title: PIG31-ALAC-Liver

source_name: Liver

value: Liver


title: CTCL018_VDJ

status: Public on Sep 11 2025

type: SRA

city: St. Louis

first: Aaron

last: Ver Heul

state: MO

address: 660 S Euclid Ave.

department: Medicine

country: USA

institute: Washington University School of Medicine

description: Full-length VDJ segments enriched from amplified cDNA

library_source: transcriptomic

data_processing:
RTA v3.4.4 was used for base calls and quality scores
cellranger mkfastq (version 2.0.1) was used to generate FASTQ files
FASTQ files were processed using cellranger-6.0.1 to combine GEX and VDJ data.
Genome_build: GRCh38-2020-A and vdj-GRCh38-alts-ensembl-5.0.0
Supplementary_files_format_and_content: Unfiltered matrix files of raw gene counts for each sample in HDF5 format
Supplementary_files_format_and_content: List of identified TCR clonotypes by cellular barcode for each sample in csv format

molecule: polyA RNA

organism: Homo sapiens

source_name: whole blood

growth_protocol: Fresh blood donated from patients was immediately processed

extract_protocol:
PBMC samples were isolated into into single cells and loaded into GEMs using the 10X Genomics Chromium instrument
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 10-14 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  TCR target enrichments were done on the full-length cDNA.  GEX and Enriched TCR libraries were prepared as recommended by the 10x Genomics Chromium Single Cell V(D)J Reagent Kits (v1 Chemistry) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x8x151 sequencing recipe according to manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library and 5000 reads/cell for each V(D)J (Tcell) library.

treatment_protocol: PBMCs were isolated by density gradient centrifugation using a standard Ficoll protocol. PBMCs were washed three times in RPMI followed by final resuspension in PBS with 0.04% BSA

tag: tissue

value: peripheral blood mononuclear cells

tag: disease

value: cutaneous t cell lymphoma


title: TMOC1

city: Harbin

first: Qiming

last: Shen

address: Thoracic Surgery, The First Hospital Of China Medical University, No.155 North Nanjing Road, Heping Area, Shenyang

country: China

description: Library name: sample1

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

source_name: Non-small cell lung cancer (organ chip)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols

value: Non-small cell lung cancer (organ chip)

tag: treatment

value: control


title: PIG8-WPI-Liver

city: Davis, CA

first: Carolyn

middle: M.

last: Slupsky

address: One Shields Ave

department: Department of Nutrition, Department of food science and technology

institute: University of California, Davis

data_processing:
Removal of low-quality reads/nucleotides and adapter sequences were performed via BBDuk from the BBTools suite (v38.72) using the recommended parameters for QuantSeq experiment (parameters: k=13, ktrim=r, useshortkmers=t, mink=5, qtrim=t, trimq=10, minlength=20, ftl=13). The trimmed-high-quality sequencing reads were then mapped to the latest reference genome for domestic pig (Sscrofa11.1) using STAR aligner (v2.7.10a) with the recommended modified-Encode settings. Quantification of per-gene counts was obtained using HT-Seq count (v2.0.2).
Assembly: Sscrofa11.1
Supplementary files format and content: Tab-delimited text file in which the first column contains the Ensembl gene ID for each reference gene, and the second column provides the corresponding gene count

molecule: total RNA

organism: Sus scrofa

extract_protocol:
Tissues were collected immediately after euthanasia, follow by snap-freezing in liquid nitrogen, and stored at -80°C until further analysis. Tissues were manually ground in liquid nitrogen using a mortar and pestle. 25-30 mg of cryoground tissue was extracted using a modified Folch extraction, and RNA was extracted from the resulting cell layer (All Prep DNA/RNA/Protein Kit, Qiagen, Germantown, MD). RNA samples were quantified using the Qubit RNA HS Assay Kit and Quibit 3.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA), and sample quality was assessed using a Lab Chip GX Touch HT (Perken Elmer, Waltham, MA).
Isolated RNA was submitted to the UC Davis DNA Technologies and Expression Analysis Core to generate 3’ Tag-Seq libraries with unique molecular indices (UMIs). To generate Illumina-compatible multiplexed sequencing libraries, barcoded 3'Tag-Seq libraries were prepared using the QuantSeq FWD kit (Lexogen, Vienna, Austria) according to the manufacturer’s recommendations.  The fragment size distribution of the libraries was verified via micro-capillary gel electrophoresis via Bioanalyzer 2100 (Agilent, Santa Clara, CA).  The libraries were quantified fluorometrically on a Qubit instrument (LifeTechnologies, Carlsbad, CA), and pooled in equimolar ratios. 232 libraries were sequenced on 2.5 lanes of NextSeq500 sequencer.

tag: crossbreed

value: Hampshire x Yorkshire x Landrace cross

tag: genotype

value: WT

tag: age

value: Postnatal day 16

tag: Sex

value: F

tag: diet

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: PIG23-WPI-Liver


title: CTCL010_VDJ


title: PIG4-WPI-Hypo

source_name: Hypothalamus

value: Hypothalamus


title: PIG19-ALAC-Liver

value: M

value: Piglet formula enriched in α-lactalbumin


title: 188 Anterior Spinal Cord

city: Kansas City

first: Jay

middle: L

last: Vivian

address: 2401 Gillham Road

department: Clinical Genetics

institute: Children's Mercy Hospital

description: Library name: 188sca

data_processing:
kallisto v0.46.1 for alignment of RNA-Seq reads to a reference
tximport to import kallisto output files and collapse the transcript counts to gene counts
Assembly: GRCm39
Supplementary files format and content: csv file with raw count values for each sample

organism: Mus musculus

source_name: anterior spinal cord

extract_protocol:
RNA was harvested using qiazol/chloroform extraction and column purification via Qiagen Rneasy Mini kit. 4ug of RNA was used in library prep of the cerebellum. 2ug of RNA was usind in library prep of the anterior spinal cord.
Library prep for cerebellum samples was performed with stranded total RNA with a RiboZero Gold library preparation kit (Illumina, San Diego CA) per the manufacturer’s protocols

value: anterior spinal cord


title: PIG5-SF-Liver

value: Sow-fed


title: CIP063_VDJ

value: chronic pruritis of unknown origin


title: PIG20-WPI-Liver


title: PIG13-WPI-Liver


title: 186 Anterior Spinal Cord

description: Library name: 186sca


title: PIG22-SF-Liver


title: CIP060_VDJ


title: PIG29-ALAC-Liver


title: 171 Anterior Spinal Cord

description: Library name: 171sca


title: CIP057_17_VDJ


title: PIG27-WPI-Liver


title: 189 Anterior Spinal Cord

description: Library name: 189sca


title: PIG9-SF-Liver


title: PIG1-ALAC-Liver


title: PIG28-ALAC-Liver


title: 179 Anterior Spinal Cord

description: Library name: 179sca


title: CIP057_12_VDJ


title: CIP055_VDJ


title: PIG3-WPI-Liver


title: PIG16-ALAC-Liver


title: 183 Anterior Spinal Cord

description: Library name: 183sca


title: PIG24-SF-Liver


title: 174 Anterior Spinal Cord

description: Library name: 174sca


title: AD061_VDJ

value: atopic dermatitis


title: PIG15-WPI-Liver

value: Liver


title: 188 Cerebellum

description: Library name: 188ce

source_name: cerebellum

value: cerebellum


title: AD059_VDJ

value: peripheral blood mononuclear cells


title: PIG12-ALAC-Liver


title: 178 Anterior Spinal Cord

description: Library name: 178sca


title: CIP062_VDJ


title: AD058_VDJ


title: PIG14-WPI-Liver


title: 174 Cerebellum

description: Library name: 174ce


title: PIG25-ALAC-Liver


title: AD057_VDJ


title: PIG4-WPI-Liver


title: PIG7-SF-Liver


title: PIG21-ALAC-Liver


title: 186 Cerebellum

description: Library name: 186ce


title: AD049_VDJ


title: AD017_VDJ


title: PIG6-ALAC-Liver


title: 189 Cerebellum

description: Library name: 189ce


title: PIG10-WPI-Liver


title: PIG11-ALAC-Liver


title: HC033_GEX

description: gene expression

value: healthy control


title: 171 Cerebellum

description: Library name: 171ce


title: PIG18-SF-Liver


title: PIG26-WPI-Liver


title: HC032_GEX

description: gene expression


title: 183 Cerebellum

description: Library name: 183ce


title: PIG1-ALAC-Hipp

source_name: Hippocampus

value: Hippocampus


title: PIG22-SF-Hipp

value: Hampshire x Yorkshire x Landrace cross


title: PIG3-WPI-Hipp

value: WT


title: 179 Cerebellum

description: Library name: 179ce


title: 178 Cerebellum

description: Library name: 178ce


title: HC029_GEX

description: gene expression


title: PIG5-SF-Hipp

value: Postnatal day 16


title: PIG15-WPI-Hipp


title: PIG23-WPI-Hipp

value: F


title: Sox2 E14.5 ChIP-seq

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description:
Library name: Sample 2
Sox2 E14.5 ChIP-seq

library_source: genomic

data_processing:
Raw FASTQ reads were trimmed by Trimmomatic
Reads were aligned to mouse refenrence genome mm10 by BWA
BAM filtering was performed by samtools and markduplicate by Picard tool
Peaks were called by MACS
BW was generated by bamCoverage
Assembly: mm10
Supplementary files format and content: BW

molecule: genomic DNA

source_name: Retina

extract_protocol:
Retinae dissected from C57/BL6 mice were flash-frozen and stored at −80°C for subsequent treatment. Retinae were thawed on ice and incubated with 1% formaldehyde in PBS at room temperature for 15 min. Fixation was stopped by the addition of 0.125 M glycine (final). Chromatin was isolated by the addition of lysis buffer and was sheared to an average length of 300-500 bp. Sheared chromatin was precleared with protein G agarose beads (Invitrogen).
Chromatin immunoprecipitation (ChIP) was performed on 30-40 μg of sheared chromatin using 6 μl of SOX2 antibody (Active Motif # 39844). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment to collect DNA. Crosslinking was reversed by incubation overnight at 65°C, and DNA was purified by phenol-chloroform extraction and ethanol precipitation.

value: Retina


title: HC027_GEX

description: gene expression


title: PIG17-WPI-Liver

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: PIG16-ALAC-Hipp


title: PIG11-ALAC-Hipp

value: M


title: CTCL019_GEX

description: gene expression

value: cutaneous t cell lymphoma


title: Sox2 E14.5 IgG CUT&RUN

description:
Library name: Sample 1
Sox2 E14.5 IgG CUT&RUN

data_processing:
Raw FASTQ reads were trimmed by Trimmomatic
Reads were aligned to mouse refenrence genome mm10 by BWA
BAM filtering was performed by samtools and markduplicate by Picard tool
Peaks were called by MACS
BW was generated by bamCoverage
Assembly: mm10
Supplementary files format and content: BW
Library strategy: CUT&Run

extract_protocol:
Freshly dissected E14.5 retinae were lysed for 10 minutes at RT in lysis buffer. Nuclei were then bound to Bio-Mag Plus Concanavalin A coated beads (Cell Signaling #86057-3). After blocking with 2mM EDTA blocking solution for 10 mins at RT, beads were washed and then bound to SOX2 antibody (Active Motif #39844) overnight. The next day, samples were treated with pA-MNase and subjected to digestion with the addition of CaCl2. The digestion reaction was stopped after 30 minutes then samples were treated with RNase for 20 mins at 37°C to release CUT&RUN fragments from beads. Fragments were then purified using phenol-chloroform extraction followed by ethanol precipitation.
Library preparation was then performed with NEBNext Ultra II DNA Library Kits for Illumina (NEB #E7645, E7103) using 10ng of CUT&RUN fragments.

value: IgG antibody


title: PIG21-ALAC-Hipp

value: Piglet formula enriched in α-lactalbumin


title: PIG31-ALAC-Hipp


title: HC030_GEX

description: gene expression


title: PIG29-ALAC-Hipp


title: CTCL018_GEX

description: gene expression


title: PIG14-WPI-Hipp


title: PIG8-WPI-Hipp


title: E16.5 mouse incisor tissue-smoc1/2 ko

city: Beijing

first: Hu

last: Zhao

address: Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District

institute: Chinese institution for brain research

description:
Library name: Sample9
10x Genomics

library_source: transcriptomic single cell

data_processing:
Quality control, mapping, and count table assembly of the library were performed using the SeekSoulTools(V1.2.0) or CellRanger pipeline(V2.1.1).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: incisor

extract_protocol:
In brief, the isolated incisor pulp or germ with dental epithelium and surrounding dental follicle were placed in 4mg/ml Dispase and 3mg/ml Collagenase I on a thermomixer at 37 °C for 15 to 30min depending on the stage of the sample to release cells from the tissue. All our samples had more than 85% viable cells.
For E13.5, E14.5, E15.5, E16.5, E18.5 and P56 wild-type mice incisors, libraries were prepared using SeekOne Digital Droplet Single-Cell 3′ library preparation kit (SeekGene). For Smoc1/2 DKO and wild-type control incisors, libraries were prepared using Single Cell 3′ Library Kit v2 (10X Genomics).

value: incisor

tag: developmental stage


title: PIG7-SF-Hipp

value: Sow-fed


title: PIG25-ALAC-Hipp


title: P56_2 mouse incisor tissue

description:
Library name: Sample7
SeekGene


title: CIP063_GEX

description: gene expression

value: chronic pruritis of unknown origin


title: CIP062_GEX

description: gene expression


title: PIG17-WPI-Hipp


title: P56_1 mouse incisor tissue

description:
Library name: Sample6
SeekGene


title: PIG26-WPI-Hipp


title: PIG13-WPI-Hipp


title: PIG18-SF-Hipp


title: PIG28-ALAC-Hipp


title: Sox2 E14.5 ChIP-seq Input

description:
Library name: Sample 1
Sox2 E14.5 ChIP-seq Input


title: E18.5 mouse incisor tissue

description:
Library name: Sample5
SeekGene


title: PIG9-SF-Hipp


title: CIP060_GEX

description: gene expression


title: CIP057_17_GEX

description: gene expression


title: E16.5 mouse incisor tissue

description:
Library name: Sample4
SeekGene


title: PIG20-WPI-Hipp


title: CIP057_12_GEX

description: gene expression


title: PIG4-WPI-Hipp


title: PIG10-WPI-Hipp


title: CTCL010_GEX

description: gene expression


title: E16.5 mouse incisor tissue-control

description:
Library name: Sample8
10x Genomics


title: PIG24-SF-Hipp


title: PIG19-ALAC-Hipp


title: PIG12-ALAC-Hipp


title: AD061_GEX

description: gene expression

value: atopic dermatitis


title: PIG6-ALAC-Hipp


title: E14.5 mouse incisor tissue

description:
Library name: Sample2
SeekGene


title: PIG27-WPI-Hipp


title: E13.5 mouse incisor tissue

description:
Library name: Sample1
SeekGene


title: PIG24-SF-STR

source_name: Striatum

value: Striatum


title: AD058_GEX

description: gene expression

value: peripheral blood mononuclear cells


title: FGF_5_Clean_Data, rep1

city: Wenzhou

first: shuxin

last: wang

state: Zhejiang

address: chashan

institute: wenzhou Medical University

description: Library name: FGF_5_Clean_Data

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: kidney

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

value: kidney

tag: cell line

value: tissue

tag: cell type

value: rFGF4 treatment


title: PIG17-WPI-STR

value: Hampshire x Yorkshire x Landrace cross

value: WT

value: Postnatal day 16


title: FGF_3_Clean_Data, rep1

description: Library name: FGF_3_Clean_Data


title: PIG31-ALAC-STR


title: PIG20-WPI-STR

value: F

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: PIG9-SF-STR

value: M


title: AD057_GEX

description: gene expression


title: PIG14-WPI-STR


title: FGF_1_Clean_Data, rep1

description: Library name: FGF_1_Clean_Data


title: AD049_GEX

description: gene expression


title: PIG25-ALAC-STR


title: E15.5 mouse incisor tissue

description:
Library name: Sample3
SeekGene


title: PIG4-WPI-STR


title: CIP055_GEX

description: gene expression


title: db_5_Clean_Data, rep1

description: Library name: db_5_Clean_Data

value: db/db model


title: AD017_GEX

description: gene expression


title: PBMCs, AD051-post_VDJ

tag: individual

value: whole blood

value: peripheral blood mononuclear cells (PBMCs)

tag: disease state

value: post-dupilumab


title: db_4_Clean_Data, rep1

description: Library name: db_4_Clean_Data


title: PIG22-SF-STR

value: Sow-fed


title: PIG29-ALAC-STR

value: Piglet formula enriched in α-lactalbumin


title: PIG28-ALAC-STR

value: Striatum


title: AD059_GEX

description: gene expression

value: peripheral blood mononuclear cells

value: atopic dermatitis


title: PBMCs, AD051-pre_VDJ

value: pre-dupilumab


title: PIG15-WPI-STR


title: PIG1-ALAC-STR


title: PIG10-WPI-STR


title: PBMCs, AD036-post_VDJ


title: PIG11-ALAC-STR


title: FGF_2_Clean_Data, rep1

description: Library name: FGF_2_Clean_Data

value: kidney

value: tissue

value: rFGF4 treatment


title: PIG19-ALAC-STR

value: Hampshire x Yorkshire x Landrace cross

value: WT

value: Postnatal day 16


title: PBMCs, AD036-pre_VDJ


title: IL9 CAR T rep3

city: Guangzhou

first: yang

last: zhou

address: South Shatai Road, Baiyun District

institute: Southern Medical University

description: Library name: Unknown_BO561-01T0005_good

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Hisat2 tools soft were used to map with reference genome. Quantification of gene expression was estimated by fragments per kilobase of transcript per million fragments (FPKM).
Assembly: GRCm38
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: splenocytes

extract_protocol:
RNAex Pro RNA Reagent was used to obtain total RNA of CAR T cells
A total amount of 500 ng RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: splenocytes

value: T cell

value: IL9 CAR virus


title: PBMCs, AD035-post_VDJ

value: whole blood

value: peripheral blood mononuclear cells (PBMCs)


title: PIG23-WPI-STR

value: F

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: PBMCs, AD035-pre_VDJ


title: PIG5-SF-STR

value: Striatum

value: M

value: Sow-fed


title: PIG7-SF-STR


title: IL9 CAR T rep2

description: Library name: Unknown_BO561-01T0004_good


title: IL9 CAR T rep1

description: Library name: Unknown_BO561-01T0003_good


title: PIG12-ALAC-STR

value: Piglet formula enriched in α-lactalbumin


title: PIG26-WPI-STR


title: PIG21-ALAC-STR


title: CXCL13 CAR T rep3

description: Library name: Unknown_BO561-01T0008_good

value: CXCL13 CAR virus


title: PBMCs, AD024-post_VDJ

value: atopic dermatitis

value: post-dupilumab


title: PIG18-SF-STR

value: Hampshire x Yorkshire x Landrace cross


title: CXCL13 CAR T rep2

description: Library name: Unknown_BO561-01T0009_good


title: db_3_Clean_Data, rep1

description: Library name: db_3_Clean_Data

value: kidney

value: tissue

value: db/db model


title: PBMCs, AD051-post_GEX

description: gene expression


title: PIG13-WPI-STR

value: WT

value: Postnatal day 16


title: PBMCs, AD024-pre_VDJ

value: whole blood

value: pre-dupilumab


title: PIG16-ALAC-STR

value: F


title: CXCL13 CAR T rep1

description: Library name: Unknown_BO561-01T0007_good

value: splenocytes

value: T cell


title: PIG3-WPI-STR

value: Striatum

value: M

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: db_2_Clean_Data, rep1

description: Library name: db_2_Clean_Data


title: PIG27-WPI-STR


title: PIG8-WPI-STR


title: PIG6-ALAC-STR

value: Piglet formula enriched in α-lactalbumin


title: PBMCs, AD051-pre_GEX

description: gene expression

value: peripheral blood mononuclear cells (PBMCs)

value: atopic dermatitis


title: Control CAR T rep3

description: Library name: Unknown_BO561-01T0002_good

value: Control CAR virus


title: PBMCs, AD036-post_GEX

description: gene expression

value: post-dupilumab


title: PIG5-SF-PFC

source_name: Prefrontal cortex

value: Hampshire x Yorkshire x Landrace cross

value: Prefrontal cortex

value: Sow-fed


title: PIG23-WPI-PFC

value: WT

value: Postnatal day 16


title: PIG19-ALAC-PFC


title: PBMCs, AD036-pre_GEX

description: gene expression

value: whole blood

value: pre-dupilumab


title: Control CAR T rep1

description: Library name: Unknown_BO561-01T0006_good

value: splenocytes


title: PIG10-WPI-PFC


title: PBMCs, AD035-post_GEX

description: gene expression


title: PIG8-WPI-PFC

value: F


title: Control CAR T rep2

description: Library name: Unknown_BO561-01T0001_good

value: T cell


title: PIG1-ALAC-PFC


title: PIG12-ALAC-PFC

value: M


title: G-CDs3

city: JiNan

first: chonglei

last: zhong

address: huaiyin district

institute: Shandong First Medical University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)   by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Assembly: GRCm38/mm10
Supplementary files format and content: Text Document  include Raw read counts for each Sample

source_name: Ascites

extract_protocol:
Total RNA was extracted using the TRIzol reagent. RNA quality and quantity were determined using a Nano Drop and Bioanalyzer 2100 system
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Ascites

value: macrophage

value: treated with LPS (1 μg/ml)


title: G-CDs2


title: PBMCs, AD035-pre_GEX

description: gene expression

value: peripheral blood mononuclear cells (PBMCs)

value: atopic dermatitis


title: PIG17-WPI-PFC

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: PBMCs, AD024-post_GEX

description: gene expression

value: post-dupilumab


title: PBMCs, AD024-pre_GEX

description: gene expression


title: PIG6-ALAC-PFC

value: Hampshire x Yorkshire x Landrace cross

value: Prefrontal cortex

value: Piglet formula enriched in α-lactalbumin


title: PIG11-ALAC-PFC

value: WT

value: Postnatal day 16


title: G-CDs1


title: PIG24-SF-PFC

value: Sow-fed


title: LPS3


title: PIG27-WPI-PFC


title: PIG16-ALAC-PFC


title: PIG22-SF-PFC


title: PIG3-WPI-PFC


title: LPS2


title: PIG28-ALAC-PFC


title: LPS1


title: PIG7-SF-PFC


title: MG_H_140_JJ

city: Amsterdam

first: Han

last: Jiao

address: 9 Meibergdreef, Endocrine Laboratory, Clin. Chemistry

country: Netherlands

institute: University of Amsterdam, Amsterdam, The Netherlands.

description:
Library name: Sample 199
column name in Raw_Counts_All_Samples.csv: MG_H_140_JJ

data_processing:
Sequencing data was filtered using SOAPnuke 68 by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Assembly: Rattus_norvegicus, GCF_000001895.5_Rnor_6.0
Supplementary files format and content: csv file includes raw counts for each Sample
Supplementary files format and content: csv file includes FPKM values for each Sample

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
To study differences in microglial gene expression, bulk RNA sequencing was performed. RNA from microglial cells was isolated using the RNeasy Micro Kit (Qiagen, 74104), according to the manufacturer’s guidelines. mRNA was enriched from total RNA with the Dynabeads® mRNA Purification Kit (Invitrogen, 61006).
A strand-specific transcriptome library was constructed using the MGIEasy RNA Directional Library Prep Set (16 RXN) (MGI, 1000006385). Briefly, after cDNA synthesis, adaptor ligation was performed to ligate adaptors with the cDNAs. Subsequently, a PCR reaction was conducted to amplify the cDNAs, after which the library quality was checked using the Agilent 2100 Bioanalyzer (Agilent, G2939AA). Finally, single-stranded cyclized products were produced from single-stranded PCR products. To perform sequencing, single-stranded circle DNA molecules were replicated via rolling cycle amplification and a DNA nanoball (DNB) was generated. Sequencing was performed through combinatorial Probe-Anchor Synthesis (cPAS) on the DNBSEQ-G400 (MGI, G400).

value: Brain

tag: strain

value: Wistar

value: Male

value: Microglia cells

value: HFD light-feeding

tag: time


title: PIG13-WPI-PFC

value: M


title: control3

value: Ascites

value: macrophage

value: untreated


title: MG_H_139_JJ

description:
Library name: Sample 198
column name in Raw_Counts_All_Samples.csv: MG_H_139_JJ


title: MG_H_137_JJ

description:
Library name: Sample 197
column name in Raw_Counts_All_Samples.csv: MG_H_137_JJ

value: HFD ad libitum


title: PIG29-ALAC-PFC


title: control2


title: MG_H_141_JJ

description:
Library name: Sample 200
column name in Raw_Counts_All_Samples.csv: MG_H_141_JJ


title: PIG4-WPI-PFC

value: F

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: PIG18-SF-PFC

value: Hampshire x Yorkshire x Landrace cross

value: Prefrontal cortex


title: PIG15-WPI-PFC

value: WT


title: PIG25-ALAC-PFC

value: Postnatal day 16

value: Piglet formula enriched in α-lactalbumin


title: MG_H_136_JJ

description:
Library name: Sample 196
column name in Raw_Counts_All_Samples.csv: MG_H_136_JJ

value: Brain


title: PIG14-WPI-PFC


title: IMQ, Keratinocyte, rep2

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

data_processing:
The low quality and TruSeq adapter sequence in mRNA-seq reads were trimmed by TrimGalore (v.0.6.6).
The alignment of sequences to the reference genome was performed using STAR (v.2.7.1a) with the ENCODE v3 parameters.
The alignment sequences were applied for transcript assembly and estimation of their abundances using RSEM (v.1.3.3).
Assembly: GRCm38.p6.101
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: Skin

growth_protocol: Seven-week-old female C57BL/6 mice and TLR2 knockout mice were housed in groups of five per cage and allowed to acclimate for one week prior to the study.

extract_protocol:
Total RNA was extracted from 100 mg of mouse retina using TRIzol solution (15596018, Invitrogen, CA, USA), according to the manufacturer’s specifications. Contaminated genomic DNA was removed from 10 μg of total RNA by the incubation with 20 units of RNase-free DNase I (New England Biolabs) and 4 units of RNase inhibitor (New England Biolabs) in DEPC-treated water. The reaction mixture was incubated for 1 h at 37 °C and then for 10 min at 60 °C. The RNA samples quantified spectrophotometrically at 260 nm and all RNA extracts had an OD260:OD280 between 1.8 and 2.0, demonstrating that RNA was suitable for subsequent analyses. Oligo‐dT (6110A, Takara) was used as the primer in the first step of cDNA synthesis. Total RNA (1 μg) was combined with 1 μl of oligo dT, and H2O and then preheated at 70 °C for 10 min to denature the secondary structures of RNA. The mix was then cooled off quickly to 4 °C, subsequent to which 10 mM DTT, 2 μl of 10X reverse-transcriptase buffer, and 200 units of reverse transcriptase (18064022, Invitrogen, CA, USA) was added to make a total volume of 20 μl. The reverse-transcriptase mixture was incubated at 40 °C for 60 min, after which it was stopped by heating at 94 °C for 20 sec.
The construction of RNA-sequencing library was performed using TruSeq RNA Sample preparation kit v2 (Illumina, Inc., San Diego, CA, cat. no. RS-122–2002). In briefly, 100 ng of total RNA from each sample was exposed to poly-T oligo-attached magnetic beads to isolate poly-A mRNA following mRNA fragmentation. The cleaved RNA fragments were constructed onto a double-stranded cDNA.  After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5’ end. Then, the double-stranded library was purified using AMPure XP beads (A63881, Beckman coulter, CA, USA) to remove all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library is purified from PCR components. Libraries were analyzed by an Agilent 2100 Bioanalyzer using the High-Sensitivity DNA Chip (Agilent Technologies, Santa Clara, CA). Then, the cDNA libraries were used for paired-end 75 sequencing using an Illumina NextSeq 500 (Illumina, Inc., San Diego, CA).

treatment_protocol: To induce psoriasis, 62.5 mg/cm² of 5% imiquimod (IMQ) cream (Aldara; 3M Pharmaceuticals) was applied topically to the shaved dorsal skin for four consecutive days. The dorsal skin was shaved using an electric clipper and treated with depilatory cream. HACNs (5 mg/cm²) or an equal volume of PBS were applied transcutaneously to the shaved dorsal skin 6 hours before IMQ application to minimize interactions between the treatments. HACNs were applied on sterile gauze patches and secured to the skin for 6 hours using transparent bio-occlusive dressings (Tegaderm, 3M Pharmaceuticals).

value: Skin

value: Keratinocyte

value: IMQ-induced


title: control1


title: MG_H_133_JJ

description:
Library name: Sample 194
column name in Raw_Counts_All_Samples.csv: MG_H_133_JJ

value: Wistar

value: Male

value: Microglia cells

value: HFD dark-feeding


title: IMQ, Keratinocyte, rep1


title: PIG26-WPI-PFC


title: MG_H_131_JJ

description:
Library name: Sample 193
column name in Raw_Counts_All_Samples.csv: MG_H_131_JJ


title: NC, Keratinocyte, rep2

value: NC


title: PIG21-ALAC-PFC


title: PIG31-ALAC-PFC

value: M


title: PIG9-SF-PFC

value: Sow-fed


title: MG_H_130_JJ

description:
Library name: Sample 192
column name in Raw_Counts_All_Samples.csv: MG_H_130_JJ

value: HFD light-feeding


title: NC, Keratinocyte, rep1


title: PIG5-SF-Colon

source_name: Colon

value: Hampshire x Yorkshire x Landrace cross

value: Colon


title: PIG20-WPI-PFC

value: Prefrontal cortex

value: WT

value: F

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: MG_H_129_JJ

description:
Library name: Sample 191
column name in Raw_Counts_All_Samples.csv: MG_H_129_JJ

value: Brain


title: MG_H_128_JJ

description:
Library name: Sample 190
column name in Raw_Counts_All_Samples.csv: MG_H_128_JJ


title: IMQ, Immune cell, rep2

value: Skin

value: Immune cell


title: PIG10-WPI-Colon

value: Postnatal day 16


title: PIG1-ALAC-Colon

value: Piglet formula enriched in α-lactalbumin


title: MG_H_135_JJ

description:
Library name: Sample 195
column name in Raw_Counts_All_Samples.csv: MG_H_135_JJ

value: Wistar

value: Male

value: Microglia cells


title: IMQ, Immune cell, rep1

value: IMQ-induced


title: MG_H_127_JJ

description:
Library name: Sample 189
column name in Raw_Counts_All_Samples.csv: MG_H_127_JJ


title: PIG17-WPI-Colon

value: M


title: MG_H_124_JJ

description:
Library name: Sample 188
column name in Raw_Counts_All_Samples.csv: MG_H_124_JJ

value: HFD dark-feeding


title: NC, Immune cell, rep1

value: NC


title: NC, Immune cell, rep2


title: PIG6-ALAC-Colon

value: Hampshire x Yorkshire x Landrace cross

value: Colon


title: PIG12-ALAC-Colon

value: WT


title: PIG27-WPI-Colon

value: F


title: MG_H_123_JJ

description:
Library name: Sample 187
column name in Raw_Counts_All_Samples.csv: MG_H_123_JJ

value: HFD light-feeding


title: MG_H_122_JJ

description:
Library name: Sample 186
column name in Raw_Counts_All_Samples.csv: MG_H_122_JJ

value: Brain


title: PIG24-SF-Colon

value: Sow-fed


title: PIG16-ALAC-Colon


title: PIG22-SF-Colon


title: PIG23-WPI-Colon

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: PIG11-ALAC-Colon

value: Postnatal day 16


title: MG_H_121_JJ

description:
Library name: Sample 185
column name in Raw_Counts_All_Samples.csv: MG_H_121_JJ


title: Control mouse gastrocnemius muscle sample 7

city: Novara

first: Francesco

last: Favero

state: NO

address: Corso Trieste 15/A

department: Translational Medicine - CAAD (Center for Translational Research on Autoimmune and Allergic Diseases)

country: Italy

institute: University of Eastern Piedmont

data_processing:
Reads were aligned to the reference mouse genome mm10, using STAR aligner (version 2.5.3a). Uniquely mapped reads were assigned to the corresponding genes using featureCounts (version1.6.4) and annotated according to Gencode basic annotations (Gencode version M22).
Assembly: mm10
Supplementary files format and content: data.matrix.RPKM.xlsx = File containing the abundance of expressed genes in every sample (RPKM).

source_name: Gastrocnemius muscle

growth_protocol: Animals were housed in pathogen-free environment. Morevoer, mice were fed standard chow diet with access to drinking water, while housed under a 12 hours light-dark cycle.

extract_protocol:
Total RNA was extracted from snap-frozen gastrocnemius muscle using RNAzol reagment (Sigma-Aldrich, R4533). Tissues were homogenized using the TissueRuptor (QIAGEN)
PolyA RNA was enriched using oligo d(T) beads. The library was prepared using the Illumina TruSeq Stranded mRNA kit.

treatment_protocol: 106 C26 murine adenocarcinoma cells in 100 μl of PBS were subcutaneously injected in the right flank of 2-month-old male Balb/c mice. Starting from day 4 post tumor inoculation, C26-bearing animals were injected intraperitoneally with rolipram (3 mg/kg) or vehicle (1,86% ethanol in saline). RNAseq was performed on gastrocnemius muscle from control (without tumor), C26 vehicle-treated, and rolipram-treated mice.

value: Gastrocnemius muscle

value: healthy


title: PIG3-WPI-Colon


title: PIG19-ALAC-Colon

value: Piglet formula enriched in α-lactalbumin


title: PIG8-WPI-Colon


title: PIG28-ALAC-Colon


title: MG_H_120_JJ

description:
Library name: Sample 184
column name in Raw_Counts_All_Samples.csv: MG_H_120_JJ

value: Wistar

value: Male

value: Microglia cells


title: Control mouse gastrocnemius muscle sample 5


title: PIG7-SF-Colon

value: M


title: Control mouse gastrocnemius muscle sample 4


title: MG_H_118_JJ

description:
Library name: Sample 183
column name in Raw_Counts_All_Samples.csv: MG_H_118_JJ

value: HFD dark-feeding


title: PIG20-WPI-Colon

value: Hampshire x Yorkshire x Landrace cross


title: PIG13-WPI-Colon

value: Colon


title: PIG29-ALAC-Colon

value: WT


title: Control mouse gastrocnemius muscle sample 3


title: MG_H_117_JJ

description:
Library name: Sample 182
column name in Raw_Counts_All_Samples.csv: MG_H_117_JJ


title: PIG4-WPI-Colon

value: F


title: Control mouse gastrocnemius muscle sample 2


title: PIG15-WPI-Colon


title: Control mouse gastrocnemius muscle sample 1


title: PIG18-SF-Colon


title: MG_H_116_JJ

description:
Library name: Sample 181
column name in Raw_Counts_All_Samples.csv: MG_H_116_JJ


title: Control mouse gastrocnemius muscle sample 6


title: PIG14-WPI-Colon


title: MG_H_113_JJ

description:
Library name: Sample 179
column name in Raw_Counts_All_Samples.csv: MG_H_113_JJ

value: HFD light-feeding


title: Cachectic mouse, rolipram treated, gastrocnemius muscle sample 5

value: injected with C26 adenocarcinoma cell line, treated with rolipram


title: Cachectic mouse, rolipram treated, gastrocnemius muscle sample 4


title: PIG26-WPI-Colon


title: PIG9-SF-Colon

value: Sow-fed


title: PIG21-ALAC-Colon


title: MG_H_114_JJ

description:
Library name: Sample 180
column name in Raw_Counts_All_Samples.csv: MG_H_114_JJ

value: Brain

value: HFD ad libitum


title: PIG31-ALAC-Colon

value: Postnatal day 16


title: Cachectic mouse, rolipram treated, gastrocnemius muscle sample 3

value: Gastrocnemius muscle


title: MG_H_111_JJ

description:
Library name: Sample 177
column name in Raw_Counts_All_Samples.csv: MG_H_111_JJ


title: PIG31-ALAC-Ile

source_name: Ileum

value: Ileum

value: Piglet formula enriched in α-lactalbumin


title: MG_H_110_JJ

description:
Library name: Sample 176
column name in Raw_Counts_All_Samples.csv: MG_H_110_JJ

value: Wistar

value: Male


title: PIG8-WPI-Ile

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: PIG5-SF-Ile

value: M


title: Cachectic mouse, rolipram treated, gastrocnemius muscle sample 1


title: PIG15-WPI-Ile

value: Hampshire x Yorkshire x Landrace cross


title: PIG28-ALAC-Ile


title: MG_H_109_JJ

description:
Library name: Sample 175
column name in Raw_Counts_All_Samples.csv: MG_H_109_JJ

value: Microglia cells

value: HFD dark-feeding


title: PIG25-ALAC-Colon

value: Colon

value: WT

value: F


title: PIG18-SF-Ile

value: Sow-fed


title: Cachectic mouse, vehicle treated, gastrocnemius muscle sample 7

value: injected with C26 adenocarcinoma cell line, treated with vehicle


title: MG_H_108_JJ

description:
Library name: Sample 174
column name in Raw_Counts_All_Samples.csv: MG_H_108_JJ

value: Brain


title: PIG11-ALAC-Ile

value: Postnatal day 16


title: PIG14-WPI-Ile


title: MG_H_107_JJ

description:
Library name: Sample 173
column name in Raw_Counts_All_Samples.csv: MG_H_107_JJ


title: Cachectic mouse, vehicle treated, gastrocnemius muscle sample 5

value: Gastrocnemius muscle


title: PIG20-WPI-Ile

value: Ileum


title: Cachectic mouse, vehicle treated, gastrocnemius muscle sample 4


title: MG_H_112_JJ

description:
Library name: Sample 178
column name in Raw_Counts_All_Samples.csv: MG_H_112_JJ

value: HFD light-feeding


title: PIG19-ALAC-Ile

value: Piglet formula enriched in α-lactalbumin


title: PIG25-ALAC-Ile


title: MG_H_102_JJ

description:
Library name: Sample 171
column name in Raw_Counts_All_Samples.csv: MG_H_102_JJ

value: Wistar

value: Male


title: PIG10-WPI-Ile

value: M

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: PIG27-WPI-Ile

value: Hampshire x Yorkshire x Landrace cross


title: PIG9-SF-Ile


title: MG_H_103_JJ

description:
Library name: Sample 172
column name in Raw_Counts_All_Samples.csv: MG_H_103_JJ

value: Microglia cells


title: Cachectic mouse, vehicle treated, gastrocnemius muscle sample 3


title: MG_H_101_JJ

description:
Library name: Sample 170
column name in Raw_Counts_All_Samples.csv: MG_H_101_JJ

value: HFD ad libitum


title: Cachectic mouse, rolipram treated, gastrocnemius muscle sample 2

value: injected with C26 adenocarcinoma cell line, treated with rolipram


title: PIG29-ALAC-Ile

value: WT


title: PIG1-ALAC-Ile

value: F


title: MG_H_100_JJ

description:
Library name: Sample 169
column name in Raw_Counts_All_Samples.csv: MG_H_100_JJ

value: HFD dark-feeding


title: PIG23-WPI-Ile


title: Cachectic mouse, vehicle treated, gastrocnemius muscle sample 1

value: injected with C26 adenocarcinoma cell line, treated with vehicle


title: MG_H_99_JJ

description:
Library name: Sample 168
column name in Raw_Counts_All_Samples.csv: MG_H_99_JJ

value: Brain


title: Cachectic mouse, vehicle treated, gastrocnemius muscle sample 6

value: Gastrocnemius muscle


title: Cachectic mouse, vehicle treated, gastrocnemius muscle sample 2


title: PIG22-SF-Ile

value: Ileum

value: Postnatal day 16

value: Sow-fed


title: PIG21-ALAC-Ile

value: Piglet formula enriched in α-lactalbumin


title: MG_H_97_JJ

description:
Library name: Sample 167
column name in Raw_Counts_All_Samples.csv: MG_H_97_JJ

value: Wistar

value: Male


title: PIG3-WPI-Ile

value: M

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: WT MSCs, Hic1:tdTom, RNA-seq

city: Vancouver

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

country: Canada

institute: University of British Columbia

data_processing:
Illumina sequencing outputs generated bcl files that were demultiplexed by bcl2fastq2.
Demultiplexed read sequences were aligned to the Mouse Genome (mm10) reference sequence using TopHat58 splice junction mapper with Bowtie 259 or STAR60 aligners (RNA-seq Alignment app, Illumina Basespace)
Assembly was performed and differential expression were estimated using Cufflinks61 and Cuffdiff62, respectively (Cufflinks Assembly & DE app; Illumina Basespace).
Assembly: mm10
Supplementary files format and content: Rpkm

growth_protocol: Mice were bred and raised to 8 weeks of age using standard approved animal care committee methodology

extract_protocol:
Tissues or sorted cells were homogenized in RNAzol lysis reagent and further processed as per manufacturers instructions to obtain RNA for library preparation and subsequent NGS.
TruSeq Stranded mRNA library kit protocol

treatment_protocol: Adult animals (for tSRC and WT sample collections) 8 weeks of age were injected with 2.5mg tamoxifen in 100uL sunflower oil daily for 5 consecutive days. For embryonic age (E) 12.5 collections, timed-pregnant females were administered a single dose of TAM at a concentration of 300 mg/kg along with 150 mg/kg progesterone (Sigma P3972-5G) in sunflower oil via oral gavage.

value: Wildtype tongue MSCs


title: PIG17-WPI-Ile

value: Hampshire x Yorkshire x Landrace cross


title: tSRC Tumor, Hic1;hSS2, RNA-seq

value: Tongue sarcoma tumor


title: PIG24-SF-Ile

value: WT


title: MG_H_96_JJ

description:
Library name: Sample 166
column name in Raw_Counts_All_Samples.csv: MG_H_96_JJ

value: Microglia cells

value: HFD ad libitum


title: PIG4-WPI-Ile

value: F


title: E12.5, Input

data_processing:
The resulting sequence reads were split by index and aligned to the reference mouse genome (mm10) using BWA alignment tool (v0.5.7)
Read-depth normalized BigWig files were generated using deepTools (v3.3.0) bamCoverage
Assembly: Mm10
Supplementary files format and content: wig

extract_protocol:
For each sample, 200K cells were sorted, counted with a hemocytometer and pelleted by centrifugation at 500 g, with no brake, for 6 min at 4°C, after which the supernatant was removed. Cell pellets were resuspended with 50 uL of 0.1% Triton X-100, 0.1% Deoxycholate, 10 mM sodium butyrate and 1x PIC, and immediately flash frozen with liquid nitrogen.
ChIP library construction and sequencing were performed following the guidelines formulated by the IHEC, and are available at https://thisisepigenetics.ca/for-scientists/protocols-and-standards. The list of antibodies used is available at https://thisisepigenetics.ca/data/CEMT/metadata/antibody_qc.html.

value: Embryonic age E12.5 MSCs

tag: chip antibody


title: PIG6-ALAC-Ile


title: MG_H_92_JJ

description:
Library name: Sample 164
column name in Raw_Counts_All_Samples.csv: MG_H_92_JJ

value: Brain

value: HFD light-feeding


title: PIG12-ALAC-Ile

value: Ileum

value: Postnatal day 16


title: PIG26-WPI-Ile


title: PIG13-WPI-Ile


title: E12.5 MSCs, Hic1;tdTom, RNA-seq


title: PIG16-ALAC-Ile

value: Piglet formula enriched in α-lactalbumin


title: PIG7-SF-Ile

value: Sow-fed


title: MG_H_90_JJ

description:
Library name: Sample 163
column name in Raw_Counts_All_Samples.csv: MG_H_90_JJ

value: Wistar

value: Male

value: HFD dark-feeding


title: MG_H_93_JJ

description:
Library name: Sample 165
column name in Raw_Counts_All_Samples.csv: MG_H_93_JJ


title: PIG12-ALAC-Jej

source_name: Jejunum

value: Jejunum

value: M


title: E12.5, H2AK119ub, ChIP


title: PIG21-ALAC-Jej

value: Hampshire x Yorkshire x Landrace cross


title: E12.5, H3K27ac, ChIP

value: H3K27ac (Abcam, ab4729)


title: MG_H_85_JJ

description:
Library name: Sample 161
column name in Raw_Counts_All_Samples.csv: MG_H_85_JJ

value: Microglia cells

value: WT


title: MG_H_89_JJ

description:
Library name: Sample 162
column name in Raw_Counts_All_Samples.csv: MG_H_89_JJ


title: PIG31-ALAC-Jej


title: PIG13-WPI-Jej

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: E12.5, H3K36me3, ChIP

value: Embryonic age E12.5 MSCs

value: H3K36me3 (Abcam, ab9050)


title: MG_H_84_JJ

description:
Library name: Sample 160
column name in Raw_Counts_All_Samples.csv: MG_H_84_JJ

value: Brain

value: HFD light-feeding


title: PIG15-WPI-Jej

value: Postnatal day 16


title: PIG4-WPI-Jej

value: F


title: PIG22-SF-Jej

value: Sow-fed


title: PIG7-SF-Jej


title: MG_H_83_JJ

description:
Library name: Sample 159
column name in Raw_Counts_All_Samples.csv: MG_H_83_JJ

value: Wistar


title: MG_H_82_JJ

description:
Library name: Sample 158
column name in Raw_Counts_All_Samples.csv: MG_H_82_JJ

value: Male


title: E12.5, H3K9me3, ChIP

value: H3K9me3 (Diagenode, C15410056)


title: E12.5, H3K4me3, ChIP

value: H3K4me3 (Cell Signaling, 9751S)


title: PIG25-ALAC-Jej

value: Jejunum

value: Piglet formula enriched in α-lactalbumin


title: PIG28-ALAC-Jej

value: Hampshire x Yorkshire x Landrace cross


title: PIG11-ALAC-Jej

value: M


title: E12.5, H3K4me1, ChIP

value: H3K4me1 (Diagenode, C15410037)


title: E12.5, H3K36me2, ChIP


title: MG_H_80_JJ

description:
Library name: Sample 157
column name in Raw_Counts_All_Samples.csv: MG_H_80_JJ

value: Microglia cells

value: WT


title: MG_H_79_JJ

description:
Library name: Sample 156
column name in Raw_Counts_All_Samples.csv: MG_H_79_JJ


title: PIG26-WPI-Jej

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: PIG27-WPI-Jej


title: PIG19-ALAC-Jej


title: WT, Input

value: Wildtype tongue MSCs


title: PIG3-WPI-Jej


title: MG_H_78_JJ

description:
Library name: Sample 155
column name in Raw_Counts_All_Samples.csv: MG_H_78_JJ

value: Brain

value: HFD light-feeding


title: PIG20-WPI-Jej

value: Postnatal day 16

value: F


title: WT, H2AK119ub, ChIP


title: MG_H_77_JJ

description:
Library name: Sample 154
column name in Raw_Counts_All_Samples.csv: MG_H_77_JJ

value: Wistar


title: E12.5, H3K27me3, ChIP

value: Embryonic age E12.5 MSCs


title: WT, H3K36me2, ChIP


title: PIG18-SF-Jej

value: Sow-fed


title: MG_H_75_JJ

description:
Library name: Sample 153
column name in Raw_Counts_All_Samples.csv: MG_H_75_JJ

value: Male

value: HFD dark-feeding


title: PIG29-ALAC-Jej

value: Jejunum

value: Piglet formula enriched in α-lactalbumin


title: PIG1-ALAC-Jej

value: Hampshire x Yorkshire x Landrace cross


title: WT, H3K27ac, ChIP

value: H3K27ac (Abcam, ab4729)


title: PIG16-ALAC-Jej


title: MG_H_74_JJ

description:
Library name: Sample 152
column name in Raw_Counts_All_Samples.csv: MG_H_74_JJ

value: Microglia cells


title: PIG6-ALAC-Jej

value: WT

value: M


title: PIG14-WPI-Jej

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: PIG23-WPI-Jej


title: PIG8-WPI-Jej


title: MG_H_72_JJ

description:
Library name: Sample 150
column name in Raw_Counts_All_Samples.csv: MG_H_72_JJ

value: Brain


title: WT, H3K36me3, ChIP

value: Wildtype tongue MSCs

value: H3K36me3 (Abcam, ab9050)


title: PIG17-WPI-Jej

value: Postnatal day 16


title: PIG24-SF-Jej

value: F


title: MG_H_70_JJ

description:
Library name: Sample 149
column name in Raw_Counts_All_Samples.csv: MG_H_70_JJ

value: Wistar

value: HFD light-feeding


title: WT, H3K27me3, ChIP


title: PIG9-SF-Jej

value: Sow-fed


title: PIG5-SF-Jej


title: WT, H3K9me3, ChIP

value: H3K9me3 (Diagenode, C15410056)


title: Hemocyte, larva

city: Ghent

first: Merel

last: Braeckman

address: Krijgslaan 281

country: Belgium

institute: Ghent University

description: Library name: Sample_larva

data_processing:
Raw data with adapter sequences or low-quality sequences was filtered. We first went through a series of data processing to remove contamination and obtain valid data. This step was completed by SOAPnuke developed by BGI. SOAPnuke software filter parameters: "-n 0.01 -l 20 -q 0.3 --adaMR 0.25 --ada_trim --polyX 50 -- minReadLen 150", steps of filtering: 1. Filter adapter: if the sequencing read matches 25.0% or more of the adapter sequence (maximum 2 base mismatches are allowed), cut the adapter; 2. Filter read length: if the length of the sequencing read is less than 150 bp, discard the entire read; 3. Remove N: if the N content in the sequencing read accounts for 1.0% or more of the entire read, discard the entire read; 4. Remove polyX: if the length of polyX (X can be A, T, G or C) in the sequencing read exceeds 50bp, discard the entire read; 5. Filter low-quality data: if the bases with a quality value of less than 20 in the sequencing read account for 30.0% or more of the entire read, discard the entire read; 6. Obtain Clean reads: the output read quality value system is set to Phred+33.
An index was constructed using the reference transcriptome of A. mellifera (GCF_003254395.2_Amel_HAv3.1_cds_from_genomic.fna) via the kallisto index command. Transcript abundance was subsequently estimated using Kallisto’s pseudo-alignment algorithm through the kallisto quant command.
Assembly: GCF_003254395.2_Amel_HAv3.1_cds_from_genomic.fna
Supplementary files format and content: Excel files with estimated counts and tpm values for each transcript (target) id

organism: Apis mellifera

source_name: hemocytes

growth_protocol: In March 2024, honey bees (A. mellifera carnica) were collected by removing closed brood frames with ready-to-emerge honey bees from the UGENT apiary (51°1’29”N, 3°42’42”E). These frames were incubated in a temperature chamber at 34°C until emergence. Honey bees were collected at 24-hour intervals. Additionally, brood frames with 8-day-old worker larvae (fifth instar) were removed from the hive and the collected larvae were immediately used for hemolymph extraction.

extract_protocol:
RNA was extracted from hemocytes from 320 µL of hemolymph, equivalent to approximately 5 million hemocytes. The hemolymph was centrifuged at 0.5G for 5 minutes at 4°C and the plasma was discarded. RNA extraction from the resulting hemocyte pellets was carried out using the Qiagen RNeasy Micro Kit. The pellet was resuspended in 350 µl of RLT lysis buffer supplemented with 1% β-mercapto-ethanol and vortexed. The lysate was then passed through a 20G needle ten times to ensure thorough disruption of the hemocytes. The RNA was purified using the Qiagen RNeasy spin column following the manufacturer’s recommendations, including an on-column DNase step. Finally, the RNA was eluted in 14 µL of RNase-free water.
RNA sequencing was performed by BGI Genomics (China). mRNA enrichment was conducted using oligo dT beads to target mRNA molecules with poly A tails. In the next step, mRNA was fragmented into smaller pieces and then converted into first-strand cDNA using random primers. The second-strand cDNA synthesis utilized dUTP. The resulting cDNA underwent end-repair and 3’ adenylation, followed by adapter ligation to the 3’ adenylated cDNA fragments. PCR amplification was employed for library fragment enrichment, followed by quality control and library circularization steps. Subsequently, the library underwent amplification to generate DNA nanoballs, enabling sequencing on the DNBSEQ platform with paired-end reads of 150 base pairs.

value: hemocytes


title: WT, H3K4me3, ChIP

value: H3K4me3 (Cell Signaling, 9751S)


title: MG_H_69_JJ

description:
Library name: Sample 148
column name in Raw_Counts_All_Samples.csv: MG_H_69_JJ

value: Male

value: HFD dark-feeding


title: MG_H_68_JJ

description:
Library name: Sample 147
column name in Raw_Counts_All_Samples.csv: MG_H_68_JJ

value: Microglia cells


title: fecal supernatant from mice with DSS-induced dysbiosis, replicate 4

city: Firenze

first: Gianluca

last: Mattei

state: FI

address: Via di S. Marta, 3

institute: Università degli Studi di Firenze

description:
Library name: FS_DSS_4
FS_DSS_4 in Salmon quant.sf raw counts in xlsx format

data_processing:
Raw counts were obtained using Salmon (v1.10.1) with the Mus musculus GRCm39 reference transcriptome, imported into R with tximport (v1.24.0), and normalized using DESeq2 (v1.36.0), with differentially expressed genes identified at p-value ≤0.05.
Assembly: Mus musculus GRCm39
Supplementary files format and content: Salmon quant.sf raw counts in xlsx format

source_name: murine epithelial colon organoids

extract_protocol:
RNA was extracted from organoid pellets and quality-checked using the Bioanalyzer 2100 System, followed by amplification and library construction according to the DNBSEQ Eukaryotic Stranded Transcriptome Sequencing protocol.
Library construction was performed following the pipeline for DNBSEQ Eukaryotic Stranded Transcriptome Sequencing.

value: murine epithelial colon organoids

value: WT

value: fecal supernatant (at 4 mg/mL) from mice with DSS-induced colitis and dysbiosis

value: Days 5


title: tSRC, Input

value: Tongue sarcoma tumor


title: Female mouse urethra

type: RNA

city: Dallas

first: Douglas

last: Strand

state: TX

address: 5323 Harry Hines Blvd JA5.150 JA5.150

department: Urology

institute: UT Southwestern Medical Center

hyb_protocol: Hybridization, imaging, and washing was performed on the Xenium Analyzer.

scan_protocol: Xenium in situ analyzer

data_processing: Data processed using Xenium Onboard Analysis, followed by visualization with Xenium Explorer software.

label: xenium

source_name: mouse female urethra

label_protocol: Xenium panel mMulti_v1 + 100 custom genes (see gene_panel.json file for full specification)

extract_protocol: 5 µm FFPE sections were mounted on a Xenium slide. Manufacturer recommendations for sample processing and operation of the Xenium analyzer were followed for downstream sample preparation and data collection.

value: female

value: urethra


title: WT, H3K4me1, ChIP

value: Wildtype tongue MSCs

value: H3K4me1 (Diagenode, C15410037)


title: fecal supernatant from mice with DSS-induced dysbiosis, replicate 2

description:
Library name: FS_DSS_2
FS_DSS_2 in Salmon quant.sf raw counts in xlsx format


title: tSRC, H2AK119ub, ChIP


title: Hemocyte, adult

description: Library name: Sample_adult


title: MG_H_73_JJ

description:
Library name: Sample 151
column name in Raw_Counts_All_Samples.csv: MG_H_73_JJ

value: Brain

value: Wistar

value: HFD light-feeding


title: fecal supernatant from healthy mice, replicate 4

description:
Library name: FS_CTR_4
FS_CTR_4 in Salmon quant.sf raw counts in xlsx format

value: treated with fecal supernatant (at 4 mg/mL) from healthy control mice


title: PIG10-WPI-Jej

value: Hampshire x Yorkshire x Landrace cross

value: Jejunum

value: Postnatal day 16

value: M

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: tSRC, H3K36me2, ChIP


title: fecal supernatant from healthy mice, replicate 2

description:
Library name: FS_CTR_2
FS_CTR_2 in Salmon quant.sf raw counts in xlsx format

value: murine epithelial colon organoids

value: WT


title: MG_H_65_JJ

description:
Library name: Sample 144
column name in Raw_Counts_All_Samples.csv: MG_H_65_JJ

value: Male

value: Microglia cells


title: MG_H_66_JJ

description:
Library name: Sample 145
column name in Raw_Counts_All_Samples.csv: MG_H_66_JJ


title: fecal supernatant from healthy mice, replicate 1

description:
Library name: FS_CTR_1
FS_CTR_1 in Salmon quant.sf raw counts in xlsx format

value: Days 5


title: fecal supernatant from healthy mice, replicate 3

description:
Library name: FS_CTR_3
FS_CTR_3 in Salmon quant.sf raw counts in xlsx format


title: tSRC, H3K27ac, ChIP

value: Tongue sarcoma tumor

value: H3K27ac (Abcam, ab4729)


title: tSRC, H3K36me3, ChIP

value: H3K36me3 (Abcam, ab9050)


title: MG_H_64_JJ

description:
Library name: Sample 143
column name in Raw_Counts_All_Samples.csv: MG_H_64_JJ

value: Brain


title: MG_H_63_JJ

description:
Library name: Sample 142
column name in Raw_Counts_All_Samples.csv: MG_H_63_JJ

value: Wistar

value: HFD dark-feeding


title: SM102_UNR_135_Day_2_Rep5

city: Waltham

first: Sudha

last: Chivukula

state: MA

address: 200 West

department: mRNA Center of Excellence

institute: Sanofi

description:
Library name: N16_s189_S135_001
Column name in count_nhp.txt: N16_s189_S135_001

data_processing:
The bcl files were demultiplexed using Illumina’s bcl2fastq software.
The fastq files were processed using Array Studio software (Qiagen) and aligned to the cynomolgus Macaque CynoWashU2013 reference genome with the WashUGene2017512 gene model.
Differential gene expression analysis was performed using the Limma-Voom method, which transforms the raw read counts into log-counts per million (log-CPM) and models the mean-variance relationship of the data.
Assembly: cynomolgus Macaque CynoWashU2013 reference genome with the WashUGene2017512 gene model.
Supplementary files format and content: Tab-delimited text file including raw counts for each sample.
Supplementary files format and content: Tab-delimited text file including log-CPM for each sample.

organism: Macaca fascicularis

source_name: Blood

growth_protocol: Primary human skeletal muscle myoblasts were obtained from Lonza (Cat. No. CC-2580) and thawed and expanded following vendor recommendations. Briefly, cryopreserved cell stocks were thawed into SkGM-2 complete media (Lonza, Cat. No. CC-3245). Media was replaced 24 h after thawing and every 48 h thereafter. Cells were expanded/passaged to P6, at which point they were seeded on 24-well culture plates pre-coated with Collagen 1 at a density of 24,000 cells/cm2 in 1 mL of culture media. The next day, media in each well was replaced with 0.5 mL of fresh media before transfection mixes were prepared. Naive male and female Mauritius origin cynomolgus macaques (Macaca fascicularis) were selected from the Sanofi NHP colony at the NIRC. Animals weighed > 2 kg and were > 2 years of age at the start of the studies. Per NIRC SOPs, all animals underwent a pre-study health assessment performed by a licensed veterinarian, which included a complete blood count and clinical chemistry analysis before being cleared for entry into the study.

extract_protocol:
Muscle cells at each collection time-point, media was aspirated, and cultures were lysed on-plate using 350 µL of RLT buffer (Qiagen Cat. No. 79216) and immediately transferred to 1.5 mL tubes and stored at -80 °C. Total RNA was extracted from whole blood NHP samples collected in PAXgene Blood RNA Tubes (Qiagen, BD Diagnostics) pre- and 2 days post-immunization using the MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit (Invitrogen) on an automated KingFisher Flex System (Thermo Scientific). The quality and yield of RNA were assessed on the 4200 TapeStation System (Agilent) and NanoDrop™ Eight Spectrophotometer (Thermo Scientific). Sequencing libraries were then prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit and sequenced on the NovaSeq 6000 Sequencing System (Illumina) using the S4 Reagent Kit v1.5 (200 cycles).
Sequencing libraries were then prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit and sequenced on the NovaSeq 6000 Sequencing System (Illumina) using the S4 Reagent Kit v1.5 (200 cycles).

treatment_protocol: Muscle cells were transfected at 2 µg of formulated RNA/million cells. For each treatment, 50 µL of transfection mix was added to the culture before an additional 0.5mL of media was added to thoroughly distribute the transfection mixture before plates were returned to the incubator for 1, 4, or 24 h. NHPs were randomized, (stratified randomization approach based on age, body weight, and sex by biostatistician) into groups of 4-6 per treatment group, were generally housed in pairs whenever possible and acclimated for at least 6 days prior to the start of the study. All NHPs were immunized with a dose of 0.5 mL of vaccine via the intramuscular (IM) route in the right forelimb on Day 0 and the left forelimb on D28 while under 10 mg/kg ketamine HCl /1 mg/kg acepromazine sedation.

value: Blood

value: PBMC

tag: timepoint

tag: dose

tag: biological replicate


title: fecal supernatant from mice with DSS-induced dysbiosis, replicate 3

description:
Library name: FS_DSS_3
FS_DSS_3 in Salmon quant.sf raw counts in xlsx format

tag: treatment

value: fecal supernatant (at 4 mg/mL) from mice with DSS-induced colitis and dysbiosis


title: tSRC, H3K27me3, ChIP


title: SM102_UNR_135_Day_2_Rep4

description:
Library name: N16_s181_S134_001
Column name in count_nhp.txt: N16_s181_S134_001

tag: tissue

value: Naive male and female Mauritius origin cynomolgus macaques


title: MG_H_67_JJ

description:
Library name: Sample 146
column name in Raw_Counts_All_Samples.csv: MG_H_67_JJ

tag: genotype


title: SM102_UNR_135_Day_2_Rep6

description:
Library name: N16_s194_S100_001
Column name in count_nhp.txt: N16_s194_S100_001


title: SM102_UNR_135_Day_2_Rep3

description:
Library name: N16_s176_S169_001
Column name in count_nhp.txt: N16_s176_S169_001


title: SM102_UNR_135_Day_2_Rep2

description:
Library name: N16_s175_S157_001
Column name in count_nhp.txt: N16_s175_S157_001


title: fecal supernatant from mice with DSS-induced dysbiosis, replicate 1

description:
Library name: FS_DSS_1
FS_DSS_1 in Salmon quant.sf raw counts in xlsx format


title: MG_H_61_JJ

description:
Library name: Sample 140
column name in Raw_Counts_All_Samples.csv: MG_H_61_JJ


title: SM102_UNR_135_Day_2_Rep1

description:
Library name: N16_s169_S85_001
Column name in count_nhp.txt: N16_s169_S85_001


title: tSRC, H3K4me3, ChIP

value: H3K4me3 (Cell Signaling, 9751S)


title: SM102_UNR_135_Day_0_Rep5

description:
Library name: N16_s155_S107_001
Column name in count_nhp.txt: N16_s155_S107_001


title: MG_H_60_JJ

description:
Library name: Sample 139
column name in Raw_Counts_All_Samples.csv: MG_H_60_JJ


title: SM102_UNR_135_Day_0_Rep4

description:
Library name: N16_s147_S106_001
Column name in count_nhp.txt: N16_s147_S106_001


title: tSRC, H3K4me1, ChIP

value: H3K4me1 (Diagenode, C15410037)


title: SM102_UNR_135_Day_0_Rep3

description:
Library name: N16_s063_S23_001
Column name in count_nhp.txt: N16_s063_S23_001


title: SM102_UNR_135_Day_0_Rep2

description:
Library name: N16_s057_S17_001
Column name in count_nhp.txt: N16_s057_S17_001


title: MG_H_58_JJ

description:
Library name: Sample 138
column name in Raw_Counts_All_Samples.csv: MG_H_58_JJ

value: HFD light-feeding


title: BV2_HBXG3

city: Wuhan

first: Xiuxiu

last: Sun

address: Shizishan Street

institute: Huazhong Agricultural University

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

source_name: brain

growth_protocol: BV2 cells were maintained in DMEM supplemented with 10% bovine serum(FBS) with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries
RNA library for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: brain

value: Glial cells

value: PRV


title: SM102_UNR_135_Day_0_Rep1

description:
Library name: N16_s049_S9_001
Column name in count_nhp.txt: N16_s049_S9_001


title: SM102_UNR_45_Day_2_Rep6

description:
Library name: N16_s190_S147_001
Column name in count_nhp.txt: N16_s190_S147_001


title: BV2_HBXG2


title: MG_H_62_JJ

description:
Library name: Sample 141
column name in Raw_Counts_All_Samples.csv: MG_H_62_JJ

value: Male

value: Microglia cells

value: WT


title: MG_H_55_JJ

description:
Library name: Sample 136
column name in Raw_Counts_All_Samples.csv: MG_H_55_JJ


title: SM102_UNR_45_Day_2_Rep2

description:
Library name: N16_s171_S109_001
Column name in count_nhp.txt: N16_s171_S109_001


title: SM102_UNR_45_Day_2_Rep3

description:
Library name: N16_s172_S121_001
Column name in count_nhp.txt: N16_s172_S121_001


title: BV2_HBXG1


title: MG_H_53_JJ

description:
Library name: Sample 134
column name in Raw_Counts_All_Samples.csv: MG_H_53_JJ


title: SM102_UNR_135_Day_0_Rep6

description:
Library name: N16_s168_S168_001
Column name in count_nhp.txt: N16_s168_S168_001


title: SM102_UNR_45_Day_2_Rep1

description:
Library name: N16_s170_S97_001
Column name in count_nhp.txt: N16_s170_S97_001


title: tSRC, H3K9me3, ChIP

value: Tongue sarcoma tumor

value: H3K9me3 (Diagenode, C15410056)


title: SM102_UNR_45_Day_0_Rep6

description:
Library name: N16_s159_S155_001
Column name in count_nhp.txt: N16_s159_S155_001


title: MG_H_54_JJ

description:
Library name: Sample 135
column name in Raw_Counts_All_Samples.csv: MG_H_54_JJ

value: Brain

value: Wistar


title: BV2_3


title: SM102_UNR_45_Day_0_Rep5

description:
Library name: N16_s151_S154_001
Column name in count_nhp.txt: N16_s151_S154_001

value: Blood


title: BV2_2


title: SM102_UNR_45_Day_2_Rep4

description:
Library name: N16_s182_S146_001
Column name in count_nhp.txt: N16_s182_S146_001

value: PBMC


title: SM102_UNR_45_Day_0_Rep3

description:
Library name: N16_s045_S5_001
Column name in count_nhp.txt: N16_s045_S5_001


title: BV2_1


title: MG_H_51_JJ

description:
Library name: Sample 132
column name in Raw_Counts_All_Samples.csv: MG_H_51_JJ


title: Ocln-/-_3

city: Shanghai

first: Zichao

last: Zhang

address: No.2005, Husong Road

institute: Fudan University

data_processing:
QC was followed manufacturer's protocols.
Differential genes were analyzed using DEseq2 package
Assembly: mm10
Supplementary files format and content: Differential genes

source_name: mammary gland

extract_protocol:
RNA was harvested using Magen RNA extraction kit
RNA libraries for RNA-seq were finished by GENEWIZ (China)

value: mammary gland

value: Luminal epthelial cells

value: Ocln knockout


title: SM102_UNR_45_Day_2_Rep5

description:
Library name: N16_s184_S170_001
Column name in count_nhp.txt: N16_s184_S170_001

value: Naive male and female Mauritius origin cynomolgus macaques


title: SM102_UNR_15_Day_2_Rep6

description:
Library name: N16_s031_S178_001
Column name in count_nhp.txt: N16_s031_S178_001


title: MG_H_56_JJ

description:
Library name: Sample 137
column name in Raw_Counts_All_Samples.csv: MG_H_56_JJ

value: HFD dark-feeding


title: SM102_UNR_45_Day_0_Rep2

description:
Library name: N16_s041_S1_001
Column name in count_nhp.txt: N16_s041_S1_001


title: SM102_UNR_45_Day_0_Rep1

description:
Library name: N16_s039_S179_001
Column name in count_nhp.txt: N16_s039_S179_001


title: Ocln-/-_2


title: MG_H_48_JJ

description:
Library name: Sample 130
column name in Raw_Counts_All_Samples.csv: MG_H_48_JJ


title: SM102_UNR_15_Day_2_Rep5

description:
Library name: N16_s030_S166_001
Column name in count_nhp.txt: N16_s030_S166_001


title: SM102_UNR_15_Day_2_Rep4

description:
Library name: N16_s028_S143_001
Column name in count_nhp.txt: N16_s028_S143_001


title: Control_2


title: MG_H_45_JJ

description:
Library name: Sample 128
column name in Raw_Counts_All_Samples.csv: MG_H_45_JJ

value: HFD ad libitum


title: Ocln-/-_1


title: SM102_UNR_45_Day_0_Rep4

description:
Library name: N16_s135_S79_001
Column name in count_nhp.txt: N16_s135_S79_001


title: SM102_UNR_15_Day_2_Rep2

description:
Library name: N16_s025_S107_001
Column name in count_nhp.txt: N16_s025_S107_001


title: SM102_UNR_15_Day_2_Rep1

description:
Library name: N16_s024_S189_001
Column name in count_nhp.txt: N16_s024_S189_001


title: SM102_UNR_15_Day_2_Rep3

description:
Library name: N16_s026_S119_001
Column name in count_nhp.txt: N16_s026_S119_001


title: Control_1


title: SM102_UNR_15_Day_0_Rep5

description:
Library name: N16_s154_S95_001
Column name in count_nhp.txt: N16_s154_S95_001


title: AV064-10

city: St. Louis

first: Aaron

last: Ver Heul

address: 660 S Euclid Ave.

institute: Washington University School of Medicine

description: gene expression

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software
RNA-seq reads were aligned and quantified to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis
The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights
Genome_build: Mouse Ensembl GRCm38.101
Supplementary_files_format_and_content: transcript quantification file - plain text

source_name: trigeminal ganglia

growth_protocol: Mice were treated for 12 days with either ethanol vehicle or 1.5 nmol calcipotriol on each cheek

extract_protocol:
RNA was extracted from trigeminal ganglia using the Nucleospin RNA purification kit
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: Fresh trigeminal ganglia from treated mice were immediately processed for RNA

value: male

tag: age

value: 8-10 week old

value: calcipotriol

value: atopic dermatitis-like disease


title: Control_3

value: WT


title: SM102_UNR_15_Day_0_Rep1

description:
Library name: N16_s050_S10_001
Column name in count_nhp.txt: N16_s050_S10_001


title: MG_H_39_JJ

description:
Library name: Sample 127
column name in Raw_Counts_All_Samples.csv: MG_H_39_JJ

tag: Sex

value: Male

value: Microglia cells


title: SM102_UNR_15_Day_0_Rep2

description:
Library name: N16_s054_S14_001
Column name in count_nhp.txt: N16_s054_S14_001


title: SM102_UNR_15_Day_0_Rep3

description:
Library name: N16_s058_S18_001
Column name in count_nhp.txt: N16_s058_S18_001


title: SM102_UNR_15_Day_0_Rep6

description:
Library name: N16_s167_S156_001
Column name in count_nhp.txt: N16_s167_S156_001


title: SM102_UNR_15_Day_0_Rep4

description:
Library name: N16_s140_S117_001
Column name in count_nhp.txt: N16_s140_S117_001


title: MG_H_35_JJ

description:
Library name: Sample 125
column name in Raw_Counts_All_Samples.csv: MG_H_35_JJ

value: Brain


title: MG_H_52_JJ

description:
Library name: Sample 133
column name in Raw_Counts_All_Samples.csv: MG_H_52_JJ

value: Wistar

value: HFD light-feeding


title: MG_H_37_JJ

description:
Library name: Sample 126
column name in Raw_Counts_All_Samples.csv: MG_H_37_JJ


title: MG_H_34_JJ

description:
Library name: Sample 124
column name in Raw_Counts_All_Samples.csv: MG_H_34_JJ


title: MG_H_47_JJ

description:
Library name: Sample 129
column name in Raw_Counts_All_Samples.csv: MG_H_47_JJ


title: SM102_UNR_5_Day_2_Rep6

description:
Library name: N16_s032_S190_001
Column name in count_nhp.txt: N16_s032_S190_001

value: Blood

value: PBMC


title: AV064-9

description: gene expression


title: MG_H_49_JJ

description:
Library name: Sample 131
column name in Raw_Counts_All_Samples.csv: MG_H_49_JJ


title: MG_H_33_JJ

description:
Library name: Sample 123
column name in Raw_Counts_All_Samples.csv: MG_H_33_JJ


title: SM102_UNR_5_Day_2_Rep5

description:
Library name: N16_s029_S155_001
Column name in count_nhp.txt: N16_s029_S155_001


title: SM102_UNR_5_Day_2_Rep4

description:
Library name: N16_s027_S131_001
Column name in count_nhp.txt: N16_s027_S131_001


title: AV064-8

description: gene expression


title: SM102_UNR_5_Day_2_Rep3

description:
Library name: N16_s023_S177_001
Column name in count_nhp.txt: N16_s023_S177_001


title: SM102_UNR_5_Day_0_Rep4

description:
Library name: N16_s130_S74_001
Column name in count_nhp.txt: N16_s130_S74_001


title: AV064-7

description: gene expression


title: MG_H_28_JJ

description:
Library name: Sample 121
column name in Raw_Counts_All_Samples.csv: MG_H_28_JJ


title: SM102_UNR_5_Day_2_Rep1

description:
Library name: N16_s021_S154_001
Column name in count_nhp.txt: N16_s021_S154_001


title: AV064-5

description: gene expression

value: vehicle

value: steady state


title: AV064-6

description: gene expression


title: SM102_UNR_5_Day_2_Rep2

description:
Library name: N16_s022_S165_001
Column name in count_nhp.txt: N16_s022_S165_001

value: Naive male and female Mauritius origin cynomolgus macaques


title: AV064-4

description: gene expression


title: MG_H_29_JJ

description:
Library name: Sample 122
column name in Raw_Counts_All_Samples.csv: MG_H_29_JJ


title: cKK-E10_UNR_135_Day_2_Rep5

description:
Library name: Flu-N10-SA137E-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-SA137E-D2-Pax_001


title: MG_H_26_JJ

description:
Library name: Sample 119
column name in Raw_Counts_All_Samples.csv: MG_H_26_JJ


title: cKK-E10_UNR_135_Day_2_Rep4

description:
Library name: Flu-N10-GB4A-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-GB4A-D2-Pax_001


title: cKK-E10_UNR_135_Day_2_Rep6

description:
Library name: Flu-N10-V863PB-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-V863PB-D2-Pax_001


title: SM102_UNR_5_Day_0_Rep5

description:
Library name: N16_s150_S142_001
Column name in count_nhp.txt: N16_s150_S142_001


title: MG_H_27_JJ

description:
Library name: Sample 120
column name in Raw_Counts_All_Samples.csv: MG_H_27_JJ


title: SM102_UNR_5_Day_0_Rep3

description:
Library name: N16_s046_S6_001
Column name in count_nhp.txt: N16_s046_S6_001


title: SM102_UNR_5_Day_0_Rep2

description:
Library name: N16_s042_S2_001
Column name in count_nhp.txt: N16_s042_S2_001


title: AV064-3

description: gene expression


title: MG_H_25_JJ

description:
Library name: Sample 118
column name in Raw_Counts_All_Samples.csv: MG_H_25_JJ


title: SM102_UNR_5_Day_0_Rep1

description:
Library name: N16_s040_S191_001
Column name in count_nhp.txt: N16_s040_S191_001


title: cKK-E10_UNR_135_Day_2_Rep3

description:
Library name: Flu-N10-AV239B-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-AV239B-D2-Pax_001


title: MG_H_24_JJ

description:
Library name: Sample 117
column name in Raw_Counts_All_Samples.csv: MG_H_24_JJ


title: AV064-2

description: gene expression


title: cKK-E10_UNR_135_Day_2_Rep1

description:
Library name: Flu-N10-AN239M-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-AN239M-D2-Pax_001


title: cKK-E10_UNR_135_Day_2_Rep2

description:
Library name: Flu-N10-AT282J-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-AT282J-D2-Pax_001


title: TG, JAK-N (ATAC)

data_processing:
RTA Version: v3.4.4 was used for base calls and quality scores.
The cellranger-arc-2.0.0 pipeline was used to generate FASTQ files, gene expression matrices, and ATAC fragment tables for each sample
Genome_build: Mousrefdata-cellranger-arc-mm10-2020-A-2.0.0e Ensembl GRCm38.101, customized with addition of the sequence for human JAK1 to detect its expression
Supplementary_files_format_and_content: Multiomic filtered feature barcode matrices (*.h5), ATAC per fragment information files (*.tsv.gz), and ATAC per fragment information indices (*.tsv.gz.tbi)

growth_protocol: Mice were maintained in standard housing conditions prior to the experiment

extract_protocol:
4-8 mice were pooled per sample; all mice used in this experiment were females. Mice were euthanized and fresh thoracic dorsal root ganglia, nodose ganglia, and trigeminal ganglia were immediately processed to yield single nuclei suspensions. Trigeminal ganglia were further enriched for neuronal nuclei by labeling with rabbit polyclonal anti-NeuN antibody (ABN78, Sigma) followed by MACS purification. The flow through containing the neuron-depleted fraction (FT) was sequenced separately from the eluate containing the neuron-enriched fraction (N).
Multiome 3v3.1 GEX and ATAC libraries were prepared as recommended by the 10x Genomics ChromiumNextGEM Multiome_ATAC_GEX_User_Guide_RevD (CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User Guide_RevD.pdf).  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 rxns PN-1000283, Chromium Next GEM Chip J Single Cell Kit, 48 rxns PN-1000234, Single Index Kit N Set A, 96 rxns PN-1000212 (ATAC), Dual Index Kit TT Set A, 96 rxns PN-1000215 (3v3.1 GEX), were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  GEX libraries were pooled and run over 0.05 of a NovaSeq6000 S4 flow cell using the XP workflow and running a 28x10x10x150 sequencing recipe in accordance with manufacturer’s protocol.  Target coverage was 500M reads per sample.  ATAC libraries were pooled and run over 0.167 of a NovaSeq6000 S1 flow cell using the XP workflow and running a 51x8x16x51 sequencing recipe in accordance with manufacturer’s protocol.  Target coverage was 250M reads per sample.

value: trigeminal ganglia

value: human JAK1 GOF heterozygous

tag: sample prep

value: neuronal enriched

value: immune dysregulation

tag: assay

value: chromatin accessibility


title: MG_H_23_JJ

description:
Library name: Sample 116
column name in Raw_Counts_All_Samples.csv: MG_H_23_JJ

value: HFD ad libitum


title: SM102_UNR_5_Day_0_Rep6

description:
Library name: N16_s158_S143_001
Column name in count_nhp.txt: N16_s158_S143_001


title: AV064-1

description: gene expression

value: male

value: 8-10 week old


title: cKK-E10_UNR_135_Day_0_Rep6

description:
Library name: Flu-N10-V863PB-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-V863PB-Pre-Pax_001


title: MG_H_21_JJ

description:
Library name: Sample 115
column name in Raw_Counts_All_Samples.csv: MG_H_21_JJ

value: Male

value: Microglia cells

value: WT


title: cKK-E10_UNR_135_Day_0_Rep4

description:
Library name: Flu-N10-GB4A-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-GB4A-Pre-Pax_001


title: cKK-E10_UNR_135_Day_0_Rep2

description:
Library name: Flu-N10-AT282J-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-AT282J-Pre-Pax_001


title: cKK-E10_UNR_135_Day_0_Rep5

description:
Library name: Flu-N10-SA137E-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-SA137E-Pre-Pax_001


title: MG_H_20_JJ

description:
Library name: Sample 114
column name in Raw_Counts_All_Samples.csv: MG_H_20_JJ

value: Brain

value: Wistar


title: cKK-E10_UNR_135_Day_0_Rep3

description:
Library name: Flu-N10-AV239B-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-AV239B-Pre-Pax_001

value: Blood

value: PBMC


title: T24NS1 replicate 3

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

country: Japan

institute: Nagoya University

data_processing:
Reads were mapped on hg38 reference genome using STAR version 2.7.3a and quantified using featureCounts version 1.6.4.
Assembly: hg38
Supplementary files format and content: comma-delimited text files include read counts for each Sample

growth_protocol: T24 cells were obtained from National Bioresource Project-Cell bank (RCB2536). Cells are cultured in DMEM (Nakalai tissue) supplemented with 10 % FBS (CCB), 1% penicillin/streptomycin (Nakalai tesque) at 37℃ in 5% CO2.

extract_protocol:
Total RNA was extracted using NuclepSpin RNA plus (Takara) following the protocol.
For mRNA isolation, NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II RNA Library Prep Kit for Illumina were used. While analysis was conducted using the NextSeq 500/550 High Output Kit v2 (75 Cycles).

tag: cell line

value: No treatment


title: TG, LM-N (ATAC)

value: wild type littermate

value: steady state


title: MG_H_18_JJ

description:
Library name: Sample 113
column name in Raw_Counts_All_Samples.csv: MG_H_18_JJ

tag: cell type


title: cKK-E10_UNR_45_Day_2_Rep10

description:
Library name: N14_s102_S157_001
Column name in count_nhp.txt: N14_s102_S157_001

value: Naive male and female Mauritius origin cynomolgus macaques


title: cKK-E10_UNR_135_Day_0_Rep1

description:
Library name: Flu-N10-AN239M-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-AN239M-Pre-Pax_001


title: MG_H_15_JJ

description:
Library name: Sample 110
column name in Raw_Counts_All_Samples.csv: MG_H_15_JJ


title: MG_H_17_JJ

description:
Library name: Sample 112
column name in Raw_Counts_All_Samples.csv: MG_H_17_JJ


title: NG, LM (ATAC)

source_name: nodose ganglia

value: nodose ganglia

value: bulk


title: T24+IAA replicate 3


title: TG, LM-FT (ATAC)

value: trigeminal ganglia

value: neuronal depleted

value: chromatin accessibility


title: T24 replicate 3


title: MG_H_16_JJ

description:
Library name: Sample 111
column name in Raw_Counts_All_Samples.csv: MG_H_16_JJ

value: HFD ad libitum


title: T24NS1+IAA replicate 3


title: T24NS1+IAA replicate 2


title: DRG, JAK (ATAC)

source_name: dorsal root ganglia

value: dorsal root ganglia

value: human JAK1 GOF heterozygous

value: immune dysregulation


title: cKK-E10_UNR_45_Day_2_Rep8

description:
Library name: N14_s094_S72_001
Column name in count_nhp.txt: N14_s094_S72_001


title: MG_H_14_JJ

description:
Library name: Sample 109
column name in Raw_Counts_All_Samples.csv: MG_H_14_JJ

value: Brain

value: Male

value: Microglia cells

value: WT


title: cKK-E10_UNR_45_Day_2_Rep7

description:
Library name: N14_s084_S47_001
Column name in count_nhp.txt: N14_s084_S47_001

value: Blood

value: PBMC


title: T24NS1 replicate 2

value: No treatment


title: DRG, LM (ATAC)

value: wild type littermate

value: steady state


title: TG, JAK-N (GEX)

value: neuronal enriched

value: gene expression


title: TG, JAK-FT (ATAC)

value: trigeminal ganglia

value: neuronal depleted


title: cKK-E10_UNR_45_Day_2_Rep4

description:
Library name: Flu-N10-BF47CC-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-BF47CC-D2-Pax_001

value: Naive male and female Mauritius origin cynomolgus macaques


title: T24+IAA replicate 2


title: cKK-E10_UNR_45_Day_2_Rep9

description:
Library name: N14_s095_S84_001
Column name in count_nhp.txt: N14_s095_S84_001


title: T24NS1+IAA replicate 1


title: T24NS1 replicate 1


title: NG, JAK (ATAC)

value: nodose ganglia

value: bulk

value: chromatin accessibility


title: T24 replicate 2


title: NG, JAK (GEX)

value: human JAK1 GOF heterozygous

value: immune dysregulation


title: TG, JAK-FT (GEX)


title: TG, LM-FT (GEX)


title: MG_H_5_JJ

description:
Library name: Sample 103
column name in Raw_Counts_All_Samples.csv: MG_H_5_JJ

value: Brain

value: Wistar

value: Male

value: Microglia cells

value: HFD ad libitum


title: cKK-E10_UNR_45_Day_2_Rep1

description:
Library name: Flu-N10-AM900N-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-AM900N-D2-Pax_001

value: Blood

value: PBMC


title: TG, LM-N (GEX)

value: wild type littermate

value: neuronal enriched

value: steady state


title: cKK-E10_UNR_45_Day_2_Rep5

description:
Library name: Flu-N10-FR284A-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-FR284A-D2-Pax_001


title: MG_H_11_JJ

description:
Library name: Sample 107
column name in Raw_Counts_All_Samples.csv: MG_H_11_JJ

value: WT


title: cKK-E10_UNR_45_Day_2_Rep6

description:
Library name: Flu-N10-GA985G-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-GA985G-D2-Pax_001

value: Naive male and female Mauritius origin cynomolgus macaques


title: MG_H_7_JJ

description:
Library name: Sample 105
column name in Raw_Counts_All_Samples.csv: MG_H_7_JJ


title: MG_H_10_JJ

description:
Library name: Sample 106
column name in Raw_Counts_All_Samples.csv: MG_H_10_JJ


title: cKK-E10_UNR_45_Day_2_Rep3

description:
Library name: Flu-N10-AT289I-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-AT289I-D2-Pax_001


title: MG_H_6_JJ

description:
Library name: Sample 104
column name in Raw_Counts_All_Samples.csv: MG_H_6_JJ


title: cKK-E10_UNR_45_Day_0_Rep10

description:
Library name: N14_s048_S90_001
Column name in count_nhp.txt: N14_s048_S90_001


title: cKK-E10_UNR_45_Day_2_Rep2

description:
Library name: Flu-N10-AP892D-D2-Pax_001
Column name in count_nhp.txt: Flu-N10-AP892D-D2-Pax_001


title: MG_H_13_JJ

description:
Library name: Sample 108
column name in Raw_Counts_All_Samples.csv: MG_H_13_JJ


title: NG, LM (GEX)

value: nodose ganglia

value: gene expression


title: T24+IAA replicate 1


title: cKK-E10_UNR_45_Day_0_Rep9

description:
Library name: N14_s047_S78_001
Column name in count_nhp.txt: N14_s047_S78_001


title: PMT-5

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

institute: Juntendo University

data_processing:
Quality of raw RNAseq reads was accessed through FastQC v0.11.5. Reads were filtered with Trimmomatic-0.38 against adapters and rRNA sequences.
Filtered RNAseq reads were aligned to primary chromosomes of hg38 UCSC genome assembly with Hisat2 v2.1.0 and counted with HTSeq v2.0.1 against Gencode v43 basic annotation.
FPKM normalization and differential expression analysis was performed in edgeR v3.42.2 package for R. Gene modules were identified with WGCNA v1.72-1.
Assembly: Hg38 UCSC
Supplementary files format and content: Tables with raw and FPKM normalized counts per transcript. Differential expression analysis results (logFC > 0 for up-regulated genes in PMT, logFC < 0 for control). WGCNA gene modules.

source_name: bone tissue

extract_protocol:
Total RNA extraction was performed using AllPrep DNA/RNA Mini Kit (QIAGEN), following the manufacturer’s protocol. RNA quality was assessed using an Agilent 5200 Fragment Analyzer, using the Agilent HS RNA (15NT) kit.
The NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) was used to isolate intact poly(A)+ RNA from 1µg of previously isolated total RNA. Libraries were prepared using the Ultra II Directional RNA Library Prep Kit for Illumina and Unique Dual Index Primer Pairs were applied following the vendor protocols from New England Biolabs. Samples were sequenced in a single run on an Illumina NextSeq 550 using the NextSeq 500/550 High Output Kit v2.5 (300 Cycles) to produce 150–base pair-end reads with a mean sequencing depth of at least 60 million reads per sample.

value: bone tissue

tag: location

value: Temporal bone

value: female

tag: state

value: tumor

tag: patient


title: T24 replicate 1

value: No treatment


title: PMT-3

value: Femur bone


title: cKK-E10_UNR_45_Day_0_Rep8

description:
Library name: N14_s042_S18_001
Column name in count_nhp.txt: N14_s042_S18_001


title: MG_H_3_JJ

description:
Library name: Sample 102
column name in Raw_Counts_All_Samples.csv: MG_H_3_JJ

value: Brain

tag: strain

value: Wistar

value: Male

value: Microglia cells

tag: time


title: DRG, JAK (GEX)

value: dorsal root ganglia

value: human JAK1 GOF heterozygous

value: bulk

tag: disease state

value: immune dysregulation


title: MG_C_151_JJ

description:
Library name: Sample 99
column name in Raw_Counts_All_Samples.csv: MG_C_151_JJ

value: WT

value: chow dark-feeding


title: DRG, LM (GEX)

value: wild type littermate

value: steady state

value: gene expression


title: PMT-2

value: bone tissue

value: Mandibula

value: female


title: PMT-4

value: Metatarsal bone

value: tumor


title: MG_C_152_JJ

description:
Library name: Sample 100
column name in Raw_Counts_All_Samples.csv: MG_C_152_JJ

value: Brain

value: Wistar

value: chow ad libitum


title: MG_H_2_JJ

description:
Library name: Sample 101
column name in Raw_Counts_All_Samples.csv: MG_H_2_JJ

value: Male

value: Microglia cells

value: HFD ad libitum


title: NG_del_JAK1

data_processing:
RTA Version: v3.4.4 was used for base calls and quality scores.
The cellranger-6.1.1 pipeline was used to generate FASTQ files and gene expression matrices
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis
Genome_build: Mouse reference genome mm10-2020-A, Ensembl GRCm38.101
Supplementary_files_format_and_content: Filtered feature barcode matrices (*.h5)

growth_protocol: Mice were maintained in standard housing conditions prior to and during the experiment

extract_protocol:
On day 5, mice (7-8 mice pooled per sample, including both males and females) were euthanized and fresh thoracic dorsal root ganglia and nodose ganglia were immediately processed to yield nuclei suspensions
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-13 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide (v3.1 Chemistry Dual Index) with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 3’ Kit v3.1, 16 rxns (PN-1000268), Chromium Next GEM Chip G Single Cell  Kit, 48 rxns (PN-1000120), and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library.

treatment_protocol: Mice were treated each day with 2 micrograms of Alternaria extract intranasally for 4 days

tag: strain background

value: Jak1 flox/flox, Nav1.8-Cre positive

value: intranasal alternaria

value: asthma-like airway inflammation

tag: tissue/cell type

value: nodose ganglia


title: MG_C_148_JJ

description:
Library name: Sample 97
column name in Raw_Counts_All_Samples.csv: MG_C_148_JJ

value: WT

tag: treatment


title: MG_C_149_JJ

description:
Library name: Sample 98
column name in Raw_Counts_All_Samples.csv: MG_C_149_JJ

tag: tissue


title: cKK-E10_UNR_45_Day_0_Rep7

description:
Library name: N14_s041_S6_001
Column name in count_nhp.txt: N14_s041_S6_001

value: Blood

value: PBMC

tag: genotype

value: Naive male and female Mauritius origin cynomolgus macaques

tag: timepoint

tag: dose

tag: biological replicate


title: NG_LM

value: Jak1 flox/flox, Nav1.8-Cre negative


title: cKK-E10_UNR_45_Day_0_Rep6

description:
Library name: Flu-N10-GA985G-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-GA985G-Pre-Pax_001


title: PMT-1

value: bone tissue

value: Mandibula

tag: age

tag: Sex

value: female


title: cKK-E10_UNR_45_Day_0_Rep5

description:
Library name: Flu-N10-FR284A-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-FR284A-Pre-Pax_001

tag: cell type


title: DRG_LM

value: dorsal root ganglia


title: Control-4

tag: location

value: Frontal  bone

value: male

value: healthy


title: MG_C_147_JJ

description:
Library name: Sample 96
column name in Raw_Counts_All_Samples.csv: MG_C_147_JJ

value: Brain

value: Wistar

value: Male

value: Microglia cells

value: chow ad libitum


title: Control-3

tag: state


title: MG_C_145_JJ

description:
Library name: Sample 95
column name in Raw_Counts_All_Samples.csv: MG_C_145_JJ

value: WT


title: DRG_del_JAK1

value: Jak1 flox/flox, Nav1.8-Cre positive

value: intranasal alternaria

value: asthma-like airway inflammation


title: Control-2

tag: patient


title: cKK-E10_UNR_45_Day_0_Rep3

description:
Library name: Flu-N10-AT289I-Pre-Pax_001
Column name in count_nhp.txt: Flu-N10-AT289I-Pre-Pax_001

value: Blood

value: PBMC

value: Naive male and female Mauritius origin cynomolgus macaques