title: CD45+ of Control tumor mice 2

description: 10X Genomics


title: mouse_mirmOTSTEO_sample_22_a (control)

status: Public on Sep 06 2024

type: SRA

city: Stockholm

first: Cheng

last: Zhao

address: Solnavägen 1, 171 77 Solna

department: Department of Clinical Science

country: Sweden

institute: Karolinska institute

library_source: transcriptomic single cell

data_processing:
Read quality was firstly checked by FastQC. Subsequently, we aligned high-quality reads to the mouse mm10 reference genome (mm10-2020-A, obtained from the 10X Genomics website) using the STAR aligner (v2.5.1b) with default settings. Raw read counts were quantified using the rsem-calculate-expression from RSEM (v1.3.0) with the option of " --single-cell-prior". Low-quality cells were filtered out by discarding those with fewer than 3000 expressed genes or with a percentage of mitochondrial genes higher than 0.1.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: embryo

growth_protocol: All mouse experiments were approved by the Centre de Recherche du Centre Hospitalier de l’Universite de Montreal (CRCHUM) Comite Institutionnel de Protection des Animaux du CHUM (CIPA) under the protocol number IP21005SPs. To induce ovulation, C57BL/6 x DBA F1 females were injected with 5 IU of pregnant mare’s serum gonadotropin (PMSG), followed by 5 IU of human chorionic gonadotropin (hCG) 48 hours later. Super-ovulated females were placed with C57BL/6 x DBA F1 male mice for mating immediately following the hCG injection and sacrificed using isoflurane anaesthetic and cervical dislocation 45 to 48 hours later.

extract_protocol:
Upon reaching the desired developmental stage (8 cell (E2.5) or 32 cell (E3.5)), several control and mimic-treated mouse embryos (3-5 embryos/group/timepoint) were collected for single cell dissociation and isolation. Embryos were briefly transferred into Tyrodes solution (Millipore, ref # MR-004-D) to digest the zona pellucida, then were dissociated through trituration in TrypLE (Life Technologies, ref # 12604-013) and picked with fine glass capillaries. Individual cells were dispensed in 4.1 uL Smart-Seq2 lysis buffer and stored at -80°C until library preparation.
Following removal from -80°C storage and thawing, cell lysis (thermocycler, 72°C for 3 minutes) and reverse transcription were performed. This was followed by two polymerase chain reactions (PCRs), the first to amplify the cDNA product (20 cycles) and second with indexes to barcode the libraries for multiplexing (11 cycles). Sample purification, downstream library preparation, sequencing with a NextSeq550 and data analysis using in-house pipelines were all performed as described in Petropoulos et al., 2016

treatment_protocol: At E1.5, uteri were dissected and flushed with 37°C EmbryoMax M2 medium (Sigma-Aldrich, cat # MR-015-D) to collect 2 cell embryos. These embryos were placed in pre-equilibrated EmbryoMax KSOM Media (Sigma-Aldrich, cat # MR-121-D) droplets covered with EmbryoMax Filtered Light Mineral Oil (Sigma-Aldrich, cat # ES-005-C). At this point, mirVana™ custom miRNA mimics (Invitrogen™ (ThermoFisher Scientific)) designed to replicate the actions of miR-381-3p were added directly to media droplets containing 2 cell embryos at a final concentration of either 5 µM or 10 µM. In parallel, a scrambled negative control mimic (Invitrogen™ (ThermoFisher Scientific), cat # 4464058) at the same concentration was used. Embryos were cultured with their respective treatments to later stages of preimplantation development in a normoxic incubator at 37°C (5% CO2, 20% O2).

tag: tissue

value: embryo

tag: developmental stage

value: 8 cell

tag: treatment

value: control


title: Pooled snRNA-seq Heart

city: Aachen

first: Tore

last: Bleckwehl

address: Pauwelsstrasse 30

department: Klinik fuer Nieren- und Hochdruckkrankheiten, rheumatologische und immunologische Erkrankungen (Medizinische Klinik II)

country: Germany

institute: RWTH Uniklinik

description:
Heart_Pooled
Pooled 10X Genomics Library

data_processing:
For the demultiplexing of CellPlex and Hashtag based sample labeling, sequencing reads were mapped to the reference genome GRCh38-2020-A applying the the cellranger multi pipeline (version 7.1.0) with default setting and the used sample barcodes for the corresponding tagging method
Assembly: GRCh38-2020-A
Supplementary files format and content: raw_feature_bc_matrix, multiplexing_assignment_tables

organism: Homo sapiens

source_name: Heart

extract_protocol:
For PBMC isolation blood was collected from patients into EDTA-tubes and mixed 1:1 with PBS. EDTA-blood was then carefully layered on to Ficoll-Paque Plus (1:1,5) and centrifuged (400 G, 40 min, RT). After centrifugation the PBMC-Layer was aspirated, resuspended in FACS-Buffer (PBS, 2% FCS, 2mM EDTA) and centrifuged (300 G, 10 min, RT). The supernatant was discarded and cells were resuspended in 300 µl FACS Buffer. At this step, PBMC were counted and ~0.5x106 cells were taken for each Bulk-RNA sequencing and WES. The remaining cells were stained with CD14-PE, CD16-APC, CD4-FITC, CD8-PE Cy7 and CD19-BB700 (30 min, 4°C, protected from light). Afterwards, cells were washed once with FACS Buffer (400 g, 5 min, 4°C) before staining PBMC with a unique CellPlex-Oligo (100 µl, 5 min, RT) for each patient. Subsequently cells were washed twice, before sorting a unique PBMC population for each patient (CD14 Monocytes, CD16 Monocytes, CD4 T-Cells, CD8 T-Cells, CD19 B-Cells) using a BD FACSMelody Cell Sorter. For lymphocytes Dapi, CD16 and CD14 positive cells were excluded to avoid dead cell and monocyte contamination. For monocytes Dapi, CD4 and CD8 positive cells were excluded to avoid dead cell and lymphocyte contamination. After sorting, PBMC were pooled and immediately loaded onto a Chromium Next GEM Chip G for snRNA-seq (10x, 3’ v3.1). For heart samples, Snap frozen tissue was crushed using a mortar and pestle, resuspended in 500 µl nuclei lysis Buffer (NLB, EZ lysis Buffer NUC101, Sigma-Aldrich with 1 Tab/10 ml  of Complete Protease Inhibitor, Roche and 10 µl/ml Recombinant RNase Inhibitor 2313A, Takara Bio and 10µl/ml Superase In RNase Inhibitor, Thermofisher) and homogenized with dounce tissue grinder pestles. The homogenized solution was spun down, supernatant discarded and the pellet resuspended in 4 ml nuclei resuspension buffer (NRB, PBS, 1% BSA, 10 µl/ml Protector RNase Inhibitor, Rochel). The suspension was then filtered via a 40 µm cell strain and centrifuged (500 G, 4°C, 5 min). Supernatant was discarded, and cells resuspended in 200 µl Nuclei resuspension Buffer (NRB, PBS, 1% BSA, 10 µl/ml Protector RNase Inhibitor, Rochel) with 3 µl of a unique TotalSeq anti-Nuclear Pore Complex Antibody Hashtag-Antibody for each sample (4°C, 20 min). Subsequently samples were washed with 1 ml NRB, centrifuged (500 G, 4°C, 5 min) and resuspended in 100 µl of a unique CellPlex Oligo for each sample (RT, 5 min). Cells were washed once more with NRB (500 G, 4°C, 5 min) before proceeding to Fluorescent-activated Nuclei-sorting of DAPI positive nuclei with a Sony SH800S. 5 minutes prior to sorting nuclei were stained with DAPI (Sigma-Aldrich). After sorting, nuclei were pooled and immediately loaded onto a Chromium Next GEM Chip G for snRNA-seq (10x, 3’ v3.1).
Single cell RNA (3’ v3.1, Dual Index) and 3’ CellPlex library preparation was performed according to the manufacturer's instructions. Hashtag-Libraries were prepared as described by Stoeckius et al.

value: Heart


title: CellPlex labeling PBMC

library_source: other

molecule: other

source_name: PBMC

value: PBMC


title: Mga_KO_2

city: Houston

first: Chang

last: Yang

state: Texas

address: 6565 MD Anderson BLVD

department: Experimental Radiation Oncology

country: USA

institute: The University of Texas MD Anderson Cancer Center

library_source: transcriptomic

data_processing:
The raw reads were first processed using AfterQC (Version 0.9.7, https://github.com/OpenGene/AfterQC) for data filtering, trimming, error removing and quality control.
Genome mapping was carried out using HISAT2 software (v2.1.0) with the mouse reference genome (UCSC GRCm38/mm10).
Reads in features were counted using htseq-count (v0.6.1p1) as a part of HTSeq (https://htseq.readthedocs.io/en/latest/).
Expression of the transcripts or genes was normalized as FPKM (fragments per kilobase of transcript per million mapped reads) for quantification.
Assembly: UCSC GRCm38/mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

molecule: total RNA

growth_protocol: 4T1 WT and Mga KO cells were cultured in DMEM medium with 10% FBS.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, 74104)  according to the manufacturer’s instructions.
The libraries were prepared with NEBNext Ploy(A) mRNA Magnetic Isolation Module (E7490L, New England Biolabs), NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L, New England Biolabs) and NEBNext Multiplex Oligos for illumina (E6609S, New England Biolabs)

treatment_protocol: With or without IFN-g stimulation (100ng/ml) for 24 hours

tag: cell line

tag: cell type

value: epithetial cell

tag: genotype

value: Mga KO

value: Mock


title: HUVECT1_model_EGB761_H2

city: Jiangsu province

first: Wei

last: Xiao

address: N0.58 Kangyuan Road, Jiangning Industrial town, Economic and development zone, Lianyun District

country: China

institute: State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process

data_processing:
Demultiplexing and basecalling performed using CASAVA version 1.8.2
QC was performed on the FASTQ files using FastQC(v0.11.5) software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens(hg19) whole genome using HISAT2(v2.1.0).
Sequence reads aligned to the human genome were imported into HTseq(v0.11.3) for sequence read counting.
Sequence reads mapped to different isoforms of individual genes were pooled together, and then were input into the DESeq(v1.36.0) differential expression analysis program to normalize and determine expression levels and differentially expressed genes.
Genome_build: Homo sapiens
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each gene per sample

source_name: cell line: Human umbilical vein endothelial cell line HUVECT1

growth_protocol: The human macrophage cell line THP-1 was maintained in RPMI 1640 medium (HyClone, USA), while the human umbilical vein endothelial cell line HUVEC-T1 and the human astroglioma cell line U251 were cultured in Modified Eagle’s medium (MEM) (HyClone, USA), both media supplemented with 10% fetal bovine serum (FBS, ExCell Bio, China). The human megakaryoblastic cell line MEG-01 was cultured in RPMI 1640 medium supplemented with 20% FBS. The human neuroblastoma cell line SH-SY5Y was cultured in (EMEM) (HyClone, USA) supplemented with 15% FBS. The human microglialcell line HMC3 was cultured in special culture medium (Procell, China). All media were supplemented with 1% penicillin, and 1% streptomycin (HyClone, UT, USA)1% penicillin, and 1% streptomycin (HyClone, UT, USA). All cell lines were authenticated and tested negative for mycoplasma contamination.

extract_protocol:
The cell lysates were directly reverse transcribed and amplified into double stranded cDNAs, which were subsequently added adaptors by Tn5 transposase. The purified and fragmented products were used for library construction and sequencing.
RNA libraries were prepared for sequencing using Illumina protocols

treatment_protocol: After seeding cells into the 96well plates following growth protocol. MEG-01 was cultured in medium containing 100 ng/mL PMA (Sigma-Aldrich, Germany) for 3 days. HUVECs-T1 and HMC3 inflammatory model were built by stimulating cells with 5 ng/mL IL-1β (GenScript, China) for 24 h. U251 was induced fibrosis related reactions with 10 ng/ml TGF-β (GenScript, China) for 24h. SH-SY5Y cell was cultured in medium containing 10 µM RA (Sigma-Aldrich, Germany) for 10 days. After 10 days, SH-SY5Y cell culture medium was replaced with sugar free medium and treated with hypoxia for 4 hours, then replaced medium and incubated for 24 hours with 5% CO2 at 37°C to build SH-SY5Y OGD model. THP-1 cell was differentiated into resting (M0) macrophages by 24 h incubation with 100 ng/ml PMA (Sigma-Aldrich, Germany) followed by treating with 1 µg/mL LPS (Sigma-Aldrich) for 24 h to polarize into M1 macrophages. Meanwhile, THP-1 cell was incubated in medium with 80 μg/mL oxLDL for 24 h to form foam cells. All cells harvested at the indicated time point.


title: Mga_KO_3


title: mouse_mirmOTSTEO_sample_21_a (control)


title: mouse_mirmOTSTEO_sample_26_a (control)


title: Pooled scRNA-seq PBMC

description:
PBMC_Pooled
Pooled 10X Genomics Library


title: HUVECT1_model_EGB761_H1


title: HUVECT1_model_DMSO_M3


title: Mga_KO_1


title: mouse_mirmOTSTEO_sample_19_a (control)


title: Heart_bulkRNA-seq_Patient_10

data_processing:
Sequencing reads from bulkRNA-seq were aligned with STAR to the same reference genome used for the single-cell RNA-seq and variants were called with freebayes using the following parameters: -iXu --min-mapping-quality 30 --min-base-quality 10 --min-coverage 5.
Assembly: hg38
Supplementary files format and content: VCF files with called SNPs
Supplementary files format and content: .

extract_protocol:
For snap frozen tissue samples, samples were shredded in RNeasy lysis buffer in a Mixer Mill prior RNA Isolation. For PBMC samples were lysed with RNeasy lysis buffer. Subsequently, RNA was extracted for both tissue and PBMC samples using the RNeasy Mini Kit (74106, Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepped with the NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760L) according to the manufacturer's instructions.

tag: subject id


title: WT_IFN-g_3

value: WT

value: IFN-g


title: HUVECT1_model_DMSO_M2


title: Heart_bulkRNA-seq_Patient_9


title: mouse_mirmOTSTEO_sample_1_a (control)


title: Heart_bulkRNA-seq_Patient_8


title: HUVECT1_model_DMSO_M1


title: WT_IFN-g_2


title: HUVECT1_model_DMSO_L3


title: Mga_KO_IFN-g_1


title: Heart_bulkRNA-seq_Patient_7


title: Heart_bulkRNA-seq_Patient_6


title: mouse_mirmOTSTEO_sample_18_a (control)


title: mouse_mirmOTSTEO_sample_17_a (control)


title: WT_3


title: mouse_mirmOTSTEO_sample_20_a (control)


title: mouse_mirmOTSTEO_sample_177_b (miR381mimic_treated)

value: 32 cell


title: HUVECT1_model_DMSO_L2


title: WT_IFN-g_1


title: PBMC_bulkRNA-seq Patient_5


title: WT_2


title: PBMC_bulkRNA-seq Patient_3


title: WT_1


title: mouse_mirmOTSTEO_sample_174_b (miR381mimic_treated)


title: mouse_mirmOTSTEO_sample_176_b (miR381mimic_treated)


title: HUVECT1_model_DMSO_L1


title: mouse_mirmOTSTEO_sample_172_b (miR381mimic_treated)


title: mouse_mirmOTSTEO_sample_171_b (miR381mimic_treated)


title: HUVECT1_model_DMSO_H2


title: 4T1 Mga KO replicate2

data_processing:
The original sequencing data file was transformed into sequenced reads (raw reads) by CASAVA base recognition (base calling). Raw reads were stored in FASTQ format files.
Cell Ranger (v6.3) was used to perform the reads alignment of sequencing raw data for the scRNA-seq matrices generation.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Breast tumors

extract_protocol:
1x10^6 WT or Mga KO 4T1 cells were implanted into BALB/c mice and incubated for 3 weeks. Tumors were harvested, minced into small pieces on ice, and digested in DMEM supplemented with 5% FBS, collagenase IA (2 mg/ml, Sigma-Aldrich #C9891), hyaluronidase (1 mg/ml, Sigma-Aldrich #H3506), and dispase II (2 mg/ml, Sigma #D4693) for 45 mins with shaking at 37 °C. The tumor lysate was filtered with 70-mm strainer and washed twice with ice-cold PBS containing 2% FBS, then re-suspended in RBC lysis buffer (ThermoFisher) for 1 min at 37 °C to lyse red blood cells. After washing twice with ice-cold PBS containing 2% FBS, single-cell suspensions with high viability were obtained via sorting with DAPI staining
Single cell Gene Expression Library was prepared according to Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics) by the Single Cell Genomics Core at Baylor College of Medicine. In Brief, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) where full length cDNA was synthesized and barcoded for each single cell. Subsequently the GEMS are broken and cDNA from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. Final library was generated by amplification.

value: Breast tumors

value: Epithelial cells


title: 4T1 Mga KO replicate3


title: HUVECT1_model_DMSO_H1


title: HUVECT1_model_DMSO_H3


title: PBMC_bulkRNA-seq Patient_1


title: HUVECT1_model_DGMIsolvent_M2


title: 4T1 Mga KO replicate1


title: HUVECT1_model_DGMIsolvent_M1


title: mouse_mirmOTSTEO_sample_170_b (miR381mimic_treated)


title: 3D, KO-3, rep3

city: La Jolla

first: Alyssa

last: Holman

state: CALIFORNIA

address: 9500 Gilman Drive Leichtag Biomedical Research Building 485

institute: University of California San Diego

data_processing:
Quality of sequencing data was assessed using FASTQC. Reads were aligned to Hg38 using STAR and counted using FeatureCounts. DESeq2 was used to identify differentially expressed genes from raw read counts comparing control and KO with biological replicates as a covariate.
Assembly: hg38
Supplementary files format and content: .txt file for featureCounts data

source_name: H9 hPSC

growth_protocol: H9 hPSCs were maintained in mTESR1 with 5% CO2 at 37C.

extract_protocol:
For HSF1 KO and control RNA-seq, total RNA from 3D day 25 cells was extracted and purified using TRIzol (Invitrogen) from three independent replicates.
Bulk RNA-seq was performed by the Institute for Genomic Medicine at UC San Diego using the Illumina Total RNA Ribodepleted Prep.

treatment_protocol: HSF1 knockout was generated in an H9 hPSC line and three clones were selected for further analysis. H9 hPSCs, WT and the three HSF1 knockouts, were differentiated into 3D CMs based on previously published protocol. DOI: 10.1016/j.stem.2010.12.008

value: H9 hPSC

value: hPSC

value: 3D cardiomyocyte differentiation


title: 3D, KO-3, rep2


title: 4T1 WT replicate3


title: PBMC_bulkRNA-seq Patient_4


title: mouse_mirmOTSTEO_sample_169_b (miR381mimic_treated)


title: HUVECT1_model_DGMIsolvent_L1


title: 3D, KO-3, rep1


title: HUVECT1_model_DGMIsolvent_L2


title: PBMC_bulkRNA-seq Patient_2


title: 4T1 WT replicate2


title: mouse_mirmOTSTEO_sample_16_a (control)


title: P13-MI-SB225002

city: Guangzhou

first: fu

last: Ai

state: Guangdong

address: Jingxijiedao

institute: Southern Medical University

data_processing:
Pre-processing of sequencing results to generate count matrices.
Further processing was done with Seurat v4.1.0 (cell and gene filtering, removing batch effect, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: Tab-delimited gene expression count values of each cell

source_name: heart

growth_protocol: C57BL/6 mice were bred and housed in a 12 h light/dark cycle in a temperature-controlled room, with adlibitum access to water and food

extract_protocol:
The heart tissues were manually divided into three zones (infarct zone, border zone and remote zone) and then digested with collagenase type II enzyme at 37  C for 30 min to generate single-cell suspensions. F4/80/CD45+ cardiac macrophages in infarct zone and border zone were collected and subjected to FACS sorting for CD45+/F4/80+ cells.
RNA libraries for RNA-seq were prepared using Genomics Library Prep Kit following manufacturer's protocols.

treatment_protocol: Myocardial infarction surgeries were performed on P10 mice. Lateral thoracotomy was performed at the fourth intercostal space and a 7-0 prolene suture was ligated through the left anterior descending coronary artery(LAD) to induce infraction. Mice were euthanized at 3 d (72 h) post-surgery.

value: heart

value: macrophage/monocyte

tag: age

value: P13 days

value: myocardial infarction


title: 3D, KO-2, rep3


title: mouse_mirmOTSTEO_sample_167_b (miR381mimic_treated)

value: embryo


title: 3D, KO-2, rep2


title: P13-MI-vehicle


title: HUVECT1_model_DGMI_M2


title: HUVECT1_model_DGMIsolvent_H2


title: mouse_mirmOTSTEO_sample_168_b (miR381mimic_treated)


title: HUVECT1_model_DGMIsolvent_H1


title: P13-Sham-vehicle

value: sham


title: mouse_mirmOTSTEO_sample_165_b (control)

value: control


title: 3D, WT, rep3


title: HUVECT1_model_DGMI_M1


title: 3D, KO-2, rep1


title: mouse_mirmOTSTEO_sample_166_b (control)


title: RANKL treated mouse intestinal organoids

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

description: 10x Genomics

data_processing:
scRNA-seq reads were processed using cellranger count v4.0.0 with default settings, using the prebuild 10X reference refdata-gex-mm10-2020-A
Assembly: mm10
Supplementary files format and content: filtered feature-barcode matrix in hdf5 format

source_name: intestinal organoid

extract_protocol:
performed according to manufacturers' instructions (10X Genomics, v2chemistry)
The libraries were sequenced on an Illumina NovaSeq 6000.

value: intestinal organoid

tag: strain

value: mouse recombinant RANKL


title: 4T1 WT replicate1

value: WT


title: mouse_mirmOTSTEO_sample_163_b (control)


title: 3D, WT, rep2


title: Control mouse intestinal organoid

description: 10x Genomics


title: 3D, WT, rep1


title: mouse_mirmOTSTEO_sample_162_b (control)


title: HUVECT1_model_DGMI_L2


title: adult_heart_bulk_rep2

library_source: genomic

data_processing:
Reads containing barcodes were de-multiplexed to generate single cell profiles by custom scripts.
Trimmed paired-end reads were mapped to a mouse mm10 genome reference genome with bowtie2.
Duplicate reads were removed using picard. Only uniquely reads>1000 cells will be remained.
Peaks were called uing macs2 2.2.7.1 with nolambda、nomedel and broad.
Bigwig files were generated using the Deeptools BamCoverage，reads were normalized to 1000000.
Assembly: mm10
Supplementary files format and content: bigWig, broadPeak
Supplementary files format and content: Fragments data contains fragment position

molecule: genomic DNA

growth_protocol: C57BL/6 mice were bred and housed in a 12 h light/dark cycle in a temperature-controlled room, with ad libitum access to water and food

extract_protocol:
The heart tissues were roughly divided into three zones (infarct zone, border zone and remote zone) and then digested with collagenase type II enzyme at 37°C for 30 min to generate single-cell suspensions. F4/80/CD45+ cardiac macrophages were collected by FACS sorting and fixed with 0.25% formaldehyde for 5 min on ice followed by methyl alcohol fixation. Before single-cell CoBATCH experiments, the cells in methyl alcohol were washed with 0.1% BSA/PBS for three times.
Custom library preparation was performed by two steps of PCR amplification. The first step was performed by addition of 0.5 μL 50 μM Truseq connector primer (Connector primer F:5′-ACACTCTTTCCCTACACGACGCTCTTCCGATCTTCGTCGGCAGCGTCTCCACGC-3′,  Connector primer R:5′-GACTGGAGTTCAGACGTGTGCTCTTCCGATCTGTCTCGTGGGCTCGGCTGTCCCTGT-3′), 25 μL 2X Taq master mix and 16.5 μL 1mM MgCI2 to the 3 μL CoBATCH cell lysis in each tube and the reaction was set up by incubation at 72°C for 5 min, 95°C for 5 min, 13-16 cycles of amplification (95°C for 30 s, 63°C for 30 s, 72°C for 1 min), and final 72°C extension for 5 min. The PCR enrichment was directly performed in the same tube as described above. Then 0.4 μL Exo1 was added and incubated at 37°C for 1 h followed by inactivation at 72°C for 20 min. The second PCR enrichment was performed by adding 0.7 μL 10 μM Truseq i5 primer (5′- AATGATACGGCGACCACCGAGATCTACAC[i5]TCGTCGGCAGCGTC-3′), 0.7 μL 25 μM i7 index primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′), 20 μL 2X Taq master mix and 8.6 μL 1 mM MgCI2 followed by incubation at 95°C for 5 min, 5-7 cycles of  95°C for 30 s, 63°C for 30 s, 72°C for 1 min, and final 72°C extension for 5 min. Finally, the PCR products were purified and selected by SPRI beads for 200-1000 bp.

treatment_protocol: Myocardial infarction surgeries were performed on 1 and 10 days post-natal mice. Lateral thoracotomy was performed at the fourth intercostal space and a 7-0 prolene suture was ligated through the left anterior descending coronary artery(LAD) to induce infraction. Mice were euthanized at 3 d (72 h) or 7 d (168 h) post-surgery.

tag: chip antibody


title: 3D, KO-1, rep3


title: HUVECT1_model_DGMI_H2


title: mouse_mirmOTSTEO_sample_164_b (control)


title: adult_heart_bulk_rep1


title: mouse_mirmOTSTEO_sample_161_b (control)


title: HUVECT1_model_DGMI_L1


title: E15.5_heart_bulk_rep2


title: E15.5_heart_bulk_rep1


title: HUVECT1_model6


title: 3D, KO-1, rep1


title: 3D, KO-1, rep2


title: HUVECT1_model_DGMI_H1


title: mouse_mirmOTSTEO_sample_160_b (control)


title: 3D D25, TNNT2+, rep3

data_processing:
The MaGeCK pipeline for the identification of essential genes using the ‘MLE’ tool was used for differential analysis of read abundances between CMs and non-CMs, as compared to day 0.
Assembly: hg38
Supplementary files format and content: .xlsx files for MLE processed counts

extract_protocol:
Three biological replicates were differentiated and sorted into TNNT2+ and TNNT2- cells amounting to 6 million cells total. Cells were snap frozen for genomic DNA.
Genomic DNA purification was performed using PureLink™ Genomic DNA Mini Kit (Invitrogen), and two rounds of PCR were performed for guide amplification and addition of indexing primers
single-end sequencing

treatment_protocol: H9 hPSCs were differentiated into 2D and 3D CMs based on previously published protocols. DOI: 10.1038/nprot.2012.150; DOI: 10.1016/j.stem.2010.12.008


title: mouse_mirmOTSTEO_sample_159_b (control)


title: E11.5_insitu_rep2


title: HUVECT1_model5


title: 3D D25, TNNT2+, rep2


title: 3D D25, TNNT2+, rep1


title: HUVECT1_model4


title: E11.5_insitu_rep1


title: HUVECT1_model3


title: mouse_mirmOTSTEO_sample_156_b (control)


title: P10_Sham_7D_RZ_rep2


title: mouse_mirmOTSTEO_sample_157_b (control)


title: HUVECT1_model2


title: 3D D25, TNNT2-, rep3


title: mouse_mirmOTSTEO_sample_154_b (control)


title: HUVECT1_ctrl6

value: untreated


title: P10_Sham_7D_RZ_rep1


title: 3D D25, TNNT2-, rep2


title: mouse_mirmOTSTEO_sample_155_b (control)

value: 32 cell


title: HUVECT1_model1


title: 3D D25, TNNT2-, rep1


title: mouse_mirmOTSTEO_sample_158_b (control)


title: P10_Sham_7D_IZ_rep2


title: 2D D25, TNNT2+, rep2

value: 2D cardiomyocyte differentiation


title: P10_Sham_7D_BZ_rep1


title: mouse_mirmOTSTEO_sample_153_b (control)


title: HUVECT1_ctrl4


title: 2D D25, TNNT2+, rep3


title: HUVECT1_ctrl5


title: P10_Sham_7D_IZ_rep1


title: HUVECT1_ctrl3


title: mouse_mirmOTSTEO_sample_151_b (miR381mimic_treated)


title: mouse_mirmOTSTEO_sample_152_b (control)


title: P10_MI_7D_RZ_rep2


title: P10_Sham_7D_BZ_rep2


title: mouse_mirmOTSTEO_sample_150_b (miR381mimic_treated)


title: 2D D25, TNNT2+, rep1


title: 2D D25, TNNT2-, rep2


title: 2D D25, TNNT2-, rep3


title: HUVECT1_ctrl2


title: mouse_mirmOTSTEO_sample_14_a (control)

value: 8 cell


title: P10_MI_7D_BZ_rep2


title: HUVECT1_ctrl1


title: 2D D25, TNNT2-, rep1

value: H9 hPSC


title: D0, rep2

value: hPSC


title: P10_MI_7D_RZ_rep1


title: mouse_mirmOTSTEO_sample_148_b (miR381mimic_treated)


title: mouse_mirmOTSTEO_sample_149_b (miR381mimic_treated)


title: P10_MI_7D_IZ_rep2


title: HMC3_model_GK_M1

source_name: cell line: Human microglialcell line HMC3


title: D0, rep1


title: P10_MI_7D_IZ_rep1


title: mouse_mirmOTSTEO_sample_146_b (miR381mimic_treated)


title: HMC3_model_GK_L2


title: HMC3_model_GK_L1


title: P10_Sham_3D_RZ_rep3


title: HMC3_model_GK_M2


title: mouse_mirmOTSTEO_sample_145_b (miR381mimic_treated)


title: mouse_mirmOTSTEO_sample_147_b (miR381mimic_treated)


title: P10_Sham_3D_RZ_rep2


title: HMC3_model_GK_H1


title: mouse_mirmOTSTEO_sample_144_b (miR381mimic_treated)


title: HMC3_model_GK_H2


title: ARPKD_2_5 Years

city: Wolverhampton

first: Paraskevi

last: Goggolidou

address: Wulfruna Street

department: Faculty of Science and Engineering

country: United Kingdom

institute: University of Wolverhampton

data_processing:
All data processing steps were performed on Usegalaxy.org
Fasta files underwent QC with FastQC and adapter sequences/low-quality sequences were trimmed using CutAdapt (Version 3.5+galaxy1)
Trimmed reads were aligned to the GRCH38 genome using Hisat2 default settings (2.1.0+galaxy5)
StringTie (Galaxy Version 2.1.1) was used to perform gene counts on aligned Bam files. Counting  was performed using a GRCH38 gtf file acquired from Ensembl.
Read count normalisation and differential expression were performed using Deseq2 (Galaxy Version 2.11.40.6+galaxy1).
Assembly: GRCH38 (Ensembl references)
Supplementary files format and content: Tab delimited text file containing raw counts for all samples

source_name: Kidney

extract_protocol:
RNA was extracted with the Qiagen Rneasy Mini kit and Qiagen QIAshredders following the  manufacturers instructions
RNA libraries for RNA-Seq were prepared using the NEBNext Ultra II Directional RNA Library  Prep Kit following the manufacturers instructions

value: Kidney

value: ARPKD


title: ARPKD_3_5 Years


title: P10_MI_7D_BZ_rep1

value: heart

value: macrophage/monocyte


title: P10_Sham_3D_BZ_rep3

value: myocardial infarction


title: P10_Sham_3D_BZ_rep2


title: HMC3_model_GB_M2


title: mouse_mirmOTSTEO_sample_141_b (miR381mimic_treated)

value: embryo


title: Normal_3_9 Years

value: Normal


title: P10_Sham_3D_IZ_rep3


title: HMC3_model_GB_M1


title: mouse_mirmOTSTEO_sample_140_b (miR381mimic_treated)


title: ARPKD_4_10 Years


title: HMC3_model_GB_L2


title: P10_MI_3D_RZ_rep3


title: HMC3_model_GB_L1


title: mouse_mirmOTSTEO_sample_139_b (miR381mimic_treated)


title: mouse_mirmOTSTEO_sample_143_b (miR381mimic_treated)


title: Normal_2_18 Months


title: P10_MI_3D_RZ_rep2


title: ARPKD_1_9 days


title: HMC3_model_GB_H1


title: HMC3_model_GB_H2


title: EU-seq RBM ERα OE  Repeat 1

city: Bangalore

first: Dimple

last: Notani

address: National Centre for Biological Sciences Tata Institute of Fundamental Research Bellary Road

department: Cellular Organization and Signallinga

country: India

institute: National Centre for Biological Sciences

data_processing:
For ChIP-seq analysis the raw reads obtained from the sequencing were aligned to the hg19 reference genome using Bowtie2. Reads with a quality score less than 20 were filtered out using the Filter Sam or Bam tool. Peaks were called using MACS2  with default settings.
For the fRIP-seq analysis the adaptor sequences were removed from the reads using Cutadapt, followed by alignment to the hg19 reference genome using RNA STAR. Duplicate reads were removed using UMI-tools deduplicate. Regions of fRIP-seq IP enrichment were called using MACS2with the fRIP-seq input as the control file. The log2FC of fRIP-seq IP /fRIP-seq input was calculated using the aligned BAM file with bamcompare.
For EU-seq analysis, the raw reads were aligned to hg19 using Bowtie2. PCR duplicates were removed using MarkDuplicates from Picard Tools. Read coverage on known E2 upregulated genes was calculated using multiBamSummary.
Assembly: hg19
Supplementary files format and content: bigwig and narrow peaks

source_name: Breast, mammary gland

growth_protocol: MCF-7 cells were maintained in DMEM with 10% FBS. For experiemtns MCF-7 cells were grown in stripping media with 5% characol stripped FBS for 72 hours.

extract_protocol:
For ChIP-seq experiment, genomic DNA was isolated as per standard ChIP-seq protocol. For fRIP-seq, RNA crosslinked to ERα were pulldown using anti ERα followed by purification of the total RNA using trizol. For EU-seq cells were chased with EU for 45 mins and total RNA was isolated using trizol. Further EU labelled RNA was biotinylated using Click Chemistry reaction and pulldown using Streptavidin beads using standard protocol. The pulldown RNA was extracted using Trizol and used for library preparation.
ChIP-seq library preparation using the NEBNext® Ultra™II DNA Library Prep kit with Sample Purification Beads (Catalogue-E7103L) following the manufacturer's protocol. The fRIP-seq purified RNA was used for preparing RNA-seq libraries, using the NEBNext rRNA Depletion Kit v2 and NEBNext Ultra II Directional RNA Library Prep, following the manufacturer's protocol. For EU-seq the nasecent RNA was converted to cDNA using the SuperScript™ IV First-Strand Synthesis System (catalogue number: 18091050). The second strand of cDNA was synthesized using the NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (Catalogue no-E7765L). The double-stranded DNA was further fragmented, and the library was prepared using the NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina (E7805L), following the manufacturer's protocol.

treatment_protocol: MCF-7 cells were treated with 100nm of 17β estradiol for 1 hour followed by the either ChIP-seq or fRIP-seq. For EU-seq MCF-7 cells were treated with 100nm of 17β estradiol and 45 mins of EU.

value: Breast, mammary gland

value: epithelial cell

value: 17beta-estradiol, 45 mins of EU


title: P10_MI_3D_BZ_rep2


title: Normal_4_4 Years


title: EU-seq WT ERα OE  Repeat 1


title: P10_MI_3D_BZ_rep3


title: HMC3_model_GA_M2


title: mouse_mirmOTSTEO_sample_12_a (control)

value: control


title: mouse_mirmOTSTEO_sample_11_a (control)


title: P10_MI_3D_IZ_rep3


title: mouse_mirmOTSTEO_sample_118_b (miR381mimic_treated)


title: mouse_mirmOTSTEO_sample_117_b (miR381mimic_treated)


title: P10_Sham_3D_IZ_rep2


title: ChIP-seq RBM ERα total PolII


title: HMC3_model_GA_M1


title: HMC3_model_GA_L2


title: mouse_mirmOTSTEO_sample_13_a (control)


title: P10_MI_3D_IZ_rep2


title: mouse_mirmOTSTEO_sample_116_b (miR381mimic_treated)


title: scMultiome_KO1_D21

first: Yingying

address: Kaiyuan Avenue

department: Chinese Academy of Sciences Guangzhou Branch

institute: Guangzhou Institutes of Biomedicine and Health

description:
Single Cell Multiome of KMT2D-SET-KO cell-induced organoid at D21
polyA RNA and genomic DNA

data_processing:
library strategy: scMultiome
The gene expression level of RNA-seq data was calculated by using  RSEM.
CUT&Tag reads were aligned to the hg38 genome using Bowtie2. Duplicate reads were removed with the function MarkDuplicates from Picard. The .bw files were generated by deepTools.
The gene expression level of scRNA-seq data was calculated by using  STAR.
The fragment files of scATAC-seq data was generated by using  Cell Ranger ATAC.
Assembly: hg38
Supplementary files format and content: .genes.results files contain the gene expression level of RNA-seq data
Supplementary files format and content: .bw files contain the CUT&Tag data that will be displayed in the Genome Browser, a web-based tool used to display a requested portion of a genome at any scale.
Supplementary files format and content: _data.tar.tar files contain the gene expression level of scRNA-seq data
Supplementary files format and content: _fragments.tsv.gz files contain the fragments of scATAC-seq data

source_name: brain organoid

growth_protocol: Cerebral organoids were generated according to the previously published protocols with dual smad inhibitors (Lancaster and Knoblich, 2014).

extract_protocol:
RNA-seq: To extract the total RNAs, organoids were collected and lysed with 1 ml TRIzol reagent (MRC, TR118-200), followed by adding 200 μL chloroform. After centrifugation (14,000 ×g for 10 min at 4°C), the total RNAs in the supernatant were precipitated with isopropanol. 1ug RNAs were subjected to RNA-seq library construction.  CUT&Tag: Brain organoids at D21 were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington, LK003153). CUT&Tag assay was performed according to the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (TD901-TD902, Vazyme).  scRNA-seq: Brain organoids at D21 and D30 were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington, LK003153).  snATAC-seq: Brain organoids at D21 were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington, LK003153). Nuclei were extracted from organoid-derived single cells following Demonstrated Protocol of Nuclei Isolation for Single Cell ATAC Sequencing (10X GENOMICS).
RNA-seq: RNA Sequencing libraries were prepared according to the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (NR611, Vazyme).   CUT&Tag: Library amplification was prepared using TruePrep Amplify Enzyme (TAE, Vazyme) followed by PCR purification (Vazyme).  scRNA-seq: 3'-library was constructed using Chromium Single Cell Reagent Kits v2 (10X GENOMICS).  snATAC-seq:Isolated nuclei were preceded to Tn5-mediated transposition, single cell barcoding, and library construction using Chromium Single Cell ATAC Reagent Kits (10X GENOMICS).

treatment_protocol: For rescue experiments, 1μM CHIR99021 (ChemBest Research Laboratories Ltd.) or PBS equivalent was added during D10 and D14

value: brain organoid

tag: time

value: untreated

tag: library strategy

value: scMultiome

tag: library source

value: TRANSCRIPTOMIC AND GENOMIC SINGLE CELL


title: Normal_1_5 Months


title: HMC3_model_GA_L1


title: mouse_mirmOTSTEO_sample_115_b (miR381mimic_treated)

value: 32 cell


title: scMultiome_WT_D21

description:
Single Cell Multiome  of HN4 cell-induced organoid at D21
polyA RNA and genomic DNA

value: WT


title: P1_Sham_7D_RZ_rep1


title: mouse_mirmOTSTEO_sample_114_b (miR381mimic_treated)


title: scATAC_seq_KO2_D21

description: Single Cell ATAC seq of KMT2D-SET-KO cell-induced organoid at D21

data_processing:
The gene expression level of RNA-seq data was calculated by using  RSEM.
CUT&Tag reads were aligned to the hg38 genome using Bowtie2. Duplicate reads were removed with the function MarkDuplicates from Picard. The .bw files were generated by deepTools.
The gene expression level of scRNA-seq data was calculated by using  STAR.
The fragment files of scATAC-seq data was generated by using  Cell Ranger ATAC.
Assembly: hg38
Supplementary files format and content: .genes.results files contain the gene expression level of RNA-seq data
Supplementary files format and content: .bw files contain the CUT&Tag data that will be displayed in the Genome Browser, a web-based tool used to display a requested portion of a genome at any scale.
Supplementary files format and content: _data.tar.tar files contain the gene expression level of scRNA-seq data
Supplementary files format and content: _fragments.tsv.gz files contain the fragments of scATAC-seq data

value: scATAC-seq

value: GENOMIC SINGLE CELL


title: HMC3_model_GA_H1


title: mouse_mirmOTSTEO_sample_113_b (miR381mimic_treated)


title: P1_Sham_7D_BZ_rep2

value: heart


title: scATAC_seq_KO1_D21


title: mouse_mirmOTSTEO_sample_112_b (miR381mimic_treated)


title: ChIP-seq WT ERα total PolII


title: HMC3_model_EGB761_M2


title: scRNA_seq_KO1_IWPMock

description: Single Cell RNA seq of KMT2D-SET-KO cell-induced organoid at D21(PBS treatment)

value: PBS

value: scRNA-seq

value: TRANSCRIPTOMIC SINGLE CELL


title: scATAC_seq_WT_D21

description: Single Cell ATAC seq  of HN4 cell-induced organoid at D21

data_processing:
The gene expression level of RNA-seq data was calculated by using  RSEM.
CUT&Tag reads were aligned to the hg38 genome using Bowtie2. Duplicate reads were removed with the function MarkDuplicates from Picard. The .bw files were generated by deepTools.
The gene expression level of scRNA-seq data was calculated by using  STAR.
The fragment files of scATAC-seq data was generated by using  Cell Ranger ATAC.
Assembly: hg38
Supplementary files format and content: .genes.results files contain the gene expression level of RNA-seq data
Supplementary files format and content: .bw files contain the CUT&Tag data that will be displayed in the Genome Browser, a web-based tool used to display a requested portion of a genome at any scale.
Supplementary files format and content: _data.tar.tar files contain the gene expression level of scRNA-seq data
Supplementary files format and content: _fragments.tsv.gz files contain the fragments of scATAC-seq data
Supplementary files format and content: CREs.zip (contains bed files for various cell types)


title: scRNA_seq_KO1_IWP

description: Single Cell RNA seq of KMT2D-SET-KO cell-induced organoid at D21(IWP treatment)

value: IWP


title: mouse_mirmOTSTEO_sample_110_b (miR381mimic_treated)

value: embryo


title: P1_Sham_7D_IZ_rep2

value: macrophage/monocyte

value: myocardial infarction


title: HMC3_model_EGB761_M1


title: P1_Sham_7D_BZ_rep1


title: HMC3_model_EGB761_L1


title: mouse_mirmOTSTEO_sample_10_a (control)

value: 8 cell

value: control


title: P1_MI_7D_RZ_rep2


title: P1_Sham_7D_IZ_rep1


title: HMC3_model_EGB761_L2


title: scRNA_seq_WT_IWPMock

description: Single Cell RNA seq of HN4 cell-induced organoid at D21(PBS treatment)

value: brain organoid


title: HMC3_model_GA_H2


title: mouse_mirmOTSTEO_sample_109_b (miR381mimic_treated)


title: P1_Sham_7D_RZ_rep2


title: P1_MI_7D_RZ_rep1


title: HMC3_model_EGB761_H2


title: scRNA_seq_WT_IWP

description: Single Cell RNA seq of HN4 cell-induced organoid at D21(IWP treatment)


title: mouse_mirmOTSTEO_sample_111_b (miR381mimic_treated)


title: scRNA_seq_KMT2D_Mut

description: Single Cell RNA seq of KMT2D_Mut cell-induced organoid at D21

value: untreated


title: HMC3_model_DMSO_M2


title: mouse_mirmOTSTEO_sample_107_b (miR381mimic_treated)


title: P1_MI_7D_BZ_rep1


title: HMC3_model_DMSO_M1


title: P1_MI_7D_BZ_rep2


title: HMC3_model_EGB761_H1


title: mouse_mirmOTSTEO_sample_106_b (miR381mimic_treated)


title: scRNA_seq_WT

description: Single Cell RNA seq of HN4 cell-induced organoid at D21


title: HMC3_model_DMSO_L2


title: scRNA_seq_iPSC_proband_line2_batch1

description: Single Cell RNA seq of Proband daughter's iPSC-induced organoid at D21


title: mouse_mirmOTSTEO_sample_105_b (miR381mimic_treated)


title: HMC3_model_DMSO_L1


title: mouse_mirmOTSTEO_sample_104_b (miR381mimic_treated)


title: mouse_mirmOTSTEO_sample_103_b (miR381mimic_treated)


title: HMC3_model_DMSO_H2


title: P1_Sham_3D_BZ_rep1


title: P1_MI_7D_IZ_rep2


title: P1_Sham_3D_RZ_rep1


title: scRNA_seq_iPSC_proband_line1_batch1


title: P1_Sham_3D_IZ_rep1


title: scRNA_seq_iPSC_mothoer_line2_batch2

description: Single Cell RNA seq of Healthy mother's iPSC-induced organoid at D21


title: HMC3_model_DGMIsolvent_M2


title: mouse_mirmOTSTEO_sample_108_b (miR381mimic_treated)


title: P1_MI_3D_RZ_rep1


title: scRNA_seq_iPSC_proband_line2_batch2


title: scRNA_seq_iPSC_proband_line1_batch2


title: P1_MI_7D_IZ_rep1


title: HMC3_model_DGMIsolvent_M1


title: scRNA_seq_iPSC_mothoer_line1_batch2


title: Gadd45β KO mice lung, 2 day bio rep 2

city: Daejeon

first: Jong-Soo

last: Lee

address: 99 Daehak-ro

department: Veterinary Medicine

country: South Korea

institute: Chungnam National University

data_processing:
Trimming was done with BBDuk (> average Q20)
Sequencing was done on the NextSeq 500/550 75bp SE system (Illumina)
Mapping using Bowtie2 to ref. Calculation read count using Bedtools
TMM+CPM Normalization using EdgeR
Assembly: mm10
Supplementary files format and content: Processed data file provide as a matrix table of Normalized data and Raw count

source_name: Lung

growth_protocol: WT and Gadd45β Knockout mice generated on a C57BL/6J background (JAX stock #029141) were maintained in a specific pathogen-free facility with free access to food and water.

extract_protocol:
Total RNA was extracted from whole lungs of 6-8 weeks old female Gadd45β+/+ and Gadd45β-/- mice, with 2 biological replicates per group obtained using the NucleoSpin RNA extraction kit (MACHEREY-NAGEL) according to the manufacturer's instructions. The quality and integrity of total RNA samples were assessed using the Agilent 4200 TapeStation (Agilent technologies) according to the manufacturer’s instructions.
cDNA library was generated using the QuantSeq 3’ mRNA-Seq library prep kit FWD for illumuna (Lexogen)

treatment_protocol: 6-8 weeks old female littermate mice were infected intranasally (IN) with SeV (16 HAU/mouse) in biosafety level-2 (BSL-2) laboratory facilitiy.

tag: Sex

value: Female

value: Lung

value: Gadd45beta knockout

value: SeV infection


title: P1_MI_3D_BZ_rep1


title: mouse_mirmOTSTEO_sample_101_b (miR381mimic_treated)

data_processing:
Read quality was firstly checked by FastQC. Subsequently, we aligned high-quality reads to the mouse mm10 reference genome (mm10-2020-A, obtained from the 10X Genomics website) using the STAR aligner (v2.5.1b) with default settings. Raw read counts were quantified using the rsem-calculate-expression from RSEM (v1.3.0) with the option of " --single-cell-prior". Low-quality cells were filtered out by discarding those with fewer than 3000 expressed genes or with a percentage of mitochondrial genes higher than 0.1.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

value: 32 cell


title: Gadd45β KO mice lung, 2 day bio rep 1


title: HMC3_model_DGMIsolvent_L1


title: scRNA_seq_iPSC_mothoer_line2_batch1

value: WT


title: Gadd45β WT mice lung, 2 day bio rep 2


title: mouse_mirmOTSTEO_sample_102_b (miR381mimic_treated)


title: scRNA_seq_iPSC_mothoer_line1_batch1


title: P1_MI_3D_IZ_rep1

value: heart


title: BCSP-KO-H3K27ac-rep2

city: wuhan

first: Jianfei

last: Liang

address: No. 237, Luoyu Road, Hongshan District,

institute: wuhan university

data_processing:
Genome_build: GRCm38
ChIP-seq data that were generated using WT and Ptip-/- (SSCs, pBCSPs and BCSPs) cells were quality-controlled and processed by Trim_Galore (v.0.6.6) for removing adapters and low-quality base pairs. Reads were aligned with bowtie2(v.2.3.5.1) to GRCm38 reference genome. Aligned reads were stripped of duplicates using samtools (v.1.9). H3K4me1/H3k4me3/H3K27ac Peaks were called with Macs2 (v.2.2.6).
Supplementary_files_format_and_content: Broad peak

source_name: bone, cartilage and stromal progenitor cells

extract_protocol:
For histone ChIP-seq, lysates were clarified from MNase digested nuclei and histone-DNA complexes were isolated with H3K4me1,H3K4me3 or H3K27ac antibodies.
For ChIP, Illumina libraries were constructed using a modified custom paired-end protocol. In brief, samples were end-repaired (1*T4 DNA ligase buffer, 0.4 mM dNTP mix, 2.25 U T4 DNA polymerase, 0.75 U Klenow DNA polymerase and 7.5 U T4 polynucleotide kinase; 30 min at 21–25 C), A-tailed (1*NEB buffer 2, 0.4 mM dNTPs and 3.75 U of Klenow (exo-); 30 min at 37 C) and ligated (1*rapid DNA ligation buffer, 1 mM Illumina PE adapters and 1,600 U DNA ligase; 1–8 h at 21–25 C). Ligated fragments were amplified using indexed primers (Illumina) for 14 PCR cycles. DNA was purified with 1.8 volume KAPA DNA purification beads between each step.

value: limbs

value: post natal day 3

tag: antibody


title: HMC3_model_DMSO_H1


title: PBCSP-KO-input-DNA-rep2

source_name: pre-bone, cartilage and stromal progenitor cells


title: scRNA_seq_KO1_Chir99021Mock

value: PBS

value: scRNA-seq

value: TRANSCRIPTOMIC SINGLE CELL


title: Gadd45β KO mice lung, 0 day bio rep 2


title: BCSP-KO-input-DNA-rep2


title: scRNA_seq_KO1_Chir99021

description: Single Cell RNA seq of KMT2D-SET-KO cell-induced organoid at D21(Chir99021 treatment)


title: Gadd45β WT mice lung, 2 day bio rep 1


title: scRNA_seq_WT_Chir99021Mock


title: HMC3_model_DGMIsolvent_H1


title: HMC3_model_DGMIsolvent_H2


title: pBCSP-KO-H3K27ac-rep2


title: HMC3_model_DGMI_M2


title: HMC3_model_DGMIsolvent_L2


title: Gadd45β KO mice lung, 0 day bio rep 1


title: HMC3_model_DGMI_M1


title: SSC-KO-input-DNA-rep2

source_name: Skeletal stem cells


title: scRNA_seq_WT_Chir99021

description: Single Cell RNA seq of HN4 cell-induced organoid at D21(Chir99021 treatment)


title: scRNA_seq_eWNT3A_KO

description: Single Cell RNA seq of WNT3A  enhancer KO cell-induced organoid at D21


title: Gadd45β WT mice lung, 0 day bio rep 2


title: scRNA_seq_KO2_D30

description: Single Cell RNA seq of KMT2D-SET-KO  cell-induced organoid at D30


title: SSC-KO-H3K27ac-rep2


title: BCSP-WT-input-DNA-rep2

value: Ptipf/f;


title: HMC3_model_DGMI_H2


title: clf_05_4

city: Shanghai

first: Minhang

last: Yuan

address: Fenglin

department: Shanghai Institute of Plant Physiology and Ecology

institute: Chinese Academy of Sciences

data_processing:
Sequencing reads were cleaned with Trim Galore v0.4.4, Trimmomatic v0.36 and sickle, including removing bases with low quality score (<25) and irregular GC content, and cutting sequencing adaptors followed by filtering short reads.
The cleaned reads were mapped to TAIR RefSeq v10 using HISAT2 2.1.020 for RNA-seq data, all with default settings.
Genome_build: TAIR 10
Supplementary_files_format_and_content: Read counts for genes (TAIR 10) were provided.

organism: Arabidopsis thaliana

source_name: clf_~95% air humidity

growth_protocol: Plants  were grown in soil in environmentally-controlled growth chambers, with relative humidity at 60% and temperature at 22℃ with 12/12h day/night photoperiod.

extract_protocol:
Total mRNA was extracted from leaves using Trizol reagent. Total RNA was treated with DNase I to remove DNA, and purified RNA was recovered with RNeasy® MinElute™ Cleanup kit. A total amount of 1 μg RNA per sample was used as input material for library preparation and Illumina sequencing.
Sequencing libraries were generated using TruSeq™ RNA Library Prep Kit for Illumina®  following manufacturer’s recommendations and sequenced on Illumina Hiseq platform and 150 bp paired-end reads were generated.

treatment_protocol: Four-week-old Arabidopsis plant leaves were treated in growth chambers, with relative humidity about 95% and temperature at 22℃ with 12/12h day/night photoperiod.

value: clf

value: ~95% air humidity

tag: time point

value: Four-week-old

value: leaf


title: Gadd45β WT mice lung, 0 day bio rep 1

value: Female


title: HMC3_model_DGMI_H1

data_processing:
Demultiplexing and basecalling performed using CASAVA version 1.8.2
QC was performed on the FASTQ files using FastQC(v0.11.5) software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens(hg19) whole genome using HISAT2(v2.1.0).
Sequence reads aligned to the human genome were imported into HTseq(v0.11.3) for sequence read counting.
Sequence reads mapped to different isoforms of individual genes were pooled together, and then were input into the DESeq(v1.36.0) differential expression analysis program to normalize and determine expression levels and differentially expressed genes.
Genome_build: Homo sapiens
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each gene per sample


title: HMC3_model_DGMI_L2


title: scRNA_seq_KO2_D21

description: Single Cell RNA seq of KMT2D-SET-KO cell-induced organoid at D21

value: brain organoid

value: untreated


title: PBCSP-WT-H3K27ac-rep2


title: scRNA_seq_WT_D30

description: Single Cell RNA seq of HN4 cell-induced organoid at D30


title: clf_05_3


title: BCSP-WT-H3K27ac-rep2


title: pBCSP-WT-input-DNA-rep2


title: clf_05_1


title: scRNA_seq_KO1_D30

description: Single Cell RNA seq of KMT2D-SET-KO  cell-induced organoid at  D30


title: clf_05_2


title: HMC3_model6


title: SSC-WT-input-DNA-rep2


title: WT_05_4

source_name: Wildtype (Col-0)_~95% air humidity

value: Wildtype (Col-0)


title: HMC3_model5


title: scRNA_seq_WT_D21


title: SSC-WT-H3K27ac-rep2


title: CUT_tag_KO1_D21_NT_IgG_rep2

description: CUT&Tag for IgG of KMT2D-SET-KO cell-induced organoid at D21

data_processing:
library strategy: Cut&Tag
The gene expression level of RNA-seq data was calculated by using  RSEM.
CUT&Tag reads were aligned to the hg38 genome using Bowtie2. Duplicate reads were removed with the function MarkDuplicates from Picard. The .bw files were generated by deepTools.
The gene expression level of scRNA-seq data was calculated by using  STAR.
The fragment files of scATAC-seq data was generated by using  Cell Ranger ATAC.
Assembly: hg38
Supplementary files format and content: .genes.results files contain the gene expression level of RNA-seq data
Supplementary files format and content: .bw files contain the CUT&Tag data that will be displayed in the Genome Browser, a web-based tool used to display a requested portion of a genome at any scale.
Supplementary files format and content: _data.tar.tar files contain the gene expression level of scRNA-seq data
Supplementary files format and content: _fragments.tsv.gz files contain the fragments of scATAC-seq data

value: GENOMIC


title: HMC3_model_DGMI_L1


title: WT_05_3


title: HMC3_model4


title: CGR8 cells, FBS_siRNA_RSL24D1_3

city: LYON

first: Mathieu

last: GABUT

address: 28 rue laennec

department: Cancer Initiation and Tumor cell Identity

country: France

institute: Cancer Research Centre of Lyon, Inserm U1052

data_processing:
Raw sequencing reads were aligned on the murine genome (GRCm38) with STAR (v2.7.0f), with the annotation of known genes from gencode vM20.
Gene expression was quantified using Salmon (0.14.1) and the annotation of protein coding genes from gencode vM20
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file with raw counts from salmon for each sample

source_name: CGR8 cells

growth_protocol: CGR8 cells were seeded in 6 well plates pre-coated with 0.2% gelatin and cultivated in DMEM media containing 10% of FBS (ESC quality) and exogenous LIF.

extract_protocol:
Cells were harvested in 1ml of TRIzol reagent (Thermo Fisher Scientific ®) and total RNA was extracted according to manufacturer’s instructions. RNA was quantified and integrity was mesured by optic density using a 2100 BioAnalyzer
TruSeq Stranded Total RNA H/M/R- Gold, ILLUMINA®. rRNAs were depleted through magnetic beads (Agencourt® RNAClean XP, BECKMAN COULTER).

treatment_protocol: Cells were transfected with siRNAs and collected after 48h for total RNA extraction.

value: CGR8 cells

tag: sirna

tag: culture condition

value: FBS

value: mouse embryonic stem cells


title: CUT_tag_KO1_D21_NT_IgG_rep1

tag: tissue


title: HMC3_model3

tag: treatment


title: CUT_tag_KO1_D21_NT_H3K4me1_rep2

description: CUT&Tag for H3K4me1 of KMT2D-SET-KO cell-induced organoid at D21


title: scRNA_seq_KO1_D21


title: CGR8 cells, FBS_siRNA_RSL24D1_1

tag: cell line


title: clf_0_4

value: Untreated


title: HMC3_model7


title: HMC3_model2


title: CGR8 cells, FBS_siRNA_RSL24D1_2

tag: cell type


title: WT_05_1

tag: genotype


title: CUT_tag_KO1_D21_NT_H3K4me1_rep1


title: CGR8 cells, FBS_Ctrl_3

value: siCtrl


title: HMC3_model1


title: CUT_tag_WT_D21_NT_IgG_rep2

description: CUT&Tag for IgG of HN4 cell-induced organoid at D21

value: WT


title: CGR8 cells, FBS_Ctrl_2


title: HMC3_ctrl6


title: clf_0_2


title: CUT_tag_WT_D21_NT_IgG_rep1


title: CGR8 cells, FBS_Ctrl_1


title: CUT_tag_WT_D21_NT_H3K4me1_rep2

description: CUT&Tag for H3K4me1 of HN4 cell-induced organoid at D21


title: clf_0_1


title: HMC3_ctrl5


title: WT_05_2


title: BCSP-KO-input-DNA

data_processing:
RNA-seq raw sequencing data processed by Trim_Galore (v.0.6.6) for removing adapters and  low-quality base pairs. Reads were aligned with bowtie2 (v.2.3.5.1) to GRCm38  reference genome. Read counts were generated by featureCounts (v.2.0.1)
ChIP-seq data that were generated using WT and Ptip-/- (SSCs, pBCSPs and BCSPs) cells were quality-controlled and processed by Trim_Galore (v.0.6.6) for removing adapters and low-quality base pairs. Reads were aligned with bowtie2(v.2.3.5.1) to GRCm38 reference genome. Aligned reads were stripped of duplicates using samtools (v.1.9). H3K4me1/H3k4me3/H3K27ac Peaks were called with Macs2 (v.2.2.6).
Genome_build: GRCm38
Supplementary_files_format_and_content: RNA-seq:  Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: ChIP-seq:  Broad peak

extract_protocol:
Total RNA were extracted with Trizol and mRNA were isolated with Oligo dT beads.
For histone ChIP-seq, lysates were clarified from MNase digested nuclei and histone-DNA complexes were isolated with H3K4me1,H3K4me3 or H3K27ac antibodies.
For RNA, libraries were prepared according to VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (Part# NR601). Briefly, mRNA was interrupted with metal ions in interrupted buffer , cDNA synthesis using random primers for reverse transcription of mRNA. The cDNA strands in the hybrid double strands were digested by RNaseH to synthesize cDNA complementary strands for cDNA second strand synthesis. Repair sticky ends were repaired to blunt ends   add A-tail,and connection connector.After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Libraries were sequenced on Illumina instrument following the manufacturer's protocols.
For ChIP, Illumina libraries were constructed using a modified custom paired-end protocol. In brief, samples were end-repaired (1*T4 DNA ligase buffer, 0.4 mM dNTP mix, 2.25 U T4 DNA polymerase, 0.75 U Klenow DNA polymerase and 7.5 U T4 polynucleotide kinase; 30 min at 21–25 C), A-tailed (1*NEB buffer 2, 0.4 mM dNTPs and 3.75 U of Klenow (exo-); 30 min at 37 C) and ligated (1*rapid DNA ligation buffer, 1 mM Illumina PE adapters and 1,600 U DNA ligase; 1–8 h at 21–25 C). Ligated fragments were amplified using indexed primers (Illumina) for 14 PCR cycles. DNA was purified with 1.8 volume KAPA DNA purification beads between each step.

value: limbs

value: bone, cartilage and stromal progenitor cells

value: post natal day 3


title: HMC3_ctrl4


title: WT_0_4

source_name: Wildtype (Col-0)_Untreated


title: WT_0_3


title: HMC3_ctrl3


title: BCSP-KO-H3K27ac


title: CUT_tag_WT_D21_NT_H3K4me1_rep1


title: clf_0_3

value: clf


title: CUT_tag_WT_D21_KMT2D_rep2

description: CUT&Tag for KMT2D of HN4 cell-induced organoid at D21


title: BCSP-KO-H3K4me3


title: CUT_tag_WT_D21_KMT2D_rep1


title: CUT_tag_WT_D21_IgG_rep2


title: BCSP-KO-H3K4me1


title: clf-05-2-H3K27me3

data_processing:
Sequencing reads were cleaned with Trim Galore v0.4.4, Trimmomatic v0.36 and sickle, including removing bases with low quality score (<25) and irregular GC content, and cutting sequencing adaptors followed by filtering short reads.
The cleaned reads were mapped to TAIR RefSeq v10 using BWA 0.7.5a-r405  for ChIP-seq, all with default settings.
For ChIP-seq, MACS1.3.7 was used to identify read-enriched regions (peaks) with combined criteria: P value < 1e–5 and fold-change >32.  ChIP-seq data Target genes were defined as genes with a peak within or nearby the gene body (±2 kb).
Genome_build: TAIR 10
Supplementary_files_format_and_content: Peak files and bigwig files were provided.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27me3 antibody.
Libraries were prepared according to Novogene Corporation (Beijing, China) protocols.Subsequently, pair-end sequencing of samples was performed on Illumuna platform (Illumina, CA, USA)

value: ~95% environment humidity

value: H3K27me3 (Upstate, USA, Cat. no. 07-449)


title: HMC3_ctrl1

extract_protocol:
The cell lysates were directly reverse transcribed and amplified into double stranded cDNAs, which were subsequently added adaptors by Tn5 transposase. The purified and fragmented products were used for library construction and sequencing.
RNA libraries were prepared for sequencing using Illumina protocols


title: CUT_tag_WT_D21_IgG_rep1


title: pBCSP-KO-H3K27ac

value: pre-bone, cartilage and stromal progenitor cells


title: Rank-knockout mouse at lactation day 5_3

data_processing:
3′ RNA-sequencing (QuantSeq) reads were prepared for analysis by removing adaptor contamination, poly(A) read through and low-quality tails using bbmap v.36.92.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with readcounts per gene

source_name: intestine

extract_protocol:
Total RNA isolation was performed using the RNA isolation kit (VBCF, Vienna) which uses a lysis step based on guanidine thiocyanate and magnetic beads applied on the KingFisher instrument.
Equivalent quantities of total RNA were used for library preparation using the Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina.
Libraries were pooled at an equimolar ratio and sequenced on an Illumina HiSeq 2500 instrument using the single-read 50-read mode.

value: intestine

value: epithelial cells

value: Rank-knockout

tag: Stage

value: lactation day5


title: RNA_seq_KO2_D21_Chir99021Mock

description: RNA seq of KMT2D-SET-KO cell-induced organoid at D12 (PBS treatment)

value: brain organoid

value: PBS

value: RNA-seq

value: TRANSCRIPTOMIC


title: clf-05-2-Input


title: Rank-knockout mouse at lactation day 5_4


title: pBCSP-KO-H3K4me3

tag: age


title: WT_0_2

value: Wildtype (Col-0)

value: Untreated

value: Four-week-old

value: leaf


title: Rank-knockout mouse at lactation day 5_1


title: Rank-knockout mouse at lactation day 5_2


title: RNA_seq_KO2_D21_Chir99021

description: RNA seq of KMT2D-SET-KO cell-induced organoid at D12 (Chir99021 treatment)


title: clf-05-1-H3K27me3


title: RNA_seq_KO1_D21_Chir99021Mock

description: RNA seq of KMT2D-SET-KO cell-induced organoid at D21 (PBS treatment)


title: HMC3_ctrl2

value: untreated


title: clf-05-1-Input

value: clf


title: pBCSP-KO-H3K4me1

tag: strain

value: limbs

value: post natal day 3


title: SSC-KO-input-DNA

value: Skeletal stem cells


title: RNA_seq_KO1_D21_Chir99021

description: RNA seq of KMT2D-SET-KO cell-induced organoid at D21 (Chir99021 treatment)


title: WT_0_1


title: W-05-2-H3K27me3

value: ~95% environment humidity

tag: chip antibody

value: H3K27me3 (Upstate, USA, Cat. no. 07-449)


title: W-05-2-Input


title: WT mouse at lactation day 5_3

value: intestine

value: epithelial cells

value: WT


title: SSC-KO-H3K27ac


title: RNA_seq_WT_D21_Chir99021Mock

description: RNA seq of HN4 cell-induced organoid at D21 (PBS treatment)

value: brain organoid

tag: time

value: PBS


title: pBCSP-KO-input-DNA

value: pre-bone, cartilage and stromal progenitor cells


title: WT mouse at lactation day 5_2

value: lactation day5


title: SSC-KO-H3K4me3


title: W-05-1-H3K27me3

value: Wildtype (Col-0)


title: RNA_seq_KO2_D60_rep3

description: RNA seq of KMT2D-SET-KO cell-induced organoid  at D60

tag: library strategy

value: RNA-seq

value: TRANSCRIPTOMIC


title: SSC-KO-H3K4me1


title: RANKL-treated organoids 4

source_name: intestinal organoids

value: intestinal organoids

value: RANKL


title: WT mouse at lactation day 5_1


title: BCSP-WT-input-DNA

value: limbs

value: bone, cartilage and stromal progenitor cells

value: Ptipf/f


title: RNA_seq_WT_D21_Chir99021

description: RNA seq of HN4 cell-induced organoid  at D21 (Chir99021 treatment)

tag: library source


title: W-05-1-Input

value: ~95% environment humidity


title: RNA_seq_KO2_D60_rep2

description: RNA seq of KMT2D-SET-KO cell-induced organoid at D60

value: untreated


title: BCSP-WT-H3K27ac

value: post natal day 3


title: RNA_seq_KO2_D60_rep1


title: clf-0-2-H3K27me3

value: clf

value: Untreated

value: H3K27me3 (Upstate, USA, Cat. no. 07-449)


title: clf-0-2-Input


title: RANKL-treated organoids 2


title: RANKL-treated organoids 3


title: WT mouse at lactation day 5_4

value: intestine

value: epithelial cells

value: WT


title: BCSP-WT-H3K4me3


title: RNA_seq_KO1_D60_rep3

value: brain organoid


title: clf-0-1-H3K27me3


title: clf-0-1-Input


title: BCSP-WT-H3K4me1


title: RNA_seq_KO1_D60_rep2

value: RNA-seq


title: control organoids 4

value: control


title: RNA_seq_KO1_D60_rep1

value: TRANSCRIPTOMIC


title: RANKL-treated organoids 1

value: intestinal organoids

value: RANKL


title: pBCSP-WT-input-DNA

value: limbs

value: pre-bone, cartilage and stromal progenitor cells


title: W-0-2-H3K27me3

value: Wildtype (Col-0)


title: W-0-2-Input


title: pBCSP-WT-H3K27ac

value: Ptipf/f


title: control organoids 3


title: RNA_seq_WT_D60_rep3

description: RNA seq of HN4 cell-induced organoid at D60

value: untreated


title: RNA_seq_WT_D60_rep2


title: control organoids 1


title: W-0-1-H3K27me3


title: pBCSP-WT-H3K4me1

value: post natal day 3


title: pBCSP-WT-H3K4me3


title: RNA_seq_WT_D60_rep1


title: EU-seq WT ERα OE  Repeat 2

value: Breast, mammary gland

value: epithelial cell

value: 17beta-estradiol, 45 mins of EU


title: EU-seq RBM ERα OE Repeat 2


title: RNA_seq_KO2_D30_rep2

description: RNA seq of KMT2D-SET-KO cell-induced organoid at D30


title: SSC-WT-H3K4me3

value: Skeletal stem cells


title: hmoDC, VLP-Man-OvaI/II-treated, 6 h, rep4

city: Cambridge

first: Valerie

last: Lensch

state: Massachusetts

address: 77 Massachusetts Avenue

institute: MIT

description: Man OVA Rep4

data_processing:
STAR 2.7.11a
Sequence reads were trimmed for adaptor sequence and trimmed sequence reads were mapped to GRCh38 using STAR (Parameters: outFilterMismatchNoverLmax 0.04, outFilterMismatchNmax 999, alignSJDBoverhangMin 1 , alignSJoverhangMin 8, outFilterMultimapNmax 20, alignIntronMin 20, alignIntronMax 1000000, alignMatesGapMax 1000000)
Read counts were extracted using STAR (quantMode GeneCounts) and normalized using DESeq2 pipeline
Assembly: GRCh38
Supplementary files format and content: comma-delimited files include DESeq2 normalized gene counts for each sample

source_name: dendritic cell

growth_protocol: moDCs grown in the presence of GM-CSF (100 ng/mL) and IL-4 (50 ng/mL) (R&D Systems) in CellGenix GMP DC media (Sartorius) for 6 to 7 days

extract_protocol:
Total RNA was isolated using NucleoSpin RNA kits
mRNA from 40ng of RNA was isolated and used to prepare Illumina libraries. Libraries were sequenced on an Illumina NextSeq500 with 40nt paired end reads.

treatment_protocol: moDCs were treated with 8 nM VLPs for 6 h at 37 °C

value: dendritic cell

value: VLP-Man-OvaI/II-treatetd, 6 h


title: hmoDC, VLP-Man-OvaI/II-treated, 6 h, rep3

description: Man OVA Rep3


title: RNA_seq_KO2_D30_rep1

value: brain organoid

value: RNA-seq


title: ChIP-seq RBM ERα FLAG pfChIP-seq


title: hmoDC, VLP-Man-OvaI/II-treated, 6 h, rep2

description: Man OVA Rep2


title: SSC-WT-H3K4me1


title: hmoDC, VLP-Man-OvaI/II-treated, 6 h, rep1

description: Man OVA Rep1


title: BCSP-Ptip-KO-rep2

description:
RNA_Raw_gene_counts_matrix.txt
RNA_KO_2_BCSP

value: bone, cartilage and stromal progenitor cells


title: RNA_seq_KO1_D30_rep5

value: TRANSCRIPTOMIC


title: ChIP-seq WT ERα FLAG pfChIP-seq


title: ChIP-seq RNaseA wo pre-extraction ERα repeat 2


title: control organoids 2

value: intestinal organoids

value: control


title: BCSP-Ptip-KO-rep1

description:
RNA_Raw_gene_counts_matrix.txt
RNA_KO_1_BCSP

value: limbs


title: hmoDC, VLP-PE-OvaI/II-treated, 6 h, rep4

description: PE OVA Rep4

value: VLP-PE-OvaI/II-treated, 6 h


title: RNA_seq_KO1_D30_rep2


title: ChIP-seq Mock wo pre-extraction ERα repeat 2


title: pBCSP-Ptip-KO-rep2

description:
RNA_Raw_gene_counts_matrix.txt
RNA_KO_2_PBCSP

value: pre-bone, cartilage and stromal progenitor cells


title: ChIP-seq RNaseA wo pre-extraction ERα repeat 1


title: hmoDC, VLP-PE-OvaI/II-treated, 6 h, rep3

description: PE OVA Rep3


title: hmoDC, VLP-PE-OvaI/II-treated, 6 h, rep5

description: PE OVA Rep5


title: pBCSP-Ptip-KO-rep1

description:
RNA_Raw_gene_counts_matrix.txt
RNA_KO_1_PBCSP


title: RNA_seq_KO1_D30_rep3

value: untreated


title: ChIP-seq Mock wo pre-extraction ERα repeat 1


title: SSC Ptip-KO-rep2

description:
RNA_Raw_gene_counts_matrix.txt
RNA_KO_2_SSC

value: post natal day 3


title: RNA_seq_KO1_D30_rep1

description: RNA seq of KMT2D-SET-KO cell-induced organoid  at D30


title: RNA_seq_KO1_D30_rep4


title: ChIP-seq RNAse A w pre-extraction ERα repeat 2

value: Breast, mammary gland


title: RNA_seq_WT_D30_rep2

description: RNA seq of HN4 cell-induced organoid at D30

value: WT


title: RNA_seq_WT_D30_rep3


title: ChIP-seq RNAseA w pre-extraction ERα repeat 1

value: epithelial cell


title: SSC Ptip-KO-rep1

description:
RNA_Raw_gene_counts_matrix.txt
RNA_KO_1_SSC

value: Skeletal stem cells


title: RNA_seq_WT_D30_rep1


title: ChIP_seq Mock w pre-extraction ERα repeat 2


title: hmoDC, unstimulated, 6 h, rep4

description: Cntrl Rep5

value: dendritic cell

value: unstimulated, 6 h


title: ChIP-seq Mock w pre-extraction ERα repeat 1


title: RNA_seq_KO2_D21_rep2

description: RNA seq of KMT2D-SET-KO cell-induced organoid at D21

value: brain organoid


title: RNA_seq_KO1_D21_rep2

value: RNA-seq


title: hmoDC, unstimulated, 6 h, rep3

description: Cntrl Rep4


title: RNA_seq_KO2_D21_rep1


title: ChIP-seq RBM FLAG ERα Repeat 2


title: pBCSP-WT rep1

description:
RNA_Raw_gene_counts_matrix.txt
RNA_WT_1_PBCSP

value: Ptipf/f


title: hmoDC, unstimulated, 6 h, rep5

description: Cntrl Rep2


title: hmoDC, unstimulated, 6 h, rep2

description: Cntrl Rep3


title: SSC-WT rep2

description:
RNA_Raw_gene_counts_matrix.txt
RNA_WT_2_SSC


title: 3D D25, rep2

data_processing:
sciATAC reads were aligned with snaptools bwa aligner and converted to fragment files using Sinto. The ArchR package was used for processing, analysis, and visualization of the data.
Assembly: hg38
Supplementary files format and content: Mtx files were generated from ArchR. PeakMatrix.mtx contains all peaks for all samples. Corresponding PeakMatrix rows and columns are provided as csv files.

source_name: H9 hPSC

extract_protocol:
Cells from hPSC, mesoderm, cardiac mesoderm, cardiac progenitor, and CM stages were dissociated and processed fresh for droplet-based snATAC-seq. Dissociated cells were stained with DAPI (Thermo Fisher Scientific). In total, 500,000 (DAPI-negative) were sorted and collected using a Sony SH800 sorter.
MinElute PCR Purification Kit (Qiagen) and size selection was performed with SPRISelect reagent (Beckman Coulter; 0.55× and 1.5×). Libraries were purified one more time with SPRISelect reagent (Beckman Coulter; 1.5×). barcoded Tn5 transposomes

value: H9 hPSC

value: hPSC

value: 3D cardiomyocyte differentiation


title: hmoDC, unstimulated, 6 h, rep1

description: Cntrl Rep1


title: ChIP-seq WT FLAG ERα Repeat 2


title: SSC-WT rep1

description:
RNA_Raw_gene_counts_matrix.txt
RNA_WT_1_SSC

value: limbs


title: 3D D25, rep1


title: fRIP-seq Veh Input Repeat 1

value: EtOH


title: pBCSP-WT rep2

description:
RNA_Raw_gene_counts_matrix.txt
RNA_WT_2_PBCSP

value: pre-bone, cartilage and stromal progenitor cells


title: hmoDC, VLP-Man-OvaI/II-treated, 6 h, rep5

description: Man OVA Rep5

value: VLP-Man-OvaI/II-treatetd, 6 h


title: RNA_seq_KO1_D21_rep1

value: untreated

value: TRANSCRIPTOMIC


title: RNA_seq_KO1_D12_rep1

description: RNA seq of KMT2D-SET-KO cell-induced organoid  at D12


title: 3D D15, rep2

value: WT


title: RNA_seq_KO2_D12_rep1

description: RNA seq of KMT2D-SET-KO cell-induced organoid at D12


title: fRIP-seq E2 Input Repeat 2

value: Breast, mammary gland

value: epithelial cell


title: 3D D7, rep2


title: PT2 group

city: Chongqing

first: Yinglian

last: Chen

address: Fengtian Road

institute: Southwest Hospital, Army Medical University (Third Military Medical University)

description:
41 years old man with ALD homozygote and no illness phenotype
TU

data_processing:
Fastp V0.23.4 Perform trimming and filtering of raw sequencing reads to ensure high-quality data; HISAT2 V2.1.0 Map the high-quality reads to a reference genome for accurate alignment; FeatureCounts V2.0.2 Count the number of reads mapped to each gene to quantify gene expression levels.
Assembly: hg38
Supplementary files format and content: csv format file and TPM values of samples had been caculated

source_name: whole blood

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols

value: whole blood

value: ALD Homozygote


title: NC1 group1

description:
7 years old Normal boy
C1

value: Normal individual


title: NC2 group

description:
33 years old normal male adult
CF


title: fRIP-seq E2 ERα IP Repeat 2

data_processing:
For ChIP-seq analysis the raw reads obtained from the sequencing were aligned to the hg19 reference genome using Bowtie2. Reads with a quality score less than 20 were filtered out using the Filter Sam or Bam tool. Peaks were called using MACS2  with default settings.
For the fRIP-seq analysis the adaptor sequences were removed from the reads using Cutadapt, followed by alignment to the hg19 reference genome using RNA STAR. Duplicate reads were removed using UMI-tools deduplicate. Regions of fRIP-seq IP enrichment were called using MACS2with the fRIP-seq input as the control file. The log2FC of fRIP-seq IP /fRIP-seq input was calculated using the aligned BAM file with bamcompare.
For EU-seq analysis, the raw reads were aligned to hg19 using Bowtie2. PCR duplicates were removed using MarkDuplicates from Picard Tools. Read coverage on known E2 upregulated genes was calculated using multiBamSummary.
Assembly: hg19
Supplementary files format and content: bigwig and narrow peaks


title: RNA_seq_WT_D12_rep1

description: RNA seq of HN4 cell-induced organoid at D12

value: brain organoid

value: RNA-seq


title: NC1 group2

description:
7 years old Normal boy
C2


title: RNA_seq_WT_D21_rep1

description: RNA seq of HN4 cell-induced organoid at D21


title: fRIP-seq E2 Input Repeat 1


title: RNA_seq_KO2_D0_rep2

description: RNA seq of KMT2D-SET-KO cell-induced organoid  cells at D0


title: 3D D15, rep1

value: H9 hPSC


title: FXX group1

description:
40 years old woman, twins's mother with ALD with Heterozygote
PM

value: ALD Heterozygote


title: RNA_seq_KO2_D0_rep1


title: 3D D5, rep1

value: hPSC

value: 3D cardiomyocyte differentiation


title: PT1 group2

description:
8 years old boy twin with ALD homozygote and no illness phenotype
T2


title: fRIP-seq E2 ERα IP Repeat 1


title: RNA_seq_KO1_D0_rep2


title: PT1 group1

description:
8 years old boy twin with ALD homozygote and illness phenotype
T1


title: CUER

city: Blacksburg

last: Sharakhova

state: VIRGINIA

address: 360 West Campus Drive

department: Entomology

institute: Virginia polytechnic institute and state university

data_processing:
The sequence quality assessment was performed using FastQC software v.0.12.1
Juicer Pipeline was used to build the contact matrices and Hi-C heatmaps
Assembly: AaegL5
Supplementary files format and content: hic files include contact meatices and Hi-C heatmaps
Supplementary files format and content: text files include experiment description for hic files

organism: Aedes aegypti

source_name: 2-5 day Adult

extract_protocol:
The proximally-ligated DNA is prepared with Arima-HiC+ for High Coverage kit (Arima Genomics)
Libraries are prepared with Arima-HiC+ for High Coverage kit (Arima Genomics)

value: 2-5 day Adult

value: CUER

tag: Sex

value: pooled male and female


title: VEBE

value: VEBE

value: male


title: 3D D7, rep1

value: WT


title: 3D D3, rep2


title: 3D D3, rep1


title: RNA_seq_KO1_D0_rep1

data_processing:
The gene expression level of RNA-seq data was calculated by using  RSEM.
CUT&Tag reads were aligned to the hg38 genome using Bowtie2. Duplicate reads were removed with the function MarkDuplicates from Picard. The .bw files were generated by deepTools.
The gene expression level of scRNA-seq data was calculated by using  STAR.
The fragment files of scATAC-seq data was generated by using  Cell Ranger ATAC.
Assembly: hg38
Supplementary files format and content: .genes.results files contain the gene expression level of RNA-seq data
Supplementary files format and content: .bw files contain the CUT&Tag data that will be displayed in the Genome Browser, a web-based tool used to display a requested portion of a genome at any scale.
Supplementary files format and content: _data.tar.tar files contain the gene expression level of scRNA-seq data
Supplementary files format and content: _fragments.tsv.gz files contain the fragments of scATAC-seq data

value: untreated

value: TRANSCRIPTOMIC


title: FXX group2

description:
68 years old woman, twins's grandmother with ALD with Heterozygote
PG

value: whole blood


title: MASC

organism: Aedes mascarensis


title: RNA_seq_WT_D0_rep2

description: RNA seq of HN4 cell-induced organoid at D0


title: 2D D25, rep2

value: 2D cardiomyocyte differentiation


title: UCPRP-treated_3

first: Ruojing

last: Huang

address: Huangpu Street 613

department: Department of Ophthalmology

institute: The First Affiliated Hospital of Jinan University

data_processing:
Adaptor and/or low-quality bases were trimmed from the sequenced reads
The clean reads were then mapped to GRCm38 using HISAT and the counts were extracted
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: cornea

extract_protocol:
RNA was extracted using Qiagen RNeasy kit as per manufacturer's protocol. RNA quality was inspected using Agilent 2100 Fragment analyzer
RNA libraries was constructed using TruSeq Stranded Total RNA Library Prep kit following manufacturer's protocol

treatment_protocol: 5 ul of 0.2% BAK was administered to each eye of the mice daily for a consecutive 14-day period. For UCS and UCPRP treatment, 5 ul of 20% UCS and UCPRP was respectively administered to the mice cornea thrice daily for a consecutive 10-day period.

value: cornea

value: BAK-injured (UCPRP treated)


title: 2D D15, rep2


title: 2D D15, rep1


title: Notch and Cph, Knockdown, Replicate1

city: Heidelberg

first: Nick

last: Hirschmüller

address: Meyerhofstrasse

department: Genome Biology

institute: European Molecular Biology Laboratory

description: 10x Genomics

data_processing:
Single cell count matricies were generated using CellRanger "count" command with the "include-introns" option (version 7.0.1). Quality control and analyses were conducted using Seurat (version 4.3.0). Raw gene expression count matrices were pre-processed and filtered using scran (version 1.24.0). In brief, droplets with RNA content below each library's inflection point were removed, along with cells meeting any of the following criteria: (a) fewer than 250 detected genes, (b) ranking in the top 1 percentile of cells by UMI count, or (c) a high percentage of mitochondrial reads. One replicate of the NotchRNAi and NotchRNAiCphRNAi condition showed an unusually high content of mitochondrial reads and were removed from subsequent analyses.
Assembly: dm6
Supplementary files format and content: Tab-separated values files and matrix files

organism: Drosophila melanogaster

extract_protocol:
Flies were starved for 3h and placed in vials with filter paper containing 5% sucrose for 16h. 20 midguts were dissected from respective condition in ice-cold PBS, taking care to remove the hindgut, Malpighian tubules and proventriculus. Samples were digested in 1 mg /ml Elastase (Sigma, #E0258) solution at 25°C for 45 min at 1000RPM and vortexed every 15min. Samples were then pelleted and resuspended in PBS and dissociated cells were then passed through a 40uM than 20uM cell strainer and subsequently counted. Approximately 20,000 live cells were used for scRNA-seq with 10X Genomics 5’ V2 kit following the manufacturers protocol for library generation. Prior to sequencing, library fragment size was determined using an Agilent Bioanalyzer high-sensitivity chip and quantified using Qubit. Libraries were multiplexed and sequenced using a Nextseq 550 at the Deep Sequencing Facility, BioQuant, Heidelberg University.
Library preperation was performed according to manufacturers instructions (10X Genomics 5’ V2 kit for knockdown experiments and 10X Genomics 3’ V2 kit for knockout experiments).

value: intestine


title: Notch and Cph, Knockdown, Replicate2

description: 10x Genomics


title: Restricted cow 1058

type: RNA

city: St Genès-Champanelle

first: Christine

last: LEROUX

address: Route de Theix

institute: INRAE

description: Holstein early lactation restricted cow

hyb_protocol: After purification (Qiagen RNeasy Mini Kit), 1,65 µg of Cy3 labeled cRNA were hybridized onto G2519F-023647 Bovine (V2) Gene Expression Microarray, 4x44K (Agilent, USA) with hybridization buffer (Agilent Gene Expression Hybridization Kit) according to the manufacturer’s instructions. After 17h of hybridization, slides were washed with the Gene Expression Wash Pack.

scan_protocol: Microarrays were scanned with Agilent G2505 scanner.

data_processing: Data were extracted with Feature Extraction 11,0 software (Agilent, USA) (no background subtraction).

organism: Bos taurus

source_name: Liver biopsy

label_protocol: 100 ng of total RNA were amplified and fluorescently labelled to produce Cy3 cRNA using the Low Input Quick Amp Labeling one colors Kit (Agilent, USA) in the presence of spike-in one color control.

growth_protocol: Twelve cows were studied at earlylactation stage,

extract_protocol: Total RNA was prepared through homogenization of approximately 50 mg of liver tissue according to manufacture protocol of mirVana miRNA extraction kit (Invitrogen Life Technologies, Cergy Pontoise, France)

treatment_protocol: At 24 ± 3 d in milk, multiparous cows were either allowed to continue ad libitum intake of a lactation diet (CON, n = 6), or the ration was diluted with barley straw (48% DM) for 4 d (RES, n = 6). On d 3, one healthy rear mammary quarter was infused with 50 µg of LPS. Liver biopsies were performed 24 h after LPS challenge

tag: physiology

value: early lactation stage, multiparous.

tag: breed

value: Holstein cow

tag: diet

value: Nutrient restricted diet


title: 2D D25, rep1

value: H9 hPSC

value: hPSC


title: Notch, Knockdown, Replicate2

description: 10x Genomics

value: NotchRNAi


title: Restricted cow 7043

description: Holstein early lactation restricted cow


title: Restricted cow 1015

description: Holstein early lactation restricted cow


title: UCPRP-treated_2


title: 2D D7, rep2


title: Restricted cow 1018

description: Holstein early lactation restricted cow


title: UCPRP-treated_1


title: UCS-treated_2

value: BAK-injured (UCS treated)


title: Notch, Knockdown, Replicate1

description: 10x Genomics


title: 2D D7, rep1


title: UCS-treated_1


title: Control, Knockdown, Replicate2

description: 10x Genomics

value: CtrlRNAi


title: Vehicle_3

value: BAK-injured (no treatment)


title: Restricted cow 0049

description: Holstein early lactation restricted cow


title: Control, Knockdown, Replicate1

description: 10x Genomics


title: Vehicle_2


title: 2D D5, rep2

value: WT


title: 2D D5, rep1


title: BCSP-WT rep1

description:
RNA_Raw_gene_counts_matrix.txt
RNA_WT_1_BCSP

value: limbs

value: bone, cartilage and stromal progenitor cells

value: post natal day 3

value: Ptipf/f


title: 2D D2, rep2

value: 2D cardiomyocyte differentiation


title: Notch, Knockout, Replicate2

description: 10x Genomics

value: NotchKO


title: Restricted cow 0078

description: Holstein early lactation restricted cow


title: Control cow 8027

description: Holstein early lactation control cow

value: Ad libitum lactation diet


title: Control cow 9040

description: Holstein early lactation control cow

value: early lactation stage, multiparous.


title: SSC-WT-H3K27ac

value: Skeletal stem cells

tag: antibody


title: Vehicle_1

tag: tissue

value: cornea


title: 2D D2, rep1

value: H9 hPSC

tag: treatment


title: Notch, Knockout, Replicate1

description: 10x Genomics

value: intestine


title: Control, Knockout, Replicate2

description: 10x Genomics

value: CtrlKO


title: Control cow 1076

description: Holstein early lactation control cow

value: Holstein cow


title: Control_3

value: no injury no treatment


title: ChIP-seq WT FLAG ERα  Repeat 1

source_name: Breast, mammary gland

extract_protocol:
For ChIP-seq experiment, genomic DNA was isolated as per standard ChIP-seq protocol. For fRIP-seq, RNA crosslinked to ERα were pulldown using anti ERα followed by purification of the total RNA using trizol. For EU-seq cells were chased with EU for 45 mins and total RNA was isolated using trizol. Further EU labelled RNA was biotinylated using Click Chemistry reaction and pulldown using Streptavidin beads using standard protocol. The pulldown RNA was extracted using Trizol and used for library preparation.
ChIP-seq library preparation using the NEBNext® Ultra™II DNA Library Prep kit with Sample Purification Beads (Catalogue-E7103L) following the manufacturer's protocol. The fRIP-seq purified RNA was used for preparing RNA-seq libraries, using the NEBNext rRNA Depletion Kit v2 and NEBNext Ultra II Directional RNA Library Prep, following the manufacturer's protocol. For EU-seq the nasecent RNA was converted to cDNA using the SuperScript™ IV First-Strand Synthesis System (catalogue number: 18091050). The second strand of cDNA was synthesized using the NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (Catalogue no-E7765L). The double-stranded DNA was further fragmented, and the library was prepared using the NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina (E7805L), following the manufacturer's protocol.

value: Breast, mammary gland

tag: cell line

value: epithelial cell


title: D0, rep2

tag: cell type

value: hPSC

value: WT


title: Control cow 1024

description: Holstein early lactation control cow


title: D0, rep1

tag: genotype


title: Control, Knockout, Replicate1

description: 10x Genomics


title: Control_2


title: Control_1


title: Control cow 0055

description: Holstein early lactation control cow


title: PD3 rep2 line DN PDL 1.5L

status: Public on Sep 05 2024

city: Moscow

first: Daniil

last: Poberezhniy

address: Kurchatov sq. 2

country: Russia

institute: National Research Centre "Kurchatov Institute"

data_processing:
Quality control of the reads was carried out using the FastQC program (v 0.12.1). Adapter removal, quality trimming and length filtration of reads was performed using the Cutadapt (v 2.6)
Mapping and quantifying of reads at the levels of individual transcripts and genes was implemented using the Salmon (v 1.10.2) and the tximport (R package, v 1.30.0) with Homo sapiens reference genome (GRCh38.14) and annotation (release 44).
Further data processing was carried out using DESeq2 (R package, v 1.42.0)
Assembly: GENCODE human genome Release 44 (GRCh38.p14)
Supplementary files format and content: tab-delimited text file includes DESeq2 normalized read counts for all samples
Supplementary files format and content: sample.sf files include raw Salmon quantification results for each sample

source_name: neuronal culture

extract_protocol:
Total RNA was extracted using Extract RNA (Eurogen, RF) and PureLink™ RNA Micro Scale Kit (Invitrogen) following manufacturer’s protocols. Total RNA was used to obtain polyA RNA fraction with oligo(dT)-coated magnetic spheres Dynabeads™ mRNA Purification Kit (Ambion) following manufacturer’s protocol.
RNA libraries were prepared using NEBNext® Ultra™ II RNA Library Prep Kit (NEB) following manufacturer’s protocol.

treatment_protocol: For the experiment glial cultures were cultivated in glial base medium (DMEM/F12 (Gibco, Billings, MT, USA), 1% NEAA (Hyclone, Logan, Utah, USA), Glutamine 2mM (PanEco, RF), N2, B27, FGF2 8 ng/ml, Heregulin 10 ng/ml, IGF1 200 ng/ml, Activin A 10 ng/ml (Stem Cell Technologies, Canada) w/o antibiotics for 48 hours. Supernatants were collected, and then HD glial mixed medium (two HD supernatants 1:1) and PD glial mixed medium (two PD supernatants 1:1) were prepared for cultivation of neurons. Neuronal cultures were seeded on 35mm Petri dishes overnight. The next day 4 types of media (base neuronal, base glial, HD glial mixed, PD glial mixed: all the media w/o antibiotics) were added to neurons. Glial mix media contained 70% of glial conditioned medium and 30% of base neuronal medium (DMEM/F12, containing 2% serum replacement (“Gibco”, USA), 1 mM non-essential aminoacids (“Paneco”, Russian Federation), 2 mM L-glutamine (“ICN Biomedicals Inc”, USA), penicillin-streptomycin (50 U/mL; 50 μg/mL) (“Paneco”, Russian Federation), 1% В27 supplement (“Life Technologies”, USA), 5 μM forskolin (“Stemgent”, USA), 20 ng/mL BDNF, 20 ng/mL GDNF, 200 μM ascorbic acid all from (“Peprotech”, USA). After 72 hours cultures were collected with Extract RNA (Eurogen, RF).

value: neuronal culture

value: line DN PDL 1.5L

value: terminally differentiated neurons

value: PARK2:homozygous deletion of 8 exon

value: conditioned medium from PD astrocytes


title: Control cow 0015

description: Holstein early lactation control cow

value: early lactation stage, multiparous.

value: Ad libitum lactation diet


title: PD3 rep1 line DN PDL 1.5L


title: PD2 rep1 line DN PDL 1.5L

value: conditioned medium from HD astrocytes


title: PD0 rep2 line DN PDL 1.5L

value: base neuronal culture medium


title: PD0 rep1 line DN PDL 1.5L


title: PD1 rep1 line DN PDL 1.5L

value: base glial culture medium


title: PD1 rep2 line DN PDL 1.5L


title: HD3 rep1 line DN HD 1.1S

value: line DN HD 1.1S

value: normal


title: HD3 rep2 line DN HD 1.1S


title: HD2 rep1 line DN HD 1.1S


title: HD1 rep2 line DN HD 1.1S


title: BCSP-WT rep2

description:
RNA_Raw_gene_counts_matrix.txt
RNA_WT_2_BCSP

source_name: bone, cartilage and stromal progenitor cells

value: limbs

value: post natal day 3

value: Ptipf/f


title: HD0 rep1 line DN HD 1.1S


title: RNA_seq_KO2_D30_rep3

last: Zhao

description: RNA seq of KMT2D-SET-KO cell-induced organoid at D30

source_name: brain organoid

extract_protocol:
RNA-seq: To extract the total RNAs, organoids were collected and lysed with 1 ml TRIzol reagent (MRC, TR118-200), followed by adding 200 μL chloroform. After centrifugation (14,000 ×g for 10 min at 4°C), the total RNAs in the supernatant were precipitated with isopropanol. 1ug RNAs were subjected to RNA-seq library construction.  CUT&Tag: Brain organoids at D21 were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington, LK003153). CUT&Tag assay was performed according to the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (TD901-TD902, Vazyme).  scRNA-seq: Brain organoids at D21 and D30 were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington, LK003153).  snATAC-seq: Brain organoids at D21 were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington, LK003153). Nuclei were extracted from organoid-derived single cells following Demonstrated Protocol of Nuclei Isolation for Single Cell ATAC Sequencing (10X GENOMICS).
RNA-seq: RNA Sequencing libraries were prepared according to the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (NR611, Vazyme).   CUT&Tag: Library amplification was prepared using TruePrep Amplify Enzyme (TAE, Vazyme) followed by PCR purification (Vazyme).  scRNA-seq: 3'-library was constructed using Chromium Single Cell Reagent Kits v2 (10X GENOMICS).  snATAC-seq:Isolated nuclei were preceded to Tn5-mediated transposition, single cell barcoding, and library construction using Chromium Single Cell ATAC Reagent Kits (10X GENOMICS).

value: brain organoid

value: untreated

value: RNA-seq

value: TRANSCRIPTOMIC


title: HD0 rep2 line DN HD 1.1S

value: neuronal culture

value: terminally differentiated neurons


title: hmoDC, VLP-PE-OvaI/II-treated, 6 h, rep2

description: PE OVA Rep2

value: dendritic cell

value: VLP-PE-OvaI/II-treated, 6 h


title: RNA_seq_WT_D21_rep2

value: WT


title: PD2 rep2 line DN PDL 1.5L

value: line DN PDL 1.5L

value: PARK2:homozygous deletion of 8 exon

value: conditioned medium from HD astrocytes


title: OSXCre N43 pelvis

city: Provo

first: Jared

middle: J

last: Barrott

state: UT

address: 701 E University Pkwy, 4005 LSB

department: Cell Biology and Physiology

institute: Brigham Young University

data_processing:
Reference fasta files were generated by combining the chromosome sequences from mm10 with splice junction sequences generated by USeq (v8.8.8) MakeTranscriptome using Ensembl transcript models
Reads were aligned with Novoalign (v2.08.01), allowing up to 50 alignments per read. USeq’s SamTranscriptomeParser selected the best alignment for each and converted the coordinates of reads aligning to splices back to genomic space.
Differential gene expression was measured using USeq DefinedRegionDifferentialSeq, which counts the number of reads aligned to each gene and then calls DESeq2 (v1.26.0) using default settings.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Osteosarcoma

growth_protocol: Mice were > 6 months of age and represented male and female

extract_protocol:
Total RNA was isolated with the RNeasy mini kit (QIAGEN) per manufactuer's recommendations.
RNA was prepared using the Illumina TruSeq RNA kit (Illumina), checked with the Bioanalyzer RNA 6000 chip (Agilent Technologies), captured using the RiboZero method (Illumina), and 50-cycle end-read sequenced on an Illumina HiSeq 2000.

treatment_protocol: Tamoxifen was administered at 1 month of age by injecting a solution of tamoxifen at a concentration of 20 mg/mL intraperitoneally at a dose of 400 μg of tamoxifen per gram of mouse.

value: Osteosarcoma


title: OSXCre N25 lung


title: hmoDC, VLP-PE-OvaI/II-treated, 6 h, rep1

description: PE OVA Rep1


title: OSXCre N42 L limb


title: OSXCre N42 L shoulder


title: OSXCre N42 R femur


title: OSXCre N42 R pelvis


title: OSXCre N43 spine


title: HD2 rep2 line DN HD 1.1S

value: line DN HD 1.1S

value: normal


title: OSXCre N215 R hind limb


title: OSXCre Zelda


title: SSC-WT-input-DNA

source_name: Skeletal stem cells

value: limbs

value: Skeletal stem cells

value: post natal day 3


title: HD1 rep1 line DN HD 1.1S

value: base glial culture medium


title: OSXCre Grilka


title: OSXCre Ohio


title: OSXCre Montana


title: OSXCre Prince


title: OSXCre Medusa


title: OSXCre Massa


title: Heart, female, WT, 2

city: Buffalo

first: Clayton

middle: Timothy

last: Brady

state: NY

address: 955 Main Street

department: Physiology and Biophysics

institute: University at Buffalo

data_processing:
Sequence reads were trimmed using Trimmomatic v.0.36
Trimmed sequence reads were mapped to the Mus musculus GRCm38 reference genome (ENSEMBL) using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated using featureCounts from Subread package v.1.5.2
DESeq2 was used to prepare normalized transcript expression counts for WT and NBCe1-B/C KO samples
Assembly: GRCm38
Supplementary files format and content: CSV (comma delimited file) with normalized expression counts for each gene (ENSEMBL ID) and sample for female WT and NBCe1-B/C KO mouse data.

source_name: Heart

extract_protocol:
Total-RNA was harvested using Rneasy micro kit (Qiagen) and dessicated RNA was stored in RNA stabilization tubes (Genewiz-Azenta). RNA sequencing was performed by standard operating procedure by Genewiz (https://www.genewiz.com/en) using Illumina HiSeq with a 2x150bp configuration.
Pre-made library (Genewiz-Azenta)

value: Heart

value: 4-5 weeks


title: Heart, female, WT, 3


title: Heart, female, NBCe1-B/C KO, 3

value: NBCe1-B/C KO


title: Heart, female, NBCe1-B/C KO, 2


title: Heart, female, WT, 1


title: jmj27 H3K9me2 30 min ChIP rep1

city: Strasbourg

first: Jean

last: Molinier

address: 12 rue du General Zimmer

institute: IBMP-CNRS

data_processing:
ChIP-seq analysis has been performed using the community curated nf-core ChIP-seq pipeline (version 1.2.2) with default parameters
Reads have been mapped on the reference genome (TAIR10) and MACS2 was used to call H3K9me2 broad peaks using H3 as a reference, and an effective genome size of 119,481,543 bp
Replicates were handled using the stringent irreproducibility discovery rate (IDR) framework and only peaks containing an IDR value superior or equal to a scaled IDR value of 540 were considered real, corresponding to an IDR of 0.05
Assembly: TAIR10
Supplementary files format and content: BigWig

source_name: Leaves

growth_protocol: Plants were cultivated in vitro on solid GM medium [MS salts (Duchefa), 1% sucrose, 0.8% Agar-agar ultrapure (Merck), pH 5.8] and in a culture chamber under a 16 h light (light intensity ∼150 μmol m−2 s−1; 21°C) and 8 h dark (19°C) photoperiod

extract_protocol:
ChIP was performed upon sonication with the Bioruptor (Diagenode) using the Universal Plant Chip-seq Kit (Diagenode: C01010152) according manufacturers’ instructions
Libraries were prepared with the MicroPlex Library Preparation Kit v3  (Diagenode: C05010001) and the 24 Dual indexes for MicroPlex Kit v3 (Diagenode-: C05010003)

value: Leaves

tag: ecotype

value: Col

value: UV-C

tag: time point

value: 30 min


title: jmj27 H3 2h ChIP rep2


title: jmj27 H3K9me2 0 ChIP rep1

value: no UV-C


title: jmj27 H3K9me2 2h ChIP rep2


title: jmj27 H3K9me2 0 ChIP rep2


title: jmj27 H3 2h ChIP rep1


title: jmj27 H3 30 min ChIP rep2


title: jmj27 H3 30 min ChIP rep1


title: WT H3K9me2 2h ChIP rep2

value: WT


title: jmj27 H3 0 ChIP rep1


title: Heart, female, NBCe1-B/C KO, 1

tag: age


title: WT H3K9me2 2h ChIP rep1

tag: chip antibody


title: WT H3K9me2 30 min ChIP rep2


title: WT H3K9me2 0 ChIP rep2


title: jmj27 H3 0 ChIP rep2


title: WT H3K9me2 0 ChIP rep1


title: jmj27 H3K9me2 2h ChIP rep1


title: WT H3K9me2 30 min ChIP rep1


title: WT H3 2h ChIP rep1


title: WT H3 30 min ChIP rep2


title: WT H3 0 ChIP rep2


title: WT H3 30 min ChIP rep1