title: lib28724

description: Library name: lib28724


title: lib28721

status: Public on Aug 07 2025

type: SRA

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

country: USA

institute: Benaroya Research Institute

description: Library name: lib28721

library_source: transcriptomic

data_processing:
Fastq files were aligned to the Ensembl version of the human genome (GRCh38) (GenBank assembly accession id GCA_000001405.15), using TopHat (version 1.4.1). The single-paired flag was set to “single,” while all other TopHat parameters were set to defaults
HTSeq-count was used to generate gene counts with mode as “Intersection (nonempty)” and minimum alignment quality set to 0 and otherwise set to default parameters
For quality control, samples were kept that had human aligned counts >250,000 and median CV coverage < 1.1. Genes were filtered to include those that had a trimmed mean of M values (TMM) normalization count of at least 1 in at least 10% of libraries and were classified as protein coding using BioMart. Normalized counts were transformed to log2 counts per million along with observations level weights using voomWithQualityWeights from the “limma” R package version 3.46
Assembly: GRCh38
Supplementary files format and content: counts_raw.tsv
Supplementary files format and content: hgnc_ensembl_id_mapping.tsv
Supplementary files format and content: modules_normalized_expr.tsv
Supplementary files format and content: voom_normalized_gene_expr.tsv

molecule: total RNA

organism: Homo sapiens

source_name: Nasal lavage

extract_protocol:
Cells were sorted into lysis buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara)
Sequencing libraries were constructed from total RNA using TruSeq RNA Sample Preparation Kits v2 (Illumina) and clustered onto a flowcell using a cBOT amplification system with a HiSeq SR v4 Cluster Kit (Illumina). Single-read sequencing was carried out on a HiSeq2500 sequencer (Illumina), using a HiSeq SBS v4 Kit to generate 58-base reads, with a target of approximately 10 million reads per sample

tag: tissue

value: Nasal lavage

tag: Sex

value: male

tag: donorid

tag: treatment

value: Mepolizumab

tag: age months

tag: visit

tag: illness

value: Cold

tag: virus _yn

value: Y

tag: eos total

tag: lym total

tag: mac total

tag: squ total

tag: epi total

tag: neut total

tag: enitrox


title: lib28719

description: Library name: lib28719

value: N


title: lib28714

description: Library name: lib28714

value: Placebo

value: cold


title: lib28713

description: Library name: lib28713


title: lib28710

description: Library name: lib28710


title: lib28712

description: Library name: lib28712


title: lib28701

description: Library name: lib28701


title: lib28692

description: Library name: lib28692


title: lib42243

description: Library name: lib42243


title: lib28690

description: Library name: lib28690


title: lib28689

description: Library name: lib28689


title: lib28680

description: Library name: lib28680


title: lib28678

description: Library name: lib28678


title: lib28676

description: Library name: lib28676


title: lib42233

description: Library name: lib42233


title: lib42228

description: Library name: lib42228

value: Exacerbation


title: lib28669

description: Library name: lib28669


title: lib28671

description: Library name: lib28671


title: lib28668

description: Library name: lib28668


title: lib28662

description: Library name: lib28662


title: lib28659

description: Library name: lib28659


title: lib28658

description: Library name: lib28658


title: lib28650

description: Library name: lib28650


title: lib28649

description: Library name: lib28649


title: lib28711

description: Library name: lib28711


title: lib28709

description: Library name: lib28709


title: lib28653

description: Library name: lib28653


title: lib28702

description: Library name: lib28702


title: lib28648

description: Library name: lib28648


title: lib28636

description: Library name: lib28636


title: lib28647

description: Library name: lib28647


title: lib28646

description: Library name: lib28646


title: lib28630

description: Library name: lib28630


title: lib28675

description: Library name: lib28675


title: lib28627

description: Library name: lib28627


title: lib28621

description: Library name: lib28621


title: lib28673

description: Library name: lib28673


title: lib28619

description: Library name: lib28619


title: lib28618

description: Library name: lib28618


title: lib28631

description: Library name: lib28631


title: lib28617

description: Library name: lib28617


title: lib28615

description: Library name: lib28615


title: lib28616

description: Library name: lib28616


title: lib28661

description: Library name: lib28661


title: lib28609

description: Library name: lib28609


title: lib28608

description: Library name: lib28608


title: lib28607

description: Library name: lib28607


title: lib28597

description: Library name: lib28597


title: lib28610

description: Library name: lib28610


title: lib28600

description: Library name: lib28600


title: lib28590

description: Library name: lib28590


title: lib28589

description: Library name: lib28589


title: lib28599

description: Library name: lib28599


title: lib28632

description: Library name: lib28632


title: lib28591

description: Library name: lib28591


title: lib28588

description: Library name: lib28588


title: lib28596

description: Library name: lib28596


title: lib28598

description: Library name: lib28598


title: lib28629

description: Library name: lib28629


title: lib28574

description: Library name: lib28574


title: lib28570

description: Library name: lib28570


title: lib28562

description: Library name: lib28562


title: lib28566

description: Library name: lib28566


title: lib28561

description: Library name: lib28561


title: lib28602

description: Library name: lib28602


title: lib28563

description: Library name: lib28563


title: lib28560

description: Library name: lib28560


title: lib28558

description: Library name: lib28558


title: lib28559

description: Library name: lib28559


title: lib28556

description: Library name: lib28556


title: lib28552

description: Library name: lib28552


title: lib28555

description: Library name: lib28555


title: lib60227

description: Library name: lib60227

value: female


title: lib60225

description: Library name: lib60225


title: lib28549

description: Library name: lib28549


title: lib60204

description: Library name: lib60204


title: lib60224

description: Library name: lib60224


title: lib60226

description: Library name: lib60226


title: lib60213

description: Library name: lib60213


title: lib60187

description: Library name: lib60187


title: lib60179

description: Library name: lib60179


title: lib60196

description: Library name: lib60196


title: lib60194

description: Library name: lib60194


title: lib60197

description: Library name: lib60197


title: lib60173

description: Library name: lib60173


title: lib60180

description: Library name: lib60180


title: lib60171

description: Library name: lib60171


title: lib60168

description: Library name: lib60168


title: lib60167

description: Library name: lib60167


title: lib60165

description: Library name: lib60165


title: lib60164

description: Library name: lib60164


title: lib60163

description: Library name: lib60163


title: lib60148

description: Library name: lib60148


title: lib60215

description: Library name: lib60215


title: lib60211

description: Library name: lib60211


title: lib60192

description: Library name: lib60192


title: lib60188

description: Library name: lib60188


title: lib60161

description: Library name: lib60161


title: lib60166

description: Library name: lib60166


title: lib60178

description: Library name: lib60178


title: lib60147

description: Library name: lib60147


title: lib60146

description: Library name: lib60146


title: lib60143

description: Library name: lib60143


title: lib60114

description: Library name: lib60114


title: lib60119

description: Library name: lib60119


title: lib60136

description: Library name: lib60136


title: lib60172

description: Library name: lib60172


title: lib60120

description: Library name: lib60120


title: lib60110

description: Library name: lib60110


title: lib60113

description: Library name: lib60113


title: lib60162

description: Library name: lib60162


title: lib60096

description: Library name: lib60096


title: lib60099

description: Library name: lib60099


title: lib60098

description: Library name: lib60098


title: lib60108

description: Library name: lib60108


title: lib60103

description: Library name: lib60103


title: lib60104

description: Library name: lib60104


title: lib60097

description: Library name: lib60097


title: lib60102

description: Library name: lib60102


title: lib60094

description: Library name: lib60094


title: lib60095

description: Library name: lib60095


title: lib60093

description: Library name: lib60093


title: lib60091

description: Library name: lib60091


title: lib60092

description: Library name: lib60092


title: lib60086

description: Library name: lib60086


title: lib60087

description: Library name: lib60087


title: lib60111

description: Library name: lib60111


title: lib60116

description: Library name: lib60116


title: lib60085

description: Library name: lib60085


title: lib60106

description: Library name: lib60106


title: lib60077

description: Library name: lib60077


title: lib60067

description: Library name: lib60067


title: lib60076

description: Library name: lib60076


title: lib60073

description: Library name: lib60073


title: lib60081

description: Library name: lib60081


title: lib60078

description: Library name: lib60078


title: lib60072

description: Library name: lib60072


title: lib60070

description: Library name: lib60070


title: lib60062

description: Library name: lib60062


title: lib60061

description: Library name: lib60061


title: lib60059

description: Library name: lib60059


title: lib60054

description: Library name: lib60054


title: lib60053

description: Library name: lib60053


title: lib60055

description: Library name: lib60055


title: lib60060

description: Library name: lib60060


title: lib60056

description: Library name: lib60056


title: lib60058

description: Library name: lib60058


title: lib60040

description: Library name: lib60040


title: lib60038

description: Library name: lib60038


title: lib60042

description: Library name: lib60042


title: lib60034

description: Library name: lib60034


title: lib60041

description: Library name: lib60041


title: ESI4_F1

city: Lawrence

first: Zijun

last: Wang

state: Kansas

address: 1251 Wescoe Hall Drive, Malott 5064

department: Pharmacology and Toxicology

institute: University of Kansas

description: Library name: Sample 12

data_processing:
After quality check using FastQC (all samples passed quality check), RNA-seq reads were first trimmed using Cutadapt to remove the 3’ end adapters and trailing sequences, and then aligned to the mouse GRCM38-mm10 RefSeq mRNAs using HISAT2 with default parameters. In GRCm38-mm10, all of the 20,423 component sequences were applied in Mapping and Annotation. Alignments with a mapping score < 10 were discarded using SAMtools. A matrix of mapped fragments per USCS RefSeq known annotated gene was generated with Feature Counts. Genes annotated as rRNA were discarded.
Assembly: mm10
Supplementary files format and content: counts

organism: Mus musculus

source_name: PrL -> VTA neurons

extract_protocol:
TRAP pull-down RNA was isolated using the Absolutely RNA Nanoprep kit (Agilent, #400753, USA)
The RNA-sequencing libraries were constructed by NEBNext Ultra II directional RNA library prep kit for Illumina via the ribosomal RNA depletion method (New England BioLabs, Ipswich, MA).

value: PrL -> VTA neurons

tag: genotype

value: ESI-HER

tag: batch


title: lib60033

description: Library name: lib60033

tag: tissue


title: ESI4_F2

description: Library name: Sample 11


title: lib60075

description: Library name: lib60075

tag: Sex


title: lib60032

description: Library name: lib60032

tag: donorid


title: ESI4_M3

description: Library name: Sample 10

tag: treatment


title: lib60031

description: Library name: lib60031

tag: age months


title: RM_3_Final_Sample

description: Library name: Sample 8

value: GH-HER


title: lib60029

description: Library name: lib60029

tag: visit


title: lib60030

description: Library name: lib60030

tag: illness


title: RF_2_Final_Sample

description: Library name: Sample 9


title: ESI4_F4_RNA

description: Library name: Sample 6

value: ESI-SAL


title: lib60025

description: Library name: lib60025

tag: virus _yn


title: RM_2 Final_Sample

description: Library name: Sample 7


title: lib60028

description: Library name: lib60028

tag: eos total


title: lib60050

description: Library name: lib60050

tag: lym total


title: ESI4_F3_RNA

description: Library name: Sample 5


title: ESI4_M4_RNA

description: Library name: Sample 4


title: lib60018

description: Library name: lib60018

tag: mac total


title: lib60016

description: Library name: lib60016

tag: squ total


title: Final_Sample

description: Library name: Sample 1

value: GH-SAL


title: RM_5_6

description: Library name: Sample 2


title: RF_3_4

description: Library name: Sample 3


title: lib60013

description: Library name: lib60013

tag: epi total


title: lib60012

description: Library name: lib60012

tag: neut total


title: lib60011

description: Library name: lib60011

tag: enitrox


title: Mouse Epithelial Organoid, Aged, 50-65wks, DMSO-culture day 10, sample128697

city: Calgary

first: Myriam

last: Hemberger

address: 3330 Hospital Dr NW

country: Canada

institute: University of Calgary

description: Library name: Mouse Epithelial Organoid-Aged-128697-DMSO

data_processing:
Reads aligned using STAR aligner
Assembly: mm10
Supplementary files format and content: tab-dilimited text files containing raw counts for each sample

source_name: primary mouse uterine epithelial organoid

extract_protocol:
Total RNA was isolated form whole uteri using TRI reagent (Sigma T9424) according to manufacturer's protocol. Minumum of 350 ng DNase-treated RNA was used for the construction of sequencing libraries.  Total RNA was isolated from organoids using Qiagen RNeasy Mini kit (Qiagen, 74104) according to manufacturer's protocol. An average of 3.2ug of total RNA was used for the construction of sequencing libraries.
RNA-seq

tag: cell type

tag: genotype

value: wildtype

tag: developmental stage

value: aged


title: lib60007

description: Library name: lib60007

tag: tissue

value: Nasal lavage

tag: Sex


title: Mouse Epithelial Organoid, Aged, 50-56wks, culture day 2, sample128697

description: Library name: Mouse Epithelial Organoid-Aged-128697-D2

value: primary mouse uterine epithelial organoid


title: Adrenal gland

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embryology

country: Poland

institute: Poznan University of Medical Sciences

description:
Library name: Adrenal_S4
Formalin-fixed paraffin-embedded (FFPE) spatial transcriptomics study

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline
Sequences were aligned to mm 10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expression count data, stored in an HDF5
Supplementary files format and content: tissue_lowres_image.png: low-res tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of detected tissue
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: cytassist_image.tiff: image from cytassist
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: cytassist_alignment.json: aligned fiducials of the tissue image
Supplementary files format and content: spatial_enrichment.csv: data on spatially enriched gene expression
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: aligned_tissue_image.jpg: aligned tissue image
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials
Library strategy: Spatial Transcriptomics

source_name: adrenal gland with adjacent adipose tissue

growth_protocol: Four sexually mature male CD-1® IGS mice, 10 weeks old with a body weight of approximately 37 g were used in this study.  Mice were housed in colony cages in a pathogen-free environment with temperature maintained at 21-23°C and relative humidity between 55-60% and under a 12h light/12 h dark cycle. All mice were given standard chow and water ad libitum.

extract_protocol:
Regions of interest (ROIs) within the mouse adrenal glands were identified based on their morphology, orientation (determined through H&E staining), and RNA quality assessment via DV200, measured using an Agilent 2100 Bioanalyzer. The FFPE tissue blocks were then sectioned into 5 μm slices using a Leica RM2255 microtome. Total RNA was extracted from the FFPE tissue using the RNeasy FFPE kit (73504, Qiagen).  FFPE Visium Spatial Gene Expression analysis (10x Genomics) was carried out on a CytAssist instrument following the manufacturer's instructions. Briefly, tissue sections were mounted on SuperFrost™ Plus Microscope Slides (#22-037-246, FisherScientific) and left to dry overnight. The slides were then incubated at 60°C for 2 hours before undergoing deparaffinization.
or the H&E-stained sections, decrosslinking was performed immediately, followed by the incorporation of probe panels targeting the entire mouse transcriptome. After the probe pairs hybridized with their corresponding target transcripts, the slides were processed on the Visium CytAssist instrument for permeabilization and RNase treatment. Subsequently, transcript capture was conducted, and the Visium Library Preparation protocol from 10x Genomics was followed. Four cDNA libraries were diluted and pooled to a final concentration of 650 pM in a 20 μl volume, then sequenced using a P1 flow cell on the Illumina NextSeq 2000 platform.

treatment_protocol: The mice were euthanized via decapitation, and the adrenal glands with surrounded adipose tissue were promptly collected and preserved in 10% buffered formalin for subsequent analysis.

value: Male

tag: age

value: 10 weeks

tag: stain

value: CD-1 IGS

tag: treatment

value: intact


title: lib60006

description: Library name: lib60006

tag: donorid

value: Placebo

tag: age months

tag: visit

tag: illness


title: lib60005

description: Library name: lib60005

tag: virus _yn

value: Y

tag: eos total

tag: lym total

tag: mac total


title: Mouse Epithelial Organoid, Aged, 41-48wks, DMSO-culture day10, sample110957

description: Library name: Mouse Epithelial Organoid-Aged-110957-DMSO


title: Mouse Epithelial Organoid, Aged, 41-48wks, culture day 14, sample110957

description: Library name: Mouse Epithelial Organoid-Aged-110957-D14


title: Mouse Epithelial Organoid, Aged, 50-65wks, culture day 14, sample128697

description: Library name: Mouse Epithelial Organoid-Aged-128697-D14


title: Mouse Epithelial Organoid, Aged, 41-48wks, culture day 2, smaple110957

description: Library name: Mouse Epithelial Organoid-Aged-110957-D2


title: lib60003

description: Library name: lib60003

value: Mepolizumab

tag: squ total

tag: epi total

tag: neut total

tag: enitrox


title: lib60004

description: Library name: lib60004

tag: tissue

value: female


title: lib60002

description: Library name: lib60002

tag: Sex


title: Mouse Epithelial Organoid, Aged, 41-48wks, DMSO-culture day 10, sample109290

description: Library name: Mouse Epithelial Organoid-Aged-109290-DMSO

tag: cell type

tag: genotype

tag: developmental stage


title: lib60001

description: Library name: lib60001

tag: donorid

tag: treatment


title: lib60000

description: Library name: lib60000

tag: age months

tag: visit

value: Exacerbation


title: lib60017

description: Library name: lib60017

tag: illness

tag: virus _yn


title: Mouse Epithelial Organoid, Aged, 50-65wks, DMSO-culture day 10, sample100761

description: Library name: Mouse Epithelial Organoid-Aged-100761-DMSO


title: lib59999

description: Library name: lib59999

tag: eos total

tag: lym total


title: Mouse Epithelial Organoid, Aged, 41-48wks, culture day 2, sample109290

description: Library name: Mouse Epithelial Organoid-Aged-109290-D2


title: Mouse Epithelial Organoid, Aged, 50-65wks, culture day 14, sample100761

description: Library name: Mouse Epithelial Organoid-Aged-100761-D14


title: Mouse Epithelial Organoid, Aged, 41-48wks, culture day 14, sample109290

description: Library name: Mouse Epithelial Organoid-Aged-109290-D14


title: lib59998

description: Library name: lib59998

value: N

tag: mac total

tag: squ total


title: lib59997

description: Library name: lib59997

value: Cold

tag: epi total

tag: neut total


title: lib59995

description: Library name: lib59995

tag: tissue

value: cold

tag: enitrox


title: Mouse Epithelial Organoid, Aged, 50-65wks, culture day 2, sample096726

description: Library name: Mouse Epithelial Organoid-Aged-096726-D2

tag: cell type


title: Mouse Epithelial Organoid, Aged, 50-65wks, culture day 2, sample100761

description: Library name: Mouse Epithelial Organoid-Aged-100761-D2

tag: genotype


title: Mouse Epithelial Organoid, Aged, 50-65wks, culture day 14, sample096726

description: Library name: Mouse Epithelial Organoid-Aged-096726-D14

tag: developmental stage


title: lib59994

description: Library name: lib59994

tag: Sex

tag: donorid


title: lib59983

description: Library name: lib59983

tag: treatment

tag: age months


title: Mouse Epithelial Organoid, Aged, 50-65wks, culture day 2, sample128699

description: Library name: Mouse Epithelial Organoid-Aged-128699-D2


title: lib59981

description: Library name: lib59981

tag: visit

tag: illness


title: Mouse Epithelial Organoid, Aged, 50-65wks, culture day 14, sample128699

description: Library name: Mouse Epithelial Organoid-Aged-128699-D14


title: lib59980

description: Library name: lib59980

tag: virus _yn

tag: eos total


title: lib59975

description: Library name: lib59975

tag: lym total

tag: mac total


title: lib59972

description: Library name: lib59972

tag: squ total

tag: epi total


title: Mouse Epithelial Organoid, Aged, 50-65wks, DMSO-culture day 10, sample128699

description: Library name: Mouse Epithelial Organoid-Aged-128699-DMSO


title: Mouse Epithelial Organoid, Young, 8-14wks, DMSO-culture day 10, sample206808

description: Library name: Mouse Epithelial Organoid-Young-206808-DMSO

value: young


title: Mouse Epithelial Organoid, Young, 8-14wks, culture day 2, sample206808

description: Library name: Mouse Epithelial Organoid-Young-206808-Day 2

value: wildtype


title: lib59967

description: Library name: lib59967

tag: tissue

tag: neut total


title: lib59996

description: Library name: lib59996

tag: enitrox


title: Mouse Epithelial Organoid, Young, 8-14wks, culture day 2, sample178218

description: Library name: Mouse Epithelial Organoid-Young-178218-Day 2

tag: cell type

tag: genotype


title: Mouse Epithelial Organoid, Young, 8-14wks, culture day 14, sample206808

description: Library name: Mouse Epithelial Organoid-Young-206808-Day 14

tag: developmental stage


title: Mouse Epithelial Organoid, Young, 8-14wks, DMSO-culture day 10, sample178218

description: Library name: Mouse Epithelial Organoid-Young-178218-DMSO


title: lib59961

description: Library name: lib59961

tag: Sex

tag: donorid


title: Mouse Epithelial Organoid, Aged, 50-65wks, DMSO-culture day 10, sample-096726

description: Library name: Mouse Epithelial Organoid-Aged-096726-DMSO

value: aged


title: lib59965

description: Library name: lib59965

value: Nasal lavage

tag: treatment

tag: age months


title: lib59956

description: Library name: lib59956

tag: visit

tag: illness


title: lib59960

description: Library name: lib59960

tag: virus _yn

tag: eos total


title: Mouse Epithelial Organoid, Young, 8-14wks, culture day 2, sample178217

description: Library name: Mouse Epithelial Organoid-Young-178217-D2

value: primary mouse uterine epithelial organoid


title: lib59951

description: Library name: lib59951

tag: lym total

tag: mac total


title: Mouse Epithelial Organoid, Young, 8-14wks, culture day 14, sample178218

description: Library name: Mouse Epithelial Organoid-Young-178218-Day 14


title: lib59950

description: Library name: lib59950

tag: squ total

tag: epi total


title: lib59954

description: Library name: lib59954

tag: tissue

tag: neut total


title: Mouse Epithelial Organoid, Young, 8-14wks, DMSO-culture day 10, sample178217

description: Library name: Mouse Epithelial Organoid-Young-178217-DMSO

tag: cell type


title: lib59949

description: Library name: lib59949

tag: enitrox


title: lib59945

description: Library name: lib59945


title: Mouse Epithelial Organoid, Young, 8-14wks, DMSO-culture Day 10, sample177437

description: Library name: Mouse Epithelial Organoid-Young-177437-DMSO

tag: genotype

tag: developmental stage


title: lib59941

description: Library name: lib59941

tag: Sex

tag: donorid


title: Mouse Epithelial Organoid, Young, 8-14wks, culture day 2, sample178216

description: Library name: Mouse Epithelial Organoid-Young-178216-D2


title: Mouse Epithelial Organoid, Young, 8-14wks, DMSO-culture day 10, sample178216

description: Library name: Mouse Epithelial Organoid-Young-178216-DMSO


title: lib59937

description: Library name: lib59937

tag: treatment

tag: age months


title: Mouse Epithelial Organoid, Young, 8-14wks, culture Day 2, sample177437

description: Library name: Mouse Epithelial Organoid-Young-177437-D2


title: Mouse Epithelial Organoid, Young, 8-14wks, culture day 14, sample178216

description: Library name: Mouse Epithelial Organoid-Young-178216-D14


title: lib59935

description: Library name: lib59935

tag: visit

tag: illness


title: lib59934

description: Library name: lib59934

tag: virus _yn

tag: eos total


title: Mouse Epithelial Organoid, Young, 8-14wks, DMSO-culture Day 10, sample206809

description: Library name: Mouse Epithelial Organoid-Young-206809-DMSO


title: Mouse Epithelial Organoid, Young, 8-14wks, culture Day 14, sample177437

description: Library name: Mouse Epithelial Organoid-Young-177437-D14


title: lib59923

description: Library name: lib59923

tag: lym total

tag: mac total


title: Mouse Epithelial Organoid, Young, 8-14wks, culture Day 2, sample206809

description: Library name: Mouse Epithelial Organoid-Young-206809-D2


title: lib59919

description: Library name: lib59919

tag: squ total

tag: epi total


title: Mouse Epithelial Organoid, Young, 8-14wks, culture day 14, sample178217

description: Library name: Mouse Epithelial Organoid-Young-178217-D14


title: siSCR control iMgls from experiment 3 rep 2

city: New York

first: Pinar

last: Ayata

state: New York

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mt Sinai

description: Library name: ID1-expt3-SCR-none2

data_processing:
Sequencing reads were quality checked and trimmed using Trim Galore (v0.6.4; a wrapper program implementing Cutadapt v2.9 and FastQC v0.11.9)
Reads were then mapped to the GRCh38 (hg38) human genome using the HISAT2 package (v2.2.0).
Quantification of reads was then performed using featureCounts (v2.0.0) against the Ensembl v99 annotation.
Assembly: hg38
Supplementary files format and content: tab separated barcode and features files

molecule: polyA RNA

source_name: iMgl

extract_protocol:
The RNA was extracted using RNeasy Plus Mini Kit (Qiagen #74136)
Libraries were prepared using the NEBNext Ultra II RNA Library Preparation Kit following the manufacturer's comments.

treatment_protocol: Cells were nucleofected with 50nM of SMARTPool ON-TARGETplus siRNA targeting human SPI1 (Dharmacon, L-010537-00-0005) or non-targeting pool (Dharmacon, D-001810-10-05).

value: iMgl

value: Female

tag: age

value: siSCR

tag: batch


title: siSPI1  iMgls from experiment 3  rep 2

description: Library name: ID1-expt3-SPI1-none2

tag: cell type


title: siSPI1  iMgls from experiment 3  rep 1

description: Library name: ID1-expt3-SPI1-none1


title: Mouse Epithelial Organoid, Young, 8-14wks, culture Day 14, sample206809

description: Library name: Mouse Epithelial Organoid-Young-206809-D14

tag: genotype


title: lib59921

description: Library name: lib59921

tag: tissue

tag: neut total

tag: enitrox


title: lib59916

description: Library name: lib59916

tag: Sex

tag: donorid

tag: treatment


title: lib59947

description: Library name: lib59947

tag: age months

tag: visit

tag: illness


title: lib59915

description: Library name: lib59915

tag: virus _yn

tag: eos total

tag: lym total


title: lib59913

description: Library name: lib59913

tag: mac total

tag: squ total

tag: epi total


title: siSPI1  iMgls from experiment 2  rep 2

description: Library name: ID1-expt2-SPI1-none2

tag: cell type

tag: age

tag: batch


title: siSCR control iMgls from experiment 3 rep 1

description: Library name: ID1-expt3-SCR-none1


title: lib59914

description: Library name: lib59914

tag: tissue

tag: neut total


title: siSPI1  iMgls from experiment 2  rep 1

description: Library name: ID1-expt2-SPI1-none1

tag: Sex


title: lib59908

description: Library name: lib59908

tag: donorid

tag: enitrox


title: siSCR control iMgls from experiment 2 rep 2

description: Library name: ID1-expt2-SCR-none2

tag: treatment


title: siSCR control iMgls from experiment 2 rep 1

description: Library name: ID1-expt2-SCR-none1


title: lib59583

description: Library name: lib59583

tag: age months

tag: visit


title: lib59581

description: Library name: lib59581

tag: illness

tag: virus _yn


title: siSPI1  iMgls from experiment 1 rep 2

description: Library name: ID1-expt1-SPI1-none2


title: lib59580

description: Library name: lib59580

tag: eos total

tag: lym total


title: siSPI1  iMgls from experiment 1 rep 1

description: Library name: ID1-expt1-SPI1-none1


title: lib59579

description: Library name: lib59579

tag: mac total

tag: squ total


title: siSCR control iMgls from experiment 1 rep 2

description: Library name: ID1-expt1-SCR-none2

tag: cell type


title: lib59563

description: Library name: lib59563

tag: epi total


title: siSCR control iMgls from experiment 1 rep 1

description: Library name: ID1-expt1-SCR-none1

tag: age

tag: batch


title: lib59561

description: Library name: lib59561

tag: tissue

tag: neut total


title: lib59557

description: Library name: lib59557

tag: Sex

tag: donorid


title: 2112-205

city: Chicago

first: Issam

middle: A

last: Awad

state: IL

address: 5841 S Maryland Avenue MC 3026, J 341 MC 3026, J 341

department: Neurological Surgery

institute: University of Chicago

description: Library name: IA1099

data_processing:
Adaptor trimming performed with sRNAbench from SRNAtoolbox version 0.0.4, with adapter minimum length of 10, adapter sequence "TGGAATTCTCGGGTGCCAAGG", no recursive trimming, and 1 allowed mismatch in the adapter.
Read Mapping to known libraries of Human miRNA was performed  using sRNAbench from SRNAtoolbox version 0.0.4. Wth hsa library as reference, species set for GRCh38_p13_mp, minimum read count of 2, number of mitmatches set to 1, seed = 19, hierarchical alignment type, isoMIR set to false.
Assembly: GRCh38_p13
Supplementary files format and content: tab-delimited text file include matrix with reads  mapped to mature miRNA from sense strand summarized by sRNAbench.

source_name: Blood plasma

extract_protocol:
RNAs was extracted using an RNA isolation kit (miRNeasy Serum/Plasma Kit (Qiagen, Venlo, Netherlands).
RNA libraries were prepared for sequencing using commercially available Illumina small RNA-Seq kits (San Diego, California, USA),

value: Blood plasma

tag: disease state

value: Familial cerebral cavernous malformations


title: CR4859

description: Library name: IA1097


title: lib59552

description: Library name: lib59552

tag: treatment

value: Placebo

tag: age months

tag: enitrox


title: lib59560

description: Library name: lib59560

tag: visit

tag: illness

tag: virus _yn


title: PO8390

description: Library name: IA1098


title: 2112-37

description: Library name: IA1095


title: lib59550

description: Library name: lib59550

tag: eos total

tag: lym total

tag: mac total


title: 2112-300

description: Library name: IA1094


title: lib59545

description: Library name: lib59545

value: Mepolizumab

tag: squ total

tag: epi total


title: lib59547

description: Library name: lib59547

value: female

value: Y


title: 2112-316

description: Library name: IA1096


title: lib59544

description: Library name: lib59544


title: lib59546

description: Library name: lib59546

value: Exacerbation

value: N


title: CD0138

description: Library name: IA1090


title: Aim3-7

description: Library name: IA1089

value: Healthy Young


title: lib59543

description: Library name: lib59543


title: JM4704

description: Library name: IA1093


title: Aim3-10

description: Library name: IA1088


title: lib59541

description: Library name: lib59541

value: Cold


title: Aim3-9

description: Library name: IA1087


title: Aim3-23

description: Library name: IA1085


title: lib59542

description: Library name: lib59542


title: Aim3-20

description: Library name: IA1086


title: lib59540

description: Library name: lib59540

value: cold


title: lib59539

description: Library name: lib59539


title: lib59530

description: Library name: lib59530


title: Aim3-24

description: Library name: IA1084


title: lib59523

description: Library name: lib59523


title: 2112-73

description: Library name: IA1092


title: Aim3-5

description: Library name: IA1082


title: Aim3-3

description: Library name: IA1083


title: lib59521

description: Library name: lib59521


title: lib59529

description: Library name: lib59529


title: lib59549

description: Library name: lib59549


title: BH6467

description: Library name: IA1078

value: Hereditary hemorrhagic telangiectasia


title: lib59524

description: Library name: lib59524

value: Nasal lavage


title: BH12948

description: Library name: IA1079


title: lib59513

description: Library name: lib59513


title: BH11775

description: Library name: IA1077


title: Aim3-4

description: Library name: IA1081


title: BH11784

description: Library name: IA1076


title: lib59504

description: Library name: lib59504


title: lib59505

description: Library name: lib59505


title: lib59518

description: Library name: lib59518


title: BH8782

description: Library name: IA1075


title: BH10405

description: Library name: IA1074


title: lib59499

description: Library name: lib59499


title: BH9468

description: Library name: IA1072


title: BH11581

description: Library name: IA1069

value: Sturge-Weber syndrome


title: BH11149

description: Library name: IA1068


title: lib59493

description: Library name: lib59493


title: lib59495

description: Library name: lib59495


title: BH14414

description: Library name: IA1067


title: lib59489

description: Library name: lib59489


title: BH11625

description: Library name: IA1066


title: lib59486

description: Library name: lib59486


title: BH11433

description: Library name: IA1064


title: lib59478

description: Library name: lib59478


title: BH11449

description: Library name: IA1063


title: lib59477

description: Library name: lib59477


title: lib59483

description: Library name: lib59483


title: BH11417

description: Library name: IA1062


title: lib59475

description: Library name: lib59475


title: BH10116

description: Library name: IA1060


title: lib59503

description: Library name: lib59503


title: lib59476

description: Library name: lib59476


title: BH4059

description: Library name: IA1073


title: lib59494

description: Library name: lib59494


title: lib59467

description: Library name: lib59467


title: lib59465

description: Library name: lib59465


title: lib59491

description: Library name: lib59491


title: lib59462

description: Library name: lib59462


title: lib59452

description: Library name: lib59452


title: BH13992

description: Library name: IA1061


title: BH11617

description: Library name: IA1065


title: lib59450

description: Library name: lib59450


title: lib59443

description: Library name: lib59443


title: lib59439

description: Library name: lib59439


title: WNA liver chronic exposure Replicate 2

type: RNA

city: Tokyo

first: Yousra

last: reda

state: 千葉県

address: Higashifukai Nagaryama Chiba, Hasumei ikei center E 103

country: Japan

institute: Tokyo University of Science

description: Biological replicate 2 of 3

hyb_protocol: Analyzed with Whole Rat Genome Microarray kit 22K (Agilent)

scan_protocol: Signal intensities were quantified with laser confocal scanner

data_processing: Analyzed with Feature Extraction software (Agilent) and R/Bioconductor version R-3.5.1.

organism: Rattus norvegicus

source_name: liver

label_protocol: RNA samples from brain or liver were labeled, linearly amplified by Low Input Quick Amp Labeling Kit and RNA Spike-In Kit (Agilent).

extract_protocol: RNA was extracted using RNase mini kit (Qiagen Inc, Maryland, USA) .

treatment_protocol: Rats were exposed to 1-bromopropane at 1,000 ppm for eight hours singly or for eight hours per dady for 28 days.

value: 4 week exposure to 1-bromoprropane

tag: strain

value: WNA/NUM

value: 4 week exposure to filtered air


title: lib59466

description: Library name: lib59466

tag: tissue


title: lib59438

description: Library name: lib59438

tag: neut total


title: lib59431

description: Library name: lib59431

tag: Sex


title: lib59427

description: Library name: lib59427

tag: donorid


title: F344 liver chronic exposure Replicate 3

description: Biological replicate 3 of 3


title: lib59428

description: Library name: lib59428


title: F344 liver chronic exposure Replicate 1

description: Biological replicate 1 of 3


title: lib59463

description: Library name: lib59463


title: lib59426

description: Library name: lib59426


title: WNA liver acute exposure Replicate 2

description: Biological replicate 2 of 3

value: 8 hour exposure to 1-bromoprropane

value: 8 hour exposure to filtered air


title: WNA liver acute exposure Replicate 3

description: Biological replicate 3 of 3


title: WNA liver chronic exposure Replicate 1

description: Biological replicate 1 of 3


title: lib59425

description: Library name: lib59425


title: WNA liver chronic exposure Replicate 3

description: Biological replicate 3 of 3


title: F344 liver acute exposure Replicate 3

description: Biological replicate 3 of 3


title: F344 liver chronic exposure Replicate 2

description: Biological replicate 2 of 3


title: WNA hippocampus chronic exposure Replicate 2

description: Biological replicate 2 of 3

source_name: hippocampus


title: lib59424

description: Library name: lib59424


title: WNA hippocampus chronic exposure Replicate 1

description: Biological replicate 1 of 3


title: lib59422

description: Library name: lib59422


title: lib59421

description: Library name: lib59421


title: lib59416

description: Library name: lib59416


title: lib59409

description: Library name: lib59409


title: lib59408

description: Library name: lib59408


title: F344 hippocampus chronic exposure Replicate 3

description: Biological replicate 3 of 3


title: lib59405

description: Library name: lib59405

value: Placebo


title: lib59407

description: Library name: lib59407


title: lib59404

description: Library name: lib59404


title: F344 hippocampus chronic exposure Replicate 2

description: Biological replicate 2 of 3


title: lib59403

description: Library name: lib59403


title: 3 month 5xfAD; Cd28-cKO, replicate 1

description:
Library name: Sample 12
10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation performed using Cell Ranger software
Assembly: mm10
Supplementary files format and content: tab separated barcode and features files

source_name: Forebrain microglia

extract_protocol:
Mouse forebrain was homogenized in ice cold HBSS to release cells. Homogenate was mixed with Percoll and spun down to get single cell suspension. Cells were stained with anti- CD45 and CD11B fluorescently tagged antibodies, and incubated for 30 minutes. DyeCycle Violet was added and microglia were sorted on the FACS Aria II (live microglia defined as DyeCycle Violet negative, CD45 intermediate, CD11B positive). Cells were then spun down, counted, and submitted for single cell RNA-seq library preparation.
Library prepared according to manufacurer's instructions (single cell 3' GEX, 10x Genomics)

value: Forebrain microglia

tag: cell type

value: microglia

tag: genotype

value: 5xFAD, Cd28fl/fl, Cx3cr1creERT2/+

tag: age

value: 3 month

tag: batch


title: Monozygotic twin, MA-10

type: genomic

city: Daejeon

first: MUNJEONG

last: CHO

address: 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

country: South Korea

institute: Korea Research Institute of Bioscience &Biotechnology

description: Monozygotic twins

hyb_protocol: Illumina standard protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended

data_processing:
R packages: minfi
normalized_data.txt (Average Beta normalized (minfi))
non-normalized_data.txt (Average Beta raw )

label: Cy5 and Cy3

molecule: genomic DNA

source_name: blood

label_protocol: Illumina beadchip kit and standard protocol

extract_protocol: DNA was extracted from placenta blood

tag: monozygotic twins

value: placenta blood

tag: gender

value: female


title: WNA liver acute exposure Replicate 1

description: Biological replicate 1 of 3

tag: treatment


title: F344 liver acute exposure Replicate 2

description: Biological replicate 2 of 3


title: Monozygotic twin, MA-6

description: Monozygotic twins


title: Monozygotic twin, MA-9

description: Monozygotic twins


title: lib59402

description: Library name: lib59402

tag: age months

tag: visit

tag: illness

tag: virus _yn

tag: eos total

tag: enitrox


title: WNA hippocampus chronic exposure Replicate 3

description: Biological replicate 3 of 3

tag: strain


title: WNA hippocampus acute exposure Replicate 2

description: Biological replicate 2 of 3


title: F344 liver acute exposure Replicate 1

description: Biological replicate 1 of 3


title: 3 month control

description:
Library name: Sample 10
10x Genomics

tag: tissue

value: Control


title: WNA hippocampus acute exposure Replicate 3

description: Biological replicate 3 of 3


title: F344 hippocampus chronic exposure Replicate 1

description: Biological replicate 1 of 3


title: Monozygotic twin, MA-5

description: Monozygotic twins


title: F344 hippocampus acute exposure Replicate 2

description: Biological replicate 2 of 3


title: lib59401

description: Library name: lib59401

tag: Sex

value: N

tag: lym total

tag: mac total

tag: squ total

tag: epi total

tag: neut total


title: Monozygotic twin, MA-8

description: Monozygotic twins

tag: monozygotic twins


title: 6 month 5xFAD; Cd28-cKO, replicate 1

description:
Library name: Sample 9
10x Genomics

tag: cell type

tag: genotype

tag: age

value: 6 month

tag: batch


title: Monozygotic twin, MA-7

description: Monozygotic twins

tag: gender


title: 3 month 5xFAD, replicate 1

description:
Library name: Sample 11
10x Genomics


title: lib59400

description: Library name: lib59400

value: Nasal lavage

tag: donorid

tag: treatment

tag: age months

tag: visit

tag: illness

tag: virus _yn


title: Monozygotic twin, MA-3

description: Monozygotic twins

tag: tissue

value: male


title: F344 hippocampus acute exposure Replicate 3

description: Biological replicate 3 of 3

tag: strain


title: 6 month 5xFAD, replicate 1

description:
Library name: Sample 8
10x Genomics


title: lib59390

description: Library name: lib59390

tag: Sex

tag: eos total

tag: lym total

tag: mac total

tag: squ total

tag: enitrox


title: Monozygotic twin, MA-2

description: Monozygotic twins

tag: monozygotic twins


title: Monozygotic twin, MA-1

description: Monozygotic twins


title: 6 month control, replicate 1

description:
Library name: Sample 7
10x Genomics

tag: cell type

tag: genotype

tag: age

tag: batch


title: Monozygotic twin, MCDA034

description: Monozygotic twins

tag: gender


title: lib59388

description: Library name: lib59388

tag: donorid

tag: treatment

value: Mepolizumab

tag: age months

tag: visit

value: Y

tag: epi total

tag: neut total


title: 3 month 5xFAD; Cd28-cKO

description:
Library name: Sample 6
10x Genomics

tag: tissue


title: Monozygotic twin, MCDA033

description: Monozygotic twins


title: Monozygotic twin, MCDA024

description: Monozygotic twins


title: Monozygotic twin, MCDA023

description: Monozygotic twins


title: WNA hippocampus acute exposure Replicate 1

description: Biological replicate 1 of 3

tag: strain

value: WNA/NUM


title: lib59386

description: Library name: lib59386

tag: Sex

value: cold

tag: illness

value: Cold

tag: virus _yn

tag: eos total

tag: lym total

tag: mac total


title: 3 month 5xFAD

description:
Library name: Sample 5
10x Genomics

tag: cell type

tag: genotype

tag: age


title: Monozygotic twin, MCDA022

description: Monozygotic twins

tag: monozygotic twins

tag: gender


title: Monozygotic twin, MCDA031

description: Monozygotic twins


title: F344 hippocampus acute exposure Replicate 1

description: Biological replicate 1 of 3

tag: treatment

value: 8 hour exposure to 1-bromoprropane

value: 8 hour exposure to filtered air


title: 8 month 5xFAD, replicate 2

description:
Library name: Sample 4
10x Genomics

value: Forebrain microglia

value: microglia

value: 8 month

tag: batch


title: 8 month control, replicate 2

description:
Library name: Sample 3
10x Genomics


title: Monozygotic twin, MA-4

description: Monozygotic twins

value: placenta blood


title: lib59384

description: Library name: lib59384

value: female

tag: donorid

value: Placebo

tag: age months

tag: visit

tag: squ total

tag: epi total

tag: enitrox


title: Monozygotic twin, MCDA021

description: Monozygotic twins

tag: tissue


title: Monozygotic twin, MCDA019

description: Monozygotic twins


title: Monozygotic twin, MCDA020

description: Monozygotic twins


title: Monozygotic twin, MCDA016

description: Monozygotic twins


title: Monozygotic twin, MCDA015

description: Monozygotic twins


title: lib59382

description: Library name: lib59382

tag: Sex

tag: illness

tag: virus _yn

tag: eos total

tag: neut total


title: lib59377

description: Library name: lib59377

tag: lym total

tag: mac total


title: 8 month control, replicate 1

description:
Library name: Sample 1
10x Genomics

tag: cell type

tag: genotype

value: Control

tag: age


title: Monozygotic twin, MCDA018

description: Monozygotic twins

tag: monozygotic twins

tag: gender


title: Mouse uterus, Aged3-9, 53-65wks

description: Library name: Mouse uterus Aged3-9 MH260

source_name: uterus

value: uterus

value: wildtype

tag: developmental stage


title: Monozygotic twin, MCDA032

description: Monozygotic twins

value: male


title: Monozygotic twin, MCDA017

description: Monozygotic twins


title: lib59387

description: Library name: lib59387

value: Nasal lavage

tag: donorid

tag: treatment

value: Mepolizumab

tag: age months

tag: visit

tag: squ total


title: lib59376

description: Library name: lib59376

tag: tissue

tag: Sex

tag: illness

tag: epi total

tag: enitrox


title: Monozygotic twin, MCDA013

description: Monozygotic twins


title: Monozygotic twin, MCDA014

description: Monozygotic twins


title: Monozygotic twin, MCDA008

description: Monozygotic twins


title: lib59385

description: Library name: lib59385

tag: virus _yn

tag: eos total

tag: lym total

tag: mac total

tag: neut total


title: Mouse uterus, Aged3-8, 53-65wks

description: Library name: Mouse uterus Aged3-8 MH249

tag: genotype


title: Monozygotic twin, MCDA007

description: Monozygotic twins

tag: monozygotic twins

tag: gender


title: Monozygotic twin, MCDA010

description: Monozygotic twins


title: Mouse uterus, Aged3-7, 53-65wks

description: Library name: Mouse uterus Aged3-7 MH34

tag: developmental stage


title: lib59375

description: Library name: lib59375

tag: donorid

tag: treatment

tag: age months

value: N


title: Monozygotic twin, MCDA009

description: Monozygotic twins

tag: tissue


title: Mouse uterus, Aged3-6, 53-65wks

description: Library name: Mouse uterus Aged3-6 MH44


title: lib59356

description: Library name: lib59356

tag: Sex

tag: visit

value: Y

tag: squ total


title: Monozygotic twin, MCDA006

description: Monozygotic twins


title: 8 month 5xFAD, replicate 1

description:
Library name: Sample 2
10x Genomics

tag: cell type

tag: age

tag: batch


title: Mouse uterus, Aged3-5, 53-65wks

description: Library name: Mouse uterus Aged3-5 MH253


title: Monozygotic twin, MCDA005

description: Monozygotic twins


title: lib59352

description: Library name: lib59352

tag: illness

tag: virus _yn

tag: eos total

tag: lym total

tag: epi total

tag: enitrox


title: Monozygotic twin, MCDA004

description: Monozygotic twins

tag: monozygotic twins

tag: gender


title: Monozygotic twin, MCDA003

description: Monozygotic twins


title: lib59343

description: Library name: lib59343

tag: donorid

tag: treatment

tag: mac total

tag: neut total


title: Monozygotic twin, MCDA002

description: Monozygotic twins

tag: tissue


title: Mouse uterus, Aged3-3, 53-65wks

description: Library name: Mouse uterus Aged3-3 MH245

tag: genotype

tag: developmental stage


title: Monozygotic twin, MCDA001

description: Monozygotic twins


title: Monozygotic twin, MC-9-2

description: Monozygotic twins


title: lib59367

description: Library name: lib59367

tag: Sex

tag: age months

tag: visit

tag: squ total


title: Mouse uterus, Aged3-2, 53-65wks

description: Library name: Mouse uterus Aged3-2 MH242


title: Monozygotic twin, MC-10-2

description: Monozygotic twins


title: Monozygotic twin, MC-9-1

description: Monozygotic twins


title: Mouse uterus, Aged3-1, 53-65wks

description: Library name: Mouse uterus Aged3-1 MH51


title: lib59338

description: Library name: lib59338

tag: illness

tag: virus _yn

tag: eos total


title: Monozygotic twin, MC-8-1

description: Monozygotic twins


title: Mouse uterus, Aged2-6, 41-48wks

description: Library name: Mouse uterus Aged2-6 MH240


title: Monozygotic twin, MC-10-1

description: Monozygotic twins


title: lib59337

description: Library name: lib59337

tag: lym total

tag: epi total

tag: enitrox


title: Monozygotic twin, MC-8-2

description: Monozygotic twins

tag: monozygotic twins

tag: gender


title: lib59336

description: Library name: lib59336

tag: donorid

tag: treatment

tag: mac total


title: Monozygotic twin, MC-7-2

description: Monozygotic twins

tag: tissue


title: Mouse uterus, Aged2-5, 41-48wks

description: Library name: Mouse uterus Aged2-5 MH236

tag: genotype

tag: developmental stage


title: lib59335

description: Library name: lib59335

tag: Sex

tag: age months

tag: neut total


title: Monozygotic twin, MC-5-2

description: Monozygotic twins


title: Mouse uterus, Aged2-4, 41-48wks

description: Library name: Mouse uterus Aged2-4 MH237


title: Mouse uterus, Aged3-4, 53-65wks

description: Library name: Mouse uterus Aged3-4 MH246


title: lib59339

description: Library name: lib59339

tag: visit

tag: illness

tag: squ total


title: Monozygotic twin, MC-6-2

description: Monozygotic twins


title: Monozygotic twin, MC-4-2

description: Monozygotic twins


title: Monozygotic twin, MC-7-1

description: Monozygotic twins


title: Monozygotic twin, MC-6-1

description: Monozygotic twins


title: lib59332

description: Library name: lib59332

tag: virus _yn

tag: eos total

tag: lym total


title: lib59334

description: Library name: lib59334

value: Exacerbation

tag: epi total

tag: enitrox


title: Mouse uterus, Aged2-2, 41-48wks

description: Library name: Mouse uterus Aged2-2 MH234


title: Monozygotic twin, MC-4-1

description: Monozygotic twins

tag: monozygotic twins

tag: gender


title: Monozygotic twin, MC-3-2

description: Monozygotic twins


title: Monozygotic twin, MC-3-1

description: Monozygotic twins


title: lib59305

description: Library name: lib59305

tag: donorid

tag: treatment

tag: mac total


title: Mouse uterus, Aged2-1, 41-48wks

description: Library name: Mouse uterus Aged2-1 MH231

tag: tissue

tag: genotype

tag: developmental stage


title: lib59300

description: Library name: lib59300

tag: Sex

tag: age months

tag: neut total


title: Monozygotic twin, MC-1-2

description: Monozygotic twins


title: Mouse uterus, Aged1-4, 27-37wks

description: Library name: Mouse uterus Aged1-4 MH228


title: Monozygotic twin, MC-1-1

description: Monozygotic twins


title: Monozygotic twin, MC-2-1

description: Monozygotic twins


title: Monozygotic twin, MC-2-2

description: Monozygotic twins


title: Monozygotic twin, DC-38-2

description: Monozygotic twins


title: Mouse uterus, Aged1-3, 27-37wks

description: Library name: Mouse uterus Aged1-3 MH227


title: Monozygotic twin, DC-38-1

description: Monozygotic twins


title: lib59299

description: Library name: lib59299

tag: visit

tag: illness

tag: squ total


title: Mouse uterus, Aged1-2, 27-37wks

description: Library name: Mouse uterus Aged1-2 MH225


title: Monozygotic twin, MC-5-1

description: Monozygotic twins


title: Monozygotic twin, DC-37-2

description: Monozygotic twins


title: lib59291

description: Library name: lib59291

tag: virus _yn

tag: eos total

tag: lym total


title: Mouse uterus, Aged2-3, 41-48wks

description: Library name: Mouse uterus Aged2-3 MH233


title: Monozygotic twin, DC-36-2

description: Monozygotic twins

tag: monozygotic twins


title: Monozygotic twin, DC-37-1

description: Monozygotic twins

tag: gender


title: lib59293

description: Library name: lib59293

tag: donorid

tag: epi total

tag: enitrox


title: Monozygotic twin, DC-36-1

description: Monozygotic twins

tag: tissue


title: Mouse uterus, Young8, 8-14wks

description: Library name: Mouse uterus Young8 MH59

tag: genotype

value: young


title: Mouse uterus, Aged1-1, 27-37wks

description: Library name: Mouse uterus Aged1-1 MH223

tag: developmental stage


title: lib59290

description: Library name: lib59290

tag: Sex

tag: treatment

tag: mac total


title: lib42569

description: Library name: lib42569

tag: age months

tag: visit

tag: neut total


title: Mouse uterus, Young7, 8-14wks

description: Library name: Mouse uterus Young7 MH55


title: Monozygotic twin, DC-34-1

description: Monozygotic twins


title: lib42566

description: Library name: lib42566

tag: illness

tag: virus _yn

tag: squ total


title: Monozygotic twin, DC-35-2

description: Monozygotic twins

tag: monozygotic twins


title: Monozygotic twin, DC-35-1

description: Monozygotic twins

tag: gender


title: Monozygotic twin, DC-33-2

description: Monozygotic twins


title: lib42564

description: Library name: lib42564

tag: donorid

tag: eos total

tag: lym total


title: Mouse uterus, Young6, 8-14wks

description: Library name: Mouse uterus Young6 MH60

tag: tissue


title: Mouse uterus, Young5, 8-14wks

description: Library name: Mouse uterus Young5 MH54

tag: genotype


title: Monozygotic twin, DC-31-2

description: Monozygotic twins


title: lib42563

description: Library name: lib42563

value: cold

value: Cold

tag: epi total

tag: enitrox


title: Monozygotic twin, DC-31-1

description: Monozygotic twins


title: Monozygotic twin, DC-29-1

description: Monozygotic twins


title: Mouse uterus, Young4, 8-14wks

description: Library name: Mouse uterus Young4 MH53

tag: developmental stage


title: lib42562

description: Library name: lib42562

tag: Sex

tag: treatment

tag: mac total


title: lib42561

description: Library name: lib42561

tag: age months

tag: visit

tag: neut total


title: Monozygotic twin, DC-30-2

description: Monozygotic twins


title: Mouse uterus, Young3, 8-14wks

description: Library name: Mouse uterus Young3 MH52


title: Monozygotic twin, DC-29-2

description: Monozygotic twins


title: Mouse uterus, Young2, 8-14wks

description: Library name: Mouse uterus Young2 MH270


title: Monozygotic twin, DC-34-2

description: Monozygotic twins


title: Monozygotic twin, DC-28-2

description: Monozygotic twins


title: Monozygotic twin, DC-27-2

description: Monozygotic twins


title: Monozygotic twin, DC-28-1

description: Monozygotic twins


title: Monozygotic twin, DC-30-1

description: Monozygotic twins


title: lib42552

description: Library name: lib42552

tag: illness

tag: virus _yn

tag: squ total


title: lib42553

description: Library name: lib42553

tag: donorid


title: Monozygotic twin, DC-27-1

description: Monozygotic twins

tag: monozygotic twins

tag: gender


title: 5xFAD CSF1Ri

description:
Library name: FAD PLX
10x Genomics

data_processing:
The raw read data were demultiplexed, aligned, and analyzed using 10X Cell Ranger (v2.1.0). To capture unspliced pre-mRNA in the single-nucleus RNA expression assay, intronic regions in the 10X Cell Ranger mm10 v1.2.0 reference were marked as exonic as suggested by 10X for pre-mRNA reference generation.
Assembly: Mouse mm10
Supplementary files format and content: Tab separated barcode and features files.

source_name: Cortex

extract_protocol:
Briefly, frozen cortex tissue was homogenized in 0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine pH 7.8. The buffers were supplemented with 10 μl/ml RNasin, Superasin, and EDTA-free protease inhibitor cocktail. The homogenate was then spun through a 29% iodixanol cushion. The resulting nuclear pellet was resuspended in 0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine pH 7.8, supplemented with 10 μM DyeCycle Ruby, and 10% donkey serum. Microglial nuclei were sorted in a BD FACS Aria cell sorter by gating for the lowest DyeCycle Ruby, which indicates nuclei singlets and a high GFP signal
Library prepared according to manufacurer's instructions (single cell 3' GEX, 10x Genomics). In brief, gel-bead in emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs using Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly-A-tailing, adaptor ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (Thermofisher) analysis and then sequenced in paired-end mode on a HiSeq 2500 instrument (Illumina, San Diego, CA) targeting a depth of 50,000–100,000 reads per nucleus/cell.

tag: tissue

value: Cortex

tag: age

value: 6 months

tag: cell type

value: Micorglia

value: PLX 5622 chow for 6 weeks

tag: batch

value: Experiment 2


title: Monozygotic twin, DC-25-2

description: Monozygotic twins

value: placenta blood

value: female


title: Monozygotic twin, DC-33-1

description: Monozygotic twins


title: Monozygotic twin, DC-25-1

description: Monozygotic twins


title: 5xFAD Control

description:
Library name: FADTV 163
10x Genomics

value: Microglia

tag: genotype

value: control chow 6 weeks


title: lib42548

description: Library name: lib42548

value: Nasal lavage

tag: Sex

value: Placebo

tag: eos total

tag: lym total

tag: epi total

tag: enitrox


title: lib42545

description: Library name: lib42545

tag: treatment

tag: age months

tag: visit

tag: mac total

tag: neut total


title: 5xFAD; PU.1-high

description:
Library name: FADTV 84
10x Genomics

value: Experiment 1


title: Monozygotic twin, DC-26-2

description: Monozygotic twins

tag: monozygotic twins


title: Monozygotic twin, DC-24-2

description: Monozygotic twins

tag: gender


title: lib42544

description: Library name: lib42544

tag: tissue

tag: donorid

tag: illness

tag: virus _yn

value: Y

tag: squ total


title: Monozygotic twin, DC-23-2

description: Monozygotic twins


title: Monozygotic twin, DC-24-1

description: Monozygotic twins


title: Monozygotic twin, DC-26-1

description: Monozygotic twins


title: lib42538

description: Library name: lib42538

tag: Sex

value: Mepolizumab


title: 5xFAD; PU.1-low

description:
Library name: FADPu 287
10x Genomics

tag: age

tag: cell type

tag: genotype

tag: batch


title: Mouse uterus, Young1, 8-14wks

description: Library name: Mouse uterus Young1 MH267

value: uterus

value: wildtype

tag: developmental stage

value: young


title: Monozygotic twin, DC-23-1

description: Monozygotic twins


title: 5xFAD

description:
Library name: FADPu 152
10x Genomics

value: Cortex


title: lib42535

description: Library name: lib42535

tag: treatment

tag: age months

tag: eos total

tag: lym total

tag: epi total

tag: enitrox


title: Monozygotic twin, DC-18-2

description: Monozygotic twins

tag: monozygotic twins

tag: tissue

tag: gender

value: male


title: Monozygotic twin, DC-22-2

description: Monozygotic twins


title: Monozygotic twin, DC-18-1

description: Monozygotic twins


title: lib42530

description: Library name: lib42530

tag: donorid

tag: visit

tag: illness

tag: virus _yn

tag: mac total

tag: neut total


title: lib42526

description: Library name: lib42526

tag: Sex

tag: squ total


title: Monozygotic twin, DC-12-2

description: Monozygotic twins


title: RNAseq_NGN3_48h_r1_2211

city: Basel

first: Sevi

last: Durdu

address: Fabrikstrasse 24

department: Genome Regulation

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Library name: Sample90

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing samples generated by Illumina HiSeq sequencing. Illumina RTA 3.4.4 and bcl2fastq2 v2.20 was used for basecalling and demultiplexing samples generated by Illumina NovaSeq sequencing. RNA-seq reads were mapped to mm10 using STAR aligner (Dobin et al, Bioinformatics 2013).
Assembly: mm10
Supplementary files format and content: Rsubread Bioconductor powered by featureCounts function (Liao et al, Nucleic Acids Research, 2019) was used to generate gene count table(s) at the level of "gene_name" based on the gene annotation from the GENCODE release M25 with default parameters.

source_name: embryonic stem cells

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma).

extract_protocol:
RNA for RNA-seq was isolated using Norgen Single Cell RNA Purification Kit, following the manufacturer’s instructions.
Sequencing libraries were prepared from purified total RNA for each sample using TruSeq stranded Total RNA Library Prep (Illumina), or TruSeq stranded mRNA Library Prep (Illumina).

treatment_protocol: mESCs were induced for differentiation by expressing NGN2 or MyoD1. 100000 cells per sample was collected for RNA extraction.

value: embryonic stem cells

tag: cell line

tag: cell type

value: mESC

tag: genotype

tag: treatment

value: 48 hours N2B27(w/oVitA)+dox

tag: mouse strain

tag: experiment id


title: RNAseq_NGN3_48h_r2_2211

description: Library name: Sample91


title: RNAseq_NGN3_6h_r2_2211

description: Library name: Sample89

value: 6 hours N2B27(w/oVitA)+dox


title: Monozygotic twin, DC-12-1

description: Monozygotic twins

tag: monozygotic twins

value: placenta blood


title: Monozygotic twin, DC-11-2

description: Monozygotic twins

tag: tissue

value: female


title: lib42523

description: Library name: lib42523

tag: age months

tag: eos total

tag: lym total

tag: epi total

tag: enitrox


title: Monozygotic twin, DC-22-1

description: Monozygotic twins

tag: gender


title: lib42519

description: Library name: lib42519

tag: donorid

tag: visit

tag: illness

tag: virus _yn

value: N

tag: mac total

tag: neut total


title: Monozygotic twin, DC-11-1

description: Monozygotic twins


title: Monozygotic twin, DC-7-2

description: Monozygotic twins


title: Monozygotic twin, DC-7-1

description: Monozygotic twins


title: ChIPseq_GFP_6h_2190

description: Library name: Sample 72

library_source: genomic

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for single-read experiments. Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for paired-read experiments. ChIP-seq samples were aligned to the mm10 assembly of the mouse genome using QuasR (Gaidatzis et al, Bioinformatics 2015), which internally uses Bowtie (Langmead, Genome Biology 2009). Bowtie was run with QuasR default parameters.
Assembly: mm10
Supplementary files format and content: ExportWig function from the QuasR package was employed to generate the wig files with default parameters except scaling=1e6 and setting shift to 80 as the average of all samples after quantifying the estimated fragment length (half) or 'halfInsert' for paired-end.

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were grown for several passages at 37℃ 7% CO2 seeded on plates coated with 0.2% gelatin (Sigma) and maintained in serum/LIF (Dulbecco’s modified Eagle medium (DMEM, Invitrogen), supplemented with 15% fetal calf serum (Invitrogen), L-glutamine (Gibco), nonessential amino acids (Gibco), 0.001% 2-Mercaptoethanol (Sigma) and leukemia inhibitory factor (produced in-house).

extract_protocol:
DNA was purified with AmpureXP beads.
Immunoprecipitated DNA was subjected to library preparation (NEBNext Ultra II DNA Library Prep Kit, Illumina).

treatment_protocol: To induce expression with TETON system, cells were washed with PBS and treated with 1 μg/ml doxycycline (Sigma, no. D989) in induction media, also referred as N2B27w/oVitA, (DMEM/F12/Glutamax (LifeTech, no. 31331-028), 1× B27 without vitamin A (LifeTech, no. 12587-010), 1× N2 supplement (LifeTech, no. 17502-048), ) or in serum/LIF media as indicated.

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: chip antibody

value: Streptavidin (Thermo Fisher, 11205D)

tag: batch


title: Monozygotic twin, DC-10-2

description: Monozygotic twins

tag: monozygotic twins

tag: tissue


title: Monozygotic twin, DC-10-1

description: Monozygotic twins


title: lib42517

description: Library name: lib42517

value: Nasal lavage

tag: Sex

tag: age months

tag: eos total

tag: lym total

tag: squ total

tag: epi total


title: lib42514

description: Library name: lib42514

tag: donorid

value: Placebo

tag: visit

tag: illness

tag: virus _yn

tag: enitrox


title: Monozygotic twin, DC-6-1

description: Monozygotic twins

tag: gender


title: Monozygotic twin, DC-6-2

description: Monozygotic twins


title: ChIPseq_NGN3mut_6h_2190

description: Library name: Sample 71

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: Monozygotic twin, DC-5-2

description: Monozygotic twins

tag: monozygotic twins

tag: tissue


title: lib42513

description: Library name: lib42513

tag: Sex

tag: age months

value: cold

value: Exacerbation

value: Y

tag: mac total

tag: neut total


title: Monozygotic twin, DC-2-1

description: Monozygotic twins


title: Monozygotic twin, DC-2-2

description: Monozygotic twins


title: ChIPseq_NGN2bHLH_24h_1848

description: Library name: Sample 70

value: 24 hours N2B27(w/oVitA)+dox

tag: chip antibody

tag: batch


title: Monozygotic twin, DC-5-1

description: Monozygotic twins


title: lib42504

description: Library name: lib42504

tag: donorid

value: Mepolizumab

tag: visit

tag: eos total

tag: lym total

tag: squ total

tag: epi total


title: ChIPseq_NGN2bHLH_12h_1848

description: Library name: Sample 69

tag: cell line

tag: cell type

value: 12 hours N2B27(w/oVitA)+dox


title: ChIPseq_NGN2bHLH_6h_1848

description: Library name: Sample 68

tag: genotype

tag: treatment


title: Monozygotic twin, DC-3-2

description: Monozygotic twins

tag: monozygotic twins

tag: tissue

tag: gender

value: male


title: Monozygotic twin, DC-1-2

description: Monozygotic twins


title: lib42502

description: Library name: lib42502

tag: Sex

tag: age months

tag: illness

tag: virus _yn

tag: mac total

tag: enitrox


title: ChIPseq_NGN3_6h_2190

description: Library name: Sample 67

value: embryonic stem cells

tag: chip antibody

tag: batch


title: DAP_gst_1781

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for single-read experiments. Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for paired-read experiments. ChIP-seq samples were aligned to the mm10 assembly of the mouse genome using QuasR (Gaidatzis et al, Bioinformatics 2015), which internally uses Bowtie 2 (Langmead, Genome Biology 2009). Bowtie was run with QuasR default parameters.
Assembly: mm10
Supplementary files format and content: ExportWig function from the QuasR package was employed to generate the wig files with default parameters except scaling=1e6 and only for single-end experiments setting shift to 120.
Library strategy: DAP-seq

growth_protocol: Rosetta(DE3)pLysS Competent Cells (Millipore) were induced to express GST-tagged protein encoded in pGEX-6P-1 plasmids for DAPseq (NGN2, MyoD1, bHLH domains of TCF3-E12,TCF3-E47,TCF4,TCF12). 2ml fresh culture were added into 50ml LB and grow to an OD600 of 0.5 and induced with IPTG for 3 hours at 37DEgC for NGN2 and MyoD1 and 16DegC for TCFs. Cells were lysed and soluble fractions were mixed in combinations. GST tagged proteins were isolated using Promega MagneGST beads.

extract_protocol:
DNA was purified by AMPure beads with a ratio of 2:1 beads to sample volume.
Isolated DNA was subjected to library preparation (NEBNext Ultra II DNA Library Prep Kit, Illumina). In the library preparation protocol, samples were amplified using 12 PCR cycles.

treatment_protocol: Protocol was performed for Small-scale DAP-seq using E. coli-expressed recombinant protein as previously described (Bartlett et al, Nature Protocols, 2017) with modifications. Brielfy, freshly isolated GST-bHLH proteins bound to magnetic beads were incubated with 10ug of gemonic DNA sonicated to an average size range of 150-200bp for 1 hour in PBS. Beads were washed 4x with 200ul of PBS + 0.05%NP40, then washed 2x with 200ul PBS. Finally, beads were resuspended in 30ul 10 mM Tris-Cl, pH 8.5 + 2ul 10mg/ml Proteinase K and incubated at 50DegC for 3 hours.

value: mESC

value: DNMT1-/-; DNMT3a-/-; DNMT3b-/-

tag: treatment (proteins)

value: GST alone

tag: mouse strain

tag: experiment id


title: Monozygotic twin, DC-3-1

description: Monozygotic twins

value: placenta blood


title: lib42501

description: Library name: lib42501

value: female

tag: donorid

tag: visit

tag: eos total

tag: lym total

tag: squ total

tag: epi total

tag: neut total


title: RNAseq_NGN3_6h_r1_2211

description: Library name: Sample88

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: 6 hours N2B27(w/oVitA)+dox


title: Monozygotic twin, DC-1-1

description: Monozygotic twins

tag: monozygotic twins

tag: gender


title: RNAseq_MYOD1_48h_2294

value: 48 hours N2B27(w/oVitA)+dox


title: lib42499

description: Library name: lib42499

value: Nasal lavage

tag: Sex

tag: age months

tag: illness

tag: virus _yn

tag: mac total

tag: enitrox


title: control T cells replicate 2

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: Library name: T-cells-WT_rep2

data_processing:
A total of 11 ATAC-Seq libraries from PU.1-low microglia (n = 3) ,PU.1-high microglia (n = 3), wild-type microglia (n = 3), and wild-type T-cells (n = 2) were processed using the same pipeline for compatibility. Read quality was assessed using FastQC (v0.11.8). Reads were trimmed for adapter sequences using Trim Galore! (v0.6.6) and aligned to the to the mouse reference genome (GRCm38, GENCODE M25) using Bowtie2 (v2.2.8) with a maximum fragment length of 2000 bp (-X 2000) with default sensitivity settings. Reads aligned to mtDNA and noncanonical chromosomes were removed. Picard (v2.2.4) was used to remove duplicated reads. Post-filtering bam files for all samples were merged using the merge function from Samtools (v1.11), followed by Peak calling using MACS2 (v2.1.0) with parameters --nomodel, --nolambda, --keep-dup all, and --slocal 10000, optimized for paired data (-f BAMPE) using the mouse genome (-g mm). Blacklisted regions were removed before downstream analysis. Peak summits were extended +/- 200bp, and quantification of reads in peaks was performed using featureCounts from Subread (v2.0.1). Peaks that fell below the top 67% of peaks across all samples were filtered out as low signal regions. Coverage tracks were generated from Bam files using deepTools (v3.2.1) bamCoverage with parameters –normalizeUsingRPKM –binsize 10.
Assembly: GRCm38
Supplementary files format and content: RPKM normalized bigwig file for each sample (.bw)

source_name: Brain

extract_protocol:
Microglia were isolated using cold mechanical homogenization followed by FACS sorting. T cells were obtained from the spleen with cold mechanical homogenization followed by RBC lysis.
ATAC-seq libraries were prepared using the OMNI-ATAC protocol (Buenrostro et al., 2015). Briefly, nuclei were isolated from 40,000 FACS-sorted eYFP+ cells. Transposition was performed using Tn5 transposase (Illumina) at 37°C for 30 min, followed by DNA purification with the Zymo DNA Clean & Concentrator kit. Libraries were pre-amplified for five cycles using NEBNext High-Fidelity 2X PCR Master Mix. Additional amplification cycles were determined via qPCR. Double-sided size selection was performed using AMPure XP beads. Libraries were quantified via Qubit and analyzed by Bioanalyzer or TapeStation. Final libraries were pooled equimolarly and sequenced on an Illumina NovaSeq (2 × 150 bp), targeting ~40 million reads per sample.

treatment_protocol: Mice were gavaged at 4-6 weeks of age with six doses of 100 mg/kg of Tamoxifen (T5648, Sigma, St. Louis, MO) in corn oil (C8267, Sigma), separated by at least 48 hours between doses

value: Brain

value: T cells

value: Wild type

value: mice were gavaged at 4-6 weeks of age with six doses of 100 mg/kg of Tamoxifen (T5648, Sigma, St. Louis, MO) in corn oil (C8267, Sigma), separated by at least 48 hours between doses

tag: batch

value: batch 1


title: control replicate 2

description: Library name: WT_rep2

value: microglia


title: control T cells replicate 1

description: Library name: T-cells-WT_rep1


title: lib42498

description: Library name: lib42498

tag: donorid

value: Placebo

tag: visit

value: cold

value: Cold

value: N

tag: eos total

tag: lym total

tag: squ total


title: control replicate 3

description: Library name: WT_rep3

tag: tissue

tag: cell type


title: RNAseq_MYOD1_nodox48h_2294

value: embryonic stem cells

tag: cell line

value: mESC

tag: genotype

tag: treatment

value: 48 hours N2B27(w/oVitA)

tag: mouse strain

tag: experiment id


title: RNAseq_MYOD1_ESM_2294

value: 0 hour mESC (FCS/LIF)


title: control replicate 1

description: Library name: WT_rep1


title: lib42497

description: Library name: lib42497

tag: Sex

value: female

tag: age months

tag: illness

tag: epi total

tag: neut total


title: PU overexpression replicate 2

description: Library name: PU_OE_rep2

tag: batch


title: lib42493

description: Library name: lib42493

tag: donorid

value: Mepolizumab

tag: visit

tag: virus _yn

tag: mac total

tag: enitrox


title: RNAseq_MYOD1_72h_r2_2022

tag: tissue

tag: cell type

value: 72 hours N2B27(w/oVitA)+dox


title: lib42495

description: Library name: lib42495

value: Nasal lavage

tag: eos total

tag: lym total

tag: squ total


title: PU overexpression replicate 1

description: Library name: PU_OE_rep1

value: Brain

tag: genotype

tag: treatment


title: PU overexpression replicate 3

description: Library name: PU_OE_rep3


title: RNAseq_GFP_72h_r2_2022

tag: cell line

tag: mouse strain

tag: experiment id


title: RNAseq_MYOD1_72h_r1_2022


title: PU knockdown replicate 1

description: Library name: PU_KO_rep1

value: Spi1fl/+ , Cx3cr1CreErt2/+(Litt)

value: Mice were gavaged at 4-6 weeks of age with six doses of 100 mg/kg of Tamoxifen (T5648, Sigma, St. Louis, MO) in corn oil (C8267, Sigma), separated by at least 48 hours between doses


title: lib42487

description: Library name: lib42487

tag: Sex

tag: age months

tag: illness

tag: epi total

tag: neut total


title: RNAseq_GFP_72h_r1_2022


title: lib42500

description: Library name: lib42500

tag: donorid

tag: visit

tag: virus _yn

tag: mac total


title: 14 weeks of Ketogenic diet  Thermoneutrality, mouse ID 4

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

institute: ETH ZURICH / University of Zurich

description: Library name: KD_TN4

data_processing:
Kallisto used for reference alignment + transcript abundance quantification
R package DESeq2 used for differential gene expression analysis
Assembly: GRCm39
Supplementary files format and content: Transcript abundances in txt format

source_name: Liver

growth_protocol: The mice were fed chow diet, ketogenic diete or HFD at RT or TN

extract_protocol:
Total RNA was extracted by using Trizol
Novogen handled the lbrary preparation

treatment_protocol: The mice were at room temperature or Thermoneutrality for 14 weeks

tag: tissue

value: Liver

tag: diet

value: Ketogenic diet

value: Thermoneutrality


title: 14 weeks of Ketogenic diet  Thermoneutrality, mouse ID 24

description: Library name: KD_TN24


title: lib42486

description: Library name: lib42486

value: Placebo

tag: eos total

tag: lym total

tag: squ total

tag: enitrox


title: 14 weeks of Ketogenic diet  Thermoneutrality, mouse ID 20

description: Library name: KD_TN20

tag: treatment


title: RNAseq_MYOD1_24h_r2_2022

tag: cell line

tag: cell type

tag: genotype

value: 24 hours N2B27(w/oVitA)+dox

tag: mouse strain

tag: experiment id


title: 14 weeks of Ketogenic diet  Room Temperature, mouse ID 25

description: Library name: KD_RT25

value: Room Temeprature


title: lib42485

description: Library name: lib42485

tag: Sex

tag: age months

tag: illness

value: N

tag: epi total

tag: neut total


title: 14 weeks of Ketogenic diet  Room Temperature, mouse ID 21

description: Library name: KD_RT21

tag: tissue


title: RNAseq_MYOD1_24h_r1_2022

value: embryonic stem cells

value: mESC


title: PU knockdown replicate 3

description: Library name: PU_KO_rep3

value: microglia

value: mice were gavaged at 4-6 weeks of age with six doses of 100 mg/kg of Tamoxifen (T5648, Sigma, St. Louis, MO) in corn oil (C8267, Sigma), separated by at least 48 hours between doses

tag: batch

value: batch 1


title: lib42480

description: Library name: lib42480

value: female

tag: donorid

tag: visit

tag: virus _yn

value: Y

tag: eos total

tag: mac total


title: PU knockdown replicate 2

description: Library name: PU_KO_rep2

value: Brain

tag: treatment


title: RNAseq_GFP_24h_r2_2022

tag: cell line

tag: cell type


title: lib42479

description: Library name: lib42479

value: Nasal lavage

tag: lym total

tag: squ total

tag: enitrox


title: 14 weeks of HFD  Thermoneutrality , mouse ID 7

description: Library name: HFD_TN7

tag: diet

value: HFD


title: 14 weeks of HFD Thermoneutrality , mouse ID 14

description: Library name: HFD_TN14

value: Liver


title: RNAseq_GFP_24h_r1_2022

tag: genotype

tag: mouse strain

tag: experiment id


title: 14 weeks of HFD Thermoneutrality, mouse ID 10

description: Library name: HFD_TN10

tag: tissue


title: lib42478

description: Library name: lib42478

tag: Sex

value: Mepolizumab

tag: age months

tag: illness

tag: epi total

tag: neut total


title: 14 weeks of Ketogenic diet  Thermoneutrality, mouse ID 23

description: Library name: KD_TN23

value: Ketogenic diet

value: Thermoneutrality


title: lib42477

description: Library name: lib42477

tag: donorid

tag: visit

tag: virus _yn

tag: eos total

tag: mac total


title: 14 weeks of HFD  Room Temperature, mouse ID 6

description: Library name: HFD_RT6

tag: treatment


title: lib42476

description: Library name: lib42476

value: cold

value: Cold

tag: lym total

tag: squ total

tag: enitrox


title: RNAseq_NGN2_48h_r2_2211

tag: cell line

tag: cell type

tag: genotype

value: 48 hours N2B27(w/oVitA)+dox

tag: mouse strain


title: 14 weeks of HFD  Room Temperature, mouse ID 2

description: Library name: HFD_RT2

tag: tissue

tag: diet

value: Room Temeprature


title: RNAseq_MYOD1_48h_r1_2211

value: embryonic stem cells

value: mESC

tag: experiment id


title: 14 weeks of Chow Diet Thermoneutrality, mouse ID 19 Control

description: Library name: CD_TN19

value: Chow diet


title: 14 weeks of Chow Diet Thermoneutrality, mouse ID 18 Control

description: Library name: CD_TN18


title: lib42475

description: Library name: lib42475

tag: Sex

value: Placebo

tag: age months

tag: illness

tag: epi total

tag: neut total


title: 14 weeks of Ketogenic diet  Room Temperature, mouse ID 22

description: Library name: KD_RT22


title: 14 weeks of Ketogenic diet  Room Temperature, mouse ID 23

description: Library name: KD_RT23


title: RNAseq_GFP_48h_r2_2211


title: 14 weeks of Chow Diet Room Temperature, mouse ID 17 Control

description: Library name: CD_RT17


title: lib42474

description: Library name: lib42474

value: female

tag: donorid

tag: visit

tag: virus _yn

value: N

tag: eos total

tag: mac total


title: lib42473

description: Library name: lib42473

tag: treatment

value: Exacerbation

value: Y

tag: lym total

tag: squ total

tag: enitrox


title: 14 weeks of Chow Diet Thermoneutrality, mouse ID 17 Control

description: Library name: CD_TN17

tag: tissue


title: 14 weeks of Chow Diet Room Temperature, mouse ID 19 Control

description: Library name: CD_RT19

tag: diet


title: 14 weeks of HFD  Room Temperature, mouse ID 8

description: Library name: HFD_RT8

value: HFD


title: RNAseq_NGN2_48h_r1_2211

tag: cell line

tag: cell type

tag: genotype

tag: mouse strain

tag: experiment id


title: RNAseq_MYOD1_48h_r2_2211


title: RNAseq_GFP_48h_r1_2211


title: 14 weeks of Chow Diet Room Temperature, mouse ID 11 Control

description: Library name: CD_RT11

value: Liver


title: GFP, control, rep5

city: Wageningen

first: Wilma

last: Van Esse

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University & Research

description:
greenscreen_merged_all_peaks.broadPeak
TB1_all_control_lambda.bdg.tdf

data_processing:
Raw paired DAP-seq reads were cleaned using Trimmomatic 0.39 (Bolger et al., 2014). (ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36), where adapters.fa is a file containing nucleotide sequences of the used adapters (Supplemental Table 1). Paired reads were mapped to the Barley MorexV3 reference genome (Mascher et al., 2021) using BWA-MEM v0.7.17 (Li, 2013, preprint; Li and Durbin, 2010). Peak calling was done using MACS2 v2.2.7.1 (Zhang et al., 2008), using the callpeak function, where the VRS5 samples were compared to the GFP control samples. The genome size parameter was set to 5.4e9, corresponding to the barley genome size. The “KEEP-DUP” parameter was set to “auto”, meaning that the MACS2 algorithm calculates the number of reads that are allowed to be identical, leading to an allowed number two identical reads.
Genomic regions that had a high number of reads in the control samples (GFP-FLAG) were identified using the “greenscreen” method (Klasfeld et al., 2022). Called peaks overlapping with a “greenscreen” region were filtered out using bedtools’ intersect function (Quinlan and Hall, 2010). Peaks with a q < 10-10 were kept and considered true peaks.
Assembly: MorexV3
Supplementary files format and content: greenscreen_merged_all_peaks.broadPeak contains enriched regions in the genome that are present in the control samples, these are later used for filtering.
Supplementary files format and content: TB1_all_q10_greenscreen.bed contains all the TB1 enriched peaks in the genome compared to the control outside of the greenscreen regions and have a q-value (p-adj) <  1E-10
Supplementary files format and content: bdg.tdf are the bedgraph files of the mapped reads agains the genome of TB1 and control
Library strategy: DAP-seq

organism: Hordeum vulgare

source_name: developing inflorescence

growth_protocol: For each replicate, genomic DNA was extracted from 100 mg developing inflorescences of barley cv. Morex, four weeks after sowing in 84-well trays (Waddington stage ~W4) using the DNeasy Plant Mini kit (Qiagen)

extract_protocol:
using the DNeasy Plant Mini kit (Qiagen)
The DNA was fragmented with ten sonication steps of ten seconds using the Sonicator 150 (MSE) and allowing 45 seconds of rest on ice between each step. The fragmented DNA was end-repaired using the End-It kit (Lucigen) and A-tailed using Klenow fragment (3’-5’ exo-; NEB). The truncated Illumina Y-adapter was ligated to the DNA using T4 DNA ligase (Promega).

value: developing inflorescence

value: Morex

value: GFP-FLAG


title: GFP, control, rep6


title: RNAseq_MYOD1_6h_r2_2211

value: 6 hours N2B27(w/oVitA)+dox


title: 14 weeks of HFD  Room Temperature, mouse ID 1

description: Library name: HFD_RT1


title: lib42472

description: Library name: lib42472

value: Nasal lavage

tag: Sex

tag: age months

tag: illness

tag: epi total

tag: neut total


title: lib42464

description: Library name: lib42464

tag: donorid

value: Mepolizumab

tag: visit

tag: virus _yn

tag: eos total

tag: mac total


title: GFP, control, rep3

tag: tissue

tag: treatment


title: RNAseq_MYOD1_6h_r1_2211

tag: cell line


title: lib42462

description: Library name: lib42462

tag: lym total

tag: squ total

tag: enitrox


title: GFP, control, rep2

tag: genotype


title: GFP, control, rep4


title: lib42460

description: Library name: lib42460

tag: Sex


title: GFP, control, rep1


title: VRS5, rep6

description:
TB1_all_q10_greenscreen.bed
TB1_all.bdg.tdf


title: 14 weeks of Chow Diet Thermoneutrality , mouse ID 16 Control

description: Library name: CD_TN16

tag: diet

value: Thermoneutrality


title: RNAseq_NGN2_6h_r2_2211

value: embryonic stem cells

tag: cell type

tag: mouse strain

tag: experiment id


title: RNAseq_NGN2_6h_r1_2211

value: mESC


title: VRS5, rep5


title: 14 weeks of Chow Diet Room Temperature, mouse ID 16 Control

description: Library name: CD_RT16

value: Chow diet

value: Room Temeprature


title: lib42458

description: Library name: lib42458

value: female

tag: donorid

tag: age months

tag: illness

tag: epi total

tag: neut total


title: VRS5, rep4

tag: tissue


title: RNAseq_GFP_6h_r1_2211

tag: treatment


title: VRS5, rep3


title: RNAseq_GFP_6h_r2_2211

tag: cell line


title: lib42455

description: Library name: lib42455

tag: visit

tag: virus _yn

tag: eos total

tag: lym total

tag: mac total


title: VRS5, rep2

tag: genotype


title: CM3-NVHL1-MKH10-3

city: Copenhagen

first: Danillo

middle: Oliveira

last: Alvarenga

address: Universitetsparken 15

country: Denmark

institute: University of Copenhagen

data_processing:
Trimming and adapter removal with Trimmomatic 0.36
De novo assembly with Trinity 2.14.0
Annotation and mapping with Comparative Metatranscriptomics Workflow 1.0.0
Mapping with BWA 0.7.17-r1188
Sequence selection for Cyanobacteria and Bryopsida with Kraken 2.1.2
Assembly: Trinity 2.14.0

organism:
Hylocomium splendens
Nostocaceae cyanobacterium

source_name: cyanobacterial cells co-incubated with feather moss shoots

extract_protocol:
RNeasy PowerPlant Kit
NEBNext rRNA Depletion Kit, QIAseq FastSelect –rRNA Plant, NEBNext Ultra II RNA Library Prep Kit

value: UCTE CB012+KH10

value: cyanobacterium+moss


title: VRS5, rep1


title: RNAseq_NGN2_ES24h_r2_1846

tag: cell type

value: 24 hours FCS/LIF+dox


title: CM2-NVHL1-MKH10-2


title: CM4-NVHL1-MKH10-4


title: RNAseq_NGN2_ES24h_r1_1846

tag: mouse strain


title: lib42450

description: Library name: lib42450

data_processing:
Fastq files were aligned to the Ensembl version of the human genome (GRCh38) (GenBank assembly accession id GCA_000001405.15), using TopHat (version 1.4.1). The single-paired flag was set to “single,” while all other TopHat parameters were set to defaults
HTSeq-count was used to generate gene counts with mode as “Intersection (nonempty)” and minimum alignment quality set to 0 and otherwise set to default parameters
For quality control, samples were kept that had human aligned counts >250,000 and median CV coverage < 1.1. Genes were filtered to include those that had a trimmed mean of M values (TMM) normalization count of at least 1 in at least 10% of libraries and were classified as protein coding using BioMart. Normalized counts were transformed to log2 counts per million along with observations level weights using voomWithQualityWeights from the “limma” R package version 3.46
Assembly: GRCh38
Supplementary files format and content: counts_raw.tsv
Supplementary files format and content: hgnc_ensembl_id_mapping.tsv
Supplementary files format and content: modules_normalized_expr.tsv
Supplementary files format and content: voom_normalized_gene_expr.tsv

source_name: Nasal lavage

extract_protocol:
Cells were sorted into lysis buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara)
Sequencing libraries were constructed from total RNA using TruSeq RNA Sample Preparation Kits v2 (Illumina) and clustered onto a flowcell using a cBOT amplification system with a HiSeq SR v4 Cluster Kit (Illumina). Single-read sequencing was carried out on a HiSeq2500 sequencer (Illumina), using a HiSeq SBS v4 Kit to generate 58-base reads, with a target of approximately 10 million reads per sample

tag: Sex

value: Placebo

value: cold

value: Cold

value: N

tag: squ total

tag: enitrox


title: C4-NHVL1-4

organism: Nostocaceae cyanobacterium

source_name: cyanobacterial cells incubated alone

value: UCTE CB012

value: cyanobacterium alone


title: CM1-NVHL1-MKH10-1


title: C3-NHVL1-3


title: lib42446

description: Library name: lib42446

value: Nasal lavage

tag: donorid

tag: age months

tag: illness


title: RNAseq_NGN2_ES12h_r2_1846

tag: tissue

value: 12 hours FCS/LIF+dox

tag: experiment id


title: lib42445

description: Library name: lib42445

tag: treatment

tag: epi total

tag: neut total


title: RNAseq_NGN2_ES12h_r1_1846

tag: cell line


title: Tead2 (Re2)

city: Helsinki

first: Sami

last: Kilpinen

address: Viikinkaari 9

department: Faculty of Biological and Environmental Sciences

country: Finland

institute: University of Helsinki

description:
Library name: E12R1_Tead2_3
E12R1_Tead2_R2

data_processing:
Reads were demultiplexed using the dual barcode sequences. Demultiplexed reads were aligned against the Mus musculus genome mm10 and the peak calling was performed, using the nf-core (Ewels et al., 2020) pipeline nf-core/cutandrun.
Following software was used in the nf-core/cutandrun pipeline: adapter trimming with TrimGalore!, aligner bowtie2, duplicate filtering with Picard, peakcaller SEACR.
Assembly: mm10
Supplementary files format and content: bigwig files contain the filtered CUT&Tag reads aligned to the mouse (Mus Musculus) genome version mm10.
Library strategy: CUT&Tag

source_name: rhombomere 1

growth_protocol: Embryonic brains were isolated from E12.5 wildtype (ICR) mouse embryos. Embryos were obtained from timed matings, where embryonic day 0.5 (E0.5) was defined as noon of the day of the vaginal plug. All animal experiments were approved by the Laboratory Animal Center, University of Helsinki, and the National Animal Experiment Board in Finland.

extract_protocol:
The samples were processed following the CUT&Tag-It Assay Kit protocol (Active Motif, cat # 53170). Shortly, the cells from freshly dissociated r1 tissues were bound to concanavalin A coated magnetic beads followed by the antibody incubations and washing steps on beads. The following primary antibodies were used: rabbit anti-Gata2 (Abcam, ab109241), rabbit anti-Gata3 (Boster, M00593), rabbit anti-Tal1 (Abcam, ab75739), rabbit anti-Vsx2 (Proteintech, 25825-1-AP-20), rabbit anti-Ebf1 (Boller et al., 2016) rabbit anti-Insm1 (Nordic BioSite, ASJ-IO4DE3-50), rabbit anti-Tead2 (Biorbyt, orb382464), rabbit anti-IgG (Cell Signalling, 66362) and rabbit anti-H3K4me3 (Cell Signalling, 9751).
The library  preparation was done as part of the CUT&Tag-It Assay Kit protocol (Active Motif, cat # 53170) that uses protein A-Tn5 transposomes (pA-Tn5) for tagmentation followed by DNA amplification with Q5 high-fidelity DNA polymerase and dual-barcoding primers. The number of PCR cycles was 14.
The DNA libraries were multiplexed at 10 nM equimolar ratios and sequenced on NextSeq 500 or Aviti. 75 bp paired-end sequences were obtained.

treatment_protocol: r1 tissues were dissected using the constriction at midbrain-hindbrain boundary anteriorly and the extent of cerebellar tissue dorsally as visual landmarks. The ventral part of the r1 was separated and used for the CUT&Tag. r1 tissues from the embryos of one mouse litter were pooled and dissociated together. Cells were then divided between samples, using 200 000 - 250 000 cells per sample. Embryos from different E12.5 mouse litters were used as biological replicates.

value: rhombomere 1

value: E12.5 embryo

value: anterior hindbrain cells

value: wild-type (ICR)

value: rabbit anti-Tead2 (Biorbyt, orb382464)

tag: batch


title: Insm1 (Re2)

description:
Library name: E12R1_Insm1_3
E12R1_Insm1_R2

value: rabbit anti-Insm1 (Nordic BioSite, ASJ-IO4DE3-50)


title: C1-NHVL1-1


title: RNAseq_NGN2_ES6h_r2_1846

value: embryonic stem cells

value: mESC

value: 6 hours FCS/LIF+dox


title: lib42456

description: Library name: lib42456

value: female

value: Mepolizumab

tag: visit

value: Exacerbation

tag: virus _yn

value: Y

tag: eos total

tag: lym total

tag: mac total


title: lib42443

description: Library name: lib42443

tag: Sex

value: N

tag: squ total


title: RNAseq_NGN2_24h_r2_1846

tag: cell type

tag: genotype

value: 24 hours N2B27(w/oVitA)+dox

tag: mouse strain


title: lib42452

description: Library name: lib42452

tag: tissue

value: Nasal lavage

tag: donorid

value: Placebo

tag: age months

tag: illness

tag: enitrox


title: Ebf1 (Re2)

description:
Library name: E12R1_Ebf1_3
E12R1_Ebf1_R2

value: rhombomere 1

tag: cell line

tag: treatment

value: rabbit anti-Ebf1 (Boller et al., 2016)


title: Insm1 (Re1)

description:
Library name: E12R1_Insm1_2
E12R1_Insm1_R1

value: E12.5 embryo

value: anterior hindbrain cells

tag: batch


title: RNAseq_NGN2_ES6h_r1_1846

tag: experiment id


title: lib42442

description: Library name: lib42442

tag: visit

value: cold

tag: virus _yn

tag: eos total

tag: epi total

tag: neut total


title: lib42441

description: Library name: lib42441

tag: Sex

tag: lym total

tag: mac total

tag: squ total


title: Tead2 (Re1)

description:
Library name: E12R1_Tead2_2
E12R1_Tead2_R1

tag: tissue

tag: cell type

tag: genotype

value: wild-type (ICR)

value: rabbit anti-Tead2 (Biorbyt, orb382464)


title: H3K4me3 (Re5)

description:
Library name: E12R1_H3K4me_186
E12R1_H3K4me_186_R1

value: rabbit anti-H3K4me3 (Cell Signalling, 9751)


title: lib42440

description: Library name: lib42440

tag: donorid

tag: age months

tag: illness

tag: enitrox


title: C2-NHVL1-2

tag: cell line

value: UCTE CB012

tag: treatment

value: cyanobacterium alone


title: Ebf1 (Re1)

description:
Library name: E12R1_Ebf1_2
E12R1_Ebf1_R1

tag: batch


title: RNAseq_NGN2_24h_r1_1846

value: embryonic stem cells

value: mESC

tag: mouse strain

tag: experiment id


title: Vsx2 (Re4)

description:
Library name: E12R1_Vsx2_4
E12R1_Vsx2_R4

value: rabbit anti-Vsx2 (Proteintech, 25825-1-AP-20)


title: IgG (Re4)

description:
Library name: E12R1_IgG_4
E12R1_IgG_R4

value: rabbit anti-IgG (Cell Signalling, 66362)


title: RNAseq_NGN2_12h_r2_1846

value: 12 hours N2B27(w/oVitA)+dox


title: lib42439

description: Library name: lib42439

value: Nasal lavage

value: female

tag: visit

value: Exacerbation

tag: virus _yn

value: N

tag: eos total

tag: epi total

tag: neut total


title: RNAseq_NGN2_12h_r1_1846

tag: tissue


title: lib42435

description: Library name: lib42435

tag: Sex

value: Placebo

value: Cold

tag: lym total

tag: mac total

tag: squ total


title: Gata2 (Re4)

description:
Library name: E12R1_Gata2_ab_4
E12R1_Gata2_R4

value: rhombomere 1

value: E12.5 embryo

tag: cell type

value: anterior hindbrain cells

tag: genotype

value: rabbit anti-Gata2 (Abcam, ab109241)


title: RNAseq_NGN2_6h_r2_1846

tag: cell line

value: 6 hours N2B27(w/oVitA)+dox


title: UGCG-KO_3

city: Grand Rapids

first: Robert

last: Fillinger

state: Michigan

address: 333 Bostwick Ave NE

institute: Van Andel Institute

description: Library name: sgUgcg_5

data_processing:
Concatenate -1 and -2 fastQ files together
Trim reads (Trim Galore 0.6.10)
Alignment (STAR 2.7.10a)
RNA-Seq analysis DESeq2 (1.44.0)
Assembly: mm10
Supplementary files format and content: FastQ

source_name: Spleen

growth_protocol: NTC and sgUgcg CD8+ OT-I T cells were maintained in IMDM + 10% Nu-Serum IV culture supplement, 50 U/mL penicillin/50 ug/mL streptomycin, 50 uM 2-mercaptoethanol, 6 mM glutamine, and 50 U/mL recombinant murine IL-2 prior to adoptive transfer into C57BL/6J mice.

extract_protocol:
Qiagen RNeasy Plus Universal Mini Kit
Takara SMART-Seq mRNA LP (with UMIs) Kit

treatment_protocol: Following adoptive transfer, mice were immunized intravenously with a sublethal dose of recombinant attenuated Listeria monocytogenes expressing ovalbumin (Lm-OVA; 2e6 colony-forming units/mouse)

value: Spleen

tag: strain

value: CD8+ T cells

value: Ugcg knockout


title: RNAseq_NGN2_6h_r1_1846

value: embryonic stem cells

value: mESC

tag: treatment


title: UGCG-KO_2

description: Library name: sgUgcg_2


title: lib42434

description: Library name: lib42434

tag: donorid

tag: age months

tag: illness

tag: enitrox


title: lib42426

description: Library name: lib42426

value: Mepolizumab

tag: visit

tag: virus _yn

tag: eos total


title: IgG (Re5)

description:
Library name: E12R1_IgG_186
E12R1_IgG_186_R1

tag: tissue

value: wild-type (ICR)

value: rabbit anti-IgG (Cell Signalling, 66362)

tag: batch