title: CuO NPs + TTM, lung, C3

city: Chengdu

first: xiaojing

last: zhang

address: Sichuan University, No. 24 South Section 1, Yanshan Road, Chengdu, Sichuan Province, China

institute: Sichuan University

description:
Library name: sample9
C3

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2[2] software. The mapped reads of each sample were assembled byStringTie[3] in a reference-based approach.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2 or DEGseq . DEGs with |log2FC| ≧ 1 and FDR≤ 0.05(DESeq2 ) or FDR ≤0.001(DEGseq) were considered to be significantly different expressed genes. In addition, functional-enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value ≤0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools and KOBAS, respectively.
Assembly: GRCm39
Supplementary files format and content: processed data.xlsx

source_name: lung tissue

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer,s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/23≥2.0, RIN≥ 6.5, 28S:18S≥1.0, > 1μg) was used toconstruct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). The XX RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequencedwith the NovaSeqXplus sequencer (Illumina, San Diego, CA, USA).

value: lung tissue


title: Effector Treg creERT2 control 2

status: Public on Jan 13 2025

type: SRA

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

description: Library name: Sample 20

library_source: transcriptomic

data_processing:
Quality of sequencing data was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were trimmed for adapters and low quality base calls using Trim Galore, with default parameters (v0.6.5; https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Reads were then mapped to the GRCm38 mouse reference genome using Hisat2 (v2.1.0; Kim et al., 2019).
BAM files were imported into Seqmonk (v1.47.0; http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), excluding those with mapping quality < 30, and reads were quantified over merged mRNA isoforms from the GRCm38 Ensembl release 90 annotation, using the RNA-seq quantitation pipeline.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file containing gene names and IDs, together with raw read counts over each gene, generated in Seqmonk using merged mRNA isoforms for the GRCm38 Ensembl release 90 annotation

molecule: total RNA

organism: Mus musculus

source_name: Spleen + lymph node

extract_protocol:
Single cell suspensions were prepared from pooled spleen and pLN, from an individual mouse of the indicated genotype. CD4+ cells were enriched by negative depletion using biotinylated anti-B220, anti-CD8 and anti-CD11b followed by Streptavidin Dynabeads (Dynal).Naïve or effector Treg and ex-Treg were sorted based on the indicated markers; all samples were sorted to >95% purity. RNA was prepared from sorted cells using the RNeasy Micro Plus kit (Qiagen), and quality was assessed using the Bioanalyzer RNA chip.
cDNA was generated using the SMARTseq v4 ultra low input RNA kit for sequencing, and libraries prepared from the cDNA using the Nextera XT DNA library preparation kit.

treatment_protocol: Mice were fed with tamoxifen for 9 weeks prior to analysis

tag: strain

tag: tissue

value: Spleen + lymph node

tag: cell type

value: Effector Treg

tag: genotype

tag: Sex

value: Male

tag: age (weeks)

tag: flow markers


title: Panc-1, AA, rep1

city: Copenhagen

first: Yifan

last: Dai

address: Ole Maaløes Vej 5

department: Department of Biology

country: Denmark

institute: Copenhagen University

library_source: transcriptomic single cell

data_processing:
De-multiplexing, alignment, and gene counting using both lanes was accomplished with CellRanger (7.2.0).
Ambient RNA was removed through CellBender (0.3.1)
Count matrices were imported into R using scCustomize(2.1.2), then quality filtered via Seurat (5.0.1). Cells with less than 1000 genes detected or with mitochondrial RNA% > 10% were filtered out. Non-protein-coding genes were removed before normalization and scaling.
Cell cycle phase score was predicted using the cyclone function from scran package (1.26.2)
Assembly: GRCh38
Supplementary files format and content: rds file containing quality filtered Seurat object.

molecule: nuclear RNA

organism: Homo sapiens

growth_protocol: Panc-1,  pancreatic cancer cells were cultured in RPMI (Sigma, #R1383) or DMEM (Gibco, #41966-029) adjusted to correct pH at 5% CO2 (7.6 and 6.5 for Ctrl and acid-adapted, respectively) either by titration with hydrochloric acid or by replacing the appropriate amount of NaHCO3- with NaCl. Cell culture media were supplemented with 5-10% Fetal Bovine Serum (FBS, Gibco, #F9665), 1% Penicillin/Streptomycin (P/S, Sigma-Aldrich, #P0781) and for RPMI also 10 mM glucose (Sigma, #G8644). To ensure correct growth conditions, medium pH was measured inside the incubator, after equilibration at 5% CO2, using a mini-pH electrode.

extract_protocol:
Nuclei were isolated from Panc-1 cells using an IgePal-based lysis buffer (protocol optimized from (Krishnaswami et al, 2016)) , see Supplemental Material for further details). Briefly, 4x106 cells were collected in BSA-coated DNA LoBind tubes (Eppendorf Cat. #022431021), lysed over ice (10 min) and centrifuged (350 RCF, 5 min, 4°C). Lysed cells/nuclei were washed in ice-cold PBS supplemented with BSA (3%), Protease and RNAse inhibitors, followed by centrifugation (800 RCF, 10 min, 4°C). This wash step was repeated twice. For optimal removal of cell membrane, nuclei were spun down through a gradient of Iodixanol (50 % over 29%, 14000 RCF, 22 min, “Optiprep”, Stemcell Cat #7820), washed and filtered through 30 µm filters (Miltenyi Biotec Cat. #130-098-458). Nuclei isolation was verified by BF imaging, and a control sample was stained with 4’,6-diamidino-2-phenylindole (DAPI) to assess nuclear membrane integrity. Nuclei were counted and adjusted to a final concentration of 700-1200 nuclei/µL in nuclei storage buffer.
cDNA libraries were prepared using 10X Genomics Chromium technology. Briefly, for each sample, 5-10*104 nuclei along with reagents, and partitioning oil were loaded onto the 10X Chromium chip (3’ V3.1) according to manufacturer's recommendations (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1, Document Number CG000204 Rev D, 10x Genomics), and processed in the 10X Chromium controller (10X Genomics). Indexed libraries were pooled, then sequenced in two lanes.

treatment_protocol: isogenic human Panc-1 cells were randomly split into control and acid adaptation groups with three replicates in each group. AA samples were cultured under acidic conditions (pH 6.7) for 4 weeks, while Ctrl samples were maintained at constant physiological pH of 7.6 for the same time. At the end of the adaptation, nuclei from each cell group were extracted and subjected to single cell RNA sequencing using the 10x Genomics snRNA-seq workflow.

tag: cell line

tag: treatment

value: Acid Adaptation


title: Effector Treg creERT2 control 1

description: Library name: Sample 19


title: chondrocyte, normal culture, IL-1β, 36h, rep1

city: Shanghai

first: Lei

last: Shi

state: 请选择

address: 115 Jinzun Road, Pudong New Area, Shanghai

country: China

institute: Shanghai Jiaotong university

description: Library name: CI136

data_processing:
The constructed libraries underwent quality control (QC), and after passing, they were subjected to sequencing. Sequencing was performed on the DNBSEQ platform with a read length of SE50. The data obtained from sequencing, referred to as raw reads or raw data, underwent QC to determine whether the sequencing data were suitable for subsequent analysis. After QC, clean reads were obtained and aligned to the reference sequence. After alignment, the alignment results were subjected to a second QC, where alignment rate, distribution of reads on the reference sequence, and other metrics were assessed. If the results passed the second QC, gene quantification analysis and various analyses based on gene expression levels (such as principal component analysis (PCA), correlation analysis, differential gene selection, etc.) were conducted.
Assembly: GRCm38
Supplementary files format and content: csv file includes FPKM values for each Sample

source_name: Primary chondrocyte

extract_protocol:
The skin tissue/cartilage tissue was cut into 1 mm diameter pieces with sterilised ophthalmic scissors. Then skin tissue was digested in 0.5 mg/ml collagenase I (Biosharp, China) and DNase I (Roche, Switzerland) for 3 hours, while cartilage tissue was digested in 0.5 mg/ml collagenase II (Biosharp, China) and DNase I (Roche, Switzerland) for 2 hours. The isolated cell suspension was passed through a 100 μm sieve and then centrifuged to remove the supernatant. DFbs were cultured in alpha-MEM with 1% penicillin-streptomycin and 10% fetal bovine serum. Chondrocytes were cultured in DMEM/F12 containing 1% ITS (OriCell, China), 1% penicillin-streptomycin and 10% fetal bovine serum.
For library construction, total RNA was processed using mRNA enrichment. The mRNA was enriched using magnetic beads with Oligo(dT) to capture mRNA with a polyA tail. The obtained RNA was fragmented using a breaking buffer, and random N6 primers were used for reverse transcription. Subsequently, double-stranded cDNA was synthesized. The ends of the synthesized double-stranded DNA were blunted and 5' end-phosphorylated. A single-base overhang "A" was added to the 3' end, and a bubble-shaped adapter with a protruding "T" at the 3' end was ligated. The ligated products were PCR-amplified using specific primers. The PCR products were denatured to form single-stranded DNA, and single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries underwent quality control, and after passing, they were subjected to sequencing

value: Primary chondrocyte

value: WT


title: Naive ex-Treg creERT2 dKO 4

description: Library name: Sample 18

value: Naive ex-Treg

value: Zfp36l1-fl/fl Zfp36l2-fl/fl Foxp3-eGFP-cre-ERT2:hemi Rosa26-flSTOP-tdRFP:hom


title: CuO NPs + TTM, lung, C2

description:
Library name: sample8
C2


title: dPrD2_PT_rep1

city: Grossbeeren

first: Maolin

last: Peng

address: Theodor-Echtermeyer-Weg 1

country: Germany

institute: Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V.

data_processing:
HISAT2 (version 2.2.1) with parameters ‘--dta, --no-mixed, --no-discordant’ was used for aligning raw RNA-seq reads to TAIR10 genome. TPM values for genes were calculated by StringTie (version 2.1.4) with default settings directed by gene annotation file TAIR10 gff3 (https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_gff3/TAIR10_GFF3_genes.gff). Mean TPM values were calculated from replicates. Differentially expressed genes were identified by edgeR with thresholds q-value < 0.01 and log fold change > 1. To perform clustering of transcriptomic data, identified differentially expressed genes at least in one pairwise comparison (Col-0 37℃ vs 22℃) out of 3 time courses (5min, 15min and 30min) were selected. TPM values were transformed into log2(TPM+1). Genes with the maximum log2(TPM+1) > 2 were kept. Gaussian Mixture Models (GMM), implemented by an R package ClusterR (https://github.com/mlampros/ClusterR), was used for the clustering. The Expectation-Maximization algorithm was used for fitting GMM. The Bayesian information criterion was used for estimating the number of clusters.
Assembly: TAIR10
Supplementary files format and content: raw count

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Seedlings were grown 22 ºC and shifted to 37 ºC  or kept at 22 ºC.

extract_protocol:
Samples were homogenizing to powder using Qiagen TissueLyser II (Cat. No. / ID: 85300). Total RNA was extracted MagMAX™ Plant RNA Isolation Kit (Applied Biosystems™A33899) according to the manufacturer's instructions.
Total RNA was quantified using Qubit4 (Thermo Fisher Scientific) according to the manufacturer's instructions and tested for integrity using an RNA screentape in an Agilent2200 tape station (Agilent).

treatment_protocol: Treated using water bath

value: seedling

tag: genotype/treatment


title: Panc-1, Ctrl, rep1

value: Control


title: CuO NPs, lung, B3

description:
Library name: sample6
B3


title: 052094_1652, ADT

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

country: USA

institute: Purdue University

description:
single-cell antibody-derived tag data from CD45+ leukocytes
0118_1344_1595_1652_feature_reference.csv
1652_barcodes.tsv.gz
1652_features.tsv.gz
1652_matrix.mtx.gz

library_source: other

data_processing:
CellRanger pipeline v3.0.0 (10x Genomics)
Cells were retained that had between 1,000 and 10,000 observed genes and less than 22% of all reads mapping to mitochondrial genes. Data normalization and unsupervised clustering of scRNA-seq data were performed using Seurat version 4.1.0. The first 15 principal components of the scaled data were then used for downstream analyses. Unsupervised clustering was performed using graph-based approaches to construct K-nearest neighbor graphs (K=15) in Seurat.
Gene ontology terms, KEGG pathways, and Reactome pathways that are enriched amongst the cluster marker genes and the differentially expressed genes were identified by the package ClusterProfiler v.4.2.2
A velocity analysis was performed on loom files generated by v.0.17.17. Scvelo v. 2.4.0 employing the dynamical model was then used for the velocity analyses.
Assembly: Ensembl Genome Reference Consortium Human Build 38 (GRCh38.p3)
Supplementary files format and content: processed data files include the feature, barcode, and count matrices generated by CellRanger. Each sample has associated CellRanger output, which includes both antibody-derived tag sequencing and cDNA sequencing in the three files provided
Library strategy: CITE-seq

molecule: protein

source_name: prostate transition zone

extract_protocol:
[tissue procurement] Human prostate transition zone tissues were ethically procured with the IRB-approved NorthShore Urologic Disease Biorepository and Database with informed consent and de-identified clinical annotation. Small prostate tissues were obtained from 10 male patients undergoing robotic-assisted laparoscopic prostatectomy (RALP) for prostate cancer, International Prostate Symptom Score (IPSS) of <15, Gleason 6-7, and estimated prostate volume of <40 grams by imaging with transrectal ultrasound (TRUS), CT scan, or MRI. Large prostate tissues were obtained from 10 male patients undergoing either RALP for prostate cancer (Gleason 6-7) or simple prostatectomy for BPH and had an estimated prostate size of >90 grams.
[isolation of CD45+ cells] The transition zone (TZ) was dissected similarly for both small and large prostate tissues and were pathologically verified to have no (or minimal) cancer burden. Tissue pieces were separated for formalin-fixed paraffin-embedded (FFPE) histology or digested and prepared for fluorescence activated cell sorting (FACS). Tissues were minced, then digested while shaking at 37°C for 2 hours in 200 U/mL Collagenase I (Gibco) + 1 mg/mL DNase I (Roche) + 1% antibiotic/antimycotic solution in Hank’s Balanced Salt Solution. Digestion solution was replaced with TrypLE Express dissociation reagent (Gibco) and allowed to shake at 37°C for 5-10 minutes. Digested samples were neutralized in RPMI + 10% FBS, then mechanically disrupted by pipetting repeatedly. Samples were passed through a 100µm cell strainer, then washed. Red blood cells were lysed in a hypotonic buffer, then cells were stained with Zombie Violet (Biolegend) and blocked with Human TruStain FcX blocking antibody (Biolegend). CD45-PE [clone HI30], EpCAM-APC [clone 9C4], and CD200-PE/Cy7 [clone OX-104] antibodies (Biolegend) were added to stain samples in preparation for FACS on a BD FACSAria II. Approximately 100,000 viable CD45+CD200-EpCAM- cells were sorted for downstream analysis.
FACS-isolated cells were spun down and washed at least twice prior to loading onto the 10X Chromium System (10X Genomics), with Single Cell 3’ Library & Gel Bead Kit, v3.0 reagents. Cells from three small and nine large tissues were stained with TotalSeq-B Antibodies (Biolegend) for CITE-seq analysis. Antibodies for CD3 [clone UCHT1], CD4 [clone RPA-T4], CD8 [clone RPA-T8], CD19 [clone HIB19], CD11b [clone ICRF44], and CD56 (NCAM) [clone 5.1H11] were used following the manufacturer’s instructions prior to loading into the Chromium System.
Cells were loaded for downstream evaluation of 5,000 cells/sample and cDNA amplification and library preparation were conducted according to 10X Genomic’s instructions.
Sequencing of normalized pools was conducted using a NovaSeq S4 flow cell on a NovaSeq 6000 system (Illumina) with 2x150 base-pair reads at a depth of 50,000 reads/cell. Libraries generated from cell surface protein labeling were sequenced at a depth of 5,000 reads/cell.

value: prostate transition zone

tag: prostate size

value: large (>90 grams)

value: leukocytes

value: male

tag: tissueid

tag: library type

value: ADT


title: dPrD2_P_rep1


title: Naive ex-Treg creERT2 dKO 3

description: Library name: Sample 17

value: Zfp36l1-fl/fl Zfp36l2-fl/fl Foxp3-eGFP-cre-ERT2:hom Rosa26-flSTOP-tdRFP:hom

value: Female


title: dPrD2_P_rep2


title: Effector Treg creERT2 control 3

description: Library name: Sample 21

value: Spleen + lymph node


title: CuO NPs, lung, B2

description:
Library name: sample5
B2

value: lung tissue


title: Naive ex-Treg creERT2 dKO 2

description: Library name: Sample 16


title: 052091_1595, GEX

description:
single-cell mRNA-seq data from CD45+ leukocytes
0118_1344_1595_1652_feature_reference.csv
1595_barcodes.tsv.gz
1595_features.tsv.gz
1595_matrix.mtx.gz

value: mRNA


title: Naive ex-Treg creERT2 control 5

description: Library name: Sample 14

value: Male


title: dPrD2_C2_rep2


title: 052092_1595, ADT

description:
single-cell antibody-derived tag data from CD45+ leukocytes
0118_1344_1595_1652_feature_reference.csv
1595_barcodes.tsv.gz
1595_features.tsv.gz
1595_matrix.mtx.gz


title: 048751_1579, ADT

description:
single-cell antibody-derived tag data from CD45+ leukocytes
1338_1579_feature_reference.csv
1579_barcodes.tsv.gz
1579_features.tsv.gz
1579_matrix.mtx.gz


title: CuO NPs, lung, B1

description:
Library name: sample4
B1


title: Naive ex-Treg creERT2 dKO 1

description: Library name: Sample 15


title: dPrD2_PT_rep2


title: dPrD2_C1_rep1


title: control, lung, A3

description:
Library name: sample3
A3


title: dPrD2_C1_rep2


title: Naive ex-Treg creERT2 control 3

description: Library name: Sample 12


title: control, lung, A1

description:
Library name: sample1
A1


title: 046785_0118, ADT

description:
single-cell antibody-derived tag data from CD45+ leukocytes
0118_1344_1595_1652_feature_reference.csv
0118_barcodes.tsv.gz
0118_features.tsv.gz
0118_matrix.mtx.gz


title: control, lung, A2

description:
Library name: sample2
A2


title: CuO NPs + TTM, lung, C1

description:
Library name: sample7
C1


title: 048750_1579, GEX

description:
single-cell mRNA-seq data from CD45+ leukocytes
1338_1579_feature_reference.csv
1579_barcodes.tsv.gz
1579_features.tsv.gz
1579_matrix.mtx.gz


title: Naive ex-Treg creERT2 control 2

description: Library name: Sample 11


title: Col-0_37C_Rep1


title: Col-0_37C_Rep3


title: PDF 24h_2

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

description: Library name: Sample 6

data_processing:
Integrative Genomcs Viewer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a standard protocol from MajorBio company. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library of MajorBio.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

source_name: embryo

extract_protocol:
Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. Illumina NovaSeq X Plus was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryo

value: 46C embryonic stem cells


title: dPrD2_C2_rep1


title: Naive ex-Treg creERT2 control 1

description: Library name: Sample 10

value: Naive ex-Treg


title: 052093_1652, GEX

description:
single-cell mRNA-seq data from CD45+ leukocytes
0118_1344_1595_1652_feature_reference.csv
1652_barcodes.tsv.gz
1652_features.tsv.gz
1652_matrix.mtx.gz


title: PDF 24h_1

description: Library name: Sample 5


title: Col_0_37C5min_rep2


title: 046784_0118, GEX

description:
single-cell mRNA-seq data from CD45+ leukocytes
0118_1344_1595_1652_feature_reference.csv
0118_barcodes.tsv.gz
0118_features.tsv.gz
0118_matrix.mtx.gz


title: PDF 12h_2

description: Library name: Sample 4


title: Col_0_37C5min


title: Naive ex-Treg creERT2 control 4

description: Library name: Sample 13


title: Col_0_37C15min_rep2


title: Naive Treg creERT2 dKO 2

description: Library name: Sample 7

value: Naive Treg


title: 046781_1338, ADT

description:
single-cell antibody-derived tag data from CD45+ leukocytes
1338_1579_feature_reference.csv
1338_barcodes.tsv.gz
1338_features.tsv.gz
1338_matrix.mtx.gz


title: 046783_1344, ADT

description:
single-cell antibody-derived tag data from CD45+ leukocytes
0118_1344_1595_1652_feature_reference.csv
1344_barcodes.tsv.gz
1344_features.tsv.gz
1344_matrix.mtx.gz


title: Naive Treg creERT2 dKO 4

description: Library name: Sample 9

value: Zfp36l1-fl/fl Zfp36l2-fl/fl Foxp3-eGFP-cre-ERT2:hemi Rosa26-flSTOP-tdRFP:hom


title: 046782_1344, GEX

description:
single-cell mRNA-seq data from CD45+ leukocytes
0118_1344_1595_1652_feature_reference.csv
1344_barcodes.tsv.gz
1344_features.tsv.gz
1344_matrix.mtx.gz


title: PD_2

description: Library name: Sample 2


title: PD_1

description: Library name: Sample 1


title: Naive Treg creERT2 dKO 3

description: Library name: Sample 8


title: Col-0_22C_Rep3

value: seedling


title: Col_0_22C_rep2


title: iRAPS,HPS1,pooled

city: New York

first: Hans-Willem

last: Snoeck

state: NY

address: 650 west 168th street

institute: Columbia University Irving Medical Centre

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cell ranger version 5.0.1 for each sample
Assembly: GRCh38 reference genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hESC-derived lung organoid

extract_protocol:
We performed single cell RNA sequencing on transitional lung organoids,iRAP,iAT1D-IRAPs. The samples were dissociated to single cells and resuspended at a concentration of 5000 cells/ul for sequencing.
Libraries were prepared and sequenced at the JP Sulzberger Columbia Genome Center High-Throughput Screening Center at Columbia University. Sequencing libraries were prepared using 10x Genomics Single Cell Gene Expression 3’ workflow

value: hESC-derived lung organoid

value: Rockefeller University Embryonic Stem Cell Line 2 (RUES2)


title: transitional AT2-like cells, iAT1, multiplexed, hashtagged

description: 10x Genomics Single Cell Gene Expression 3’


title: PDF 12h_1

description: Library name: Sample 3


title: Col-0_22C_Rep1


title: Naive Treg creERT2 control 3

description: Library name: Sample 3


title: CONTROL 5

type: RNA

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 15, from SAS. miRNA expression profiling was performed using arrays of GeneChip™ miRNA 4.0 Arrays (Thermo Fisher Scientific Inc., Waltham, MA, USA) . The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotine

source_name: Urine

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol:
miRNA was obtained using the extracellular vesicle extraction process.  Urine samples were pre clarified spinning 15 min. at 3000 rpm. To isolate the extracellular vesicles, the supernatants were again ultra-centrifuged for 1 h at 28,000g
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Following this, the mirVana™ miRNA Isolation Kit (Invitrogen, Thermofisher Scientific Inc., Waltham, MA, USA) was utilized for the rest of the miRNA purification, also according to manufacturer’s protocol.

tag: group


title: Col_0_37C15min


title: KOA synovial fibroblasts, rep3

description: Library name: OA08FILB

data_processing:
The constructed libraries underwent quality control (QC), and after passing, they were subjected to sequencing. Sequencing was performed on the DNBSEQ platform with a read length of SE50. The data obtained from sequencing, referred to as raw reads or raw data, underwent QC to determine whether the sequencing data were suitable for subsequent analysis. After QC, clean reads were obtained and aligned to the reference sequence. After alignment, the alignment results were subjected to a second QC, where alignment rate, distribution of reads on the reference sequence, and other metrics were assessed. If the results passed the second QC, gene quantification analysis and various analyses based on gene expression levels (such as principal component analysis (PCA), correlation analysis, differential gene selection, etc.) were conducted.
Assembly: GRCh38
Supplementary files format and content: csv file includes FPKM values for each Sample

source_name: Primary fibroblasts

extract_protocol:
The synovial tissue/ prepuce tissue was cut into 1 mm diameter pieces with sterilised ophthalmic scissors, while it was later digested in 0.5 mg/ml collagenase I (Biosharp, China) and DNase I (Roche, Switzerland) for 3 hours. The isolated cell suspension was passed through a 100 μm sieve and then centrifuged to remove the supernatant. FLSs and DFbs were cultured in DMEM with 1% penicillin-streptomycin (Gibco, USA) and 10% fetal bovine serum (FBS, Hyclone, USA). FLSs and DFbs (Vimentin positive) were identified at the 3rd passage (P3), and FLSs at P3 with a purity over 90% were used for the function and mechanism experiments.
For library construction, total RNA was processed using mRNA enrichment. The mRNA was enriched using magnetic beads with Oligo(dT) to capture mRNA with a polyA tail. The obtained RNA was fragmented using a breaking buffer, and random N6 primers were used for reverse transcription. Subsequently, double-stranded cDNA was synthesized. The ends of the synthesized double-stranded DNA were blunted and 5' end-phosphorylated. A single-base overhang "A" was added to the 3' end, and a bubble-shaped adapter with a protruding "T" at the 3' end was ligated. The ligated products were PCR-amplified using specific primers. The PCR products were denatured to form single-stranded DNA, and single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries underwent quality control, and after passing, they were subjected to sequencing.

value: Primary fibroblasts


title: LIM1215 cells, IACS, biol rep 1

city: Callaghan

first: Xiaohong

last: Zhao

address: University Drive

country: Australia

institute: University of Newcastle

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: Homo Sapiens GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: Colo205 and LIM1215 cells were maintained in DMEM supplemented with 5% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
RNA was harvested using ISOLATE II RNA Mini Kit (Bioline, Cat#BIO-52073, UK). 400 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit

treatment_protocol: Cells were treated with 100 nM IACS for 24 hour

value: Colorectal cancer cell

value: wildtype p53

value: IACS


title: 046780_1338, GEX

description:
single-cell mRNA-seq data from CD45+ leukocytes
1338_1579_feature_reference.csv
1338_barcodes.tsv.gz
1338_features.tsv.gz
1338_matrix.mtx.gz

value: prostate transition zone

value: large (>90 grams)

value: leukocytes

value: male


title: LIM1215 cells, DMSO, biol rep 2

value: DMSO


title: KOA synovial fibroblasts, rep1

description: Library name: OA06FILB


title: CONTROL 4


title: Naive Treg creERT2 control 5

description: Library name: Sample 5

value: Spleen + lymph node

value: Male


title: Naive Treg creERT2 dKO 1

description: Library name: Sample 6


title: T34R172H/LOH

city: Cold Spring Harbor

first: David

middle: A

last: Tuveson

state: New York

address: 1 Bungtown Road

department: Cancer Center

institute: Cold Spring Harbor Laboratory

data_processing:
The quality of the RNA-seq reads was first confirmed using FastQC version 0.11.5 (Babraham Bioinformatics).
Reads were then mapped to transcripts from GENCODE release M16 on mus musculus GRCm38.p5 genome using STAR alignment software version 2.5.2b.
RSEM version 1.3.0 was used to calculate expression estimates per gene and per isoform.
DESeq2 version 1.44.0 was used to perform count normalization. A pre-filtering step was performed to remove genes that have reads in less than two samples. A first normalization was done using all remaining genes. A second normalization was done using only protein coding genes as  identifed by BioMart.
Assembly: mus musculus NCBI genome build 38.p5
Supplementary files format and content: The gene.results files are tab-delimited text files that include expected counts, TPM and FKPM values per gene for each sample as generated by RSEM.
Supplementary files format and content: The isoforms.results files are tab-delimited text files that include expected counts, TPM and FKPM values per isoform for each sample as generated by RSEM.
Supplementary files format and content: The mouse_organoids_TPM_M16.csv file is a comma-separated text file that includes the transcript per million (TPM) per transcript for all samples as extracted from the files generated by RSEM.
Supplementary files format and content: The mouse_organoids_expected_counts_M16.csv file is a comma-separated text file that includes the expected count per transcript for all samples as extracted from the files generated by RSEM.
Supplementary files format and content: The mouse_organoids_normalized_expected_counts_M16.csv file is a comma-separated text file that includes the normalized counts per transcript for all samples as obtained by DESeq2 after pre-filtering for genes expressed in less than two samples.
Supplementary files format and content: The mouse_organoids_normalized_expected_counts_protein_coding_only_M16.csv file is a comma-separated text file that includes the normalized counts per protein-coding transcript for all samples as obtained by DESeq2 after pre-filtering for genes expressed in less than two samples and not identified as protein-coding in BioMart.

source_name: KPC tumor

growth_protocol: Organoids were grown in a matrigel dome in mouse complete organoid medium.

extract_protocol:
Organoids were harvested in Trizol (Invitrogen), total RNA was extracted using the TRIzol Plus RNA Purification Kit (ThermoFisher) per manufacturer’s instructions. RNA samples were treated on column with PureLink DNase (ThermoFisher). The quality of purified RNA samples was determined using a Bioanalyzer 2100 (Agilent) with an RNA 6000 Nano Kit.
Libraries for RNA-Seq were prepared with the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat (Illumina) following manufacturer instructions.

value: KPC tumor


title: Healthy synovial fibroblasts, rep3

description: Library name: H03F


title: T23R172H/LOH


title: Hi-C_Lwaltii

city: Paris

first: Axel

last: Cournac

address: 28 rue du docteur Roux

country: France

institute: Institut Pasteur

library_source: genomic

data_processing:
Reads were aligned and contact maps generated and processed using Hicstuff (https://github.com/koszullab/hicstuff). Briefly, pairs of reads were aligned iteratively and independently using Bowtie2 (Langmead and Salzberg, 2012) in its most sensitive mode against their reference genome. Each uniquely mapped read was assigned to a restriction fragment.
Quantification of pairwise contacts between restriction fragments was performed with default parameters: uncuts, loops and circularization events were filtered as described in (Cournac et al., 2012)).
PCR duplicates (defined as multiple pairs of reads positioned at the exact same position) were discarded.
Contacts were binned at 1kb resolution and multiple-resolution balanced contact maps (in mcool format) were generated using cooler (Abdennur and Mirny, 2020).
Assembly: GCA_900074765.1 for L.fermentati / GCA_030580015.1 for L.waltii
Supplementary files format and content: Contact matrices are provided in multiple resolution mcool files.

molecule: genomic DNA

organism: Lachancea waltii

extract_protocol:
Cell fixation with 3% formaldehyde (Sigma-Aldrich, Cat. F8775) was performed as described in Dauban et al. (2020). Quenching of formaldehyde with 300 mM glycine was performed at 4°C for 20 min. Hi-C experiments were performed with a Hi-C kit (Arima Genomics) with a double DpnII + HinfI restriction digestion following manufacturer instructions. Briefly, Cells were resuspended in 500ul water and transferred in VK05-0.5ml (ozyme, P000934-LYSK0-A.0) tubes containing glass beads before mechanical cells lysis. 8ul of samples were permeabilized by sequentially adding lysis buffer (15min at 4C), conditioning solution (10min at 62C) and stop solution 2 (15min at 37C) to the samples. DNA was digested using a mix of buffer A, DpnII, and Hinf1 (45min at 37C followed by 20min at 65C).
DNA was repaired and biotin was added by adding a mix of buffer B and enzyme B for 45min at room temperature. DNA was re-ligated by adding a mix of buffer C and enzyme C during 15min at room temperature. Samples were then digested by protease and de-crosslinked by adding a mix of buffer D, enzyme D and buffer E during 30 min à 55°C followed by 90 min at 68°C. Samples were purified using AMPure XP beads (Beckman A63882), recovered in 120ul H2O and sonicated using Covaris (DNA 300bp) in Covaris microTUBE (Covaris, 520045). Biotinylated DNA was loaded on Dynabeads™ Streptavidin C1 (FISHER SCIENTIFIC, 10202333). Preparation of the samples for paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed using Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina and following manufacturer instructions.

value: WT


title: CONTROL 1


title: Naive Treg creERT2 control 4

description: Library name: Sample 4

value: Naive Treg

value: Female


title: HSCR PATIENT 5


title: Colo205 cells, IACS, biol rep 1

value: mutant p55


title: Healthy synovial fibroblasts, rep1

description: Library name: H01F


title: LIM1215 cells, IACS, biol rep 2


title: Naive Treg creERT2 control 2

description: Library name: Sample 2


title: Colo205 cells, DMSO, biol rep 1

value: mutant p53


title: T23R172H/+


title: KOA synovial fibroblasts, rep2

description: Library name: OA07FILB

value: Primary fibroblasts


title: Naive Treg creERT2 control 1

description: Library name: Sample 1


title: LIM1215 cells, DMSO, biol rep 1

value: Colorectal cancer cell


title: CONTROL 3


title: CONTROL 2


title: T6R172H/LOH


title: Healthy synovial fibroblasts, rep2

description: Library name: H02F


title: 14_sperm_BJL_2

status: Public on Jan 12 2025

city: London

first: James

last: Turner

address: The Francis Crick Institute, 1 Midland Road

institute: The Francis Crick Institute

data_processing:
Read trimming was performed with TrimGalore v0.6.0 using these parameters: --clip_R1 6 --3_prime_clip_R1 6
Mapping was performed with Bismark v0.18.0 using these parameters: --non_directional --un --ambiguous
SNP splitting was performed with SNPsplit v0.3.4 using these parameters: --bisulfite –conflicting
Methylation analysis was performed with R v3.4.3 using the methylKit v1.4.1 package
Plotting was performed with R v3.4.3 using the ggplot2 v3.2.0 and Gviz v1.22.3 packages
Assembly: MonDom5
Supplementary files format and content: bedGraph

molecule: other

organism: Monodelphis domestica

source_name: sperm

extract_protocol:
direct lysis
EZ Methylation Kit (#D5020, Zymo)
post-bisulfite adapter tagging style whole-genome bisulfite sequencing libraries Clark et al 2017 Nature Protocols

value: sperm


title: Colo205 cells, IACS, biol rep 2

value: mutant p56

value: IACS


title: 13_sperm_BJL_1


title: 12_sperm_SM_4


title: 11_sperm_SM_3


title: Colo205 cells, DMSO, biol rep 2

value: mutant p54


title: T34R172H/+


title: HSCR PATIENT 4


title: HSCR PATIENT 3


title: dermal fibroblasts, rep2

description: Library name: D02


title: 1_pool_E2_5

tag: developmental stage

value: embryo


title: HSCR PATIENT 2


title: emb5_cell5_20221214_E6.5

data_processing:
Single-cell RNA-seq data was aligned to the opossum ASM229v1 genome, using the nf-core rnaseq pipeline (3.2), using the parameters –aligner star_rsem –bam-csi-index.
Raw counts were loaded into Seurat (4.3.0) for analysis in R (4.2.2).. Each dataset was normalised using NormalizeData, then datasets were integrated together using the functions SelectIntegrationFeatures, FindIntegrationAnchors then IntegrateData
The integrated dataset was scaled used ScaleData. Principle Component Analysis was applied using RunPCA. Uniform Manifold Approximation and Projection was estimated for the integrated dataset using RunUMAP.
Assembly: ASM229v1
Supplementary files format and content: tab delimited file containing the raw gene counts from rsem, rsem.merged.gene_counts.tsv

molecule: polyA RNA

source_name: single cell from embryo

growth_protocol: single cells were disaggregated from opossum embryos by incubation in TrypLE and washed through multiple drops of PBS

extract_protocol:
direct lysis followed by polyA mRNA capture on polydT magnetic beads
RNA-seq library preparation following the scNMT-seq method of Clark et al 2018 https://doi.org/10.1038/s41467-018-03149-4
scNMT-seq RNA-seq

treatment_protocol: incubation for 15 minutes in M.CviPI

value: single cell from embryo


title: 5_pool_E3_5


title: T6R172H/+


title: 7_pool_oocytes_20230320

source_name: oocyte

value: oocyte


title: dermal fibroblasts, rep1

description: Library name: D01


title: emb5_cell4_20221214_E6.5


title: induced respiratory airway progenitors  (iRAPs), scRNAseq, pooled

description: 10x Genomics Single Cell  3’ Gene Expression

data_processing:
Sequencing data were aligned and quantified using the Cell Ranger Single-Cell Software Suite (version 6.1.2, 10x Genomics) against the provided GRCh38 (Ensembl 98) human reference genome.
All further computational analysis of scRNA-seq data was performed using R version 4.1.3 and Python (https://www.R-project.org/.) unless otherwise stated.
RNA velocity was calculated in python using the packages Velocyto and scVelo, according to the developer's manual
Assembly: GRCh38 reference genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hESC- derived transitional lung organoids

extract_protocol: Single-cell RNA-seq was performed on these samples using the Chromium platform (10x Genomics, Pleasanton, CA) with the 3’ gene expression (3’ GEX) V3 kit, using an input of ~10,000 cells. Briefly, Gel-Bead in Emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (Thermofisher) analysis and were sequenced in paired end mode on a NovaSeq instrument (Illumina, San Diego, CA) targeting a depth of 50,000-100,000 reads per cell.

value: Rockefeller University Embryonic Stem Cell Line 2 (RUES2)


title: emb5_cell3_20221214_E6.5


title: HSCR PATIENT 1


title: emb3_cell24_20221214_E6.5


title: emb3_cell20_20221214_E6.5


title: 16_sperm_BJL_4


title: emb3_cell18_20221214_E6.5


title: 15_sperm_BJL_3


title: emb3_cell17_20221214_E6.5


title: 10_sperm_SM_2


title: emb3_cell8_20221214_E6.5


title: dermal fibroblasts, rep3

description: Library name: D03


title: emb3_cell12_20221214_E6.5


title: emb3_cell6_20221214_E6.5


title: 9_sperm_SM_1


title: emb3_cell27_20221214_E6.5


title: 3_pool_oocytes


title: emb5_cell6_20221214_E6.5


title: GpC_embryo1_troph_B03_20221110_E7.5


title: emb5_cell2_20221214_E6.5


title: emb5_cell1_20221214_E6.5


title: emb1_cell31_20221214_E6.5


title: emb3_cell26_20221214_E6.5


title: emb3_cell25_20221214_E6.5


title: emb3_cell23_20221214_E6.5


title: emb3_cell21_20221214_E6.5


title: emb1_cell28_20221214_E6.5


title: emb3_cell22_20221214_E6.5


title: emb1_cell27_20221214_E6.5


title: emb1_cell26_20221214_E6.5


title: GpC_embryo1_epi_E02_20221110_E7.5


title: GpC_embryo1_epi_E03_20221110_E7.5


title: emb1_cell19_20221214_E6.5


title: emb1_cell18_20221214_E6.5


title: emb3_cell13_20221214_E6.5


title: emb1_cell17_20221214_E6.5


title: emb1_cell25_20221214_E6.5


title: emb1_cell22_20221214_E6.5


title: emb1_cell16_20221214_E6.5


title: emb3_cell7_20221214_E6.5


title: emb1_cell32_20221214_E6.5


title: emb3_cell3_20221214_E6.5


title: emb1_cell13_20221214_E6.5


title: emb1_cell15_20221214_E6.5


title: emb3_cell2_20221214_E6.5


title: emb1_cell30_20221214_E6.5


title: emb1_cell12_20221214_E6.5


title: emb1_cell10_20221214_E6.5


title: emb1_cell9_20221214_E6.5


title: GpC_embryo1_epi_D08_20221110_E7.5


title: emb1_cell8_20221214_E6.5


title: emb1_cell7_20221214_E6.5


title: emb1_cell21_20221214_E6.5


title: emb1_cell6_20221214_E6.5


title: emb1_cell5_20221214_E6.5


title: emb1_cell4_20221214_E6.5


title: GpC_embryo1_troph_B02_20221110_E7.5


title: emb1_cell2_20221214_E6.5


title: emb1_cell3_20221214_E6.5


title: CTRL_embryo1_epi_D12_20221110_E7.5

value: no M.CviPI


title: emb1_cell1_20221214_E6.5


title: GpC_embryo1_troph_B01_20221110_E7.5


title: GpC_embryo1_epi_D03_20221110_E7.5


title: CTRL_embryo1_epi_D10_20221110_E7.5


title: GpC_embryo1_troph_A11_20221110_E7.5


title: CTRL_embryo1_epi_D09_20221110_E7.5


title: CTRL_embryo1_epi_B12_20221110_E7.5


title: emb1_cell11_20221214_E6.5


title: emb1_cell14_20221214_E6.5


title: GpC_embryo1_troph_A12_20221110_E7.5


title: GpC_embryo1_troph_A10_20221110_E7.5


title: CTRL_embryo1_epi_B11_20221110_E7.5


title: GpC_embryo1_epi_D02_20221110_E7.5


title: emb4_cell20_20230288_E5.5


title: emb4_cell19_20230287_E5.5


title: emb4_cell17_20230285_E5.5


title: emb4_cell18_20230286_E5.5


title: GpC_embryo1_epi_D01_20221110_E7.5


title: GpC_embryo1_epi_D06_20221110_E7.5


title: emb4_cell15_20230283_E5.5


title: emb4_cell12_20230280_E5.5


title: CTRL_embryo1_epi_D11_20221110_E7.5


title: CTRL_embryo1_epi_B09_20221110_E7.5


title: CTRL_embryo1_epi_B10_20221110_E7.5


title: emb4_cell16_20230284_E5.5


title: emb4_cell14_20230282_E5.5


title: emb4_cell11_20230279_E5.5


title: emb4_cell6_20230274_E5.5


title: emb4_cell5_20230273_E5.5


title: emb4_cell3_20230271_E5.5


title: emb4_cell4_20230272_E5.5


title: emb4_cell9_20230277_E5.5


title: emb4_cell2_20230270_E5.5


title: emb4_cell7_20230275_E5.5


title: emb4_cell10_20230278_E5.5


title: GpC_embryo1_troph_A09_20221110_E7.5


title: emb4_cell21_20230289_E5.5


title: emb4_cell8_20230276_E5.5


title: emb4_cell1_20230269_E5.5


title: emb3_cell22_20230268_E5.5


title: emb3_cell20_20230266_E5.5


title: emb3_cell21_20230267_E5.5


title: emb4_cell13_20230281_E5.5


title: emb3_cell18_20230264_E5.5


title: emb3_cell15_20230261_E5.5


title: GpC_embryo1_epi_C12_20221110_E7.5


title: emb3_cell11_20230259_E5.5


title: emb3_cell10_20230258_E5.5


title: emb3_cell13_20230260_E5.5


title: emb3_cell9_20230257_E5.5


title: emb3_cell5_20230253_E5.5


title: emb3_cell8_20230256_E5.5


title: emb3_cell6_20230254_E5.5


title: emb3_cell7_20230255_E5.5


title: emb3_cell3_20230252_E5.5


title: emb3_cell2_20230251_E5.5


title: GpC_embryo1_epi_C11_20221110_E7.5


title: GpC_embryo1_epi_C10_20221110_E7.5


title: emb2_cell21_20230249_E5.5


title: emb2_cell14_20230244_E5.5


title: emb3_cell1_20230250_E5.5


title: emb2_cell15_20230245_E5.5


title: emb2_cell11_20230242_E5.5


title: emb2_cell18_20230247_E5.5


title: emb3_cell17_20230263_E5.5


title: emb2_cell19_20230248_E5.5


title: emb2_cell16_20230246_E5.5


title: emb2_cell8_20230240_E5.5


title: CTRL_embryo1_troph_B08_20221110_E7.5


title: emb2_cell13_20230243_E5.5


title: emb2_cell10_20230241_E5.5


title: emb3_cell16_20230262_E5.5


title: emb3_cell19_20230265_E5.5


title: emb2_cell5_20230237_E5.5


title: emb2_cell7_20230239_E5.5


title: emb2_cell6_20230238_E5.5


title: emb2_cell2_20230235_E5.5


title: emb1_cell17_20230231_E5.5


title: emb1_cell21_20230233_E5.5


title: emb2_cell1_20230234_E5.5


title: emb1_cell19_20230232_E5.5


title: emb1_cell16_20230230_E5.5


title: GpC_embryo1_troph_A08_20221110_E7.5


title: emb1_cell15_20230229_E5.5


title: emb1_cell14_20230228_E5.5


title: emb1_cell12_20230227_E5.5


title: emb1_cell11_20230226_E5.5


title: emb1_cell10_20230225_E5.5


title: emb1_cell9_20230224_E5.5


title: emb1_cell7_20230222_E5.5


title: fibroblasts, DNMT1_2_d8

data_processing:
RNA-seq nf-core pipeline (v3.2), star_rsem was used to generate raw reads counts. The read coutns were processed in R using the DESeq2 package (v1.36).
Assembly: ASM229v1
Supplementary files format and content: normalised count matrix

source_name: immortalised fibroblast

growth_protocol: Primary opossum fibroblasts were derived from a newborn male and immortalised using SV40-tag virus infection. Cells were grown in DMEM with 20% FBS, 1% Glutamax, and pen-strep

extract_protocol:
RNAqueous-Micro Total RNA Isolation kit
NEBNext Ultra II Directional PolyA mRNA

treatment_protocol: DNMT1-KO by transfection of CRISPR cas9 reagents targeting DNMT1A and 1B genes. Puromycin selection for sucessful tranfection applied one day later for 48h. Note experiment was done on pool of targeted cells i.e. mosiac pool not clonal isolate

value: immortalised fibroblast

tag: time


title: fibroblasts, DNMT1_3_d8


title: emb1_cell6_20230221_E5.5

value: WT


title: fibroblasts, DNMT1_1_d8


title: emb1_cell8_20230223_E5.5


title: GpC_embryo1_epi_C09_20221110_E7.5


title: fibroblasts, DNMT1_3_d4


title: emb2_cell4_20230236_E5.5


title: emb1_cell4_20230219_E5.5


title: emb1_cell3_20230218_E5.5


title: fibroblasts, DNMT1_1_d4


title: emb1_cell2_20230217_E5.5


title: fibroblasts, NC_3_d8


title: fibroblasts, NC_2_d8


title: fibroblasts, DNMT1_2_d4


title: emb1_cell1_20230216_E5.5


title: CTRL_embryo1_troph_B07_20221110_E7.5


title: GpC_embryo1_troph_A07_20221110_E7.5


title: emb1_cell5_20230220_E5.5


title: GpC_embryo1_epi_C08_20221110_E7.5


title: fibroblasts, NC_2_d4


title: GpC_embryo1_epi_C07_20221110_E7.5


title: fibroblasts, NC_3_d4


title: GpC_embryo1_epi_C06_20221110_E7.5


title: fibroblasts, day4 deltaDNMT1 rep2

data_processing:
mapped using Bismark
Assembly: ASM229v1
Supplementary files format and content: bigwig files with average methylation for every site covered at least 3x

source_name: immortalised male opossum fibroblast

extract_protocol:
Purelink gDNA kit
BS-seq library prep following the method of Clark et al 2017 Nature Protocols PMID: 28182018, for bulk samples

value: immortalised male opossum fibroblast


title: fibroblasts, day4 deltaDNMT1 rep1


title: emb6_cell29_20221214_E6.5


title: emb6_cell27_20221214_E6.5


title: fibroblasts, day4 control rep3


title: fibroblasts, day4 control rep2


title: GpC_embryo1_epi_C05_20221110_E7.5


title: emb6_cell26_20221214_E6.5


title: emb6_cell25_20221214_E6.5


title: DT_AHR_03

city: Los Angeles

first: youssef

last: errami

state: CA

address: 650 Charles E Young Dr S

department: MIMG

institute: University of California Los Angeles

description: Library name: Sample 12

data_processing:
The Ensembl GRCh38.p14 reference genome was used to map genes, and the RASflow RNA sequencing workflow was used for analysis. Normalized Raw counts were used to generate the gene expression signature by comparing gene expression levels between the control 8505c cells and the AhR-generated knock-out cells group. The heatmap was generated using clustergrammer. Before displaying the heatmap, the raw gene counts were normalized using the logCPM method, filtered by selecting the 2500 genes with the most variable expression, and finally transformed using the Z-score method. The Augmented Gene Set Enrichment Analysis (AGSEA) Appyter was used to perform and visualize standard gene set enrichment analysis (GSEA).  Wikipathways was the chosen gene set library selected. The Transcription Factor Enrichment Analysis Enrichment results were generated by analyzing the up-regulated and down-regulated gene sets using Enrichr. The following libraries were used for the analysis: ARCHS4_TFs_Coexp. Significant results are determined by using a cut-off of p-value<0.1 after applying the Benjamini-Hochberg correction. The same filtered gene of the 2500 most differentiated was used for the transcription factor target over-representation analysis using ChEA3.
Assembly: Human GRCh38
Supplementary files format and content: Gene count contains gene read count for each condition. DESeq2 contains normalized differential expression of AHR vs NTC.

growth_protocol: 8505c was purchased from Millipore-Sigma Cat. No. 94090184 and cultured in EMEM (HBSS) supplemented with 2mM Glutamine + 1% Non-Essential Amino Acids (NEAA) + 10% Fetal Bovine Serum (FBS) + 1% penicillin-streptomycin.

extract_protocol:
The cell pellets were collected by scraping, and the total RNA was isolated using the QIAGEN RNeasy Purification Kit (Cat. No. 74104), following the manufacturer’s instructions.
TruSeq library preparation and paired-end sequencing (2 × 100 bp) on the Illumina NextSeq 2000 instrument (Illumina) were performed at the Genomics Core at the Tulane Center for Aging. Around 100 million total reads were obtained for each sample.

treatment_protocol: Cells were transduced with lentiCas9-Blast (Addgene plasmid # 52962) and pLenti-U6sgbbBsmbI-puro-2A-Fluc (Addgene plasmid # 100277). In NTC the sgRNA cassette was left empty, for AhR sgRNA targeting AhR Fwd: CGTAAGATGGTTAGCTTGTC, the corresponding oligos were synthesized, annealed and cloned into BsmBI linearized pLenti-U6sgbbBsmbI-puro-2A-Fluc lentiviral knockout vector.   Treatment was done for 4 days with Dabrafenib (Cat. No. S2807) and Trametinib (Cat. No. S2673) purchased from Selleck Chemicals, TX, USA.

value: Anaplastic thyroid carcinoma

value: AHR-KO

value: Dabrafenib(10uM)+Trametinib (10nM)

value: day 4


title: emb6_cell24_20221214_E6.5


title: DT_AHR_02

description: Library name: Sample 11


title: emb6_cell23_20221214_E6.5


title: fibroblasts, day4 control rep1


title: DT_AHR_01

description: Library name: Sample 10


title: fibroblasts, NC_1_d8


title: C_AHR_03

description: Library name: Sample 9

value: DMSO

value: day 0


title: emb6_cell22_20221214_E6.5


title: emb6_cell20_20221214_E6.5


title: fibroblasts, NC_1_d4


title: emb6_cell19_20221214_E6.5


title: DT_NTC_03

description: Library name: Sample 6


title: C_AHR_01

description: Library name: Sample 7


title: emb6_cell18_20221214_E6.5


title: GpC_embryo1_troph_A06_20221110_E7.5


title: fibroblasts, day4 deltaDNMT1 rep3


title: DT_NTC_01

description: Library name: Sample 4


title: emb6_cell16_20221214_E6.5


title: emb6_cell17_20221214_E6.5


title: C_NTC_03

description: Library name: Sample 3


title: emb6_cell15_20221214_E6.5


title: C_NTC_02

description: Library name: Sample 2


title: C_NTC_01

description: Library name: Sample 1


title: emb6_cell14_20221214_E6.5


title: Human blastocyst, extracellular vesicles 12

city: Valencia

first: Hortensia

last: Ferrero

state: Valencia

address: Avenida Fernando Abril Martorell 106, Torre A

department: Reproductive Medicine

country: Spain

institute: Instituto de Investigación Sanitaria La Fe / Fundación IVI

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

source_name: Human blastocyst cells

growth_protocol: Day 5 human blastocysts were cultured for 24 hours at 37°C, 6% CO2 and 5% O2.in Blastocyst Medium.

extract_protocol:
Total embryonic RNA was extracted from all 24 blastocysts (12 blastocysts from control-embryos group and 12 blastocysts from EV-embryos group) using a SMART-Seq v4 ultra-low input RNA kit for sequencing (Takara Bio). RNA from each blastocyst was reversed transcribed into cDNA, amplified and purified with the same kit.
cDNA libraries were constructed using the Nextera XT DNA library preparation protocol (Illumina), according to the manufacturer’s protocol.

treatment_protocol: Control-embryos were cultured in Blastocyst Medium (Genea Biomedx), EV-embryos were cultured in Blastocyst Medium in combination with 20 µg/mL of endometrial extracellular vesicles.

value: Human blastocyst cells

value: Endometrial extracellular vesicles


title: emb6_cell12_20221214_E6.5


title: Human blastocyst, extracellular vesicles 11


title: emb6_cell10_20221214_E6.5


title: emb6_cell21_20221214_E6.5


title: Human blastocyst, extracellular vesicles 9


title: Human blastocyst, extracellular vesicles 10


title: emb6_cell8_20221214_E6.5


title: emb6_cell9_20221214_E6.5


title: C_AHR_02

description:
Library name: Sample 8
read2 file not provided for this sample.


title: emb6_cell7_20221214_E6.5


title: Human blastocyst, extracellular vesicles 8


title: GpC_embryo1_troph_A05_20221110_E7.5


title: emb6_cell6_20221214_E6.5


title: Human blastocyst, extracellular vesicles 5


title: DT_NTC_02

description: Library name: Sample 5


title: Human blastocyst, extracellular vesicles 7


title: Human blastocyst, extracellular vesicles 6


title: Human blastocyst, extracellular vesicles 4


title: emb6_cell3_20221214_E6.5


title: emb6_cell2_20221214_E6.5


title: Human blastocyst, extracellular vesicles 2


title: emb6_cell1_20221214_E6.5


title: Human blastocyst, extracellular vesicles 3


title: Human blastocyst, extracellular vesicles 1


title: emb6_cell11_20221214_E6.5


title: Human blastocyst, control 12


title: emb4_cell23_20221214_E6.5


title: Human blastocyst, control 11


title: emb4_cell21_20221214_E6.5


title: Human blastocyst, control 10


title: Human blastocyst, control 8


title: emb4_cell22_20221214_E6.5


title: emb4_cell18_20221214_E6.5


title: Human blastocyst, control 9


title: Human blastocyst, control 7


title: emb4_cell16_20221214_E6.5


title: Human blastocyst, control 6


title: emb6_cell4_20221214_E6.5


title: Human blastocyst, control 5


title: emb4_cell14_20221214_E6.5


title: Human blastocyst, control 4


title: emb4_cell12_20221214_E6.5


title: emb4_cell11_20221214_E6.5


title: emb4_cell8_20221214_E6.5


title: Human blastocyst, control 2


title: emb4_cell24_20221214_E6.5


title: Human blastocyst, control 1


title: emb4_cell25_20221214_E6.5


title: emb4_cell7_20221214_E6.5


title: Zinc3

city: Murcia

first: Carlos

last: Lax

address: Facultad de Biología

department: Genetics and Microbiology

institute: University of Murcia

description: Library name: Zinc3_MKRN240027024-1A_22HH5WLT4_L3_1.fq.gz

data_processing:
Raw paired-end (PE) reads from  R. microsporus RNA-seq datasets were quality-checked using FastQC v0.11.9
Adapters were removed with Trim Galore! V0.6.7
Reads with a Phred quality score (q) ≤ 33 and/or a total length < 20 nt were removed from the analysis
Assembly: Rhizopus microsporus (ATCC 11559) v2 (https://mycocosm.jgi.doe.gov/Rhimi59_2/Rhimi59_2.home.html)
Supplementary files format and content: Spreadsheet including deseq results with log2FC, differential expression statistics and functional annotation for every gene

organism: Rhizopus microsporus

source_name: Mycelium

growth_protocol: ATCC 11559 strain was grown on solid YNBmedia with zinc (ZnSO4) (20mg/L)  and in unsupplemented media during 24 hours at 30ºC

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) and treated with DNase (Sigma, On-Column DNaseI treatment set)
NEBNext® Ultra™ Directional RNA Library Prep Kit

value: Mycelium

value: R. microsporus ATCC 11559

value: with Zinc (20mg/L)


title: emb4_cell5_20221214_E6.5

value: single cell from embryo


title: emb4_cell3_20221214_E6.5


title: Zinc1

description: Library name: Zinc1_MKRN240027022-1A_22HH7WLT4_L6_1.fq.gz


title: emb4_cell2_20221214_E6.5


title: GpC_embryo1_epi_C04_20221110_E7.5


title: YNB2

description: Library name: YNB2_MKRN240027027-1A_22HH7WLT4_L6_1.fq.gz

value: without Zinc (0mg/L)


title: emb4_cell1_20221214_E6.5


title: YNB3

description: Library name: YNB3_MKRN240027028-1A_22HH7WLT4_L6_1.fq.gz


title: YNB1

description: Library name: YNB1_MKRN240027026-1A_22HH7WLT4_L6_1.fq.gz


title: emb2_cell31_20221214_E6.5


title: UM67_0

data_processing:
Raw reads were checked with FastQC
adapters were trimmed using Cutadapt
Trimmed reads were mapped to the R. microsporus v2 reference genome using bwa-mem for medium and long reads with default parameters
Assembly: Rhizopus microsporus v2

extract_protocol:
R. microsporus mycelium was crosslinked with formaldehyde at a final concentration of 1% for 20 minutes in a shaker (80rpm).  For each treatment, we used 20 U of micrococcal nuclease (Thermo Scientific) for 15 minutes at 30 ºC. Digestions were stopped with 100µ of MNase Stop Buffer (80mM EDT and 1.5% SDS). Tubes were centrifuged for 5 minutes at 2700 x g. The supernatant was transferred to a new tube and incubated for 10 min at 95 ºC for reversal crosslinking
Truseq library preration kit was used and 30 ng were used for library preparation


title: Human blastocyst, control 3


title: emb2_cell32_20221214_E6.5


title: UM67_10


title: a1WT_1


title: emb2_cell29_20221214_E6.5


title: emb2_cell27_20221214_E6.5


title: emb2_cell30_20221214_E6.5


title: emb4_cell15_20221214_E6.5


title: emb2_cell28_20221214_E6.5


title: UM67_0_t0


title: Zinc2

description: Library name: Zinc2_MKRN240027023-1A_22HH7WLT4_L6_1.fq.gz


title: p1mCIP_2

data_processing:
Raw reads were checked with FastQC
adapters were trimmed using Cutadapt
Trimmed reads were mapped to the R. microsporus v2 reference genome using bwa-mem for medium and long reads with default parameters
BAM files were sorted and deepTools bamCoverage function127 (bin size = 10, CPM normalization)
Assembly: Rhizopus microsporus ATCC 11559 v2
Supplementary files format and content: bigWig

extract_protocol:
R. microsporus mycelium was crosslinked with formaldehyde at a final concentration of 1% for 20 minutes in a shaker (80rpm). Crosslinking was quenched by adding glycine at a final concentration of 135 mM for 10 minutes. The lysates were sonicated using a Bioruptor Pico sonicator (Diogenode) with 30s ON/OFF pulses for 25 cycles in a thermostated bath (4 ºC).
Truseq library preration kit was used and 30 ng were used for library preparation


title: H3K27_IP_Z


title: H3K27_IP_Y


title: emb2_cell24_20221214_E6.5


title: emb2_cell26_20221214_E6.5


title: emb2_cell25_20221214_E6.5


title: H3K27_IP_WT


title: UM67_20


title: emb2_cell19_20221214_E6.5


title: H3K9InputWT


title: emb2_cell15_20221214_E6.5


title: H3K9_IP_Z


title: emb2_cell14_20221214_E6.5


title: H3K9_IP_Y


title: emb2_cell13_20221214_E6.5


title: H3K9_IP_WT


title: H3K9_b_WT


title: emb2_cell12_20221214_E6.5


title: H3K4InputZ


title: emb2_cell11_20221214_E6.5


title: H3K4InputWT


title: H3K4InputY


title: Konjac,leaf (petiole) , 48H ,rep3

city: 陕西省

first: longfei

last: duan

address: 陕西杨凌示范区西农路22号

institute: 西北农林科技大学

description: Library name: T3_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the amorphophallus albus reference genome using HISAT2 package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: Konjac ，V1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Amorphophallus albus

source_name: leaf (petiole)

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: leaf (petiole)

value: tissue

tag: time point


title: emb2_cell20_20221214_E6.5

value: WT


title: p1mCInput_2


title: Konjac,leaf (petiole) , 48H ,rep2

address: 陕西杨凌示范区西农路22号

description: Library name: T3_2


title: emb2_cell9_20221214_E6.5


title: GpC_embryo1_epi_C03_20221110_E7.5


title: Konjac,leaf (petiole) , 48H ,rep1

address: 陕西杨凌示范区西农路22号

description: Library name: T3_1


title: H3K4_IP_WT


title: emb2_cell10_20221214_E6.5


title: Konjac,leaf (petiole) , 24H ,rep3

address: 陕西杨凌示范区西农路22号

description: Library name: T2_3


title: H3K4_b_Z


title: H3K4_IP_Z


title: Konjac,leaf (petiole) , 24H ,rep2

address: 陕西杨凌示范区西农路22号

description: Library name: T2_2


title: H3K4_IP_Y


title: Konjac,leaf (petiole) , 24H ,rep1

address: 陕西杨凌示范区西农路22号

description: Library name: T2_1


title: H3K4_b_Y


title: Konjac,leaf (petiole) , 12H ,rep2

address: 陕西杨凌示范区西农路22号

description: Library name: T1_2


title: H3K4_b_WT


title: biol rep 2 of Peter Stuyvesant perianth tube at full-anthesis stage

city: Shatin

first: Kwan-Ho

last: WONG

address: The Chinese University of Hong Kong, Ma Liu Shui

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Library name: PS2tA

data_processing:
After removal of adaptor trimming and quality trimming, the qualified sequences were adopted for mRNA de novo assembly using Trinity software. The gene expressions were then quantification into read counts by mapping the reads to a set of reference transcript sequences using RNA-Seq by Expectation Maximization (RSEM), and calculated the relative abundance of unigene based on the alignment of reads against the reference transcript using Bowtie. The read counts were then normalized into Fragments Per Kilobase of transcript sequence per Millions (FPKM) value.
Assembly: Absence of reference genome.
Supplementary files format and content: Excel Binary File Format (XLS) file containing raw read counts for each sample
Supplementary files format and content: Excel Binary File Format (XLS) file containing FPKM values for each sample

organism: Hyacinthus orientalis

source_name: Perianth tube

growth_protocol: The bulbs were imported from the Netherlands (Simple Pleasures Flowerbulbs & Perennials Inc.) in September 2022. They were firstly immersed in tetrachlorophthalonitrile for 1 hour to prevent fungal infection. Air-dried bulbs were stored at 4 °C for three months. The vernalised bulbs were planted on 3rd January 2023, in an outdoor environment outside Li Dak Sum Yip Yio Chin R&D Centre for Chinese Medicine (GPS: 22.419292, 114.210200) with natural sunlight. Perianth were collected during 16th January to 4th February 2023.

extract_protocol:
The collected tissues were immediately immersed in RNAlater™ Stabilization Solution and stored at appropriate conditions before RNA extraction. Total RNA was extracted using Qiagen RNeasy Plant Mini Kit (Qiagen Co., Hilden, Germany) following the instructions of manufacturer. The quality and quantity of extracted RNA were assessed by 1.5% agarose gel electrophoresis and Nanodrop Lite Spectrophotometer (Thermo Fisher Scientific, MA, USA), respectively.
Libraries of mRNA with poly-A enrichment were sequenced on Illumnia NovaSeq X Plus platform, with paired-end sequencing of 150 nucleotides. About 6 Gb data were targeted for each sample.

value: Perianth tube

tag: cultivar

value: Peter Stuyvesant

value: In full anthesis


title: emb2_cell7_20221214_E6.5

tag: tissue


title: H2AZ_IP_Y


title: emb2_cell8_20221214_E6.5


title: H2AZ_IP_WT


title: emb2_cell6_20221214_E6.5


title: Konjac,leaf (petiole) , 12H ,rep3

address: 陕西杨凌示范区西农路22号

description: Library name: T1_3


title: H2AZ_b_Y


title: H2AZ_IP_Z


title: biol rep 3 of Peter Stuyvesant perianth tube at full-anthesis stage

description: Library name: PS3tA


title: biol rep 3 of Peter Stuyvesant outer perianth lobes at full-anthesis stage

description: Library name: PS3oA

source_name: Outer perianth lobes

value: Outer perianth lobes


title: biol rep 1 of Peter Stuyvesant inner perianth lobes at full-anthesis stage

description: Library name: PS1nA

source_name: Inner perianth lobes

value: Inner perianth lobes


title: biol rep 2 of Peter Stuyvesant inner perianth lobes at full-anthesis stage

description: Library name: PS2nA


title: emb2_cell5_20221214_E6.5


title: biol rep 2 of Peter Stuyvesant outer perianth lobes at full-anthesis stage

description: Library name: PS2oA


title: Konjac,leaf (petiole) , 12H ,rep1

address: 陕西杨凌示范区西农路22号

description: Library name: T1_1


title: biol rep 3 of Peter Stuyvesant inner perianth lobes at full-anthesis stage

description: Library name: PS3nA


title: H2AZ_b_Z


title: biol rep 3 of Peter Stuyvesant perianth tube at coloured-bud stage

description: Library name: PS3tC

value: Coloured flower buds


title: emb2_cell4_20221214_E6.5


title: emb2_cell3_20221214_E6.5


title: emb2_cell2_20221214_E6.5


title: Konjac,leaf (petiole) , 0H ,rep2

address: 陕西杨凌示范区西农路22号

description: Library name: CK2


title: Konjac,leaf (petiole) , 0H ,rep3

address: 陕西杨凌示范区西农路22号

description: Library name: CK3


title: GpC_embryo1_epi_C02_20221110_E7.5


title: biol rep 3 of Peter Stuyvesant inner perianth lobes at coloured-bud stage

description: Library name: PS3nC


title: biol rep 1 of Peter Stuyvesant outer perianth lobes at full-anthesis stage

description: Library name: PS1oA


title: emb2_cell16_20221214_E6.5


title: biol rep 1 of Peter Stuyvesant perianth tube at coloured-bud stage

description: Library name: PS1tC


title: biol rep 1 of Peter Stuyvesant perianth tube at full-anthesis stage

description: Library name: PS1tA


title: ChIP_antiGATA_V_IP

city: Hangzhou

first: Shudi

address: Yuhangtang Road No.866

institute: Zhejiang University

description: Library name: ChIP_antiGATA_V_IP

data_processing:
Raw data was cleaned by Trim Galore (Version 0.6.6) with the parameters "-q 25 --phred33 --length 36 -e 0.1 --stringency 5" and maped to silkworm genome using Bowtie 2 (Version 2.4.4). Afterwards, the resulted SAM files were converted into BAM format using SAMtools (Version 1.12), and MACS2 (Version 2.2.7.1) was adopted for peaks calling with the parameters "-p 0.1 -f BAMPE -g 4.6e8".
Assembly: SilkBase November 2016
Supplementary files format and content: tab-delimited narrowPeak files includes narrow peaks for each ChIP-seq sample
Supplementary files format and content: bigWig files indicating binding density for each ChIP-seq sample

organism: Bombyx mori

source_name: BmN cells

extract_protocol:
Cells were collected and cross-linked with 1% formaldehyde for 10 min at 25˚C. The reaction was then quenched by addition of glycine to a final concentration of 125 mM. Afterwards, cells were lysed and chromatin was obtained on ice. Chromatin was sheared to a mean fragment size of 200-500 base pairs. The samples were immunoprecipitated by anti-GATA antibody (Abcam, ab199428).
Sequencing libraries were generated using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) following the instructions.

value: BmN cells


title: emb5_cell27_20221214_E6.5


title: emb5_cell26_20221214_E6.5


title: biol rep 1 of Peter Stuyvesant outer perianth lobes at coloured-bud stage

description: Library name: PS1oC


title: emb2_cell1_20221214_E6.5


title: biol rep 2 of Peter Stuyvesant perianth tube at green-bud stage

description: Library name: PS2tB

value: Green flower buds


title: ChIP_antiGATA_V_input

description: Library name: ChIP_antiGATA_V_input


title: biol rep 1 of Peter Stuyvesant inner perianth lobes at coloured-bud stage

description: Library name: PS1nC


title: biol rep 2 of Peter Stuyvesant perianth tube at coloured-bud stage

description: Library name: PS2tC


title: emb5_cell24_20221214_E6.5


title: biol rep 2 of Peter Stuyvesant inner perianth lobes at coloured-bud stage

description: Library name: PS2nC


title: biol rep 3 of Peter Stuyvesant outer perianth lobes at coloured-bud stage

description: Library name: PS3oC


title: emb5_cell25_20221214_E6.5


title: biol rep 1 of Peter Stuyvesant perianth tube at green-bud stage

description: Library name: PS1tB


title: ChIP_antiGATA_Mock_input

description: Library name: ChIP_antiGATA_Mock_input


title: biol rep 2 of Peter Stuyvesant inner perianth lobes at green-bud stage

description: Library name: PS2nB


title: biol rep 2 of Peter Stuyvesant outer perianth lobes at coloured-bud stage

description: Library name: PS2oC


title: biol rep 3 of Peter Stuyvesant perianth tube at green-bud stage

description: Library name: PS3tB


title: ChIP_antiGATA_Mock_IP

description: Library name: ChIP_antiGATA_Mock_IP


title: biol rep 2 of Peter Stuyvesant outer perianth lobes at green-bud stage

description: Library name: PS2oB


title: emb5_cell22_20221214_E6.5


title: Konjac,leaf (petiole) , 0H ,rep1

address: 陕西杨凌示范区西农路22号

description: Library name: CK1


title: Old-28dpi, replicate 3

first: Guiping

last: Kong

address: 55-96, Du Cane Road

department: Brain Sciences

institute: Imperial College London

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting were made using the Cell Ranger software v7.1.0.
Assembly: GRCm39
Supplementary files format and content: Cell Range output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Spinal cord

extract_protocol:
To prepare the cell suspension for 3’ 10X genomic single cell RNA sequencing, mice were anaesthetized (80 mg of ketamine and 10 mg of xylazine per kilogram of body weight via i.p. injection) and transcardially perfused with 20 ml of oxygenated cold artificial cerebrospinal fluid (CSF) solution (93 mM NMDG, 2.5 mM KCl, 1.2 mM NaH2PO4, 30 mM NaHCO3, 20mM HEPES, 25mM glucose, 5 mM Sodium Ascorbate, 2 mM Thiourea, 0.5 mM CaCl2, and 10 mM MgSO4). 2mm spinal cord including the lesion site or the corresponding location in the naïve spinal cord segment was immediately dissected. After, spinal cord tissues were processed using the Neural Tissue Dissociation Kit (Miltenyi Biotec, 130-092-628) following the manufacturer’s protocol combined with some modifications as described previously (Milich et al., 2021). The dissociated cells were incubated with 20ul of myelin removal beads (Miltenyi Biotec, 130-096-433) to remove myelin debris following the manufacturer’s protocol. After centrifugation, cell pellets were resuspended in 1X PBS (Thermo Fisher Scientific, 14190250) + 0.04%BSA (Jackson Immuno Research, 001-000-162). An aliquot of cells was stained with Acridine Orange/Propidium Iodide dye (AO/PI Cell Viability Kit, Labtech, F23001). Cell concentration and viability were measured using the LUNA-FL Dual Fluorescence Cell Counter (Logos, L20001-LG). Cells were immediately proceeded to the 10X single cell RNA sequencing procedures.
Library was performed according to the manufacturer’s instructions (single cell 3’ V2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with portioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for the subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample dual index were added.

value: Spinal cord

tag: strain


title: emb5_cell28_20221214_E6.5

tag: genotype


title: Old-28dpi, replicate 1

description: 10x Genomics


title: emb5_cell23_20221214_E6.5


title: biol rep 1 of Peter Stuyvesant outer perianth lobes at green-bud stage

description: Library name: PS1oB


title: Old-14dpi, replicate 3

description: 10x Genomics


title: emb5_cell21_20221214_E6.5


title: Old-naïve, replicate 3

description: 10x Genomics

value: naïve


title: biol rep 2 of Delft Blue perianth tube at full-anthesis stage

description: Library name: DB2tA

value: Delft Blue


title: biol rep 3 of Peter Stuyvesant inner perianth lobes at green-bud stage

description: Library name: PS3nB


title: biol rep 1 of Delft Blue perianth tube at full-anthesis stage

description: Library name: DB1tA


title: emb5_cell20_20221214_E6.5


title: Old-naïve, replicate 2

description: 10x Genomics


title: emb5_cell19_20221214_E6.5


title: biol rep 1 of Delft Blue inner perianth lobes at full-anthesis stage

description: Library name: DB1nA


title: biol rep 2 of Delft Blue inner perianth lobes at full-anthesis stage

description: Library name: DB2nA


title: Old-naïve, replicate 1

description: 10x Genomics


title: emb5_cell18_20221214_E6.5


title: biol rep 1 of Peter Stuyvesant inner perianth lobes at green-bud stage

description: Library name: PS1nB


title: biol rep 3 of Peter Stuyvesant outer perianth lobes at green-bud stage

description: Library name: PS3oB


title: biol rep 3 of Delft Blue outer perianth lobes at full-anthesis stage

description: Library name: DB3oA


title: Old-28dpi, replicate 2

description: 10x Genomics


title: Young-28dpi, replicate 3

description: 10x Genomics


title: biol rep 2 of Delft Blue outer perianth lobes at full-anthesis stage

description: Library name: DB2oA


title: biol rep 3 of Delft Blue perianth tube at coloured-bud stage

description: Library name: DB3tC


title: Young-28dpi, replicate 2

description: 10x Genomics


title: biol rep 1 of Delft Blue outer perianth lobes at full-anthesis stage

description: Library name: DB1oA


title: emb5_cell17_20221214_E6.5


title: biol rep 2 of Delft Blue perianth tube at coloured-bud stage

description: Library name: DB2tC


title: GpC_embryo1_epi_C01_20221110_E7.5


title: biol rep 1 of Delft Blue perianth tube at coloured-bud stage

description: Library name: DB1tC


title: biol rep 3 of Delft Blue inner perianth lobes at coloured-bud stage

description: Library name: DB3nC


title: emb5_cell16_20221214_E6.5


title: Young-28dpi, replicate 1

description: 10x Genomics


title: biol rep 3 of Delft Blue perianth tube at full-anthesis stage

description: Library name: DB3tA


title: Young-14dpi, replicate 3

description: 10x Genomics


title: emb5_cell15_20221214_E6.5


title: biol rep 2 of Delft Blue inner perianth lobes at coloured-bud stage

description: Library name: DB2nC


title: biol rep 3 of Delft Blue inner perianth lobes at full-anthesis stage

description: Library name: DB3nA


title: biol rep 1 of Delft Blue inner perianth lobes at coloured-bud stage

description: Library name: DB1nC


title: biol rep 3 of Delft Blue outer perianth lobes at coloured-bud stage

description: Library name: DB3oC


title: emb5_cell14_20221214_E6.5


title: Young-14dpi, replicate 2

description: 10x Genomics


title: Young-14dpi, replicate 1

description: 10x Genomics


title: Young-naïve, replicate 3

description: 10x Genomics

value: Young-naïve


title: biol rep 2 of Delft Blue outer perianth lobes at coloured-bud stage

description: Library name: DB2oC


title: emb5_cell13_20221214_E6.5

value: single cell from embryo


title: biol rep 2 of Delft Blue perianth tube at green-bud stage

description: Library name: DB2tB


title: biol rep 1 of Delft Blue outer perianth lobes at coloured-bud stage

description: Library name: DB1oC


title: emb5_cell12_20221214_E6.5


title: biol rep 3 of Delft Blue perianth tube at green-bud stage

description: Library name: DB3tB


title: emb5_cell11_20221214_E6.5


title: biol rep 1 of Delft Blue perianth tube at green-bud stage

description: Library name: DB1tB


title: biol rep 2 of Delft Blue outer perianth lobes at green-bud stage

description: Library name: DB2oB


title: emb5_cell9_20221214_E6.5


title: Young-naïve, replicate 1

description: 10x Genomics


title: biol rep 1 of Delft Blue outer perianth lobes at green-bud stage

description: Library name: DB1oB


title: Young-naïve, replicate 2

description: 10x Genomics


title: biol rep 3 of Delft Blue inner perianth lobes at green-bud stage

description: Library name: DB3nB


title: Young-28dpi_TCR, replicate 4

description: TCR (5' mRNA)  library, 10X Genomic

data_processing:
The demultiplexing, barcode processing, 5’ gene counting, and V(D)J transcript sequence assembly were made using the Cell Ranger software v7.1.0.
Assembly: mm10
Supplementary files format and content: Cell Range output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig_annotations.csv
Library strategy: scTCR-seq

extract_protocol:
To prepare the cell suspension for 5’ 10X genomic single cell RNA sequencing, mice were anaesthetized (80 mg of ketamine and 10 mg of xylazine per kilogram of body weight via i.p. injection) and transcardially perfused with 20 ml of cold 1XPBS (Thermo Fisher Scientific, 14287080). 4mm spinal cord including the lesion site or the corresponding location in the naive spinal cord segment was immediately dissected. After, spinal cord tissues were processed using the Multi Tissue Dissociation Kit 1 (Miltenyi Biotec, 130-110-201) following the manufacturer’s protocol. The dissociated cells were incubated with 40ul of myelin removal beads (Miltenyi Biotec, 130-096-433) to remove myelin debris following the manufacturer’s protocol. After centrifugation of the final step in the myelin removal procedures, cell pellets were resuspended in 50ul 1X MojoSort Buffer (Biolegend, 480017) and 0.5ul of TruStain FcX PLUS anti-mouse CD16/32 antibody (Biolegend, 156604) was added to the cell suspension to block Fc receptors for 10 min on ice. Antibody cocktails were prepared in 50ul Brilliant Stain Buffer (Thermo Fisher Scientific, 00-4409-42). Antibodies used for sorting were: APC anti-CD45 (30-F11, 2 µg/ml, 103111, Biolegend), Brilliant Violet 711 anti-CD8a (53-6.7, 2 µg/ml, 100759, Biolegend), Brilliant Violet 605 anti-CD4 (RM4-5, 2 µg/ml, 100547, Biolegend), FITC anti-TCR β (H57-597, 5 µg/ml, 109205, Biolegend) and LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit (Thermo Fisher Scientific, L34966, 1:1000). Cells were stained with the antibody cocktails in the dark at 4°C for 20 min followed by two times washing with 1X MojoSort Buffer. Cell sorting was conducted using BD FACSAria III flow cytometer. After FACS, cells were washed twice with 1XPBS+0.04%BSA and immediately proceeded to the 10X TCR single cell RNA sequencing procedures.
Library was performed according to the manufacturer’s instructions (single cell 5’ V2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with portioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, and amplified by PCR for the subsequent V(D)J library and 5ʹ gene expression (GEX) library construction. For the V(D)J library construction, full-length V(D)J segments were amplified via PCR from the full-length cDNA using primers specific to the TCR. The appropriated sized V(D)J fragments were selected with SPRIselect reagent and used for the library construction. Full length of amplified and purified cDNA was used for the 5ʹ gene expression (GEX) library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample dual index were added.

tag: cell type

value: CD8+ and CD4+ T cells

tag: age

value: 20-24 months old


title: emb5_cell8_20221214_E6.5


title: Young-28dpi_GEX, replicate 4

description: GEX (5' mRNA) library, 10X Genomic

data_processing:
The demultiplexing, barcode processing, 5’ gene counting, and V(D)J transcript sequence assembly were made using the Cell Ranger software v7.1.0.
Assembly: mm10
Supplementary files format and content: Cell Range output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig_annotations.csv


title: biol rep 2 of China Pink perianth tube at full-anthesis stage

description: Library name: CP2tA

value: China Pink


title: biol rep 3 of China Pink inner perianth lobes at full-anthesis stage

description: Library name: CP3nA


title: Young-28dpi_GEX, replicate 3

description: GEX (5' mRNA) library, 10X Genomic


title: biol rep 3 of China Pink perianth tube at full-anthesis stage

description: Library name: CP3tA


title: emb5_cell7_20221214_E6.5

value: WT


title: Young-28dpi_TCR, replicate 3

description: TCR (5' mRNA)  library, 10X Genomic


title: biol rep 2 of China Pink inner perianth lobes at full-anthesis stage

description: Library name: CP2nA


title: biol rep 2 of Delft Blue inner perianth lobes at green-bud stage

description: Library name: DB2nB


title: biol rep 1 of China Pink perianth tube at full-anthesis stage

description: Library name: CP1tA

value: Perianth tube


title: biol rep 3 of China Pink outer perianth lobes at full-anthesis stage

description: Library name: CP3oA


title: biol rep 1 of Delft Blue inner perianth lobes at green-bud stage

description: Library name: DB1nB


title: biol rep 1 of China Pink outer perianth lobes at full-anthesis stage

description: Library name: CP1oA


title: biol rep 2 of China Pink outer perianth lobes at full-anthesis stage

description: Library name: CP2oA


title: GpC_embryo1_troph_A02_20221110_E7.5


title: biol rep 1 of China Pink inner perianth lobes at full-anthesis stage

description: Library name: CP1nA


title: biol rep 3 of China Pink perianth tube at coloured-bud stage

description: Library name: CP3tC


title: biol rep 2 of China Pink perianth tube at coloured-bud stage

description: Library name: CP2tC


title: biol rep 1 of China Pink perianth tube at coloured-bud stage

description: Library name: CP1tC


title: Young-28dpi_TCR, replicate 2

description: TCR (5' mRNA)  library, 10X Genomic


title: Young-28dpi_GEX, replicate 1

description: GEX (5' mRNA) library, 10X Genomic


title: GpC_embryo1_troph_A03_20221110_E7.5


title: LEE63A21

description: offspring of SAMN26894108 and SAMN26894109

data_processing:
Read trimming was performed with TrimGalore v0.6.0 using these parameters: --paired --clip_R1 10 --clip_R2 10
Mapping was performed with HISAT2 v2.1.0 using these parameters: --no-softclip --no-mixed --no-discordant
Postprocessing was performed with SAMtools v1.4
SNP splitting was performed with SNPsplit v0.3.4 using these parameters: --paired -–conflicting
Differential gene expression analysis was performed in R v3.4.3 using the Rsubread v1.28.1 and DESeq2 v1.18.1 packages
Assembly: MonDom5

source_name: Brain

extract_protocol:
Ambion RNAqueous Micro Kit (#AM1931, ThermoFisher)
SMART-Seq v4 Ultra Low Input RNA Kit (#634894, Takara); Nextera XT DNA Library Preparation Kit (FC-131-1096, Illumina)

value: Brain

tag: stock

tag: Sex

value: Female


title: biol rep 3 of Delft Blue outer perianth lobes at green-bud stage

description: Library name: DB3oB

value: Outer perianth lobes


title: Young-28dpi_GEX, replicate 2

description: GEX (5' mRNA) library, 10X Genomic

tag: treatment


title: LEE63A17

source_name: Liver

value: Liver

value: Male


title: Young-28dpi_TCR, replicate 1

description: TCR (5' mRNA)  library, 10X Genomic


title: biol rep 1 of China Pink inner perianth lobes at coloured-bud stage

description: Library name: CP1nC

value: Inner perianth lobes

value: Coloured flower buds


title: LEE63A18

source_name: Spleen

value: Spleen


title: biol rep 2 of China Pink inner perianth lobes at coloured-bud stage

description: Library name: CP2nC


title: LEE63A16


title: Old-28dpi_GEX,  replicate 4

description: GEX (5' mRNA) library, 10X Genomic

value: Spinal cord


title: biol rep 3 of China Pink perianth tube at green-bud stage

description: Library name: CP3tB

value: Green flower buds


title: Old-28dpi_TCR, replicate 4

description: TCR (5' mRNA)  library, 10X Genomic


title: LEE63A15


title: Old-28dpi_GEX, replicate 3

description: GEX (5' mRNA) library, 10X Genomic


title: biol rep 3 of China Pink outer perianth lobes at coloured-bud stage

description: Library name: CP3oC


title: biol rep 1 of China Pink perianth tube at green-bud stage

description: Library name: CP1tB


title: LEE63A12


title: LEE63A14


title: biol rep 2 of China Pink outer perianth lobes at coloured-bud stage

description: Library name: CP2oC


title: biol rep 1 of China Pink outer perianth lobes at coloured-bud stage

description: Library name: CP1oC


title: biol rep 2 of China Pink inner perianth lobes at green-bud stage

description: Library name: CP2nB


title: LEE63A13


title: Old-28dpi_TCR, replicate 3

description: TCR (5' mRNA)  library, 10X Genomic


title: LEE63A10


title: biol rep 3 of China Pink outer perianth lobes at green-bud stage

description: Library name: CP3oB


title: Old-28dpi_TCR, replicate 1

description: TCR (5' mRNA)  library, 10X Genomic


title: biol rep 1 of China Pink inner perianth lobes at green-bud stage

description: Library name: CP1nB


title: biol rep 3 of City of Haarlem perianth tube at full-anthesis stage

description: Library name: CH3tA

value: City of Haarlem

value: In full anthesis


title: biol rep 2 of China Pink perianth tube at green-bud stage

description: Library name: CP2tB


title: biol rep 1 of City of Haarlem perianth tube at full-anthesis stage

description: Library name: CH1tA


title: biol rep 3 of China Pink inner perianth lobes at coloured-bud stage

description: Library name: CP3nC


title: Old-naive_TCR, replicate 4

description: TCR (5' mRNA)  library, 10X Genomic

value: CD8+ and CD4+ T cells

value: Naive


title: biol rep 3 of China Pink inner perianth lobes at green-bud stage

description: Library name: CP3nB

value: China Pink


title: Old-28dpi_TCR, replicate 2

description: TCR (5' mRNA)  library, 10X Genomic

value: 20-24 months old


title: LEE63A11

value: WT


title: Old-28dpi_GEX, replicate 2

description: GEX (5' mRNA) library, 10X Genomic


title: Old-naive_GEX, replicate 4

description: GEX (5' mRNA) library, 10X Genomic


title: biol rep 1 of China Pink outer perianth lobes at green-bud stage

description: Library name: CP1oB


title: biol rep 3 of City of Haarlem outer perianth lobes at full-anthesis stage

description: Library name: CH3oA


title: biol rep 2 of China Pink outer perianth lobes at green-bud stage

description: Library name: CP2oB


title: biol rep 2 of City of Haarlem outer perianth lobes at full-anthesis stage

description: Library name: CH2oA


title: biol rep 1 of City of Haarlem outer perianth lobes at full-anthesis stage

description: Library name: CH1oA


title: LEE63A9


title: LEE63A5


title: Old-naive_GEX, replicate 3

description: GEX (5' mRNA) library, 10X Genomic


title: Old-28dpi_GEX, replicate 1

description: GEX (5' mRNA) library, 10X Genomic


title: biol rep 2 of City of Haarlem perianth tube at full-anthesis stage

description: Library name: CH2tA

value: Perianth tube


title: LEE63A4

value: Brain

value: Female


title: LEE63A8

value: Liver


title: Old-naive_TCR, replicate 2

description: TCR (5' mRNA)  library, 10X Genomic


title: biol rep 1 of City of Haarlem inner perianth lobes at full-anthesis stage

description: Library name: CH1nA


title: LEE63A7


title: LEE63A6


title: biol rep 3 of City of Haarlem inner perianth lobes at full-anthesis stage

description: Library name: CH3nA


title: LEE63A3


title: biol rep 2 of City of Haarlem inner perianth lobes at full-anthesis stage

description: Library name: CH2nA


title: Old-naive_TCR, replicate 3

description: TCR (5' mRNA)  library, 10X Genomic


title: biol rep 3 of City of Haarlem inner perianth lobes at coloured-bud stage

description: Library name: CH3nC


title: biol rep 3 of City of Haarlem perianth tube at coloured-bud stage

description: Library name: CH3tC


title: biol rep 2 of City of Haarlem inner perianth lobes at coloured-bud stage

description: Library name: CH2nC


title: biol rep 3 of City of Haarlem outer perianth lobes at coloured-bud stage

description: Library name: CH3oC

value: Outer perianth lobes


title: LEE63A2


title: Old-naive_TCR, replicate 1

description: TCR (5' mRNA)  library, 10X Genomic


title: biol rep 1 of City of Haarlem perianth tube at coloured-bud stage

description: Library name: CH1tC


title: LEE63A1


title: biol rep 2 of City of Haarlem perianth tube at coloured-bud stage

description: Library name: CH2tC


title: biol rep 2 of City of Haarlem outer perianth lobes at coloured-bud stage

description: Library name: CH2oC


title: Old-naive_GEX, replicate 1

description: GEX (5' mRNA) library, 10X Genomic


title: LEE62A18

data_processing:
Read trimming was performed with TrimGalore v0.6.0 using these parameters: --clip_R1 6 --3_prime_clip_R1 6
Mapping was performed with Bismark v0.18.0 using these parameters: --non_directional --un --ambiguous
SNP splitting was performed with SNPsplit v0.3.4 using these parameters: --bisulfite –conflicting
Methylation analysis was performed with R v3.4.3 using the methylKit v1.4.1 package
Plotting was performed with R v3.4.3 using the ggplot2 v3.2.0 and Gviz v1.22.3 packages
Assembly: MonDom5

extract_protocol:
PureLink Genomic DNA Mini kit
EZ Methylation Kit (#D5020, Zymo)
post-bisulfite adapter tagging style whole-genome bisulfite sequencing libraries Clark et al 2017 Nature Protocols

value: Male


title: biol rep 3 of City of Haarlem perianth tube at green-bud stage

description: Library name: CH3tB