title: Whole blood_Placebo_Before_No3


title: Hippocampus, WT, m, K, 2339, biol rep 3

status: Public on Jan 24 2025

type: SRA

city: Münster

first: Christa

last: Hohoff

address: Albert-Schweitzer-Campus 1, A9

department: Department of Psychiatry

country: Germany

institute: University of Muenster

description:
WT_m_K_2339_H
59__73_RNA_r_v_Hip_2339_m

library_source: transcriptomic

data_processing:
Demultiplexing and conversion of samples to fastq data (bcl2fastq2 conversion software v. 2.20; Illumina) and quality control (FastQC v. 0.11.9; Babraham Bioinformatics)
Adapter trimming and read filtering (Trimmomatic v. 0.38)
Alignment of resulting reads (HISAT2 v. 2.1.0) to reference genome (Ensembl GRCm38)
Sorting (SAMtools v. 1.9) and counting of reads into genomic features (htseq-count v .0.11.1)
Assembly: Ensembl GRCm38
Supplementary files format and content: .xlsx file includes raw read counts aligned to Ensembl GRCm38 genome

molecule: total RNA

organism: Mus musculus

source_name: hippocampus (ventral)

growth_protocol: Controlled housing conditions (1 same-sex KO-WT-littermate pair per cage), filtertops, 22±2°C, 55±10% humidity,12h:12h light-dark cycle, sawdust as bedding plus nesting material, tab water and standard diet ad libitum

extract_protocol:
RNA was harvested using Direct-zol RNA Micro- or Mini-Prep Kit (Zymo Research) resulting in total RNA of good quality (RIN > 7.5) and sufficient amount (110-250ng for hippocampus samples, 200-500ng for prefrontal cortex samples) to be used for library construction
RNA libraries for mRNA-seq were prepared using the NEBNext Ultra II RNA directional kit (BioLabs) following manufacturer protocols

treatment_protocol: Four weeks of non-stress control condition or chronic stress paradigm (unpredictably applied different mild stressors) followed by sacrificing (5% isoflurane, 50 sec.; decapitation 10 sec. later) to dissect hippocampi and prefrontal cortices (stored in RNAlater 6 to 8 min. after decapitation)

tag: brain part

value: right hemisphere

tag: tissue

value: hippocampus (ventral)

tag: genotype

value: wildtype (WT)

tag: Sex

value: male

tag: treatment

value: non-stress (K)


title: H2al2y_2_2

city: London

first: Jeremie

last: Subrini

address: 1 Midland road

country: United Kingdom

institute: The Francis Crick Intitute

description:
batch 4
SUB4754A50_2

data_processing:
Raw RNA-seq reads were processed using the RNA-seq nf-core pipeline (v3.2), star_rsem was used to generate raw reads counts.  The read counts were processed in R using the DESeq2 (v1.34) package. Very lowly expressed genes were filtered out by applying a rowSums filter of >=5 to the raw counts table. Principal component analysis (PCA) plots were generated using the top 500 most variable genes, applying the vst()  function and limma::removeBatchEffect() to remove batch effects for PCA visualisation. Raw counts were batch corrected and normalised using the DESeq() function, specifying “~batch + Sample_Genotype” in the design formula.  Log2 fold change (log2FC) and adjusted p-values between KO and WT were calculated using the results() function in DESeq2, specifying the “BH” (Benjamini-Hochberg p-value adjustment). Log2FCs were shrunk using the lfcShrink(type=”apeglm”) function.
Assembly: mm39
Supplementary files format and content: tab-deliminted file containing raw counts for each sample

source_name: testis

extract_protocol:
About 20mg of frozen testis pieces were placed in Precellys Homogenizer tubes 2.8 mm ceramic reinforced (Precellys 50722019, Bertin Technologies, France) on dry ice. 500μl of Trizol reagent (Sigma-Aldrich, USA) was added to the tubes and the samples placed in a Bertin Precellys 24-Dual High-throughput Tissue Homogenizer (Bertin Technologies, France). The machine was then run with the factory programme 5: 6,500 rpm for 20 seconds, automatic 25 seconds of pause and a repeat of 6500 rpm for 20 seconds. The lysate was then centrifuged for 5 minutes at 12,000 x g at 4°C and the clear supernatant transferred to a MaXtract High Density phase lock tube (Qiagen, UK). After 5 minutes of incubation at room temperature, 100μl of chloroform was added and tubes shaken vigorously for 2-3 minutes. Tubes were spun down for 15 minutes at 12,000 x g at 4°C. The upper aqueous phase was transferred to a new tube and 250μl of isopropanol added and mixed by pipetting. After 10 minutes of incubation at room temperature samples were spun down for 10 minutes at 12,000 x g at 4°C. The supernatant was discarded, the RNA pellet washed with 1ml of 75% ethanol and the samples spun down for 5 minutes at 7,500 x g at 4°C. Finally, the pellet was air-dried for 5-10 minutes and resuspended in 40μl of nuclease-free water.
Libraries were prepared using the NEBNext Ultra II Directional PolyA mRNA kits according to manufacturer instructions.

value: testis


title: B5__CML_RNA

city: New York

first: Cameron

last: Park

state: NY

country: USA

institute: Columbia University

library_source: transcriptomic single cell

data_processing:
10x genomics pipeline
CellRanger 5.0.0
Assembly: GRCh38-2020-A
Supplementary files format and content: zipped csv file for counts and metadata

organism: Homo sapiens

source_name: bone  marrow

extract_protocol:
CML data were obtained from previously described sequencing runs and all cells were analyzed for the current study, whereas we previously reported only the subset of data originating from T cells. For preparation of AML samples, cryopreserved primary bone marrow mononuclear cells (BMMCs) or peripheral blood mononuclear cells (PBMCs, for the matched sample from R 3501) were thawed on the day of sequencing at 37°C and dispensed into a warmed solution of 10% FBS, 10% DNaseI (StemCell Technologies, cat. No. 07900) in PBS. The cell suspension was centrifuged at 200g for 10 minutes at room temperature. Viable cells were negatively selected using MACS Dead Cell Removal Kit (Miltenyi Biotec, cat. No. 130-090-101). Collected live cells were resuspended in warmed Cell Staining Buffer (BioLegend). Cells were stained with TotalSeq C hashtag antibodies as well as CITE-seq antibodies according to manufacturer instructions. For batch AML1, after washing three times, cells from four samples were combined into one pool with approximately 20,000 cells from each sample and diluted to a final concentration of 1000 cells/ μl in 0.04% UltraPure BSA (ThermoFisher). Seven total pools were processed in this way. Subsequent samples (i.e. those in batch AML2, DLI products, and controls samples) were run individually.
Approximately 50,000 cells from each of the pooled samples or 10,000 cells from each of the individual samples were loaded into one lane of a 10x Genomics ChromiumTM instrument (10x Genomics) according to the manufacturer’s instructions. The scRNA-seq libraries were processed using Chromium Single Cell 5’ Library & Gel Bead v2 Kit (10x Genomics), and coupled scCITE-seq libraries were obtained using ChromiumTM single cell Feature Barcode kit. Quality control for amplified cDNA libraries and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent).

value: bone  marrow

value: DLI


title: Teyorf_1

description:
batch 4
SUB4754A53


title: B42__CML_RNA


title: mPFC, KO, f, CS, 2399, biol rep 4

description:
KO_f_CS_2399 _P
16__16_RNA_r_mPFC_2399_f

source_name: medial prefrontal cortex

value: medial prefrontal cortex

value: knockout (KO)

value: female

value: chronic stress (CS)


title: Whole blood_Placebo_After_No25

type: RNA

city: Kawasaki

first: Fumika

last: SHINOZAKI

address: 3-25-13 Tonomachi, Kawasaki-ku

country: Japan

institute: Kanagawa Institute of Industrial Science and Technology

hyb_protocol: Following fragmentation, 2.3 microgram of ss-cDNA were hybridized for 16 hr at 45C on Clariom S Array, human. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: CEL files were quantified with the qFARMs, using the statistical language R (R-4.0.3) and Bioconductor 3.12

label: biotin

source_name: Human whole blood after placebo ingestion and cognitive measure test

label_protocol: Biotinylated ss-cDNA were prepared according to the Thermo Fisher Scientific (Affymetrix) protocol from 50ng total RNA (Manual Target Preparation for GeneChip Whole Transctipt Expression Arrays, Publication Number MAN0018137, Revision B.0, 2020, Thermo Fisher Scientific).

extract_protocol: Total RNA from whole blood was extracted using PAXgene Blood miRNA Kit according to the manufacturer's instructions.

treatment_protocol: Blood was collected using a PAX gene Blood RNA tube.

value: Female


title: Hippocampus, WT, m, K, 2302, biol rep 2

description:
WT_m_K_2302_H
55__69_RNA_r_v_Hip_2302_m


title: Whole blood_Placebo_After_No24


title: B40__CML_RNA


title: H2al2y_2

description:
batch 4
SUB4754A50


title: B44__CML_CONTROL_RNA


title: H2al2y_1_2

description:
batch 4
SUB4754A49_2


title: Whole blood_Placebo_After_No23

value: Male


title: Hippocampus, WT, m, K, 2244, biol rep 1

description:
WT_m_K_2244_H
51__65_RNA_r_v_Hip_2244_m


title: B3__CML_RNA


title: B43__CML_RNA


title: H2al2y_1

description:
batch 4
SUB4754A49


title: Hippocampus, WT, m, CS, 2395, biol rep 4

description:
WT_m_CS_2395_H
79__76_RNA_r_v_Hip_2395_m


title: Whole blood_Placebo_After_No22


title: B39__CML_RNA


title: Whole blood_Placebo_After_No21


title: B41__CML_RNA


title: B38__CML_RNA


title: Hippocampus, WT, m, CS, 2434, biol rep 3

description:
WT_m_CS_2434_H
62__80_RNA_r_v_Hip_2434_m


title: Whole blood_Placebo_After_No20


title: Uty_4

description:
batch 4
SUB4754A48


title: Hippocampus, WT, m, CS, 2257, biol rep 2

description:
WT_m_CS_2257_H
58__72_RNA_r_v_Hip_2257_m


title: B37__CML_RNA


title: Uty_3_2

description:
batch 4
SUB4754A47_2


title: Hippocampus, WT, m, CS, 2271, biol rep 1

description:
WT_m_CS_2271_H
54__68_RNA_r_v_Hip_2271_m


title: Whole blood_Placebo_After_No19


title: Uty_3

description:
batch 4
SUB4754A47


title: Hippocampus, WT, f, K, 2429, biol rep 6

description:
WT_f_K_2429_H
75__63_RNA_r_v_Hip_2429_f


title: B36__CML_RNA


title: Uty_2_2

description:
batch 4
SUB4754A46_2


title: Hippocampus, WT, f, K, 2342, biol rep 5

description:
WT_f_K_2342_H
69__53_RNA_r_v_Hip_2342_f


title: Whole blood_Placebo_After_No17


title: Whole blood_Placebo_After_No16


title: B34__CML_RNA


title: Uty_2

description:
batch 4
SUB4754A46


title: B33__CML_RNA


title: Hippocampus, WT, f, K, 2337, biol rep 4

description:
WT_f_K_2337_H
68__52_RNA_r_v_Hip_2337_f


title: Whole blood_Placebo_After_No15


title: Uty_1_2

description:
batch 4
SUB4754A45_2


title: Hippocampus, WT, f, K, 2408, biol rep 3

description:
WT_f_K_2408_H
49__58_RNA_r_v_Hip_2408_f


title: B32__CML_RNA


title: Uty_4_2

description:
batch 4
SUB4754A48_2


title: Uty_1

description:
batch 4
SUB4754A45


title: Hippocampus, WT, f, K, 2253, biol rep 2

description:
WT_f_K_2253_H
44__46_RNA_r_v_Hip_2253_f


title: B31__CML_RNA


title: B30__CML_RNA


title: Hippocampus, WT, f, K, 2278, biol rep 1

description:
WT_f_K_2278_H
40__42_RNA_r_v_Hip_2278_f


title: Zfy2_1r

description:
batch 3
SUB4754A43


title: Whole blood_Placebo_After_No18


title: Hippocampus, WT, f, CS, 2417, biol rep 6

description:
WT_f_CS_2417_H
74__62_RNA_r_v_Hip_2417_f


title: B35__CML_RNA


title: Whole blood_Placebo_After_No13


title: wt_2r

description:
batch 3
SUB4754A42

value: control


title: Whole blood_Placebo_After_No12


title: Hippocampus, WT, f, CS, 2397, biol rep 5

description:
WT_f_CS_2397_H
70__55_RNA_r_v_Hip_2397_f


title: Whole blood_Placebo_After_No10


title: B29__CML_RNA


title: Whole blood_Placebo_After_No11


title: Hippocampus, WT, f, CS, 2315, biol rep 4

description:
WT_f_CS_2315_H
67__49_RNA_r_v_Hip_2315_f


title: B28__CML_RNA


title: Zfy12_2r

description:
batch 3
SUB4754A40


title: B27__CML_RNA


title: Whole blood_Placebo_After_No9


title: Hippocampus, WT, f, CS, 2285, biol rep 3

description:
WT_f_CS_2285_H
66__48_RNA_r_v_Hip_2285_f


title: Hippocampus, WT, f, CS, 2409, biol rep 2

description:
WT_f_CS_2409_H
50__59_RNA_r_v_Hip_2409_f


title: Whole blood_Placebo_After_No14


title: B26__CML_RNA


title: Whole blood_Placebo_After_No8


title: Zfy2_2r

description:
batch 3
SUB4754A44


title: Hippocampus, WT, f, CS, 2274, biol rep 1

description:
WT_f_CS_2274_H
41__43_RNA_r_v_Hip_2274_f


title: Ddx3y_2r

description:
batch 3
SUB4754A38


title: B25__CML_RNA


title: Zfy12_1r

description:
batch 3
SUB4754A37


title: B24__CML_RNA


title: Hippocampus, KO, m, K, 2341, biol rep 4

description:
KO_m_K_2341_H
77__74_RNA_r_v_Hip_2341_m


title: Whole blood_Placebo_After_No6


title: Whole blood_Placebo_After_No5


title: Kdm5d_2r

description:
batch 3
SUB4754A36


title: B2__CML_RNA


title: wt_1r

description:
batch 3
SUB4754A41


title: Hippocampus, KO, m, K, 2412, biol rep 3

description:
KO_m_K_2412_H
60__78_RNA_r_v_Hip_2412_m


title: B23__CML_RNA


title: B22__CML_RNA


title: Hippocampus, KO, m, K, 2303, biol rep 2

description:
KO_m_K_2303_H
56__70_RNA_r_v_Hip_2303_m


title: Kdm5d_1r

description:
batch 3
SUB4754A35


title: Whole blood_Placebo_After_No4


title: Ddx3y_1r

description:
batch 3
SUB4754A39


title: Hippocampus, KO, m, K, 2246, biol rep 1

description:
KO_m_K_2246_H
52__66_RNA_r_v_Hip_2246_m


title: B21__CML_RNA


title: Zfy1_2r

description:
batch 3
SUB4754A34


title: Zfy1_1r

description:
batch 3
SUB4754A33


title: Hippocampus, KO, m, CS, 2393, biol rep 4

description:
KO_m_CS_2393_H
78__75_RNA_r_v_Hip_2393_m


title: B20__CML_RNA


title: Hippocampus, KO, m, CS, 2433, biol rep 3

description:
KO_m_CS_2433_H
61__79_RNA_r_v_Hip_2433_m


title: Zfy12_4

description:
batch 2
SUB4754A32


title: B1__CML_RNA


title: Whole blood_Placebo_After_No7


title: Whole blood_Placebo_After_No2


title: Whole blood_Taxifolin_Before_No28

source_name: Human whole blood before taxifolin ingestion and cognitive measure test


title: Hippocampus, KO, m, CS, 2269, biol rep 1

description:
KO_m_CS_2269_H
53__67_RNA_r_v_Hip_2269_m


title: Hippocampus, KO, m, CS, 2256, biol rep 2

description:
KO_m_CS_2256_H
57__71_RNA_r_v_Hip_2256_m


title: Zfy12_3

description:
batch 2
SUB4754A31


title: Zfy12_2

description:
batch 2
SUB4754A30


title: B19__CML_RNA


title: Ddx3y_1

description:
batch 2
SUB4754A29


title: Whole blood_Taxifolin_Before_No27


title: B17__CML_RNA


title: B12__CML_RNA


title: Hippocampus, KO, f, K, 2406, biol rep 5

description:
KO_f_K_2406_H
71__57_RNA_r_v_Hip_2406_f


title: Whole blood_Taxifolin_Before_No25


title: Ddx3y_4

description:
batch 2
SUB4754A28


title: Whole blood_Taxifolin_Before_No26


title: Whole blood_Taxifolin_Before_No24


title: Whole blood_Placebo_After_No1


title: B11__CML_RNA


title: Ddx3y_3

description:
batch 2
SUB4754A27


title: Whole blood_Placebo_After_No3


title: Hippocampus, KO, f, K, 2273, biol rep 4

description:
KO_f_K_2273_H
64__41_RNA_r_v_Hip_2273_f


title: Whole blood_Taxifolin_Before_No23


title: Hippocampus, KO, f, K, 2343, biol rep 3

description:
KO_f_K_2343_H
47__54_RNA_r_v_Hip_2343_f


title: B10__CML_RNA


title: Whole blood_Taxifolin_Before_No22


title: Ddx3y_2

description:
batch 2
SUB4754A26


title: Zfy12_1

description:
batch 2
SUB4754A25


title: B18__CML_RNA


title: Hippocampus, KO, f, K, 2336, biol rep 2

description:
KO_f_K_2336_H
46__51_RNA_r_v_Hip_2336_f


title: 3516_product_DLI_RNA

source_name: peripheral blood

value: peripheral blood


title: Hippocampus, KO, f, K, 2252, biol rep 1

description:
KO_f_K_2252_H
43__45_RNA_r_v_Hip_2252_f


title: 3516_2_AML_RNA


title: Kdm5d_4

description:
batch 2
SUB4754A24


title: Whole blood_Taxifolin_Before_No21


title: Hippocampus, KO, f, K, 2430, biol rep 6

description:
KO_f_K_2430_H
76__64_RNA_r_v_Hip_2430_f


title: Hippocampus, KO, f, CS, 2416, biol rep 6

description:
KO_f_CS_2416_H
73__61_RNA_r_v_Hip_2416_f


title: Kdm5d_3

description:
batch 2
SUB4754A23


title: Whole blood_Taxifolin_Before_No20


title: 3516_1_AML_RNA


title: Hippocampus, KO, f, CS, 2407, biol rep 5

description:
KO_f_CS_2407_H
72__60_RNA_r_v_Hip_2407_f


title: Kdm5d_2

description:
batch 2
SUB4754A22


title: 3514_product_DLI_RNA


title: Whole blood_Taxifolin_Before_No19


title: Hippocampus, KO, f, CS, 2284, biol rep 4

description:
KO_f_CS_2284_H
65__47_RNA_r_v_Hip_2284_f


title: Whole blood_Taxifolin_Before_No18


title: 3514_2_AML_RNA


title: Kdm5d_1

description:
batch 2
SUB4754A21


title: 3514_1_AML_RNA


title: Hippocampus, KO, f, CS, 2399, biol rep 3

description:
KO_f_CS_2399_H
48__56_RNA_r_v_Hip_2399_f


title: Zfy1_4

description:
batch 2
SUB4754A20


title: Whole blood_Taxifolin_Before_No17


title: Hippocampus, KO, f, CS, 2317, biol rep 2

description:
KO_f_CS_2317_H
45__50_RNA_r_v_Hip_2317_f


title: Zfy1_3

description:
batch 2
SUB4754A19


title: Hippocampus, KO, f, CS, 2277, biol rep 1

description:
KO_f_CS_2277_H
42__44_RNA_r_v_Hip_2277_f


title: 3512_3_AML_RNA


title: Zfy1_2

description:
batch 2
SUB4754A18


title: Zfy1_1

description:
batch 2
SUB4754A17


title: Whole blood_Taxifolin_Before_No16


title: Whole blood_Taxifolin_Before_No14


title: 3512_2_AML_RNA


title: Single-cell RNA-seq profiling of in vitro differentiating ependymal cells, replicate 2

city: Paris

first: Romain

last: Koszul

address: 25 Rue du Dr Roux

department: Genetics and Genomics

country: France

institute: Institut Pasteur

description:
10x Genomics
MCCs_cell-metadata.csv
MCCs_gene-metadata.csv
MCCs_count-matrix.csv

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1
Assembly: mm10
Supplementary files format and content: Count matrix was generated using Cellranger v3 and saved as a .csv file
Supplementary files format and content: Aggregated cell metadata provided as a .csv file
Supplementary files format and content: Gene metadata provided as a .csv file

source_name: brain

growth_protocol: Newborn mice (P0-P2) were sacrificed by decapitation. The brains were then dissected in Hank’s solution (10% HBSS, 5% HEPES, 5% sodium bicarbonate, 1% penicillin/streptomycin (P/S) in pure water) and the extracted ventricular walls were cut manually into pieces, followed by enzymatic digestion (DMEM glutamax, 33% papain (Worthington 3126), 17% DNase at 10 mg/ml, 42% cysteine at 12 mg/ml) for 45 min at 37 °C in a humidified 5% CO2 incubator. Digestion was stopped by addition of a solution of trypsin inhibitors (Leibovitz Medium L15, 10% ovomucoid at 1 mg/ml, 2% DNase at 10 mg/ml). The cells were then washed in L15 and resuspended in DMEM glutamax supplemented with 10% fetal bovine serum (FBS) and 1% P/S in a Poly-L-lysine (PLL)-coated flask (equivalent of 2 ventricular walls per 25cm2 flask). Ependymal progenitors proliferated for 4-5 days until confluence, followed by shaking (250rpm) overnight to remove contaminant cells (neurons, oligodendrocytes, etc.).

extract_protocol:
After 2 days of in vitro differentiation, flasks were rinsed with PBS 1X twice and treated by enzymatic cell dissociation (Trypsin, 1mL) for 10 min and trituration to obtain a single cell suspension. Digestion was stopped by addition of 1 ml of fetal bovine serum (FBS). The cells were then washed in serum-free DMEM glutamax 1% P/S and resuspended in HBSS-0.1% BSA for single-cell RNA-seq library preparation.
Samples were labelled using a cell surface protein labelling strategy following manufacturer’s instructions, single-cell RNA-seq libraries were prepared with a Chromium equipment using the standard Single Cell 3’ v3 protocol (10X Genomics) and sequencing was performed on an Illumina NextSeq 500 sequencing machine following manufacturer’s instructions.

treatment_protocol: The day after shaking, the flasks’ medium was changed to warm serum-free DMEM glutamax 1% P/S to trigger ependymal cell differentiation for 2 days. At this time point, cells at all stages of cell cycle or ependymal differentiation are present in the flask.

value: brain

tag: age

tag: developmental stage

value: newborn

tag: cell type

value: Differentiating ependymal cells

value: Primary culture of dissected brain lateral ventricular walls


title: Zfy2_4

description:
batch 1
SUB4754A16


title: 3512_1_AML_RNA


title: Whole blood_Taxifolin_Before_No13


title: 3512_product_DLI_RNA


title: Single-cell RNA-seq profiling of in vitro differentiating ependymal cells, replicate 1


title: Whole blood_Taxifolin_Before_No15


title: Zfy2_3

description:
batch 1
SUB4754A15


title: VHL and HIF1A Rod Specific Knockout Retinal Samples at 3 Weeks Age -- Mouse 5

first: Salvatore

last: Caruso

state: New York

address: 701 West 168th Street, RM211E

institute: Columbia

description:
Library name: 488742-I1
Column Name in All_Samples_Raw_Counts.csv: VHL_HIF1A_KO_5

data_processing:
Low count genes (<10 reads per sample) were filtered out
Assembly: mm10
Data processing and Analysis was handled using DESeq2
Supplementary files format and content: CSV file includes raw counts for every sample

source_name: Retina

growth_protocol: Experimental and control mice were housed in Columbia animal facilities in accordance with appropriate protocols and exposed to standard light cycles (12hr on/12hr off)

extract_protocol:
Mice were euthanized at p21 and retinas were extracted and dissected for isolation / analysis. Tissue disections were immediately snapfrozen on liquid nitrogen and then transported to external sequencing service provider where further sample preparation was performed.
Libraries were constructed at the New York  Genome Center using standard kits and procedures.

treatment_protocol: Mice were injected with tamoxifen at 3 separate time points between p7 and p10 via IP injection

value: Retina

tag: cell line

value: Retinal Cells

value: Mixed

value: VHL and HIF1A KO

value: Tamoxifen at p7-p10


title: 3510_3_AML_RNA

value: bone  marrow

value: DLI


title: Whole blood_Taxifolin_Before_No12


title: Zfy2_2

description:
batch 1
SUB4754A14

value: testis


title: 3510_2_AML_RNA


title: VHL and HIF1A Rod Specific Knockout Retinal Samples at 3 Weeks Age -- Mouse 4

description:
Library name: 488741-I1
Column Name in All_Samples_Raw_Counts.csv: VHL_HIF1A_KO_4


title: Zfy2_1

description:
batch 1
SUB4754A13


title: Whole blood_Taxifolin_Before_No10


title: 3510_1_AML_RNA


title: Whole blood_Taxifolin_Before_No9


title: Usp9y_4

description:
batch 1
SUB4754A12


title: VHL and HIF1A Rod Specific Knockout Retinal Samples at 3 Weeks Age -- Mouse 2

description:
Library name: 488739-I1
Column Name in All_Samples_Raw_Counts.csv: VHL_HIF1A_KO_2


title: Whole blood_Taxifolin_Before_No8


title: Usp9y_3

description:
batch 1
SUB4754A11


title: 3509_product_DLI_RNA


title: 3509_2_AML_RNA


title: VHL and HIF1A Rod Specific Knockout Retinal Samples at 3 Weeks Age -- Mouse 1

description:
Library name: 488738-I1
Column Name in All_Samples_Raw_Counts.csv: VHL_HIF1A_KO_1


title: Whole blood_Taxifolin_Before_No7


title: 3509_1_1_AML_RNA


title: Usp9y_2

description:
batch 1
SUB4754A10


title: 3509_1_2_AML_RNA


title: Usp9y_1

description:
batch 1
SUB4754A9


title: VHL and HIF1A Floxed Control Retinal Samples at 3 Weeks Age -- Mouse 3

description:
Library name: 445894
Column Name in All_Samples_Raw_Counts.csv: VHL_HIF1A_CTRL_3

value: VHL and HIF1A Floxed


title: Whole blood_Taxifolin_Before_No11

value: Female


title: VHL and HIF1A Floxed Control Retinal Samples at 3 Weeks Age -- Mouse 4

description:
Library name: 445895
Column Name in All_Samples_Raw_Counts.csv: VHL_HIF1A_CTRL_4


title: Whole blood_Taxifolin_Before_No6


title: Uba1y_4

description:
batch 1
SUB4754A8


title: Whole blood_Taxifolin_Before_No5


title: VHL and HIF1A Rod Specific Knockout Retinal Samples at 3 Weeks Age -- Mouse 3

description:
Library name: 488740-I1
Column Name in All_Samples_Raw_Counts.csv: VHL_HIF1A_KO_3


title: VHL and HIF1A Floxed Control Retinal Samples at 3 Weeks Age -- Mouse 2

description:
Library name: 445893
Column Name in All_Samples_Raw_Counts.csv: VHL_HIF1A_CTRL_2


title: Whole blood_Taxifolin_Before_No4


title: 3507_product_DLI_RNA


title: 3507_4_AML_RNA


title: VHL and HIF1A Floxed Control Retinal Samples at 3 Weeks Age -- Mouse 1

description:
Library name: 445892
Column Name in All_Samples_Raw_Counts.csv: VHL_HIF1A_CTRL_1


title: Uba1y_3

description:
batch 1
SUB4754A7


title: Whole blood_Taxifolin_Before_No3

value: Male


title: 3507_3_AML_RNA


title: Uba1y_2

description:
batch 1
SUB4754A6


title: VHL Rod Specific Knockout Retinal Samples at 3 Weeks Age -- Mouse 4

description:
Library name: 445904
Column Name in All_Samples_Raw_Counts.csv: VHL_KO_4

value: VHL KO


title: 3507_2_AML_RNA


title: Uba1y_1

description:
batch 1
SUB4754A5


title: Whole blood_Taxifolin_Before_No1


title: wt_4

description:
batch 1
SUB4754A4

value: control


title: 3507_1_AML_RNA


title: VHL Rod Specific Knockout Retinal Samples at 3 Weeks Age -- Mouse 2

description:
Library name: 445902
Column Name in All_Samples_Raw_Counts.csv: VHL_KO_2


title: Whole blood_Taxifolin_After_No28

source_name: Human whole blood after taxifolin ingestion and cognitive measure test


title: VHL Rod Specific Knockout Retinal Samples at 3 Weeks Age -- Mouse 1

description:
Library name: 445901
Column Name in All_Samples_Raw_Counts.csv: VHL_KO_1


title: wt_3

description:
batch 1
SUB4754A3


title: VHL Floxed Control Retinal Samples at 3 Weeks Age -- Mouse 4

description:
Library name: 445899
Column Name in All_Samples_Raw_Counts.csv: VHL_CTRL_4

value: VHL Floxed


title: wt_2

description:
batch 1
SUB4754A2


title: wt_1

description:
batch 1
SUB4754A1


title: VHL Floxed Control Retinal Samples at 3 Weeks Age -- Mouse 3

description:
Library name: 445898
Column Name in All_Samples_Raw_Counts.csv: VHL_CTRL_3


title: Whole blood_Taxifolin_After_No27


title: Whole blood_Taxifolin_After_No26


title: 3505_4_AML_RNA


title: VHL Floxed Control Retinal Samples at 3 Weeks Age -- Mouse 2

description:
Library name: 445897
Column Name in All_Samples_Raw_Counts.csv: VHL_CTRL_2


title: AZFa_KO_5

data_processing:
Replicates from the P10 and adult 10x nuclei datasets were aligned to the mm39 genome using STARsolo (v2.7.9), specifying the parameters –soloMultiMappers EM –outFilterScoreMin 30 --soloFeatures Gene GeneFull --soloType CB_UMI_Simple --soloFeatures Gene GeneFull --soloUMIlen 12 --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIdedup 1MM_CR. Empty droplets were separated from nuclei using the proportion of reads mapping to intronic reads. Replicates were then processed in the Seurat R package (v4.3.0). Cells were retained if they had <5% reads aligning to mitochondrial and rRNA genes, if the total number of molecules within a cell was between 1000 and 50000 and the number of genes detected per cell was between 500 and 10000. The data was normalised using NormalizeData, then FindVariableFeatures. The dataset was scaled using ScaleData. Principle Component Analysis was applied using RunPCA followed by FindNeighbours and FindClusters. Uniform Manifold Approximation and Projection was estimated for the integrated dataset using RunUMAP. Doublets were identified using the DoubletFinder R package (v2.0.3). Replicates from each KO were integrated together, then the integrated KOs from their respective P10 and adult datasets were integrated with each other using SelectIntegrationFeatures, FindIntegrationAnchors and IntegrateData, generating one integrated dataset for the P10 10x data, and another for the adult 10x data. Each dataset was processed using ScaleData, then RunPCA and RunUMAP. Clusters were identified using a 0.5 resolution for both the adult and P10 datasets. In the adult dataset, ambient RNA clusters were identified using the FindAllMarkers function, and subsequently removed.
Assembly: mm39
Supplementary files format and content: tab-separated matrix files

molecule: nuclear RNA

extract_protocol:
On ice, around 10mg of frozen testis was homogenised in 1ml of lysis buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8, 1% BSA, 0.1% IGEPAL and freshly added 1 µM DTT, 0.4 U µl−1 RNase Inhibitor (New England BioLabs), 0.2 U µl−1 SUPERasIn (ThermoFischer Scientific)) and incubated on ice for 4 minutes. The lysate was filtered through a 30µm filter and then centrifuged at 500g for 5 minutes at 4C. The supernatant was removed, and the pellet resuspended in 1ml of wash buffer 1 (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8, 1% BSA, and freshly added 1 µM DTT, 0.4 U µl−1 RNase Inhibitor, 0.2 U µl−1 SUPERasIn). This was spun down at 500g for 5 minutes at 4°C and washing step repeated. Next the pellet was resuspended in 670 µl of freshly diluted dithio-bis (succinimidyl propionate) (DSP) (1mg/ml in PBS) and incubated at room temperature for 30 minutes. Fixation was quenched by adding 14.07µl Tris-HCL, pH8. Nuclei were spined down at 500g for 5 minutes at 4C and resuspended in 1ml of wash buffer 2 (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10mM Tris-HCL, pH8, 1% BSA, and freshly added 1 µM DTT, 0.4 U µl−1 RNase Inhibitor, 0.2 U µl−1 SUPERasIn). The sample were spun down one more time at 500g for 4 minutes at 4°C and the pellet resuspended in 0.04% BSA in PBS.  Testis nuclei isolation was adapted from a previously published protocol36. On ice, around 10mg of frozen testis was homogenised in 1ml of lysis buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8, 1% BSA, 0.1% IGEPAL and freshly added 1 µM DTT, 0.4 U µl−1 RNase Inhibitor (New England BioLabs), 0.2 U µl−1 SUPERasIn (ThermoFischer Scientific)) and incubated on ice for 4 minutes. The lysate was filtered through a 30µm filter and then centrifuged at 500g for 5 minutes at 4C. The supernatant was removed, and the pellet resuspended in 1ml of wash buffer 1 (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8, 1% BSA, and freshly added 1 µM DTT, 0.4 U µl−1 RNase Inhibitor, 0.2 U µl−1 SUPERasIn). This was spun down at 500g for 5 minutes at 4°C and washing step repeated. Next the pellet was resuspended in 670 µl of freshly diluted dithio-bis (succinimidyl propionate) (DSP) (1mg/ml in PBS) and incubated at room temperature for 30 minutes. Fixation was quenched by adding 14.07µl Tris-HCL, pH8. Nuclei were spined down at 500g for 5 minutes at 4C and resuspended in 1ml of wash buffer 2 (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10mM Tris-HCL, pH8, 1% BSA, and freshly added 1 µM DTT, 0.4 U µl−1 RNase Inhibitor, 0.2 U µl−1 SUPERasIn). The sample were spun down one more time at 500g for 4 minutes at 4°C and the pellet resuspended in 0.04% BSA in PBS.
Libraries were prepared according to the manufacturers protocol from 10X Genomics for 10X_3prime_mRNA


title: Whole blood_Taxifolin_After_No25


title: VHL Rod Specific Knockout Retinal Samples at 3 Weeks Age -- Mouse 3

description:
Library name: 445903
Column Name in All_Samples_Raw_Counts.csv: VHL_KO_3


title: VHL Floxed Control Retinal Samples at 3 Weeks Age -- Mouse 1

description:
Library name: 445896
Column Name in All_Samples_Raw_Counts.csv: VHL_CTRL_1


title: AZFa_KO_4


title: Whole blood_Taxifolin_After_No23


title: Whole blood_Taxifolin_Before_No2


title: Whole blood_Taxifolin_After_No24


title: 3505_2_AML_RNA


title: AZFa_KO_3


title: 3505_product_DLI_RNA

value: peripheral blood


title: 3503_product_DLI_RNA


title: AccuTOX_10uM_n3_human

city: Montreal

first: Moutih

last: Rafei

address: Montreal

country: Canada

institute: Universite de Montreal

description:
Library name: Sample 13
ARMX human MSC
S13_S16

data_processing:
Basecalls performed using Illumina RTA 2.4.11. followed by STAR v2.7 aligner Genecounts
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Assembly: Mouse mm10 and Human hg38
Supplementary files format and content: Files are tabular in tsv format (ensembl genes in row and samples in columns)

molecule: polyA RNA

source_name: Bone marrow

growth_protocol: Murine mesenchymal stromal cells (MSCs) were maintained in AMEM supplemented with 10% fetal bovine serum (FBS) and 50 U/mL Penicillin-Streptomycin in humidified atmosphere with 5% CO2 at 37C. Human MSCs were mainained in the RoosterBio media (RoosterKit-hBM-1M-XF) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

treatment_protocol: Treatment was added post confluency of 80%. AccuTOX condition consisted of 25uM of the compound diluted in AMEM supplemented with 10% fetal bovine serum (FBS) and 50 U/mL Penicillin-Streptomycin. AccuTOX+OVA/lysate condition consisted of 25uM of the compound, plus 1 mg/mL of Albumin from chicken egg white, diluted in AMEM supplemented with 10% fetal bovine serum (FBS) and 50 U/mL Penicillin-Streptomycin/ml insulin (Sigma). Cell were treated and incubated for 6h in humidified atmosphere with 5% CO2 at 37C. Similar treatments were done for the human cells except AccuTOX was used at 10uM.

value: Bone marrow

value: Primary cell

value: Mesenchymal stromal cell

value: WT

value: 10 uM of AccuTOX


title: 3503_6_AML_RNA


title: Whole blood_Taxifolin_After_No22


title: AccuTOX_10uM_n2_human

description:
Library name: Sample 12
ARMX human MSC
S12_S15


title: AZFa_KO_2


title: Whole blood_Taxifolin_After_No21


title: AZFa_KO_1


title: 3505_3_AML_RNA


title: AccuTOX_10uM_n1_human

description:
Library name: Sample 10
ARMX human MSC
S10_S14


title: 3503_4_AML_RNA


title: Whole blood_Taxifolin_After_No20


title: Negative_n3_human

description:
Library name: Sample 9
ARMX human MSC
S9_S13

value: Untreated


title: 3505_1_AML_RNA


title: 3503_3_AML_RNA


title: RNAseq_mut3_rep2

city: Guangzhou

first: HongXin

last: Zhong

address: No. 190, Open Source Avenue, Luogang District, Guangzhou, China

country: China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
Paired-end reads were handled with Trim Galore, and then mapped to mouse (mm10) genome using STAR aligner.
Transcript abundance were quantified using RSEM. Differentially expressed genes (DEGs) were determined using DESeq2.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include TPM values.

source_name: Embryo

extract_protocol:
Total RNAs from each mouse tissue or cells were extracted, and were purified by two rounds of mRNA purification with mRNA capture beads to ensure removal of rRNA.
RNA-seq libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina, and the method was performed according to the manufacturer's instructions.

treatment_protocol: ANKRD11 Y347A mutation were generated by CRISPR/Cas9-mediated genome editing.

value: Embryo

value: mESC

value: ANKRD11 Y347A mutated

value: Matate


title: RNAseq_mut3_rep1


title: Negative_n2_human

description:
Library name: Sample 8
ARMX human MSC
S8_S12


title: Whole blood_Taxifolin_After_No19


title: 3503_2_AML_RNA

value: bone  marrow

value: DLI


title: Whole blood_Taxifolin_After_No18

value: Female


title: RNAseq_mut2_rep2


title: Neagtive_n1_human

description:
Library name: Sample 7
ARMX human MSC
S7_S11


title: RNAseq_mut2_rep1


title: 3501_product_DLI_RNA


title: 3503_1_AML_RNA


title: IDH2R172K_rep3

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing reads from all RNA-seq experiments were aligned to human (hg38) reference genome by STAR 2.7.3.a with the parameters: --outFilterMultimapNmax 1
The number of reads aligned to GENCODE annotated genes' exons were counted using HTseq and further normalized to be of unit TPM (transcripts per million)using RSEM.
Differentially expressed genes (DEGs) were identified by DESeq2
Assembly: hg38
Supplementary files format and content: text file of gene TPM values

source_name: Human cell line

growth_protocol: Human TF-1 cells were cultured in RPMI-1640 medium containing 10% FBS and 1% penicillin/streptomycin and supplemented with recombinant human GM-CSF (2 ng/ml). Base-edited TF-1 cells with different IDH mutations were cultured without human GM-CSF.

extract_protocol: 0.1-1 ug of total human leukemia cell line RNA was processed for library generation using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and NEBNext Ultra II Directional RNA Library Prep Kit.

value: Leukemia cell line


title: Whole blood_Taxifolin_After_No17


title: IDH2R172K_rep2


title: RNAseq_mut1_rep2


title: Whole blood_Taxifolin_After_No16

value: Male


title: 3501_3_AML_RNA_PBMC


title: IDH2R172K_rep1


title: RNAseq_mut1_rep1


title: IDH2R140W_rep3


title: Whole blood_Taxifolin_After_No15


title: 3501_3_AML_RNA


title: RNAseq_wt2_rep2

value: wild type

value: Untreatment


title: 3501_2_AML_RNA


title: Whole blood_Taxifolin_After_No13


title: Whole blood_Taxifolin_After_No14


title: IDH2R140W_rep2


title: RNAseq_wt1_rep2


title: IDH2R140W_rep1


title: Whole blood_Taxifolin_After_No11


title: RNAseq_wt1_rep1


title: Whole blood_Taxifolin_After_No12


title: 3501_1_AML_RNA


title: 3501_4_AML_RNA


title: 3028_2_AML_CONTROL_RNA


title: BMDMs, Nudt21 KO4, IFNγ/LPS 4hr

city: Shanghai

first: Yunzhu

last: Chen

address: 280 South Chong Qing Rd

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
The clean reads were aligned to the mouse genome (mm10, GRCm38) using hisat2 2.2.1(Kim et al., 2015), and RefSeq gene expressions were quantified by Stringtie 2.1.7(Pertea et al., 2015).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: bone marrow

extract_protocol:
Total RNA of BMDMs from WT and Nudt21-cKO mice was extracted using TRIZOL (catalog no. 15596026, Invitrogen) and was used as input material for the RNA sample preparations. RNA purification, reverse transcription, library construction, and sequencing were performed by Novogene Co., Ltd. Paired-end RNA-Seq was performed to yield more than 250 million reads per sample, which allowed us to obtain not only transcript expression but also alternative PAS usage.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: bone marrow

value: bone marrow derived macrophages

value: Nudt21 KO

value: IFNγ/LPS stimulation


title: IDH2R140Q_rep3


title: IDH2R140Q_rep2


title: IDH2R140Q_rep1


title: Whole blood_Taxifolin_After_No10


title: BMDMs, Nudt21 KO3, IFNγ/LPS 4hr


title: RNAseq_wt2_rep1


title: BMDMs, WT2, IFNγ/LPS 4hr

value: WT


title: 3028_1_AML_CONTROL_RNA


title: Whole blood_Taxifolin_After_No8


title: 3026_2_AML_CONTROL_RNA


title: 3024_2_AML_CONTROL_RNA


title: BMDMs, WT1, IFNγ/LPS 4hr


title: IDH1R132H_rep1


title: 3501_1_AML_RNA_PBMC

value: peripheral blood


title: 3026_1_AML_CONTROL_RNA


title: BMDMs, Nudt21 KO4, 0hr


title: Whole blood_Taxifolin_After_No6


title: Whole blood_Taxifolin_After_No7


title: IDH1R132H_rep2


title: Whole blood_Taxifolin_After_No9


title: BMDMs, Nudt21 KO3, 0hr


title: BMDMs, WT2, 0hr


title: 3022_1_AML_CONTROL_RNA


title: Parental_rep2

value: Parental


title: Parental_rep3


title: Parental_rep1


title: BMDMs, WT1, 0hr


title: IDH1R132H_rep3


title: 3020_1_AML_CONTROL_RNA


title: Replicate 2 of scRNAseq of bone marrow immune cells, GEX

status: Public on Jan 23 2025

city: Wien

first: Jörg

last: Menche

state: Wien

address: Augasse 2-6,

country: Austria

institute: Ludwig Boltzmann Institute for Network Medicine

description:
Library name: MR_33_10X_SA_PBS_BM_Transcriptome
polyA RNA

data_processing:
The demultiplexing, bacoded processing, gene counting and aggregation were performed using cellranger count pipeline using Cell Ranger v6.1.2.
Assembly: mm10
Supplementary files format and content: Feature count matrices in h5 format with raw and filtered barcodes along with HTO assignment for each barcode.

extract_protocol:
Bone marrow cells were then sorted into PBS with 0.02% BSA to exclude erythrocytes and dead cells as well as limit the numbers of abundant immune cell types such as neutrophils, monocytes and T and B cells. In brief, 30,000 target cells from each panel were sort-purified independently from  PBS and SA treated mice using a FACSAria Fusion flow cytometer (BD). Subsequently, 3 and 4 samples were pooled per replicate experiment respectively (Replicate experiment 1 : MR_30_10X_SA_PBS_BM_22112021_Transcriptome, replicate experiment 2: MR_33_10X_SA_PBS_BM_Transcriptome). Those  cell fractions were pooled . for processing as a single sample according to the manufacturer’s protocol, while the antibody-linked barcodes enabled sample-specific demultiplexing of the sequencing data.
Both scRNA-seq libraries were generated using the Chromium Controller and the Next GEM Single Cell 3’ Reagent Kit (v3, 10x Genomics) according to the manufacturer’s instructions

treatment_protocol: Bone marrow cells were collected from 9 week old female C57BL/6J mice at day 7 post Staphylococcus aureus skin infection or PBS. Cells were stained for flow cytometry markers for major immune cell populations and tagged with TotalSeq™ anti-mouse CD45/MHCI from Biolegend).

value: Bone marrow

value: Bone marrow immune cells

value: C57BL6/J (WT)

value: S.aureus skin infection or PBS

tag: library

value: mRNA


title: Replicate 2 of scRNAseq of bone marrow immune cells, HTO

description:
Library name: MR_33_10X_SA_PBS_BM_Antibody_Multiplex
Hastag-derived oligonucleotide (HTO)

library_source: other

data_processing:
The demultiplexing, bacoded processing, gene counting and aggregation were performed using cellranger count pipeline using Cell Ranger v6.1.2.
Assembly: mm10
Supplementary files format and content: Feature count matrices in h5 format with raw and filtered barcodes along with HTO assignment for each barcode.
Library strategy: CITE-seq

molecule: protein

value: HTO

tag: hto

value: TotalSeq™-A0301 anti-mouse Hashtag 1 Antibody, TotalSeq™-A0302 anti-mouse Hashtag 2 Antibody, TotalSeq™-A0303 anti-mouse Hashtag 3 Antibody, TotalSeq™-A0304 anti-mouse Hashtag 4 Antibody


title: Whole blood_Taxifolin_After_No1

value: Male


title: Replicate 1 of scRNAseq of bone marrow immune cells, GEX

description:
Library name: MR_30_10X_SA_PBS_BM_22112021_Transcriptome
polyA RNA


title: FACS-sorted bone marrow Eosinophil progenitor_RNA _SA6

description:
Library name: MR_54_48
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)

data_processing:
NGS reads were mapped to the Genome Reference Consortium GRCm38 assembly via STAR aligner, version2.7.9a.
NGS read alignments overlapping Ensembl exon features were counted with the Bioconductor (3.16) Genomi-cAlignments (1.34.0) package via the summarizeOverlaps function in Union mode, ignoring secondary alignments and alignments not passing vendor quality filtering.
Exon-level counts were aggregated to gene-level counts.
Assembly: GRCm38
Supplementary files format and content: tab-delimieted text file includes raw counts for each sample
Supplementary files format and content: tab-delimieted text file includes normalized counts for each sample
Supplementary files format and content: tab-delimieted text file includes FPKM values for each sample

extract_protocol:
RNA was precipitated with ice cold absolute ethanol, LPA (Linear Polyacrylamide (Sigma Aldrich) and 3 M Sodium Acetate (NaOAc PH 5.2; ThermoFisher) overnight and resuspended in 10 µl of 10 mM Tris buffer (pH 8.0; Invitrogen). RNA concentrations were measured by flurometric analysis (Qubit).
The Quantseq libraries were prepared with an input of 10 ng RNA using the QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen) in combination with the PCR add-on Kit for Illumina (Lexogen) (16 amplification cycles) following the manufacturer’s protocol. Sample quality was assessed with a Bioanalyzer 2100 (Agilent Technologies)

treatment_protocol: Bulk RNA-seq analysis was performed on bone marrow eosinophils and eosinophil progenitors from PBS control or S.aureus-infected mice at day 7 post infection. Cells (10000 - 100000) were sorted from the bone marrow into cold RLT Buffer (Qiagen), followed by RNA isolation using the RNeasy Micro kit (Qiagen). RNA was precipitated with ice cold absolute ethanol, LPA (Linear Polyacrylamide (Sigma Aldrich) and 3 M Sodium Acetate (NaOAc PH 5.2; ThermoFisher) overnight and resuspended in 10 µl of 10 mM Tris buffer (pH 8.0; Invitrogen). RNA concentrations were measured by flurometric analysis (Qubit).

value: Eosinophil progenitor

value: SA

tag: strain


title: FACS-sorted bone marrow Eosinophil progenitor_RNA _SA4

description:
Library name: MR_54_46
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: Whole blood_Taxifolin_After_No3


title: Whole blood_Taxifolin_After_No5

value: Female


title: FACS-sorted bone marrow Eosinophil progenitor_RNA _SA2

description:
Library name: MR_54_44
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: FACS-sorted bone marrow Eosinophil progenitor_RNA _SA3

description:
Library name: MR_54_45
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: 3024_1_AML_CONTROL_RNA

value: bone  marrow


title: FACS-sorted bone marrow Eosinophil progenitor_RNA _SA5

description:
Library name: MR_54_47
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: Whole blood_Taxifolin_After_No4


title: FACS-sorted bone marrow Eosinophil progenitor_RNA _PBS6

description:
Library name: MR_54_42
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)

value: PBS


title: FACS-sorted bone marrow Eosinophil progenitor_RNA _PBS1

description:
Library name: MR_54_37
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: FACS-sorted bone marrow Eosinophil progenitor_RNA _PBS5

description:
Library name: MR_54_41
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: FACS-sorted bone marrow Eosinophil progenitor_RNA _PBS2

description:
Library name: MR_54_38
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: FACS-sorted bone marrow Eosinophil_RNA_SA6

description:
Library name: MR_54_12
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)

value: Eosinophil


title: FACS-sorted bone marrow Eosinophil_RNA_SA3

description:
Library name: MR_54_9
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)

value: WT


title: FACS-sorted bone marrow Eosinophil_RNA_SA5

description:
Library name: MR_54_11
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: Replicate 1 of scRNAseq of bone marrow immune cells, HTO

description:
Library name: MR_30_10X_SA_PBS_BM_22112021_Antibody_Multiplex
Hastag-derived oligonucleotide (HTO)

value: TotalSeq™-A0301 anti-mouse Hashtag 1 Antibody, TotalSeq™-A0302 anti-mouse Hashtag 2 Antibody, TotalSeq™-A0303 anti-mouse Hashtag 3 Antibody


title: FACS-sorted bone marrow Eosinophil_RNA_SA1

description:
Library name: MR_54_7
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: FACS-sorted bone marrow Eosinophil_RNA_SA2

description:
Library name: MR_54_8
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: FACS-sorted bone marrow Eosinophil_RNA_PBS5

description:
Library name: MR_54_5
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: FACS-sorted bone marrow Eosinophil_RNA_PBS6

description:
Library name: MR_54_6
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: Whole blood_Taxifolin_After_No2


title: FACS-sorted bone marrow Eosinophil_RNA_PBS3

description:
Library name: MR_54_3
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: FACS-sorted bone marrow Eosinophil_RNA_PBS4

description:
Library name: MR_54_4
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: FACS-sorted bone marrow Eosinophil_RNA_PBS2

description:
Library name: MR_54_2
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: FACS-sorted bone marrow Eosinophil progenitor_RNA _SA1

description:
Library name: MR_54_43
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: FACS-sorted bone marrow Eosinophil_RNA_PBS1

description:
Library name: MR_54_1
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: FACS-sorted bone marrow Eosinophil progenitor_RNA _PBS4

description:
Library name: MR_54_40
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: AOM+Saline cycle2-1

city: chongqing

first: Ruyi

last: HANG

address: Yuzhong District

institute: Army Medical Center of PLA

description:
Library name: AOM+Saline cycle2-1
AOM_D100_1

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

source_name: colon

growth_protocol: C57BL/6J mice (male, 6-10 weeks old, weight 22±3 g) were kept in individually ventilated cages (IVC) which had been thoroughly sterilized, with constant temperature, humidity and pressure, and regular disinfection. The light/dark cycle was simulated by alternating 12 hours. Mice ad libitum access to filtered air, sterile water, and sterile feed.

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

treatment_protocol: All mice were treated with AOM (10 mg/kg) by intraperitoneal injection on day 0. On days 7-11, 28-32, and 49-53 of the experiment, the only drinking water of the mice was replaced by 2.5% DSS solution, and the mice had free access to it. The mice were treated with sterilized drinking water for the rest of the experiment. In addition, the in vivo working solution of APX3330 was configured according to the method provided by the supplier. APX3330 was injected intraperitoneally once a day at a dose of 25mg/kg on days 7-11, 28-32, and 49-53. The placebo group was injected intraperitoneally with an equal volume of saline on days 7-11, 28-32, and 49-53.

value: colon


title: AOM+Saline cycle1-2

description:
Library name: AOM+Saline cycle1-2
AOM_D48_2


title: AOM+Saline cycle1-3

description:
Library name: AOM+Saline cycle1-3
AOM_D48_3


title: AOM+Saline cycle2-2

description:
Library name: AOM+Saline cycle2-2
AOM_D100_2


title: AOM+E3330-3

description:
Library name: AOM+E3330-3
AOM_E330_3

value: C57BL/6, AOM/DSS-induced CAC,APX3330


title: FACS-sorted bone marrow Eosinophil progenitor_RNA _PBS3

description:
Library name: MR_54_39
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)

value: Bone marrow


title: AOM+E3330-2

description:
Library name: AOM+E3330-2
AOM_E330_2


title: AOM+E3330-1

description:
Library name: AOM+E3330-1
AOM_E330_1


title: AOM+Saline-3

description:
Library name: AOM+Saline-3
AOM_D27_3

value: C57BL/6, AOM/DSS-induced CAC,Saline


title: AOM+Saline cycle1-1

description:
Library name: AOM+Saline cycle1-1
AOM_D48_1


title: FACS-sorted bone marrow Eosinophil_RNA_SA4

description:
Library name: MR_54_10
Bulk RNA-seq (QuantSeq 3' mRNA-Seq)


title: Control-3

description:
Library name: Control-3
Control_3

value: C57BL/6, WT


title: Control-2

description:
Library name: Control-2
Control_2


title: Control-1

description:
Library name: Control-1
Control_1


title: heart, Old_UA, 90D

city: Ecublens

first: Davide

last: D'Amico

address: EPFL Innovation Park, Building C

country: Switzerland

institute: Amazentis SA

description:
Library name: lib687629
Old_UA_90D

data_processing:
RNA-seq instrument: NovaSeq6000 using S4 flowcells with 2x150bp
Assembly: High quality RNA-seq read pairs were mapped to the Ensembl mouse GRCm38 reference genome, using a transcriptome annotation GTF file (version GRCm38.94).
Supplementary files format and content: For the alignment process, a bespoke index was built using the annotation file, and an expected read length of 151 bps. Read counting was performed on the gene-level, using htseq-count.

source_name: heart

extract_protocol:
Excess OCT was trimmed away from the frozen tissues block with a sterile scalpel blade. The tissues were cut into sections of 20 µM using a cryostat previously cleaned with a RNAse away solution. 10 sections per sample were collected in microtubes containing 1mL of Trizol. The RNA was isolated using the TRIZOL/Chloroform extraction method. RNA was quality controlled with Agilent Fragment Analyzer System.
Library preparation was performed by Strand-specific cDNA library, purification of poly-A containing mRNA molecules, mRNA fragmentation, random primed cDNA synthesis (strand-specific), adapter ligation and adapter specific PCR amplification.

value: heart

value: UA

value: Old


title: AOM+Saline-2

description:
Library name: AOM+Saline-2
AOM_D27_2


title: heart, Old_UA, 13NS

description:
Library name: lib681036
Old_UA_13NS


title: AOM+Saline-1

description:
Library name: AOM+Saline-1
AOM_D27_1


title: heart, Old_UA, 10OD

description:
Library name: lib687630
Old_UA_10OD


title: heart, Old, 14OD

description:
Library name: lib681035
Old_14OD

value: Control


title: heart, Old, 14OG

description:
Library name: lib681034
Old_14OG


title: heart, Old, 8OG

description:
Library name: lib681032
Old_8OG


title: heart, Old, 4OG

description:
Library name: lib681030
Old_4OG


title: AOM+Saline cycle2-3

description:
Library name: AOM+Saline cycle2-3
AOM_D100_3


title: heart, Old, 4OD

description:
Library name: lib681031
Old_4OD


title: heart, Young_UA, 12NS

description:
Library name: lib681027
Young_UA_12NS

value: Young


title: heart, Young_UA, 2OD

description:
Library name: lib681025
Young_UA_2OD


title: heart, Young, 11OD

description:
Library name: lib681023
Young_11OD


title: heart, Young, 11OG

description:
Library name: lib681022
Young_11OG


title: heart, Young, 1OD

description:
Library name: lib681019
Young_1OD


title: MB_RNA

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

description: SPACE-seq (utilizing the 10X Visium CytAssist v2 workflow)

data_processing:
FASTQ files were trimmed, filtered, and aligned using the spaceranger pipeline from 10X genomics.
Spatial RNA-seq profiles were clustered and visualized using Seurat.
Spatial ATAC-seq fastqs were re-aligned using hisat2, processed into fragment files, and then clustered and visualized using ArchR.
Assembly: mm10 or hg38
Supplementary files format and content: Filtered cell by gene counts matrices (spatial RNA) and fragments files (spatial ATAC) for use in downstream analyses.

source_name: mouse brain

extract_protocol:
Tissue sections were isolated from mouse brain or human glioblastoma, imaged, and then used for spatial multi-omics (SPACE-seq).
Spatial multi-ome (paired spatial RNA and spatial ATAC) libraries were constructed using the SPACE-seq protocol and commercially available reagents from 10X Genomics.

value: mouse brain

value: F

value: 8 weeks

tag: disease state

value: healthy brain


title: heart, Young_UA, 6OG

description:
Library name: lib681026
Young_UA_6OG


title: MB_ATAC

library_source: genomic

molecule: genomic DNA


title: H3K27ac_WD_WD

city: tianjin

first: kan

last: li

address: Tianjin Medical University, 22 Qixiangtai Road, Tianjin, China

institute: Tianjin Medical University

data_processing:
Samples were quality controlled using FastQC (version 0.12.1) to remove low-quality reads. The adapters of raw reads were removed using Trim Galore (version 0.6.10). Paired end reads of 150 bp were aligned to the GENCODE Mus musculus reference genome (build GRCm38/mm10) using Bowtie2 (version 2.4.5). The SAM files were converted into BAM files and duplicate reads were removed by Samtools (version 1.13). Mitochondrial genome reads were manually removed.
The genomic region was divided into several 500 bp bins and the reads of each bin were counted as a table using deepTools (version 3.5.4), and R package corrplot (version 0.92) was used for correlation analysis between samples. The BAM files with a correlation greater than 0.8 in the same group were merged through Samtools (version 1.13). Peaks detection was made on the merged BAMs using " -q 5e-2 -f BAMPE" by MACS2 (version 2.2.9.1), and the peaks in the ENCODE mm10 blacklist were filtered out. DeepTools (version 3.5.4) bamCoverage was used to generate Bigwigs with RPGC normalization and presented by Integrative Genomics Viewer (IGV, version 0.12.9) software.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig,narrowPeak
Library strategy: CUT&Tag

source_name: MAECs

extract_protocol:
DNA was purified with VAHTS DNA Clean Beads (N41101, Vazyme, Nanjing, China) for final library construction and high-throughput sequencing on the Illumina NovaSeq platform.
The DNA libraries were sequenced on the illumina Novaseq™ 6000 platform.
CUT&Tag,ATAC-seq

value: MAECs


title: H3K27ac_WD_CD


title: heart, Young_UA, 2OG

description:
Library name: lib681024
Young_UA_2OG


title: ATAC_CD_WD_2

data_processing:
Samples were quality controlled using FastQC (version 0.12.1) to remove low-quality reads. The adapters of raw reads were removed using Trim Galore (version 0.6.10). Paired end reads of 150 bp were aligned to the GENCODE Mus musculus reference genome (build GRCm38/mm10) using Bowtie2 (version 2.4.5). The SAM files were converted into BAM files and duplicate reads were removed by Samtools (version 1.13). Mitochondrial genome reads were manually removed.
The genomic region was divided into several 500 bp bins and the reads of each bin were counted as a table using deepTools (version 3.5.4), and R package corrplot (version 0.92) was used for correlation analysis between samples. The BAM files with a correlation greater than 0.8 in the same group were merged through Samtools (version 1.13). Peaks detection was made on the merged BAMs using " -q 5e-2 -f BAMPE" by MACS2 (version 2.2.9.1), and the peaks in the ENCODE mm10 blacklist were filtered out. DeepTools (version 3.5.4) bamCoverage was used to generate Bigwigs with RPGC normalization and presented by Integrative Genomics Viewer (IGV, version 0.12.9) software.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig,narrowPeak


title: muscle, 16 hours post injection, 1st shot of adenoviral vaccine (Ad(S))

city: Daejeon

first: Jong-Eun

address: 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description:
Library name: M_adeno
10X 3' chemistry

data_processing:
Sequence data were processed with CellRanger (v.6.0.2) to generate count matrices
Assembly: mm10
Supplementary files format and content: CellRanger filtered cellxgene count matrices in h5 format

source_name: muscle

extract_protocol:
To make single cell suspension, freshly collected anterior thigh muscles were chopped with scissors and enzymatically dissociated with collagenase, inguinal lymph nodes were physically dissociated with mesh strainer, and blood cells were RBC-lysed with RBC lysis buffer.
Library was constucted according to the manufacturer's instructions (10X 3' v3)

value: muscle


title: H3K27ac_CD_WD


title: heart, Old, 14NS

description:
Library name: lib687628
Old_14NS


title: H3K27ac_CD_CD


title: ATAC_WD_CD_2


title: heart, Young, 7OG

description:
Library name: lib681020
Young_7OG


title: heart, Young_UA, 12OG

description:
Library name: lib687627
Young_UA_12OG


title: ATAC_CD_CD_2


title: muscle, 16 hours post injeciton, 2nd shot of cross vaccination (Ad(S)-mRNA)

description:
Library name: M_cross
10X 3' chemistry


title: ATAC_WD_WD_1


title: ATAC_CD_CD_1


title: LEC,KrasG12D, scRNAseq

city: Dallas

first: Michael

last: Dellinger

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Centre

description: 10X Genomics

data_processing:
Demultiplexing was performed using bcl2fastq v2.20.0 (Illumina). Barcode processing, Gene counting and aggregation were performed using cellranger v7.0.0 (10x Genomics). (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: Lymphatic endothelial cells

extract_protocol:
The lungs were perfused with Heparin/DPBS pH 7.2 solution to remove red blood cells. The lobes of the lung were isolated and cut into pieces with a scalpel before placing them into milteny C-tubes (Miltenyi Biotec; catalog # 130-093-237) containing 5 ml of the lung dissociation cocktail (Miltenyi Biotec; catalog # 130-095-927). The C-tubes containing the tissue/enzyme mix were then placed into the sleeve of the gentleMACS dissociator and the m_lung_01 program was run once to dissociate the cells. The C-tubes were then placed in a 37°C incubator under continuous agitation for 45 minutes. Following incubation, the C-tubes containing the tissue/enzyme mix were placed into the gentleMACS dissociator and the m_lung_02 program was run to dissociate the cells. The C-tubes were then centrifuged at 300xg to collect the sample at the bottom of the tube. The sample was resuspended with 1x Buffer S and applied to a prewet 100 µm cell strainer in a 50 ml conical tube. This process was repeated with a 70 µm and 40 µm cell strainer to ensure that all cells were in a single cell suspension. The cell suspension was transferred to a 15 ml conical tube and centrifuged at 300xg to collect a pellet. The pellet was resuspended in 3% FBS in 1XDPBS for subsequent FACS sorting and live GFP positive lymphatic endothelial cells were submited to the genomics core for sequencing.
The 10x Genomics Chromium Next GEM Single Cell Reagent Kits v3.1 (Dual Index) was used according to the manufacturer's protocol (Chromium Next GEM Single Cell 3’ Kit v3.1, 4 rxns PN-1000269). The 10X Genomics Chromium iX Single Cell Analysis System which utilizes the NEXT GEM technology was used for partitioning and barcoding cells. The Eppendorf Mastercycler X50S was used for PCR amplification for 12 PCR cycles. libraries were sequenced on the illumina NovaSeq6000 sequencer with S4 200 cycle flow cell PE-100.

value: Lymphatic endothelial cells

tag: cell purification_method

value: FACS sorting

value: pooled male and female

value: 3 Weeks old

tag: chemistry

value: Single Cell 3' v3


title: PWKM5

city: Bar Harbor

last: MacLean

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
Raw FASTQ files were processed using standard quality control practices. High quality read pairs were aligned to a custom pseudogenome produced by incorporating strain-specific variants (single nucleotide variants and short insertions/deletions derived from Mouse Genomes Project REL-1505) into the mouse reference genome (GRCm38/mm10) using g2gtools version 0.2.7 (https://github.com/churchill-lab/g2gtools). Reads were aligned using STAR version 2.7.10a. Transcript counts were generated using RSEM version 1.3.3.
Differential expression analyses were completed using edgeR v3.40.2 within the R environment v4.2.3 using the glmQLFtest function. filterByExpr within edgeR was used to filter our very lowly expressed genes prior to TMM normalization. Differential expression was analyzed using generalized linear models via edgeR, with either 1) groups defined as a combination of strain, sex, age and a library batch term (~0+Group+Batch) and contrasts designed to test for average strain effect, average age effect within each strain; or 2) age as a continuous variable to control and test for differential expression related to strain differences or determining the impact of aging while controlling for strain and sex differences.
Assembly: mm10
Supplementary files format and content: tab delimited text file of normalized counts (library size and log10)
Supplementary files format and content: tab delimited text of metadata
Supplementary files format and content: tab delimited text of library prep information

extract_protocol:
Total RNA was isolated from retinal tissue aliquots using RNeasy Micro kits (Qiagen), according to the manufacturers’ protocols, including the optional DNase digest step. Tissues were homogenized in RLT buffer (Qiagen) using a Pellet Pestle Motor (Kimbal). RNA concentration and quality were assessed using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and the RNA 6000 Nano and Pico Bioanalyzer Assay (Agilent Technologies)
. Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol. Libraries were assessed using D5000 ScreenTape (Agilent Technologies) and the Qubit dsDNA HS Assay (ThermoFisher) according to the manufacturers’ instructions.

value: Retina

value: PWK

value: Male


title: PWKM4


title: muscle, 16 hours post injection, 2nd shot of adenoviral vaccine (Ad(S)-Ad(S))

description:
Library name: M-Adn
10X 3' chemistry


title: LEC,Control, scRNAseq

description: 10X Genomics


title: PWKM2


title: PWKF5

value: Female


title: PWKM3


title: PWKF4


title: PWKF2


title: BALBF4

value: Balbc/j


title: ATAC_WD_WD_2


title: PWKF1


title: ATAC_CD_WD_1


title: BALBF3


title: BALBF2


title: BALBF1


title: Balb_YM3


title: Balb_YM2


title: Balb_YM1


title: Balb_YF1


title: Balb_YF2


title: B6M2


title: B6M5


title: B6F5


title: B6M3


title: ATAC_WD_CD_1


title: B6F4


title: B6F3


title: B6M4


title: B6F2


title: AJ_M4

value: A/J


title: AJ_M3


title: AJ_M6


title: AJ_M1


title: AJ_F5


title: AJ_F3


title: AJ_F1


title: 3517_B


title: 3517_1R


title: Balb_YF4


title: 3515_B


title: 3515_2L


title: 3515_1R


title: 2976_B


title: Balb_YM4


title: 3515_1L


title: 3517_1L


title: 2972_2R


title: 2972_1R


title: 2972_2L


title: 2969_1L


title: 2969_2R


title: 2944_1L


title: 2943_1L


title: 2976_1L


title: 2943_B


title: 2861_B


title: AJ_F2


title: 2974_1L


title: 3474_1L


title: 2943_1R


title: 2711_1R


title: 2712_1L


title: 2861_1R


title: 2272_1R

value: NZO


title: 2271_2L


title: 2861_2L


title: 2712_B


title: 2861_1L


title: 1855_1R


title: 2711_1L


title: 2271_1L


title: 1855_2R


title: 2271_B


title: 1855_1L


title: 1829_1R

value: NOD


title: 1829_2L


title: 1830_B


title: 1816_2L


title: 1829_B


title: 1816_1L


title: 1712_1L


title: 1712_1R


title: 1711_2L


title: 1708_B


title: 479298

value: WSB


title: 1711_1L


title: 1708_2L


title: 479294


title: 1855_B


title: 479297


title: 460796


title: 460795


title: 460793


title: 89880

value: CAST


title: 460792


title: 89875


title: 89879


title: 76272


title: 89874


title: 76269


title: 70030


title: 76271


title: 76268


title: 70029


title: 70027


title: 70028


title: 61808


title: 61740


title: 61730


title: 61729


title: 61725


title: 61718


title: 61708


title: 61707


title: 61706


title: 61695


title: 61694


title: 61690


title: 61681


title: 61689


title: 61666


title: 61665


title: 61663


title: 61606


title: 61632


title: 61621


title: 61498


title: 61631


title: 61633


title: 61733


title: 61492


title: 61495


title: 61493


title: 61722


title: 61488


title: 61489


title: 61481


title: 61485


title: 61475


title: 61467


title: 61464


title: 61469


title: 61478


title: 61462


title: 61452


title: 61447


title: 61427


title: 61432


title: 61420


title: 60921


title: 60919


title: 60917


title: 59127


title: 59024


title: 57478


title: 57477


title: 61470


title: 57458


title: 57460


title: 57473


title: 57456


title: 57462


title: 57472


title: 57463


title: 57464


title: 57457


title: 57454


title: 57453


title: 61421


title: 57450


title: 57449


title: 57403


title: 56266


title: 56265


title: 56264


title: 56259


title: 57176


title: 60920


title: 56156


title: 53395


title: 56056


title: 57410


title: 56062


title: 53393


title: 53392


title: 53391


title: 53385


title: 53390


title: 53381


title: 53384


title: 53382


title: 53387


title: 53380


title: 53378


title: 53371


title: 53372


title: 53368


title: 53080


title: 53370


title: RGC, PSCL_3mpi, cell27

city: Hong Kong

first: Kai

last: Liu

address: Clear water bay

department: LIFS

institute: HKUST

data_processing:
Raw reads were aligned to the GRCm38 (mm10) mouse reference genome using the “Subread” aligner from the Rsubread package, and gene counts were generated using the featureCounts function.
Assembly: mm10
Supplementary files format and content: Comma-separated values (CSV) file includes raw counts for each sample

source_name: retina

extract_protocol:
The RGC-labeled retina was quickly dissected out from mice after cervical dislocation and incubated with 0.5 mg/ml papain at 37 °C for 30 minutes. The retina was then washed with Neurobasal-A medium and triturated into a single-cell suspension by pipetting. After centrifugation at 300g for 6 minutes at 4 °C, the retinal cells were resuspended in Neurobasal-A medium supplemented with 10% B27.Mouth-pipetting was employed to pick single-labeled RGCs manually. A small volume of the RGC suspensions was transferred through a series of 1% BSA-containing PBS drops until a single targeted RGC was isolated. This RGC was then transferred into 4.2 µl lysis buffer, as per the Smart-seq2 protocol, and stored at -80 °C for subsequent processing.The single-cell RGC lysate underwent further processing according to the Smart-seq2 protocol. RNA was reversely transcribed into cDNA using superscript II and TSO primer and followed by amplification with KAPA HiFi HotStart ReadyMix and ISPCR primer for 27 cycles. The amplified product was purified using Ampure XP beads. A fragment analyzer assessed cDNA quality and Qubit dsDNA High Sensitivity (HS) kit measured cDNA concentration. qPCR measured the relative expression level of the Sncg and Rbpms genes. Samples with low cDNA quality or low expression levels of both genes were excluded from downstream library construction.
Library construction utilized the TruePrep DNA Library Prep Kit V2 for Illumina (vazyme) and TruePrep Index Kit V2 for Illumina, following the manufacturer’s instructions. The constructed library was then sent to Novogene company for sequencing with NovaSeq PE150.

value: retina

value: RGC


title: 53078


title: RGC, PSCL_3mpi, cell28


title: RGC, PSCL_3mpi, cell19


title: 56155


title: 53011


title: RGC, PSCL_3mpi, cell16


title: 53020


title: RGC, PSCL_3mpi, cell22


title: RGC, PSCL_1.5mpi, cell20


title: RGC, PSCL_3mpi, cell23


title: RGC, PSCL_3mpi, cell24


title: RGC, PSCL_3mpi, cell25


title: RGC, PSCL_3mpi, cell18


title: RGC, PSCL_3mpi, cell26


title: RGC, PSCL_1.5mpi, cell19


title: 53079


title: RGC, PSCL_1.5mpi, cell21


title: RGC, PSCL_1.5mpi, cell17


title: RGC, PSCL_3mpi, cell17


title: RGC, PSCL_3mpi, cell20


title: RGC, PSCL_1.5mpi, cell18


title: RGC, PSCL_5dpi, cell25


title: RGC, PSCL_1.5mpi, cell22


title: RGC, PSCL_1.5mpi, cell16


title: RGC, PSCL_5dpi, cell24


title: RGC, PSCL_5dpi, cell23


title: RGC, PSCL_5dpi, cell26


title: 53366


title: RGC, PSCL_3mpi, cell21


title: RGC, PSCL_5dpi, cell20


title: RGC, PSCL_5dpi, cell21


title: RGC, PSCL_5dpi, cell18


title: RGC, PSCL_5dpi, cell19


title: RGC, PSCL_intact, cell30


title: RGC, PSCL_intact, cell27


title: RGC, PSCL_intact, cell21


title: RGC, PSCL_5dpi, cell14


title: RGC, PSCL_intact, cell22


title: RGC, PSCL_intact, cell19


title: RGC, PSCL_intact, cell28


title: RGC, PSCL_intact, cell26


title: RGC, PSCL_intact, cell20


title: RGC, PSCL_intact, cell24


title: RGC, PSCL_intact, cell17


title: RGC, PSCL_intact, cell23


title: RGC, GFP_3mpi, cell22


title: RGC, PSCL_intact, cell18


title: RGC, GFP_3mpi, cell20


title: RGC, GFP_3mpi, cell19


title: RGC, GFP_3mpi, cell18


title: RGC, PSCL_5dpi, cell22


title: RGC, PSCL_5dpi, cell17


title: RGC, PSCL_5dpi, cell16


title: RGC, PSCL_intact, cell29


title: RGC, PSCL_5dpi, cell15


title: RGC, GFP_3mpi, cell17


title: RGC, PSCL_intact, cell25


title: RGC, GFP_3mpi, cell16


title: RGC, GFP_3mpi, cell15


title: RGC, PSCL_intact, cell16


title: RGC, GFP_3mpi, cell11


title: RGC, GFP_3mpi, cell23


title: RGC, GFP_3mpi, cell13


title: RGC, GFP_1.5mpi, cell27


title: RGC, GFP_3mpi, cell10


title: RGC, GFP_1.5mpi, cell26


title: RGC, GFP_1.5mpi, cell25


title: RGC, GFP_1.5mpi, cell24


title: RGC, GFP_3mpi, cell21


title: RGC, GFP_1.5mpi, cell22


title: RGC, GFP_1.5mpi, cell21


title: RGC, GFP_1.5mpi, cell23


title: RGC, GFP_1.5mpi, cell20


title: RGC, GFP_1.5mpi, cell17


title: RGC, GFP_1.5mpi, cell18


title: RGC, GFP_1.5mpi, cell16


title: RGC, GFP_1.5mpi, cell15


title: RGC, GFP_1.5mpi, cell14


title: RGC, GFP_5dpi, cell29


title: RGC, GFP_5dpi, cell30


title: RGC, GFP_5dpi, cell28


title: RGC, GFP_3mpi, cell14


title: RGC, GFP_3mpi, cell12


title: RGC, GFP_5dpi, cell27


title: RGC, GFP_5dpi, cell26


title: RGC, GFP_5dpi, cell25


title: RGC, GFP_5dpi, cell24


title: RGC, GFP_5dpi, cell23


title: RGC, GFP_5dpi, cell22


title: RGC, GFP_1.5mpi, cell19


title: RGC, GFP_5dpi, cell20


title: RGC, GFP_5dpi, cell18


title: RGC, GFP_5dpi, cell16


title: RGC, GFP_intact, cell24


title: RGC, GFP_5dpi, cell21


title: RGC, GFP_intact, cell25


title: RGC, GFP_intact, cell30


title: RGC, GFP_5dpi, cell19


title: RGC, GFP_intact, cell21


title: RGC, GFP_intact, cell23


title: RGC, GFP_intact, cell29


title: RGC, GFP_intact, cell28


title: RGC, GFP_intact, cell26


title: RGC, GFP_intact, cell20


title: RGC, GFP_intact, cell19


title: RGC, GFP_intact, cell18


title: RGC, GFP_intact, cell16


title: RGC, GFP_intact, cell17


title: RGC, PSCL_3mpi, cell15


title: RGC, PSCL_3mpi, cell13


title: RGC, PSCL_3mpi, cell14


title: RGC, PSCL_3mpi, cell11


title: RGC, PSCL_3mpi, cell10


title: RGC, GFP_intact, cell27


title: RGC, PSCL_3mpi, cell9


title: RGC, GFP_5dpi, cell17


title: RGC, PSCL_3mpi, cell8


title: RGC, GFP_intact, cell22


title: RGC, PSCL_3mpi, cell7


title: RGC, PSCL_3mpi, cell4


title: RGC, PSCL_3mpi, cell3


title: RGC, PSCL_3mpi, cell6


title: RGC, PSCL_1.5mpi, cell15


title: RGC, PSCL_1.5mpi, cell14


title: RGC, PSCL_1.5mpi, cell13


title: RGC, PSCL_1.5mpi, cell11


title: RGC, PSCL_3mpi, cell1


title: RGC, PSCL_1.5mpi, cell9


title: RGC, PSCL_1.5mpi, cell10


title: RGC, PSCL_3mpi, cell12


title: RGC, PSCL_1.5mpi, cell6


title: RGC, PSCL_1.5mpi, cell8


title: RGC, PSCL_1.5mpi, cell7


title: RGC, PSCL_1.5mpi, cell5


title: RGC, PSCL_5dpi, cell13


title: RGC, PSCL_1.5mpi, cell4


title: RGC, PSCL_1.5mpi, cell3


title: RGC, PSCL_1.5mpi, cell2


title: RGC, PSCL_1.5mpi, cell1


title: RGC, PSCL_3mpi, cell2


title: RGC, PSCL_5dpi, cell10


title: RGC, PSCL_3mpi, cell5


title: RGC, PSCL_5dpi, cell12


title: RGC, PSCL_5dpi, cell8


title: RGC, PSCL_5dpi, cell9


title: RGC, PSCL_1.5mpi, cell12


title: RGC, PSCL_5dpi, cell6


title: RGC, PSCL_5dpi, cell3


title: RGC, PSCL_5dpi, cell7


title: RGC, PSCL_intact, cell14


title: RGC, PSCL_5dpi, cell4


title: RGC, PSCL_5dpi, cell1


title: RGC, PSCL_intact, cell15


title: RGC, PSCL_intact, cell12


title: THP-6, ATAC-seq

city: Ann Arbor

first: Mark

middle: Yat-fung

last: Chiang

state: MI

address: 109 Zina Pitcher Place

department: Internal Medicine/Heme-onc

institute: University of Michigan

data_processing:
Data processing was performing using Chipseq ATACseq Pipelines 1.0.1 (https://github.com/russell-ryan-lab/ChIPseq_ATACseq_pipelines).
Paired-end reads were aligned to hg38 using BWA-ALN (v 0.7.17).
Bam files were filtered (samtools view) to retain only paired reads in a proper pair (flags: 0x1, 0x2), and to remove reads flagged as secondary alignments, not passing quality control, PCR or optical duplicates, and supplementary alignments (flags: 0x100, 0x200, 0x400, 0x800).
Reads were filtered to retain only read-pairs mapping to <=2 sites genome-wide (X0 tag <=2 for both reads).
Display files were generated with deeptools bamCoverage (options: "--binSize 25 --normalizeUsing CPM --extendReads")
Assembly: hg19
Supplementary files format and content: bigwig (hg19 fragment coverage, normalized to fragments per million post-filtering)

source_name: T-cell acute lymphoblastic leukemia

growth_protocol: T-ALL cell lines were grown in RPMI 1640 (Invitrogen) supplemented with 20% fetal bovine serum (Hyclone or Gibco), 2 mM L-glutamine, 2-mercaptoethanol (0.0005% (v/v), Sigma), penicillin and streptomycin.

extract_protocol: Nuclei were isolated from 50,000 cells for each sample using Nuclei EZ prep-Nuclei Isolation Kit (Sigma-Aldrich, USA). The transposition reaction mix (25μl of 2X TD buffer, 2.5μl of Tn5 transposase (Illumina, San Diego, CA, USA), 15ul of PBS and 7.5μl of nuclease free water) was added to nuclei and incubated at 37°C for 1hour in an orbital shaker at 300RPM. 50uL Qiagen buffer PB was added to each sample to stop the reaction and DNA was isolated with AMPure XP beads (Beckman Coulter). 15 cycles of PCR were performed with transposed DNA using the dual index primers and NEBNext PCR Master Mix, followed by AMPure XP purification.

value: T-cell acute lymphoblastic leukemia


title: LOUCY, ATAC-seq

value: LOUCY


title: RGC, PSCL_intact, cell11


title: RGC, PSCL_intact, cell8


title: RGC, PSCL_5dpi, cell11


title: 8_SMJ_20m_31M_AF_(Clariom_S_Mouse)

city: Philadelphia

first: Emanuel

middle: José

last: Novais

state: PA

address: 1025 Walnut St., Suite 511 College Bldg.

department: Department of Orthopaedic Surgery

institute: Thomas Jefferson

description: Gene expression data from  20-month annulus fibrosis SM/J mouse Exp

hyb_protocol: Gene chips (Mouse Clariom S) were hybridized with fragmented and biotin-labeled cDNA. Arrays were washed and stained with GeneChip hybridization wash & stain kit

scan_protocol: scanned on an Affymetrix Gene Chip Scanner 3000 7G, using Command Console Software.

data_processing: Chp files were generated by sst-rma normalization from Affymetrix cel file using Expression Console Software. Experimental group was compared with control group by using Transcriptome array console 4.0 software. The SST-RMA algorithm was used for data normalization.

source_name: 20M AF SM/J

label_protocol: Fragmented biotin labeled cDNA was synthesized using the GeneChip WT Plus kit according to ABI protocol (Thermo Fisher Scientific).

growth_protocol: DRG and AF tissue were dissected from lumbar discs from BL6 and SM/J mice (n=5-6 per group).

extract_protocol: Pooled tissue from single animal served as an individual sample. Samples were homogenized and total RNA was extracted using RNeasy® Mini kit (Qiagen).

value: Annulus Fibrosus

value: SM/J


title: pathogenic KO Th2 #3

city: Vienna

first: Nicole

last: Boucheron

address: Lazarettgasse 19

institute: Institute of Immunology

data_processing:
Following the raw data acquisition (HiSeq Control Software) and base calling (Real-Time Analysis Software, RTA, v2.7.7) that was performed on-instrument, the subsequent raw data processing involved programs based on Picard tools (https://broadinstitute.github.io/picard/) to generate sample-specific, unaligned BAM files
Sequence reads were subsequently mapped onto the mouse reference genome assembly build mm10 (a flavor of GRCm38) using Spliced Transcripts Alignment to a Reference (STAR) aligner (Dobin et al, 2013) which was run with options recommended by the ENCODE project
Aligned reads that overlapped Ensembl transcript features were counted with the Bioconductor (v3.12) GenomicAlignments (v1.26.0) package.
Differential expression was tested using the Bioconductor DESeq2 package (v1.30.0) (Love et al, 2014).
Assembly: mm10
Supplementary files format and content: tab-delimited text file including Raw counts for each sample
Supplementary files format and content: tab-delimited text file including FPKM values for each sample

source_name: Spleen/peripheral lymph nodes

extract_protocol:
RNA was extracted using the RNAeasy mini plus kit (Qiagen).
RNA-Seq libraries were generated  using a Sciclone NGS Workstation (PerkinElmer) and a Zepyhr NGS Workstation (PerkinElmer) with the TruSeq Stranded mRNA LT sample preparation kit (Illumina). Library concentrations were determined with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA)

value: Spleen/peripheral lymph nodes

value: cultured naive CD4+ T cells

value: KO

value: pathogenic Th2 differentiation


title: 7_SMJ_20m_30F_AF_(Clariom_S_Mouse)


title: RGC, PSCL_5dpi, cell5


title: RGC, PSCL_intact, cell13


title: RGC, PSCL_5dpi, cell2


title: pathogenic KO Th2 #1


title: 5_SMJ_20m_25F_AF_(Clariom_S_Mouse)


title: RGC, PSCL_intact, cell3


title: RGC, PSCL_intact, cell10


title: RGC, PSCL_intact, cell9


title: pathogenic WT Th2 #2

value: WT


title: RGC, GFP_3mpi, cell7


title: RGC, PSCL_intact, cell7


title: 6_SMJ_20m_0M_AF_(Clariom_S_Mouse)


title: RGC, PSCL_intact, cell6


title: 1_B6_20m_0F_AF_(Clariom_S_Mouse)

description: Gene expression data from  20-month annulus fibrosis C57BL/6 mouse Ctr

source_name: 20M AF BL/6


title: pathogenic WT Th2 #1


title: RGC, PSCL_intact, cell4


title: RGC, PSCL_intact, cell5


title: RGC, GFP_3mpi, cell4


title: pathogenic KO Th2 #2


title: KO Th2 #2

value: Th2 differentiation


title: 4_B6_20m_37M_AF_(Clariom_S_Mouse)

source_name: 20M AF BL/9


title: RGC, PSCL_intact, cell2


title: RGC, GFP_3mpi, cell2


title: pTh1_cells, ORAI1KO 3, biorep1

city: Los Angeles

first: Yousang

last: Gwack

state: CA

address: 10833 Le Conte Ave, 53-159 CHS

department: Physiology

institute: Uuniversity of California Los Angeles

description:
Library name: Orai1KO-3-pTh17_S24
Orai1KO-3-pTh17_S24

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software
The reads were mapped by STAR 2.7.8a [1] and read counts per gene were quantified using the mouse Ensembl GRCm39.105 GTF file.
In Partek Flow, read counts were normalized by CPM +1.0E-4.
Assembly: mm10
Supplementary files format and content: tab-delimited files include RAW and CPM normalized counts for each sample

source_name: Lymph nodes, Spleen

growth_protocol: Naive CD4+ T-cells were isolated and purified from either wild-type or ORAI1 KO mice. Naïve CD4+ T cells were enriched by magnetic sorting from single-cell suspensions generated by mechanical disruption of spleens and lymph nodes of adult mice using MagniSort naïve CD4+ T cell enrichment kit (catalog # 8804-6824-74,ThermoFisher Scientific). For effector T cell differentiation, cells were stimulated with anti-CD3 antibody (1452C11, Bio X Cell) and anti-CD28 antibody (Clone 37.51, Bio X Cell) for 48 hours on a plate coated with rabbit anti-hamster antibody (MP Biomedicals). CD4 + CD25 - T cells were cultured with anti-IL-4 antibody (Peprotech) and 10 μg/ml anti-IFN-γ antibody, 30 ng/ml IL-6 (Peprotech), 10 ng/ml IL-23 (R&D Systems) and 10 ng/ml IL-1β (R&D Systems) for pathogenic Th17 differentiation and cultured in T cell medium. For non-pathogenic Th17 cell differentiation,CD4 + CD25 - T cells were cultured with  10 μg/ml anti-IL-4 antibody, 10 μg/ml anti-IFN-γ antibody, 30 ng/ml IL-6 (Peprotech) and 1 ng/ml TGF-β (Peprotech). Cells were taken off the plate on D2 (48h) and  ~3 million control and ORAI1−/− p and np-Th17 cells  harvested in TriZol reagent (Invitrogen) for RNA preparation.

extract_protocol:
~3 million control and ORAI1 CD4cre −/− p and np 17 cells were harvested in TriZol reagent (Invitrogen) for RNA preparation.  3 Biological replicates per genotype were pooled after harvesting and divided into 3 technical replicates per condition. RNA was isolated using RNA purification kit (ThermoFisher Scientific), quantified and used for purification of mRNA, cDNA synthesis and library preparation using  KAPA stranded RNA seq-kit Sample following manufacturer’s instructions.
Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consists of depletion of rRNA by hybridization of complementary DNA oligonucleotides, followed by treatment with RNase H and DNase and RNA fragmentaion. First strand cDNA synthesis using random priming followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporates dUTP into the second cDNA strand. cDNA generation is followed by A-tailing, adaptor ligation and PCR amplification. Different adapters were used for multiplexing samples in one lane. Sequencing was performed on Illumina HiSeq3000 for a SE 1x50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.

treatment_protocol: Wild-type vs ORAi1 Knock-Out _ CD4Cre Genetic System, np vs p-Th17 cells, 48 hours differentiation

value: Lymph nodes, Spleen

value: Female

value: knock-out (ORAI1)

tag: batch


title: RGC, PSCL_intact, cell1


title: RGC, GFP_3mpi, cell1


title: RGC, GFP_3mpi, cell9


title: KO Th2 #1


title: pTh1_cells, ORAI1KO 2, biorep1

description:
Library name: Orai1KO-2-pTh17_S23
Orai1KO-2-pTh17_S23


title: 3_B6_20m_34F_AF_(Clariom_S_Mouse)

source_name: 20M AF BL/8


title: RGC, GFP_3mpi, cell8


title: RGC, GFP_1.5mpi, cell13


title: RGC, GFP_3mpi, cell6


title: WT Th2 #3


title: 2_B6_20m_32F_AF_(Clariom_S_Mouse)

source_name: 20M AF BL/7


title: RGC, GFP_3mpi, cell5


title: WT Th2 #2


title: npTh1_cells, ORAI1KO 3, biorep1

description:
Library name: Orai1KO-3-npTh17_S18
Orai1KO-3-npTh17_S18


title: KO Th2 #3


title: pathogenic WT Th2 #3


title: RGC, GFP_3mpi, cell3


title: npTh1_cells, ORAI1KO 2, biorep1

description:
Library name: Orai1KO-2-npTh17_S17
Orai1KO-2-npTh17_S17


title: WT Th2 #1


title: pTh1_cells, ORAI1KO 1, biorep1

description:
Library name: Orai1KO-1-pTh17_S22
Orai1KO-1-pTh17_S22


title: 24_2470_smj_Emanuel_4-7-21

description: Gene expression data from old dorsal root ganglion SM/J mouse Exp

source_name: Old DRG SM/J

value: Dorsal root ganglion


title: heart, vehicle, Rat_12_1

description:
Library name: lib652481
Rat_12_1

data_processing:
RNA-seq instrument: NovaSeq6000 using S4 flowcells with 2x150bp
Assembly: High quality RNA-seq read pairs were mapped to the Ensembl rat mRatBN7.2
Supplementary files format and content: An in-house RNA-sequencing alignment pipeline that utilizes the STAR aligner version 2.6.1c was applied. For the alignment process, a bespoke index was built using the annotation file, and an expected read length of 151 bps. Read counting was performed on the gene-level, using htseq-count. To inspect the alignment results, MultiQC version 1.8.dev0 was applied.

organism: Rattus norvegicus

extract_protocol:
The protocol was performed according to the manufacture instructions using the kit RNeasy FFPE (Qiagen, 73504). Tissues blocks deriving from the middle region were cut into sections of 20 µM and collected in microtubes. Samples were incubated for 3 minutes at 56°C in a deparaffinization solution (Qiagen, 19093). A step of digestion with Proteinase K was performed followed by a treatment with DNAses. RNA was purified using the RNeasy MinElute column and eluted in 30uL of RNAse free water. Data were grouped into three categories based on experimental conditions: Vehicle (Sham) with 4 samples, MI with 4 samples, and MI+UA with 5 samples. RNA-seq library preparation and Illumina pair-end read sequencing
RNA-seq library preparation and Illumina pair-end read sequencing Library preparation: Strand-specific cDNA library • rRNA depletion • mRNA fragmentation • Random primed cDNA synthesis (strand-specific) • Adapter ligation and adapter specific PCR amplification

value: heart

value: vehicle


title: RGC, GFP_1.5mpi, cell11

value: retina

value: RGC


title: 21_154_smj_Emanuel_4-7-21


title: RGC, GFP_1.5mpi, cell12


title: RGC, GFP_1.5mpi, cell9


title: RGC, GFP_1.5mpi, cell10


title: RGC, GFP_1.5mpi, cell8


title: npTh1_cells, ORAI1KO 1, biorep1

description:
Library name: Orai1KO-1-npTh17_S16
Orai1KO-1-npTh17_S16


title: 22_1523_smj_Emanuel_4-7-21


title: pTh1_cells, Control 3, biorep1

description:
Library name: Control_3_pTh17_S21
Control_3_pTh17_S21

value: Wild-type


title: 20_153_smj_Emanuel_4-7-21


title: heart, surgery, Rat_89

description:
Library name: lib652491
Rat_89

value: surgery


title: 23_7_smj_Emanuel_4-7-21

value: SM/J


title: 17_5_smj_Emanuel_4-7-21

description: Gene expression data from young dorsal root ganglion SM/J mouse Exp

source_name: Young DRG SM/J


title: pTh1_cells, Control 2, biorep1

description:
Library name: Control_2_pTh17_S20
Control_2_pTh17_S20


title: 16_4_smj_Emanuel_4-7-21


title: RGC, GFP_1.5mpi, cell7


title: 15_2_smj_Emanuel_4-7-21


title: pTh1_cells, Control 1, biorep1

description:
Library name: Control_1_pTh17_S19
Control_1_pTh17_S19


title: heart, surgery_UA, Rat_64

description:
Library name: lib652497
Rat_64

value: surgery+UA


title: heart, surgery_UA, Rat_66

description:
Library name: lib652496
Rat_66


title: RGC, GFP_1.5mpi, cell6


title: 18_6_smj_Emanuel_4-7-21


title: heart, surgery, Rat_61

description:
Library name: lib652488
Rat_61


title: 19_152_smj_Emanuel_4-7-21


title: RGC, GFP_1.5mpi, cell5


title: npTh17_cells, Control 3, biorep1

description:
Library name: Control_3_npTh17_S15
Control_3_npTh17_S15


title: heart, surgery_UA, Rat_58

description:
Library name: lib652492
Rat_58


title: 14_3_smj_Emanuel_4-7-21


title: npTh17_cells, Control 2, biorep1

description:
Library name: Control_2_npTh17_S14
Control_2_npTh17_S14


title: heart, surgery, Rat_57

description:
Library name: lib652486
Rat_57


title: RGC, GFP_1.5mpi, cell4


title: heart, vehicle, Rat_38

description:
Library name: lib652484
Rat_38


title: Batch 2, scRNAseq

first: Dongzhao

last: Ma

address: No.58 Zhongshan Second Road

institute: First Affiliated Hospital of Sun Yat-sen University

description: BD Bioscience

data_processing:
Raw files are base called and transformed into .fastq file by Bcl2Fastq.
Assembly: hg38
Supplementary files format and content: Tab seperated-values files and matrix files

source_name: Urine

extract_protocol:
Urine samples were collected in the morning of each patient. Once the samples were obtained, they were immediately transported on ice to the laboratory for processing. 150-200ml urine were collected and divided into 50ml centrifuge tubes for centrifugation (1000 rpm for 5min). The urine sediment was suspended in PBS and treated by ACK lysing buffer (Gibco A1049201) to remove erythrocyte.  After cleaning twice with PBS (1000 rpm for 5min), living cells were enriched with Dead cell removal kit (Miltenyi, 130-091-286) according to the manufacturer’s protocol. Then, after labeling the collected cells, mixed samples were carried out and sequenced using the BD single cell sequencing platform. All steps were performed on ice or at 4 degrees.
Microwell-based scRNA-seq was performed according to the manufacturer’s instruction provided by BD Biosciences.

value: Urine

value: 49–78 years old


title: 13_1_smj_Emanuel_4-7-21


title: RGC, GFP_1.5mpi, cell3


title: npTh17_cells, Control 1, biorep1

description:
Library name: Control_1_npTh17_S13
Control_1_npTh17_S13


title: RGC, GFP_1.5mpi, cell2


title: 10_2471_bl6_Emanuel_4-7-21

description: Gene expression data from old dorsal root ganglion BL/6 mouse Ctr

source_name: Old DRG BL/6


title: heart, surgery, Rat_36

description:
Library name: lib652485
Rat_36

source_name: heart


title: 12_9_bl6_Emanuel_4-7-21


title: heart, vehicle, Rat_32

description:
Library name: lib652483
Rat_32


title: Batch 1, scRNAseq

description: BD Bioscience


title: 11_2132_bl6_Emanuel_4-7-21


title: rat, MII oocyte, single cell sample 9

city: Stockton

first: Yangqi

last: Su

address: 4142 E Morada Ln, Apt 6303

department: Bioinformatics

institute: UNC Charlotte

description: Library name: RU9

data_processing:
Raw sequences were trimmed using Trim_galore (Krueger, 2015), with parameters length > 35 and q > 10, and subsequently mapped to the respective reference genome using STAR v2.7.10b (Dobin et al., 2013) with parameters adapted from nf-core/rnaseq workflow settings: --quantMode TranscriptomeSAM --twopassMode Basic --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend --outSAMstrandField intronMotif.
Quantification of read coverage of nascent transcripts was performed using velocyto ( 0.17.17) (La Manno et al., 2018) under the run-smartseq2 option with default parameters.
STAR aligned mappings  were also quantified via HTSeq (Anders et al., 2015) and a custom GTF file of 1kb intergenic regions to obtain intergenic transcription counts.
The resulting mappings were quantified using Salmon (Patro et al., 2017) with default settings to obtain estimated expression levels for transcripts in transcript per million (TPM) units. Transcript TPM values were then aggregated via tximport package to obtain estimated gene counts.
BEDGRAPH files for 3'UTR regions were obtained via processing GTF annotation files for each organism via custom scripts. Estimated alternative polyadenylation was obtained via a modified version of the DaPars2 package.
Assembly: GRCm39 with assembly GCF_000001635.27 for Mice; mRatBN7.2 with assembly GCF_015227675.2 for Rat
Supplementary files format and content: tab delimited files of transcript TPM and  transcript lengths for each sample estimated by Salmon pseudoaligner .
Supplementary files format and content: tab delimited files of nascent and spliced counts for all samples and genes.
Supplementary files format and content: BigWig files of samtools depth output for all samples
Supplementary files format and content: tab delimited files of DaPars2 estimated long, short UTR coverage, PDUI and UTR region information for samples tested for differential alternative polyadenylation.

source_name: MII oocyte

growth_protocol: Mouse and rat oocytes and zygotes were isolated at Horizon Discovery, St. Louis site, operated under approved animal protocols overseen by Horizon Discovery's Institutional Animal Care and Use Committee (IACUC). C57BL/6N mice and Sprague Dawley rats purchased from Taconic Farms were housed in standard cages and maintained on a 12-h light/dark cycle with ad libitum access to food and water.

extract_protocol:
Full-length double-strand cDNA for each oocyte or zygote was prepared using an sc-RNA-seq libraries SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, Mountain View, CA) following the vendor’s instruction, which was based on the Smartseq2 protocol (Picelli et al., 2013).
cDNA-seq libraries were constructed using a Nextera® XT DNA Library Preparation Kit (Illumina, Sandiago, CA, Cat. Nos. FC-131-1024, FC-131-1096) following the vendor’s instruction. The libraries were quantified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara) and sequenced on an Illumina 2500 machine with 150 bp paired end reads.

treatment_protocol: Three- to four-week-old female mice were injected with PMS (5 IU/mouse) 48 hr before hCG (5 IU/mouse) injection, followed by with or without mating to stud males. Fertilized eggs and oocytes were harvested 1 d later, respectively. Four- to five-week-old female rats were injected with 20 units of PMS, which was followed by an injection of 50 units of hCG 48 h later, followed by with or without mating to stud males. Fertilized eggs and oocytes of both species were harvested 1 d later.

value: MII oocyte


title: heart, surgery_UA, Rat_29

description:
Library name: lib652495
Rat_29


title: RGC, GFP_5dpi, cell15


title: RGC, GFP_1.5mpi, cell1


title: rat, MII oocyte, single cell sample 8

description: Library name: RU8


title: 08_2467_bl6_Emanuel_4-7-21


title: RGC, GFP_5dpi, cell14


title: RGC, GFP_5dpi, cell13


title: rat, MII oocyte, single cell sample 6

description: Library name: RU6


title: rat, MII oocyte, single cell sample 7

description: Library name: RU7


title: 35_AXL 3

city: STANFORD

first: James

last: Brooks

address: 300 PASTEUR DR

institute: STANFORD UNIVERSITY

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Supplementary files format and content: Tab-delimited excel file

source_name: LuCaP 35

growth_protocol: Different Prostate cancer PDXs are implanted into the RAG2-/- mice through the intratibial injection  methods, then treated by different componds.The tumors were harvested for the RNAseq.

extract_protocol:
Total RNA was isolated from fresh frozen mouse tibial PDX tumor tissues using an Allprep DNA/RNA mini kit (Qiagen).
After RNA fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: LuCaP 35

value: Tumor Tissue

value: batiraxcept

tag: time

value: 30 days


title: 35_Vehicle 4


title: 07_2466_bl6_Emanuel_4-7-21


title: RGC, GFP_5dpi, cell12


title: rat, MII oocyte, single cell sample 5

description: Library name: RU5


title: 35_Vehicle 3


title: RGC, GFP_5dpi, cell11


title: RGC, GFP_5dpi, cell10


title: rat, MII oocyte, single cell sample 4

description: Library name: RU4


title: 35_AXL 2


title: 09_2468_bl6_Emanuel_4-7-21


title: rat, MII oocyte, single cell sample 3

description: Library name: RU3


title: RGC, GFP_5dpi, cell9


title: 04_17_bl6_Emanuel_4-7-21

description: Gene expression data from young dorsal root ganglion BL/6 mouse Ctr

source_name: Young DRG BL/6


title: 35_Vehicle 2


title: 03_16_bl6_Emanuel_4-7-21


title: 06_101_bl6_Emanuel_4-7-21


title: rat, MII oocyte, single cell sample 2

description: Library name: RU2