title: 7231_L6b-pyramidal-neuron_HSB2341, HD

description: 706 nuclei


title: 7044_L6b-pyramidal-neuron_BEB19025, CTRL

status: Public on Jan 17 2024

type: SRA

city: New York

first: Christina

last: Pressl

state: NY

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

description: 2299 nuclei

library_source: transcriptomic

data_processing:
Sequence and transcript coordinates for human hg38 UCSC genome and gene models were retrieved from the BSgenome.Hsapiens.UCSC.hg38 Bioconductor package (version 1.4.1) and TxDb.Haspiens.UCSC.hg38.knownGene (version 3.4.0) Bioconductor libraries respectively. FANSseq reads were aligned to the genome using Rsubread's subjunc method (version 1.30.6).
Aligned reads were exported as bigWigs normalized to reads per million using the rtracklayer package (version 1.40.6).
Aligned reads in genes were counted using the featurecounts function within the Rsubread package against gene exons.
Cell-type specific differential gene expression analyses were performed using DESeq2. Results were filtered for genes with accessible promoters for each cell-type and GO analyses were performed for cell-type specific comparisons between HD and NC as well as between L5a and L6 cells in HD.
Assembly: BSgenome.Hsapiens.UCSC.hg38
Supplementary files format and content: BigWig files, Counts files, DESeq2 and GO analyses results in .csv and .xlsx file format

molecule: nuclear RNA

organism: Homo sapiens

source_name: Cortex BA22

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

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

tag: tissue

value: Cortex BA22

tag: cell type

value: L6b pyramidal neuron

tag: donor

tag: age

tag: Sex

value: M

tag: pmi (hrs)

tag: donor category

value: CTRL


title: 7045_L5a-pyramidal-neuron_BEB19025, CTRL

description: 12282 nuclei

value: L5a pyramidal neuron


title: 7012_L5a-pyramidal-neuron_BEB18135, CTRL

description: 8437 nuclei


title: 7230_L6a-pyramidal-neuron_HSB2341, HD

description: 1316 nuclei

value: L6a pyramidal neuron

tag: genotype

value: F

value: HD


title: 7043_L6a-pyramidal-neuron_BEB19025, CTRL

description: 10421 nuclei


title: 6937_VENs_BEB18116, CTRL

description: 967 nuclei

source_name: Cortex BA9

value: Cortex BA9

value: VENs


title: 6938_L6a-pyramidal-neuron_BEB18116, CTRL

description: 6716 nuclei


title: 6940_L5a-pyramidal-neuron_BEB18116, CTRL

description: 8194 nuclei


title: 7009_L5rs_BEB18135, CTRL

description: 944 nuclei


title: 6913_L5a-pyramidal-neuron_BEB18116, CTRL

description: 8562 nuclei

source_name: Cortex BA24

value: Cortex BA24


title: 6939_L6b-pyramidal-neuron_BEB18116, CTRL

description: 813 nuclei


title: 7010_L6a-pyramidal-neuron_BEB18135, CTRL

description: 7036 nuclei


title: 6912_L6b-pyramidal-neuron_BEB18116, CTRL

description: 1134 nuclei


title: 6910_VENs_BEB18116, CTRL

description: 808 nuclei


title: 6911_L6a-pyramidal-neuron_BEB18116, CTRL

description: 8955 nuclei


title: 6740_VENs_HSB2341, HD

description: Tube 3


title: 6738_L6b-pyramidal-neuron_HSB2341, HD

description: Tube 3


title: 6700_L6b-pyramidal-neuron_S04002, HD

description: 827 nuclei

source_name: Cortex BA4

value: Cortex BA4


title: 6701_L5a-pyramidal-neuron_S04002, HD

description: 6110 nuclei


title: 6739_L5a-pyramidal-neuron_HSB2341, HD

description: Tube 3


title: 6737_L6a-pyramidal-neuron_HSB2341, HD

description: Tube 3


title: 6699_L6a-pyramidal-neuron_S04002, HD

description: 5281 nuclei


title: 6698_Betz-cell_S04002, HD

description: 1455 nuclei

value: Betz cell


title: 6642_L5a-pyramidal-neuron_S01891, HD

description: 12,037 nuclei - CW PREP


title: 6643_Betz-cell_S01891, HD

description: 1,454 nuclei - CW PREP


title: 6641_L6b-pyramidal-neuron_S01891, HD

description: 2,514 nuclei - CW PREP


title: 6636_Betz-cell_S13630, HD

description: 3,421 nuclei - CW PREP


title: 6639_Betz-cell_S02205, HD

description: 688 nuclei - CW PREP


title: 6640_L6a-pyramidal-neuron_S01891, HD

description: 5,431 nuclei - CW PREP


title: 6631_L5a-pyramidal-neuron_S15682, HD

description: 9,332 nuclei - CW PREP


title: 6634_L6b-pyramidal-neuron_S13630, HD

description: 3,727 nuclei - CW PREP


title: 6635_L5a-pyramidal-neuron_S13630, HD

description: 18,046 nuclei - CW PREP


title: 6572_L6a-pyramidal-neuron_HCTSU, CTRL

description: 28,423 nuclei - CW PREP

value: HCTSU


title: 6587_L6b-pyramidal-neuron_BEB18116, CTRL

description: 3,414 nuclei - CW PREP

source_name: Insular cortex

value: Insular cortex


title: 6586_L6a-pyramidal-neuron_BEB18116, CTRL

description: 22,561 nuclei - CW PREP


title: 6632_Betz-cell_S15682, HD

description: 2,260 nuclei - CW PREP


title: 6629_L6a-pyramidal-neuron_S15682, HD

description: 14,656 nuclei - CW PREP


title: 6529_L5a-pyramidal-neuron_HCT-17-HFG, CTRL

description: 5022 nuclei


title: 6527_L6a-pyramidal-neuron_HCT-17-HFG, CTRL

description: 1657 nuclei


title: 6463_L6b-pyramidal-neuron_HSB3167, HD

description: 907 nuclei


title: 6266_VENs_HSB3730, HD

description: 744 nuclei


title: 6267_L6a-pyramidal-neuron_HSB3730, HD

description: 1884 nuclei


title: 6268_L6b-pyramidal-neuron_HSB3730, HD

description: 1037 nuclei


title: 6219_L6b-pyramidal-neuron_HSB3358, HD

description: 425 nuclei


title: 6220_L5a-pyramidal-neuron_HSB3358, HD

description: 1274 nuclei


title: 6217_VENs_HSB3358, HD

description: 489 nuclei


title: 6045_L5a-pyramidal-neuron_BEB18117, CTRL

description: 5448 nuclei


title: 6218_L6a-pyramidal-neuron_HSB3358, HD

description: 1479 nuclei


title: 6637_L6a-pyramidal-neuron_S02205, HD

description: 1,435 nuclei - CW PREP


title: 6638_L5a-pyramidal-neuron_S02205, HD

description: 2,628 nuclei - CW PREP


title: 6633_L6a-pyramidal-neuron_S13630, HD

description: 7,528 nuclei - CW PREP


title: 6630_L6b-pyramidal-neuron_S15682, HD

description: 2,585 nuclei - CW PREP


title: 6573_L6b-pyramidal-neuron_HCTSU, CTRL

description: 4,330 CW PREP


title: 6588_L5a-pyramidal-neuron_BEB18116, CTRL

description: 21,103 nuclei - CW PREP


title: 6044_L6b-pyramidal-neuron_BEB18117, CTRL

description: 1328 nuclei


title: 6574_L5a-pyramidal-neuron_HCTSU, CTRL

description: 29,006 nuclei - CW PREP


title: 6043_L6a-pyramidal-neuron_BEB18117, CTRL

description: 5391 nuclei


title: 5963_L6b-pyramidal-neuron_BEB19025, CTRL

description: 569 nuclei


title: 6042_Betz-cell_BEB18117, CTRL

description: 1410 nuclei


title: 5964_L5a-pyramidal-neuron_BEB19025, CTRL

description: 2414 nuclei


title: 5928_L5a-pyramidal-neuron_HSB3358, HD

source_name: Cortex BA17

value: Cortex BA17


title: 5962_L6a-pyramidal-neuron_BEB19025, CTRL

description: 3051 nuclei


title: 6269_L5a-pyramidal-neuron_HSB3730, HD

description: 3616 nuclei


title: 5961_VENs_BEB19025, CTRL

description: 385 nuclei


title: 5929_L6a-pyramidal-neuron_HSB3167, HD


title: 5930_L6b-pyramidal-neuron_HSB3167, HD


title: 5924_L5a-pyramidal-neuron_HSB3358, HD


title: 5927_L6b-pyramidal-neuron_HSB3358, HD


title: 5922_L6a-pyramidal-neuron_HSB3358, HD


title: 5926_L6a-pyramidal-neuron_HSB3358, HD


title: 5916_VENs_HSB3358, HD

description: 22-2-1 sort


title: 5923_L6b-pyramidal-neuron_HSB3358, HD


title: 5925_VENs_HSB3358, HD


title: 5914_L6b-pyramidal-neuron_HSB3358, HD

description: 22-2-1 sort


title: 5913_L6a-pyramidal-neuron_HSB3358, HD

description: 22-2-1 sort


title: 5915_L5a-pyramidal-neuron_HSB3358, HD

description: 22-2-1 sort


title: 5912_VENs_HSB3167, HD

description: 22-2-1 sort


title: 5908_VENs_HSB2341, HD

description: 22-2-1 sort


title: 5909_L6b-pyramidal-neuron_HSB3167, HD

description: 22-2-1 sort


title: 5907_L5a-pyramidal-neuron_HSB2341, HD

description: 22-2-1 sort


title: 5892_VENs_HSB3167, HD

description: 970 nuclei


title: 5906_L6b-pyramidal-neuron_HSB2341, HD

description: 22-2-1 sort


title: 5911_L5a-pyramidal-neuron_HSB3167, HD

description: 22-2-1 sort


title: 5891_L5a-pyramidal-neuron_HSB3167, HD

description: 4575 nuclei


title: 5884_VENs_BEB18135, CTRL

description: 798 nuclei


title: 5889_L6a-pyramidal-neuron_HSB3167, HD

description: 3497 nuclei


title: 5890_L6b-pyramidal-neuron_HSB3167, HD

description: 1376 nuclei


title: 5880_VENs_HCTSU, CTRL

description: 7142 nuclei


title: 5885_L6a-pyramidal-neuron_HSB2341, HD

description: 2735 nuclei


title: 5881_L6a-pyramidal-neuron_BEB18135, CTRL

description: 2101 nuclei


title: 5879_L5a-pyramidal-neuron_HCTSU, CTRL

description: 9262 nuclei


title: 5876_VENs_BEB19025, CTRL

description: 5015 nuclei


title: 5883_L5a-pyramidal-neuron_BEB18135, CTRL

description: 2565 nuclei


title: 5875_L5a-pyramidal-neuron_BEB19025, CTRL

description: 20638 nuclei


title: 5877_L6a-pyramidal-neuron_HCTSU, CTRL

description: 13806 nuclei


title: 5870_L6b-pyramidal-neuron_BEB18135, CTRL

description: 10958 nuclei


title: 5873_L6a-pyramidal-neuron_BEB19025, CTRL

description: 25408 nuclei


title: 5868_VENs_HCTSU, CTRL

description: 1004 nuclei


title: 5866_L6b-pyramidal-neuron_HCTSU, CTRL

description: 1447 nuclei


title: 5867_L5a-pyramidal-neuron_HCTSU, CTRL

description: 4598 nuclei


title: 5871_L5a-pyramidal-neuron_BEB18135, CTRL

description: 35271 nuclei


title: 5865_L6a-pyramidal-neuron_HCTSU, CTRL

description: 2809 nuclei


title: 5869_L6a-pyramidal-neuron_BEB18135, CTRL

description: 31698 nuclei


title: 5874_L6b-pyramidal-neuron_BEB19025, CTRL

description: 7442 nuclei


title: 5864_Betz-cell_HSB3167, HD

description: 482 nuclei


title: 5863_L5a-pyramidal-neuron_HSB3167, HD

description: 2884 nuclei


title: 5862_L6b-pyramidal-neuron_HSB3167, HD

description: 488 nuclei


title: 5861_L6a-pyramidal-neuron_HSB3167, HD

description: 2573 nuclei


title: 5806_L5a-pyramidal-neuron_BEB18135, CTRL

description: 23,611 nuclei (Prepared by Cuidong)


title: 5888_VENs_HSB2341, HD

description: 2975 nuclei


title: 5569_L5a-pyramidal-neuron_HSB2385, HD

description: 1495 nuclei


title: 5804_L6a-pyramidal-neuron_BEB18135, CTRL

description: 22,101 nuclei (Prepared by Cuidong)


title: 5803_Betz-cell_BEB18135, CTRL

description: 2,967 nuclei (Prepared by Cuidong)


title: 5805_L6b-pyramidal-neuron_BEB18135, CTRL

description: 3,797 nuclei (Prepared by Cuidong)


title: 5568_L6b-pyramidal-neuron_HSB2385, HD

description: 1605 nuclei


title: 5566_Betz-cell_HSB2385, HD

description: 3242 nuclei


title: 5541_Betz-cell_HSB3383, HD

description: 910 nuclei


title: 5528_L6b-pyramidal-neuron_HSB3730, HD

description: 592 nuclei


title: 5872_VENs_BEB18135, CTRL

description: 7815 nuclei


title: 5529_L5a-pyramidal-neuron_HSB3730, HD

description: 3711 nuclei


title: 5526_Betz-cell_HSB3730, HD

description: 1723 nuclei


title: 5356_Betz-cell_BEB18116, CTRL

description: 2,725 nuclei


title: 5441_VENs_HCTSU, CTRL

description: 1,331 nuclei


title: 5442_L6a-pyramidal-neuron_HCTSU, CTRL

description: 13,814 nuclei


title: 5444_L5a-pyramidal-neuron_HCTSU, CTRL

description: 9,027 nuclei


title: 5358_L6b-pyramidal-neuron_BEB18116, CTRL

description: 1,743 nuclei


title: 5359_L5a-pyramidal-neuron_BEB18116, CTRL

description: 5378 nuclei


title: 5357_L6a-pyramidal-neuron_BEB18116, CTRL

description: 5,413 nuclei


title: 5223_L6b-pyramidal-neuron_HCT-17-HFG, CTRL

description: 767 nuclei (test)

source_name: Extrastriate cortex, BA18

value: Extrastriate cortex, BA18


title: 5222_L6a-pyramidal-neuron_HCT-17-HFG, CTRL

description: 2,053 nuclei


title: 5224_L5a-pyramidal-neuron_HCT-17-HFG, CTRL

description: 1,072 nuclei


title: 5023_Betz-cell_HSB3358, HD

description: 9,204 nuclei


title: 5024_L6a-pyramidal-neuron_HSB3358, HD

description: 6,126 nuclei


title: 5012_L5a-pyramidal-neuron_HCT-17-HFG, CTRL

description: 4,638 nuclei


title: 5543_L6b-pyramidal-neuron_HSB3383, HD

description: 1374 nuclei


title: 5011_L6a-pyramidal-neuron_HCT-17-HFG, CTRL

description: 7,090 nuclei


title: 4952_L6b-pyramidal-neuron_BEB19025, CTRL

description: 344 nuclei


title: 4942_L5a-pyramidal-neuron_BEB19025, CTRL

description: 4298 nuclei


title: 5518_L6b-pyramidal-neuron_HSB3881, HD

description: 546 nuclei


title: 4941_L6b-pyramidal-neuron_BEB19025, CTRL

description: 1350 nuclei


title: 4951_L6a-pyramidal-neuron_BEB19025, CTRL

description: 1008 nuclei


title: TDF 2

type: protein

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

country: Japan

institute: Kanazawa University

scan_protocol: The array was washed with Tris Buffered Saline with 0.05% Tween20 (TBST) and stained with the 4G10 phosphorylated protein-specific antibody (Merck, #05-1050) and a secondary fluorescein-conjugated antibody (Thermo, #A21235) to detect the phosphorylated tyrosine residues.

data_processing: Signal data were averaged (n=6), filtered and normalized by BRB-ArrayTools (https://brb.nci.nih.gov/BRB-ArrayTools).

label: Alexa Fluor 647

molecule: protein

source_name: HeG2 xenografted

label_protocol: Cell lysates of 100 μg total protein were applied to the array with additional ATP at 30°C for 3 h. After termination of the kinase reaction, the array was washed with Tris-buffered saline containing 0.05% Tween 20 and stained with a 4G10 phosphorylated protein-specific antibody (Merck, #05-1050) and a secondary fluorescein-conjugated antibody (Thermo, #A21235) to detect the phosphorylated tyrosine residues.

growth_protocol: NOD-SCID mice were purchased from The Jackson Laboratory. Six-week-old male mice were used for study. Dimethyl sulfoxide (DMSO), ETV, ADV, and TDF were administered intraperitoneally to the mice at a concentration of 90 mg/kg every 3 days. At 7 days after first treatment with the NAs, the mice were injected subcutaneously with 5.0 × 106 HepG2 cells in the right flank. At day 50, tumor volume was evaluated and phosphorylation activity was measured.

extract_protocol: Cell lysates were extracted from each tumor and100 μg total protein was used for labbelling.

value: HeG2 xenografted in subcutaneus of NOD-SCID mice

tag: treatment

value: TDF treated


title: ETV 2

hyb_protocol: Cell lysates of 100 μg total protein were applied to the array with additional ATP at 30°C for 3 h.

treatment_protocol: Six-week-old male mice were used for study. Dimethyl sulfoxide (DMSO), ETV, ADV, and TDF were administered intraperitoneally to the mice at a concentration of 90 mg/kg every 3 days. At 7 days after first treatment with the NAs, the mice were injected subcutaneously with 5.0 × 106 HepG2 cells in the right flank. At day 50, tumor volume was evaluated and phosphorylation activity was measured.

value: ETV treated


title: 4940_L6a-pyramidal-neuron_BEB19025, CTRL

description: 7711 nuclei

value: M

value: CTRL


title: TDF 1


title: ETV 1


title: ADV 1

value: ADV treated


title: 4838_L6b-pyramidal-neuron_BEB18135, CTRL

description: 1,824 nuclei

value: L6b pyramidal neuron


title: DMSO 1

value: Control


title: S_latifolia16_3

city: Fuzhou

first: mengting

last: weng

address: Xin dian town, jin'an district

country: China

institute: Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences

data_processing:
Cutadapt (V 2.7) was used to filter the original sequences and trim the reads with low sequencing quality
Fastqc (v 0.11.8) was used for data statistics.
HISAT2 (v 2.1.0) was used to align clean reads to the reference sequence
RSeQC (V 3.0.1) was used to evaluate the quality of the comparison results of sequencing
StringTie (v 1.3.3b) was used to evaluate the expression levels of mRNA and lncRNA, respectively
Assembly: Sparassis latifolia genome
Supplementary files format and content: text files include RPKM values for each Sample

molecule: total RNA

organism: Sparassis latifolia

source_name: fruiting body, cold storage, Day16

extract_protocol:
Total RNA was extracted from S. latifolia samples using the TRIzol reagent.
Ribosomal RNA was removed using Epicentre Ribo-Zero™ Gold Kits(Human/Mouse/Rat/other) (Epicentre, USA). Subsequently, the sequencing libraries were generated following manufacture commendations with varied index label by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA).

value: fruiting body

value: 4℃ storage

tag: time

value: Day 16


title: S_latifolia16_2


title: S_latifolia24_2

source_name: fruiting body, cold storage, Day24

value: Day 24


title: DMSO 2


title: 5542_L6a-pyramidal-neuron_HSB3383, HD

description: 1338 nuclei

value: Cortex BA4

value: L6a pyramidal neuron

value: F

value: HD


title: S_latifolia24_3


title: 4839_L5a-pyramidal-neuron_BEB18135, CTRL

description: 5,672 nuclei

value: L5a pyramidal neuron


title: S_latifolia8_3

source_name: fruiting body, cold storage, Day8

value: Day 8


title: S_latifolia16_1


title: 4821_L5a-pyramidal-neuron_HCTSU, CTRL

description: 3,704 nuclei

value: HCTSU


title: ADV 2

value: HeG2 xenografted in subcutaneus of NOD-SCID mice


title: S_latifolia8_2


title: S_latifolia0_2

source_name: fruiting body, cold storage, Day0

value: Day 0


title: 4820_L6b-pyramidal-neuron_HCTSU, CTRL

description: 1,698 nuclei

value: CTRL


title: S_latifolia24_1


title: 4680_L6a-pyramidal-neuron_HSB2341, HD

description: 2,192 nuclei

value: Cortex BA17


title: 4819_L6a-pyramidal-neuron_HCTSU, CTRL

description: 5,923 nuclei


title: 4953_L5a-pyramidal-neuron_BEB19025, CTRL

description: 915 nuclei

value: M


title: S_latifolia0_1


title: 5583_Betz-cell_HSB2116, HD

description: 2291 nuclei

value: Betz cell


title: S_latifolia0_3

value: fruiting body


title: 4909_L5a-pyramidal-neuron_BEB18135, CTRL

description: 1,880 nuclei


title: 4546_L6a-pyramidal-neuron_HCTSU, CTRL

description: 6,225 nuclei

source_name: Cortex BA19

value: Cortex BA19


title: 4818_Betz-cell_HCTSU, CTRL

description: 2,067 nuclei


title: 4548_L6b-pyramidal-neuron_HCTSU, CTRL

description: 1,401 nuclei

value: L6b pyramidal neuron


title: 4547_L5a-pyramidal-neuron_HCTSU, CTRL

description: 8,485 nuclei


title: 4908_L6a-pyramidal-neuron_BEB18135, CTRL

description: 9,064 nuclei


title: G⍺13-deficient, pLN, scRNAseq

city: Bethesda

first: David

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0
Clustering analysis by R Seurat package
Assembly: mm10
Supplementary files format and content: gene-cell-read-count in 10X H3 format

organism: Mus musculus

source_name: peripheral lymph node

extract_protocol:
RNA from isolated cells was extracted using the Qiagen Plus Micro kit
Libraries were generated for sequencing using standard Illumina protocols

value: GC B cells

value: peripheral lymph node

tag: strain

value: Cr2-cre Gna13f/f

value: 12 weeks old


title: 4837_L6a-pyramidal-neuron_BEB18135, CTRL

description: 5,882 nuclei

value: Cortex BA4

value: L6a pyramidal neuron


title: Control, pLN, scRNAseq

description: 10x Genomics


title: 4836_Betz-cell_BEB18135, CTRL

description: 2,388 nuclei


title: G⍺13-deficient, mLN, scRNAseq

description: 10x Genomics

source_name: mesenteric lymph node

value: mesenteric lymph node


title: Control, mLN, scRNAseq

description: 10x Genomics


title: HSB2385_BA4_NeuN-Ab_pos_SATB2-Ab_plusplus_fansExpID-1111

data_processing:
The snRNAseq raw data was processed using the count function in Cell Ranger (10X Genomics, version 6.0). Reads were aligned to the human genome (hg38) and including the intron regions, genes were mapped and counted in each nucleus. Counting matrices were generated in Cell Ranger and utilized in downstream analyses. Data was read into R and further processed using Seurat algorithms as well as other Bioconductor packages and custom code.
Assembly: BSgenome.Hsapiens.UCSC.hg38
Supplementary files format and content: raw and filtered feature, barcode, and matrix files

extract_protocol:
Nuclei were loaded and processed on the 10X platform for snRNAseq. 1000121 Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1, 16 rxns, 1000215 Dual Index Kit TT Set A 96 rxns, and Chromium Single Cell Controller were used.
snRNA/scRNA-seq

value: Nuclei from Mixed Neuronal Populations

tag: sort-gate

value: NeuNpos SATB2plus

value: HD


title: HSB2385_BA4_NeuN-Ab_pos_SATB2-Ab_med_fansExpID-1111

value: NeuNpos SATB2med


title: Sunn4_96h

city: Gainesville

first: Matias

last: Kirst

address: 367 Newins-Ziegler Hall, PO Box 110410

institute: University of Florida

description:
Roots, 96h
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Medicago truncatula (v5, release 1.9)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Medicago truncatula

source_name: Roots

growth_protocol: After removing M. truncatula seeds from their fruit, they were scarified and stratified to initiate germination. Seeds were sown on 1% agar plates with 1 μM of GA3. The plates were kept at 4 °C for three days to induce stratification. After incubating plates at 24 °C for 12 h in the dark, four seedlings were transferred to germination pouches. Each pouch contained four seedlings and 10 mL of Modified Nodulation Medium. Pouches were placed vertically in polypap stands, and the stands were placed in a tray and 7.5” (L) x 11’’ (W) x 21.25’’ (H) humidity dome. After 3 days, pouches were replenished with 10 mL of Modified Nodulation Medium. The growth chamber was kept at 24 °C with long-day light conditions (16 h light/8 h dark; 150 μmol m−2 s−1 light intensity).

extract_protocol:
Nuclei isolation was carried out at 4. Forty root segments were moved to a glass plate with 200 μL of modified Nuclei Isolation Buffer containing 0.5 U/uL Protector Rnase Inhibitor. After samples were fragmented with a sterile razor blade, the homogenate was washed into a 50 mL tube with NIB and incubated on a shaker for 5 min. All samples went through at least two stages of filtration, first with Miracloth and then with a 40 μm cell strainer. The samples were centrifuged for 5 min at 600 g before the supernatant was discarded without disturbing the pellet. The pellet was resuspended with 4 mL of NIB WASH. Centrifugation and resuspension were repeated once more. After the final centrifugation, 300 μL of NIB WASH was used to resuspend the pellet. Samples that contained debris underwent an additional filtration step with a 40 uM cell strainer with an attached 5 mL tube. Next, the suspension was transferred to a sterile tube compatible with the BD FACSAria™ IIU/III upgraded cell sorter. Nuclei were stained with 5 μg/mL DAPI for 5 min at 28 °C before sorting. The sample was used for Florescence Activated Nuclei Sorting (FANS) before being loaded onto the 10× Genomics microfluid chip.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Plants were inoculated by pipetting 1 mL of the S. meliloti 1021 suspension into each pouch

value: multiple

value: Roots

value: sunn-4 mutant

value: 1 week


title: HSB2385_BA4_NeuN-Ab_pos_SATB2-Ab_neg_fansExpID-1111

value: NeuNpos SATB2neg

value: M


title: Sunn4_48h

description:
Roots, 48h
10x Genomics


title: HSB2385_BA4_NeuN-Ab_neg_fansExpID-1111

value: Glial Nuclei

value: NeuNneg


title: BEB18135_BA4_NeuN-Ab_pos_SATB2-Ab_plusplus_fansExpID-1059

value: CTRL


title: S_latifolia8_1

value: fruiting body

value: 4℃ storage

value: Day 8


title: A17_96h

description:
Roots, 96h
10x Genomics

value: Jemalong A17 - WT


title: Sunn4_24h

description:
Roots, 24h
10x Genomics


title: A17_48h

description:
Roots, 48h
10x Genomics


title: BEB18135_BA4_NeuN-Ab_pos_SATB2-Ab_med_fansExpID-1059

value: Cortex BA4

value: Nuclei from Mixed Neuronal Populations


title: A17_24h

description:
Roots, 24h
10x Genomics


title: Control 24h U46619, replicate 2

description:
2x50 cycle
control_24h_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 human genome using STAR2
Raw read counts per gene were called with Htseq-Count
FPKM Normalization and median shift
Assembly: hg19
Supplementary files format and content: NUDUL1_GNA13_RNAseq_Normalized_Log2.txt

growth_protocol: NUDUL1 (Control or GNA13-deficient) cells were grown in advanced RPMI supplemented with 4% FBS with pen/strep and glutamine.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini kit
Libraries were generated for sequencing using standard Illumina protocols

treatment_protocol: NUDUL1 (Control or GNA13-deficient) cells were grown at 1 x 10^6 cells/ml and treated in duplicates with U46619 10nM for 24h.

tag: cell line

value: human DLBCL cell line

value: Cas9 engineered


title: HSB2116_BA4_NeuN-Ab_pos_SATB2-Ab_plusplus_fansExpID-1054

value: NeuNpos SATB2plus

value: F

value: HD


title: HSB2116_BA4_NeuN-Ab_pos_SATB2-Ab_med_fansExpID-1054

value: NeuNpos SATB2med


title: GNA13-deficient 24h U46619, replicate 2

description:
2x50 cycle
GNA13_24h_2


title: HCTSU_BA4_NeuN-Ab_pos_SATB2-Ab_plusplus_fansExpID-1058

value: HCTSU


title: HSB2116_BA4_NeuN-Ab_neg_fansExpID-1054


title: BEB18135_BA4_NeuN-Ab_pos_SATB2-Ab_neg_fansExpID-1059

value: NeuNpos SATB2neg

value: M


title: HCTSU_BA4_NeuN-Ab_pos_SATB2-Ab_neg_fansExpID-1058


title: HSB2116_BA4_NeuN-Ab_pos_SATB2-Ab_neg_fansExpID-1054


title: BEB18135_BA4_NeuN-Ab_neg_fansExpID-1058

value: Glial Nuclei

value: NeuNneg


title: GNA13-deficient 24h U46619, replicate 1

description:
2x50 cycle
GNA13_24h_1


title: Control 24h U46619, replicate 1

description:
2x50 cycle
control_24h_1


title: T1DAL_243767, week 104, CD57pos_DP_NN_CD8

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

library_source: genomic

data_processing:
Following sequencing, base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. The FASTQs were aligned to the University of California Santa Cruz (UCSC) Human genome assembly version 38.91, using STAR (v.2.4.2a). Duplicate filtering, QC and metrics analysis was performed using the Picard (v 1.134) family of tools. For peak calls, MACS (v 2.1.0) was run in paired-end mode with a q-value cutoff of 0.05 on filtered reads.
Assembly: GRCh38.91
Supplementary files format and content: "macs2_peaks-narrow.bed" files contain peak calling output from MACS2 in bed format.

molecule: genomic DNA

source_name: PBMC

extract_protocol:
Bulk ATAC-seq was performed using the method described by Buenrostro et al. 2015. 50,000 cells were lysed to produce a crude nuclei preparation
50,000 cells were lysed to produce a crude nuclei preparation, followed by transposition and PCR amplification of the transposed DNA fragments to add Illumina-compatible indexed adapters. After 1.8x Ampure XP (Beckman Coulter) size selection, concentration of each library was assessed using a 100-1000 bp gate on a Tapestation 4200 (Agilent). Pooled libraries were run with paired-end 59 base sequencing on a NextSeq 2000 with a P3 sequencing kit (Illumina) with a target of 50M reads.

value: PBMC

tag: maskeddonorid

value: R

value: CD57+ DP Non-naive CD8 T cells:singlet, live, CD14-CD19-CD56-CD3+CD8+CD4-, not CD45RA+CCR7+, KLRG1+TIGIT+, CD57+

tag: lib id

tag: timepoint

value: Week 104

value: alefacept


title: HCTSU_BA4_NeuN-Ab_neg_fansExpID-1058

value: Cortex BA4

value: CTRL


title: T1DAL_243767, week 104, DN_NN_CD8

value: DN Non-naive CD8 T cells:singlet, live, CD14-CD19-CD56-CD3+CD8+CD4-, not CD45RA+CCR7+, KLRG1-TIGIT-


title: T1DAL_243767, baseline, DN_NN_CD8

value: Baseline


title: T1DAL_243767, week 104, CD57neg_DP_NN_CD8

value: CD57- DP Non-naive CD8 T cells:singlet, live, CD14-CD19-CD56-CD3+CD8+CD4-, not CD45RA+CCR7+, KLRG1+TIGIT+, CD57-


title: T1DAL_243767, baseline, CD57pos_DP_NN_CD8


title: A17_0h

description:
Roots, 0h
10x Genomics

value: multiple

value: Roots

value: Jemalong A17 - WT

value: 1 week


title: 6048_Oligodendrocyte_BEB18117_CTRL

description: 124471 nuclei

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

value: Oligodendrocyte

value: M


title: Sunn4_0h

description:
Roots, 0h
10x Genomics

value: sunn-4 mutant


title: T1DAL_323347, week 104, DN_NN_CD8

value: PBMC


title: T1DAL_243767, baseline, CD57neg_DP_NN_CD8

value: R


title: 6042_Betz-cell_BEB18117_CTRL

description: 1410 nuclei

value: Betz cell


title: 6037_L2-L3-pyramidal-neuron_BEB18117_CTRL

description: 52758 nuclei

value: L2/L3 pyramidal neuron


title: 5962_L6a-pyramidal-neuron_BEB19025_CTRL

description: 3051 nuclei

value: Cortex BA9

value: L6a pyramidal neuron


title: 5876_VENs_BEB19025_CTRL

description: 5015 nuclei

value: Insular cortex

value: VENs

value: CTRL


title: T1DAL_323347, baseline, CD57pos_DP_NN_CD8

value: CD57+ DP Non-naive CD8 T cells:singlet, live, CD14-CD19-CD56-CD3+CD8+CD4-, not CD45RA+CCR7+, KLRG1+TIGIT+, CD57+

value: Baseline

value: alefacept


title: T1DAL_323347, baseline, CD57neg_DP_NN_CD8

value: CD57- DP Non-naive CD8 T cells:singlet, live, CD14-CD19-CD56-CD3+CD8+CD4-, not CD45RA+CCR7+, KLRG1+TIGIT+, CD57-


title: T1DAL_323347, baseline, DN_NN_CD8

value: DN Non-naive CD8 T cells:singlet, live, CD14-CD19-CD56-CD3+CD8+CD4-, not CD45RA+CCR7+, KLRG1-TIGIT-


title: HCTSU_BA4_NeuN-Ab_pos_SATB2-Ab_med_fansExpID-1058

value: Cortex BA4

value: Nuclei from Mixed Neuronal Populations

value: NeuNpos SATB2med

value: HCTSU

value: F


title: 5866_L6b-pyramidal-neuron_HCTSU_CTRL

description: 1447 nuclei

value: L6b pyramidal neuron


title: 5810_Oligodendrocyte-progenitor_BEB18135_CTRL

description: 7,065 nuclei (Prepared by Cuidong)

value: Oligodendrocyte progenitor

value: M


title: 5473_Oligodendrocyte_HCT-17-HFG_CTRL

description: 103,918 nuclei

value: Oligodendrocyte


title: T1DAL_769151, week 104, CD57pos_DP_NN_CD8

value: PBMC

value: R

value: Week 104


title: 5868_VENs_HCTSU_CTRL

description: 1004 nuclei

value: Insular cortex

value: VENs

value: CTRL


title: T1DAL_323347, week 104, CD57pos_DP_NN_CD8

value: CD57+ DP Non-naive CD8 T cells:singlet, live, CD14-CD19-CD56-CD3+CD8+CD4-, not CD45RA+CCR7+, KLRG1+TIGIT+, CD57+

value: alefacept


title: T1DAL_769151, week 104, DN_NN_CD8

value: DN Non-naive CD8 T cells:singlet, live, CD14-CD19-CD56-CD3+CD8+CD4-, not CD45RA+CCR7+, KLRG1-TIGIT-


title: 5798_Interneuron--RELN_BEB18135_CTRL

description: 12,560 nuclei (Prepared by Cuidong)

value: Cortex BA9

value: Interneuron, RELN


title: 5471_Microglia_HCT-17-HFG_CTRL

description: 29,363 nuclei

value: Cortex BA4

value: Microglia


title: 5873_L6a-pyramidal-neuron_BEB19025_CTRL

description: 25408 nuclei

value: L6a pyramidal neuron


title: T1DAL_769151, baseline, DN_NN_CD8

value: Baseline


title: T1DAL_769151, baseline, CD57pos_DP_NN_CD8


title: 5468_Interneuron--PVALB_HCT-17-HFG_CTRL

description: 3,740 nuclei

value: Interneuron, PVALB

value: M


title: 5467_Interneuron--RELN_HCT-17-HFG_CTRL

description: 5,820 nuclei


title: 5466_L2-L3-pyramidal-neuron_HCT-17-HFG_CTRL

description: 60,525 nuclei

value: L2/L3 pyramidal neuron


title: 5449_Oligodendrocyte-progenitor_HCTSU_CTRL

description: 24,710 nuclei

value: Oligodendrocyte progenitor

value: HCTSU

value: F


title: T1DAL_616755, week 104, DN_NN_CD8

value: PBMC

value: R

value: Week 104


title: T1DAL_616755, week 104, CD57neg_DP_NN_CD8

value: CD57- DP Non-naive CD8 T cells:singlet, live, CD14-CD19-CD56-CD3+CD8+CD4-, not CD45RA+CCR7+, KLRG1+TIGIT+, CD57-

value: alefacept


title: Blood_NMO_monocyte_rep3

city: Seouol

first: Moonhang

last: Kim

state: Seoul

address: 71, Daehak-ro, Jongno-gu, Seoul, Korea

country: South Korea

institute: Biomedical Research Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Blood

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Blood

value: Monocytes

value: WT

tag: injury model

value: NMO

tag: sampling time

value: 1 day

tag: number of_samples


title: T1DAL_323347, week 104, CD57neg_DP_NN_CD8

tag: tissue

tag: cell type


title: Blood_NMO_monocyte_rep2


title: 5448_Oligodendrocyte_HCTSU_CTRL

description: 98,828 nuclei

source_name: Cortex BA9

value: Cortex BA9

value: Oligodendrocyte

tag: donor

tag: age

tag: Sex

value: CTRL


title: T1DAL_616755, week 104, CD57pos_DP_NN_CD8

value: CD57+ DP Non-naive CD8 T cells:singlet, live, CD14-CD19-CD56-CD3+CD8+CD4-, not CD45RA+CCR7+, KLRG1+TIGIT+, CD57+

tag: genotype


title: Blood_NMO_monocyte_rep1


title: 5472_Astrocyte_HCT-17-HFG_CTRL

description: 12,999 nuclei

value: Cortex BA4

value: Astrocyte

value: M

tag: pmi (hrs)

tag: donor category


title: T1DAL_616755, baseline, DN_NN_CD8

value: PBMC

value: DN Non-naive CD8 T cells:singlet, live, CD14-CD19-CD56-CD3+CD8+CD4-, not CD45RA+CCR7+, KLRG1-TIGIT-

value: Baseline

tag: treatment


title: Brain_NMO_monocyte_rep3

source_name: Brain

value: Brain


title: 5442_L6a-pyramidal-neuron_HCTSU_CTRL

description: 13,814 nuclei

value: L6a pyramidal neuron

value: HCTSU

value: F


title: T1DAL_769151, week 104, CD57neg_DP_NN_CD8

value: R

value: CD57- DP Non-naive CD8 T cells:singlet, live, CD14-CD19-CD56-CD3+CD8+CD4-, not CD45RA+CCR7+, KLRG1+TIGIT+, CD57-

value: Week 104

value: alefacept


title: 5447_Astrocyte_HCTSU_CTRL

description: 22,278 nuclei

value: Cortex BA9


title: T1DAL_769151, baseline, CD57neg_DP_NN_CD8


title: 5436_Interneuron--RELN_HCTSU_CTRL

description: 6,270 nuclei

value: Interneuron, RELN

value: CTRL


title: Brain_NMO_monocyte_rep2

value: Monocytes

value: WT

value: NMO

value: 1 day


title: 5358_L6b-pyramidal-neuron_BEB18116_CTRL

description: 1,743 nuclei

source_name: Cortex BA4

value: Cortex BA4

value: L6b pyramidal neuron

value: M


title: T1DAL_616755, baseline, CD57pos_DP_NN_CD8

value: PBMC

value: CD57+ DP Non-naive CD8 T cells:singlet, live, CD14-CD19-CD56-CD3+CD8+CD4-, not CD45RA+CCR7+, KLRG1+TIGIT+, CD57+

value: Baseline


title: 5437_Interneuron--LAMP5_HCTSU_CTRL

description: 7,824 nuclei

value: Interneuron, LAMP5

value: HCTSU

value: F


title: 5350_L2-L3-pyramidal-neuron_BEB18116_CTRL

description: 35,205 nuclei

value: L2/L3 pyramidal neuron


title: 5221_L4-granular-neuron_HCT-17-HFG_CTRL

description: 4,908 nuclei

value: Extrastriate cortex, BA18

value: L4 granular neuron


title: 5220_Interneuron--PVALB_HCT-17-HFG_CTRL

description: 4,341 nuclei

value: Interneuron, PVALB

value: CTRL


title: Blood_Normal_monocyte_rep3

value: Blood

value: Monocytes

value: WT

value: Normal


title: 5219_Interneuron--LAMP5_HCT-17-HFG_CTRL

description: 6,127 nuclei


title: donor T1DAL_243767, alefacept treated, 104 wk post-treatment, responder (R), single cell RNA-seq

description:
10X Genomics
11_6313_GEX

data_processing:
Sequence data were processed from raw reads to gene-barcode count matrices and assembled into TCR sequences using 10x Genomics Cell Ranger v4.0.059. Reads were demultiplexed by sample and library type using index sequence pools. Gene expression reads were aligned to the human genome (GRCh38.91), and reads were collapsed to molecule counts per gene using unique molecular identifiers (UMIs). TCR sequence reads were assembled into consensus contigs, assessed for in-frame and productive sequences, and aligned to the 10x V(D)J reference v. 4.0.0 to determine gene usage. Barcodes were called as cells or background using default settings in CellRanger (10X), which utilizes both the distribution of UMI counts by barcode and expression comparisons of low-UMI-count barcodes to assumed background. Data from all samples were aggregated without normalization prior to downstream analysis.
Assembly: GRCh38.91
Supplementary files format and content: For RNA-seq files: processed data is unfiltered 10X output of single cell RNA-seq in h5 format.
Supplementary files format and content: For TCR-seq files: processed output is in a csv file with information for the assembled TCR chains in each cell output from the 10X Genomics Cell Ranger program.

source_name: CD3+ CD8+ CD45RA+/- CCR7+/- sorted from PBMC

extract_protocol:
PBMCs were stained with a flow cytometry panel (Figure S12) and sorted into non-naive CD8+ T cells (singlet, live, CD14- CD19- CD56- CD3+ CD8+ CD4-, not CD45RA+ CCR7+) from 12 donors (6 alefacept responders, 6 non-responders, as defined by preservation of C-peptide levels11,58) with new onset T1D at 104 wk (Visit 30) post-treatment with alefacept (T1DAL Trial, ITN) using the FACS Aria Fusion (Becton Dickinson) cell sorter. Cell viability and purity were >90%. Samples were sorted into RPMI with 2% human serum prior to single cell RNA-seq. A single cell suspension was prepared from sorted cells and loaded onto the 10x Chromium Controller (10X Genomics) according to the manufacturer’s protocol, with a target capture of 5,000 cells per channel.
Sequencing libraries were generated using the NextGEM Single Cell 5' v1.1 kit (10x Genomics). Three pools of gene expression and TCR libraries, each from two responders and two non-responders, were generated, with a ratio of 4:1 GEX:TCR. Each pool was run on a NextSeq P2 flowcell on a NextSeq 2000 sequencer (Illumina), with a target depth of 20,000 reads/cell for GEX and 5000 reads/cell for TCR libraries.

value: non-naive CD8 T cells

value: R

tag: cellnumber

value: alefacept

tag: stimulation

value: Week 104

tag: visit


title: Blood_Normal_monocyte_rep2

value: 1 day


title: 5008_Interneuron--LAMP5_HCT-17-HFG_CTRL

description: 7,147 nuclei

value: Cortex BA4

value: Interneuron, LAMP5

value: M


title: donor T1DAL_769151, alefacept treated, 104 wk post-treatment, responder (R), single cell RNA-seq

description:
10X Genomics
10_5562_GEX

value: CD3+ CD8+ CD45RA+/- CCR7+/- sorted from PBMC

tag: cell line

tag: maskeddonorid

tag: lib id


title: 5444_L5a-pyramidal-neuron_HCTSU_CTRL

description: 9,027 nuclei

value: Cortex BA9

value: L5a pyramidal neuron

value: HCTSU

value: F


title: Blood_Normal_monocyte_rep1

value: Blood

tag: injury model

tag: sampling time


title: 5446_Microglia_HCTSU_CTRL

description: 31,573 nuclei

tag: tissue

value: Microglia

value: CTRL


title: 5006_Interneuron--VIP_HCT-17-HFG_CTRL

description: 2,468 nuclei

tag: cell type

value: Interneuron, VIP


title: 4953_L5a-pyramidal-neuron_BEB19025_CTRL

description: 915 nuclei

tag: donor


title: NMO+Clodronate_Brain_microglia_rep3

value: Brain

value: WT

value: NMO

tag: nember of_samples

value: clodronate


title: donor T1DAL_323347, alefacept treated, 104 wk post-treatment, responder (R), single cell RNA-seq

description:
10X Genomics
8_4610_GEX

value: non-naive CD8 T cells

value: R

value: alefacept

tag: timepoint

value: Week 104


title: 4943_Microglia_BEB19025_CTRL

description: 59900 nuclei

source_name: Cortex BA17

value: Cortex BA17

tag: age

tag: Sex

value: M


title: 4939_L4-granular-neuron_BEB19025_CTRL

description: 9505 nuclei

value: L4 granular neuron

tag: pmi (hrs)

tag: donor category


title: NMO+Clodronate_Brain_microglia_rep2

tag: genotype

value: 1 day

tag: treatment


title: 4938_Interneuron--PVALB_BEB19025_CTRL

description: 8719 nuclei

value: Interneuron, PVALB


title: donor T1DAL_442289, alefacept treated, 104 wk post-treatment, non-responder (NR), single cell RNA-seq

description:
10X Genomics
7_4512_GEX

value: CD3+ CD8+ CD45RA+/- CCR7+/- sorted from PBMC

value: NR

tag: cellnumber

tag: stimulation

tag: visit


title: donor T1DAL_576351, alefacept treated, 104 wk post-treatment, non-responder (NR), single cell RNA-seq

description:
10X Genomics
12_8085_GEX

tag: cell line

tag: maskeddonorid

tag: lib id


title: NMO+Clodronate_Brain_microglia_rep1

tag: tissue

value: Microglia

tag: injury model

tag: sampling time


title: 4838_L6b-pyramidal-neuron_BEB18135_CTRL

description: 1,824 nuclei

value: Cortex BA4

tag: cell type

value: L6b pyramidal neuron

tag: donor

value: CTRL


title: donor T1DAL_923889, alefacept treated, 104 wk post-treatment, non-responder (NR), single cell RNA-seq

description:
10X Genomics
6_8083_GEX

tag: timepoint


title: T1DAL_616755, baseline, CD57neg_DP_NN_CD8

value: PBMC

value: CD57- DP Non-naive CD8 T cells:singlet, live, CD14-CD19-CD56-CD3+CD8+CD4-, not CD45RA+CCR7+, KLRG1+TIGIT+, CD57-

value: Baseline


title: 5216_Interneuron--VIP_HCT-17-HFG_CTRL

description: 6,812 nuclei

source_name: Extrastriate cortex, BA18

value: Extrastriate cortex, BA18

value: Interneuron, VIP

tag: age

tag: Sex


title: NMO_Brain_microglia_rep3

value: Brain

value: WT

value: NMO

tag: nember of_samples

value: no treatment


title: 4552_Astrocyte_HCTSU_CTRL

description: 105,971 nuclei

value: Cortex BA19

value: Astrocyte

value: HCTSU

value: F

tag: pmi (hrs)

tag: donor category


title: 4554_Oligodendrocyte-progenitor_HCTSU_CTRL

description: 15,975 nuclei

value: Oligodendrocyte progenitor


title: donor T1DAL_616755, alefacept treated, 104 wk post-treatment, responder (R), single cell RNA-seq

description:
10X Genomics
5_4546_GEX

value: CD3+ CD8+ CD45RA+/- CCR7+/- sorted from PBMC

value: non-naive CD8 T cells

value: R

tag: cellnumber

tag: treatment

value: alefacept

value: Week 104

tag: genotype


title: 5833_L6b-pyramidal-neuron_BEB18116_CTRL

description:
nuclear Transposase-Accessible Chromatin
2,733 nuclei

data_processing:
The ATACseq reads were aligned with the hg38 genome from the BSgenome.Hsapiens.UCSC.hg38 Bioconductor package (version 1.4.1) with Rsubread's align method in paired-end mode.
Normalized, fragment signal bigWigs were created with the rtracklayer package.
Peak calls were made with MACS2 software in BAMPE mode (Feng et al. 2012) (Zhang et al. 2008).
Assembly: BSgenome.Hsapiens.UCSC.hg38
Supplementary files format and content: BigWig files, Counts files

extract_protocol:
Follwing nuclei isolation and incubation in lysis and tagmentation buffer, DNA extraction was carried out with AllPrep DNA/RNA FFPE Kit (Qiagen, #80234).
The  ATACseq protocol utilized in this work was adapted from Corces et al. 2017.

value: Cortex BA4

value: L6b pyramidal neuron

value: M

value: CTRL


title: 5834_L5a-pyramidal-neuron_BEB18116_CTRL

description:
nuclear Transposase-Accessible Chromatin
13,628 nuclei

value: L5a pyramidal neuron


title: NMO_Brain_microglia_rep2

value: Brain

value: Microglia

value: WT

value: NMO

value: 1 day


title: Brain_NMO_monocyte_rep1

value: Monocytes

tag: number of_samples


title: 4946_Interneuron--VIP_BEB19025_CTRL

description: 2212 nuclei

value: Interneuron, VIP


title: donor T1DAL_671942, alefacept treated, 104 wk post-treatment, non-responder (NR), single cell RNA-seq

description:
10X Genomics
4_4611_GEX

value: CD3+ CD8+ CD45RA+/- CCR7+/- sorted from PBMC

tag: cell line

tag: maskeddonorid

value: NR

tag: stimulation

tag: visit


title: donor T1DAL_947702, alefacept treated, 104 wk post-treatment, non-responder (NR), single cell RNA-seq

description:
10X Genomics
9_4901_GEX

tag: tissue

value: non-naive CD8 T cells

tag: lib id


title: 5832_L6a-pyramidal-neuron_BEB18116_CTRL

description:
nuclear Transposase-Accessible Chromatin
17,357 nuclei

tag: cell type

value: L6a pyramidal neuron

tag: donor


title: 5831_Betz-cell_BEB18116_CTRL

description:
nuclear Transposase-Accessible Chromatin
3,378 nuclei

value: Betz cell

tag: age


title: NMO_Brain_microglia_rep1

tag: injury model

tag: sampling time

value: no treatment


title: donor T1DAL_325261, alefacept treated, 104 wk post-treatment, non-responder (NR), single cell RNA-seq

description:
10X Genomics
3_4509_GEX

value: alefacept

tag: timepoint

value: Week 104


title: 5764_L5a-pyramidal-neuron_BEB18135_CTRL

description:
nuclear Transposase-Accessible Chromatin
14,158 nuclei

value: Cortex BA4

tag: Sex

value: M

tag: pmi (hrs)

tag: donor category

value: CTRL


title: 5763_L6b-pyramidal-neuron_BEB18135_CTRL

description:
nuclear Transposase-Accessible Chromatin
4,818 nuclei

value: L6b pyramidal neuron


title: Normal_Brain_microglia_rep3

value: Brain

value: Microglia

tag: genotype

value: WT

value: Normal

tag: nember of_samples

tag: treatment


title: donor T1DAL_799347, alefacept treated, 104 wk post-treatment, responder (R), single cell RNA-seq

description:
10X Genomics
2_4505_GEX

tag: cell line

tag: maskeddonorid

value: R

tag: cellnumber


title: Normal_Brain_microglia_rep2

tag: tissue

value: 1 day


title: 4907_L4-granular-neuron_BEB18135_CTRL

description: 17,118 nuclei

value: Cortex BA17

value: L4 granular neuron


title: 5761_Betz-cell_BEB18135_CTRL

description:
nuclear Transposase-Accessible Chromatin
5,012 nuclei


title: 5760_L5a-pyramidal-neuron_BEB19025_CTRL

description:
nuclear Transposase-Accessible Chromatin
4,163 nuclei

value: L5a pyramidal neuron


title: 5964_L5a-pyramidal-neuron_BEB19025_CTRL

description: 2414 nuclei

value: Cortex BA9


title: donor T1DAL_365106, alefacept treated, 104 wk post-treatment, responder (R), single cell RNA-seq

description:
10X Genomics
1_1223_GEX

value: CD3+ CD8+ CD45RA+/- CCR7+/- sorted from PBMC

value: non-naive CD8 T cells

tag: stimulation

tag: lib id

tag: visit


title: Normal_Brain_microglia_rep1

tag: cell type

value: no treatment


title: 5759_L6b-pyramidal-neuron_BEB19025_CTRL

description:
nuclear Transposase-Accessible Chromatin
1,890 nuclei

value: Cortex BA4

tag: donor

tag: age


title: donor T1DAL_576351, alefacept treated, 104 wk post-treatment, non-responder (NR), single cell TCR-seq

description:
10X Genomics
12_8085_TCR

data_processing:
Sequence data were processed from raw reads to gene-barcode count matrices and assembled into TCR sequences using 10x Genomics Cell Ranger v4.0.059. Reads were demultiplexed by sample and library type using index sequence pools. Gene expression reads were aligned to the human genome (GRCh38.91), and reads were collapsed to molecule counts per gene using unique molecular identifiers (UMIs). TCR sequence reads were assembled into consensus contigs, assessed for in-frame and productive sequences, and aligned to the 10x V(D)J reference v. 4.0.0 to determine gene usage. Barcodes were called as cells or background using default settings in CellRanger (10X), which utilizes both the distribution of UMI counts by barcode and expression comparisons of low-UMI-count barcodes to assumed background. Data from all samples were aggregated without normalization prior to downstream analysis.
Assembly: GRCh38.91
Supplementary files format and content: For RNA-seq files: processed data is unfiltered 10X output of single cell RNA-seq in h5 format.
Supplementary files format and content: For TCR-seq files: processed output is in a csv file with information for the assembled TCR chains in each cell output from the 10X Genomics Cell Ranger program.
Library strategy: scTCR-seq

value: NR

value: alefacept

tag: timepoint

value: Week 104


title: 5758_L6a-pyramidal-neuron_BEB19025_CTRL

description:
nuclear Transposase-Accessible Chromatin
10,738 nuclei

value: L6a pyramidal neuron

tag: Sex

value: M

value: CTRL


title: 5754_Betz-cell_HCTSU_CTRL

description:
nuclear Transposase-Accessible Chromatin
1,442 nuclei

value: Betz cell

value: HCTSU

value: F

tag: pmi (hrs)


title: 5755_L6a-pyramidal-neuron_HCTSU_CTRL

description:
nuclear Transposase-Accessible Chromatin
1,351 nuclei

tag: donor category


title: donor T1DAL_243767, alefacept treated, 104 wk post-treatment, responder (R), single cell TCR-seq

description:
10X Genomics
11_6313_TCR

value: R

tag: genotype


title: donor T1DAL_769151, alefacept treated, 104 wk post-treatment, responder (R), single cell TCR-seq

description:
10X Genomics
10_5562_TCR


title: 5411_L6a-pyramidal-neuron_HCT-17-HFG_CTRL

description:
nuclear Transposase-Accessible Chromatin
6,042 nuclei


title: 5252_L6b-pyramidal-neuron_HCTSU_CTRL

description: nuclear Transposase-Accessible Chromatin

value: L6b pyramidal neuron


title: 5412_L5a-pyramidal-neuron_HCT-17-HFG_CTRL

description:
nuclear Transposase-Accessible Chromatin
4,524 nuclei

value: L5a pyramidal neuron


title: donor T1DAL_947702, alefacept treated, 104 wk post-treatment, non-responder (NR), single cell TCR-seq

description:
10X Genomics
9_4901_TCR


title: A375_sample3_10X_tnp

city: Iowa City

first: Adam

middle: J

last: Dupuy

state: IA

address: 375 Newton Road

institute: University of Iowa

data_processing:
raw sequence data were analyzed using the 10X Genomics Cell Ranger software.
Assembly: grch38-2020
Library strategy: scCNV

source_name: xenograft tumor

extract_protocol:
Genomic DNA was extracted from frozen samples using the GenElute™ Mammalian Genome DNA miniprep Kit (Sigma #G1N350-KT).
Tumor nuclei were isolated following the 10X Genomics protocol (CG000167.RevA). Preparation of samples for sequencing was completed using the 10X Genomics Chromium Single Cell CNV platform protocol, in which a transposon specific PCR is utilized in leu of ligation with Read 2 primers. 10X Chromium Library Prep (CG000153: Single-Cell DNA Reagent Kits User Guide, Rev C) was followed as written with the following exceptions.

value: xenograft tumor

value: melanoma


title: 5762_L6a-pyramidal-neuron_BEB18135_CTRL

description:
nuclear Transposase-Accessible Chromatin
14,587 nuclei


title: A375_sample2_10X_tnp


title: donor T1DAL_323347, alefacept treated, 104 wk post-treatment, responder (R), single cell TCR-seq

description:
10X Genomics
8_4610_TCR

value: CD3+ CD8+ CD45RA+/- CCR7+/- sorted from PBMC

value: non-naive CD8 T cells


title: SW480-shCYP1B1 2

city: Shanghai

first: Lei

last: Jin

state: Shanghai

address: Shanghai Fenglin Road

institute: Fudan University

data_processing:
CLC Genomics Workbenchv 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to NCBI_GRCh38.p13 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: tab-delimited text files include count and FPKM values for each Sample

source_name: colon tissue

growth_protocol: RKO and SW480 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
Then the libraries were constructed using TruSeq Stranded mRNALTSample Prep Kit(Ilumina,San Diego, CA, USA) . 1 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: RKO and SW480 cells were transfected with CYP1B1 lentivirus for 24hpf

value: colon tissue

value: Human colon cancer cells

value: CYP1B1 knockdown


title: A375_sample4_10X_tnp


title: donor T1DAL_442289, alefacept treated, 104 wk post-treatment, non-responder (NR), single cell TCR-seq

description:
10X Genomics
7_4512_TCR

value: NR

value: alefacept

value: Week 104


title: SW480-shCYP1B1 1


title: SW480-shNT 2

value: CYP1B1 normal control


title: donor T1DAL_616755, alefacept treated, 104 wk post-treatment, responder (R), single cell TCR-seq

description:
10X Genomics
5_4546_TCR


title: cartana_iri6w_male

type: RNA

city: St. Louis

first: Haojia

last: Wu

state: Missouri

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

description: ISS by Cartana

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing:
ISS data processing: ISS data was processed using our in-house pipeline called CellScopes https://github.com/TheHumphreysLab/CellScopes.jl.
Cell segmentation: Cell segmentation was performed using Baysor https://github.com/kharchenkolab/Baysor.
genome assembly: mm10

label: not applicable

label_protocol: not applicable

extract_protocol: RNA hybridization-based in situ sequencing protocol: Fresh kidneys were incubated in 2-methylbutane (Millipore, Sigma) equilibrated in liquid nitrogen to maintain RNA integrity. Tissues were then stored at −80°C and embedded in cryomolds using OCT (Tissue-Tek 4583) on dry ice. For frozen sectioning, OCT blocks were equilibrated to −18°C, and 10 μm-thick sections were mounted onto the glass slides (1358W; Globe Scientific). Libraries were prepared using the high sensitivity (HS) library preparation kit provided by CARTANA (Sweden) per manufacturer’s instruction. In brief, slides were fixed in freshly prepared formaldehyde diluted in 0.01% DEPC treated PBS, followed by permeabilization in 0.1M HCl (DEPC treated). After dehydration and rehydration in series of alcohol gradients, slides were incubated in RM1-mix (provided by the library kit) overnight at 37°C. Kidney sections were incubated in WB4 (library kit) at 37°C for 30 min. Gene probes were ligated in ligases dissolved in RM2 (library kit) at 37°C for 2 hours. Transcripts were amplified in RM3-mix (library kit) at 30°C overnight. Slides were stained with DAPI for quality control imaging and shipped to 10x Genomics for in situ sequencing.

value: male

tag: surgery

value: IRI 6 weeks

value: Kidney


title: donor T1DAL_671942, alefacept treated, 104 wk post-treatment, non-responder (NR), single cell TCR-seq

description:
10X Genomics
4_4611_TCR

tag: treatment


title: JC475_G007LK

city: Tokyo

first: Tetsuo

last: Mashima

address: Koto-ku, Ariake 3-8-31

department: Cancer Chemotherapy Center

institute: Japanese Foundation for Cancer Research

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Gene-level expression signals were obtained by processing of raw data with the MAS5 procedure using GeneSpring GX (Agilent Technologies).

label: biotin

source_name: Human Colorectal Cancer

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: JC21 and JC475 cells were maintained in in the StemPro ESC medium (Life technologies) supplemented with 10 μM Y-27632 in a humidified atmosphere of 5% CO2 and 95% air at 37 °C.

extract_protocol: Total RNAs were extracted using Fast Gene RNA Basic kit (Nippon Genetics) according to the manufacturer's instructions.

treatment_protocol: The patient-derived CRC cells, JC21 and JC475, were left untreated (DMSO) or treated with 0.3 µM G007LK or RK582 for 24 h.

tag: cell line

value: 0.3 uM G007LK for 24 h


title: SW480-shNT 1


title: RKO-CYP1B1 1

value: RKO

value: CYP1B1 overexpression


title: cartana_iri12h_male

description: ISS by Cartana

value: IRI 12 hours


title: JC475_DMSO

value: DMSO


title: cartana_iri4h_male

description: ISS by Cartana

value: IRI 4 hours


title: JC21_RK582

value: 0.3 uM RK582 for 24 h


title: JC21_G007LK


title: cartana_sham_female

description: ISS by Cartana

value: female

value: sham


title: cartana_sham_male

description: ISS by Cartana


title: JC475_RK582


title: donor T1DAL_325261, alefacept treated, 104 wk post-treatment, non-responder (NR), single cell TCR-seq

description:
10X Genomics
3_4509_TCR

value: CD3+ CD8+ CD45RA+/- CCR7+/- sorted from PBMC

value: non-naive CD8 T cells

tag: maskeddonorid


title: donor T1DAL_923889, alefacept treated, 104 wk post-treatment, non-responder (NR), single cell TCR-seq

description:
10X Genomics
6_8083_TCR

value: NR

tag: cellnumber

value: alefacept


title: JC494_G007LK

growth_protocol: JC11 and JC494 cells were maintained in in the StemPro ESC medium (Life technologies) supplemented with 10 μM Y-27632 in a humidified atmosphere of 5% CO2 and 95% air at 37 °C.

treatment_protocol: The patient-derived CRC cells, JC11 and JC494, were left untreated (DMSO) or treated with 0.3 µM G007LK or RK582 for 24 h.


title: JC494_RK582


title: JC21_DMSO


title: RKO-Control 1

tag: tissue

value: colon tissue

value: Human colon cancer cells

value: CYP1B1 normal control


title: donor T1DAL_365106, alefacept treated, 104 wk post-treatment, responder (R), single cell TCR-seq

description:
10X Genomics
1_1223_TCR

value: R

tag: stimulation

value: Week 104


title: Rice Input_rep2

city: Nanjing

first: huang

middle: ran

last: ran

address: weigang 1

institute: Nanjing Agricultural College

data_processing:
Sequenced reads were trimmed for adaptor sequences using trim_galore
BWA (Burrows-Wheeler Aligner) with default parameters was used to align all cleaned reads to the MSU v7.0 reference genom
MACS  was used to call IP-G4 (referred to as G4s pulled down by anti-BG4 antibody) peaks from reads with an alignment length greater than 50.
Assembly: MSU v7.0
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: BG4-DNA-IP-Seq

organism: Oryza sativa

source_name: seedling

growth_protocol: temperature of 28–30 °C and a 14 h/10 h light/dark cycle

extract_protocol:
collected and cut into small slices of 1–1.5 cm in size, followed by cross-linking with a 1% final concentration of formaldehyde for 10 min under vacuum.
DNA immunoprecipitation with anti-BG4 antibody coupled with sequencing termed BG4-DNA-IP-seq. Briefly, 5 μg of fragmented genomic DNA was denatured and reassociated in the G4 stabilization buffer (40% PEG200, 10 mM Tris-HCl, pH 7.5, with 150 mM KCl or NaCl), which was then followed by incubation with anti-BG4-FLAG antibody in the IP incubation buffer (50 mM HEPES, 150 mM KCl, 1 mM MgCl2, 130 nM CaCl2, 1% BSA, 40% PEG200, Complete Mini, pH 7.5). After adding anti-FLAG antibody (D110005, BBI, Shanghai, China) and washed protein G Dynalbeads (10004D, Invitrogen, Carlsbad, CA, USA) for additional 4 h followed by washing two times, anti-BG4 recognized DNA-G4s was finally recovered for library preparation. IPed and input DNA was used for library preparation using the NEBNext®Ultra™ II DNA Library Prep Kit for Illumina (E7645S, NEB). All libraries were sequenced on the Illumina platform.

value: seedling

tag: antibody

value: WT


title: Human endometrial organoids, gestational phase, adenomyosis 17 [ADENO17-GEST]

city: Valencia

first: Hortensia

last: Ferrero

state: Valencia

address: Avenida Fernando Abril Martorell 106, Torre A

department: Reproductive Medicine

country: Spain

institute: Instituto de Investigación Sanitaria La Fe / Fundación IVI

description:
ADENO17-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx

data_processing:
Data was processed in R computing environment (version 4.1.3).
The quality of sequencing was evaluated by FastQC.
Raw FASTQ files from sequencing were processed to remove adapters and filter read sequences by size using BBDuk package.
mRNAs were aligned using Subread software and annotated using the human genome reference HG38.
The number of reads per sample was normalized using the geometric median method of ratios on each mRNA implemented in the DESeq2 R package.
Assembly: HG38
Supplementary files format and content: Raw_counts.xlsx, column-delimited excel file include raw count values for each sample
Supplementary files format and content: Normalized_counts.xlsx, column-delimited excel file include normalized count values for each sample

source_name: Human endometrial epithelial cells

growth_protocol: Established human endometrial organoids were cultured for 7 days at 37°C, 6% CO2 and 5% O2 in Organoid Expansion Medium (ExM).

extract_protocol:
Total RNA was extracted from the ADENO-SECorg, CONTROL-SECorg, ADENO-GESTorg and CONTROL-GESTorg groups (n=15/group) using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol, and quantified with a Qubit 3 Fluorometer (Invitrogen).
cDNA libraries were generated employing the TruSeq Stranded mRNA Library Prep (Illumina) and TruSeq RNA CD Index Plate (Illumina) according to manufacturer’s instructions.

treatment_protocol: Control and adenomyosis organoids were cultured in ExM treated with 10 nM estradiol (E2; Sigma-Aldrich), 1 µM progesterone (P4; Sigma-Aldrich) and 1 µM 8-bromoadenosine 3′,5′-cyclic monophosphate sodium salt (cAMP; Sigma-Aldrich) for mid-secretory phase differentiation. For gestational phase differentiation, control and adenomyosis organoids were treated with 10 nM E2, 1 µM P4, 1 µM cAMP, with an additional 20 ng/mL prolactin (Peprotech) and 20 ng/mL human placental lactogen (R&D).

value: Human endometrial epithelial cells

tag: differentiation phase

value: gestational phase

value: Adenomyosis


title: donor T1DAL_799347, alefacept treated, 104 wk post-treatment, responder (R), single cell TCR-seq

description:
10X Genomics
2_4505_TCR

tag: cell type

tag: lib id

tag: visit


title: HCT116_ENL_Ab2

city: Shenzhen

first: Xing-sheng

last: Shu

state: Guangdong

address: No 3688, Nanhai Avenue

department: Medical School

institute: Shenzhen University

data_processing:
Raw reads were aligned to hg19 using bwa. The sam files were converted to bam with samtools.
MACS2 was used to call peaks on the bam files with signals from input DNA as reference.
Assembly: hg19
Supplementary files format and content: Bigwig files were generated using bamCoverage from Deeptools.

source_name: HCT116 colon cancer cells

growth_protocol: HCT116 cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum. For selection of AID clones, HCT116 cells transfected with indicated plasmids were cultured with 2 ug/ml puromycin and 3 ug/ml blasticidin.

extract_protocol:
Cells were cross-linked in 1% formaldehyde for 10 min at room temperature (RT) with gentle swirling, and crosslinking was stopped by adding glycine to a final concentration of 0.125 M and incubating at RT for 5 min. Cells were harvested and an aliquot of 1 × 107 cells were used per ChIP reaction. Each cell aliquot was resuspended in 0.5 mL of RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS in PBS, pH 7.4), and chromatin was fragmented on ice to 200 to 500 bp in size with 5 pulses of 30 sec at 50% power with a Sonics VibraCell sonicator. 5-10 μg primary antibodies or control IgG were pre-conjugated with Protein G magnetic beads (Pierce) at 4°C overnight. 1% of sheared chromatin was saved as input, and the rest was incubated with pre-conjugated antibody on a rotator at 4°C overnight. The beads were washed 5 times with LiCl wash buffer (0.1 M Tris, 0.5 M LiCl, 1% NP-40, 1% sodium deoxycholate, pH 7.5) followed by a single wash with TE buffer (10 mM Tris-HCl, 0.1 mM Na2EDTA, pH 7.5). The beads were then resuspended in 200 μL IP elution buffer (1% SDS, 0.1 M NaHCO3) and incubated at 65°C for 1 hour in a heat block with vortexing. The supernant was collected and together with input was incubated at 65°C for 16 hours to reverse cross-links. DNA was purified with QIAquick PCR Purification Kit (Qiagen) and eluted in 50 μL EB.
ChIP’s DNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated fragments. Fragments were amplified by PCR and PCR products were purified and selected with the Agencourt AMPure XP-Medium kit. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. Library was qualified by Qubit ssDNA kit.

treatment_protocol: The HCT116 ENL-AID cells was treated with or without 500 um auxin (IAA) for 3 hours and an additional group of IAA treated cells were subjected to PBS washout and subsequent culture in normal medieum for another 48 hours . The resulting cells were harvested for analysis as described below.

value: colon cancer cells


title: APP/PS1 NLRP3.KO brain 9m

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

description: 10x Genomics

data_processing:
Raw data bcl files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
Assembly: mm10
Supplementary files format and content: comma-delimited text files including raw UMI counts and metadata with information per cell

source_name: whole brain

extract_protocol: All methods listed in Srinivasan et al. Inflammasome signaling is dispensable for ß-amyloid-induced neuropathology in preclinical models of Alzheimer's disease. 2024

value: whole brain

value: APP/PS1 NLRP3.KO

tag: age


title: Human endometrial organoids, mid-secretory phase, adenomyosis 17 [ADENO17-SEC]

description:
ADENO17-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: mid-secretory phase


title: HCT116_ENL_Ab1


title: APP/PS1 brain 9m

description: 10x Genomics


title: RKO-Control 2

value: RKO


title: JC11_RK582


title: cartana_iri2d_male

description: ISS by Cartana

tag: Sex

value: male

value: IRI 2 days

value: Kidney


title: Human endometrial organoids, gestational phase, adenomyosis 16 [ADENO16-GEST]

description:
ADENO16-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: Rice K+PDS_rep2

value: K+PDS G4 stabilizing buffers


title: JC11_DMSO

value: DMSO


title: JC11_G007LK


title: HCT116_IgG

value: IgG


title: Rice K+PDS_rep1


title: NLRP3.KO brain 9m

description: 10x Genomics


title: Human endometrial organoids, mid-secretory phase, adenomyosis 16 [ADENO16-SEC]

description:
ADENO16-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: Human endometrial organoids, gestational phase, adenomyosis 14 [ADENO14-GEST]

description:
ADENO14-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: NLRP3.KO brain 6m

description: 10x Genomics


title: JC494_DMSO


title: Fenretinide

city: İZMİR

first: Serap

last: Erkek Özhan

state: BALÇOVA

address: İzmir Biyotıp ve Genom Merkezi (IBG), Dokuz Eylül Üniversitesi Sağlık Yerleşkesi, Mithatpaşa Caddesi No:58/5

country: Turkey

institute: Izmir Biomedicine and Genome Center

data_processing:
Sequenced and demultiplexed FastQ files were obtained for four groups, which are Vehicle Control, GSK-126, Fenretinide, and Combination.
FastQ files were aligned with the reference FASTA file (GRCh38) by using Subread (v2.0.3). The number of aligned reads and the number of reads mapped to genes were obtained.
Reads were mapped to the reference GTF file (gencode v32 annotation) by using R Subread (v2.11.2), and sample specific BAM files were obtained. After that, count and FPKM files were obtained.
Assembly: GRCh38
Supplementary files format and content: FPKM values for each sample

growth_protocol: T24 cells were maintained in DMEM (Gibco) medium with non-essential amino acids, L-glutamine, and 4.5g/L D-glucose supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Thermo Fisher), in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA Midi Kit from Macherey-Nagel.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep with Ribo-Zero H/M/R Kit following manufacturer's protocols. Library Protocol: TruSeq Stranded Total RNA Reference Guide (1000000040499 v00)

treatment_protocol: T24 were treated with DMSO (Vehicle Control); or GSK-126 (Selleck Chemicals) (5 μM for 72 h); or fenretinide (5 μM for 72 h) (Merck) or their combination (5 μM fenretinide and GSK-126 for 72 h)

value: Human Urinary Bladder Cancer

value: Fenretinide


title: WT brain 9m

description: 10x Genomics

value: WT


title: Rice K+PEG_rep2

value: seedling

value: K+PEG G4 stabilizing buffers


title: Rice K+PEG_rep1


title: Human endometrial organoids, mid-secretory phase, adenomyosis 14 [ADENO14-SEC]

description:
ADENO14-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: Human endometrial epithelial cells

value: Adenomyosis


title: GSK-126


title: WT brain 6m

description: 10x Genomics

value: whole brain


title: Rice Input_rep1


title: Human endometrial organoids, gestational phase, adenomyosis 12 [ADENO12-GEST]

description:
ADENO12-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: gestational phase


title: Vehicle Control


title: APP/PS1 NLRP3.KO brain 3m

description: 10x Genomics

value: APP/PS1 NLRP3.KO


title: Traumatic brain injury repl. 4

city: Berlin

first: Denise

last: Jahn

state: Berlin

address: Augustenburger Platz 1

department: Julius Wolff Institut

country: Germany

institute: Charité - Universitätsmedizin Berlin

data_processing:
Sequencing reads were mapped to the mouse GRCm38 genome
Features count extraction and normalization were performed using STAR
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file with raw counts for each sample
Supplementary files format and content: Tab-delimited text file with DESeq-normalised count data for each sample

source_name: femur

extract_protocol:
Total RNA was isolated by crushing the femur with an Ultraturrax in Trizol, phase separation was induced through mixing and centrifugation with chlorophorm, and the aqueous phase together with ethanol were transferred to the Qiagen Rneasy Kit. We followed the instructions of the manufacturer.
libraries were prepared using the TruSeq Stranded mRNA Kit following the manufacturer's protocol

value: femur

value: wild type

value: traumatic brain injury


title: Traumatic brain injury repl. 3


title: APP/PS1 brain 3m

description: 10x Genomics


title: Traumatic brain injury repl. 2


title: Human endometrial organoids, gestational phase, adenomyosis 11 [ADENO11-GEST]

description:
ADENO11-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: HAoSMC - Na+-lactate (pH 7.4) - sample group: 5

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

institute: Martin Luther University - Halle-Wittenberg

data_processing:
Read alignment (HISAT2 2.1.0)
Read counting (featureCounts - 2.0.0)
Annotation with biomaRt and Ensembl 101
Assembly: hg38
Supplementary files format and content: .csv file including annotation raw counts (output of featureCounts) for each sample

source_name: smooth muscle

growth_protocol: Seeding of HAoSMCs on 10 cm Petri dishes until confluence with medium change every 3 days

extract_protocol:
Total RNA was isolated using BlueZol Reagent; eventual genomic DNA contamination was removed from the RNA samples using the TURBO DNA-free™ Kit; RNA sample were cleaned by ethanol precipitation with sodium acetate, glycogen and 100 % ethanol; quality check of the purified RNA samples with 2100 Bioanalyzer System
polyA enrichment (performed by Novogene Europe)

treatment_protocol: HAoSMCs were synchronized by incubation in supplement- and serum free DMEM medium for 24 h. Treatment in DMEM medium for 48 h under the following conditions: (i) pH 7.4, control condition; (ii) pH 6.8 with hydrochloric acid (HCl) ; (iii) pH 6.8 with lactic acid ; (iv) pH 7.4 with Na+-Lactate (anion of lactic acid).

value: male

value: smooth muscle

tag: organ

value: aorta

tag: celltype

value: HAoSMC

value: Na+-lactate (pH 7.4)

tag: sample group


title: NLRP3.KO brain 3m

description: 10x Genomics

tag: genotype


title: HAoSMC - Lactic acid (pH 6.8) - sample group: 5

tag: treatment

value: Lactic acid (pH 6.8)


title: Combination

tag: cell line

value: Human Urinary Bladder Cancer

value: Combination


title: Human endometrial organoids, mid-secretory phase, adenomyosis 11 [ADENO11-SEC]

description:
ADENO11-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: mid-secretory phase


title: WT brain 3m

description: 10x Genomics

value: WT


title: Traumatic brain injury repl. 1


title: HAoSMC - HCl (pH 6.8) - sample group: 5

value: HCl (pH 6.8)


title: Human endometrial organoids, gestational phase, adenomyosis 10 [ADENO10-GEST]

description:
ADENO10-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: Human endometrial epithelial cells

value: Adenomyosis


title: HAoSMC - Control (pH 7.4) - sample group: 5

value: Control (pH 7.4)


title: Human endometrial organoids, mid-secretory phase, adenomyosis 10 [ADENO10-SEC]

description:
ADENO10-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: D7-OS-3

city: Wuxi

first: Yanshan

last: Liu

address: No1800, Lihu Road

institute: Jiangnan University

data_processing:
reads were aligned to mouse whole genome (mm10) with STAR (v2.7.0)
Differential expression was pairwisely analyzed by Bioconductor package edgeR (v3.28.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: polyA RNA

source_name: Retina

extract_protocol:
Total RNA was extracted from retina samples (n=3) using RNApure Tiss&Cell kit (CWBIO, China) according to the manufacturer’s protocol.
Libraries were generated following manufacturer recommendations with varied index labels by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA).

tag: strain

value: Retina

value: retinal cells

value: wildtype

value: control


title: HAoSMC - Na+-lactate (pH 7.4) - sample group: 4

value: male

value: smooth muscle


title: D7-OD-3

value: laser treated


title: Control repl. 1

value: femur

value: wild type


title: Control repl. 2


title: D7-OS-2


title: Human endometrial organoids, mid-secretory phase, adenomyosis 12 [ADENO12-SEC]

description:
ADENO12-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: Human endometrial organoids, gestational phase, adenomyosis 9 [ADENO9-GEST]

description:
ADENO9-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: gestational phase


title: HAoSMC - HCl (pH 6.8) - sample group: 4

value: aorta

value: HAoSMC


title: D7-OS-1


title: Human endometrial organoids, mid-secretory phase, adenomyosis 9 [ADENO9-SEC]

description:
ADENO9-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: mid-secretory phase


title: Human endometrial organoids, gestational phase, adenomyosis 8 [ADENO8-GEST]

description:
ADENO8-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: day15,treat12,scRNAseq

city: Tianjin

first: Chunqiu

last: Zhang

address: NO 94 Weijin Road

institute: Nankai University

data_processing:
SeekSoul Tools pipeline were used to process the cleaned reads and generated the transcript expression matrix.Firstly, the cell barcodes  and UMI sequences were extracted based on the defined pattern about the localization of the barcode, linker and UMI within a read. The barcode was corrected with whitelist. The corrected barcode , together with UMI, were put in the header of their corresponding reads.Secondly, the reads were mapped to the reference genomes using STAR 2.7.2a.Then, the reads with barcode and UMI information were assigned to transcriptome using featureCounts of package Subread  v2.0.1.
Assembly: mm10
Supplementary files format and content: matrix files

source_name: skin

extract_protocol:
The skin tissues without separating dermis and epidermis were dissociated from the diabetic mice wound and washed with pre-cold PBS buffer. And skin tissues were minced as smaller as possible in digestive enzyme mixture and then incubated at 37°C for 1.5 h. Digestive enzyme mixture contains collagenase IV ( 200 mg/ml), Deoxyribonuclease I (1 mg/ml) , HEPES buffer solution (25mM) and RPIM-1640 medium supplemented with 10% fetal bovine serum. Subsequently, digestion process was terminated by adding the medium, and the digested skin tissues were further milled and filtered through a 40 μm strainer. Cell count and viability was estimated using fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after removal erythrocytes (Miltenyi 130-094-183). Afterward, fresh cells were washed with ice-cold RPMI 1640 containing 2% FBS for twice and then resuspended at 1×106 cells per ml in 1×PBS and 0.04% BSA.
Single-cell RNA-seq libraries were prepared using SeekOne® Digital Droplet (SeekOne® DD) Single Cell 3’ library preparation kit V2.1.  Briefly, appropriate number of cells were mixed with reverse transcription reagent and then loaded to the sample well in SeekOne® DD Chip S3 (ChipS3). Subsequently, Barcoded Hydrogel Beads (BHBs) and partitioning Oil were dispensed into corresponding wells separately in chip. After emulsion droplet generation reverse transcription were performed at 42°C for 90 minutes and inactivated at 85°C for 5 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally the indexed PCR were performed to amplified the DNA representing 3’ polyA part of expressing genes which also contained Cell Bar code and Unique Molecular Index. The indexed sequencing libraries were cleanup with SPRI beads, quantified by quantitative PCR (KAPA Biosystems KK4824) and then sequenced on illumina NovaSeq 6000 with PE150 read length

value: skin

value: skin cells

value: TSeL with light irradiation (TSeL+L)


title: HepG2-derived xenograft-sorlef-3

city: nanjing

first: ying

last: zheng

address: 639 Longmian Avenue, Jiangning District

institute: China pharmaceutical university

data_processing:
CLC Genomics Workbench V11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length faction: 0.8 similarity faction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

source_name: tumor

growth_protocol: 4-week-old Balb/c nude mice were subcutaneously injected with HepG2 cells, when the xenografts were palpable, mice were treated with vehicle, sorafenib(30mg/kg), lefamulin(50mg/kg), or the combination for 3 weeks.

extract_protocol:
RNA was harvested using RNeasy Plus Mini Kit (Qiagen). 1.3μg total RNA was used for the construction of suquencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufaturer's protocols.

treatment_protocol: Mouse tumor xenografts, rapidly frozen in liquid nitrogen, were stored at -80°C for subsequent RNA extraction

value: tumor

value: Sorafenib+Lefamulin


title: day15,control08,scRNAseq

value: PBS as control


title: Human endometrial organoids, mid-secretory phase, adenomyosis 8 [ADENO8-SEC]

description:
ADENO8-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: Human endometrial epithelial cells

value: Adenomyosis


title: HAoSMC - Lactic acid (pH 6.8) - sample group: 4

value: male

value: Lactic acid (pH 6.8)


title: HAoSMC - Na+-lactate (pH 7.4) - sample group: 3

value: smooth muscle

value: Na+-lactate (pH 7.4)


title: D7-OD-2

value: Retina

value: retinal cells

value: wildtype

value: laser treated


title: Control repl. 3

value: femur

value: wild type

value: control


title: HepG2-derived xenograft-sorlef-2


title: D3-OS-3


title: HAoSMC - Lactic acid (pH 6.8) - sample group: 3

value: aorta

value: HAoSMC


title: Human endometrial organoids, gestational phase, adenomyosis 7 [ADENO7-GEST]

description:
ADENO7-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: gestational phase


title: HepG2-derived xenograft-sorlef-1

value: tumor

value: Sorafenib+Lefamulin


title: D7-OD-1


title: Human endometrial organoids, mid-secretory phase, adenomyosis 7 [ADENO7-SEC]

description:
ADENO7-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: Human endometrial epithelial cells

value: mid-secretory phase

value: Adenomyosis


title: D3-OD-3


title: HepG2-derived xenograft-sor-3

value: Sorafenib


title: HAoSMC - HCl (pH 6.8) - sample group: 3

value: male

value: smooth muscle

value: HCl (pH 6.8)


title: Human endometrial organoids, gestational phase, adenomyosis 6 [ADENO6-GEST]

description:
ADENO6-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: HAoSMC - Control (pH 7.4) - sample group: 3

value: Control (pH 7.4)


title: D3-OS-2

value: Retina

value: retinal cells

value: wildtype


title: HepG2-derived xenograft-sor-2


title: HAoSMC - Na+-lactate (pH 7.4) - sample group: 2

value: Na+-lactate (pH 7.4)


title: Human endometrial organoids, mid-secretory phase, adenomyosis 6 [ADENO6-SEC]

description:
ADENO6-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: D3-OD-2

value: laser treated


title: HAoSMC - Control (pH 7.4) - sample group: 4

value: aorta

value: HAoSMC


title: HepG2-derived xenograft-sor-1

value: tumor


title: Human endometrial organoids, gestational phase, adenomyosis 5 [ADENO5-GEST]

description:
ADENO5-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: gestational phase


title: HAoSMC - Lactic acid (pH 6.8) - sample group: 2

value: Lactic acid (pH 6.8)


title: D3-OS-1

value: control


title: HepG2-derived xenograft-lef-3

value: Lefamulin


title: D3-OD-1


title: HAoSMC - HCl (pH 6.8) - sample group: 2


title: HepG2-derived xenograft-lef-2


title: Human endometrial organoids, mid-secretory phase, adenomyosis 5 [ADENO5-SEC]

description:
ADENO5-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: Human endometrial epithelial cells

value: mid-secretory phase

value: Adenomyosis


title: Human endometrial organoids, gestational phase, adenomyosis 4 [ADENO4-GEST]

description:
ADENO4-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: HepG2-derived xenograft-lef-1


title: HAoSMC - Na+-lactate (pH 7.4) - sample group: 1

value: male

value: smooth muscle


title: Human endometrial organoids, mid-secretory phase, adenomyosis 4 [ADENO4-SEC]

description:
ADENO4-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: iPSC-derived cortical organoid, Control -4

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

data_processing:
Reads were aligned to the human reference genome hg38. Mayo Clinic RNA-Seq analytic pipeline (MAP-RSeq Version 3.1.3) was used to generate raw gene read counts and sequencing quality control metrics.
Assembly: hg38
Supplementary files format and content: text delimited file containing raw gene counts of all samples

source_name: iPSC-derived cortical organoids

growth_protocol: iPSC-derived cortical organoids were maintained in STEMdiff™ Cerebral Organoid Kit (Stemcell Technologies).

extract_protocol:
RNA was harvested using RNeasy Mini Kit (quiagen). 600ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared fusing the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA) according to the manufacturer’s instructions

value: iPSC-derived cortical organoids

value: Control

value: Differentiation


title: HAoSMC - Control (pH 7.4) - sample group: 2

value: Control (pH 7.4)


title: iPSC-derived cortical organoid, Control -5


title: Human endometrial organoids, gestational phase, adenomyosis 3 [ADENO3-GEST]

description:
ADENO3-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: HepG2-derived xenograft-ctrl-3

value: Vehicle


title: HAoSMC - Lactic acid (pH 6.8) - sample group: 1

value: aorta


title: HepG2-derived xenograft-ctrl-2


title: HAoSMC - HCl (pH 6.8) - sample group: 1

value: HAoSMC

value: HCl (pH 6.8)


title: iPSC-derived cortical organoid, Control -3


title: iPSC-derived cortical organoid, Control -2


title: Human endometrial organoids, mid-secretory phase, adenomyosis 3 [ADENO3-SEC]

description:
ADENO3-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: HepG2-derived xenograft-ctrl-1

value: tumor


title: Human endometrial organoids, gestational phase, adenomyosis 2 [ADENO2-GEST]

description:
ADENO2-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: gestational phase


title: HAoSMC - Control (pH 7.4) - sample group: 1


title: iPSC-derived cortical organoid, Control -1


title: Human endometrial organoids, mid-secretory phase, adenomyosis 2 [ADENO2-SEC]

description:
ADENO2-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: 12yPT, snRNA-seq

city: Houston

first: Xiao

last: Li

state: TX

address: 6770 Bertner Ave

institute: Texas Heart Institute

description: 10x Genomics

data_processing:
All newly generated and published snRNA-seq data sets were processed using a uniformed pipeline. Raw sequencing reads were aligned to the genome (build GRCh38) using the 10X Genomics toolkit CellRanger version 5.0.1 (cellranger count) with --include-introns set to true. All other parameters were left as defaults.
Assembly: GRCh38
Supplementary files format and content: TSV files: Tab-separated tables. MTX files: long-format matrix files. CSV files: comma-seperated tables.

source_name: Left ventricle

extract_protocol:
Cardiac tissue was collected in the operating room during redo heart transplantation. Cardiac tissue samples were kept in cold saline on ice during transfer to the laboratory for preservation. Cardiac tissue samples were carefully dissected into multiple aliquots, which were flash-frozen and stored at –80 °C Nuclear isolation was performed as described previously. Briefly, frozen cardiac tissue was dissociated by using a Dounce homogenizer. Single nuclei were isolated via fluorescence-activated cell sorting (FACS).
SnRNA-seq was performed by using the 10X Genomics platform. Isolated nuclei and cells were loaded into the 10X Genomics Chromium Controller to obtain the gel beads in emulsion. The sequencing libraries were then prepared according to the manufacturer’s protocols for the Single-cell 3’ Reagents Kits v2 or v3. Sequencing was performed by using the NextSeq 500 and NovaSeq 6000 systems.

value: Cardiac cells

value: Left ventricle

tag: donor sex

value: Unknown

tag: donor age

tag: recipient age

tag: recipient sex

value: Male

tag: patient id


title: iPSC-derived cortical organoid, ABCA7-/- -5

tag: cell type


title: Human endometrial organoids, gestational phase, adenomyosis 1 [ADENO1-GEST]

description:
ADENO1-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: Human endometrial epithelial cells

tag: differentiation phase

value: Adenomyosis


title: Human endometrial organoids, mid-secretory phase, adenomyosis 1 [ADENO1-SEC]

description:
ADENO1-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: mid-secretory phase


title: HFpEF_TYA018_V2548

city: South San Francisco

first: Farshad

last: Farshidfar

state: CA

address: 171 Oyster Point Blvd Ste 500

institute: Tenaya Therapeutics Inc.

data_processing:
After sequencing, clean reads were analyzed with mouse reference genome mm10-2020-A using Cell Ranger v6.1.2 software. Output from Cell Ranger in the form of filtered gene expression matrix h5 files were analyzed using R package Seurat version 4.
Assembly: mm10-2020
Supplementary files format and content: h5

extract_protocol:
Approximately 100 mg of mouse heart tissue were lysed with TRI Reagent (Zymo Research) and frozen at -80 °C to ensure complete cell lysis. Nuclei isolation was performed as per instructions from 10xGenomics "Nuclei Isolation from Cell Suspensions & Tissues for Single Cell RNA Sequencing" protocol (CG000124, Rev F) to reach the target concentration of 700-1,200 nuclei/µl. The suspension was processed using 10X Genomics Single Cell protocol (CG00053, Rev D).
We constructed 3’ single cell gene expression libraries (Next GEM v3.1) using the 10x Genomics Chromium system. Each library was sequenced with Illumina NovaSeq (PE150).
snRNA-seq

treatment_protocol: Control and HFD+L-NAME mice were randomized to different groups to receive oral doses of 15 mg/kg TYA-018, 10 mg/kg empagliflozin,  or vehicle (5% DMSO + 45% PEG-300 + 50% purified water) at 10 mL/kg once per day for 6-9 weeks. TYA-018 was formulated in vehicle.

tag: tissue

tag: disease state

value: HFD/L-NAME HFpEF model

value: WT

value: TYA018 15mg/kg


title: HFpEF_Empagliflozin_V2562

value: Empagliflozin 10 mg/kg


title: iPSC-derived cortical organoid, ABCA7-/- -3

value: iPSC-derived cortical organoids

value: Differentiation


title: Human endometrial organoids, gestational phase, control 24 [B24-GEST]

description:
CONTROL24-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: None; contraol


title: Hela-nucleosome-fragments-rep3

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

description: 140-150 bp DNA fragmants were sampled

data_processing:
Adapter DNAs were trimmed using Trim Galore (version 0.6.7) with the options: --paired.
The paired-end reads were mapped to the GRCh38 for the Hela samples and the tandemly connected three Widom 601 sequences for the in vtiro sample using bowtie (version 2.3.5.1) with the default options.
Data of Hela samples were filtered using the following specifications; OLTN: 337 (+/- 5) bp, OLDN: 248 (+/- 5) bp and mono-nucleosome: 147 (+/- 5) bp, respectively.
For Hela data, the bigWig files were created by 50 bp intervals on the genome, and then the counts were normalized as CPM (Reads Per Million reads) using deepTools (version 3.5.1) with the option: -bs 1 --normalizeUsing CPM --minMappingQuality 60 --ignoreDuplicates --normalizeUsing CPM.
For in vitro data, a count file was created by counting fragments by lengths.
Assembly: GRCh38
Supplementary files format and content: bigwig files were genelated using deepTools (version 3.5.1, bamCoverage function)  with the option

source_name: Hela cells

growth_protocol: The HeLa cells were commercially obtained and stored at -80ºC until use.

extract_protocol:
The HeLa cells were suspended in the washing solution containing 15 mM Tris-HCl (pH 8.0), 15 mM NaCl, 60 mM KCl, 300 mM sucrose, and a proteinase inhibitor (Roche). The detergent buffer containing 15 mM Tris-HCl (pH 8.0), 15 mM NaCl, 60 mM KCl, 300 mM sucrose, proteinase inhibitor (Roche), and 1% NP-40 was then added to the cell suspension, and the mixture was rotated at 4 ºC for 10 minutes. The HeLa nuclei were collected by centrifugation and were resuspended in the washing solution. A large amount of MNase (3 units/µL) and CaCl2 (2 mM) were added to the HeLa nuclei suspension. The MNase treatment was performed under 37 ºC for 30 minutes, and was terminated by EDTA (pH 8.0) addition. The MNase fragments were precipitated by ethanol, and were electrophoresed by 4% agarose gel.
Libraries were prepared using ThruPLEX DNA-Seq Kit (Clontech, #R400674).

value: Hela

value: nucleosome-fragments


title: HFpEF_TYA018_V2547


title: 5dPT, snRNA-seq

description: 10x Genomics


title: Hela-nucleosome-fragments-rep2

description: 140-150 bp DNA fragmants were sampled


title: iPSC-derived cortical organoid, ABCA7-/- -2


title: iPSC-derived cortical organoid, ABCA7-/- -1


title: Human endometrial organoids, mid-secretory phase, control 24 [B24-SEC]

description:
CONTROL24-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: Hela-nucleosome-fragments-rep1

description: 140-150 bp DNA fragmants were sampled


title: Ctrl_vehicle_V2507

value: Control

value: Vehicle


title: HFpEF_vehicle_V2521

value: Left ventricle


title: CD5C5ANXX_3#136780_GAGTGG [KEV sRNA]

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
fastQ quality assessment
cutadapt adater trimming
bowtie1 genome alignment
miRDeep2 miRNA quantification (mirbase)
Assembly: GRCh38.p12; mirbase version v22.1
Supplementary files format and content: CSV with miRNA quantifications (raw and rpm)

source_name: HUVEC

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit
RealSeq Biofluids Plasma/Serum miRNA Library Kit

tag: sample type

value: EV

value: HUVEC

tag: donor

value: K

tag: molecule subtype

value: small RNA


title: Human endometrial organoids, mid-secretory phase, control 21 [B21-SEC]

description:
CONTROL21-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: Human endometrial epithelial cells

value: mid-secretory phase


title: Human endometrial organoids, gestational phase, control 18 [B18-GEST]

description:
CONTROL18-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: gestational phase


title: Hela-OLDN-fragments-rep3

description: 200-300 bp DNA fragmants were sampled

tag: sample group

value: OLDN-fragments


title: CD5C5ANXX_3#136779_CGTACG [JEV sRNA]

source_name: LEC

value: LEC

value: J


title: iPSC-derived cortical organoid, ABCA7-/- -4

value: iPSC-derived cortical organoids

tag: genotype

value: Differentiation


title: Human endometrial organoids, mid-secretory phase, control 18 [B18-SEC]

description:
CONTROL18-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx

tag: treatment

value: None; contraol


title: 15mPT, snRNA-seq

description: 10x Genomics

value: Cardiac cells

value: Female

value: Male


title: CD5C5ANXX_3#136778_GTTTCG [IEV sRNA]

source_name: BEC

value: BEC

value: I


title: HFpEF_Empagliflozin_V2561

value: Left ventricle

value: HFD/L-NAME HFpEF model

value: WT

value: Empagliflozin 10 mg/kg


title: HFpEF + TYA-018_2299

data_processing:
Adapter trimming by FASTP (ver. 0.23.2)
Read alignment by Salmon (ver. 1.6.0)
tximport to generate gene expression matrix in Transcript Per Million (TPM)
Protein-coding genes identification by Ensembl human reference genome release 100
Exclusion of mitochondrial genes and renormalization to TPM.
Assembly: hg38 v.13
Supplementary files format and content: TXT

extract_protocol:
Approximately 106 cells or 20-30 mg of mouse heart tissue were lysed with TRI Reagent (Zymo Research) and frozen at -80 °C to ensure complete cell lysis. Total RNA was extracted and washed from lysed cells using the Direct-zol-96 RNA Kit (Zymo Research) according to the manufacturer’s instructions. Samples were treated with DNase I for 15 min at room temperature. cDNA was reverse transcribed from approximately 1 μg of RNA through random hexamers using the SuperScript III First-Strand Synthesis System according to the manufacturer’s instructions (Thermo Fisher Scientific). Real-time qPCR reactions were performed using the TaqMan universal PCR master mix (Thermo Fisher Scientific) with the TaqMan probes listed. RT-qPCR reactions were performed using the QuantStudio7 Flex Real-Time PCR systems (Thermo Fisher Scientific). Each reaction was performed in triplicate for a given RT-qPCR run, and each condition had four experimental replicates. Relative expression of the gene of interest was normalized to GAPDH as the housekeeping control using the 2–ΔΔCT method. P values were calculated with Student’s t-tests.
From each replicate, 100 ng total RNA was extracted via the polyA-tail-specific protocol according to Illumina, Inc.. The RNA libraries were prepared using a TruSeq Stranded mRNA kit (Illumina), which also removes ribosomal RNA. The libraries were sequenced as 100 base pair single-end reads using Illumina NovaSeq SP with an average of 29.8 million reads per sample.

treatment_protocol: HFD+L-NAME mice were randomized to different groups to receive oral doses of 15 mg/kg TYA-018 or vehicle (5% DMSO + 45% PEG-300 + 50% purified water) at 10 mL/kig once per day for 6-9 weeks. TYA-018 was formulated in vehicle.

value: TYA018 15mg/kg


title: Human endometrial organoids, gestational phase, control 17 [B17-GEST]

description:
CONTROL17-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: Human endometrial epithelial cells

value: gestational phase


title: Hela-OLDN-fragments-rep1

description: 200-300 bp DNA fragmants were sampled

tag: cell line

value: Hela

value: OLDN-fragments


title: HFpEF_vehicle_V2523

tag: strain

value: Vehicle


title: HFpEF + TYA-018_2298


title: Human endometrial organoids, mid-secretory phase, control 17 [B17-SEC]

description:
CONTROL17-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: mid-secretory phase


title: CD5C5ANXX_3#136777_GTGGCC [HEV sRNA]

value: EV

value: H

value: small RNA


title: Human endometrial organoids, gestational phase, control 16 [B16-GEST]

description:
CONTROL16-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: None; contraol


title: Hela-OLTN-fragments-rep3

description: 300-400 bp DNA fragmants were sampled

value: OLTN-fragments


title: CD5C5ANXX_3#136776_GTGAAA [GEV sRNA]

source_name: HDMEC

value: HDMEC

value: G


title: Hela-OLTN-fragments-rep2

description: 300-400 bp DNA fragmants were sampled


title: HFpEF + TYA-018_2297

value: Left ventricle

value: HFD/L-NAME HFpEF model


title: CD5C5ANXX_3#136775_GTCCGC [FEV sRNA]

value: LEC

value: F


title: HFpEF + TYA-018_2296

value: WT

value: TYA018 15mg/kg


title: Human endometrial organoids, mid-secretory phase, control 16 [B16-SEC]

description:
CONTROL16-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: Human endometrial epithelial cells


title: CD5C5ANXX_3#136774_GTAGAG [EEV sRNA]

source_name: LECtert

value: LECtert

value: E


title: Hela-OLTN-fragments-rep1

description: 300-400 bp DNA fragmants were sampled

value: Hela