title: SOA4-2_Zone_DZ_Condition_WB_Rep1

city: Xi'an

first: Yue

last: Fan

address: Yanta West Road No.76

institute: Xi'an Jiaotong University

data_processing:
Alignment was performed using HISAT2 software with hg19 reference genomes to convert FASTQ files into BAM files.
RNA-seq gene expression levels were quantified with featureCounts with basic gene annotation(ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/GRCh37_mapping/gencode.v26lift37.annotation.gtf.gz)
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: comma-delimited text file includes annotation information for each Sample

source_name: Cartilage

extract_protocol:
Fresh cartilage tissue obtained from patients with OA and non-OA controls was placed in cold RNase-free PBS. The tissue was then gently transferred to pre-cooled optimum cutting temperature (OCT) compound, ensuring that the entire tissue was embedded. The tissue was immediately frozen in liquid nitrogen or dry ice and transferred to -80 °C. The OCT-embedded samples were cryosectioned at −20 °C at 14 μm thickness. The sections were then mounted on polyethylene-terephthalate-coated slides, fixed immediately with ethanol, and stained with 1% cresyl violet acetate dissolved in 75% ethanol solution. Afterward, targeted regions of sections were collected by laser capture microdissection (LCM), and transcriptome analyses of those collected samples were performed by Geo-seq.
cDNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina and sequenced on Illumina NovaSeq 6000 with PE150 mode.

value: Cartilage


title: HET, replicate 3, 10X multiome scRNA

status: Public on Feb 05 2024

type: SRA

city: Houston

first: Michael

last: Green

state: Texas

address: 7455 Fannin Street

department: Department of Lymphoma/Myeloma

country: USA

institute: The University of Texas MD Anderson Cancer Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, gene counting were done using the Cell Ranger ARC software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
Analyses were performed in R (version 4.2.1) using various R packages. FASTQ files were processed using cellranger-arc count (10x genomics). This pipeline aligns reads to the mm10 mouse reference genome, performs barcode error correction, PCR duplicate marking, peak calling, and ATAC and gene expression molecule counting to produce expression and fragment count matrices.  The gene expression matrices and ATAC fragments were loaded into R and processed with Signac (version 1.9.0, https://github.com/timoast/signac) and Seurat (version 4.3.0, https://github.com/satijalab/seurat) for downstream analyses.
Assembly: mm10
Supplementary files format and content: Tab-separated matrix files and fragments files

molecule: nuclear RNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
GC B cells were isolated from mice spleens at day 10 post-immunization using the Germinal Center B Cell (PNA) MicroBead Kit (Miltenyi Biotec,130-110-479). To improve the quality of single cell ATAC libraries, pre-enriched cells were stained with Zombie Green (BioLegend) and sorted by FACS. Cells were washed in PBS containing 0.04% BSA 2 times. Determine the cell concentration using a Countess II FL Automated Cell counter and viable cell number was counted by the trypan blue dye exclusion method, before proceeding to nuclei isolation. Pellet 100,000~200,000 cells at 300 rcf for 5 min at 4 °C, remove all supernatant and resuspend in lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin, 1% BSA, 1 mM DTT and 1 U/µl RNase inhibitor). Incubate for 5 min on ice. After a total of 3 washes, nuclei were resuspended in diluted nuclei buffer (10x Genomics) and nuclei concentration was determined.
Proceed immediately to Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338). Briefly, 10,000 nuclei/sample were loaded on the Chromium Controller. The 10X libraries were then prepared following the manufacturer’s instruction (Next GEM Single Cell Multiome)
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression

tag: tissue

value: Spleen

tag: strain

tag: age

value: 8-10 weeks

tag: genotype

tag: cell type

value: Germinal Center B Cells


title: patient6_postACT_1

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

country: Switzerland

institute: Centre hospitalier universitaire vaudois

data_processing:
The scTCR-Seq reads were aligned to the GRCh38 reference genome (refdata-cellranger-vdj-GRCh38-alts-ensembl-4.0.0) and quantified using cellranger vdj (10X Genomics, version 4.0.0).
Assembly: GRCh38
Supplementary files format and content: csv file ("all_contig_annotations.csv" output from Cellranger) containing the mapping of unique cells to TCR

molecule: total RNA

organism: Homo sapiens

source_name: melanoma

extract_protocol:
Resected tumors were chopped into 1-2 mm2 pieces and, along with post-infusion biopsies, cryopreserved in 90% human serum + 10% dimethyl sulfoxide (DMSO) and additional pieces were snap frozen for bulk RNA extraction. For single-cell experiments, both frozen and fresh material were used as starting material. PBMCs were isolated from blood collected in EDTA tubes and cryopreserved in 90% human serum + 10% DMSO. The day of the assay, pathofrozen pieces were thawed in RPMI + 10% FBS and chopped in small pieces using a scalpel. Tissue was dissociated in RPMI + 2% Gelatin (#G7041, Sigma-Aldrich) + 200 IU/mL Collagenase I (#17100-017, ThermoFisher Scientific) + 400 IU/mL Collagenase IV (#17104-019, ThermoFisher Scientific) + 5 IU/mL Deoxyribonuclease I (#D4527, Sigma-Aldrich) + 0.1% RNasin Plus RNase Inhibitor (#N2618, Promega) for 15-30min (depending of sample size and consistency) at 37°C and shaken at 160rpm. Digested cells were filtered using a 70 mm strainer and resuspended in PBS + 1% Gelatin + 0.1% RNasin. Cells were manually counted with hematocymeter then stained for viability with 50uM/mL of Calcein AM (#C3099, Thermo Fisher Scientific) and FcR blocked (#130-059-901, Miltenyi Biotec) for 15min at RT. After incubation and washing, cells were stained with CD45-APC (#304012, BioLegend) for 20min at 4°C. After washing, cells were resuspended in PBS + 0.04% BSA (Sigma-Aldrich) + 0.1% RNasin and DAPI staining (Invitrogen) was performed.
40’000 CD45+ cells and 40’000 total live cells were sorted on a MoFlo Astrios (Beckman Coulter) and collected in separated 0.2mL PCR tubes containing 10ml in PBS + 0.04% BSA + 0.1% RNasin. After sorting, cells were manually counted with hemocytometer and viability was assessed using Trypan blue exclusion. Ex vivo CD45 cells from tumor were resuspended at a density of 600-1200 cells/ml when possible with a viability of >90% and subjected to a 10x Chromium instrument for single-cell analysis. Single-cell RNA libraries were generated using the Chromium Next GEM Single Cell 5’ Library and Gel beads kit v1.1 for the CD45-sorted population or using the Chromium Next GEM Single Cell 3’ Library and Gel beads kit v3.1 for the live-sorted cells, according to the manufacturer’s instructions. For each sample, 15’000 cells were loaded into the Chromium machine when possible (i.e. the total of sorted cells if <15’000), encapsulated and barcoded following the manual (CG000388 for 3’ or CG000207 for 5’ technology). After encapsulation and reverse transcription, 14 PCR cycles were used to amplify cDNA. All library construction steps were performed according to the manufacturer's protocol. For the FACS sorting of post-ACT biopsies, depending of the percentage of CD45+ fraction in the sample, two sorting strategies were adopted. If the CD45+ fraction was inferior to 75% of total viable cells, 40’000 CD45+ and 40’000 CD45- viable cells were sorted in two separated tubes. If the CD45+ fraction was superior to 75% of total viable cells, 40’000 total viable cells were collected in one tube.  All cells were sorted on a MoFlo Astrios (Beckman Coulter) and collected in separated 0.2mL PCR tubes containing 10l in PBS + 0.04% BSA + 0.1% RNasin. After sort, cells were manually counted with hemacytometer and viability was assessed using Trypan blue exclusion. If CD45+ and CD45- were sorted separately, cells were mixed with a ratio of 70% CD45+ and 30% CD45-. All cells were resuspended at a density of 600-1200 cells/mL if possible with a viability >90% and subjected to a 10x Chromium instrument for single-cell analysis. Only the CD45+ compartment was analyzed in this study.

value: melanoma

tag: patient

tag: time

value: post-ACT

tag: biopsy site


title: patient10_preACT_2

value: pre-ACT


title: patient11_preACT_1


title: SOA3-2_Zone_DZ_Condition_WB_Rep1

country: China

library_source: transcriptomic


title: HET, replicate 3, 10X multiome scATAC

description: 10x Genomics

library_source: genomic

molecule: genomic DNA


title: SOA3-2_Zone_DZ_Condition_WB_Rep2


title: ROSA26 rep 3, miRNA-seq

city: Paris

first: Angelique

last: Gougelet

address: 15 rue de l'école de médecine

country: France

institute: INSERM U1138

description:
Raw-Mir-Matrix.csv
Rosa4

data_processing:
STAR version 2.7.6a:  STAR --genomeDir $reference_dir --sjdbGTFfile $reference_GTF --runThreadN 20 --readFilesIn $fq1 $fq2 --outFileNamePrefix $echantillon --twopassMode Basic --sjdbOverhang 74 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped Within --outFilterType BySJout --quantMode TranscriptomeSAM
RSEM version 1.3.1:  rsem-calculate-expression -p 20 --paired-end --bam --no-bam-output $alignedToTransciptomFile $reference_RSEM $resultats_RSEM
R version 3.6.3:  DESeq2_1.26.0
Assembly: Ensembl release 96:  Mus_musculus.GRCm38
Supplementary files format and content: RSEM count file:  count file from the rsem-calculate-expression program
Design DESeq2:  tabulated file with the name of the sample file, the sample name, and each factor integrated in the deseq2 design
Normalized matrix:  matrix with normalized values from DESeq2
Raw UMI matrix:  matrix with raw count value from the QIAGEN pipeline

source_name: mouse ApcDHep hepatocytes

extract_protocol: RNAs were extracted by Trizol

treatment_protocol: RNA profiles from hepatocytes isolated from  ApcDHep livers by perfusion with collagenase in three-month old mice injected with AAV8 containing SaCas9 constructs for 1 month and treated with tamoxifen for 7 days

value: liver

value: hepatocytes

value: ApcDHep

tag: condition

tag: treatment

value: tamoxifen 2mg 7 days


title: ROSA26 rep 2, miRNA-seq

description:
Raw-Mir-Matrix.csv
Rosa3


title: ROSA26 rep 1, miRNA-seq

description:
Raw-Mir-Matrix.csv
Rosa2


title: HET, replicate 2, 10X multiome scATAC

description: 10x Genomics


title: patient9_preACT_1


title: patient8_preACT_1


title: SOA2-2_Zone_DZ_Condition_WB_Rep4


title: SOA2-2_Zone_DZ_Condition_WB_Rep3


title: SOA2-2_Zone_DZ_Condition_WB_Rep2


title: DLK1DWRE rep 3, miRNA-seq

description:
Raw-Mir-Matrix.csv
DDLK168


title: WT, replicate 1, bulkRNA

data_processing:
Demultiplexed FASTQ files were QC checked using FASTQC and processed using custom pipeline which involves read alignment using STAR-aligner. Count matrices were created using featureCounts of subread package.
Downstream analyses were performed in R (version 4.2.1) using various R packages.
Assembly: hg38
Supplementary files format and content: Tab-separated matrix file

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN) according to the manufacturers protocol.
mRNA-seq library preparation was performed using KAPA RNA HyperPrep Kit with RiboErase (HMR), following the manufacturer’s protocol. Library size distribution and concentration was evaluated using the Agilent 4200 TapeStation system and Qubit dsDNA HS Assay Kit (ThermoFisher Scientific), respectively.

tag: cell line


title: DLK1DWRE rep 2, miRNA-seq

description:
Raw-Mir-Matrix.csv
DDLK170


title: S46

city: Singapore

first: Jing

last: Guo

state: State...

address: 8 Collage Road, DUKE-NUS Medical School, level 5

department: Center for Computational Biology

country: Singapore

institute: Duke-NUS Medical School

data_processing:
Sequencing reads were aligned and quantified to the mouse genome GRCm38 (mm10-3.0.0 provided by 10x Genomics) using 10x Genomics cellranger count (v3.1.0).
For each of the four samples, quality control and preprocessing were performed individually. Genes present in less than 50 cells and cells below the 10th and above the 90th percentile in terms of both the number of genes and number of counts were filtered out. Cells with percentage of mitochondrial content greater than 40% and haemoglobin gene accounting more than 1% of total counts were also filtered. In addition, cells above the 99th percentile in terms of percentage of total counts being stress genes (Hochane et al. 2019) were removed.
Assembly: mm10
Supplementary files format and content: tab seperated matrix files

source_name: kidney

extract_protocol:
Mouse kidneys was perfused, excised, minced, digested to obtain single cell suspension as described before. Cells were collected by centrifugation, subjected to live-death dye and sorted by flow cytometry using BD FACS ARIA system.
Isolated living single cell suspensions were converted to barcoded scRNA-seq libraries by using the Chromium Single Cell 3′ Library, Gel Bead & Multiplex Kit, and Chip Kit V3, loading an estimated 7,000–12,000 cells per library/well, and following the manufacturer's instructions. Indexed libraries were sequenced using Illumina NovaSeq 6000 platform, where 150bp pair-end sequences were obtained.

value: kidney

value: wwp2 KO


title: HET, replicate 1, 10X multiome scRNA

description: 10x Genomics


title: patient7_preACT_1


title: DLK1DWRE rep 1, miRNA-seq

description:
Raw-Mir-Matrix.csv
DDLK169


title: HET, replicate 1, 10X multiome scATAC

description: 10x Genomics


title: SOA1-2_Zone_DZ_Condition_WB_Rep5


title: ROSA26 rep 5, RNA-seq

description:
Normalized-matrix.tsv
Rosa4_r595


title: patient6_preACT_1


title: SOA2-2_Zone_DZ_Condition_WB_Rep1


title: WT, replicate 4, 10X multiome scRNA

description: 10x Genomics


title: WT, replicate 3, 10X multiome scRNA

description: 10x Genomics


title: patient10_preACT_1


title: patient5_preACT_1


title: SOA1-2_Zone_DZ_Condition_WB_Rep3


title: ROSA26 rep 4, RNA-seq

description:
Normalized-matrix.tsv
Rosa2_r595


title: patient4_preACT_1


title: WT, replicate 4, 10X multiome scATAC

description: 10x Genomics


title: SOA1-2_Zone_DZ_Condition_WB_Rep4


title: GFP_LOW, replicate 1, 24hr, bulkATAC

data_processing:
Demultiplexed FASTQ files were QC checked using FASTQC and processed using custom pipeline which involves read trimming, read alignment using bwa, filtering low-quality, unmapped and duplicated reads. BIGWIG files were generated using deeptools RPKM normalization.
Downstream analyses were performed in R (version 4.2.1) using various R packages.
Assembly: hg38
Supplementary files format and content: Tab-separated count matrix file and RPKM normalized bigwig files

source_name: Raji

extract_protocol:
DNA was purified using a Zymo DNA Clean and Concentrator-5 Kit (D4014, Zymo Research)
ATAC-seq libraries were generated following the Omni-ATAC protocol. Libraries were barcoded and amplified with KAPA HiFi HotStart ReadyMix (KK2602, Roche). Library size distribution and concentration was evaluated using the Agilent 4200 TapeStation system and Qubit dsDNA HS Assay Kit (ThermoFisher Scientific), respectively.

value: Raji


title: patient3_preACT_1


title: ROSA26 rep 3, RNA-seq

description:
Normalized-matrix.tsv
R229_r770


title: ROSA26 rep 2, RNA-seq

description:
Normalized-matrix.tsv
R194_r770


title: SOA1-2_Zone_DZ_Condition_WB_Rep2


title: SOA1-2_Zone_DZ_Condition_WB_Rep1


title: WT, replicate 2, 10X multiome scRNA

description: 10x Genomics


title: patient1_preACT_1


title: ROSA26 rep 1, RNA-seq

description:
Normalized-matrix.tsv
R168_r770


title: WT, replicate 3, 10X multiome scATAC

description: 10x Genomics


title: WT, replicate 2, 10X multiome scATAC

description: 10x Genomics


title: HET, replicate 2, 10X multiome scRNA

description: 10x Genomics


title: WT, replicate 1, 10X multiome scRNA

description: 10x Genomics


title: patient2_preACT_1


title: SOA4-2_Zone_MZ_Condition_WB_Rep3


title: SOA4-2_Zone_MZ_Condition_WB_Rep2


title: patient13_preACT_2 [scRNA-Seq]

data_processing:
The scRNA-Seq reads were aligned to the GRCh38 reference genome and quantified using cellranger count (10X Genomics, version 4.0.0). Filtered gene-barcode matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the threshold for cell detection were used and processed using the Seurat R package version 4.0.1.
Assembly: GRCh38
Supplementary files format and content: Processed gene expression raw count with Gene Symbol mapping in tab-separted format

extract_protocol:
Resected tumors were chopped into 1-2 mm2 pieces and, along with post-infusion biopsies, cryopreserved in 90% human serum + 10% dimethyl sulfoxide (DMSO) and additional pieces were snap frozen for bulk RNA extraction. For single-cell experiments, both frozen and fresh material were used as starting material. PBMCs were isolated from blood collected in EDTA tubes and cryopreserved in 90% human serum + 10% DMSO. The day of the assay, pathofrozen pieces were thawed in RPMI + 10% FBS and chopped in small pieces using a scalpel. Tissue was dissociated in RPMI + 2% Gelatin (#G7041, Sigma-Aldrich) + 200 IU/mL Collagenase I (#17100-017, ThermoFisher Scientific) + 400 IU/mL Collagenase IV (#17104-019, ThermoFisher Scientific) + 5 IU/mL Deoxyribonuclease I (#D4527, Sigma-Aldrich) + 0.1% RNasin Plus RNase Inhibitor (#N2618, Promega) for 15-30min (depending of sample size and consistency) at 37°C and shaken at 160rpm. Digested cells were filtered using a 70 mm strainer and resuspended in PBS + 1% Gelatin + 0.1% RNasin. Cells were manually counted with hematocymeter then stained for viability with 50uM/mL of Calcein AM (#C3099, Thermo Fisher Scientific) and FcR blocked (#130-059-901, Miltenyi Biotec) for 15min at RT. After incubation and washing, cells were stained with CD45-APC (#304012, BioLegend) for 20min at 4°C. After washing, cells were resuspended in PBS + 0.04% BSA (Sigma-Aldrich) + 0.1% RNasin and DAPI staining (Invitrogen) was performed.
40’000 CD45+ cells and 40’000 total live cells were sorted on a MoFlo Astrios (Beckman Coulter) and collected in separated 0.2mL PCR tubes containing 10ml in PBS + 0.04% BSA + 0.1% RNasin. After sorting, cells were manually counted with hemocytometer and viability was assessed using Trypan blue exclusion. Ex vivo CD45 cells from tumor were resuspended at a density of 600-1200 cells/ml when possible with a viability of >90% and subjected to a 10x Chromium instrument for single-cell analysis. Single-cell RNA libraries were generated using the Chromium Next GEM Single Cell 5’ Library and Gel beads kit v1.1 for the CD45-sorted population or using the Chromium Next GEM Single Cell 3’ Library and Gel beads kit v3.1 for the live-sorted cells, according to the manufacturer’s instructions. For each sample, 15’000 cells were loaded into the Chromium machine when possible (i.e. the total of sorted cells if <15’000), encapsulated and barcoded following the manual (CG000388 for 3’ or CG000207 for 5’ technology). After encapsulation and reverse transcription, 14 PCR cycles were used to amplify cDNA. All library construction steps were performed according to the manufacturer's protocol. For the FACS sorting of post-ACT biopsies, depending of the percentage of CD45+ fraction in the sample, two sorting strategies were adopted. If the CD45+ fraction was inferior to 75% of total viable cells, 40’000 CD45+ and 40’000 CD45- viable cells were sorted in two separated tubes. If the CD45+ fraction was superior to 75% of total viable cells, 40’000 total viable cells were collected in one tube.  All cells were sorted on a MoFlo Astrios (Beckman Coulter) and collected in separated 0.2mL PCR tubes containing 10l in PBS + 0.04% BSA + 0.1% RNasin. After sort, cells were manually counted with hemacytometer and viability was assessed using Trypan blue exclusion. If CD45+ and CD45- were sorted separately, cells were mixed with a ratio of 70% CD45+ and 30% CD45-. All cells were resuspended at a density of 600-1200 cells/mL if possible with a viability >90% and subjected to a 10x Chromium instrument for single-cell analysis. Only the CD45+ compartment was analyzed in this study.The full baseline sorted viable cell dataset (3’) contained real stoichiometry for all cell types except for patient 1 where the scRNAseq library was enriched for malignant cells to reach an approximate rate of CD45+ and non-CD45+ cells of fifty percent each for a better characterization of the malignant compartment. Thus, for analyses involving stoichiometrical comparisons, the real stoichiometry of cell types was deduced and used by forcing the CD45+ cells to represents 93.9% (value obtained by FACS analysis) of the total number of cells.


title: WT, replicate 1, 10X multiome scATAC

description: 10x Genomics


title: DLK1DWRE rep 5, RNA-seq

description:
Normalized-matrix.tsv
DDLK1_170_r711


title: patient13_preACT_1 [scRNA-Seq]


title: DLK1DWRE rep 4, RNA-seq

description:
Normalized-matrix.tsv
DDLK1_169_r711


title: wt4

first: Evgeniya

last: Petrova

address: 24 Boulevard du Montparnasse

department: Imagine Institute

institute: INSERM UMR1163

data_processing:
RASflow pipeline in Python
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2 aligner.
Read count extraction and normalization were performed using DESeq2.
Assembly: mm10
Supplementary files format and content: excel file with normalized counts by DEseq2
Supplementary files format and content: excel file with normalized counts by DEseq2

source_name: Back skin

extract_protocol:
RNA was extracted using RNeasy Firbous Tissue kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using a TruSeq stranded mRNA kit version 2019 (Illumina) following manufacturer's protocols.

value: Back skin

value: WT

tag: Sex

value: male

tag: age (weeks)


title: patient11_preACT_1 [scRNA-Seq]


title: wt5


title: DLK1DWRE rep 3, RNA-seq

description:
Normalized-matrix.tsv
D69_r770


title: patient10_preACT_2 [scRNA-Seq]


title: SOA3-2_Zone_MZ_Condition_WB_Rep3

value: Cartilage


title: patient10_preACT_1 [scRNA-Seq]


title: wt3

value: female


title: DLK1DWRE rep 6, RNA-seq

description:
Normalized-matrix.tsv
DDLK169_r595


title: DLK1DWRE rep 1, RNA-seq

description:
Normalized-matrix.tsv
D192_r770


title: DLK1DWRE rep 2, RNA-seq

description:
Normalized-matrix.tsv
D230_r770


title: SOA3-2_Zone_MZ_Condition_WB_Rep1


title: patient9_preACT_1 [scRNA-Seq]


title: wt2


title: patient8_preACT_1 [scRNA-Seq]


title: patient7_preACT_1 [scRNA-Seq]


title: SOA2-2_Zone_MZ_Condition_WB_Rep2


title: SOA2-2_Zone_MZ_Condition_WB_Rep1


title: SOA2-2_Zone_MZ_Condition_WB_Rep3


title: wt1


title: LNCaP, R1881+MEL-6, biol rep3

city: Leuven

first: Christine

last: Helsen

address: Herestraat 49

department: Cellular and Molecular Medicine

country: Belgium

institute: KU Leuven

description:
HSR9
M2

data_processing:
CASAVA v1.8
assembly: GRCh37/hg19
The 'GEO LNCaP summary.xls' file includes gene counts of each sample and whether the gene counts within a treatment group differ significantly from the others.

molecule: polyA RNA

source_name: LNCaP

extract_protocol:
RNA was isolated using the Rneasy Mini kit from Qiagen
RNA was converted into cDNA using the TruSeq RNA Sample Preparation Kit from Illumina

value: LNCaP

value: prostate cancer cell


title: SOA4-2_Zone_MZ_Condition_WB_Rep1


title: LNCaP, R1881+MEL-6, biol rep2

description:
HSR8
L2


title: Tg3


title: patient4_preACT_1 [scRNA-Seq]

value: melanoma


title: SOA1-2_Zone_MZ_Condition_WB_Rep4


title: patient3_preACT_1 [scRNA-Seq]


title: SOA1-2_Zone_MZ_Condition_WB_Rep3


title: Tg2


title: SOA3-2_Zone_MZ_Condition_WB_Rep2


title: LNCaP, R1881+MEL-6, biol rep1

description:
HSR7
K2


title: patient2_preACT_1 [scRNA-Seq]


title: SOA1-2_Zone_MZ_Condition_WB_Rep2


title: LNCaP, R1881, biol rep3

description:
HSR6
J2


title: SOA1-2_Zone_MZ_Condition_WB_Rep1


title: Tg5


title: patient1_preACT_1 [scRNA-Seq]


title: Tg4


title: LN_WT4

data_processing:
RASflow pipeline in Python
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2 aligner.
Read count extraction and normalization were performed using DESeq2.
Assembly: mm10
Supplementary files format and content: excel file with normalized counts by DEseq2

source_name: inguinal lymph node

value: inguinal lymph node


title: LNCaP, R1881, biol rep1

description:
HSR4
H2


title: SOA4-2_Zone_SZ_Condition_WB_Rep4


title: LNCaP, vehicle, biol rep3

description:
HSR3
G2

value: vehicle


title: patient6_T30_CD45

data_processing:
The scRNA-Seq reads were aligned to the GRCh38 reference genome and quantified using cellranger count (10X Genomics, version 4.0.0). Filtered gene-barcode matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the threshold for cell detection were used and processed using the Seurat R package version 4.0.1.
For CD45+-sorted cells from tumor data (5`GEX), we defined and removed low-quality cells containing more than 10% of mitochondrial reads.
Assembly: GRCh38
Supplementary files format and content: Processed gene expression raw count with Gene Symbol mapping for filtered non-apoptotic cells in tab-separted format

value: post-ACT


title: LNCaP, R1881, biol rep2

description:
HSR5
I2


title: patient8_T30_CD45


title: LN_WT3


title: SOA4-2_Zone_SZ_Condition_WB_Rep3


title: LN_WT5


title: LNCaP, vehicle, biol rep2

description:
HSR2
F2


title: LN_WT2


title: patient7_T30_CD45


title: SOA4-2_Zone_SZ_Condition_WB_Rep2


title: SOA4-2_Zone_SZ_Condition_WB_Rep1


title: LNCaP, vehicle, biol rep1

description:
HSR1
E2


title: patient5_T30_CD45


title: LN_WT1


title: SOA3-2_Zone_SZ_Condition_WB_Rep3


title: patient1_T30_CD45


title: LN_NS5


title: patient13_T30_CD45


title: SOA3-2_Zone_SZ_Condition_WB_Rep2


title: USB1 KO_shPARN_3

city: boulder

first: Roy

last: parker

address: colorado ave

institute: university of colorado boulder

description: KOsh.csv

data_processing:
Adapters were trimmed and reads shorter than 19nt were dropped using Cutadapt 2.5
Trimmed reads were aligned to human mature miRNA release from miRbase 22 using Bowtie2 2.2.9
Aligned reads were co-ordinate shorted to BAM files using Samtools 1.3.1
miRNA counts were extracted from BAM files
Differential expression between WT and USB1 mutant miRome was calculated using DEseq2
Assembly: miRbase 22
Supplementary files format and content: CSV file containing counts of miRNA reads

extract_protocol:
Cells were collected and lysed using Trizol
Lexogen Small RNA-seq library prep kit

value: CML

value: USB1 KO


title: Tg1


title: LN_NS4

value: K14-CreERT2(Tg/0) / Spink5{delta}ex3/-


title: patient10_T30_CD45


title: SOA3-2_Zone_SZ_Condition_WB_Rep1


title: USB1 KO_shPARN_1

description: KOsh.csv


title: SOA2-2_Zone_SZ_Condition_WB_Rep3


title: Control_shPARN_2

description: WTsh.csv


title: patient9_T0_CD45

value: pre-ACT


title: LN_NS2


title: Control_shPARN_3

description: WTsh.csv


title: Control_shPARN_1

description: WTsh.csv


title: patient8_T0_CD45


title: LN_NS1


title: patient7_T0_CD45


title: SOA2-2_Zone_SZ_Condition_WB_Rep1


title: skin_WT5

description:
skin_WT5
norm_counts_Spink5cond_WT_skin.xlsx

value: 8.1 weeks


title: patient6_T0_CD45


title: SOA1-2_Zone_SZ_Condition_WB_Rep4


title: SOA1-2_Zone_SZ_Condition_WB_Rep3


title: patient5_T0_CD45


title: skin_WT4

description:
skin_WT4
norm_counts_Spink5cond_WT_skin.xlsx

value: 6.3 weeks


title: USB1 mutants_shPAPD5_2

value: Human embryonic stem cells

value: USB1 mut


title: USB1 KO_shPARN_2

description: KOsh.csv


title: skin_WT3

description:
skin_WT3
norm_counts_Spink5cond_WT_skin.xlsx

value: Back skin

value: 2.3 weeks


title: patient4_T0_CD45


title: USB1 mutants_shPAPD5_1


title: skin_WT2

description:
skin_WT2
norm_counts_Spink5cond_WT_skin.xlsx

value: male

value: 3.6 weeks


title: patient3_T0_CD45


title: LN_NS3


title: SOA1-2_Zone_SZ_Condition_WB_Rep1

value: Cartilage


title: SOA2-2_Zone_SZ_Condition_WB_Rep2


title: USB1 mutants_iUSB1-WT +Dox_3

value: with Dox


title: patient2_T0_CD45

value: melanoma


title: skin_WT1

description:
skin_WT1
norm_counts_Spink5cond_WT_skin.xlsx

value: 4.7 weeks


title: USB1 mutants_iUSB1-WT +Dox_2


title: USB1 mutants_iUSB1-WT +Dox_1


title: skin_NS4

description:
skin_NS4
norm_counts_Spink5cond_NS_skin.xlsx

value: female


title: USB1 mutants_shPAPD5_3


title: patient1_T0_CD45


title: USB1 mutants_iUSB1-WT -Dox_3

value: without Dox


title: SOA3-2_Zone_AS_Condition_WB_Rep5


title: skin_NS5

description:
skin_NS5
norm_counts_Spink5cond_NS_skin.xlsx

value: 5.3 weeks


title: SOA3-2_Zone_AS_Condition_WB_Rep4


title: SOA3-2_Zone_AS_Condition_WB_Rep2


title: SOA3-2_Zone_AS_Condition_WB_Rep3


title: skin_NS3

description:
skin_NS3
norm_counts_Spink5cond_NS_skin.xlsx

value: K14-CreERT2(Tg/0) / Spink5{delta}ex3/-

value: 7.3 weeks


title: SOA1-2_Zone_SZ_Condition_WB_Rep2


title: patient13_T01_CD45

value: pre-ACT


title: SOA3-2_Zone_AS_Condition_WB_Rep1


title: skin_NS1

description:
skin_NS1
norm_counts_Spink5cond_NS_skin.xlsx


title: patient12_T0_CD45


title: patient11_T0_CD45


title: SOA2-2_Zone_AS_Condition_WB_Rep4


title: patient13_T02_CD45


title: USB1 mutants_iUSB1-WT -Dox_1


title: USB1 KO_3

description: KO.csv

value: CML

value: USB1 KO


title: patient10_T02_CD45


title: SOA2-2_Zone_AS_Condition_WB_Rep3


title: Otx2, D0, ATAC

city: AUSTIN

first: Qingqing

state: TX

address: 2506 Speedway

institute: The University of Texas at Austin

data_processing:
The FASTQ files of bioChIP-seq and ATAC-seq were trimmed with Trim Galore v0.6.7
The reads were mapped to the mm10 mouse reference genome using bowtie2 v2.4.4 with default parameters.
All alignments were further sorted by Picard Tools v2.27.2 and filtered by Samtools v1.14 with MAPQ >= 10.
The PCR duplicates were removed using Picard Tools v2.27.2.
Peaks were identified using MACS2 v2.2.7.1 with a cutoff of FDR<0.05
Assembly: RPGC normalized bigwig files were generated using deeptools bamcoverage v3.5.0.
Supplementary files format and content: Bigwig files normalized by 1x depth (reads per genome coverage, RPGC)

source_name: pre-implantation embryo

extract_protocol:
bioChIP were performed by cross-linking proteins to DNA using 1% formaldehyde solution. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNAs were applied for the generation of sequencing libraries using the NEBNext Ultra II DNA Library Prep Kit (E7103L) and NEBNext Multiplex Oligos for Illumina (E7600S) following the manufacturer’s protocol.

value: pre-implantation embryo

value: J1 ES cells

value: mouse embryonic stem cells


title: patient10_T01_CD45


title: SOA2-2_Zone_AS_Condition_WB_Rep2


title: Otx2, D1, ATAC

value: 1 day of doxycycline treatment


title: USB1 KO_1

description: KO.csv


title: SOA2-2_Zone_AS_Condition_WB_Rep1


title: USB1 mutants_iUSB1-WT -Dox_2

value: Human embryonic stem cells

value: USB1 mut


title: USB1 KO_2

description: KO.csv


title: Gcm1, D0, ATAC


title: patient13_preACT_1

data_processing:
Illumina paired-end sequencing reads were aligned to the human reference GRCh37.75 genome using STAR aligner (version 2.6.0c) and the 2-pass method as briefly follows: the reads were aligned in a first round using the --runMode alignReads parameter, then a sample-specific splice-junction index was created using the --runMode genomeGenerate parameter. Finally, the reads were aligned using this newly created index as a reference. The number of counts was summarized at the gene level using htseq-count (version 0.9.1). The Ensembl ID were converted into gene symbols using the biomaRt package and only protein-coding, immunoglobulin and TCR genes were conserved for the analysis.
Assembly: GRCh37
Supplementary files format and content: Processed coding gene expression raw count with Gene Symbol mapping

extract_protocol:
Resected tumors were chopped into 1-2 mm2 pieces and, along with post-infusion biopsies, cryopreserved in 90% human serum + 10% dimethyl sulfoxide (DMSO) and additional pieces were snap frozen for bulk RNA extraction. For single-cell experiments, both frozen and fresh material were used as starting material. PBMCs were isolated from blood collected in EDTA tubes and cryopreserved in 90% human serum + 10% DMSO. The day of the assay, pathofrozen pieces were thawed in RPMI + 10% FBS and chopped in small pieces using a scalpel. Tissue was dissociated in RPMI + 2% Gelatin (#G7041, Sigma-Aldrich) + 200 IU/mL Collagenase I (#17100-017, ThermoFisher Scientific) + 400 IU/mL Collagenase IV (#17104-019, ThermoFisher Scientific) + 5 IU/mL Deoxyribonuclease I (#D4527, Sigma-Aldrich) + 0.1% RNasin Plus RNase Inhibitor (#N2618, Promega) for 15-30min (depending of sample size and consistency) at 37°C and shaken at 160rpm. Digested cells were filtered using a 70 mm strainer and resuspended in PBS + 1% Gelatin + 0.1% RNasin. Cells were manually counted with hematocymeter then stained for viability with 50uM/mL of Calcein AM (#C3099, Thermo Fisher Scientific) and FcR blocked (#130-059-901, Miltenyi Biotec) for 15min at RT. After incubation and washing, cells were stained with CD45-APC (#304012, BioLegend) for 20min at 4°C. After washing, cells were resuspended in PBS + 0.04% BSA (Sigma-Aldrich) + 0.1% RNasin and DAPI staining (Invitrogen) was performed.
Total RNA was extracted from snap frozen tissues. Samples were lyzed in TRIzol reagent (Invitrogen) using a tissue lyzer (Qiagen) and the RNA was purified with the RNeasy kit (Qiagen). RNA quality was assessed with a Fragment Analyzer (Agilent) and Nanodrop spectrophotometer (Thermofisher). Quantification was performed with the Qubit HS RNA assay kit (InVitrogen). RNA sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA reagents according to the protocol supplied by the manufacturer and sequenced using HiSeq 4000.

tag: sequencing batch


title: Gcm1, D1, ATAC


title: patient13_preACT_2


title: skin_NS2

description:
skin_NS2
norm_counts_Spink5cond_NS_skin.xlsx

value: Back skin

value: 4.9 weeks


title: patient11_preACT_1

value: melanoma


title: USB1 mutants_3


title: patient10_postACT_2

value: post-ACT


title: Otx2, D1, bioChIP

description: Chromatin IP against biotinylated protein


title: Gcm1, D1, bioChIP


title: patient10_postACT_1


title: SOA1-2_Zone_AS_Condition_WB_Rep1

value: Cartilage


title: Otx2, D0, bioChIP


title: patient12_preACT_1


title: Control_2

description: WT.csv

value: WT


title: Control_1

description: WT.csv


title: USB1 mutants_2


title: SOA1-2_Zone_AS_Condition_WB_Rep2


title: Nanog, bioChIP


title: SOA2-1_Zone_DZ_Condition_NWB_Rep3


title: SOA4-1_Zone_DZ_Condition_NWB_Rep1


title: SOA2-1_Zone_DZ_Condition_NWB_Rep2


title: USB1 mutants_1


title: WT_2


title: Control_3

description: WT.csv


title: day5, scRNA-seq

city: Austin

first: Muyoung

last: Lee

department: Molecular Biosciences

institute: University of Texas at Austin

description: 10x Genomics

data_processing:
Sequencing reads alignment and feature counts generation were performed by Cell Ranger v6.0.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: J1 ES cells

extract_protocol:
Cells were dissociated into single cells with 0.25% trypsin. The dissociated cells were washed twice with 0.04% BSA in PBS and resuspended to a concentration of 1000 cells/uL. Then the cells were subjected to single-cell RNA sequencing.
Library was performed according to the manufacturer's instructions (Chromium Next GEM Single Cell 3' Library Kit v3.1,10x genomics).

value: embryonic stem cells

tag: time point

value: 5 days

tag: agent

value: doxycycline


title: patient10_preACT_2

value: pre-ACT


title: Gcm1, D0, bioChIP


title: SOA2-1_Zone_DZ_Condition_NWB_Rep4


title: patient9_postACT_1


title: SOA1-1_Zone_DZ_Condition_NWB_Rep4


title: day3, scRNA-seq

description: 10x Genomics

value: 3 days


title: SOA1-1_Zone_DZ_Condition_NWB_Rep3


title: iWAT-KO-HFD-3

city: Milan

first: Tanja

last: Eberhart

address: Via Olgettina

country: Italy

institute: IRCCS San Raffaele Scientific Institute

data_processing:
The 3' adaptors were removed using cutadapt and trimmed reads with a length of less than 18bp were discarded
The trimmed reads were filtered with a contaminants database consisting of rDNA sequences
The recovered non matching reads were aligned to the genome/transcriptome using STAR-align
Unique mappers from the resulting BAM file were used to create unstranded, stranded and reverse stranded coverage tracks for visualisation using bedtools
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: iWAT

extract_protocol:
RNA from iWAT and eWAT was harvested from snap-frozen tissues using TRIZOL followed by the ReliaPrep RNA Tissue Miniprep System (Promega  Cat#Z6111)
Barcoded mRNA Libraries were prepared usingNEBNext RNA Ultra II Directional Library Kit (New England Biolabs)

treatment_protocol: C57BL/6NJ male wild type and Acod1-/- mice were challenged with HFD. HFD was started at 5 weeks of age and continued for 16 weeks.

value: iWAT

value: high fat diet

value: 18 weeks

value: male


title: day1, scRNA-seq

description: 10x Genomics

value: J1 ES cells

value: 1 day


title: WT_1

value: Human embryonic stem cells


title: HeLa_Normoxia

city: Kyoto

first: Peter

middle: Wai Tik

last: LEE

address: Sakyo Ward, Yoshidakonoecho

department: Graduate School of Biostudies

country: Japan

institute: Kyoto University

data_processing:
All analyses were performed using CLC Genomics Workbench v 10.1.1.
Sequence reads were imported to CLC GW as paired-end reads, and then mapped to hg19.
Raw quantification output was the read per kiloobase per million reads (RPKM) value, and normalisation was performed by quantile method.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes the normalised expression values of each gene

source_name: HeLa

growth_protocol: HeLa cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with high glucose (4.5g/L-Glucose), L-Gln, and sodium pyruvate,  supplemented with 10% (v/v) FBS and 1% (v/v) penicillin-streptomycin. Cells were maintained at 37˚C in a 95% air/5% CO2 moisturised incubator.

extract_protocol:
Cells were lysed in Sepasol-RNA I Super G (Nacalai tesque) and chloroform was added for phase separation in order to extract total RNA.
500 ng of total RNA was used for rRNA depletion, followed by directional library synthesis (NEB, E7420).

treatment_protocol: HeLa cells were seeded and allowed to adhere completely, before being transferred into the RUSKINN INVIVO2 500 Hypoxic Work Station set at <0.1% oxygen, 5% CO2. After incubation for 24 hours, total RNA was extracted. For normoxia control, cells were seeded and maintained in a 95% air/5% CO2 moisturised incubator.

value: HeLa

value: Human cervical adenocarcinoma

value: Normoxia (20% oxygen) 24h


title: SOA1-1_Zone_DZ_Condition_NWB_Rep2

data_processing:
Alignment was performed using HISAT2 software with hg19 reference genomes to convert FASTQ files into BAM files.
RNA-seq gene expression levels were quantified with featureCounts with basic gene annotation(ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/GRCh37_mapping/gencode.v26lift37.annotation.gtf.gz)
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: comma-delimited text file includes annotation information for each Sample

value: Cartilage


title: patient9_preACT_1

value: melanoma


title: SOA1-1_Zone_DZ_Condition_NWB_Rep1


title: iWAT-KO-HFD-2

value: 17 weeks


title: patient8_postACT_1

value: post-ACT


title: patient10_preACT_1


title: 2-1_J12_S125,HyperSeq, scRNASeq

city: Kensington

first: Yike

last: Xie

state: NSW

address: Lowy 2, Cnr High and Botany St

country: Australia

institute: UNSW Sydney

description: A single cell was imaged by a hyperspectral microscope and then captured by CellCelector

data_processing:
The sequencing reads were demultiplexed using bcl2fastq 2.20 (Illumina, San Diego, CA, USA), mapped and counted to human genome reference (GRCh38) for MCF-7 cells using STAR aligner. HTSeq 2.0 was used to map the sequencing reads of MCF-7 cells into exon level. Quality of datasets were evaluated based on the number of genes expressed in the count matrix, the total counts per cell and the percentage of counts in mitochondrial genes. Genes that were expressed in less than ten cells were excluded. Datasets were normalised by the total reads, multiplied by 1,000,000 (cpm). During analyses but doublet deconvolution, datasets were log2 transformed after addition of a pseudo count of 1. GSEAPY was used for pathway analysis.
Assembly: GRCh38
Supplementary files format and content: fastq files of each cell are provided

source_name: Breast

extract_protocol:
MCF-7 cells were washed twice with PBS, then placed into equilibrated Hank’s balanced salt solution (HBSS) (Thermo Fisher Scientific, Waltham MA, USA) and maintained at 37°C during hyperspectral imaging. Subsequently, imaged cells were captured by CellCelector to a 384-well PCR plate with lysis buffer.
Library was prepared following Smart-seq2 protocol. Briefly, cells were picked into 384 well lysis plates followed by reverse transcription, template switching and 26 cycles of PCR to generate and amplify the cDNA. MANTIS automated liquid handler (Tecan, Zürich, Switzerland) was used during the process. cDNA was normalised to 0.1 - 1ng/µl according to the qualification by Quant-iT™ PicoGreen™ dsDNA Assay Kit (Thermo Fisher Scientific, Waltham MA, USA) via automated liquid handling robot Mosquito (SPT Labtech, Melbourn, Cambridgeshire, UK). Nextera XT kit (Illumina, San Diego, CA, USA) with 14 cycles of amplification was used for tagmenting MCF-7 cells. Purification was conducted to remove primer by Agencourt Ampure XP (Beckman Coulter, Brea CA, USA) magnetic beads at a ratio of 0.7x for two times. Libraries were quantified using Bioanalyzer 2100 (Agilent Technologies, Waldbronn, Germany).

value: Breast

value: Breast cancer cells


title: HeLa_Hypoxia

value: Hypoxia (<0.1% oxygen) 24h


title: patient8_preACT_1

value: pre-ACT


title: 2-1_K12_S126,HyperSeq, scRNASeq


title: patient7_preACT_1


title: WT_3

value: WT


title: SOA4-1_Zone_MZ_Condition_NWB_Rep2

extract_protocol:
Fresh cartilage tissue obtained from patients with OA and non-OA controls was placed in cold RNase-free PBS. The tissue was then gently transferred to pre-cooled optimum cutting temperature (OCT) compound, ensuring that the entire tissue was embedded. The tissue was immediately frozen in liquid nitrogen or dry ice and transferred to -80 °C. The OCT-embedded samples were cryosectioned at −20 °C at 14 μm thickness. The sections were then mounted on polyethylene-terephthalate-coated slides, fixed immediately with ethanol, and stained with 1% cresyl violet acetate dissolved in 75% ethanol solution. Afterward, targeted regions of sections were collected by laser capture microdissection (LCM), and transcriptome analyses of those collected samples were performed by Geo-seq.
cDNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina and sequenced on Illumina NovaSeq 6000 with PE150 mode.


title: 2-1_H12_S123,HyperSeq, scRNASeq


title: patient7_postACT_1


title: SOA2-1_Zone_DZ_Condition_NWB_Rep1


title: iWAT-KO-HFD-1

value: iWAT

value: high fat diet

value: 16 weeks


title: iWAT-WT-HFD-4

value: male


title: patient6_postACT_1


title: 2-1_G12_S122,HyperSeq, scRNASeq


title: SOA4-1_Zone_MZ_Condition_NWB_Rep1


title: iWAT-WT-HFD-3


title: iWAT-WT-HFD-5


title: patient6_preACT_1


title: SOA4-1_Zone_MZ_Condition_NWB_Rep3


title: SOA3-1_Zone_MZ_Condition_NWB_Rep3


title: patient5_preACT_1


title: SOA3-1_Zone_MZ_Condition_NWB_Rep2


title: 2-1_C12_S118,HyperSeq, scRNASeq


title: SOA3-1_Zone_MZ_Condition_NWB_Rep1


title: iWAT-WT-HFD-1


title: 2-1_F12_S121,HyperSeq, scRNASeq


title: iWAT-WT-HFD-2


title: 2-1_N11_S116,HyperSeq, scRNASeq


title: patient4_postACT_1


title: 2-1_O11_S117,HyperSeq, scRNASeq


title: patient4_preACT_1


title: iWAT-WT-ND-2

value: normal chow diet


title: SOA2-1_Zone_MZ_Condition_NWB_Rep5


title: iWAT-WT-ND-1


title: 2-1_J11_S112,HyperSeq, scRNASeq


title: iWAT-WT-ND-3


title: 2-1_K11_S113,HyperSeq, scRNASeq


title: patient3_postACT_1


title: SOA2-1_Zone_MZ_Condition_NWB_Rep3


title: SOA2-1_Zone_MZ_Condition_NWB_Rep4


title: eWAT-KO-HFD-5

source_name: eWAT

value: eWAT


title: SOA2-1_Zone_MZ_Condition_NWB_Rep2


title: 2-1_H11_S110,HyperSeq, scRNASeq


title: patient2_postACT_1


title: eWAT-KO-HFD-4


title: patient3_preACT_1


title: patient5_postACT_1


title: 2-1_G11_S109,HyperSeq, scRNASeq


title: eWAT-KO-HFD-3


title: patient2_preACT_1


title: 2-1_F11_S108,HyperSeq, scRNASeq


title: SOA1-1_Zone_MZ_Condition_NWB_Rep3


title: 2-1_E11_S107,HyperSeq, scRNASeq


title: eWAT-KO-HFD-2


title: patient1_postACT_1


title: eWAT-WT-HFD-4


title: 2-1_D11_S106,HyperSeq, scRNASeq


title: SOA2-1_Zone_MZ_Condition_NWB_Rep1


title: WT_CDK9_1024c_Biol_Rep_2

first: Martino

last: Ugolini

address: Genopode

department: CIG

institute: UNIL

description: nascent RNA with base conversion (SLAM chemistry)

library_source: other

data_processing:
Trimming using Trimmomatic (Paired-end mode, LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Mapping using HISAT-3N (--base-change T,C --repeat --rna-strandness RF --fr --no-discordant)
Uniquely mapped fragments were filtered with Samtools and mate information was fixed with Picard FixMateInformation (--IGNORE_MISSING_MATES FALSE)
To distinguish between naturally occurring SNPs and SLAM-Seq-specific mismatches, we first identified naturally occurring SNPs by analysing the four IAA-minus samples (one per stage) in which the iodoacetamide treatment – and therefore the base conversion – was not performed. The bam files were converted to a suitable format with the Samtools mpileup function and then SNPs were identified by Varscan pileup2snp (--min-coverage 20 --min-reads2 5 --min-avg-qual 15 --min-var-freq0.25 --p-value 0.01). The union of the SNPs that were identified was used as a consensus list. Then the splbam.py script from pulseR was used to select fragments with at least one SLAM-Seq-specific mismatch.
To assess gene expression levels of annotated genes, raw read counts were obtained using FeatureCounts (-p --countReadPairs -B --minOverlap 10 -s 2 -t exon -g gene_id).
Normalization, Principal Component Analysis (PCA) and call for differential expression (alpha = 0.01 and log2(Fold Change) threshold = 2) was performed using DESeq2.
Assembly: Zebrafish GRCz11.105
Supplementary files format and content: raw_counts_proper_orientation_filtered_with_genename_2.txt: Raw counts of all genes as obtained by FeatureCounts. Gene names were added.
Supplementary files format and content: Table_S2.xlsx: Results of DESEQ2 comparison, for each of the 2 stages, of the comparison WT vs. WT + inj. MiR430 and WT vs. WT + cdk9 mRNA

molecule: other

organism: Danio rerio

source_name: whole embryo

growth_protocol: Synchronized WT embryos were collected, dechorionated with Pronase and injected with s4UTP, s4UTP and MiR430 miRNA and s4UTP and CDK9 mRNA. Embryos were then grown to the desired stages at 28 degrees.

extract_protocol:
Total RNA was extracted at the desired stages and genomic DNA removed by DNAse treatment. RNA containing s4UTP was then biotinylated and enriched with magnetic beads. Incorporated s4UTP was then chemically treated with IAA (SLAM chemistry) to introduce specific point mutatinos during retrotranscription step. 4 WT samples (one fro each stage) were not treated with IAA and used to determine SNPs.
Libraries were prepared with the TruSeq stranded mRNA Kit (Illumina, #20020594) and TruSeq RNA UD Indexes (Illumina, #20022371). The polyA enrichment step was not performed. Fragmentation was performed for 1 minute at 94°C.

value: whole embryo

value: wild type

value: CDK9 overexpression

value: IAA treatment


title: 2-1_O10_S104,HyperSeq, scRNASeq


title: eWAT-WT-HFD-5


title: WT_CDK9_1024c_Biol_Rep_1


title: WT_CDK9_1024c_Biol_Rep_3


title: eWAT-WT-HFD-3


title: SOA4-1_Zone_SZ_Condition_NWB_Rep4

value: Cartilage


title: 2-1_N10_S103,HyperSeq, scRNASeq


title: SOA1-1_Zone_MZ_Condition_NWB_Rep2


title: WT_MiR430_1024c_Biol_Rep_3

value: MiR430 injection


title: SOA1-1_Zone_MZ_Condition_NWB_Rep1


title: 2-1_L10_S101,HyperSeq, scRNASeq

value: Breast


title: eWAT-WT-HFD-2


title: 2-1_C11_S105,HyperSeq, scRNASeq

value: Breast cancer cells


title: eWAT-WT-HFD-1


title: SOA1-1_Zone_MZ_Condition_NWB_Rep4


title: WT_MiR430_1024c_Biol_Rep_2


title: eWAT-KO-HFD-1


title: patient1_preACT_1

value: melanoma


title: SOA4-1_Zone_SZ_Condition_NWB_Rep2


title: 2-1_K10_S100,HyperSeq, scRNASeq


title: WT_MiR430_1024c_Biol_Rep_1


title: SOA4-1_Zone_SZ_Condition_NWB_Rep1


title: eWAT-WT-ND-4


title: 2-1_I10_S98,HyperSeq, scRNASeq


title: SOA4-1_Zone_SZ_Condition_NWB_Rep5


title: SOA4-1_Zone_SZ_Condition_NWB_Rep3


title: eWAT-WT-ND-3


title: 2-1_H10_S97,HyperSeq, scRNASeq


title: SOA3-1_Zone_SZ_Condition_NWB_Rep4


title: eWAT-WT-ND-2


title: SOA3-1_Zone_SZ_Condition_NWB_Rep3


title: eWAT-WT-ND-1


title: 2-1_G10_S96,HyperSeq, scRNASeq


title: WT_CDK9_256c_Biol_Rep_3


title: WT_1024c_Biol_Rep_1

value: No treatment


title: P0, WT, scRNAseq

first: Silvia

last: Fre

address: 26 rue d’Ulm

department: Genetics and Developmental Biology

institute: Institut Curie

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mammary gland

extract_protocol:
For mammary rudiments at E13.5, E14.5 and E15.5, single cell dissociation was performed through enzymatic digestion with 300 U/ml collagenase A and 300 U/ml hyaluronidase for 90 minutes at 37°C under shaking. Cells were further treated with 0.1 mg/ml DNase I for 3 minutes. 10% FBS diluted in PBS was added to quench the DNase I. For mammary glands at P0, single cell dissociation was performed through enzymatic digestion with 600 U/ml collagenase A and 150 U/ml hyaluronidase for 90 minutes at 37°C under shaking were used for enzymatic digestion. Cells were further treated with 0.1 mg/ml DNase I for 3 min and an additional incubation in 0.63% NH4Cl for 1 min allowed lysis of red blood cells. Cells were pelleted by centrifugation at 320 g for 10 minutes. For all developmental times, after careful removal of the supernatant, cells were incubated in fluorescently labelled primary antibodies for 15 minutes on ice. Cells were washed from unbound antibodies with 2% FBS in HBSS and the cell suspension was passed through a 40 µm cell strainer filter to eliminate cell clumps. Cell viability was determined with DAPI and doublets were systematically excluded during analysis. CD45+, CD31+, Ter119+ (Lin+) non-epithelial cells were excluded. FACS analysis was performed using an ARIA flow cytometer (BD).
Single cell capture and library construction were performed using the 10x Genomics Chromium Single Cell 3’ v3.1 kit following the manufacturer’s instructions. Briefly, sorted mammary gland cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, P5 and P7 primers used for Illumina bridge amplification and a sample index were added.

value: Mammary gland

value: WT C57B6 mice

value: Female

tag: developmental stage


title: 2-1_D10_S93,HyperSeq, scRNASeq

tag: tissue


title: SOA3-1_Zone_SZ_Condition_NWB_Rep1

source_name: Cartilage


title: 2-1_C10_S92,HyperSeq, scRNASeq


title: SOA3-1_Zone_SZ_Condition_NWB_Rep2


title: WT_CDK9_256c_Biol_Rep_2


title: SOA2-1_Zone_SZ_Condition_NWB_Rep4


title: E15, WT, scRNAseq

description: 10x Genomics

tag: strain


title: 2-1_J9_S86,HyperSeq, scRNASeq


title: WT_CDK9_256c_Biol_Rep_1


title: 2-1_I9_S85,HyperSeq, scRNASeq


title: SOA2-1_Zone_SZ_Condition_NWB_Rep3


title: E14, WT, scRNAseq

description: 10x Genomics


title: E13, WT, scRNAseq

description: 10x Genomics


title: 2-1_H9_S84,HyperSeq, scRNASeq


title: WT_1024c_Biol_Rep_3


title: WT_1024c_Biol_Rep_2


title: hfq-3XFLAG #2

city: Jena

first: Eric

last: Ruhland

address: Winzerlaer Str. 2

country: Germany

institute: Friedrich Schiller University Jena

description: instrument should be Illumina NextSeq 1000; molecule is Hfq bound RNA

data_processing:
Analysis with "ChimericFragments" DOI: 10.5281/zenodo.8376810
default parameters, exept: min_seed_length=15; autocomplete_utrs=false; bp_shift_weight=0.0; max_bp_fdr=0.35; min_reads=5
Assembly: NCBI Reference Sequence: NC_009648.1 - NC_009653.1
Supplementary files format and content: xlsx workbook with single and chimeric counts for each gene, as well as RNA-RNA interactions

organism: Klebsiella pneumoniae subsp. pneumoniae

growth_protocol: Growth in LB-Medium, 200 rpm shaking, 37 °C until OD 2

extract_protocol:
RNA-protein crosslinking, cell lysis, CoIP using anti-FLAG-antibody, RNA ends trimmed using RNase A/T1, ligation of neighboring RNAs, Protein digestion using Proteinase K, RNA extraction, fragmentaton and DNase digestion, ribosomal RNA depletion and purification with AMPure XP beads
first strand cDNA synthesis using SuperScript III and Primer AR2, RNA degradation, cDNA cleanup, ligation of second adaptor(3Tr3) to cDNA 3' ends, cDNA cleanup and PCR enrichment using P5_Enr primer and P7_BC1_Enr primer
RIL-seq (doi: 10.1038/nprot.2017.115)


title: WT_MiR430_256c_Biol_Rep_2


title: hfq-3XFLAG #1


title: SOA1-1_Zone_SZ_Condition_NWB_Rep4


title: 2-1_F9_S82,HyperSeq, scRNASeq


title: WT_MiR430_256c_Biol_Rep_1


title: 2-1_G9_S83,HyperSeq, scRNASeq


title: SOA2-1_Zone_SZ_Condition_NWB_Rep1


title: wt #2

value: wt


title: SOA1-1_Zone_SZ_Condition_NWB_Rep3


title: wt #1


title: WT_256c_Biol_Rep_3


title: 2-1_E9_S81,HyperSeq, scRNASeq


title: SOA2-1_Zone_SZ_Condition_NWB_Rep2


title: WT_MiR430_256c_Biol_Rep_3


title: SOA1-1_Zone_SZ_Condition_NWB_Rep1


title: WT_256c_Biol_Rep_1


title: WT_256c_Biol_Rep_2


title: 2-1_O8_S78,HyperSeq, scRNASeq


title: SOA1-1_Zone_SZ_Condition_NWB_Rep2


title: 2-1_D9_S80,HyperSeq, scRNASeq


title: SOA3-1_Zone_AS_Condition_NWB_Rep4


title: miR430_Sphere_Biol_Rep_3

description:
nascent RNA with base conversion (SLAM chemistry)
miR430_D3

data_processing:
Trimming using Trimmomatic (Paired-end mode, LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Mapping using HISAT-3N (--base-change T,C --repeat --rna-strandness RF --fr --no-discordant)
Uniquely mapped fragments were filtered with Samtools and mate information was fixed with Picard FixMateInformation (--IGNORE_MISSING_MATES FALSE)
To distinguish between naturally occurring SNPs and SLAM-Seq-specific mismatches, we first identified naturally occurring SNPs by analysing the four IAA-minus samples (one per stage) in which the iodoacetamide treatment – and therefore the base conversion – was not performed. The bam files were converted to a suitable format with the Samtools mpileup function and then SNPs were identified by Varscan pileup2snp (--min-coverage 20 --min-reads2 5 --min-avg-qual 15 --min-var-freq0.25 --p-value 0.01). The union of the SNPs that were identified was used as a consensus list. Then the splbam.py script from pulseR was used to select fragments with at least one SLAM-Seq-specific mismatch.
To assess gene expression levels of annotated genes, raw read counts were obtained using FeatureCounts (-p --countReadPairs -B --minOverlap 10 -s 2 -t exon -g gene_id).
Normalization, Principal Component Analysis (PCA) and call for differential expression (alpha = 0.01 and log2(Fold Change) threshold = 2) was performed using DESeq2.
Assembly: Zebrafish GRCz11.105
Supplementary files format and content: raw_counts_proper_orientation_filtered_with_genename.txt: Raw counts of all genes as obtained by FeatureCounts. Gene names were added.
Supplementary files format and content: Table_S1.xlsx: Results of DESEQ2 comparison, for each of the 4 stages, of the comparison WT vs. mir430-/- + inj. MiR430

growth_protocol: Synchronized WT and mir430-/- embryos were collected, dechorionated with Pronase and injected with s4UTP and MiR430 rescue solution (only mir430-/-). Embryos were then grown to the desired stages at 28 degrees.

tag: Stage

value: Sphere


title: 2-1_J8_S73,HyperSeq, scRNASeq


title: 2-1_K8_S74,HyperSeq, scRNASeq


title: SOA3-1_Zone_AS_Condition_NWB_Rep2


title: SOA3-1_Zone_AS_Condition_NWB_Rep3


title: 2-1_I8_S72,HyperSeq, scRNASeq


title: miR430_Oblong_Biol_Rep_3

description:
nascent RNA with base conversion (SLAM chemistry)
miR430_C3

value: Oblong

tag: genotype


title: SOA3-1_Zone_AS_Condition_NWB_Rep1


title: 2-1_H8_S71,HyperSeq, scRNASeq

tag: cell type


title: 2-1_G8_S70,HyperSeq, scRNASeq


title: miR430_Oblong_Biol_Rep_2

description:
nascent RNA with base conversion (SLAM chemistry)
miR430_C2


title: SOA2-1_Zone_AS_Condition_NWB_Rep4


title: miR430_Oblong_Biol_Rep_1

description:
nascent RNA with base conversion (SLAM chemistry)
miR430_C1


title: SOA2-1_Zone_AS_Condition_NWB_Rep5


title: 2-1_F8_S69,HyperSeq, scRNASeq


title: 2-1_E8_S68,HyperSeq, scRNASeq


title: miR430_1024c_Biol_Rep_3

description:
nascent RNA with base conversion (SLAM chemistry)
miR430_B3


title: SOA2-1_Zone_AS_Condition_NWB_Rep3


title: 2-1_D8_S67,HyperSeq, scRNASeq


title: miR430_1024c_Biol_Rep_1

description:
nascent RNA with base conversion (SLAM chemistry)
miR430_B1


title: miR430_1024c_Biol_Rep_2

description:
nascent RNA with base conversion (SLAM chemistry)
miR430_B2


title: SOA2-1_Zone_AS_Condition_NWB_Rep2


title: miR430_256c_Biol_Rep_3

description:
nascent RNA with base conversion (SLAM chemistry)
miR430_A3


title: SOA2-1_Zone_AS_Condition_NWB_Rep1


title: 2-1_C8_S66,HyperSeq, scRNASeq


title: SOA1-1_Zone_AS_Condition_NWB_Rep3


title: 2-1_N7_S64,HyperSeq, scRNASeq


title: SOA1-1_Zone_AS_Condition_NWB_Rep2


title: miR430_256c_Biol_Rep_2

description:
nascent RNA with base conversion (SLAM chemistry)
miR430_A2


title: miR430_Sphere_Biol_Rep_2

description:
nascent RNA with base conversion (SLAM chemistry)
miR430_D2


title: miR430_Sphere_Biol_Rep_1

description:
nascent RNA with base conversion (SLAM chemistry)
miR430_D1


title: SOA1-1_Zone_AS_Condition_NWB_Rep1


title: WT_Sphere_Biol_Rep_4_NO_IAA

description:
nascent RNA without base conversion (SLAM chemistry)
WT_D4

value: No IAA treatment


title: miR430_256c_Biol_Rep_1

description:
nascent RNA with base conversion (SLAM chemistry)
miR430_A1

value: whole embryo


title: SC1_Zone_DZ_Condition_Control_Rep5


title: 2-1_L7_S62,HyperSeq, scRNASeq


title: 2-1_K7_S61,HyperSeq, scRNASeq


title: WT_1024c_Biol_Rep_4_NO_IAA

description:
nascent RNA without base conversion (SLAM chemistry)
WT_B4

value: wild type


title: 2-1_J7_S60,HyperSeq, scRNASeq

description: A single cell was imaged by a hyperspectral microscope and then captured by CellCelector


title: WT_Oblongc_Biol_Rep_4_NO_IAA

description:
nascent RNA without base conversion (SLAM chemistry)
WT_C4


title: SC1_Zone_DZ_Condition_Control_Rep4


title: 2-1_I7_S59,HyperSeq, scRNASeq


title: SC1_Zone_DZ_Condition_Control_Rep3


title: SC1_Zone_DZ_Condition_Control_Rep1


title: WT_Sphere_Biol_Rep_3

description:
nascent RNA with base conversion (SLAM chemistry)
WT_D3


title: WT_Sphere_Biol_Rep_2

description:
nascent RNA with base conversion (SLAM chemistry)
WT_D2


title: 2-1_G7_S57,HyperSeq, scRNASeq


title: SC1_Zone_MZ_Condition_Control_Rep4


title: SC1_Zone_MZ_Condition_Control_Rep3


title: WT_Oblong_Biol_Rep_3

description:
nascent RNA with base conversion (SLAM chemistry)
WT_C3


title: SC1_Zone_DZ_Condition_Control_Rep2


title: 2-1_H7_S58,HyperSeq, scRNASeq


title: 2-1_D7_S54,HyperSeq, scRNASeq


title: WT_Oblong_Biol_Rep_2

description:
nascent RNA with base conversion (SLAM chemistry)
WT_C2


title: 2-1_M7_S63,HyperSeq, scRNASeq


title: dpp_library_2

city: New York

first: Felix

last: Simon

state: New York

address: 24 Waverly Place

department: Biology

institute: NYU

description: 10x genomics

data_processing:
Fastq files were generated using cell ranger cellranger/6.0.1 with default parameters
We mapped the reads to the D. melanogaster genome assembly BDGP6.88 using cellranger 6.0.1 with default parameters except the "cell_number" parameter that was set to 7000.
Building of the filtered and annotated seurat objects is detailed in the "Methods" section of the corresponding paper.
Assembly: BDGP6.88
Supplementary files format and content: Processed data files named "Library_filtered_feature_bc_matrix.zip" contain the "Filtered feature-barcode matrices MEX" cellranger count output for the corresponding library.
Supplementary files format and content: Processed data files named "Library_filtered_normalized.RDS" are the filtered and annotated seurat objects for the corresponding libraries.

organism: Drosophila melanogaster

source_name: Optic lobe

extract_protocol:
Whole brains were extracted in ice-cold Schneider's media. The brains were then transferred into DPBS, we used an epifluorescence microscope to remove brains with ectopic mOPC GFP expression, and placed the brains back in Schneider’s media. The brains were then incubated at 25˚C in Schneider’s media with 2mg/mL Collagenase and 2mg/mL Dispase, for 1hr 30min (adult brains) or for 30min (pupal brains), then washed 3 times with ice-cold Schneider’s media to stop the dissociation. Optic lobes were then separated from the central brain, transferred in ice-cold DPBS + 0.04% BSA, and washed twice with ice-cold DPBS + 0.04% BSA. For pupal brains, the separation between central brain and optic lobes can be seen as a difference in texture: the optic lobe forms a smoother and cohesive structure that can be removed using a fine tungsten needle. Optic lobes and 150μL of DPBS + 0.04% BSA were then transferred to a low-bind Eppendorf, and dissociated by pipetting vigorously 50 times, resting the cells for 1 minute on ice, and pipetting 50 times more. The cell suspension was then checked under a dissecting microscope, and we pipetted up to 50 more times if the size of remaining clumps was too significant. We did not try to dissociate small clumps since they are most likely neuropils, not soma, and indeed we empirically noticed a better quality of the data obtained after lowering pipetting repetitions. The suspension was then passed through a 20µm mini-PluriStrainer, and the filter was washed with 400μL of DPBS + 0.04% BSA which we also collected (pipetting from the opposite side may be necessary to collect the entire cell suspension).
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index )

value: Optic lobe

tag: group

value: dpp


title: WT_Sphere_Biol_Rep_1

description:
nascent RNA with base conversion (SLAM chemistry)
WT_D1

value: IAA treatment


title: SC1_Zone_MZ_Condition_Control_Rep1

first: Yue

institute: Xi'an Jiaotong University

value: Cartilage


title: WT_Oblong_Biol_Rep_1

description:
nascent RNA with base conversion (SLAM chemistry)
WT_C1


title: 2-1_C7_S53,HyperSeq, scRNASeq

value: Breast


title: SC1_Zone_MZ_Condition_Control_Rep2


title: SC1_Zone_SZ_Condition_Control_Rep5


title: WT_256c_Biol_Rep_4_NO_IAA

description:
nascent RNA without base conversion (SLAM chemistry)
WT_A4


title: WT_1024c_Biol_Rep_3

description:
nascent RNA with base conversion (SLAM chemistry)
WT_B3


title: hh_library_2

description: 10x genomics

value: hh


title: SC1_Zone_SZ_Condition_Control_Rep4


title: hh_library_1

description: 10x genomics


title: 1-1_O6_S52,HyperSeq, scRNASeq

value: Breast cancer cells


title: 1-1_N6_S51,HyperSeq, scRNASeq


title: 2-1_F7_S56,HyperSeq, scRNASeq


title: 1-1_M6_S50,HyperSeq, scRNASeq


title: WT_1024c_Biol_Rep_2

description:
nascent RNA with base conversion (SLAM chemistry)
WT_B2


title: WT_1024c_Biol_Rep_1

description:
nascent RNA with base conversion (SLAM chemistry)
WT_B1


title: SC1_Zone_SZ_Condition_Control_Rep2


title: Optix_library_3

description: 10x genomics

value: Optix


title: SC1_Zone_SZ_Condition_Control_Rep3


title: 1-2_K6_S48,HyperSeq, scRNASeq


title: WT_256c_Biol_Rep_3

description:
nascent RNA with base conversion (SLAM chemistry)
WT_A3


title: Optix_library_2

description: 10x genomics


title: 1-2_J6_S47,HyperSeq, scRNASeq


title: dpp_library_1

description: 10x genomics


title: SC1_Zone_SZ_Condition_Control_Rep1


title: SC1_Zone_AS_Condition_Control_Rep7


title: Optix_library_1

description: 10x genomics


title: WT_256c_Biol_Rep_1

description:
nascent RNA with base conversion (SLAM chemistry)
WT_A1


title: WT_256c_Biol_Rep_2

description:
nascent RNA with base conversion (SLAM chemistry)
WT_A2


title: 1-2_I6_S46,HyperSeq, scRNASeq


title: SC1_Zone_AS_Condition_Control_Rep6


title: 1-2_H6_S45,HyperSeq, scRNASeq


title: SC1_Zone_AS_Condition_Control_Rep5


title: 1-2_G6_S44,HyperSeq, scRNASeq


title: SC1_Zone_AS_Condition_Control_Rep4


title: 1-2_F6_S43,HyperSeq, scRNASeq


title: SC1_Zone_AS_Condition_Control_Rep3


title: 833-10, n5-Rc, Naïve, 500um, ratn5, Right Hemisphere

city: EAST LANSING

first: Erin

middle: K

last: Purcell

state: MI

address: 775 WOODLOT DRIVE

department: Biomedical Engineering

institute: MICHIGAN STATE UNIVERSITY

data_processing:
Sequencing adapters were trimmed using Cutadapt (v2.3). FastQC (v0.11.8) was used to ensure the quality of data.
Reads are mapped to the reference genome Rattus_norvegicus.Rnor_6.0.9, using STAR (v2.6.1b) and assigned count estimates to genes with RSEM (v1.3.1). Alignment options follow ENCODE standards for RNA-seq.
FastQC is used in an additional post-alignment step to ensure that only high-quality data gets used for expression quantitation and differential expression.
Data was pre-filtered to remove genes with 0 counts in all samples. Differential gene expression analysis is performed using DESeq2, using a negative binomial generalized linear model (thresholds: linear fold change >1.5 or <-1.5, Benjamini–Hochberg FDR (Padj) <0.05).
Assembly: Rnor_6.0.9
Supplementary files format and content: deseq2_raw_counts.txt

organism: Rattus norvegicus

source_name: Brain Tissue

growth_protocol: Single shank ‘Michigan’-style probes (16-channel A1 × 16−3 mm, 15 µm thick, 703 µm2 site size, 100 µm site spacing, Neuronexus Technologies) were stereotaxically implanted in the motor cortex (M1) of male Sprague–Dawley rats (aged 12–14 weeks). Animals were isoflurane anesthetized and a craniotomy was performed over M1 (+3.0 mm anterior posterior, 2.5 medio lateral from Bregma), dura was resected, and the probe was stereotaxically inserted to a depth of 2 mm from the cortical surface.

extract_protocol:
RNA was extracted from LCM-collected tissue using a specialized RNAstorm extraction kit (Cell Data Sciences).
cDNA library preparation and RNA sequencing was carried out by the University of Michigan Advanced Genomics Core. cDNA libraries were prepped using a Takara SMART-stranded kit and subsequently subjected to 150 paired-end cycles on the NovaSeq-6000 platform (Illumina).

treatment_protocol:
At the terminal time point, animals were deeply anesthetized with sodium pentobarbital, perfused with 4% paraformaldehyde transcardially, and the brains were extracted. Following graded sucrose protection (5%–20%) and cryo-embedding, the brains were sliced via cryostat (Leica) as 20 µm thick sectionsand mounted on SuperfrostTM Plus slides (Fisher Scientific). Six tissue sections (n = 6) were collected for analysis at each time point (24 h, n = 3 rats; 1 week, n = 5 rats; 6 weeks, n = 4 rats) in addition to six samples collected from naïve, unimplanted rats. Depth of collection spanned the implant shank (∼600–1700 µm from cortical surface).
Tissue near the implant injury, or ‘interfacial’ (within 100 µm) was extracted using LCM (Zeiss Palm MicroBeam IV). Distal tissue of an approximately equivalent total surface area was extracted from ∼500 µm away from the implant site to assess distance-dependent effects. These samples were collected and pooled from four smaller sections obtained at locations equidistant from the implant site. Using similar collection methods, control tissue from naïve brains was used to compare implanted tissue to unimplanted tissue.

value: Sprague-Dawley

value: Brain Tissue

value: WT

value: Naïve

tag: time


title: 1-2_E6_S42,HyperSeq, scRNASeq


title: 833-8, n3-Lc, Naïve, 500um, ratn3, Left Hemisphere


title: 1-2_O5_S39,HyperSeq, scRNASeq


title: 833-9, n5-R, Naïve, 100um, ratn5, Right Hemisphere


title: 833-7, n3-L, Naïve, 100um, ratn3, Left Hemisphere


title: 1-2_C6_S40,HyperSeq, scRNASeq


title: Retinal organoid differentiated from hPSCs, Day6, LDN treated, Biological replicate 4

city: Indianapolis

first: Chi

last: Zhang

state: IN

address: 410 W. 10th Street, Suite 5000

institute: Indiana University School of Medicine

data_processing:
The sequencing data was next assessed using FastQC (Babraham Bioinfomatics, Cambridge, UK) and then mapped to the Human genome (GRCH38) using STAR RNA-seq aligner (Dobin et al., 2013) with the parameter: “— outSAMmapqUNIQUE 60”. Uniquely mapped sequencing reads were assigned to GRCH38 reference genome using featureCounts.
Assembly: hg19
Supplementary files format and content: raw_counts.txt

source_name: Retinal organoid

growth_protocol: Human induced pluripotent stem cells were differentiated to a neural/retinal lineage following described protocols in neural induction medium (DMEM/F12 with 1% N2 supplement, 1x MEM NEAA, and 2 ug/ml heparin). Samples were collected for RNA on either day 6 of differentiation, or on day 8 after treatment for 2 days with either BMP4 or LDN-193189

extract_protocol:
Total RNA was collected from untreated aggregates on day 6 and treated aggregates on day 8 using the Picopure RNA extraction kit (Life Technologies).
mRNAseq was then performed upon these samples to identify transcriptional changes across all conditions using a NovaSeq 6000 sequencer at the Indiana University Center for Medical Genomics. RNA quality was determined with an Agilent Bioanalyzer 2011, with a RIN number of 7 or higher.
cDNA library preparation included mRNA purification/enrichment, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification, following the KAPA mRNA Hyper Prep Kit Technical Data Sheet, KR1352 – v4.17 (Roche Corporation). Approximately 30M reads per library were generated.

treatment_protocol: Cultures were treated at day 6 of differentiation with either BMP4 (50 ng/ml) or LDN-193189 (200nM) for 2 days, at which point other samples were collected for day 8 timepoints.

value: Retinal organoid

value: LDN treated


title: SC1_Zone_AS_Condition_Control_Rep2

last: Fan

address: Yanta West Road No.76


title: Retinal organoid differentiated from hPSCs, Day6, LDN treated, Biological replicate 3


title: 1-2_M5_S37,HyperSeq, scRNASeq


title: 833-6, n3-Rc, Naive, 500um, ratn3, Right Hemisphere


title: 1-2_N5_S38,HyperSeq, scRNASeq


title: 1-2_L5_S36,HyperSeq, scRNASeq


title: 833-12, n5-Lc, Naïve, 500um, ratn5, Left Hemisphere


title: Retinal organoid differentiated from hPSCs, Day6, LDN treated, Biological replicate 1


title: Retinal organoid differentiated from hPSCs, Day6, LDN treated, Biological replicate 2


title: 1-2_K5_S35,HyperSeq, scRNASeq


title: Retinal organoid differentiated from hPSCs, Day6, BMP4 treated, Biological replicate 4

value: BMP4 treated


title: 833-3, n2-L, Naïve, 100um, ratn2, Left Hemisphere


title: 833-11, n5-L, Naïve, 100um, ratn5, Left Hemisphere


title: 2-1_E7_S55,HyperSeq, scRNASeq


title: 833-4, n2-Lc, Naïve, 500um, ratn2, Left Hemisphere


title: 1-2_G5_S31,HyperSeq, scRNASeq


title: RNA_WT_P3_rep3

city: Bunkyo-ku

first: Soichiro

last: Yamanaka

institute: The University of Tokyo

data_processing:
Basecalls were performed using bcl2fastq v2.20 for HiSeqX output.
RNA-seq reads were trimmed down to 90 bp from 3' end, using Seqkit v0.10.2, Cutadapt v1.18, discarding reads left with < 20 bp
RNA-seq reads were aligned to the UCSC mm10 genome using Hisat2 version 2.1.0, with following option, --dta.
FeatureCount v1.5.2 to calculate read counts on transposons or genes with following parameters: -p, -M (When calculating read counts on genes, -M is removed). For gene annotation, we used mus_musculus_GRCm38_102.gtf (http://asia.ensembl.org/Mus_musculus/Info/Index)
Read counts were normalized to RLE using DESeq2 v1.26.0
Assembly: mm10
Supplementary files format and content: bigWig : read coverage file
Supplementary files format and content: txt : files include RLE normalized read count

source_name: gonocyte from WT mouse at P3

growth_protocol: Male germ cells were isolated from Mvh-Venus transgenic mouse at indicated developmental timepoints

extract_protocol:
RNA was extracted with RNA plus XS (Machery and Nagel), following manufacturer's instruction.
RNA libraries for RNA-seq were prepared using SMART-seq v4 Ultra Low input RNA kit (Clontech) and TruSeq mRNA library prep kit (Illumina) following manufacturer's protocols.

value: testis


title: 833-2, n2-Rc, Naïve, 500um, ratn2, Right Hemisphere


title: Retinal organoid differentiated from hPSCs, Day6, BMP4 treated, Biological replicate 3


title: 1-2_F5_S30,HyperSeq, scRNASeq


title: RNA_WT_P3_rep2


title: 833-1, n2-R, Naïve, 100um, ratn2, Right Hemisphere


title: SC1_Zone_AS_Condition_Control_Rep1

city: Xi'an


title: Retinal organoid differentiated from hPSCs, Day6, BMP4 treated, Biological replicate 2


title: RNA_WT_P3_rep1


title: 134238, 19c, 6 Weeks, 500um, rat19, Right Hemisphere

value: Silicon Microelectrode Implant  (16-channel A1 × 16−3 mm, 15 µm thick, 703 µm2 site size,100 µm site spacing, Neuronexus Technologies)

value: 6 Weeks


title: 833-5, n3-R, Naïve, 100um, ratn3, Right Hemisphere


title: Retinal organoid differentiated from hPSCs, Day6, BMP4 treated, Biological replicate 1


title: 1-2_D5_S28,HyperSeq, scRNASeq


title: 1-2_C5_S27,HyperSeq, scRNASeq


title: 134237, 19, 6 Weeks, 100um, rat19, Right Hemisphere


title: Retinal organoid differentiated from hPSCs, Day6, Basline, Biological replicate 3

value: Baseline


title: Retinal organoid differentiated from hPSCs, Day6, Basline, Biological replicate 4


title: 134236, 18c, 6 Weeks, 500um, rat19, Left Hemisphere


title: 1-2_N4_S25,HyperSeq, scRNASeq


title: Retinal organoid differentiated from hPSCs, Day6, Basline, Biological replicate 2


title: RNA_WT_P0_rep1

source_name: gonocyte from WT mouse at P0


title: 134235, 18, 6 Weeks, 100um, rat19, Left Hemisphere


title: 134234, 17c, 6 Weeks, 500um, rat17, Right Hemisphere


title: 1-2_M4_S24,HyperSeq, scRNASeq


title: Retinal organoid differentiated from hPSCs, Day6, Basline, Biological replicate 1


title: RNA_WT_E165_rep3

source_name: gonocyte from WT mouse at E16.5


title: 1-2_L4_S23,HyperSeq, scRNASeq


title: RNA_WT_E165_rep2


title: RNA_WT_E165_rep1


title: 134233, 17, 6 Weeks, 100um, rat17, Right Hemisphere


title: 1-2_K4_S22,HyperSeq, scRNASeq


title: iPSC-neurons, sildenafil 75 µM, Day 5_2

city: CLEVELAND

first: Feixiong

last: Cheng

state: OH

address: 9620 Carnegie Ave.

department: Genome center

institute: The Cleveland Clinic Lerner Research Institute

data_processing:
Raw fastq reads were first subjected to the quality filtering using fastp v0.23.2 with qualified phred quality score cut-off of 20 (>=Q20) and 30% bases allowed to be unqualified.
Quality filtered reads were aligned to the reference human genome hg38 (GRCh38/108 build) employing Rsubread 2.8.1 package with default settings except multiple threads.
Gene-wise read counts were obtained with feature Counts utilizing inbuilt hg38 RefSeq annotation and duplicates were ignored in read summarization.
Assembly: hg38
Supplementary files format and content: tab-delimited file includes raw counts for each sample.

source_name: iPSC-neurons

growth_protocol: Briefly, iPSC lines were cultured and maintained in mTeSR™1 medium. Cells were cultured in neural induction medium (05839, STEMCELL Technologies) in a 37°C, 5% CO2 incubator to form monolayer neural progenitor cells (NPCs). Further, forebrain neuron differentiation medium (08600, STEMCELL Technologies) and forebrain neuron maturation medium (08605, STEMCELL Technologies).

extract_protocol:
RNA was extracted using RNeasy mini kit, in combination with RNAase-free DNAase to remove the potential genomic DNA contamination (Qiagen).
Libraries were constructed using the lllumina Stranded kits following the recommended protocol.

treatment_protocol: After 10 days of maturation (day 35), neurons were treated with sildenafil at different concentrations (10-100 µM) along with DMSO for 5 days.

tag: disease state

value: Alzheimer’s disease (AD)

value: iPSC-neurons

value: AD patient-derived iPSC (HVRDi001-A-1)

value: Male

value: sildenafil 75 uM

value: Day 5


title: iPSC-neurons, sildenafil 100 µM, Day 5_2

value: sildenafil 100 uM


title: 134232, 16c, 6 Weeks, 500um, rat17, Left Hemisphere

value: Sprague-Dawley

value: Brain Tissue


title: RNA_WT_P0_rep3


title: 1-2_J4_S21,HyperSeq, scRNASeq

value: Breast

value: Breast cancer cells


title: 1-2_E5_S29,HyperSeq, scRNASeq


title: 134231, 16, 6 Weeks, 100um, rat17, Left Hemisphere

value: WT


title: RNA_WT_E135_rep3

source_name: gonocyte from WT mouse at E13.5


title: RNA_WT_P0_rep2


title: RNA_WT_E135_rep2


title: 134229, 14, 6 Weeks, 100um, rat11, Left Hemisphere


title: RNA_WT_E135_rep1


title: 1-2_F4_S17,HyperSeq, scRNASeq


title: iPSC-neurons, sildenafil 25 µM, Day 5_2

value: sildenafil 25 uM


title: 1-2_E4_S16,HyperSeq, scRNASeq


title: RNA-seq_P3_KO_rep3

data_processing:
Basecalls were performed using bcl2fastq v2.20 for HiSeqX output.
RNA-seq reads were trimmed down to 90 bp from 3' end, using Seqkit v0.10.2, Cutadapt v1.18, discarding reads left with < 20 bp
RNA-seq reads were aligned to the UCSC mm10 genome using Hisat2 version 2.1.0, with following option, --dta.
FeatureCount v1.5.2 to calculate read counts on transposons or genes with following parameters: -p, -M (When calculating read counts on genes, -M is removed). For gene annotation, we used mus_musculus_GRCm38_102.gtf (http://asia.ensembl.org/Mus_musculus/Info/Index)
Read counts were normalized to RLE using DESeq2 v1.26.0
Assembly: mm10
Supplementary files format and content: bigWig : read coverage file
Supplementary files format and content: txt, cvs : files include RLE normalized read count

source_name: gonocyte from Morc1 (-/-) mice at P3

growth_protocol: Male germ cells were isolated from Mvh-Venus transgenic mouse at indicated developmental timepoints for Morc1 KO or Morc1 het mice

value: testis


title: iPSC-neurons, sildenafil 10 µM, Day 5_2

value: sildenafil 10 uM


title: 1-2_C4_S14,HyperSeq, scRNASeq


title: iPSC-neurons, DMSO, Day 5_2

value: DMSO


title: RNA-seq_P3_KO_rep2


title: 134228, 13c, 6 Weeks, 500um, rat2, Left Hemisphere

value: Silicon Microelectrode Implant  (16-channel A1 × 16−3 mm, 15 µm thick, 703 µm2 site size,100 µm site spacing, Neuronexus Technologies)

value: 6 Weeks


title: iPSC-neurons, sildenafil 100 µM, Day 5_1

value: Alzheimer’s disease (AD)

value: iPSC-neurons


title: 1-2_O3_S13,HyperSeq, scRNASeq


title: 134227, 13, 6 Weeks, 100um, rat2, Left Hemisphere


title: iPSC-neurons, sildenafil 75 µM, Day 5_1

value: AD patient-derived iPSC (HVRDi001-A-1)

value: Male


title: 1-2_N3_S12,HyperSeq, scRNASeq


title: 1-2_H4_S19,HyperSeq, scRNASeq


title: iPSC-neurons, sildenafil 50 µM, Day 5_2

value: sildenafil 50 uM

value: Day 5


title: iPSC-neurons, sildenafil 50 µM, Day 5_1


title: 1-1_M3_S11,HyperSeq, scRNASeq


title: RNA-seq_P3_het_rep2

source_name: gonocyte from Morc1 (+/-) mice at P3


title: RNA-seq_P3_het_rep3


title: 134224, 11c, 1 Week, 500um, rat23, Left Hemisphere

value: Sprague-Dawley

value: 1 Week


title: 134230, 14c, 6 Weeks, 500um, rat11, Left Hemisphere

value: Brain Tissue


title: iPSC-neurons, sildenafil 25 µM, Day 5_1


title: 1-1_L3_S10,HyperSeq, scRNASeq

value: Breast

value: Breast cancer cells


title: 134223, 11, 1 Week, 100um, rat23, Left Hemisphere

value: WT


title: iPSC-neurons, sildenafil 10 µM, Day 5_1


title: 1-1_K3_S9,HyperSeq, scRNASeq


title: RNA-seq_P3_het_rep1

value: testis


title: 134222, 10c, 1 Week, 500um, rat22, Right Hemisphere


title: RNA-seq_P0_KO_rep3

source_name: gonocyte from Morc1 (-/-) mice at P0


title: RNA-seq_P0_KO_rep2


title: RNA-seq_P3_KO_rep1


title: iPSC-neurons, DMSO, Day 5_1


title: 134226, 12c, 1 Week, 500um, rat23, Right Hemisphere


title: RNA-seq_P0_KO_rep1


title: 1-1_J3_S8,HyperSeq, scRNASeq


title: shPHF19_rep3 ATAC-seq

city: Beijing

first: Xiao-ning

last: Gao

state: Beijing

address: 28 Fuxing Road

department: Department of Hematology

institute: Chinese PLA General Hospital

data_processing:
ATAC-seq reads were trimmed from 3' end until the final base had a quality score >30, using Fastp v0.20
ATAC-seq reads were aligned to the UCSC hg38 genome using Bowtie2 v2.4.1
Picard v2.2.4 was used to obtain the unique mapping reads
Deeptools v1.5.12 was used to generate coverage plots in bigwig file
Peaks were called using MACS2 v2.2.6
Assembly: hg38
Supplementary files format and content: Excel file includes information of increased or decreased peaks

source_name: Homo sapiens

growth_protocol: Kasumi-1 cells were maintained in RPMI 1640 medium supplemented with 50 µg/ml streptomycin, 50 IU/ml penicillin and 10% fetal calf serum at 37°C in a humidified atmosphere containing 5% CO2 (v/v).

extract_protocol:
ATAC-seq libraries were generated by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme #TD502) following the manufacturer’s instructions.
For each sample, 10,000 fresh cells were lysed using pre-cooled lysis buffer and then centrifuged at 500 × g for 10 min at 4°C to obtain nuclei. Nuclei were resuspended in TruePrep tagment enzyme mix and incubated for 30 min at 37°C. DNA fragments were purified the with VAHTS DNA Clean Beads and then subjected to PCR amplification. After size selected by VAHTS DNA Clean Beads, the samples were sequenced by the Illumina nova6000 platform (Geekgene, China) under paired-end 150 nt mode.

treatment_protocol: Kasumi-1 cells were seeded into 6-well plates overnight before PHF19 shRNA or scrambled control shRNA transfection and the medium was changed approximately 12 to 16 hours after transfection. Forty-eight hours after shRNA transfection, cells were selected with puromycin (2 microgram per milliliter) for at least 24 hours before further investigations.

value: Homo sapiens

value: acute myeloblastic leukemia cell

value: PHF19 knockdown


title: 134221, 10, 1 Week, 100um, rat22, Right Hemisphere

value: Silicon Microelectrode Implant  (16-channel A1 × 16−3 mm, 15 µm thick, 703 µm2 site size,100 µm site spacing, Neuronexus Technologies)


title: 134220, 9c, 1 Week, 500um, rat20, Left Hemisphere


title: 134225, 12, 1 Week, 100um, rat23, Right Hemisphere


title: shPHF19_rep2 ATAC-seq


title: shPHF19_rep1 ATAC-seq


title: 1-1_C3_S1,HyperSeq, scRNASeq

source_name: Breast


title: 134218, 8c, 1 Week, 500um, rat10, Right Hemisphere


title: RNA-seq_P0_het_rep3

source_name: gonocyte from Morc1 (+/-) mice at P0


title: RNA-seq_P0_het_rep2


title: 1-1_H3_S6,HyperSeq, scRNASeq


title: 134219, 9, 1 Week, 100um, rat20, Left Hemisphere


title: Control_rep4 ATAC-seq


title: RNA-seq_P0_het_rep1


title: Control_rep3 ATAC-seq


title: 134217, 8, 1 Week, 100um, rat10, Right Hemisphere


title: 134216, 7c, 1 Week, 500um, rat9, Right Hemisphere


title: H3_ChIP_P3_KO_rep2

data_processing:
Basecalls were performed using bcl2fastq v2.20 for HiSeqX output.
ChIP-seq reads were trimmed down to 50 bp from 3' end, using Seqkit v0.10.2, Cutadapt v1.18, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie2 version 2.3.4.1 Only uniquely mapping reads were retained. No mismatch was allowed.
To normalized coverage plots (reads per million, rpm) (bigWig file format) were created by deeptools v3.5.0.
Peaks were called uing homer v4.10 with following settings: -style histone, -size 1000, -minDist 2500
Assembly: mm10
Supplementary files format and content: bigWig : read coverage file
Supplementary files format and content: bed : bed files with peak coordinates

source_name: ChIP-seq for H3 using gonocyte from Morc1 (-/-) mice at P3

extract_protocol:
Germ cells were fixed with 1% FA. Chromatin fraction was extracted after processing with sonication. Chromatin extract was served for immunoprecipitation with H3K9me3 antibody. DNA was purified from co-precipitaed fraction.
ChIP-seq library was prepared using QIAseq ultralow input library kit (QIAGEN), following manufacturer's instruction.

tag: antibody

value: MBL, #MABI0301


title: 1-1_I3_S7,HyperSeq, scRNASeq


title: H3_ChIP_P3_KO_rep1


title: 134215, 7, 1 Week, 100um, rat9, Right Hemisphere

tag: treatment


title: Control_rep1 ATAC-seq

tag: cell line


title: 134213, 6, 24 Hours, 100um, rat30, Right Hemisphere

value: 24 Hours


title: H3_ChIP_P3_het_rep2

source_name: ChIP-seq for H3 using gonocyte from Morc1 (+/-) mice at P3


title: shPHF19_rep2

data_processing:
Sequence was trimmed using Fastp v0.20 to remove adaptor and low quality reads
Trimmed reads were further mapping to hg38 genome using hisat2 v2.1.0
The read counts of each gene was quantified by HTseq v0.11.2
Assembly: hg38
Supplementary files format and content: Excel file includes differentially expressed gene list

extract_protocol:
Total RNA was isolated and purified from cultured cells using TRIzol reagent (Invitrogen #15596026) following the manufacturer's procedure.
KAPA Hyper Prep Kit (KAPA #KK8504) was used to generate the sequencing libraries following the manufacturer’s instructions.


title: 134214, 6c, 24 Hours, 500um, rat30, Right Hemisphere


title: shPHF19_rep3


title: H3_ChIP_P0_KO_rep2

source_name: ChIP-seq for H3 using gonocyte from Morc1 (-/-) mice at P0


title: SC243vsSC104_HA-Gsm1vsNotag_rds2delta_20180502_rep2

type: genomic

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

description: Biological replicate 2 of 2.  Gsm1-HA occupancy by ChIP-chip in rds2∆ cells. Gsm1-HA ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against no tag ChIP sample (Cy3-labeled).

hyb_protocol: standard protocol

scan_protocol: Microarrays were scanned using an InnoScan900 (Innopsys) at 2 µm resolution.

data_processing:
BED description: A genome browser-ready file for Gsm1-HA occupancy by ChIP-chip (Gsm1-HA/no tag) in rds2∆ cells.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)

organism: Saccharomyces cerevisiae

label_protocol: The ChIP samples were blunted as follow. 40 µL of ChIP DNA were added to 70 µL of blunting mix (11 µL 10X NEBuffer 2 (NEB, B7002S), 0.5 µL 10 mg/mL BSA, 0.5 µL 20 mM dNTPs and 0.2 µL (0.6 units) of T4 DNA polymerase (NEB, M0203L)) and incubated at 12˚C for 20 min. Then, the blunted DNA was extracted with phenol/chloroform/isoamyl alcohol (25:24:1) in the presence of 280 mM of NaOAc pH 5.2 and 10 μg of glycogen, precipitated with ethanol and resuspended in 25 µL ddH2O. Blunted DNA was ligated to 100 pmol of annealed linkers (see Table S2) with 2.5 units of T4 DNA ligase (Thermo Fisher Scientific, 15224041) in the supplied buffer, in a final volume of 50 µL, overnight at 16˚C. Samples were precipitated with 6 µL of 3 M NaOAc pH 5.2 and 130 µL ethanol, and resuspended in 25 µL ddH2O. 15 µL of labeling mix (4 µL 10X ThermoPol Reaction buffer (NEB, B9004S), 2 µL of 5 mM aa-dUTP/dNTP mix (5 mM each dATP, dGTP and dCTP, 3 mM dTTP and 2 mM 5-(3-aminoallyl)-dUTP (Thermo Fisher Scientific, AM8439)) and 1.25 µL of 40 µM oligo 1) were added to each sample. Samples were placed in a thermocycler and when temperature reached 55˚C, 10 µL of enzyme mix (1 µL 10X ThermoPol Reaction buffer, 1 µL (5 units) Taq DNA polymerase (Thermo Fisher Scientific, 18038240) and 0.01 µL (0.025 units) Pfu DNA polymerase (Thermo Fisher Scientific, EP0502)) were added and the following program was run. 1) 72˚C, 5 min; 2) 95˚C, 2 min; 3) 32 cycles: 95˚C, 30sec; 55˚C, 30sec; 72˚C, 1 min; 4) 72˚C, 4 min; 5) 4˚C, forever. PCR products were purified using QIAquick PCR Purification kit (QIAGEN, 28106) with few modifications: PE buffer was replaced by Phosphate wash buffer (5 mM KPO4 pH 8.5 and 80% ethanol) and EB buffer was replace by Phosphate elution buffer (4 mM KPO4 pH 8.5). Eluates were dried by SpeedVac and pellets were resuspended in 4.5 µL of freshly prepared 0.1 M Na2CO3 pH 9.0 buffer. 4.5 µL of Cy5 Mono-Reactive NHS Ester Fluorescent Dye (ChIP samples) or Cy3 Mono-Reactive NHS Ester Fluorescent Dye (control samples no-tag ChIP) (GE Healthcare, PA25001 and PA23001) were added. Samples were incubated 1 hr in the dark at room temperature. 35 µL of 0.1 M NaOAc pH 5.2 were added and samples were purified using QIAquick PCR Purification kit according to the manufacturers’ instructions.

growth_protocol: Strains were grown in YPD to an OD600 ≈0.7. Cells were washed twice in water, resuspended in YEP containing 2% ethanol, and grown for 3 h. The culture was poured in a 50mL Falcon tube containing 1.4mL 37% formaldehyde and incubated on a rotating wheel for 30 min. Crosslinking was stopped by adding 2.5mL 2.5M Glycine to quench formaldehyde (optional). Crosslinked cells were pelleted at 4'C, 3000 rpm, resuspended in 40mL ice-cold TBS and pelleted again. This wash was repeated a second time. Cell pellets were resuspended in the remaining liquid (~1mL) and transferred to 1.5mL screw cap tubes. Cells were pelleted by centrifugation, the supernatant removed by pipetting, and the cells pellet snap-freeze in liquid nitrogen and stored at -80'C.

extract_protocol: Cell pellets were resuspended in 400 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed using a vortex for 2 hrs at 4C. The lysate was then sonicated 30 cycles, 30 sec ON and 30 sec OFF at High settings (Diagenode Bioruptor). Soluble fragmented chromatin was recovered by centrifugation. 350 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 3.5 μL (1%) were saved as Input sample. 20 μL of Dynabeads coated with protein G pre-coupled with the indicated antibody were added to the chromatin sample and incubated overnight at 4°C. Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 200uL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 50°C for 1 hr and subsequently subjected to Proteinase K (5.5 μL 20% SDS, 7.5 μL 10 mg/mL Proteinase K) digestion at 50°C for 1 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 70 % EtOH. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

treatment_protocol: 2% ethanol for 3 h

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 rds2{delta}::KanMX [GSM1 tagged with three HA epitopes at the C-terminus]

value: anti-HA (F7 from Santa-Cruz; 15uL)


title: 134212, 5c, 24 Hours, 500um, rat30, Left Hemisphere


title: SC243vsSC104_HA-Gsm1vsNotag_rds2delta_20180502_rep1

description: Biological replicate 1 of 2.  Gsm1-HA occupancy by ChIP-chip in rds2∆ cells. Gsm1-HA ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against no tag ChIP sample (Cy3-labeled).

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 rds2{delta}::KanMX


title: SC242vsSC106_HA-Rds2vsNoTag_gsm1delta_20180502_rep2

description: Biological replicate 2 of 2.  HA-Rds2 occupancy by ChIP-chip in gsm1∆ cells. HA-Rds2 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against no tag ChIP sample (Cy3-labeled).

data_processing:
BED description: A genome browser-ready file for HA-Rds2 occupancy by ChIP-chip (HA-Rds2/no tag) in gsm1∆ cells.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 gsm1{delta}::KanMX [RDS2 tagged with three HA epitopes at the N-terminus]


title: H3_ChIP_P3_het_rep1


title: 134211, 5, 24 Hours, 100um, rat30, Left Hemisphere

value: Sprague-Dawley


title: H3_ChIP_P0_het_rep2

source_name: ChIP-seq for H3 using gonocyte from Morc1 (+/-) mice at P0


title: shPHF19_rep1


title: Control_rep2


title: 134210, 4c, 24 Hours, 500um, rat29, Right Hemisphere

source_name: Brain Tissue


title: SC242vsSC106_HA-Rds2vsNoTag_gsm1delta_20180502_rep1

description: Biological replicate 1 of 2.  HA-Rds2 occupancy by ChIP-chip in gsm1∆ cells. HA-Rds2 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against no tag ChIP sample (Cy3-labeled).

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 gsm1{delta}::KanMX


title: H3_ChIP_P0_het_rep1


title: SC175vsCS1_HA-Gsm1vsNoTag_WT_20180502_rep2

description: Biological replicate 2 of 2.  Gsm1-HA occupancy by ChIP-chip in WT cells. Gsm1-HA ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against no tag ChIP sample (Cy3-labeled).

data_processing:
BED description: A genome browser-ready file for Gsm1-HA occupancy by ChIP-chip (Gsm1-HA/no tag) in WT cells.
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 [GSM1 tagged with three HA epitopes at the C-terminus]


title: Control_rep3


title: Control_rep2 ATAC-seq


title: ChIP-seq_D12_JB_Input

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

institute: GReD CNRS

data_processing:
ChIP-seq were mapped on the mouse genome (mm39 masked  for JF1 SNPs)using Bowtie2 .
Alignments filtering was realized with samtools (view -q 20).
peaks were called using MACS1.4.2. (--nomodel --shiftsize 73 --pvalue 1e-5 ) and the coverage was computed using bamCoverage (--normalizeUsing RPKM --extendReads 200  --ignoreDuplicates  --binSize 20).
Assembly: mm39
Supplementary files format and content: bigWig

growth_protocol: ES cell lines were maintained in gelatin-coated dishes with ESGRO complete plus medium (Millipore, SF001-500P) containing LIF, BMP4, and a GSK3-β inhibitor. ES-derived neural precursor cells were generated using in vitro corticogenesis as described in Montibus et al 2021 (PMID: 32405722).

extract_protocol:
ChiP-seq experiments on native chromatin were performed on ESC and NPC for the JF1xB6 genetic backgrounds as previously in Le Boiteux et al., 2021 (PMID: 33720519).
Library preparation (TruSeq® ChIP Sample Preparation) and sequencing on a HiSeq 2500 instrument (Illumina) were performed by MGX, according to the manufacturer’s recommendations

value: ES-derived neural precursor cells

value: JF1 x C57BL/6

value: In vitro corticogenesis Day 12

tag: chip antibody


title: 134209, 4, 24 Hours, 100um rat29, Right Hemisphere

value: Brain Tissue

value: WT


title: H3_ChIP_E165_KO_rep2

source_name: ChIP-seq for H3 using gonocyte from Morc1 (-/-) mice at E16.5

value: testis


title: ChIP-seq_D12_JB_H3K4me2

value: H3K4me2 (abcam Ab32356)