's Application Note "Chromatin Immunoprecipitation (ChIP) Protocol for A. thaliana" (https://www.ptglab.com/products/pictures/pdf/ChIP_Apps_Note_GFP-Trap_for_A_thaliana.pdf). Formaldehyde crosslinking was performed on ice and under vacuum for 2x10min. The chromatin solution was sonicated (on a Bandelin Sonopuls) for seven cycles (15 seconds each) at 10% power. Input samples were set aside after this step. Samples were pre-cleared with binding-control agarose beads. Following elution from beads and reversal of crosslinking, all samples (IP and Input) were purified using Qiagen's Min Elute Kit.
Library construction (repair of DNA fragments, A-tailing and adapter ligation, size selection and PCR amplification) and sequencing (150bp paired end using Illumina's NovaSeq6000) were carried out as a custom service by Novogene (Cambridge, UK).

value: whole seedlings

tag: time

value: 7 days after germination

tag: chip antibody


title: p35S::AtH2B-GFP, IP, rep2

value: GFP-Trap® Agarose (ChromoTek Cat# gta-20, RRID:AB_2631357)


title: 224e_4716


title: d30_WT fly head_2

description: WT flies


title: d30_WT fly head_1

description: WT flies


title: d30_WT fly head_3

description: WT flies


title: d15_WT fly head_1

description: WT flies


title: p35S::AtH2B-GFP, Input, rep1


title: p35S::AtH2B-GFP, IP, rep1


title: d15_WT fly head_3

description: WT flies


title: d15_WT fly head_2

description: WT flies


title: d3_WT fly head_3

description: WT flies


title: d3_WT fly head_2

description: WT flies


title: d3_WT fly head_1

description: WT flies


title: gbpl3-5/pAtGBPL3::AtGBPL3genomic-GFP, IP, rep2


title: TNcc_AtNUDX23_rep3

city: Copenhagen N

first: Jeppe

last: Vinther

address: Ole Maaloes Vej 5

country: Denmark

institute: University of Copenhagen

description:
CapZyme-seq protocol
FeatureCount_TNcc_triplicate_output.txt

data_processing:
Illumina bcl2fastq was used to create fastq files
Sequenced reads were trimmed for adaptor sequence (cutadapt -a AGATCGGAAGAGCACACGTCT -q 20 -m 15) and mapped to RNA sequences (viral RNA, rRNA, snoRNA, tRNA and mRNA (TPM>2) using  (bowtie2 --norc --very-sensitive)
Counts for the 5' end of different RNA were obtained using the featureCounts function from the Subread package using a SAF file specifing the first 100 nts of each RNA.
Example code for the processing of the sequencing data is available at https://github.com/jeppevinther/CapZyme
Supplementary files format and content: Tab-delimited text files include FeatureCounts output, raw counts
Supplementary files format and content: Matrix table with raw 5'  counts for every RNA (first 100nt) and every sample in experiment
Library strategy: CapZyme-seq

organism:
Homo sapiens
Hepacivirus hominis

source_name: Huh7.5 hepatoma cells

extract_protocol:
RNA extraction was performed by Trizol treatment followed on-column DNase I digestion and RNA purification using RNA Clean & Concentrator kit-5
RNA was enzymatically treated with de-capping enzymes that specifically convert different 5’ cap structures to 5’ monophosphates. 5’-phosphate dependent adapter ligation was performed followed by reverse transcription. Libraries were generated using PCR with custom Illumina compatible primers.

tag: cell type

value: Huh7.5 hepatoma cells

tag: enzymatic treatment

tag: virus

value: HCV genotype 1a:TNcc

tag: molecule subtype

value: TEX treated total RNA


title: TNcc_neg_rep3

value: negative


title: 9a54_426f

value: Female


title: gbpl3-5/pAtGBPL3::AtGBPL3genomic-GFP, Input, rep1

tag: genotype


title: gbpl3-5/pAtGBPL3::AtGBPL3genomic-GFP, IP, rep1


title: TNcc_Rpp_rep3

value: Rpp


title: TNcc_neg_rep2


title: TNcc_AtNUDX23_rep2


title: RNA-Seq, whole seedlings 4dag  (SALK_025347 SALK_079296) crwn1-1crwn4-1_2 (crwn1-1crwn4-1 biol rep 2)

description:
c1c4_2
DESeq2_ncts.txt
FPKM.txt

data_processing:
BBDuk (from the BBTools suite, v38.96; Bushnell, 2014) was used for adapter-trimming (parameters: k=23, mink = 11, hdist=1, tpe, tbo for right- and subsequent left-trimming, respectively), quality-trimming (of bases with a PHRED score < 30) and pre-filtering (reads with average quality below 30 and/or shorter than 35bp were discarded).
intermediate quality checks were performed on raw and trimmed data using fastQC v0.11.9 (Andrews et al., 2010) and multiQC v1.12 (Ewels et al., 2016), respectively.
Transcript abundance was quantified for each individual sample from corresponding cleaned reads using Salmon (v1.9.0; Patro et al., 2017) in selective alignment mode (additional parameters: --validateMappings --gcBias) after indexing of the transcriptome (TAIR10; Arabidopsis_thaliana.TAIR10.cdna.all.fa via ENSEMBL) and using the full genome (TAIR10; Arabidopsis_thaliana.TAIR10.dna.toplevel.fa via ENSEMBL) as decoy sequence (corresponding to the “SAF” pipeline layed out in detail by Srivastava et al., 2020). (See files: "quant_[sample].sf").
Subsequent analyses used resources from Bioconductor release 3.16 (Huber et al., 2015) in R (v4.2.0; R Core Team, 2021): transcript-level abundance estimates were summarized to gene-level (annotation: Arabidopsis_thaliana.TAIR10.42.gtf via ENSEMBL) using the tximport package (Soneson et al., 2016) and genes with a total of < 10 counts (summed over all 18 individual samples in the study) were discarded (22603 genes remaining). DeSeq2 (Love et al., 2014) was used for count normalization (over all samples together using DESeq2's median-of-ratios method, see file: "DESeq2_ncts.txt"; alternatively, FPKMs were extracted, see file: "fpkm.txt") and analysis of differential gene expression (pairwise comparisons with the wild-type [WT]).
Assembly: TAIR10
Supplementary files format and content: Salmon output (tab delimited; quantification of mapped reads); FPKMs (fragments per kilobase of exon per million mapped fragments) for all samples; normalized count data over all samples based on DESeq2's median-of-ratios method

source_name: whole seedling

growth_protocol: surface sterilized seeds were plated on 1/2MS supplemented with 2% sucrose, stratified at 4°C for 2 days and transferred to Long-Day conditions (16h Light/8h Dark, 22°C). Whole seedlings were harvested 4 days after germination.

extract_protocol:
total RNA was extracted using NucleoSpin™ RNA Plus Kit (Macherey-Nagel™); ≥ 1 µg per replicate was used for library preparation.
Library preparation (poly(A)-enrichment, fragmentation, first strand cDNA synthesis using random hexamer primers and second strand cDNA synthesis, end-repair, A-tailing, adapter ligation, size selection, amplification and purification) and sequencing (150bp paired-end, PE150 using Illumina's NovaSeq6000) were carried out as a custom service by Novogene (Cambridge, UK).

value: whole seedling

tag: growth conditions

value: 1/2MS+2%Suc, photoperiod 16h-Light/8h-Dark, 22°C

value: 4 dag


title: gbpl3-5/pAtGBPL3::AtGBPL3genomic-GFP, Input, rep2


title: RNA-Seq, whole seedlings 4dag  (SALK_025347 SALK_079296) crwn1-1crwn4-1_1 (crwn1-1crwn4-1 biol rep 1)

description:
c1c4_1
DESeq2_ncts.txt
FPKM.txt


title: TNcc_Rpp_rep2


title: TNcc_neg_rep1


title: RNA-Seq, whole seedlings 4dag (SALK_079296) crwn4-1_3 (crwn4-1 biol rep 3)

description:
c4_3
DESeq2_ncts.txt
FPKM.txt


title: Tcells_hBD-2_4

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

hyb_protocol: Labeled fragments were hybridized to Affymetrix Clariom S Mouse arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: T cells, hBD-2, 48h

label_protocol: We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol: Spleens were isolated from 4 wildtype (WT) C57BL/6 mice and meshed through a 100 µM cell strainer into a PBS filled dish. T cells were isolated using the Pan T cell isolation kit (Miltenyi). 200 000 CD4/CD8 T cells were cultured in 96-well format in 200µL RPMI+10%FCS per well.

extract_protocol: Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: T cells were stimulated with anti-CD3/anti-CD28 microbeads in a 1:1 bead-to-cell ratio. PBS or hBD-2 (60µL/mL) were added, respectively. Cells were cultured for 48h at 37°C, 5% CO2.

value: splenic CD4/CD8 T cells

value: spleen

value: C57BL/6 wildtype

tag: gender

value: male

tag: treatment


title: Tcells_hBD-2_2

tag: tissue


title: Tcells_PBS_3

source_name: T cells, PBS, 48h

value: PBS


title: TNcc_AtNUDX23_rep1


title: Tcells_hBD-2_3


title: Tcells_hBD-2_1


title: Tcells_PBS_4


title: Tcells_PBS_2


title: GVHD_Colon_hBD-2_4

description: Recipient mouse after allo-HCT with C57BL/6 BM and T cells

source_name: Colon, GVHD mouse, hBD-2, day7

growth_protocol: 8 BALB/c mice were lethally irradiated followed by allogeneic transplantation with C57BL/6 BM cells and T cells on day 0.

treatment_protocol: Mice were treated orally with PBS or hBD-2 (1.2 mg/kg) from day 0-7 after irradiation and allo-HCT. Colon was isolated for RNA isolation on day 7 post allo-HCT

tag: disease state

value: graft-versus-host disease (GVHD)

value: Colon whole tissue

value: WT BALB/c


title: Tcells_PBS_1


title: RNA-Seq, whole seedlings 4dag  (SALK_025347 SALK_079296) crwn1-1crwn4-1_3 (crwn1-1crwn4-1 biol rep 3)

description:
c1c4_3
DESeq2_ncts.txt
FPKM.txt


title: RNA-Seq, whole seedlings 4dag (SALK_079296) crwn4-1_2 (crwn4-1 biol rep 2)

description:
c4_2
DESeq2_ncts.txt
FPKM.txt


title: RNA-Seq, whole seedlings 4dag (SALK_079296) crwn4-1_1 (crwn4-1 biol rep 1)

description:
c4_1
DESeq2_ncts.txt
FPKM.txt


title: TNcc_Rpp_rep1

value: Huh7.5 hepatoma cells


title: DBN3acc_neg_rep3

description:
CapZyme-seq protocol
FeatureCount_DBN3acc_triplicate_output.txt

value: HCV genotype 3a:DBN3acc


title: RNA-Seq, whole seedlings 4dag (gbpl3-5/pAtGBPL3::AtGBPL3K83A-GFP) K83A_3 (K83A biol rep 3)

description:
KA_3
DESeq2_ncts.txt
FPKM.txt


title: DBN3acc_AtNUDX23_rep3

value: TEX treated total RNA


title: RNA-Seq, whole seedlings 4dag (gbpl3-5/pAtGBPL3::AtGBPL3K83A-GFP) K83A_2 (K83A biol rep 2)

description:
KA_2
DESeq2_ncts.txt
FPKM.txt


title: RNA-Seq, whole seedlings 4dag (gbpl3-5/pAtGBPL3::AtGBPL3K83A-GFP) K83A_1 (K83A biol rep 1)

description:
KA_1
DESeq2_ncts.txt
FPKM.txt


title: DBN3acc_neg_rep2

value: negative


title: DBN3acc_Rpp_rep3


title: DBN3acc_AtNUDX23_rep2


title: RNA-Seq, whole seedlings 4dag (gbpl3-5/pAtGBPL3::AtGBPL3genomic-GFP) comp2_3 (comp2 biol rep 3)

description:
co_3
DESeq2_ncts.txt
FPKM.txt


title: RNA-Seq, whole seedlings 4dag (gbpl3-5/pAtGBPL3::AtGBPL3genomic-GFP) comp2_2 (comp2 biol rep 2)

description:
co_2
DESeq2_ncts.txt
FPKM.txt


title: GVHD_Colon_hBD-2_3


title: GVHD_Colon_hBD-2_1


title: GVHD_Colon_PBS_4

source_name: Colon, GVHD mouse, PBS, day7


title: DBN3acc_Rpp_rep2


title: 9E

first: Atul

last: Anand

address: Ole Maaløes Vej 5, building 2, 3 floor

department: Department of Pathology

institute: Rigshospitalet

hyb_protocol: An Affymetrix GeneChip Fluidics Station was used for hybridization and washing using a GeneChip™ Hybridization, Wash, and Stain Kit (ThermoFischer).

scan_protocol: scanned on  a GeneChipTM Scanner.

data_processing: Data from the Microarray Scanner was extracted using the Affymetrix Data Transfer Tool (Version 1.1)

source_name: PAXgene Blood miRNA

label_protocol: 50 ng of total RNA was used for RNA Clariom D Pico Assays using a GeneChip™ Hybridization, Wash, and Stain Kit (ThermoFischer)

extract_protocol: 10 full blood samples were collected before and after treatment in PAXgene tubes April 2018 and kept in 80oC. In 2020, the RNA was extracted with RNeasy Micro Kit from Qiagen. Quality and quantity assessment of extracted RNA on NanoDrop 2000c spectrophotometer (ThermoFischer) and 2100 bioanalyzer (Agilent).

treatment_protocol: Blood samples of healthy individuals before and after garlic ingestion.

value: whole blood

tag: person id

tag: garlic consumption (0=prior garlic consumption; 1=post garlic consumption)

tag: Sex

value: female


title: 4E


title: GVHD_Colon_hBD-2_2


title: 5E


title: 10E


title: GVHD_Colon_PBS_3


title: GVHD_Colon_PBS_1


title: DA28102 transconjugant with PCU1 plasmid in TB media, biol rep 3

city: Durham

first: Lingchong

last: You

state: NC

address: 101 Science Drive

institute: Duke University

description:
PCU1Tdeseq.csv
TB-PCU1T-4

data_processing:
Reads were trimmed using Trimmomatic v0.36 and mapped to MG1655 and pathogen reference genomes using Bowtie2 v2.2.6. Unique gene hit counts were calculated using Subread package v1.5.2 and analyzed via transcripts per million (TPM) and DESeq2
Assembly: Chromosome: SAMN27361452; plasmids from matching pathogens in BioProjects: PRJNA551684 and PRJNA823807
Supplementary files format and content: DESeq2 csv output

organism: Escherichia coli

growth_protocol: Grown overnight for 18 hours, 37C, shaking, in M9 or TB media / diluted and resuspended in M9CA for 2 hours before freezing

extract_protocol:
Samples were submitted to GeneWiz for extraction
rRNA depletion, followed by RNA fragmention and random priming, cDNA synthesis with end repair, adaptor ligation, PCR enrichment

tag: cell line

value: TB


title: GVHD_Colon_PBS_2


title: 6E


title: 10F


title: RNA-Seq, whole seedlings 4dag (gbpl3-5/pAtGBPL3::AtGBPL3genomic-GFP) comp2_1 (comp2 biol rep 1)

description:
co_1
DESeq2_ncts.txt
FPKM.txt

value: whole seedling

value: 1/2MS+2%Suc, photoperiod 16h-Light/8h-Dark, 22°C


title: 9F


title: 8E


title: 3E


title: DA28102 transconjugant with PCU1 plasmid in TB media, biol rep 2

description:
PCU1Tdeseq.csv
TB-PCU1T-5


title: 7E


title: 1E


title: DBN3acc_neg_rep1


title: RNA-Seq, whole seedlings 4dag (GK028F01) gbpl3-5_3 (gbpl3-5 biol rep 3)

description:
gb_3
DESeq2_ncts.txt
FPKM.txt

value: 4 dag


title: DA28102 transconjugant with PCU1 plasmid in TB media, biol rep 1

description:
PCU1Tdeseq.csv
TB-PCU1T-6


title: DBN3acc_AtNUDX23_rep1


title: RNA-Seq, whole seedlings 4dag (GK028F01) gbpl3-5_2 (gbpl3-5 biol rep 2)

description:
gb_2
DESeq2_ncts.txt
FPKM.txt


title: DA28102 transconjugant with PCU1 plasmid in M9 media, biol rep 3

description:
PCU1Tdeseq.csv
M9-PCU1T-2


title: DA28102 transconjugant with PCU1 plasmid in M9 media, biol rep 2

description:
PCU1Tdeseq.csv
M9-PCU1T-3


title: H77cc_neg_rep3

description:
CapZyme-seq protocol
FeatureCount_H77cc_triplicate_output.txt

value: HCV genotype 1a:H77cc


title: DA28102 transconjugant with PCU1 plasmid in M9 media, biol rep 1

description:
PCU1Tdeseq.csv
M9-PCU1T-1


title: RNA-Seq, whole seedlings 4dag wt_3 (wt biol rep 3)

description:
wt_3
DESeq2_ncts.txt
FPKM.txt

value: WT


title: RNA-Seq, whole seedlings 4dag (GK028F01) gbpl3-5_1 (gbpl3-5 biol rep 1)

description:
gb_1
DESeq2_ncts.txt
FPKM.txt


title: DA28102 transconjugant with pathogen 5243 plasmid(s) in TB media, biol rep 3

description:
5243Tdeseq.csv
TB-5243T-4


title: H77cc_AtNUDX23_rep3


title: RNA-Seq, whole seedlings 4dag wt_2 (wt biol rep 2)

description:
wt_2
DESeq2_ncts.txt
FPKM.txt


title: DBN3acc_Rpp_rep1

value: Rpp


title: H77cc_Rpp_rep3


title: DA28102 transconjugant with pathogen 5243 plasmid(s) in TB media, biol rep 2

description:
5243Tdeseq.csv
TB-5243T-5


title: H77cc_neg_rep2


title: H77cc_AtNUDX23_rep2


title: DA28102 transconjugant with pathogen 5243 plasmid(s) in TB media, biol rep 1

description:
5243Tdeseq.csv
TB-5243T-6


title: DA28102 transconjugant with pathogen 5243 plasmid(s) in M9 media, biol rep 3

description:
5243Tdeseq.csv
M9-5243T-1


title: H77cc_Rpp_rep2


title: Peds NIBD Ileum 51

city: Ithaca

first: Praveen

last: Sethupathy

email: as3999@cornell.edu, pr46@cornell.edu

address: T7 006D Veterinary Research Tower, Box 17

department: Department of Biomedical Sciences

institute: Cornell University

description:
Ileum_Peds_normalized_counts.csv
PNIBD51 D

data_processing:
miRquant 2.0 used for 3' adapter trimming (Cutadapt), two tier read alignment (Bowtie and SHRiMP), and miRNA annotation (miRBase, GtRNAdb, and GENCODE). Normalization and differential analysis was then performed using DESeq2.
RNA-seq data were mapped to the mm6 genome with STAR.Transcripts were quantified with Salmon using GENCODE release 25 transcript annotations. Normalization and differential analysis was then performed using DESeq2.
Assembly: Genome_build: hg19 (GRCh37) for small-RNA seq. mm6 genome for RNA-seq.
Supplementary files format and content: Normalized counts

source_name: NIBD, Terminal ileum mucosal biopsy

growth_protocol: FFPE samples from the index colonoscopies from treatment naive pediatric patients were collected as part of the University of North Carolina IRB protocol 15-0024.

extract_protocol:
Small RNA libraries were generated using Illumina TruSeq Small RNA Sample Preparation Kit (San Diego, CA).
miRNA was enriched from FFPE tissue samples using the Roche High Pure miRNA Isolation Kit (Penzberg, Germany). RNA purity and integrity were assessed with Thermo Scientific NanoDrop 2000 (Waltham, MA) and Agilent 2100 Bio- analyzer (Santa Clara, CA), respectively.
Single-end (50 bp) sequencing was performed on the Illumina HiSeq 2500 platform.

tag: age

value: Pediatric

value: Terminal ileum mucosal biopsy

tag: phenotypic status

value: Non-IBD

value: Naïve


title: Peds NIBD Ileum 47

description:
Ileum_Peds_normalized_counts.csv
PNIBD47 G


title: 6F

value: male


title: 5F


title: 7F


title: 2E


title: 8F


title: 4F


title: DA28102 transconjugant with pathogen 5243 plasmid(s) in M9 media, biol rep 2

description:
5243Tdeseq.csv
M9-5243T-4


title: Peds NIBD Ileum 01

description:
Ileum_Peds_normalized_counts.csv
PNIBD01 D


title: Peds CD Ileum 214

description:
Ileum_Peds_normalized_counts.csv
PB214 B6

source_name: CD, Terminal ileum mucosal biopsy

value: Crohn's disease


title: RNA_transferred_Th2_48h_TxnipKO_rep2

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

country: Japan

institute: Chiba univercity

description: Takara

data_processing:
Base calls for RNA-seq were performed using bcl2fastq v2.20 for Nextseq output.
RNA-seq reads were aligned to the UCSC mm10 genome using Bowtie version 2.3.4. and Top Hat 1.3.2.
Fragments per kilobase of exon per million mapped reads for each gene for RNA-seq were calculated using the Cufflinks 2.2.1.
Base calls for ChIP-seq were performed using bcl2fastq v2.20 for Nextseq output.
ChIP-seq reads were aligned to the UCSCmm10 genome using Bowtie version 2.3.4. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called using MACS v2.1.2 with the significance cut-off q-value <=0.1.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: ATAC-seq: bigWig files
Supplementary files format and content: RNA-seq: genes.fpkm_tracking files

source_name: Spleen

extract_protocol:
The scRNA-seq samples of Th2 at day7 and day11 in vivo that were freshly prepared from KJ1+CD4+ T cells sorted using a BD FACS Aria III (10,000 cells each, cell viability >98%). The Effector Th2 and transferred Th2 that were also freshly prepared from KJ1+CD4+ T cells sorted using a BD FACS Aria III (10,000 cells each, cell viability >98%). The scRNA-seq , RNA-seq and ATAC-seq samples of Wild-type or Txnip KO mice that were also freshly prepared from CD4+CD44high T cells sorted using a BD FACS Aria III (10,000 cells each, cell viability >98%).
Libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3.1 according to manufacturer’s protocol (10X Genomics). The generated scRNA-seq libraries were sequenced using a 128 cycle (paired-end reads) with a NovaSeq 6000 (Illumina).

treatment_protocol: Splenic naïve CD4+ T cells (CD44loCD62Lhi) from DO11.10 OVA-specific TCR transgenic mice were purified with a magnetic cell sorter (atomics; Miltenyi Biotec, Tokyo, Japan), yielding a purity exceeding 90%. Purified naïve CD4+ T cells were stimulated by irradiated (3500 rad) Thy-1.2 depleted splenic cells (i.e. APCs) with OVA peptides (Loh15, 0.3 μM) in the presence of IL-2 (25 U/mL) for IL-2 (25 U/mL), IL-4 (100 U/mL) (Pep Rotech, New Jersey, USA), and anti-IFN-γ maybe (R46A2, 2.5% [v/v]) for Th2 cell differentiation.

value: Spleen

value: KJ1+CD4+ T cells

tag: time point

value: Txnip KO

tag: assay

value: RNA-seq


title: RNA_transferred_Th2_48h_TxnipKO_rep1

description: Takara

tag: cell type


title: RNA_transferred_Th2_48h_TxnipKO_rep3

description: Takara


title: 3F

value: whole blood

value: female


title: 2F


title: DA28102 transconjugant with pathogen 5243 plasmid(s) in M9 media, biol rep 1

description:
5243Tdeseq.csv
M9-5243T-5


title: RNA-Seq, whole seedlings 4dag wt_1 (wt biol rep 1)

description:
wt_1
DESeq2_ncts.txt
FPKM.txt

value: whole seedling

value: 1/2MS+2%Suc, photoperiod 16h-Light/8h-Dark, 22°C

tag: time


title: H77cc_neg_rep1

value: Huh7.5 hepatoma cells

tag: enzymatic treatment

value: negative

tag: virus

value: HCV genotype 1a:H77cc

tag: molecule subtype

value: TEX treated total RNA


title: H77cc_Rpp_rep1

value: Rpp


title: 1F


title: RNA_transferred_Th2_48h_TxnipWT_rep4

description: Takara

tag: genotype

value: Txnip WT


title: DA28102 transconjugant with pathogen 2560 plasmid(s) in TB media, biol rep 2

description:
2560Tdeseq.csv
TB-2560T-5

tag: treatment

value: TB


title: DA28102 transconjugant with pathogen 2560 plasmid(s) in TB media, biol rep 3

description:
2560Tdeseq.csv
TB-2560T-4


title: Peds CD Ileum 149

description:
Ileum_Peds_normalized_counts.csv
PB149 E

value: Pediatric

tag: tissue

value: Terminal ileum mucosal biopsy

value: Naïve


title: RNA_transferred_Th2_48h_TxnipWT_rep2

description: Takara

value: Spleen

value: KJ1+CD4+ T cells


title: RNA_transferred_Th2_48h_TxnipWT_rep3

description: Takara

value: RNA-seq


title: Peds NIBD Colon 52

description:
Colon_Peds_normalized_counts.csv
PNIBD52 E

source_name: NIBD, Ascending colon mucosal biopsy

value: Ascending colon mucosal biopsy

value: Non-IBD


title: DA28102 transconjugant with pathogen 2560 plasmid(s) in M9 media, biol rep 3

description:
2560Tdeseq.csv
M9-2560T-2


title: Peds CD Ileum 122

description:
Ileum_Peds_normalized_counts.csv
PB122 E

value: Crohn's disease


title: H77cc_AtNUDX23_rep1


title: DA28102 transconjugant with pathogen 2560 plasmid(s) in TB media, biol rep 1

description:
2560Tdeseq.csv
TB-2560T-6


title: mpra_IMR_diff_1

institute: Stanford University

value: cell line

value: day 6

tag: growth

value: IMR-32 neuroblastoma cells (ATCC, CCL-127) were grown in EMEM media. IMR-32 cells were differentiation by adding 1 mM dibutyryl-cAMP (Fisher:Stem Cell Technologies cat. no. 73884) and 2.5 µM BrdU (Fisher Scientific cat. no. B23151) in EMEM for 6 days. A full media change was done on day 3.


title: mpra_IMR_prog_3

value: day 0


title: mpra_IMR_diff_3


title: mpra_IMR_diff_2


title: ATAC_transferred_Th2_48h_TxnipKO_rep3

description: Illumina

value: Txnip KO

value: ATAC-seq


title: RNA_transferred_Th2_48h_TxnipWT_rep1

description: Takara

value: Txnip WT


title: DA28102 transconjugant with pathogen 2560 plasmid(s) in M9 media, biol rep 2

description:
2560Tdeseq.csv
M9-2560T-4


title: ATAC_transferred_Th2_48h_TxnipKO_rep2

description: Illumina


title: Peds CD Ileum 110

description:
Ileum_Peds_normalized_counts.csv
PB110 D1


title: mpra_IMR_prog_1


title: DA28102 transconjugant with pathogen 92 plasmid(s) in TB media, biol rep 2

description:
92Tdeseq.csv
TB-92T-5

value: TB


title: Peds NIBD Colon 51

description:
Colon_Peds_normalized_counts.csv
PNIBD51 E

value: Pediatric


title: DA28102 transconjugant with pathogen 2560 plasmid(s) in M9 media, biol rep 1

description:
2560Tdeseq.csv
M9-2560T-5


title: ATAC_transferred_Th2_48h_TxnipKO_rep1

description: Illumina


title: Peds NIBD Colon 46

description:
Colon_Peds_normalized_counts.csv
PNIBD46 A


title: mpra_IMR_prog_2


title: ATAC_transferred_Th2_48h_TxnipWT_rep3

description: Illumina


title: ATAC_transferred_Th2_48h_TxnipWT_rep1

description: Illumina


title: Peds NIBD Colon 01

description:
Colon_Peds_normalized_counts.csv
PNIBD01 E


title: DA28102 transconjugant with pathogen 92 plasmid(s) in TB media, biol rep 3

description:
92Tdeseq.csv
TB-92T-6


title: ATAC_transferred_Th2_48h_TxnipWT_rep2

description: Illumina


title: Peds CD Colon 217

description:
Colon_Peds_normalized_counts.csv
PB217 G1

source_name: CD, Ascending colon mucosal biopsy


title: mpra_D341_3

value: D341 medulloblastoma cells (ATCC, HTB-187) were grown in suspension in EMEM media supplemented with 20% FBS.


title: mpra_D341_2


title: DA28102 transconjugant with pathogen 92 plasmid(s) in TB media, biol rep 1

description:
92Tdeseq.csv
TB-92T-1


title: DA28102 transconjugant with pathogen 92 plasmid(s) in M9 media, biol rep 3

description:
92Tdeseq.csv
M9-92T-3


title: mpra_D341_1


title: mpra_D283_3

value: D283 medulloblastoma cells (ATCC, HTB-185) were grown in EMEM media in suspension.


title: Peds CD Colon 119

description:
Colon_Peds_normalized_counts.csv
PB119 E1

value: Naïve


title: DA28102 transconjugant with pathogen 92 plasmid(s) in M9 media, biol rep 1

description:
92Tdeseq.csv
M9-92T-1


title: DA28102 transconjugant with pathogen 92 plasmid(s) in M9 media, biol rep 2

description:
92Tdeseq.csv
M9-92T-2


title: Invivo_SingleCell_StrepCGRP_L2

city: St Louis

first: Felipe

last: Almeida de Pinho Ribeiro

state: MO

address: 4515 McKinley Ave

institute: Washington University in St Louis

data_processing:
For bulk RNA-seq (in vitro samples) data, the raw data was converted to fastq files using bcl2fastq 2.17.1.14 with options “--minimum-trimmed-read-length 10 --mask-short-adapter-reads 10”. Transcript quantification was done using Salmon 1.9.0 with the mm10 mouse genome annotation, and transcript counts were then converted to gene counts and normalized TPM values using the R package tximport (Soneson et al., 2015). Differential gene expression analysis was performed in sequencing datasets using the R package DESeq2.
For single-cell RNA-sequencing samples, Cell Ranger (10x Genomics) analysis pipelines were used to demultiplex raw sequencing data and to perform alignment, filtering, and counting of barcodes and UMIs. Reference mouse genome mm10 version 2020-A was used. Count matrices generated by Cell Ranger imported into R (v.4.0.3) for further analysis using Seurat package (v. 4.1.0). Analysis was performed using only high-quality cells that had UMI counts between 4000 and 70000 and less than 25% of their genes corresponding to the mitochondrial genome. Samples were normalized and scaled using Seurat’s SCTransform function followed by Principal component analysis (PCA). Clustering and visualization were performed by running Uniform Manifold Approximation and Projection (UMAP) dimensional reduction of 15 principal components for each cluster resolution of 0.3. Cell types were defined by comparing cluster marker genes with previously published single-cell RNA-sequencing datasets of mouse meninges. Visualization of genes illustrating expression levels was performed using R/Seurat commands (DoHeatmap, FeaturePlot, and DotPlot) and R/Nebulosa package. Differential gene expression analysis was performed in sequencing datasets using Seurat.
Assembly: mm10

source_name: Meningeal immune cells

extract_protocol:
Sorted CD45+ cells were encapsulated into droplets, and libraries were prepared using 10x Single Cell 3′ Reagent Kits according to manufacturer’s protocol (10x Genomics). The generated scRNA-seq libraries were sequenced on a NovaSeq using a read structure of 28 bp for Read 1, 8 bp for Index 1, and 96 bp for Read 2.
Meningeal cells were processed using Liberase TL and subsequently enriched for CD45 positive and negative cells using CD45 MicroBeads (Miltenyi Biotec).
see library construction protocol for each sample above

treatment_protocol: Animals were injected with vehicle, S. pneumoniae, or S. pneumoniae+CGRP, and meningeal cells were isolated 24h later using MACS CD45 beads (Miltenyi).

tag: strain

tag: lane

tag: s. pneumoniae-stimulated

value: Yes

tag: cgrp-treated

tag: in vitro vs. in vivo

value: In vivo

tag: rna-seq method

value: ScRNA-seq (10x)


title: mpra_D283_2

tag: cell line


title: Invivo_SingleCell_StrepCGRP_L1


title: Invivo_SingleCell_Strep_L2

value: No


title: DA28102 transconjugant with pathogen 41 plasmid(s) in TB media, biol rep 3

description:
41Tdeseq.csv
TB-41T-6


title: mpra_D283_1


title: SC-EC, +ifn, biol rep 3

first: Dario

last: Gerace

address: 7 Divinity Ave

institute: Harvard University

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into FASTQ files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison.

growth_protocol: SC-endothelial and CD49a+ SC-beta cells were magnetically-enriched and seeded at a concentration of 1M cells/well of a matrigel-coated 6-well plate and incubated at 370C/5% CO2 for 24 h.

extract_protocol:
Total RNA was extracted from cell pellet samples using RNeasy Plus Mini Kit (Qiagen, Germantown, MD, USA) and quantified using Qubit Fluorometer (Life Technologies, Carlsbad, CA, USA).
SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA), and Illumina Nextera XT library was used for sequencing library preparation. Multiplexed sequencing libraries were loaded on the Illumina HiSeq instrument and sequenced using a 2x150 Paired End (PE) configuration.

treatment_protocol: After 24 h of culture, the medium was replaced and IFN-G (10ng/ml) added to half the wells containing SC-beta or SC-EC, and the cells incubated for a further 24 h at 370C/5% CO2.

value: endothelial cell

value: WT

value: IFN-gamma (10ng/ml)


title: Invivo_SingleCell_Strep_L1


title: SC-EC, +ifn, biol rep 2


title: DA28102 transconjugant with pathogen 41 plasmid(s) in TB media, biol rep 2

description:
41Tdeseq.csv
TB-41T-5


title: SC-EC, -ifn, biol rep 3

value: No treatment


title: Peds CD Colon 220

description:
Colon_Peds_normalized_counts.csv
PB220 G1

tag: age

value: Ascending colon mucosal biopsy

tag: phenotypic status

value: Crohn's disease


title: DA28102 transconjugant with pathogen 41 plasmid(s) in TB media, biol rep 1

description:
41Tdeseq.csv
TB-41T-4

tag: cell type


title: Invivo_SingleCell_CD45neg_basal

source_name: Meningeal non-immune cells

extract_protocol:
Sorted CD45- cells were encapsulated into droplets, and libraries were prepared using 10x Single Cell 3′ Reagent Kits according to manufacturer’s protocol (10x Genomics). The generated scRNA-seq libraries were sequenced on a NovaSeq using a read structure of 28 bp for Read 1, 8 bp for Index 1, and 96 bp for Read 2.
Meningeal cells were processed using Liberase TL and subsequently enriched for CD45 positive and negative cells using CD45 MicroBeads (Miltenyi Biotec).
see library construction protocol for each sample above

treatment_protocol: Meningeal cells were isolated from uninfected/untreated mice using MACS CD45 beads (Miltenyi).


title: Invivo_SingleCell_Vehicle_L2


title: SC-EC, -ifn, biol rep 2


title: mpra_SH-SY5Y_diff_2

value: cell line

value: day 6

value: SH-SY5Y cells (ATCC, CRL-2266) were grown in 1:1 F12 (Lonza, cat. no. 12-615F):EMEM (Thermo Fisher Scientific cat. no. 50-188-268FP). SH-SY5Y cells were differentiated in Neurobasal medium (Thermo Fisher no 21103049) with B27 (Thermo Fisher no 17504044) and Glutamax (Thermo Fisher no 35050061) supplements and 10 µM all-trans-retinoic acid (ATRA) according to the published protocol11. Half-media changes were made every day for 6 days.


title: DA28102 transconjugant with pathogen 41 plasmid(s) in M9 media, biol rep 3

description:
41Tdeseq.csv
M9-41T-5


title: Invivo_SingleCell_Vehicle_L1


title: mpra_SH-SY5Y_diff_1


title: SC-EC, -ifn, biol rep 1


title: Invitro_BMDM_StrepCGRP_4_L2

description:
tx2gene.rda
txi.rda

source_name: Bone marrow-derived macrophages

extract_protocol:
Four biologically independent replicates were sequenced. After incubation, supernatant was removed and replaced by 500 μL of Trizol, and plates were frozen at −80°C until RNA extraction. For total RNA extraction, samples were thawed at room temperature, mixed with 100 μL of chloroform, and centrifuged at 12,000 g for 15 min at 4°C. The aqueous phase was collected to a new tube and combined with equal parts of isopropyl alcohol, mixed well, and centrifuged at 12,000 g for 10 min at 4°C. After discarding the supernatant, 500 μL of 75% ethanol was added to the samples, vortexed well, and centrifuged at 7,500 g for 5 min. Supernatant was then discarded and the pellet containing RNA was resuspended in 50 μL of nuclease-free water. RNA-seq library preparation (Kapa mRNA Hyperprep, Roche) and sequencing (NovaSeq SP, 2x50bp, Illumina) was conducted by the Bauer Sequencing Core at Harvard University.
Meningeal cells were processed using Liberase TL and subsequently enriched for CD45 positive and negative cells using CD45 MicroBeads (Miltenyi Biotec).
see library construction protocol for each sample above

treatment_protocol: BMDM co-incubated for 4h with vehicle, S. pneumoniae, or Spneumoniae+CGRP

value: In vitro

value: Bulk RNA-seq


title: mpra_SH-SY5Y_prog_3

value: day 0


title: DA28102 transconjugant with pathogen 41 plasmid(s) in M9 media, biol rep 2

description:
41Tdeseq.csv
M9-41T-4


title: Invitro_BMDM_StrepCGRP_4_L1

description:
tx2gene.rda
txi.rda


title: SC-beta, +ifn, biol rep 3

value: beta cell


title: DA28102 transconjugant with pathogen 41 plasmid(s) in M9 media, biol rep 1

description:
41Tdeseq.csv
M9-41T-3


title: mpra_SH-SY5Y_prog_2


title: SC-beta, +ifn, biol rep 2


title: Postive Dox 3

description:
Paneth_normalized_counts.csv
MS6c

source_name: jejunal epithelial cell fraction one (IEC-1), miR-29b overexpression mice /doxycycline exposed

growth_protocol: Harvested small intestine from doxycycline exposed and unexposed WT and miR-29b overexpressing mice was measured and divided into three equal segments.  The middle region was considered jejunum.

extract_protocol:
NEBNext Ultra II Directional Library Prep Kit (New England Biolabs, Ipswich, MA) with ribosomal RNA depletion
Total RNA was isolated using the Total RNA Purification kit (Norgen Biotek).
NextSeq500 platform (Illumina, San Diego, CA) at the Genomics Facility in the Biotechnology Research Center at Cornell University

value: 60 Days

value: miR-29b overexpression mice

value: doxycycline exposed


title: Invitro_BMDM_StrepCGRP_3_L2

description:
tx2gene.rda
txi.rda

value: Yes


title: SC-EC, +ifn, biol rep 1

value: endothelial cell


title: mpra_SH-SY5Y_diff_3


title: SC-beta, +ifn, biol rep 1

value: WT


title: Postive Dox 2

description:
Paneth_normalized_counts.csv
MS5c

value: jejunal epithelial cell fraction one (IEC-1)


title: Postive Dox 1

description:
Paneth_normalized_counts.csv
MS4c


title: mpra_P-NPC_4

value: neuron

value: Stem cells were plated in clumps in the presence of Y27632 (10mg/ml, 1000x, Axon MedChem). The hES colonies were allowed to grow in mTESR for another day before the media was switch to differentiation media (1X N2, 1X B27, DMEM/F12:Neurobasal=1:1 (Invitrogen), 0.1mM Ascorbic acid (Sigma)) with small molecules [SB431542, LDN193189 and CHIR99021 (Final concentration:10µM, 100nM and 3µM from Stemgent and Tocris)]. To obtain anterior or posterior neural stem cells, SB431542/LDN194189 and SB431542/LDN193189/CHIR99021 were added respectively. The cells were allowed to differentiate in the media for 6 days before they were dissociated with Accutase and plated at the density of 1 million cells per well of 6 wells for infection. For Ngn2 day 2 post-dox induction cells, TetO-Ngn2-t2a-puro and FUW-rtTA were infected at day 0 in differentiation media followed by adding doxycycline and puromycin the next day. The cells were selected for two days in puromycin before collection for downstream HiChIP experiment.


title: SC-beta, -ifn, biol rep 3

value: No treatment


title: Invitro_BMDM_StrepCGRP_2_L2

description:
tx2gene.rda
txi.rda


title: Invitro_BMDM_StrepCGRP_3_L1

description:
tx2gene.rda
txi.rda


title: mpra_P-NPC_3


title: SC-beta, -ifn, biol rep 2


title: mpra_P-NPC_2


title: Negative Dox 3

description:
Paneth_normalized_counts.csv
MS3c

source_name: jejunal epithelial cell fraction one (IEC-1), miR-29b overexpression mice / doxycycline unexposed WT

value: doxycycline unexposed WT


title: Invitro_BMDM_StrepCGRP_2_L1

description:
tx2gene.rda
txi.rda


title: Invitro_BMDM_StrepCGRP_1_L2

description:
tx2gene.rda
txi.rda


title: Negative Dox 2

description:
Paneth_normalized_counts.csv
MS2c


title: mpra_P-NPC_1


title: Acute_Hippocampus_H24

city: Leiden

first: Eva

last: Viho

email: e.viho@lumc.nl, viho.eva@gmail.com

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

description:
H24
Acute_rawcounts.csv, DNBSEQ-PE100

data_processing:
The BioWDL pipeline was used for reads quality control, alignment, and quantification.
Quality control was performed using FastQC and MultiQC.
Reads were aligned to mm10 using STAR and gene-read quantification was performed using HTSeq-count
Assembly: mm10
Supplementary files format and content: Matrix tables with gene raw counts for every feature according to Ensembl97 for each sample

source_name: hippocampus

extract_protocol:
Total RNA was isolated from frozen hippocampus and liver tissue using the NucleoSpin® RNA kit (Macherey-Nagel)
mRNA was enriched and purified and a stranded library was constructed for 100 bp paired-end sequencing on BGI's DNBseq platform

value: hippocampus

value: AS

value: acute corticosterone


title: Negative Dox 1

description:
Paneth_normalized_counts.csv
MS1c


title: Acute_Hippocampus_H23

description:
H23
Acute_rawcounts.csv, DNBSEQ-PE100


title: mpra_A-NPC_4


title: mpra_SH-SY5Y_prog_1

value: cell line

value: SH-SY5Y cells (ATCC, CRL-2266) were grown in 1:1 F12 (Lonza, cat. no. 12-615F):EMEM (Thermo Fisher Scientific cat. no. 50-188-268FP). SH-SY5Y cells were differentiated in Neurobasal medium (Thermo Fisher no 21103049) with B27 (Thermo Fisher no 17504044) and Glutamax (Thermo Fisher no 35050061) supplements and 10 µM all-trans-retinoic acid (ATRA) according to the published protocol11. Half-media changes were made every day for 6 days.


title: mpra_A-NPC_3


title: Acute_Hippocampus_H22

description:
H22
Acute_rawcounts.csv, DNBSEQ-PE100


title: LV Tissue WT [WLV_7]

city: BALTIMORE

first: Kirill

middle: V

last: Tarasov

state: Maryland

address: 251 Bayview Boulevard, Room 9B133, Room 9B133

department: NIA

institute: NIH

data_processing:
Analysis was performed by DNA Link USA, Inc.
Basecalling Software: RTA2.0;  Fastq Quality Score: ASCII Qscore Offset 64
Trimmed reads were aligned to the reference genome using TopHat v2.1.1
Cufflinks v.2.1.1 was used to calculate FPKM for each sample. Differential gene expression analysis was performed with a Cuffdiff package (Cufflinks v2.1.1)
Assembly: UCSC mm10 mouse reference genome; ADCY8HS - https://www.ncbi.nlm.nih.gov/gene/?term=NM_001115
Supplementary files format and content: Excel file w/the following columns: tracking_id, gene_id, gene_short_name, locus, FPKM for each sample, statistics

source_name: Left Ventricles

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Takara Bio USA, Inc.) following manufacturer's protocols.

value: Left Ventricles

tag: strain background


title: Acute_Hippocampus_H21

description:
H21
Acute_rawcounts.csv, DNBSEQ-PE100


title: Invitro_BMDM_Strep_4_L1

description:
tx2gene.rda
txi.rda

value: No

value: In vitro

value: Bulk RNA-seq