title: Tag, Subjects UNC0119 and UNC0223

description:
Library name: TAG119A223A
Hashtag-derived oligonucleotide (HTO)


title: AbSeq, Subjects UNC0142 and UNC0229

status: Public on Sep 22 2025

type: SRA

city: Chapel Hill

first: Austin

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

country: USA

institute: UNC Chapel Hill

description:
Library name: ABSEQ142C229C
Antibody-derived oligonucleotide (ADT)

library_source: other

data_processing:
CITE-Seq and multiplexed files were demultiplexed using the Lex plug-in in SeqGeq.
The Seurat plug-in in SeqGeq was used for multimodal analysis.
Assembly: Human
Supplementary files format and content: CSV file containing DBEC moleculers per cell.
Supplementary files format and content: CSV file containing sample tag call
Library strategy: CITE-seq

molecule: protein

organism: Homo sapiens

source_name: PBMCs

extract_protocol:
Peripheral blood mononuclear cell preparations were enriched for B cells from the same patient and sequentially labeled with sample tags using the BD Human Single-Cell Multiplexing Kit and BD AbSeq oligo-conjugated antibodies.
Single cells were captured, and cDNA was synthesized on beads, followed by targeted amplification of transcripts using the Human Immune Response Panel primers (399 genes) and a custom supplemental panel set (20 targets), as well as amplification of cDNA of sample Tag and AbSeq. Final RNA-seq libraries were prepared by performing the index PCR using a combination of 3 forward index primers (TreSeq D501-D503) and 12 reverse index primers (TrueSeq D701-D712).

tag: cell type

value: PBMCs

tag: treatment

value: Control

tag: library type

value: ADT


title: AbSeq, Subjects UNC0119 and UNC0223

description:
Library name: ABSEQ119A223A
Antibody-derived oligonucleotide (ADT)

value: AGS


title: AbSeq, Subjects UNC0211 and UNC0212

description:
Library name: ABSEQ211A212A
Antibody-derived oligonucleotide (ADT)


title: Primary human neutrophils LPS 6h biol rep 3

city: Montreal

first: Aiten

last: Ismailova

address: 3655 Sir William Osler

country: Canada

institute: McGill University

description:
Library name: Sample 11
Column name in counts_ALL_SAMPLES.xlsx: Lps3

library_source: transcriptomic

data_processing:
All samples met quality standards as determined by QC reports from Genome Quebec and were included in the analysis. The quality of sequence reads was verified using FastQC, with poor-quality reads identified based on the Phred score, which is logarithmically related to base calling error probabilities. For all RNA-seq datasets, the Phred offset quality score exceeded 30, and the minimum fragment size for alignment was set to 50. Low-quality bases were trimmed from read ends using default settings in Trimmomatic, and quality was re-assessed using FastQC. Reads were mapped to the human GRCh38 genome assembly using HISAT2. Gene expression was quantified by counting uniquely mapped reads with StringTie, using default parameters.
Assembly: hg38
Supplementary files format and content: excel file includes raw counts for each sample

molecule: total RNA

source_name: primary human neutrophils

extract_protocol:
Briefly, total RNA was extracted from three isolates of 1,25D-, LPS-, 1,25D+LPS- and vehicle-treated neutrophils using the FavorPrep Blood/Cultured Cell Total RNA Mini Kit (FABRK 001, Favorgen) according to the manufacturer's protocol.
Library preparation was performed using the polyA Enriched RNA Library Preparation.

value: primary human neutrophils

value: 100ng/ml LPS


title: AbSeq, Subjects UNC0039 and UNC0085

description:
Library name: ABSEQ039C095C
Antibody-derived oligonucleotide (ADT)


title: Primary human neutrophils 1,25D 6h biol rep 3

description:
Library name: Sample 10
Column name in counts_ALL_SAMPLES.xlsx: Vitd3


title: Primary human neutrophils 1,25D+LPS 6h biol rep 3

description:
Library name: Sample 12
Column name in counts_ALL_SAMPLES.xlsx: Lpsd3


title: AbSeq, Subjects UNC0221 and UNC0222

description:
Library name: ABSEQ221A222A
Antibody-derived oligonucleotide (ADT)


title: Primary human neutrophils LPS 6h biol rep 2

description:
Library name: Sample 7
Column name in counts_ALL_SAMPLES.xlsx: Lps2


title: Primary human neutrophils 1,25D 6h biol rep 2

description:
Library name: Sample 6
Column name in counts_ALL_SAMPLES.xlsx: Vitd2


title: Primary human neutrophils control 6h (treated with DMSO) biol rep 3

description:
Library name: Sample 9
Column name in counts_ALL_SAMPLES.xlsx: Ctl3

value: DMSO


title: Primary human neutrophils control 6h (treated with DMSO) biol rep 2

description:
Library name: Sample 5
Column name in counts_ALL_SAMPLES.xlsx: Ctl2


title: Primary human neutrophils LPS 6h biol rep 1

description:
Library name: Sample 3
Column name in counts_ALL_SAMPLES.xlsx: Lps1


title: Primary human neutrophils 1,25D 6h biol rep 1

description:
Library name: Sample 2
Column name in counts_ALL_SAMPLES.xlsx: Vitd1


title: Primary human neutrophils control 6h (treated with DMSO) biol rep 1

description:
Library name: Sample 1
Column name in counts_ALL_SAMPLES.xlsx: Ctl1


title: Primary human neutrophils 1,25D+LPS 6h biol rep 1

description:
Library name: Sample 4
Column name in counts_ALL_SAMPLES.xlsx: Lpsd1


title: PBMC, healthy, 6

city: Seoul

first: Namphil

last: Kim

address: Gwanak-ro 1

department: Electrical and Computer Engineering

country: South Korea

institute: Seoul National University

description: Library name: HC6

data_processing:
The raw NGS forward (R1) and reverse (R2) reads were merged, filtered based on Phred scores, and subclustered using UMI using paired-end read merger (PEAR), v0.9.10, and Clustal Omega, v1.2.4, with the default setting .
The sequence annotation process used the IMGT (International Immunogenetics Information System) constant gene database (PMID: 12529691) to obtain the isotype, and IgBLAST, v1.17.1 (PMID: 23671333) to obtain VJ genes, CDR1/2/3 sequences, and the number of mutations from the corresponding V genes.
Sequences from technical duplicates were merged after processing.
Assembly: GRCh38
Supplementary files format and content: Format in TSV, BCR repertoire related fields.

molecule: polyA RNA

source_name: PBMC

extract_protocol:
Total RNA was isolated from PBMCs, using the TRIzol Reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s protocols.
Genes encoding VH and part of the first constant domain of the heavy chain (CH1) domain were amplified using specific primers. NGS sequencing was performed using NovaSeq6000 SP chip (250PE).

tag: diagnosis

value: Healthy

tag: severity(mgfa)

value: X

tag: age

tag: Sex

value: F

tag: tissue

value: PBMC

value: B cell


title: PBMC, healthy, 4

description: Library name: HC4


title: PBMC, healthy, 5

description: Library name: HC5


title: PBMC, healthy, 9

description: Library name: HC9


title: PBMC, healthy, 7

description: Library name: HC7


title: PBMC, healthy, 3

description: Library name: HC3


title: PBMC, MG, 17

description: Library name: MP68_t1

value: MuSK-MG


title: PBMC, healthy, 1

description: Library name: HC1


title: PBMC, MG, 21

description: Library name: MP93_t1


title: PBMC, healthy, 11

description: Library name: HC11

value: M


title: PBMC, MG, 20

description: Library name: MP82_t1


title: PBMC, healthy, 2

description: Library name: HC2


title: PBMC, healthy, 13

description: Library name: HC13


title: PBMC, MG, 13

description: Library name: MP32_t2


title: Primary human neutrophils 1,25D+LPS 6h biol rep 2

description:
Library name: Sample 8
Column name in counts_ALL_SAMPLES.xlsx: Lpsd2


title: PBMC, MG, 22

description: Library name: MP93_t2


title: PBMC, MG, 19

description: Library name: MP68_t3


title: PBMC, MG, 14

description: Library name: MP45_t1


title: PBMC, MG, 16

description: Library name: MP45_t3


title: PBMC, healthy, 12

description: Library name: HC12


title: PBMC, MG, 18

description: Library name: MP68_t2


title: PBMC, healthy, 10

description: Library name: HC10


title: PBMC, MG, 11

description: Library name: MP153_t1


title: PBMC, MG, 12

description: Library name: MP168_t1


title: PBMC, MG, 10

description: Library name: MP152_t1


title: PBMC, MG, 9

description: Library name: MP149_t3


title: PBMC, MG, 8

description: Library name: MP149_t2


title: PBMC, healthy, 8

description: Library name: HC8


title: PBMC, MG, 5

description: Library name: MP136_t1


title: PBMC, MG, 6

description: Library name: MP145_t1


title: PBMC, MG, 4

description: Library name: MP126_t1


title: PBMC, MG, 2

description: Library name: MP115_t2


title: PBMC, MG, 3

description: Library name: MP115_t3


title: PBMC, MG, 15

description: Library name: MP45_t2


title: PBMC, NHD, 9

description: Library name: NHD9


title: PBMC, NHD, 4

description: Library name: NHD4


title: PBMC, NHD, 5

description: Library name: NHD5


title: PBMC, NHD, 7

description: Library name: NHD7


title: PBMC, NHD, 1

description: Library name: NHD1


title: PBMC, RA, 10

description: Library name: RA10

value: Rheumatoid Arthritis


title: PBMC, MG, 7

description: Library name: MP149_t1


title: PBMC, RA, 13

description: Library name: RA13


title: PBMC, NHD, 2

description: Library name: NHD2


title: PBMC, RA, 11

description: Library name: RA11


title: PBMC, NHD, 6

description: Library name: NHD6


title: PBMC, RA, 14

description: Library name: RA14


title: PBMC, RA, 12

description: Library name: RA12


title: PBMC, RA, 7

description: Library name: RA7


title: PBMC, MG, 1

description: Library name: MP115_t1


title: PBMC, RA, 6

description: Library name: RA6


title: PBMC, RA, 9

description: Library name: RA9


title: PBMC, RA, 3

description: Library name: RA3


title: PBMC, RA, 4

description: Library name: RA4


title: PBMC, RA, 5

description: Library name: RA5


title: PBMC, RA, 2

description: Library name: RA2


title: PBMC, RA, 1

description: Library name: RA1


title: PBMC, HC, 11

description: Library name: HC11


title: PBMC, HC, 9

description: Library name: HC9


title: PBMC, HC, 8

description: Library name: HC8


title: PBMC, RA, 15

description: Library name: RA15


title: PBMC, NHD, 8

description: Library name: NHD8


title: PBMC, NHD, 3

description: Library name: NHD3


title: PBMC, HC, 6

description: Library name: HC6


title: PBMC, HC, 3

description: Library name: HC3


title: PBMC, HC, 4

description: Library name: HC4


title: PBMC, SS, 18

description: Library name: SS18

value: Sjogren's Syndrome


title: PBMC, SS, 17

description: Library name: SS17


title: PBMC, RA, 8

description: Library name: RA8


title: PBMC, SS, 19

description: Library name: SS19


title: PBMC, HC, 5

description: Library name: HC5


title: PBMC, HC, 1

description: Library name: HC1


title: PBMC, SS, 14

description: Library name: SS14


title: PBMC, SS, 16

description: Library name: SS16


title: PBMC, SS, 11

description: Library name: SS11


title: PBMC, HC, 2

description: Library name: HC2


title: PBMC, SS, 10

description: Library name: SS10


title: PBMC, SS, 20

description: Library name: SS20


title: PBMC, SS, 12

description: Library name: SS12


title: PBMC, SS, 15

description: Library name: SS15


title: PBMC, SS, 13

description: Library name: SS13


title: PBMC, SS, 9

description: Library name: SS9


title: PBMC, HC, 10

description: Library name: HC10


title: PBMC, SS, 6

description: Library name: SS6


title: PBMC, SS, 8

description: Library name: SS8


title: PBMC, SS, 5

description: Library name: SS5


title: PBMC, SS, 7

description: Library name: SS7


title: PBMC, SS, 4

description: Library name: SS4


title: PBMC, SS, 3

description: Library name: SS3


title: PBMC, HC, 7

description: Library name: HC7


title: PBMC, SS, 1

description: Library name: SS1


title: PBMC, SS, 2

description: Library name: SS2


title: neural progenitor cell, differentiated 6 days [scATAC-seq]

city: Hangzhou

first: Hongtao

last: Yu

state: Zhejiang

address: No.600 Dunyu Road, Xihu District

country: China

institute: Westlake University

description:
Library name: NPC_D6
10X Genomics

library_source: genomic single cell

data_processing:
The demultiplexing, barcode processing, reads mapping, chromatin accessibility fragments calculation and aggregation were made  using Cell Ranger ARC 1.0.1 software. Refence human genome for Cell Ranger ARC was downloaded from https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-GRCh38-2020-A-2.0.0.tar.gz.
Assembly: GRCh38
Supplementary files format and content: HDF5 files include filtered cell barcode × feature matrices for both gene expression and chromatin accessibility;  direct outputs of Cell Ranger ARC count command (v1.0.1).
Supplementary files format and content: csv files include descriptive statistics and quality control metrics for each cell barcode
Supplementary files format and content: tsv.gz files include the record of ATAC-seq fragments with genomic location, barcode and duplicate count

molecule: genomic DNA

extract_protocol:
Live cells were lysed on ice for 5 minutes and isolated nuclei were transposed and loaded onto the Chromium Next GEM Chip J (10×Genomics)
The chip containing the cells was then loaded onto a Chromium Controller, and the library construction was carried out in accordance with the manufacturer's instructions

tag: cell line

value: neural progenitor cell

tag: genotype

value: WT

value: neurogenic differentiation

tag: time

value: 6 days


title: neural progenitor cell, differentiated 72h [scATAC-seq]

description:
Library name: NPC_72h
10X Genomics


title: neural progenitor cell, differentiated 52h [scATAC-seq]

description:
Library name: NPC_52h
10X Genomics


title: neural progenitor cell, differentiated 54h [scATAC-seq]

description:
Library name: NPC_54h
10X Genomics


title: neural progenitor cell, differentiated 50h [scATAC-seq]

description:
Library name: NPC_50h
10X Genomics


title: neural progenitor cell, differentiated 44h [scATAC-seq]

description:
Library name: NPC_44h
10X Genomics


title: neural progenitor cell, differentiated 46h [scATAC-seq]

description:
Library name: NPC_46h
10X Genomics


title: neural progenitor cell, differentiated 48h [scATAC-seq]

description:
Library name: NPC_48h
10X Genomics


title: neural progenitor cell, differentiated 3 days replication1

address: Dunyu Street

description: Library name: NPC_D3_rep1

library_source: genomic

data_processing:
Sequencing data was mapped to hg38 reference genome with Bowtie2
SAM-format mapping files were sorted, quality-checked, and transformed into BAM with SAMtools and duplicate reads were removed using picard. BAM format mapping files were transformed into bigWig format with RPKM normalization by deeptools.
Peak calling was performed with MACS2
Assembly: GRCh38
Supplementary files format and content: bigWig files after dropping duplicate reads
Library strategy: CUT&Tag

extract_protocol:
Fresh cell cultures were harvested and counted to obtain 1×10^⁵ cells per sample.  Cells were then incubated with Concanavalin A-coated beads at room temperature for 10 min.  After removal of the supernatant, cells were resuspended in ice-cold Antibody Buffer containing the PAX6 antibody (Cell Signaling Technology, #60433) and incubated overnight at 4˚C.  The primary antibody solution was then removed, and the cells were incubated with the secondary Goat Anti-Rabbit IgG H&L (Vazyme, Ab206-01) diluted in DIG Wash Buffer for 1 h at room temperature.  After thorough washing, CUT&Tag pA/G-Tn5 Transposomes were added and incubated for 1 h at room temperature.  Following additional washes, tagmentation was performed at 37˚C for 1 h.  DNA was extracted using magnetic DNA purification beads.
The purified DNA was amplified via PCR using indexed i7 and i5 primers (Vazyme, TruePrep DNA Library Prep Kit V2 for Illumina, #TD501).

value: Day 3


title: H9 embryonic stem cell replication2

description: Library name: H9_ESC_rep2

value: embryonic stem cell

value: Day 0


title: H9 embryonic stem cell [scATAC-seq]

description:
Library name: H9_ESC
10X Genomics


title: neural progenitor cell, differentiated 3 days replication2

description: Library name: NPC_D3_rep2


title: HBCx218 treated with Capecitabine, residual tumor

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

description:
Library name: HBCx218_AC
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (v.7.1) for scRNA-seq experiments.
Assembly: hg38
Supplementary files format and content: Sparse-matrix in 10X format, corresponding to the ‘*barcodes.tsv’ files containing the cell barcode sequence ; the ‘*features.tsv’ files containing the features (transcripts) and the ‘*matrix.mtx’ files containing the matrix non-zeroes values and row and column indexes.

source_name: Breast

growth_protocol: For PDX model, female Swiss nude mice were purchased from Charles River Laboratories and maintained under specific-pathogen-free conditions. Mouse care and housing were in accordance with institutional guidelines and the rules of the French Ethics Committee (project authorization no. 02163.02). In this study, we used xenograft models generated from 5 residual triple-negative breast cancer post-neoadjuvant chemotherapy (HBCx39, HBCx95, HBCx172, HBCx221 and HBCx218) established previously at Institut Curie with informed consent from the patient.

extract_protocol:
For PDX model, before downstream analysis, control and treated tumors were digested for 2 h at 37 °C with a cocktail of Collagenase I (Roche, Ref: 11088793001) and Hyaluronidase (Sigma-Aldrich, Ref: H3506). Cells were then individualized at 37°C using a cocktail of 0.25% Trypsin-Versen (Thermo Fisher Scientific, Ref: 15040-033), Dispase II (Sigma-Aldrich, Ref: D4693) and DNase I (Roche, Ref: 11284932001) as described previously53. Then, eBioscience red blood cell lysis buffer (Thermo Fisher Scientific, Ref: 00-4333-57) was added to the cell suspension to remove red blood cells. To increase the viability of the final cell suspension, dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec, Ref:130-090-101).
For each single-cell suspension or PDX dissociated cell sample (7), approximately 3,000 cells were loaded on a Chromium Single Cell Controller Instrument according to the manufacturer’s instructions. Samples and libraries were prepared according to the manufacturer's instructions. Libraries were sequenced on a NovaSeq 6000 (Illumina) in PE 28-8-91 with a coverage of 50,000 reads/cell.

treatment_protocol: Mice were treated with various methods (Table S2): capecitabine (Xeloda; Roche Laboratories) at a dose of 540 mg/kg, orally 5 d/week, for 25 to 51 days (i.e. pCR); adriamycine (Accord) at 2 mg/kg, intraperitoneal (i.p.)  1×/21 days; cyclophosphamide (Baxter) at 100 mg/kg, i.p. 1×/21 days; cisplatin (Mylan) at 6 mg/kg, i.p. 1×/21 days; or carboplatine (Accord) at 90 mg/kg, i.p. 1x/21 days. Relative tumor volumes (mm3) were measured as described previously. Before downstream analysis, cell suspensions were prepared as previously described (7).

value: Breast

tag: disease

value: TNBC

tag: model

value: patient-derived xenograft (PDX)

value: Anthracyclines


title: HBCx172, chemonaive tumor

description:
Library name: HBCx172_chemonaive
10x Genomics

value: chemonaive


title: HBCx221, chemonaive tumor

description:
Library name: HBCx221_chemonaive
10x Genomics


title: HBCx14 treated with Anthracyclines, residual tumor, biological rep 5

description:
Library name: HBCx14_AC5
Column name : HBCx14_AC5

data_processing:
The alignement, gene counting and aggregation were made using the RNA-seq pipeline (10.5281/zenodo.7443721)
Assembly: hg38
Supplementary files format and content: csv files includes raw counts for each Sample.

growth_protocol: For PDX model, female Swiss nude mice were purchased from Charles River Laboratories and maintained under specific-pathogen-free conditions. Mouse care and housing were in accordance with institutional guidelines and the rules of the French Ethics Committee (project authorization no. 02163.02). In this study, we used xenograft models generated from a primary triple-negative breast cancer (HBCx14) established previously at Institut Curie with informed consent from the patient.

extract_protocol:
After mechanical dissociation with Mixer Mill for 2 min at 30 Hz in 500 µL of Qiazol, RNA was extracted following Qiazol/chloroform extraction protocol (Qiagen, ref. 139046, MaXtract High density) and RNeasy Mini column (Qiagen, ref. 74106), following manufacturer’s instructions. RNA quality was checked on the Agilent TapeStation using RNA reagents. RNA extracts were sequenced on a NovaSeq 6000 (Illumina) in PE100 mode.
RNA-seq libraries were prepared using the Illumina® Stranded mRNA Prep, Ligation kit (96 Samples) (Cat# 20040534, Illumina) following the manufacturer’s protocol. Unique dual indexes were added using the IDT for Illumina DNA/RNA UD Indexes (Set A) (Cat# 20040553, Illumina).


title: HBCx39, chemonaive tumor

description:
Library name: HBCx39_chemonaive
10x Genomics


title: HBCx221 treated with Capecitabine, residual tumor

description:
Library name: HBCx221_Capecitabine
10x Genomics

value: Capecitabine


title: HBCx95, chemonaive tumor

description:
Library name: HBCx95_chemonaive
10x Genomics


title: HBCx218, chemonaive tumor

description:
Library name: HBCx218_chemonaive
10x Genomics


title: HBCx39 treated with Capecitabine, residual tumor

description:
Library name: HBCx39_Capecitabine
10x Genomics


title: HBCx172 treated with Capecitabine, residual tumor

description:
Library name: HBCx172_Capecitabine
10x Genomics


title: HBCx95 treated with Capecitabine, residual tumor

description:
Library name: HBCx95_Capecitabine
10x Genomics


title: H9 embryonic stem cell replication1

description: Library name: H9_ESC_rep1


title: HBCx14 treated with Anthracyclines, residual tumor, biological rep 3

description:
Library name: HBCx14_AC3
Column name : HBCx14_AC3


title: HBCx14 treated with Anthracyclines, residual tumor, biological rep 4

description:
Library name: HBCx14_AC4
Column name : HBCx14_AC4


title: HBCx14 treated with Carboplatin, residual tumor, biological rep 5

description:
Library name: HBCx14_Carboplatin5
Column name : HBCx14_Carboplatin5

value: Carboplatin


title: HBCx14 treated with Anthracyclines, residual tumor, biological rep 1

description:
Library name: HBCx14_AC1
Column name : HBCx14_AC1


title: HBCx14 treated with Carboplatin, residual tumor, biological rep 4

description:
Library name: HBCx14_Carboplatin4
Column name : HBCx14_Carboplatin4


title: HBCx14 treated with Carboplatin, residual tumor, biological rep 3

description:
Library name: HBCx14_Carboplatin3
Column name : HBCx14_Carboplatin3


title: neural progenitor cell, differentiated 24h [scATAC-seq]

description:
Library name: NPC_24h
10X Genomics


title: HBCx14 treated with Carboplatin, residual tumor, biological rep 1

description:
Library name: HBCx14_Carboplatin1
Column name : HBCx14_Carboplatin1


title: HBCx14 treated with Anthracyclines, residual tumor, biological rep 2

description:
Library name: HBCx14_AC2
Column name : HBCx14_AC2


title: HBCx14 treated with Carboplatin, residual tumor, biological rep 2

description:
Library name: HBCx14_Carboplatin2
Column name : HBCx14_Carboplatin2


title: HBCx14 treated with Cisplatin, residual tumor, biological rep 4

description:
Library name: HBCx14_Cisplatin4
Column name : HBCx14_Cisplatin4

value: Cisplatin


title: HBCx14 treated with Cisplatin, residual tumor, biological rep 5

description:
Library name: HBCx14_Cisplatin5
Column name : HBCx14_Cisplatin5


title: HBCx14 treated with Cisplatin, residual tumor, biological rep 3

description:
Library name: HBCx14_Cisplatin3
Column name : HBCx14_Cisplatin3


title: HBCx14 treated with Cisplatin, residual tumor, biological rep 2

description:
Library name: HBCx14_Cisplatin2
Column name : HBCx14_Cisplatin2


title: HBCx14 treated with Cisplatin, residual tumor, biological rep 1

description:
Library name: HBCx14_Cisplatin1
Column name : HBCx14_Cisplatin1


title: HBC14 untreated, chemonaive tumor, biological rep 2

description:
Library name: HBCx14_chemonaive2
Column name : HBCx14_chemonaive2


title: EVT, TP53KO, D6, rep2

city: Pokfulam

first: Yunying

last: Huang

state: Hong Kong

address: Rm503, JCBIR, 5 Sassoon Road

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

description:
Library name: EVT_TP53KO_D6_2
normal-counts-EVT-D6.csv

data_processing:
Raw data of RNA-seq was processed using the current best practice pipeline implemented in nfcore.
Sequence reads were mapped to mm10 mouse reference genome or hg38 human reference genome.
RSEM was applied to estimate gene expression levels with default settings.
Assembly: mm10; hg38 human genome
Supplementary files format and content: comma-separated values file or tab-delimited file including raw counts or normal counts for each sample

source_name: EVT

extract_protocol:
Total RNA was harvetsed using Trizol reagents 1.0µg of total RNA was used for the construction of sequencing libraries.
RNA libraris for RNA-seq were prepared using magnetic beads for mRNA enrichment followed by cDNA synthesis, adapter ligation and PCR amplification.

value: EVT

value: KO

tag: time point


title: EVT, WT, D6, rep2

description:
Library name: EVT_WT_D6_2
normal-counts-EVT-D6.csv


title: EVT, WT, D6, rep1

description:
Library name: EVT_WT_D6_1
normal-counts-EVT-D6.csv


title: EVT, WT, D3, rep2

description:
Library name: EVT_WT_D3_2
normal-counts-EVT-D3.csv


title: EVT, TP53KO, D3, rep2

description:
Library name: EVT_TP53KO_D3_2
normal-counts-EVT-D3.csv


title: EVT, TP53KO, D3, rep1

description:
Library name: EVT_TP53KO_D3_1
normal-counts-EVT-D3.csv


title: RNA-seq of EVs from uterine fluid , ART patient, sample 42

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospdale San Raffaele

description:
Library name: EUF97
Failed implantation after transfer

data_processing:
Sequencing was performed on the Illumina NovaSeq 6000 platform, in order to obtain 30 millions of single-end reads per sample
The raw reads generated by sequencing were trimmed using Trimmomatic, version 0.32, to remove adapters and exclude low-quality reads from the analysis
The remaining reads were then aligned to the human genome GRCh38 using STAR, version 2.5.3a and  assigned to genes according to the Gencode basic annotations, version 31.
Uniquely mapped reads were assigned to the corresponding genes using the featureCounts function in the Rsubread R package.Only reads mapped to exons were considered in the counting procedure.
The quality of sequencing and alignment was assessed using the FastQC and MultiQC tools
Assembly: hg38
Supplementary files format and content: format: ".txt", tab delimited file,   content: Raw Counts Matrix

source_name: Uterine fluid derived Extracellular Vescicles

extract_protocol:
Uterine fluid samples were obtained by lavage of the endometrial cavity with 2.5 of physiologic solution using a balloon hysterosonosonography catheter to avoid vaginal contamination. Extracellular vesicles were isolated- after mucus disgregation by vortexing- using standard ultracentrifugation protocol.  RNA was harvested using  RNase micro KIT of QIAGEN with DNAse treatment step in coloumn.
To perform transcriptome sequencing on UF-EVs, cDNA libraries were prepared using the SMART-Seq V4 Ultra Low Input RNA kit

tag: population

value: Women undergoing ART and transfer of an euploid blastocyst

value: menstrual cycle_phase:secretory

value: mentrual cycle_day_(counted_from_the_first_day_of_menstrual_bleeding_and_expressed_as_n_or_from_the_day_of_urinary_lh_surge_detection_and_expressed_an_lh+n):LH+7 (within window of implantation)

tag: batch


title: RNA-seq of EVs from uterine fluid , ART patient, sample 43

description:
Library name: EUF99
Failed implantation after transfer

value: Uterine fluid derived Extracellular Vescicles


title: RNA-seq of EVs from uterine fluid , ART patient, sample 41

description:
Library name: EUF96
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 40

description:
Library name: EUF95
Successful implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 39

description:
Library name: EUF94
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 37

description:
Library name: EUF92
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 38

description:
Library name: EUF93
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 36

description:
Library name: EUF91
Successful implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 35

description:
Library name: EUF90
Successful implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 31

description:
Library name: EUF85
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 33

description:
Library name: EUF87
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 32

description:
Library name: EUF86
Failed implantation after transfer


title: HBC14 untreated, chemonaive tumor, biological rep 1

description:
Library name: HBCx14_chemonaive1
Column name : HBCx14_chemonaive1


title: RNA-seq of EVs from uterine fluid , ART patient, sample 28

description:
Library name: EUF82
Successful implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 34

description:
Library name: EUF89
Successful implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 27

description:
Library name: EUF80
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 30

description:
Library name: EUF84
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 26

description:
Library name: EUF79
Failed implantation after transfer


title: EVT, TP53KO, D6, rep1

description:
Library name: EVT_TP53KO_D6_1
normal-counts-EVT-D6.csv


title: HBC14 untreated, chemonaive tumor, biological rep 3

description:
Library name: HBCx14_chemonaive3
Column name : HBCx14_chemonaive3


title: RNA-seq of EVs from uterine fluid , ART patient, sample 25

description:
Library name: EUF78
Successful implantation after transfer


title: EVT, WT, D3, rep1

description:
Library name: EVT_WT_D3_1
normal-counts-EVT-D3.csv

value: WT


title: RNA-seq of EVs from uterine fluid , ART patient, sample 24

description:
Library name: EUF77
Successful implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 22

description:
Library name: EUF70
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 15

description:
Library name: EUF60
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 18

description:
Library name: EUF65
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 20

description:
Library name: EUF67
Successful implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 17

description:
Library name: EUF64
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 16

description:
Library name: EUF62
Successful implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 23

description:
Library name: EUF72
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 21

description:
Library name: EUF69
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 13

description:
Library name: EUF55
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 12

description:
Library name: EUF53
Successful implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 10

description:
Library name: EUF18
Successful implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 9

description:
Library name: EUF108
Successful implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 29

description:
Library name: EUF83
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 6

description:
Library name: EUF105
Excluded from analysis due to high number genes with outliers expression values


title: RNA-seq of EVs from uterine fluid , ART patient, sample 7

description:
Library name: EUF106
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 4

description:
Library name: EUF103
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 2

description:
Library name: EUF101
Successful implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 3

description:
Library name: EUF102
Successful implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 5

description:
Library name: EUF104
Failed implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 8

description:
Library name: EUF107
Successful implantation after transfer


title: neural progenitor cell, differentiated 72h

description:
Library name: NPC_72h
10X Genomics

data_processing:
The demultiplexing, barcode processing, reads mapping, gene counting and aggregation were made  using Cell Ranger ARC 1.0.1 software. Refence human genome for Cell Ranger ARC was downloaded from https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-GRCh38-2020-A-2.0.0.tar.gz.
Assembly: GRCh38
Supplementary files format and content: tsv files include barcodes and features and matrix files includes counts matrix for each sample

molecule: nuclear RNA

value: neural progenitor cell

value: neurogenic differentiation


title: RNA-seq of EVs from uterine fluid , ART patient, sample 1

description:
Library name: EUF100
Successful implantation after transfer


title: RNA-seq of EVs from uterine fluid , ART patient, sample 19

description:
Library name: EUF66
Successful implantation after transfer


title: conidia germination, mushroom powder medium, stage 4, rep3

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were filtered using fastp v0.21.0 using default parameters.
Trimmed reads were mapped to the Tolypocladium ophioglossoides reference genome (JGI Tolop 1) with hisat2 v2.1.1 indicating that reads correspond to the reverse complement of the transcripts. Alignments with quality score below 20 were excluded from further analysis.
Gene counts were produced with stringtie v1.3.3b and the python script “prepDE.py” provided in the package. Stringtie was limited to reads matching the reference annotation.
LOX v1.4 was applied to the tallies for each sample for each gene to estimate gene expression levels and credible intervals across developmental stages. LOX provides relative gene expression levels standardized by the lowest sample, with credible intervals
Assembly: Tolypocladium ophioglossoides JGI Tolop 1
Supplementary files format and content: CSV with raw counts for PDA and mushroom powder mediums.

organism: Tolypocladium ophioglossoides

source_name: fungal hyphae

growth_protocol: The project was set to compare fungal conidial germination on different culture media . For this experiment, the conidial germination was sampled on PDA medium and on mushroom powder agar at 25C. CULTURES were performed by applying 2 ml of the suspension of conidia in 1.5% Tween 60 (105 - 106 conidia/ml) to the surface of medium plates that were covered with cellophane membranes. Conidia germination were monitored with microscope, and roughly over 70% individual conidia showing same development stage were used to decide the sampling time points.

extract_protocol:
For transcriptomic analysis, all tissues and perithecia were immediately and rapidly frozen in liquid nitrogen as they were sampled, then stored at -80°C. RNA was isolated from homogenized mycelia with TRI REAGENT (Invitrogen) and mRNA was purified using Dynabeads oligo(dT) magnetic separation (Invitrogen)
Preparation of cDNA for sequencing followed the Illumina mRNA Sequencing Sample Preparation Guide. Complementary DNA was prepared using N6 primers.
Sequencing libraries were produced from purified total RNA samples by the Illumina TruSeq stranded protocol. The libraries underwent 101 bp pair-end sequencing using Illumina HiSeq 6000 according to Illumina protocols.

value: fungal hyphae

value: fungal spore and hyphae

value: mushroom powder medium


title: neural progenitor cell, differentiated 6 days

description:
Library name: NPC_D6
10X Genomics

value: 6 days


title: conidia germination, mushroom powder medium, stage 4, rep2


title: RNA-seq of EVs from uterine fluid , ART patient, sample 14

description:
Library name: EUF6
Successful implantation after transfer


title: neural progenitor cell, differentiated 54h

description:
Library name: NPC_54h
10X Genomics


title: conidia germination, mushroom powder medium, stage 3, rep3


title: conidia germination, mushroom powder medium, stage 4, rep1


title: neural progenitor cell, differentiated 48h

description:
Library name: NPC_48h
10X Genomics


title: conidia germination, mushroom powder medium, stage 2, rep3


title: neural progenitor cell, differentiated 52h

description:
Library name: NPC_52h
10X Genomics


title: neural progenitor cell, differentiated 46h

description:
Library name: NPC_46h
10X Genomics


title: neural progenitor cell, differentiated 44h

description:
Library name: NPC_44h
10X Genomics


title: conidia germination, mushroom powder medium, stage 2, rep2


title: RNA-seq of EVs from uterine fluid , ART patient, sample 11

description:
Library name: EUF3
Successful implantation after transfer


title: neural progenitor cell, differentiated 24h

description:
Library name: NPC_24h
10X Genomics


title: conidia germination, mushroom powder medium, stage 2, rep1


title: conidia germination, mushroom powder medium, stage 1, rep3


title: neural progenitor cell, differentiated 6 days rep1

description: Library name: NPC_D6_rep1

data_processing:
Quality control of the ATAC-seq fastq files was conducted using cutadapt
Sequencing data was aligned to the GRCh38 human genome assembly using bwa. Duplicate reads were removed using picard, and only non-duplicate reads in the BAM format were used for subsequent analysis.
Peak calling on the nucleosome-free reads was performed with MACS2. BAM files were converted to the bigWig format using deepTools with CPM
Assembly: GRCh38
Supplementary files format and content: bigWig file

extract_protocol:
Cells were lysed in an ice-cold ATAC lysis Buffer, nuclei were incubated in a tagmentation Master Mix for 30 minutes at 37°C, and the resulting DNA was purified using DNA purification columns.
PCR amplification of the tagmented DNA was then carried out to generate libraries with appropriate indexed primers. DNA libraries were cleaned up with SPRI bead.

value: Day 6


title: neural progenitor cell, differentiated 6 days rep2

description: Library name: NPC_D6_rep2


title: H9 embryonic stem cell

description:
Library name: H9_ESC
10X Genomics


title: conidia germination, mushroom powder medium, stage 1, rep1


title: neural progenitor cell, differentiated 3 days rep2

description: Library name: NPC_D3_rep2

value: Day 3


title: conidia germination, PDA medium, stage 4, rep3

value: PDA


title: neural progenitor cell, differentiated 3 days rep1

description: Library name: NPC_D3_rep1


title: neural progenitor cell, differentiated 2 days rep1

description: Library name: NPC_D2_rep1

value: Day 2


title: conidia germination, mushroom powder medium, stage 3, rep2


title: conidia germination, PDA medium, stage 4, rep1


title: conidia germination, PDA medium, stage 3, rep2


title: neural progenitor cell, differentiated 1 day rep2

description: Library name: NPC_D1_rep2

value: Day 1


title: conidia germination, mushroom powder medium, stage 3, rep1


title: H9 embryonic stem cell rep2

description: Library name: H9_ESC_rep2

value: embryonic stem cell

value: Day 0


title: conidia germination, PDA medium, stage 2, rep3


title: H9 embryonic stem cell rep1

description: Library name: H9_ESC_rep1


title: conidia germination, PDA medium, stage 3, rep1


title: Neuron, differentiated 35 days replication2

description:
Library name: NPC_D35_rep2
Column name in raw_counts.csv: NPC_D35_2

data_processing:
Quality control of raw sequences was checked with fastqc (v0.11.9)
Sequences reads were trimmed for adaptor sequences and low quality sequences with fastp (v0.23.2)
Trimmed sequences were mapped to reference genome GRCh38.p13 with STAR (v2.7.8a)
Raw counts were generated with featureCounts (v2.0.2)
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: csv file includes raw counts for each sample

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, #RC112-01) for library construction
Sequencing libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, #E7530L) following the manufacturer’s instruction

value: Neuron

value: Day 35


title: conidia germination, PDA medium, stage 2, rep1


title: Neuron, differentiated 35 days replication1

description:
Library name: NPC_D35_rep1
Column name in raw_counts.csv: NPC_D35_1


title: conidia germination, PDA medium, stage 2, rep2


title: neural progenitor cell, differentiated 18 days replication2

description:
Library name: NPC_D18_rep2
Column name in raw_counts.csv: NPC_D18_2

value: Day 18


title: neural progenitor cell, differentiated 50h

description:
Library name: NPC_50h
10X Genomics

value: WT


title: conidia germination, mushroom powder medium, stage 1, rep2


title: conidia germination, PDA medium, stage 1, rep2


title: neural progenitor cell, differentiated 18 days replication1

description:
Library name: NPC_D18_rep1
Column name in raw_counts.csv: NPC_D18_1

value: neural progenitor cell


title: conidia germination, PDA medium, stage 4, rep2


title: neural progenitor cell, differentiated 6 days replication1

description:
Library name: NPC_D6_rep1
Column name in raw_counts.csv: NPC_D6_1

value: neurogenic differentiation


title: conidia germination, PDA medium, stage 1, rep1

value: fungal hyphae


title: RNAseq, ultrasound+drought, rep3

city: Nyíregyháza

first: Judit

last: Dobránszki

state: Szabolcs-Szatmár-Bereg

address: Westsik Vilmos út 4-6.

department: Centre for Agricultural Genomics and Biotechnology

country: Hungary

institute: University of Debrecen

description: Library name: P12

data_processing:
RNA-seq: raw sequencing reads were trimmed and QC filtered with fastp.
Clean reads were aligned to tomato reference genome SL4.0 (Sol Genomics Network) with HISAT2.
DESeq2 tool was used for read count normalization and identification of the differentially expressed genes (log2FC > 0.58 and P < 0.05)
Assembly: Solanum lycopersicum assembly 4.0 (SL4.0, GCA_000188115.5)
Supplementary files format and content: RNA-seq raw read count table: RNAseq_AllSamples_raw_read_counts.txt

organism: Solanum lycopersicum

source_name: leaves

growth_protocol: In the experiments tomato (Solanum lycopersicum L. cv. Micro Tom) plants were used. Tomato seeds were individually sown in Jiffy-7® peat cylinders (mentioned later as Jiffy), which were put individually in a Veg-box and placed in a climate chamber (24 °C, photoperiod of 16/8 h day/night with a PPFD of 89 µmol m-2 s-1; relative humidity was RH: 65%).

extract_protocol:
Total RNA isolation: Total RNA was extracted from tomato leaves in three biological replicates (S1, 48h) using Quick-RNA™ Plant Miniprep Kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s protocol. RNA quantity and quality was assessed via microcapillary electrophoresis using a NanoPhotometer® N50 (Implen, Munchen, Germany), and by fragment analysis with an Agilent Bioanalyzer 2100 system using RNA 6000 Nano Kit (Agilent, Santa Clara, CA, USA).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Drought stress (D) was induced by irrigating each plant with 10 ml of a solution that contained 20% PEG (polyethylene glycol 6000). Ultrasonication (US) was made under an ultrasonicator applying 30 KHz, 120 W ultrasound treatment for 5 minutes when the average distance between the plants and the ultrasonic head was 6 cm, and the medium of transmission was air. In the combined treatment (US+D) ultrasonicated plants were irrigated with the aforementioned PEG solution immediately after ultrasonication.

tag: cultivar

value: Micro Tom

value: leaves

value: ultrasound and drought combined


title: neural progenitor cell, differentiated 6 days replication2

description:
Library name: NPC_D6_rep2
Column name in raw_counts.csv: NPC_D6_2

tag: cell type

value: Day 6


title: RNAseq, ultrasound+drought, rep2

description: Library name: P11

tag: treatment


title: neural progenitor cell, differentiated 3 days replication1

description:
Library name: NPC_D3_rep1
Column name in raw_counts.csv: NPC_D3_1

value: Day 3


title: neural progenitor cell, differentiated 3 days replication2

description:
Library name: NPC_D3_rep2
Column name in raw_counts.csv: NPC_D3_2


title: RNAseq, drought, rep3

description: Library name: P9

value: drought stress treated


title: neural progenitor cell, differentiated 2 days replication2

description:
Library name: NPC_D2_rep2
Column name in raw_counts.csv: NPC_D2_2

value: Day 2


title: conidia germination, PDA medium, stage 3, rep3

value: fungal spore and hyphae

value: PDA


title: RNAseq, drought, rep2

description: Library name: P8


title: neural progenitor cell, differentiated 2 days replication1

description:
Library name: NPC_D2_rep1
Column name in raw_counts.csv: NPC_D2_1


title: RNAseq, drought, rep1

description: Library name: P7


title: RNAseq, ultrasound+drought, rep1

description: Library name: P10


title: neural progenitor cell, differentiated 1 day replication1

description:
Library name: NPC_D1_rep1
Column name in raw_counts.csv: NPC_D1_1

value: Day 1


title: neural progenitor cell, differentiated 1 day replication2

description:
Library name: NPC_D1_rep2
Column name in raw_counts.csv: NPC_D1_2


title: H9 embryonic stem cell replication1

description:
Library name: H9_ESC_rep1
Column name in raw_counts.csv: H9_ESC_1

value: embryonic stem cell

value: Day 0


title: conidia germination, PDA medium, stage 1, rep3


title: RNAseq, control, rep3

description: Library name: P3

value: control


title: RNAseq, ultrasound, rep2

description: Library name: P5

value: ultrasound treated


title: RNAseq, control, rep2

description: Library name: P2


title: RNAseq, ultrasound, rep1

description: Library name: P4


title: H9 embryonic stem cell replication2

description:
Library name: H9_ESC_rep2
Column name in raw_counts.csv: H9_ESC_2

value: WT


title: RNAseq, control, rep1

description: Library name: P1


title: H1644-EPC-1

city: Research Triangle Park

first: Francesco

middle: John

last: DeMayo

state: North Carolina

address: 111 T W Alexander Dr

department: DIR

institute: NIEHS

description:
Library name: H1644-EPC-1
column name in Partek_THESC_72h_RNAseq_all_samples_Normalization_Normalized_counts:NOVA0435.1644-EPC72-1_20221011_111334.L001.1

data_processing:
FASTQ files were imported into Partek Flow (Illumina), aligned to hg38 using Bowtie 2, then quantified to Refseq genes and reads were normalized.
the sample group NOVA0414 and NOVA0435 are technical replicates of the same libraries. In NOVA0414, library THESC-EPC-3 had very few reads for read-2, so all of the libraries were re-sequenced; for data processing, all reads from both techinal replicates were combined EXCEPT for THESC-EPC-3 which only included data from NOVA0435
Assembly: hg38
Supplementary files format and content: tab delimited text file containing normalized counts  exported  from Partek Flow analysis into a single file.

growth_protocol: 150,000 THESC or H1644 cells per well were seeded in 6 wells each and cultured in hESC media (DMEM/F12; Gibco Thermo Fisher) with 10% fetal bovine serum (Gibco Thermo Fisher) 1% Penicillin-Streptomycin (Gibco Thermo Fisher). In the case of H1644 cells, the media also contained  and 2 mm Sodium Pyruvate (Gibco Thermo Fisher). Cells were cultured  for 24 hours. Wells were washed with PBS and Media was changed to decidual media (OptiMEM with 2% Charcoal Stripped Serum and 1% Penicillin-Streptomycin) containing either 0.2% Ethanol (vehicle) or 10 nM estradiol (Sigma Chemical), 1 µM medroxyprogesterone acetate (Sigma Chemical) and 100 µM dibutyral cyclic AMP (Sigma Chemical) (EPC). Media was changed after 2 days and cells were imaged (EVOS microscope, Thermo Fisher) and collected on the third day of decidualization for RNA isolation.

extract_protocol:
Trizol (Thermo Fisher) was used to isolate RNA from cells according to the manufacturer’s protocol. Following chloroform extraction, RNA was prepared from the aqueous layer using the Direct-zol RNA Miniprep Kit (Zymo Research).
Libraries were made using the Illumina Tru Seq Stranded mRNA kit

value: endometrial stromal


title: H1644-EPC-3

description:
Library name: H1644-EPC-3
column name in Partek_THESC_72h_RNAseq_all_samples_Normalization_Normalized_counts:NOVA0435.1644-EPC72-3_20221011_111334.L001.3


title: H1644-V3

description:
Library name: H1644-V3
column name in Partek_THESC_72h_RNAseq_all_samples_Normalization_Normalized_counts:NOVA0435.1644-V72-3_20221011_111334.L001.3


title: H1644-EPC-2

description:
Library name: H1644-EPC-2
column name in Partek_THESC_72h_RNAseq_all_samples_Normalization_Normalized_counts:NOVA0435.1644-EPC72-2_20221011_111334.L001.2


title: WGBS, ultrasound+drought, rep2

description: Library name: Pa8

data_processing:
Whole Genome Bisulfite Sequencing (WGBS): Bisulfite-treated sequencing reads were processed using fastp for adapter trimming and quality control filtering to ensure high-quality data.
Cleaned reads were aligned to the tomato reference genome (SL4.0, Sol Genomics Network) using Bismark with the Bowtie 2 aligner, which simultaneously extracted methylation calls.
Methylation data were imported into MethylKit in R for downstream analysis. Methylation calls were filtered to retain only cytosine positions with a minimum of 10x read coverage. Differentially methylated regions (DMRs) were identified using MethylKit with a 200-bp sliding window, requiring a methylation percentage difference greater than 10% and a P-value ≤ 0.05. Differentially methylated genes (DMGs) were defined as genes harboring DMRs within their gene body or up to 3 kb upstream in their promoter regions.
Gene annotation of DMRs was performed using the Genomation R package.
Assembly: Solanum lycopersicum assembly 4.0 (SL4.0, GCA_000188115.5)
Supplementary files format and content: Tab separated, context specific (CHH,CHG,CpG) raw methylation data files from MethylKit for each sample (Pa1-Pa8 : (Pa1-Pa8)_(CHH,CHG,CpG).txt

extract_protocol:
Genomic DNA isolation: DNA isolation from tomato leaves was performed in two biological replicates from each treatment and control groups from the first sampling time (S1, 48h) according to the Macherey-Nagel Nucleospin® Plant II kit protocol. Concentration and purity of the extracted DNA was measured on NanoPhotometer® N50 (Implen, Munchen, Germany).
Firstly, the genomic DNA spiked with lambda DNA were fragmented to 200-400 bp. The DNA fragments were bisulfite treated to generate single strand DNA (ssDNA). During the bisulfite conversion, unmethylated cytosine were converted into uracil, while methylated cytosine staid unchanged. Methylation sequencing adapters were ligated, followed by double strand DNA synthesis. The library was ready after size selection and PCR amplification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.


title: H1644-V2

description:
Library name: H1644-V2
column name in Partek_THESC_72h_RNAseq_all_samples_Normalization_Normalized_counts:NOVA0435.1644-V72-2_20221011_111334.L001.2


title: WGBS, drought, rep2

description: Library name: Pa6


title: H1644-V1

description:
Library name: H1644-V1
column name in Partek_THESC_72h_RNAseq_all_samples_Normalization_Normalized_counts:NOVA0435.1644-V72-1_20221011_111334.L001.1


title: WGBS, drought, rep1

description: Library name: Pa5


title: RNAseq, ultrasound, rep3

description: Library name: P6


title: THESC-EPC-3

description:
Library name: THESC-EPC-3
column name in Partek_THESC_72h_RNAseq_all_samples_Normalization_Normalized_counts:NOVA0435.THESC-EPC72-3_20221011_111334.L001.3

source_name: THESC

value: THESC


title: THESC-EPC-2

description:
Library name: THESC-EPC-2
column name in Partek_THESC_72h_RNAseq_all_samples_Normalization_Normalized_counts:NOVA0435.THESC-EPC72-2_20221011_111334.L001.2


title: WGBS, ultrasound, rep2

description: Library name: Pa4

value: Micro Tom


title: THESC-EPC-1

description:
Library name: THESC-EPC-1
column name in Partek_THESC_72h_RNAseq_all_samples_Normalization_Normalized_counts:NOVA0435.THESC-EPC72-1_20221011_111334.L001.1


title: WGBS, ultrasound, rep1

description: Library name: Pa3

value: leaves


title: THESC-V3

description:
Library name: THESC-V3
column name in Partek_THESC_72h_RNAseq_all_samples_Normalization_Normalized_counts:NOVA0435.THESC-V72-3_20221011_111334.L001.3


title: WGBS, control, rep1

description: Library name: Pa1


title: WGBS, control, rep2

description: Library name: Pa2


title: FU [CLG98]

type: protein

city: San Francisco

first: Jessica

last: Neely

state: California

address: 550 16th Street

department: Pediatrics

institute: UCSF

data_processing:
NPX values per Olink
Data is presented as NPX values. NPX is Olink's relative protein quantification unit on log2 scale. NPX  values are calculated from the number of matched counts, using NGS (Next Generation Sequencing) as  readout. The NPX values are presented in a separate results file. Data values for measurements below  limit of detection (LOD) are reported for all samples.

source_name: plasma

extract_protocol: Olink Explore 3072

tag: site

value: Duke

tag: disease status

value: FU

value: Female


title: H1644, siZMIZ1-V-3

description:
Library name: siZMIZ1-3
row name in Partek_siZMIZ-H1644_Normalization_Normalized_counts: NS51430.siZMIZ1-V3_20230811_143205.L001

data_processing:
FASTQ files were imported into Partek Flow (Illumina), aligned to hg38 using Bowtie 2, then quantified to Refseq genes and reads were normalized.
Assembly: hg38
Supplementary files format and content: tab delimited text file containing normalized counts  exported  from Partek Flow analysis into a single file.

growth_protocol: 100,000 H1644 cells per well were seeded in 6-well dishes and cultured in hESC media (DMEM/F12; Gibco Thermo Fisher) with 10% fetal bovine serum (Gibco Thermo Fisher) 1% Penicillin-Streptomycin (Gibco Thermo Fisher) and 2 mm Sodium Pyruvate (Gibco Thermo Fisher) for 24 hours. Wells were washed with PBS and 1 ml of transfection media (OptiMEM (Gibco Thermo Fisher) with 2% Charcoal Stripped Serum (Gibco Thermo Fisher) was added.  For each well, 3 µl of siNT (control) or siZMIZ1 siRNA (ON-TARGETplus siRNA Smartpool, Dharmacon/Horizon Discovery) was diluted to 100 µl in OpitMEM and 5 µl of RNAiMax (Thermo Fisher) was diluted to 150 µl  with OptiMEM and pre incubated for 10 minutes. siRNA and RNAiMax mixtures were combined, incubated for 20 min and added to cells. Cells were incubated for 48 hours

treatment_protocol: Media was changed to decidual media (OptiMEM with 2% Charcoal Stripped Serum and 1% Penicillin-Streptomycin) containing 0.2% Ethanol (vehicle). Media was changed after 2 days and cells were collected on the third day  for RNA isolation

value: ZMIZ1 siRNA knockdown

value: vehicle


title: H1644, siZMIZ1-V-2

description:
Library name: siZMIZ1-2
row name in Partek_siZMIZ-H1644_Normalization_Normalized_counts: NS51430.siZMIZ1-V2_20230811_143205.L001


title: THESC-V1

description:
Library name: THESC-V1
column name in Partek_THESC_72h_RNAseq_all_samples_Normalization_Normalized_counts:NOVA0435.THESC-V72-1_20221011_111334.L001.1


title: BL [CLG94]

value: BL


title: H1644, siZMIZ1-V-1

description:
Library name: siZMIZ1-1
row name in Partek_siZMIZ-H1644_Normalization_Normalized_counts: NS51430.siZMIZ1-V1_20230811_143205.L001


title: FU [CLG96]


title: BL [CLG93]


title: BL [CLG92]


title: WGBS, ultrasound+drought, rep1

description: Library name: Pa7

value: ultrasound and drought combined


title: FU [CLG95]


title: BL [CLG90]

value: male


title: H1644, siNT-V-1

description:
Library name: siNT-V1
row name in Partek_siZMIZ-H1644_Normalization_Normalized_counts: NS51430.siNT-V1_20230811_143205.L001

value: non targeting siRNA knockdown


title: H1644, siNT-V-2

description:
Library name: siNT-V2
row name in Partek_siZMIZ-H1644_Normalization_Normalized_counts: NS51430.siNT-V2_20230811_143205.L001


title: BL [CLG9]

value: CARRA


title: H3K27Ac-ChIP of vehicle treated H1644 cells

description: Library name: H1644-V-H3K27Ac-ChIP

data_processing:
FASTQ file was imported into Partek Flow (Illumina), and aligned to hg38 using Bowtie 2, and filtered to remove duplicates and reads with mapping quality <20.
the resulting .bam file was exported from Partek Flow, converted to .bedgraph, sorted, and converted to a bigwig file using samtools
Assembly: hg38
Supplementary files format and content: bigwig file

growth_protocol: H1644 cells were seeded in 100 mm dishes and cultured in hESC media (DMEM/F12; Gibco Thermo Fisher) with 10% fetal bovine serum (Gibco Thermo Fisher) 1% Penicillin-Streptomycin (Gibco Thermo Fisher)  and 2 mm Sodium Pyruvate (Gibco Thermo Fisher). Cells were cultured  for 24 hours. Wells were washed with PBS and Media was changed to decidual media (OptiMEM with 2% Charcoal Stripped Serum and 1% Penicillin-Streptomycin) containing  0.2% Ethanol (V, vehicle). Media was changed after 2 days and on the 3rd day, cells were fixed and collected for ChIP according to the protocol provided by Active Motif, Inc.

extract_protocol:
The frozen, fixed cell pellet was shipped to Active Motif for H3K27Ac ChIP seq& library construction
Libraries were prepared by Active Motif Services HistonePath assays for H3K27ac (Active Motif cat# 25015)


title: H1644-EPC-72h

description: Library name: H1644-EPC-72h

data_processing:
technical replicates are included from additional sequencing from each library to obtain sufficient reads for analysis.
raw reads were mapped to human reference genome (GRCh38/hg38) using HiCUP
Juicer  was used to identify chromatin loops
Assembly: HG38
Supplementary files format and content: .BED interact files of loops

growth_protocol: H1644 cells  were seeded in 100 mm dishes and cultured in hESC media (DMEM/F12; Gibco Thermo Fisher) with 10% fetal bovine serum (Gibco Thermo Fisher) 1% Penicillin-Streptomycin (Gibco Thermo Fisher)  and 2 mm Sodium Pyruvate (Gibco Thermo Fisher). Cells were cultured  for 24 hours. Wells were washed with PBS and Media was changed to decidual media (OptiMEM with 2% Charcoal Stripped Serum and 1% Penicillin-Streptomycin) containing either 0.2% Ethanol (vehicle) or 10 nM estradiol (Sigma Chemical), 1 µM medroxyprogesterone acetate (Sigma Chemical) and 100 µM dibutyral cyclic AMP (Sigma Chemical) (EPC). Media was changed after 2 days and cells were imaged (EVOS microscope, Thermo Fisher) and collected on the third day of decidualization. Frozen pellets contaiining 8.5x10^6 cells (V) and 3x10^6 cells (EPC) were shipped to Active Motif for HiC.

extract_protocol:
Cells were sent to Active Motif Epigenomics Services for HiC and library construction.
Libraries were prepared by Active Motif Services Hi-C Service cat#25280


title: H1644, siNT-V-3

description:
Library name: siNT-V3
row name in Partek_siZMIZ-H1644_Normalization_Normalized_counts: NS51430.siNT-V3_20230811_143205.L001


title: BL [CLG89]


title: BL [CLG88]


title: THESC-V2

description:
Library name: THESC-V2
column name in Partek_THESC_72h_RNAseq_all_samples_Normalization_Normalized_counts:NOVA0435.THESC-V72-2_20221011_111334.L001.2


title: MM468_VPRFOSL1_gRNA3

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger multi software (v.6.0.0) with default parameters
Assembly: hg38
Supplementary files format and content: Raw sparse matrices with feature and barcode sequences as tsv files, corresponding to row and column indices respectively (10X format).
Supplementary files format and content: Table in CSV format obtained with cellranger multi, that contains all information from the tag assignment algorithm for each cell-associated barcode.
Library strategy: CITE-seq

growth_protocol: MDA-MB-468 cells were cultured in DMEM (Gibco-BRL, Ref: 11966025), supplemented with 10% heat-inactivated fetal calf serum (Gibco-BRL, Ref: 10270-106). HCC38 and BT20 cell lines were cultured in RPMI 1640 (Gibco-BRL, Ref: 11875085), supplemented with 10% heat-inactivated fetal calf serum. All cell lines were cultured in a humidified 5% CO2 atmosphere at 37°C, and were tested as mycoplasma negative.

extract_protocol:
1x10^6 cells were blocked for 10min at 4°C with 5uL of human Trustain FcX (Biolegend, Ref: 422301) and stained for 30min at 4°C with 1ug of TotalSeq A antibodies (Biolegend, 1 antibody per sample for MDA-MB-468 GOF VPR control, VPR FOSL1 gRNA2, VPR FOSL1 gRNA3, HA control and HA FOSL1). After washes, cells were filtered and counted. A pool of 6 stained samples was prepared by mixing of 25 000 cells per sample (finale concentration of the pool: 2000 cells/uL)
Approximately 16,000 cells were loaded on a Chromium Single Cell Controller Instrument (Chromium Single Cell 3ʹv3, 10X Genomics, Ref: PN-1000075) according to the manufacturer’s instructions. Samples and libraries were prepared according to the manufacturer's instructions. Libraries were sequenced on a NovaSeq 6000 (Illumina) in PE 28-8-91 with a coverage of 50,000 reads/cell.

treatment_protocol: Cells were treated with 5 μM of 5-FU (Sigma, Ref: F6627) for 7 to 21 days as indicated.


title: BL [CLG87]


title: BL [CLG91]


title: H1644-V72

description: Library name: H1644-V72


title: BL [CLG86]


title: MM468_VPRCtrl


title: CTL [CLG85]

value: UCSF

value: CTL


title: CTL [CLG83]


title: MM468_HAFOSL1


title: MM468_HACtrl


title: CTL [CLG82]


title: CTL [CLG81]


title: FU [CLG8]


title: MM468_WT_d0_n3_FOSL1

data_processing:
Reads were aligned to hg38 Human reference genome using bowtie with options ‘-k 1 -N 1 --end-to-end’
Coverage BigWigs files were created from sorted deduplicated files using Deeptools bamCoverage function with options ‘--normalizeUsing CPM --binSize 10 --smoothLength 50 --extendReads 150 --ignoreForNormalization chrX'
Assembly: hg38
Supplementary files format and content: Bigwig binary file of coverage
Library strategy: CUT&Tag

growth_protocol: MDA-MB-468 cells were cultured in DMEM (Gibco-BRL, Ref: 11966025), supplemented with 10% heat-inactivated fetal calf serum (Gibco-BRL, Ref: 10270-106). All cell lines were cultured in a humidified 5% CO2 atmosphere at 37°C, and were tested as mycoplasma negative.

extract_protocol:
The CUT&Tag-IT™ Assay Kit (Active Motif, Ref: 53160) was used with 1:50 Anti-Rabbit antibodies for FOSL1 (Cell Signaling, Ref: #5281), HA (Epicypher, Ref: 13-2010) and H3K27ac (Cell Signaling, Ref: #8173) following manufacturer instructions. Starting cell number was 500 000 cells for control and GOF cells down to 100 000 for persister cells. Digitonin concentration (0,05%) was maintained in all buffers, completing the kit with additional digitonin (Cell Signaling, Ref: #16359).
Sequencing libraries were prepared using Nextera™- Compatible Multiplex Primers (Active Motif, Ref: 53155). CUT&Tag libraries were sequenced on a NovaSeq 6000 (Illumina) in PE100 mode.

treatment_protocol: Cells were treated with 5 μM of 5-FU (Sigma, Ref: F6627) for 35 days as indicated.


title: MM468_WT_d0_n3_H3K27ac


title: BL [CLG78]


title: MM468_WT_d0_n2_H3K27ac


title: BL [CLG76]


title: MM468_WT_d0_n2_FOSL1


title: BL [CLG74]


title: MM468_WT_d0_n1_FOSL1


title: BL [CLG72]


title: MM468_WT_5FU_d35_n3_FOSL1


title: MM468_WT_5FU_d35_n3_H3K27ac


title: BL [CLG66]


title: MM468_VPRFOSL1_gRNA2


title: BL [CLG7]


title: BL [CLG68]


title: neural progenitor cell, differentiated 2 days rep2

description: Library name: NPC_D2_rep2

value: neural progenitor cell

value: WT

value: neurogenic differentiation

value: Day 2


title: MM468_WT_5FU_d35_n2_H3K27ac


title: BL [CLG63]


title: BL [CLG61]


title: MM468_WT_5FU_d35_n1_H3K27ac


title: MM468_WT_5FU_d35_n2_FOSL1


title: BL [CLG54]


title: MM468_VPRCtrl_d0_n1_FOSL1


title: FU [CLG6]


title: MM468_HAFOSL1_d0_n3_H3K27ac


title: BL [CLG52]


title: MM468_HAFOSL1_d0_n2_HAFOSL1


title: BL [CLG58]


title: BL [CLG56]


title: MM468_HAFOSL1_d0_n2_H3K27ac


title: MM468_HAFOSL1_d0_n1_HAFOSL1


title: MM468_HAFOSL1_d0_n3_HAFOSL1


title: MM468_WT_5FU_d35_n1_FOSL1


title: BL [CLG50]


title: MM468_WT_d0_n1_H3K27ac


title: MM468_HACtrl276_d0_n2_HAFOSL1


title: MM468_HAFOSL1_d0_n1_H3K27ac


title: BL [CLG46]


title: BL [CLG49]


title: BL [CLG5]


title: FU [CLG44]


title: MM468_HACtrl276_d0_n3_HAFOSL1


title: BL [CLG47]


title: FU [CLG48]


title: MM468_VPRFOSL1_d0_n1_FOSL1


title: KO, H3K27me3, ChIP, rep2

data_processing:
Raw data was processed using the current best practice pipeline implemented in nfcore.
Bowtie2 with default parameters was applied for raw reads mapping to hg38 human reference genome.
MAC2 supplemented with IDR was used to identify highly reproducible peaks which were then annotated by their nearest gene using ChIPseeker.
Assembly: hg38 human reference genome
Supplementary files format and content: BigWig, narrow peak for p53 and ATAC-seq, broad peak for H3K27ac, H3K4me3 and H3K27me3.

source_name: TSC

extract_protocol:
For ChIP-seq, cells were fixed with 1% formaldehyde, lysed and sonicated using Diagenode BioruptorPico UltraSonication System; For ATAC-seq, 50,000 fresh isolated beads conjured nuclei were extracted.
ChIP-seq and ATAC-seq libraries were prepared using TruePrep DNA Library Prep Kit according to the manufacturer's protocol.

value: TSC

value: KO


title: FU [CLG41]

value: FU


title: MM468_HACtrl275_d0_n1_HAFOSL1


title: WT, ATAC, rep2


title: KO, ATAC, rep2


title: WT, ATAC, rep1


title: BL [CLG38]

value: Female


title: FU [CLG45]


title: KO, ATAC, rep1


title: KO, H3K27me3, ChIP, rep1


title: BL [CLG4]


title: WT, H3K27me3, ChIP, rep2


title: KO, H3K4me3, ChIP, rep1


title: FU [CLG35]


title: FU [CLG37]


title: WT, H3K4me3, ChIP, rep2


title: FU [CLG51]


title: BL [CLG31]


title: KO, H3K4me3, ChIP, rep2


title: KO, Input 2


title: WT, H3K4me3, ChIP, rep1


title: FU [CLG3]


title: neural progenitor cell, differentiated 1 day rep1

description: Library name: NPC_D1_rep1

value: Day 1


title: WT, H3K27me3, ChIP, rep1


title: BL [CLG42]


title: BL [CLG43]


title: FU [CLG39]


title: BL [CLG29]


title: WT, H3K27ac, ChIP, rep1


title: WT, Input 2


title: KO, p53, ChIP, rep2


title: FU [CLG30]


title: KO, H3K27ac, ChIP, rep2


title: BL [CLG24]


title: WT, p53, ChIP, rep2


title: WT, p53, ChIP, rep1


title: FU [CLG23]


title: KO, Input 1


title: KO, H3K27ac, ChIP, rep1


title: BL [CLG22]


title: TSC, TP53KO, rep2

data_processing:
Raw data of RNA-seq was processed using the current best practice pipeline implemented in nfcore.
Sequence reads were mapped to mm10 mouse reference genome or hg38 human reference genome.
RSEM was applied to estimate gene expression levels with default settings.
Assembly: mm10; hg38 human genome
Supplementary files format and content: comma-separated values file or tab-delimited file including raw counts for each sample


title: WT, Input 1


title: BL [CLG40]


title: TSC, TP53KO, rep1


title: WT, H3K27ac, ChIP, rep2


title: BL [CLG28]


title: BL [CLG19]


title: FU [CLG27]


title: BL [CLG18]


title: BL [CLG26]


title: FU [CLG2]


title: BL [CLG21]


title: KO, p53, ChIP, rep1


title: TSC, WT, rep2


title: TSC, WT, rep1


title: Differentiated, D7 TP53KO, rep1

source_name: Extraembryonic cells

value: Extraembryonic cells


title: BL [CLG20]

value: BL


title: FU [CLG25]


title: BL [CLG17]


title: BL [CLG15]


title: FU [CLG16]


title: Differentiated, D7 TP53KO, rep2


title: Differentiated, D7 WT, rep2


title: FU [CLG14]


title: Differentiated, D7 WT, rep1


title: Differentiated, D4 TP53KO, rep1


title: Differentiated, D4 WT, rep2


title: CTL [CLG122]

value: U-M


title: CTL [CLG120]

value: male


title: Differentiated, D4 WT, rep1


title: BL [CLG13]


title: Differentiated, D2 TP53KO, rep2


title: CTL [CLG119]


title: CTL [CLG121]


title: Differentiated, D2 TP53KO, rep1


title: Differentiated, D2 WT, rep2


title: Differentiated, D4 TP53KO, rep2


title: BL [CLG115]


title: BL [CLG12]


title: EPSC, TP53KO, rep2

source_name: EPSC

value: EPSC


title: BL [CLG114]


title: BL [CLG113]


title: EPSC, TP53KO, rep1


title: BL [CLG111]


title: EPSC, WT, rep2


title: FU [CLG11]

value: CARRA


title: EPSC, WT, rep1


title: BL [CLG106]


title: BL [CLG104]


title: BL [CLG1]


title: B. oleracea_young_leaves_BS-seq

city: Wuhan

first: Jie

last: Zhou

address: 1 Lion Rock Street

institute: Huazhong Agricultural University

description: Library name: BOBS-14

data_processing:
Evaluated the quality of sequencing data using FastQC.
The clean reads were mapped to the corresponding reference genomes using BatMeth2
Assembly: Brassica_oleracea_JZS; Brapa_chiifu
Supplementary files format and content: DNA methylation level matrix

organism: Brassica oleracea

source_name: young leaf

growth_protocol: For the collection of young leaves, the plants were planted in greenhouses. Germinated seeds were grown in a phytotron with a day/night cycle of 16 h/8 h and a temperature of 22°C/18°C. Young leaves were collected from 2-week-old hydroponically grown seedlings.

extract_protocol:
Tissues were evenly cut into small pieces, crosslinked with 1% formaldehyde in vacuum for 10 min, and then quenched with 0.2 M glycine for 5 min at room temperature.
The libraries were sequenced on an Illumina HiSeq X Ten system (paired-end 150-bp reads).

value: young leaf

value: JZS

value: 14d young leaves cells


title: B. oleracea_young_leaves_input_rep2

description: Library name: B.oleracea_young_leaves_input_rep2

data_processing:
Evaluated the quality of sequencing data using Fastp.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Assembly: Brassica_oleracea_JZS; Brapa_chiifu
Supplementary files format and content: peak

extract_protocol:
Tissues were evenly cut into small pieces, crosslinked with 1% formaldehyde in vacuum for 10 min, and then quenched with 0.2 M glycine for 5 min at room temperature.
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina and sequenced on an Illumina HiSeq X Ten system (paired-end 150-bp reads).

value: input


title: B. oleracea_young_leaves_ATAC-seq_rep2

description: Library name: BARS-6_ATAC

data_processing:
Evaluated the quality of sequencing data using Fastp.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-B -q 1e-5 -f BAMPE”
Assembly: Brassica_oleracea_JZS; Brapa_chiifu
Supplementary files format and content: peak

extract_protocol:
Tissues were evenly cut into small pieces, crosslinked with 1% formaldehyde in vacuum for 10 min, and then quenched with 0.2 M glycine for 5 min at room temperature.
Libraries were size-selected and sequenced (2 × 150 bp) on an Illumina HiSeq X-Ten system.


title: B. oleracea_young_leaves_ATAC-seq_rep1

description: Library name: BRAS-5_ATAC


title: neural progenitor cell, treated with DMSO in 4 days differentiation replication1

description:
Library name: NPC_D4_rep1
Column name in raw_counts.csv: D4_Ctrl_1

treatment_protocol: 250 μM hydroxyurea (HU) was added to the neural induction medium from day 1 or day 2 of differentiation, and these cells were further cultured for 48 hours or 24 hours, respectively, until day 3 of differentiation

value: neural progenitor cell

value: WT

value: neurogenic differentiation + DMSO


title: B. oleracea_young_leaves_RNA-seq_rep2

description: Library name: CC_RNA_rep2

data_processing:
Evaluated the quality of sequencing data using Fastp.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
hisat2 with “-p 10” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping.
Assembly: Brassica_oleracea_JZS; Brapa_chiifu.
Supplementary files format and content: csv files include FPKM values for each Sample.

extract_protocol:
Total RNA from young leaves was isolated using the RNeasy Plant Mini Kit (QIAGEN, 74904). Approximately 2 μg of RNA was used for library preparation with the Illumina TruSeq RNA kit following the manufacturer’s protocol.
The libraries were sequenced on an Illumina HiSeq X-Ten system.


title: Human retinal organoid_1

city: Schlieren

first: Elvir

last: Becirovic

state: Zurich

address: Wagistrasse 14

department: Department of Ophthalmology

country: Switzerland

institute: University of Zurich

description:
Library name: ret_organoid_1
Library: Kinnex Full-Length RNAseq

data_processing:
HiFi circular consensus (CCS) reads were processed using the PacBio Iso-Seq pipeline (v4.3.0).
Skera (v1.4.0) was used for deconcatenation.
Primers were removed with lima (v2.13.0), and full-length reads were refined and clustered into high-confidence isoforms.
Reads were aligned to the GRCh38 primary assembly using pbmm2 (v1.17.0) with the ISOSEQ preset.
Isoforms were collapsed using isoseq collapse and further classified and filtered with Pigeon (v1.4.0).
Assembly: human GENCODE v45 genome and annotation
Supplementary files format and content: csv files include classifications of different isoforms and read count before and after deduplication

source_name: Human retinal organoid

growth_protocol: Human retinal organoids were differentiated from the human derived iPSCs (F49B7). Pluripotency markers and germ layer differentiation potential was determined as previously described (Cowan CS, et al.). IPSCs were seeded in matrigel-coated 6-well plates and cultured in mTeSR plus medium at 37 °C, 5% CO2. The iPSCs were passaged using 0.5 mM EDTA. Differentiation of iPSCs into human retinal organoids was performed according to the protocol developed by (Kim S, et al.), with some modifications. All organoids at the different maturation stages were cultured in a humidified incubator at 37 °C, 5% CO2. On day 0, the iPSCs were dissociated using 0.5 mM EDTA. The aggregates were suspended in cold Matrigel and incubated at 37 °C for 20 min. Afterwards, the iPSC/Matrigel aggregates were dispersed in neural induction medium and cultivated in ultra-low adherent 6-well plates. On day 5, floating cysts were seeded in matrigel-coated 6-well plates. On day 15, cysts were detached by adding dispase, washed with DMEM/F12 and further cultured in retinal differentiation medium. On day 25, the immature retinal organoids were transferred to retinal maturation medium. On day 230, mature organoids were used for RNA isolation and subsequent experiments.

extract_protocol:
RNA isolation from human retinal organoids was done with the Direct-zol DNA/RNA miniprep kit.
Using the Kinnex full-length RNA kit Poly-A-RNA without prior fragmentation was reverse-transcribed into cDNA, amplified, and concatenated to SMRT bell libraries with approx. 16 kb insert size (MAS Seq method). Sequencing was performed on a Revio device at 24 h video time.

value: Human retinal organoid


title: neural progenitor cell, treated with DMSO in 4 days differentiation replication2

description:
Library name: NPC_D4_rep2
Column name in raw_counts.csv: D4_Ctrl_2

data_processing:
Quality control of raw sequences was checked with fastqc (v0.11.9)
Sequences reads were trimmed for adaptor sequences and low quality sequences with fastp (v0.23.2)
Trimmed sequences were mapped to reference genome GRCh38.p13 with STAR (v2.7.8a)
Raw counts were generated with featureCounts (v2.0.2)
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: csv file includes raw counts for each sample


title: Differentiated, D2 WT, rep1

extract_protocol:
Total RNA was harvetsed using Trizol reagents 1.0µg of total RNA was used for the construction of sequencing libraries.
RNA libraris for RNA-seq were prepared using magnetic beads for mRNA enrichment followed by cDNA synthesis, adapter ligation and PCR amplification.


title: B. oleracea_young_leaves_input

description: Library name: BOCS-256_input


title: H1

type: RNA

city: Cheongju

first: Hyo Youn

last: Jo

address: 1, Chungdae-ro, Seowon-gu, Cheongju-si, Chungcheongbuk-do

department: Veterinary medicine

institute: Chungbuk National University

description: UCB-MSCs cultured in high glucose (25 mM) for 72 h. Gene expression profiling was performed using the Bioneer AccuTarget™ Human qPCR Screening Kit (Pathway No. 60: Glucose Metabolism). Normalized expression values were calculated using the ΔΔCt method with ACTB as the internal control gene.

hyb_protocol: Not applicable (gene expression was measured using qPCR array rather than hybridization-based microarray).

scan_protocol: For qPCR array analysis, each reaction mixture (20 μL) contained primers, cDNA, and AccuPower™ 2X GreenStar qPCR Master Mix (Bioneer, #K-6251). Reactions were run using a two-step PCR program: initial pre-denaturation at 95 °C for 5 min (1 cycle), followed by 45 cycles of denaturation at 95 °C for 15 s and annealing/extension at 58 °C for 5–30 s. Amplification data were collected with CFXTM Connect real-time PCR detection system (BIO-RAD, #1855201).

data_processing: Cq values were obtained for each gene and normalized against the housekeeping gene ACTB included in the array. Normalized relative expression values were calculated using the ΔΔCt method and used as the matrix values.

label: unlabeled

source_name: Umbilical cord blood derived-mesenchymal stem cells

label_protocol: No additional labeling was performed. Gene expression was quantified by SYBR Green-based qPCR detection.

growth_protocol: UCB-MSCs were cultured in standard mesenchymal stem cell medium until reaching approximately 70% confluency, then switched to serum-free medium for 24 hours to induce starvation.

extract_protocol: Total RNA was extracted from UCB-MSCs using the miniBEST Universal RNA Extraction Kit (TaKaRa, #9767A) according to the manufacturer’s instructions. One microgram of RNA was reverse-transcribed into cDNA prior to analysis.

treatment_protocol: After starvation, cells were exposed to either 25 mM D-glucose for 72 h (H group) or pretreated with 100 nM everolimus for 30 min followed by 25 mM D-glucose for 72 h (HE group). Two biological replicates were prepared for each group.

value: UCB-MSCs

value: High glucose

tag: replicate


title: H2


title: HE2

description: UCB-MSCs pretreated with everolimus (100 nM, 30 min) followed by high glucose (25 mM) for 72 h. Gene expression profiling was performed using the Bioneer AccuTarget™ Human qPCR Screening Kit (Pathway No. 60: Glucose Metabolism). Normalized expression values were calculated using the ΔΔCt method with ACTB as the internal control gene.

value: High glucose with everolimus


title: neural progenitor cell, treated with hydroxyurea for 48h in 3 days differentiation replication1

description:
Library name: NPC_D3_HU48h_rep1
Column name in raw_counts.csv: D3_HU48h_1

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, #RC112-01) for library construction
Sequencing libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, #E7530L) following the manufacturer’s instruction

value: neurogenic differentiation + hydroxyurea for 48h


title: B. oleracea_young_leaves_RNA-seq_rep1

description: Library name: CC_RNA_rep1


title: HE1


title: neural progenitor cell, treated with hydroxyurea for 48h in 3 days differentiation replication2

description:
Library name: NPC_D3_HU48h_rep2
Column name in raw_counts.csv: D3_HU48h_2


title: B. oleracea_young_leaves_H3K9me2_ChIP-seq_rep2

description: Library name: BOCS-265_H3K9me2


title: neural progenitor cell, treated with hydroxyurea for 24h in 3 days differentiation replication2

description:
Library name: NPC_D3_HU24h_rep2
Column name in raw_counts.csv: D3_HU24h_2

value: neurogenic differentiation + hydroxyurea for 24h


description:
Library name: NPC_D3_rep2
Column name in raw_counts.csv: D3_Ctrl_2

value: neurogenic differentiation


title: BL [CLG108]

value: U-M

value: BL

tag: age

value: male


title: FU [CLG100]

value: Duke

value: FU

tag: Sex

value: Female


title: neural progenitor cell, treated with hydroxyurea for 24h in 3 days differentiation replication1

description:
Library name: NPC_D3_HU24h_rep1
Column name in raw_counts.csv: D3_HU24h_1


title: B. oleracea_young_leaves_H3K9me2_ChIP-seq_rep1

description: Library name: BOCS-255_H3K9me2

tag: tissue

value: young leaf

value: JZS

value: 14d young leaves cells


title: neural progenitor cell, differentiated 2 days replication2

description:
Library name: NPC_D2_rep2
Column name in raw_counts.csv: D2_2

tag: cell line

value: neural progenitor cell

value: WT


title: neural progenitor cell, differentiated 3 days replication1

description:
Library name: NPC_D3_rep1
Column name in raw_counts.csv: D3_Ctrl_1

tag: genotype


title: FU [CLG10]

value: CARRA


title: B. oleracea_young_leaves_H3K27me3_ChIP-seq_rep2

description: Library name: BOCS-268_H3K27me3


title: neural progenitor cell, differentiated 2 days replication1

description:
Library name: NPC_D2_rep1
Column name in raw_counts.csv: D2_1


title: Human retinal organoid_2

description:
Library name: ret_organoid_2
Library: Kinnex Full-Length RNAseq

value: Human retinal organoid


title: neural progenitor cell, differentiated 1 day replication2

description:
Library name: NPC_D1_rep2
Column name in raw_counts.csv: D1_2


title: B. oleracea_young_leaves_H3K27me3_ChIP-seq_rep1

description: Library name: BOCS-251_H3K27me3


title: Induced_senescent_BJ_cells_VS_2h_rep2_KAS-seq

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

data_processing:
The Trim_Galore tool was employed to remove low-quality bases and adapter-containing reads from the raw KAS-seq data. Reads that were trimmed to shorter than 30 bp were discarded.
The remaining reads were aligned to the reference genome (hg19) using Bowtie2 (v2.3.3.1), with the alignment carried out under default parameters. The SAM files were then converted and sorted into BAM files using samtools sort (v1.9).
Duplicate reads were removed with the assistance of Picard MarkDuplicates (v1.141), and the deduplicated, uniquely mapped reads were extended to 150 bp to align with the average length of DNA fragments, a process executed using the awk command. The extended data, in BED file format, were converted to BedGraph files using bedtools genomecov, and subsequently transformed into BigWig files through bedGraphToBigWig, part of the University of California, Santa Cruz (UCSC) precompiled utilities.
Shell scripts for KAS-seq data mapping and quality control can be accessed at GitHub (https://github.com/Ruitulyu/KAS-Analyzer).
The metagene profile plots and heatmaps were constructed using deepTools plotProfile and plotHeatmap. For peak calling, MACS2 was utilized to identify broad KAS-seq peaks, and 2kb bins overlapping with KAS-seq peaks were used to detect differentially generated time-course KAS-seq signals. Finally, the k-means clustering method was applied to segregate the differential 2kb bins into 4 clusters.
Assembly: hg19
Supplementary files format and content: bigWig, KAS-seq read density
Supplementary files format and content: bed, KAS-seq peaks
Library strategy: KAS-seq

source_name: BJ cells

growth_protocol: BJ cells were grown in EMEM (Corning, 10009-CV) supplemented with penicillin and streptomycin (Gibco, 15070), 10% FBS (Sigma, F2442).

extract_protocol:
After treatment, cells were collected for genomic DNA (gDNA)purification using the PureLink genomic DNA mini kit (Thermo Fisher, K182002). In a 100 µL volume, around 1 µg gDNA was incubated with 1 mM DBCO-PEG4-biotin (Sigma, 760749) in 1× PBS at 37 °C for 1.5 h with gentle shake for biotinylation. gDNA was then purified by DNA Clean & Concentrator-5 kit (Zymo Research, D4013) and fragmented to around 250 bp by sonication. 10 µL Dynabeads MyOne Streptavidin C1 (Thermo Fisher, 65001) were then applied to pull-down biotinylated DNA fragments following the manufacturer’s protocol. DNA was eluted from the bead by heating the beads in 15 µL H2O at 95 °C for 10 min.
Library construction was performed using the xGen™ methyl-seq DNA library prep kit (IDT, 10009860).

treatment_protocol: Cells were treated with 5 mM N3-kethoxal in 6-well plates for 10 min under their normal culture condition.

value: BJ cells

value: Fibroblasts established from skin taken from normal foreskin from a neonatal male

value: Vanadyl sulfate, 2 hs

tag: time

value: 2 hours


title: neural progenitor cell, differentiated 1 day replication1

description:
Library name: NPC_D1_rep1
Column name in raw_counts.csv: D1_1

value: neurogenic differentiation


title: B. rapa_young_leaves_input_rep2

description: Library name: B.rapa_young_leaves_input_rep2

organism: Brassica rapa

value: Chiffu

value: input


title: B. oleracea_young_leaves_H3K4me1_ChIP-seq_rep2

description: Library name: BOCS-266_H3K4me1


title: B. rapa_young_leaves_BS-seq

description: Library name: BRBS-13


title: Induced_senescent_BJ_cells_VS_2h_rep1_KAS-seq


title: B. oleracea_young_leaves_H3K4me1_ChIP-seq_rep1

description: Library name: BOCS-254_H3K4me1


title: B. rapa_young_leaves_input

description: Library name: BRCS-237_input


title: Induced_senescent_BJ_cells_VS_40min_rep1_KAS-seq

value: Vanadyl sulfate, 40 mins

value: 40 minutes


title: B. rapa_young_leaves_RNA-seq_rep2

description: Library name: AA_RNA_rep2


title: B. oleracea_young_leaves_H3K4me3_ChIP-seq_rep2

description: Library name: BOCS-267_H3K4me3


title: B. rapa_young_leaves_RNA-seq_rep1

description: Library name: AA_RNA_rep1


title: B. rapa_young_leaves_ATAC-seq_rep1

description: Library name: BORS-7_ATAC


title: Induced_senescent_BJ_cells_VS_40min_rep2_KAS-seq


title: B. oleracea_young_leaves_H3K4me3_ChIP-seq_rep1

description: Library name: BOCS-250_H3K4me3


title: B. rapa_young_leaves_H3K9me2_ChIP-seq_rep1

description: Library name: BRCS-212_H3K9me2


title: B. rapa_young_leaves_H3K9me2_ChIP-seq_rep2

description: Library name: BRCS-233_H3K9me2


title: B. rapa_young_leaves_H3K27me3_ChIP-seq_rep2

description: Library name: BRCS-231_H3K27me3


title: Induced_senescent_BJ_cells_VS_20min_rep2_KAS-seq

value: Vanadyl sulfate, 20 mins

value: 20 minutes


title: mRNAseq_Flower_b2_rim-cr_rep2

city: La Jolla

first: Julie

middle: A

last: Law

state: CA

address: 10010 North Torrey Pines Rd

department: Plant Molecular and Cellular Biology

institute: Salk Institute for Biological Studies

description:
Library name: sample68
experiment batch2

data_processing:
Reads were mapped to the TAIR10 reference genome using STAR (v2.7.10a) allowing 2 mismatches and only uniquely mapped reads with the following options: --alignIntronMin 20 --alignIntronMax 6000 --outFilterMismatchNmax 2 --outFilterMultimapNmax 1 and --alignMatesGapMax 7500. To facilitate expression quantification, Tag Directories were generated from the resulting bam files using the makeTagDirectory function of HOMER (v4.10) with the following options: -format sam -mis 2 and -unique. mRNA expression was quantified using the analyzeRepeats.pl function of HOMER (v4.10). A custom gtf file containing genes, transposons, and repeats was used for quantification with the option -condenseGenes to report the highest expressed transcript, and -noadj to report raw read count. UCSC format track files were generated using the makeUCSCfile function of HOMER (v4.10) with the following options: -fragLength given -norm 10000000 -style rnaseq and -strand both.
Assembly: TAIR10
Supplementary files format and content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

organism: Arabidopsis thaliana

source_name: stage 12 and younger flower buds

growth_protocol: For wild-type plants (Col-0 ecotype), T-DNA insertion lines, rim-cr CRISPR deletion lines, and rim22-3 EMS lines, seeds were stratified in 0.1% agar (Phyto Agar, Cat# P1003) at 4˚C for 4 days before sowing directly onto soil and grown under Salk greenhouse conditions. Approximately five weeks after planting, stage 12 and younger flower buds were collected and frozen in liquid nitrogen.

extract_protocol:
Total RNA was extracted from flower buds (stage 12 and younger) using the Zymo Quick-RNA Miniprep Kit (R1055).
1 μg of DNase I treated total RNA was used for mRNA isolation with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, Cat# E7490L). Library preparation was performed using the NEBNext Ultra II RNA Library Prep Kit (NEB, Cat# E7770L). Pooled libraries were sequenced using a 50 bp single-end kit (SE50) or paired-end kit (PE50) on the Illumina Nextseq 2000 or Novaseq X plus platforms.

value: stage 12 and younger flower buds

value: Columbia

value: rim-cr


title: mRNAseq_Flower_b2_rim-cr_rep1

description:
Library name: sample67
experiment batch2


title: B. rapa_young_leaves_H3K4me1_ChIP-seq_rep2

description: Library name: BRCS-234_H3K4me1

value: young leaf

value: 14d young leaves cells


title: B. rapa_young_leaves_H3K27me3_ChIP-seq_rep1

description: Library name: BRCS-230_H3K27me3


title: Induced_senescent_BJ_cells_Ctrl_rep2_KAS-seq

value: Vanadyl sulfate, 0 mins

value: WT

value: 0 minutes


title: Induced_senescent_BJ_cells_VS_20min_rep1_KAS-seq

value: BJ cells

value: Fibroblasts established from skin taken from normal foreskin from a neonatal male


title: B. rapa_young_leaves_H3K4me1_ChIP-seq_rep1

description: Library name: BRCS-213_H3K4me1


title: mRNAseq_Flower_b2_rim22-2_rep2

description:
Library name: sample66
experiment batch2


title: B. rapa_young_leaves_H3K4me3_ChIP-seq_rep2

description: Library name: BRCS-235_H3K4me3


title: B. rapa_young_leaves_H3K4me3_ChIP-seq_rep1

description: Library name: BRCS-217_H3K4me3


title: mRNAseq_Flower_b2_rim22-2_rep1

description:
Library name: sample65
experiment batch2


title: B. rapa_young_leaves_ATAC-seq_rep2

description: Library name: BOAS-8_ATAC


title: mRNAseq_Flower_b2_rim16_rep2

description:
Library name: sample64
experiment batch2


title: mRNAseq_Flower_b2_rim16_rep1

description:
Library name: sample63
experiment batch2


title: IntestiCult™ Plus, Colon, Illumina, rep2

city: Vancouver

first: STEMCELL

last: Technologies

state: BC

address: 1618 Station st

department: RND

institute: STEMCELL Technologies

description:
Library name: Illumina-7-Colon-IntPlus_S7
scRNA-seq data from the colon expanded in IntestiCult™ Plus

data_processing:
10X libraries: the barcoded processing, gene counting and aggregation were made using the 10X Genomics Cell Ranger software v3.1.0. Sequencing data was demultiplexed using Illumina's cellranger multi.
Illumina libraries: the barcoded processing, gene counting and aggregation were made using the Fluent BioSciences PIPSeeker software v3.3. Processed data at sensitivity 3 are provided.
Downstream analysis were performed with Seurat v5.2.1. Cells with gene count between 2,000 and 10,000 genes and less than 10% mitochondrial genes were retained for analysis. RPCA integration was performed in order to incorporate all samples under a single UMAP. Gene expression of key markers was used to identify cell types.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon

extract_protocol:
Intestinal organoids in matrigel domes were digested using gentle cell dissociation reagent for 10 minutes, followed by centrifugation at 300g for 5 minutes. The cell pellet is washed with DMEM-F12 + 0.5% BSA, and centrifuged at 300g for 5 minutes. After removal of the supernatant, the pellet is resuspended in 1mL of warmed (37°C) Trypsin-EDTA (0.05%), and incubated at 37°C for 5-10 minutes. The cell suspension is then mixed thoroughly until large fragments have dissociated into single cells. An equal volume of DMEM/F-12 + 1% BSA is added to the suspension to deactivate the trypsin. A pre-wet a 37um reversible strainer is used to remove any large fragments that remain. Cell concentration, viability and percent of clumps are determined using a Nucleocounter. Single cells are centrifuged at 200g for 5 mins (RT). The supernatant was removed, and 1mL of pre-warmed cell suspension buffer is added with a wide bore pipette and gentle mixing to resuspend the pellet. Cells are then centrifuged at 200g for 3 minutes (RT), followed by aspiration of the supernatant. 200-400uL of cold cell suspension buffer is added to the pellet and gently mixed 10-15 times to resuspend. The single cell concentration is determined using the laboratory’s preferred method. A suspension of 2,500 live cells/uL is prepared in a cell suspension buffer to achieve an input volume of 4uL (10,000 live cells/uL) into a PIP reaction.
10X libraries: Library was prepared using Chromium Single Cell 3ʹ v1 protocol with GEM-X Universal Multiplex technology (10x Genomics). Sample quality control was performed using the Agilent 2100 Bioanalyzer or the Agilent 4200 TapeStation. Qualifying samples were then prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina). Sequencing was performed on the Illumina NextSeq 2000 with Paired End 59 bp × 59 bp reads. Illumina libraries: Library preparation was performed according to the manufacturer’s instructions (Illumina Single Cell 3′ RNA Prep, T10, Illumina). Briefly, single cells were combined with Particle-templated Instant Partitions (PIPs) and barcoded beads to generate emulsified partitions. Following chemical lysis, mRNA released from each partition was reverse transcribed into barcoded cDNA. The cDNA was then amplified by whole transcriptome amplification, isolated from PIPs, and purified using magnetic beads. Quality control included Qubit quantification and fragment analysis. For library construction, cDNA underwent fragmentation, end repair and A-tailing, adapter ligation, and sample index PCR to add Illumina P5, P7, and index sequences. Final libraries were cleaned with magnetic beads and prepared for sequencing on Illumina platforms.

value: Colon

value: Primary Organoid Intestinal epithelial


title: IntestiCult™ Plus, Ileum, Illumina, rep2

description:
Library name: Illumina-8-Ileum-IntPlus_S8
scRNA-seq data from the ileum expanded in IntestiCult™ Plus

source_name: Ileum

value: Ileum


title: mRNAseq_Flower_b2_WTCol-0_rep3

description:
Library name: sample62
experiment batch2


title: IntestiCult™ Plus, Duodenum, Illumina, rep2

description:
Library name: Illumina-2-Duodenum-IntPlus_S2
scRNA-seq data from the duodenum expanded in IntestiCult™ Plus

source_name: Duodenum

value: Duodenum


title: IntestiCult™ OGM, Ileum, Illumina, rep2

description:
Library name: Illumina-6-Ileum-OGM_S6
scRNA-seq data from the ileum expanded in IntestiCult™ OGM


title: IntestiCult™ OGM, Duodenum, Illumina, rep1

description:
Library name: Illumina-1-Duodenum-OGM_S1
scRNA-seq data from the duodenum expanded in IntestiCult™ OGM


title: IntestiCult™ Plus, Colon, 10X, rep1

description:
Library name: OCM2-2-Colon-IntPlus
scRNA-seq data from the colon expanded in IntestiCult™ Plus


title: mRNAseq_Flower_b2_WTCol-0_rep2

description:
Library name: sample61
experiment batch2


title: IntestiCult™ Plus, Ileum, 10X, rep1

description:
Library name: OCM2-3-Ileum-IntPlus
scRNA-seq data from the ileum expanded in IntestiCult™ Plus