title: AGS cells treated with C. concisus rep3

city: Sydney

first: Li

last: Zhang

state: NSW

address: Botany Street

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

data_processing:
Quality was checked using FastQC (v 0.11.8)
Trimmomatic (v 0.38) was used to trim Illumina adapter sequences and filter the raw reads
The quality filtered reads were mapped to the reference human genome GRCh38.p14 using HISAT2 (v 2.1.0)
The Subread package Featurecount (v 2.0.1) was used to generate a set of per-gene read counts for each sample using default options
The count data files were loaded into R and analyzed with DESeq2 (v 1.36.0)
Assembly: Reference human genome GRCh38.p14
Supplementary files format and content: Tab-delimited text files of raw counts

source_name: cell line

extract_protocol:
Total RNA was extracted using the Isolate II RNA minikit (Bioline)
Libraries were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina) and sequenced on Illumina’s NextSeq 500

value: cell line

value: AGS

value: gastric epithelial

value: C. concisus


title: Case CTL_09

status: Public on Dec 27 2023

type: genomic

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg, Intitute of Pathology

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: IDHmut Astro_ctl

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: disease state

value: IDHmut Astro_ctl

tag: material

value: FFPE

tag: Sex

value: M

tag: tissue

value: brain


title: Female cortical_Mouse 2

type: SRA

city: San Francisco

first: Marci

middle: F

last: Rosenberg

state: CA

address: 1651 4th Street

department: Psychiatry

country: USA

institute: UCSF

library_source: transcriptomic

data_processing:
Samples were analyzed as previously described (Vainchtein et al. 2018; R. T. Han et al. 2023). Briefly, after assessing read quality with FastQC (v0.11.5; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), samples were aligned to the Mus musculus genome (Ensembl GRC m39) using STAR aligner (v2.6.0) (Dobin et al. 2013). Aligned reads were then counted with HTSeq (v0.9.0) (Anders, Pyl, and Huber 2015), and loaded into R, where count normalization and differential expression analysis (between cortical vs. subcortical astrocytes) was performed using DESeq2 (v1.35.0) (Love, Huber, and Anders 2014).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include normalized counts for each sample
Supplementary files format and content: tab-delimited text files include raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Astrocytes

extract_protocol:
After thawing the lysed astrocytes in RLT Plus buffer, mRNA was isolated from each sample using the RNeasy Plus Micro Kit (74034, Qiagen)
cDNA libraries were then prepared using a QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen).

tag: cell type

value: Astrocytes

value: Female

tag: age

tag: genotype

value: WT


title: Case CTL_14


title: 3xFS HeLa clone

city: Dundee

first: Ralitsa

middle: Radostinova

last: Madsen

address: Dow Street

department: Medical Research Council Protein Phosphorylation and Ubiquitylation Unit

country: United Kingdom

institute: School of Life Sciences, University of Dundee

data_processing:
Nextflow (version 20.07.1) nf-core RNAseq pipeline (version 1.1), with Spliced Transcripts Aligment to a Reference (STAR) for read alignment to the human genome (Homo_sapiens.GRCh38.96.gtf) and featureCounts for counting of mapped reads (multimapped reads were discarded)
All subsequent analysis steps using the raw gene counts were performed in R. Filtering of low gene expression counts was performed with the TCGAbiolinks package with quantile value 0.75 (chosen empirically based on the observed count distribution).
Read count normalization was performed with the gene length-corrected trimmed mean of M-values (GeTMM) method.
The mean-variance relationship was modelled with voom(), followed by linear modelling and computation of moderated t-statistics using the lmFit() and eBayes() functions in the limma package.
The associated p-values for assessment of differential gene expression were adjusted for multiple comparisons with the Benjamini-Hochberg method at false-discovery rate (FDR) = 0.05. Adjustments were performed with option = “separate”, comparing PIK3CAH1047R mutant clones against wild-type clones.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing all raw gene counts for each sample

source_name: HeLa

growth_protocol: HeLa cells were cultured in complete medium consisting of DMEM (with 4 mM L-Glutamine and 1 mM sodium pyruvate; Thermo Fisher Scientific #41966-029) supplemented with another 2 mM of L-Glutamine (Sigma #G7513) and 10 % fetal bovine serum (FBS; Pan-Biotech #P30-8500).

extract_protocol:
Direct-zol RNA Miniprep Kit from ZymoResearch (#R2051)
NEB Next® Ultra™ RNA Library Prep Kit (NEB #E7770)

treatment_protocol: Cells were fed fresh growth medium 3 hours prior to colelction for RNA extraction.

tag: cell line

value: HeLa

value: cervical cancer

value: PIK3CA exon21 frameshift on all three alleles

tag: clone


title: Female cortical_Mouse 3


title: Case ID_15

source_name: IDHmut Astro_MS

value: IDHmut Astro_MS


title: PAEC_6

city: Providence

first: Navneet

last: Singh

state: Rhode Island

address: 593 Eddy Street, POB Suite 334

department: Medicine

institute: Brown University

description:
1052N1
PAEC RNAseq Counts_GEO1.09.11.23.xlsx

data_processing:
Quality control performed using FastQC (Babraham Bioinformatics, Cambridge, UK)
Supplementary files format and content: tab-limited text files include raw counts for each sample

source_name: pulmonary artery endothelial cell

growth_protocol: Pulmonary artery catheter tips with balloon were placed directly into one well of a 24 well plate with Attachment Factor Solution (Cell Applications, Inc; San Diego, CA) and washed with fresh media (EndoGRO-vascular endothelial growth factor [VEGF] complete media kit; Millipore Sigma, Billerica, MA) every two days.Cells were then seeded into T-25 and T-75 flasks until passaged cells reached confluence over the next four to five days.

extract_protocol:
RNA was extracted from frozen cell pellets by Genewiz (Azenta) per their protocol.
Libraries were constructed by Genewiz (Azenta) per their protocol.

value: pulmonary artery endothelial cell

tag: ph group/control

value: Group 1 PAH

tag: ph subtype

value: IPAH


title: 2xH1047R HeLa clone_3

value: PIK3CA H1047R on two alleles, exon21 frameshift on the third


title: Case ID_05


title: Case CTL_07


title: Male cortical_Mouse 4

value: Male


title: AGS cells without treatment rep3

value: cell line

value: AGS

value: gastric epithelial

tag: treatment

value: Negative control


title: 2xH1047R HeLa clone_2


title: WT, low dose LPS neutrophil

city: Blacksburg

first: Liwu

last: Li

state: VA

address: 1015 Life Science Cir

institute: Virginia Tech

library_source: transcriptomic single cell

data_processing:
Cellranger 3.1.0 version
All the data were merged using Seurat's integration workflow. The merged data was then saved in RDS format using the "saveRDS" function.
Assembly: mm10
Supplementary files format and content: Seurat RDS (gz file with matrix can be read by Seurat)

source_name: neutrophil

growth_protocol: Murine bone marrow neutrophils were purified by the percoll gradient method, and cultured in complete RPMI medium (10% fetal bovine serum, 2 mM L-glutamine, and 1% penicillin/streptomycin) supplemented with 100 ng/ml G-CSF.

extract_protocol:
cDNA libraries were generated from treated cells by using the 10X Genomics Chromium Single Cell 3' Reagent Kits (version 3 Chemistry)
Single-cell suspensions were loaded onto the Chromium Controller to generate 1,000 single-cell gel beads in emulsion per sample. The cDNA of each sample after amplification of 12 cycles was quantified by Qubit and quality-checked by Bioanalyzer to verify the size distribution of cDNA samples and determine indexed PCR amplification of 15 cycles to yield a sufficient and unbiased library for sequencing. After library quality control by Tapestation, indexed library samples were quantified by KAPA library quantification kit (Universal) and pooled with 15 ul of 5 nM for each sample.
Libraries were pooled togegther for sequencing on Illumina Hiseq4000

treatment_protocol: Cultured bone marrow neutrophils from WT  mice were treated with PBS, 100 pg/ml LPS or 100 ng/ml LPS for 24 h.

value: BM-derived neutrophil

value: LLPS


title: 3xWT HeLa clone_1

value: PIK3CA WT with silent mutation in exon 21 on all three alleles


title: WT, high dose LPS neutrophil

value: WT

value: HLPS


title: Case ID_14

value: FFPE

value: F

value: brain


title: Case ID_20


title: WT, PBS neutrophil

value: PBS


title: Case ID_12


title: FBC: CD45- lymph node cells from D5 TCRb WT/KO mice, W2 TCRb WT/KO mice, W5 TCRb WT/KO mice, 2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: 6 samples (3 TCRbWT and 3 TCRbKO CD45- LN cells) were hashed together into a single 10X scRNA-seq run

data_processing:
Sequenced reads were demultiplexed, aligned, assigned to cells, and output as count matrices using Cell Ranger (10x Genomics).
Hash-by-cell matrices were computed using CITE-seq-count.
Cells with no or multiple hashes, high mitochondrial content, low gene number, low UMI number, or lineage markers of contaminants were filtered out in Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: LN

extract_protocol:
Cells were released by digestion in Collagenase P, Dispase and DNaseI followed by filtering and washed in RPMI containing 5% fetal calf serum (FCS). CD45+ and CD45- cells were purified by fluorescence-activated cell sorting. Single cells were then sent to the Broad Institute Genomics Platform, which performed encapsulation following 10x Genomics protocols.
10x Genomics library prep, 3' v3 chemistry

value: LN

value: CD45- immune cells

tag: strain

value: Female


title: AGS cells without treatment rep1


title: FBC: CD45+ lymph node cells from D5 TCRb WT/KO mice, W2 TCRb WT/KO mice, W5 TCRb WT/KO mice, 2

description: 6 samples (3 TCRbWT and 3 TCRbKO CD45+ LN cells) were hashed together into a single 10X scRNA-seq run

value: CD45+ immune cells


title: Case CTL_08

value: M


title: AGS cells without treatment rep2

value: cell line

value: AGS


title: FBC: CD45+ lymph node cells from D5 Aire WT/KO mice, W2 Aire WT/KO mice, W5 Aire WT/KO mice,

description: 6 samples (3 AireWT and 3 AireKO CD45+ LN cells) were hashed together into a single 10X scRNA-seq run


title: Uterine_neuroendocrine [OE180716630-04]

city: Shanghai

first: Yin

last: Liu

state: Shanghai

address: Building #2, 507 Zhengmin Road

department: Department of Laboratory Medicine

country: China

institute: Shanghai Pulmonary Hospital, Tongji University School of Medicine

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10xGenomics was used to process reads. Fastq files generated from Illumina sequencing output were mapped to the human reference genome (GRCh37) and transcriptome using the STAR aligner, and then read count matrices were generated by counting unique molecular identifiers (UMIs). Finally, a gene-barcode matrix containing the barcoded cells and gene expression counts was generated. The count data was imported into the Seurat (version 3.1.2) R package to remove low quality cells and likely multiplet captures.
Assembly: hg38
Supplementary files format and content: zip

source_name: uterine neuroendocrine tumor

extract_protocol: Single-cell library preparation was carried out using Chromium Single cell 3’ Reagent v2 Kits (10 × Genomics, USA) according to the manufacturer’s protocol. Cells were loaded on the Chromium Single Cell Controller Instrument to generate single cell gel beads in emulsions (GEMs). Next, reverse transcription was performed, cDNA was cleaned up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific, USA), and was then amplified by PCR with appropriate cycles. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, index adaptor-ligated and subjected to library amplification.

value: uterine neuroendocrine tumor

value: neuroendocrine

tag: diagnosis

value: endometrial neuroendocrine carcinoma


title: Uterine_neuroendocrine [OE180716630-03]


title: AGS cells treated with C. concisus rep2

value: gastric epithelial

value: C. concisus


title: Uterine_neuroendocrine [OE180716630-02]


title: FBC: CD45- lymph node cells from D5 Aire WT/KO mice, W2 Aire WT/KO mice, W5 Aire WT/KO mice

description: 6 samples (3 AireWT and 3 AireKO CD45- LN cells) were hashed together into a single 10X scRNA-seq run


title: GEX: CD45+ lymph node cells from D5 TCRb WT/KO mice, W2 TCRb WT/KO mice, W5 TCRb WT/KO mice, 2


title: Uterine_neuroendocrine [OE180716630-01]


title: GEX: CD45- lymph node cells from D5 Aire WT/KO mice, W2 Aire WT/KO mice, W5 Aire WT/KO mice


title: GEX: CD45- lymph node cells from D5 TCRb WT/KO mice, W2 TCRb WT/KO mice, W5 TCRb WT/KO mice, 2


title: GEX: CD45+ lymph node cells from D5 Aire WT/KO mice, W2 Aire WT/KO mice, W5 Aire WT/KO mice,


title: Male cortical_Mouse 1

value: Astrocytes

value: Male

value: WT


title: AGS cells treated with C. concisus rep1


title: Peripheral blood CD4+ T cell, Asthmatic, JH9

city: Manchester

first: Mauro

last: Tutino

address: Oxford road

institute: University of Manchester

data_processing:
Reads were quality trimmed with Trimmomatic and poly-G and poly-A tails were removed with Cutadapt
STAR was used to map the reads on the hg38 reference genome version
Reads were de-duplicated with UMI-tools
Gene counts were calculated with HTSeq
Assembly: hg38
Supplementary files format and content: The tab-delimited text file include the (UMI de-duplicated) gene counts for all samples

source_name: Peripheral blood

extract_protocol:
CD4+ Enrichment Kit Easysep (Stemcell); RNeasy mini extraction kit - between 100ng and 250ng of RNA were used for library construction
QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen)
3'-UTR RNA-Seq

value: Peripheral blood

value: CD4+ T cell

value: Asthmatic

tag: individual


title: HSC3 cells, Treated with  CPA + S66 Sample 3

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

data_processing:
Trimming of reads using trimmomatic V.0.36
Star (2.5.2a) alignment using Ensemble GRCh38
Raw Gene count generation using htseq-count program (0.6.1p1)
Assembly: Ensembl Homo_sapiens.GRCh38
Supplementary files format and content: htseq-Count text fiile

growth_protocol: Human oral cancer cell lines (HSC-3) were cultured in Dulbecco’s modified eagle medium (DMEM, Gibco, #11885-084) supplemented with 10% fetal bovine serum (FBS, Gibco, #26140-079) and 1% penicillin-streptomycin (PS, Gibco, #15140-122). Cells were harvested by treating 0.25 % Trypsin/EDTA (Gibco, #25200-072) and subcultured (2-3x105 cells) in 100 mm dishes at 37oC in a humidified 20 % O2/ 5 % CO2 incubator for 3-4 days. Cells were stimulated with 25 µM cyclopiazonic acid (CPA, Sigma, #1530) in the presence/absence of the ORAI inhibitor synta-66 for 3 hours before washing the cells and isolating the mRNA.

extract_protocol:
Total RNA was isolated using miRNeasy Mini Kit (Qiagen, #1038703) for RNASeq and RNeasy mini kit (Qiagen, #74106). A NanoDrop spectrophotometer (Thermo Scientific, #13400519) was used to measure the 260/280
The Illumina sequencing run produced 774,131,516 raw paired-end reads from 12 samples (54,874,503-71,100,845 reads). Quality control of raw sequencing reads was performed using FastQC (v0.11.5).Low-quality reads, sequencing adapters and overrepresented K-mers were removed using Trimmomatic (v0.32) resulting a total of 708,579,673 trimmed reads (46,791,160-66,701,914). The reads were aligned to the Human reference genome (Ensembl release 84-GRCh38) using the STAR aligner (v2.5.2a) and default alignment parameters to produce BAM files. HTSeq-Count (v0.6.1p1) was then used to generate read counts per gene based on the 84-GRCh38 GTF considering that the RNASeq library is stranded. The counts generated were then filtered to remove unexpressed or very lowly expressed genes to retain only genes with a minimum of 5 reads in 50% of samples in at least one of the three conditions investigated.
The Illumina sequencing run produced 774,131,516 raw paired-end reads from 12 samples (54,874,503-71,100,845 reads). Quality control of raw sequencing reads was performed using FastQC (v0.11.5).Low-quality reads, sequencing adapters and overrepresented K-mers were removed using Trimmomatic (v0.32) resulting a total of 708,579,673 trimmed reads (46,791,160-66,701,914). The reads were aligned to the Human reference genome (Ensembl release 84-GRCh38) using the STAR aligner (v2.5.2a) and default alignment parameters to produce BAM files. HTSeq-Count (v0.6.1p1) was then used to generate read counts per gene based on the 84-GRCh38 GTF considering that the RNASeq library is stranded. The counts generated were then filtered to remove unexpressed or very lowly expressed genes to retain only genes with a minimum of 5 reads in 50% of samples in at least one of the three conditions investigated.

value: oral cancer cell


title: HSC3 cells, Treated with  CPA + S66 Sample 4

treatment_protocol: Cells were stimulated with 25 µM cyclopiazonic acid (CPA, Sigma, #1530) in the presence/absence of the ORAI inhibitor synta-66 for 3 hours before washing the cells and isolating the mRNA.


title: experiment 3 replicate 2, scRNAseq

city: Tempe

first: Leandra

last: Brettner

state: AZ

address: 1001 S McAllister Ave

department: Biodesign Center for Mechanisms of Evolution

institute: Arizona State University

description: SPLiTseq

data_processing:
Due to an unforeseen and irreversible data loss, 3 of the 14 files were truncated, resulting in minor loss of approximately 5% of the data. The trimmed files are indicated with _trim.
The original, untruncated fastq files were processed into barcode-by-gene count matrices using STARsolo version 2.7.9a. These files were unaffected by the data loss.
Assembly: R46 s288c and/or sc5314 V4
Supplementary files format and content: tab separated value and matrix files

organism: Saccharomyces cerevisiae

source_name: mixed sample (s288c, BY4741)

extract_protocol:
At the time of sampling, 3 mL of yeast cultures were immediately spun down in a room temperature centrifuge at 3000G for 5 minutes. The media supernatant was removed, and the cell pellet was resuspended in 2 mL of cold 4% formaldehyde in molecular grade PBS. The cells were then fixed cold in a 4C refrigerator for approximately 18 hours. After fixation, the samples were spun down in a 4C centrifuge at 3000G for 5 minutes. The formaldehyde supernatant was removed, and the pellet was resuspended in 1 mL cold molecular grade 100 mM Tris HCl pH 7 plus 0.1 U/uL SUPERase-In RNase inhibitor (Invitrogen) to quench the formaldehyde. Cells were then centrifuged, resuspended in 250 uL of a zymolyase enzymatic solution of 0.1M Na2EDTA, 1M sorbitol, and 0.005 U/uL zymolyase (Zymo Research) (pH ~7.5), and incubated at 37C for 15 minutes. At the end of the incubation, 1 mL of cold PBS plus 0.1 U/uL SUPERase-In RNase inhibitor and 0.1 U/uL Enzymatics RNase inhibitor (Enzymatics) was immediately added, and the cells were centrifuged at 4C, 3000G for 5 minutes. The cells were then resuspended in 250 uL of cold 0.4% Triton X-100 in PBS plus RNase inhibitors and incubated on ice for 3 minutes. Again, 1 mL of cold PBS plus RNase inhibitors was added at the end of the 3 minutes and the cells were centrifuged. They were then resuspended in 500 uL of cold PBS plus RNase inhibitors, vortexed on high for ~30 seconds, and lightly filtered through a 40 µm pluriStrainer (pluriSelect). The cells were then counted using a Beckman Coulter Cell Counter and diluted to 1 million cells/mL into fresh cold PBS plus RNase inhibitors.
The cells were then processed according to the standard SPLiTseq protocol. Briefly, in situ reverse transcription and ligation steps were performed and then the cells were lysed and cDNA collected and amplified for sequencing.

value: mixed sample (s288c, BY4741)

value: yeast cells

tag: ploidy

value: diploid, haploid

value: mixed sample (naive, MATa ura3A0 his3{delta}1 met17{delta}0 P ACT1-GAL3::SpHIS5 gall1{delta}gal10{delta}::LEU2 leu2{delta}0::P PGK1 -mCherry-KanMX6 ybr209w{delta}::B103-HphMX6, and MATa ura3A0 his3{delta}1 met17{delta}0 P ACT1-GAL3::SpHIS5 gall1{delta}gal10{delta}::LEU2 leu2{delta}0::P GAL1 -YFP-KanMX6 ybr209w{delta}::BC3-HphMX9)

value: log growth


title: Peripheral blood CD4+ T cell, Asthmatic, JH8


title: Peripheral blood CD4+ T cell, Asthmatic, JH7


title: Peripheral blood CD4+ T cell, Control, JH6

value: Healthy control


title: HSC3 cells, Treated with  CPA + S66 Sample 2


title: HSC3 cells, Treated with  CPA + S66 Sample 1


title: HSC3 cells, Treated with  CPA Sample 4

value: CPA


title: experiment 3 replicate 1, scRNAseq

description: SPLiTseq

value: mixed sample (naive, MATa ura3A0 his3{delta}1 met17{delta}0 P ACT1-GAL3::SpHIS5 gall1{delta}gal10{delta}::LEU2 leu2{delta}0::P PGK1 -mCherry-KanMX6 ybr209w{delta}::B103-HphMX6, and MATa ura3A0 his3{delta}1 met17{delta}0 P ACT1-GAL3::SpHIS5 gall1{delta}gal10{delta}::LEU2 leu2{delta}0::P GAL1 -YFP-KanMX6 ybr209w{delta}::BC3-HphMX8)


title: Case ID_09

value: FFPE

value: M

value: brain


title: HSC3 cells, Treated with  CPA Sample 3


title: Peripheral blood CD4+ T cell, Asthmatic, JH55


title: SVZ375

city: Montreal

first: Kevin

last: Petrecca

state: Quebec

address: 3801 Rue University

department: Neuro

country: Canada

institute: McGill

data_processing:
Illumina HiSeq 1000 reads were demultiplexed and aligned to the GRCh38 reference using CellRanger to produce raw counts. The latter was processed with Seurat pipeline : for each cell, counts (number of UMIs) per gene were normalized to the total counts of the cell and scaled by 10000. The data were natural-log transformed  (log(counts+1)). All cells expressing more than 200 and less than 3500 genes, with lower than  8% expression for mitochondrial genes were included for further analyses. The most significant  8305 PCAs were selected (S:35;F:30;M:20), using jackstraw method and elbow visualization to cluster  the cells based on a shared nearest neighbor (SNN), applying the Louvain algorithm with the resolution of 0.6-0.8 (S:0.6;F:0.6;M:0.8).  Markers, for each cluster/program compared to all other programs, were identified using the  FindAllMarkers function with default Wilcoxon test
Assembly: HGRC38

source_name: brain

extract_protocol:
1. Weight empty 10cm dish (same that will be used tissue) ex: 18.42g 2. Weight tissue 18.69g 3. Wash tissue 2x with PBS+ antibiotics (PS) 4. Remove necrosis area and blood vessels with scalpels 5. Add 0.5mL digestion buffer and cut tissue in 2 or 3 in order to have ~ 1mm piece 6. Transfer tissue + digestion buffer in 15ml tube 7. Add 0.5ml of digestion buffer and inc 20min in 37C and invert tube few times every hour and Triturate with 1000ul pipette tip few time 8. Leave tissue to be digest o/n at 37C (or until tissue can be dissociate by pipetting ) 9. Centrifuge 1400 rpm for 10min 10. Remove supernatant 11. Add 9ml PBS + PS 12. Resuspend pellet using 5ml pipette 13. Add 21 ml percoll to ultracentrifugation tube, then add 9 ml of cells mix well by inverting tube 14. Centrifuge 15000 rpm 30min 4C (program #2) in Jack Antel’s lab 15. Remove debris from top of tube 16. Transfer cells (middle layer) to 50 ml tube and count cells 17. Filled up to 50ml with PBS+PS 18. Centrifuge 1400 rpm 10min 19. Count cells
Single Cell 3′ Reagent Kits v2 User Guide

value: Metastatic adenocarcinoma

tag: brain region

value: subventricular zone


title: SVZ395

value: Glioblastoma


title: SVZ379

value: Astrocytoma grade 2


title: SVZ423


title: SVZ400


title: SVZ391

value: Large cell carcinoma


title: SVZ420


title: SVZ383


title: SVZ428


title: SVZ444


title: Input ChIP [Input2_S5_L004]

city: Houston

first: Komal Kumar

last: Bollepogu Raja

state: TX

address: One Baylor plaza

department: Pathology and Immunology

institute: baylor college of medicine

library_source: genomic

data_processing:
overrepresented sequences such as sequencing adapters from fastQ files using ‘cutadapt’ and ‘trimmomatic’ tools. We next aligned the reads to Drosophila melanogaster genome dm6 with ‘Bowtie2,’ using sensitive local alignment presets to generate a set of BAM files for the ChIP-seq data. Since we received data from four sequencing lanes (technical repeats), we merged BAM files to generate a single merged BAM file for each sample using 'SAMtools.' Merged BAM data were then filtered based on the MAPQ quality score such that only mapped reads that have a MAPQ quality score of at least 20 were retained. Any PCR or optical duplicates were also removed at this step. The resulting filtered BAM files were then sorted with SAMtools. MACS2 was run on the filtered and sorted BAM files using the anti-GFP or anti-FLAG ChIP as the ChIP-seq treatment file, and input control as the control file.
Assembly: Dm6
Supplementary files format and content: bed file

organism: Drosophila melanogaster

source_name: Larval eye disc

growth_protocol: Flies were grown at room temperature

extract_protocol:
120 late third instar larval heads, containing 240 eye discs, were dissected into ice cold PBS. Dissected heads were then fixed in 1.5% formaldehyde in PBS for 15 minutes at room temperature. Fixed heads were quenched with 0.125 M glycine + PBS solution on ice for 5 minutes. Heads were washed in ice cold wash buffer A (10 mM Hepes pH 7.6, 10 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 0.25% Triton X-100) for 10 minutes followed by another wash in wash buffer B (10 mM Hepes pH 7.6, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 0.01% Triton X-100) for 10 minutes at 4°C. Eye discs were dissected away from the heads and placed in ice cold wash buffer B. The eye discs were pelleted by centrifugation at 800 g for 30 seconds at 4°C. Eye discs were resuspended in 1 mL of sonication buffer (50 mM Hepes pH 7.6, 140 mM NaCl, 1 mM EDTA pH 8.0, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, supplemented with proteinase inhibitors (GenDepot P3100-001)) and then transferred to a 15 ml Falcon tube. Eye discs were then sonicated on ice with a Misonix S-4000 Sonicator, 3.2 mm probe. The sonication cycle was as follows: 10 s at 65 amplitude, 30 s rest on ice, total sonication time: 3 minutes. 10 µL of 10% SDS, 100 µL 1% sodium deoxycholate, 100 µL 10% Triton X-100, and 28 µL of 5M NaCl were added to the sonicated eye discs and incubated at 4°C for 10 minutes. Sonicated eye discs were then centrifuged at maximum speed for 5 minutes at 4°C to remove any debris. Supernatant containing the sonicated chromatin was transferred to a new tube.For ChIP-seq experiments, 30 µL of antibody conjugated Protein G Dynabeads were added to the supernatant and immunoprecipitated overnight at 4°C in a tube rotator. 5 µL rabbit anti-GFP (Invitrogen A-6455) and 5 µL of mouse anti-FLAG (M2, Sigma Aldrich, F1804) antibodies were used for each ChIP-seq experiment. Beads were washed once in each of the following buffers: sonication buffer, ChIP wash buffer A (same recipe as sonication buffer but with 500 mM NaCl), ChIP wash buffer B (20 mM Tris pH 8.0, 1 mM EDTA pH8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate), and finally TE buffer for 5 minutes each at 4°C. To remove crosslinks, all supernatant was replaced with 150 µL of elution buffer (50 mM Tris pH 8.0, 50 mM NaCl, 2 mM EDTA, 0.75% SDS, 20 μg/mL RNase A) and incubated overnight at 65°C. Eluted chromatin was removed from the beads and set aside and 150 µL of fresh elution buffer was added to the beads and incubated at 65°C for 30 minutes. Supernatant was pooled with previously eluted chromatin to yield ~300 µL of eluted chromatin. 60 µg of Proteinase K was added to the eluted chromatin and incubated at 37°C for 2 hours to complete the crosslink removal process. ChIP DNA was subjected to phenol-chloroform extraction and ethanol precipitation. Total input controls were treated with the same protocol as the ChIP samples, except that there were no immunoprecipitation steps. Sonicated chromatin from total input controls was directly subjected to the crosslink removal protocol followed by Proteinase K treatment, phenol chloroform extraction, and ethanol precipitation. Libraries for next generation sequencing were generated from these DNA samples.
ChIP-seq libraries were prepared and paired-end sequencing (PE75) was performed with an Illumina NextSeq 500 system. Samples were sequenced to a depth of 40 million reads. All samples passed the initial quality controls on the fastQ files.

value: Larval eye disc

tag: developmental stage

value: late third instar larva

value: pnt-GFP-FPTB; pntd88/pnt2

tag: antibody

value: none; input


title: SVZ376


title: Peripheral blood CD4+ T cell, Asthmatic, JH57

value: Peripheral blood

value: CD4+ T cell

tag: disease state

value: Asthmatic


title: case_B_sc

city: shanghai

first: Junfeng

last: Chen

address: Gaoke Xi Road 2699

institute: Tongji university

description: one sample from Human endometrial tissue

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: Human endometrial tissue

extract_protocol:
Samples are fixed in a 4% formaldehyde fixative solution, as described in the Fixation of Cells & Nuclei for Chromium Fixed RNA Profiling (Demonstrated Protocol CG000478) and using Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics PN-1000414).
RNA libraries  were prepared with Chromium Single Cell Gene Expression Flex kits according to the manufacturer’s protocol.

tag: tissue

value: Human endometrial tissue

value: nonresponder  to anti-PD-1 therapy


title: case_A_st

data_processing:
The Space Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus spots
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell
Library strategy: Spatial Transcriptomics

extract_protocol:
The tissues were cut into 4-5 mm pieces and treated with cleanroom wipers. After removing blood stains on the tissue surface, fresh tissue was embedded with OCT then snap frozen. Cryosections were cut at 10-um thickness, mounted onto the ST arrays.Next, the tissue was dehydrated with isopropanol for 1 min followed by staining with HE. Brightfield images were taken on a Leica SCN400 F whole-slide scanner at 40x resolution.
Library preparation slides used were purchased from the Spatial Transcriptomics team. Each of the spots printed onto the array is 55um in diameter and 100um from center to center, covering an area of 6.5x6.5 mm2. Each slide includes 4 Capture Areas, each with ~5,000 unique gene expression spots.

value: responder to anti-PD-1 therapy


title: case_A_sc


title: case_B_st


title: Peripheral blood CD4+ T cell, Asthmatic, JH54

tag: cell type


title: Input ChIP [Input2_S5_L003]


title: Input ChIP [Input2_S5_L002]


title: HSC3 cells, Treated with  CPA Sample 1

value: oral cancer cell

value: CPA


title: HSC3 cells, Treated with  CPA Sample 2


title: Input ChIP [Input2_S5_L001]


title: Peripheral blood CD4+ T cell, Asthmatic, JH53


title: Peripheral blood CD4+ T cell, Control, JH52

value: Healthy control


title: SVZ359

value: Astrocytoma grade 3

tag: age

value: subventricular zone

value: brain


title: HSC3 cells, Untreated Sample 4

value: Untreated


title: Input ChIP [Input1_S4_L004]

value: Larval eye disc

tag: genotype


title: HSC3 cells, Untreated Sample 3

tag: cell line


title: HSC3 cells, Untreated Sample 2


title: Input ChIP [Input1_S4_L002]

value: late third instar larva


title: Input ChIP [Input1_S4_L003]

value: pnt-GFP-FPTB; pntd88/pnt2


title: Peripheral blood CD4+ T cell, Asthmatic, JH51


title: Case CTL_06

tag: material

value: FFPE

tag: Sex

value: M


title: HSC3 cells, Untreated Sample 1


title: Peripheral blood CD4+ T cell, Asthmatic, JH50

value: Peripheral blood

value: CD4+ T cell


title: Input ChIP [Input1_S4_L001]

value: none; input


title: SVZ373

value: Glioblastoma


title: SVZ350


title: Case CTL_05


title: Peripheral blood CD4+ T cell, Asthmatic, JH5

value: Asthmatic


title: laneM141-ESRP1_IP_1_BKDL210007688-1a-AK15931-AK15932

city: Wuhan

first: Chengguo

state: Hubei

address: Union Hospital, No. 1277 Jiefang Avenue

institute: Wuhan Union Hospital

library_source: other

data_processing:
Illumina NovaSeq 6000, 150 nt
The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base. Those reads need to be filtered before the data analysis for reliability analysis results.
We used TopHat 2 to align the clean reads to the reference genome.
We used HOMER(Hypergeometric Optimization of Motif EnRichment) to analyze motif.
Assembly: GRCh38, version 23(Ensembl 81)
Supplementary files format and content: tab-delimited text file includes raw reads for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: other

source_name: gastric cancer

extract_protocol:
SGC7901 cells were irradiated once for 400 mJ/cm2, and lysed in ice-cold wash buffer (1× PBS, 0.1% SDS, 0.5% NP-40 and 0.5% sodium deoxycholate) supplemented with a 200 U/mL RNase inhibitor (Takara) and protease inhibitor cocktail (Roche) and incubate on ice for 30 min. After centrifuge, RQ I(Promega) with a final concentration of 1 U/μL was added to the supernatant and incubate for 30 min at 37°C. Immediately afterward, a stop solution was added to the lysates to quench DNase. The mixture was then vibrated vigorously and centrifuged at 13,000 g for 20 min at 4℃ to remove cell debris. Then RNA digestion by MNase (Thermo Fisher Scientific) was performed.
libraries were prepared with the KAPA RNA Hyper Prep Kit (#KK8541, KAPA) according the manufacturer’s procedure.
crosslinking-immunoprecipitation and high-throughput sequencing (CLIP seq)

value: gastric cancer

value: gastric cancer cells

value: ESRP1 overexpression


title: laneM141-ESRP1_IP_2_BKDL210007688-1a-AK15933-AK15934


title: myocardium,  Ischemia3, 30 min, rep3

city: Daqing

first: Long

middle: Pi

last: Shi

state: Heilongjiang

address: No.39, Xinyang Road, Longfeng District, Daqing City

department: Department of Pharmacology

institute: Harbin Medical University

data_processing:
Paired-end sequencing was performed on cDNA library using Illumina instrument.
The qualified reads were mapped to Rat6 using STAR split mapping algorithm.
The expression level of genes was determined based on the value of FPKM which was calculated by htseq-count.
Assembly: Rat6
Supplementary files format and content: tab-delimited text files include counts and FPKM values for each Sample

organism: Rattus norvegicus

source_name: Myocardial tissue

growth_protocol: The rats were placed in a colony room with controlled temperature and humidity, where food and water were freely available in a 12-h light/dark cycle.

extract_protocol:
Total RNA was harvested from the cells using Trizol reagent. TruSeq Stranded Total RNA Library Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Male rats were anesthetized, placed supine, and surgically assisted breathing with animal ventilator, and left thoracotomy was performed through a horizontal incision in the fourth intercostal space.
Ischemia (model rat) was observed when the left anterior descending (LAD) coronary artery was ligated around the PE-10 tube with moving nodule with 6-0 sutures, and occlusion of the left anterior descending coronary artery was confirmed by elevation of the ST segment of the electrocardiogram.

value: Myocardial tissue

value: WT

value: Ischemia


title: myocardium, Ischemia2, 30 min, rep2


title: Flag_ChIP [Flag2_S3_L002]

value: mouse anti-FLAG (M2, Sigma Aldrich, F1804)


title: laneM141-Input_2_BKDL210007688-1a-AK8223-AK15937


title: Peripheral blood CD4+ T cell, Asthmatic, JH49


title: Flag_ChIP [Flag2_S3_L003]

value: Larval eye disc


title: Peripheral blood CD4+ T cell, Asthmatic, JH48


title: laneM141-Input_1_BKDL210007688-1a-AK2701-AK4510


title: Peripheral blood CD4+ T cell, Asthmatic, JH47


title: Flag_ChIP [Flag2_S3_L004]

value: late third instar larva


title: myocardium, Ischemia1, 30 min, rep1


title: HCAEC, EGF, biol rep 8

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

institute: Martin Luther University - Halle-Wittenberg

description: Human coronary artery endothelial cells

data_processing:
Read alignment (HISAT2 2.1.0).
Read counting (featureCounts - 2.0.0).
Annotation with biomaRt and Ensembl 101.
Assembly: hg38
Supplementary files format and content: annotatedCounts.csv: Comma-separated file including annotation raw counts (output of featureCounts) for each sample.

source_name: HCAEC

growth_protocol: HAoEC and HCAEC were obtained from PromoCell (C-12271) and Lonza (CC-2585), respectively. Both cells types were cultivated with Endothelial Cell Growth Medium MV2 (PromoCell, C-22121) supplemented with Endothelial Cell Growth Medium MV2 SupplementMix (PromoCell, C-39226. Final concentrations after addition to the medium: 5% FCS, 5ng/mL EGF, 10ng/mL FBF, 20ng/mL IGF-1, 0.5ng/mL VEGF, 1µg/mL Ascorbic acid and 0.2µg/mL Hydrocortisone).

extract_protocol:
Total RNA was isolated with BluZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNase (Ambion, Life Technologies).
PolyA enrichment (performed by Novogene Europe).

treatment_protocol: Cells were synchronized for 24h in media with minimal supplementation (Endothelial Cell Growth Medium MV2 with 1% HSA, 1µg/mL Ascorbic acid and 0.2µg/mL Hydrocortisone only) and then incubated for 48h -/+ 10µg/L EGF.

value: HCAEC

tag: gender

value: female

tag: donor

tag: replicate

value: biol rep 8

value: EGF


title: SVZ337

tag: diagnosis

value: Astrocytoma grade 3

value: subventricular zone

value: brain


title: myocardium, Ischemia, 30 min, rep1, H2Aub ChIP

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. 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 uing MACS v2.1.0 with the significance cut-off q-value <=0.01
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: Rat6
Supplementary files format and content: bigWig, narrowPeak

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

tag: treatment

tag: chip antibody

value: H2Aub(cell siginaling, #8240)


title: Case CTL_03

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta

extract_protocol: Illumina protocol

value: FFPE

value: M


title: Flag_ChIP [Flag2_S3_L001]

value: pnt-GFP-FPTB; pntd88/pnt2


title: Peripheral blood CD4+ T cell, Asthmatic, JH46

value: Peripheral blood

value: CD4+ T cell

value: Asthmatic

tag: individual


title: Flag_ChIP [Flag1_S2_L004]

tag: developmental stage

value: mouse anti-FLAG (M2, Sigma Aldrich, F1804)


title: HCAEC, Control, biol rep 8

description: Human coronary artery endothelial cells

value: Control


title: myocardium, sham3, 30 min, rep3

value: Myocardial tissue

value: WT

value: Sham


title: HCAEC, EGF, biol rep 7

description: Human coronary artery endothelial cells

value: HCAEC

value: female

value: biol rep 7


title: Peripheral blood CD4+ T cell, Control, JH38

value: Healthy control


title: Peripheral blood CD4+ T cell, Control, JH4


title: Peripheral blood CD4+ T cell, Asthmatic, JH39


title: myocardium, sham2, 30 min, rep2


title: myocardium, sham1, 30 min, rep1


title: HCAEC, EGF, biol rep 6

description: Human coronary artery endothelial cells

value: biol rep 6

value: EGF


title: Flag_ChIP [Flag1_S2_L002]

value: Larval eye disc

value: late third instar larva

tag: antibody


title: HCAEC, Control, biol rep 7

description: Human coronary artery endothelial cells


title: Case CTL_02

tag: disease state

value: FFPE

value: F

value: brain


title: Flag_ChIP [Flag1_S2_L003]

tag: tissue

value: pnt-GFP-FPTB; pntd88/pnt2


title: Flag_ChIP [Flag1_S2_L001]

value: mouse anti-FLAG (M2, Sigma Aldrich, F1804)


title: Peripheral blood CD4+ T cell, Control, JH37

value: Peripheral blood

tag: cell type

value: CD4+ T cell


title: GFP_ChIP [GFP1_S1_L003]

value: rabbit anti-GFP (Invitrogen A-6455)


title: myocardium, Ischemia, 30 min, rep1, input

value: Myocardial tissue

value: Ischemia

value: none (input)


title: Peripheral blood CD4+ T cell, Asthmatic, JH35

value: Asthmatic


title: Case CTL_04

value: M


title: HCAEC, Control, biol rep 6

description: Human coronary artery endothelial cells

value: HCAEC

value: female

value: biol rep 6

value: Control


title: Case ID_08

value: FFPE


title: GFP_ChIP [GFP1_S1_L004]

value: Larval eye disc

value: late third instar larva


title: HCAEC, EGF, biol rep 5

description: Human coronary artery endothelial cells

value: biol rep 5

value: EGF


title: Case CTL_01

value: brain


title: HCAEC, EGF, biol rep 4

description: Human coronary artery endothelial cells

value: biol rep 4


title: ABPS3

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10 (ref 1). The processed reads were aligned to the Caenorhabditis elegans transcriptome and genome version WBcel235 with annotations from Ensembl release 106 using TopHat v2.1.1 (ref 2). Counts per gene quantification was done with htseq-count v2.01 (ref. 3). Normalization and differential expression analysis were done with the DESeq2 package v 1.36.0 (ref 4.). The normalized counts were further batch corrected for the effect of the 3 repeats of the biological procedure.
Assembly: WBcel235
Supplementary files format and content: txt table with DESeq2 normalized and batch corrrected counts per gene (rows) per sample (column)

organism: Caenorhabditis elegans

source_name: pool of whole worms

growth_protocol: Synchronized CL2006 worms were grown @20C on the indicated RNAi (EV or AB) to day 1 of adulthood and were bleached again. Eggs were placed on the same RNAi (EV or AB). Worms of the second generation were washed and transferred onto new plates every day to remove progeny and harvested at day 6 of adulthood.

extract_protocol:
RNA was extracted using the NucleoSpin® RNA kit (MACHEREY-NAGEL; 740955) according to the manufacturer instructions.
PolyA-selection, mRNA libraries were prepared using KAPA Stranded mRNA kit with mRNA Capture Beads (KAPA Biosystems, KK8421). In brief, 1µg was used for the library construction; library was eluted in 20µl of elution buffer. All DNA samples libraries were pooled to 10nM sample. Multiplex samples Pool were loaded on NovaSeq 6000 (Illumina), using NovaSeq 6000 SP Reagent Kit v1.5 100 cycles (cat# 20028401), with 122 cycles
Single End 122bp length

treatment_protocol: At day 1 of adulthood, worms of the second generation were soaked in M9 buffer (untreated groups) or with the 5MER peptide (5MER treated). The same treatment (M9 or 5MER) was added daily to the plates until harvesting.

value: pool of whole worms

tag: strain

tag: harvest time

value: harvested at day 6 of adulthood

value: AB RNAi

value: Grown on AB RNAi -  exposed to the 5MER peptide


title: HCAEC, Control, biol rep 5

description: Human coronary artery endothelial cells


title: GFP_ChIP [GFP1_S1_L001]

tag: genotype

value: pnt-GFP-FPTB; pntd88/pnt2

value: rabbit anti-GFP (Invitrogen A-6455)


title: GFP_ChIP [GFP1_S1_L002]


title: Case ID_11

city: Heidelberg

first: Daniel

address: Im Neuenheimer Feld 224

institute: University Hospital Heidelberg, Intitute of Pathology

tag: material

value: F


title: HCAEC, Control, biol rep 4

description: Human coronary artery endothelial cells

value: HCAEC

value: female


title: Peripheral blood CD4+ T cell, Asthmatic, JH33

value: Peripheral blood

value: CD4+ T cell

value: Asthmatic


title: Non-metastatic HNSCC-2

type: RNA

city: Beijing

first: Yujia

last: Wang

address: 22 Zhongguancun South Avenue, Haidian District

institute: Peking University School and Hospital of Stomatology

description: Non-metastatic HNSCC samples from anterior portions of the tongue of patient #6

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: Non-metastatic HNSCC

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: No growth protocol, all paired metastatic HNSCC samples from anterior portions of the tongue and non-metastatic HNSCC samples were obtained from 8 patients who were admitted to the Department of Oral and Maxillofacial Surgery of Peking University of Stomatology between  May 2008 and August 2011.

extract_protocol: Total RNA was isolated from tumor samples by using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA)

treatment_protocol: No treatment

value: Human tongue tissues

tag: tissue type

value: Non-metastatic HNSCC


title: Peripheral blood CD4+ T cell, Asthmatic, JH32


title: ABPS1


title: Non-metastatic HNSCC-4

description: Non-metastatic HNSCC samples from anterior portions of the tongue of patient #8


title: Non-metastatic HNSCC-3

description: Non-metastatic HNSCC samples from anterior portions of the tongue of patient #7


title: ABPS2


title: AB0S3

value: Grown on AB RNAi - not exposed to the 5MER peptide


title: HCAEC, EGF, biol rep 3

description: Human coronary artery endothelial cells

tag: gender

value: biol rep 3

value: EGF


title: Non-metastatic HNSCC-1

description: Non-metastatic HNSCC samples from anterior portions of the tongue of patient #5


title: Peripheral blood CD4+ T cell, Asthmatic, JH31


title: HCAEC, EGF, biol rep 2

description: Human coronary artery endothelial cells

tag: donor

value: biol rep 2


title: Metastatic HNSCC-3

description: Metastatic HNSCC samples from anterior portions of the tongue of patient #3

source_name: Metastatic HNSCC

value: Metastatic HNSCC


title: Metastatic HNSCC-4

description: Metastatic HNSCC samples from anterior portions of the tongue of patient #4


title: AB0S2

value: pool of whole worms

value: harvested at day 6 of adulthood

value: AB RNAi


title: Peripheral blood CD4+ T cell, Asthmatic, JH34


title: Metastatic HNSCC-2

description: Metastatic HNSCC samples from anterior portions of the tongue of patient #2


title: Peripheral blood CD4+ T cell, Control, JH24

value: Healthy control


title: Metastatic HNSCC-1

description: Metastatic HNSCC samples from anterior portions of the tongue of patient #1


title: HCAEC, Control, biol rep 2

description: Human coronary artery endothelial cells

tag: replicate

value: Control


title: EVPS3

value: WT

value: Exposed to 5MER peptide


title: Peripheral blood CD4+ T cell, Asthmatic, JH22

value: Peripheral blood


title: Peripheral blood CD4+ T cell, Asthmatic, JH23

value: CD4+ T cell


title: AB0S1


title: HCAEC, EGF, biol rep 1

description: Human coronary artery endothelial cells

value: HCAEC

value: female

value: biol rep 1


title: HCAEC, Control, biol rep 1

description: Human coronary artery endothelial cells


title: Peripheral blood CD4+ T cell, Asthmatic, JH3

value: Asthmatic


title: HCAEC, Control, biol rep 3

description: Human coronary artery endothelial cells

value: biol rep 3


title: EVPS2


title: Peripheral blood CD4+ T cell, Asthmatic, JH21


title: HAoEC, EGF, biol rep 8

description: Human aortic endothelial cells

source_name: HAoEC

value: HAoEC

value: biol rep 8

value: EGF


title: Peripheral blood CD4+ T cell, Asthmatic, JH20


title: EVPS1

value: pool of whole worms


title: 3d_post_IR_rep1

city: Chongqing

first: Weinian

last: Liao

address: Gaotanyan street 30

institute: Army Medical University

description: Gene expression of MKs from mice at 3 day post IR

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression v2 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained

source_name: MK, 3dpi

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All mice used were randomized, background-matched. All mice used were housed in individually ventilated specific pathogen-free (SPF) conditions and fed with autoclaved water and food.

extract_protocol: RNA was extracted from sorted mMKs using a TRIzol Plus reagent (TaKaRa, Shiga, Japan).

treatment_protocol: With or without exposed to IR.

value: Bone marrow

value: megakaryocyte (MK)

value: male

value: 3 day post IR


title: 3d_post_IR_rep2


title: EV0S3

value: harvested at day 6 of adulthood

value: WT

value: Untreated worms


title: 1d_post_IR_rep3

description: Gene expression of MKs from mice at 1 day post IR

source_name: MK, 1dpi

value: 1 day post IR


title: Peripheral blood CD4+ T cell, Asthmatic, JH2

value: Peripheral blood

value: CD4+ T cell


title: 3d_post_IR_rep3


title: HAoEC, Control, biol rep 8

description: Human aortic endothelial cells

value: female

value: Control


title: Peripheral blood CD4+ T cell, Asthmatic, JH19

value: Asthmatic


title: HAoEC, EGF, biol rep 7

description: Human aortic endothelial cells

value: HAoEC

value: biol rep 7


title: EV0S2


title: 1d_post_IR_rep2


title: Peripheral blood CD4+ T cell, Asthmatic, JH18


title: HAoEC, EGF, biol rep 6

description: Human aortic endothelial cells

value: biol rep 6

value: EGF


title: HAoEC, Control, biol rep 7

description: Human aortic endothelial cells


title: Peripheral blood CD4+ T cell, Asthmatic, JH17


title: E5_RNA

city: Baltimore

first: Seth

last: Blackshaw

state: MD

address: 733 N Broadway

department: Neuroscience

institute: Johns Hopkins University

data_processing:
Reads were aligned to chicken genome GRCg7b and analyzed using the chicken annotation from Ensembl Release 109 and 10X Genomics Cell Ranger ARC (v2.0.2).
Assembly: GRCg7b
Supplementary files format and content: h5 file is the combined output of samples from CellRanger ARC, containing both RNA and ATAC count matricies.

organism: Gallus gallus

source_name: Eye

growth_protocol: Fertile Specific Pathogen Free eggs (Charles River Laboratories, 10100329) were incubated in a rotating, humidified incubator at 37° C.

extract_protocol:
Whole chicken eyes were enucleated at E4 or E5 in PBS containing 0.2 U / µl RNasin Plus RNase Inhibitor (Promega, N2615). Eyes from 3 embryos were pooled for each biological replicate. Nuclei were immediately extracted and fixed for snRNA-seq. For combined snRNA-seq and scATAC-seq, samples were first cryopreserved via snap freezing in an isopentane bath on liquid nitrogen and briefly stored at -80°C prior to nuclei extraction. In brief, nuclei extraction was carried out via an optimized variation of the demonstrated protocols described in 10X Genomics Protocol CG000124 Rev E and 10X Genomics Protocol CG000366 Rev D. Lysis was performed via trituration and 30 second incubation in a buffer containing 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.005% Tween-20, 0.005% Surfact-Amps NP-40, 0.0005% digitonin (Thermo Fisher Scientific, BN2006), 1% fraction V bovine serum albumin, 1 mM DTT, and 1 U / µl Sigma Protector RNase inhibitor (MilliporeSigma, 3335402001). Nuclei were washed twice by resuspending in cold buffer containing 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 1% fraction V bovine serum albumin, 0.1% Tween-20, 1 mM DTT, and 1 U / µl Sigma Protector RNase inhibitor. Nuclei were passed twice through 20 µm cell strainers (pluriSelect, 43-10020-40) during isolation to filter debris and cell aggregates.
Nuclei were subjected to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression library preparation workflow (10X Genomics, 1000285 & 1000230) following 10X Genomics protocol CG000338 Rev F, loading approximately 16,000 nuclei per reaction. The 10X Genomics Chromium Controller was used for GEM generation. ATAC libraries were amplified with 7 total PCR cycles, and RNA libraries were amplified with 15 PCR cycles. Indexes were incorporated from Single Index Kit N, Set A (10X Genomics, PN-1000212) and Dual Index Plate TT Set A (10X Genomics, PN-1000215). Libraries were sequenced at the Novogene Sequencing Core (Sacramento, CA) on the Illumina NovaSeq 6000. ATAC libraries were sequenced to generate 49,000-54,000 reads per nucleus and RNA libraries were sequenced to generate 29,000-56,000 reads per nucleus.

value: Eye

value: Embryonic day 5


title: 1d_post_IR_rep1

value: Bone marrow

value: megakaryocyte (MK)

value: male


title: HAoEC, Control, biol rep 6

description: Human aortic endothelial cells


title: 0 minute Control, rep2

city: New Delhi

first: Agam

middle: Prasad

state: Delhi

address: Aruna Asaf Ali Marg

department: IDL

country: India

institute: NII

data_processing:
Illumina Casava1.8 software used for basecalling.
All sequence reads were trimmed off adaptor sequences and YPD grown sample sequence reads wer trimmed to make it 36 base pairs to maintain uniformity across the samples. Sequence reads were independently aligned using QIAGEN CLC Genomics Workbench 21.0.3 with default setting against Candida albicans genome (Assembly 22).
Differential expression, p-value and fold changes for each gene were determined using QIAGEN CLC Genomics Workbench 21.0.3 with default parameters.
Genome_build: Candida albicans SC5314 genome assembly 22.
Supplementary_files_format_and_content: Excel files include RPKM values for each mRNA of respective samples.

organism: Candida albicans

source_name: whole organism total RNA

growth_protocol: Candida albicans NCCPF 400034 was grown at 37 °C overnight in YPD medium. The cells were then washed with PBS and counted using the hemocytometer.

extract_protocol:
RNA was extracted using the Ribopure Yeast Kit (Ambion).  The total RNA extraction was performed as per the mannual described in the Kit protocol. Briefly, Candida albicans grown in serum for different time points were washed with the PBS and then the total RNA was extracted using the Ribopure yeast kit. RNA purity was confirmed by the nandrop and RNA integrity were confirmed by analysis on an Agilent 2100 bioanalyzer, using the RNA 6000 nano kit (Agilent) to conform RINs above 8.0. The YPD grown samples was also extracted with the above kit and the RNA purity was checked by Nanodrop.
RNA library was prepared as recommended by the IlluminaTruseq RNA sample preparation kit V2 for serum +butanol grown samples and sequencing was performed using Genome Analyzer IIx for 36 cycles. For the YPD grown sample RNA library was prepared using Ribo-zero gold kit and sequencing was performed on Illumina Hiseq for 150 cycles.

treatment_protocol: The overnight grown Candida albicans NCCPF 400034 was then placed in complete human serum (O+ve) supplemented with 1 % butanol and incubated in 5 % CO2 at 37 °C. The cells were then harvested at different time points to extract the total mRNA. The YPD grown Candida cells were treated as control and RNA was sequenced using next generation techniques.

value: 0 minutes overnight growth in YPD at 150 RPM (control)


title: Peripheral blood CD4+ T cell, Control, JH16

data_processing:
Reads were quality trimmed with Trimmomatic and poly-G and poly-A tails were removed with Cutadapt
STAR was used to map the reads on the hg38 reference genome version
Reads were de-duplicated with UMI-tools
Gene counts were calculated with HTSeq
Assembly: hg38
Supplementary files format and content: The tab-delimited text file include the (UMI de-duplicated) gene counts for all samples

extract_protocol:
CD4+ Enrichment Kit Easysep (Stemcell); RNeasy mini extraction kit - between 100ng and 250ng of RNA were used for library construction
QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen)
3'-UTR RNA-Seq

value: Healthy control


title: E4_RNA

value: Embryonic day 4


title: Ctrl_rep3

description: Gene expression of Ctrl mice MKs

source_name: MK, Ctrl

value: Ctrl


title: 0 minute Control, rep1


title: HAoEC, EGF, biol rep 5

description: Human aortic endothelial cells

value: biol rep 5


title: Ctrl_rep2

description: Gene expression of Ctrl mice MKs


title: Ctrl_rep1

description: Gene expression of Ctrl mice MKs


title: Peripheral blood CD4+ T cell, Control, JH14

source_name: Peripheral blood

value: Peripheral blood

value: CD4+ T cell


title: E5_ATAC


title: E4_ATAC


title: Peripheral blood CD4+ T cell, Control, JH13


title: Peripheral blood CD4+ T cell, Control, JH12


title: HAoEC, Control, biol rep 5

description: Human aortic endothelial cells

value: female

value: Control


title: C92×MH63_rep2

first: Xuncheng

address: 5 Yiheyuan Road

institute: Peiking University

description:
PolyA RNA isolated
F1 hybrid

data_processing:
C92 and MH63 RNA-seq reads were mapped to the corresponding assembled genomes, respectively, using HISAT2 (version 2.0.5) software with default parameters (Kim et al. 2015). Reads that can map to multiple position were discarded before subsequent analyses. For F1 hybrid, we aligned RNA-seq reads to both of the parental genomes. We then split F1 RNA-seq reads into reads that can mapped to both of the parental genomes (common reads) or only to one of the genome (allele reads) based upon the highest quality alignment. Both of the common reads and allele reads were used to calculation mRNA expression levels in F1 hybrid.
Genome_build: MSU 7.0 (http://rice.plantbiology.msu.edu)
Supplementary_files_format_and_content: FPKM.txt: Tab-delimited text files include FPKM values for each Sample.

organism: Oryza sativa Indica Group x Oryza sativa Japonica Group

source_name: 14-day-old seedling

growth_protocol: Rice cultivar C92, MH63 and their hybrid were used for all experiments in this study. Seeds were grown in water under long-day conditions (16-h light at 28°C and 8-h dark at 28°C) in a growth chamber (100 μmol·m-2·s-1) for 2 weeks.

extract_protocol:
Total RNA was extracted using an RNeasy Plant Mini Kit (Qiagen) and treated with RNase-free DNase I (Promega) to remove any contaminating genomic DNA.
First- and second-strand cDNAs were generated using SuperScript II reverse transcriptase (Invitrogen) and random hexamer primers. Double-stranded cDNAs were fragmented by nebulization and used for RNA-seq library construction following the standard Illumina protocol.

tag: cultivar

value: MH63 x C92

value: Shoot

tag: age

value: 14 days


title: C92×MH63_rep3

description:
PolyA RNA isolated
F1 hybrid


title: C92×MH63_rep1

description:
PolyA RNA isolated
F1 hybrid


title: Sublibrary_7

data_processing:
Reads were aligned to chicken genome GRCg7b and analyzed using the chicken annotation from Ensembl Release 109 using the Parse Biosciences alignment suite (v1.0.3)
Assembly: GRCg7b
Supplementary files format and content: all_genes.csv contains the list of genes output from the Parse Biosciences alignment suite
Supplementary files format and content: cell_metadata.csv contains the list of cell barcodes and gene counts output from the Parse Biosciences alignment suite
Supplementary files format and content: DGE.mtx contains the digital gene expression matrix output from the Parse Biosciences alignment suite

extract_protocol:
Whole chicken eyes were enucleated at E4 or E5 in PBS containing 0.2 U / µl RNasin Plus RNase Inhibitor (Promega, N2615). Eyes from 3 embryos were pooled for each condition. Nuclei were immediately extracted and fixed for snRNA-seq. In brief, nuclei extraction was carried out via an optimized variation of the demonstrated protocols described in 10X Genomics Protocol CG000124 Rev E and 10X Genomics Protocol CG000366 Rev D. For snRNA-seq, cell lysis was performed by triturating sample and incubating in a cold buffer comprised of 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.01% Surfact-Amps NP-40 (Thermo Fisher Scientific, 28324), and 0.2 U / µl RNase Inhibitor. Nuclei were washed 3 times by resuspending in cold PBS containing 2% fraction V bovine serum albumin and 0.2 U / µl RNase inhibitor (Promega, N2615). Nuclei were passed twice through 20 µm cell strainers (pluriSelect, 43-10020-40) during isolation to filter debris and cell aggregates.
snRNA-seq libraries were generated via the split-pool barcoding method using the Parse Biosciences Single Cell Whole Transcriptome Kit Chemistry Version 1 (Parse Biosciences, SB2001). Nuclei were fixed according to the Nuclei Fixation Kit Protocol (Parse Biosciences, SB1003) and stored at -80°C. During library preparation, nuclei were loaded for library prep as follows: embryonic day 4 (wells A1-A6), embryonic day 5 (wells A7-B1), embryonic day 4 6 hours post-retinectomy (wells B2-B8), and embryonic day 4 6 hours post-retnectomy + FGF2 (wells B9-C3). cDNA was amplified with 13 total PCR cycles. Final libraries were assessed with the Agilent Bioanalyzer and Qubit 4. Libraries were sequenced across two lanes of HiSeq X Ten and a lane of NovaSeq 6000 at the Novogene Sequencing Core (Sacramento, CA).

treatment_protocol: Retinectomies and FGF2 delivery were performed by creating an incision around the anterior eye chamber with surgical scissors and the neural retina was dislodged with a wire probe. For FGF2-delivery, approximately 20 acrylic beads with immobilized surface heparin (MilliporeSigma, H5263) were incubated overnight in 4 µl of 250 ng/µl of bovine basic FGF2 (R&D Biosystems, 133-FB-025). At the time of surgery, FGF2 beads were deposited into the posterior chamber of the eye cup and the eye was closed. Embryos were incubated for 6 hours before enucleating the eyes for use with the Parse Biosciences snRNA-seq workflow.

value: Eye

tag: treatment

value: Embryonic day 4, Embryonic day 5, Embryonic day 4 6 hours post-retinectomy, Embryonic day 4 6 hours post-retinectomy + FGF2


title: EV0S1

value: pool of whole worms

value: harvested at day 6 of adulthood

value: WT

value: Untreated worms


title: HAoEC, Control, biol rep 4

description: Human aortic endothelial cells

value: HAoEC

value: biol rep 4


title: HAoEC, EGF, biol rep 3

description: Human aortic endothelial cells

value: biol rep 3

value: EGF


title: Sublibrary_6


title: HYs-3 (miRNA-Seq)

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss Omyk_1.1
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each Sample

organism: Oncorhynchus mykiss

source_name: dorsal skin

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: dorsal skin

value: yellow mutant


title: Peripheral blood CD4+ T cell, Control, JH10

first: Mauro

address: Oxford road

institute: University of Manchester

value: Peripheral blood

value: CD4+ T cell

value: Healthy control

tag: individual


title: HYs-2 (miRNA-Seq)


title: HAoEC, Control, biol rep 3

description: Human aortic endothelial cells

value: female

value: Control


title: Sublibrary_5

value: Eye


title: Peripheral blood CD4+ T cell, Asthmatic, JH1

value: Asthmatic


title: Sublibrary_4

value: Embryonic day 4, Embryonic day 5, Embryonic day 4 6 hours post-retinectomy, Embryonic day 4 6 hours post-retinectomy + FGF2


title: HAoEC, EGF, biol rep 2

description: Human aortic endothelial cells

value: biol rep 2


title: Sublibrary_3


title: C92_rep3

description: PolyA RNA isolated

organism: Oryza sativa Japonica Group

value: Shoot

value: 14 days


title: HWs-3 (miRNA-Seq)

value: wild-type


title: HYs-1 (miRNA-Seq)


title: HAoEC, Control, biol rep 2

description: Human aortic endothelial cells

value: HAoEC


title: C92_rep2

description: PolyA RNA isolated


title: HAoEC, EGF, biol rep 4

description: Human aortic endothelial cells

value: biol rep 4


title: Sublibrary_2


title: HWs-2 (miRNA-Seq)


title: Peripheral blood CD4+ T cell, Asthmatic, JH11


title: HAoEC, EGF, biol rep 1

description: Human aortic endothelial cells

value: biol rep 1

value: EGF


title: HAoEC, Control, biol rep 1

description: Human aortic endothelial cells


title: C92_rep1

description: PolyA RNA isolated


title: HWs-1 (miRNA-Seq)

value: dorsal skin


title: nascentRNA_FX5

status: Public on Dec 26 2023

city: Chicago

first: Christopher

last: Futtner

state: Il

address: 303 E. Superior St, Lurie 7-220

department: Endocrinology

institute: Northwestern University

data_processing:
Alignment:  ChIP-seq reads were obtained and mapped to the mouse mm10 genome using Bowtie 1.2 with --best and -m 1  parameters. RNA-seq and Ribo-seq reads were mapped to an mm10 reference genome using STAR version 2.4.0.
ChIP-seq Peaks. Tag directories were generated in HOMER using the -tbp 1 command to remove clonal reads. Homer getDifferentialPeaksReplicates.pl was used to call ChIP-seq peaks in comparison to input controls using default settings.
RNA-seq gene expression was quantified using HOMER. Differnetially expressed RNA's were normalized and identified using DESeq2 version 1.14.1.
Ribo-seq data was processed via Homer and RiboDiff. Raw RPF and RNA read counts matrices were generated with Homer using the analyzerepeats.pl command with the -noadj option. Changes in translation efficiency were detected with RiboDiff.
Assembly: mm10
Supplementary files format and content: Tab-delimited text (txt) files with annotated peak lists

source_name: skeletal muscle - quadricep

extract_protocol:
Skeletal muscle for ChIP-Seq was dissected and finely minced. ChIP-seq samples were subjected to cross linking in 1% formaldehyde for 30 minutes and quenched with glycine. Tissue was dounced to release nuclei. Nuclei were sonicated to shear the chromatin and subjected to immunoprecipitation. Precipitates were washed and DNA was purified by column (Qiagen Min-Elute). Tissues for RNA-Seq were homogenized in Trizol using a MoBio PowerLyzer 24. Lysates were purified via Qiagen RNAeasy purification column. RiboSeq samples pulverized in liquid nitrogen then lysed in polysome lysis buffer supplemnted with 100ug/ml cyclohexamide. Lysate were dounced, then cleared by centrifugation. Cleared lysates were next treated with 3000U of T1RNase and ribosomes immunoprecipitated with HA tag magnetic beads. RNA was extracted from the immunoprecipitated ribosomes and subjected to library prep.
ChIP-seq libraries were prepared with the KAPA Hyper Prep Kit (Kapa Biosciences). RNA-seq libraries were prepared with the Illumina Tru-seq stranded mRNA kit. Ribo-seq libraries were prepared with the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs).

value: skeletal muscle - quadricep

value: wild type

tag: molecule subtype

value: nascent RNA


title: nascentRNA_FX4


title: nascentRNA_FX2


title: nascentRNA_FX3


title: nascentRNA_DMSO5

value: DMSO


title: nascentRNA_FX1


title: nascentRNA_DMSO1


title: nascentRNA_DMSO2


title: nascentRNA_DMSO3


title: nascentRNA_DMSO4


title: Yy1 KD Morula RNA rep3

city: Kofu

first: Mizuki

last: Sakamoto

country: Japan

institute: University of Yamanashi

description: RNA-seq

data_processing:
Paired-end reads were aligned to the mouse genome (mm10) using Hisat2 (version 2.2.1) after removing adaptor sequences and low quality reads by Trim Galore! (version 0.6.7) with a ‘--clip_R2 3’ option. Reads corresponding to ribosomal RNA were removed using a bedtools ‘intersectBed’ function. Read counts were calculated by featureCounts (version 2.0.1) with option ‘-p -O --fraction -s 0’ and the expression of each gene annotated by GENCODE vM25 was quantified by calculating TPM.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files indicating TPM values

source_name: BDF1 x BDF1

growth_protocol: Early embryos were cultured in KSOM.

extract_protocol:
Total RNA from embryos was used in SMART-Seq stranded kit (TAKARA).
Libraries were prepared with SMART-seq stranded kit (TAKARA).

treatment_protocol: Morulae were collected after siRNA injection at the zygote stage.

value: BDF1 x BDF1

tag: developmental stage

value: Morula

value: Yy1 knocked down


title: Yy1 KD Morula RNA rep1

description: RNA-seq


title: Yy1 KD Morula RNA rep2

description: RNA-seq


title: K27Ac_chronic_imKO_1802

description:
acute_k27Ac_counts.txt
chronic_k27Ac_counts.txt

value: AEC-Esr Cre (+):Bcl6 fl/fl

value: TMX

tag: chip primary_antibody

value: rabbit anti-H3K27Ac, Active Motif 39133


title: K27Ac_chronic_imKO_1794

tag: tissue


title: Control KD Morula RNA rep3

description: RNA-seq

value: control knockdown


title: Control KD Morula RNA rep2

description: RNA-seq


title: K27Ac_chronic_Ctr_Input

value: Bcl6 fl/fl


title: Control KD Morula RNA rep1

description: RNA-seq


title: Sublibrary_1

value: Eye

value: Embryonic day 4, Embryonic day 5, Embryonic day 4 6 hours post-retinectomy, Embryonic day 4 6 hours post-retinectomy + FGF2


title: Peripheral blood CD4+ T cell, Asthmatic, JH36

city: Manchester

value: Peripheral blood

tag: cell type

value: CD4+ T cell

tag: disease state

value: Asthmatic


title: sgRNA_rep2-cd69n2

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Raw reads for gene expression were processed using CellRanger v6 for the mm10 reference transcriptome
sgRNA counts were computed using kallisto | bustools for a custom kite index of gRNAs present in the library
Assembly: mm10
Supplementary files format and content: h5 of gene expression counts matrices; barcodes/genes/counts for sgRNA content from CRISPR perturbation

source_name: Tissue Resident Memory T cells

extract_protocol:
Cells were isolated from frozen, flow cytometry sorted CD8+ T cell subsets according to the sort markers noted in the per-sample descriptions
Perturb-seq libraries were constructed using 10x Genomics reagents and protocols for 5' feature barcoding and gene expression

tag: infection

value: 14 dpi of LCMV

tag: mouse replicate

value: Liver N


title: sgRNA_rep2-cd69p1

value: Liver P


title: K27Ac_chronic_imKO_Input

value: skeletal muscle - quadricep

tag: strain

tag: genotype


title: sgRNA_rep2-Spl2

value: Spleen


title: sgRNA_rep2-cd69n1


title: K27Ac_chronic_imKO_1803


title: sgRNA_rep2-Spl1


title: sgRNA_cd69n1


title: sgRNA_cd69n2


title: sgRNA_Spl2


title: sgRNA_Spl1


title: GEX_rep2-Spl2


title: GEX_rep2-cd69n2


title: GEX_rep2-cd69n1


title: GEX_rep2-cd69p1


title: GEX_rep2-Spl1


title: sgRNA_cd69p1


title: GEX_cd69p1


title: GEX_cd69n2


title: GEX_cd69n1


title: GEX_Spl2


title: GEX_Spl1


title: K27Ac_acute_Ctr_Input


title: K27Ac_acute_Ctr_6366


title: K27Ac_acute_Ctr_6371


title: Carm1_KO_3w_RNAseq_Rep2

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University

data_processing:
Data quality was checked with FastQC and MultiQC.
Reads were aligned to the mm10 reference genome using hisat2
featureCounts was used for computing gene expression level
DESeq2 was used to obtain the differentially expressed genes between CTRL and KO samples.
Assembly: mm10
Supplementary files format and content: CTRL_KO_1w_3w_raw_count.csv

source_name: Heart

extract_protocol:
Briefly, mosaic heart that contained AAV9-Cre infected Carm1KO or control AAV9-GFP infected cardiomyocytes was isolated. And the cardiomyocytes were isolated using Langendorff system. Total RNA was purified and used for mRNA library preparation.
The libraries are constructed with SMARTrHT + NEXTERA XT .

value: Heart

value: Cardiomyocyte

value: Mouse was Injected with AAV-CRE at Postnatal Day 4


title: Carm1_KO_1w_RNAseq_Rep1

value: Mouse was Injected with AAV-CRE at Postnatal Day 1


title: Carm1_KO_3w_RNAseq_Rep1

value: Mouse was Injected with AAV-CRE at Postnatal Day 3


title: Carm1_KO_1w_RNAseq_Rep2

value: Mouse was Injected with AAV-CRE at Postnatal Day 2


title: Carm1_CTRL_3w_RNAseq_Rep2

value: Mouse was Injected with AAV-GFP at Postnatal Day 4


title: E13.5 EDNRB-GFP bowel, GFP positive cells 3 [miRNA]

city: Philadelphia

first: Robert

middle: O

last: Heuckeroth

state: PA

address: 3615 Civic Center Blvd Rm 1115

institute: Children's Hospital of Philadelphia Research Institute

description: GFP-Pos 3

data_processing:
Sequencing reads were aligned with STAR v2.4.2a, then normalized with PORT v0.8.5-beta.
STAR alignment was performed with the additional arguments --outFilterScoreMinOverLread 0.3 and --outFilterMatchNminOverLread 0.3 to account for short alignments with miRNA
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized CPM values for each gene and sample

source_name: E13.5 bowel

extract_protocol:
RNA was purified from frozen samples in QIAzol using the Qiagen miRNAeasy Mini Kit (Qiagen #217004); a total of 750pg was used to begin library preparation
Libraries were prepared with the Illumina truSeq smRNA kit (Illumina #RS-200)

value: E13.5 bowel

value: Enteric neural crest-derived cells

value: Wild-type


title: E13.5 EDNRB-GFP bowel, GFP positive cells 4 [miRNA]

description: GFP-Pos 4


title: E13.5 EDNRB-GFP bowel, GFP positive cells 2 [miRNA]

description: GFP-Pos 2


title: P42adultRGC ATAC replicate2

first: Ying

last: Xin

address: 400 N Broadway (Smith Building)

description: S4 200 cycle

data_processing:
Feature-barcode matrices were generated using the Cell Ranger software v3.0.2
Assembly: mm10
Supplementary files format and content: Tab-saparated values files and matrix files

source_name: enriched RGC from mouse retina

extract_protocol:
Retinas of the vGlut2-Cre;LSL-Sun1GFP mice were quickly and carefully dissected out from enucleated eyeballs. Through gentle pipette trituration, the retinas were dissociated in ice-cold neurobasal medium on ice. According to the 10X Genomics protocol, whole retinal cells were then incubated in the nuclear lysis buffer on ice for 3-min to expose and penetrate the cell nuclei, and then centrifuged to pellet the nuclei. The cell nuclei were then resuspended in ice-cold MACS buffer (Miltenyi Biotec, Gaithersburg, MD) for anti-GFP MACS microbeads incubation. The whole retina nuclei were then passed through and eluted from the Miltenyi MACS MS column to enrich GFP+ RGC nuclei, then being centrifuged to pellet.
Final concentration of 4000~5000 nuclei/uL loading onto the 10X Genomics multiome platform.
10X Genomics multiome platform

value: enriched RGC from mouse retina

value: postnatal day 42


title: K27Ac_acute_Ctr_6345

value: Bcl6 fl/fl

value: TMX

value: rabbit anti-H3K27Ac, Active Motif 39133


title: E13.5 EDNRB-GFP bowel, GFP positive cells 1 [miRNA]

description: GFP-Pos 1


title: P42adultRGC ATAC replicate1

description: S4 200 cycle


title: Carm1_CTRL_3w_RNAseq_Rep1

value: Mouse was Injected with AAV-GFP at Postnatal Day 3


title: E13.5 EDNRB-GFP bowel, GFP negative cells 4 [miRNA]

description: GFP-Neg 4

value: Non-enteric neural crest-derived cells


title: K27Ac_acute_imKO_6348

value: skeletal muscle - quadricep

value: AEC-Esr Cre (+):Bcl6 fl/fl


title: K27Ac_acute_imKO_6349


title: K27Ac_acute_imKO_Input


title: K27Ac_chronic_Ctr_1795


title: K27Ac_chronic_Ctr_1801


title: K27Ac_chronic_Ctr_7362


title: Carm1_CTRL_1w_RNAseq_Rep2

value: Heart

value: Cardiomyocyte

value: Mouse was Injected with AAV-GFP at Postnatal Day 2


title: K27Ac_acute_imKO_6346


title: mycelium, d_xyr1_2_fru_rep_1

city: Nanjing

first: Paul

last: Daly

state: Jiangsu

address: 50 Zhongling St

institute: Jiangsu Academy of Agricultural Sciences

data_processing:
Raw data (raw reads) of fastq format were first processed through in-house Perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter sequences, reads containing poly-N, and low-quality reads from raw data. At the same time, Q20, Q30, GC-content, and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality. These clean reads were then mapped to the reference genome sequence by STAR aligner (v2.5.2b) (Dobin et al. 2013). The percentage of uniquely mapped reads was at least 95% in all of the samples. HTSeq (v 0.5.4) (Anders et al. 2015) was used to count the reads numbers mapped to each gene. Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped (FPKM).  Anders S, Pyl P T, Huber W. 2015. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics, 31, 166-169. Dobin A, Davis C A, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras T R. 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29, 15-21.
Assembly: T. harzianum CBS 226.95 strain from NCBI (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_003025095.1/) (Druzhinina et al. 2018). Druzhinina I S, Chenthamara K, Zhang J, Atanasova L, Yang D, Miao Y, Rahimi M J, Grujic M, Cai F, Pourmehdi S, Salim K A, Pretzer C, Kopchinskiy A G, Henrissat B, Kuo A, Hundley H, Wang M, Aerts A, Salamov A, Lipzen A, et al. 2018. Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts. PLoS Genetics, 14, e1007322.
Supplementary files format and content: tab-delimited text file of counts for each sample
Supplementary files format and content: tab-delimited text file of FPKM values for each sample

organism: Trichoderma harzianum

source_name: mycelium

growth_protocol: To inoculate pre-cultures, spores were harvested from a PDA plate using a 0.05% tween 20 solution, filtered with a nappy gauze, and inoculated into a 250 mL flask containing 50 mL minimal medium supplemented with 1% w/v D-fructose and 0.1% w/v peptone to give a 1x10^4/mL spore final concentration. The composition of the minimal medium (MM) used was 5 g/L (NH₄)₂SO₄, 15 g/L KH2PO4, 0.6 g/L MgSO₄, 0.6 g/L CaCl₂ and 2 mL/L Vishniac solution 500X stock, and adjusted to pH 5.5 with KH2PO4 or K2HPO4 (Penttilä, Nevalainen et al. 1987). The pre-cultures were incubated at 28°C and 200 RPM for 36 h in the dark. For transfer, the mycelia were collected using a 38 µm nylon net filter and washed twice with ~200 mL MM solution. Then 1 g wet weight of mycelia was transferred into 250 mL flasks containing 50 mL of MM with either 25 mM D-fructose, 1% w/v cellulose (microcrystalline from cotton linters) or without an added carbon source, and incubated for 18 h at 28°C with 200 RPM in the dark. For transcriptomic analysis, mycelia were collected from cultures from the 18 h time-point, flash-frozen in liquid nitrogen, and stored at -80°C. To take account of variability from different spore plates, separate spore plates were used to inoculate each of the three sets of replicate pre-cultures, and each set of replicate pre-cultures was transferred to their respective replicate cultures with various carbon sources.

extract_protocol:
Total RNA was extracted using the Magnetic Tissue/Cell/Blood Total RNA Kit (Tiangen, China) according to the manufacturer’s instructions. RNA purity and quantity were evaluated using a NanoDrop spectrophotometer (Thermo Scientific, USA), and RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
For the library preparation for transcriptome sequencing, a total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). To select cDNA fragments of preferentially 200-250 bp in length, the library fragments were purified with the AMPure XP system (Beckman Coulter, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. The purified PCR products (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The library preparations were sequenced on an Illumina NovaSeq 6000 platform by Beijing Allwegene Technology (China), and paired-end 150 bp reads were generated. About ~40 M raw reads for each sample were generated.

treatment_protocol: See the growth protocol section for information on the treatments.

value: mycelium

value: D-fructose


title: mycelium, d_xyr1_2_noC_rep_1

value: no added carbon source


title: mycelium, d_xyr1_2_fru_rep_2


title: mycelium, d_xyr1_2_noC_rep_2


title: mycelium, d_xyr1_2_noC_rep_3


title: mycelium, d_xyr1_2_fru_rep_3


title: in vivo_2

city: Seattle

first: Rene

last: Cheng

state: WA

address: 1900 9th AVE

institute: Seattle children research institute

description: in vivo_2

data_processing:
FASTQ files were filtered and adaptors were trimmed using Trimmomatic .
We then use STAR to map high-quality reads to the human genome reference sequence (version hg38) and associate read counts with each gene.
Assembly: hg38
Supplementary files format and content: gene count matrix in csv.

extract_protocol:
Enriched hCD45+ in vivo expanded tranformed human B cells derived from NSG mice receiving human differentitated B cells
Clontech’s SMARTseq and Illumina’s NexteraXT kits

value: Primary cells


title: in vivo_1

description: in vivo_1

source_name: Enriched hCD45+ in vivo expanded tranformed human B cells


title: P42adultRGC rNA replicate2

description: S4 200 cycle


title: Carm1_CTRL_1w_RNAseq_Rep1

value: Mouse was Injected with AAV-GFP at Postnatal Day 1


title: mycelium, d_xyr1_2_cel_rep_3

value: cellulose


title: E13.5 EDNRB-GFP bowel, GFP negative cells 3 [miRNA]

description: GFP-Neg 3

value: E13.5 bowel

value: Wild-type


title: P42adultRGC RNA replicate1

description: S4 200 cycle

value: enriched RGC from mouse retina

value: postnatal day 42


title: E13.5 EDNRB-GFP bowel, GFP negative cells 1 [miRNA]

description: GFP-Neg 1


title: E13.5 EDNRB-GFP bowel, GFP positive cells 4

description: GFP-Pos 4

data_processing:
Sequencing reads were aligned with STAR v2.4.2a, then normalized with PORT v0.8.5-beta.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized CPM values for each gene and sample

extract_protocol:
RNA was purified from frozen samples in QIAzol using the Qiagen miRNAeasy Mini Kit (Qiagen #217004); a total of 750pg was used to begin library preparation
Libraries were prepared with the Clontech SMARTer PCR cDNA Synthesis Kit (Clontech #634925) followed by the Illumina NexteraXT kit (Illumina #FC-131)

value: Enteric neural crest-derived cells


title: carm1_1_ChIPseq

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Reads were aligned to the mm10 reference genome using Bowtie2.
Genome_build: mm10 genome
Supplementary_files_format_and_content: two bed files containing H3R17m2a ChIPseq peaks for WT and carm1 samples

source_name: Primary mouse cardiac fibroblast

growth_protocol: Mice were raised and maintained under standard laboratory conditions.

extract_protocol:
Hearts were extracted according to standard protocol
Homogenized frozen cardiac tissue was resuspended in hypotonic buffer, followed by sonication to separate chromatin. Chromatin was then immunoprecipitated by using antibody against H3R17me2 for library construction and deep sequencing.

value: wild type


title: E13.5 EDNRB-GFP bowel, GFP positive cells 3

description: GFP-Pos 3


title: E13.5 EDNRB-GFP bowel, GFP positive cells 2

description: GFP-Pos 2


title: control5dayONC

description: S2 100

molecule: nuclear RNA

source_name: enriched RGC mouse retina

extract_protocol:
Retinas of the vGlut2-Cre;LSL-Sun1GFP mice were quickly and carefully dissected out from enucleated eyeballs. Through gentle pipette trituration, the retinas were dissociated in ice-cold neurobasal medium on ice. According to the 10X Genomics protocol, whole retinal cells were then incubated in the nuclear lysis buffer on ice for 3-min to expose and penetrate the cell nuclei, and then centrifuged to pellet the nuclei. The cell nuclei were then resuspended in ice-cold MACS buffer (Miltenyi Biotec, Gaithersburg, MD) for anti-GFP MACS microbeads incubation. The whole retina nuclei were then passed through and eluted from the Miltenyi MACS MS column to enrich GFP+ RGC nuclei, then being centrifuged to pellet.
The pellet was then resuspended to reach concentration of 4000~5000 nuclei/uL loading onto the 10X Genomics Single-Nuclei 3’ HT platform.
10X Genomics Single-Nuclei 3’ HT

treatment_protocol: AAV-based transduction and mice optic nerve crush surgery

value: enriched RGC mouse retina

value: 5day ONC


title: E13.5 EDNRB-GFP bowel, GFP positive cells 1

description: GFP-Pos 1


title: hOprm1OE5dayONC

description: S2 100

value: hOprm1OE 5day ONC


title: 17ZR101, scRNAseq

city: Hong Kong

first: QI

last: XU

address: B2530, Yeung Kin Man Academic Building, City University of Hong Kong, Hong Kong

department: Department of Infectious Disease and Public Health

institute: City University of Hong Kong

description: 10x Genomics

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

source_name: Lung

extract_protocol:
Lung tissues were excised and incubated in HBSS containing 1 x HEPES and Collagenase type I. The tissue fragments were forced through a 70-μm strainer as described above. Red blood cells were lysed with ACK lysing buffer.
Rootine Library consctruction was performed  by BGI.

value: Lung

value: 6-8 weeks old

value: bacteria-infection


title: E13.5 EDNRB-GFP bowel, GFP negative cells 2 [miRNA]

description: GFP-Neg 2

value: Non-enteric neural crest-derived cells


title: E13.5 EDNRB-GFP bowel, GFP negative cells 4

description: GFP-Neg 4


title: carm1_2_ChIPseq

value: Heart


title: IECs from uninfected neonatal mice

city: Aachen

first: Matthias

middle: W

last: Hornef

address: Pauwellstr 30

department: Medical Microbiology

institute: Uniklinik Aachen

data_processing:
Gene quantification and compared the differential gene expression using DESeq2.
You have the DESeq2 result table with annotations.
Additionally, plotting file with a histogram of the log2 fold-changes and MA-plot.
Assembly: for Salmonella, we used this as our referencehttps://www.ncbi.nlm.nih.gov/nuccore/CP001363. for host, we used the official mouse reference genome (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCA_000001635.9/.
Supplementary files format and content: File `Mouse_Salmonella_plus vs_Salmonella_minus_vs_mock` in Excel Sheets. It compares mouse genes expression in Salmonella+ and Salmonella- neonatal intestinal epithelial cells
Supplementary files format and content: File `Salmonella_plus_vs_Salmonella_reference`in Excel Sheets. It compares Salmonella gene expression in Salmonella+ neonatal intestinal epithelial cells and Salmonella reference

source_name: Neonatal intestinal epithelial cells

extract_protocol:
C57BL/6 mice will be infected on day 1 after birth with 100 CFU S. Tm. carrying a FPV-mCherry plasmid (pmCherry, kindly provided by Leigh Knodler, NIH, Hamilton, USA). Enterocytes will be isolated from total small intestinal tissues using a previously established EDTA-based protocol at d4p.i. (Lotz et al., 2006). Alexa Fluor® conjugated EpCam and CD45 antibodies in combination with flow cytometric (FACS) sorting will be used to further enrich enterocytes and remove immune cells. EpCam+ CD45- enterocytes (Ep+) will then be pooled from several animals of an infected litter and individually gated and sorted according to their intracellular Salmonella status (Ep+Sal+ = pmCherry+ or Ep+Sal- = pmCherry-). In parallel, EpCam+ CD45- enterocytes (Ep+) will be sorted from non-infected age-matched (5 day old) neonates using a similar protocol and allow defining the gate for Salmonella negative enterocytes. RNA will be isolated from the four independent FACS sorting experiments using the QIAGEN RNeasy Micro or RNeasy Midi Kit for Ep+Sal+ population or Ep+Sal- population and Ep+ population from non-infected neonates, respectively. cDNA libraries were generated according to published protocol (Westermann et al., 2016)
The integrity of the DNase-treated RNA samples was assessed in a Bioanalyzer (Agilent).Ribosomal transcripts were removed using the Ribo-Zero Gold (epidemiology) kit (Illumina).rRNA-depleted RNA was precipitated in ethanol for 3 h at −20 °C.ForcDNA library generation, rRNA-free RNA samples were first sheared via ultrasound sonication (four 30-s pulses at 4 °C) to generate on average 200- to 400-nt fragments. Fragments of 20 nt were removed using the Agencourt RNAClean XP kit (Beckman Coulter Genomics) and the Illumina TruSeq adapter was ligated to the 3′ ends of the remaining fragments. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase (NEB) wherein the 3′ adapter served as a primer. The first-strand cDNA was purified, and the 5′ Illumina TruSeq sequencing adapter was ligated to the 3′ end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10–20 ng/μl using a high-fidelity DNA polymerase. The TruSeq barcode sequences were part of the 5′ and 3′ TruSeq sequencing adapters. The cDNA library was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis (Shimadzu MultiNA microchip). For sequencing, cDNA libraries were pooled in approximately equimolar amounts. The cDNA pool was size fractionated in the size range of 200–600 bp using a differential cleanup with the Agencourt AMPure kit (Beckman Coulter Genomics). Aliquots of the cDNA pools were analyzed by capillary electrophoresis (Shimadzu MultiNA microchip). Sequencing was performed on a NextSeq 500 platform (single-end mode; 75 cycles).
Dual RNA Seq according to Alexander Westermann et al., 2016

value: Neonatal intestinal epithelial cells

value: wildtype

value: no treatment


title: IECs containing Salmonella sorted from infected neonatal mice

value: infected on day 1 after birth with 100 CFU S. Tm. carrying a FPV-mCherry plasmid


title: Sham, scRNAseq

description: 10x Genomics

value: mock-infection


title: IECs containing no Salmonella sorted from infected neonatal mice


title: mycelium, wt_noC_rep_2

value: mycelium

value: wild type (CBS 226.95)

value: no added carbon source


title: mycelium, wt_noC_rep_3


title: mycelium, d_xyr1_2_cel_rep_2

value: cellulose


title: mycelium, wt_fru_rep_2

value: D-fructose


title: mycelium, wt_fru_rep_3


title: mycelium, wt_noC_rep_1


title: mycelium, d_xyr1_2_cel_rep_1


title: mycelium, wt_fru_rep_1


title: E13.5 EDNRB-GFP bowel, GFP negative cells 1

description: GFP-Neg 1

value: E13.5 bowel

value: Wild-type


title: E13.5 EDNRB-GFP bowel, GFP negative cells 3

description: GFP-Neg 3


title: mycelium, wt_cel_rep_3


title: mycelium, wt_cel_rep_2