title: 30C-1d-Naive-rep6

description:
Library name: 10500-LM-0131
Paired-end 150bp, targeting 50M reads per sample


title: 27C-5d-Naive-rep5

status: Public on Jul 01 2025

type: SRA

city: Nashville

first: Julian

middle: F

last: Hillyer

state: TN

address: VU Station B, 35-1634

department: Department of Biological Sciences

country: USA

institute: Vanderbilt University

description:
Library name: 10500-LM-0101
Paired-end 150bp, targeting 50M reads per sample

library_source: transcriptomic

data_processing:
RNA sequencing reads were adapter-trimmed and quality-filtered using Trimgalore v0.6.7.
An alignment reference was generated from the AgamP4.14 A. gambiae genome (VectorBase-66_AgambiaePEST_Genome.fasta) and gene annotations (VectorBase-66_AgambiaePEST.gff), to which trimmed reads were aligned and counted using Spliced Transcripts Alignment to a Reference (STAR) v2.7.9a with the –quantMode GeneCounts parameter.
About 20 million uniquely mapped reads were sequenced per sample. DESeq2 package v1.36.0 was used to perform sample-level quality control, low count filtering, normalization, and downstream differential gene expression analysis.
Of the 120 samples, 115 were used in downstream analyses. Five samples were removed from downstream analyses because PCA clustering analysis deemed that four samples were mislabeled (immune treatment was swapped in samples 127 and 128, and 135 and 136), and one sample was a statistical outlier by Cook’s distance (sample 38).
Assembly: AgamP4.14 VectorBase-66_AgambiaePEST_Genome.fasta
Supplementary files format and content: tab-delimited text file containing raw counts for each sample
Supplementary files format and content: tab-delimited text file containing normalized counts for each sample

molecule: polyA RNA

organism: Anopheles gambiae

source_name: whole body

growth_protocol:
A colony of Anopheles gambiae mosquitoes (Giles sensu stricto, G3 strain; Diptera: Culicidae) was maintained at the standard rearing temperature of 27°C, 75% relative humidity, and a 12h:12h light:dark photoperiod.
Eggs produced by the 27°C colony were hatched and reared to adulthood at 27°C, 30°C or 32°C in environmental chambers maintained under the same humidity and light conditions defined above. Larvae were fed koi food mixed with baker’s yeast. Pupae were separated daily, and adults were fed 10% sucrose ad libitum.

extract_protocol:
RNA was extracted using TRIzol per manufacturer’s instructions. RNA was then resuspended in Buffer RLT (Qiagen) containing 1% 2-mercaptoethanol (Fisher Scientific), and re-purified using the RNeasy Mini Kit (Qiagen). The re-purification included DNase treatment in the column, and elution in RNase-free water.
Library preparation for sequencing was completed using the stranded mRNA NEBNext Poly(A) mRNA library preparation kit (New England BioLabs) with an input of 300 ng of total RNA.

treatment_protocol:
At each temperature, adult females that were 1, 5, 10, and 15 days post-eclosion were divided into two immune treatment groups: (i) naïve and (ii) immune induced with heat-killed bacteria.
Naïve mosquitoes were left unmanipulated. Immune induced mosquitoes were intrathoracically injected at the thoracic anepisternal cleft with 69 nL of heat-killed, DH5α Escherichia coli modified to express GFP and tetracycline-resistance (OD600 = 2, or ~9,300 colony forming units).

tag: tissue

value: whole body

tag: strain

value: G3 strain

tag: temperature

tag: age

tag: treatment

value: Naive

tag: replicate


title: 32C-15d-Naive-rep5

description:
Library name: 10500-LM-0099
Paired-end 150bp, targeting 50M reads per sample


title: 32C-15d-HKEC-rep5

description:
Library name: 10500-LM-0100
Paired-end 150bp, targeting 50M reads per sample

value: Heat killed E. coli


title: 30C-10d-Naive-rep5

description:
Library name: 10500-LM-0103
Paired-end 150bp, targeting 50M reads per sample


title: 27C-5d-HKEC-rep5

description:
Library name: 10500-LM-0102
Paired-end 150bp, targeting 50M reads per sample


title: 27C-1d-Naive-rep5

description:
Library name: 10500-LM-0097
Paired-end 150bp, targeting 50M reads per sample


title: 30C-5d-HKEC-rep5

description:
Library name: 10500-LM-0096
Paired-end 150bp, targeting 50M reads per sample


title: 30C-5d-Naive-rep5

description:
Library name: 10500-LM-0095
Paired-end 150bp, targeting 50M reads per sample


title: 32C-5d-HKEC-rep4

description:
Library name: 10500-LM-0094
Paired-end 150bp, targeting 50M reads per sample


title: 32C-5d-HKEC-rep5

description:
Library name: 10500-LM-0116
Paired-end 150bp, targeting 50M reads per sample


title: 27C-1d-HKEC-rep5

description:
Library name: 10500-LM-0098
Paired-end 150bp, targeting 50M reads per sample


title: 27C-10d-HKEC-rep5

description:
Library name: 10500-LM-0114
Paired-end 150bp, targeting 50M reads per sample


title: 32C-10d-HKEC-rep4

description:
Library name: 10500-LM-0092
Paired-end 150bp, targeting 50M reads per sample


title: 27C-15d-HKEC-rep5

description:
Library name: 10500-LM-0110
Paired-end 150bp, targeting 50M reads per sample


title: 27C-15d-Naive-rep4

description:
Library name: 10500-LM-0089
Paired-end 150bp, targeting 50M reads per sample


title: 30C-15d-HKEC-rep5

description:
Library name: 10500-LM-0108
Paired-end 150bp, targeting 50M reads per sample


title: 27C-1d-HKEC-rep4

description:
Library name: 10500-LM-0088
Paired-end 150bp, targeting 50M reads per sample


title: 32C-10d-Naive-rep4

description:
Library name: 10500-LM-0091
Paired-end 150bp, targeting 50M reads per sample


title: 27C-1d-Naive-rep4

description:
Library name: 10500-LM-0087
Paired-end 150bp, targeting 50M reads per sample


title: 32C-1d-HKEC-rep5

description:
Library name: 10500-LM-0106
Paired-end 150bp, targeting 50M reads per sample


title: 27C-15d-HKEC-rep4

description:
Library name: 10500-LM-0090
Paired-end 150bp, targeting 50M reads per sample


title: 30C-15d-Naive-rep5

description:
Library name: 10500-LM-0107
Paired-end 150bp, targeting 50M reads per sample


title: 30C-10d-HKEC-rep4

description:
Library name: 10500-LM-0084
Paired-end 150bp, targeting 50M reads per sample


title: 32C-15d-HKEC-rep4

description:
Library name: 10500-LM-0086
Paired-end 150bp, targeting 50M reads per sample


title: 32C-1d-HKEC-rep4

description:
Library name: 10500-LM-0082
Paired-end 150bp, targeting 50M reads per sample


title: 32C-1d-Naive-rep4

description:
Library name: 10500-LM-0081
Paired-end 150bp, targeting 50M reads per sample


title: 32C-5d-Naive-rep4

description:
Library name: 10500-LM-0093
Paired-end 150bp, targeting 50M reads per sample


title: 27C-10d-Naive-rep4

description:
Library name: 10500-LM-0075
Paired-end 150bp, targeting 50M reads per sample


title: 30C-15d-HKEC-rep4

description:
Library name: 10500-LM-0078
Paired-end 150bp, targeting 50M reads per sample


title: 27C-10d-HKEC-rep4

description:
Library name: 10500-LM-0076
Paired-end 150bp, targeting 50M reads per sample


title: 30C-15d-Naive-rep4

description:
Library name: 10500-LM-0077
Paired-end 150bp, targeting 50M reads per sample


title: 27C-5d-Naive-rep4

description:
Library name: 10500-LM-0079
Paired-end 150bp, targeting 50M reads per sample


title: 30C-1d-HKEC-rep4

description:
Library name: 10500-LM-0074
Paired-end 150bp, targeting 50M reads per sample


title: 30C-1d-Naive-rep4

description:
Library name: 10500-LM-0073
Paired-end 150bp, targeting 50M reads per sample


title: 32C-5d-HKEC-rep3

description:
Library name: 10500-LM-0072
Paired-end 150bp, targeting 50M reads per sample


title: 32C-5d-Naive-rep3

description:
Library name: 10500-LM-0071
Paired-end 150bp, targeting 50M reads per sample


title: 27C-15d-Naive-rep3

description:
Library name: 10500-LM-0069
Paired-end 150bp, targeting 50M reads per sample


title: 30C-10d-HKEC-rep3

description:
Library name: 10500-LM-0068
Paired-end 150bp, targeting 50M reads per sample


title: 32C-15d-Naive-rep4

description:
Library name: 10500-LM-0085
Paired-end 150bp, targeting 50M reads per sample


title: 30C-10d-Naive-rep4

description:
Library name: 10500-LM-0083
Paired-end 150bp, targeting 50M reads per sample


title: 27C-5d-Naive-rep3

description:
Library name: 10500-LM-0063
Paired-end 150bp, targeting 50M reads per sample


title: 27C-5d-HKEC-rep3

description:
Library name: 10500-LM-0064
Paired-end 150bp, targeting 50M reads per sample


title: 30C-15d-Naive-rep3

description:
Library name: 10500-LM-0065
Paired-end 150bp, targeting 50M reads per sample


title: 27C-15d-HKEC-rep3

description:
Library name: 10500-LM-0070
Paired-end 150bp, targeting 50M reads per sample


title: 32C-1d-Naive-rep3

description:
Library name: 10500-LM-0061
Paired-end 150bp, targeting 50M reads per sample


title: 30C-15d-HKEC-rep3

description:
Library name: 10500-LM-0066
Paired-end 150bp, targeting 50M reads per sample


title: 30C-10d-Naive-rep3

description:
Library name: 10500-LM-0067
Paired-end 150bp, targeting 50M reads per sample


title: 27C-1d-HKEC-rep3

description:
Library name: 10500-LM-0058
Paired-end 150bp, targeting 50M reads per sample


title: 32C-10d-HKEC-rep3

description:
Library name: 10500-LM-0060
Paired-end 150bp, targeting 50M reads per sample


title: 32C-1d-HKEC-rep3

description:
Library name: 10500-LM-0062
Paired-end 150bp, targeting 50M reads per sample


title: 27C-5d-HKEC-rep4

description:
Library name: 10500-LM-0080
Paired-end 150bp, targeting 50M reads per sample


title: 27C-1d-Naive-rep3

description:
Library name: 10500-LM-0057
Paired-end 150bp, targeting 50M reads per sample


title: 32C-10d-Naive-rep3

description:
Library name: 10500-LM-0059
Paired-end 150bp, targeting 50M reads per sample


title: 32C-15d-HKEC-rep3

description:
Library name: 10500-LM-0054
Paired-end 150bp, targeting 50M reads per sample


title: 30C-5d-Naive-rep3

description:
Library name: 10500-LM-0055
Paired-end 150bp, targeting 50M reads per sample


title: 32C-15d-Naive-rep3

description:
Library name: 10500-LM-0053
Paired-end 150bp, targeting 50M reads per sample


title: 30C-1d-HKEC-rep3

description:
Library name: 10500-LM-0052
Paired-end 150bp, targeting 50M reads per sample


title: 27C-10d-HKEC-rep3

description:
Library name: 10500-LM-0050
Paired-end 150bp, targeting 50M reads per sample


title: 27C-10d-Naive-rep3

description:
Library name: 10500-LM-0049
Paired-end 150bp, targeting 50M reads per sample


title: 30C-1d-Naive-rep3

description:
Library name: 10500-LM-0051
Paired-end 150bp, targeting 50M reads per sample


title: 30C-15d-HKEC-rep1

description:
Library name: 10500-LM-0048
Paired-end 150bp, targeting 50M reads per sample


title: 30C-15d-Naive-rep1

description:
Library name: 10500-LM-0047
Paired-end 150bp, targeting 50M reads per sample


title: 30C-1d-HKEC-rep2

description:
Library name: 10500-LM-0046
Paired-end 150bp, targeting 50M reads per sample


title: 30C-1d-Naive-rep2

description:
Library name: 10500-LM-0045
Paired-end 150bp, targeting 50M reads per sample


title: 32C-10d-Naive-rep2

description:
Library name: 10500-LM-0037
Paired-end 150bp, targeting 50M reads per sample


title: 32C-15d-HKEC-rep2

description:
Library name: 10500-LM-0040
Paired-end 150bp, targeting 50M reads per sample


title: 30C-15d-HKEC-rep2

description:
Library name: 10500-LM-0042
Paired-end 150bp, targeting 50M reads per sample


title: 32C-10d-HKEC-rep2

description:
Library name: 10500-LM-0038
Paired-end 150bp, targeting 50M reads per sample


title: 30C-5d-HKEC-rep3

description:
Library name: 10500-LM-0056
Paired-end 150bp, targeting 50M reads per sample


title: 32C-15d-Naive-rep2

description:
Library name: 10500-LM-0039
Paired-end 150bp, targeting 50M reads per sample


title: 30C-5d-HKEC-rep2

description:
Library name: 10500-LM-0044
Paired-end 150bp, targeting 50M reads per sample


title: 32C-5d-Naive-rep2

description:
Library name: 10500-LM-0035
Paired-end 150bp, targeting 50M reads per sample


title: 30C-15d-Naive-rep2

description:
Library name: 10500-LM-0041
Paired-end 150bp, targeting 50M reads per sample


title: 27C-1d-Naive-rep2

description:
Library name: 10500-LM-0033
Paired-end 150bp, targeting 50M reads per sample


title: 27C-1d-HKEC-rep2

description:
Library name: 10500-LM-0034
Paired-end 150bp, targeting 50M reads per sample


title: 27C-10d-HKEC-rep2

description:
Library name: 10500-LM-0032
Paired-end 150bp, targeting 50M reads per sample


title: 32C-5d-HKEC-rep2

description:
Library name: 10500-LM-0036
Paired-end 150bp, targeting 50M reads per sample


title: 32C-15d-HKEC-rep1

description:
Library name: 10500-LM-0030
Paired-end 150bp, targeting 50M reads per sample


title: 27C-10d-Naive-rep2

description:
Library name: 10500-LM-0031
Paired-end 150bp, targeting 50M reads per sample


title: 32C-15d-Naive-rep1

description:
Library name: 10500-LM-0029
Paired-end 150bp, targeting 50M reads per sample


title: 32C-1d-HKEC-Rep2

description:
Library name: 10500-LM-0028
Paired-end 150bp, targeting 50M reads per sample


title: 30C-10d-HKEC-Rep2

description:
Library name: 10500-LM-0026
Paired-end 150bp, targeting 50M reads per sample


title: 32C-1d-Naive-Rep2

description:
Library name: 10500-LM-0027
Paired-end 150bp, targeting 50M reads per sample


title: 30C-10d-Naive-Rep2

description:
Library name: 10500-LM-0025
Paired-end 150bp, targeting 50M reads per sample


title: 27C-15d-HKEC-Rep2

description:
Library name: 10500-LM-0024
Paired-end 150bp, targeting 50M reads per sample


title: 27C-5d-HKEC-Rep2

description:
Library name: 10500-LM-0022
Paired-end 150bp, targeting 50M reads per sample


title: 27C-5d-Naive-Rep2

description:
Library name: 10500-LM-0021
Paired-end 150bp, targeting 50M reads per sample


title: 27C-15d-Naive-Rep2

description:
Library name: 10500-LM-0023
Paired-end 150bp, targeting 50M reads per sample


title: 30C-5d-Naive-rep2

description:
Library name: 10500-LM-0043
Paired-end 150bp, targeting 50M reads per sample


title: Hs294T, MZB1 KO 1

type: RNA

city: Madison

first: Nihal

last: Ahmad

state: Wisconsin

address: WIMR II, 1111 Highland Ave

department: Dermatology

institute: University of Wisconsin

hyb_protocol: According to NanoString nCounter user manual

data_processing:
nSolver software with an advanced analysis module (NanoString Technologies, Seattle, WA) was used for the QC, normalization, differential gene expression, and functional pathways score analyses in accordance with guidance provided by Nanostring. Principle component analysis (PCA) was performed to assess sample grouping.
The expression levels of each gene were normalized to housekeeping genes. Fold changes greater than 1.5-fold upregulation or downregulation with p-values <0.05 between the two groups were considered significant.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MZB1 CRISP KO Hs294T human melanoma cells

extract_protocol: RNA was extracted from from control and MZB1 KO melanoma cells, followed by determination of expression of 785 genes (including 12 internal reference genes) via the NanoString Immune Profiling Panel using the nCounter platform at the TRIP lab UW-Madison.

treatment_protocol: CRISPR/Cas9 mediated MZB1 knockout (KO) melanoma lines were generated by the Genome editing services of the Biotechnology Center at the University of Wisconsin-Madison.

tag: cancer type

value: Melanoma


title: Hs294T, Control 4

scan_protocol: According to NanoString nCounter user manual

source_name: Hs294T human melanoma cells


title: Hs294T, MZB1 KO 3

label_protocol: According to NanoString nCounter user manual


title: DSP-1001660013119-E-H10

city: Ann Arbor

first: Mohamed

last: Noureldein

address: 109 Zina Pitcher Place

department: Neurology

institute: University of Michigan

data_processing:
Fastq files were converted to DCC files using the GeoMx NGS Pipeline software and the mm10 reference genome.
Digital Count Conversion files, containing expression count data and sequencing quality metadata, and Probe Kit Configuration files, containing probe assay and sample metadata, were imported into R. Gene expression counts with a value of 0 were shifted to 1 to facilitate downstream transformations. ROI segments were filtered and removed if they met the criteria: “<1000 raw reads”, “below 80% Aligned or 80% Trimmed”, “80% Stitched”, and “below 50% sequencing saturation”. Genes were filtered and removed if they were not detected in at least 10% of segments. Next, counts were normalized using quartile 3 normalization and visualized by uniform manifold approximation and projection, a non-linear dimensionality reduction visualization tool. Gene expression in both datasets was relatively well separated according to ROI brain region.
Assembly: mm10
Supplementary files format and content: Early_stage_count_table.csv. A count table containing normalized counts for probes and segments that passed the quality control steps mentioned in the data processing step.
Library strategy: Spatial transcriptomics

organism: Mus musculus

source_name: Brain

growth_protocol: Two slides were for early-stage analysis and were duplicates of 4 brain sections (n=2 5XFAD 12 wk, n=2 controls 12 wk)

extract_protocol:
One brain hemisphere was fixed in 4% paraformaldehyde (PFA) for 24 h, cryoprotected in escalating sucrose gradients, embedded, and cryosectioned in coronal plane sections onto histologic slides [10 μm thickness for spatial transcriptomics sections, 14 μm thickness for subsequent fluorescent in situ hybridization (FISH)] and stored at –80 °C.
Spatial transcriptomics was performed by GeoMx DSP (NanoString, Seattle, WA), a platform for spatially analyzing gene expression in tissue in a highly multiplexed manner
Other: Spatial transcriptomics-Nanostring GeoMx DSP

value: Brain

tag: genotype

value: WT


title: DSP-1001660013119-E-H06


title: DSP-1001660013119-E-H09


title: DSP-1001660013119-E-H08


title: DSP-1001660013119-E-H12


title: Hs294T, MZB1 KO 2


title: DSP-1001660013119-E-H07


title: DSP-1001660013119-E-H11


title: Hs294T, Control 3


title: DSP-1001660013119-E-H03


title: DSP-1001660013119-E-H05


title: DSP-1001660013119-E-H02


title: DSP-1001660013119-E-H01


title: DSP-1001660013119-E-H04


title: Hs294T, Control 2


title: DSP-1001660013119-E-G09


title: DSP-1001660013119-E-G12


title: DSP-1001660013119-E-G11


title: Hs294T, Control 1


title: DSP-1001660013119-E-G10


title: DSP-1001660013119-E-G08


title: DSP-1001660013119-E-G05


title: DSP-1001660013119-E-G06


title: DSP-1001660013119-E-G03


title: DSP-1001660013119-E-G04


title: DSP-1001660013119-E-G02


title: DSP-1001660013119-E-F12


title: DSP-1001660013119-E-G01


title: DSP-1001660013119-E-F10


title: DSP-1001660013119-E-F09


title: DSP-1001660013119-E-F08


title: DSP-1001660013119-E-F06


title: DSP-1001660013119-E-F01


title: DSP-1001660013119-E-F03


title: DSP-1001660013119-E-E12


title: DSP-1001660013119-E-F07


title: DSP-1001660013119-E-F02


title: DSP-1001660013119-E-E11


title: DSP-1001660013119-E-F05


title: DSP-1001660013119-E-E09


title: DSP-1001660013119-E-F04


title: DSP-1001660013119-E-E10


title: DSP-1001660013119-E-E08


title: DSP-1001660013119-E-E06


title: DSP-1001660013119-E-F11


title: DSP-1001660013119-E-E04


title: DSP-1001660013119-E-E05


title: DSP-1001660013119-E-G07


title: DSP-1001660013119-E-E03


title: DSP-1001660013119-E-E02


title: DSP-1001660013119-E-E01


title: DSP-1001660013119-E-D12


title: DSP-1001660013119-E-D11


title: DSP-1001660013119-E-D10


title: DSP-1001660013119-E-D09


title: DSP-1001660013119-E-D06


title: DSP-1001660013119-E-D08


title: DSP-1001660013119-E-D07


title: DSP-1001660013119-E-D04


title: DSP-1001660013119-E-D02


title: DSP-1001660013119-E-D03


title: DSP-1001660013119-E-C09


title: DSP-1001660013119-E-C11


title: DSP-1001660013119-E-D01


title: DSP-1001660013119-E-C10


title: DSP-1001660013119-E-C01


title: DSP-1001660013119-E-C12


title: DSP-1001660013119-E-C02


title: DSP-1001660013119-E-C07


title: DSP-1001660013119-E-B12


title: DSP-1001660013119-E-C08


title: DSP-1001660013119-E-C04


title: DSP-1001660013119-E-D05


title: DSP-1001660013119-E-C05


title: DSP-1001660013119-E-B11


title: DSP-1001660013119-E-B09

value: AD


title: DSP-1001660013119-E-B10


title: DSP-1001660013119-E-B08


title: DSP-1001660013119-E-B07


title: DSP-1001660013119-E-B06


title: DSP-1001660013119-E-B04


title: DSP-1001660013119-E-B03


title: DSP-1001660013119-E-C06


title: DSP-1001660013119-E-B02


title: DSP-1001660013119-E-B01


title: DSP-1001660013119-E-C03


title: DSP-1001660013119-E-A12


title: DSP-1001660013119-E-A10


title: DSP-1001660013119-E-A11


title: DSP-1001660013119-E-A08


title: DSP-1001660013119-E-A09


title: DSP-1001660013119-E-A05


title: DSP-1001660013119-E-A06


title: DSP-1001660013119-E-A02


title: DSP-1001660013119-E-A01


title: DSP-1001660013119-E-A04


title: DSP-1001660013119-E-A03


title: DSP-1001660013109-D-H11


title: DSP-1001660013109-D-H12

value: No Template Control


title: DSP-1001660013109-D-H10


title: DSP-1001660013109-D-H06


title: DSP-1001660013109-D-H03


title: DSP-1001660013109-D-H02


title: DSP-1001660013109-D-G12


title: DSP-1001660013109-D-G10


title: DSP-1001660013109-D-H01


title: DSP-1001660013119-E-B05


title: DSP-1001660013109-D-G09


title: DSP-1001660013109-D-G11


title: DSP-1001660013109-D-G08


title: DSP-1001660013109-D-G05


title: DSP-1001660013109-D-G06


title: DSP-1001660013119-E-A07


title: DSP-1001660013109-D-H09


title: DSP-1001660013109-D-G04


title: DSP-1001660013109-D-H07


title: DSP-1001660013109-D-H08


title: DSP-1001660013109-D-G03


title: DSP-1001660013109-D-G07


title: DSP-1001660013109-D-H05


title: DSP-1001660013109-D-F10


title: DSP-1001660013109-D-G02


title: DSP-1001660013109-D-F07


title: DSP-1001660013109-D-F09


title: DSP-1001660013109-D-G01


title: DSP-1001660013109-D-F12


title: DSP-1001660013109-D-F08


title: DSP-1001660013109-D-F11


title: DSP-1001660013109-D-H04


title: DSP-1001660013109-D-F06


title: DSP-1001660013109-D-F04


title: DSP-1001660013109-D-F05


title: DSP-1001660013109-D-F02


title: DSP-1001660013109-D-E11


title: DSP-1001660013109-D-E10


title: DSP-1001660013109-D-F03


title: DSP-1001660013109-D-E09


title: DSP-1001660013109-D-E07


title: DSP-1001660013109-D-E06


title: DSP-1001660013109-D-E08


title: DSP-1001660013109-D-E05


title: DSP-1001660013109-D-E04


title: DSP-1001660013109-D-E02


title: DSP-1001660013109-D-E03


title: DSP-1001660013109-D-D12


title: DSP-1001660013109-D-D11


title: DSP-1001660013109-D-E01


title: DSP-1001660013109-D-D10


title: DSP-1001660013109-D-D09


title: DSP-1001660013109-D-D07


title: DSP-1001660013109-D-D06


title: DSP-1001660013109-D-D08


title: DSP-1001660013109-D-D05


title: DSP-1001660013109-D-F01


title: DSP-1001660013109-D-D04


title: DSP-1001660013109-D-D02


title: DSP-1001660013109-D-E12


title: DSP-1001660013109-D-D03


title: DSP-1001660013109-D-C08


title: DSP-1001660013109-D-C07


title: DSP-1001660013109-D-C03


title: DSP-1001660013109-D-C05


title: DSP-1001660013109-D-C12


title: DSP-1001660013109-D-C04


title: DSP-1001660013109-D-C11


title: DSP-1001660013109-D-B11


title: DSP-1001660013109-D-C09


title: DSP-1001660013109-D-B12


title: DSP-1001660013109-D-B10


title: DSP-1001660013109-D-B09


title: DSP-1001660013109-D-C06


title: DSP-1001660013109-D-C01


title: DSP-1001660013109-D-B04


title: DSP-1001660013109-D-C02


title: DSP-1001660013109-D-B03


title: DSP-1001660013109-D-B08


title: DSP-1001660013109-D-B07


title: DSP-1001660013109-D-B01


title: DSP-1001660013109-D-C10


title: DSP-1001660013109-D-B05


title: DSP-1001660013109-D-D01


title: DSP-1001660013109-D-A11


title: DSP-1001660013109-D-A12


title: DSP-1001660013109-D-B02


title: DSP-1001660013109-D-A10


title: DSP-1001660013109-D-A09


title: DSP-1001660013109-D-A07


title: DSP-1001660013109-D-A06


title: DSP-1001660013109-D-A05


title: DSP-1001660013109-D-A04


title: DSP-1001660013109-D-A08


title: DSP-1001660013109-D-B06


title: DSP-1001660013108-C-H11


title: DSP-1001660013108-C-H12


title: DSP-1001660013109-D-A01


title: DSP-1001660013109-D-A03


title: ATAC_Ca_D7_Smarca5_480

city: Beijing

first: Jing

last: Han

address: qinghuayuan

country: China

institute: Tsinghua university

library_source: genomic

data_processing:
The adaptors of paired-end reads were trimmed by trim-galore (v.0.6.4) with the parameters set as: -q 25 --phred33 --length 50 -e 0.1 --fastqc --stringency 5 --paired.
Trimmed reads were aligned to the mm10 genome with the following parameters: --very-sensitive -k 10 by Bowtie2 (v.2.3.5.1)
Aligned reads stored in SAM format were manipulated to generate BAM files and PCR duplicates were removed using SAMtools (v.1.10)
ATAC-seq peaks were called by Genrich (v.0.6) using the parameters: -j -y -r -e chrM -v.
All peaks from all samples were merged and raw counts of merged peaks in each sample were counted by featureCounts (v.2.0.1). Size factor for each sample were calculated using DESeq2 (v.1.24.0). Normalized bigwig files were generated with 1/(size factor) using bamCoverage from deepTools (v.3.4.3).
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: pancreas

extract_protocol:
10,000 GFP-positive cells were sorted by FACS for ATAC-seq. 10% HEK-293T cells were mixed in ATAC-seq samples for spike-in normalization. ATAC-seq was performed with Chromatin Profile Kit for Illumina (Novoprotein, N248-01A).
ATAC-seq was performed with Chromatin Profile Kit for Illumina (Novoprotein, N248-01A).

value: pancreas

tag: cell line

tag: cell type

value: pancreatitis

value: no


title: DSP-1001660013109-D-A02


title: DSP-1001660013108-C-H10


title: ATAC_Ca_D7_Smarca5_475


title: DSP-1001660013108-C-H08


title: DSP-1001660013108-C-H07


title: ATAC_Ca_D7_Rosa_476

value: control


title: ATAC_Ca_D7_Rosa_474


title: ATAC_Ca_D5_Smarca5_434


title: DSP-1001660013108-C-H09


title: DSP-1001660013108-C-H05


title: ATAC_Ca_D5_Smarca5_429


title: DSP-1001660013108-C-H03


title: ATAC_Ca_D5_Rosa_433


title: DSP-1001660013108-C-H04


title: DSP-1001660013119-E-E07


title: DSP-1001660013108-C-H02


title: ATAC_KCa_0h_Rosa_211

value: acinar


title: DSP-1001660013108-C-H01


title: DSP-1001660013108-C-G12


title: DSP-1001660013108-C-G11


title: DSP-1001660013108-C-G10


title: ATAC_Ca_D2_Smarca5_459


title: ATAC_Ca_D2_Rosa_457


title: DSP-1001660013108-C-G09


title: ATAC_Ca_D2_Rosa_456


title: DSP-1001660013108-C-H06


title: ATAC_Ca_8h_Smarca5_455


title: DSP-1001660013108-C-G07


title: ATAC_Ca_D5_Smarca5_428


title: DSP-1001660013108-C-G06


title: DSP-1001660013108-C-G05


title: ATAC_Ca_8h_Smarca5_438


title: ATAC_Ca_8h_Rosa_453


title: ATAC_Ca_D5_Rosa_423


title: ATAC_Ca_8h_Rosa_452


title: ATAC_Ca_D2_Smarca5_472


title: ATAC_Ca_D2_Smarca5_470


title: ATAC_Ca_8h_Rosa_435


title: DSP-1001660013108-C-G03


title: DSP-1001660013108-C-F12


title: DSP-1001660013108-C-G04


title: DSP-1001660013108-C-F10


title: DSP-1001660013108-C-F11


title: DSP-1001660013108-C-G02


title: ATAC_Ca_0h_Smarca5_70


title: DSP-1001660013108-C-G01


title: ATAC_Ca_0h_Rosa_60


title: ATAC_Ca_D5_Rosa_422


title: DSP-1001660013108-C-G08


title: EAE4

city: kai feng

first: zejin

last: liu

address: ximen street

institute: henan university

description:
EAE4:fpkm
CCK4

data_processing:
Sequencing data was trimmed for high quality sequence（Clean Data）using Cutadapt
The reference genome and gene annotation files were downloaded from genome website.
The filtered reads were mapping to the reference genome using HISAT2 v2.0.5.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: spinal cord

extract_protocol:
RNA was harvested using Trizol Reagent (Invitrogen Life Technologies). Three micrograms of RNA were used as input material for the RNA sample preparations.
Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides andSuper Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina) by Suzhou PANOMIX Biomedical Tech Co., LTD

value: spinal cord

tag: time

value: 14 day

value: Naringenin


title: ATAC_Ca_8h_Smarca5_454


title: EAE1

description:
EAE1:fpkm
CCK1


title: DSP-1001660013108-C-F05


title: EAE2

description:
EAE2:fpkm
CCK2


title: DSP-1001660013108-C-F06


title: EAE5

description:
EAE5:fpkm
CCK5


title: EAE3

description:
EAE3:fpkm
CCK3


title: Nar5

description:
Nar5:fpkm
CNar5


title: DSP-1001660013108-C-F07


title: Nar4

description:
Nar4:fpkm
CNar4


title: DSP-1001660013108-C-F08


title: ATAC_Ca_0h_Smarca5_69


title: DSP-1001660013108-C-F03


title: DSP-1001660013108-C-F04


title: ATAC_Ca_0h_Rosa_58


title: DSP-1001660013108-C-F09


title: Nar3

description:
Nar3:fpkm
CNar3


title: Nar2

description:
Nar2:fpkm
CNar2


title: DSP-1001660013108-C-E12


title: Nar1

description:
Nar1:fpkm
CNar1


title: DSP-1001660013108-C-F01


title: sample_DIZE4

city: Gwangju

first: Woo

middle: Ju

last: JEONG

address: 123 Cheomdangwagi-ro

country: South Korea

institute: Gwangju Institute of Science and Technology

data_processing:
Reads were trimmed under quality score 30 using Cutadaptor(v.2.10) then aligned mm10 RefSeq through STAR (v2.7.3) followed by excluding duplicated reads using MarkDuplicates v2.23.3
Raw read counts were generated using Htseq count (v0.6.1p1).
Raw read counts were processed using the 'edgeR' package with R software (version 4.1) to generate counts per million (cpm), which were then transformed to a log2 scale and standardized using quantile normalization. The adjusted log2-cpm was then used in an integrative statistical technique to detect the differentially expressed genes (DEGs). For each gene, the Student's t-test and log2-median-ratio were used to calculate the observed T-value and the log2-median-ratio between the two conditions. Subsequently, random sampling of 1,000 times was used to produce empirical null distributions for the T-value and log2-median-ratio. To obtain an overall p-value for each gene, we first computed the adjusted p-values by running a two-tailed test on the measured T-value and log2-median-ratio using their respective empirical distributions. The adjusted p-values were then merged using Stouffer’s method. DEGs were chosen for each comparison based on two criteria: an overall p-value of less than 0.05, and an absolute log2-median-ratio greater than the median of the empirical distribution's 2.5th and 97.5th percentiles for the log2-median-ratio.
mm10
Assembly: tab-delimited text file includes raw read counts for each Sample

source_name: heart

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s protocol. Total RNA (1 μg) was reverse-transcribed using the High-Capacity cDNA Reverse Transcription kit (Applied Biosystems, Waltham, MA, USA; Thermo Fisher Scientific) according to the manufacturer’s protocol.
The libraries were prepared for 151bp paired-end sequencing using TruSeq stranded mRNA Sample Preparation Kit (Illumina, CA, USA). Namely, mRNA molecules were purified and fragmented from 1μg of total RNA using oligo (dT) magnetic beads. The fragmented mRNAs were synthesized as single-stranded cDNAs through random hexamer priming. By applying this as a template for second strand synthesis, double-stranded cDNA was prepared. After sequential process of end repair, A-tailing and adapter ligation, cDNA libraries were amplified with PCR (Polymerase Chain Reaction). Quality of these cDNA libraries was evaluated with the Agilent 2100 BioAnalyzer (Agilent, CA, USA). They were quantified with the KAPA library quantification kit (Kapa Biosystems, MA, USA) according to the manufacturer’s library quantification protocol. Following cluster amplification of denatured templates, sequencing was progressed as paired-end (2×151bp) using Illumina NovaSeq6000 (Illumina, CA, USA).

value: heart

value: db/db

value: DIZE


title: DSP-1001660013108-C-E11


title: sample_DIZE3


title: sample_DB_A4


title: DSP-1001660013108-C-E10


title: DSP-1001660013108-C-F02


title: DSP-1001660013108-C-E09


title: sample_dbA1


title: 7-day-old rice and sorghum seedlings undergoing deetiolation - technical replicate 123

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
Library name: 6_21_21_JS_Sorghum_Rice_vegetative_shoot_Light_1_123
sci-RNA-seq3
L1_rice_combined.RData

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed using the Cell Ranger software. Data filtering was performed with Seurat
Assembly: Os-Nipponbare-Reference-IRGSP-1.0  and Sorghum bicolor v3.0.1
Supplementary files format and content: Seurat object
Library strategy: sci-RNA-seq3

molecule: nuclear RNA

organism: Oryza sativa

source_name: seedling

growth_protocol: 5 day old seedlings grown on soil were exposed to light and harvested at different time points during de-etiolation.

extract_protocol:
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter. To enrich the filtered solution for nuclei, an Optiprep (Sigma) gradient was used. Enriched nuclei were then stained with Hoechst, before being FACS purified.
Library construction was performed according to the manufacturer's specification (Chromium Next GEM Single Cell 3' HT Kit v3.0, 10x Genomics)

value: seedling


title: DSP-1001660013108-C-E08


title: sample_DV6

value: vehicle


title: sample_DBV4


title: DSP-1001660013108-C-E07

value: Brain


title: DSP-1001660013108-C-E06


title: sample_db_v1


title: DSP-1001660013108-C-E04


title: DSP-1001660013108-C-E03


title: WT-2 Single cells aorta

city: New Haven

first: George

last: Tellides

state: CT

address: 10 Amistad st, 337B

department: Surgery

institute: Yale University

description: 6,263 cells before, 4,300 cells after filtering

data_processing:
Samples were sequenced on Novaseq 6000
The data from sequencer was processed to obtain the fastq sequences using the "cellranger mkfastq" program provided by the vendor (10X genomics).
The raw reads were aligned to the mouse reference genome (mm10 with added sequences for GFP and tdTomato) and gene expression in cells was quantified using the "cellranger count" program provided by the vendor (10X genomics).
The gene expression data was further processing using the Seurat package (version 4.0), including data filtering, normalization, data dimension reduction, cell clustering, marker identification, cell type identity assignment, and data visualization.
keep cells with all criteria of: eGFP > 1, at least 200 genes detected, UMI between 5000 and 25000, and mitochondria percentage < 10%; keep genes detected in at least 10 cells
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every cell, or under specific clusters/cell types

source_name: aortic cells

growth_protocol: Mice were bred and housed under standard conditions

extract_protocol:
Thoracic aortas were enzymatically digested under cold conditions, single (based on SSC-W vs SSC-H and FSC-W vs FSC-H gating), viable (based on exclusion of viability dye) cells were sorted into buffer with 0.04% BSA, and 4,300 to 6,278 cells from individual aortas were analyzed for each sample
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1

treatment_protocol: GFPiSMC (WT) mice were administered tamoxifen at 1 mg/d i.p. for 5 days at 3 weeks of age and the thoracic aortas were analyzed at 12 weeks of age

value: thoracic aorta

value: GFPiSMC


title: DSP-1001660013108-C-E02

value: AD


title: KO3-DESC (Bulk KO vs. WT SMC)

description:
KO3-DESC
12,000 SMCs

data_processing:
Illumina Casava1.7 software for basecalling
RNA-seq reads were aligned to the mouse reference genome (mm10) using the HISAT2
Gene models were downloaded from the GENCODE project (M15).
read counts were extracted from StringTie output using the prepDE.py script (http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#deseq)
DESeq2 was used to determine differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every sample

source_name: aortic SMCs

extract_protocol:
Ascending aorta/aortic arch or descending thoracic aorta segments were enzymatically digested under cold conditions, single (based on SSC-W vs SSC-H and FSC-W vs FSC-H gates), viable (based on exclusion of viability dye), GFP+ SMCs were sorted into NEB lysis buffer, and between 9,000-20,000 cells from individual aortic segments were analyzed for each sample
NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB #E6420)

treatment_protocol: GFPiSMC (WT) and Tgfbr1/2iSMCKO (KO) mice were administered tamoxifen for 5 days at a dose of 1 mg/d or 2 mg/d i.p. at 4 or 11 weeks of age, respectively, and aorta segments were analyzed at 12 weeks of age

value: descending thoracic aorta


title: WT-1 Single cells aorta

description: 8,947 cells before, 6,278 cells after filtering


title: KO3-ASC (Bulk KO vs. WT SMC)

description:
KO3-ASC
11,825 SMCs

value: ascending aorta/aortic arch


title: DSP-1001660013108-C-D12


title: DSP-1001660013108-C-D11


title: DSP-1001660013108-C-E01


title: KO2-ASC (Bulk KO vs. WT SMC)

description:
KO2-ASC
14,360 SMCs


title: KO2-DESC (Bulk KO vs. WT SMC)

description:
KO2-DESC
20,000 SMCs


title: KO1-DESC (Bulk KO vs. WT SMC)

description:
KO1-DESC
15,914 SMCs


title: KO1-ASC (Bulk KO vs. WT SMC)

description:
KO1-ASC
20,000 SMCs


title: DSP-1001660013108-C-D10


title: DSP-1001660013108-C-D08


title: WT3-ASC (Bulk KO vs. WT SMC)

description:
WT3-ASC
16,292 SMCs


title: DSP-1001660013108-C-D09


title: DSP-1001660013108-C-D07


title: sample_DV4


title: WT3-DESC (Bulk KO vs. WT SMC)

description:
WT3-DESC
16,114 SMCs


title: DSP-1001660013108-C-E05


title: DSP-1001660013108-C-D06


title: WT2-DESC (Bulk KO vs. WT SMC)

description:
WT2-DESC
9,208 SMCs


title: DSP-1001660013108-C-D05


title: WT1-DESC (Bulk KO vs. WT SMC)

description:
WT1-DESC
11,088 SMCs


title: WT1-ASC (Bulk KO vs. WT SMC)

description:
WT1-ASC
12,526 SMCs


title: DSP-1001660013108-C-D03


title: DSP-1001660013108-C-D04


title: WT2-ASC (Bulk KO vs. WT SMC)

description:
WT2-ASC
20,000 SMCs


title: DSP-1001660013108-C-D02


title: DSP-1001660013108-C-D01


title: KO-2 Bulk KO vs. WT Aorta

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were aligned to the mouse reference genome (mm10) using the HISAT2
Gene models were downloaded from the GENCODE project (M15).
read counts were extracted from StringTie output using the prepDE.py script (http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#deseq)
DESeq2 was used to determine differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every sample

source_name: aorta

extract_protocol:
Thoracic aortas were procured and total RNA was extracted via RNeasy Mini Kit from QIAGEN (cat. 74104).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C57BL/6J (WT) mice were untreated, whereas Tgfbr1/2iSMCKO (KO) mice were injected with tamoxifen for 5 days at a dose of 2 mg/d i.p. for 5 days at 11 weeks of age, and aortas of both strains were analyzed at 12 weeks of age

value: Tgfbr1/2iSMCKO (KO)


title: KO-1 Bulk KO vs. WT Aorta


title: DSP-1001660013108-C-C11


title: DSP-1001660013108-C-C09


title: WT-3 Bulk KO vs. WT Aorta

value: C57BL/6J (WT)


title: WT-2 Bulk KO vs. WT Aorta


title: DSP-1001660013108-C-C10


title: DSP-1001660013108-C-C12


title: WT-1 Bulk KO vs. WT Aorta


title: WT-4 Bulk KO vs. WT Aorta


title: Th17 SNAT1 KO replicate 3

first: Jeff

last: Rathmell

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

description: Cas9 transgenic

data_processing:
trim adapters with Cutadapt (v2.10)
Align with STAR (v2.7.3a)
featureCounts (v2.0.0)
Genome_build: mm10
Supplementary_files_format_and_content: txt file for raw counts

source_name: Th17 cells

growth_protocol: CD4+ cells were isolated from Cas9-transgenic mice by negative selection, activated with anti-CD3 and anti-CD28 antibodies and polarized to Th1 or Th17 cells with cytokines and blocking antibodies.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit (Cat# 74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were transduced with either retrovirus carrying NTC or SNAT1 gRNA with Thy1.1 reporter. Thy1.1+ cells were isolated by positive selection before RNA extraction.

value: spleen

value: 9 weeks

tag: tranduction

value: SNAT1 gRNA


title: DSP-1001660013108-C-C08


title: Th17 SNAT1 KO replicate 2

description: Cas9 transgenic


title: DSP-1001660013108-C-C05


title: Th17 NTC replicate 3

description: Cas9 transgenic

value: non-targeting control (NTC)


title: DSP-1001660013108-C-C06


title: DSP-1001660013108-C-C07


title: DSP-1001660013108-C-C03


title: DSP-1001660013108-C-C04


title: Th17 NTC replicate 2

description: Cas9 transgenic


title: Th17 SNAT1 KO replicate 1

description: Cas9 transgenic


title: Th17 NTC replicate 1

description: Cas9 transgenic


title: Th1 SNAT1 KO  replicate 3

description: Cas9 transgenic

source_name: Th1 cells


title: DSP-1001660013108-C-C01


title: DSP-1001660013108-C-B12


title: Th1 NTC replicate 3

description: Cas9 transgenic


title: DSP-1001660013108-C-C02


title: Th1 SNAT1 KO  replicate 2

description: Cas9 transgenic


title: Th1 NTC replicate 2

description: Cas9 transgenic


title: DSP-1001660013108-C-B11


title: Th1 SNAT1 KO replicate 1

description: Cas9 transgenic


title: DSP-1001660013108-C-B09


title: Th1 NTC replicate 1

description: Cas9 transgenic


title: DSP-1001660013108-C-B08


title: DMSO

city: Guiyang

first: Jiankun

last: Hong

state: Guizhou

address: Province science city, high tech, zone, Baiyun district

department: State Key Laboratory for Functions and Applications of Medicinal Plants

institute: Guizhou Medical University

data_processing:
Sequencing data is called raw reads or raw data, and quality control (QC) is then performed on the raw reads to determine whether the sequencing data is suitable for subsequent analysis. After quality control, the filtered clean reads were aligned to the reference sequence. After the alignment, the statistics of the mapping rate and the distribution of reads on the reference sequence are used to determine whether the alignment result passes the second QC of alignment. If it passes, we perform gene quantification analysis and other analysis based on gene expression (principal component, correlation, differential gene screening, etc.), and perform significant enrichment analysis of GO function on differentially expressed genes among the screened samples, significance enrichment analysis of pathway, clustering, protein interaction networks, and transcription factors, and more in-depth mining analysis. SNP & InDel, differential splicing gene detection can also be done.
Assembly: Reference Genome Version: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: FPKM values, different expression genes for each sample

source_name: HEL

growth_protocol: HEL cells were cultured using 1640 medium until full-grown petri dishes were passaged.

extract_protocol:
Total RNA was extracted fusing TRIzol reagent kit (Life Technologies; Thermo Fisher Scientific, USA).
In this project, we sequence 2 samples used BGISEQ platform, averagely generating about 6.67G Gb bases per sample. The average mapping ratio with reference genome is 96.37%, the average mapping ratio with gene is 74.82%; 15540 genes were identified.

treatment_protocol: Red leukaemia cells HEL were used as experimental subjects and HEL cells were treated with 25 µmol of calcitriol for 24 hours.

value: HEL

value: erythroleukaemia cell

value: normal

value: Transfection


title: DSP-1001660013108-C-B07


title: CA

value: 25 µmol of calcitriol for 24 hours


title: DSP-1001660013108-C-B06

value: Brain


title: DSP-1001660013108-C-B05


title: PDGF-BB, rep3

city: Guangzhou

first: Hanyan

last: Yang

address: Zhujiang Hospital, Southern Medical University, Haizhu District, Guangzhou City, Guangdong Province

institute: Southern Medical University

description: Library name: sample 6

data_processing:
Raw Data Filtering: Use SOAPnuke to remove adapter-contaminated, low-quality (≥20% Q≤15 bases), and high-N-content (≥5%) reads, generating clean FASTQ data.
Genome Alignment: Align clean reads to the reference genome using HISAT2 with sensitive mode and strand-specific parameters
Transcript Assembly & Quantification: Assemble transcripts and quantify gene expression (FPKM) via RSEM after mapping clean reads to the reference gene set with Bowtie2.
Differential Expression Analysis: Identify differentially expressed genes using DESeq2 (or DEGseq/PoissonDis) with a threshold of Q value ≤0.05 or FDR ≤0.001.
Functional Enrichment: Perform GO and KEGG enrichment analysis on differentially expressed genes using Phyper with hypergeometric testing (Q value ≤0.05).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

source_name: human aortic isolated SMCs (HASMCs)

growth_protocol: Human primary aortic smooth muscle cells (HASMCs) were cultured in a low-serum primary smooth muscle cell culture system. The cells were carefully incubated under controlled conditions in a humidified incubator at 37°C with a 5% CO2 atmosphere.

extract_protocol:
RNA from HASMCs lysed with TRIzol (Invitrogen, 15596026) was extracted using the RNeasy Micro Kit (QIAGEN, Germany) following the manufacturer’s instructions. Briefly, TRIzol-lysed samples were thawed and mixed with 1/5 volume of chloroform/iso-amyl alcohol (24:1), then centrifuged at 12,000×g for 10 min. The supernatant was transferred to a new tube and mixed with an equal volume of 75% ethanol. The mixture was applied to an RNeasy MinElute spin column, followed by sequential washing with RW1 and RPE buffers. DNA digestion was performed using DNase I and Buffer RDD at room temperature for 15 min. Finally, RNA was eluted with 20 µL RNase-free water and quantified/qualified using a Fragment Analyzer, Agilent 2100 Bioanalyzer, or Qseq-400 with fluorescent dye-based methods.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA treated with Hieff NGS MaxUp Human rRNA Depletion Kit (Yeasen-Shanghai, China) to remove rRNA. After reacting at a suitable temperature for a fixed time period, RNAs are fragmented with fragmentation reagents. Then First-strand cDNA is generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis in a new reaction system containing dUTP. The synthesized double strand cDNA is subject to end repairment reaction. After cDNA end repairment, a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments through A tailing reaction. Then the reaction system for adaptor ligation is configured to ligate adaptors with the cDNAs, and finally, the library products are amplified through PCR reaction and subjected to quality control. Next, the single-stranded library products are produced via denaturation. The reaction system for circularization is set up to get the single-stranded circularized DNA products. Any single stranded linear DNA molecules will be digested. The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs are loaded into the patterned nanoarray and sequencing reads of PE150 bases length are generated on T7 platform (BGI-Shenzhen, China).

treatment_protocol: HASMCs were treated with 0.1% BSA solution (Ctrl) or PDGF-BB dissolved in 0.1% BSA solution (PDGF-BB group) for 48 h.

value: human aortic isolated SMCs (HASMCs)

value: Treat with PDGF-BB dissolved in 0.1% BSA solution for 48h


title: PDGF-BB, rep1

description: Library name: sample 4


title: Ctrl, rep2

description: Library name: sample 2

value: Treat with 0.1% BSA solution for 48h


title: DSP-1001660013108-C-B02

value: AD


title: DSP-1001660013108-C-A12


title: DSP-1001660013108-C-B03


title: Ctrl, rep1

description: Library name: sample 1


title: DSP-1001660013108-C-B04


title: DSP-1001660013108-C-B01


title: DSP-1001660013108-C-A10


title: Ctrl, rep3

description: Library name: sample 3


title: DSP-1001660013108-C-A11


title: PDCC,DMSO,rep2

description: Library name: RNA_pateint_DMSO_2

data_processing:
The adaptors of paired-end reads were trimmed by trim-galore (v.0.6.4) with the parameters set as: -q 25 --phred33 --length 50 -e 0.1 --fastqc --stringency 5 --paired.
Adaptor-trimmed reads were aligned to the mm10 genome with the following parameters: --readFilesCommand zcat --outFilterMismatchNoverLmax 0.2 by STAR (v.2.7.9a)
Aligned reads stored in SAM format were converted to BAM files using SAMtools with parameter: samtools view -bS -h -F 4 -f 2 -q 7.
FeatureCounts counted reads stored in BAM format to exon sites of genes included in GTF files from Ensembl
Assembly: mm10/hg19
Supplementary files format and content: raw counts

extract_protocol:
300 GFP-positive cells and 10,000 GFP-positive cells were sorted by FACS for small scale RNA-seq and ATAC-seq. 10% HEK-293T cells were mixed in ATAC-seq samples for spike-in normalization. ATAC-seq was performed with Chromatin Profile Kit for Illumina (Novoprotein, N248-01A). Small scale RNA-seq library was constructed using Smart-seq2 method with modifications allowing higher quality library generation from pancreatic cells. Briefly, mouse pancreatic cells were directly sorted into 8 μl of denaturing lysis buffer (6 M guanidine HCl, 0.2% (vol/vol) Triton X-100 and 1% (vol/vol) β-mercaptoethanol). RNA SPRI beads (RNA Clean XP beads, Beckman A63987) were added (2.2X) to the lysis buffer and RNA was purified, followed by library preparation by the standard Smart-seq2 protocol, except with a 12-cycle PCR pre-amplification step.
Smart-seq2 protocol.

value: pancreas

value: PDAC

value: DMSO


title: PDCC,DMSO,rep1

description: Library name: RNA_pateint_DMSO_1


title: PDCC,GSK2801,rep2

description: Library name: RNA_pateint_GSK2801_2


title: PDCC,GSK2801,rep1

description: Library name: RNA_pateint_GSK2801_1


title: DSP-1001660013108-C-A08


title: DSP-1001660013108-C-B10


title: PDCC,shSMARCA5,rep2

description: Library name: RNA_pateint_shSMARCA5_2


title: DSP-1001660013108-C-A07


title: PDCC,shSMARCA5,rep1

description: Library name: RNA_pateint_shSMARCA5_1


title: PDCC,shScramble,rep2

description: Library name: RNA_pateint_shScramble_2

value: control


title: PDGF-BB, rep2

description: Library name: sample 5


title: DSP-1001660013108-C-A06


title: DSP-1001660013108-C-A04


title: PDCC,shRUNX1,rep2

description: Library name: RNA_pateint_shRUNX1_2


title: DSP-1001660013108-C-A03


title: PDCC,shRUNX1,rep1

description: Library name: RNA_pateint_shRUNX1_1


title: DSP-1001660013108-C-A01


title: DSP-1001660013108-C-A02


title: BxPC3,SMARCA5,shRUNX1

description: Library name: BxPC3_SMARCA5_shRUNX1

data_processing:
The adaptors of paired-end reads were trimmed by trim-galore (v.0.6.4) with the parameters set as: -q 25 --phred33 --length 50 -e 0.1 --fastqc --stringency 5 --paired.
Adaptor-trimmed reads were aligned to the mm10 genome with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 by Bowtie2.
Aligned reads stored in SAM format were converted to BAM files and PCR duplicates were removed using SAMtools.
Peaks were called by MACS2(v.2.2.7.1)56 using the parameters: macs2 callpeak -g mm -B -p 0.01 -f BEDPE.
Assembly: mm10/hg19
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

extract_protocol:
30,000-60,000 GFP-positive cells were sorted by FACS and the CUT&RUN sequencing was performed as previously described44 with minor modifications. 10% Kasumi-1 cells were added as spike-in. Concanavalin-A (ConA) beads were activated by washed twice using activation buffer (20 mM HEPES–KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). Sorted cells were resuspended in room temperature (RT) wash buffer (20 mM HEPES–KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, protease inhibitor cocktail) and added into ConA beads. After incubating 10 min in RT, ConA-beads-bound cells were incubated overnight at 4 °C in antibody buffer (wash buffer supplemented with 0.01% digitonin and 2 mM EDTA) and antibody. The following primary antibodies were used: SMARCA5 (EpiCypher, 13-2007, 2.5 μl) and CTCF (CST, 3418S, 1μl). After antibody incubation, ConA-beads-bound nuclei were washed once with Digitonin buffer (wash buffer supplemented with 0.01% digitonin) then resuspended and incubated at 4 °C for 1 h in Digitonin buffer and 0.1 μl pAG-MNase (a gift from Dr. Wei Xie, Tsinghua University). ConA-beads-bound nuclei were then washed twice with Digitonin buffer and resuspended in 98 μl of Digitonin buffer and incubated on ice for 5 min. Then, 2 μl 100 mM CaCl2 was added and mixed gently to each 100 μl ConA-bound nuclei. The reaction was then incubated at 4 °C for 30 min. The reaction was stopped by addition of 100 μl 2× stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% Digitonin and 50 μg/ml RNaseA, 50 μg/ml Glycogen) and incubated at 37 °C for 10 min. All buffers mentioned above were filtered with 0.22 μm filter before use. After incubation, ConA-bound nuclei were captured using a magnet and supernatant containing CUT&RUN DNA fragments were collected. Supernatant was incubated at 70 °C for 10 min with 2 μl 10% sodium dodecyl sulfate, 3 μL 10 mg/ml proteinase K and 2 μL 20ng/μL carrier RNA (Qiagen, 1068337). DNA was purified using PCI reagent (Solarbio, P1012) and overnight ethanol precipitation with glycogen at -20 °C.
DNA was resuspended in water and repaired to 5´phosphorylated and 3´ dA-tailed DNA with NEBNext® Ultra™ II End Repair/dA-Tailing Module (NEB, E7546S). Barcodes (BIOO Scientific, 514153) were ligated with Quick Ligation kit (NEB, M2200). After size selection, 16 cycles of PCR were used to amplify the library. PCR-amplified libraries were purified using KAPA beads (Kapa biosystems) and sent for sequencing.


title: BxPC3,SMARCA5,shScramble

description: Library name: BxPC3_SMARCA5_shScramble


title: PDCC,SMARCA5KD,rep2

description: Library name: ATAC_patient_shSMARCA5_2

data_processing:
The adaptors of paired-end reads were trimmed by trim-galore (v.0.6.4) with the parameters set as: -q 25 --phred33 --length 50 -e 0.1 --fastqc --stringency 5 --paired.
Trimmed reads were aligned to the mm10 genome with the following parameters: --very-sensitive -k 10 by Bowtie2 (v.2.3.5.1)
Aligned reads stored in SAM format were manipulated to generate BAM files and PCR duplicates were removed using SAMtools (v.1.10)
ATAC-seq peaks were called by Genrich (v.0.6) using the parameters: -j -y -r -e chrM -v.
All peaks from all samples were merged and raw counts of merged peaks in each sample were counted by featureCounts (v.2.0.1). Size factor for each sample were calculated using DESeq2 (v.1.24.0). Normalized bigwig files were generated with 1/(size factor) using bamCoverage from deepTools (v.3.4.3).
Assembly: mm10/hg19
Supplementary files format and content: bigwig


title: DSP-1001660001371-F-B02

value: WT


title: DSP-1001660001371-F-A12


title: BxPC3,RUNX1,shScramble

description: Library name: BxPC3_RUNX1_shScramble


title: DSP-1001660001371-F-B03

value: No Template Control


title: PDCC,control,rep2

description: Library name: ATAC_patient_shScramble_2


title: DSP-1001660001371-F-B01


title: PDCC,SMARCA5KD,rep1

description: Library name: ATAC_patient_shSMARCA5_1


title: DSP-1001660001371-F-A11


title: DSP-1001660001371-F-A10


title: DSP-1001660001371-F-A09


title: PDCC,control,rep1

description: Library name: ATAC_patient_shScramble_1


title: PDCC,shScramble,rep1

description: Library name: RNA_pateint_shScramble_1


title: PDCC,RUNX1KD,rep2

description: Library name: ATAC_patient_shRUNX1_2


title: DSP-1001660013108-C-A05


title: DSP-1001660001371-F-A08


title: PDCC,RUNX1KD,rep1

description: Library name: ATAC_patient_shRUNX1_1


title: KCa,8h,Smarca5,714

description: Library name: ATAC_KCa_8h_Smarca5_714

value: pancreatitis


title: DSP-1001660001371-F-A07


title: DSP-1001660001371-F-A05


title: KCa,8h,Rosa,711

description: Library name: ATAC_KCa_8h_Rosa_711


title: KCa,0h,Rosa,223

description: Library name: ATAC_KCa_0h_Rosa_223

value: acinar


title: KCa,0h,Smarca5,226

description: Library name: ATAC_KCa_0h_Smarca5_226


title: DSP-1001660001371-F-A03


title: Ca,D7,Smarca5,215

description: Library name: ATAC_CA_D7_Smarca5_215


title: DSP-1001660001371-F-A04


title: Ca,D2,Rosa,713

description: Library name: ATAC_CA_D2_Rosa_713


title: DSP-1001660016239-C-H12

data_processing:
Fastq files were converted to DCC files using the GeoMx NGS Pipeline software and the mm10 reference genome.
Digital Count Conversion files, containing expression count data and sequencing quality metadata, and Probe Kit Configuration files, containing probe assay and sample metadata, were imported into R. Gene expression counts with a value of 0 were shifted to 1 to facilitate downstream transformations. ROI segments were filtered and removed if they met the criteria: “<1000 raw reads”, “below 80% Aligned or 80% Trimmed”, “80% Stitched”, and “below 50% sequencing saturation”. Genes were filtered and removed if they were not detected in at least 10% of segments. Next, counts were normalized using quartile 3 normalization and visualized by uniform manifold approximation and projection, a non-linear dimensionality reduction visualization tool. Gene expression in both datasets was relatively well separated according to ROI brain region.
Assembly: mm10
Supplementary files format and content: Late_stage_count_table.csv. A count table containing normalized counts for probes and segments that passed the quality control steps mentioned in the data processing step.
Library strategy: Spatial Transcriptomics

growth_protocol: Two slides were for late-stage analysis and were duplicates of 4 brain sections (n=2 5XFAD 30 wk, n=2 controls 30 wk)


title: Ca,D7,Rosa,210

description: Library name: ATAC_CA_D7_Rosa_210


title: Ca,0h,Smarca5,259

description: Library name: ATAC_CA_0h_Smarca5_259


title: DSP-1001660001371-F-A02


title: DSP-1001660016239-C-H10


title: DSP-1001660016239-C-H09


title: isolated Microglia-set 2, hashtaged for the different conditions

city: Dresden

first: Fanny

last: Ehret

address: Fetscherstraße 74

department: Medical faculity

country: Germany

institute: TU Dresden

description: Library name: ADM-set2

library_source: transcriptomic single cell

data_processing:
The reference was created with cellranger mkref (v5.01) as similarly to what is described by 10x (https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build#mm10_2020A), with the difference that “pseudogene” was added to the allowed biotype patterns.
The raw sequencing data was then processed with the ‘cellranger count’ command using Cell Ranger (6.0.1).
Next, demultiplexing of individual samples was performed following the Seurat workflow “Demultiplexing with hashtag oligos (HTOs)” as implemented in https://github.com/ktrns/scrnaseq. The following feature barcodes were used: id,name,read,pattern,sequence,feature_type MouseHashTag1,MouseHashTag1,R2,5P(BC),ACCCACCAGTAAGAC,Antibody Capture MouseHashTag2,MouseHashTag2,R2,5P(BC),GGTCGAGAGCATTCA,Antibody Capture MouseHashTag3,MouseHashTag3,R2,5P(BC),CTTGCCGCATGTCAT,Antibody Capture MouseHashTag4,MouseHashTag4,R2,5P(BC),AAAGCATTCTTCACG,Antibody Capture MouseHashTag5,MouseHashTag5,R2,5P(BC),CTTTGTCTTTGTGAG,Antibody Capture MouseHashTag6,MouseHashTag6,R2,5P(BC),TATGCTGCCACGGTA,Antibody Capture MouseHashTag7,MouseHashTag7,R2,5P(BC),GAGTCTGCCAGTATC,Antibody Capture MouseHashTag8,MouseHashTag8,R2,5P(BC),TATAGAACGCCAGGC,Antibody Capture
The resulting count matrices were further processed using scanpy 1.8.1 and saved as h5ad
Assembly: mm10 / Ensembl 98
Supplementary files format and content: count matrix in h5ad format

source_name: hippocampus

extract_protocol:
Hippocampal tissue was chopped and mechanically dissociated in HBSS with 15 strokes using a Ddounce homogenizer usingwith a loose pestle. The supernatant was transferred to a falcon and the cell pellet was again pulsed 10-15 times with the tight pestle in HBSS. The supernatant was again collected and filtered through a 70µm strainer followed by 40% Percoll density gradient centrifugation at 500g for 30 min at 4˚C. Cell pellet was collected and blocked with CD16/32 for 30min and then stained with live/dead BD700 and the following antibodies: CD45-BV421, CD11b-PE-Cy7, Cd11c-FITC, F4/80 BV786, Celc7a-PE  and Ly6C APC-Cy7. Cells from the four different conditions were stained with 8 Totalseq-A anti-mouse hashtag antibodies and sorted with a FACS device to pool equal numbers of cells from each individual.
All sorted cells (~8,000) were carefully mixed with reverse transcription mix before loading cells on the 10X Genomics Chromium controller in a Chromium Single Cell G Chip targeting ~4,800 cells per reaction. The droplets were directly subjected to reverse transcription, the emulsion was broken and cDNA was purified using Dynabeads MyOne Silane (10X Genomics). After amplification of cDNA with 13 cycles using primers to enrich cDNA as well as Totalseq-A hashtag sequences, the samples underwent a purification with SPRIselect beads (Beckman Coulter) with 0.6x volume of beads to enrich cDNA fragments (>400 bp), followed by an additional purification of the supernatant with 2x volume of SPRI beads to separately enrich the small fragments from the hashtag sequences. After quality check and quantification of the cDNA on the Fragment Analyzer (using the DNF-473 NGS Fragment Kit, Agilent), the 10X Genomics single cell RNA-seq library preparation - involving fragmentation, dA-Tailing, adapter ligation and 14 cycles indexing PCR – was performed based on the manufacturer’s protocol. In parallel, the hashtag library was prepared by a 12 cycles index PCR with the 10x Genomics TT-index set A. After quantification, both libraries were sequenced on Illumina NovaSeq 6000 S4 flowcells in 200 bp paired-end mode, generating 125 million fragment pairs for the gene expression libraries and 55 million fragment pairs for the hashtag library.

treatment_protocol: The different hashtags correspond to different treatment conditions: NL-STD set1_1, set2_1, set2_2; NL-ENR= set1_6, set1_7, set2_6, set2_7, set2_8; NL-G-F-STD=set1_2, set1_3, set2_3; NL-G-F-ENR=set1_4, set1-5, set1-8, set2_4, set2_5

value: hippocampus

value: 7 months

tag: Sex

value: female

value: microglia

value: App-NL-G-F and App-NL

value: Standard housing and Enrichment

tag: batch


title: DSP-1001660016239-C-H08

value: Brain


title: DSP-1001660001371-F-A06


title: DSP-1001660016239-C-H07


title: 5FU_HTO

city: Farmington

first: Harshpreet

last: Chandok

address: 10 Discovery Dr

institute: The Jackson Laboratory

description: Library name: LSK5FU-HT

data_processing:
After sequencing, cDNA and Hashtag Oligo reads were demultiplexed and aligned to the genome using the 10X Genomics CellRanger Software. The output matrix file, features file, and barcode file were imported into R. The Seurat package was using for downstream analysis. The output files were used to create a Seurat object and HTO counts were extracted and normalized, and a genotype was assigned to each cell. Quality control filters were used to isolate high-quality cells that were singlets for all downstream analysis.
LSKs were assigned a subset based on previously published transcriptional signatures of LT-HSCs, ST-HSCs, MPP2s, MPP3s, and MPP4s. Principal Component Analysis (PCA) was computed and the Jackstraw package used to determine statistically significant PCs to use for the Uniform Manifold Approximation Projections (UMAP). Differentially expressed genes were determined using the FindMarkers function in Seurat using a DESeq2 framework.
For the stress dataset, the same workflow to import the data and isoalte high quality cells and a genotype as well as subtype scores was followed as in the homeostasis dataset. For integration, we utilized the IntegrateData function from Seurat.
The pseudotime analysis was computed by first exporting the Seurat object to a CellDataSet format and then using the Monocle3 package in R. The learn_graph function was used to determine cell trajectories and the order_cells function used to determine the order of psueudotime, with the LT-HSC cluster manually selected as the start node. The graph autocorrelation analysis was completed using the graph_test function and relevant modules were determined with find_gene_modules. The aggregate_gene_expression function was used to generate heat maps. Module gene lists were exported to Enrichr for all gene ontology analysis.
For cell cycle analysis, previously pubished datasets were used to score M/G1, G0, G0/G1, G1/S, S, G2/M, and M cell cycles and LT-HSCs were then ordered based on lowest to highest expression of G0 score.
Assembly: mm9
Supplementary files format and content: Processed data contains output file from CellRanger

source_name: Hematopoietic

growth_protocol: Cells were freshly isolated from C57BL/6 mice housed in a pathogen-free barrier facility with a 12h light/dark cycle and given food and water ad libitum.

extract_protocol:
Mice were humanely euthanized via CO2 inhalation followed by a secondary cervical dislocation. The femurs, tibiae, pelvis, spine, humerus, and sternum were all taken and crushed to release bone marrow. After red blood cell lysis with ACK buffer, cells were magnetically enriched for cKit+ cells and then stained with Lineage, cKit, and Sca-1 antibodies to sort on L-S+K+ cells. Cells were combined from 2 mice for each genotype. Cells were then placed in a 10X Genomics Chromium Chip to generate single cell suspensions and to isolate RNA and reverse transcribe to cDNA, following the manufacturer's instructions.
Reactions from 10X Genomics chip were stored at -20ºC and then quality of cDNA was checked with an Agilent 2100 Bioanalyzer. Libraries were generated using the 10X Genomics 3' GEM protocol with HTO primers and then sequenced on an Illumina NovaSeq

treatment_protocol: Mice under stress conditions were given 100mg/kg 5-Fluorouracil via intraperitoneal injection 9 days before harvest.

value: Hematopoietic

value: LSK

value: WT/3B KO


title: DSP-1001660016239-C-H06


title: isolated Microglia-set 1, hashtaged for the different conditions

description: Library name: ADM-set1


title: 5FU_cDKA

description: Library name: LSK5FU


title: LSK_HTO

description: Library name: Combined_LSKs-HT


title: DSP-1001660016239-C-H05


title: Mus,XZSW4

city: Wenzhou

first: Liting

last: Zhu

address: Chashan Street

institute: Wenzhou Medical University

description:
Library name: Sample12
M4

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: kidney

extract_protocol:
Total RNA was isolated using TRIzol (Thermo 15596018), quantified by NanoDrop (concentration >50ng/μL), and assessed for integrity with Bioanalyzer 2100 (RIN>7.0; total RNA>1μg).
Library construction for transcriptome sequencing employed a strand-specific approach (fr-firstrand).

value: kidney


title: LSK_cDNA

description: Library name: Combined_LSKs


title: DSP-1001660016239-C-H04


title: DSP-1001660016239-C-H03


title: Mus,XZSW3

description:
Library name: Sample11
M3


title: Ca,D2,Smarca5,744

description: Library name: ATAC_CA_D2_Smarca5_744

value: pancreas


title: DSP-1001660001371-F-A01

data_processing:
Fastq files were converted to DCC files using the GeoMx NGS Pipeline software and the mm10 reference genome.
Digital Count Conversion files, containing expression count data and sequencing quality metadata, and Probe Kit Configuration files, containing probe assay and sample metadata, were imported into R. Gene expression counts with a value of 0 were shifted to 1 to facilitate downstream transformations. ROI segments were filtered and removed if they met the criteria: “<1000 raw reads”, “below 80% Aligned or 80% Trimmed”, “80% Stitched”, and “below 50% sequencing saturation”. Genes were filtered and removed if they were not detected in at least 10% of segments. Next, counts were normalized using quartile 3 normalization and visualized by uniform manifold approximation and projection, a non-linear dimensionality reduction visualization tool. Gene expression in both datasets was relatively well separated according to ROI brain region.
Assembly: mm10
Supplementary files format and content: Early_stage_count_table.csv. A count table containing normalized counts for probes and segments that passed the quality control steps mentioned in the data processing step.
Library strategy: Spatial transcriptomics


title: DSP-1001660016239-C-H11


title: Mus,XZSW2

description:
Library name: Sample10
M2


title: Ca,0h,Rosa,58

description: Library name: ATAC_CA_0h_Rosa_258

value: control


title: DSP-1001660016239-C-H01


title: DSP-1001660016239-C-G12


title: DSP-1001660016239-C-G11


title: Mus,HUA4

description:
Library name: Sample8
N4

value: WT


title: DSP-1001660016239-C-G10


title: Mus,HUA3

description:
Library name: Sample7
N3


title: Mus,HUA1

description:
Library name: Sample5
N1


title: DSP-1001660016239-C-G09


title: Mus,HUA2

description:
Library name: Sample6
N2


title: DSP-1001660016239-C-G08


title: DSP-1001660016239-C-G07


title: Mus,CTL4

description:
Library name: Sample4
C4


title: Mus,CTL2

description:
Library name: Sample2
C2


title: Mus,CTL1

description:
Library name: Sample1
C1


title: Mus,CTL3

description:
Library name: Sample3
C3


title: DSP-1001660016239-C-G06


title: DSP-1001660016239-C-G05


title: DSP-1001660016239-C-H02


title: DSP-1001660016239-C-G03


title: Mus,XZSW1

description:
Library name: Sample9
M1


title: DSP-1001660016239-C-G04


title: DSP-1001660016239-C-G02


title: WT sgSCR_ILO_REP 1

city: Grand Rapids

first: Russell

last: Jones

state: MI

address: 333 Bostwick Ave NE

department: Department of Metabolism and Nutritional Programming

institute: Van Andel Insitute

description: Library name: M16

data_processing:
Adaptor sequences and low-quality reads were trimmed using Trim Galore (v0.6.0; Martin, 2011). Trimmed reads were aligned to the mm10 reference genome using STAR (v2.7.8; Dobin et al., 2013) with --quantMode GeneCounts.
Assembly: mm10
Supplementary files format and content: raw counts of all samples with ensembl id, gene symbol, and gene names.

source_name: spleen derived

growth_protocol: Wildtpe (WT) and Keap1 KO CD8 T cells were isolated from spleens of mice using a CD8 T cell isolation kit (Stemcell, #19853) and activated (1 million cells/mL) using plate bound anti-CD3 (2 µg/mL) and anti-CD28 1 µg/mL) antibodies for 48h in T cell media. Cells were then passaged (400,000 cells/mL) for an additional 48 hours in the absence of plate bound antibodies, in T cell media.

extract_protocol:
mRNA was captured using polyA, and stranded libraries were constructed.
RNA-seq

treatment_protocol: On day 4, cells were seeded at 400,000 cells/mL and treated with either vehicle (DMSO), or iloprost (5 µM) for 24h, both in technical triplicate, then harvested for downstream RNA-seq.

value: spleen derived

value: CD8 T cell


title: WT sgSCR_ILO_REP 2

description: Library name: M17


title: DSP-1001660016239-C-G01

extract_protocol:
One brain hemisphere was fixed in 4% paraformaldehyde (PFA) for 24 h, cryoprotected in escalating sucrose gradients, embedded, and cryosectioned in coronal plane sections onto histologic slides [10 μm thickness for spatial transcriptomics sections, 14 μm thickness for subsequent fluorescent in situ hybridization (FISH)] and stored at –80 °C.
Spatial transcriptomics was performed by GeoMx DSP (NanoString, Seattle, WA), a platform for spatially analyzing gene expression in tissue in a highly multiplexed manner
Other: Spatial transcriptomics-Nanostring GeoMx DSP


title: WT sgSCR_VEH_REP 3

description: Library name: M15


title: WT sgSCR_VEH_REP 2

description: Library name: M14


title: DSP-1001660016239-C-F11


title: DSP-1001660016239-C-F12


title: WT sgSCR_VEH_REP 1

description: Library name: M13


title: WT OE_ILO_REP 3

description: Library name: M12


title: DSP-1001660016239-C-F10


title: WT OE_ILO_REP 2

description: Library name: M11


title: DSP-1001660016239-C-F08


title: DSP-1001660016239-C-F07


title: WT OE_VEH_REP 2

description: Library name: M8


title: DSP-1001660016239-C-F06


title: DSP-1001660016239-C-F09


title: WT OE_VEH_REP 3

description: Library name: M9


title: DSP-1001660016239-C-F05


title: WT OE_VEH_REP 1

description: Library name: M7


title: WT MIGR1_ILO_REP 3

description: Library name: M6


title: DSP-1001660016239-C-F04


title: WT MIGR1_ILO_REP 2

description: Library name: M5


title: WT sgSCR_ILO_REP 3

description: Library name: M18


title: DSP-1001660016239-C-F03


title: WT MIGR1_ILO_REP 1

description: Library name: M4


title: DSP-1001660016239-C-F01


title: DSP-1001660016239-C-E12


title: WT MIGR1_VEH_REP 3

description: Library name: M3


title: WT MIGR1_VEH_REP 2

description: Library name: M2


title: DSP-1001660016239-C-E11


title: WT MIGR1_VEH_REP 1

description: Library name: M1


title: DSP-1001660016239-C-E10


title: DSP-1001660016239-C-E08


title: WT OE_ILO_REP 1

description: Library name: M10


title: RNA-Seq of mus musculus: adult male iWAT,SH_1

city: Shanghai

first: Chao

last: Wu

state: 上海

address: 上海市普陀区真南路500号同济大学

institute: Tongji University

description: Library name: LGM16959

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm39
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: iWAT

growth_protocol: The temperature and lighting are normal, and the mice can move around freely.

extract_protocol:
Total RNA was extracted from frozen mouse iWAT using TRIzol (Invitrogen), followed by DNase I treatment and purification with RNeasy Mini Kit (Qiagen). RNA integrity was confirmed by Bioanalyzer (RIN > 8).
RNA libraries were prepared using the protocol of Genewiz.

treatment_protocol: Group housing: 4-6 mice per cage; socially isolated group: 1 mouse per cage

value: iWAT

value: single housing


title: RNA-Seq of mus musculus: adult male iWAT,SH_3

address: 上海市普陀区真南路500号同济大学

description: Library name: LGM16961


title: RNA-Seq of mus musculus: adult male iWAT,SH_2

address: 上海市普陀区真南路500号同济大学

description: Library name: LGM16960


title: RNA-Seq of mus musculus: adult male iWAT,GH_3

address: 上海市普陀区真南路500号同济大学

description: Library name: LGM16958

value: group housing


title: RNA-Seq of mus musculus: adult male iWAT,GH_2

address: 上海市普陀区真南路500号同济大学

description: Library name: LGM16957


title: DSP-1001660016239-C-E07

source_name: Brain


title: DSP-1001660016239-C-E06


title: DSP-1001660016239-C-E04


title: RNA-Seq of mus musculus: adult male iWAT,GH_1

address: 上海市普陀区真南路500号同济大学

description: Library name: LGM16956


title: DSP-1001660016239-C-F02


title: DSP-1001660016239-C-E05


title: male SCFA-treated, 14 dpi, sample3

city: Berlin

first: Susanne

middle: A.

last: Wolf

state: Berlin

address: Augustenburger Platz 1

department: Klinik für Augenheilkunde

institute: Charite

description: Library name: M14SCFA3

data_processing:
Illumina Novaseq 6000 platform
Paired-end 150 strategy.
The data was reported as raw read counts and fragments per kilobase of transcripts per million.
DEseq2 was used to calculate the normalized read counts.
Assembly: mm10
Supplementary files format and content: Excel file containing Read Counts

source_name: retina

growth_protocol: Each RNA sample was a pool of two laser induced retinas extracted from mice on the same group. We pooled 2 retinae from two different animals per n.

extract_protocol:
RNeasy Mini  (Cat#74104, Qiagen, Germany)
Novogene NGS RNA Library Prep Set (PT042)

treatment_protocol: Nine-week-old C57BL/6J mice  received a retinal, laser-induced choroidal neovascularization (CNV) lesion. C57BL/6J mice were randomly divided into two groups: the control group received only the laser lesion without SCFA supplementation, and the SCFA-treated group received SCFA before the laser lesion until the mice were euthanized and samples were collected. SCFA was administered to mice ad libitum via drinking water, and the SCFA concentrations of choice were 67.5mM sodium acetate (5.54 g/L), 25mM sodium butyrate (4.4 g/L) and 40mM sodium propionate (2.48 g/L).

value: retina

value: bulk


title: DSP-1001660016239-C-E03


title: male SCFA-treated, 14 dpi, sample1

description: Library name: M14SCFA1


title: male SCFA-treated, 14 dpi, sample2

description: Library name: M14SCFA2


title: DSP-1001660016239-C-E02


title: male control, 14 dpi, sample3

description: Library name: M14CTR3


title: DSP-1001660016239-C-E01


title: DSP-1001660016239-C-E09


title: male control, 14 dpi, sample2

description: Library name: M14CTR2


title: DSP-1001660016239-C-D11


title: male control, 14 dpi, sample1

description: Library name: M14CTR1


title: DSP-1001660016239-C-D12


title: male SCFA-treated, 7 dpi, sample5

description: Library name: M7SCFA5


title: DSP-1001660016239-C-D09


title: male SCFA-treated, 7 dpi, sample4

description: Library name: M7SCFA4


title: male SCFA-treated, 7 dpi, sample3

description: Library name: M7SCFA3


title: DSP-1001660016239-C-D08


title: EU-RNAseq_L36plClone2_dTAG_4h_Rep3

city: Stuttgart

first: Steven

middle: A

last: Johnsen

address: Auerbachstrasse 112

institute: Robert Bosch Center for Tumor Diseases

description: Library name: Sample070

data_processing:
Paired end sequencing reads were mapped to the reference genome assembly hg38 using bowtie2. chrM, chrUn, alt and random chromosomes were removed from bam files with ‘grep -v’ command. PCR duplicates were removed with samtools markdup. Forward and reverse bigwig files were generated ignoring duplicates and blacklist regions using bamCoverage using counts per million (cpm) normalization and --filterRNAstrand forward and reverse.
Assembly: hg38
Supplementary files format and content: Forward strand bigwig for each condition
Supplementary files format and content: Reverse strand bigwig for each condition

source_name: cell line

growth_protocol: L36pl cells were maintained in phenol free MEM with 10% FBS and 1% Pen-Strep in a humidified 5% CO2 incubator at 37C.

extract_protocol:
Nascent RNA capture was performed by plating 5 x 105 cells in a 6 well plate, incubated overnight and treated with dTAGV-1 for 0, 1, 4 or 24 hr. 0.5 mM 5-ethynyl uridine (EU) in 2 mL of cell culture media was added to cells during the last 1 hr of dTAGV-1 treatment. Cells were washed twice with PBS after removing cell culture medium and total RNA was extracted from cells by adding 700 µL of QIAzol, incubated for 5 min on rocker, scraped and transferred to a new tube. 140 µL chloroform was added to the samples, vortexed for 15 sec, incubated for 3 min at room temperature, and centrifuged. Aqueous phase was transferred to a new tube and mixed with an equal volume of isopropanol. Samples were incubated at -80°C 1 hour and centrifuged. RNA pellet was washed twice with 70% ethanol and the pellet was air-dried at room temperature for 5-10 min. 50 µL of RNAse-free water was used to resuspend the pellet. 2 µg of isolated RNA was used for the click reaction using the Click-iT Nascent RNA Capture Kit (ThermoFisher Scientific, C10365) following supplier’s protocol.
Following the click reaction, RNA was extracted and 500 ng of isolated RNA was used for binding to Dynabeads MyOne Streptavidin T1 beads, washed and proceeded immediately to library preparation using the Universal Plus Total RNA-Seq with NuQuant kit (Tecan Life Sciences, M01523). The library fragment size was determined by TapeStation.

value: cell line

value: Pancreatic ductal adenocarcinoma


title: male SCFA-treated, 7 dpi, sample2

description: Library name: M7SCFA2


title: DSP-1001660016239-C-D06

value: Brain


title: male control, 7 dpi, sample2

description: Library name: M7CTR2


title: EU-RNAseq_L36plClone2_dTAG_4h_Rep2

description: Library name: Sample069


title: male SCFA-treated, 3 dpi, sample3

description: Library name: M3SCFA3


title: male SCFA-treated, 7 dpi, sample1

description: Library name: M7SCFA1


title: male control, 7 dpi, sample1

description: Library name: M7CTR1


title: EU-RNAseq_L36plClone2_dTAG_24h_Rep3

description: Library name: Sample067


title: DSP-1001660016239-C-D05


title: male SCFA-treated, 3 dpi, sample2

description: Library name: M3SCFA2


title: EU-RNAseq_L36plClone2_dTAG_24h_Rep2

description: Library name: Sample066


title: DSP-1001660016239-C-D10


title: DSP-1001660013108-C-A09

value: AD


title: male control, 3 dpi

description: Library name: M3CTR4


title: DSP-1001660016239-C-D03


title: male control, 3 dpi, sample3

description: Library name: M3CTR3


title: male control, 3 dpi, sample2

description: Library name: M3CTR2


title: EU-RNAseq_L36plClone2_dTAG_1h_Rep3

description: Library name: Sample064


title: male control, 3 dpi, sample1

description: Library name: M3CTR1


title: EU-RNAseq_L36plClone2_dTAG_24h_Rep1

description: Library name: Sample065


title: female SCFA-treated, 14 dpi

description: Library name: F14SCFA4


title: DSP-1001660016239-C-D02


title: DSP-1001660016239-C-D01


title: male control, 7 dpi, sample3

description: Library name: M7CTR3


title: EU-RNAseq_L36plClone2_dTAG_1h_Rep2

description: Library name: Sample063


title: female SCFA-treated, 14 dpi, sample2

description: Library name: F14SCFA2


title: DSP-1001660016239-C-D07


title: EU-RNAseq_L36plClone2_dTAG_4h_Rep1

description: Library name: Sample068


title: male SCFA-treated, 3 dpi, sample1

description: Library name: M3SCFA1


title: female SCFA-treated, 14 dpi, sample1

description: Library name: F14SCFA1


title: DSP-1001660016239-C-C12


title: EU-RNAseq_L36plClone2_dTAG_0h_Rep3

description: Library name: Sample061


title: DSP-1001660016239-C-D04


title: female control, 14 dpi, sample2

description: Library name: F14CTR2


title: female SCFA-treated, 7 dpi, sample4

description: Library name: F7SCFA4


title: female control, 14 dpi, sample3

description: Library name: F14CTR3


title: DSP-1001660016239-C-C11


title: EU-RNAseq_L36plClone2_dTAG_0h_Rep2

description: Library name: Sample060


title: DSP-1001660016239-C-C10


title: EU-RNAseq_L36plClone2_dTAG_0h_Rep1

description: Library name: Sample059


title: female SCFA-treated, 7 dpi, sample3

description: Library name: F7SCFA3


title: female SCFA-treated, 7 dpi, sample2

description: Library name: F7SCFA2


title: DSP-1001660016239-C-C09


title: female SCFA-treated, 14 dpi, sample3

description: Library name: F14SCFA3


title: DSP-1001660016239-C-C08


title: ChIPseq_L36plClone2_dTAG_4h_KLF5_Rep1

description: Library name: Sample057

data_processing:
Paired or end sequencing reads were mapped to the reference genome assembly hg38 using bowtie2. PCR duplicates were removed with samtools markdup and replicates were merged using samtools merge. Bigwig files were generated removing blacklist regions using reads per genomic content (RPGC) normalization with bamCoverage . MACS3 callpeak was used to call the significant peaks with non-broad cutoff of 0.05 for while using input files from respective conditions as background.
Assembly: hg38
Supplementary files format and content: Normalized bigwig for each condition
Supplementary files format and content: peaks.narrowPeak file for each condition

growth_protocol: AsPC1 and BxPC3 (RPMI, 10% FBS, 1% Pen-Strep), HPAFII and L36pl (phenol red free MEM, 10% FBS, 1% Pen-Strep) were maintained in humidified 5% CO2 incubator at 37C.

extract_protocol:
Chromatin immunoprecipitation was performed by crosslinking cells with 1% formaldehyde for 20 min and quenched by 1.25 M glycine for 5 min. Cells were lysed with lysis buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 0.5% v/v NP-40, 1% v/v Triton X-100, 10 mM NaF). Nuclear pellets were resuspended and sonicated in sonication buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 1% v/v NP-40, 0.5% v/v sodium deoxycholate, 10 mM NaF, 0.1% SDS) using a Bioruptor Pico (Diagenode) and a cycle setting of 30 sec on/off until fragment sizes around 200-500 bp was reached. Protease and phosphatase inhibitors were added to both lysis and sonication buffers. Samples were precleared by 50% slurry of sepharose resuspended in sonication buffer. Antibodies were added and incubated rotating overnight. Sepharose beads coupled with Protein A (rabbit antibodies) or Protein G (mouse or goat antibodies) were added to samples and incubated for 2 hr, washed, de-crosslinked, RNAse A and proteinase K treated, and DNA was extracted.
ChIP DNA was quantified with Qubit using the Qubit 1X dsDNA High Sensitivity Kit and libraries were prepped per supplier’s protocol using the MicroPlex Library Preparatioin Kit v3 (Diagenode, C05010001). The library fragment size was determined by TapeStation using the High Sensitivity D1000 Sample Buffer and High Sensitivity D1000 ScreenTape.

tag: sample group


title: female control, 7 dpi, sample3

description: Library name: F7CTR3


title: female control, 7 dpi, sample2

description: Library name: F7CTR2


title: ChIPseq_L36plClone2_dTAG_4h_KLF5_Rep2

description: Library name: Sample058


title: DSP-1001660016239-C-C07


title: female SCFA-treated, 3 dpi, sample 4

description: Library name: F3SCFA4


title: female control, 7 dpi, sample1

description: Library name: F7CTR1


title: EU-RNAseq_L36plClone2_dTAG_1h_Rep1

description: Library name: Sample062


title: DSP-1001660016239-C-C06


title: female SCFA-treated, 3 dpi, sample 5

description: Library name: F3SCFA5


title: ChIPseq_L36plClone2_dTAG_4h_H3K4me3_Rep2

description: Library name: Sample055


title: female SCFA-treated, 3 dpi, sample3

description: Library name: F3SCFA3


title: female SCFA-treated, 3 dpi, sample1

description: Library name: F3SCFA1


title: female control, 14 dpi, sample1

description: Library name: F14CTR1


title: ChIPseq_L36plClone2_dTAG_4h_H3K27ac_Rep3

description: Library name: Sample053


title: DSP-1001660016239-C-C04


title: female SCFA-treated, 7 dpi, sample1

description: Library name: F7SCFA1


title: female control, 3 dpi, sample3

description: Library name: F3CTR3


title: female SCFA-treated, 3 dpi, sample2

description: Library name: F3SCFA2


title: female control, 3 dpi, sample1

description: Library name: F3CTR1


title: ChIPseq_L36plClone2_dTAG_4h_H3K4me3_Rep1

description: Library name: Sample054


title: DSP-1001660016239-C-C03


title: female control, 3 dpi, sample2

description: Library name: F3CTR2


title: Tibialis anterior muscle tissue from BAY2416964-treated Female C57BL/6 mice (18 months old)-4

city: Augusta

first: Meghan

middle: E.

last: McGee-Lawrence

state: Georgia

address: 1120 15th Street

department: Department of Cellular Biology and Anatomy

institute: Augusta University

description: Library name: MB4

data_processing:
Illumina Partek FLOW was used to process the raw RNA-seq files (fastq.gz files)
Trimmed sequencing reads were alogned to mm39 using STAR 2.7.8a aligner
aligned reads were quantified using ensemble transcripts release 104
quantified data were then normalized using CPM, offset and log base 2 transformation
Assembly: mm39
Supplementary files format and content: normalized counts
Supplementary files format and content: txt file inclduing normalized counts for each sample

source_name: Tibialis anterior muscle

extract_protocol:
for cortical bone, RNA was isolated with TRIzol.  For skeletal muscle, RNA was extracted using the Promega Maxwell RSC simplyRNA Tissue kit (cat#AS1340).
RNA libraries for RNA-seq were generated using the Illumina NovaSeq 6000 platform for 300 cycles according to manufacturer’s instructions

value: Tibialis anterior muscle


title: Tibialis anterior muscle tissue from BAY2416964-treated Female C57BL/6 mice (18 months old)-3

description: Library name: MB3


title: ChIPseq_L36plClone2_dTAG_4h_H3K4me3_Rep3

description: Library name: Sample056


title: DSP-1001660016239-C-C02

first: Mohamed

last: Noureldein

institute: University of Michigan


title: Tibialis anterior muscle tissue from BAY2416964-treated Female C57BL/6 mice (18 months old)-2

description: Library name: MB2


title: ChIPseq_L36plClone2_dTAG_4h_H3K27ac_Rep1

description: Library name: Sample051


title: DSP-1001660016239-C-C01


title: Tibialis anterior muscle tissue from Vehicle-treated Female C57BL/6 mice (18 months old)-4

description: Library name: MC4

value: Vehicle


title: DSP-1001660016239-C-C05


title: Tibialis anterior muscle tissue from Vehicle-treated Female C57BL/6 mice (18 months old)-2

description: Library name: MC2


title: Tibialis anterior muscle tissue from BAY2416964-treated Female C57BL/6 mice (18 months old)-1

description: Library name: MB1


title: ChIPseq_L36plClone2_dTAG_24h_KLF5_Rep2

description: Library name: Sample050


title: ChIPseq_L36plClone2_dTAG_24h_KLF5_Rep1

description: Library name: Sample049


title: ChIPseq_L36plClone2_dTAG_4h_H3K27ac_Rep2

description: Library name: Sample052


title: cortical bone tissue from BAY2416964-treated Female C57BL/6 mice (18 months old)-4

description: Library name: B4

source_name: cortical bone

value: cortical bone


title: Tibialis anterior muscle tissue from Vehicle-treated Female C57BL/6 mice (18 months old)-1

description: Library name: MC1


title: Tibialis anterior muscle tissue from Vehicle-treated Female C57BL/6 mice (18 months old)-3

description: Library name: MC3


title: DSP-1001660016239-C-B11


title: DSP-1001660016239-C-B10


title: cortical bone tissue from BAY2416964-treated Female C57BL/6 mice (18 months old)-3

description: Library name: B3


title: cortical bone tissue from BAY2416964-treated Female C57BL/6 mice (18 months old)-2

description: Library name: B2


title: ChIPseq_L36plClone2_dTAG_24h_H3K4me3_Rep3

description: Library name: Sample048


title: cortical bone tissue from BAY2416964-treated Female C57BL/6 mice (18 months old)-1

description: Library name: B1


title: ChIPseq_L36plClone2_dTAG_24h_H3K4me3_Rep2

description: Library name: Sample047


title: cortical bone tissue from Vehicle-treated Female C57BL/6 mice (18 months old)-3

description: Library name: C3


title: ChIPseq_L36plClone2_dTAG_24h_H3K4me3_Rep1

description: Library name: Sample046


title: cortical bone tissue from Vehicle-treated Female C57BL/6 mice (18 months old)-4

description: Library name: C4


title: DSP-1001660016239-C-B08


title: cortical bone tissue from Vehicle-treated Female C57BL/6 mice (18 months old)-2

description: Library name: C2


title: ChIPseq_L36plClone2_dTAG_24h_H3K27ac_Rep3

description: Library name: Sample045


title: DSP-1001660016239-C-B07


title: Ventricle, Pos Cre, Sample 4

city: Iowa City

first: Chad

middle: E

last: Grueter

state: IA

address: 169 Newton Rd, 4332 PBDB

department: Internal Medicine

institute: University of Iowa

description:
Library name: poscre-6M
poscre-6M-trim_FPKM

data_processing:
BaseSpace (Illumina) FastQ Toolkit 2.2.6
Raw sequences were aligned to UCSC mm10 using Bowtie2 v2.2.6 on RNAseq Alignment v1.1.1 in BaseSpace.
Alignments were uploaded into the Cufflinks Assembly and DE v2.1.0 (BaseSpace, Illumina)
Assembly: UCSC mm10
Supplementary files format and content: txt file includes FPKM values for all samples

source_name: ventricular lysate

extract_protocol:
RNA isolation was performed using Monarch Total RNA isolation kit (NEB) according to the instruction manual.
RNA libraries were prepped using TruSeq Stranded Total RNA with RiboZero Gold Kit (Illumina) according to manufacturer's instructions

value: ventricular lysate

value: Med13/13L fl/fl

value: Cre Positive

value: Male

value: Tamoxifen Chow

value: 12 weeks


title: ChIPseq_L36plClone2_dTAG_24h_H3K27ac_Rep2

description: Library name: Sample044


title: DSP-1001660016239-C-B12

city: Ann Arbor

address: 109 Zina Pitcher Place


title: cortical bone tissue from Vehicle-treated Female C57BL/6 mice (18 months old)-1

description: Library name: C1


title: ChIPseq_L36plClone2_dTAG_24h_H3K27ac_Rep1

description: Library name: Sample043


title: Ventricle, Pos Cre, Sample 2

description:
Library name: poscre-4M
Poscre-4M-Correct_FPKM


title: DSP-1001660016239-C-B06


title: Ventricle, Pos Cre, Sample 1

description:
Library name: poscre-1M
poscre-1M-trim_FPKM


title: Ventricle, Neg Cre, Sample 4

description:
Library name: negcre-4M
Negcre-4M-trim_FPKM

value: Cre Negative


title: DSP-1001660016239-C-B05


title: DSP-1001660016239-C-B04


title: ChIPseq_L36plClone2_dTAG_1h_KLF5_Rep2

description: Library name: Sample042


title: Ventricle, Pos Cre, Sample 3

description:
Library name: poscre-5M
pos5-trim_FPKM


title: Ventricle, Neg Cre, Sample 2

description:
Library name: negcre-2M-2
Negcre-2M-2_FPKM


title: Ventricle, Neg Cre, Sample 3

description:
Library name: negcre-3M
Negcre-3M-trim_FPKM


title: DSP-1001660016239-C-B09


title: DSP-1001660016239-C-B03


title: Ventricle, Neg Cre, Sample 1

description:
Library name: negcre-2M
Negcre-2M-trim_FPKM


title: DSP-1001660016239-C-B02


title: ChIPseq_L36plClone2_dTAG_1h_KLF5_Rep1

description: Library name: Sample041


title: ChIPseq_L36plClone2_dTAG_1h_H3K4me3_Rep3

description: Library name: Sample040


title: whole organoids at d100

city: Darmstadt

first: Tamara

last: Bender

address: Planckstraße 1

institute: GSI Helmholtzzentrum für Schwerionenforschun

description:
Library name: hols
10X Genomics

data_processing:
Raw reads were preprocessed and aligned to the human genome (hg38) using the Cell ranger pipeline (10X Genomics). Initial quality control and visualization of the data was performed in the Loupe browser (10X Genomics). Data analysis of the filtered feature matrix was performed using the R software (https://www.r-project.org/) with Seurat package and Seurat workflow (https://satijalab.org/seurat/). Cells that had unique feature counts over 2500 or less than 200, and cells that had >5% mitochondrial count were filtered out from the dataset. The data was normalized using a SCTransform function for data normalization, scaling and reduction prior to graph-based clustering and visualization of the merged and integrated datasets for organoids and organoid slices.
Assembly: Human (hg38)
Supplementary files format and content: Tab-separated values and matrix files

source_name: cerebral organoid

extract_protocol:
Organoid slices (n = 3) and organoids (n = 3), each pooled from the same biological replicate in one tube, were washed in cold PBS at 300xg, 5 min. After complete removal of PBS, organoid slices and organoids were placed on dry ice for 5 min, and then stored in liquid nitrogen. Preparation of samples for sequencing including the isolation of the nuclei, and initial quality control were performed as a service by GENEWIZ/AZENTA (USA).
Library preparation, sequencing and initial data processing were performed as a service by GENEWIZ/AZENTA (USA). The RNA-seq library was prepared using 10X Genomics Chromium® 3` expression, and the 10X library sequencing was performed on the Illumina series. The target number of cells per sample was 6000, and number of reads per cell 50000.

value: cerebral organoid

value: neural and glia cells

value: WT

value: control


title: organoid slices at d100

description:
Library name: ALI
10X Genomics


title: DSP-1001660016239-C-B01