title: 24hpf_TrunkNC_3

city: Berkeley

first: Megan

last: Martik

state: California

address: 163 Weill Hall

department: Molecular and Cell Biology

institute: University of California Berkeley

description:
Library name: Sample 9
19733

data_processing:
Reads were mapped zebrafish genome GRCz10 using Bowtie 2.
Transcript counts were determined using featureCounts (Subread).
Differential gene expression was performed using DEseq.
Assembly: GRCz10
Supplementary files format and content: tab delimited text file included for cardiac neural crest and non-neural crest samples

source_name: trunk NC tissue from somite 7 to somite 16

extract_protocol:
mch+ CdNC cells and mch- non-neural crest cells from 16 somite-stage Tg(-4.9sox10:GAL4-UAS-cre;UAS:NfsB-mCherry;myl7:nucGFP) embryos were dissected, dissociated and FAC-sorted. GFP+ cells were sorted from 24hpf Tg(-4.9sox10:eGFP) embryos were dissected, dissociated, and FAC-sorted.
Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART-Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory (California Institute of Technology, Pasadena, CA) for 50 million, single-ended reads.

value: migratory trunk neural crest

tag: transgenic line

tag: age

tag: fluorophore

value: GFP+


title: LCLs, WT_ESGO, ZBTB24

status: Public on Jan 30 2025

type: SRA

city: Paris

first: Guillaume

last: Velasco

address: 35 rue Hélène Brion

department: UMR7216 Epigenetics and Cell Fate

country: France

institute: Université Paris Cité

library_source: genomic

data_processing:
Sequencing was done using a NextSeq 500 instrument (Illumina) in paired-end mode (2x75 cycles). After sequencing, a primary analysis based on AOZAN software  was applied to demultiplex and control the quality of the raw data (based on bcl2fastq v2.20 and FastQC modules / v0.11.5).
Quality of raw data has been evaluated with FastQC. Poor quality sequences have been trimmed or removed with Trimmomatic software.
ChIP-seq reads were mapped to the reference genomes (mm10/hg38) using Bowtie2 v2.3.4.3 with the option -k 2. Then, peaks were called with Macs2 v2.2.4  using the input as control, an FDR of 0.01 and keeping all the duplicates. Peaks from multiple replicates were combined by taking regions covered by at least 2 replicates.
Peak annotation was performed with ChiPseeker v1.18.0  and Bedtools intersect v2.28.0 was used to annotate peaks with repeated elements obtained on the repeatmasker website, enhancers obtained on FANTOM5 and genome segmentation from ENCODE data.
Assembly: mm10 or hg38
Supplementary files format and content: bigWig files for visualization of ChIP-seq tracks

molecule: genomic DNA

organism: Homo sapiens

source_name: LCLs

growth_protocol: mESCs  were maintained in the absence of feeder cells, on plates coated with 1x Laminin in serum-free 2i medium containing  Dulbecco’s modified Eagle’s medium (DMEM) F12 Glutamax supplemented with  50% Neurobasal medium , N2 and B27 Supplements, penicillin/streptomycin, non-essential amino acids, 2-mercaptoethanol, CHIR99201, PD032552 inhibitors and Leukemia Inhibitory Factor. Cells were passaged every two days and maintained at 37°C with 8% CO2 in a humidified chamber. Human Lymphoblastoid Cell Lines (LCLs) from healthy donors and ICF2 patients were cultured in RPMI 1640 supplemented with 15% FCS and antibiotics.

extract_protocol:
Mouse ESCs and LCLs were crosslinked with 1% formaldehyde for 10min at room temperature (RT) and the reaction was quenched by adding glycine at a final concentration of 0.125M for 5min at RT. Fixed cells were washed and adherent cells were harvested with phosphate-buffered saline (PBS). Cell nuclei were isolated using a cell lysis buffer (5mM Pipes pH8.0, 85mM KCl, 0.5% NP40, Complete protease inhibitor cocktail) for 20min, at 4°C. Nuclei were then pelleted by centrifugation and lysed in a nuclei lysis buffer (50mM Tris HCl pH8.1, 150mM NaCl, 10mM EDTA, 1% SDS, Complete protease inhibitor cocktail) for 20min, 4°C. Chromatin was subjected to sonication with a Bioruptor (Diagenode) yielding genomic DNA fragments with a bulk size of 150- 300 bp.
ChIP-seq libraries were prepared using the MicroPlex Library Preparation Kit v2 (Diagenode) according to the manufacturer’s protocol. After adapters ligation, fragments were amplified with Illumina primers for 10 cycles. Libraries were purified using AMPure XP beads protocol (Beckman Coulter) and quantified using the Qubit fluorometer (Thermo Fisher Scientific). Libraries’ size distribution was assessed using the Bioanalyzer High Sensitivity DNA chip (Agilent Technologies). Libraries were normalized and pooled at 2nM and spike-in PhiX Control v3 (Illumina) was added.

treatment_protocol: For in vitro differentiation, mESCs were grown in bacteriological Petri dish with differentiation medium containing 25% Advanced DMEM, 25% DMEM/F12 GlutaMAX, 50% Neurobasal medium, penicilline/streptavidin, β-mercatoethanol and 11% of knock out serum, at 37°C with 5% CO2. The differentiation medium was changed every day and embryoid bodies were collected by centrifugation and resuspended in fresh medium.

tag: cell line

value: LCLs

tag: cell type

value: lymphobalstoid cells

tag: genotype

value: WT

tag: treatment

tag: Sex

value: Female

tag: chip antibody

value: ZBTB24 (MBL life science, #PM086)


title: PBMCs, scRNA-seq, sublibrary 1

city: Stanford

first: Leslie

last: Chan

state: CA

address: 300 Pasteur Dr Bldg S131, Grant

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
ParseBiosciences-Pipeline.1.0.3p was used to identify barcodes, align sequencing reads, assign transcript counts to genes, and generate a cell-by-gene count matrix
After running each sublibrary through the pipeline, the outputs of each sublibrary were combined into a single dataset
Assembly: Custom genome containing the human genome (HG38) and the annotated Wuhan-Hu-1 SARS-CoV-2 reference sequence (NC_045512.2)
Supplementary files format and content: .mtx file containing expression matrix

molecule: polyA RNA

source_name: Peripheral blood

extract_protocol:
PBMCs were fixed using Parse fixation reagents, frozen at -80°C for less than 6 months, and prepped according to Parse Evercode WT Mega v2 protocol. In this combinatorial split pool barcoding process, samples were first loaded into a 96-well plate and underwent reverse transcription with barcoded primers, pooled, split and barcoded again, followed by cell lysis using Parse reagents.
According to Parse Evercode WT Mega v2 protocol. First, cDNA was amplified, then underwent fragmentation, adaptor ligation, sublibrary index PCR, and double-sided size selection. Sequencing was performed on a NovaSeq S4 instrument (Illumina; Chan Zuckerberg Biohub). The read structure was paired-end with i7 index, i5 index, and the 4th barcode (6bp) that tags each sublibrary acting as a standard Illumina index.

tag: tissue

value: Peripheral blood

value: Cryopreserved PBMCs

tag: participant group

value: Pooled PBMCs


title: Germinating basidiospores, 0h, replica 1

city: Szeged

first: Botond

last: Hegedüs

state: Csongrád-Csanád

address: Temesvári krt. 62

department: Institute of Biochemistry

country: Hungary

institute: Biological Research Center

description:
Library name: BS_0h_1
QuantSeq 3′ mRNA-Seq library

data_processing:
The raw reads were trimmed using the BBduk.sh script from BBtools 38.92 and then mapped to the reference genome using STAR version 2.6.1a_08-27. The trimming and mapping parameters were set according to the manufacturer’s recommendations (https://www.lexogen.com/quantseq-data-analysis/).
The number of reads overlapping the transcript annotations was determined using the featureCounts function of the Rsubread package version 2.6.4
Assembly: CopciAB_V2_genome.fasta
Supplementary files format and content: Genome sequence of the Corinopsis cinerea AmutBmut V2 strain used for read alignment (CopciAB_V2_genome.fasta).
Supplementary files format and content: GTF-formatted annotation file of the Coprinopsis cinerea AmutBmut V2 strain, which was used to determine the read count values (CopciAB_V2_annotation.gtf).
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample (CopciAB_V2_rawCounts.tsv)
Supplementary files format and content: Text file includes detailed description of the growth conditions (growth_protocol.pdf).

organism: Coprinopsis cinerea AmutBmut pab1-1

source_name: Basidiospore

growth_protocol: A detailed description of the growth conditions can be found in the document growth_protocol.pdf

extract_protocol:
RNA was extracted using Quick-RNA Miniprep kit (Zymo Research, USA, catalog number: R1054), following the manufacturer’s instructions.
The libraries were generated using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna). To begin, 100 ng of total RNA was used as input for first strand cDNA generation with an oligo-dT primer, followed by RNA removal. Next, second strand synthesis was initiated with random priming and the resulting products were purified with magnetic beads. Finally, the libraries were amplified and barcoded using PCR. The Agilent 4200 TapeStation (Agilent) was used to assess all libraries for the formation of adapter dimers during PCR. The QuantSeq libraries were sequenced on the Illumina NextSeq550 platform, producing 75 bp single-end reads.

value: Basidiospore


title: 24hpf_TrunkNC_2

description:
Library name: Sample 8
19731

molecule: total RNA

organism: Danio rerio

value: trunk NC tissue from somite 7 to somite 16


title: LCLs, WT_2592, ZBTB24


title: Germinating Oidia, 18h, replica 3

description:
Library name: OIDIA_18h_3
QuantSeq 3′ mRNA-Seq library

source_name: Oidia

value: Oidia


title: 24hpf_TrunkNC_1

description:
Library name: Sample 7
19729


title: Myometrium_4, snRNAseq

city: Newcastle Upon Tyne

first: Michael

last: Taggart

state: Tyne And Wear

address: International Centre for Life,

department: Biosciences Institute,

country: United Kingdom

institute: Newcastle University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Illumina BCL files were ran through 10X Cell Ranger software v7.01 to generate Fastq files and count matrices.
Assembly: GRCh38
Supplementary files format and content: 10x hdf file contains filtered count matrix

molecule: nuclear RNA

source_name: utero-placental tissue

extract_protocol:
Single-nuclei RNA sequencing (snRNA-seq) was performed on the three matched tissue types from four healthy pregnant women. 1-5 mg samples were processed using the 10X Genomics Chromium Nuclei isolation Kit (PN-1000494, 10X Genomics, UK). Tissue chunks were cut to 1 mm cubes on dry ice. Samples were transferred to dissociation tubes in 200ul lysis buffer and homogenized using the pestles with 30 strokes. Further 300ul lysis buffer was added and samples homogenized with 20 further strokes. Samples were incubated at 4oC for 15 minutes. Nuclei were isolated and purified following the manufacturer’s instructions with minimal alterations. To avoid loss of nuclei, centrifugation times were extended to 15 minutes and only one wash was performed in resuspension buffer. For the final step, pellets were resuspended in approximately 50ul resuspension buffer.For nuclei counts, 10ul isolated nuclei were mixed with 10ul VitaStain AOPI Staining Solution (CS2-0106-5ml, Nexcelom) and counted using a Countess™ II FL automated cell counter (AMQAF1000, ThermoFisher Scientific, UK). For each samples, two full fields of view were imaged using brightfield, GFP and RFP wavelengths. Isolated nuclei were manually counted using Fiji Cell counter application (Schindelin et al 2012).
The freshly prepared nuclei were further processed to sequencing libraries using 10X Genomics Chromium Next GEM Single Cell 3′ Kit v3.1 (PN-1000268, 10X Genomics, UK) following the manufacturer’s protocol (CG000315 revC). Libraries were analysed using TapeStation HSD5000 (Agilent Technologies).
sn-RNA sequencing

value: myometrial strips


title: Myometrium_3, snRNAseq

description: 10x Genomics


title: Germinating Oidia, 18h, replica 2

description:
Library name: OIDIA_18h_2
QuantSeq 3′ mRNA-Seq library


title: 17hpf_Positive_CNC_3

description:
Library name: Sample 6
22028

source_name: cardiac neural crest from midbrain-hindbrain boundary to somite 6

value: migratory cardiac neural crest

value: 16 somite stage (17hpf)

value: mcherry +


title: Myometrium_2, snRNAseq

description: 10x Genomics


title: LCLs, WT_2591, ZBTB24

value: Male


title: Germinating Oidia, 18h, replica 1

description:
Library name: OIDIA_18h_1
QuantSeq 3′ mRNA-Seq library


title: PBMCs, scRNA-seq, sublibrary 2


title: Germinating Oidia, 0h, replica 3

description:
Library name: OIDIA_0h_3
QuantSeq 3′ mRNA-Seq library


title: LCL_ESGO [RNA-Seq]

data_processing:
Paired end (2 × 75) sequencing was performed on an Illumina NextSeq 500 platform, demultiplexing and quality control were performed with the AOZAN software (based on bcl2fastq v2.20 and FastQC modules / v0.11.5).
The quality of raw data has been evaluated with FastQC. Poor quality sequences have been trimmed or removed with Trimmomatic software. Star v2.5.3a has been used to align reads on reference genome (mm10/hg38) using standard options.
Quantification of gene and isoform abundances has been done with rsem 1.2.28, prior to normalisation on library size with DESEq2 bioconductor R package. Finally, differential analysis has been conducted with edgeR bioconductor R package.
Assembly: mm10 or hg38
Supplementary files format and content: bigWig files for visualization of RNA-seq tracks

growth_protocol: mESCs  were maintained in the absence of feeder cells, on plates coated with 1x Laminin in serum-free 2i medium containing  Dulbecco’s modified Eagle’s medium (DMEM) F12 Glutamax supplemented with  50% Neurobasal medium , N2 and B27 Supplements, penicillin/streptomycin, non-essential amino acids, 2-mercaptoethanol, CHIR99201, PD032552 inhibitors and Leukemia Inhibitory Factor. Cells were passaged every two days and maintained at 37ºC with 8% CO2 in a humidified chamber. Human Lymphoblastoid Cell Lines (LCLs) from healthy donors and ICF2 patients were cultured in RPMI 1640 supplemented with 15% FCS and antibiotics.

extract_protocol:
Total RNAs from cell lines were isolated using TRI Reagent according to manufacturer’s instructions. Contaminant genomic DNA was eliminated with TURBO DNA-free Kit . RNA quality was verified using the Bioanalyzer RNA 6000 Nano kit.
The libraries were prepared following the TruSeq Stranded Total RNA protocol from Illumina, starting from 1 µg of high-quality total RNA (RIN > 7)

treatment_protocol: For in vitro differentiation, mESCs were grown in bacteriological Petri dish with differentiation medium containing 25% Advanced DMEM, 25% DMEM/F12 GlutaMAX, 50% Neurobasal medium, penicilline/streptavidin, β-mercatoethanol and 11% of knock out serum, at 37ºC with 5% CO2. The differentiation medium was changed every day and embryoid bodies were collected by centrifugation and resuspended in fresh medium.


title: LCLs, WT_ESGO, IgG

value: IgG (MBL life science, # PM067)


title: 17hpf_Positive_CNC_1

description:
Library name: Sample 4
21309

value: cardiac neural crest from midbrain-hindbrain boundary to somite 6


title: 17hpf_Negative_CNC_3

description:
Library name: Sample 3
22029

source_name: non neural crest from midbrain-hindbrain boundary to somite 6

value: non-neural crest

value: mcherry -


title: LCLs, WT_2591, IgG

value: LCLs

value: lymphobalstoid cells

value: WT


title: Myometrial_Arteries_4, snRNAseq

description: 10x Genomics

value: myometrial arteries


title: Myometrial_Arteries_3, snRNAseq

description: 10x Genomics


title: Germinating Oidia, 0h, replica 1

description:
Library name: OIDIA_0h_1
QuantSeq 3′ mRNA-Seq library


title: Germinating Oidia, 0h, replica 2

description:
Library name: OIDIA_0h_2
QuantSeq 3′ mRNA-Seq library


title: 17hpf_Negative_CNC_2

description:
Library name: Sample 2
21339

value: non neural crest from midbrain-hindbrain boundary to somite 6


title: LCLs, WT_ESGO, input_IgG

value: Female


title: Myometrial_Arteries_2, snRNAseq

description: 10x Genomics


title: MC3T3 cells were treated with HUVEC-derived exosomes  48 hours,Biology Repeat #3

city: Guangzhou

first: Zhilong

last: Pi

address: 111 Liuhua Road

country: China

institute: General Hospital of Southern Theater Command of PLA

description: Library name: Exo3

data_processing:
RNA Extraction
mRNA Enrichment
Fragmentation of mRNA
Reverse Transcription to Generate cDNA
CLC Genomics Workbench v11.0.1
Assembly: Mus_musculus_Ensembl_104(http://may2021.archive.ensembl.org/Mus_musculus/Info/Index)
Supplementary files format and content: Deg_genes_fpkm_of_all_samples.xlsx

organism: Mus musculus

source_name: bone

growth_protocol: MC3T3 cells were maintained in MEM-α supplemented with 10%6fetal bovne serum (FBS) and antibiotics in humidifed atmosphere with 5% CO2 at 37 ℃

extract_protocol:
RNA was harvested using trizol. 1.3 µg of total RNA was used to construct the sequencing library.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols.

treatment_protocol: MC3T3 cells were treated with HUVEC-derived exosomes for 48 hours. The control group was untreated. Three replicates per group.

value: bone

value: stem cells

value: HUVEC-derived exosomes


title: 17hpf_Negative_CNC_1

description:
Library name: Sample 1
21310


title: LCLs, WT_2592, input_IgG


title: Myometrial_Arteries_1, snRNAseq

description: 10x Genomics


title: 16ss_Neg_2_ATAC

description:
Library name: Sample 4
ATACseq

data_processing:
Reads were trimmed and mapped to GRCz11 using Bowtie2.
Samtools was used to downsample each replictate to ~95 million reads.
PCR and mitochondrial reads were filtered out and peaks were called with Genrich.
Differential accessibility between samples was determined using Diffbind.
Assembly: GRCz11
Supplementary files format and content: bam files and bigwig files for each replicate.

extract_protocol:
mch+ CdNC cells and mch- non-neural crest cells from 16 somite-stage Tg(-4.9sox10:GAL4-UAS-cre;UAS:NfsB-mCherry;myl7:nucGFP) embryos were dissected, dissociated and FAC-sorted.
Cells were lysed with a cold lysis buffer, regions of open chromatin were fragmented and tagged with Tn5 transposase and sequencing libraries were constructed according to standard protocols with barcoded primers.

value: Non-neural crest

value: mcherry-


title: Placental_Arteries_34, snRNAseq

description: 10x Genomics

value: placental chorionic plate arteries


title: LCLs, WT_2591, input_IgG

value: Male


title: MC3T3 cells were treated with HUVEC-derived exosomes  48 hours,Biology Repeat #1

description: Library name: Exo1


title: MC3T3 cells were treated with HUVEC-derived exosomes  48 hours,Biology Repeat #2

description: Library name: Exo2


title: 17hpf_Positive_CNC_2

description:
Library name: Sample 5
21338

value: migratory cardiac neural crest

value: 16 somite stage (17hpf)

value: mcherry +


title: 16ss_Neg_1_ATAC

description:
Library name: Sample 3
ATACseq


title: LCLs, WT_ESGO, input_ZBTB24


title: MC3T3 cells, control group,Biology Repeat #3

description: Library name: Con3

value: The control group was untreated


title: LCLs, WT_2592, IgG

value: LCLs

value: IgG (MBL life science, # PM067)


title: Placental_Arteries_3b, snRNAseq

description: 10x Genomics


title: Myometrium_1, snRNAseq

description: 10x Genomics

value: myometrial strips


title: LCLs, WT_2592, input_ZBTB24

value: lymphobalstoid cells

value: WT


title: 16ss_CNC_2_ATAC

description:
Library name: Sample 2
ATACseq

value: cardiac neural crest from midbrain-hindbrain boundary to somite 6

value: Migratory cardiac neural crest

value: mcherry+


title: Placental_Arteries_2, snRNAseq

description: 10x Genomics


title: MC3T3 cells, control group,Biology Repeat #2

description: Library name: Con2

value: bone

value: stem cells


title: 16ss_CNC_1_ATAC

description:
Library name: Sample 1
ATACseq


title: LCLs, WT_2591, input_ZBTB24


title: MC3T3 cells, control group,Biology Repeat #1

description: Library name: Con1


title: Placental_Arteries_1, snRNAseq

description: 10x Genomics


title: mch+ CdNC cells from 16ss zebrafish embryos

description:
Library name: Sample 1
10X Genomics

data_processing:
Reads were mapped to GRCz11 and initial quality control was performed using Cell Ranger v7.20.
Scanpy was used for further quality control, filtering, clustering, and downstream analysis.
Assembly: GRCz11
Supplementary files format and content: tab-separated barcodes and features files as well as matrix file.

source_name: midbrain-hindbrain boundary to somite 6

extract_protocol:
mch+ CdNC cells from 16 somite-stage Tg(-4.9sox10:GAL4-UAS-cre;UAS:NfsB-mCherry;myl7:nucGFP) embryos were dissected, dissociated and FAC-sorted.
Single cell libraries were prepared using the Chromium Single Cell 3’ v3.1 reagent kit (10X Genomics, PN-1000075) according to manufacturer's protocol.

value: midbrain-hindbrain boundary to somite 6

value: Cardiac Neural Crest

value: 16 somite stage


title: Serum_7Gy_rep4

status: Public on Jan 29 2025

type: RNA

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

country: Japan

institute: Hirosaki University

description: gene expression in serum of 8-week-old mouse

hyb_protocol: SurePrint G3 mouse miRNA microarray slides (8 × 60 K, Ver.21.0) were hybridized with the Cy3-labeled miRNA in a hybridization solution prepared with a Gene Expression Hybridization Kit (Agilent Technologies) for 20 hours at 55°C in a rotating hybridization oven (Agilent Technologies), according to the manufacturer’s instructions. After hybridization, microarray slides were washed for 5 min at room temperature with GE Wash Buffer 1 (Agilent Technologies) and for 5 min at 37°C with GE Wash buffer 2 (Agilent Technologies), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarray Scanner (G4900DA) (Agilent Technologies) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2 μm high sensitivity, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5 (Agilent Technologies) using default parameters (Protocol name: miRNA_1105_Oct12 and Grid name: 070155_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Serum

label_protocol: The miRNA Complete Labeling and Hyb kit (Agilent Technologies) were used to label miRNAs in 30 ng of serum total RNA with cyanine 3 (Cy3) fluorescent dye following the manufacturer’s instructions.

extract_protocol: RNAs from serum were extracted using the Isogen II reagent and ethachinmate (Nippongene) according to manufacturer’s instruction. The concentration of extracted serum RNAs were examined using a Quant-iT RiboGreen RNA Reagent and kit (Thermo Fisher Scientific) and a Fluoroskan Ascent (Thermo Fisher Scientific) according to manufacturer’s instructions.

treatment_protocol: Male C57BL/6NJcl mice were delivered at 7 weeks of age from the breeding facilities of Clea, Japan. Eight-weeks old mice were exposed to X-rays (MBR-1520R-3 X-ray machine, Hitachi Medical Corporation, Tokyo, Japan) at a dose rate of 1.0 Gy/min (150 kVp, 20 mA, 0.5 mm aluminum and 0.3 mm copper filters). Blood obtained from the irradiated and non-irradiated mice was collected in BD Microtainer tubes with serum separator additive BD Microgard closure (Becton Dickinson Biosciences). Blood was then centrifuged at 6000 × G at room temperature for 3 min, and sera were collected.

tag: gender

value: male

value: 8 weeks


title: Serum_7Gy_rep2


title: 257015510296_2_2

city: Chongqing

first: Jing

last: Chen

address: Chongqing

institute: Chongqing Medical University

hyb_protocol: The miRNAs were labelled with Agilent miRNA labeling reagent (Agilent Technologies). Then, the dephosphorylated RNA was linked with PCP-Cy3 and the labeled RNA was purified and hybridized to an miRNA microarray.

scan_protocol: Images were scanned with an Agilent array scanner (Agilent Technologies) .

data_processing: Data was analyzed with Agilent feature extraction version 10.10 to obtain chip data.

source_name: mouse primary peritoneal macrophages+C. albicans infected for 36h

label_protocol: Briefly, the miRNAs were labelled with Agilent miRNA labeling reagent (Agilent Technologies). Then, the dephosphorylated RNA was linked with PCP-Cy3 and the labeled RNA was purified and hybridized to an miRNA microarray.

growth_protocol: Mouse primary peritoneal macrophages stimulated with thioglycolate were prepared as described,and murine peritoneal macrophages were isolated from female BALB/c mice (6–8 week of age, purchased from the Chong Qing Medical Animal Laboratory in china). Mice were intraperitoneally injected with 1 mL 3% thioglycolate (B2551; Sigma Aldrich, St. Louis, MO, USA). After 3 days, peritoneal macrophages were obtained by collecting and centrifuging from ascites in mice. After resuspending the cells in red blood cell lysis buffer, mouse peritoneal macrophages were cultured in medium supplemented with 10% fetal calf serum (Life Technologies, Inc, Gibco/BRL Division, Grand Island, NY, USA), 100 U/mL of penicillin, and 100 mg/mL streptomycin (Gibco) in a5% CO2 atmosphere. After 6 h, the cells were washed twice with phosphate-buffered saline (PBS) to remove unattached cells, and then the adherent cells were cultured in fresh culture medium. After 12 h, the cells were used for the following experiments.

extract_protocol: Primary peritoneal macrophages infected (infected group) and not infected (control group) with C. albicans were extracted using TRIzol reagent (Invitrogen Corporation) and an mirVanamiRNA Isolation Kit (Ambion, Austin, Tex) to obtain high-quality total RNA, according to the manufacturer’s instructions.

treatment_protocol: C. albicans strain (ATCC 14053) was maintained on solid yeast-extract peptone dextrose agar plates (1%D glucose, 1% yeast extract, and 2% agar) at 30℃. Prior to performing the experiment, the C. albicans cells were transferred to fresh yeast-extract peptone dextrose agar and cultured for 24 h at 30℃. To prepare heat-inactivated (HI)C. albicans, cells were collected, suspended in PBS, heated at 65℃ for 2 h, washed twice with PBS, and then resuspended in the same buffer. Inactivation was confirmed by the absence of growth, when 200uL of the yeast suspension was spread over yeast-extract peptone dextrose agar plates and incubated for 48 h at 30℃. Mouse peritoneal macrophages were prepared at a cell density of 3 x 10^6cells/mL in 2mL of medium in a 6-well plate and infected with HI C. albicans for 36h.

value: peritoneal macrophage

value: female


title: Serum_7Gy_rep1


title: 257015510296_2_1


title: 257015510296_1_4


title: 257015510296_1_2

source_name: mouse primary peritoneal macrophages


title: Serum_0Gy_rep1


title: 257015510296_1_1


title: 257015510296_1_3


title: OV90CisR2_3

city: Jinju

first: Hyonok

last: Yoon

state: Gyeongnam

address: 501 Jinju-Daero

department: Pharmacy

country: South Korea

institute: Gyeongsang National University

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2 (Langmead and Salzberg, 2012). Bowtie2 indices were either generated from genome assembly sequence or the representative transcript sequences for aligning to the genome and transcriptome. The alignment file was used for assembling transcripts, estimating their abundances and detecting differential expression of genes. Differentially expressed gene were determined based on counts from unique and multiple alignments using coverage in Bedtools (Quinlan AR, 2010). The RC (Read Count) data were processed based on TMM+CPM normalization method using EdgeR within R (R development Core Team, 2020) using Bioconductor (Gentleman et al.,2004). Gene classification was based on searches done by DAVID (http://david.abcc.ncifcrf.gov/) and Medline databases(http://www.ncbi.nlm.nih.gov/).
Assembly: GRCh38
Supplementary files format and content: Normalized counts for each sample as a xlsx file format

growth_protocol: OV90 cells were maintained in MCDB-105 medium with 15% fetal bovine serum (FBS) and antibiotics cultured at 37°C and 5% CO2.  While OV90CisR1 and OV90CisR2 were maintained in cisplatin containing MCDB-105 medium at same conditions.

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed by Agilent 2100 bioanalyzer using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and RNA quantification was performed using ND-2000 Spectrophotometer (Thermo Inc., DE, USA).
For control and test RNAs, the construction of library was performed using QuantSeq 3’ mRNASeq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions.
High-throughput sequencing was performed as single-end 75 sequencing using NextSeq 550 (Illumina, Inc., USA).

value: Ovarian cancer cells

value: Resistant


title: OV90CisR2_2


title: OV90CisR1_1


title: OV90_3

value: Sensitive


title: OV90_1


title: OV90CisR1_2


title: OV90_2


title: OV90CisR2_1


title: UPN254_BM_RNA_MDS

first: David

last: Rombaut

address: 22 rue Méchain

institute: Institut Cochin

data_processing:
FASTQ files were mapped using STAR (v2.7.9) to align the reads against the human reference genome GRCh37 (UCSC version hg19). Read count normalizations and groups comparisons were performed using DESeq2 (v1.30.1), using the Wald test for significance testing. Genes with low counts were filtered, if at least half the samples have less than 20 normalized reads.
For differential expression study, the results obtained after DESeq2 comparison were selected for further analysis and filtered at Benjamini-Hochberg (BH)- adjusted P-value < 0.05 and log2(FC) > |1|.
To identify differentially expressed splicing events, we used KisSplice (v2.6.2), KisSplice2refgenome (v2.0.7) and KissDE (v1.15.3), and filtered results at BH adjusted P-value < 0.05 and ΔPSI > |0.10|.
Assembly: GRCh37
Supplementary files format and content: count_MDS.tar.gz : raw count table and metadata (tabulated txt file).
Supplementary files format and content: event.tar.gz : event_k2ref_SF3B1.tsv, event_k2ref_SRSF2.tsv, event_k2ref_U2AF1.tsv (kissplice2refgenome outputs, splicing raw count, txt files) and input_order_kissplice_SF3B1, input_order_kissplice_SRSF2, input_order_kissplice_U2AF1 (txt files, order necessary to run splicing differential analysis with kissDE).

source_name: Bone marrow

extract_protocol:
Samples were controled with an Agilent 2100 Bioanalyzer. RNA polyA was realized with the NEBNext polyA kit + Ultra II < 150ng.
Libraries were constructed using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA), > 150ng BA-mRNA. Bank were normalized and controled with a Bioanalyzer.

value: Bone marrow

tag: disease

value: LR-MDS

tag: progression

value: MDS

tag: mdsdiag

value: RARS

value: SF3B1 MUT SRSF2 WT U2AF1 WT


title: UPN252_BM_RNA_NA

value: Not Known


title: UPN251_BM_RNA_MDS


title: UPN256_BM_RNA_MDS

value: SF3B1 WT SRSF2 WT U2AF1 WT


title: OV90CisR1_3


title: Serum_7Gy_rep3


title: UPN253_BM_RNA_NA


title: Serum_0Gy_rep2


title: UPN255_BM_RNA_MDS

value: SF3B1 WT SRSF2 WT U2AF1 MUT


title: UPN249_BM_RNA_MDSp

value: MDSp

value: RCMD


title: Serum_0Gy_rep4

value: male


title: UPN250_BM_RNA_NA

value: RCMD-RS


title: UPN248_BM_RNA_MDS


title: UPN246_BM_RNA_MDS


title: UPN247_BM_RNA_NA


title: UPN245_BM_RNA_MDS


title: Serum_0Gy_rep3

value: 8 weeks


title: UPN244_BM_RNA_MDS


title: UPN242_BM_RNA_NA


title: UPN239_BM_RNA_NA


title: UPN241_BM_RNA_NA


title: UPN240_BM_RNA_NA


title: UPN238_BM_RNA_NA


title: UPN237_BM_RNA_NA


title: UPN236_BM_RNA_MDS


title: UPN233_BM_RNA_NA

value: SF3B1 WT SRSF2 MUT U2AF1 WT


title: UPN235_BM_RNA_NA


title: UPN234_BM_RNA_MDSp


title: UPN232_BM_RNA_NA


title: UPN229_BM_RNA_NA


title: UPN231_BM_RNA_NA


title: UPN226_BM_RNA_MDSp


title: UPN228_BM_RNA_MDS


title: UPN230_BM_RNA_MDSp


title: UPN224_BM_RNA_MDS


title: UPN227_BM_RNA_MDS


title: UPN243_BM_RNA_NA


title: UPN223_BM_RNA_MDS


title: UPN220_BM_RNA_MDSp


title: UPN222_BM_RNA_MDS

value: MDS-U


title: UPN218_BM_RNA_MDS


title: UPN221_BM_RNA_MDSp


title: UPN225_BM_RNA_MDS

value: RA


title: UPN213_BM_RNA_MDSp


title: UPN216_BM_RNA_MDS


title: UPN214_BM_RNA_MDS


title: UPN215_BM_RNA_MDS


title: UPN212_BM_RNA_MDS


title: UPN210_BM_RNA_MDS


title: UPN209_BM_RNA_MDS


title: UPN205_BM_RNA_CTRL

value: Healthy control

value: CTRL


title: UPN211_BM_RNA_MDS

value: Bone marrow

value: LR-MDS


title: UPN207_BM_RNA_CTRL


title: UPN203_BM_RNA_CTRL


title: UPN202_BM_RNA_CTRL


title: UPN201_BM_RNA_CTRL


title: UPN204_BM_RNA_CTRL


title: UPN200_BM_RNA_MDS

value: MDS


title: UPN206_BM_RNA_CTRL


title: UPN197_BM_RNA_MDS


title: UPN195_BM_RNA_MDS

value: SF3B1 MUT SRSF2 WT U2AF1 WT


title: UPN217_BM_RNA_MDS


title: UPN198_BM_RNA_MDS


title: UPN194_BM_RNA_MDSp


title: UPN193_BM_RNA_MDSp


title: UPN192_BM_RNA_MDSp


title: UPN196_BM_RNA_MDSp


title: UPN189_BM_RNA_MDS


title: UPN187_BM_RNA_MDS


title: UPN188_BM_RNA_MDS

value: RARS


title: UPN179_BM_RNA_MDS


title: UPN182_BM_RNA_MDS


title: UPN176_BM_RNA_MDS

value: SF3B1 WT SRSF2 WT U2AF1 WT


title: UPN180_BM_RNA_MDS

value: SF3B1 WT SRSF2 WT U2AF1 MUT


title: UPN175_BM_RNA_MDS


title: UPN172_BM_RNA_MDS


title: UPN170_BM_RNA_MDS


title: UPN169_BM_RNA_MDS


title: UPN171_BM_RNA_MDS


title: UPN165_BM_RNA_MDSp

value: MDSp

value: SF3B1 WT SRSF2 MUT U2AF1 MUT


title: UPN178_BM_RNA_MDSp

value: SF3B1 MUT SRSF2 WT U2AF1 MUT


title: UPN159_BM_RNA_MDS

value: RCMD


title: UPN168_BM_RNA_MDS


title: UPN158_BM_RNA_MDS

value: RCMD-RS


title: UPN162_BM_RNA_MDS


title: UPN164_BM_RNA_MDS


title: UPN151_BM_RNA_MDS


title: UPN155_BM_RNA_MDS

value: SF3B1 WT SRSF2 MUT U2AF1 WT


title: UPN153_BM_RNA_MDS


title: UPN150_BM_RNA_MDS


title: UPN145_BM_RNA_MDS


title: UPN149_BM_RNA_MDS


title: UPN146_BM_RNA_MDS


title: UPN186_BM_RNA_MDS


title: UPN144_BM_RNA_MDS


title: UPN142_BM_RNA_MDS


title: UPN143_BM_RNA_MDS


title: UPN141_BM_RNA_MDS


title: UPN136_BM_RNA_MDS


title: UPN124_BM_RNA_MDSp


title: UPN129_BM_RNA_MDS


title: UPN117_BM_RNA_MDS


title: UPN115_BM_RNA_MDS


title: UPN114_BM_RNA_MDS


title: UPN157_BM_RNA_MDS


title: UPN108_BM_RNA_MDS


title: UPN109_BM_RNA_MDS


title: UPN152_BM_RNA_MDS


title: UPN100_BM_RNA_MDSp


title: UPN106_BM_RNA_MDS


title: UPN105_BM_RNA_MDS


title: UPN97_BM_RNA_MDS


title: UPN94_BM_RNA_MDS


title: UPN148_BM_RNA_MDS


title: UPN92_BM_RNA_MDS


title: UPN90_BM_RNA_MDSp


title: UPN98_BM_RNA_MDS


title: UPN91_BM_RNA_MDS


title: UPN93_BM_RNA_MDS


title: UPN88_BM_RNA_MDSp


title: UPN84_BM_RNA_MDS


title: UPN89_BM_RNA_MDS


title: UPN87_BM_RNA_MDS


title: UPN82_BM_RNA_MDS


title: UPN119_BM_RNA_MDS


title: UPN81_BM_RNA_MDS


title: UPN86_BM_RNA_MDS


title: UPN123_BM_RNA_MDS


title: UPN122_BM_RNA_MDS


title: UPN80_BM_RNA_MDS


title: UPN79_BM_RNA_MDS


title: UPN77_BM_RNA_MDS


title: UPN76_BM_RNA_MDS


title: UPN74_BM_RNA_MDS


title: UPN72_BM_RNA_MDS


title: UPN71_BM_RNA_MDS


title: UPN69_BM_RNA_MDS


title: UPN64_BM_RNA_MDSp


title: UPN68_BM_RNA_MDS


title: UPN60_BM_RNA_MDS


title: UPN58_BM_RNA_MDS


title: UPN54_BM_RNA_MDSp


title: UPN55_BM_RNA_MDS


title: UPN52_BM_RNA_MDS


title: UPN83_BM_RNA_MDS


title: UPN56_BM_RNA_MDS


title: UPN49_BM_RNA_MDS


title: UPN53_BM_RNA_MDSp


title: UPN47_BM_RNA_MDS


title: UPN48_BM_RNA_MDS


title: UPN46_BM_RNA_MDS


title: UPN50_BM_RNA_MDS


title: UPN78_BM_RNA_MDS


title: UPN41_BM_RNA_MDSp


title: UPN42_BM_RNA_MDS


title: UPN73_BM_RNA_MDS


title: UPN39_BM_RNA_MDS


title: UPN40_BM_RNA_MDS


title: UPN38_BM_RNA_MDS


title: UPN35_BM_RNA_MDS


title: UPN61_BM_RNA_MDSp


title: UPN33_BM_RNA_MDS


title: UPN32_BM_RNA_MDS


title: UPN31_BM_RNA_MDS


title: UPN44_BM_RNA_MDS


title: UPN34_BM_RNA_MDS


title: UPN30_BM_RNA_MDS


title: UPN28_BM_RNA_MDS


title: UPN27_BM_RNA_MDS


title: UPN26_BM_RNA_MDS


title: UPN18_BM_RNA_MDS


title: UPN20_BM_RNA_MDS


title: UPN19_BM_RNA_MDSp

value: MDS-U


title: UPN45_BM_RNA_MDSp


title: UPN25_BM_RNA_MDS


title: UPN23_BM_RNA_MDSp


title: UPN24_BM_RNA_MDS


title: UPN15_BM_RNA_MDS


title: UPN22_BM_RNA_MDSp


title: UPN36_BM_RNA_MDS

value: RA


title: UPN14_BM_RNA_MDS


title: UPN5_BM_RNA_MDSp


title: UPN8_BM_RNA_MDS


title: UPN29_BM_RNA_MDS


title: UPN4_BM_RNA_MDS


title: UPN1_BM_RNA_MDS


title: Liver, Paracetamol injury, PBS, rep 5

city: Edinburgh

first: Stuart

last: Forbes

address: 5 Little France Drive

department: Centre for Regenerative Medicine

institute: The University of Edinburgh

data_processing:
Base call data generated by Illumina NextSeq 2000
Read quality assessed using FastQC and MultiQC (v.1.25)
Adapter, poly-G and low-quality base trimming with Cutadapt (v.4.6)
Read alignment with STAR (v.2.7.1a)
Read counting with GenomicAlignments (v.1.34.1)
Differential expression computed using DESeq2 (v.1.38.3)
Assembly: GRCm38.100
Supplementary files format and content: Tab separated matrix table with raw gene counts for all genes and samples

source_name: liver

extract_protocol:
Approximately 10 mg frozen liver tissue was homogenized in 900 µL Qiazol lysis reagent (Qiagen) using the tissue tearor. Chloroform was mixed and incubated (5 min) before centrifugation (12000 g, 15 min, 4 °C). Aqueous phase was separated and RNA extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
14 Libraries were prepared from total-RNA samples using the NEBNext Ultra 2 Directional RNA library prep kit for Illumina (#E7760) and the NEBNext rRNA Depletion kit (Human/Mouse/Rat) (#E6310) according to the provided protocol. 500ng of total-RNA was added to the ribosomal RNA (rRNA) depletion reaction using the NEBNext rRNA depletion kit (Human/mouse/rat). This step uses specific probes that bind to the rRNA in order to cleave it. rRNA-depleted RNA was then DNase treated and purified using Agencourt RNAClean XP beads (Beckman Coulter Inc, #66514). RNA was then fragmented using random primers before undergoing first strand and second strand synthesis to create cDNA. Fragmentation time was dependent upon the quality of each total RNA sample. cDNA was end-repaired before ligation of sequencing adapters, and adapter-ligated libraries were enriched by 10 cycles of PCR using NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) (NEB, #E6440 or E6442).

treatment_protocol: Mice were either untreated (control; n=3), or treated with 350mg/kg APAP. APAP-treated animals were given either PBS vehicle (n=5) or hAAM cells (n=4).

value: liver

tag: injury

value: Paracetamol

value: PBS vehicle


title: UPN17_BM_RNA_MDS

value: Bone marrow

value: LR-MDS


title: UPN16_BM_RNA_MDS

value: MDS

value: SF3B1 MUT SRSF2 WT U2AF1 WT


title: UPN13_BM_RNA_MDS

value: SF3B1 WT SRSF2 WT U2AF1 WT


title: UPN12_BM_RNA_MDSp


title: UPN21_BM_RNA_MDS


title: UPN10_BM_RNA_MDS


title: Liver, Paracetamol injury, hAAM, rep 3

value: hAAM cells


title: UPN9_BM_RNA_MDSp

value: MDSp

value: RARS


title: UPN3_BM_RNA_MDS


title: Liver, Paracetamol injury, PBS, rep 2


title: Liver, Control, rep 3

value: No injury

value: No treatment


title: DMSO_3h_489

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

description:
YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients
Sample_Rogatsky.XC.13468_2022_12_08_3h_dmso_489

data_processing:
Read quality filtering and adapter trimming were performed with fastP. Filtered reads were mapped to the mouse genome (mm10) or human genome (hg38) with the STAR aligner (2.7.0) and exonic reads were counted against GENCODE release 27 annotation with featureCount  sing a customised pipeline available at https://gitlab.com/hssgenomics/pipelines/RNAseq.
Differential gene expression analysis was performed with edgeR(3.38.4, ) using quasi-likelihood framework. Genes with low expression levels (<2 counts per million in at least one group) were filtered from all downstream analyses. P values were adjusted to correct for multiple testing using the Benhamini-Hochberg FDR procedure.
Assembly: mm10 or hg38
Supplementary files format and content: edgeR_DEGs_*.xlsx excel file with the results of differential analysis and datanormalization/transformation

source_name: Synovial tissues from Rheumatoid arthritis patients

growth_protocol:
1.YKL, LPS Mouse  time course experiment: Bone marrow derived Macrophages from tibiae and femora were flushed and incubated for 5 days in DMEM (Corning, 1 g/L glucose) supplemented with 20% FBS and 20% L-Cell conditioned media. Adherent cells were then scraped, seeded into 150 mm or 6-well plates in DMEM -20% FBS and treated the following day
2. TNF, IFNg polarized human macrophages YKL time course experiment: Deidentified human buffy coats were purchased from New York Blood Center. PBMC were isolated by gradient centrifugation of buffy coats with Lymphoprep (STEMCELL Technologies, 07851). Human monocytes were purified from PBMC with anti-CD14 magnetic beads (Miltenyi Biotec, 130-050-201) as recommended by the manufacturer. Purified human monocytes were seeded into 150 mm plates (1.5 x 107 cells/ plate) or 6-well plates (2x106 cells/well) and cultured for 5 days in DMEM supplemented with 20% heat-inactivated FBS, penicillin/streptomycin, L-glutamine, with 20 ng/ml human macrophage colony-stimulating factor (hM-CSF) added fresh every other day.
3. YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients: Synovial tissue was obtained from patients consented into the HSS FLARE study (IRB no. 2014–233). De-identified 3x3 mm synovial biopsy specimens were collected from patients undergoing synovectomy and cryopreserved in Cryostor CS10 (Sigma-Aldrich). Cryopreserved synovial tissues were digested with Liberase TL (100 μg/ml, Roche) and DNAase I (100 μg/ml, NEB) for 15 min, single cells were separated using 70-μm cell strainers and resuspended in RBC lysis buffer for 3’ before plating in RPMI 1640 - 10% FBS - 1% glutamine in 96-well plates at 2 x 105 viable cells/well.

extract_protocol:
Total RNA was isolated from cells with RNeasy Plus micro kit (Qiagen)
The integrity of total RNA samples was evaluated with BioAnalyzer 2100 system (Agilent). Sequencing compatible libraries are prepared with NEBNext Ultra II RNA Kits (NEB) and NEBNext Multiplex Oligos for Illumina – 96 Unique Dual Index Primer Pairs (NEB) following instructions from manufacturer. In brief, total RNA was poly(A)-enriched, fragmented, and reverse transcribed to cDNA. cDNA were ligated with adaptors and indexes. Sequencing compatible libraries were then quality-controlled with BioAnalyzer 2100 system (Agilent) and sequenced

treatment_protocol:
1.YKL, LPS Mouse  time course experiment: Mouse bone marrow derived macrophages were pretreated with YKL-5-124 for (250 nM, 6h), followed by treatment with LPS (10 ng/ml) for 1, 6 and 12 hours
2. TNF, IFNg polarized human macrophages: human macrophages were cultured in TNF+IFNγ for 24 hours(ab259410; 20 ng/ml and ab259377; 5 ng/ml, respectively), YKL-5-124  (250nm) added for the last 3 or 6 h,
3. YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients: Synovial cell suspensions were prepared from deidentified synovial tissue samples collected from RA patients, placed in culture and treated  YKL-5-124 (250 nm) for 3 or 6 hours

value: primary

value: Synovial single-cell suspensions

value: unknown

value: Female

tag: batch


title: UPN2_BM_RNA_MDSp


title: Liver, Control, rep 2

value: liver


title: Liver, Paracetamol injury, PBS, rep 4

value: Paracetamol


title: Pearl millet lateral roots replicate three

city: Montpellier

first: Laurent

last: Laplaze

address: 911 avenue Agropolis

department: DIADE

institute: IRD

description:
Library name: PM_L3
Column name in normalized_counts_deseq2.csv: PML_3

data_processing:
After sequencing, low-quality reads and adapters were removed from the raw reads and sequencing quality checks were performed using FastQC.
The toolbox for generic NGS analyses (TOGGLE, version 3; Monat et al., 2015) was further used to obtain read counts for each pearl millet gene. The TOOGLE analysis pipeline included an additional cleaning step using CutAdapt (version 3.1; Martin, 2011) before mapping the reads against the pearl millet genome (ASM217483v2; Varshney et al., 2017) using Hisat2 (version 2.0.1; Kim et al., 2015).
The percentage of mapping was checked using Samtools (version 1.9; Li et al., 2009).
Analysis of the data was performed using the online DIANE software (version 1.0.6; Cassan et al., 2021). Data were normalised and differentially expressed genes were identified using the DESeq2 method (implemented in EdgeR) with a minimal gene count sum across samples set at 90. The adjusted p-value (FDR) threshold for detection of genes differentially expressed was set 0.01, and an absolute Log Fold change threshold of 1 was considered.
Assembly: Transcriptome assembly was performed using Stringtie (version 1.3.4; Pertea et al., 2015) with guidance from the pearl millet genes coding sequences (ASM217483v2; Varshney et al., 2017).
Supplementary files format and content: The processed data file is a Excel sheet with reads counts.

organism: Cenchrus americanus

source_name: Lateral roots

growth_protocol: Plants were grown in 400 mm x 700 mm x 20 mm rhizotrons as in Passot et al (2016).

extract_protocol:
After fifteen days of growth, the plexiglass was carefully removed to avoid damaging the roots and samples were taken from different root types: the primary root tip (5 cm apex), the crown root tips (5 cm apex) and lateral roots on primary roots. Roots from three plants were pooled together to make one sample. Roots tissues from three replicates were stored at -80°C before RNA extraction using the RNAeasy Plant Mini Kit (QIAGEN).
RNA sequencing was performed by the Novogene Company Limited (United-Kingdom) on an Illumina platform. Briefly, messenger RNA was purified and double strand cDNA was synthesized. Library construction involved end repair, A-tailing, adaptor ligation, size selection, amplification and purification as per the provider’s protocols.

value: Lateral roots


title: Liver, Paracetamol injury, hAAM, rep 2


title: Liver, Paracetamol injury, hAAM, rep 4


title: Liver, Control, rep 1


title: Liver, Paracetamol injury, hAAM, rep 1


title: Pearl millet crown roots replicate one

description:
Library name: PM_C1
Column name in normalized_counts_deseq2.csv: PMC_1

source_name: Crown roots

value: Crown roots


title: Pearl millet crown roots replicate two

description:
Library name: PM_C2
Column name in normalized_counts_deseq2.csv: PMC_2


title: UPN11_BM_RNA_MDS

value: Bone marrow

value: LR-MDS


title: Liver, Paracetamol injury, PBS, rep 3

value: PBS vehicle


title: Pearl millet primary root replicate one

description:
Library name: PM_P1
Column name in normalized_counts_deseq2.csv: PMP_1

source_name: Primary roots

value: Primary roots


title: Liver, Paracetamol injury, PBS, rep 1


title: 35_rep2

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

institute: Chungbuk National University

data_processing:
mRNA-Seq reads were mapped to reference Poecilia reticulata genome using STAR with default parameters.
Transcript abundance was quantified using StringTie, and gene expression levels were measured in transcripts per million (TPM).
Differential gene expression analysis was conducted utilizing the DESeq2 package, with a cutoff threshold set at more than 2-fold change and a false discovery rate (FDR) of less than 0.05.
Assembly: Poecilia reticulata
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Poecilia reticulata

source_name: intestine

growth_protocol: Adult wild-type guppies were housed in a standard circulating water system at 28°C with a 14-hour light/10-hour dark cycle.

extract_protocol:
Total RNA was isolated using the TRIzol reagent according to the manufacturer's instructinos.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 3‰ salt was added every 2 days to tanks containing guppies. The osmotic challenge continued until reaching a salt concentration of 35‰ for guppies over a period of 24 days.

value: intestine

value: 35% salt


title: YKL_6h_489

description:
YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients
Sample_Rogatsky.XC.13468_2022_12_08_6h_ykl_489

value: Synovial tissues from Rheumatoid arthritis patients


title: 18_rep2

value: 18% salt


title: YKL_3h_489

description:
YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients
Sample_Rogatsky.XC.13468_2022_12_08_3h_ykl_489


title: Pearl millet lateral roots replicate one

description:
Library name: PM_L1
Column name in normalized_counts_deseq2.csv: PML_1


title: Pearl millet crown roots replicate three

description:
Library name: PM_C3
Column name in normalized_counts_deseq2.csv: PMC_3


title: Pearl millet lateral roots replicate two

description:
Library name: PM_L2
Column name in normalized_counts_deseq2.csv: PML_2


title: DMSO_6h_489

description:
YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients
Sample_Rogatsky.XC.13468_2022_12_08_6h_dmso_489


title: 18_rep1


title: Pearl millet primary root replicate two

description:
Library name: PM_P2
Column name in normalized_counts_deseq2.csv: PMP_2


title: Pearl millet primary root replicate three

description:
Library name: PM_P3
Column name in normalized_counts_deseq2.csv: PMP_3


title: 411-SPH-3

city: London

first: Gabriel

middle: E

last: DiMattia

state: ONTARIO

address: 750 Base Line Rd E

department: Biochemistry

country: Canada

institute: Western University

description:
Library name: Sample 27
ENTREZID_normalized_counts

data_processing:
Galaxy Platform
Raw sequencing reads were uploaded to the Galaxy platform and tested for quality using FastQC and MultiQC to measure the per base sequence quality, GC content, N content, overrepresented sequences, and adapter content.
Reads were mapped to the human genome (hg38) using HISAT2. Differential gene expression was determined using DESeq2.
Gene set enrichment analysis was performed using the gene set collections from the Molecular Signatures Database, with focus on the Cancer Hallmark gene set
Assembly: hg38
Supplementary files format and content: xlsx file contains counts (normalized) for each sample

growth_protocol:
iOvCa cell lines were maintained with DMEM/F12 with 10% fetal bovine serum on adherent cultures.
[in vitro culture protocol] For spheroids, cells were seeded in suspension on 6-well Ulta-Low Attachment plates and supplemented with DMEM/F12 with 10% fetal bovine serum and collected after 3 days.For organoids, cells were resuspended in 50uL of Cultrex BME as droplets on 24-well plates and overald with EOC organoid specific media (refer to paper), then collected after 21 days.

extract_protocol:
RNA was harvested using RNEasy Spin Column Kit (Qiagen) and a minimum of 125ng/uL was required for analysis.
Total RNA samples were processed using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (PN NR603) from Vazyme Biotech Co. Ltd.

tag: replicate number

tag: 3d in_vitro_model_system

value: spheroid

value: high grade serous ovarian cancer cells


title: 411-SPH-T

description:
Library name: Sample 28
ENTREZID_normalized_counts


title: 256-SPH-2

description:
Library name: Sample 24
ENTREZID_normalized_counts


title: 256-SPH-1

description:
Library name: Sample 23
ENTREZID_normalized_counts


title: 35_rep1


title: 0_rep2

value: 0% salt


title: 246-SPH-3

description:
Library name: Sample 21
ENTREZID_normalized_counts


title: 0_rep1


title: 246-SPH-4

description:
Library name: Sample 22
ENTREZID_normalized_counts


title: 398-SPH-6

description:
Library name: Sample 26
ENTREZID_normalized_counts


title: 195-SPH-1

description:
Library name: Sample 17
ENTREZID_normalized_counts


title: 198-SPH-6

description:
Library name: Sample 20
ENTREZID_normalized_counts


title: 198-SPH-5

description:
Library name: Sample 19
ENTREZID_normalized_counts


title: 411-ORG-T

description:
Library name: Sample 14
ENTREZID_normalized_counts

value: organoid


title: 182-SPH-2

description:
Library name: Sample 16
ENTREZID_normalized_counts


title: 398-ORG-6

description:
Library name: Sample 12
ENTREZID_normalized_counts


title: 411-ORG-3

description:
Library name: Sample 13
ENTREZID_normalized_counts


title: 195-SPH-2

description:
Library name: Sample 18
ENTREZID_normalized_counts


title: 182-SPH-1

description:
Library name: Sample 15
ENTREZID_normalized_counts


title: 398-ORG-5

description:
Library name: Sample 11
ENTREZID_normalized_counts


title: 256-ORG-2

description:
Library name: Sample 10
ENTREZID_normalized_counts


title: 246-ORG-3

description:
Library name: Sample 7
ENTREZID_normalized_counts


title: 198-ORG-3

description:
Library name: Sample 6
ENTREZID_normalized_counts


title: 198-ORG-2

description:
Library name: Sample 5
ENTREZID_normalized_counts


title: 398-SPH-5

description:
Library name: Sample 25
ENTREZID_normalized_counts


title: 256-ORG-1

description:
Library name: Sample 9
ENTREZID_normalized_counts


title: 246-ORG-4

description:
Library name: Sample 8
ENTREZID_normalized_counts


title: 195-ORG-2

description:
Library name: Sample 4
ENTREZID_normalized_counts


title: 182-ORG-2

description:
Library name: Sample 2
ENTREZID_normalized_counts


title: 195-ORG-1

description:
Library name: Sample 3
ENTREZID_normalized_counts


title: Pt8, scRNAseq

city: Birmingham

first: Paul

last: Moss

state: West Midlands

address: Vincent Drive

department: Immunology and Immunotherapy

institute: University of Birmingham

description: 10x Genomics; Illumina NextSeq 500 (150 bps, paired-end) at a sequencing depth of >50,000 raw reads/cell.

data_processing:
Raw reads were processed using CellRanger (10X Genomics, v5.0.1) functions mkfastq and count. Raw bcl files were converted to fastq and aligned to the human reference genome GRCh38
Doublets were removed using DoubletFinder (v3.0).
Cells were eliminated if they had fewer than 500 genes, greater than 3500 genes or high proportion (>10%) mitochondrial transcripts
Genes were removed if they were expressed in only 3 or less cells.
Assembly: GRCh38
Supplementary files format and content: Comma separated values containing the raw UMI counts matrix

source_name: Omental metastasis from HGSOC post NACT

growth_protocol: Tumor tissue was collected and cut into small fragments (2mm size pieces) following surgical resection and digested using using collagenase (1500 units), hyaluronidase (500 units; StemCell Technologies;07912), liberase TL (500μl; Sigma-Aldrich (RRID:SCR_008988); 05401020001) and benzonase nuclease (500 units; Merck; E1014) at 37°C for 90 minutes. The resulting single cell solution was centrifuged, added to 2ml red blood cell lysis buffer and washed with 4ml sterile MACS buffer (PBS, 2mM of EDTA (Corning) and 2% of newborn calf bovine serum (Thermo Fisher Scientific (RRID:SCR_008452)). Samples were stained with 15μl Fc receptor blocking solution (Biolegend; 422302) and antibodies CD45 - BV785 (Biolegend 304047), Epcam - APC (Biolegend 324207) and Podoplanin - FITC (Biolegend 337025), before being suspended in 500μl MACS buffer for cell sorting. Here cells were separated into immune cells (high CD45 expression), epithelial cells (high Epcam and low podoplanin expression), and fibroblasts (low Epcam and high podoplanin expression). Cell populations were combined, with CD45 positive cells making up 75% and the Epcam/podoplanin cells 25% of the final sample, in a concentration of 1 x 106 cells per ml of basic media.

extract_protocol:
PI was added prior to sorting to exclude non-viable cells. Live CD45+ and CD45- populations were sorted and adjusted to 1 x 103/ml.
Samples with >85% cell viability were processed at the Genomics Birmingham Sequencing Facility (University of Birmingham, UK) for gene expression profiling using the 10X Genomics platform. Around 1.7 x 104 cells per sample were processed using the Chromium Controller (10X Genomics) for a recovery of 1 x 104 cells per sample, and library preparation was performed using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 according to manufacturer’s instructions. Library quantification and quality control was performed using TapeStation (Agilent). Samples were sequenced on an Illumina NextSeq 500 (150 bps, paired-end) at a sequencing depth of >50,000 raw reads/cell.

value: Omental metastasis from HGSOC post NACT

value: Female

value: Mixed

value: post NACT

tag: barcode tag


title: Pt10, scRNAseq

source_name: Omental metastasis from HGSOC pre NACT

value: Omental metastasis from HGSOC pre NACT

value: pre NACT


title: Pt7, scRNAseq


title: Pt9, scRNAseq


title: Pt3, scRNAseq


title: Pt1, scRNAseq


title: Pt6, scRNAseq


title: Human PGCLC KLF4-AID clone13 noIAA

city: Seoul

first: SUN-MIN

last: LEE

state: Other

address: 120, Neungdong-ro, Gwangjin-gu

institute: Konkuk University

data_processing:
RNA-seq: The low-quality reads and adaptor sequences were removed by Trim Galore. The pre-processed reads were mapped to human reference genome (GENCODE, GRCh38.p13) using STAR with parameters --outFilterMultimapNmax 1 --outFilterMatchNmin 35. The raw read counts per gene were extracted by the --quantMode GeneCounts option. The HOMER functions makeTagDirectory and makeUCSCfile were used to create bedGraph files.  Cut&Run: The leeHom package program with —ancientdna option was used to trim the reads. The pre-processed reads were mapped to the human reference genome (GENCODE, GRCh38.p13) using Bowtie2 with options –very-sensitive –no-mixed –no-discordant -q –phred33 -I 10 -X 700. The macs2 function —bdg were used to create be
Assembly: hg38
Supplementary files format and content: bedGraph

source_name: Embryonic stem cells

growth_protocol: 4i ESCs were maintained on irradiated mouse embryonic fibroblasts (MEFs) in knockout DMEM supplemented with knockout serum replacement, non-essential amino acids, 2-mercaptoethanol, penicillin, streptomycin, l-glutamine, human LIF, bFGF, TGFβ, GSK3i, ERKi, p38i, and JNKi. Before seeding on MEFs, ROCKi was added. For PGCLC induction, 4i ESCs were trypsinized into single cells and seeded in Ultra-Low attachment plates at 4,000 cells per well in hPGCLC induction medium with BMP2, human LIF, SCF, EGF, and ROCKi, and cultured as floating aggregates for 4–6 days.

extract_protocol:
RNA-seq: TNAP+ NANOS3-tdTomato+ PGCLCs were lysed in 50 μL RNA extraction buffer. RNA was extracted with the Arcturus PicoPure kit following the manufacturer’s instructions.  Cut&Run:  TNAP+ NANOS3-tdTomato+ PGCLCs were washed and bound to 10 μl Concanavalin A-coated magnetic beads. The cell-bound beads were incubated with wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, protease inhibitor) containing 0.1% digitonin and 1 μg of KLF4 antibody (ab215036, Abcam) for 2 hours at 4°C on a rotator. After two washes, the beads were resuspended in Protein A/G-MNase fusion protein at 70 ng/ml in digitonin–wash buffer and incubated for 1 hour at 4°C. Following two more washes, the beads were resuspended in ice-cold calcium incubation buffer (3.5 mM HEPES pH 7.5, 10 mM CaCl2, 0.1% digitonin). After 15 minutes, 2x stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM egtazic acid, 0.1% digitonin, 100 μg/ml RNase A, 50 μg/ml glycogen) was added, and the beads were incubated at 37°C for 30 minutes. The liquid was then transferred to a fresh tube and DNA was extracted using phenol–chloroform.
RNA-seq: Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB #E7760) following the manufacturer’s protocol. Sequencing was performed on an Illumina NextSeq 500.   Cut&Run: Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645S) from Illumina according to the manufacturer’s instructions. PCR enrichment of adaptor-ligated DNA was conducted with the KAPA HiFi Real-Time PCR Library Amplification Kit (Roche, KK2702) as per the manufacturer’s guidelines. SPRIselect beads (Beckman Coulter, B23317) were utilized for PCR product clean-up and size selection. Libraries were sequenced for 150 cycles in paired-end mode on the NovaSeq platform.

treatment_protocol: AID experiments, indole-3-acetic acid (IAA) was added to the cell culture medium at a final concentration of 100 μM.

value: Embryonic stem cells

tag: cell line

value: Primordial germ cell-like cells

value: PGCLC differentiation


title: Human PGCLC KLF4-AID clone13 IAA

tag: cell type

value: PGCLC differentiation, IAA


title: Human PGCLC KLF4-AID clone11 noIAA


title: Human PGCLC KLF4-AID clone11 IAA


title: YKL_6h_RA3

description:
YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients
Sample_Rogatsky.XC.12907_2022_08_29_6h_YKL_3

value: primary

value: Synovial single-cell suspensions

tag: genotype

tag: age

value: unknown


title: DMSO_6h_RA3

description:
YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients
Sample_Rogatsky.XC.12907_2022_08_29_6h_DMSO_3

value: Synovial tissues from Rheumatoid arthritis patients

tag: Sex

tag: treatment


title: YKL_3h_RA3

description:
YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients
Sample_Rogatsky.XC.12907_2022_08_29_3h_YKL_3

tag: tissue


title: DMSO_3h_RA3

description:
YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients
Sample_Rogatsky.XC.12907_2022_08_29_3h_DMSO_3


title: Human PGCLC KLF4-AID clone3 IAA


title: Human PGCLC KLF4-AID clone3 noIAA


title: YKL_3h_RA2

description:
YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients
Sample_Rogatsky.XC.12907_2022_08_29_3h_YKL_2


title: 182-ORG-1

description:
Library name: Sample 1
ENTREZID_normalized_counts

value: high grade serous ovarian cancer cells


title: DMSO_3h_RA2

description:
YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients
Sample_Rogatsky.XC.12907_2022_08_29_3h_DMSO_2


title: YKL_6h_RA2

description:
YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients
Sample_Rogatsky.XC.12907_2022_08_29_6h_YKL_2


title: YKL_6h_RA1

description:
YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients
Sample_Rogatsky.XC.12907_2022_08_29_6h_YKL_1


title: DMSO_6h_RA1

description:
YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients
Sample_Rogatsky.XC.12907_2022_08_29_6h_DMSO_1


title: DMSO_6h_RA2

description:
YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients
Sample_Rogatsky.XC.12907_2022_08_29_6h_DMSO_2


title: Pt2, scRNAseq


title: s271, scRNAseq

source_name: Normal Omentum tissue

value: Normal Omentum tissue

value: Normal


title: Batch6_Unctrl.CBF91_S19

city: Chicago

first: Yong

last: Peng

state: IL

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

data_processing:
library strategy: 5hmC-Seal-Seq
Basecalls were performed using bcl2fastq or Illumina nextseq 500 output.
5hmC-Seal-Seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.39, discarding reads left with < 25 bp
5hmC-Seal-Seq reads were aligned to the GENCODE V40  hg38 genome using BWA-aln version 0.7.17-r1198-dirty. Only uniquely mapping reads with at most two mismatches were retained.
To create GENCODE coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments.
Peaks were called uing MACS v2.2.7.1 with the significance cut-off q-value <=0.05
Assembly: bigWig files were generated using the deepTools.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak

source_name: plasma

extract_protocol:
All blood samples were stored at -80°C and then thawed on ice prior to use. Plasma was obtained by centrifuging whole blood at 1,350 × g for 12 minutes. Following centrifugation, plasma was removed from the pellet via pipette and recentrifuged at 1,350 × g for 12 minutes and then at 13,500 × g for 5 minutes to ensure full removal of pellet. cfDNA was isolated from 1 to 2 mL of plasma using the QIAamp Circulating Nucleic Acid Kit (Qiagen) following manufacturer's instructions. Final elution was done using 25 μL of IDTE pH 8.0 buffer and purified DNA was stored at -80°C until use.
In summary, sequencing adapters were ligated using the KAPA Hyper Prep Kit (KAPA Biosciences). cfDNA subsequently underwent T4 β-glucosyltransferase enzymatic modification with UDP-N3-glucose, followed by chemical modification with biotin-PEG4-dibenzocyclooctyne (DBCO). Biotin-labeled cfDNA fragments were then pulled down using streptavidin M270 Dynabeads (Invitrogen). Resulting pulled down DNA was then PCR amplified to construct sequencing libraries. Libraries were purified using AMPure XP beads (Beckman Coulter) following a standard purification protocol.

value: plasma

tag: molecule type

value: cell free DNA

tag: group

value: UNCONTROLLED


title: Batch6_Ctrl.CBF09_S9

value: CONTROLLED


title: Batch6_Ctrl.CBF90_S18


title: YKL_3h_RA1

description:
YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients
Sample_Rogatsky.XC.12907_2022_08_29_3h_YKL_1

value: Female


title: Batch6_Ctrl.CBF89_S17


title: Batch6_Ctrl.CBF88_S16


title: Batch6_Unctrl.CBF86_S14


title: Batch6_Ctrl.CBF85_S13


title: Batch6_Ctrl.CBF84_S12


title: Batch6_Ctrl.CBF83_S11


title: Batch6_Ctrl.CBF82_S10


title: Batch6_Ctrl.CBF87_S15


title: Batch6_Unctrl.CBF78_S6


title: Batch6_Ctrl.CBF79_S7


title: Batch6_Ctrl.CBF80_S8


title: Batch6_Ctrl.CBF81_S9


title: Batch6_Ctrl.CBF08_S8


title: Batch6_Unctrl.CBF77_S5


title: Batch6_Ctrl.CBF76_S4


title: Batch6_Ctrl.CBF74_S2


title: Batch6_Ctrl.CBF75_S3


title: Batch6_Ctrl.CBF72_S24


title: DMSO_3h_RA1

description:
YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients
Sample_Rogatsky.XC.12907_2022_08_29_3h_DMSO_1


title: Batch6_Ctrl.CBF71_S23


title: Batch6_Ctrl.CBF94_S22


title: Batch6_Ctrl.CBF70_S22


title: Batch6_Unctrl.CBF69_S21


title: Batch6_Ctrl.CBF68_S20


title: Batch6_Ctrl.CBF07_S7


title: Batch6_Ctrl.CBF65_S17


title: Batch6_Ctrl.CBF66_S18


title: Batch6_Ctrl.CBF64_S16


title: Batch6_Ctrl.CBF67_S19


title: Batch6_Ctrl.CBF63_S15


title: Batch6_Ctrl.CBF61_S13


title: Batch6_Ctrl.CBF60_S12


title: Batch6_Ctrl.CBF06_S6


title: Batch6_Ctrl.CBF58_S10


title: Batch6_Ctrl.CBF57_S9


title: Batch6_Ctrl.CBF56_S8


title: Batch6_Ctrl.CBF54_S6


title: Batch6_Ctrl.CBF53_S5


title: Batch6_Ctrl.CBF52_S4


title: Batch6_Unctrl.CBF51_S3


title: Batch6_Ctrl.CBF05_S5


title: UPN37_BM_RNA_MDS

value: Bone marrow

tag: disease

value: LR-MDS

value: MDS

value: SF3B1 WT SRSF2 WT U2AF1 WT


title: Batch6_Ctrl.CBF50_S2


title: Batch6_Ctrl.CBF43_S19


title: Batch6_Ctrl.CBF45_S21


title: Batch6_Ctrl.CBF47_S23


title: Batch6_Ctrl.CBF42_S18


title: Batch6_Ctrl.CBF48_S24


title: Batch6_Ctrl.CBF49_S1


title: Batch6_Ctrl.CBF62_S14


title: Batch6_Ctrl.CBF59_S11


title: Batch6_Ctrl.CBF38_S20


title: Batch6_Ctrl.CBF44_S20


title: Batch6_Ctrl.CBF46_S22


title: Batch6_Ctrl.CBF40_S16


title: Batch6_Ctrl.CBF39_S21


title: Batch6_Ctrl.CBF37_S13


title: Batch6_Ctrl.CBF04_S4


title: Batch6_Ctrl.CBF34_S10


title: Batch6_Ctrl.CBF55_S7


title: Batch6_Ctrl.CBF35_S11


title: Batch6_Ctrl.CBF33_S9


title: Batch6_Unctrl.CBF31_S7


title: Batch6_Unctrl.CBF03_S3


title: Batch6_Ctrl.CBF30_S6


title: Batch6_Unctrl.CBF29_S5


title: Batch6_Unctrl.CBF41_S17


title: Batch6_Ctrl.CBF27_S3


title: Batch6_Ctrl.CBF28_S4


title: Batch6_Unctrl.CBF26_S2


title: Batch6_Ctrl.CBF25_S1


title: Batch6_Ctrl.CBF22_S22


title: Batch6_Ctrl.CBF20_S20


title: Batch6_Ctrl.CBF23_S23


title: Batch6_Ctrl.CBF21_S21


title: Batch6_Ctrl.CBF02_S2


title: Batch6_Ctrl.CBF36_S12


title: Batch6_Ctrl.CBF24_S24


title: Batch6_Ctrl.CBF19_S19


title: Batch6_Ctrl.CBF13_S13


title: Batch6_Ctrl.CBF11_S11


title: Batch6_Ctrl.CBF10_S10


title: Batch6_Ctrl.CBF18_S18


title: Batch6_Ctrl.CBF17_S17


title: Batch5_Ctrl.CBE77_S15


title: Batch6_Ctrl.CBF14_S14


title: Batch6_Ctrl.CBF15_S15


title: Batch6_Ctrl.CBF32_S8


title: Batch5_Ctrl.CBE08_S8


title: Batch6_Ctrl.CBF16_S16


title: Batch6_Ctrl.CBF12_S12


title: Batch5_Ctrl.CBE76_S14


title: Batch5_Ctrl.CBE09_S9


title: Batch6_Ctrl.CBF01_S1


title: Batch5_Unctrl.CBE70_S8


title: Batch5_Ctrl.CBE74_S12


title: Batch5_Ctrl.CBE75_S13


title: Batch5_Ctrl.CBE73_S11


title: Batch5_Ctrl.CBE69_S7


title: Batch5_Unctrl.CBE07_S7


title: Batch5_Ctrl.CBE72_S10


title: Batch5_Ctrl.CBE66_S4


title: Batch5_Ctrl.CBE71_S9


title: Batch5_Unctrl.CBE64_S2


title: Batch5_Ctrl.CBE67_S5


title: Batch5_Ctrl.CBE65_S3


title: Batch5_Ctrl.CBE63_S1


title: Batch5_Ctrl.CBE06_S6


title: Batch5_Ctrl.CBE62_S16


title: Batch5_Ctrl.CBE60_S14


title: Batch5_Unctrl.CBE61_S15


title: Batch5_Unctrl.CBE59_S13


title: Batch5_Ctrl.CBE56_S10


title: Batch5_Ctrl.CBE57_S11


title: Batch5_Ctrl.CBE54_S8


title: Batch5_Ctrl.CBE55_S9


title: Batch5_Ctrl.CBE53_S7


title: Batch5_Ctrl.CBE51_S5


title: Batch5_Ctrl.CBE68_S6


title: Batch5_Ctrl.CBE52_S6


title: Batch5_Ctrl.CBE05_S5


title: Batch5_Unctrl.CBE49_S3


title: Batch5_Ctrl.CBE47_S1


title: Batch5_Ctrl.CBE50_S4


title: Batch5_Ctrl.CBE43_S13


title: Batch5_Ctrl.CBE44_S14


title: Batch5_Ctrl.CBE42_S12


title: Batch5_Ctrl.CBE46_S16


title: Batch5_Ctrl.CBE48_S2


title: Batch5_Ctrl.CBE41_S11


title: Batch5_Ctrl.CBE40_S10


title: Batch5_Ctrl.CBE39_S9


title: Batch5_Ctrl.CBE38_S8


title: Batch5_Ctrl.CBE04_S4


title: Batch5_Ctrl.CBE35_S5


title: Batch5_Ctrl.CBE34_S4


title: Batch5_Ctrl.CBE58_S12


title: Batch5_Ctrl.CBE33_S3


title: Batch5_Unctrl.CBE32_S2


title: Batch5_Ctrl.CBE03_S3


title: Batch5_Ctrl.CBE30_S16


title: Batch5_Ctrl.CBE45_S15


title: Batch5_Ctrl.CBE29_S15


title: Batch5_Ctrl.CBE28_S14


title: Batch5_Unctrl.CBE25_S11


title: Batch5_Unctrl.CBE27_S13


title: Batch5_Ctrl.CBE26_S12


title: Batch5_Ctrl.CBE23_S9


title: Batch5_Ctrl.CBE24_S10


title: Batch5_Ctrl.CBE17_S3


title: Batch5_Ctrl.CBE20_S6


title: Batch5_Ctrl.CBE16_S2


title: Batch5_Ctrl.CBE22_S8


title: Batch5_Ctrl.CBE37_S7


title: Batch5_Ctrl.CBE36_S6


title: Batch5_Unctrl.CBE19_S5


title: Batch5_Ctrl.CBE18_S4


title: Batch5_Unctrl.CBE21_S7


title: Batch5_Unctrl.CBE02_S2


title: Batch5_Ctrl.CBE15_S1


title: Batch5_Ctrl.CBE13_S13


title: Batch5_Unctrl.CBE14_S14


title: Batch5_Unctrl.CBE11_S11


title: Batch5_Ctrl.CBE12_S12


title: Batch5_Ctrl.CBE10_S10


title: Batch5_Unctrl.CBE01_S1


title: Batch5_Ctrl.CBE31_S1


title: Batch4_Ctrl.CBF24_S24


title: Batch4_Ctrl.CBF23_S23


title: Batch4_Ctrl.CBF21_S21


title: Batch4_Ctrl.CBF20_S20


title: Batch4_Ctrl.CBF17_S17


title: Batch4_Ctrl.CBF14_S14


title: Batch4_Ctrl.CBF18_S18


title: Batch4_Ctrl.CBF12_S12


title: Batch4_Ctrl.CBF11_S11


title: Batch4_Ctrl.CBF8_S8


title: Batch4_Ctrl.CBF5_S5


title: Batch4_Ctrl.CBF6_S6


title: Batch4_Ctrl.CBF4_S4


title: Batch3_Ctrl.CBA40_S20


title: Batch4_Ctrl.CBF2_S2


title: Batch4_Ctrl.CBF3_S3


title: Batch3_Ctrl.CBA39_S19


title: Batch3_Ctrl.CBA38_S18


title: Batch3_Unctrl.CBA37_S17


title: Batch3_Ctrl.CBA35_S15


title: Batch3_Unctrl.CBA36_S16


title: Batch3_Unctrl.CBA33_S13


title: Batch3_Unctrl.CBA34_S14


title: Batch4_Ctrl.CBF22_S22


title: Batch3_Unctrl.CBA32_S12


title: Batch3_Ctrl.CBA30_S10


title: Batch3_Unctrl.CBA29_S9


title: Batch3_Ctrl.CBA28_S8


title: Batch4_Unctrl.CBF19_S19


title: Batch3_Ctrl.CBA27_S7


title: Batch3_Ctrl.CBA25_S5


title: Batch4_Ctrl.CBF13_S13


title: Batch4_Ctrl.CBF15_S15


title: Batch4_Ctrl.CBF10_S10


title: Batch3_Ctrl.CBA24_S4


title: Batch3_Ctrl.CBA23_S3


title: Batch3_Ctrl.CBA20_S20


title: Batch3_Ctrl.CBA17_S17


title: Batch3_Unctrl.CBA19_S19


title: Batch3_Unctrl.CBA18_S18


title: Batch3_Ctrl.CBA14_S14


title: Batch3_Unctrl.CBA15_S15


title: Batch3_Unctrl.CBA21_S1


title: Batch3_Ctrl.CBA16_S16


title: Batch3_Ctrl.CBA31_S11


title: Batch3_Ctrl.CBA12_S12


title: Batch3_Unctrl.CBA10_S10


title: Batch3_Unctrl.CBA9_S9


title: Batch3_Ctrl.CBA13_S13


title: Batch3_Ctrl.CBA8_S8


title: Batch3_Unctrl.CBA7_S7


title: Batch3_Ctrl.CBA26_S6


title: Batch3_Ctrl.CBA6_S6


title: Batch3_Unctrl.CBA5_S5


title: Batch3_Ctrl.CBA4_S4


title: Batch3_Ctrl.CBA2_S2


title: Batch3_Unctrl.CBA22_S2


title: Batch3_Ctrl.CBA3_S3


title: Batch2_Ctrl.CB56_S17


title: Batch2_Ctrl.CB51_S13


title: Batch2_Ctrl.CB55_S16


title: Batch2_Ctrl.CB54_S19


title: Batch2_Ctrl.CB57_S18


title: Batch2_Ctrl.CB48_S10


title: Batch2_Ctrl.CB50_S12


title: Batch2_Ctrl.CB49_S11


title: Batch2_Ctrl.CB45_S8


title: Batch2_Ctrl.CB44_S18


title: Batch3_Ctrl.CBA11_S11


title: Batch2_Ctrl.CB42_S16


title: Batch2_Ctrl.CB47_S9


title: Batch2_Ctrl.CB43_S17


title: Batch2_Ctrl.CB41_S15


title: Batch2_Unctrl.CB40_S14


title: Batch2_Ctrl.CB37_S7


title: Batch2_Ctrl.CB39_S13


title: Batch2_Ctrl.CB34_S5


title: Batch2_Unctrl.CB33_merge


title: Batch3_Unctrl.CBA1_S1


title: Batch2_Ctrl.CB35_S6


title: Batch2_Ctrl.CB38_S12


title: Batch2_Unctrl.CB31_S3


title: Batch2_Unctrl.CB28_S1


title: Batch2_Ctrl.CB30_S2


title: Batch2_Unctrl.CB26_S15


title: Batch2_Unctrl.CB29_S17


title: Batch2_Unctrl.CB27_S16


title: Batch2_Unctrl.CB25_S11


title: Batch2_Ctrl.CB24_S10


title: Batch2_Ctrl.CB23_S9


title: Batch2_Ctrl.CB21_S8


title: Batch2_Ctrl.CB20_S13


title: Batch2_Ctrl.CB19_S7


title: Batch2_Ctrl.CB16_S12


title: Batch2_Unctrl.CB15_S11


title: Batch2_Ctrl.CB13_S9


title: Batch1_Ctrl.JK36_S8


title: Batch1_Ctrl.JK35_S7


title: Batch2_Ctrl.CB17_S5


title: Batch1_Unctrl.JK34_S6


title: Batch1_Ctrl.JK33_S8


title: Batch1_Ctrl.JK32_S5


title: Batch1_Ctrl.JK28_S8


title: Batch1_Ctrl.JK31_S7


title: Batch1_Unctrl.JK29_S11


title: Batch1_Unctrl.JK27_S11


title: Batch1_Ctrl.JK26_S10


title: Batch1_Ctrl.JK24_S6


title: Batch1_Unctrl.JK25_S4


title: Batch1_Ctrl.JK22_S3


title: Batch1_Unctrl.JK23_S7


title: Batch1_Ctrl.JK20_S9


title: Batch2_Unctrl.CB22_S14


title: Batch1_Ctrl.JK18_S10


title: Batch1_Ctrl.JK21_S2


title: Batch1_Ctrl.JK19_S6


title: Batch1_Unctrl.JK17_S5


title: Batch1_Ctrl.JK15_S9


title: Batch1_Ctrl.JK10_S9


title: Batch1_Unctrl.JK8_S12


title: Batch1_Ctrl.JK9_S1


title: Batch1_Unctrl.JK11_S10


title: Batch1_Ctrl.JK14_S11


title: Batch1_Ctrl.JK12_S3


title: Batch1_Ctrl.JK7_S2


title: Batch1_Ctrl.JK4_S3


title: Batch1_Ctrl.JK5_S4


title: Batch1_Ctrl.JK3_S2


title: Batch1_Ctrl.JK2_S1


title: spatial transcriptome for patient 1

city: Nanjing

first: Dijun

state: Jiangsu

address: Xianlin

department: Life Sciences

institute: Nanjing University

description:
ST_normal
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx, peaks.bed).
Supplementary files format and content: Image files (.jpg).
Library strategy: spatial transcriptomics

source_name: Endometrium

extract_protocol: scRNA-seq, scATAC-seq data and ST-seq generated in this study were performed on the 10× Chromium platform using single-cell 3’ V3.1 (scRNA-seq) or V1.1 (scATAC-seq) according to the manufacturer’s protocols including sample preparation, library preparation and instrument and sequencing settings. All libraries were sequenced on the NextSeq 500 platform (Illumina) with paired-end sequencing and dual indexing.

value: Endometrium

value: All cells

tag: diagnosis

value: No

tag: patient


title: scATAC-seq for patient 7

description:
ATAC_EH1
10x Genomics

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx, peaks.bed).
Supplementary files format and content: Image files (.jpg).

value: Endometrial hyperplasia


title: scATAC-seq for patient 8

description:
ATAC_EH2
10x Genomics


title: Batch1_Ctrl.JK1_S1


title: scATAC-seq for patient 6

description:
ATAC_EN2
10x Genomics

value: Endometritis


title: scATAC-seq for patient 4

description:
ATAC_Normal4
10x Genomics


title: scATAC-seq for patient 5

description:
ATAC_EN1
10x Genomics


title: endometritis from the patient 23

description:
EN6
10x Genomics


title: scATAC-seq for patient 1

description:
ATAC_Normal1
10x Genomics


title: endometritis from the patient 24

description:
EN7
10x Genomics


title: scATAC-seq for patient 3

description:
ATAC_Normal3
10x Genomics


title: scATAC-seq for patient 2

description:
ATAC_Normal2
10x Genomics


title: Batch1_Ctrl.JK16_S12


title: endometritis from the patient 22

description:
EN5
10x Genomics


title: Batch1_Ctrl.JK13_S4


title: Batch1_Unctrl.JK6_S5


title: endometritis from the patient 21

description:
EN4
10x Genomics


title: endometritis from the patient 20

description:
EN3
10x Genomics


title: endometritis from the patient 18

description:
EN1
10x Genomics


title: endometritis from the patient 19

description:
EN2
10x Genomics


title: endometrial hyperplasia from the patient 15

description:
EH8
10x Genomics


title: endometrial hyperplasia from the patient 16

description:
EH9
10x Genomics


title: endometrial hyperplasia from the patient 14

description:
EH7
10x Genomics


title: spatial transcriptome for patient 2

description:
ST_EH
10x Genomics


title: endometrial hyperplasia from the patient 13

description:
EH6
10x Genomics


title: endometrial hyperplasia from the patient 10

description:
EH3
10x Genomics


title: endometrial hyperplasia from the patient 12

description:
EH5
10x Genomics


title: endometrial hyperplasia from the patient 11

description:
EH4
10x Genomics


title: normal endometrium from the patient 7

description:
Normal7
10x Genomics


title: endometrial hyperplasia from the patient 8

description:
EH1
10x Genomics


title: normal endometrium from the patient 6

description:
Normal6
10x Genomics


title: endometrial hyperplasia from the patient 9

description:
EH2
10x Genomics


title: normal endometrium from the patient 5

description:
Normal5
10x Genomics


title: normal endometrium from the patient 3

description:
Normal3
10x Genomics


title: normal endometrium from the patient 4

description:
Normal4
10x Genomics


title: normal endometrium from the patient 1

description:
Normal1
10x Genomics


title: Control mAb treated spheroids

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

description: Cells derived from HCC tissue

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used for identification of the Illumina library barcode, cel barcode and UMI. R2 was assigned 60 base pairs and used to map to the reference transcriptome of Hg38 with BWA (Anders and Huber, 2010).
Data was demultiplexed as described in Grün et al. 2014.
Mapping and generation of count tables was automated using the MapAndGo script (https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell of every sample

source_name: Liver spheroids

growth_protocol: HCC tumor tissue was dissociated into single cells and spheroids were generated and cultured in 96 well ultra-low attachment plates with 20 spheroids per treatment group

extract_protocol: scRNA-Seq was performed by Single-Cell Discoveries B.V. using SORT-seq protocol

treatment_protocol: HCC spheroids were treated with 50 µg/ml CLDN1 mAb or Control mAb for 24h and then single cells were sorted into 384 well cell capture plates (Single Cell Discovery, https://www.scdiscoveries.com) using SH800 cell sorter (Sony).

value: Control mAb-treated

value: HCC


title: CLDN1 mAb treated spheroids

description: Cells derived from HCC tissue

value: CLDN1 mAb-treated


title: hBES-blastoids

city: beijing

first: yuxin

last: luo

address: NO.49 Huanyuanbei Road Haidian District

institute: Peking University Third Hospital

description: synthetic embryos

data_processing:
Alignment, filtering, barcode counting, and UMI counting were performed with Cell Ranger count module to generate feature-barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principal components were used to generate clusters by K-means algorithm and graph-based algorithm, respectively. The other clustering method is Seurat 4.0.3 (R package).
The R package Seurat 4.0.3 was used to analyze feature-barcode matrix as following steps: First, cells whose gene numbers were less than 100, unique features count over 60,000, and mitochondrial gene ratio was more than 20% according to quality control matrix plots, were regarded as abnormal and filtered out.
Then UMI counts were normalized with NormalizeData function using defalult settings. A nonlinear dimensionality reduction was performed using PCA, clustered with resolution setting at 0.6, and visualized by TSNE and UMAP.
Differentially expressed genes (DEGs) in clusters were determined by the FindAllMarkers function (Seurat 4.0.3) using a minimum upregulation of 0.25 log-fold. DEGs between lineages with uncorrected P values were smaller than 0.01, and log-fold change was larger than 0.25 (log2FC > 0.25) in one group were regarded as DEGs. The GO terms of DEGs in biological process were enriched using DAVID. Heat map of top DEGs between clusters was performed with DoHeatmap (Seurat 4.0.3). Then the overlapped DEGs between blastoids and blastocysts were normalized and showed in heat map by DoHeatmap.
Assembly: hg38
Supplementary files format and content: processed tsv files contain information on barcodes and gene annotations; the processed mtx files contain gene umi counts

source_name: fibroblasts

extract_protocol:
hPES-blastoids and hBES-blastoids were manually picked up using mouthpipette and washed three times. ~150 hPES-blastoids or hBES-blastoids were harvested and dissciated with a homemade enzyme mix composed of 0.5 X versene (Lonza, 17711E), 0.5 X Acumax (Innovative Cell Tech, AM105), and 0.05 X Dnase (STEMCELL Tech, 07900) at 37°C for 30 min with agitation. Dissociated cells were spinned down and wash with PBS + 0.05% BSA for three times and resuspended in the same buffer. Cell density was determined by a TC10 cell counter (Biorad, 1450001).
Dissociated cells (~6000 cells for hPES-blastoids and ~8000 cells for hBES-blastoids) were loaded into the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. The library was generated using the Chromium Single Cell 3‘ Reagent Kits according to the manufacturer’s manual. The two libraries were pooled and sequenced using Nextseq 500 (150 cycles, high output).

value: fibroblasts

value: human naive induced pluripotent stem cells


title: hPES-blastoids

description: synthetic embryos

source_name: embryos

value: embryos

value: human naive parthenogenetic embryonic stem cells


title: endometrial hyperplasia from the patient 17

description:
EH10
10x Genomics

value: Female


title: S11

city: Xi 'an

first: Bing

last: Qi

state: Select

address: No. 1, Xinwang Road, Weiyang District

institute: Xi'an Medical University

description: Control PANC-1 samples were treated with an empty plasmid vector under the same transfection conditions to ensure any observed effects were specifically due to GLI1 overexpression.

hyb_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were tailed with Poly A and then labeled with Biotin. Afer, the labeled RNAs were hybridized onto the microarray.

scan_protocol: Having washed and staining the slides, the arrays were scanned by the Affymetrix Scanner 3000 (Affymetrix).

data_processing: Affymetrix GeneChip Command Console software (version4.0, Affymetrix) was used to analyze array images to get raw data

label: biotin

label_protocol: RNA integrity was assessed using Agilent 2100 (Agilent Technologies)

growth_protocol: PDAC cells, including SW1990 and Panc-1, were procured from the Type Culture Collection of the Chinese Academy of Sciences (Shanghai, China). These cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, Gibco, USA) supplemented with 10% fetal bovine serum (FBS, Gibco, USA) and penicillin-streptomycin solution (100 U/mL penicillin/100 ng/mL streptomycin, Hyclone, USA) at 37°C with 5% CO2. Recombinant human SHH, TNF-α and IL-1β were acquired from R&D Systems, USA. The cells were seeded in T25 culture dishes (Corning, USA).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The cells in the logarithmic phase were transfected with  Gli1 cDNA and their corresponding controls.

tag: transfection

value: control


title: S8


title: PANC-1 LIP-2

description: GLI1 overexpression was achieved in PANC-1 cells via plasmid transfection. This involved introducing a GLI1-expressing plasmid into the cells using a lipid-mediated transfection reagent, allowing for elevated GLI1 expression to study its effects on cellular functions.

source_name: PANC-1 LIP-2


title: PANC-1 LIP-1

source_name: PANC-1 LIP-1


title: a

description: Control SW1990 samples were treated with an empty plasmid vector under the same transfection conditions to ensure that any observed effects were specifically due to GLI1 overexpression.

source_name: a


title: PANC-1 LIP

source_name: PANC-1 LIP


title: Arabidopsis emf2 callus, biol rep3

city: Rehovot

first: Leor

middle: Eshed

last: Eshed Williams

address: P.O.Box 12

department: Faculty of Agriculture

country: Israel

institute: Hebrew university

description: Library name: SAMPLES 3 biol rep 3

data_processing:
Each NGS analysis included quality control using FastQC
adaptor trimming using cutadapt
NGS reads were mapped to the Arabidopsis thaliana reference transcriptome TAIR10 using TopHat
Assembly: TAIR10
Supplementary files format and content: No processed data

organism: Arabidopsis thaliana

source_name: Callus

growth_protocol: For all experiments, seeds were surface sterilized for 10 minutes in 3% Sodium Hypochlorite containing 0.1% Triton X-100 and washed 4 times with DDW before sowing. seeds were sown on Murashige and Skoog (MS) basal medium 87, and kept under continuous light at 23°C for one week. Seedlings were then transplanted to soil and grown under long-day conditions (16h light/8h dark) at 21°C. Rosette leaves were harvested two weeks after transplanting.

extract_protocol:
Samples were ground, and total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's instructions, including treatment with RNase-free DNase (Qiagen). Each RNA sample was loaded on agarose gel for integrity validation and quantified using NanoDrop.
Sequencing was done at the Technion Genome Centre (TGC) according to Illumina's protocols. The TruSeq RNA V2 sample prep kit (RS-122) was used. Total RNA was polyA-selected, followed by fragmentation and random hexamer-primed reverse transcription. Indexed adapters were added, and cDNA was amplified by PCR for 15 cycles. Every four indexed libraries were loaded onto an individual lane of Illumina's HiSeq 2500 system.

treatment_protocol: To generate callus from Col-0 and emf2 cotyledons, sterilized seeds were sown directly on callus-inducing medium (CIM): Gamborg B5 medium with 0.5g/L MES, 2% dextrose, 0.9% phytagel, supplemented with 2.2μM 2,4-dichlorophenoxyacetic acid and 0.46μM kinetin. Following two days at 4°C, plates were transferred to a continuous light growth room at 23°C. After seven days, cotyledons were trimmed and transferred to a new CIM plate placed in the dark. During the next 5-6 weeks, calli were re-cultured to new CIM plates every 7-10 days. All analyses were done on 6-8 weeks-old calli.

value: Callus


title: c

source_name: c


title: S10


title: Arabidopsis emf2 callus, biol rep2

description: Library name: SAMPLES 3 biol rep 2


title: Arabidopsis Wild type callus, biol rep3

description: Library name: SAMPLES 2 biol rep 3

value: Wild Type


title: 1990 LIP-1

description: GLI1 overexpression was achieved in SW1990 cells via plasmid transfection. This involved introducing a GLI1-expressing plasmid into the cells using a lipid-mediated transfection reagent, allowing for elevated GLI1 expression to study its effects on cellular functions.


title: b

source_name: b


title: Arabidopsis thaliana Wild type leaves, biol rep 3

description: Library name: SAMPLES 1 biol rep 3

source_name: Leaf

value: Leavs

value: Leaf


title: normal endometrium from the patient 2

description:
Normal2
10x Genomics

value: Endometrium

value: All cells

value: Normal


title: 1990 LIP


title: BBROA2

first: Sun

address: 101 Longmian Avenue

institute: Nanjing Medical University

data_processing:
Filtering of Clean Reads
Alignment with Ribosome RNA (rRNA)
Alignment with Reference Genome
Transcripts Reconstruction
Novel Gene Transcripts Identification and Annotation
Quantification of Gene Abundance
Assembly: mm10
Supplementary files format and content: Text file includes raw counts and FPKM values for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted from tissue samples using the Trizol RNA extraction kit
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and  buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeqTM 2500 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: liver

value: BBROA


title: Arabidopsis thaliana Wild type leaves, biol rep 1

description: Library name: SAMPLES 1 biol rep 1


title: BBROA1


title: BBR3

value: BBR


title: Arabidopsis thaliana Wild type leaves, biol rep 2

description: Library name: SAMPLES 1 biol rep 2


title: BBROA3


title: BBR2


title: BBR1


title: ConOA3

value: ConOA


title: Arabidopsis Wild type callus, biol rep1

description: Library name: SAMPLES 2 biol rep 1


title: Con3

value: Con


title: Arabidopsis emf2 callus, biol rep1

description: Library name: SAMPLES 3 biol rep 1


title: ConOA2


title: Con1


title: ConOA1


title: Arabidopsis Wild type callus, biol rep2

description: Library name: SAMPLES 2 biol rep 2


title: Wild Type aorta 4

city: Madrid

first: Pablo

last: Minguez

state: Madrid

address: Av. Reyes Catolicos 2

department: Genetics and Genomics

country: Spain

institute: Health Research Institute Fundación Jiménez Díaz (IIS-FJD), UAM

description: Total RNA

data_processing:
Tophat2 applied to align reads to GrCM38/mm10 genome
Htseq-count was used to extract counts
Assembly: mm10
Supplementary files format and content: raw counts for each Sample

source_name: aorta

extract_protocol:
Total aorta were harvested using Trizol reagent. Rnaeasy plus mini kit was used to isolate RNA. 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: aorta

value: normal diet

tag: time

value: 40 week-old mice


title: Wild Type aorta 3

description: Total RNA


title: Wild Type aorta 1

description: Total RNA


title: ApoE aorta 4

description: Total RNA

value: ApoE knockout


title: ApoE aorta 3

description: Total RNA


title: 1990 LIP-2


title: ApoE aorta 2

description: Total RNA


title: s8

value: control


title: ApoE aorta 1

description: Total RNA


title: Human PGCLC KLF4 Cut&Run replicate 2

data_processing:
RNA-seq: The low-quality reads and adaptor sequences were removed by Trim Galore. The pre-processed reads were mapped to human reference genome (GENCODE, GRCh38.p13) using STAR with parameters --outFilterMultimapNmax 1 --outFilterMatchNmin 35. The raw read counts per gene were extracted by the --quantMode GeneCounts option. The HOMER functions makeTagDirectory and makeUCSCfile were used to create bedGraph files.  Cut&Run: The leeHom package program with —ancientdna option was used to trim the reads. The pre-processed reads were mapped to the human reference genome (GENCODE, GRCh38.p13) using Bowtie2 with options –very-sensitive –no-mixed –no-discordant -q –phred33 -I 10 -X 700. The macs2 function —bdg were used to create be
Assembly: hg38
Supplementary files format and content: bedGraph
Library strategy: CUT&Run

source_name: Embryonic stem cells

value: Embryonic stem cells

value: Primordial germ cell-like cells

value: PGCLC differentiation


title: Con2


title: b


title: s10


title: Runx3

city: Tianjin

first: Yun Huan

last: Gao

address: 94 Weijin Road, Nankai District, Tianjin

institute: Nankai University

description:
Library name: SAMPLES 2
10X Genomics

data_processing:
Single-cell RNA-seq data were pre-processed and qualitied with Seurat (version 4). We removed the cells that had greater than 15% expression originating from mitochondrial genes as well as expressed less than 200 genes or greater than 6,000 genes to filter out low-quality cells and doublets.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separted values files and matrix files

source_name: gut

extract_protocol:
For the collection of the immune cells in colon, mice were sacrificed by CO2 overdose and colon was removed and placed in ice-cold HBSS (GIBCO) with 5% FBS. Isolated cells were resuspended in 10 ml of the 40% fraction of a 40: 80 Percoll gradient and overlaid on 5 ml of the 80% fraction in a 15 ml Falcon tube. Percoll gradient separation was performed by centrifugation for 20 min at 1,800 rpm at room temperature. lymphocytes were collected at the interphase of the Percoll gradient, washed and resuspended in medium, and then stained for sorting and analyzed by flow cytometry. Dead cells were eliminated through 7-AAD staining.
According to the manufacture’s introduction, single-cell RNA-seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

value: gut

value: gut lamina propria


title: PANC-1LIP-C2


title: Human PGCLC KLF4 Cut&Run replicate 1


title: S11


title: 1990 LIP-C1


title: 1990 LIP-C2


title: Runx3_fl

description:
Library name: SAMPLES 1
10X Genomics


title: PANC-1LIP-C1


title: c


title: 9m_Male_Naive_2

city: Bristol

first: Alison

middle: Jane

last: Clare

address: University Walk

institute: University of Bristol

data_processing:
The Illumina NextSeq 500/550 High Output v2 kit (75 cycles) on an Illumina NextSeq 500 Sequencing System was used to sequence samples, to depths of up to 2.9 million single-end 75 nt length reads per sample. NextSeq Control Software v2.0 (NCS) and Real-Time Analysis Software v2 (RTA), were used for image analysis, base calling, and generation of sequence reads, before conversion to FASTQ files using the bcl2fastq2 v2.20 software (Illumina Inc.), producing four FASTQ files per sample.
Data were processed to read counts using Galaxy (https://academic.oup.com/nar/article/50/W1/W345/6572001): STAR (v2.7.8a) was used to map to reference index mm10. Resulting bam files were concatenated using mergeSAMfiles (v2.18.2.1) and read counts determined using feature counts (v2.0.1) with refGene (https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/genes/) for annotation.
Exported raw counts were further processed in R studio (v 2022.12.0+353 and R v4.2.2): combatseq (sva package) was used to correct for batch effect from collection days.
Assembly: mm10
Supplementary files format and content: comma seperated value file containing raw counts for each sample
Supplementary files format and content: comma seperated value file containing raw counts for each sample after combatseq batch correction

source_name: Retina

extract_protocol:
Exactly 600 microglia were sorted from mechanically dissociated retinas (kept ice cold) directly into lysis buffer from the SMART-seq v4 kit. All samples were collected within 2 h from cull. Each batch was randomised to include a mix of all conditions to mitigate batch effects of sort and cDNA preparation. Samples were collected over two days, with all samples collected in one day processed to cDNA preparations together (sorted samples were stored in lysis buffer on ice until all samples were collected).
The SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, was used for cDNA preparation and amplification (16 PCR cycles), according to the user manual, before cDNA isolation using the Agencourt AMPure XP Kit (Beckman Coulter, Brea, CA). Quantification of cDNA was performed using the Agilent High Sensitivity DNA Kit on an Agilent 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA) and 150 pg of cDNA was used for library preparation using the Nextera XT DNA Library Preparation Kit (Illumina Inc., San Diego, CA).

treatment_protocol: Animals received an intravitreal injection of AAV2 (no transgene) at 1E10 gc/eye. Eyes were collected naïve, 12 or 28 days post-injection.

tag: batch

value: two

value: M

value: Retina

value: Microglia

value: Cx3cr1CreER:R26-tdTomato +/-

value: Naive

tag: time-point


title: 18m_Male_D12_3


title: PANC-1LIP-C


title: Wild Type aorta 2

description: Total RNA

value: Wild Type


title: 1990 LIP-C


title: 18m_Male_D28_4


title: 3m_Female_Naive_4

value: F


title: 18m_Female_D12_4