title: Gli1_12wk_20180822BJ_C18

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_C20

status: Public on Nov 03 2020

type: SRA

city: Zürich

first: Baptiste

middle: N

last: Jaeger

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zürich

description: dentate gyrus dissection

library_source: transcriptomic

data_processing:
Single-end 126nt-long reads were adaptor removed and trimmed using cutadapt v1.16 and sickle v1.33 with default parameters. Reads were mapped against the mouse GRCm38.90 primary assembly 126 with the Ensembl GRCm38.90 GTF annotation using STAR v2.6.0c
cells / genes filtered with scater v.1.12.2 and Seurat v3.0.2. Cells with 1000-6000 genes detected, less than 8% of mitochondrial reads and more than 50000 total reads were kept for downstream analysis.
Data normalized with Seurat v3.0.2 pipeline (log normalization)
Analysis(UMAP,DEG) performed with Seurat v3.0.2
RNA velocity was run with velocyto.R v0.6 using default parameters
Slingshot and pseudotime were computed using slingshot v1.3.2 and fastICA v1.2-2 Packages
Prediction was computed using caret caret_6.0-84 package
Data analysis was carried out in R v3.6.1
Supplementary_files_format_and_content: metadata and matrix with counts for all cells in txt file

molecule: total RNA

organism: Mus musculus

source_name: dentate gyrus tdTomato+ single cells

extract_protocol:
single-cell
illumina nextera
Smart-seq2

tag: mouse strain

value: Gli1_CreERT2 x CAG_tdTomato

tag: age of the mice at time of injection

value: 7-8 week old

tag: time of dissection

value: 12 weeks after last tamoxifen injection

tag: cells

value: Hoechst- tdTomato+ single cells


title: Gli1_12wk_20180822BJ_C17

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_C19

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_C15

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_C14

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_C13

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D15

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F01

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_C11

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D12

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D10

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_C10

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_C06

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_C09

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_C04

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_C03

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_C02

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_C01

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B19

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B17

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_C05

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B23

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B16

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B20

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B15

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B13

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B14

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B18

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B10

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B07

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B12

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B06

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B05

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B01

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B03

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_A17

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_A18

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_A20

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B04

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_A14

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_B22

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_A13

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_A10

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_A09

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_A08

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_A04

description: dentate gyrus dissection


title: 20190219_Gli1_5d_O06

description: dentate gyrus dissection

value: 5 days after last tamoxifen injection


title: Gli1_12wk_20180822BJ_B11

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_A06

description: dentate gyrus dissection


title: 20190219_Gli1_5d_N20

description: dentate gyrus dissection


title: 20190219_Gli1_5d_N16

description: dentate gyrus dissection


title: 20190219_Gli1_5d_N15

description: dentate gyrus dissection


title: 20190219_Gli1_5d_N11

description: dentate gyrus dissection


title: 20190219_Gli1_5d_N04

description: dentate gyrus dissection


title: 20190219_Gli1_5d_N03

description: dentate gyrus dissection


title: 20190219_Gli1_5d_M11

description: dentate gyrus dissection


title: 20190219_Gli1_5d_M12

description: dentate gyrus dissection


title: 20190219_Gli1_5d_N12

description: dentate gyrus dissection


title: 20190219_Gli1_5d_L22

description: dentate gyrus dissection


title: 20190219_Gli1_5d_L17

description: dentate gyrus dissection


title: 20190219_Gli1_5d_L15

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_A11

description: dentate gyrus dissection


title: 20190219_Gli1_5d_L11

description: dentate gyrus dissection


title: 20190219_Gli1_5d_L10

description: dentate gyrus dissection


title: 20190219_Gli1_5d_L02

description: dentate gyrus dissection


title: 20190219_Gli1_5d_L01

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_A07

description: dentate gyrus dissection


title: 20190219_Gli1_5d_O03

description: dentate gyrus dissection


title: 20190219_Gli1_5d_N19

description: dentate gyrus dissection


title: 20190219_Gli1_5d_K12

description: dentate gyrus dissection


title: 20190219_Gli1_5d_K23

description: dentate gyrus dissection


title: 20190219_Gli1_5d_K20

description: dentate gyrus dissection


title: 20190219_Gli1_5d_J15

description: dentate gyrus dissection


title: 20190219_Gli1_5d_J09

description: dentate gyrus dissection


title: 20190219_Gli1_5d_K03

description: dentate gyrus dissection


title: P52

type: RNA

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

country: USA

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Hybriziation was performed by following Affymetrix standard procedure.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Gene-level intensity data were extracted and normalized by RMA stretch in Affymetrix Expression Console and Batch effects from different labeling protocols were adjusted using the ComBat R package (Johnson WE)

label: spia

organism: Homo sapiens

source_name: non-AR_percutaneous allograft biopsy

label_protocol: ENCORE amplification and labeling kit (NuGen, San Carlos, CA) was applied to the first batch of samples starting with approximately 100ng of total RNA to generate biotin-labeled RNA fragments for hybridization to the chip. For samples with a low RNA concentration, the Nugen Ovation SPIA amplification kit (NuGen, San Carlos, CA) was applied.

extract_protocol: Total RNA was extracted from biopsy samples obtained at 12 month after transplantation using All prep kit (QIAGEN-ALLprep kit, Valencia, CA USA). RNA quality was assessed using Bioanalyzer 2100 (Agilent Technologies)

tag: rejection at 12months post transplant

value: non-AR

tag: tissue

value: percutaneous allograft biopsy


title: P51

source_name: AR_percutaneous allograft biopsy

value: AR


title: P50


title: 20190219_Gli1_5d_J19

description: dentate gyrus dissection


title: P46


title: 20190219_Gli1_5d_J04

description: dentate gyrus dissection


title: 20190219_Gli1_5d_J05

description: dentate gyrus dissection


title: P48


title: 20190219_Gli1_5d_J02

description: dentate gyrus dissection


title: P47


title: 20190219_Gli1_5d_I20

description: dentate gyrus dissection


title: P45


title: 20190219_Gli1_5d_K07

description: dentate gyrus dissection


title: P39


title: 20190219_Gli1_5d_I09

description: dentate gyrus dissection


title: P43


title: P41


title: P42


title: P44


title: P40


title: P49


title: P36


title: 20190219_Gli1_5d_H24

description: dentate gyrus dissection


title: 20190219_Gli1_5d_H20

description: dentate gyrus dissection


title: 20190219_Gli1_5d_I05

description: dentate gyrus dissection


title: 20190219_Gli1_5d_H19

description: dentate gyrus dissection


title: P38


title: P37


title: 20190219_Gli1_5d_I21

description: dentate gyrus dissection


title: 20190219_Gli1_5d_H13

description: dentate gyrus dissection


title: 20190219_Gli1_5d_H09

description: dentate gyrus dissection


title: P34


title: 20190219_Gli1_5d_H07

description: dentate gyrus dissection


title: 20190219_Gli1_5d_H03

description: dentate gyrus dissection


title: 20190219_Gli1_5d_G23

description: dentate gyrus dissection


title: 20190219_Gli1_5d_G22

description: dentate gyrus dissection


title: P33


title: P27

label: encor


title: P28


title: P35


title: 20190219_Gli1_5d_G18

description: dentate gyrus dissection


title: P30


title: P31


title: 20190219_Gli1_5d_G14

description: dentate gyrus dissection


title: P29


title: 20190219_Gli1_5d_G07

description: dentate gyrus dissection


title: 20190219_Gli1_5d_H11

description: dentate gyrus dissection


title: P26


title: 20190219_Gli1_5d_G04

description: dentate gyrus dissection


title: 20190219_Gli1_5d_F24

description: dentate gyrus dissection


title: 20190219_Gli1_5d_F19

description: dentate gyrus dissection


title: 20190219_Gli1_5d_F16

description: dentate gyrus dissection


title: 20190219_Gli1_5d_F15

description: dentate gyrus dissection


title: P20


title: P19


title: P23


title: P21


title: P22


title: P24


title: P18


title: 20190219_Gli1_5d_F03

description: dentate gyrus dissection


title: 20190219_Gli1_5d_F11

description: dentate gyrus dissection


title: 20190219_Gli1_5d_F02

description: dentate gyrus dissection


title: P25


title: 20190219_Gli1_5d_F01

description: dentate gyrus dissection


title: P17


title: P12


title: 20190219_Gli1_5d_E16

description: dentate gyrus dissection


title: 20190219_Gli1_5d_E20

description: dentate gyrus dissection


title: 20190219_Gli1_5d_E13

description: dentate gyrus dissection


title: 20190219_Gli1_5d_E10

description: dentate gyrus dissection


title: P16


title: P13


title: P15


title: P14


title: 20190219_Gli1_5d_E02

description: dentate gyrus dissection


title: 20190219_Gli1_5d_E09

description: dentate gyrus dissection


title: P11


title: 20190219_Gli1_5d_D20

description: dentate gyrus dissection


title: P9


title: 20190219_Gli1_5d_F05

description: dentate gyrus dissection


title: P8


title: P6


title: 20190219_Gli1_5d_D15

description: dentate gyrus dissection


title: P5


title: 20190219_Gli1_5d_D12

description: dentate gyrus dissection


title: P32


title: P7


title: P4


title: P10


title: 20190219_Gli1_5d_C23

description: dentate gyrus dissection


title: P2


title: 20190219_Gli1_5d_C17

description: dentate gyrus dissection


title: 20190219_Gli1_5d_C22

description: dentate gyrus dissection


title: P1


title: 20190219_Gli1_5d_C14

description: dentate gyrus dissection


title: P3


title: 20190219_Gli1_5d_D19

description: dentate gyrus dissection


title: 20190219_Gli1_5d_C05

description: dentate gyrus dissection


title: 20190219_Gli1_5d_B20

description: dentate gyrus dissection


title: 20190219_Gli1_5d_B06

description: dentate gyrus dissection


title: 20190219_Gli1_5d_A12

description: dentate gyrus dissection


title: 20190219_Gli1_5d_D04

description: dentate gyrus dissection


title: 20190219_Gli1_5d_A07

description: dentate gyrus dissection


title: 20190219_Gli1_5d_A06

description: dentate gyrus dissection


title: mgamma,m8_2

city: Linkoping

first: Srivathsa

last: Magadi

address: Campus US, Building 463 Cellbiologen, Entrance 64

department: Department of Biomedical and Clinical Sciences (BKV) Division of Molecular Medicine and Virology (MMV)

country: Sweden

institute: Linkoping University

description: Gene expression data from Hes induced neural hyperplasia

hyb_protocol: Fragmented cRNA preparations were hybridized to Drosophila genome oligonucleotide arrays (GeneChip Drosophila Genome 2.0 Array (3' IVT Expression_Affymetrix)] using an Affymetrix hybridization Oven 640, washed, and then scanned on a GeneChip Scanner 3000

scan_protocol: GeneChip Scanner 3000

data_processing: Data were analysed using Transcription activation console to generate CHP files, further Quantile normalised using R for Differential expression analysis. Trimmed mean expression intensity of >75 arbitrarily set as minimal expression

label: Affymetrix array

organism: Drosophila melanogaster

source_name: 3rd instar arval CNS

label_protocol: Synthesis of double-stranded cDNA and biotin-labelled cRNA was performed according to manufacturer’s instructions (Affymetrix)

growth_protocol: Animals from the following genotype, control animals: tubGal80ts;grhGal4/UAS-cd8GFP, overexpressing activated Notch:  tubGal80ts;grhGal4/UAS-NΔECD, Hes overexpressing animals:  tubGal80ts;grhGal4/UAS-dpn,  tubGal80ts;grhGal4/UAS-mgamma,UAS-m8,  tubGal80ts;grhGal4/UAS-dpn,UAS-mgamma,  were grown at restrictive temperature 18°C till late 2nd instar 8days and moved to permissive temperature 30°C for 24 hours.

extract_protocol: RNA was isolated from 300 larval CNSs dissected in cold PBS using the RNeasy Plus Mini Kit (Qiagen)

treatment_protocol: 24h post incubation at 30°C, wandering 3rd instar lavae were harvested

tag: genotype

value: 3rd instar larval brains


title: 20190219_Gli1_5d_A03

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_O23

description: dentate gyrus dissection


title: Deadpan,mgamma_3


title: immune cells_unstimulated_3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Fluorescence images were transformed to BCL files with the Illumina BaseCaller software and samples were demultiplexed to FASTQ files with CASAVA (version 1.8.2)
Assessment of quality control of sequences using FastQC 0.10.1
Alignment of sequences to human reference genome using STAR 2.3.0e_r291
SAM files converted to sorted BAM files and filtered for unique hits using SAMtools 0.1.19
Counting unique reads within genes using HTSeq 0.6.1p1
Data normalization and testing for differentially expressed genes using DESeq2 1.8.2
Genome_build: hg19

source_name: blood of healthy donors

growth_protocol: Primary human epidermal keratinocytes were cultured in KGM-Gold medium (Lonza);  dermal microvascular endothelial cells were cultured in Endothelial cell proliferation medium (Provitro);  dermal fibroblasts were cultured in FGM-2 medium (Lonza); peripheral blood mononuclear cells were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum and 2 mM L-alanyl-L-glutamine) (all from Biochrom).

extract_protocol:
Total RNA was extracted from cells using Invisorb RNA Kit II (Invitek/Stratec molecular).
RNA-samples prepared with the "TruSeq RNA Sample Prep Kit v2" according to the manufacturer's protocol (Illumina)

treatment_protocol: Primary human epidermal keratinocytes,  dermal microvascular endothelial cells,  dermal fibroblasts and peripheral blood mononuclear cells were stimulated with human recombinant IL-1b (5 ng/ml, R and D Systems) or left unstimulated for 24h.

tag: cell type

value: immune cells

tag: treatment

value: unstimulated


title: immune cells_IL-1b-stimulated_1


title: 20190219_Gli1_5d_C11

description: dentate gyrus dissection


title: Deadpan_3


title: Deadpan_1


title: mgamma,m8_3


title: Deadpan,mgamma_1


title: Deadpan_2


title: immune cells_unstimulated_2


title: mgamma,m8_1


title: immune cells_IL-1b-stimulated_3


title: immune cells_unstimulated_1


title: Gli1_20180503BJ_Plate_I_O14

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_O05

description: dentate gyrus dissection


title: dermal endothelial cells_IL-1b-stimulated_3

value: dermal endothelial cells


title: Gli1_20180503BJ_Plate_I_O03

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_N21

description: dentate gyrus dissection


title: immune cells_IL-1b-stimulated_2


title: dermal endothelial cells_IL-1b-stimulated_2


title: dermal endothelial cells_IL-1b-stimulated_1


title: Deadpan,mgamma_2


title: Gli1_20180503BJ_Plate_I_N20

description: dentate gyrus dissection


title: dermal endothelial cells_unstimulated_3


title: Gli1_20180503BJ_Plate_I_N18

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_N03

description: dentate gyrus dissection


title: dermal endothelial cells_unstimulated_2


title: Gli1_20180503BJ_Plate_I_M24

description: dentate gyrus dissection


title: dermal endothelial cells_unstimulated_1


title: dermal fibroblasts_IL-1b-stimulated_3

value: dermal fibroblasts


title: dermal fibroblasts_IL-1b-stimulated_2


title: Gli1_20180503BJ_Plate_I_M20

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_M21

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_M23

description: dentate gyrus dissection


title: dermal fibroblasts_unstimulated_2


title: keratinocytes_IL-1b-stimulated_1

value: keratinocytes


title: dermal fibroblasts_IL-1b-stimulated_1


title: Gli1_20180503BJ_Plate_I_M18

description: dentate gyrus dissection


title: dermal fibroblasts_unstimulated_1


title: Gli1_20180503BJ_Plate_I_M17

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_M22

description: dentate gyrus dissection


title: keratinocytes_IL-1b-stimulated_3


title: Gli1_20180503BJ_Plate_I_M07

description: dentate gyrus dissection


title: dermal fibroblasts_unstimulated_3


title: keratinocytes_IL-1b-stimulated_2


title: Gli1_20180503BJ_Plate_I_M12

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_M05

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_M04

description: dentate gyrus dissection


title: keratinocytes_unstimulated_2


title: Gli1_20180503BJ_Plate_I_L21

description: dentate gyrus dissection


title: keratinocytes_unstimulated_1


title: Gli1_20180503BJ_Plate_I_L24

description: dentate gyrus dissection


title: keratinocytes_unstimulated_3


title: Gli1_20180503BJ_Plate_I_L20

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_L18

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_L07

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_L05

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_L04

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_K24

description: dentate gyrus dissection


title: patient 2_DSE+TGFb, rep2

city: Cambridge

first: Viviana

last: Cremasco

state: MA

address: 250 Massachusetts Avenue

institute: Novartis Institutes for BioMedical Research

data_processing:
Sequence intensity files were generated using the Illumina Real Time Analysis
Intensity files were demultiplexed and then aligned to the transcriptome using the 10x Genomics Cellranger software package (v3.1)
bam files were generated and sorted using 10x Genomics Cellranger software
Count matrices were generated using 10x Genomics Cellranger software
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix csv files contains cell by gene matrix for all samples, cell barcodes are appended by library id, metadata.csv file contains all the related metadata including patient ID, treatment condition and library ID.

source_name: Dissociated colorectal cancer tumor

growth_protocol: Dissociated human colorectal cancer tumor samples were thawed and cultured in vitro

extract_protocol:
All cells were harvested as input for 10x Genomics Chromium Single Cell platform
Libraries were prepared according to 10x Genomics Chromium Single Cell platform

treatment_protocol: The cells were treated by isotype control or TGFb blockade (DSE or NIS) for 24hr

value: Dissociated colorectal cancer tumor

value: DSE+TGFb

tag: timepoint

value: 24 hr

tag: individual

value: patient 2

tag: library id


title: patient 2_NIS+TGFb, rep2

value: NIS+TGFb


title: patient 2_DSE+TGFb, rep1


title: patient 2_NIS+TGFb, rep1


title: patient 2_Isotype+TGFb, rep2

value: Isotype+TGFb


title: Gli1_20180503BJ_Plate_I_K10

description: dentate gyrus dissection

value: Gli1_CreERT2 x CAG_tdTomato

value: 7-8 week old

value: Hoechst- tdTomato+ single cells


title: patient 1_NIS+TGFb, rep2

value: patient 1


title: patient 1_NIS+TGFb, rep1


title: Gli1_20180503BJ_Plate_I_K06

description: dentate gyrus dissection

value: 5 days after last tamoxifen injection


title: patient 1_Isotype+TGFb, rep2


title: Gli1_20180503BJ_Plate_I_J09

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_J06

description: dentate gyrus dissection


title: patient 1_DSE+TGFb, rep1


title: Gli1_20180503BJ_Plate_I_K01

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_J05

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_J01

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_I23

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_I20

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_I02

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_H06

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_G20

description: dentate gyrus dissection


title: Human TM, medial (fib)

city: San Francisco

first: Aaron

last: Tward

address: 505 Parnassus AVE

institute: UCSF

description: A healthy human TM was removed during a surgical procedure under an IRB-approved protocol. It was mechanically spearated into more lateral and medial portions. The lateral portion was dissociated into single cells using collagenase P and DNAse, and the more medial portion was first dissociated in dispase and then collagenase/DNAse.

data_processing:
10X Genomics Cell Ranger pipeline
See their website for their proprietary steps
the output matrix files are here and are included for postprocessing for R analysis
The web summaries for the experiments are attached as a guide to how the sequencing results turned out.
Genome_build: mm10 for mouse, and hg19 for human

source_name: tympanic membrane

growth_protocol: See tissue dissociation protocol in SAMPLES section

extract_protocol:
Cells were resuspended at 1,000 cells/μL in 0.04% BSA in PBS and loaded onto the Chromium Controller from 10x Genomics for single cell capture.
cDNA library for RNA-seq

value: tympanic membrane


title: Gli1_20180503BJ_Plate_I_G13

description: dentate gyrus dissection


title: Human TM, lateral (epi)


title: patient 1_Isotype+TGFb, rep1


title: patient 1_DSE+TGFb, rep2


title: Gli1_20180503BJ_Plate_I_K05

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_F04

description: dentate gyrus dissection


title: healthy donor skin_4

description:
Heal14-015
Skin sample of healthy control donor.
mRNA-seq

data_processing:
Base-calling performed with bcl2fastq (version 2.17.1.14).
Sequencing quality control performed with FastQC (version 0.11.5).
Reads aligned to reference transcriptome using STAR (version 2.5.2a).
Number of reads counted for each gene using featureCounts (version 1.5.0-p1).
Differentially expressed genes searched for using DESeq2 (version 1.14.1) filtered for adjusted p-value <0.05 and absolute log2 fold-change >1.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include counts.

source_name: Healthy donor skin

extract_protocol:
Total RNA was extracted from cells using Invisorb RNA Kit II (Invitek/Stratec molecular).
RNA-samples prepared with the "TruSeq RNA Sample Prep Kit v2" according to the manufacturer's protocol (Illumina).

value: Skin

tag: disease status

value: Healthy


title: Gli1_20180503BJ_Plate_I_F18

description: dentate gyrus dissection


title: Acne inversa skin_3

description:
ROS11E
Lesional skin sample of Acne inversa patient.
mRNA-seq

source_name: Acne inversa skin

value: Acne inversa


title: Gli1_20180503BJ_Plate_I_F24

description: dentate gyrus dissection


title: Acne inversa skin_2

description:
ROS8C1
Lesional skin sample of Acne inversa patient.
mRNA-seq


title: Gli1_20180503BJ_Plate_I_D20

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_G09

description: dentate gyrus dissection


title: Acne inversa skin_1

description:
ROS4D1
Lesional skin sample of Acne inversa patient.
mRNA-seq


title: Gli1_20180503BJ_Plate_I_E22

description: dentate gyrus dissection


title: healthy donor skin_2

description:
Heal14-012
Skin sample of healthy control donor.
mRNA-seq


title: As72hpp6

city: Hilo

first: Kelsey

last: Coffman

state: HI

address: 64 Nowelo St

department: Tropical Pest Genetics and Molecular Biology Research Unit

institute: USDA-ARS

description: developing parasitoid wasp was removed prior to collection

data_processing:
Reads were filtered with the fastx toolkit (hannonlab.cshl.edu/fastx_toolkit/) to retain reads with >90% of bases with a PHRED score of 30 or higher for both reads in a pair.
Quality reads for each sample were separately mapped to the DlEPV reference genome using bowtie2 v2.2.4
Cuffquant from Cufflinks v2.2.1 was used to calculate the average FPKM value for each DlEPV ORF in both wasp and fly tissues.
Cuffdiff from Cufflinks v2.2.1 was used to test for differential expression between the two tissue types.
Differential expression for a gene was considered significant for FDR-adjusted q-values < 0.05.
Genome_build: GenBank accession KR095315 (not yet released)
Supplementary_files_format_and_content: allgene_repFPKM.txt is a space-delimited text file inidicating the FPKM value of each DlEPV gene for each sample.
Supplementary_files_format_and_content: allgene_diffData.txt is a space-delimited text file containing the average FPKM value for each tissue type, as well as differential expression testing generated from Cuffdiff for each DlEPV gene.

organism:
Anastrepha suspensa
Diachasmimorpha longicaudata entomopoxvirus

source_name: fly whole body

growth_protocol: D. longicaudata wasps and A. suspensa flies were both reared with a 16L:8D photoperiod at 26–27 °C and 55–60% relative humidity.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN) with on-column DNase digestion, followed by a secondary DNase treatment using the TURBO DNA-free Kit after RNA isolation.
Illumina-compatible stranded RNA libraries for all 12 samples were constructed with the Kapa Biosystems RNA library preparation chemistry using 3ug RNA from each fly sample and 1ug RNA from each venom gland sample. All libraries were sequenced on one run of an Illumina NextSeq instrument, which generated an average of 18.5 million and 14.2 million 75bp paired-end reads for each wasp and fly sample, respectively.

tag: developmental stage

value: pupa, 72 hours post parasitism

value: whole body tissue


title: healthy donor skin_3

description:
Heal14-013
Skin sample of healthy control donor.
mRNA-seq


title: healthy donor skin_1

description:
Heal14-011
Skin sample of healthy control donor.
mRNA-seq


title: Gli1_20180503BJ_Plate_I_D19

description: dentate gyrus dissection


title: As72hpp5


title: As72hpp4


title: Gli1_20180503BJ_Plate_I_D09

description: dentate gyrus dissection


title: As72hpp3


title: Gli1_20180503BJ_Plate_I_C20

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_C19

description: dentate gyrus dissection


title: patient 2_Isotype+TGFb, rep1

value: Dissociated colorectal cancer tumor


title: As72hpp2


title: Gli1_20180503BJ_Plate_I_C18

description: dentate gyrus dissection


title: As72hpp1


title: Gli1_20180503BJ_Plate_I_B23

description: dentate gyrus dissection


title: Gli1_20180503BJ_Plate_I_B20

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_P20

description: dentate gyrus dissection

value: Ascl1_CreERT2 x CAG_tdTomato


title: INPUT_WT_MA_1

city: Boston

first: Camron

middle: D

last: Bryant

address: 72 East Concord St

department: Pharmacology

institute: Boston University School of Medicine

data_processing:
Reads were trimmed for quality using Trimmomatic: trimmomatic PE -phred33 ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30
Unique Molecular Identifier (UMI) sequences were extracted from Read 2 for removal of PCR amplification duplicates using the ‘extract’ command in UMI-tools: umi_tools extract --extract-method=string --bc-pattern=NNNNNNNNNN
STAR to map reads to mouse genome (mm10): STAR --runMode alignReads --runThreadN 16 --limitBAMsortRAM 15000000000 --genomeLoad NoSharedMemory --outReadsUnmapped Fastx --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outFilterScoreMinOverLread 0.2 --outFilterMatchNminOverLread 0.2 --sjdbScore 2
Bedtools to remove rRNA (rRNA annotation exported from UCSC Table Browser): bedtools intersect -f 0.90
Using the ‘dedup’ command in UMI_tools, PCR duplicates from the rRNA-depleted bam files were removed based on UMI extracted in the previous step.
Peaks were called in multi-replicate mode of CLAM (Zhang and Xing 2017): --binsize 100. Prior to peak calling, the de-duplicated bam files were preprocessed and realigned in CLAM. Once peaks were called, the genome regions of peaks were annotated in CLAm using "peak_annotator."
Deduplicated BAM files were merged across all 12 CLIP samples and deduplicated BAM files were merged across all 12 input (bulk RNA-seq) samples to generate two merged BAM files as the input for peak calling in CLAM as described above. The called peaks were then annotated. The file containing all the peaks was formatted into a file in GTF format to be used for strand-specific feature counting in individual BAM files using Subread FeatureCounts (Liao et al., 2014). FeatureCount (Liao et al., 2014) in Subread was used to sum reads under each peak for each of the four conditions. To examine the effect of Genotype, Treatment, and the interactive effects on hnRNP H binding, differential binding sites and peak analysis were performed using limma (Ritchie et al., 2015) and edgeR (Robinson et al., 2009) based on summed counts for each peak derived from Subread FeatureCount. The interaction of Genotype and Treatment is expressed as: I = (MUT_MA – MUT_SAL) – (WT_MA – WT_SAL).
Genome_build: mm10
Supplementary_files_format_and_content: peak.text files contain output from CLAM showing genomic positions of the called peaks for each of the four experimental conidtions
Supplementary_files_format_and_content: bed file contains output from CLAM showing genomic positions of called peaks from merged bam files from all 12 CLIP samples
Supplementary_files_format_and_content: count.txt files contain output from featureCount showing read counts for either CLIP samples or RNA-seq samples

source_name: Striatum

growth_protocol: Mice were generated by mating heterozygous Hnrnph1 mutant males with C57BL/6J females purchased from The Jackson Laboratory (Bar Harbor, ME USA).

extract_protocol:
Dissected whole striata were stored in RNAlater (ThermoFisher) following manufacturer’s instructions to stabilize the RNA and protein followed by cross-linking immunoprecipitation library preparation. Prior to crosslinking, a portion of the pooled tissue from each replicate was removed and stored in -80C for later RNA extraction and bulk RNA-seq library preparation. Following the completion of membrane transfer, the membrane was cut with a clean razor to obtain a vertical membrane slice per lane from 50 kDa (molecular weight of hnRNP H) to 75 kDa, which translates to 30 to 70 nucleotide RNA fragments crosslinked to the protein. RNA was then extracted from the membrane slices following a previously described procedure (Rieger et al., 2018). The same extraction procedure (starting with the addition of 7M urea) was used to isolate RNA from samples previously stored for total RNA-seq.
Following RNA extraction, sample concentration was quantified with Agilent Bioanalyzer and approximately 0.2 ng of RNA was used to prepare next-generation sequencing libraries following a protocol for library preparation (Rieger et al., 2018; BioRxiv). Because the RNA adapter on each sample contained a unique barcode, the cDNA libraries generated from the sample (12 CLIP-seq and 12 RNA-seq libraries) were multiplexed and pooled for increased throughput. A pooled library at a concentration of 10 nM were shipped to University of Chicago Sequencing core and subjected to 100 bp paired-end 2 x 100 sequencing in a single lane on Illumina HiSEQ4000. To increase read coverage for the RNA-seq samples, those 12 cDNA libraries were pooled (10 nM concentration) for sequencing for a second time in one lane using Illumina HiSEQ4000.
CLIP-seq and RNA-seq

treatment_protocol: On Days 1 and 2, all mice received a saline injection (10 ml/kg, i.p.) and were recorded for locomotor activity in Plexiglas chambers (40 cm length x 20 cm width x 45 cm height) for 1 h. On Day 3, mice receive either saline again or MA (2 mg/kg, i.p.; Sigma Aldrich) and were recorded for locomotor activity for 30 min and the whole striata (left and right sides) were dissected from each mouse at 30 min post-injection.

tag: strain

value: brain

tag: tissue region

value: striatum (from 2 females and 2 males)

value: wild type

value: methamphetamine

tag: age

value: post-natal day 50 - 100

tag: clip antibody


title: Ascl1_5d_II_20190403BJ_P18

description: dentate gyrus dissection

tag: mouse strain

tag: age of the mice at time of injection

value: 7-8 week old


title: INPUT_WT_MA_2


title: INPUT_WT_MA_3


title: Ascl1_5d_II_20190403BJ_P15

description: dentate gyrus dissection

tag: time of dissection

tag: cells

value: Hoechst- tdTomato+ single cells


title: INPUT_WT_SAL_3

tag: tissue

value: saline


title: Ascl1_5d_II_20190403BJ_P14

description: dentate gyrus dissection

value: 5 days after last tamoxifen injection


title: INPUT_WT_SAL_1

tag: genotype


title: Ascl1_5d_II_20190403BJ_P12

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_P17

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_P05

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_P08

description: dentate gyrus dissection


title: INPUT_WT_SAL_2


title: Ascl1_5d_II_20190403BJ_P11

description: dentate gyrus dissection


title: CLIP_WT_SAL_1

value: hnRNP H (Bethyl Cat #A300-511A)


title: CLIP_WT_SAL_3


title: CLIP_WT_MA_1


title: CLIP_WT_SAL_2


title: CLIP_WT_MA_3


title: x15

city: Iowa City

first: Serena

last: Gumusoglu

state: IA

address: 200 Hawkins Dr

institute: University of Iowa

description: [S20] geo_submission_processed_data.txt

data_processing:
Illumina adaptors were removed using Trim Galore (version 0.4.1) and verified by FastQC (version 0.5.2).
Data were quasi-mapped to GENCODE version M16 GRCm38 (mm10) assembly and quantified using parameters –bias –bootstrap-samples=200 –rf-stranded in Kallisto (version 0.43.1)(25-27). The average mapping efficiency  was ~89%, with an average of 28,335,347 mapped reads per sample.
Read data were pooled across lanes (average reads/sample: 31,707,708) and differential gene expression was determined using the Sleuth version 0.29.0 pipeline in R statistical computing.
Transcript abundance (via Kallisto) was normalized to gene length for gene level analysis.
Principle components analysis was used to assess variance between samples and  data were analyzed using a linear model (scaled reads per base as the response variable, treatment group as the explanatory variable), with males and females analyzed separately. One AVP female sample was excluded for high variance.
Statistical differences between treatment groups (false discovery rate < 0.05) were calculated via the Wald test, with beta values (Sleuth) as effect sizes. Significantly changed genes (p<0.05) were functionally annotated via PANTHER (version 15.0) GO-Biological Process binomial overrepresentation testing.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: E18 dorsal forebrain

extract_protocol:
E18 dorsal forebrains were dissected from four brains per sex per condition (16 total samples from 8 litters). Tissues were treated with RNAlater and flash frozen on dry ice. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany).
mRNA-seq library preparation (TruSeq® Stranded mRNA Library Prep, Illumina, Madison, WI) was tested using the DNA 1000 kit (Agilent) and 2100 Bioanalyzer Tapestation. 150 bp paired-end reactions across two lanes were used to sequence libraries (HiSeq 4000, Illumina).

value: Dorsal forebrain

value: embryonic day 18

value: vehicle

tag: gender

value: female


title: x14

description: [S19] geo_submission_processed_data.txt

tag: treatment


title: Gli1_20180503BJ_Plate_I_E20

description: dentate gyrus dissection

value: Gli1_CreERT2 x CAG_tdTomato


title: Ascl1_5d_II_20190403BJ_O17

description: dentate gyrus dissection


title: x13

description: [S18] geo_submission_processed_data.txt

value: male


title: Ascl1_5d_II_20190403BJ_P16

description: dentate gyrus dissection

value: Ascl1_CreERT2 x CAG_tdTomato


title: Ascl1_5d_II_20190403BJ_O16

description: dentate gyrus dissection


title: CLIP_WT_MA_2

value: brain


title: x12

description: [S17] geo_submission_processed_data.txt


title: Ascl1_5d_II_20190403BJ_P07

description: dentate gyrus dissection


title: x11

description: [S16] geo_submission_processed_data.txt

value: AVP


title: Ascl1_5d_II_20190403BJ_O15

description: dentate gyrus dissection


title: x10

description: [S15] geo_submission_processed_data.txt


title: Ascl1_5d_II_20190403BJ_O13

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_O14

description: dentate gyrus dissection


title: x9

description: [S14] geo_submission_processed_data.txt


title: Ascl1_5d_II_20190403BJ_O10

description: dentate gyrus dissection


title: x8

description: [S13] geo_submission_processed_data.txt


title: x7

description: [S8] geo_submission_processed_data.txt


title: x6

description: [S7] geo_submission_processed_data.txt


title: Ascl1_5d_II_20190403BJ_O18

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_O07

description: dentate gyrus dissection


title: x5

description: [S6] geo_submission_processed_data.txt


title: x2

description: [S2] geo_submission_processed_data.txt


title: x4

description: [S5] geo_submission_processed_data.txt


title: Ascl1_5d_II_20190403BJ_O06

description: dentate gyrus dissection


title: x3

description: [S4] geo_submission_processed_data.txt


title: x1

description: [S1] geo_submission_processed_data.txt


title: Ascl1_5d_II_20190403BJ_N17

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_N18

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_O05

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_N16

description: dentate gyrus dissection


title: Mouse 4 fenoterol 4h

city: Molndal

first: Kasparas

last: Petkevicius

address: Pepparedsleden 1

department: CVRM Metabolism

institute: AstraZeneca

data_processing:
Sequence reads were mapped onto the GRCm38 genome using TopHat v2.0.11
Genes were counted using HTseq-count (V0.8.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: BMDMs_1uM fenoterol for 4h

growth_protocol: Bone marrow cells were isolated from femur and tibia and differentiated in the presence of RPMI+10%FCS+20% L929 cell conditioned medium for 1 week.

extract_protocol:
Total RNA was extracted using QIAGEN RNEasy Mini kit, according to manufacturer's protocol, and eluted in 30 microliters of water.
1 µg of total RNA was quality checked (RIN >8.5) using an Agilent Bioanalyser 2100 system and then used to construct barcoded sequencing libraries with Illumina’s TruSeq Stranded mRNA Library Prep Kit following manufacturer’s instruction.

treatment_protocol: Differentiated cells were plated in 12-well plates in the same culture medium and cultured overnight. Next day, cells were stimulated with fenoterol for indicated periods of time without changing the medium, and then lysed immediately after.

tag: cell type

value: Bone marrow-derived macrophages (BMDMs)

value: treated with 1uM fenoterol for 4h


title: Ascl1_5d_II_20190403BJ_O12

description: dentate gyrus dissection


title: Mouse 3 fenoterol 4h


title: Mouse 1 fenoterol 4h


title: Mouse 2 fenoterol 4h


title: Ascl1_5d_II_20190403BJ_N13

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_O09

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_N15

description: dentate gyrus dissection


title: Mouse 4 fenoterol 1h

source_name: BMDMs_1uM fenoterol for 1h

value: treated with 1uM fenoterol for 1h


title: Mouse 2 fenoterol 1h


title: Mouse 3 fenoterol 1h


title: Ascl1_5d_II_20190403BJ_O04

description: dentate gyrus dissection

value: 7-8 week old


title: Ascl1_5d_II_20190403BJ_N10

description: dentate gyrus dissection

value: Hoechst- tdTomato+ single cells


title: Mouse 1 fenoterol 1h


title: Ascl1_5d_II_20190403BJ_N07

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_N09

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_N08

description: dentate gyrus dissection


title: Mouse 4 control

value: untreated


title: Ascl1_5d_II_20190403BJ_N03

description: dentate gyrus dissection

value: 5 days after last tamoxifen injection


title: Mouse 3 control


title: Mouse 1 control


title: Ascl1_5d_II_20190403BJ_N04

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_N02

description: dentate gyrus dissection


title: Mouse 2 control


title: Ascl1_5d_II_20190403BJ_N01

description: dentate gyrus dissection


title: RORa -T2A ChIPseq_3 Input DNA

first: Alastair

last: Crisp

address: Francis Crick Avenue

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

library_source: genomic

data_processing:
Pooled libraries were sequenced using an Illumina Hiseq4000 running a single-read 50bp protocol
Sequenced reads were aligned to the mouse genome (GRCm38) using Bowtie2 (v2.3.5.1) with default parameters
reads that could not be uniquely mapped were removed from further analysis
Peak calling analysis was performed using Macs2 (v2.1.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: macs2 output files with peak calling data

molecule: genomic DNA

growth_protocol: ILC2s Purified from MLN of IL-25 and IL-2/anti–IL-2 complex treated mice  were maintained for 7 days in RPMI-1640, 10% FCS plus penicillin/streptomycin and 2-mercaptoethanol, supplemented with IL-7 (10 ng/ml) and IL-33 (10 ng/ml)

extract_protocol:
Chromatin extracts from in vitro expanded ILC2 (10 million) were prepared using truChIP Chromatin Shearing kit (Covaris), with 5 min of crosslink and optimized shearing conditions (peak power 75, duty factor 10.0, cycles/burst 200, duration 300 sec) to obtain fragments of ~500bp
Chromatin-antibody-bead complexes were then subjected to tagmentation, followed by DNA elution, and libraries amplification and purification, as described previously (Schmidl et al., 2015)

value: lymphonodes

tag: chip antibody

value: Rora-Teal/Teal


title: WT- ChIPseq

value: Wild Type


title: Ascl1_5d_II_20190403BJ_M21

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_N12

description: dentate gyrus dissection


title: RORa -T2A ChIPseq_2 Input DNA


title: Ascl1_5d_II_20190403BJ_M18

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_M16

description: dentate gyrus dissection


title: RORa -T2A ChIPseq_3


title: GATA3-T2A ChIPseq_2


title: RORa -T2A ChIPseq_2


title: Ascl1_5d_II_20190403BJ_M13

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_M15

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_N05

description: dentate gyrus dissection


title: DN3 ATACseq_3

data_processing:
Pooled libraries were sequenced using an Illumina Hiseq4000 running a single-read 50bp protocol
Sequenced reads were aligned to the mouse genome (GRCm38) using Bowtie2 (v2.3.5.1) with default parameters
reads that could not be uniquely mapped were removed from further analysis
Peak calling analysis was performed using Macs2 (v2.1.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: bed file and macs2 output

source_name: Embryonic Thymus

extract_protocol:
FACS purified cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) to obtain nuclei extract
Nuclei were immediately used in the transposase reaction (25 μl 2× TD buffer, 2.5 μl transposase (Illumina) and 22.5 μl nuclease- free water) for 30 min at 37 °C, followed by sample purification (Qiagen MinElute kit). Then, we amplified library fragments using Kappa HiFi HotStart Ready mix and 1.25 M of custom Nextera PCR primers. Libraries were purified using dual (0.5x-0.7x) SPRI Ampure XP beads (Beckman Coulter), pooled and were subjected to high-throughput sequencing

value: Embryonic Thymus

value: 5x polychromILC mice


title: DN3 ATACseq_2


title: Ascl1_5d_II_20190403BJ_M12

description: dentate gyrus dissection


title: DN3 ATACseq_1


title: Ascl1_5d_II_20190403BJ_M08

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_M11

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_M06

description: dentate gyrus dissection


title: DN2 ATACseq_1


title: DN2 ATACseq_3


title: Ascl1_5d_II_20190403BJ_M09

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_M05

description: dentate gyrus dissection


title: NKp ATACseq_3

value: NKp


title: NKp ATACseq_2


title: Ascl1_5d_II_20190403BJ_M02

description: dentate gyrus dissection


title: ILC2p ATACseq_3


title: Ascl1_5d_II_20190403BJ_L20

description: dentate gyrus dissection


title: ILC2p ATACseq_2


title: Ascl1_5d_II_20190403BJ_M17

description: dentate gyrus dissection


title: ETP ATACseq_3

value: ETP


title: Ascl1_5d_II_20190403BJ_L19

description: dentate gyrus dissection

value: Ascl1_CreERT2 x CAG_tdTomato


title: ETP ATACseq_2


title: Ascl1_5d_II_20190403BJ_L17

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_L18

description: dentate gyrus dissection


title: DN2/DN3 ATACseq


title: ETP ATACseq


title: DN2 ATACseq_2


title: ILC2p ATACseq


title: Ascl1_5d_II_20190403BJ_L14

description: dentate gyrus dissection


title: Input DNA-2

description:
processed data file: sample_GATA3_ChIPseq2.peaks_peaks_ChIPm2_G3T2A_aT2A.txt
SLX-16314.i712_i502.HWMFJBBXX.s_8.r

extract_protocol:
The T2A antibody was bespoke generated using a T2A synthetic peptide and is now available from CRB (Cambridge Research Biochemicals, crb2005269).
Chromatin extracts from in vitro expanded ILC2 (10 million) were prepared using truChIP Chromatin Shearing kit (Covaris), with 5 min of crosslink and optimized shearing conditions (peak power 75, duty factor 10.0, cycles/burst 200, duration 300 sec) to obtain fragments of ~500bp
Chromatin-antibody-bead complexes were then subjected to tagmentation, followed by DNA elution, and libraries amplification and purification, as described previously (Schmidl et al., 2015)


title: Input DNA

description:
processed data file: sample.peaks_peaks_ChIPm2_RORaT2A_aT2A.txt
SLX-16314.i711_i502.HWMFJBBXX.s_8.r


title: Ascl1_5d_II_20190403BJ_L12

description: dentate gyrus dissection


title: GATA3-T2A ChIPseq

description:
processed data file: sample_GATA3_ChIPseq2.peaks_peaks_ChIPm2_G3T2A_aT2A.txt
SLX-16314.i705_i502.HWMFJBBXX.s_8.r


title: RORa -T2A ChIPseq

description:
processed data file: sample.peaks_peaks_ChIPm2_RORaT2A_aT2A.txt
SLX-16314.i701_i502.HWMFJBBXX.s_8.r


title: NKp ATACseq


title: FT_E19_pop2_M2

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGH01.H2KVHBBXY.s_7.r

data_processing:
Samples were sequenced using an Illumina Hiseq 4000 running a single-read 50bp protocol
Sequence data were trimmed to remove adaptors and sequences with a quality score below 30 using Trim Galore (v0.50, Babraham Bioinformatics)
sequences were aligned to the mouse genome (GRCm38) using STAR (v2.6.0a, Spliced Transcripts Alignment to a Reference, Alexander Dobin)
differential expression calculated using DEseq2 (v1.18.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: DEseq2 output file

extract_protocol:
Cells were flow sorted into PBS 50% FCS and RNA was extracted using RNeasy Plus micro kit (Qiagen). After assessment using a Bioanalyser (Agilent), RNA was processed for RNA-sequencing using an Ovation RNA-seq System V2 (Nugen), fragmented using the Covaris M220, and bar-coded using Ovation Ultralow Library Systems (Nugen)
and bar-coded using Ovation Ultralow Library Systems (Nugen)


title: FT_E19_DN2_M4

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGH03.H2KVHBBXY.s_7.r


title: Ascl1_5d_II_20190403BJ_M01

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_L15

description: dentate gyrus dissection


title: FT_E19_pop5_M4

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGG03.H2KVHBBXY.s_7.r


title: Ascl1_5d_II_20190403BJ_L11

description: dentate gyrus dissection


title: FT_E19_pop1_M2

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGG01.H2KVHBBXY.s_7.r


title: Ascl1_5d_II_20190403BJ_L08

description: dentate gyrus dissection


title: FT_E19_pop4_M4

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGF03.H2KVHBBXY.s_7.r


title: Ascl1_5d_II_20190403BJ_L04

description: dentate gyrus dissection


title: FT_E19_DN2_M1

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGF01.H2KVHBBXY.s_7.r


title: Ascl1_5d_II_20190403BJ_L16

description: dentate gyrus dissection


title: FT_E19_pop3_M4

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGE03.H2KVHBBXY.s_7.r


title: Ascl1_5d_II_20190403BJ_L01

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_K20

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_L03

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_L13

description: dentate gyrus dissection


title: FT_E19_pop5_M1

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGE01.H2KVHBBXY.s_7.r


title: Ascl1_5d_II_20190403BJ_K19

description: dentate gyrus dissection


title: FT_E19_pop2_M4

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGD03.H2KVHBBXY.s_7.r


title: Ascl1_5d_II_20190403BJ_K17

description: dentate gyrus dissection


title: FT_E19_DN2_M2

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGD02.H2KVHBBXY.s_7.r


title: Ascl1_5d_II_20190403BJ_K16

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_L10

description: dentate gyrus dissection


title: FT_E19_pop4_M1

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGD01.H2KVHBBXY.s_7.r


title: FT_E19_pop5_M2

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGC02.H2KVHBBXY.s_7.r


title: Ascl1_5d_II_20190403BJ_K13

description: dentate gyrus dissection


title: FT_E19_pop3_M1

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGC01.H2KVHBBXY.s_7.r


title: Ascl1_5d_II_20190403BJ_K12

description: dentate gyrus dissection


title: FT_E19_pop4_M2

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGB02.H2KVHBBXY.s_7.r


title: Ascl1_5d_II_20190403BJ_L02

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_K11

description: dentate gyrus dissection


title: FT_E19_pop3_M2

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGA02.H2KVHBBXY.s_7.r


title: Ascl1_5d_II_20190403BJ_K08

description: dentate gyrus dissection


title: FT_E19_pop1_M1

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGA01.H2KVHBBXY.s_7.r


title: Ascl1_5d_II_20190403BJ_K10

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_K05

description: dentate gyrus dissection


title: FT_E15_pop4_M3

description:
processed data file: samples_4fded22d.csv_DESeq_norm_read_counts.txt
SLX-16318.L2V18DRBC14.H23JTBBXY.s_5.r


title: FT_E15_pop3_M3

description:
processed data file: samples_4fded22d.csv_DESeq_norm_read_counts.txt
SLX-16318.L2V18DRBC13.H23JTBBXY.s_5.r


title: Ascl1_5d_II_20190403BJ_K06

description: dentate gyrus dissection


title: FT_E15_pop2_M3

description:
processed data file: samples_4fded22d.csv_DESeq_norm_read_counts.txt
SLX-16318.L2V18DRBC12.H23JTBBXY.s_5.r


title: Ascl1_5d_II_20190403BJ_K01

description: dentate gyrus dissection


title: FT_E15_pop1_M3

description:
processed data file: samples_4fded22d.csv_DESeq_norm_read_counts.txt
SLX-16318.L2V18DRBC11.H23JTBBXY.s_5.r


title: FT_E15_DN2_M2

description:
processed data file: samples_4fded22d.csv_DESeq_norm_read_counts.txt
SLX-16318.L2V18DRBC10.H23JTBBXY.s_5.r


title: Ascl1_5d_II_20190403BJ_K03

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_K15

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_J19

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_J18

description: dentate gyrus dissection


title: FT_E15_pop4_M2

description:
processed data file: samples_4fded22d.csv_DESeq_norm_read_counts.txt
SLX-16318.L2V18DRBC09.H23JTBBXY.s_5.r


title: Ascl1_5d_II_20190403BJ_K14

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_J17

description: dentate gyrus dissection


title: FT_E19_pop1_M4

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGC03.H2KVHBBXY.s_7.r


title: Ascl1_5d_II_20190403BJ_J16

description: dentate gyrus dissection


title: FT_E15_pop2_M2

description:
processed data file: samples_4fded22d.csv_DESeq_norm_read_counts.txt
SLX-16318.L2V18DRBC07.H23JTBBXY.s_5.r


title: Ascl1_5d_II_20190403BJ_J14

description: dentate gyrus dissection


title: FT_E15_pop1_M2

description:
processed data file: samples_4fded22d.csv_DESeq_norm_read_counts.txt
SLX-16318.L2V18DRBC06.H23JTBBXY.s_5.r


title: FT_E19_pop2_M1

description:
processed data file: samples_e197be57.csv_DESeq_norm_read_counts.txt
SLX-16928.NGB01.H2KVHBBXY.s_7.r


title: FT_E15_DN2_M1

description:
processed data file: samples_4fded22d.csv_DESeq_norm_read_counts.txt
SLX-16318.L2V18DRBC05.H23JTBBXY.s_5.r


title: Ascl1_5d_II_20190403BJ_J10

description: dentate gyrus dissection


title: FT_E15_pop4_M1

description:
processed data file: samples_4fded22d.csv_DESeq_norm_read_counts.txt
SLX-16318.L2V18DRBC04.H23JTBBXY.s_5.r


title: Ascl1_5d_II_20190403BJ_J09

description: dentate gyrus dissection


title: FT_E15_pop3_M1

description:
processed data file: samples_4fded22d.csv_DESeq_norm_read_counts.txt
SLX-16318.L2V18DRBC03.H23JTBBXY.s_5.r


title: FT_E15_pop2_M1

description:
processed data file: samples_4fded22d.csv_DESeq_norm_read_counts.txt
SLX-16318.L2V18DRBC02.H23JTBBXY.s_5.r


title: Ascl1_5d_II_20190403BJ_J07

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_J06

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_J04

description: dentate gyrus dissection


title: E19.5_DN1 [10X]

data_processing:
The reads were aligned to the mouse transcriptome (GRCm38) and expression calculated using the 10X Cellranger (v3.0.2) wrapper for the STAR aligner (Spliced Transcripts Alignment to a Reference, Alexander Dobin)
Separate libraries were generated using cells from E15.5 (7,700 DN1 cells plus 300 DN2 cells) and E19.5 (7,700 DN1 cells plus 300 DN2 cells), then combined using Cellranger.
Genome_build: GRCm38
Supplementary_files_format_and_content: Cloupe file, tab separated per cell raw expression values

extract_protocol:
FACS purified cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) to obtain nuclei extract
10X Single cell library preparation was performed using the 10X Genomics technology platform. The 10X Genomics Chromium Single Cell 3’ v3 protocol was followed to obtain 3’ libraries for subsequent sequencing


title: E15.5_DN1 [10X]


title: FT_E15_pop3_M2

description:
processed data file: samples_4fded22d.csv_DESeq_norm_read_counts.txt
SLX-16318.L2V18DRBC08.H23JTBBXY.s_5.r


title: Ascl1_5d_II_20190403BJ_J03

description: dentate gyrus dissection


title: JW8_9

data_processing:
Reads aligned to a modified mouse genome (addition of the reporters found in the mouse) using the Salmon pseudoaligner (v0.8.2)
Pseudocounts analysis with the scater library (v1.6.3) (McCarthy et al., 2017), scran library (v1.6.9) (Lun et al., 2016), and sva library (sva: Surrogate Variable Analysis. R package v3.26.0).
Cells with pseudocounts below 3 median-absolute-deviations away from the median were removed. Genes with an average count across all remaining cells of less than 1 were removed.
Size factors were calculated with the scran library (based on the gene counts) and the data normalised by them.
Batch effects were removed using the ComBat empirical Bayes framework from the sva library
Genome_build: GRCm38.68
Supplementary_files_format_and_content: RDS of R SCE object containing metadata and gene expression generated using R,scater,scran and sva; tab-separated normalised gene expression from the SCE object

source_name: Sample 2B_embryonic thymus

extract_protocol:
Individual cells were flow cytometrically purified on a 96 well format into 0.2% Triton X-100 containing RNase inhibitor, dNTPs and oligo-dT primers and stored at -80oC.
On thawing, lysates were heated to 72 oC for 3 minutes and subject to reverse transcription, PCR preamplification (26 cycles) and PCR purification.  cDNA library quality was assessed for all samples by qualitative PCR using primers for 18s RNA with an additional check by Bioanalyzer using an Agilent high sensitivity DNA chip on a small subset of libraries. A subset of libraries was quantified using the Qubit dsDNA HS assay kit and an average value used to calculate library dilution to 100-150 pg/ml. cDNA library tagmentation and amplification was performed using the Illumina Nextera XT DNA Library Preparation Kit according to manufacturer’s instructions except that all volumes were reduced 4-fold and tagmentation performed at 55oC for 20 minutes. Nextera index and Illumina adapter sequences were incorporated at the amplification stage (N7xx and S5xx). Amplified and indexed libraries were pooled and purified using Agencourt AMPure XP beads at a ratio of 1:0.9 library to beads and washed with 70% ethanol. Two rounds of purification were performed before a final elution in 1.25x total library volume of Nextera Resuspension buffer

tag: mouse id

value: Sample 2B


title: JW8_8


title: Ascl1_5d_II_20190403BJ_J02

description: dentate gyrus dissection

extract_protocol:
single-cell
illumina nextera
Smart-seq2


title: JW8_7


title: JW8_6


title: Ascl1_5d_II_20190403BJ_I19

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_J01

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_I18

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_J12

description: dentate gyrus dissection


title: JW8_4


title: JW8_5


title: Ascl1_5d_II_20190403BJ_I16

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_L06

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_I17

description: dentate gyrus dissection


title: JW8_30


title: FT_E15_pop1_M1

description:
processed data file: samples_4fded22d.csv_DESeq_norm_read_counts.txt
SLX-16318.L2V18DRBC01.H23JTBBXY.s_5.r


title: Ascl1_5d_II_20190403BJ_J08

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_I14

description: dentate gyrus dissection


title: JW8_29


title: Ascl1_5d_II_20190403BJ_I12

description: dentate gyrus dissection


title: JW8_27


title: Ascl1_5d_II_20190403BJ_I15

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_I11

description: dentate gyrus dissection


title: JW8_26


title: Ascl1_5d_II_20190403BJ_I09

description: dentate gyrus dissection


title: JW8_28


title: Ascl1_5d_II_20190403BJ_I07

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_I06

description: dentate gyrus dissection


title: JW8_25


title: Ascl1_5d_II_20190403BJ_I02

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_I03

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_I01

description: dentate gyrus dissection


title: JW8_24


title: Ascl1_5d_II_20190403BJ_H15

description: dentate gyrus dissection


title: JW8_20


title: JW8_22


title: JW8_21


title: JW8_2


title: JW8_3


title: JW8_23


title: Ascl1_5d_II_20190403BJ_H11

description: dentate gyrus dissection


title: JW8_19


title: Ascl1_5d_II_20190403BJ_H12

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_H10

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_H08

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_H07

description: dentate gyrus dissection


title: JW8_17


title: JW8_18


title: Ascl1_5d_II_20190403BJ_H06

description: dentate gyrus dissection


title: JW8_16


title: JW8_15


title: Ascl1_5d_II_20190403BJ_H04

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_H03

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_H01

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_H02

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_G20

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_G19

description: dentate gyrus dissection


title: JW8_14


title: JW8_12


title: JW8_13


title: JW8_11


title: JW8_10


title: Ascl1_5d_II_20190403BJ_G16

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_G15

description: dentate gyrus dissection


title: JW8_1


title: JW7_94


title: Ascl1_5d_II_20190403BJ_G14

description: dentate gyrus dissection


title: JW7_96


title: JW7_93


title: JW7_95


title: Ascl1_5d_II_20190403BJ_G11

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_G09

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_G08

description: dentate gyrus dissection


title: JW7_91


title: JW7_92


title: Ascl1_5d_II_20190403BJ_G07

description: dentate gyrus dissection


title: JW7_90


title: Ascl1_5d_II_20190403BJ_G06

description: dentate gyrus dissection


title: JW7_89


title: Ascl1_5d_II_20190403BJ_G05

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_G03

description: dentate gyrus dissection


title: JW7_88


title: JW7_87


title: Ascl1_5d_II_20190403BJ_F20

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_F17

description: dentate gyrus dissection


title: JW7_84


title: JW7_83


title: JW7_85


title: Ascl1_5d_II_20190403BJ_F18

description: dentate gyrus dissection


title: JW7_82


title: Ascl1_5d_II_20190403BJ_F15

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_F11

description: dentate gyrus dissection


title: JW7_81


title: Ascl1_5d_II_20190403BJ_F12

description: dentate gyrus dissection


title: JW7_80


title: JW7_79


title: JW7_78


title: Ascl1_5d_II_20190403BJ_F10

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_F07

description: dentate gyrus dissection


title: JW7_74


title: JW7_76


title: Ascl1_5d_II_20190403BJ_F04

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_F05

description: dentate gyrus dissection


title: JW7_75


title: Ascl1_5d_II_20190403BJ_F06

description: dentate gyrus dissection


title: JW7_73


title: Ascl1_5d_II_20190403BJ_G01

description: dentate gyrus dissection


title: JW7_86


title: Ascl1_5d_II_20190403BJ_F03

description: dentate gyrus dissection


title: JW7_72


title: Ascl1_5d_II_20190403BJ_E19

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_F16

description: dentate gyrus dissection


title: JW7_71


title: JW7_70


title: Ascl1_5d_II_20190403BJ_E17

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_E18

description: dentate gyrus dissection


title: JW7_69


title: JW7_77


title: Ascl1_5d_II_20190403BJ_F09

description: dentate gyrus dissection


title: JW7_68


title: Ascl1_5d_II_20190403BJ_E15

description: dentate gyrus dissection


title: JW7_67


title: JW7_65


title: Ascl1_5d_II_20190403BJ_E16

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_E12

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_E14

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_E13

description: dentate gyrus dissection


title: JW7_64


title: Ascl1_5d_II_20190403BJ_E11

description: dentate gyrus dissection


title: JW7_63


title: Ascl1_5d_II_20190403BJ_E09

description: dentate gyrus dissection


title: JW7_62


title: JW7_61


title: JW7_60


title: JW7_59


title: Ascl1_5d_II_20190403BJ_E06

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_E04

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_E08

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_E03

description: dentate gyrus dissection


title: JW7_66


title: Ascl1_5d_II_20190403BJ_E02

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_E01

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_D18

description: dentate gyrus dissection


title: JW7_53

source_name: Sample 2A_embryonic thymus

value: Sample 2A


title: Ascl1_5d_II_20190403BJ_D21

description: dentate gyrus dissection

source_name: dentate gyrus tdTomato+ single cells


title: JW7_57


title: JW7_54


title: Ascl1_5d_II_20190403BJ_D20

description: dentate gyrus dissection


title: JW7_56


title: JW7_51


title: Ascl1_5d_II_20190403BJ_E10

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_D16

description: dentate gyrus dissection


title: JW7_52


title: Ascl1_5d_II_20190403BJ_D14

description: dentate gyrus dissection


title: JW7_48


title: Ascl1_5d_II_20190403BJ_D15

description: dentate gyrus dissection


title: JW7_50


title: JW7_47


title: Ascl1_5d_II_20190403BJ_D13

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_D17

description: dentate gyrus dissection


title: JW7_46


title: Ascl1_5d_II_20190403BJ_D12

description: dentate gyrus dissection


title: JW7_45


title: Ascl1_5d_II_20190403BJ_D10

description: dentate gyrus dissection


title: JW7_58


title: Ascl1_5d_II_20190403BJ_D09

description: dentate gyrus dissection


title: JW7_55


title: JW7_44


title: Ascl1_5d_II_20190403BJ_D08

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_D06

description: dentate gyrus dissection


title: JW7_43


title: JW7_40


title: JW7_41


title: JW7_42


title: Ascl1_5d_II_20190403BJ_D03

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_D05

description: dentate gyrus dissection


title: JW7_38


title: JW7_49


title: Ascl1_5d_II_20190403BJ_C23

description: dentate gyrus dissection


title: JW7_37


title: Ascl1_5d_II_20190403BJ_C22

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_C19

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_C17

description: dentate gyrus dissection


title: JW7_36


title: JW7_34


title: JW7_33


title: Ascl1_5d_II_20190403BJ_C16

description: dentate gyrus dissection


title: JW7_35


title: JW7_32


title: Ascl1_5d_II_20190403BJ_C15

description: dentate gyrus dissection


title: JW7_31


title: Ascl1_5d_II_20190403BJ_C13

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_C12

description: dentate gyrus dissection


title: JW7_30


title: Ascl1_5d_II_20190403BJ_D02

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_D04

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_C11

description: dentate gyrus dissection


title: JW7_39


title: Ascl1_5d_II_20190403BJ_C10

description: dentate gyrus dissection


title: JW7_28


title: Ascl1_5d_II_20190403BJ_C09

description: dentate gyrus dissection


title: JW7_29


title: Ascl1_5d_II_20190403BJ_C07

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_C18

description: dentate gyrus dissection


title: JW7_23


title: Ascl1_5d_II_20190403BJ_C06

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_C08

description: dentate gyrus dissection


title: JW7_25


title: JW7_26


title: JW7_27


title: Ascl1_5d_II_20190403BJ_C05

description: dentate gyrus dissection


title: JW7_24


title: Ascl1_5d_II_20190403BJ_C03

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_C02

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_B20

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_B18

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_B19

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_B17

description: dentate gyrus dissection


title: JW7_20


title: JW7_22


title: AF2_95


title: JW7_21


title: JW7_19


title: AF2_96


title: AF2_94


title: Ascl1_5d_II_20190403BJ_B15

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_B14

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_B13

description: dentate gyrus dissection


title: AF2_92


title: Ascl1_5d_II_20190403BJ_B12

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_B10

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_B09

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_C01

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_B11

description: dentate gyrus dissection


title: AF2_89


title: Ascl1_5d_II_20190403BJ_B08

description: dentate gyrus dissection


title: AF2_88


title: AF2_90


title: AF2_87


title: AF2_86


title: Ascl1_5d_II_20190403BJ_B06

description: dentate gyrus dissection


title: AF2_85


title: AF2_93


title: AF2_91


title: AF2_84


title: AF2_83


title: Ascl1_5d_II_20190403BJ_B05

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_B03

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_B01

description: dentate gyrus dissection


title: AF2_82


title: Ascl1_5d_II_20190403BJ_B02

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_A18

description: dentate gyrus dissection


title: AF2_9


title: Ascl1_5d_II_20190403BJ_B04

description: dentate gyrus dissection


title: AF2_80


title: AF2_8


title: AF2_79


title: Ascl1_5d_II_20190403BJ_A16

description: dentate gyrus dissection


title: AF2_78


title: Ascl1_5d_II_20190403BJ_B07

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_A15

description: dentate gyrus dissection


title: AF2_77


title: Ascl1_5d_II_20190403BJ_A12

description: dentate gyrus dissection


title: Ascl1_5d_II_20190403BJ_A11

description: dentate gyrus dissection


title: AF2_76


title: Ascl1_5d_II_20190403BJ_A14

description: dentate gyrus dissection


title: exp 4

city: irvine

first: Siwei

last: Chen

state: CA

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

description: Intracortical injection with LNA oligonucleotide complementary to miR-29a (miR-29a)

data_processing:
Basecalling performed using RTA version 1.18.64
Demultiplexing performed using CASAVA version 1.8.2
Alignment to reference assembly mm10 using Tuxedo bowtie
Mapping results filtering performed using Tuxedo cuffquant
Read counting for each gene and normalization to FPKM values performed using Tuxedo cuffnorm
Genome_build: mm10
Supplementary_files_format_and_content: FPKM value for each gene in tsv table format

source_name: amiR-29a 4

extract_protocol:
RNA was extracted by the addiction of Phenol/guanidine-based QIAzol Lysis Reagent (Qiagen, cat. no. 79306)
RNA libraries were constructed using the TruSeq RNA Sample preparation kit v2 (Illumina) and sequenced (2 × 100 bp reads, about 30 M reads/sample) on a Illumina Hiseq2000 platform at the Istituto di Genomica Applicata (Udine, Italy).

value: visual cortex

tag: age at intracortical injection

value: Postnatal day 122

tag: time of harvest

value: Post-natal day 129


title: exp 3

source_name: amiR-29a 3

tag: strain


title: Ascl1_5d_II_20190403BJ_A10

description: dentate gyrus dissection

data_processing:
Single-end 126nt-long reads were adaptor removed and trimmed using cutadapt v1.16 and sickle v1.33 with default parameters. Reads were mapped against the mouse GRCm38.90 primary assembly 126 with the Ensembl GRCm38.90 GTF annotation using STAR v2.6.0c
cells / genes filtered with scater v.1.12.2 and Seurat v3.0.2. Cells with 1000-6000 genes detected, less than 8% of mitochondrial reads and more than 50000 total reads were kept for downstream analysis.
Data normalized with Seurat v3.0.2 pipeline (log normalization)
Analysis(UMAP,DEG) performed with Seurat v3.0.2
RNA velocity was run with velocyto.R v0.6 using default parameters
Slingshot and pseudotime were computed using slingshot v1.3.2 and fastICA v1.2-2 Packages
Prediction was computed using caret caret_6.0-84 package
Data analysis was carried out in R v3.6.1
Supplementary_files_format_and_content: metadata and matrix with counts for all cells in txt file

value: 7-8 week old


title: AF2_74


title: AF2_81


title: AF2_73


title: exp 2

source_name: amiR-29a 2


title: exp 1

source_name: amiR-29a 1


title: control 4

description: Intracortical injection with LNA oligonicleotide with scrambeld sequence (control)


title: Ascl1_5d_II_20190403BJ_A08

description: dentate gyrus dissection

value: Hoechst- tdTomato+ single cells


title: control 3


title: AF2_71


title: AF2_72


title: Ascl1_5d_II_20190403BJ_A06

description: dentate gyrus dissection


title: control 2


title: control 1


title: Dl3vg5

description: venom glands were collected in triplicate for each biological replicate

organism:
Diachasmimorpha longicaudata
Diachasmimorpha longicaudata entomopoxvirus

source_name: wasp venom gland

tag: developmental stage

value: unemerged adult

value: venom gland


title: AF2_70


title: Ascl1_5d_II_20190403BJ_A04

description: dentate gyrus dissection

value: 5 days after last tamoxifen injection


title: AF2_75


title: AF2_7


title: Dl3vg4


title: Ascl1_5d_II_20190403BJ_A03

description: dentate gyrus dissection


title: AF2_69


title: Dl3vg6


title: Ascl1_5d_II_20190403BJ_A02

description: dentate gyrus dissection


title: Dl3vg3


title: Dl3vg2


title: AF2_68


title: AF2_67


title: Ascl1_5d_II_20190403BJ_A09

description: dentate gyrus dissection


title: 09A018.09A5072_016

city: New Haven

first: Jen-hwa

last: Chu

state: CT

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale University School of Medicine

description:
09A5072_IonXpressRNA_016
processed data file: A1AT-PBMC_gradsids_added.tsv
09A018:09A5072_016_FPKM

data_processing:
Basecalls using Torrent Suite Software Version 5.0.5
mRNA-seq reads were aligned to hg19 using a two stage mapping strategy. In the first stage, tophat version 2.0.12 was used with annotation and the --b2-very-sensitive option. In the second stage, bowtie 2.0.5 was used with local alignment and the --very-sensitive option.
Data were filtered using principal component analysis to remove outleirs.
Genome_build: hg19
Supplementary_files_format_and_content: text files that contain the  Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were generated using cufflinks 2.2.0

source_name: PBMC_PiZZ on Augmenation Therapy

extract_protocol:
Total RNA was extracted from BALF\ and PBMC samples using Qiazol following Qiagen’s miRNeasy protocol (Qiagen 217004) and using QiaCube
cDNA libraries were made from 1ug of total RNA that had RNA Integrity Number (RINe) over 6.5 upon Poly-A selection using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Ambion 61021) and fragmentation using the AB Library Builder™ System (Life Technologies 4463592) with the Ion Total RNA-Seq Kit for AB Library Builder™ System (Life Technologies 4482416).

tag: subject status

value: Alpha-1 Antitrypsin Deficiency patients

value: PiZZ on Augmenation Therapy

value: peripheral blood mononuclear cell (PBMC)


title: 09A009.09A5074_014

description:
09A5074_IonXpressRNA_014
processed data file: A1AT-PBMC_gradsids_added.tsv
09A009:09A5074_014_FPKM


title: 10A008.10A5086_004

description:
10A5086_IonXpressRNA_004
processed data file: A1AT-PBMC_gradsids_added.tsv
10A008:10A5086_004_FPKM


title: 09A011.09A5135_003

description:
09A5135_IonXpressRNA_003
processed data file: A1AT-PBMC_gradsids_added.tsv
09A011:09A5135_003_FPKM


title: AF2_65

value: 5x polychromILC mice

value: Embryonic Thymus


title: 10A016.10A5091_007

description:
10A5091_IonXpressRNA_007
processed data file: A1AT-PBMC_gradsids_added.tsv


title: 10A005.10A5083_010

description:
10A5083_IonXpressRNA_010
processed data file: A1AT-PBMC_gradsids_added.tsv
10A005:10A5083_010_FPKM


title: 09A002.09A5071_008

description:
09A5071_IonXpressRNA_008
processed data file: A1AT-PBMC_gradsids_added.tsv
09A002:09A5071_008_FPKM


title: AF2_64


title: AF2_63


title: Dl3vg1


title: 05A011.05A5046_010

description:
05A5046_IonXpressRNA_010
processed data file: A1AT-PBMC_gradsids_added.tsv
05A011:05A5046_010_FPKM


title: 04A013.04A5128_009

description:
04A5128_IonXpressRNA_009
processed data file: A1AT-PBMC_gradsids_added.tsv
04A013:04A5128_009_FPKM


title: 05A003.05A5041_008

description:
05A5041_IonXpressRNA_008
processed data file: A1AT-PBMC_gradsids_added.tsv
05A003:05A5041_008_FPKM


title: 05A005.05A5043_010

description:
05A5043_IonXpressRNA_010
processed data file: A1AT-PBMC_gradsids_added.tsv
05A005:05A5043_010_FPKM


title: 16S_YoungvAged_Ctrl and ABX [YC2-R_END]

city: Dallas

first: Siyuan

address: 6001 Forest Park Rd

institute: UT Southwestern Medical Center

description: microbiome

data_processing:
Base calling and demultiplexing were performed by MiSeq Controller Software. Nextera XT Indices were used for sample level demultiplexing.
DADA2 (v1.16.0) R package was used for reads filtering, mergein forward/reserve reads, construct sequence table, and remove remove chimeras.
Divisive Amplicon Denoising Algorithm version 2 (DADA2) R package was used to analyze the 16S amplicon reads and construct the operational taxonomic units (OTUs).
Genome_build: silva_nr99_v138_train_set.fa.gz and silva_species_assignment_v138.fa.gz
Supplementary_files_format_and_content: tab-delimited text files
Supplementary_files_format_and_content: Metadata
Supplementary_files_format_and_content: constructed sequence table with out chimeras
Supplementary_files_format_and_content: taxa assigned
Supplementary_files_format_and_content: metagenome file
Supplementary_files_format_and_content: metagenome file

source_name: fecal pellet bacterial DNA

extract_protocol:
DNA was extracted using the ZymoBIOMICS DNA Miniprep Kit (Cat# D4300).
Libraries were constructed following the the Illumina 16S Metagenomic Sequencing Library Preparation protocol (PN 15044223 Rev. B).
Libraries were normalized and multiplexed into a single pool prior to validation by Qubit High-Sensitivity dsDNA, Agilent Bioanalyzer DNA 7500 Chip, and Kapa Illumina Library Quantification qPCR analyses. The final library (8.5pM) and PhiX (0.7pM) were sequenced on the MiSeq System using MiSeq V2 500 cycle kit (250-PE with 8-bp dual indexing).

tag: 1 brain or pooled

value: V3/V4 Amplicons from 12 fecal pellets


title: 16S_YoungvAged_Ctrl and ABX [YC1-R_END]

description: microbiome

tag: mouse strain


title: 16S_YoungvAged_Ctrl and ABX [Standard]

description: microbiome


title: 16S_YoungvAged_Ctrl and ABX [YC1-L_END]

description: microbiome


title: AF2_66


title: 04A033.04A5124_002

description:
04A5124_IonXpressRNA_002
processed data file: A1AT-PBMC_gradsids_added.tsv
04A033:04A5124_002_FPKM


title: 04A032.04A5125_016

description:
04A5125_IonXpressRNA_016
processed data file: A1AT-PBMC_gradsids_added.tsv
04A032:04A5125_016_FPKM


title: T1: Pancreas of P48-Cre; KrasG12D; G9aflox/flox mice 1

city: Tokyo

first: Keisuke

last: Tateishi

address: Bunkyo-ku, Hongo7-3-1

country: Japan

institute: University of Tokyo

description: Gene expression data from pancreas of P48-Cre; KrasG12D; G9aflox/flox mice 1

hyb_protocol: Hybridization, Wash, and Stain Kit (Affymetrix cat.#900720), GeneChip Hybridization Oven.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix® Expression Console™ Software  (Affymetrix, Inc)

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (GeneChip WT PLUS Reagent Kit User Manual, Affymetrix).

growth_protocol: Mice were maintained in a temperature- and light-controlled facility and permitted ad libitum regular chow diet and autoclaved water. All mice were backcrossed with the C57BL/6 strain.

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mouse pancreas were harvested and minched quickly.

value: Pancreas

value: P48-Cre; KrasG12D; G9aflox/flox


title: T2: Pancreas of P48-Cre; KrasG12D; G9aflox/flox mice 2

description: Gene expression data from pancreas of P48-Cre; KrasG12D; G9aflox/flox mice 2


title: AF2_60

source_name: Sample 1A_embryonic thymus

value: Sample 1A


title: AF2_6


title: 03A022.03A5106_007

description:
03A5106_IonXpressRNA_007
processed data file: A1AT-PBMC_gradsids_added.tsv
03A022:03A5106_007_FPKM


title: AF2_62

value: Sample 2A


title: 08A015.08A5068_013

description:
08A5068_IonXpressRNA_013
processed data file: A1AT-PBMC_gradsids_added.tsv
08A015:08A5068_013_FPKM


title: 03A044.03A5212_013

description:
03A5212_IonXpressRNA_013
processed data file: A1AT-PBMC_gradsids_added.tsv
03A044:03A5212_013_FPKM


title: 04A034.04A5126_012

description:
04A5126_IonXpressRNA_012
processed data file: A1AT-PBMC_gradsids_added.tsv
04A034:04A5126_012_FPKM


title: 16S_YoungvAged_Ctrl and ABX [YA1-R_END]

description: microbiome


title: 03A019.03A5102_015

description:
03A5102_IonXpressRNA_015
processed data file: A1AT-PBMC_gradsids_added.tsv
03A019:03A5102_015_FPKM


title: 16S_YoungvAged_Ctrl and ABX [YA2-LL_END]

description: microbiome


title: AF2_58


title: 10A032.10A5192_005

description:
10A5192_IonXpressRNA_005
processed data file: A1AT-PBMC_gradsids_added.tsv
10A032:10A5192_005_FPKM

source_name: PBMC_PiZZ Not on Augmenation Therapy

value: PiZZ Not on Augmenation Therapy


title: 03A013.03A5027_002

description:
03A5027_IonXpressRNA_002
processed data file: A1AT-PBMC_gradsids_added.tsv
03A013:03A5027_002_FPKM


title: 16S_YoungvAged_Ctrl and ABX [YA2-R_END]

description: microbiome


title: 03A014.03A5028_002

description:
03A5028_IonXpressRNA_002
processed data file: A1AT-PBMC_gradsids_added.tsv
03A014:03A5028_002_FPKM


title: AF2_59


title: 10A026.10A5151_002

description:
10A5151_IonXpressRNA_002
processed data file: A1AT-PBMC_gradsids_added.tsv
10A026:10A5151_002_FPKM


title: 16S_YoungvAged_Ctrl and ABX [OC2-R_END]

description: microbiome


title: AF2_57


title: AF2_61


title: C1: Pancreas of P48-Cre; KrasG12D mice 1

description: Gene expression data from pancreas of P48-Cre; KrasG12D mice 1

value: P48-Cre; KrasG12D


title: C2: Pancreas of P48-Cre; KrasG12D mice 2

description: Gene expression data from pancreas of P48-Cre; KrasG12D mice 2


title: 10A010.10A5097_008

description:
10A5097_IonXpressRNA_008
processed data file: A1AT-PBMC_gradsids_added.tsv
10A010:10A5097_008_FPKM


title: 16S_YoungvAged_Ctrl and ABX [OC1-RL_END]

description: microbiome


title: 10A017.10A5095_011

description:
10A5095_IonXpressRNA_011
processed data file: A1AT-PBMC_gradsids_added.tsv
10A017:10A5095_011_FPKM


title: AF2_56


title: 03A023.03A5107_009

description:
03A5107_IonXpressRNA_009
processed data file: A1AT-PBMC_gradsids_added.tsv
03A023:03A5107_009_FPKM


title: 10A003.10A5089_004

description:
10A5089_IonXpressRNA_004
processed data file: A1AT-PBMC_gradsids_added.tsv
10A003:10A5089_004_FPKM


title: 16S_YoungvAged_Ctrl and ABX [OC1-R_END]

description: microbiome


title: AF2_55


title: 03A012.03A5026_015

description:
03A5026_IonXpressRNA_015
processed data file: A1AT-PBMC_gradsids_added.tsv
03A012:03A5026_015_FPKM


title: 10A004.10A5082_002

description:
10A5082_IonXpressRNA_002
processed data file: A1AT-PBMC_gradsids_added.tsv
10A004:10A5082_002_FPKM


title: 10A002.10A5081_014

description:
10A5081_IonXpressRNA_014
processed data file: A1AT-PBMC_gradsids_added.tsv
10A002:10A5081_014_FPKM


title: 10A007.10A5087_008

description:
10A5087_IonXpressRNA_008
processed data file: A1AT-PBMC_gradsids_added.tsv
10A007:10A5087_008_FPKM


title: 16S_YoungvAged_Ctrl and ABX [OA2-R_END]

description: microbiome


title: AF2_54


title: 10A001.10A5080_009

description:
10A5080_IonXpressRNA_009
processed data file: A1AT-PBMC_gradsids_added.tsv
10A001:10A5080_009_FPKM


title: AF2_53


title: 09A023.09A5076_001

description:
09A5076_IonXpressRNA_001
processed data file: A1AT-PBMC_gradsids_added.tsv
09A023:09A5076_001_FPKM


title: 05A002.05A5040_001

description:
05A5040_IonXpressRNA_001
processed data file: A1AT-PBMC_gradsids_added.tsv
05A002:05A5040_001_FPKM


title: 05A012.05A5045_002

description:
05A5045_IonXpressRNA_002
processed data file: A1AT-PBMC_gradsids_added.tsv
05A012:05A5045_002_FPKM


title: AF2_52


title: 16S_YoungvAged_Ctrl and ABX [OA2-L_END]

description: microbiome


title: 16S_YoungvAged_Ctrl and ABX [OA1-RR_END]

description: microbiome


title: 08A005.08A5060_013

description:
08A5060_IonXpressRNA_013
processed data file: A1AT-PBMC_gradsids_added.tsv
08A005:08A5060_013_FPKM


title: 04A014.04A5032_011

description:
04A5032_IonXpressRNA_011
processed data file: A1AT-PBMC_gradsids_added.tsv
04A014:04A5032_011_FPKM


title: 04A017.04A5036_014

description:
04A5036_IonXpressRNA_014
processed data file: A1AT-PBMC_gradsids_added.tsv
04A017:04A5036_014_FPKM


title: 03A026.03A5170_006

description:
03A5170_IonXpressRNA_006
processed data file: A1AT-PBMC_gradsids_added.tsv
03A026:03A5170_006_FPKM


title: AF2_51


title: AF2_50


title: AF2_5


title: 03A025.03A5109_013

description:
03A5109_IonXpressRNA_013
processed data file: A1AT-PBMC_gradsids_added.tsv
03A025:03A5109_013_FPKM


title: 03A024.03A5108_016

description:
03A5108_IonXpressRNA_016
processed data file: A1AT-PBMC_gradsids_added.tsv
03A024:03A5108_016_FPKM


title: 04A007.04A5037_005

description:
04A5037_IonXpressRNA_005
processed data file: A1AT-PBMC_gradsids_added.tsv
04A007:04A5037_005_FPKM


title: WYK3382 Patient UC Sample

city: Chapel Hill

first: Kim Lab

last: UNC

state: NC

address: 450 West Drive, Room 21-209

institute: UNC-CH LCCC

data_processing:
Sequence reads were aligned to the human reference genome hg38 using MapSplice v2.2.1
Gene-level counts were quantified using RSEM v.1.3.0 and normalized for variations in read counts
Normalized read counts were log2 transformed
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: Urothelial cancer FFPE tissue

extract_protocol:
RNA was isolated from 10uM FFPE slides from all patient samples using the Roche High Pure RNA Paraffin Kit according to manufacturer’s protocol, a minimum of 2 µg of total RNA was isolated from FFPE tissues
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Male

tag: race

value: White

tag: age

tag: smoking status

value: Former

tag: pathology stage

tag: rnaseq base47 classification

value: Basal

tag: nanostring base47 classification

tag: overall survival status

tag: overall survival months


title: WYK3384 Patient UC Sample

tag: gender

value: Female

value: Luminal


title: WYK3383 Patient UC Sample

value: Never


title: WYK3385 Patient UC Sample


title: 03A017.03A5100_007

description:
03A5100_IonXpressRNA_007
processed data file: A1AT-PBMC_gradsids_added.tsv
03A017:03A5100_007_FPKM

value: Alpha-1 Antitrypsin Deficiency patients

tag: genotype

tag: tissue

value: peripheral blood mononuclear cell (PBMC)


title: 03A015.03A5029_005

description:
03A5029_IonXpressRNA_005
processed data file: A1AT-PBMC_gradsids_added.tsv
03A015:03A5029_005_FPKM


title: 03A010.03A5025_012

description:
03A5025_IonXpressRNA_012
processed data file: A1AT-PBMC_gradsids_added.tsv
03A010:03A5025_012_FPKM


title: AF2_49

tag: mouse id

value: 5x polychromILC mice

value: Embryonic Thymus


title: WYK3381 Patient UC Sample


title: AF2_48

tag: strain


title: WYK3379 Patient UC Sample


title: 03A009.03A5024_011

description:
03A5024_IonXpressRNA_011
processed data file: A1AT-PBMC_gradsids_added.tsv
03A009:03A5024_011_FPKM


title: WYK3377 Patient UC Sample


title: AF2_46


title: AF2_47


title: WYK3376 Patient UC Sample


title: 03A001.03A5020_014

description:
03A5020_IonXpressRNA_014
processed data file: A1AT-PBMC_gradsids_added.tsv
03A001:03A5020_014_FPKM


title: 03A008.03A5023_003

description:
03A5023_IonXpressRNA_003
processed data file: A1AT-PBMC_gradsids_added.tsv
03A008:03A5023_003_FPKM


title: 01A004.01A5013_011

description:
01A5013_IonXpressRNA_011
processed data file: A1AT-PBMC_gradsids_added.tsv
01A004:01A5013_011_FPKM


title: 03A004.03A5022_009

description:
03A5022_IonXpressRNA_009
processed data file: A1AT-PBMC_gradsids_added.tsv
03A004:03A5022_009_FPKM


title: 01A002.01A5011_012

description:
01A5011_IonXpressRNA_012
processed data file: A1AT-PBMC_gradsids_added.tsv
01A002:01A5011_012_FPKM


title: 01A003.01A5012_011

description:
01A5012_IonXpressRNA_011
processed data file: A1AT-PBMC_gradsids_added.tsv
01A003:01A5012_011_FPKM


title: AF2_45


title: AF2_44


title: 10A040.10A5232_010

description:
10A5232_IonXpressRNA_010
processed data file: A1AT-PBMC_gradsids_added.tsv
10A040:10A5232_010_FPKM

value: PiMZ


title: 10A036.10A5235_011

description:
10A5235_IonXpressRNA_011
processed data file: A1AT-PBMC_gradsids_added.tsv
10A036:10A5235_011_FPKM


title: AF2_43


title: 10A037.10A5231_013

description:
10A5231_IonXpressRNA_013
processed data file: A1AT-PBMC_gradsids_added.tsv
10A037:10A5231_013_FPKM


title: WYK3375 Patient UC Sample


title: WYK3373 Patient UC Sample

value: Current


title: AF2_42

value: Sample 1A


title: WYK3374 Patient UC Sample


title: 10A038.10A5236_005

description:
10A5236_IonXpressRNA_005
processed data file: A1AT-PBMC_gradsids_added.tsv
10A038:10A5236_005_FPKM


title: WYK3372 Patient UC Sample


title: 10A028.10A5199_001

description:
10A5199_IonXpressRNA_001
processed data file: A1AT-PBMC_gradsids_added.tsv
10A028:10A5199_001_FPKM


title: 10A041.10A5230_009

description:
10A5230_IonXpressRNA_009
processed data file: A1AT-PBMC_gradsids_added.tsv
10A041:10A5230_009_FPKM


title: 10A033.10A5191_012

description:
10A5191_IonXpressRNA_012
processed data file: A1AT-PBMC_gradsids_added.tsv
10A033:10A5191_012_FPKM


title: WYK3371 Patient UC Sample


title: 10A029.10A5197_005

description:
10A5197_IonXpressRNA_005
processed data file: A1AT-PBMC_gradsids_added.tsv
10A029:10A5197_005_FPKM


title: AF2_40


title: 10A027.10A5159_004

description:
10A5159_IonXpressRNA_004
processed data file: A1AT-PBMC_gradsids_added.tsv
10A027:10A5159_004_FPKM


title: 10A024.10A5158_003

description:
10A5158_IonXpressRNA_003
processed data file: A1AT-PBMC_gradsids_added.tsv
10A024:10A5158_003_FPKM


title: 10A018.10A5156_003

description:
10A5156_IonXpressRNA_003
processed data file: A1AT-PBMC_gradsids_added.tsv
10A018:10A5156_003_FPKM


title: AF2_4


title: 10A013.10A5090_001

description:
10A5090_IonXpressRNA_001
processed data file: A1AT-PBMC_gradsids_added.tsv
10A013:10A5090_001_FPKM


title: WYK3367 Patient UC Sample


title: 10A006.10A5088_007

description:
10A5088_IonXpressRNA_007
processed data file: A1AT-PBMC_gradsids_added.tsv
10A006:10A5088_007_FPKM


title: AF2_39


title: WYK3366 Patient UC Sample


title: 09A033.09A5180_008

description:
09A5180_IonXpressRNA_008
processed data file: A1AT-PBMC_gradsids_added.tsv
09A033:09A5180_008_FPKM


title: AF2_38


title: WYK3364 Patient UC Sample


title: 09A036.09A5134_002

description:
09A5134_IonXpressRNA_002
processed data file: A1AT-PBMC_gradsids_added.tsv
09A036:09A5134_002_FPKM


title: 09A031.09A5133_001

description:
09A5133_IonXpressRNA_001
processed data file: A1AT-PBMC_gradsids_added.tsv
09A031:09A5133_001_FPKM


title: AF2_37


title: AF2_41


title: 09A028.09A5131_009

description:
09A5131_IonXpressRNA_009
processed data file: A1AT-PBMC_gradsids_added.tsv
09A028:09A5131_009_FPKM


title: 09A029.09A5077_006

description:
09A5077_IonXpressRNA_006
processed data file: A1AT-PBMC_gradsids_added.tsv
09A029:09A5077_006_FPKM


title: AF2_36


title: WYK3363 Patient UC Sample


title: WYK3362 Patient UC Sample


title: 05A015.05A5049_006

description:
05A5049_IonXpressRNA_006
processed data file: A1AT-PBMC_gradsids_added.tsv
05A015:05A5049_006_FPKM


title: 04A039.04A5240_007

description:
04A5240_IonXpressRNA_007
processed data file: A1AT-PBMC_gradsids_added.tsv
04A039:04A5240_007_FPKM


title: AF2_35


title: 04A035.04A5127_008

description:
04A5127_IonXpressRNA_008
processed data file: A1AT-PBMC_gradsids_added.tsv
04A035:04A5127_008_FPKM


title: WYK3361 Patient UC Sample


title: WYK3369 Patient UC Sample


title: AF2_34


title: WYK3360 Patient UC Sample


title: 04A030.04A5123_009

description:
04A5123_IonXpressRNA_009
processed data file: A1AT-PBMC_gradsids_added.tsv
04A030:04A5123_009_FPKM


title: 10A015.10A5085_012

description:
10A5085_IonXpressRNA_012
processed data file: A1AT-PBMC_gradsids_added.tsv
10A015:10A5085_012_FPKM


title: WYK3359 Patient UC Sample


title: 04A024.04A5120_009

description:
04A5120_IonXpressRNA_009
processed data file: A1AT-PBMC_gradsids_added.tsv
04A024:04A5120_009_FPKM


title: AF2_32


title: 04A004.04A5038_015

description:
04A5038_IonXpressRNA_015
processed data file: A1AT-PBMC_gradsids_added.tsv
04A004:04A5038_015_FPKM


title: 04A025.04A5122_006

description:
04A5122_IonXpressRNA_006
processed data file: A1AT-PBMC_gradsids_added.tsv
04A025:04A5122_006_FPKM


title: 03A043.03A5211_011

description:
03A5211_IonXpressRNA_011
processed data file: A1AT-PBMC_gradsids_added.tsv
03A043:03A5211_011_FPKM


title: AF2_33


title: WYK3357 Patient UC Sample

value: Hispanic


title: 03A040.03A5179_009

description:
03A5179_IonXpressRNA_009
processed data file: A1AT-PBMC_gradsids_added.tsv
03A040:03A5179_009_FPKM


title: AF2_31


title: 03A039.03A5178_008

description:
03A5178_IonXpressRNA_008
processed data file: A1AT-PBMC_gradsids_added.tsv
03A039:03A5178_008_FPKM


title: 05A017.05A5112_003

description:
05A5112_IonXpressRNA_003
processed data file: A1AT-PBMC_gradsids_added.tsv
05A017:05A5112_003_FPKM


title: AF2_30


title: WYK3356 Patient UC Sample


title: 03A038.03A5177_007

description:
03A5177_IonXpressRNA_007
processed data file: A1AT-PBMC_gradsids_added.tsv
03A038:03A5177_007_FPKM


title: WYK3354 Patient UC Sample


title: 03A035.03A5175_011

description:
03A5175_IonXpressRNA_011
processed data file: A1AT-PBMC_gradsids_added.tsv
03A035:03A5175_011_FPKM


title: 03A029.03A5173_005

description:
03A5173_IonXpressRNA_005
processed data file: A1AT-PBMC_gradsids_added.tsv
03A029:03A5173_005_FPKM


title: AF2_29


title: WYK3352 Patient UC Sample


title: AF2_3


title: 03A034.03A5174_006

description:
03A5174_IonXpressRNA_006
processed data file: A1AT-PBMC_gradsids_added.tsv
03A034:03A5174_006_FPKM


title: 03A027.03A5171_014

description:
03A5171_IonXpressRNA_014
processed data file: A1AT-PBMC_gradsids_added.tsv
03A027:03A5171_014_FPKM


title: 03A016.03A5103_004

description:
03A5103_IonXpressRNA_004
processed data file: A1AT-PBMC_gradsids_added.tsv
03A016:03A5103_004_FPKM


title: 03A021.03A5105_004

description:
03A5105_IonXpressRNA_004
processed data file: A1AT-PBMC_gradsids_added.tsv
03A021:03A5105_004_FPKM


title: 10A008.10B9191_014

description:
10B9191_IonXpressRNA_014
processed data file: A1AT-BAL_gradsids_added.tsv
10A008:10B9191_014_FPKM

source_name: BAL_PiZZ on Augmenation Therapy

value: PiZZ on Augmenation Therapy

value: bronchoalveolar lavage (BAL)


title: 10A005.10B9185_001

description:
10B9185_IonXpressRNA_001
processed data file: A1AT-BAL_gradsids_added.tsv
10A005:10B9185_001_FPKM


title: AF2_27


title: 09A011.09B9178_015

description:
09B9178_IonXpressRNA_015
processed data file: A1AT-BAL_gradsids_added.tsv
09A011:09B9178_015_FPKM


title: 10A016.10B9194_007

description:
10B9194_IonXpressRNA_007
processed data file: A1AT-BAL_gradsids_added.tsv
10A016:10B9194_007_FPKM


title: AF2_26


title: WYK3347 Patient UC Sample

value: Male


title: WYK3349 Patient UC Sample

value: White


title: AF2_28


title: 03A041.03A5210_012

description:
03A5210_IonXpressRNA_012
processed data file: A1AT-PBMC_gradsids_added.tsv
03A041:03A5210_012_FPKM


title: WYK3355 Patient UC Sample

value: Former


title: WYK3346 Patient UC Sample

value: Basal


title: AF2_24


title: AF2_25


title: 08A015.08B9318_001

description:
08B9318_IonXpressRNA_001
processed data file: A1AT-BAL_gradsids_added.tsv
08A015:08B9318_001_FPKM


title: WYK3343 Patient UC Sample

value: Female


title: WYK3350 Patient UC Sample


title: AF2_23


title: 04A033.04B9409_015

description:
04B9409_IonXpressRNA_015
processed data file: A1AT-BAL_gradsids_added.tsv
04A033:04B9409_015_FPKM


title: AF2_22