title: IMR32_COMBO_3

status: Public on Jan 27 2022

city: Memphis

first: Brian

middle: J

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
RNA-seq reads were aligned to a reference genome comprised of the non-random chromosomes of the hg19 human reference plus the ERCC92 probe sequences using tophat v2.1.1 (PMID: 23618408) with –no-novel-juncs and -G set to a database of RefSeq genes downloaded 7/5/2017 that also contain the ERCC probe coordinates as separate chromosomes.
Per-gene expression was quantified in these same RefSeq genes using htseq-count (PMID: 25260700) using -m intersection-strict.
Supplementary_files_format_and_content: Counts files contain RefSEq gene names and numbers of reads assigned to each gene

source_name: Neuroblastoma

growth_protocol: Three biologic replicate lines of IMR-32 human neuroblastoma cells treated with DMSO/ JQ1/YKL-5-124 or combionation of JQ1 and YKL-5-124  were used.  Cells were grown in were grown in RPMI supplemented with 10% FBS and 1% penicillin/streptomycin. ine/penicillin/streptomycin.

extract_protocol:
Library prepped with the Illumina TruSeq stranded mRNA kit.
RNA extraction was performed with mirVana miRNA isolation kit (Invitrogen). Total RNA was treated with DNase I (Invitrogen). Sequencing libraries were prepared with the Illumina TruSeq stranded mRNA kit  and with ERCC spike-in controls for sample normalization. All samples were sequenced on an Illumina SE75 sequencer.

value: Neuroblastoma

value: JQ1 and YKL-5-124


title: IMR32_YKL_3

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment


title: IMR32_COMBO_2


title: IMR32_COMBO_1


title: IMR32_YKL_1


title: IMR32_JQ1_2


title: IMR32_YKL_2


title: IMR32_DMSO_2

value: DMSO


title: NP(elderly)_2

type: RNA

city: Tampa

first: Seong

middle: H

last: Cho

state: FL

address: 3802 Spectrum Blvd Suite 303

department: Internal Medicine

institute: University of South Florida

description: Nasal polyp and uncinate tissues were obtained from patients during endoscopic sinus surgeries.

hyb_protocol: 5.5ug labeled cDNA was hybridized to Affymetrix Human Gene 2.1ST array following the manufacturer’s protocol (Affymetrix Inc., Santa Clara, CA).

scan_protocol: Chip processing and image capturing were performed using Affymetrix AGCC software.

data_processing: Samples underwent RMA Normalization. Samples grouped according to phenotype and replicates were averaged and p value assigned using Transcriptome Analysis Console, v 4.0.1.

label: biotin

molecule: total RNA

source_name: Nasal polyp tissue from CRSwNP patient

label_protocol: Purified total RNA was reverse transcribed and biotin labeled to produce biotinylated cRNA targets according to GeneAtlas™ WT Expression Kit User Manual.

extract_protocol: For microarray analyses, total RNA was purified using QIazol (Qiagen, Valencia, CA) followed by quality assessment using bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: age

tag: classification

value: CRS Revision

tag: polyposis

value: Polyp


title: IMR32_DMSO_1


title: Con(non-elderly)_3

source_name: Uncinate tissues from normal controls

value: Normal Tumor

value: No Polyp


title: Con(elderly)_3

value: Normal


title: Con(non-elderly)_2


title: Con(elderly)_4


title: NP(non-elderly)_2

value: CRS


title: Con(non-elderly)_1


title: NP(elderly)_3


title: NP(elderly)_4


title: Con(elderly)_1


title: Con(elderly)_2


title: pri-miR-9-2 with GU

city: Frederick

first: Xavier

last: Bofill-De Ros

state: MD

address: 1050 Boyles St., blg 560

department: RNA Biology Laboratory

institute: National Cancer Institute

data_processing:
Adaptor removal using custom scripts. Described in Gu et al. Cell (2012)
miRNA mapping with QuagmiR. Described in Bofill-De Ros et al. Bioinformatics (2019).
Genome_build: miRBase21
Supplementary_files_format_and_content: tsv files reporting number of reads, length, 5' fidelity, trimming and tailoring events.

growth_protocol: HEK293T cells were maintained in DMEM high glucose (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (Hyclone), 100 U/ml penicillin-streptomycin (Gibco) at 37℃. Cells were tested to be free of mycoplasma contamination.

extract_protocol:
Phenol-cholorphorm total RNA extraction
5µg of total RNA was ligated with RNA 3’ adaptor using T4 RNA Ligase 2 - truncated (NEB), in the presence of RNase Inhibitor (NEB). RNA 5’ adaptor was ligated using T4 RNA Ligase 1 - high concentration (NEB) and 10 mM ATP. Ligated small RNAs were reverse transcribed using SuperScript ® IV Reverse Transcriptase (Thermo-Fisher). Small RNA library cDNA was amplified and indexed using Phusion® High-Fidelity DNA polymerase (NEB). Constructs were purified in a 6% (w/v) native acrylamide gel based on the expected product size and purified by ethanol precipitation.

treatment_protocol: Transfections were performed using PolyJet™ DNA Transfection Reagent (SignaGen) according to the manufacturer's instructions.

tag: transfection


title: pri-miR-9-1 Suboptimal 2


title: pri-miR-9-1 with GU


title: pri-miR-9-1 Suboptimal 1


title: NP(non-elderly)_1


title: NP(non-elderly)_3


title: pri-miR-9-1 variant B


title: IMR32_JQ1_1


title: IMR32_JQ1_3


title: Cipc-/-

city: suzhou

first: zheng

middle: ji

last: qing

address: renairoad

country: China

institute: szdx

data_processing:
Illumina Casava  bcl2fastqv2.19 software used for basecalling.
Filter the Raw Reads obtained by sequencing to obtain clean Reads that can be used for data analysis, and apply Seqtk to filter. The main steps are as follows: 1. Remove the linker sequence contained in the reads; 2. Remove the 3'end quality Q less than 20 Bases, that is, the base error rate is less than 0.01, where Q=-10logerror_ratio; 3. Removal of reads less than 25 in length; 4. Removal of ribosome RNA reads of the species.
Use Hisat2 (version: 2.0.4) split mapping algorithm to perform Genome mapping on the preprocessed reads. This algorithm allows the splitting of reads that cannot be matched to the full length to be mapped, and is more suitable for eukaryotic (with intron inter-regions). ) Transcriptome sequencing data; default parameters are used.
In transcriptome sequencing, we can estimate the level of gene expression by mapping the number of reads to the gene region, but the number of reads is not only proportional to the level of gene expression, but also related to the length of the gene itself and the amount of sequencing data. In order to make the gene expression levels of different genes and different samples comparable, the reads were converted into FPKM (Fragments Per Kilobase of exon model per Million mapped reads) to standardize the gene expression levels.
We first use Stringtie (version: 1.3.0) to count the number of Fragments of each gene after Hisat2 comparison, then use the TMM (trimmed mean of M values) method to normalize, and finally use the perl script to calculate each gene FPKM value.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: satellite cells

extract_protocol:
Cipc+/+ and Cipc-/- Satellite cells was isolated from TA muscle of CIPC-flox/flox mice and CIPC-scko mice. Total RNA was extracted using the RNAsimple total RNA Kit per manufacturer’s instructions. The quality of the total RNA was inspected by Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA). Qualified total RNA was further purified by RNAClean XP Kit (Cat# A63987, Beckman Coulter, Inc, Brea, CA). The cDNA library was generated using a VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Cat# NR604-02, Vazyme, Nanjing, China) and sequenced on an Illumina system (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: Tibialis anterior muscle

tag: genotype

value: Cipc-scko

value: satellite cells


title: Cipc+/+

value: Cipc-flox/flox


title: pri-miR-9-1 variant A


title: NP(elderly)_1


title: MGI0370_1_SLAB-85-0

city: St Louis

first: Ashley

last: Steed

state: Missouri

address: 660 South Euclid Ave

institute: Washington University In St Louis

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to hg38 genome build via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Genome_build: hg38
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: PBMC

extract_protocol: 10x Genomcis Chromium single cell preparation

tag: patient id

value: blood

value: PBMC

tag: disease state

tag: status

value: deceased

tag: Sex

value: male

tag: ethnicity

value: Caucasian

tag: time

value: day 0


title: MGI0370_1_SLAB-80-0

value: alive


title: MGI0370_1_SLAB-79-7

value: female

value: African American

value: day 7


title: IMR32_DMSO_3

value: Neuroblastoma

value: DMSO


title: MGI0370_1_SLAB-72-7


title: MGI0370_1_SLAB-62-7


title: MGI0370_1_SLAB-72-0


title: MGI0370_1_SLAB-283-0


title: MGI0370_1_SLAB-276-0


title: MGI0370_1_SLAB-283-7


title: MGI0370_1_SLAB-272-7


title: MGI0370_1_SLAB-272-0


title: MGI0369_1_SLAB-C8-C8

value: control 8

value: control


title: MGI0369_1_SLAB-C7-C7

value: control 7


title: P14 CTRL- Replicative senescence (old passage)

city: Redmond

first: Renuka

last: Kandhaya Pillai

state: WA

department: aging

institute: university of washington

description:
Gene expression data from replicative senescence
Control Passage 14
CTRL2

hyb_protocol: The labeled samples were hybridized to Human Gene ST 1.0 Arrays (Affymetrix)

scan_protocol: The arrays were scanned in a GeneChip Scanner 3000 (Affymetrix). CEL files were generated from DAT files using GCOS software (Affymetrix).

data_processing: To generate the log2 expression estimates, overall array intensity was  normalized between arrays and the probe intensity of all probes in a probeset summarized to a single value using RMA (Robust Multichip Average) algorithm . Comparisons were made between TNF vs CTRL (Cytokine induced senescence vs control), TNF VS CTRL2 (Cytokine induced senesence vs Replicative senescence) and CTR2 VS CTR1 (Replicative senescence vs Non-senescent or young cells)

source_name: HUVEC (Lonza)

label_protocol: Briefly, cDNA library preparation and amplification were performed from 50ng total RNA using WTA2 (Sigma-Aldrich) with 17cycles of amplification. 10 µg cDNA was subsequently fragmented by DNAseI and biotinylated by terminal transferase obtained from GeneChip Mapping 10Kv2 Assay Kit (Affymetrix).

growth_protocol: Human umbilical vein endothelial cells (HUVECs) purchased from Clonetics/Lonza (Bazel, Switzerland) were grown in EGM-2 medium supplemented with growth factors (EGM-2 bullet kit; Clonetics/Lonza).

extract_protocol: RNA was collected using TRIzol.

treatment_protocol: Human umbilical vein endothelial cells (HUVECs) were untreated or treated with TNF (5ng/ml) for 26 days (or Passged until senecence with TNF α) or control cells are grown until replicative arrest (Replicative senescence)

value: umbilical vein endothelial cells (HUVEC)

tag: phenotype

value: Senescent Cells (Replicative senescence)


title: P15 CTRL - Replicative senescence (old passage)

description:
Gene expression data from replicative senescence
Control Passage 15
CTRL2


title: MGI0369_1_SLAB-C6-C6

value: control 6

value: blood


title: MGI0369_1_SLAB-C4-C4

value: control 4

value: PBMC


title: MGI0369_1_SLAB-C1-C1

value: control 1

value: deceased

value: male

value: Caucasian


title: MGI0369_1_SLAB-C2-C2

value: control 2

value: female


title: MGI0369_1_SLAB-251-7

value: African American

value: day 7


title: MGI0369_1_SLAB-85-7


title: MGI0369_1_SLAB-163-7


title: MGI0369_1_SLAB-251-0

value: day 0


title: MGI0369_1_SLAB-163-0


title: MGI0369_1_SLAB-154-0

value: alive


title: MGI0369_1_SLAB-154-7


title: MGI0369_1_SLAB-145-7


title: MGI0369_1_SLAB-145-0


title: MGI0370_1_SLAB-80-7


title: Fetal_1_villi

city: New Haven

first: Liza

last: Konnikova

state: CT

address: 375 Congress Ave LSOG 407

department: Pediatrics

institute: Yale University

data_processing:
Basecalls performed using CLC Genomics Workbench
CLC Genomics Workbench was used to first trim paired reads with a quality limit of 0.05, ambiguous limit of 2 with automated read through adapter trimming from the 3’-end with a maximum length of 150.
Trimmed reads were then mapped to the homo_sapiens_sequence_hg38 reference sequence
Gene expression was calculated as Transcripts per Kilobase Million (TPM)
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text files include TPM values for every sample

source_name: mid-gestation Placenta

extract_protocol:
Placental layers were separated with forceps under a dissecting microscope. Samples were snap frozen with dry ice and shipped to MedGenome for RNA isolation using the Qiagen All-Prep Kit (#80204)
cDNA synthesis wasprepped with the Takara SMART-seq kit (#634894)and NexteraXT (FC-131-1024, Illumina) was used to fragment and add sequencing adaptors. Quality control was completed by MedGenome via Qubit Fluorometric Quantitation and TapeStation BioAnalyzer.

tag: patient number

value: villi


title: Fetal_3_fetal_membrane

value: fetal membrane


title: Fetal_2_decidua

value: decidua


title: Fetal_2_villi


title: Fetal_3_villi


title: Fetal_3_decidua


title: MGI0370_1_SLAB-79-0

tag: cell type


title: Fetal_1_fetal_membrane


title: MGI0370_1_SLAB-62-0


title: Fetal_1_decidua


title: MGI0370_1_SLAB-276-7


title: siSA.Riboseq

city: Guangzhou

first: Yizhao

last: Luan

state: Guangdong

address: Xianlie South Rd. 54, Yuexiu Dist

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen university

description: ribosome-protected fragments

data_processing:
Library strategy: Ribo-Seq
Base calling in bcl files were demultiplexed and converted into fastq files by Bcl2fastq (v2.20.0.422). Adapters and low-quality reads ending with quality scores < 20 were trimmed by Cutadapt (v1.8.1). Trimmed reads with length < 20nt were discarded. Reads aligned to human rRNA and tRNA sequences were further excluded. For Ribo-seq libraries, trimmed reads with length <26nt or >34nt were excluded. Remaining reads were aligned to the human genome (Ensembl GRCh38.88) by STAR (v2.6.1-d).
Genome_build: Ensembl GRCh38.88
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for each Sample

source_name: Cell line:A549

growth_protocol: A549 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS) (Gibco, 10270-106) and antibiotics (100μg/ml penicillin and 50μg/ml streptomycin sulfate) (Gibco, 15140122).

extract_protocol:
A549 cells were harvested 5min after treatment with 100 μg/ml cycloheximide (CHX) in DMEM, washed twice in PBS with 100 μg/ml CHX. Samples were lysed with 1 ml mammalian lysis buffer containing 200 µl 5x Mammalian Polysome Buffer, 100 µl 10% Triton X-100, 10 µl 100 mM DTT, 12.5 µl Turbo DNase, 1 µl 100 mg/ml CHX, and 675.5 µl nuclease-free water. After incubation for 20min on ice, lysates were centrifuged at 12,000rpm, 4°C for 10min. For each sample, lysate was divided into two aliquots.
For the 600-μl aliquots lysates, 6 units of ARTseq Nuclease was added to each A260 lysate, and the mixtures were incubated for 60min at room temperature with rotation. Nuclease digestion was stopped by 10μL SUPERase·In RNase Inhibitor. Lysates were applied to MicroSpin S-400 HR spin columns. Total RNA was purified with Zymo RNA Clean & Concentrator-25 kit. The rRNA was depleted with Ribo-Zero Gold rRNA Removal Kit. The rRNA-depleted samples were run on a 10% TBE-Urea polyacrylamide gel. RPF between 28-nt and 30-nt were selected. Ribo-seq libraries were then constructed following a protocol described previously. For the 150-μl aliquots lysates, total RNA was isolated with Zymo RNA Clean & Concentrator-25 kit, RNA-seq libraries were constructed with VAHTS Total RNA-seq (H/M/R) Library Prep Kit according to the manufacturer’s instructions. All libraries were sequenced with PE150 mode by Illumina Hiseq X10 or NovaSeq 6000.

treatment_protocol: A549 cells were transfected for 24h with RP-targeting or non-targeting (control) siRNAs at a final concentration of 40nM using Lipofectamine RNAiMAX reagent (Invitrogen, 13778150) following the manufacturer's protocol.

tag: cell line


title: siS28.Riboseq

description: ribosome-protected fragments


title: siS29.Riboseq

description: ribosome-protected fragments


title: siS27.Riboseq

description: ribosome-protected fragments


title: siS27L.Riboseq

description: ribosome-protected fragments


title: P2 CTRL - Early Passage (Young or Non-senescent)

description:
Gene expression data from Early passage
Early Passage 2
CTRL1

value: umbilical vein endothelial cells (HUVEC)

value: Non-senescent Cells


title: siS26_5_1.Riboseq

description: ribosome-protected fragments


title: siS26_5_2.Riboseq

description: ribosome-protected fragments


title: siS25.Riboseq

description: ribosome-protected fragments


title: siS23.Riboseq

description: ribosome-protected fragments


title: siS24.Riboseq

description: ribosome-protected fragments


title: siS21.Riboseq

description: ribosome-protected fragments


title: siS17_4_1.Riboseq

description: ribosome-protected fragments


title: siS18.Riboseq

description: ribosome-protected fragments


title: siS17_4_2.Riboseq

description: ribosome-protected fragments


title: siS16_2.Riboseq

description: ribosome-protected fragments


title: siS19.Riboseq

description: ribosome-protected fragments


title: siS15A_19_1.Riboseq

description: ribosome-protected fragments


title: siS16_1.Riboseq

description: ribosome-protected fragments


title: siS11_16_1.Riboseq

description: ribosome-protected fragments


title: siS12_3_1.Riboseq

description: ribosome-protected fragments


title: Fetal_2_fetal_membrane


title: siS11_16_2.Riboseq

description: ribosome-protected fragments


title: siS15_18_1.Riboseq

description: ribosome-protected fragments


title: siS12_3_2.Riboseq

description: ribosome-protected fragments


title: siS14.Riboseq

description: ribosome-protected fragments


title: siS13.Riboseq

description: ribosome-protected fragments


title: siS10_15_2.Riboseq

description: ribosome-protected fragments


title: siS9_2_2.Riboseq

description: ribosome-protected fragments


title: siS9_2_1.Riboseq

description: ribosome-protected fragments


title: siS15_18_2.Riboseq

description: ribosome-protected fragments


title: siS10_15_1.Riboseq

description: ribosome-protected fragments


title: siS7_13_2.Riboseq

description: ribosome-protected fragments


title: siS8_14_1.Riboseq

description: ribosome-protected fragments


title: siS7_13_1.Riboseq

description: ribosome-protected fragments


title: siS6.Riboseq

description: ribosome-protected fragments


title: siS8_14_2.Riboseq

description: ribosome-protected fragments


title: siS4Y.Riboseq

description: ribosome-protected fragments


title: siS4X.Riboseq

description: ribosome-protected fragments


title: siS3A.Riboseq

description: ribosome-protected fragments


title: siS3_1_2.Riboseq

description: ribosome-protected fragments


title: siS2.Riboseq

description: ribosome-protected fragments


title: siP1.Riboseq

description: ribosome-protected fragments


title: siP2.Riboseq

description: ribosome-protected fragments


title: siNC9.Riboseq

description: ribosome-protected fragments


title: siNC7.Riboseq

description: ribosome-protected fragments


title: siNC3.Riboseq

description: ribosome-protected fragments


title: siNC5.Riboseq

description: ribosome-protected fragments


title: siS15A_19_2.Riboseq

description: ribosome-protected fragments


title: siNC1.Riboseq

description: ribosome-protected fragments


title: siL36.Riboseq

description: ribosome-protected fragments


title: siL36A.Riboseq

description: ribosome-protected fragments


title: siL35A.Riboseq

description: ribosome-protected fragments


title: siNC_11_1.Riboseq

description: ribosome-protected fragments


title: siL39.Riboseq

description: ribosome-protected fragments


title: siNC_22.Riboseq

description: ribosome-protected fragments


title: siL37.Riboseq

description: ribosome-protected fragments


title: siNC_11_2.Riboseq

description: ribosome-protected fragments


title: siL41.Riboseq

description: ribosome-protected fragments


title: siNC_20_1.Riboseq

description: ribosome-protected fragments


title: siNC_21.Riboseq

description: ribosome-protected fragments


title: siL32.Riboseq

description: ribosome-protected fragments


title: siL34.Riboseq

description: ribosome-protected fragments


title: siL37A.Riboseq

description: ribosome-protected fragments


title: siL31.Riboseq

description: ribosome-protected fragments


title: siL30.Riboseq

description: ribosome-protected fragments


title: siS5.Riboseq

description: ribosome-protected fragments


title: siS3_1_1.Riboseq

description: ribosome-protected fragments


title: siL28.Riboseq

description: ribosome-protected fragments


title: siL29_10_2.Riboseq

description: ribosome-protected fragments


title: siL26.Riboseq

description: ribosome-protected fragments


title: siL29_10_1.Riboseq

description: ribosome-protected fragments


title: siL23.Riboseq

description: ribosome-protected fragments


title: siL24_9_2.Riboseq

description: ribosome-protected fragments


title: siL23A.Riboseq

description: ribosome-protected fragments


title: siL24_9_1.Riboseq

description: ribosome-protected fragments


title: siP0.Riboseq

description: ribosome-protected fragments


title: siL18A.Riboseq

description: ribosome-protected fragments


title: siL15_7_2.Riboseq

description: ribosome-protected fragments


title: siL38.Riboseq

description: ribosome-protected fragments


title: siL22.Riboseq

description: ribosome-protected fragments


title: siL21_8_1.Riboseq

description: ribosome-protected fragments


title: siL19.Riboseq

description: ribosome-protected fragments


title: siL12.Riboseq

description: ribosome-protected fragments


title: siL10.Riboseq

description: ribosome-protected fragments


title: siL7.Riboseq

description: ribosome-protected fragments


title: siL8.Riboseq

description: ribosome-protected fragments


title: siL17.Riboseq

description: ribosome-protected fragments


title: siL6.Riboseq

description: ribosome-protected fragments


title: siL14.Riboseq

description: ribosome-protected fragments


title: siL15_7_1.Riboseq

description: ribosome-protected fragments


title: siL13A.Riboseq

description: ribosome-protected fragments


title: siNC_20_2.Riboseq

description: ribosome-protected fragments


title: siL13.Riboseq

description: ribosome-protected fragments


title: siL35.Riboseq

description: ribosome-protected fragments


title: siL11.Riboseq

description: ribosome-protected fragments


title: siL10A.Riboseq

description: ribosome-protected fragments


title: siL9.Riboseq

description: ribosome-protected fragments


title: siL18.Riboseq

description: ribosome-protected fragments


title: siL7A.Riboseq

description: ribosome-protected fragments


title: siL4.Riboseq

description: ribosome-protected fragments


title: siL5.Riboseq

description: ribosome-protected fragments


title: siL3.Riboseq

description: ribosome-protected fragments


title: pancreatic cells for patch-seq [P2H9]

city: Gothenburg

first: Joan

last: Camunas-Soler

address: Medicinaregatan 9C

country: Sweden

institute: University of Gothenburg

data_processing:
Mapped to GRCh38 using STAR.
Gene counts using htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: pclamp_v2_counts.tab: Tab-delimited text file includes gene counts.

source_name: pancreatic islets

extract_protocol: SmartSeq2 (21X-23X PCR cycles).

tag: diagnosis

value: Nondiabetic

value: Pancreatic islets

value: Female

tag: patched

value: Yes


title: pancreatic cells for patch-seq [P2H8]


title: siL21_8_2.Riboseq

description: ribosome-protected fragments


title: pancreatic cells for patch-seq [P2H6]

value: Male


title: pancreatic cells for patch-seq [P2H7]


title: pancreatic cells for patch-seq [P2H4]


title: pancreatic cells for patch-seq [P2H3]


title: pancreatic cells for patch-seq [P2G8]


title: pancreatic cells for patch-seq [P2H5]


title: pancreatic cells for patch-seq [P2G9]


title: pancreatic cells for patch-seq [P2G3]


title: pancreatic cells for patch-seq [P2G11]


title: pancreatic cells for patch-seq [P2H2]


title: pancreatic cells for patch-seq [P2H11]


title: pancreatic cells for patch-seq [P2H10]


title: pancreatic cells for patch-seq [P2G5]


title: pancreatic cells for patch-seq [P2H1]


title: pancreatic cells for patch-seq [P2G10]


title: pancreatic cells for patch-seq [P2G1]


title: pancreatic cells for patch-seq [P2F9]


title: pancreatic cells for patch-seq [P2F8]


title: pancreatic cells for patch-seq [P2F6]


title: pancreatic cells for patch-seq [P2F5]


title: pancreatic cells for patch-seq [P2F3]


title: pancreatic cells for patch-seq [P2F4]


title: pancreatic cells for patch-seq [P2F12]


title: pancreatic cells for patch-seq [P2E9]


title: pancreatic cells for patch-seq [P2F1]


title: pancreatic cells for patch-seq [P2F2]


title: pancreatic cells for patch-seq [P2E6]


title: pancreatic cells for patch-seq [P2E3]


title: pancreatic cells for patch-seq [P2E4]


title: pancreatic cells for patch-seq [P2E5]


title: pancreatic cells for patch-seq [P2E7]


title: pancreatic cells for patch-seq [P2F11]


title: pancreatic cells for patch-seq [P2E12]


title: pancreatic cells for patch-seq [P2E11]


title: pancreatic cells for patch-seq [P2E10]


title: pancreatic cells for patch-seq [P2E2]


title: pancreatic cells for patch-seq [P2E1]


title: pancreatic cells for patch-seq [P2D8]


title: pancreatic cells for patch-seq [P2C9]


title: pancreatic cells for patch-seq [P2D1]


title: pancreatic cells for patch-seq [P2D4]


title: pancreatic cells for patch-seq [P2D3]


title: pancreatic cells for patch-seq [P2D12]


title: pancreatic cells for patch-seq [P2D10]


title: pancreatic cells for patch-seq [P2D5]


title: pancreatic cells for patch-seq [P2G12]


title: pancreatic cells for patch-seq [P2C8]


title: pancreatic cells for patch-seq [P2C7]


title: pancreatic cells for patch-seq [P2C5]


title: pancreatic cells for patch-seq [P2C6]


title: pancreatic cells for patch-seq [P2G2]


title: pancreatic cells for patch-seq [P2C4]


title: pancreatic cells for patch-seq [P2C2]


title: pancreatic cells for patch-seq [P2C3]


title: pancreatic cells for patch-seq [P2C12]


title: pancreatic cells for patch-seq [P2B8]


title: pancreatic cells for patch-seq [P2C1]


title: pancreatic cells for patch-seq [P2C11]


title: pancreatic cells for patch-seq [P2B9]


title: pancreatic cells for patch-seq [P2C10]


title: pancreatic cells for patch-seq [P2B7]


title: pancreatic cells for patch-seq [P2B2]


title: pancreatic cells for patch-seq [P2B6]


title: pancreatic cells for patch-seq [P2B3]


title: pancreatic cells for patch-seq [P2B5]


title: pancreatic cells for patch-seq [P2B12]


title: pancreatic cells for patch-seq [P2B11]


title: pancreatic cells for patch-seq [P2B10]


title: pancreatic cells for patch-seq [P2B1]


title: pancreatic cells for patch-seq [P2A4]


title: pancreatic cells for patch-seq [P2A6]


title: pancreatic cells for patch-seq [P2A7]


title: pancreatic cells for patch-seq [P2A3]


title: pancreatic cells for patch-seq [P2A11]


title: pancreatic cells for patch-seq [P2D6]


title: pancreatic cells for patch-seq [O2H9]


title: pancreatic cells for patch-seq [P2A1]


title: pancreatic cells for patch-seq [P2A10]


title: pancreatic cells for patch-seq [O2H8]


title: pancreatic cells for patch-seq [O2H7]


title: pancreatic cells for patch-seq [O2H5]


title: pancreatic cells for patch-seq [O2H4]


title: pancreatic cells for patch-seq [O2H3]


title: pancreatic cells for patch-seq [O2H1]


title: pancreatic cells for patch-seq [O2G9]


title: pancreatic cells for patch-seq [O2G8]


title: pancreatic cells for patch-seq [O2H2]


title: pancreatic cells for patch-seq [O2H10]


title: pancreatic cells for patch-seq [O2H12]


title: pancreatic cells for patch-seq [O2G4]


title: pancreatic cells for patch-seq [O2G5]


title: pancreatic cells for patch-seq [O2G3]


title: pancreatic cells for patch-seq [O2G12]


title: pancreatic cells for patch-seq [O2G11]


title: pancreatic cells for patch-seq [O2G10]


title: pancreatic cells for patch-seq [O2F8]


title: pancreatic cells for patch-seq [O2G1]


title: pancreatic cells for patch-seq [O2F6]


title: pancreatic cells for patch-seq [O2F5]


title: pancreatic cells for patch-seq [O2F4]


title: pancreatic cells for patch-seq [O2F7]


title: pancreatic cells for patch-seq [O2F3]


title: pancreatic cells for patch-seq [P2A9]


title: pancreatic cells for patch-seq [P2A5]


title: pancreatic cells for patch-seq [P2A2]


title: pancreatic cells for patch-seq [O2F2]


title: pancreatic cells for patch-seq [O2F11]


title: pancreatic cells for patch-seq [O2F10]


title: pancreatic cells for patch-seq [O2F1]


title: pancreatic cells for patch-seq [O2E9]


title: pancreatic cells for patch-seq [O2H6]


title: pancreatic cells for patch-seq [O2E6]


title: pancreatic cells for patch-seq [O2E7]


title: pancreatic cells for patch-seq [O2E3]


title: pancreatic cells for patch-seq [O2E5]


title: pancreatic cells for patch-seq [O2E12]


title: pancreatic cells for patch-seq [O2E11]


title: pancreatic cells for patch-seq [O2E2]


title: pancreatic cells for patch-seq [O2E10]


title: pancreatic cells for patch-seq [O2E1]


title: pancreatic cells for patch-seq [O2D8]


title: pancreatic cells for patch-seq [O2D7]


title: pancreatic cells for patch-seq [O2D5]


title: pancreatic cells for patch-seq [O2D9]


title: pancreatic cells for patch-seq [O2D4]


title: pancreatic cells for patch-seq [O2D3]


title: pancreatic cells for patch-seq [O2D12]


title: pancreatic cells for patch-seq [O2D11]


title: pancreatic cells for patch-seq [O2D2]


title: pancreatic cells for patch-seq [O2G7]


title: pancreatic cells for patch-seq [O2D1]


title: pancreatic cells for patch-seq [O2C8]


title: pancreatic cells for patch-seq [O2F9]


title: pancreatic cells for patch-seq [O2C7]


title: pancreatic cells for patch-seq [O2C5]


title: pancreatic cells for patch-seq [O2C3]


title: pancreatic cells for patch-seq [O2C4]


title: pancreatic cells for patch-seq [O2C2]


title: pancreatic cells for patch-seq [O2C12]


title: pancreatic cells for patch-seq [O2C1]


title: pancreatic cells for patch-seq [O2B7]


title: pancreatic cells for patch-seq [O2C11]


title: pancreatic cells for patch-seq [O2B8]


title: pancreatic cells for patch-seq [O2B5]


title: pancreatic cells for patch-seq [O2B12]


title: pancreatic cells for patch-seq [O2A9]


title: pancreatic cells for patch-seq [O2B1]


title: pancreatic cells for patch-seq [O2A8]


title: pancreatic cells for patch-seq [O2E4]


title: pancreatic cells for patch-seq [O2A7]


title: pancreatic cells for patch-seq [O2A6]


title: pancreatic cells for patch-seq [O2A5]


title: pancreatic cells for patch-seq [O2A4]


title: pancreatic cells for patch-seq [O2A3]


title: pancreatic cells for patch-seq [O2A2]


title: pancreatic cells for patch-seq [O2A10]


title: pancreatic cells for patch-seq [O2A11]


title: pancreatic cells for patch-seq [O2A1]


title: pancreatic cells for patch-seq [O2D10]


title: pancreatic cells for patch-seq [N2H8]


title: pancreatic cells for patch-seq [N2H6]


title: pancreatic cells for patch-seq [N2H4]


title: pancreatic cells for patch-seq [N2H5]


title: pancreatic cells for patch-seq [N2H11]


title: pancreatic cells for patch-seq [N2H1]


title: pancreatic cells for patch-seq [N2H2]


title: pancreatic cells for patch-seq [N2H7]


title: pancreatic cells for patch-seq [N2H10]


title: pancreatic cells for patch-seq [N2G9]


title: pancreatic cells for patch-seq [N2G8]


title: pancreatic cells for patch-seq [O2B9]


title: pancreatic cells for patch-seq [N2G5]


title: pancreatic cells for patch-seq [N2G7]


title: pancreatic cells for patch-seq [N2G6]


title: pancreatic cells for patch-seq [O2B6]


title: pancreatic cells for patch-seq [N2G4]


title: pancreatic cells for patch-seq [N2G2]


title: pancreatic cells for patch-seq [N2G12]


title: pancreatic cells for patch-seq [N2G11]


title: pancreatic cells for patch-seq [N2G3]


title: pancreatic cells for patch-seq [N2F8]


title: pancreatic cells for patch-seq [O2B10]


title: pancreatic cells for patch-seq [O2B4]


title: pancreatic cells for patch-seq [N2G1]


title: pancreatic cells for patch-seq [N2F6]


title: pancreatic cells for patch-seq [N2F9]


title: pancreatic cells for patch-seq [N2F3]


title: pancreatic cells for patch-seq [N2F2]


title: pancreatic cells for patch-seq [N2F10]


title: pancreatic cells for patch-seq [N2H9]


title: pancreatic cells for patch-seq [N2E9]


title: pancreatic cells for patch-seq [N2E5]


title: pancreatic cells for patch-seq [N2E4]


title: pancreatic cells for patch-seq [N2E3]


title: pancreatic cells for patch-seq [N2E2]


title: pancreatic cells for patch-seq [N2E10]


title: pancreatic cells for patch-seq [N2E11]


title: pancreatic cells for patch-seq [N2E1]


title: pancreatic cells for patch-seq [N2D9]


title: pancreatic cells for patch-seq [N2D8]


title: pancreatic cells for patch-seq [N2D7]


title: pancreatic cells for patch-seq [N2D4]


title: pancreatic cells for patch-seq [N2D5]


title: pancreatic cells for patch-seq [N2D3]


title: pancreatic cells for patch-seq [N2D12]


title: pancreatic cells for patch-seq [N2D2]


title: pancreatic cells for patch-seq [N2D11]


title: pancreatic cells for patch-seq [N2C9]


title: pancreatic cells for patch-seq [N2C8]


title: pancreatic cells for patch-seq [N2D10]


title: pancreatic cells for patch-seq [N2C6]


title: pancreatic cells for patch-seq [N2G10]


title: pancreatic cells for patch-seq [N2C5]


title: pancreatic cells for patch-seq [N2D1]


title: pancreatic cells for patch-seq [N2C4]


title: pancreatic cells for patch-seq [N2C2]


title: pancreatic cells for patch-seq [N2C12]


title: pancreatic cells for patch-seq [N2C1]


title: pancreatic cells for patch-seq [N2C10]


title: pancreatic cells for patch-seq [N2B9]


title: pancreatic cells for patch-seq [N2F12]


title: pancreatic cells for patch-seq [N2B7]


title: pancreatic cells for patch-seq [N2B8]


title: pancreatic cells for patch-seq [N2B4]


title: pancreatic cells for patch-seq [N2E7]


title: pancreatic cells for patch-seq [N2B5]


title: pancreatic cells for patch-seq [N2E6]


title: pancreatic cells for patch-seq [N2B3]


title: pancreatic cells for patch-seq [N2B11]


title: pancreatic cells for patch-seq [N2B6]


title: pancreatic cells for patch-seq [N2B10]


title: pancreatic cells for patch-seq [N2A8]


title: pancreatic cells for patch-seq [N2B2]


title: pancreatic cells for patch-seq [N2E12]


title: pancreatic cells for patch-seq [N2B12]


title: pancreatic cells for patch-seq [N2B1]


title: pancreatic cells for patch-seq [N2A9]


title: pancreatic cells for patch-seq [N2A7]


title: pancreatic cells for patch-seq [N2A6]


title: pancreatic cells for patch-seq [N2A5]


title: pancreatic cells for patch-seq [N2A4]


title: pancreatic cells for patch-seq [N2A2]


title: pancreatic cells for patch-seq [N2A10]


title: pancreatic cells for patch-seq [N2A11]


title: pancreatic cells for patch-seq [N2A12]


title: pancreatic cells for patch-seq [M2H9]


title: pancreatic cells for patch-seq [M2H8]


title: pancreatic cells for patch-seq [M2H7]


title: pancreatic cells for patch-seq [N2C11]


title: pancreatic cells for patch-seq [M2H6]


title: pancreatic cells for patch-seq [M2H5]


title: pancreatic cells for patch-seq [M2H10]


title: pancreatic cells for patch-seq [M2G9]


title: pancreatic cells for patch-seq [M2H1]


title: pancreatic cells for patch-seq [M2H3]


title: pancreatic cells for patch-seq [M2G8]


title: pancreatic cells for patch-seq [M2G7]


title: pancreatic cells for patch-seq [M2G10]


title: pancreatic cells for patch-seq [M2G12]


title: pancreatic cells for patch-seq [M2G6]


title: pancreatic cells for patch-seq [M2G5]


title: pancreatic cells for patch-seq [M2G2]


title: pancreatic cells for patch-seq [M2G4]


title: pancreatic cells for patch-seq [M2G11]


title: pancreatic cells for patch-seq [M2F9]


title: pancreatic cells for patch-seq [M2F5]


title: pancreatic cells for patch-seq [M2F8]


title: pancreatic cells for patch-seq [M2F7]


title: pancreatic cells for patch-seq [M2G1]


title: pancreatic cells for patch-seq [N2A3]


title: pancreatic cells for patch-seq [M2F3]


title: pancreatic cells for patch-seq [M2F2]


title: pancreatic cells for patch-seq [M2F12]


title: pancreatic cells for patch-seq [M2F10]


title: pancreatic cells for patch-seq [M2F1]


title: pancreatic cells for patch-seq [M2E9]


title: pancreatic cells for patch-seq [M2E7]


title: pancreatic cells for patch-seq [M2E5]


title: pancreatic cells for patch-seq [M2E6]


title: pancreatic cells for patch-seq [M2E4]


title: pancreatic cells for patch-seq [N2A1]


title: pancreatic cells for patch-seq [M2E3]


title: pancreatic cells for patch-seq [M2E10]


title: pancreatic cells for patch-seq [M2D9]


title: pancreatic cells for patch-seq [M2E11]


title: pancreatic cells for patch-seq [M2D8]


title: pancreatic cells for patch-seq [M2D6]


title: pancreatic cells for patch-seq [M2D5]


title: pancreatic cells for patch-seq [M2D4]


title: pancreatic cells for patch-seq [M2D3]


title: pancreatic cells for patch-seq [M2D2]


title: pancreatic cells for patch-seq [M2D12]


title: pancreatic cells for patch-seq [M2D11]


title: pancreatic cells for patch-seq [M2G3]


title: pancreatic cells for patch-seq [M2D10]


title: pancreatic cells for patch-seq [M2C9]


title: pancreatic cells for patch-seq [M2D1]


title: pancreatic cells for patch-seq [M2C7]


title: pancreatic cells for patch-seq [M2F4]


title: pancreatic cells for patch-seq [M2C6]


title: pancreatic cells for patch-seq [M2C4]


title: pancreatic cells for patch-seq [M2F11]


title: pancreatic cells for patch-seq [M2C12]


title: pancreatic cells for patch-seq [M2C2]


title: Day 15-2

city: Newark

first: Jason

last: Weinstein

state: NJ

address: New Jersey Medical School Cancer Center 205 South Orange Ave

department: Center for Immunity and Inflmmation

institute: Rutgers New Jersey Medical School

description:
D15-2
Temporal Tbet B cells processed data.csv

data_processing:
Base calling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and Alignment (Cutadapt v2.5, STAR vSTAR_2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Genome_build: Genome_build: GRCm38
Supplementary_files_format_and_content: Comma delimited file (csv) for differential gene expression counts via DESeq2.

source_name: Spleen

extract_protocol:
RNA was extracted using the RNAeasy plus mini kit (Qiagen)
Paired end strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols at Genewiz.

tag: infected with

value: LCMV Armsttrong

tag: timepoint

value: Day 15 post LCMV infection


title: pancreatic cells for patch-seq [M2C3]


title: Day 15-3

description:
D15-3
Temporal Tbet B cells processed data.csv

tag: strain


title: pancreatic cells for patch-seq [M2C11]

tag: tissue


title: Day 15-1

description:
D15-1
Temporal Tbet B cells processed data.csv


title: Day 10-2

description:
D10-2
Temporal Tbet B cells processed data.csv

value: Day 10 post LCMV infection


title: pancreatic cells for patch-seq [M2C1]


title: Day 10-1

description:
D10-1
Temporal Tbet B cells processed data.csv


title: pancreatic cells for patch-seq [M2E8]


title: pancreatic cells for patch-seq [M2B9]


title: pancreatic cells for patch-seq [M2B8]


title: pancreatic cells for patch-seq [M2E12]


title: Day 10-3

description:
D10-3
Temporal Tbet B cells processed data.csv


title: Day 8-3

description:
D8-3
Temporal Tbet B cells processed data.csv

value: Day 8 post LCMV infection


title: pancreatic cells for patch-seq [M2B7]


title: pancreatic cells for patch-seq [M2B6]


title: Day 8-2

description:
D8-2
Temporal Tbet B cells processed data.csv


title: Day 8-1

description:
D8-1
Temporal Tbet B cells processed data.csv


title: pancreatic cells for patch-seq [M2E1]


title: pancreatic cells for patch-seq [M2B5]


title: pancreatic cells for patch-seq [M2B4]


title: pancreatic cells for patch-seq [M2B3]


title: GR_KO_5

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Paired-end reads were mapped to the mouse genome assembly mm10 using HISAT2 software (v 2.1.0) (Kim et al., 2019a)
Quantification of the number of mapped reads of each gene was performed using iRNA-seq (v 1.1) specifying the "-count gene" option (Madsen et al., 2015)
Differential expression was determined using DESeq2 (v 1.24.0) (Love et al., 2014)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing unnormalized counts (output from iRNA-seq)
Supplementary_files_format_and_content: Tab-delimited text with log2FC and differential gene expression analyses (output from DESeq2)

source_name: Liver

extract_protocol:
Liver tissue were homogenized directly in Trizol using a Tissuelyzer II (Qiagen) and RNA purification was performed using EconoSpin columns (Epoch).
A total amount of 800ng of total RNA was used and sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
Prepared PCR products were purified and size-selected on AMPure XP beads (Beckman A63881), and library quality was assessed on the Agilent Bioanalyzer 2100 system. The prepared libraries were sequenced (paired-end) on a Illumina platform.

value: Liver

tag: genotype

value: GRMAC

tag: treatment


title: GR_KO_4


title: pancreatic cells for patch-seq [M2B2]


title: GR_KO_2


title: pancreatic cells for patch-seq [M2C8]


title: pancreatic cells for patch-seq [M2B12]


title: pancreatic cells for patch-seq [M2B11]


title: GR_KO_3


title: GR_WT_5

value: GRflox


title: pancreatic cells for patch-seq [M2B10]


title: GR_WT_4


title: GR_WT_2


title: GR_WT_3


title: pancreatic cells for patch-seq [M2A8]


title: GR_WT_1


title: MUC6724_Input_P8_24h_ad_24h_Ad_MAC_WL

description: Whole liver nuclei from MAC-INTACT mice

data_processing:
The STAR aligner (v 2.4.2a) (Dobin et al., 2013) with modified parameter settings (--twopassMode=Basic) was used for split-read alignment against the mouse genome assembly mm10 and UCSC knownGene annotation.
Quantification of the number of mapped reads of each gene was performed using iRNA-seq (v 1.1) specifying the "-count gene" option (Madsen et al., 2015)
Differential expression was determined using DESeq2 (v 1.24.0) (Love et al., 2014)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing unnormalized counts (output from iRNA-seq)
Supplementary_files_format_and_content: Tab-delimited text with log2FC and differential gene expression analyses (output from DESeq2)

source_name: Whole Liver Nuclei, pool of 4 mice

extract_protocol:
Whole liver nuclei as well as bead-bound and supernatant nuclei prepared from INTACT mice were directly resuspended in Trizol. RNA purification was performed using EconoSpin columns (Epoch) with on-column DNase digestion (Qiagen).
Total RNA (50-100ng) was prepared for sequencing using VAHTS Stranded mRNA-seq Library Kit for Illumina (Vazyme NR602) following manufacturer’s recommendations, except that no selection for poly-adenylated RNA was used.
Prepared PCR products were purified and size-selected on AMPure XP beads (Beckman A63881), and library quality was assessed on the Agilent Bioanalyzer 2100 system. RNA libraries were sequenced as 50 bp paired-end runs on a HiSeq 4000 platform (Illumina, San Diego, USA).

value: Whole Liver Nuclei, pool of 4 mice

tag: feeding state


title: pancreatic cells for patch-seq [M2A7]


title: MUC6723_Input_P7_24h_fast_24h_fast_MAC_WL

description: Whole liver nuclei from MAC-INTACT mice


title: MUC6722_Input_P6_16h_ad_16h_Ad_MAC_WL

description: Whole liver nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [M2A5]


title: pancreatic cells for patch-seq [M2A6]


title: pancreatic cells for patch-seq [M2A2]


title: pancreatic cells for patch-seq [M2A4]


title: MUC6721_Input_P5_16h_fast_16h_fast_MAC_WL

description: Whole liver nuclei from MAC-INTACT mice


title: MUC6720_Input_P4_8h_ad_8h_Ad_MAC_WL

description: Whole liver nuclei from MAC-INTACT mice


title: MUC6719_Input_P3_8h_fast_8h_fast_MAC_WL

description: Whole liver nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [M2A3]


title: pancreatic cells for patch-seq [M2A12]


title: pancreatic cells for patch-seq [M2A11]


title: MUC6718_Input_P2_3h_ad_3h_Ad_MAC_WL

description: Whole liver nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [M2A10]


title: MUC6716_11593_24h_Ad_24h_Ad_MAC

description: IP'ed nuclei from MAC-INTACT mice

source_name: Macrophage Nuclei

value: Macrophage Nuclei


title: MUC6717_Input_P1_3h_fast_3h_fast_MAC_WL

description: Whole liver nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [M2A1]


title: pancreatic cells for patch-seq [L2H9]


title: S449_11_386f_WT_3

city: Freiburg

first: Gianni

last: Monaco

address: Breisacher Straße

country: Germany

institute: Freiburg Medical Center

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.9.2. The resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software.
The RNA-seq data was aligned with STAR v2.7.8a to the mouse reference genome Gencode M26. Counts were obtained using FeatureCounts v2.0.2.
Genome_build: Gencode M26
Supplementary_files_format_and_content: Counts

source_name: CAMs

growth_protocol: SPF breeding facility

extract_protocol:
Cells were sorted into RNAprotect Cell Reagend (QIAGEN) according to the manufacturers recommendations. RNA was extracted using Picopure RNA extraction kit (Life Technologies) according to manufacturer’s protocol. The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 500 pg total-RNA.
Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA)

tag: strain background

value: wild type

tag: age

value: 6-8 weeks

tag: batch

value: CNS-associated macrophages (CAMs)


title: MUC6715_11718_24h_fast_24h_fast_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [L2H7]

value: Nondiabetic

tag: Sex


title: MUC6713_11658_16h_fast_16h_fast_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: S449_09_379m_WT_1


title: MUC6712_11585_8h_Ad_8h_Ad_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [L2H8]

value: Pancreatic islets


title: MUC6714_11574_16h_Ad_16h_Ad_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [L2H2]


title: pancreatic cells for patch-seq [M2B1]


title: MUC6710_11591_3h_Ad_3h_Ad_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [L2H5]

value: Female


title: pancreatic cells for patch-seq [L2H11]

value: Yes


title: pancreatic cells for patch-seq [L2H10]

value: Male


title: pancreatic cells for patch-seq [L2H3]


title: S449_10_381m_WT_2


title: GR_KO_1


title: MUC6711_11762_8h_fast_8h_fast_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: S449_08_385f_Cre-pos_4


title: pancreatic cells for patch-seq [L2H12]


title: MUC6709_11768_3h_fast_3h_fast_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: S449_06_383m_Cre-pos_2


title: S449_04_395f_Cre-Cre_4


title: pancreatic cells for patch-seq [L2G8]


title: pancreatic cells for patch-seq [L2G7]


title: S449_05_380m_Cre-pos_1


title: pancreatic cells for patch-seq [L2G9]


title: MUC6708_11592_24h_Ad_24h_Ad_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: S449_03_394f_Cre-Cre_3


title: S449_02_391m_Cre-Cre_2


title: pancreatic cells for patch-seq [L2G6]


title: pancreatic cells for patch-seq [L2G5]


title: pancreatic cells for patch-seq [L2G4]


title: MUC6707_11719_24h_fast_24h_fast_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: S449_01_382m_Cre-Cre_1


title: MUC6705_11724_16h_fast_16h_fast_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [L2G12]


title: MUC6704_11584_8h_Ad_8h_Ad_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: Ga(NO3 )3-treated  rep2 [SY2]

city: wenzhou

first: Changrui

last: Qian

state: zhejiang

address: wenzhou medical university

institute: wenzhou medical university

data_processing:
The RNA-seq data of 6 samples was filtered with SOAP nuke (v1.5.2).
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean  reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12).
differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Genome_build: BM2333

organism: Acinetobacter baumannii

source_name: Bacterial cells

growth_protocol: A. baumannii BM-2333 cultured in M9CA medium with and without Ga(NO3)3 were defined as the experimental group and the control group, respectively. Logarithmic phase cultures were cultured at 37℃ with constant shaking (200 rpm) for 6 h

extract_protocol:
Bacterial cells were pelleted and flash frozen on dry ice. Pellets were shipped to Genewiz for RNA extraction, Illumina Ribo-Zero rRNA removal, Illumina library construction, and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ga(NO3)3 (8 × MIC, 512 μg/mL) and sterile water was added to the medium of the experimental group and the control group, respectively. The cells of BM-2333 were harvested 6 h later and prepared for RNA-seq.

value: Ga(NO3 )3-treated


title: pancreatic cells for patch-seq [L2F8]


title: pancreatic cells for patch-seq [L2F7]


title: pancreatic cells for patch-seq [L2F6]


title: MUC6701_11586_3h_fast_3h_fast_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [L2G3]


title: pancreatic cells for patch-seq [L2G2]


title: control rep2 [C2]

value: control


title: pancreatic cells for patch-seq [L2F3]


title: Ga(NO3 )3-treated  rep3 [SY3]


title: pancreatic cells for patch-seq [L2F2]


title: pancreatic cells for patch-seq [L2G1]


title: pancreatic cells for patch-seq [L2H6]


title: MUC6698_11659_16h_Ad_16h_Ad_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: MUC6703_11589_8h_fast_8h_fast_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [L2F9]


title: MUC6697_11737_16h_fast_16h_fast_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: Ga(NO3 )3-treated  rep1 [SY1]


title: pancreatic cells for patch-seq [L2E9]


title: control rep3 [C3]


title: pancreatic cells for patch-seq [L2F5]


title: pancreatic cells for patch-seq [L2E8]


title: PVN P80 1

city: Atlanta

first: Kim

last: Huhman

state: Georgia

department: Neuroscience Institute

institute: Georgia State University

data_processing:
Data was processed using the standard Illumina processing pipeline to segregate each multiplexed samples’ reads. The resulting data files were in fastq format.
FASTQ quality filter  was used to filter low quality sequences (base quality score less than 30) leaving only sequences with high quality scores.
High quality reads were then aligned to mm10 mus musculus reference genome using Bowtie2 to identify gene sequences
Gene expression levels were measured using Cufflinks and differential expression was measured using Cuffdiff
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) expression scores were obtained for each gene. Log2fold differential expression scores for each gene are calculated by dividing the average FPKM score for each experimental group by the average FPKM score for the water control group and converting the fold change to a logarithmic 2 scale after which a p-value was calculated. P-score values were FDR adjusted  (q-value) using the Benjamini-Hochberg correction
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited cuffdiff text files include the following columns: test_id, gene_id gene, locus, sample_1, sample_2, status, value_1, value_2, log2(fold_change), test_stat, p_value, q_value, significant

source_name: PVN

extract_protocol:
Brains were removed and flash frozen on dry ice. A 1mm tissue punch was used to isolate Amygdala and PVN regions. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep v2 Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Subjects consumed drinking water containing either 1% sodium carboxymethylcellulose (CMC), 1% polysorbate-80 (P80) or water without emulsifier for 12 weeks

value: Brain- PVN

value: 20 weeks


title: MUC6696_11576_8h_Ad_8h_Ad_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [L2E7]


title: PVN CMC 1

value: CMC


title: PVN Water 2

value: Water


title: MUC6699_11578_24h_fast_24h_fast_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [L2E5]


title: control rep1 [C1]


title: PVN Water 1


title: PVN P80 2


title: pancreatic cells for patch-seq [L2E2]


title: MUC6693_11579_3h_fast_3h_fast_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: MUC6700_11731_24h_Ad_24h_Ad_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [L2F1]


title: pancreatic cells for patch-seq [L2F10]


title: pancreatic cells for patch-seq [L2E12]


title: MUC6706_11575_16h_Ad_16h_Ad_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [L2E6]


title: Amygdala P80 2

source_name: Amygdala

value: Brain- Amygdala


title: MUC6695_11740_8h_fast_8h_fast_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [L2E4]


title: MUC6702_11590_3h_Ad_3h_Ad_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: MUC6692_11730_24h_Ad_24h_Ad_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [L2D9]


title: pancreatic cells for patch-seq [L2D8]


title: MUC6690_11739_16h_Ad_16h_Ad_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [L2E3]


title: Amygdala CMC 1


title: pancreatic cells for patch-seq [L2F11]


title: pancreatic cells for patch-seq [L2E11]


title: Amygdala P80 1


title: pancreatic cells for patch-seq [L2D6]


title: pancreatic cells for patch-seq [L2E10]


title: Amygdala Water 2


title: pancreatic cells for patch-seq [L2D4]


title: pancreatic cells for patch-seq [L2E1]


title: MUC6691_11577_24h_fast_24h_fast_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: MUC6688_11594_8h_Ad_8h_Ad_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: PVN CMC 2


title: Amygdala CMC 2


title: pancreatic cells for patch-seq [L2D5]


title: MUC6689_11716_16h_fast_16h_fast_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: MUC6694_11735_3h_Ad_3h_Ad_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [L2D12]


title: pancreatic cells for patch-seq [L2D10]


title: B_igg_kid

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Quality controls using FastQC (v0.11.2) were generated and raw sequencing reads were then aligned to the mouse mm10 genome using default settings of Bowtie (v2.2.0).
Peak-calling was performed using MACS (v2.1.1) (Zhang et al., 2008) with various P-value cutoffs. The peak bed files were generated from peak calling against genomic input control or IgG control with the default setting (10-5 cutoff).
The common peaks from these two bed files were used for subsequent analyses. The overlapping peaks of bed files were identified using the bedtools from Galaxy (https://usegalaxy.org/) (Afgan et al., 2018).
Genome_build: mm10
Supplementary_files_format_and_content: bed

source_name: Kidney

extract_protocol:
Kidneys from E13.5-14.0 Eya1Six1 embryos were collected for ChIP-seq assay. ChIP-seq was performed according to previous protocols with some modifications (Li et al., 2020, Xu et al., 2021). Briefly, the kidneys were cross-linked, homogenized and lysed and chromatin was sonicated as described (Li et al., 2021). Sonicated chromatin was cleared by pelleting insoluble material at 13,000 RPM at 4°C, followed by preclear with protein A/G beads and incubation with 1~2 mg anti-Six1 overnight or 1~2 mg rabbit IgG as a negative control.
The pulldown and input control sequencing libraries were generated using the ThruPLEX DNA-seq Kit (R400429, Rubicon Genomics) and sequenced on Illumina NextSeq 500.

value: mixed; C57BL/6 and 129SV

value: Kidney

tag: chip antibody

value: rabbit IgG


title: MUC6687_11741_8h_fast_8h_fast_MAC

description: IP'ed nuclei from MAC-INTACT mice

value: Macrophage Nuclei


title: Amygdala Water 1

value: wild type


title: MUC6498_P8_24h_ad_24h_Ad_HEP_WL

description: Whole liver nuclei from HEP-INTACT mice

value: Whole Liver Nuclei, pool of 4 mice


title: pancreatic cells for patch-seq [L2D11]

value: Pancreatic islets


title: MUC6686_11734_3h_Ad_3h_Ad_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: 7_Six1_Eya1-Six1/+_kidneys_S4_C

value: anti-Six1 (Cell Signaling Technology #12891)


title: pancreatic cells for patch-seq [L2D1]

value: Nondiabetic

value: Yes


title: pancreatic cells for patch-seq [L2C7]

value: Female


title: pancreatic cells for patch-seq [L2C6]


title: pancreatic cells for patch-seq [L2C5]


title: MUC6497_P7_24h_fast_24h_fast_HEP_WL

description: Whole liver nuclei from HEP-INTACT mice


title: S363_03_Graft-3

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v2.4.11. The resulting .bcl files were converted into .fastq files with the bcl2fastq v2.18 software.
FastQ files were aligned to the mouse genome (Gencode M21 genome version and transcriptome annotation) using the STAR aligner (Version 2.7.2a) with command line: STAR   --runThreadN xx   --genomeDir /gencode_M21_075bp   --genomeLoad LoadAndKeep   --readFilesIn xyz      --readFilesCommand zcat      --limitBAMsortRAM 20000000000   --outFileNamePrefix xyz   --outSAMtype BAM   SortedByCoordinate      --outSAMstrandField intronMotif   --outBAMcompression 10   --outFilterIntronMotifs RemoveNoncanonical   --seedSearchStartLmax 30   --quantMode GeneCounts
Aligned BAM files were further processed using featureCounts (Version 1.6.2) with command line: featureCounts -a ./gencode.vM21.annotation.gtf -G ./GRCm38.p6.genome.fa -o counts.txt -F GTF -g gene_name -t exon -T N --largestOverlap xyz.bam
Genome_build: GRCm38 / Gencode M21
Supplementary_files_format_and_content: counts.txt - tab delimited text file with gene counts as output by featureCounts

source_name: cortex

growth_protocol: Grafts were isolated from the cortex of 5xFAD mice four weeks p.i. Briefly, mice were overdosed through i.p. injection of ketamine and xylazine and transcardially perfused with 10 ml ice-cold PBS. Brains were immediately isolated and divided coronally at the injection site. The cortical grafts were identified under a stereo-microscope and carefully isolated with a small scalpel; as control, small cortical pieces near the transplant were also isolated. The cortical samples were collected in FACS medium and maintained on ice until further use.  CD11b+CD45low microglia were directly FACS-sorted into cell lysis buffer with MoFlo Astrios (Beckman Coulter).

extract_protocol:
Total RNA extraction using ARCTURUS® PicoPure® RNA Isolation Kit (ThermoFisher, cat. no. KIT0204) was performed according to the manufacturer`s protocol.
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 300 pg total-RNA. Double stranded cDNA was amplified by LD PCR (13 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA Library Quantification Kit - Illumina/ABI Prism User Guide (Roche Sequencing Solutions, Inc., Pleasanton, CA, USA). Equimolar amounts of each library were sequenced on a NextSeq 500 instrument controlled by the NextSeq Control Software (NCS) v2.2.0, using two 75 Cycles High Output Kits with the dual index, single-read (SR) run parameters.

value: primary microglia


title: MUC6496_P6_16h_ad_16h_Ad_HEP_WL

description: Whole liver nuclei from HEP-INTACT mice


title: S363_01_Graft-1


title: S363_02_Graft-2


title: pancreatic cells for patch-seq [L2C2]

value: Male


title: MUC6495_P5_16h_fast_16h_fast_HEP_WL

description: Whole liver nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [L2D7]


title: pancreatic cells for patch-seq [L2C11]


title: MUC6494_P4_8h_ad_8h_Ad_HEP_WL

description: Whole liver nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [L2C10]


title: pancreatic cells for patch-seq [L2C1]


title: MUC6493_P3_8h_fast_8h_fast_HEP_WL

description: Whole liver nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [L2B9]


title: S363_05_Control-2


title: pancreatic cells for patch-seq [L2D3]


title: pancreatic cells for patch-seq [L2B8]


title: pancreatic cells for patch-seq [L2B7]


title: S363_04_Control-1


title: MUC6492_P2_3h_ad_3h_Ad_HEP_WL

description: Whole liver nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [L2B5]


title: MUC6491_P1_3h_fast_3h_fast_HEP_WL

description: Whole liver nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [L2B4]


title: HSC_shRNA_M3-14-KO.rep1

city: Chicago

first: Yong

last: Peng

state: IL

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

description:
Ribo-minus RNA
METTL3_METTL14 knockout

data_processing:
Basecalls performed using CASAVA version 1.4.
Adapters of all raw RNA-seq data sets  were clipped away by Cutadapt v1.15.
All reads from pre-processed RNA-seq data sets were mapped to the human genome (hg38) and the GENCODE v27 gene annotation using STAR v2.5.3a with default parameters.
Gene expression level (TPM) were calculated by Kallisto v0.46.1.
Genome_build: Human hg38
Supplementary_files_format_and_content: BAM

source_name: human CD34+ hematopoietic stem/progenitor cells

growth_protocol: Human CD34+ hematopoietic stem/progenitor cells (HSPCs) were isolated from umbilical cord blood (UBC) samples.

extract_protocol:
Isolated RNAs after ribosomal RNA depletion.
Libraries were made with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: shRNA knockout of METTL3 and METTL14.

value: HPSC

value: METTL3_METTL14 knockout


title: HSC_shRNA_M3-14-KO.rep2

description:
Ribo-minus RNA
METTL3_METTL14 knockout


title: pancreatic cells for patch-seq [L2B2]


title: MUC6685_11717_3h_fast_3h_fast_MAC

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [L2B12]


title: pancreatic cells for patch-seq [L2B10]


title: MUC6490_9899_24h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice

source_name: Hepatocyte Nuclei

value: Hepatocyte Nuclei


title: MUC6489_10097_24h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: HSC_shRNA_control.rep2

description:
Ribo-minus RNA
Control

value: Control


title: pancreatic cells for patch-seq [L2B1]


title: pancreatic cells for patch-seq [L2B11]


title: pancreatic cells for patch-seq [L2A9]


title: pancreatic cells for patch-seq [L2A8]


title: MUC6486_9856_8h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [L2C4]


title: HSC_shRNA_control.rep1

description:
Ribo-minus RNA
Control


title: MUC6487_9642_16h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: PDR-FM-4

city: Nanjing

first: Songtao

last: Yuan

address: 300 Guangzhou Road

institute: First Affiliated Hospital of Nanjing Medical University

data_processing:
Novaseq 6000 software used for basecalling.
After removing R1 reads without poly-T tails, the cell barcodes and unique molecular identifiers (UMIs) were extracted. Meanwhile, the R2 reads were mapped to reference genome hg38 (STAR v2.5.4a and featureCounts 1.6.2) using Star (version 2.5.2b) reference.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cells

source_name: Fibrous membrane

extract_protocol:
FMs were cut by the vitrectomy cutter at 5000 cpm and the pellets were aspirated through the cutter tub into syringe. FMs were digested with collagenase type IV, followed by TrypLE™ Express Enzyme.
The single-cell suspensions (1×105 cells/mL in PBS) were loaded onto microfluidic devices and scRNA-Seq libraries were constructed according to the Singleron GEXSCOPE protocol with GEXSCOPE Single-Cell RNA Library Kit (Singleron Biotechnologies, Jiangsu, China) (Dura B. et al.Nucleic acids research 2019). The individual library of each sample was diluted to 4 nM and pooled for sequencing on Illumina HiSeq X Ten platform.

value: Fibrous membrane

tag: disease state

value: Proliferative diabetic retinopathy


title: pancreatic cells for patch-seq [L2A7]


title: S363_07_Control-4

tag: cell type


title: pancreatic cells for patch-seq [L2A5]


title: PDR-FM-5


title: MUC6488_9858_16h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [L2A3]


title: NC9_RNAseq

data_processing:
Base calling in bcl files were demultiplexed and converted into fastq files by Bcl2fastq (v2.20.0.422). Adapters and low-quality reads ending with quality scores < 20 were trimmed by Cutadapt (v1.8.1). Trimmed reads with length < 20nt were discarded. Reads aligned to human rRNA and tRNA sequences were further excluded. For Ribo-seq libraries, trimmed reads with length <26nt or >34nt were excluded. Remaining reads were aligned to the human genome (Ensembl GRCh38.88) by STAR (v2.6.1-d).
Genome_build: Ensembl GRCh38.88
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for each Sample

tag: cell line


title: MUC6485_10098_8h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: MUC6483_9864_3h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [L2A4]

tag: diagnosis


title: S363_06_Control-3


title: MUC6484_9639_3h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [L2A2]

tag: patched


title: NC7_RNAseq


title: pancreatic cells for patch-seq [L2A12]


title: MUC6482_9902_24h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [L2A11]


title: pancreatic cells for patch-seq [L2B3]


title: pancreatic cells for patch-seq [L2A10]


title: pancreatic cells for patch-seq [L2A1]


title: MUC6481_10095_24h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [J2H9]


title: NC3_RNAseq


title: MUC6480_9850_16h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [J2H8]


title: pancreatic cells for patch-seq [J2H6]


title: NC1_RNAseq


title: MUC6479_9641_16h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [J2H5]


title: pancreatic cells for patch-seq [J2H3]


title: NC_22_RNAseq


title: pancreatic cells for patch-seq [L2A6]


title: NC_21_RNAseq


title: pancreatic cells for patch-seq [J2H2]


title: MUC6478_9857_8h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: MUC6477_10107_8h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [J2H10]


title: PDR-FM-3


title: NC_20_2_RNAseq


title: pancreatic cells for patch-seq [J2H1]


title: MUC6476_9640_3h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [J2G8]


title: NC_20_1_RNAseq


title: pancreatic cells for patch-seq [J2G7]


title: MUC6475_10116_3h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [J2G5]


title: NC_11_2_RNAseq


title: MUC6474_10105_24h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: NC5_RNAseq


title: NC_11_1_RNAseq


title: pancreatic cells for patch-seq [J2G2]


title: MUC6473_10106_24h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: siSA_RNAseq


title: pancreatic cells for patch-seq [J2G10]


title: MUC6472_9870_24h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [J2F9]


title: siS29_RNAseq


title: pancreatic cells for patch-seq [J2H7]


title: siS28_RNAseq


title: pancreatic cells for patch-seq [J2F10]


title: pancreatic cells for patch-seq [J2E9]


title: MUC6469_10096_24h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [J2F8]


title: MUC6471_9869_16h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: MUC6470_9898_16h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [J2G6]


title: siS27L_RNAseq


title: pancreatic cells for patch-seq [J2F2]


title: pancreatic cells for patch-seq [J2E5]


title: siS27_RNAseq


title: MUC6468_10099_16h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: siS26_5_2_RNAseq


title: pancreatic cells for patch-seq [J2F1]


title: siS25_RNAseq


title: pancreatic cells for patch-seq [J2E7]


title: pancreatic cells for patch-seq [J2G9]


title: MUC6467_10101_16h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: siS26_5_1_RNAseq


title: pancreatic cells for patch-seq [J2E8]


title: pancreatic cells for patch-seq [J2F6]


title: pancreatic cells for patch-seq [J2D9]


title: pancreatic cells for patch-seq [J2E6]


title: pancreatic cells for patch-seq [J2E1]


title: MUC6465_9851_8h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: MUC6466_9901_8h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: MUC6463_10108_8h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [J2G3]


title: MUC6464_9897_8h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [J2D8]


title: siS21_RNAseq


title: pancreatic cells for patch-seq [J2D7]


title: MUC6461_9594_3h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: MUC6460_9860_3h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: siS17_4_2_RNAseq


title: MUC6459_10115_3h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [J2D5]


title: siS18_RNAseq


title: MUC6788_11593_24h_MAC_Ad_B

description: IP'ed nuclei from MAC-INTACT mice

library_source: genomic

data_processing:
Sequence tags from ATAC-seq libraries were aligned to the mm10 using the BWA aligner (version 0.7.5a-r405) (Li and Durbin, 2009).
Post-alignment processing of reads was performed with Samtools (0.1.19-44428cd) (Li et al., 2009) by removing duplicate reads and filtering for high quality reads using Samtools view using the following settings ”-b -h -f 1 -F 4 -F 8 -F 256 -F 2048 -q 30”. Furthermore, only reads with a fragment length<100bp was used corresponding to the reads located in nucleosome-free regions.
ATAC seq peaks were identified, annotated and tags in peaks were counted using HOMER (Heinz et al., 2010). Tag directories from conditions with technical duplicates were combined into one before further analyses. Peaks were called in each library with HOMER findPeaks using the following settings: ‘peaks’, ‘-fragLength 70’, ‘-style factor’, ‘-minDist 140’, ‘-size 70’.
For all peak files, overlapping peaks were merged and collected in one master peak file. Tags were then counted in a 200bp window around the peak centers for each individual library in the resulting master peak file.
Differential accessible sites (fed vs fasted) were determined using DESeq2 using default parameters.
Bedgraph files for individual libraries were generated using HOMER makeUCSCfile specifying ‘-fragLength 70’ and ‘-fsize 20e’
Bedgraph files for each condition were generated by merging the individual tag directories of one condition into one and using HOMER makeUCSCfile specifying ‘-fragLength 70’ and ‘-fsize 20e’
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text with norm counts and log2FC (fed vs fasted) (output from DESeq2)
Supplementary_files_format_and_content: Bedgraph files for individual libraries
Supplementary_files_format_and_content: Bedgraph files (merged) - one from each condition

molecule: genomic DNA

extract_protocol:
Approximately 25,000 bead-bound nuclei from INTACT reactions were transposed in a 50 μL volume of 1X TTBL buffer and 3.5 μL TTE Mix V50 (from TruePrep™ DNA Library Prep Kit V2 for Illumina, Vazyme TD501) for 30 minutes at 37°C. Fragmented genomic DNA was recovered using Buffer ERC coupled with MinElute spin column purification (Qiagen). Samples originating from MAC INTACT mice were run in technical duplicates.
Transposed genomic DNA was amplified by 12 cycles of quantitative PCR. Amplified DNA was purified and size-selected on AMPure XP beads (Beckman A63881), analyzed on an Agilent Bioanalyzer, and sequenced (paired-end) on an Illumina HiSeq 4000 platform.


title: pancreatic cells for patch-seq [J2D3]


title: siS24_RNAseq


title: siS17_4_1_RNAseq


title: pancreatic cells for patch-seq [J2E10]


title: pancreatic cells for patch-seq [J2D10]


title: siS15A_19_2_RNAseq


title: siS16_1_RNAseq


title: siS16_2_RNAseq


title: Subject 078 VisitDay 028 Cohort IMRAS_Cohort 1_True Immunized

city: Seattle

first: Raphael

last: Gottardo

address: 1100 Fairview Ave N

department: VIDD

institute: Fred Hutch

description:
IMRAS078.028
processed data file: GEO_IMRAS_mapped_rawCounts.tsv

data_processing:
a. Reads were aligned to the UCSC hg38 genome using Kallisto alignment tool.
b. Reads were quantified with RSEM.
c. Raw counts from two separate batches were combined into one matrix.
d. Original sample names used during processing were mapped to standardized sample names to include subjectId and visit day.
e. Four samples that could not be mapped to standardized subject-visit day format were excluded.
Genome_build: UCSC hg38 (GRCh38)
Supplementary_files_format_and_content: GEO_IMRAS_mapped_rawCounts.tsv: Tab-delimited file with raw counts for 265 samples.

source_name: Whole Blood

extract_protocol:
Whole blood samples taken from participants via venipuncture and collected into PaxGene tubes. Total RNA was extracted using PAXgene Blood Kit (PreAnalytiX) and globin mRNA removed using GLOBINclear Human Kit (Ambion).
RNA libraries were generated using standard manufacturers’ protocols for the two platforms (BGI’s BGIseq500 and Illumina’s HiSeq2000).

tag: cohort

value: Cohort 1

tag: subject

value: Whole Blood

value: True Immunized

tag: visit day


title: siS15A_19_1_RNAseq


title: siS19_RNAseq


title: Subject 002 VisitDay 014 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.014
processed data file: GEO_IMRAS_mapped_rawCounts.tsv

tag: tissue


title: Subject 071 VisitDay 007 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.007
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: MUC6787_11718_24h_MAC_fast_B

description: IP'ed nuclei from MAC-INTACT mice

value: Macrophage Nuclei


title: siS23_RNAseq


title: MUC6786_11574_16h_MAC_Ad_B

description: IP'ed nuclei from MAC-INTACT mice


title: Subject 078 VisitDay 007 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.007
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: pancreatic cells for patch-seq [J2D2]

value: Pancreatic islets


title: MUC6785_11658_16h_MAC_fast_B

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [J2C9]


title: MUC6462_9595_3h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: MUC6783_11719_24h_MAC_fast_B

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [J2C7]


title: MUC6784_11592_24h_MAC_Ad_B

description: IP'ed nuclei from MAC-INTACT mice


title: Subject 060 VisitDay 007 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.007
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: pancreatic cells for patch-seq [J2C8]


title: Subject 039 VisitDay 007 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.007
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: siS15_8_2_RNAseq


title: siS14_RNAseq


title: Subject 057 VisitDay 007 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.007
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: pancreatic cells for patch-seq [J2C5]


title: siS15_8_1_RNAseq


title: Subject 033 VisitDay 007 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.007
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 061 VisitDay 007 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.007
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: pancreatic cells for patch-seq [J2C3]


title: pancreatic cells for patch-seq [J2C2]


title: MUC6782_11575_16h_MAC_Ad_B

description: IP'ed nuclei from MAC-INTACT mice


title: Subject 045 VisitDay 007 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.007
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: MUC6778_11574_16h_MAC_Ad_A

description: IP'ed nuclei from MAC-INTACT mice


title: MUC6781_11724_16h_MAC_fast_B

description: IP'ed nuclei from MAC-INTACT mice


title: MUC6779_11718_24h_MAC_fast_A

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [J2C6]


title: siS11_16_2_RNAseq


title: MUC6780_11593_24h_MAC_Ad_A

description: IP'ed nuclei from MAC-INTACT mice


title: siS12_3_2_RNAseq


title: siS13_RNAseq


title: siS12_3_1_RNAseq


title: Subject 021 VisitDay 007 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.007
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 007 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.007
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 005 VisitDay 007 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.007
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: MUC6777_11658_16h_MAC_fast_A

description: IP'ed nuclei from MAC-INTACT mice


title: siS11_16_1_RNAseq


title: pancreatic cells for patch-seq [J2C1]


title: MUC6776_11592_24h_MAC_Ad_A

description: IP'ed nuclei from MAC-INTACT mice


title: Subject 078 VisitDay 003 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.003
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: siS10_15_2_RNAseq


title: MUC6775_11719_24h_MAC_fast_A

description: IP'ed nuclei from MAC-INTACT mice


title: Subject 071 VisitDay 003 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.003
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: pancreatic cells for patch-seq [J2B8]


title: pancreatic cells for patch-seq [J2B9]


title: Subject 060 VisitDay 003 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.003
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: siS9_2_2_RNAseq


title: Subject 057 VisitDay 003 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.003
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: MUC6774_11575_16h_MAC_Ad_A

description: IP'ed nuclei from MAC-INTACT mice


title: siS9_2_1_RNAseq


title: MUC6773_11724_16h_MAC_fast_A

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [J2B5]


title: siS8_14_2.RNAseq


title: Subject 071 VisitDay 001 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.001
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: MUC6771_11762_8h_MAC_fast_B

description: IP'ed nuclei from MAC-INTACT mice


title: siS8_14_1_RNAseq


title: pancreatic cells for patch-seq [J2B3]


title: pancreatic cells for patch-seq [J2B6]


title: siS7_13_2_RNAseq


title: MUC6769_11768_3h_MAC_fast_B

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [J2B2]


title: Subject 045 VisitDay 003 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.003
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 003 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.003
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: MUC6770_11591_3h_MAC_Ad_B

description: IP'ed nuclei from MAC-INTACT mice


title: Subject 033 VisitDay 003 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.003
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: MUC6772_11585_8h_MAC_Ad_B

description: IP'ed nuclei from MAC-INTACT mice


title: siS7_13_1_RNAseq


title: pancreatic cells for patch-seq [J2B10]


title: MUC6768_11584_8h_MAC_Ad_B

description: IP'ed nuclei from MAC-INTACT mice


title: Subject 021 VisitDay 003 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.003
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: siS6_RNAseq


title: MUC6767_11589_8h_MAC_fast_B

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [J2B1]


title: siS10_15_1_RNAseq


title: siS5_RNAseq


title: Subject 005 VisitDay 003 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.003
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: pancreatic cells for patch-seq [J2A9]


title: MUC6766_11590_3h_MAC_Ad_B

description: IP'ed nuclei from MAC-INTACT mice


title: Subject 002 VisitDay 003 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.003
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: siS4Y_RNAseq


title: pancreatic cells for patch-seq [J2B7]


title: MUC6765_11586_3h_MAC_fast_B

description: IP'ed nuclei from MAC-INTACT mice


title: Subject 078 VisitDay 001 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.001
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: pancreatic cells for patch-seq [J2A7]


title: siS3A_RNAseq


title: Subject 060 VisitDay 001 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.001
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: MUC6764_11585_8h_MAC_Ad_A

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [J2A8]


title: siS4X_RNAseq


title: Subject 057 VisitDay 001 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.001
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: siS3_1_2_RNAseq


title: MUC6762_11591_3h_MAC_Ad_A

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [J2A6]


title: pancreatic cells for patch-seq [J2A5]


title: Subject 045 VisitDay 001 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.001
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: siS3_1_1_RNAseq


title: pancreatic cells for patch-seq [J2A3]


title: MUC6761_11768_3h_MAC_fast_A

description: IP'ed nuclei from MAC-INTACT mice


title: siS2_RNAseq


title: Subject 039 VisitDay 001 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.001
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: MUC6760_11584_8h_MAC_Ad_A

description: IP'ed nuclei from MAC-INTACT mice


title: siP2_RNAseq


title: pancreatic cells for patch-seq [J2A10]


title: Subject 033 VisitDay 001 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.001
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 001 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.001
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: siP1_RNAseq


title: MUC6758_11590_3h_MAC_Ad_A

description: IP'ed nuclei from MAC-INTACT mice


title: siP0_RNAseq


title: pancreatic cells for patch-seq [H2H9]


title: Subject 005 VisitDay 001 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.001
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 001 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.001
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: MUC6757_11586_3h_MAC_fast_A

description: IP'ed nuclei from MAC-INTACT mice


title: siL41_RNAseq


title: pancreatic cells for patch-seq [H2H8]


title: Subject 045 VisitDay 028 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.028
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: pancreatic cells for patch-seq [H2H7]


title: Subject 039 VisitDay 028 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.028
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: MUC6755_11578_24h_MAC_fast_B

description: IP'ed nuclei from MAC-INTACT mice


title: siL39_RNAseq


title: MUC6763_11762_8h_MAC_fast_A

description: IP'ed nuclei from MAC-INTACT mice


title: siL38_RNAseq


title: pancreatic cells for patch-seq [H2H6]


title: MUC6754_11659_16h_MAC_Ad_B

description: IP'ed nuclei from MAC-INTACT mice


title: siL37A_RNAseq


title: pancreatic cells for patch-seq [H2H5]


title: Subject 033 VisitDay 028 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.028
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 028 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.028
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: pancreatic cells for patch-seq [J2A2]


title: siL37_RNAseq


title: MUC6753_11737_16h_MAC_fast_B

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [H2H4]


title: Subject 005 VisitDay 028 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.028
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: MUC6752_11730_24h_MAC_Ad_B

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [H2H3]


title: MUC6759_11589_8h_MAC_fast_A

description: IP'ed nuclei from MAC-INTACT mice


title: Subject 078 VisitDay 014 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.014
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 028 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.028
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: MUC6750_11739_16h_MAC_Ad_B

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [J2A1]


title: siL35A_RNAseq


title: pancreatic cells for patch-seq [H2H12]


title: MUC6749_11716_16h_MAC_fast_B

description: IP'ed nuclei from MAC-INTACT mice


title: Subject 071 VisitDay 014 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.014
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: MUC6756_11731_24h_MAC_Ad_B

description: IP'ed nuclei from MAC-INTACT mice


title: siL35_RNAseq


title: MUC6748_11731_24h_MAC_Ad_A

description: IP'ed nuclei from MAC-INTACT mice


title: Subject 061 VisitDay 014 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.014
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: siL34_RNAseq


title: MUC6747_11578_24h_MAC_fast_A

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [H2H10]


title: siL36_RNAseq


title: MUC6746_11659_16h_MAC_Ad_A

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [H2H1]


title: siL31_RNAseq


title: Subject 057 VisitDay 014 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.014
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: siL36A_RNAseq


title: siL30_RNAseq


title: MUC6745_11737_16h_MAC_fast_A

description: IP'ed nuclei from MAC-INTACT mice


title: Subject 045 VisitDay 014 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.014
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: pancreatic cells for patch-seq [H2G8]


title: MUC6744_11730_24h_MAC_Ad_A

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [H2G7]


title: Subject 039 VisitDay 014 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.014
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: siL29_10_2_RNAseq


title: MUC6743_11577_24h_MAC_fast_A

description: IP'ed nuclei from MAC-INTACT mice


title: siL29_10_1_RNAseq


title: MUC6751_11577_24h_MAC_fast_B

description: IP'ed nuclei from MAC-INTACT mice


title: Subject 033 VisitDay 014 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.014
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: siL28_RNAseq


title: pancreatic cells for patch-seq [H2H2]


title: Subject 021 VisitDay 014 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.014
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 005 VisitDay 014 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.014
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: pancreatic cells for patch-seq [H2G6]


title: MUC6742_11739_16h_MAC_Ad_A

description: IP'ed nuclei from MAC-INTACT mice


title: siL26_RNAseq


title: MUC6741_11716_16h_MAC_fast_A

description: IP'ed nuclei from MAC-INTACT mice


title: Subject 071 VisitDay 028 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.028
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 060 VisitDay 014 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.014
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: siL24_9_2_RNAseq


title: pancreatic cells for patch-seq [H2G3]


title: siL24_9_1_RNAseq


title: Subject 057 VisitDay 028 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.028
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: siL32_RNAseq


title: pancreatic cells for patch-seq [H2G2]


title: MUC6738_11735_3h_MAC_Ad_B

description: IP'ed nuclei from MAC-INTACT mice


title: MUC6739_11740_8h_MAC_fast_B

description: IP'ed nuclei from MAC-INTACT mice


title: Subject 061 VisitDay 028 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.028
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: pancreatic cells for patch-seq [H2G12]


title: Subject 060 VisitDay 028 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.028
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: siL23_RNAseq


title: MUC6736_11594_8h_MAC_Ad_B

description: IP'ed nuclei from MAC-INTACT mice


title: MUC6737_11579_3h_MAC_fast_B

description: IP'ed nuclei from MAC-INTACT mice


title: Old_Enrich_rep4

city: Shanghai

first: Dean

last: Li

address: Haike Road 100

institute: Chinese Academy of Science

data_processing:
For RNA-Seq comparison, Sequencing reads were mapped to human with STAR by default parameter. The read counts for each genes were calculated by featurecounts. The count files were used as input to DESeq2 for differential expression analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Counts from featurecounts output were merged into csv table with each gene in rows and each sample in columns.

source_name: Liver tissue

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa, catalog: 9108)
RNA libraries were prepared according to instructions of Abclonal mRNA-seq Library Prep Kit for Illumina (RK20302)

value: Liver

tag: strain

tag: condition

value: Old

tag: assay

value: Enrich


title: siL22_RNAseq

source_name: Cell line:A549


title: Old_Enrich_rep3


title: MUC6735_11741_8h_MAC_fast_B

description: IP'ed nuclei from MAC-INTACT mice

tag: feeding state


title: MUC6734_11734_3h_MAC_Ad_B

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [H2G10]

source_name: pancreatic islets

value: Nondiabetic

value: Yes


title: siL21_8_1_RNAseq


title: pancreatic cells for patch-seq [H2F9]

value: Male


title: siL21_8_2_RNAseq


title: pancreatic cells for patch-seq [H2G1]


title: pancreatic cells for patch-seq [H2G4]


title: MUC6740_11576_8h_MAC_Ad_B

description: IP'ed nuclei from MAC-INTACT mice


title: Old_Enrich_rep1


title: siL19_RNAseq


title: pancreatic cells for patch-seq [H2F8]


title: MUC6732_11576_8h_MAC_Ad_A

description: IP'ed nuclei from MAC-INTACT mice


title: Young_Enrich_rep3

value: Young


title: siL18A_RNAseq


title: siL18_RNAseq


title: MUC6731_11740_8h_MAC_fast_A

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [H2F6]


title: MUC6730_11735_3h_MAC_Ad_A

description: IP'ed nuclei from MAC-INTACT mice


title: siL17_RNAseq


title: pancreatic cells for patch-seq [H2F5]


title: Young_Enrich_rep2


title: MUC6728_11594_8h_MAC_Ad_A

description: IP'ed nuclei from MAC-INTACT mice


title: siL15_7_2_RNAseq


title: MUC6727_11741_8h_MAC_fast_A

description: IP'ed nuclei from MAC-INTACT mice


title: siL14_RNAseq


title: Old_Enrich_rep2


title: siL23A_RNAseq


title: MUC6733_11717_3h_MAC_fast_B

description: IP'ed nuclei from MAC-INTACT mice


title: Old_Input_rep4

value: Input


title: pancreatic cells for patch-seq [H2F11]


title: MUC6729_11579_3h_MAC_fast_A

description: IP'ed nuclei from MAC-INTACT mice


title: siL12_RNAseq


title: MUC6725_11717_3h_MAC_fast_A

description: IP'ed nuclei from MAC-INTACT mice


title: siL13A_RNAseq


title: pancreatic cells for patch-seq [H2F3]


title: siL13_RNAseq


title: siL15_7_1_RNAseq


title: pancreatic cells for patch-seq [H2F2]


title: Old_Input_rep3


title: Young_Input_rep3


title: MUC5860_10097_24h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice

value: Hepatocyte Nuclei


title: Young_Enrich_rep1


title: Old_Input_rep2


title: MUC6726_11734_3h_MAC_Ad_A

description: IP'ed nuclei from MAC-INTACT mice


title: pancreatic cells for patch-seq [H2F12]


title: Old_Input_rep1


title: Young_Enrich_rep4


title: MUC5859_9858_16h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [H2F10]


title: siL10A_RNAseq


title: siL10_RNAseq


title: With_NudC_Enrich_rep2

value: NudC+


title: siL9_RNAseq


title: siL11_RNAseq


title: pancreatic cells for patch-seq [H2F1]


title: pancreatic cells for patch-seq [H2E7]


title: MUC5856_10098_8h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: siL8_RNAseq


title: MUC5855_9639_3h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: Without_NudC_Enrich_rep2

value: NudC-


title: siL7A_RNAseq


title: Young_Input_rep2


title: pancreatic cells for patch-seq [H2E4]


title: MUC5853_9902_24h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [H2E9]


title: MUC5858_9642_16h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: Young_Input_rep1


title: Young_Input_rep4


title: MUC5861_9899_24h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [H2E8]


title: MUC5857_9856_8h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: With_NudC_Enrich_rep1


title: pancreatic cells for patch-seq [H2E11]


title: pancreatic cells for patch-seq [H2E6]


title: Without_NudC_Enrich_rep1


title: siL7_RNAseq


title: With_NudC_Input_rep2


title: PDR-FM-2

source_name: Fibrous membrane_PDR

extract_protocol:
FMs were cut by the vitrectomy cutter at 5000 cpm and the pellets were aspirated through the cutter tub into syringe. FMs were digested with collagenase type IV, followed by TrypLE™ Express Enzyme.
The single-cell suspensions (1×10^5 cells/mL in PBS) were loaded onto microfluidic devices and scRNA-Seq libraries were constructed according to the Singleron GEXSCOPE protocol with GEXSCOPE Single-Cell RNA Library Kit (Singleron Biotechnologies, Jiangsu, China) (Dura B. et al.Nucleic acids research 2019). The individual library of each sample was diluted to 4 nM and pooled for sequencing on Illumina HiSeq X Ten platform.

value: Proliferative diabetic retinopathy (PDR)

tag: age

value: 51 years

value: Fibrous membrane


title: siL6_RNAseq


title: pancreatic cells for patch-seq [H2E3]


title: MUC5852_10095_24h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [H2E10]


title: MUC5854_9864_3h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: With_NudC_Input_rep1


title: MUC5851_9850_16h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: MUC5848_10107_8h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: NAD10_Enrich_rep2

value: 10% NAD-RNA spike-in


title: NAD10_Enrich_rep1


title: siL4_RNAseq


title: MUC5847_9640_3h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [H2E12]


title: siL3_RNAseq


title: MUC5850_9641_16h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: NAD10_Enrich_rep3


title: PVR-FM

source_name: Fibrous membrane_PVR

value: Proliferative vitreoretinopathy (PVR)

value: 59 years


title: pancreatic cells for patch-seq [H2D9]

value: Pancreatic islets


title: siL5_RNAseq


title: PDR-FM-1


title: Without_NudC_Input_rep2

value: Liver


title: MUC5846_10116_3h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: NAD5_Enrich_rep3

value: 5% NAD-RNA spike-in

value: Enrich


title: pancreatic cells for patch-seq [H2D8]

value: Nondiabetic

value: Yes


title: MUC5845_10105_24h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: NAD5_Enrich_rep2


title: Without_NudC_Input_rep1


title: MUC5844_10106_24h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice