title: ABM-LPSp [LPSp]

description:
LPSp is LPS treated single stained transmigrated to lung
gene_counts.txt
gene_norm_corrected.txt

data_processing:
We used cutadapt to trim Truseq adapters and low quality ends from the 3' end of raw reads; a minimum trimmed length of 40bp was required. Trimmed reads were mapped to the reference genome using STAR, and gene expression quantified using featureCounts. Batch effect correction was computed for log2-CPM normalized expression using removeBatchEffect() in edgeR based on the sample batches.
Assembly: mm10
Supplementary files format and content: gene_counts.txt: tab-delimited text file of counts per gene for each sample
Supplementary files format and content: gene_norm_corrected.txt: tab-delimited text file of batch effect corrected log2 CPM normalized expression for each sample

extract_protocol:
Neutrophils were mobilized to lung of 8-10 weeks old male Catchup (heterozygous) or non-labelled C57BL/6-background mice by exposure to 1mg/ml of nebulized LPS (Sigma, Escherichia coli O55:B5) inside the fumigation chamber. 20 mg of anti-Ly6G-BV421 antibody (Biolegend, #127628) was i.v. injected 2 minutes before sacrifice. Lungs were perfused with 10 ml of PBS through right ventricle of heart and collected for PMN isolation, biochemical, and histopathological analyses. For PMN isolation, a single cell suspension was prepared by digestion of minced lung lobes with collagenase A (1 mg/ml; Millipore-Sigma # SCR103) at a 370C shaking water bath for 45 min. Digested lung samples were passed through 16-17G needle and filtered through 40 mm cell strainer (Thermo Fisher, #08-771-1). Red blood cells were removed by using RBC lysis buffer (Thermo Fisher, #00-4333-57). A single cell suspension prepared from Catchup (heterozygous) mice were directly subjected to flow sorting for separation of td-Tomato-positive or double td-Tomato and anti-Ly6G-BV421-positive PMN. PMN, labelled with td-Tomato (or anti-Ly6G-AF-594) and td-Tomato and anti-Ly6G-BV-421 (or anti-Ly6G-AF-594 and anti-Ly6G-BV-421), were sorted in a sterile environment by MoFlo Astrios and MoFlo Astrios EQ (Beckman Coulter) cell sorter equipped with 405, 488, 561 and 635 nm lasers, and collected in RPMI-1640 medium (Thermo Fisher #72400047). Both the sorters are Gates were initially established on forward and side scatter, based on granularity and relative size. Aggregates were gated out accordingly. Selective gates were drawn to sort the single positive and dual positive PMN. Software SUMMIT, 6.1 (Beckman Coulter) was used for sorting and analysis.
RNA quality and quantity was assessed using the Agilent bio-analyzer. All samples showed RNA integrity number > 8. Strand-specific RNA-SEQ libraries were prepared using a TruSEQ mRNA RNA-SEQ library protocol (Illumina provided). Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000 (Illumina provided reagents and protocols).
TruSEQ mRNA RNA-SEQ library protocol (Illumina provided)

value: LPSp

tag: batch


title: ABM-LPSpp [LPSpp]

status: Public on Dec 04 2023

type: SRA

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

country: USA

institute: University of Illinois at Chicago

description:
LPSpp is LPS treated dual stained vascular
gene_counts.txt
gene_norm_corrected.txt

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

source_name: Lung

tag: tissue

value: Lung

tag: cell type

value: Neutrophil

tag: treatment

value: LPSpp


title: Bulk RNAseq of nasal OSN cells (Pou2f3). Treatment: Alt.Day1 and sample id: 221220_F1

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

data_processing:
10X Chromium V3 Chemistry Single-cell RNA Seq
log transformation and TPM normalization (Seurat R package)
PCA (Seurat R package)
UMAP and clustering (Seurat R)
Assembly: mm10
Supplementary files format and content: Log2(Transcripts per million (TPM) + 1) expression values (derived from kallisto bustools  for each gene (rows) in each single-cell (columns)

molecule: total RNA

source_name: Mouse nasal epithelial cells sorted using FACS

growth_protocol: To isolate respiratory epithelium from olfactory mucosa, the tissue overlying the proximal part of the nasal septal and lateral wall, together with vomeronasal organ, was separated from olfactory epithelium, covering the distal portions of nasal cavity. The isolated olfactory and respiratory mucosa were processed as described previously (40). The separated tissue including cartilages and bone fragments was first incubated in a PBS solution with dispase (16 U/ml) and deoxyribonuclease I (DNase I; 20 μg/ml) for 30 min at room temperature on a shaker at 120 rpm. The digestion was terminated by adding cold DMEM supplemented with 5% fetal bovine serum (FBS).

extract_protocol:
Then, the nasal mucosa was separated from the bones mechanically and incubated in Tyrode's Solution with bicarbonate, HEPES, 0.25% BSA, without Ca2+ and added 31 U/ml of papain, 0.25 mg/ml L-cysteine and 20 μg/ml DNase I for 40 min at 37 °C on a rotating shaker at 220 rpm. The papain enzymatic activity was terminated with Tyrode's Solution with HEPES and Ca2+ and with 0.01 mg/ml leupeptin and the digested mucosa was triturated thoroughly and prepared for flow cytometric staining. All samples were pre-incubated with TruStain FcX™ (Biolegend) at 1µg per 106 cells in 100 µl volume for 10 minutes prior to immunostaining (Fig. S1A). 6,000-10,000 cells per sample were collected into PBS and 0.04% (w/v) bovine serum albumin (BSA) and submitted for scRNA-seq. Single-cell suspensions for low input (bulk) RNA-sequencing at 1,000 cells per sample were sorted into TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol. We analyzed a total of 10 mice, treated with PBS (n=4), with one Alternaria challenge (n=4), and with two challenges (n=2).
Sorted samples, containing 6,000-10,000 cells each, were submitted for droplet-based single-cell RNA-sequencing (10X Genomics) to the Single Cell Genomic Core at Brigham and Women’s Hospital. Cells were washed and resuspended in PBS and 0.04% (w/v) bovine serum albumin (BSA) per the manufacturer’s guidelines. Purified samples were run through 10X controller and individually bar-coded libraries were generated and pooled. Pooled library samples were sequenced on a NovaSeq S1 (Illumina) in partnership with Dana Farber Cancer Institute (DFCI) Molecular Biology Core Facilities.
10X Chromium V3 Chemistry Single-cell RNA Seq

treatment_protocol: For assessment of the inflammatory and epithelial response to Alternaria by scRNAseq, the olfactory and respiratory epithelium were processed separately and CD45+ and EpCAM+ cells were sorted to represent 50% of cells in each location. The experiment was performed twice with the collected cells from olfactory mucosa of one mouse and respiratory mucosa from a different mouse of the opposite sex combined together to contribute equal proportions of a single sample.

tag: genotype

tag: time point


title: 4577_Interneuron--Fast-Spiking_BEB19051_CTRL

city: New York

first: Kert

last: Matlik

state: NY

address: 1230 York Avenue

institute: Rockefeller University

description:
4577
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

data_processing:
Sequence and transcript coordinates for human hg38 UCSC genome and gene models were retrieved from the BSgenome.Hsapiens.UCSC.hg38 Bioconductor package (version 1.4.1) and TxDb.Haspiens.UCSC.hg38.knownGene (version 3.4.0) Bioconductor libraries respectively. FANSseq reads were aligned to the genome using Rsubread's subjunc method (version 1.30.6).
Aligned reads were exported as bigWigs normalized to reads per million using the rtracklayer package (version 1.40.6).
Aligned reads in genes were counted using the featurecounts function within the Rsubread package against gene exons.
Assembly: BSgenome.Hsapiens.UCSC.hg38
Supplementary files format and content: BigWig files, Counts files

molecule: nuclear RNA

organism: Homo sapiens

source_name: Posterior caudate

extract_protocol:
RNA extraction was carried out with AllPrep DNA/RNA FFPE Kit (Qiagen, #80234).
RNA-seq libraries were prepared with Trio RNA-Seq™ library preparation kit (Tecan, #0506-A01) and pooled for sequencing on NovaSeq6000 (SP 2 x 150bp).

treatment_protocol: Nuclei were isolated from fresh-frozen post-mortem human caudate nucleus and putamen, labeled with cell type-specific probes and separated by FACS as described by Matlik et al. 2023.

value: Posterior caudate

value: Interneuron, Fast Spiking

tag: donor

tag: age

tag: Sex

value: Male

tag: pmi (hrs)

tag: disease

value: CTRL


title: Bulk RNAseq of nasal OSN cells (Pou2f3). Treatment: Naive and sample id: 221220_E9

value: Naive


title: 4576_Interneuron--Other_BEB19051_CTRL

description:
4576
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

value: Interneuron, Other


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Alt.Day1 and sample id: 221220_E8

value: WT


title: 4703_Interneuron--Other_HSB2116_HD

description:
4703
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

source_name: Caudate

value: Caudate

value: 44CAG / 17CAG

value: Female

value: HD


title: ABM-Cpp [Cpp]

description:
Cpp is control dual stained vascular
gene_counts.txt
gene_norm_corrected.txt

value: Cpp


title: 4575_Interneuron--Non-Fast-Spiking_BEB18117_CTRL

description:
4575
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

value: Interneuron, Non-Fast Spiking


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Alt.Day1 and sample id: 221220_E7


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Naive and sample id: 221220_E6


title: AM-AM-04_D1_TM

description:
AM-AM-04
gene_counts_v2.txt
gene_norm_v2.txt

data_processing:
We used cutadapt to trim Truseq adapters and low quality ends from the 3' end of raw reads; a minimum trimmed length of 40bp was required. Trimmed reads were mapped to the reference genome using STAR, and gene expression quantified using featureCounts. For comparisons between KO groups, batch effect correction was performed based on the Day and Animal ID.
Assembly: mm10
Supplementary files format and content: gene_counts.txt: tab-delimited text file of counts per gene for each sample
Supplementary files format and content: gene_norm.txt: tab-delimited text file of CPM normalized expression for each sample

extract_protocol:
Neutrophils were mobilized to lung of 8-10 weeks old male Catchup (heterozygous) or non-labelled C57BL/6-background mice by exposure to 1mg/ml of nebulized LPS (Sigma, Escherichia coli O55:B5) inside the fumigation chamber. 20 micro grams of anti-Ly6G-BV421 antibody (Biolegend, #127628) was i.v. injected 2 minutes before sacrifice. Lungs were perfused with 10 ml of PBS through right ventricle of heart and collected for PMN isolation, biochemical, and histopathological analyses. For PMN isolation, a single cell suspension was prepared by digestion of minced lung lobes with collagenase A (1 mg/ml; Millipore-Sigma # SCR103) at a 370C shaking water bath for 45 min. Digested lung samples were passed through 16-17G needle and filtered through 40 mm cell strainer (Thermo Fisher, #08-771-1). Red blood cells were removed by using RBC lysis buffer (Thermo Fisher, #00-4333-57). A single cell suspension prepared from Catchup (heterozygous) mice were directly subjected to flow sorting for separation of td-Tomato-positive or double td-Tomato and anti-Ly6G-BV421-positive PMN. PMN, labelled with td-Tomato (or anti-Ly6G-AF-594) and td-Tomato and anti-Ly6G-BV-421 (or anti-Ly6G-AF-594 and anti-Ly6G-BV-421), were sorted in a sterile environment by MoFlo Astrios and MoFlo Astrios EQ (Beckman Coulter) cell sorter equipped with 405, 488, 561 and 635 nm lasers, and collected in RPMI-1640 medium (Thermo Fisher #72400047). Both the sorters are Gates were initially established on forward and side scatter, based on granularity and relative size. Aggregates were gated out accordingly. Selective gates were drawn to sort the single positive and dual positive PMN. Software SUMMIT, 6.1 (Beckman Coulter) was used for sorting and analysis.
RNA quality and quantity was assessed using the Agilent bio-analyzer. All samples showed RNA integrity number > 8. Strand-specific RNA-SEQ libraries were prepared using a TruSEQ mRNA RNA-SEQ library protocol (Illumina provided). Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000 (Illumina provided reagents and protocols).
TruSEQ mRNA RNA-SEQ library protocol (Illumina provided)

value: Transmigrated

tag: time

value: day 1

tag: animal id


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Aspergillus and sample id: 221220_G4

value: Aspergillus


title: Bulk RNAseq of nasal OSN cells (Pou2f3). Treatment: Alt.Day1 and sample id: 221220_F4


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Naive and sample id: 221220_E5


title: Bulk RNAseq of nasal HBC cells (Pou2f3). Treatment: Alt.Day1 and sample id: 221220_E4


title: Bulk RNAseq of nasal HBC cells (Pou2f3). Treatment: Alt.Day1 and sample id: 221220_E3


title: 4573_Interneuron--Other_BEB18117_CTRL

description:
4573
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)


title: ABM-AM-8 [LPSpp]

value: Lung

value: Neutrophil

value: LPSpp


title: 4574_Interneuron--Fast-Spiking_BEB18117_CTRL

description:
4574
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

value: Posterior caudate

value: Interneuron, Fast Spiking

value: Male


title: 4572_Interneuron--Non-Fast-Spiking_BEB18116_CTRL

description:
4572
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

source_name: Anterior caudate

value: Anterior caudate

value: CTRL


title: ABM-AM-6 [LPSp]

value: LPSp


title: Bulk RNAseq of nasal OSN cells (Pou2f3). Treatment: Naive and sample id: 221220_E10

value: Naive


title: Bulk RNAseq of nasal HBC cells (Pou2f3). Treatment: Alt.Day1 and sample id: 221220_E2


title: Bulk RNAseq of nasal OSN cells (Pou2f3). Treatment: Alt.Day1 and sample id: 221220_F2


title: Bulk RNAseq of nasal OSN cells (Pou2f3). Treatment: Naive and sample id: 221220_E12


title: Bulk RNAseq of nasal OSN cells (Pou2f3). Treatment: Alt.Day1 and sample id: 221220_F3


title: ABM-AM-7 [Cpp]


title: Bulk RNAseq of nasal HBC cells (Pou2f3). Treatment: Naive and sample id: 221220_D9


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Alt.Day1 and sample id: 221220_D4

value: WT


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Alt.Day1 and sample id: 221220_D5


title: 4571_Interneuron--Fast-Spiking_BEB18116_CTRL

description:
4571
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)


title: ABM-AM-5 [LPSpp]


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Naive and sample id: 221220_D3


title: 4570_Interneuron--Other_BEB18116_CTRL

description:
4570
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

value: Interneuron, Other


title: ABM-AM-9 [LPSp]


title: ABM-AM-4 [Cpp]

value: Cpp


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Naive and sample id: 221220_D2


title: 4544_Oligodendrocyte_BEB18117_CTRL

description:
4544
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

value: Oligodendrocyte


title: Bulk RNAseq of nasal HBC cells (Pou2f3). Treatment: Naive and sample id: 221220_D10


title: Bulk RNAseq of nasal HBC cells (Pou2f3). Treatment: Naive and sample id: 221220_D11


title: 4543_Astrocyte_BEB18117_CTRL

description:
4543
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

value: Astrocyte


title: TmlL-3

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

country: China

institute: Qinghai university

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss Omyk_1.1
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each Sample

organism: Oncorhynchus mykiss

source_name: liver tissues

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver tissues

value: hypoxia stress

tag: phenotype

value: wild-type


title: TmlL-2


title: Bulk RNAseq of nasal HBC cells (Pou2f3). Treatment: Naive and sample id: 221220_D12


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Alt.Day1 and sample id: 221220_C9


title: TmlL-1


title: 4484_Interneuron--Other_HMC_HD

description:
4484
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

source_name: Anterior putamen

value: Anterior putamen

value: 42CAG / 15CAG

value: HMC

value: HD


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Alt.Day1 and sample id: 221220_C10


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Alt.Day1 and sample id: 221220_A7


title: ClL-2

value: control


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Naive and sample id: 221220_A1


title: 4482_Interneuron--Non-Fast-Spiking_HMC_HD

description:
4482
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

value: Interneuron, Non-Fast Spiking

value: Male


title: ClL-3


title: 4481_Striatopallidal-medium-spiny-neuron_UWA-7026_HD

description:
4481
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Anterior caudate

value: Striatopallidal medium spiny neuron

value: 43CAG / 17CAG


title: 4483_Interneuron--Fast-Spiking_HMC_HD

description:
4483
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

value: Interneuron, Fast Spiking


title: Bulk RNAseq of nasal OSN cells (IL7R). Treatment: Alt.Day1 and sample id: 221014_H8


title: Bulk RNAseq of nasal OSN cells (IL7R). Treatment: Alt.Day1 and sample id: 221014_H9


title: Bulk RNAseq of nasal OSN cells (IL7R). Treatment: Naive and sample id: 221014_H7

value: Naive


title: Bulk RNAseq of nasal OSN cells (IL7R). Treatment: Naive and sample id: 221014_H6


title: ClL-1


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Alt.Day1 and sample id: 221014_H4

value: WT


title: 4480_Striatonigral-medium-spiny-neuron_UWA-7026_HD

description:
4480
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Striatonigral medium spiny neuron


title: 4479_Interneuron--Other_BEB20057_CTRL

description:
4479
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

value: Interneuron, Other

value: CTRL


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Alt.Day1 and sample id: 221014_H5


title: Bulk RNAseq of nasal OSN cells (STAT6). Treatment: Alt.Day1 and sample id: 221014_H10


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Alt.Day1 and sample id: 221014_H3


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Naive and sample id: 221220_C4


title: 4478_Interneuron--Fast-Spiking_BEB20057_CTRL

description:
4478
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)


title: Bulk RNAseq of nasal OSN cells (STAT6). Treatment: Naive and sample id: 221014_G7


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Naive and sample id: 221014_G3


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Naive and sample id: 221014_G2


title: 4477_Interneuron--Non-Fast-Spiking_BEB20057_CTRL

description:
4477
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)


title: 56_11

type: RNA

city: Columbus

first: Jose

middle: Javier

last: Otero

state: Ohio

address: 333 W 10th Ave, 4170 Graves Hall

department: Pathology

institute: The Ohio State University

description: FFPE-derived RNA was evaluated using Nanostring nCounter Human Pancancer 360 IO panels containing 784 genes. Positive and negative control housekeeping genes are included in the panel for quality control analysis and normalization.

hyb_protocol: Hybridization was performed as per manufacturer's protocol.

scan_protocol: Samples were analysed in the nCounter Digital Analyser at 555 FOV.

data_processing: Normalization was performed using the ROSALIND Platform for nCounter analysis software following standard pipelines.

label: Nanostring bar coding

source_name: brain

label_protocol: RNA samples that passed concentration and degredation standards were labeled using input RNA and Nanostring Pancancer 360 IO barcodes.

extract_protocol: 5 um-thick FFPE sections (total scrolls based on slide tissue area) were prepared for RNA extraction using a FFPE RNA Purification Kit (Cat. 25300, 25400). Concentration of RNA was performed using both Nanodrop and Qubit RNA assay. RNA degradation was evaluated using RIN scores taken by an Agilent Tapestation.

tag: diagnosis

value: glioblastoma

tag: disease state

value: psPD

tag: slide tissue area

tag: side

value: Right

tag: lobe

value: Temporal

tag: vital status

tag: overall survival (months)

tag: tissue preparation

value: FFPE


title: 4391_Astrocyte_BEB18135_CTRL

description:
4391
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

source_name: Posterior putamen

tag: tissue

value: Posterior putamen

tag: cell type

value: Astrocyte


title: 55_10

value: Left

value: Occipital


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Alt.Day1 and sample id: 221014_G1

tag: genotype

tag: treatment

tag: time point


title: Bulk RNAseq of nasal OSN cells (IL7R). Treatment: Naive and sample id: 221014_G11


title: Bulk RNAseq of nasal OSN cells (STAT6). Treatment: Naive and sample id: 221014_F9


title: 4390_Microglia_BEB18135_CTRL

description:
4390
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: Microglia

tag: donor

tag: age

tag: Sex

value: Male

tag: pmi (hrs)

tag: disease


title: Bulk RNAseq of nasal OSN cells (STAT6). Treatment: Naive and sample id: 221014_F8


title: Bulk RNAseq of nasal OSN cells (STAT6). Treatment: Alt.Day1 and sample id: 221014_F7


title: 54_09

tag: diagnosis

tag: disease state


title: 4388_Astrocyte_HCTSU_CTRL

description:
4388
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

value: HCTSU

value: Female


title: Bulk RNAseq of nasal OSN cells (STAT6). Treatment: Naive and sample id: 221014_F5

value: Naive


title: Bulk RNAseq of nasal OSN cells (STAT6). Treatment: Alt.Day1 and sample id: 221014_F6


title: Bulk RNAseq of nasal OSN cells (IL7R). Treatment: Alt.Day1 and sample id: 221014_F4


title: 4387_Microglia_HCTSU_CTRL

description:
4387
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)


title: 53_08

tag: slide tissue area

tag: side

value: Parietal


title: Bulk RNAseq of nasal OSN cells (IL7R). Treatment: Alt.Day1 and sample id: 221014_F3


title: 4385_Astrocyte_HCTSU_CTRL

description:
4385
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

value: Posterior caudate


title: 4384_Microglia_HCTSU_CTRL

description:
4384
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: CTRL


title: Bulk RNAseq of nasal OSN cells (IL7R). Treatment: Alt.Day1 and sample id: 221014_F2


title: 48_05

value: glioblastoma

tag: lobe

value: Frontal

tag: vital status


title: 49_06

value: psPD

value: Right

tag: overall survival (months)

tag: tissue preparation


title: 50_07

value: Temporal

value: FFPE


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Naive and sample id: 221014_F12

value: WT


title: Bulk RNAseq of nasal OSN cells (STAT6). Treatment: Alt.Day1 and sample id: 221014_F11


title: Bulk RNAseq of nasal OSN cells (IL7R). Treatment: Naive and sample id: 221014_F1


title: 45_03

value: Left


title: 46_04


title: 4383_Oligodendrocyte_HCTSU_CTRL

description:
4383
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

tag: tissue

tag: cell type

value: Oligodendrocyte


title: 44_02

value: Occipital


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Alt.Day1 and sample id: 221014_E12

tag: genotype

tag: treatment


title: 4382_Astrocyte_BEB19025_CTRL

description:
4382
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

value: Astrocyte

tag: donor

value: Male


title: Bulk RNAseq of nasal OSN cells (IL7R). Treatment: Naive and sample id: 221014_E4

tag: time point


title: 4381_Microglia_BEB19025_CTRL

description:
4381
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: Microglia

tag: age

tag: Sex


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Alt.Day1 and sample id: 221014_E10


title: 43_01


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Alt.Day1 and sample id: 221014_E11


title: 4380_Oligodendrocyte_BEB19025_CTRL

description:
4380
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

tag: pmi (hrs)

tag: disease


title: 41_12

tag: diagnosis

tag: disease state


title: Bulk RNAseq of nasal HBC cells (IL7R). Treatment: Naive and sample id: 221014_D7

value: Naive


title: Bulk RNAseq of nasal HBC cells (IL7R). Treatment: Alt.Day1 and sample id: 221014_D9


title: 4378_Microglia_BEB18117_CTRL

description:
4378
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Alt.Day1 and sample id: 221014_D6


title: 40_11

tag: slide tissue area

tag: side


title: Bulk RNAseq of nasal HBC cells (IL7R). Treatment: Naive and sample id: 221014_D8


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Alt.Day1 and sample id: 221014_D5


title: 39_10

tag: lobe

tag: vital status


title: Bulk RNAseq of nasal OSN cells (STAT6). Treatment: Alt.Day1 and sample id: 221014_F10


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Alt.Day1 and sample id: 221014_D4


title: 4375_Microglia_BEB18116_CTRL

description:
4375
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: Posterior putamen


title: 4376_Astrocyte_BEB18116_CTRL

description:
4376
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)


title: 4238_Astrocyte_BEB19051_CTRL

description:
4238
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)


title: 38_09

tag: overall survival (months)

tag: tissue preparation


title: 37_08


title: Bulk RNAseq of nasal OSN cells (STAT6). Treatment: Naive and sample id: 221014_E7


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Naive and sample id: 221014_D12


title: Bulk RNAseq of nasal HBC cells (IL7R). Treatment: Alt.Day1 and sample id: 221014_D10


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Naive and sample id: 221014_C4


title: Bulk RNAseq of nasal HBC cells (STAT6). Treatment: Alt.Day1 and sample id: 221014_D11


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Naive and sample id: 221014_C3


title: Bulk RNAseq of nasal HBC cells (STAT6). Treatment: Naive and sample id: 221014_C8


title: 4229_Interneuron--Other_BEB19051_CTRL

description:
4229
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

tag: tissue

tag: cell type

value: Interneuron, Other


title: 4228_Interneuron--Non-Fast-Spiking_BEB19051_CTRL

description:
4228
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

value: Interneuron, Non-Fast Spiking

value: CTRL


title: 4227_Interneuron--Fast-Spiking_BEB19051_CTRL

description:
4227
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

value: Interneuron, Fast Spiking


title: 24_4152, youngster, RNA-seq

city: Hamburg

first: Agata

last: Bienkowska

address: Beiersdorfstraße 1-9

country: Germany

institute: Beiersdorf AG

data_processing:
FastQC version 0.11.7 was used for quality control evaluation.
The read sequences were trimmed using Trimmomatic 0.36.
Salmon 0.8.1 was used to map reads against the GRCh38 build of the human transcriptome.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes gene counts for each subject

source_name: epidermis

extract_protocol:
Suction blister roofs, each 7 mm in diameter, were obtained from the volar forearms by applying negative pressure at 180 mbar for 30 minutes, followed by 320 mbar until blister formation. The blister roofs were then carefully prepared using surgical scissors and tweezers. They were immediately snap frozen in liquid nitrogen and stored at -80°C until further use. Total RNA was extracted from the roofs of the suction blisters using the RNAeasy Fibrous Tissue Mini Kit (Qiagen, Inc.) according to the manufacturer's instructions.
Libraries were prepared using TruSeq Library Prep Kit (Illumina) following manufacturer’s instructions.

value: epidermis

value: female

tag: appearance

value: youngster


title: 35_06

description: FFPE-derived RNA was evaluated using Nanostring nCounter Human Pancancer 360 IO panels containing 784 genes. Positive and negative control housekeeping genes are included in the panel for quality control analysis and normalization.

value: glioblastoma

value: psPD

value: Temporal

value: FFPE


title: 3888_Astrocyte_BEB20057_CTRL

description:
3888
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

value: Anterior putamen

tag: donor


title: 33_05

value: Right


title: 25_23507, oldie, RNA-seq

value: oldie


title: 36_07

value: Left

value: Frontal


title: Bulk RNAseq of nasal HBC cells (IL7R). Treatment: Naive and sample id: 221014_C12

tag: genotype

tag: treatment

value: Naive

tag: time point


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Naive and sample id: 221014_C1

value: WT


title: 32_04


title: 3907_Oligodendrocyte_BEB20057_CTRL

description:
3907
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

value: Posterior putamen

value: Oligodendrocyte

tag: age

tag: Sex

value: Male

tag: pmi (hrs)


title: Bulk RNAseq of nasal HBC cells (STAT6). Treatment: Naive and sample id: 221014_B9


title: 26_02

tag: diagnosis

tag: disease state

value: PD


title: 3887_Microglia_BEB20057_CTRL

description:
3887
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: Microglia

tag: disease

value: CTRL


title: 28_03

value: glioblastoma

tag: slide tissue area

tag: side

tag: lobe

value: Parietal


title: Bulk RNAseq of nasal HBC cells (STAT6). Treatment: Alt.Day1 and sample id: 221014_B8


title: 3886_Oligodendrocyte_BEB20057_CTRL

description:
3886
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)


title: 25_01

tag: vital status

tag: overall survival (months)

tag: tissue preparation


title: Bulk RNAseq of nasal HBC cells (STAT6). Treatment: Alt.Day1 and sample id: 221014_B7


title: 21_17393, oldie, RNA-seq

tag: tissue

value: epidermis

value: female

tag: appearance


title: Btaurus_thymus_MAIT

city: Paris

first: Martin

last: MESTDAGH

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: BosTau9
Supplementary files format and content: Tab-separated values files and matrix files

organism: Bos taurus

source_name: Thymus

extract_protocol:
A freshly isolated thymus was maintained in CO2-independent medium (Gibco) at 4°c until processing. Sample processing started less than 6 hours after euthanasia.  The thymus was minced with a sterile scalpel in a petri dish containing 5 mL of CO2-independent medium. Tissue pieces were then washed with 40 mL of FACS buffer (PBS supplemented with 2% fetal calf serum (FCS) and 2.5 mM EDTA) to recover single cell suspensions of thymocytes.  To generate scRNAseq data from B. taurus, 109 thymocytes were stained for 30 min at room temperature with a PE-labeled cattle MR1 tetramer loaded with 5-OP-RU, then washed and stained with 70 mL of anti-PE microbeads (Miltenyi).  Magnetic enrichment of tetramer-labeled thymocytes was then performed. Following magnetic enrichment, thymocytes were stained for 30 min at 4°C with the following primary antibodies: mouse anti-bovine CD3 (clone MM1A, Bio-rad MCA6080) and mouse anti-bovine gd TCR (clone GB21A, Monoclonal Antibody Center BOV2058).  After washing with FACS buffer, cattle cells were stained with secondary anti-mouse IgG1 AF700 (clone RMG1-1, Biolegend 406631) and anti-mouse IgG2b PE-Cy7 (clone RMG2b-1, Biolegend 406713). Cells were then washed with FACS buffer and stained with DAPI (Sigma). A population of gd thymocytes were found to bind to the cattle MR1 tetramer and were gated out and excluded from the FACS-sorted population. DAPI- Tetramer+ CD3+ gd- thymocytes were flow-sorted (Aria III, BD) into PBS supplemented with 0.35% BSA (Sigma). Sorted cells were centrifuged, counted and 5,000 – 10,000 cells were loaded onto the Chromium 3’ chip. Reverse transcription, library preparation and sequencing were performed according to manufacturer’s recommendations (10x Genomics).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: cell type

value: MAIT

value: Thymus

tag: condition

value: Steady State


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Alt.Day1 and sample id: 221014_C2

tag: genotype

tag: treatment

tag: time point


title: 3885_Interneuron--Other_HCT-17-HFG_CTRL

description:
3885
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

value: Interneuron, Other

tag: donor

tag: age

tag: Sex

tag: pmi (hrs)


title: 20_36277, youngster, RNA-seq

value: youngster


title: 24_12

tag: diagnosis

tag: disease state

tag: slide tissue area

value: Left

value: Temporal

value: FFPE


title: 23_11

tag: side

value: Right

tag: lobe

value: Frontal

tag: vital status


title: 3884_Interneuron--Fast-Spiking_HCT-17-HFG_CTRL

description:
3884
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

tag: tissue

value: Posterior putamen

value: Interneuron, Fast Spiking

value: Male

tag: disease


title: Bulk RNAseq of nasal HBC cells (STAT6). Treatment: Naive and sample id: 221014_B6

value: Naive


title: 19_14434, oldie, RNA-seq

tag: appearance

value: oldie


title: 18_33260, oldie, RNA-seq

value: epidermis


title: 23_3420, oldie, RNA-seq

value: female


title: 3882_Oligodendrocyte_BEB18116_CTRL

description:
3882
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

value: Anterior putamen

tag: cell type

value: Oligodendrocyte

value: CTRL


title: 3883_Interneuron--Non-Fast-Spiking_HCT-17-HFG_CTRL

description:
3883
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

value: Interneuron, Non-Fast Spiking


title: Bulk RNAseq of nasal HBC cells (IL7R). Treatment: Alt.Day1 and sample id: 221014_B3

tag: genotype


title: 17_13342, youngster, RNA-seq

value: youngster


title: 22_10

value: glioblastoma

value: PD

value: Parietal

tag: overall survival (months)

tag: tissue preparation


title: Bulk RNAseq of nasal HBC cells (IL7R). Treatment: Alt.Day1 and sample id: 221014_B5

tag: treatment

tag: time point


title: 20_08

value: Right

value: Temporal

value: FFPE


title: Bulk RNAseq of nasal HBC cells (IL7R). Treatment: Alt.Day1 and sample id: 221014_B4


title: 3881_Oligodendrocyte_BEB18117_CTRL

description:
3881
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

tag: donor

tag: age

tag: Sex


title: 22_2940, oldie, RNA-seq


title: 21_09

tag: diagnosis

tag: disease state


title: Bulk RNAseq of nasal HBC cells (IL7R). Treatment: Naive and sample id: 221014_B2


title: 16_32921, youngster, RNA-seq


title: 3879_Interneuron--Fast-Spiking_BEB19025_CTRL

description:
3879
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

value: Posterior putamen

value: Interneuron, Fast Spiking

tag: pmi (hrs)


title: Bulk RNAseq of nasal HBC cells (STAT6). Treatment: Alt.Day1 and sample id: 221014_B11


title: 3880_Interneuron--Other_BEB19025_CTRL

description:
3880
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

value: Interneuron, Other

value: Male


title: 19_07

tag: slide tissue area

tag: side

value: Left

tag: lobe


title: Bulk RNAseq of nasal HBC cells (STAT6). Treatment: Alt.Day1 and sample id: 221014_B12


title: 3877_Astrocyte_BEB18135_CTRL

description:
3877
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

tag: tissue

value: Posterior caudate

value: Astrocyte

tag: disease


title: 14_5622, oldie, RNA-seq

value: epidermis

value: female

tag: appearance

value: oldie


title: 18_06

tag: vital status


title: Bulk RNAseq of nasal HBC cells (STAT6). Treatment: Naive and sample id: 221014_B10

tag: genotype

value: Naive


title: 12_229, oldie, RNA-seq


title: 13_236, youngster, RNA-seq

value: youngster


title: 16_04

value: glioblastoma

value: PD

tag: overall survival (months)

tag: tissue preparation


title: Bulk RNAseq of nasal HBC cells (STAT6). Treatment: Naive and sample id: 221014_A8

tag: treatment

tag: time point


title: 11_221, youngster, RNA-seq


title: 3875_Oligodendrocyte_BEB18135_CTRL

description:
3875
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

tag: cell type

value: Oligodendrocyte

tag: donor

tag: age

value: CTRL


title: 10_167, youngster, RNA-seq

tag: Sex


title: 15_31542, oldie, RNA-seq


title: 15_03

tag: diagnosis

tag: disease state

value: Temporal

value: FFPE


title: 3874_Interneuron--Other_BEB18135_CTRL

description:
3874
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

value: Posterior putamen

tag: pmi (hrs)


title: 9_149, oldie, RNA-seq


title: 14_02

tag: slide tissue area

tag: side

value: Right

tag: lobe


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Alt.Day1 and sample id: 221014_A12

value: WT


title: Bulk RNAseq of nasal HBC cells (IL7R). Treatment: Naive and sample id: 221014_A5


title: 17_05


title: 3872_Interneuron--Non-Fast-Spiking_BEB18135_CTRL

description:
3872
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

tag: tissue

value: Interneuron, Non-Fast Spiking

value: Male

tag: disease


title: 13_01

value: Left

tag: vital status


title: 3871_Astrocyte_BEB18116_CTRL

description:
3871
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

value: Anterior caudate

value: Astrocyte


title: 8_100, oldie, RNA-seq

value: epidermis

value: female

tag: appearance

value: oldie


title: 3876_Microglia_BEB18135_CTRL

description:
3876
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: Posterior caudate

value: Microglia


title: 12_12

description: FFPE-derived RNA was evaluated using Nanostring nCounter Human Pancancer 360 IO panels containing 784 genes. Positive and negative control housekeeping genes are included in the panel for quality control analysis and normalization.

value: glioblastoma

value: PD

value: Parietal

tag: overall survival (months)

tag: tissue preparation


title: 57_12

value: psPD

value: Frontal

value: FFPE


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Alt.Day1 and sample id: 221014_A11

tag: genotype

value: WT

tag: treatment

tag: time point


title: 3853_Astrocyte_BEB20057_CTRL

description:
3853
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

value: Posterior putamen

tag: cell type

tag: donor

tag: age

value: CTRL


title: 3869_Oligodendrocyte_BEB18116_CTRL

description:
3869
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

value: Oligodendrocyte

tag: Sex

value: Male


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Alt.Day1 and sample id: 221014_B1


title: 6_075, oldie, RNA-seq


title: 11_11

tag: diagnosis

tag: disease state

value: Left


title: 10_10

tag: slide tissue area

tag: side


title: 9_09

tag: lobe


title: 3850_Astrocyte_BEB18116_CTRL

description:
3850
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

tag: tissue

value: Anterior putamen

value: Astrocyte

tag: pmi (hrs)

tag: disease


title: 5_060, youngster, RNA-seq

value: epidermis

value: female

tag: appearance

value: youngster


title: Bulk RNAseq of nasal ISN cells (WT). Treatment: Naive and sample id: 220512_G3

value: Naive


title: 3849_Microglia_BEB18116_CTRL

description:
3849
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: Microglia


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Naive and sample id: 220512_G2


title: 4_056, youngster, RNA-seq


title: 3_033, oldie, RNA-seq

value: oldie


title: 7_095, oldie, RNA-seq


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Alt.Day1 and sample id: 220512_F7


title: 7_07

value: glioblastoma

value: PD

tag: vital status

tag: overall survival (months)

tag: tissue preparation


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Naive and sample id: 221014_A1

tag: genotype

tag: treatment

tag: time point


title: 3848_Astrocyte_BEB18117_CTRL

description:
3848
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

tag: cell type

tag: donor

tag: age


title: 6_06

tag: diagnosis

tag: disease state

value: Frontal

value: FFPE


title: 3847_Microglia_BEB18117_CTRL

description:
3847
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

tag: Sex


title: 2_007, youngster, RNA-seq


title: 3837_Interneuron--Fast-Spiking_BEB18116_CTRL

description:
3837
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

value: Posterior putamen

value: Interneuron, Fast Spiking


title: 1_002, oldie, RNA-seq


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Alt.Day1 and sample id: 220512_F6

value: WT


title: Bulk RNAseq of nasal ISN cells (WT). Treatment: Alt.Day7 and sample id: 220512_F4


title: 3836_Interneuron--Other_BEB18116_CTRL

description:
3836
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

value: Interneuron, Other

value: Male

value: CTRL


title: NALF Exosome, Control 10

city: Seoul

first: Daeun

last: Jeong

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei university

data_processing:
Illumina HCS v2.2.70 software used for basecalling.
The raw reads of small RNAs were pre-processed to eliminate adapter sequences. Adapters in the raw reads were trimmed using cutadapt program. The first 3nt of all reads were trimmed to remove extra bases, which were inserted during the SMART template-switching activity process. If a sequence was matched to more than the first 5 bp of 3' adapter sequence, it was regarded as an adapter sequence, and then trimmed from the read. Trimmed reads, whose length is longer than 18 bp, were selected for mapping reliability.
To minimize the sequence redundancy for computational efficiency, processed reads were clustered by a sequence. A unique cluster consists of the reads whose sequences and length are same.
In order to eliminate rRNA, reads were excluded that aligned to the 45S pre-rRNA and mitochondrial rRNA of Homo sapiens
Sequence alignment and detection of known and novel microRNAs were performed using miRDeep2 software algorithm. rRNA-filtered reads were aligned to the matured and precursor miRNAs of Homo sapiens obtained from miRBase v22.1 using bowtie 1.1.2 (option : -f -v 0 -a --best --strata --norc).
Expression profile (the reads for each miRNA) was quantified by miRDeep2 quantifier module.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include read counts for each Sample ...

source_name: nose

extract_protocol:
Exosomes were isolated from pre-filtered NAL fluid samples, total exosomal RNA were prepared using the exoRNeasy Serum/Plasma Midi Kit (77044; QIAGEN, Hilden, Germany) according to the manufacturer’s instructions.
RNA libraries were generated using SMARTer smRNA-Seq for Illumina Kit, library protocol was SMARTer smRNA-Seq Kit for Illumina User Manual.

value: nose

tag: cell line

value: nasal lavage fluid

value: exosome

tag: group

value: control


title: 5_05

tag: slide tissue area

tag: side

value: Left

tag: lobe


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Alt.Day7 and sample id: 220512_F3


title: 3835_Interneuron--Non-Fast-Spiking_BEB18116_CTRL

description:
3835
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

tag: tissue

value: Interneuron, Non-Fast Spiking

tag: pmi (hrs)

tag: disease


title: NALF Exosome, Control 9


title: 3_03

value: Right

value: Parietal

tag: vital status

tag: overall survival (months)

tag: tissue preparation


title: 4_04

value: glioblastoma

value: PD


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Naive and sample id: 220512_G1

tag: genotype

tag: treatment

value: Naive

tag: time point


title: NALF Exosome, Control 8

tag: cell type


title: 3834_Interneuron--Fast-Spiking_BEB20057_CTRL

description:
3834
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

value: Posterior putamen

tag: donor

tag: age


title: 3833_Interneuron--Other_BEB20057_CTRL

description:
3833
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

tag: Sex


title: 8_08

tag: diagnosis

tag: disease state

value: Temporal

value: FFPE


title: Bulk RNAseq of nasal ISN cells (WT). Treatment: Naive and sample id: 220512_E8

value: WT


title: stop1-NAA-3

city: qingdao

first: jia

middle: jia

last: liu

address: qingdaojimoaoshanwei

institute: shandong university

data_processing:
The RNA was purified by electrophoresis through a TBE-urea polyacrylamide gel. The gel regions harboring 18-30 nt fragments were excised and the RNA recovered. The resulting population of sRNAs was 5' and 3' RNA adapter-ligated using T4 RNA ligase, and amplified for 18 PCR cycles
The amplicons were purified and sequenced using an Illumina/Solexa Genome Analyzer (Beijing Genomics Institute, Shenzhen, China).
Raw reads were trimmed by removing low-quality and adaptor sequences, then aligned to the A. thaliana genome using SOAP2 software.
Transcript frequency was calculated using the reads per kilobase per million reads method. Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the P value and the false discovery rate (FDR) (Audic and Claverie, 1997).

organism: Arabidopsis

source_name: root

extract_protocol:
Total RNA was isolated using a RNeasy Mini Kit (Qiagen).
First strand cDNA was generated using reverse transcriptase and random primers. The constructed cDNA libraries was qualified and quantified with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, and then sequenced via Illumina HiSeqTM 2000 or other sequencer when necessary at the Beijing Genomics Institute, Shenzhen, China.

value: root

value: NAA


title: NALF Exosome, Control 6

value: nose

tag: cell line

tag: group


title: 3832_Interneuron--Non-Fast-Spiking_BEB20057_CTRL

description:
3832
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

tag: tissue

value: Male

value: CTRL


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Naive and sample id: 220512_E7


title: 1_01

tag: slide tissue area

tag: side

tag: lobe


title: stop1-NAA-2


title: stop1-NAA-1


title: Bulk RNAseq of nasal ISN cells (WT). Treatment: Alt.Day7 and sample id: 220512_E4


title: 3831_Interneuron--Fast-Spiking_BEB18117_CTRL

description:
3831
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

value: Anterior putamen

value: Interneuron, Fast Spiking

tag: pmi (hrs)

tag: disease


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Naive and sample id: 220512_E6

tag: genotype


title: 3830_Interneuron--Other_BEB18117_CTRL

description:
3830
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

value: Interneuron, Other


title: 3829_Interneuron--Non-Fast-Spiking_BEB18117_CTRL

description:
3829
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

value: Interneuron, Non-Fast Spiking


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Alt.Day7 and sample id: 220512_F2

tag: treatment


title: stop1-CK-2


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Alt.Day7 and sample id: 220512_E3

tag: time point


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Alt.Day7 and sample id: 220512_E2


title: 2_02

value: Left

value: Frontal

tag: vital status

tag: overall survival (months)

tag: tissue preparation


title: 3669_Striatopallidal-medium-spiny-neuron_HSB3358_HD

description:
3669
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Anterior caudate

tag: cell type

value: Striatopallidal medium spiny neuron

value: 43CAG / 21CAG

tag: donor

tag: age

tag: Sex

value: Female

value: HD


title: NALF Exosome, AR 7

tag: cell line

value: nasal lavage fluid

value: exosome

tag: group

value: AR


title: NALF Exosome, Control 3

tag: tissue

value: nose

value: control


title: 3668_Striatonigral-medium-spiny-neuron_HSB3358_HD

description:
3668
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Striatonigral medium spiny neuron


title: stop1-CK-1

value: root


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Alt.Day7 and sample id: 220512_E11

value: WT


title: NALF Exosome, Control 7


title: Bulk RNAseq of nasal ISN cells (WT). Treatment: Alt.Day7 and sample id: 220512_E12


title: col-NAA-2

value: col

value: NAA


title: NALF Exosome, Control 4


title: col-NAA-3


title: NALF Exosome, AR 6


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Alt.Day7 and sample id: 220512_E10


title: NALF Exosome, Control 5


title: 3660_Striatonigral-medium-spiny-neuron_HCT-17-HFG_CTRL

description:
3660
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Posterior caudate

value: Male

value: CTRL


title: NALF Exosome, AR 5


title: col-NAA-1


title: 3661_Striatopallidal-medium-spiny-neuron_HCT-17-HFG_CTRL

description:
3661
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Striatopallidal medium spiny neuron


title: NALF Exosome, AR 4


title: col-CK-3


title: NALF Exosome, AR 8


title: 3657_Striatopallidal-medium-spiny-neuron_HSB3167_HD

description:
3657
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Caudate

value: 45CAG / 17CAG


title: Bulk RNAseq of nasal ISN cells (Pou2f3). Treatment: Naive and sample id: 220512_C9

value: Naive


title: stop1-CK-3


title: NALF Exosome, AR 3

value: nasal lavage fluid


title: col-CK-2


title: col-CK-1


title: 3656_Striatonigral-medium-spiny-neuron_HSB3167_HD

description:
3656
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: HD


title: Bulk RNAseq of nasal HBC cells (Pou2f3). Treatment: Naive and sample id: 220512_C7


title: Bulk RNAseq of nasal OSN cells (Pou2f3). Treatment: Naive and sample id: 220512_C8


title: NALF Exosome, Control 2

value: exosome


title: arf2-NAA-3


title: 3655_Striatopallidal-medium-spiny-neuron_BEB20057_CTRL

description:
3655
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)


title: Bulk RNAseq of nasal ISN cells (Pou2f3). Treatment: Naive and sample id: 220512_C12


title: NALF Exosome, Control 1

value: nose


title: NALF Exosome, AR 2

value: AR


title: arf2-NAA-2


title: Bulk RNAseq of nasal OSN cells (Pou2f3). Treatment: Naive and sample id: 220512_C11


title: NALF Exosome, AR 1


title: Bulk RNAseq of nasal ISN cells (Pou2f3). Treatment: Alt.Day1 and sample id: 220512_A6


title: Bulk RNAseq of nasal OSN cells (Pou2f3). Treatment: Alt.Day1 and sample id: 220512_A5


title: arf2-NAA-1


title: Hsapiens_thymus_NKT

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: thymus

extract_protocol:
A freshly isolated thymus was maintained in CO2-independent medium (Gibco) at 4°c until processing.  The thymus was minced with a sterile scalpel in a petri dish containing 5 mL of CO2-independent medium. Tissue pieces were then washed with 40 mL of FACS buffer (PBS supplemented with 2% fetal calf serum (FCS) and 2.5 mM EDTA) to recover single cell suspensions of thymocytes.  To generate scRNAseq data from H. sapiens, 109 thymocytes were stained for 30 min at room temperature with PE-labeled human MR1:5-OP-RU, CD1d:aGalCer or MelanA:A2 tetramers, then washed and stained with 70 mL of anti-PE microbeads (Miltenyi).  Magnetic enrichment of tetramer-labeled thymocytes was then performed. Following magnetic enrichment, thymocytes were stained for 30 min at 4°C with the following primary antibodies: anti-CD3 AF700 (clone HIT3a, Biolegend 300324), anti-CD161 APC (clone HP-3G10, Biolegend 339912) anti-CD27 PECy7 (clone O323, Biolegend 302838).  Cells were then washed with FACS buffer and stained with DAPI (Sigma). DAPI- Tetramer+ CD3+ thymocytes were flow-sorted (Aria III, BD) into PBS supplemented with 0.35% BSA (Sigma). Sorted cells were centrifuged, counted and 5,000 – 10,000 cells were loaded onto the Chromium 3’ chip. Reverse transcription, library preparation and sequencing were performed according to manufacturer’s recommendations (10x Genomics).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: MAIT

value: thymus

tag: condition

value: Steady State


title: arf2-CK-3

value: root


title: 3648_Striatonigral-medium-spiny-neuron_BEB20057_CTRL

description:
3648
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Anterior putamen

value: Striatonigral medium spiny neuron


title: Hsapiens_thymus_Tconv

description: 10x Genomics


title: 3585_Microglia_BEB19025_CTRL

description:
3585
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: Posterior putamen

value: Microglia

value: Male


title: Bulk RNAseq of nasal HBC cells (Pou2f3). Treatment: Alt.Day1 and sample id: 220512_A4


title: 3654_Striatonigral-medium-spiny-neuron_BEB20057_CTRL

description:
3654
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Posterior caudate

value: CTRL


title: Bulk RNAseq of nasal ISN cells (Pou2f3). Treatment: Alt.Day1 and sample id: 220512_A3


title: 3577_Striatonigral-medium-spiny-neuron_BEB20057_CTRL

description:
3577
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Anterior caudate


title: arf2-CK-2


title: Bulk RNAseq of nasal OSN cells (Pou2f3). Treatment: Alt.Day1 and sample id: 220512_A2


title: 3576_Striatopallidal-medium-spiny-neuron_BEB20057_CTRL

description:
3576
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Striatopallidal medium spiny neuron


title: Bulk RNAseq of nasal HBC cells (Pou2f3). Treatment: Alt.Day1 and sample id: 220512_A1


title: 3649_Striatopallidal-medium-spiny-neuron_BEB20057_CTRL

description:
3649
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: DerP.Day1 and sample id: 210602_E2

value: WT


title: toxIN_tifAK55AR56AR59A_lysate_rep2

city: Cambridge

first: Chantal

middle: K

last: Guegler

state: MA

address: 31 Ames Street

department: Biology

institute: MIT

description:
230605_bl21_rpm_middlemapped.csv
230605_toxItifA_rpm_middlemapped.csv
230605_toxN_rpm_middlemapped.csv
230605_log2eluent-log2lysate_bl21_ratios.csv
sample 8

data_processing:
Paired-end reads mapped to the E. coli BL21(DE3) genome and the sequences for pACYCDuet1-toxI-tifA and pTXB1-toxN using bowtie2 with default settings.
For all mapped fragments, at all aligned positions a count was added (fragment density mapping).
Counts were depth normalized to a pseudo-reference sample calculated from all samples (fragment density mapping).
For all mapped fragments, a count was added to the middle position of the fragment (counts per million measurements).
Counts were depth-normalized using counts per million counts and log2 transformed (counts per million measurements).
Assembly: NCBI reference sequence for E. coli BL21(DE3): NZ_CP053602.1
Supplementary files format and content: 230605_bl21_rpm_middlemapped.csv is a list of sequencing depth-normalized counts for every gene in the BL21 genome in all samples.
Supplementary files format and content: 230605_toxItifA_rpm_middlemapped.csv is a list of sequencing depth-normalized counts for every gene in pACYCDuet1-toxI-tifA in all samples.
Supplementary files format and content: 230605_toxN_rpm_middlemapped.csv is a list of sequencing depth-normalized counts for every gene in pTXB1-toxN in all samples.
Supplementary files format and content: 230605_log2eluent-log2lysate_bl21_ratios.csv is a list of the log2-transformed ratio of fragment density counts in every position in the E. coli Bl21(DE3) genome for eluent versus lysate samples for every biological replicate (e.g, sample 1 - sample 2; sample 3 - sample 4; sample 5 - sample 6; sample 7 - sample 8)

organism: Escherichia coli

source_name: T7 express (NEB)

growth_protocol: Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in LB supplemented. Overnight cultures were back diluted into fresh media and grown 4-6 hours to an OD600 of ~0.8 at 37°C in an orbital shaker at 200 RPM. To induce protein overexpression, 0.4 mM IPTG was added to each culture, the temperature was shifted to 16 C, and cultures were grown overnight in an orbital shaker at 200 RPM.

extract_protocol:
RNA from lysate samples was harvested immediately after lysis with a Microfluidizer via subsequent rounds of extraction with 1x volume acid-buffered phenol, acid-buffered phenol chloroform, and chloroform, followed by isopropanol precipitation. RNA was isolated from purified proteins following elution from chitin resin via subsequent rounds of extraction with acid-buffered phenol chloroform and chloroform, followed by isopropanol precipitation.
200 ng of each RNA sample was used to make RNA-seq libraries using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® following the manufactures’ protocol for use with purified mRNA or rRNA depleted RNA.

treatment_protocol: Cells were harvested by centrifugation, resuspended in lysis/column buffer (20 mM Tris-HCl pH 8.5, 500 mM NaCl, 1 mM EDTA, 0.05% Tween-20, SIGMAFAST Protease Inhibitor Tablet (Sigma), 5% glycerol), and lysed using a Microfluidizer (three passes, 18,000 psi). The cell lysate was clarified by centrifugation at 15,000 rpm for 30 min and passed over chitin resin (NEB) pre-equilibrated with lysis/column buffer at 4 C. The resin was then washed with 25 column volumes of lysis/column buffer. To induce self-cleavage of the C-terminal intein-CBD tag, the resin was quickly washed with 3 column volumes of lysis/column buffer supplemented with 50 mM DTT (column cleavage buffer), capped, and incubated overnight at 4 C. The next day, 5 column volume of lysis/column buffer was added to each column to elute untagged ToxN and its binding partners.

tag: strain

value: T7 express (NEB)

tag: plasmid

value: pTXB1-toxN, pACYCDuet1-tifA(K55A R56A R59A)-toxI

tag: fraction

value: whole cell lysate


title: toxIN_tifAK55AR56AR59A_chitineluent_rep2

description:
230605_bl21_rpm_middlemapped.csv
230605_toxItifA_rpm_middlemapped.csv
230605_toxN_rpm_middlemapped.csv
230605_log2eluent-log2lysate_bl21_ratios.csv
sample 7

library_source: other

molecule: other

value: chitin resin eluent


title: 3564_Microglia_HCT-17-HFG_CTRL

description:
3564
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

tag: pmi (hrs)

tag: disease


title: 3565_Astrocyte_HCT-17-HFG_CTRL

description:
3565
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

value: Astrocyte


title: toxIN_tifAK55AR56AR59A_lysate_rep1

description:
230605_bl21_rpm_middlemapped.csv
230605_toxItifA_rpm_middlemapped.csv
230605_toxN_rpm_middlemapped.csv
230605_log2eluent-log2lysate_bl21_ratios.csv
sample 6


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: DerP.Day1 and sample id: 210602_D10

tag: genotype

tag: treatment

tag: time point


title: toxIN_tifAK55AR56AR59A_chitineluent_rep1

description:
230605_bl21_rpm_middlemapped.csv
230605_toxItifA_rpm_middlemapped.csv
230605_toxN_rpm_middlemapped.csv
230605_log2eluent-log2lysate_bl21_ratios.csv
sample 5


title: Mouse, ChIP, Cortex, E18, TCF4, Rep2

city: San Francisco

first: Kenneth

last: Lim

state: CA

department: Psychiatry

institute: UCSF

library_source: genomic

data_processing:
Sequence reads were aligned to the mm10 genome assembly using BWA version 0.7.15
Data was filtered using samtools view version 1.10 using a MAPQ cutoff of 30.
Bigwig files were generated using deepTools bamCoverage version 3.4.3 with the following setting: output type (bigwig), bin-size (10), fragment extension (200), normalize (RPKM), ignore duplicates (active). Scores represent: RPKM.
Peaks were called using MACS v2.2.7 with the following setting: narrow peak calling, WT background used as input, qvalue cutoff of 0.01, fragment extension of 200, no-model, no-lambda.
Assembly: UCSC mm10
Supplementary files format and content: Bigwig files (.bw)
Supplementary files format and content: Peak bed files (.narrowPeak)

molecule: genomic DNA

source_name: Cortex

growth_protocol: Not applicable

extract_protocol:
Tissues were mechanically dissociated in ice-cold HBSS and fixed in 1% PFA for 10 min at RT. Fixed cells were lysed in a hypotonic buffer. Nuclei was extracted by centrifugation at 13,500 rpm for 10 min at 4°C and sheared into 200 - 1,000 bp fragments using a Covaris S2
Ovation Ultralow System V2 Multiplex System (NuGEN) following manufacturer's protocol.
SE50

treatment_protocol: Not applicable

value: Cortex

tag: chip antibody

value: Experiment

tag: replicate


title: Mouse, ChIP, Cortex, E18, TCF4, Rep1


title: Mouse, ChIP, Cortex, E18, TCF4, INPUT, Rep2

value: Control


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: DerP.Day1 and sample id: 210602_D6


title: Mouse, ChIP, Cortex, E18, TCF4, INPUT, Rep1


title: 3578_Striatopallidal-medium-spiny-neuron_BEB20057_CTRL

description:
3578
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

tag: cell type

tag: donor


title: Mouse, ChIP, Cortex, E18, TBR1, INPUT, Rep1

tag: age


title: 3563_Oligodendrocyte_HCT-17-HFG_CTRL

description:
3563
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

value: Oligodendrocyte

tag: Sex


title: toxIN_tifAWT_lysate_rep2

description:
230605_bl21_rpm_middlemapped.csv
230605_toxItifA_rpm_middlemapped.csv
230605_toxN_rpm_middlemapped.csv
230605_log2eluent-log2lysate_bl21_ratios.csv
sample 4

value: pTXB1-toxN, pACYCDuet1-tifA-FLAG-toxI


title: arf2-CK-1

value: root


title: 3562_Astrocyte_BEB18117_CTRL

description:
3562
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

value: Posterior putamen

value: Male


title: Late elongating spermatids, replicate 3

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

description:
LES_3
DeNovo_globalTranscriptome.gtf.gz
Gill_RNA_Seq_log2RPKM_DeNovo.csv.gz
Gill_RNA_Seq_log2RPKM_Gencode.csv.gz

data_processing:
PE 150 bp reads
TrimGalore + STAR
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR
Read count extraction and normalization were performed in R using the QuasR package
Assembly: mm10
Supplementary files format and content: comma separated text files include log2RPKM values for each Sample (counts performed on Gencode v19 or De Novo transcriptome assembly (see GTF file)); GTF file describing de novo transcriptome annotation

source_name: testes

growth_protocol: Single cell suspensions were generated from adult testis tissue by sequential digestion with collagenase and trypsin

extract_protocol:
Total RNA was extracted using a DirectZol kit (Zymo research)
RNA libraries for RNA-seq were prepared using the Illumina TruSeq kit following manufacturer's recommendations

treatment_protocol:
Single cell suspensions were then stained either with Hoechst 33342 alone (RS_23_dpp & Prm_EGFP_ES) or Hoechst 33342 and SYTO 16 (all other samples)
Stained cells were then isolated via FACS

value: 3 months

value: male

value: testes

value: Late elongating spermatid


title: Mouse, ChIP, Cortex, E18, TBR1, Rep2

value: WT


title: toxIN_tifAWT_chitineluent_rep2

description:
230605_bl21_rpm_middlemapped.csv
230605_toxItifA_rpm_middlemapped.csv
230605_toxN_rpm_middlemapped.csv
230605_log2eluent-log2lysate_bl21_ratios.csv
sample 3

value: T7 express (NEB)


title: 3561_Microglia_BEB18117_CTRL

description:
3561
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: Microglia

value: CTRL


title: Mouse, ChIP, Cortex, E18, TBR1, Rep1


title: 3575_Striatonigral-medium-spiny-neuron_BEB20057_CTRL

description:
3575
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Striatonigral medium spiny neuron


title: Hsapiens_thymus_MAIT

description: 10x Genomics

extract_protocol:
A freshly isolated thymus was maintained in CO2-independent medium (Gibco) at 4°c until processing.   The thymus was minced with a sterile scalpel in a petri dish containing 5 mL of CO2-independent medium. Tissue pieces were then washed with 40 mL of FACS
Library was performed according to the manufacters instructions (single cell 3 v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-

value: MAIT

value: thymus

value: Steady State


title: toxIN_tifAWT_lysate_rep1

description:
230605_bl21_rpm_middlemapped.csv
230605_toxItifA_rpm_middlemapped.csv
230605_toxN_rpm_middlemapped.csv
230605_log2eluent-log2lysate_bl21_ratios.csv
sample 2

value: whole cell lysate


title: Late elongating spermatids, replicate 2

description:
LES_2
DeNovo_globalTranscriptome.gtf.gz
Gill_RNA_Seq_log2RPKM_DeNovo.csv.gz
Gill_RNA_Seq_log2RPKM_Gencode.csv.gz


title: Late elongating spermatids, replicate 1

description:
LES_1
DeNovo_globalTranscriptome.gtf.gz
Gill_RNA_Seq_log2RPKM_DeNovo.csv.gz
Gill_RNA_Seq_log2RPKM_Gencode.csv.gz


title: 3560_Oligodendrocyte_BEB18117_CTRL

description:
3560
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

value: Oligodendrocyte


title: Mouse, ChIP, Cortex, E18, FOXP1, INPUT, Rep2

value: Cortex

value: Control


title: 3545_Oligodendrocyte_BEB18116_CTRL

description:
3545
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

value: Posterior putamen

value: Male


title: H63.Macia.T15.H3

city: Riverside

first: Dawn

last: Nagel

address: 900 University Avenue

institute: UC Riverside Department of Botany and Plant Sciences

data_processing:
Sequencing reads were not trimmed and mapped on the Sbicolor_454_v3.1.1 genome using Hisat2 and the SystemPipeR pipeline (genome downloaded from Phytozome: https://data.jgi.doe.gov/refine-download/phytozome?organism=Sbicolor&expanded=45).
Read counting was performed with the summarizeOverlaps function from the GenomicRanges Package, and using the Sbicolor_454_v3.1.1.gene.gff3.gz file for the annotation.
Normalized transcript abundance was then calculated using the rlog function from the R package ‘DESeq2’ (Love et al., 2014, 10.1186/s13059-014-0550-8)
Assembly: Sbicolor_454_v3.0.1
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample

organism: Sorghum bicolor

source_name: Macia, Heat stress, ZT15, replicate 3

extract_protocol:
Between ~2 and ~40 ug of total RNA was extracted from three biological replicates of sorghum samples for each genotype and treatment (control, heat, cold stress) using GeneJET Plant RNA Extraction Kit (Thermofisher K0801) followed by DNAse I treatment (Thermofisher EN0521). Total mRNAs were isolated using biotinylated oligo(dT) and streptavidin magnetic beads (New England Biolabs) as previously described (Wang et al., 2011, 10.1371/journal.pone.0026426)
Purified mRNAs were used for library preparation as previously described with the following modifications. In the final enrichment step, indexed adapter enrichment primers were used (Townsley et al., 2015, 10.3389/fpls.2015.00366) and 12 cycles were performed to amplify the libraries. The libraries were quantified using a Qubit 2.0 Fluorescence Reader (Thermo Fisher Scientific) and quality was verified using a Bioanalyzer 2100 (Agilent Genomics). Final libraries were multiplexed and sequenced on the NextSeq 500 (Illumina) at the UC Riverside (UCR) Institute for Integrated Genome Biology (IIGB) Genomics Core facility to obtain 75 nt single-end reads.

treatment_protocol: Plants were grown under controlled (30/20°C; day/night) conditions and then subjected to 1 h of cold (10°C) or 1 h of heat (42°C) at four times of the day (ZT0, ZT6, ZT9, and ZT15).

tag: experiment

value: Heat stress

value: leaves

value: Macia

tag: time of_day


title: 3500_Striatopallidal-medium-spiny-neuron_BEB18116_CTRL

description:
3500
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

tag: tissue

value: Posterior caudate

value: Striatopallidal medium spiny neuron


title: Early elongating spermatids, replicate 2

description:
EES_2
DeNovo_globalTranscriptome.gtf.gz
Gill_RNA_Seq_log2RPKM_DeNovo.csv.gz
Gill_RNA_Seq_log2RPKM_Gencode.csv.gz

tag: strain

value: 3 months

value: WT

value: male

value: testes

value: Early elongating spermatid


title: Early elongating spermatids, replicate 3

description:
EES_3
DeNovo_globalTranscriptome.gtf.gz
Gill_RNA_Seq_log2RPKM_DeNovo.csv.gz
Gill_RNA_Seq_log2RPKM_Gencode.csv.gz


title: Mouse, ChIP, Cortex, E18, FOXP1, INPUT, Rep1


title: H59.Macia.T15.C3

source_name: Macia, Control, ZT15, replicate 3


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Naive and sample id: 210602_A6

source_name: Mouse nasal epithelial cells sorted using FACS

value: Naive


title: 3499_Striatonigral-medium-spiny-neuron_BEB18116_CTRL

description:
3499
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

source_name: Posterior caudate

value: Striatonigral medium spiny neuron

value: CTRL


title: Mouse, ChIP, Cortex, E18, FOXP1, Rep2

value: Cortex

value: Experiment


title: 3498_Striatopallidal-medium-spiny-neuron_BEB18116_CTRL

description:
3498
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Anterior putamen


title: Mouse, ChIP, Cortex, E18, FOXP1, Rep1


title: H55.RTX.T15.H3

source_name: RTX430, Heat stress, ZT15, replicate 3


title: Early elongating spermatids, replicate 1

description:
EES_1
DeNovo_globalTranscriptome.gtf.gz
Gill_RNA_Seq_log2RPKM_DeNovo.csv.gz
Gill_RNA_Seq_log2RPKM_Gencode.csv.gz


title: toxIN_tifAWT_chitineluent_rep1

description:
230605_bl21_rpm_middlemapped.csv
230605_toxItifA_rpm_middlemapped.csv
230605_toxN_rpm_middlemapped.csv
230605_log2eluent-log2lysate_bl21_ratios.csv
sample 1

value: T7 express (NEB)

tag: plasmid

value: pTXB1-toxN, pACYCDuet1-tifA-FLAG-toxI

value: chitin resin eluent


title: H51.RTX.T15.C3

source_name: RTX430, Control, ZT15, replicate 3

value: Heat stress

value: leaves

value: Control


title: 3497_Striatonigral-medium-spiny-neuron_BEB18116_CTRL

description:
3497
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

source_name: Anterior putamen

value: Male


title: Mouse, ChIP, Cortex, E18, BCL11A, INPUT, Rep1

value: WT


title: Mouse, ChIP, Cortex, E18, BCL11A, Rep1


title: H47.Macia.T9.H3

source_name: Macia, Heat stress, ZT9, replicate 3

value: Macia


title: Round spermatids, replicate 2

description:
RS_2
DeNovo_globalTranscriptome.gtf.gz
Gill_RNA_Seq_log2RPKM_DeNovo.csv.gz
Gill_RNA_Seq_log2RPKM_Gencode.csv.gz

value: 3 months

value: male

value: testes

value: Round spermatid


title: H43.Macia.T9.C3

source_name: Macia, Control, ZT9, replicate 3


title: 3496_Striatopallidal-medium-spiny-neuron_BEB18117_CTRL

description:
3496
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Striatopallidal medium spiny neuron

value: CTRL


title: Mouse, ChIP, Cortex, E18, ARID1B, INPUT, Rep2

value: Cortex


title: Round spermatids, replicate 1

description:
RS_1
DeNovo_globalTranscriptome.gtf.gz
Gill_RNA_Seq_log2RPKM_DeNovo.csv.gz
Gill_RNA_Seq_log2RPKM_Gencode.csv.gz


title: 3495_Striatonigral-medium-spiny-neuron_BEB18117_CTRL

description:
3495
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Anterior putamen

value: Striatonigral medium spiny neuron


title: Pachytene/Diplotene spermatocytes, replicate 3

description:
PD_3
DeNovo_globalTranscriptome.gtf.gz
Gill_RNA_Seq_log2RPKM_DeNovo.csv.gz
Gill_RNA_Seq_log2RPKM_Gencode.csv.gz

value: Pachytene/Diplotene spermatocyte


title: Mouse, ChIP, Cortex, E18, ARID1B, INPUT, Rep1


title: H39.RTX.T9.H3

source_name: RTX430, Heat stress, ZT9, replicate 3


title: 3494_Striatopallidal-medium-spiny-neuron_HCTSU_CTRL

description:
3494
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: HCTSU

value: Female


title: H35.RTX.T9.C3

source_name: RTX430, Control, ZT9, replicate 3

value: Heat stress

value: leaves


title: 3493_Striatonigral-medium-spiny-neuron_HCTSU_CTRL

description:
3493
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)


title: Pachytene/Diplotene spermatocytes, replicate 1

description:
PD_1
DeNovo_globalTranscriptome.gtf.gz
Gill_RNA_Seq_log2RPKM_DeNovo.csv.gz
Gill_RNA_Seq_log2RPKM_Gencode.csv.gz


title: Pachytene/Diplotene spermatocytes, replicate 2

description:
PD_2
DeNovo_globalTranscriptome.gtf.gz
Gill_RNA_Seq_log2RPKM_DeNovo.csv.gz
Gill_RNA_Seq_log2RPKM_Gencode.csv.gz


title: 3476_Striatopallidal-medium-spiny-neuron_BEB18117_CTRL

description:
3476
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Posterior caudate

value: Male


title: H31.Macia.T6.H3

source_name: Macia, Heat stress, ZT6, replicate 3

value: Macia


title: Round spermatids, replicate 3

description:
RS_3
DeNovo_globalTranscriptome.gtf.gz
Gill_RNA_Seq_log2RPKM_DeNovo.csv.gz
Gill_RNA_Seq_log2RPKM_Gencode.csv.gz

value: 3 months

value: WT


title: Mouse, ChIP, Cortex, E18, ARID1B, Rep2

value: Experiment


title: Mouse, ChIP, Cortex, E15, TCF4, INPUT, Rep2

description: SFDJLR152_E15_5_TCF4-Input_S28_L005_R1_001

value: Control


title: H27.Macia.T6.C3

source_name: Macia, Control, ZT6, replicate 3


title: Mouse, ChIP, Cortex, E18, ARID1B, Rep1


title: Mouse, ChIP, Cortex, E15, TCF4, INPUT, Rep1

description: SFDJLR151_E15_5_TCF4-Input-Rep1_S19_L004_R1_001


title: 3475_Striatonigral-medium-spiny-neuron_BEB18117_CTRL

description:
3475
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)


title: Leptotene/Zygotene spermatocytes, replicate 3

description:
LZ_3
DeNovo_globalTranscriptome.gtf.gz
Gill_RNA_Seq_log2RPKM_DeNovo.csv.gz
Gill_RNA_Seq_log2RPKM_Gencode.csv.gz

value: male

value: testes

value: Leptotene/Zygotene spermatocyte


title: Mouse, ChIP, Cortex, E15, TCF4, Rep2

description: SFDJLR152_E15_5_TCF4_Rep2_S29_L005_R1_001

value: Cortex


title: Leptotene/Zygotene spermatocytes, replicate 2

description:
LZ_2
DeNovo_globalTranscriptome.gtf.gz
Gill_RNA_Seq_log2RPKM_DeNovo.csv.gz
Gill_RNA_Seq_log2RPKM_Gencode.csv.gz


title: Leptotene/Zygotene spermatocytes, replicate 1

description:
LZ_1
DeNovo_globalTranscriptome.gtf.gz
Gill_RNA_Seq_log2RPKM_DeNovo.csv.gz
Gill_RNA_Seq_log2RPKM_Gencode.csv.gz


title: H19.RTX.T6.C3

source_name: RTX430, Control, ZT6, replicate 3


title: 3473_Striatonigral-medium-spiny-neuron_HMC_HD

description:
3473
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Anterior putamen

value: Striatonigral medium spiny neuron

value: 42CAG / 15CAG

value: HMC

value: HD


title: H23.RTX.T6.H3

source_name: RTX430, Heat stress, ZT6, replicate 3

value: Heat stress

value: leaves


title: 3474_Striatopallidal-medium-spiny-neuron_HMC_HD

description:
3474
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Striatopallidal medium spiny neuron

value: Male


title: Mouse, ChIP, Cortex, E15, TCF4, Rep1

description: SFDJLR151_E15_5_TCF4_Rep1_S20_L004_R1_001

source_name: Cortex


title: H15.Macia.T1.H3

source_name: Macia, Heat stress, ZT1, replicate 3

value: Macia


title: 3472_Striatopallidal-medium-spiny-neuron_HCTSU_CTRL

description:
3472
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Posterior caudate

value: HCTSU

value: Female

value: CTRL


title: Mouse, ChIP, Cortex, E15, TBR1, Rep2

value: Experiment

value: WT


title: H11.Macia.T1.C3

source_name: Macia, Control, ZT1, replicate 3

value: Control


title: PHZ_SPL_HSC_3 [bisulfite-seq]

city: Houston

first: Rebecca

last: Murdaugh

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
The reads were aligned with bsmapz.
Methylation calculations were done using MethPipe.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include methylation measurements from MethPipe

source_name: Spleen

growth_protocol: Mice were housed in AAALAC-accredited, specific-pathogen-free animal care facilities at Baylor College of Medicine (BCM) with 12-hour light-dark cycle and received standard chow ad libitum. All procedures were approved by the BCM (protocol #AN-5858) Institutional Animal Care and Use Committees.

extract_protocol:
Genomic DNA was purified from sorted HSCs followed by bisulfite conversion and bisulfite PCR to amplify the region of interest (Tfrc gene).
The PCR products were purified and prepped for amplicon-seq using the Illumina Nextera XT kit.

treatment_protocol: 60mg/kg of phenylhydrazine (PHZ) was injected intraperitoneally for two constitutive days. Cells were sorted at day 3 after the last injection.

value: Splenic hematopoietic stem cells

value: PHZ


title: PHZ_SPL_HSC_2 [bisulfite-seq]


title: 3471_Striatonigral-medium-spiny-neuron_HCTSU_CTRL

description:
3471
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Striatonigral medium spiny neuron


title: Mouse, ChIP, Cortex, E15, TBR1, Rep1

value: Cortex


title: H7.RTX.T1.H3

source_name: RTX430, Heat stress, ZT1, replicate 3


title: Mouse, ChIP, Cortex, E15, FOXP1, INPUT, Rep2


title: PHZ_SPL_HSC_1 [bisulfite-seq]


title: 3470_Striatopallidal-medium-spiny-neuron_HCTSU_CTRL

description:
3470
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

source_name: Anterior caudate

value: Anterior caudate


title: PHZ_BM_HSC_3 [bisulfite-seq]

source_name: Bone marrow

value: Bone marrow hematopoietic stem cells

value: PBS


title: 3469_Striatonigral-medium-spiny-neuron_HCTSU_CTRL

description:
3469
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)


title: H3.RTX.T1.C3

source_name: RTX430, Control, ZT1, replicate 3

value: Heat stress

value: leaves


title: C63.SC224.T15.Cold3

source_name: SC224, Cold stress, ZT15, replicate 3

value: Cold stress


title: Mouse, ChIP, Cortex, E15, FOXP1, Rep2


title: Mouse, ChIP, Cortex, E15, FOXP1, INPUT, Rep1


title: PHZ_BM_HSC_2 [bisulfite-seq]


title: C62.SC224.T15.Cold2

source_name: SC224, Cold stress, ZT15, replicate 2


title: PHZ_BM_HSC_1 [bisulfite-seq]


title: Mouse, ChIP, Cortex, E15, FOXP1, Rep1


title: WT_SPL_HSC_2 [bisulfite-seq]


title: 3467_Striatonigral-medium-spiny-neuron_HCTSU_CTRL

description:
3467
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

source_name: Posterior putamen

value: Posterior putamen


title: C58.SC224.T9.Cold2

source_name: SC224, Cold stress, ZT9, replicate 2


title: Mouse, ChIP, Cortex, E15, BCL11A, INPUT, Rep1


title: WT_SPL_HSC_1 [bisulfite-seq]


title: 3466_Striatopallidal-medium-spiny-neuron_BEB19051_CTRL

description:
3466
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Striatopallidal medium spiny neuron

value: Male


title: C55.SC224.T6.Cold3

source_name: SC224, Cold stress, ZT6, replicate 3


title: Mouse, ChIP, Cortex, E15, BCL11A, Rep1


title: WT_BM_HSC_3 [bisulfite-seq]


title: 3464_Striatopallidal-medium-spiny-neuron_BEB19025_CTRL

description:
3464
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

source_name: Anterior putamen

value: Anterior putamen

value: CTRL


title: Mouse, ChIP, Cortex, E15, ARID1B, INPUT, Rep2

description: SFDJLR152_E15_5_Arid1b_Input_S34_L005_R1_001

value: WT


title: WT_BM_HSC_2 [bisulfite-seq]


title: C54.SC224.T6.Cold2

source_name: SC224, Cold stress, ZT6, replicate 2


title: 3463_Striatonigral-medium-spiny-neuron_BEB19025_CTRL

description:
3463
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)


title: Mouse, ChIP, Cortex, E15, ARID1B, INPUT, Rep1

description: SFDJLR151_E15_5_Arid1b_Input_S25_L004_R1_001

value: Control


title: 3468_Striatopallidal-medium-spiny-neuron_HCTSU_CTRL

description:
3468
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: HCTSU

value: Female


title: C51.SC224.T1.Cold3

source_name: SC224, Cold stress, ZT1, replicate 3


title: WT_BM_HSC_1 [bisulfite-seq]


title: C50.SC224.T1.Cold2

source_name: SC224, Cold stress, ZT1, replicate 2


title: 3462_Striatopallidal-medium-spiny-neuron_BEB18135_CTRL

description:
3462
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)


title: PHZ_SPL_HSC_2

data_processing:
Reads were aligned to mm10 genome assembly using STAR aligner.
FPKM was calculated using DeSeq2.
Differentially expressed genes were identified using DeSeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: comma-separated value files include log2foldchange calculations for significant differentially expressed genes

extract_protocol:
HSCs  were sorted into Trizol and RNA purified according to the manufacturer's instructions. DNase I-treated RNA samples were purified using the QIAGEN MinElute kit before cDNA was made and amplified with a SMART-Seq2 kit.
The cDNA was then fragmented and barcoded for sequencing using a Nextera XT kit.

value: Splenic hematopoietic stem cells

value: PHZ


title: C59.SC224.T9.Cold3

source_name: SC224, Cold stress, ZT9, replicate 3


title: Mouse, ChIP, Cortex, E15, ARID1B, Rep2

description: SFDJLR152_E15_5_Arid1b_Rep2_S35_L005_R1_001

source_name: Cortex

value: Cortex

value: Experiment


title: Mouse, ChIP, Cortex, E15, ARID1B, Rep1

description: SFDJLR151_E15_5_Arid1b_Rep1_S26_L004_R1_001


title: PHZ_SPL_HSC_1


title: 3456_Astrocyte_BEB19025_CTRL

description:
3456
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

value: Astrocyte


title: 3461_Striatonigral-medium-spiny-neuron_BEB18135_CTRL

description:
3461
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Striatonigral medium spiny neuron


title: C47.SC224.T15.Cont3

source_name: SC224, Control, ZT15, replicate 3

value: leaves


title: C46.SC224.T15.Cont2

source_name: SC224, Control, ZT15, replicate 2

value: Cold stress


title: Panc02, CRISPR 1G2 rep3

city: Atlanta

first: Tenzin

last: Passang

state: Georgia

address: 1365 Clifton Road NE

department: Hematology and Medical Oncology

institute: Emory University

data_processing:
The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software. Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove adapter sequences. The trimmed reads were mapped to the mouse reference genome GRCm38 available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison. A PCA analysis was performed using the "plotPCA" function within the DESeq2 R package. The plot shows the samples in a 2D plane spanned by their first two principal components. The top 500 genes, selected by highest row variance, were used to generate the plot.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: tab-delimited text files includes RPKM value for each sample

source_name: pancreas

growth_protocol: Panc02 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% HEPES with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from frozen cell pellet samples using Qiasymphony RNA kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles.The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: No treatment

value: pancreas

tag: cell line

value: ductal adenocarcinoma cells

value: CRISPR-wild type


title: 3465_Striatonigral-medium-spiny-neuron_BEB19051_CTRL

description:
3465
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

source_name: Anterior caudate

extract_protocol:
RNA extraction was carried out with AllPrep DNA/RNA FFPE Kit (Qiagen, #80234).
RNA-seq libraries were prepared with Trio RNA-Seq™ library preparation kit (Tecan, #0506-A01) and pooled for sequencing on NovaSeq6000 (SP 2 x 150bp).

value: Anterior caudate

value: Male

tag: pmi (hrs)


title: PHZ_BM_HSC_3

source_name: Bone marrow

value: WT

value: Bone marrow hematopoietic stem cells


title: C43.SC224.T9.Cont3

source_name: SC224, Control, ZT9, replicate 3

value: Control


title: 3455_Striatopallidal-medium-spiny-neuron_BEB18135_CTRL

description:
3455
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

source_name: Posterior caudate

value: Posterior caudate

value: Striatopallidal medium spiny neuron

tag: disease

value: CTRL


title: PHZ_BM_HSC_2

tag: genotype

value: PHZ


title: Panc02, CRISPR 1G2 rep1

tag: treatment


title: Panc02, CRISPR 1G2 rep2


title: C42.SC224.T9.Cont2

source_name: SC224, Control, ZT9, replicate 2


title: PHZ_BM_HSC_1


title: 3454_Striatonigral-medium-spiny-neuron_BEB18135_CTRL

description:
3454
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)


title: Panc02, VPAC2KO 1E7 rep3

value: VPAC2 knock out


title: C39.SC224.T6.Cont3

source_name: SC224, Control, ZT6, replicate 3


title: WT_BM_HSC_3

value: PBS


title: C38.SC224.T6.Cont2

source_name: SC224, Control, ZT6, replicate 2


title: Panc02, VPAC2KO 1E7 rep2


title: Panc02, VPAC2KO 1E7 rep1


title: WT_BM_HSC_2


title: 3451_Striatopallidal-medium-spiny-neuron_BEB19025_CTRL

description:
3451
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)


title: C35.SC224.T1.Cont3

source_name: SC224, Control, ZT1, replicate 3


title: WT_BM_HSC_1


title: C34.SC224.T1.Cont2

source_name: SC224, Control, ZT1, replicate 2


title: 3450_Striatonigral-medium-spiny-neuron_BEB19025_CTRL

description:
3450
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Striatonigral medium spiny neuron


title: 3449_Striatopallidal-medium-spiny-neuron_BEB18116_CTRL

description:
3449
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)


title: Panc02, parental, rep3

value: Wild type