title: 7 Days HFD Secretory Enriched- Duo

first: Jacob

last: Enriquez

state: IL

institute: University of Chicago

description: Live+, Epcam+, TdTom+

data_processing:
Standard CellRanger Pipeline to generate FASTQ
Initial filtering by only including cells greater than 100 and less than 7500 genes. Only including cells less than 50 percent mitochondrial related genes
SCTransform pipeline and cell cycle regression for each sample
DoubletDecon standard pipeline for each sample (rhop values in methods)
Seurat Reference- Based Integration SCTransform Pipeline using Normal Chow as Reference Dataset (Epithelial Samples)
Seurat Reference- Based Integration SCTransform Pipeline using Normal Chow as Reference Dataset (Secretory Enriched Samples)
Differential expression using Seurat
STREAM pseudotime standard pipeline
Assembly: mm10
Supplementary files format and content: Saved as Rds files to upload directly into Seurat

source_name: intestine

growth_protocol: Adult Mouse Intestine

extract_protocol:
Performed by the CCHMC Gene Expression Core using the Chromium 3’v3 GEM Kit (10x Genomics)
RNA libraries were prepared using standard Illumina protocols

treatment_protocol: Normal Chow- 5010 ; HFD Chow- D12492

value: Neurog3Cre x TdTom

tag: region

value: Duodenum

tag: condition

value: 7 Days HFD


title: Saline Brain, S1, Sample 2, Batch 1

status: Public on Nov 15 2022

type: SRA

city: Rockville

first: Danielle

last: Sambo

state: MD

address: 5625 Fishers Lane

country: USA

institute: National Institute on Alcohol Abuse and Alcoholism

library_source: transcriptomic single cell

data_processing:
10X Genomics Cell Ranger Single Cell pipeline was used to demultiplex samples, process and align barcodes, and integrate samples using the default and recommended parameters.
Assembly: Cellranger’s default mm10 reference dataset was used for alignment.
Supplementary files format and content: Data files contain the raw counts per cell for each sample and cluster. No processed data is included for Sal5 because this sample was excluded from downstream analysis.

molecule: polyA RNA

organism: Mus musculus

source_name: Brain, cortex

extract_protocol:
Nuclei were isolated. RNA was extracted during library preparation using the Single Cell 3’ V3.1 Reagent Kit.
Nuclei were isolated and library preparation was completed using the 10X Single Cell Version 3.1 chemistry per the manufacturer’s instructions.

tag: tissue

value: Brain, cortex

tag: age

value: Embrynoic day 14

tag: pregnant dam

tag: treatment

value: Saline


title: YZWJs524_Ectoderm

type: RNA

city: Kyoto

first: Masayoshi

last: Tsukahara

state: Kyoto

address: Shogoin kawahara-cho, sakyo-ku,

department: Research and Develpoment center

country: Japan

institute: CiRA foundation

description: SAMPLE 366

hyb_protocol: Gene expression hybridizatoin kits (Agilent) were used for hybridization.

scan_protocol: Slides were scanned on the SureScan microarray scanner system (Agilent).

data_processing: Fluorescent intensities were loaded and processed for backgroud correction by limma package of R software. Values were log-transformed and normalized by quantile normalization.

molecule: total RNA

organism: Homo sapiens

source_name: Differentiated cells from HLA homozygous iPSC

label_protocol: Low input quick amp labeling kits (Agilent) were used for cRNA labeling.

growth_protocol: Human iPSCs were maintained on iMatrix-511 (Nippi) coated plate with StemFit (AK03N, Ajinomoto).

extract_protocol: RNA was extracted by using TRIzol reagent (Thermo Fisher) and purifed by using RNA easy mini kit (QIAGEN).

treatment_protocol: Differentiation into three germ layers were conducted by using STEMDiff Trilineage differentiation kit (STEMCELL Technologies).

tag: cell type

tag: gender

value: Male

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: Patient 1293, acute sample

city: Chicago

first: Yan

last: Che

state: Illinois

address: 303 E Superior St

institute: Northwestern University

description:
1293x1q1
DENV_gene_count_matrix.csv

library_source: transcriptomic

data_processing:
Sequencer-generated base call (BCL) files were converted to FASTQ files and the multiplexed samples were separated using bcl2fastq
Demultiplexed fastq were assessed for sequencing quality using FastQC (version 0.11.4, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The fastq files were quality filtered by using FASTAX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) with the invocation fastq_quality_filter -q 30 -p 50 -v -Q 33
Sequencing reads that met all quality control requirements were aligned to the latest human reference genome (GRCh38) using HISAT2 (version 2.0.4)
Gene expression in units of overlapping read counts per million were obtained by using the script from ballgown on gtf files of preprocessed RNA-seq alignments.
Counts per million were normalized using the voom methodology and expression profiles were modeled using mixed-effect models in limma (version 3.30.6)
Genome_build: GRCh38
Supplementary_files_format_and_content: DENV_gene_count_matrix.csv

source_name: Whole blood

extract_protocol:
Total RNA was extracted from PAXgene RNA blood solution with the MagNA Pure96 Cellular RNA Large Volume Kit on Roche MagNA Pure96 (MP96) Automated Nucleic Acid Isolator  by following manufacturers’ instructions and an additional clean-up using RNAClean XP beads from Beckman Coulter. Purified RNA samples were quantified by Qubit 3.0 fluorometer with RNA High Sensitivity Assay kit. Quality of the RNA samples was confirmed with the RNA High Sensitivity ScreenTape using the TapeStation 2200.
Sample libraries were then prepared from the 136 samples’ libraries (from two time points of 68 paired patient samples). First, ribosomal RNA (rRNA) and globin mRNA were removed from 200 ng total RNA, and the remaining RNA was fragmented and primed for cDNA synthesis using TruSeq Total Stranded RNA HT kit with Ribo-Zero Globin on a Microlab STAR automated liquid handling system. The libraries were barcoded with TruSeq HT indices to allow for multiplexing, and ligation-mediated PCR was performed to enrich barcoded libraries for 15 cycles, then purified with the Agencourt AMPure XP beads system. The libraries were assessed for quality with the high-sensitivity DNA chip in a TapeStation 2200 and quantified with KAPA Library Quantification Kits for Illumina platforms. The libraries were diluted to 2nM and combined equimolarly in pools of 12. These pools were then clustered using a cBot with a HiSeq 3000/4000 paired-end cluster kit on a patterned flow cell over 8 lanes. The flow cell was sequenced on a HiSeq4000 using a HiSeq 3000/4000 SBS kit.

tag: timepoint

value: 5d post symptom onset

tag: age (years)

tag: Sex

value: M

tag: infection

value: Secondary

tag: symptom

value: Dengue Hemorrhagic Fever/Dengue Shock Syndrome

tag: virus type


title: Patient 1303, acute sample

description:
1303x1q1
DENV_gene_count_matrix.csv

value: F

value: Dengue Fever


title: Saline Brain, S1, Sample 1, Batch 1


title: SEc6-D9

city: Cambridge

first: Anna

last: Greka

state: MA

address: 415 Main St

department: Kidney Disease Initiative

institute: Broad Institute of MIT and Harvard

description: 10x Genomics

data_processing:
cellranger-6.0.2
Samples raw base calls demultiplexing, barcoded processing, sequence alignment and gene counting  were made using the Cell Ranger software 6.0.2 function. Raw sequence reads were aligned to the latest mouse reference genome (mm10).
Downstream analysis were performed in the R programming language for graphics and statistical computing version 4.0.3 (R-v4.0.3).
Data analysis and visualization were performed using Seurat within R.
Assembly: mm10_v3.0.0
Supplementary files format and content: h5 files from CellRanger

source_name: Whole kidney cell suspensions

extract_protocol: Each animal was perfused with 20 ml of cold PBS, and then 1/2 of the kidney was sampled and quicly placed in media with 2% FBS on ice. After micing with razor blade, the remainings were transferred to 1X Liberase TH (Millipore Sigma) dissociation medium and subjected to single cell dissociation.

treatment_protocol:
Mice were injected with either vehicle or PTH (1-34, 300 ug/kg) or SK-124 (40 mg/kg) and sacrified using CO2 inhalation, 90 minutes or 2.5 hours post injection, resectively.
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)

tag: cell line

value: Whole kidney cell suspensions

value: Kidney

value: PTH

tag: age (weeks)


title: 7 Days HFD Secretory Enriched-  Jej

description: Live+, Epcam+, TdTom+

tag: strain

value: Neurog3Cre x TdTom

tag: region

value: Proximal Jejunum

tag: condition


title: Patient 1269, convalescent sample

description:
1269x9q2
DENV_gene_count_matrix.csv

value: 14d post symptom onset


title: 3 Days HFD Secretory Enriched- Jej

description: Live+, Epcam+, TdTom+

value: 3 Days HFD


title: SEc5-D8

description: 10x Genomics

value: VEH


title: Patient 1269, acute sample

description:
1269x1q1
DENV_gene_count_matrix.csv

value: 4d post symptom onset


title: YZWJs513_Mesoderm

description: SAMPLE 365

value: Male

value: Cord blood


title: 3 Days HFD Secretory Enriched- Duo

description: Live+, Epcam+, TdTom+

value: Duodenum


title: YZWJs513_Endoderm

description: SAMPLE 364

value: pCE episomal vector


title: Patient 1250, convalescent sample

description:
1250x9q1
DENV_gene_count_matrix.csv

value: 16d post symptom onset

value: M

value: Secondary


title: 1 Day HFD Secretory Enriched- Jej

description: Live+, Epcam+, TdTom+

value: 1 Day HFD


title: YZWJs513_Ectoderm

description: SAMPLE 363


title: PolyA RNASeq 1

city: Pasadena

first: Isabel

last: Goronzy

state: CA

address: 1200 E California Blvd

department: Biology and Biological Engineering

institute: California Institute of Technology

description: Female ES cells (pSM44 ES cell line) derived from a 129 × castaneous F1 mouse cross. These cells express Xist from the endogenous locus under control of a tetracycline-inducible promoter. The dox-inducible Xist gene is on the 129 allele, enabling allele-specific analysis of Xist induction and X chromosome silencing

data_processing:
Adapters were trimmed from raw paired-end fastq files using Trimmomatic v0.38.
Reads were aligned to GRCm38.p6 with the Ensembl GRCm38 v95 gene model annotation using Hisat2 v2.1.01 with a high penalty for soft-clipping (--sp 1000,1000) and excluding mixed or discordant alignments (--no-mixed --no-discordant). Unmapped reads and reads with a low MapQ score (samtools view -bq 20) were filtered out.
Mapped reads were annotated with the featureCounts tool from the subread package v1.6.4 using the Gencode release M25 annotations for GRCm38.p6 and a subset of the Repeat and Transposable element annotation from the Hammel lab. Reads that recieved a single annotation for a protein coding gene were counted.

source_name: Mouse Embryonic Stem cells

growth_protocol:
All mouse ES cell lines were cultured in serum-free 2i/LIF medium
Cells were cultured in serum-free 2i/LIF medium

extract_protocol:
Total RNA isolation was performed with Qiagen RNeasy kit. Polyadenylated RNA transcripts were isolated using two rounds of poly-A capture on Oligo dT(25) magnetic beads.
Isolated polyadenylated RNA was fragmented by heating, treated with DNAse and dephosphorylated using FastAP and T4 PNK. Then, RNA was ligated with a ssRNA adaptor and reverse transcribed into cDNA. The cDNA was ligated with the second adaptor and amplified using standard Illumina library prep. Libraries were gel cut and sequenced on a HiSeq 2500 (90 cycle x 125 cycle).

treatment_protocol: Cells were treated with 2 μg/mL doxycycline for 24 hrs

tag: drug treatment

value: 24hr DOX


title: SEc7-D10

description: 10x Genomics

value: Whole kidney cell suspensions

value: Kidney

tag: treatment


title: Patient 1250, acute sample

description:
1250x1q1
DENV_gene_count_matrix.csv

value: 3d post symptom onset

value: Dengue Hemorrhagic Fever/Dengue Shock Syndrome


title: RWMH23s01_Mesoderm

description: SAMPLE 362

tag: cell type

value: PBMC


title: Patient 1247, convalescent sample

description:
1247x9q1
DENV_gene_count_matrix.csv

value: 24d post symptom onset


title: Normal Chow Secretory Enriched- Jej

description: Live+, Epcam+, TdTom+

value: Neurog3Cre x TdTom

value: Proximal Jejunum

value: Normal Chow


title: RWMH23s01_Endoderm

description: SAMPLE 361

tag: gender

value: Male


title: Patient 1247, acute sample

description:
1247x1q2
DENV_gene_count_matrix.csv

value: 2d post symptom onset


title: Patient 1240, convalescent sample

description:
1240x9q1
DENV_gene_count_matrix.csv

value: 19d post symptom onset


title: GLKVs31_Mesoderm

description: SAMPLE 359

tag: source cell

value: Cord blood

value: pCE episomal vector


title: Normal Chow Secretory Enriched- Duo

description: Live+, Epcam+, TdTom+

value: Duodenum


title: GLKVs31_Endoderm

description: SAMPLE 358

tag: generation method


title: RWMH23s01_Ectoderm

description: SAMPLE 360


title: 7 Days HFD Epithelial- Duo

description: Live+, Epcam+

value: 7 Days HFD


title: Patient 1240, acute sample

description:
1240x1q1
DENV_gene_count_matrix.csv

tag: timepoint

value: 5d post symptom onset

value: M

value: Secondary


title: Patient 1231, convalescent sample

description:
1231x9q1
DENV_gene_count_matrix.csv

value: 15d post symptom onset

tag: age (years)

value: Primary

value: Dengue Fever


title: PolyA RNASeq 2

value: 24hr DOX


title: GLKVs13_Mesoderm

description: SAMPLE 356


title: 3 Days HFD Epithelial- Duo

description: Live+, Epcam+

value: 3 Days HFD


title: 7 Days HFD Epithelial-  Jej

description: Live+, Epcam+

value: Proximal Jejunum


title: Patient 1231, acute sample

description:
1231x2q1
DENV_gene_count_matrix.csv

value: 4d post symptom onset

tag: Sex


title: 3 Days HFD Epithelial- Jej

description: Live+, Epcam+


title: GLKVs13_Endoderm

description: SAMPLE 355

value: Male


title: 1 Day HFD Epithelial- Jej

description: Live+, Epcam+

value: 1 Day HFD


title: Patient 1221, convalescent sample

description:
1221x9q1
DENV_gene_count_matrix.csv

value: 28d post symptom onset

value: F

tag: infection


title: GLKVs13_Ectoderm

description: SAMPLE 354

value: Cord blood

value: pCE episomal vector


title: Patient 1221, acute sample

description:
1221x1q2
DENV_gene_count_matrix.csv

tag: symptom


title: Patient 1214, convalescent sample

description:
1214x9q1
DENV_gene_count_matrix.csv

value: 16d post symptom onset

tag: virus type


title: 1 Day HFD Secretory Enriched- Duo

description: Live+, Epcam+, TdTom+

value: Neurog3Cre x TdTom

value: Duodenum


title: QHJI14s04-2_Endoderm

description: SAMPLE 352

value: PBMC


title: QHJI14s04-2_Mesoderm

description: SAMPLE 353


title: Normal Chow Epithelial- Jej

description: Live+, Epcam+

value: Normal Chow


title: Normal Chow Epithelial- Duo

description: Live+, Epcam+


title: Patient 1214, acute sample

description:
1214x1q2
DENV_gene_count_matrix.csv

value: 5d post symptom onset

value: Primary


title: Patient 1213, convalescent sample

description:
1213x9q1
DENV_gene_count_matrix.csv

value: 17d post symptom onset

value: Dengue Fever


title: QHJI14s04_Mesoderm

description: SAMPLE 350


title: GLKVs31_Ectoderm

description: SAMPLE 357


title: QHJI14s04-2_Ectoderm

description: SAMPLE 351


title: Patient 1194, convalescent sample

description:
1194x9q1
DENV_gene_count_matrix.csv

value: 15d post symptom onset

value: M

value: Secondary


title: QHJI14s04_Endoderm

description: SAMPLE 349

value: Male


title: WT(Chd2+/+)

city: Changsha

first: Ziqian

last: Min

state: Hunan

address: Tianma road

country: China

institute: Hunan University

data_processing:
Cutadapt (V 2.7) was used to filter the connector sequence of the original sequence, trim the reads ends with low sequencing quality (sequencing quality value less than 20), and remove the reads containing 10% N.
The small fragments with a length less than 20bp after the adapter and quality pruning are discarded, and high-quality clean data is finally obtained.
Fastqc (V 0.11.8) was used for data statistics, and clean data was used for subsequent analysis.
An index of the reference genome was constructed using HISAT2(V 2.1.0), and clean reads were compared to the reference sequence using HISAT2(V 2.1.0) for gene alignment.
Meanwhile, RSeQC (V 3.0.1) was used to evaluate the quality of the comparison results of this transcriptome sequencing, including the distribution of sequencing saturation, gene coverage and Reads in different regions of the reference genome.
Assembly: GRCm38
Supplementary files format and content: matrix_gene.fpkm.annot.xls

source_name: testis

extract_protocol:
Testes were removed, flash frozen with liquid nitrogen,and RNA was harvested using RNAiso Plus(Takara).NR604-VAHTS® Fast RNA-seq Library Prep Kit was used for Illumina（Vazyme，China). 1 ug of total RNA was used for the construction of sequencing libraries.
Illumina Novaseq6000 was used for transcriptome library sequencing, and PE150 (double-end 150bp) sequencing process was performed.

tag: tissue

value: testis

tag: age

value: 12 week

tag: genotype


title: Patient 1194, acute sample

description:
1194x2q2
DENV_gene_count_matrix.csv


title: 981/982PosRetONC

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

data_processing:
Following sequencing, reads were trimmed, aligned, differential expression statistics, and correlation analyses were performed in Strand NGS software package (Version 3.1, Bangalore, India).
Reads were aligned against the Mm10 build of the mouse genome with (2013.04.01) annotation build. Alignment and filtering criteria included: adapter trimming, fixed 2bp trim from 5’ and 6bp from 3’ ends, a maximum number of one novel splice allowed per read, a minimum of 90% identity with the reference sequence, a maximum of 5% gap, trimming of 3’ end with Q<30.
Alignment was performed directionally with Read 1 aligned in reverse and Read 2 in forward orientation. Reads were filtered based on the mapping status and only those reads that aligned normally (in the appropriate direction) were retained.
Normalization was performed with the DESeq algorithm.
Transcripts with an average read count value >5 in at least 100% of the samples in at least one group were considered expressed at a level sufficient for quantitation per tissue and those transcripts below this level were considered not detected/not expressed and excluded, as these low levels of reads are close to background and are highly variable.
Genome_build: mm10
Supplementary_files_format_and_content: txt file, raw read counts and normalized read counts for all expressed genes

source_name: Retina

extract_protocol:
The purification of cell-specific, ribosomally loaded RNA from retina tissue from Tam-induced Aldh1l1-cre/ERT2+; NuTRAP+ mice was achieved following established protocol, with slight modifications23,31,32. For each sample, two retinae were pooled and homogenized in 1.0 mL ice-cold homogenization buffer (50 mM Tris, pH 7.4; 12 mM MgCl2; 100 mM KCl; 1% NP-40; 1 mg/mL sodium heparin; 1 mM DTT) supplemented with 100 µg/mL cycloheximide (#C4859-1ML, Millipore Sigma), 0.5 mM spermidine (#05292-1ML-F, Millipore Sigma), 200 units/mL RNaseOUT Recombinant Ribonuclease Inhibitor (#10777019; Thermofisher), and 1X cOmplete, EDTA-free Protease Inhibitor Cocktail (#11836170001; Millipore Sigma) with a glass dounce tissue grinder set (#D8938; 10 times with pestle A only). The homogenate was transferred to a 2 mL round-bottom tube and centrifuged at 10,000 x g for 10 minutes at 4°C. After centrifugation, 150 µL of the supernatant was saved as input. The remaining supernatant was transferred to a 2 mL round-bottom tube and incubated with 5 µg/µL of anti-GFP antibody (ab290; Abcam) at 4°C with end-over-end rotation overnight. Dynabeads Protein G for Immunoprecipitation (#10003D; Thermofisher) were washed three times in 1 mL ice-cold low-salt wash buffer (50mM Tris, pH 7.5; 12mM MgCl2; 100mM KCl; 1% NP-40; 100?g/mL cycloheximide; 1mM DTT). After removal of the last wash, the homogenate/antibody mixture was transferred to the 2 mL round-bottom tube containing the washed Protein-G Dynabeads and incubated at 4°C overnight with end-over-end rotation. Magnetic beads were collected using a DynaMag-2 magnet. Beads were then washed three times with 1 mL of high-salt wash buffer (50 mM Tris, pH 7.5; 12 mM MgCl2; 300 mM KCl; 1% NP-40; 100 ?g/mL cycloheximide; 1 mM DTT). Following the last wash, 350 µL of Buffer RLT (Qiagen) supplemented with 3.5 µL 2-? mercaptoethanol was added directly to the beads and incubated with mixing on a ThermoMixer (Eppendorf) for 10 minutes at room temperature. The beads were magnetically separated and the supernatant containing the target bead-bound ribosomes and associated RNA was transferred to a new tube. 350 µL of 100% ethanol was added to the tube (“positive” fraction: enriched in translatome associated to EGFP-tagged ribosomes) and then loaded onto a RNeasy MinElute column. RNA was isolated using RNeasy Mini Kit (#74104, Qiagen), according to manufacturer’s instructions. RNA was quantified with a Nanodrop One spectrophotometer (Thermofisher Scientific) and its quality assessed by HSRNA ScreenTape with a 4150 TapeStation analyzer (Agilent Technologies, Santa Clara, CA).
The NEBNext Ultra II Directional Library Prep Kit for Illumina (#NEBE7760L; New England Biolabs Inc., Ipswich, MA) was used on 25 ng of total RNA for the preparation of strand-specific sequencing libraries from each TRAP-isolated RNA sample (input and positive fraction) and from conventionally isolated RNA samples from brain (tissue), according to manufacturer's instructions. Briefly, polyA containing mRNA was purified using oligo-dT attached magnetic beads. mRNA was chemically fragmented and cDNA synthesized. For strand-specificity, the incorporation of dUTP instead of dTTP in the second strand cDNA synthesis does not allow amplification past this dUTP with the polymerase. Following cDNA synthesis, each product underwent end repair process, the addition of a single ‘A’ base, and finally ligation of adapters. The cDNA products were further purified and enriched using PCR to make the final library for sequencing. Library sizing was performed with HS RNA ScreenTape (#5067-5579; Agilent Technologies).

treatment_protocol: Mice were anesthetized by intraperitoneal injection of 80-100 mg/kg ketamine and 5-10 mg/kg xylazine. For each mouse, one eye was subjected to ONC procedure while the fellow  was left untreated as control, or was subjected to sham procedure. The optic nerve crush (ONC) procedure was performed as previously described, with minor modifications33,34. Briefly, the bulbar conjunctiva was bundled and lifted with sterile forceps and temporally cut 90° to the anterior-posterior eye globe axis using sterile spring scissors. Using a pair of self-closing forceps, the orbital blood sinuses were retracted to expose the optic nerve. The self-closing forceps were opened, were placed over the optic nerve, and were released approximately 1 mm from the posterior pole to clamp the optic nerve for 3 seconds. After clamping, the forceps were carefully removed from the surgical window and the eye was treated with Bacitracin Antibiotic Ointment. Mice were then injected with 0.2 mg/kg buprenorphine subcutaneously for post-surgical analgesia. After recovery from anesthesia, mice were returned to cages and monitored for normal habits to detect any ill effects until time of collection, at 72h post-procedure.

value: Aldhl1l-Cre/Ert2+; NuTRAP+

tag: fraction

value: Positive

tag: animal number

value: ONC


title: QHJI14s04_Ectoderm

description: SAMPLE 348

value: pCE episomal vector


title: Patient 1190, convalescent sample

description:
1190x9q1
DENV_gene_count_matrix.csv

value: 14d post symptom onset

value: F


title: 1 Day HFD Epithelial- Duo

description: Live+, Epcam+

tag: strain

tag: region

value: Duodenum

tag: condition

value: 1 Day HFD


title: 976/978PosRetONC

tag: treatment


title: QHJI01s04_Endoderm

description: SAMPLE 346

tag: cell type

tag: gender

tag: source cell

value: PBMC


title: Patient 1213, acute sample

description:
1213x1q2
DENV_gene_count_matrix.csv

tag: timepoint

value: 4d post symptom onset

tag: age (years)

value: Primary


title: QHJI01s04_Mesoderm

description: SAMPLE 347

tag: generation method


title: Patient 1181, convalescent sample

description:
1181x9q1
DENV_gene_count_matrix.csv

value: 15d post symptom onset

tag: Sex

tag: infection

tag: symptom

value: Dengue Fever


title: Patient 1190, acute sample

description:
1190x1q2
DENV_gene_count_matrix.csv

tag: virus type


title: QHJI01s04_Ectoderm

description: SAMPLE 345


title: 938/88PosRetONC

tag: genotype


title: Patient 1181, acute sample

description:
1181x1q2
DENV_gene_count_matrix.csv

value: Secondary


title: KO (Chd2+/-)

tag: tissue

tag: age


title: KthES14_P15

description: SAMPLE 344

source_name: ESC (Kyoto university)

value: ESC

value: Female


title: 938/88PosRetCTL

tag: fraction

tag: animal number

value: Control


title: KthES14_P14

description: SAMPLE 343


title: Patient 1172, convalescent sample

description:
1172x9q1
DENV_gene_count_matrix.csv


title: 914/92PostRetONC

value: Aldhl1l-Cre/Ert2+; NuTRAP+


title: Patient 1172, acute sample

description:
1172x1q2
DENV_gene_count_matrix.csv


title: KthES13_P14

description: SAMPLE 342


title: 914/92PostRetCTL

value: Positive


title: Chronic_B1

city: Groningen

first: Bart

last: Eggen

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences

country: Netherlands

institute: UMCG Groningen

data_processing:
reads were trimmed to bp 1-60 using FastX Trimmer (0.013)
reads were alignment with HiSat2 with default parameters
reads were sorted and QCed using Samtools (1.3.1) and Picard (2.6.4)
reads were quantified to gene counts using HTSeq (0.6.1)
counts were evaluated on quality using RSeQC (2.6.4)
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: spinal cord

extract_protocol:
RNA was extracted using the RNeasy Plus Micro kit (Qiagen) according to the manufacturer’s protocol. Reverse transcription was performed for both qPCR and sequencing libraries using a mixture of random hexamers, dNTPs, M-MLV buffer, RibolockTMRNase Inhibitor, and RevertAidTM M-MuLV Reverse Transcriptase (Fermantas).
Sequencing libraries were generated using a Nextera XT Sample Prep Kit according to the manufacturer’s protocol.
RNAseq. Single-read. Libraries were sequenced using Illumina NextSeq500 using one 75 bp high output flow cell.

tag: strain

value: Biozzi ABH

tag: disease state

value: crEAE

tag: eae phase

value: Chronic

value: spinal cord

value: microglia

tag: sample barcode

value: CGTACTAG-ATAGAGAG


title: 913/986PosRetONC

tag: treatment

value: ONC


title: Patient 1170, convalescent sample

description:
1170x9q1
DENV_gene_count_matrix.csv

tag: timepoint

value: 22d post symptom onset

value: M


title: KthES13_P13

description: SAMPLE 341

tag: cell type

tag: gender

tag: source cell


title: 976/978PosRetCTL


title: Patient 1170, acute sample

description:
1170x1q2
DENV_gene_count_matrix.csv

value: 5d post symptom onset

tag: age (years)

tag: Sex

tag: infection


title: Acute_C1

value: Acute

value: AGGCAGAA-AGAGGATA


title: KthES12_P13

description: SAMPLE 340

value: ESC

tag: generation method


title: Chronic_E1

tag: tissue

value: GGACTCCT-CTCCTTAC


title: 55nucRNAPos

extract_protocol:
The purification of viable, cell-specific nuclei from brain tissue from Tam-induced Aldh1l1-cre/ERT2+; NuTRAP+ mice was achieved by combining two previously published protocols, with modifications32,37,38. For each sample, two retinae were homogenized in 1 mL ice-cold nuclei EZ lysis buffer (#NUC-101, Millipore Sigma) supplemented with 1X Halt protease inhibitor cocktail (ThermoFisher Scientific) and 1 mM DTT using a glass dounce tissue grinder set (20 times with pestle A and 20 times with pestle B). Undissociated tissue, largely composed of blood vessels, was removed by centrifugation at 200 x g for 1.5 min at 4°C, and the supernatant containing the nuclear material filtered through a 30 µm strainer and centrifuged at 500 x g for 5 min at 4°C. The resulting nuclear pellet was resuspended in nuclei lysis EZ buffer, incubated on ice for 5 min, washed by centrifugation, and resuspended in 200 µL nuclei EZ storage buffer by gentle trituration with a micropipette. From the total resuspended pellet volume, 10% was reserved as input nuclei fraction and the rest was diluted with 1.6 mL nuclei purification buffer (NPB: 20 mM HEPES, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 1X Halt protease inhibitor cocktail, 1mM DTT), and subjected to the INTACT protocol. Briefly, 30 µL of resuspended M-280 Streptavidin Dynabeads (#11205, ThermoFisher Scientific) were added into a fresh 2 mL microcentrifuge tube and washed with 1 mL of NPB using a DynaMag-2 magnet (#12321; ThermoFisher Scientific) for a total of three washes (1 min incubation/each). The washed beads were reconstituted to their initial volume (30 µL) with NPB and gently mixed with the nuclear suspension. The mixture of nuclei and magnetic beads was incubated at 4°C for 40 min under gentle rotation settings to allow the affinity binding of streptavidin beads to the cell-specific, biotinylated nuclei. After incubation, the streptavidin-bound nuclei were magnetically separated with the DynaMag-2 magnet for a period of 3 min. The nuclei bound to the beads were washed in the magnet for three washes (1 min/each), resuspended in 30 µL of NPB, and reserved as the positive nuclei fraction. From the nuclear fraction [input and positive (enriched in biotinylated nuclei)], an aliquot was mixed with equal volume of DAPI counterstain and used for confocal microscopy visualization. The AllPrep DNA/RNA kit Micro (#80284, Qiagen, Germantown, MD) was used to extract gDNA and nuclear RNA from each sample. gDNA and nuclear RNA were quantified with a Nanodrop One spectrophotometer (Thermofisher Scientific) and its quality assessed by genomic DNA D1000 (#5067-5582) and HSRNA ScreenTape, respectively, with a 4150 TapeStation analyzer.
The NEBNext Ultra II Directional Library Prep Kit for Illumina (#NEBE7760L; New England Biolabs Inc., Ipswich, MA) was used on 25 ng of total RNA for the preparation of strand-specific sequencing libraries from each TRAP-isolated RNA sample (input and positive fraction) and from conventionally isolated RNA samples from brain (tissue), according to manufacturer's instructions. Briefly, polyA containing mRNA was purified using oligo-dT attached magnetic beads. mRNA was chemically fragmented and cDNA synthesized. For strand-specificity, the incorporation of dUTP instead of dTTP in the second strand cDNA synthesis does not allow amplification past this dUTP with the polymerase. Following cDNA synthesis, each product underwent end repair process, the addition of a single ‘A’ base, and finally ligation of adapters. The cDNA products were further purified and enriched using PCR to make the final library for sequencing. Library sizing was performed with HS RNA ScreenTape (#5067-5579; Agilent Technologies).

tag: genotype


title: KthES12_P12

description: SAMPLE 339

value: Female


title: Patient 1169, convalescent sample

description:
1169x9q1
DENV_gene_count_matrix.csv

value: 19d post symptom onset

value: F

value: Secondary

tag: symptom

value: Dengue Hemorrhagic Fever/Dengue Shock Syndrome

tag: virus type


title: 40nucRNAPos

value: Aldhl1l-Cre/Ert2+; NuTRAP+

tag: fraction

value: Positive

tag: animal number


title: Patient 1169, acute sample

description:
1169x2q2
DENV_gene_count_matrix.csv

value: 4d post symptom onset


title: KthES11_P13

description: SAMPLE 338


title: Remission_F1

tag: strain

value: Biozzi ABH

tag: disease state

value: crEAE

tag: eae phase

value: Remission

value: spinal cord

value: microglia

value: TAGGCATG-TATGCAGT


title: 981/982PosRetCTL

tag: treatment

value: Control


title: Patient 1165, convalescent sample

description:
1165x9q1
DENV_gene_count_matrix.csv

tag: timepoint

value: 18d post symptom onset

value: M

value: Primary

value: Dengue Fever


title: KthES11_P12

description: SAMPLE 337

tag: cell type

value: ESC

tag: gender

value: Female


title: 40nucRNAInput

value: Input


title: Chronic_G1

value: Chronic

tag: sample barcode

value: CTCTCTAC-TACTCCTT


title: Patient 1165, acute sample

description:
1165x1q2
DENV_gene_count_matrix.csv

value: 1d post symptom onset

tag: age (years)

tag: Sex


title: Control_A1

value: Biozzi ABH

value: TAAGGCGA-TCTTACGC


title: Remission_H1

value: crEAE

value: Remission

value: CAGAGAGG-AGGCTTAG


title: YZWJs31_3_P11

description: SAMPLE 336

source_name: HLA homozygous iPSC

value: iPSC

value: Male

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: Patient 1162, convalescent sample

description:
1162x9q1
DENV_gene_count_matrix.csv

value: 20d post symptom onset

value: F

tag: infection

value: Secondary

value: Dengue Hemorrhagic Fever/Dengue Shock Syndrome


title: 843PosRet

tag: genotype

value: Aldhl1l-Cre/Ert2+; NuTRAP+

value: Positive


title: Control_D1

value: Control

tag: tissue

value: spinal cord

value: microglia

value: TCCTGAGC-TCTACTCT


title: YZWJs31_2_P11

description: SAMPLE 335


title: Remission_A2

value: Biozzi ABH

value: crEAE

value: GCTACGCT-TCTTACGC


title: YZWJs31_1_P11

description: SAMPLE 334

value: iPSC


title: Control_B2

value: CGAGGCTG-ATAGAGAG


title: 55nucRNAInput

tag: fraction

value: Input


title: 843InputRet

tag: animal number


title: Patient 1162, acute sample

description:
1162x1q2
DENV_gene_count_matrix.csv

value: 3d post symptom onset

tag: symptom

tag: virus type


title: Patient 1153, convalescent sample

description:
1153x9q1
DENV_gene_count_matrix.csv

value: 30d post symptom onset


title: YZWJs28_3_P11

description: SAMPLE 333

value: Male

value: Cord blood

value: pCE episomal vector


title: 842PosRet

value: Aldhl1l-Cre/Ert2+; NuTRAP+


title: Acute_C2

tag: strain

tag: disease state

tag: eae phase

value: Acute

value: AAGAGGCA-AGAGGATA


title: 842InputRet


title: YZWJs28_2_P11

description: SAMPLE 332

tag: cell type


title: Patient 1153, acute sample

description:
1153x1q2
DENV_gene_count_matrix.csv

tag: timepoint

value: 4d post symptom onset

value: F

value: Secondary

value: Dengue Hemorrhagic Fever/Dengue Shock Syndrome


title: YZWJs28_1_P11

description: SAMPLE 331

tag: gender


title: 841PosRet

value: Positive


title: Wild-type enteroid RNA-seq sample #2

city: Ithaca

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

department: Biomedical Science

institute: Cornell University

description:
M2
Batch 1. WT
RNA_RLOG-LIMMA_normalized_counts.csv

data_processing:
Sequencing was aligned and quantiitated using miRquant2.0 (small RNAseq), aligned and quantified using STAR/Salmon (RNA-seq), or proseq2.0 (leChRO).
RNA- and leChRO-seq HCT116 data was normalized using DESeq2. Mutant enteroid RNA- and smRNA-seq data was rlog transformed followed by limma batch correction.
Genome_build: Mouse enteroids: mm9 (small RNAseq) or vM10 (RNAseq). HCT116: hg19 for both RNA- and leChRO-seq datasets.
Supplementary_files_format_and_content: Normalized counts

source_name: Small Intestine

extract_protocol:
Libraries were prepared according to the NEBNext Ultra II Directional RNA kit protocol following Ribosomal Depletion
Cells were lysed using the lysis buffer described in Chu, T. et al. Nature Genetics (2018). Chromatin was pelleted and supernatant was collected and stored in Trizol LS. RNA was isolated using manufacturer's protocol.

value: Small Intestine

tag: genotype/variation

value: Wild-type enteroid


title: 12nucRNAPos


title: YZWJs27_3_P11

description: SAMPLE 330

value: iPSC


title: Patient 1150, acute sample

description:
1150x2q2
DENV_gene_count_matrix.csv

tag: age (years)

tag: Sex

value: M

value: Primary

value: Dengue Fever


title: 841InputRet

value: Input


title: 1386InputRet

tag: age

value: Young


title: Rspo3 mutant enteroid RNA-seq sample #2

description:
PR3_2
Batch 1. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement.
RNA_RLOG-LIMMA_normalized_counts.csv

value: Rspo3 mutant enteroid


title: Rspo3 mutant enteroid RNA-seq sample #1

description:
PR3_1
Batch 1. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement.
RNA_RLOG-LIMMA_normalized_counts.csv


title: 1386PosRet

value: Aldhl1l-Cre/Ert2+; NuTRAP+


title: YZWJs27_2_P11

description: SAMPLE 329

value: Male

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: YZWJs27_1_P11

description: SAMPLE 328


title: YZWJs26_2_P11

description: SAMPLE 326


title: Kras/Rspo3/Smad4 mutant enteroid RNA-seq sample #3

description:
961_KRS19
Batch 2. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Smad4KO mutations induced using CRISPR/Cas9.
RNA_RLOG-LIMMA_normalized_counts.csv

extract_protocol:
Libraries were prepared according to the NEBNext Ultra II Directional RNA kit protocol following Ribosomal Depletion
RNA was isolated using the the Norgen Total RNA Purification Kit according to the manufacturer's protocol.

tag: tissue

value: Kras/Rspo3/Smad4 mutant enteroid


title: Patient 1142, acute sample

description:
1142x1q2
DENV_gene_count_matrix.csv

value: 3d post symptom onset

tag: infection

value: Secondary


title: Patient 1136, convalescent sample

description:
1136x9q1
DENV_gene_count_matrix.csv

value: 21d post symptom onset


title: 1383InputRet

tag: genotype

tag: fraction

tag: animal number


title: Patient 1150, convalescent sample

description:
1150x9q1
DENV_gene_count_matrix.csv

value: 16d post symptom onset

tag: symptom

tag: virus type


title: Acute_D2

tag: strain

value: Biozzi ABH

tag: disease state

value: crEAE

tag: eae phase

value: Acute

value: spinal cord

value: microglia

tag: sample barcode

value: GTAGAGGA-TCTACTCT


title: Kras/Rspo3/Smad4 mutant enteroid RNA-seq sample #1

description:
47_KRS19
Batch 2. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Smad4KO mutations induced using CRISPR/Cas9.
RNA_RLOG-LIMMA_normalized_counts.csv

value: Small Intestine

tag: genotype/variation


title: Kras/Rspo3/Smad4 mutant enteroid RNA-seq sample #2

description:
72_KRS19
Batch 2. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Smad4KO mutations induced using CRISPR/Cas9.
RNA_RLOG-LIMMA_normalized_counts.csv


title: Patient 1142, convalescent sample

description:
1142x9q1
DENV_gene_count_matrix.csv

tag: timepoint

value: 23d post symptom onset

tag: age (years)

value: M

value: Dengue Fever


title: Patient 1148, acute sample

description:
1148x2q2
DENV_gene_count_matrix.csv

value: 4d post symptom onset

tag: Sex

value: F

value: Dengue Hemorrhagic Fever/Dengue Shock Syndrome


title: 1382InputRet

value: Aldhl1l-Cre/Ert2+; NuTRAP+

value: Input

tag: age

value: Young


title: Patient 1136, acute sample

description:
1136x1q2
DENV_gene_count_matrix.csv

value: Primary


title: YZWJs24_3_P11

description: SAMPLE 324

tag: cell type

value: iPSC

tag: gender

value: Male

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: Patient 1148, convalescent sample

description:
1148x9q1
DENV_gene_count_matrix.csv

value: 25d post symptom onset

tag: infection

value: Secondary


title: 523InputRet

tag: genotype

tag: fraction

tag: animal number

value: Old


title: YZWJs26_1_P11

description: SAMPLE 325


title: YZWJs26_3_P11

description: SAMPLE 327


title: Kras/Rspo3/p53/Smad4 mutant enteroid RNA-seq sample #3

description:
N4_1
Batch 1. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Trp53-/- and Smad4KO mutations induced using CRISPR/Cas9.
RNA_RLOG-LIMMA_normalized_counts.csv

tag: tissue

value: Small Intestine

value: Kras/Rspo3/p53/Smad4 mutant enteroid


title: R4_RF_rep2

city: Beijing

first: Yi

last: Zuo

address: No. 50 Road Zhanghua

institute: Beijing Academy of Agriculture and Forestry Science

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed using fastp（version:0.20.1）, then mapped to 970103 V2 using hisat2（version:2.1.0）.
The unique reads were normalized as Fragments Per Kilobase of exon model per Million mapped reads (FPKM) using samtools v1.5
Genome_build: CuGenDB 97103-v2 watermelon
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

organism: Citrullus lanatus

source_name: rind

extract_protocol:
RNA was extracted from flesh with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: flesh

value: 30 DAP

tag: cultivar


title: Kras/Rspo3/p53/Smad4 mutant enteroid RNA-seq sample #4

description:
N4_2
Batch 1. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Trp53-/- and Smad4KO mutations induced using CRISPR/Cas9.
RNA_RLOG-LIMMA_normalized_counts.csv


title: Patient 1134, convalescent sample

description:
1134x9q2
DENV_gene_count_matrix.csv

value: 15d post symptom onset

value: F

tag: symptom

value: Dengue Fever

tag: virus type


title: Patient 1134, acute sample

description:
1134x1q2
DENV_gene_count_matrix.csv

value: 4d post symptom onset


title: 1383PosRet

value: Aldhl1l-Cre/Ert2+; NuTRAP+

value: Positive

value: Young


title: 523PosRet


title: Kras/Rspo3/p53/Smad4 mutant enteroid RNA-seq sample #2

description:
N3
Batch 1. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Trp53-/- and Smad4KO mutations induced using CRISPR/Cas9.
RNA_RLOG-LIMMA_normalized_counts.csv

tag: genotype/variation


title: Wild-type enteroid RNA-seq sample #1

description:
F2
Batch 1. WT
RNA_RLOG-LIMMA_normalized_counts.csv

value: Wild-type enteroid


title: R2_RF_rep1


title: Patient 1132, convalescent sample

description:
1132x9q1
DENV_gene_count_matrix.csv

tag: timepoint

value: 14d post symptom onset

value: M


title: Kras/Rspo3/p53 mutant enteroid RNA-seq sample #1

description:
KRP_1
Batch 1. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Trp53-/- mutation induced using CRISPR/Cas9.
RNA_RLOG-LIMMA_normalized_counts.csv

value: Kras/Rspo3/p53 mutant enteroid


title: Ctnnb1/Kras/p53 mutant enteroid RNA-seq sample #1

description:
S33KP
Batch 1. Ctnnb1S33F mutation induced using CRISPR base editing. KrasG12D and Trp53-/- mutations induced using enteroids from LSL-Kras/p53fl/fl mouse model
RNA_RLOG-LIMMA_normalized_counts.csv

value: Ctnnb1/Kras/p53 mutant enteroid


title: R2_RF_rep2


title: 215InputRet

value: Input

value: Old


title: 521InputRet


title: Ctnnb1 mutant enteroid RNA-seq sample #5

description:
S33_M2
Batch 2. Ctnnb1S33F mutation induced using CRISPR base editing
RNA_RLOG-LIMMA_normalized_counts.csv

value: Small Intestine

value: Ctnnb1 mutant enteroid


title: 521PosRet


title: 215PosRet


title: Patient 1126, convalescent sample

description:
1126x9q1
DENV_gene_count_matrix.csv

value: 17d post symptom onset

tag: age (years)

value: Primary


title: Kras/Rspo3/p53 mutant enteroid RNA-seq sample #2

description:
KRP_2
Batch 1. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Trp53-/- mutation induced using CRISPR/Cas9.
RNA_RLOG-LIMMA_normalized_counts.csv


title: R4_CT_rep1

value: flesh

value: 20 DAP


title: Patient 1130, convalescent sample

description:
1130x9q1
DENV_gene_count_matrix.csv

value: 16d post symptom onset

tag: Sex

value: Secondary

value: Dengue Hemorrhagic Fever/Dengue Shock Syndrome


title: Kras/Rspo3/p53/Smad4 mutant enteroid RNA-seq sample #1

description:
N1
Batch 1. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Trp53-/- and Smad4KO mutations induced using CRISPR/Cas9.
RNA_RLOG-LIMMA_normalized_counts.csv

value: Kras/Rspo3/p53/Smad4 mutant enteroid


title: Patient 1132, acute sample

description:
1132x1q2
DENV_gene_count_matrix.csv

value: 2d post symptom onset

value: Dengue Fever


title: Patient 1126, acute sample

description:
1126x1q2
DENV_gene_count_matrix.csv

value: 4d post symptom onset

value: F


title: R4_RF_rep1

tag: age

value: 30 DAP


title: W_RF small RNA-Seq rep1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed using fastp（version:0.20.1）, then mapped to 970103 V2 using bwa（version:0.7.15）.
The unique reads were calculated as count using miRDeep2 (version:2.0.5)
Genome_build: CuGenDB 97103-v2 watermelon
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

source_name: flesh

extract_protocol:
RNA was extracted from flesh with Trizol reagent. Total RNA was then separated on denaturing polyacrylamide gels, and < 100-nt fractions were cut out and purified for standard small RNA library preparation.
Small RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Citrullus lanatus germplasm PI296341FR


title: W_RF small RNA-Seq rep2


title: Patient 1122, convalescent sample

description:
1122x9q1
DENV_gene_count_matrix.csv

value: 18d post symptom onset

value: M


title: 214PosRet

value: Aldhl1l-Cre/Ert2+; NuTRAP+

value: Positive

value: Old


title: Ctnnb1 mutant enteroid RNA-seq sample #3

description:
S33_F2
Batch 2. Ctnnb1S33F mutation induced using CRISPR base editing
RNA_RLOG-LIMMA_normalized_counts.csv

value: Small Intestine

value: Ctnnb1 mutant enteroid


title: H011

city: Hangzhou

first: Yang

last: Wang

state: Zhejiang

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
The data were aligned to the GRCm38 reference genome using Cell Ranger v4.0
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: heart

extract_protocol:
The hearts were isolated and digested. Cells were stained with relative antibodies and dyes. After incubation, live nucleated CD45+ and CD45- cells were sorted and collected.
Sorted single-cell suspensions were loaded to 10× Chromium to capture no more than 10000 single cells according to the manufacturer's instructions of Chromium Single Cell 3' Reagent Kits v3 (10× Genomics). Libraries were sequenced on a Novaseq 6000 (Illumina) .

tag: strain

tag: cell type

value: live nucleated CD45+

value: heart

tag: time point

value: 7 days post CLP

value: Wild-type littermate control


title: W_BW small RNA-Seq rep2

value: flesh

value: 10 DAP


title: R4_CT_rep2

value: 20 DAP


title: Patient 1130, acute sample

description:
1130x2q2
DENV_gene_count_matrix.csv

value: 4d post symptom onset

value: Secondary

value: Dengue Hemorrhagic Fever/Dengue Shock Syndrome


title: 214InputRet

value: Input


title: Patient 1122, acute sample

description:
1122x3q2
DENV_gene_count_matrix.csv

value: 1d post symptom onset

value: M

value: Primary

value: Dengue Fever


title: Ctnnb1 mutant enteroid RNA-seq sample #4

description:
S33_M1
Batch 2. Ctnnb1S33F mutation induced using CRISPR base editing
RNA_RLOG-LIMMA_normalized_counts.csv

value: Small Intestine


title: Ctnnb1 mutant enteroid RNA-seq sample #1

description:
F2S333
Batch 1. Ctnnb1S33F mutation induced using CRISPR base editing
RNA_RLOG-LIMMA_normalized_counts.csv

value: Ctnnb1 mutant enteroid


title: Patient 1117, acute sample

description:
1117x2q2
DENV_gene_count_matrix.csv

value: 2d post symptom onset


title: Apc mutant enteroid RNA-seq sample  #3

description:
Apc_Min
Batch 3. ApcQ883* mutation induced using CRISPR base editing
RNA_RLOG-LIMMA_normalized_counts.csv

value: Apc mutant enteroid


title: Ctnnb1 mutant enteroid RNA-seq sample #2

description:
S33_F1
Batch 2. Ctnnb1S33F mutation induced using CRISPR base editing
RNA_RLOG-LIMMA_normalized_counts.csv


title: C_RF small RNA-Seq rep2

value: 30 DAP


title: H005

value: live nucleated CD45+

value: heart

value: steady state


title: Patient 1114, acute sample

description:
1114x1q2
DENV_gene_count_matrix.csv


title: H007

value: 7 days post CLP

value: Wild-type


title: W_BW small RNA-Seq rep1

value: flesh

value: 10 DAP

value: Citrullus lanatus germplasm PI296341FR


title: C_RF small RNA-Seq rep1


title: Patient 1114, convalescent sample

description:
1114x9q1
DENV_gene_count_matrix.csv

value: 17d post symptom onset

value: Secondary


title: C_BW small RNA-Seq rep1


title: H009

value: 21 days post CLP


title: H004

value: 3 days post CLP


title: Apc/Kras/p53 mutant enteroid RNA-seq sample #1

description:
Min_PlusKP
Batch 1. ApcQ883* mutation induced using CRISPR base editing. KrasG12D and Trp53-/- mutations induced using enteroids from LSL-Kras/p53fl/fl mouse model
RNA_RLOG-LIMMA_normalized_counts.csv

value: Small Intestine

value: Apc/Kras/p53 mutant enteroid


title: Apc mutant enteroid RNA-seq sample  #2

description:
M2_Min
Batch 1. ApcQ883* mutation induced using CRISPR base editing
RNA_RLOG-LIMMA_normalized_counts.csv


title: Apc mutant enteroid RNA-seq sample  #1

description:
F2_MIN
Batch 1. ApcQ883* mutation induced using CRISPR base editing
RNA_RLOG-LIMMA_normalized_counts.csv

value: Apc mutant enteroid RNA-seq sample  #1


title: RF small RNA-Seq rep3


title: Patient 1110, convalescent sample

description:
1110x9q1
DENV_gene_count_matrix.csv

value: M

value: Dengue Fever


title: 1382PosRet

value: Aldhl1l-Cre/Ert2+; NuTRAP+

value: Positive

value: Young


title: H003

value: live nucleated CD45+

value: heart

value: steady state


title: enFNE_pooled_7-8h_15d

city: Freiburg

first: Valérie

last: Hilgers

address: Stübeweg 51

country: Germany

institute: MPI of Immunobiology and Epigenetics

description: Comparison of differentially expressed exons and 3' UTRs between mutants and the corresponding wild type control.

data_processing:
Bases were called on an Illumina NovaSeq 6000 platform
Within snakePipes standard RNAseq workflow (https://snakepipes.readthedocs.io/en/latest/content/workflows/mRNA-seq.html#mrna-seq), reads were aligned with STAR (Settings: --sjdbOverhang 100 --outSAMunmapped Within, otherwise default)
For 3' UTR quantification, mapped reads were quantified using featureCounts (within Subread) and a neuronal 3' UTR aware custom annotation.
For alternative exon quantification, standard DEXseq analysis was executed using default settings and the D. melanogaster dm6 release 79 annotation.
Fold changes of nodes corresponding to known neuronal alternative 3' UTRs (Carrasco et al., 2020) were subset.
Assembly: D. melanogaster: dm6 Ensembl, release 79
Supplementary files format and content: Original (alternative exons) or subset (alternative 3' UTRs) DEXseq output tables in tsv format

organism: Drosophila melanogaster

source_name: Whole embryo

growth_protocol: Flies were grown at 25C, following standard fly husbandry protocols.

extract_protocol:
Total RNA was isolated using TRIzol LS Reagent (Ambion 10296028) according to manufacturer's instructions.
Libraries were prepared with 100 ng of total RNA using Stranded mRNA Prep reagents (Illumina) according to manufacturer’s instructions.

treatment_protocol: Untreated

tag: developmental stage

value: Embryo - 7-8 h AEL

value: elavnFNE

value: male


title: RF small RNA-Seq rep2

value: flesh

value: 30 DAP


title: H006

value: 3 days post CLP


title: Patient 1110, acute sample

description:
1110x1q2
DENV_gene_count_matrix.csv

value: 4d post symptom onset

tag: infection

value: Secondary


title: H008

value: 7 days post CLP

tag: genotype


title: Patient 1106, convalescent sample

description:
1106x9q1
DENV_gene_count_matrix.csv

value: 19d post symptom onset

value: M

value: Primary


title: C_BW small RNA-Seq rep2

value: 10 DAP


title: H002

value: live nucleated CD45+ and CD45- (~1:1mixed)

value: Wild-type littermate control


title: Patient 1117, convalescent sample

description:
1117x9q1
DENV_gene_count_matrix.csv

value: 16d post symptom onset

value: Dengue Fever


title: RF small RNA-Seq rep1


title: CT small RNA-Seq rep3

value: 20 DAP


title: H001

value: heart

value: steady state


title: enFNE_pooled_7-8h_15a

value: Embryo - 7-8 h AEL

value: elavnFNE

value: male


title: CT small RNA-Seq rep1

value: flesh


title: enFNE_pooled_7-8h_15c


title: Patient 1086, acute sample

description:
1086x2q2
DENV_gene_count_matrix.csv

value: 3d post symptom onset

value: Secondary


title: hfq_hcd_1

city: Jena

first: Malte

last: Siemers

address: Winzerlaer Straße 2

department: Institute of Microbiology

institute: Friedrich Schiller University

description: whole bacterial cells

data_processing:
Library strategy: RIL-seq
demultiplexing of raw fastq files using custom script.
reads trimming and barcode removal using fastp version 0.23.1. Default parameters were used except for the following: --umi-loc=read1 –umi-length=9 –cut-front –cut-tail –cut-mean-quality=25 –trim-poly-x
trimmed reads were mapped to the reference genome using bwa-mem2 version 2.2.1. Default parameter  were used except for the following: -U 9 -T 20
alignments of trimmed reads were used to compute table of significant interactions using custom script.
Assembly: NC_002505, NC_002506
Supplementary files format and content: table_s1.xlsx contains the table of significant interactions in .xlsx format.

organism: Vibrio cholerae

source_name: Hfq::3XFLAG rep I

growth_protocol: V. cholerae wild-type and hfq::3XFLAG-tagged strains were grown in LB medium to low (OD600 of 0.2) and high (OD600 of 2.0) cell densities.

extract_protocol:
RNA was extracted according to the protocol found in this paper: doi:10.1038/nprot.2017.115
Libraries were built according to the protocol found in this paper: doi:10.1038/nprot.2017.115

treatment_protocol: Cells equivalent to 40 OD600 units were collected and subjected to RIL-seq.

tag: growth phase

value: stationary

tag: density (od600)

tag: protocol

value: RIL-seq


title: Patient 1106, acute sample

description:
1106x1q2
DENV_gene_count_matrix.csv

value: 4d post symptom onset

value: M

value: Primary


title: wt_hcd_2

description: whole bacterial cells

source_name: control rep II

value: wild-type


title: elav-resc_pooled_7-8h_12d

value: delta-elav,fnenFNE


title: Patient 1076, convalescent sample

description:
1076x9q2
DENV_gene_count_matrix.csv

value: 18d post symptom onset

value: F

value: Dengue Fever


title: CT small RNA-Seq rep2

tag: tissue

value: 20 DAP


title: Patient 1086, convalescent sample

description:
1086x9q1
DENV_gene_count_matrix.csv

value: 17d post symptom onset

tag: symptom


title: elav-resc_pooled_7-8h_12c

value: Embryo - 7-8 h AEL


title: BW small RNA-Seq rep3

value: 10 DAP


title: wt_hcd_1

description: whole bacterial cells

source_name: control rep I


title: Patient 1076, acute sample

description:
1076x3q2
DENV_gene_count_matrix.csv

value: 2d post symptom onset

tag: virus type


title: BW small RNA-Seq rep2

value: flesh


title: elav-resc_pooled_7-8h_12b

value: male


title: Patient 1068, convalescent sample

description:
1068x9q2
DENV_gene_count_matrix.csv

value: 22d post symptom onset


title: hfq_lcd_2

description: whole bacterial cells

source_name: Hfq::3XFLAG rep II

value: exponential

value: RIL-seq


title: Patient 1068, acute sample

description:
1068x1q2
DENV_gene_count_matrix.csv

source_name: Whole blood

value: 3d post symptom onset

value: M


title: elav-resc_pooled_7-8h_12a


title: hfq_hcd_2

description: whole bacterial cells

value: stationary


title: enFNE_pooled_7-8h_15b

value: elavnFNE


title: hfq_lcd_1

description: whole bacterial cells


title: BW small RNA-Seq rep1


title: SW small RNA-Seq rep3

value: 5 DAP


title: RRM34_pooled_7-8h_11c

value: elavmin,fnenFNE


title: RRM34_pooled_7-8h_11d


title: wt_lcd_1

description: whole bacterial cells

value: wild-type


title: SW small RNA-Seq rep1


title: SW small RNA-Seq rep2


title: RRM34_pooled_7-8h_11b


title: RRM34_pooled_7-8h_11a


title: resc_pooled_7-8h_14d

value: fnenFNE - control group


title: AP small RNA-Seq rep3

value: 1 DAP


title: PB-EZ 2

city: Tokyo

first: Tomohiro

last: Mizutani

address: 1-5-45 Yushima, Bunkyo-ku,

department: Department of Gastroenterology and Hepatology

institute: Institute of Science Tokyo

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots' signal intensities of 95% confidence intervals.

source_name: iPS cell-derived hidgut spheroids

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Maintained iPS cells were differentiate into definitive endoderm and then treated with mid/hindgut differentiation medium following published protocol (Nature 2011, Nature protocol 2011).

extract_protocol: Total RNA extracted using RNeasy Mini kit (Quiagen) following manufacturer's instructions.

treatment_protocol: Formed mid/hindgut floating spheroids were collected as floating intestinal spheroids (fl). Cells were dissociated with TrypLE and seeded on EZSPHERE 6-well plates to generate spheroids (EZ).

tag: iPS cell line

tag: treatment

value: EZ


title: resc_pooled_7-8h_14c

value: Embryo - 7-8 h AEL


title: Micorwell-seq datasets of TwoYearsUterus_3

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-6,22-27,43-48 merge (18bp)； UMI:In read1, the　bases　49-54 (6bp)
ScRNA-seq reads were aligned to the Mus_musculus.GRCm38.88 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cell barcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Assembly: Mus_musculus.GRCm38.88 genome
Supplementary files format and content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq protocol

value: Uterus

value: Female


title: AP small RNA-Seq rep1

value: flesh


title: PB-EZ 3


title: resc_pooled_7-8h_14b

value: male


title: Micorwell-seq datasets of TwoYearsUterus_4


title: PD small RNA-Seq rep3

value: 0 DAP


title: wt_lcd_2

description: whole bacterial cells

value: exponential

value: RIL-seq


title: Micorwell-seq datasets of TwoYearsStomach_5

value: Stomach


title: resc_pooled_7-8h_14a


title: Micorwell-seq datasets of TwoYearsStomach_4


title: Micorwell-seq datasets of TwoYearsSpleen_7

value: Spleen


title: elav-resc_pooled_heads_12c

source_name: Heads

value: Adult - 72 h AH

value: delta-elav,fnenFNE


title: PD small RNA-Seq rep2


title: Micorwell-seq datasets of TwoYearsUterus_5


title: PD small RNA-Seq rep1


title: elav-resc_pooled_heads_12b


title: AP small RNA-Seq rep2


title: 5_Aza_rep3

value: 20 DAP

value: 5-zazcytidine treatment


title: 2F-EZ 2


title: 2F-EZ 3


title: Micorwell-seq datasets of TwoYearsSpleen_6


title: Micorwell-seq datasets of TwoYearsSpleen_5


title: 2F-EZ 1


title: PB-fl 3

value: fl


title: elav-resc_pooled_heads_12a


title: PB-fl 2


title: 5_Aza_rep2


title: RRM34_pooled_heads_11c

value: elavmin


title: Micorwell-seq datasets of TwoYearsPancreas_7

value: Pancreas


title: 5_Aza_rep1


title: PB-fl 1


title: Micorwell-seq datasets of TwoYearsPancreas_6


title: RRM34_pooled_heads_11b


title: Mock_rep3

value: Wild-type


title: 2F-fl 2


title: PB-EZ 1

value: EZ


title: SCAN-seq2 of Isoginkgetin treated Hela and HepG2 cells (48 h) [IGG48]

first: Zhenyu

last: Liu

address: Peking University, No.5 Yiheyuan Road, Haidian District, Beijing, China

department: Biomedical Pioneering Innovation Center

institute: Peking University

description: SCAN-seq2; OXFORD_NANOPORE PromethION

data_processing:
Base calling was performed on the electric signals of nanopore sequencing to generate fastq files using Guppy (v4.0.1). Single-cell barcodes were extracted from 150 bp on both ends of the reads by nanoplexer (v0.1.2, https://github.com/hanyue36/nanoplexer). Reads with low quality (q < 7) and short length (< 100 bp) were filtered out using NanoFilt (v2.7.1). Pychopper (v2.5.0, https://github.com/nanoporetech/pychopper) was utilized to trim adaptors, identify and orient full-length cDNA sequence. UMIs were extracted from 3’ end of reads and added to header by UMI-tools (v1.0.1) extract command. Poly-A sequences were trimmed using cutadapt (v3.2) with parameters ‘-a "A{10}" -e 0.2’. Clean reads were mapped to a merged reference transcriptome of human (GRCh38.p13) and mouse (GRCm38.p6) cDNAs from Ensembl release 101 using minimap2 (v 2.17-r941). PCR duplications were filtered based on UMI sequence and mapping position using dedup command of UMI-tools (v1.0.1) with parameters “--method=directional --edit-distance-threshold=1 --per-gene --per-contig --buffer-whole-contig”. Expression levels of each transcript and each gene were quantified using Salmon (v1.3.0) in alignment-based mode.
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text files for UMI count matrix

organism:
Homo sapiens
Mus

source_name: cell line

extract_protocol:
Cells from each line were sorted into 96-well plates containing lysis buffer. The lysis buffer comprised 2U RNase Inhibitor (Takara, Cat. 2313B), 0.475% Triton X-100 (Sigma-Aldrich, Cat. X100), 2.5 mM dNTP mixture (Thermo, Cat. R0193), 0.75 μM RT primer (TCAGACGTGTGCTCTTCCGATC-XXXXXXXXXXXXXXXXXXXXXXXX-N8-T25, with X representing the nucleotide of cell-specific barcode, N8 representing unique molecular identity), and 0.025% ERCC spike-in. Plates were thoroughly vortexed for 60 seconds and incubated at 72˚C for 10 minutes, so that the linearized RNA molecules were released. Then they were immediately transferred on ice.
After reverse transcription, mRNA-cDNA hybrid strands from each 32 cells were pooled together for PCR amplification. All PCR products were pooled together then purified with Ampure XP beads. Library was constructed using the Oxford Nanopore Ligation Sequencing Kit 1D (ONT, 313 Cat. SQK-LSK109) and sequenced with PromethION 48.

value: cell line

tag: cell line

value: Hela, HepG2

value: mixed


title: wt_pooled_heads_8c

value: wild type

tag: Sex

value: male


title: SCAN-seq2 of Isoginkgetin treated Hela and HepG2 cells (24 h) [IGG24]

description: SCAN-seq2; OXFORD_NANOPORE PromethION


title: Mock_rep2

value: flesh

tag: age


title: 2F-fl 3


title: Micorwell-seq datasets of TwoYearsLung_5

tag: strain

value: Lung

value: Female


title: Mock_rep1


title: Micorwell-seq datasets of TwoYearsLung_4


title: Micorwell-seq datasets of TwoYearsPancreas_5


title: Micorwell-seq datasets of TwoYearsLung_3


title: RF_rep3

value: 30 DAP

tag: cultivar


title: SCAN-seq2 UMI_200 library of 96 K562 cells and 96 3T3 cells [UMI_200]

description: SCAN-seq2; OXFORD_NANOPORE PromethION

tag: cell type


title: SCAN-seq2 of Isoginkgetin treated Hela and HepG2 cells (6h) [IGG6]

description: SCAN-seq2; OXFORD_NANOPORE PromethION


title: RF_rep2


title: 2F-fl 1


title: wt_pooled_heads_8a

tag: developmental stage

value: Adult - 72 h AH


title: SCAN-seq2 UMI_100 library of 48 K562 cells and 48 3T3 cells [UMI_100]

description: SCAN-seq2; OXFORD_NANOPORE PromethION


title: elav-resc_pooled_14-16h_12d

value: Embryo - 14-16 h AEL

value: delta-elav,fnenFNE


title: Micorwell-seq datasets of TwoYearsLiver_7

value: Liver


title: Micorwell-seq datasets of TwoYearsLiver_6


title: SCAN-seq2 4CL library of 2 human cell lines and 2 mouse cell lines [4CL]

description: SCAN-seq2; OXFORD_NANOPORE PromethION


title: elav-resc_pooled_14-16h_12c


title: RF_rep1


title: SCAN-seq2 9CL_Mix library of 6 human cell lines and 3 mouse cell lines [9CL_Mix]

description: SCAN-seq2; OXFORD_NANOPORE PromethION


title: RRM34_pooled_heads_11a

value: elavmin


title: CT_rep3

value: 20 DAP


title: Micorwell-seq datasets of TwoYearsLiver_5


title: CT_rep2


title: elav-resc_pooled_14-16h_12b


title: Micorwell-seq datasets of TwoYearsKidney_6

value: Kidney


title: elav-resc_pooled_14-16h_12a


title: wt_pooled_heads_8b


title: RRM34_pooled_14-16h_11d


title: Micorwell-seq datasets of TwoYearsKidney_5


title: CT_rep1


title: BW_rep3

value: 10 DAP


title: 9CL: Mix of 6 human cell line and 3 mouse cell line [9CL]

description: SCAN-seq2; OXFORD_NANOPORE PromethION

value: cell line


title: RRM34_pooled_14-16h_11c


title: Micorwell-seq datasets of TwoYearsIntestine_6

value: Intestine


title: BW_rep2


title: RRM34_pooled_14-16h_11a


title: Control_#4 Kidney

city: Columbia

first: Rocío

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri, Columbia

description: Original fetal ID: C008

data_processing:
Quality of raw reads was assessed using FastQC version 0.11.7 and SolexaQA++ version 3.1.7 dynamictrim function was used to trim low quality reads (Phred < 20). The lengthsort function of SolexaQA++ was used to remove trimmed reads less than 30 bases in length. Hisat2-build was used to create an index of the reference genome, ARS-UCD1.2, and hisat2 version 2.1.0 was used for alignment of the paired end reads to the reference genome with –dta-cufflinks option. Samtools sort was used to sort bam files based on position. Featurecounts was used for read count estimation with read counting performed at a gene feature level (parameter -t gene). EdgeR v3.24.3 was used for differential expression analysis, using the trimmed mean of M values (TMM) method for normalization and a likelihood ratio test to identify differentially expressed genes. Only genes with at least 5 counts per million in all of the control-AI, or all of the ART-normal, or at least 2 of the ART-LOS were used for differential expression analysis. Genes with a false discovery rate (FDR) ≤ 0.05 were considered significant.
Assembly: ARS-UCD1.2
Supplementary files format and content: Plain text files contain raw read count and edgeR output for annotated genes.

organism: Bos indicus x Bos taurus

source_name: ~Day 105 fetal kidney

growth_protocol: Refers to Chen et al. 2013 (PMID: 23751783 and GEO: GSE63509).

extract_protocol:
Total RNA was isolated using TRIzol™ Reagent (Invitrogen, 15596026) following the manufacturer’s instructions. The concentration of RNA samples was measured by using the NanoDrop® ND-1000 Spectrophotometer. RNA samples were stored at -80°C.
This RNA-seq was conducted by Novogene (Sacramento, CA, USA). Briefly, total RNA samples were shipped on dry ice to Novogene overnight. Quality controls were performed for all samples using agarose gel electrophoresis to test RNA degradation and potential contamination and using Agilent 2100 Bioanalyzer to check RNA integrity and quantitation. All samples showed RNA integrity numbers (RIN) of 7.5 to 9.1 and passed the quality control. For strand specific sequencing library preparation, mRNA was enriched using oligo(dT) beads and fragmented randomly using fragmentation buffer. cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs (dUTP instead of dTTP), RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Then, double-stranded cDNA was subjected to terminal repair, 3’ adenylation, sequencing adaptor ligation, uracil-DNA glycosylase degradation, size selection for 250-300bp insert, and PCR enrichment. Quality controls were performed for all libraries including Qubit concentration measurement, testing insert size using Agilent 2100 Bioanalyzer, and quantifying effective concentration using qPCR. Qualified libraries were pooled and sequenced on Illumina HiSeq platform for 150bp paired end reads.

tag: conception method

value: Artificial insemination

value: ~D105 fetus

tag: disease status

value: Healthy


title: Control_#2 Muscle

description: Original fetal ID: B892

source_name: ~Day 105 fetal skeletal muscle

treatment_protocol: Refers to Chen et al. 2013 (PMID: 23751783 and GEO: GSE63509).


title: Control_#4 Liver

description: Original fetal ID: C008

source_name: ~Day 105 fetal liver


title: Control_#4 Muscle

description: Original fetal ID: C008


title: Micorwell-seq datasets of TwoYearsIntestine_5


title: BW_rep1

value: flesh


title: Control_#2 Liver

description: Original fetal ID: B892


title: Micorwell-seq datasets of TwoYearsIntestine_4


title: elav_pooled_14-16h_2d

tag: genotype

value: delta-elav

value: male


title: SW_rep3

value: 5 DAP


title: ART_#4 Muscle

description: Original fetal ID: R893

value: Assisted reproductive technology


title: Micorwell-seq datasets of TwoYearsIntestine_3

value: Female


title: SW_rep2


title: SW_rep1


title: ART_#4 Liver

description: Original fetal ID: R893


title: elav_pooled_14-16h_2b

value: Embryo - 14-16 h AEL


title: elav_pooled_14-16h_2c


title: AP_rep3

value: 1 DAP


title: ART_#4 Kidney

description: Original fetal ID: R893


title: Micorwell-seq datasets of TwoYearsHeart_7

value: Heart


title: Micorwell-seq datasets of TwoYearsIntestine_7


title: ART_#3 Muscle

description: Original fetal ID: J817B


title: elav_pooled_14-16h_2a


title: RRM34_pooled_14-16h_11b

value: elavmin


title: Micorwell-seq datasets of TwoYearsHeart_6


title: ART_#3 Liver

description: Original fetal ID: J817B


title: wt_pooled_14-16h_8d

value: wild type


title: PD_rep3

value: 0 DAP


title: ART_#3 Kidney

description: Original fetal ID: J817B


title: AP_rep1


title: wt_pooled_14-16h_8b


title: Micorwell-seq datasets of TwoYearsBladder_5

value: Bladder


title: Micorwell-seq datasets of TwoYearsBladder_4


title: ART_#2 Liver

description: Original fetal ID: J619


title: PD_rep2


title: wt_pooled_14-16h_8a


title: Micorwell-seq datasets of TwoYearsBladder_3


title: PD_rep1


title: Micorwell-seq datasets of TwoYearsHeart_8


title: Micorwell-seq datasets of TwoYearsBrain_8

value: Brain


title: VEGFA

city: Birmingham

first: Abdullah

middle: Obaid

last: Khan

state: West Midlands

address: MDS, Wolfson Drive

department: Institute of Cardiovascular Science

country: United Kingdom

institute: University of Birmingham

data_processing:
Raw files processed with CellRanger Count 6.0.1
Resulting data analysed by SingleCellaR as described by vignette: https://supatt-lab.github.io/SingCellaR.Doc/
VEGFA and VEGFAC samples analysed individual and subsequently integrated via SingelCellaR's supervised Harmony approach.
Genome_build: GRCh38-2020-A
Supplementary_files_format_and_content: R objects containing annotated SingleCellaR objects.

source_name: Human bone marrow organoid

growth_protocol: iPSCs treated with a directed differentiation protocol to induce step wise endothelial and haematopoeitic commitment.

extract_protocol:
Chromium Next GEM Single Cell 3ʹ v3.1
RNA libraries were prepared for sequencing using standard 10X Genomics protocols (single indexing)

treatment_protocol: VEGFA samples differentiated with VEGFA alone, VEGFA + C samples differentiated with both VEGFA and VEGFC in combination.

value: Humam induced pluripotent stem cell derived cells

value: Differentiation with VEGA alone


title: AP_rep2


title: Micorwell-seq datasets of TwoYearsBrain_7


title: ART_#2 Kidney

description: Original fetal ID: J619

value: ~D105 fetus

value: Healthy


title: VEGFAC

value: Differentiation with VEGFA and VEGFC


title: ART_#1 Muscle

description: Original fetal ID: J649


title: Streptococcus suis in the biofilm state 1

city: Luoyang

address: Ancient city street

institute: College of Animal Science and Technology, Henan University of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Seguenced reads were trimmed for adaptor seguence, and masked for low-complexity or low-quality seguence, then mapped to ZY05H33 whole genome using bowtie v0.12 2 with parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Assembly: ZY05H33
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Streptococcus suis

source_name: culture

growth_protocol: Streptococcus suis was cultured on Todd-Hewitt Broth

extract_protocol:
RNA was harvested using Trizol reagent. Ilumina TruSeg RNA Sample Prep Kit (CatFC-122-1001) was used with 1 ug of total RNA for the construction
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: culture


title: Micorwell-seq datasets of TwoYearsBrain_6


title: ART_#1 Liver

description: Original fetal ID: J649


title: MHC region enriched GM12878 rep3

city: Shanghai

first: Yun

address: 130 Dong An Road

institute: Fudan University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
data were aligned to BS-converted MHC haplotype 1 + hg38 non-MHC and MHC haplotype 2 + hg38 non-MHC using bowtie2 v2.2.3 with options score-min L,0,0; and aligned to hg38 with default options
CpG evidence was extracted using bismarker v0.22.1
Genome_build: hg38
Supplementary_files_format_and_content: plain text, methylated and unmethylated reads per CpG site within MHC region captured by haplotype 1, haplotype 2 and hg38

molecule: genomic DNA

growth_protocol: GM12878 is cultrured in T25 tissue culture flask that has been filled with 20ml RPMI1640 medium supplemented with 15% FBS and Pen-Strep (1X).

extract_protocol:
Cultured cells were harvested and embed into low melting point agrose.After in-gel cleavege, the MHC moleculars were seperated and enriched by Pulse field gel electrophoresis .
20ng enriched MHC was fragmented to an average size of 250 bp using a Covaris M220 ultrasonicator. End repair and methylated adaptor ligation was performed with NEBNext Ultra End Repair/dA-Tailing Module, Ligation Module and NEBNext Multiplex Oligos for Illumina.Samples then underwent bisulfite conversion using an EZ DNA Methylation kit (Zymo Research, Irvine, CA, USA), with modified single stranded DNA fragments amplified using a Kapa HiFi U + HotStart ReadyMix (Kapa Biosystems, Wilmington, MA, USA) with primers (NEBNext Multiplex Oligos for Illumina). A final size selection was performed to enrich the library to a range between 300 and 500 bp. Constructed libraries were evaluated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) to assess quality and sequenced on an Illumina HiSeq X Ten using the 150-bp paired-end mode.

value: B cell


title: Streptococcus suis in the biofilm state 2


title: wt_pooled_14-16h_8c

value: male


title: Streptococcus suis in the planktonic state 2


title: Micorwell-seq datasets of TwoYearsBrain_5

value: Female


title: ART_#2 Muscle

description: Original fetal ID: J619

value: Assisted reproductive technology


title: Streptococcus suis in the planktonic state 1


title: MHC region enriched GM12878 rep1


title: Micorwell-seq datasets of TwoYearsBrain_4


title: MHC region enriched GM12878 rep2


title: ART_#1 Kidney

description: Original fetal ID: J649


title: CIC-NUTM2A 5

status: Public on Nov 14 2022

city: Palo Alto

first: Tanja

middle: A

last: Gruber

address: 1000 Welch Road Suite 300

department: Pediatrics

institute: Stanford University

data_processing:
RNA-seq reads from the mouse models were mapped by the mapping pipeline STRONGARM. Reads were aligned by using the BWA (12) (0.5.10) aligner to the following database files: (i) the mouse MGSCv37 reference sequence; (ii) RefSeq; (iii) a sequence file representing all possible combinations of non-sequential pairs in RefSeq exons; and (iv) the AceView database flat file downloaded from the UCSC Genome Browser, which represents transcripts constructed from ESTs. The mapping results from databases (ii)–(iv) were aligned to reference genome coordinates, and a BAM file was constructed by selecting the best alignment from the 4 databases. Mapped reads were counted with HTseq(13) and normalized to FPKM (fragments per kilobase of transcript per million mapped reads).
Assembly: MGSCv37
Supplementary files format and content: tab-delimited gene counts include RPKM values for each Sample

source_name: Bone Marrow

extract_protocol:
Trizol extraction
RNA sequencing was performed according to the manufacturer's instructions using the Illumina TrueSeq total stranded RNA kit.

value: Bone Marrow

value: Leukemia


title: CIC-NUTM2A 3


title: CIC-NUTM2A 4


title: CIC-NUTM2A 1


title: MLL-AF6 2


title: MLL-AF6 3


title: MLL-AF6 1


title: NUP98-KDM5A 3


title: CBAF2T3-GLIS2/Jak2 3


title: NUP98-KDM5A 1


title: NUP98-KDM5A 2


title: CBAF2T3-GLIS2/Jak2 2


title: Splenocytes_GFP_3

city: Cologne

first: Giuliano

last: Crispatzu

address: Joseph-Stelzmann-Straße 26

department: CECAD

institute: University of Cologne (UoC), Germany

hyb_protocol: Mouse Gene 1.0 ST Arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al.

label: biotin

source_name: Splenocytes from mice transplanted with HPCs expressing GFP

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

extract_protocol: RNA was extracted with the RNeasy Micro Kit from Qiagen. RNA was amplified using the Ovation Pico WTA System V2 from NUGEN applied for 50ng total RNA.

treatment_protocol: No treatment. Freshly isolated splenocytes from C57BL/6 (CD45.2) recipient mice of transduced HSCs/HPCs were collected for RNA isolation.

value: Splenocytes

value: Day 100 post transplant

tag: transplant

value: GFP-transgenic HSC/HSP cells


title: AML1-ETO9a 3


title: Splenocytes_GFP_1

growth_protocol: Freshly isolated splenocytes from C57BL/6 (CD45.2) recipient mice of transduced HSCs/HPCs were collected for RNA isolation.


title: AML1-ETO9a 2


title: AML1-ETO9a 1


title: Splenocytes_GFP_2


title: CD63+ MSC from IL-1rn-KO

city: Oslo

first: Lorena

last: Arranz

address: Forskningsveien 1

department: CRESCO - Centre for Embryology and Healthy Development

country: Norway

institute: University of Oslo

data_processing:
Cellranger demultiplexing and quantification
Genome_build: mm10 (cellranger 1.2.0 build)
Supplementary_files_format_and_content: Cellranger filtered bc matrixes with genes, barcodes and counts.

source_name: CD63, plus, KO

extract_protocol:
For CD11b and HSPC sorting, BM from 1 femur and 1 tibia from one mouse was flushed by centrifugation. For MSC sorting, the rest of the bones (femur, tibia, sternum, hips, humerus, spine) were pooled with all the bones of another mouse and were crushed and digested for 1 hour with collagenase. After erythrocyte lysis, cells were stained with antibody mixes and FACS-sorted using BD Aria II cell sorter. Single cells were encapsulated into emulsion droplets using the Chromium Controller (10x Genomics). Each cell suspension was loaded into one port of a Chromium Next GEM Chip G (10x Genomics) with a target output of 4000-10000 cells. Single cell RNA-Seq libraries were prepared using the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics) following the manufacturer instructions using a SureCycler 8800 thermal cycler (Agilent Technologies). The average size of each library was calculated using a high sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies) and the concentration was determined using the Qubit fluorometer (Thermo Fisher). Individual libraries were diluted to 10 nM and pooled for sequencing. Library pool was sequenced at 700 pM in paired-end reads (28bp Read1, 10bp Index1, 10 pb Index 2 and 90bp Read2) using one P3 flow cell (100 cycles) on a NextSeq 2000 (Illumina). FastQ files for each sample were obtained using cellranger demux pipeline (10x Genomics).
Single cell RNA-Seq libraries were prepared using the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics) following the manufacturer instructions using a SureCycler 8800 thermal cycler (Agilent Technologies). The average size of each library was calculated using a high sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies) and the concentration was determined using the Qubit fluorometer (Thermo Fisher). Individual libraries were diluted to 10 nM and pooled for sequencing. Library pool was sequenced at 700 pM in paired-end reads (28bp Read1, 10bp Index1, 10 pb Index 2 and 90bp Read2) using one P3 flow cell (100 cycles) on a NextSeq 2000 (Illumina). FastQ files for each sample were obtained using cellranger demux pipeline (10x Genomics).
Single-cell RNA-Seq

value: female

value: 12 weeks

value: mesenchymal stromal cells (MSC)

tag: membrane phenotype


title: CD63+ MSC from WT

source_name: CD63, plus, WT

value: WT


title: BM HSPC from IL-1rn-KO

source_name: LSK, KO

value: hematopoietic stem and progenitor cells (HSPC)


title: CIC-NUTM2A 2

tag: tissue


title: BM HSPC from WT

source_name: LSK, WT


title: Primary tumors isolated from mice, day10

city: Nanjing

first: Jie

last: Dong

address: Hankou road 22

institute: Nanjing University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: sgRNA library
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: tumor

growth_protocol: Primary tumors isolated from mice

extract_protocol:
RNA was harvested using Trizol. 1.1 ug of total RNA was used for the construction of sequencing libraries.
End Repair, 5’Phosphorylation and dA-Tailing, Adapter Ligation, Clean Up, PCR Enrichement and Clean Up were used for RNA libraries preparation.

value: tumor

value: breast cancer

value: Tumor progression

tag: time

tag: disease state

value: model of TNBC


title: 08_MCL_100w

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

institute: Osaka university

data_processing:
Sequencing outputs were demultiplexed using bcl2fastq2 (https://jp.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html)
Fastq files were aligned to Mus musculus GRCm38 reference using STAR aligner (2.7.6a; https://github.com/alexdobin/STAR)
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tar-archived STAR output directory (Solo.out).

source_name: MCL

extract_protocol:
After euthanasia, ligaments were isolated and dissociated into single cells by the enzyme.To obtain live cells, isolated cells were labeled with the following fluorescence-conjugated antibodies which were applied and incubated for 20 min at 4 °C: anti-mouse CD45-APC  and anti-mouse H-2-FITC.
Cells were sorted into 384-well plates with barcoded oligo dT primer for each well (1 cell / well). After reverse transcription in each well, cDNA was pre-amplified using the Accel-NGS 1S Plus DNA Library Kit (Swift Biosciences). Purified cDNAs were tagmentationed with Amplicon Tagment enzyme (Illumina) and PCR for library construction was done by using NEBNext High-Fidelity 2× PCR Master Mix (NEB).

value: post natal week 100

tag: cell sorting

value: H2+, Cd45+, Sytox-


title: 07_MCL_100w


title: 06_MCL_100w


title: Primary tumors isolated from mice, day5

tag: treatment


title: 03_ACL_100w

source_name: ACL


title: 02_ACL_100w


title: 01_ACL_100w


title: 04_ACL_100w


title: 09_MCL10w

value: post natal week 10


title: CBAF2T3-GLIS2/Jak2 1

value: Bone Marrow


title: 10_MCL10w


title: 07_MCL10w


title: 06_MCL10w


title: 05_ACL10w


title: 08_MCL10w


title: 02_ACL10w


title: 04_ACL10w


title: 03_ACL10w


title: 01_ACL10w


title: BM myeloid cells from C57BL/6J

source_name: CD11b, WT

value: myeloid cells


title: BM myeloid cells from IL-1rn-KO

source_name: CD11b, KO


title: 05_ACL_100w


title: Myc1L

city: Nagoya

first: Satoru

last: Ato

state: Aichi

address: Gokiso-cho, Showa-ku

department: Department of life science and applied chemistry

institute: Nagoya Institute of Technology

data_processing:
 Illumina Miniseq Control Software Ver. 1.1.8.0 was used for base-calling
Read quality control was conducted by FASTQC Ver. 0.11.5(-t8)
Trimming low quality tails, polyA read-through and adaptor contamination was performed with Bbduk Ver. 35.92
samtools index Ver 1.3 was used for read indexing
Alignment was performed with STAR Ver 2.5.2a
Mapping Quality Control was performed with RSEQC Ver 2.6.4
Gene Read Counting was performed with HTseq Ver 0.6.0
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Left lower leg (control)

extract_protocol:
Skeletal muscle was removed, rapidly frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared with QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina

value: post natal week 11

tag: genotype/variation

value: c-myc over-expression

value: gastrocnemius muscle


title: Myc1R

source_name: Right lower leg (contracted)

tag: Sex

value: female


title: Myc3L

tag: age


title: Myc2R

tag: strain


title: Con2R

value: control


title: Myc2L


title: Con3L


title: Con3R


title: Con2L


title: Con1R


title: PHx, biological rep 1

city: Jerusalem

first: Rinat

last: Abramovitch

address: Hadassah Ein Kerem

department: Institute for Gene Therapy

country: Israel

institute: Hadassah Medical Organization

data_processing: Data was analysed with Affymetrix Analysis Power Tools (APT) command apt-probeset-summarize. Analysis type was set to plier-gcbg, implementing the PLIER (Probe Logarithmic Intensity Error) method. Full quantile normalization and background noise reduction by median probe intensity (GC corrected) was applied. Summarization was utilized collectively to all samples of all groups under test.

organism: Rattus norvegicus

source_name: partial hepatectomy (50% PHx)

label_protocol: Biotinylated sense-strand DNA was prepared according to the standard Affymetrix protocol

extract_protocol: Total RNA was isolated from frozen liver tissues with TRIzol reagent according to the manufacturer’s instructions (n= 3 rats/group). Amplified and biotinylated sense-strand DNA was prepared according to the standard Affymetrix protocol from a total of 100ng RNA (Expression Analysis WT PLUS Technical Manual 2013, Affymetrix). Following fragmentation, 2.3µg of biotinylated sense-strand DNA was hybridized for 16 hours at 45oC on a GeneChip Rat Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidic Station 450 and were then scanned using an Affymetrix Gene Chip Scanner 3000.

treatment_protocol: Adult male Sprague-Dawley rats were cannulated (femoral artery) for bleeding the animals (controlled haemorrhage;  3ml of blood was extracted at a rate of 1 ml/min) and for administration of blood/fluids (resuscitation). PHx- partial liver resection of 50% of the total liver mass was performed.

value: liver

value: Sprague-Dawley


title: Con1L


title: bleeding, biological rep 3

hyb_protocol: Following fragmentation, 2.3µg of biotinylated sense-strand DNA was hybridized for 16 hours at 45oC on a GeneChip Rat Gene 2.0 ST Array.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidic Station 450 and were then scanned using an Affymetrix Gene Chip Scanner 3000.

source_name: 50% PHx & bleeding


title: Fresh RBC, biological rep 2

source_name: 50% PHx + bleeding + fresh RBC


title: HAES , biological rep 2

source_name: 50% PHx + bleeding + HAES 10%


title: Myc3R


title: Fresh RBC, biological rep 1


title: Naive, biological rep 3

source_name: naive


title: PHx, biological rep 3


title: Naive, biological rep 2


title: PHx, biological rep 2


title: bleeding, biological rep 2


title: Naive, biological rep 1


title: Stored RBC, biological rep 2

source_name: 50% PHx + bleeding + 7 days stored RBC


title: HAES , biological rep 1


title: Stored RBC, biological rep 3


title: Freash RBC, biological rep 3


title: HAES, biological rep 3


title: Stored RBC, biological rep 1


title: bleeding, biological rep 1


title: OLD sham mice #3 - CL

city: Barcelona

first: Laura

last: Ramiro

state: Barcelona

address: Passeig De La Vall D'hebrón 119-129, Edificio Mediterránea, Laboratorio 120

country: Spain

institute: Vall d'Hebron Institute of Research

description: Gene expression data from mouse brain

hyb_protocol: cDNA was hybridizated in GeneChip Mouse Clariom S Affymetrix microarrays for 16 hours with rotation at 45 ºC with rotation

scan_protocol: Microarrays were scanned in Affymetrix GeneChip Scanner 3000

data_processing: the images were processed with the Affymetrix GeneChip Command Console software for CEL file generation. To check the array image quality, Affymetrix Expression Console was used. Samples that demonstrated good quality results (pm mean, bgrd mean, pos vs neg auc,...) were subjected to subsequent analysis

source_name: mouse brain, contralateral hemisphere (CL)

label_protocol: Samples were amplified and labeled using GeneChip WT Plus Reagent Kit

growth_protocol: Saline-perfused mouse brain samples were isolated; IP and CL hemispheres were separated and flash frozen with liquid N2 until RNA isolation.

extract_protocol: RNA was isolated from frozen brain samples with the MirVana™ Paris™ (Thermo Fisher Scientific Inc., USA) and kept at -80ºC until the array was performed.

treatment_protocol: flash frozen at -80ºC

value: 18 months

tag: condition

value: aged

value: male

value: sham

value: brain

tag: brain hemisphere

value: CL


title: OLD sham mice #3 - IP

description: Gene expression data from mouse brain

source_name: mouse brain, ipsilateral hemisphere (IP)

value: IP


title: OLD sham mice #2 - CL

description: Gene expression data from mouse brain


title: OLD sham mice #2 - IP

description: Gene expression data from mouse brain


title: OLD sham mice #4 - IP

description: Gene expression data from mouse brain


title: OLD ischemic mice #7 - CL

description: Gene expression data from mouse brain

source_name: mouse brain, healthy hemisphere (CL)

value: ischemic


title: OLD ischemic mice #8 - IP

description: Gene expression data from mouse brain

source_name: mouse brain, ischemic hemisphere (IP)


title: OLD sham mice #1 - IP

description: Gene expression data from mouse brain


title: OLD sham mice #1 - CL

description: Gene expression data from mouse brain


title: OLD ischemic mice #8 - CL

description: Gene expression data from mouse brain


title: OLD ischemic mice #6 - CL

description: Gene expression data from mouse brain


title: OLD ischemic mice #4 - CL

description: Gene expression data from mouse brain


title: OLD ischemic mice #3 - IP

description: Gene expression data from mouse brain


title: OLD ischemic mice #3 - CL

description: Gene expression data from mouse brain


title: OLD ischemic mice #5 - CL

description: Gene expression data from mouse brain


title: OLD sham mice #4 - CL

description: Gene expression data from mouse brain


title: OLD ischemic mice #7 - IP

description: Gene expression data from mouse brain


title: OLD ischemic mice #1 - CL

description: Gene expression data from mouse brain


title: DIABETIC sham mice #3 - CL

description: Gene expression data from mouse brain

value: BKS-Leprdb/db/JOrlRj

value: 8-12 weeks

value: diabetic


title: OLD ischemic mice #2 - CL

description: Gene expression data from mouse brain


title: OLD ischemic mice #2 - IP

description: Gene expression data from mouse brain


title: DIABETIC sham mice #4 - CL

description: Gene expression data from mouse brain


title: OLD ischemic mice #5 - IP

description: Gene expression data from mouse brain


title: DIABETIC sham mice #4 - IP

description: Gene expression data from mouse brain


title: DIABETIC sham mice #2 - CL

description: Gene expression data from mouse brain


title: OLD ischemic mice #6 - IP

description: Gene expression data from mouse brain


title: OLD ischemic mice #4 - IP

description: Gene expression data from mouse brain


title: DIABETIC sham mice #3 - IP

description: Gene expression data from mouse brain


title: OLD ischemic mice #1 - IP

description: Gene expression data from mouse brain


title: DIABETIC sham mice #2 - IP

description: Gene expression data from mouse brain


title: DIABETIC ischemic mice #8 - CL

description: Gene expression data from mouse brain


title: DIABETIC ischemic mice #5 - CL

description: Gene expression data from mouse brain


title: DIABETIC ischemic mice #7 - CL

description: Gene expression data from mouse brain


title: DIABETIC ischemic mice #6 - CL

description: Gene expression data from mouse brain


title: DIABETIC ischemic mice #5 - IP

description: Gene expression data from mouse brain


title: DIABETIC ischemic mice #8 - IP

description: Gene expression data from mouse brain


title: DIABETIC ischemic mice #7 - IP

description: Gene expression data from mouse brain


title: DIABETIC ischemic mice #4 - CL

description: Gene expression data from mouse brain


title: DIABETIC ischemic mice #3 - IP

description: Gene expression data from mouse brain


title: DIABETIC ischemic mice #3 - CL

description: Gene expression data from mouse brain


title: DIABETIC sham mice #1 - CL

description: Gene expression data from mouse brain


title: FEMALE sham mice #4 - IP

description: Gene expression data from mouse brain

value: young


title: DIABETIC ischemic mice #4 - IP

description: Gene expression data from mouse brain


title: DIABETIC sham mice #1 - IP

description: Gene expression data from mouse brain


title: DIABETIC ischemic mice #2 - CL

description: Gene expression data from mouse brain


title: FEMALE sham mice #3 - CL

description: Gene expression data from mouse brain


title: DIABETIC ischemic mice #6 - IP

description: Gene expression data from mouse brain


title: FEMALE sham mice #3 - IP

description: Gene expression data from mouse brain


title: DIABETIC ischemic mice #1 - IP

description: Gene expression data from mouse brain


title: DIABETIC ischemic mice #2 - IP

description: Gene expression data from mouse brain


title: DIABETIC ischemic mice #1 - CL

description: Gene expression data from mouse brain


title: FEMALE sham mice #2 - IP

description: Gene expression data from mouse brain


title: FEMALE sham mice #1 - IP

description: Gene expression data from mouse brain


title: FEMALE sham mice #2 - CL

description: Gene expression data from mouse brain


title: FEMALE sham mice #1 - CL

description: Gene expression data from mouse brain


title: FEMALE ischemic mice #8 - CL

description: Gene expression data from mouse brain


title: FEMALE sham mice #4 - CL

description: Gene expression data from mouse brain


title: FEMALE ischemic mice #7 - IP

description: Gene expression data from mouse brain


title: FEMALE ischemic mice #7 - CL

description: Gene expression data from mouse brain


title: FEMALE ischemic mice #8 - IP

description: Gene expression data from mouse brain


title: FEMALE ischemic mice #5 - IP

description: Gene expression data from mouse brain


title: FEMALE ischemic mice #6 - IP

description: Gene expression data from mouse brain


title: FEMALE ischemic mice #3 - IP

description: Gene expression data from mouse brain


title: FEMALE ischemic mice #4 - CL

description: Gene expression data from mouse brain


title: FEMALE ischemic mice #5 - CL

description: Gene expression data from mouse brain


title: FEMALE ischemic mice #3 - CL

description: Gene expression data from mouse brain


title: FEMALE ischemic mice #1 - CL

description: Gene expression data from mouse brain


title: FEMALE ischemic mice #6 - CL

description: Gene expression data from mouse brain


title: FEMALE ischemic mice #2 - CL

description: Gene expression data from mouse brain


title: FEMALE ischemic mice #4 - IP

description: Gene expression data from mouse brain


title: MALE sham mice #3 - CL

description: Gene expression data from mouse brain


title: MALE sham mice #1 - IP

description: Gene expression data from mouse brain


title: MALE ischemic mice #6 - IP

description: Gene expression data from mouse brain


title: MALE ischemic mice #7 - IP

description: Gene expression data from mouse brain