title: mESC HiC rep1

city: Basel

first: Filippo

middle: M.

last: RIJLI

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
The Hi-C data was mapped and quality controlled with HiCUP  (version 0.6.1) {Wingett, 2015}, the interaction matrix was created with Juicer (version 1.6) {Durand, 2016}, and was transformed into a cool matrix {Abdennur, 2020} with hic2cool (https://github.com/4dn-dcic/hic2cool, version 0.8.3) and HiCExplorer’s hicConvertFormat (version 3.7.2) {Wolff, 2020}.
Assembly: mm10/ GRCm38
Supplementary files format and content: hic

source_name: mESCs

extract_protocol:
Dissected tissue from E10.5 and E12.5 embryos was kept in 1× PBS on ice, then treated with 0.5% trypsin/1× EDTA at 37 °C for 10 minutes and immediately put on ice. Dissected tissue from E14.5 embryos was kept in 1× PBS on ice, then treated with papain digestion mix (10 mg ml−1 papain, 2.5 mM cysteine, 10 mM HEPES (pH 7.4), 0.5 mM EDTA and 0.9× DMEM) for 7 min at 37 °C and immediately put on ice. The tissue was rinsed once in ice-cold 1× DMEM/10% FBS, followed by two washes in ice-cold 1× DMEM. Tissue was dissociated by pipetting. Dissociated cells were cross-linked with 2% paraformaldehyde for 10 min at room temperature (RT) and quenched with 125 mM glycine for 5 min at RT. Cells were spun down (1600 rpm, 10 minutes, 4 °C) and resuspended in cold 1× PBS. Cranial NCCs with genotype Wnt1::Cre;ROSARFP or Hoxa2EGFP were filtered and collected by FACS. Cells were spun down (1600 rpm, 10 minutes, 4°C), supernatant removed, and cell pellets were flesh-frozen and stored at -80°C.
The input material per Hi-C experiment was 1-2 × 106 cells. Cells were incubated in 500 µL ice-cold lysis buffer (10 mM Tris-HCl pH 8, 0.2% (vol/vol) NP-40, 10 mM NaCl,1× protease inhibitor cocktail (Roche)) for 30 min with periodical mixing, followed by centrifugation to pellet nuclei (760xg, 5 min., 4°C). Cell nuclei were resuspended in 179 µL ice-cold 1.25× NEBuffer 2, 5.5 µL of 10% SDS was added, and nuclei were incubated at 37°C, shaking at 950 rpm, for 1 hour. Then 37.5 µL of 10% Triton X-100 was added and cell nuclei incubated at 37°C, shaking at 950 rpm, for 1 hour. A 5 μL aliquot was taken as a control for undigested chromatin (stored at − 20 °C). For HindIII digestion 5 µL of HindIII enzyme (NEB, cat. no. R0104T) was added, incubated 6 hours at 37°C shaking at 950 rpm, followed by addition of another 5 µL of HindIII and overnight incubation at 37°C shaking at 950 rpm. A 5 μL aliquot was taken to test digestion efficiency (stored at − 20 °C). To fill in and biotinylate the restriction fragment overhangs 30 µL of biotinylation master mix (3 µL 10× NEBuffer 2, 1 µL H2O, 0.75 µL 10 mM dATP, 0.75 µL 10 mM dGTP, 0.75 µL 10 mM dTTP, 18.75 µL 0.4 mM biotin-14-dATP, and 5 µL 5U/μl Klenow (DNA polymerase I large fragment, NEB M0210L)) was added, incubated for 75 min at 37°C mixing regularly by pipetting, and then placed on ice. Next, 227 µL ligation master mix (50 µL 10× ligation buffer (NEB B0202), 5 µL 10 mg/mL BSA, 172 µL nuclease-free H2O) and 12.5 µL 1U/µL T4 DNA ligase (Invitrogen 15224-024) was added for overnight blunt end ligation in a water bath at 16°C. The next day ligated samples were incubated for a further 30 min at room temperature. The re-ligated chromatin products and test aliquots were de-cross-linked for at least 6 hours by adding 50 µL and 2.5 μL proteinase K (10 mg/mL), incubated at 65 °C. Afterwards, 6 µL or 0.5 μL of 10 mg/ml RNase A was added to the samples and test aliquots, respectively, and incubated for 60 min at 37 °C. Next, chromatin was precipitated by adding 1 volume of phenol:chloroform:isoamyl alcohol (25:24:1) (PC) to the samples and test aliquots, vigorously shaking them, followed by centrifugation at maximum speed of a table top centrifuge (~ 13,000 rpm) at room temperature for 5 min. The upper phase containing the chromatin was transferred to a new 15 mL tube. To reduce loss of DNA 1 mL of TLE buffer (10 mM Tris HCl (pH 8.0), 0.1 mM EDTA) was added to tube containing PC and residual chromatin, tube was vigorously mixed, followed by centrifugation at maximum speed of a table top centrifuge (~ 13,000 rpm) at room temperature for 5 min. The upper phase containing the chromatin was transferred to the 15 mL tube. One tenth volume of 3 M sodium acetate was added to the chromatin sample mixed by vortexing, followed by the addition of 3 volumes 100% ethanol and vortexing to mix. The samples were frozen at − 80 °C for at least 2h. The precipitated chromatin was isolated by centrifugation at maximum speed for 45 min at 4 °C. The chromatin pellet was washed twice with 2mL freshly prepared 70% ethanol and centrifuged at maximum speed for 15 min at 4 °C in between washes. Finally, the chromatin pellet was dried at room temperature and resuspended in 100 μL TLE buffer. To check the Hi-C library DNA, 1:50 dilution of the sample, and the undigested and digested controls were loaded on a 1.5% agarose gel. The DNA concentration of the Hi-C library was determined using Qubit™ dsDNA HS assay kit. 5 µg DNA was used for library preparation. The next steps were performed per 5 µg aliquot. The DNA was sonicated using Covaris S220 (peak incidence power: 175W; duty factor: 10%; cycles per burst: 200; time: 120s) in a volume of 130 µL in a Covaris microTUBE to obtain 100 – 1000 bp long DNA fragments. End repair, dATP-tailing and Adapter ligation was performed on beads. For this, 100 µL of Dynabeads™ MyOne™ Streptavidin T1 (Invitrogen) were washed twice with 400 µL Tween Buffer (TWB; 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween 20) and resuspended in 400 µL 2× binding buffer (2×BB; 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 2 M NaCl). The volume of the sonicated DNA was increased to 400 µL with TLE. DNA was mixed with washed beads (800 µL total volume) and incubated at RT for 45 min rotating at 5 rpm. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by a wash with 400 µL 1×BB, then with 100 µL 1×ligation buffer, and resuspended in 50 µL 1× ligation buffer. For end repair each aliquot was mixed on ice with 50 µL 2.5 mM dNTP mix (12.5 μL of 10 mM of each dNTP), 18 μL of T4 DNA Polymerase (NEB M0203), 18 μL of T4 PNK (NEB M0201), 3.7 μL of DNA polymerase I large fragment (Klenow; NEB M0210), and 360.1 μL of H2O, and then incubated at 20°C for 60 min. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by two washes with 500 µL 1×TWB, one wash with 500 µL 1×BB, one wash with 500 µL TLE and resuspended in 415 µL TLE. For dATP-tailing each aliquot was mixed with 50 µL 10× NEBuffer 2, 5 µL 10 mM dATG and 20 µL 5 U/µL Klenow exo-minus, and then incubated at 37°C for 30 min. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by two washes with 500 µL 1×TWB, one wash with 500 µL 1×BB, one wash with 200 µL 1× ligation buffer and resuspended in 100 µL 1× ligation buffer. For Hi-C 10 µL 15 µM TruSeq DNA Sgl index adapters (Illumina, Cat. No. 20016329) and 4 µL NEB T4 Ligase 400 U/mL (NEB, M0202) were added to each aliquot and incubated 2 h at room temperature. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by two washes with 500 µL 1×TWB, one wash with 500 µL 1× BB, one wash with 200 µL 1×BB, one wash with 100 µL 1× NEBuffer 2, one wash with 50 µL 1× NEBuffer 2 and resuspended in 50 µL 1× NEBuffer 2. For Hi-C library amplification a reaction master mix was prepared, reaction volume per PCR tube was 25 µL (PCHi-C: 5 µL 5× Herculase II reaction buffer (Agilent), 0.25 µL 100 mM dNTPs, 2 µL PE PCR primer 1.0 {Schoenfelder, 2018}, 2 µL PE PCR primer 2.0 {Schoenfelder, 2018}, 0.5 µL Polymerase (Herculase, Agilent), 2.5 µL Hi-C DNA on beads, 12.75 µL nuclease-free H2O; Hi-C: 12.5 µL KAPA HiFi HotStart ReadyMix (Roche), 2.5 µL Illumina primer mix (contained in KAPA HiFi HotStart Library Amplification Kit), 2.5 µL Hi-C DNA on beads, 7.5 µL nuclease-free H2O) and PCR was run under the following conditions: 30s at 98 °C; 6-7 cycles of: 10 s at 98 °C, 30 s at 65 °C, 30 s at 72 °C; 7 min at 72 °C. Post-amplification PCR reactions per sample were pooled and DNA was cleaned up using AMPure XP beads and eluted in nuclease-free H2O. Obtained DNA was used directly for Hi-C

value: mESCs

value: WT


title: mESC HiC rep2

status: Public on Apr 29 2023

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: genotype


title: 200s_I5

city: Huddinge

first: Ping

last: Chen

address: Alfred Nobels allé 8

department: Department of Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description: Mouse non-parenchymal single cells

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were de-multiplexed and converted into fastq format for each cell by using Illumina bcl2fastq with default setting.
Reads were aligned to human genome mm10 using the STAR aligner.
Uniquely aligned reads mapping to the RefSeq gene annotations were used for gene expression estimates at reads per kilobase transcript and million mapped reads (RPKMs) using rpkmforgenes.
Low quality cells were excluded from downstream analysis when they failed to meet the following criteria for retaining cells: 1) >= 50,000 sequence reads; 2) >= 20% of reads uniquely aligned to the genome; 3) >= 40% of these reads mapping to RefSeq annotated exons; 4) >= 1000 genes with RPKM >= 1; and 5) < 25% of mitochondrial gene expression. In addition, doublets detected by Scrublet were further removed.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each single cell.

molecule: total RNA

source_name: Mouse non-parenchymal single cells

growth_protocol: Not applicable

extract_protocol:
Not applicable
The reverse-transcribed cDNA from single cells was amplified followed by tagmentation and a standard index PCR. The single cell libraries were prepared according to Smart-seq2 protocol. The sequencing was performed on HISEQ 3000 (IIlumina).
Smart-seq2 single cell RNA-Seq

treatment_protocol: Not applicable

tag: tissue

value: Liver

tag: disease state


title: 200s_I7

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1071

city: Cardiff

first: Jimena

last: Monzón-Sandoval

address: Maindy Road

country: United Kingdom

institute: UK Dementia Research Institute at Cardiff University

data_processing:
The quality of the sequences was assessed using FastQC (version 0.11.8) and results summarized using MultiQC.
After removing adapters by TrimGalore (version 0.5.0) transcript abundances was quantified using Kallisto (version 0.46.0)
The reference index used include the all cDNA, ncRNA sequences from Ensembl (release 99, GRCh38) as well as the Array Control RNA spike sequences from Thermo Fisher. Sequences in scaffold chromosomes were removed and we kept only chromosomes 1-22, X and Y.
We removed cells with less than 25% of reads mapping to protein coding genes and retained cells with at least half a million reads. We further removed an outlier sample from 12 PCW. We filtered out lowly expressed genes, keeping only those with more the 5 counts in at least 1% of the cells. The filtered dataset consisted of 14673 protein coding genes across 358 cells.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: MGE_counts_gene_level.txt: estimated counts per gene in tab separated values
Supplementary files format and content: MGE_metadata_filtered.txt metadata in tab separated values

molecule: polyA RNA

organism: Homo sapiens

source_name: medial ganglionic eminence (MGE)

extract_protocol:
Human fetal tissue was collected from medical terminations of pregnancy with full donor consent, through the SWIFT human fetal tissue bank (http://www.biobankswales.org.uk/swift-research-tissue-bank), under UK Human Tissue Authority research license (No. 12457) held by Cardiff University and with ethical approval of the project from the Bro Taf local research ethics committee. Gestational age was estimated through ultrasound scan prior to the procedure in combination with measurement of fetal regions. MGE tissue was harvested from seven fetuses corresponds to approximately 10, 12-15  post conception weeks (PCW). MGEs were individually incubated at 37°C for 20 min in TrypLE Express containing Donase-α. Tissue was dissociated by trituration in 200 μl of DMEM/D to obtain a quasi-single-cell suspension. The cell concentration was calculated by manual counting and viability measured by Trypan Blue assay.
Single cells were captured according to the manufacturer's protocol on a C1 Single-Cell IFC microfluidic chip designed for 10- to 17-μm cells (Fluidigm, Inc). This captured one cell in each of up to 96 capture chambers. Capture efficiency and cell viability was determined by microscopy before cDNA amplification and library preparation using the SMART-Seq 46 v4 Ultra Low Input RNA kit chemistry (Clontech) and Nextera XT DNA Library Prep Index Kit (Illumina). Single cell sequencing was carried out on HiSeq 4000 Illumina platform with the following parameters: paired-end reads, read length 2 x 75bp and read depth of approximately 1 million reads per cell.

value: medial ganglionic eminence (MGE)

tag: group

tag: developmental stage_pcw

tag: batch

tag: sample id


title: 200s_I3

description: Mouse non-parenchymal single cells


title: 200s_I4

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1070


title: 200s_I22

description: Mouse non-parenchymal single cells


title: 200s_I21

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1069


title: MGE_B_10pcw_1068


title: 200s_I19

description: Mouse non-parenchymal single cells


title: 200s_I17

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1074


title: 200s_I20

description: Mouse non-parenchymal single cells


title: 200s_I18

description: Mouse non-parenchymal single cells


title: TY-3_2week, replicate 3, scRNAseq

city: New York City

first: Dan

last: Li

state: NY

department: HOPP

country: USA

institute: Memorial Sloan-Kettering Cancer Center

description:
10x Genomics
TY-3_2week

data_processing:
Reads obtained from the 10x Genomics scRNAseq platform were mapped to mouse genome (mm9) using the Cell Ranger package (10X Genomics). True cells are distinguished from empty droplets using scCB2 package (Ni et al., 2020). The levels of mitochondrial reads and numbers of unique molecular identifiers (UMIs) were similar among the samples, which indicates that there were no systematic biases in the libraries from mice with different genotypes. Cells were removed if they expressed fewer than 600 unique genes, less than 1,500 total counts, more than 50,000 total counts or greater than 20% mitochondrial reads. Genes detected in less than 10 cells and all mitochondrial genes were removed for subsequent analyses. Putative doublets were removed using the Doublet Detection package (Chi et al., 2020). The average gene detection in each cell type was similar among the samples. Combining samples in the entire cohort yielded a filtered count matrix of 48,926 cells by 19,854 genes, with a median of 6,944 counts and a median of 1,973 genes per cell and a median of 2,039 cells per sample. The count matrix was then normalized to CPM (counts per million), and log2(X+1) transformed for analysis of the combined dataset. The top 1000 highly variable genes were found using SCANPY (version 1.6.1) (Wolf et al., 2018). Principal Component Analysis (PCA) was performed on the 1,000 most variable genes with the top 50 principal components (PCs) retained with 29% variance explained.
To visualize single cells of the global atlas, we used UMAP projections (https://arxiv.org/abs/1802.03426). We then performed Leiden clustering (Traag et al., 2019). Marker genes for each cluster were found with scanpy.tl.rank_genes_groups. Cell types were determined using the SCSA package, an automatic tool, based on a score annotation model combining differentially expressed genes (DEGs) and confidence levels of cell markers from both known and user-defined information (Cao et al., 2020). Heat-map were performed for single cells based on log-normalized and scaled expression values of marker genes curated from literature or identified as highly differentially expressed.
Differentially expressed genes between different clusters were found using MAST package (Finak et al., 2015), which were shown in heat-map. The logFC of MAST output was used for the ranked gene list in GSEA analysis (Subramanian et al., 2005). The custom gene sets used in GSEA analysis are shown in Supplementary Table 2.
Assembly: mm9
Supplementary files format and content: Tab-separated values files and matrix files

source_name: prostate

extract_protocol:
Tmprss2-CreERT2, EYFP; Tmprss2-CreERT2, ETV4WT; Tmprss2-CreERT2, ETV4AAA; and Tmprss2-CreERT2, ETV4AAA; Trp53L/L mice were euthanized 2 weeks or 4 months after tamoxifen treatment (n=3 mice for each genotype and time point). After euthanasia, the prostates were dissected out and minced with scalpel, and then processed for 1h digestion with collagenase/hyaluronidase (#07912, STEMCELL Technologies) and 30min digestion with TrypLE (#12605010, Gibco). Live single prostate cells were sorted out by flow cytometry as DAPI-. For each mouse, 5,000 cells were directly processed with 10X genomics Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 according to manufacturer’s specifications. For each sample, 200 million reads were acquired on NovaSeq platform S4 flow cell.
Cells were directly processed with 10X genomics Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 according to manufacturer’s specifications. For each sample, 200 million reads were acquired on NovaSeq platform S4 flow cell.

value: prostate cells

value: prostate

tag: treatment

value: 2 week after tamoxifen

tag: strain

tag: age

value: 8-10 weeks old


title: MGE_B_15pcw_1067


title: 200s_I13

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1073


title: 200s_I12

description: Mouse non-parenchymal single cells


title: 200s_I10

description: Mouse non-parenchymal single cells


title: 200s_I1

description: Mouse non-parenchymal single cells


title: 200s_H9

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1064


title: MGE_B_15pcw_1063


title: 200s_H3

description: Mouse non-parenchymal single cells


title: 200s_I14

description: Mouse non-parenchymal single cells


title: 200s_H19

description: Mouse non-parenchymal single cells


title: TY-1_4months, replicate 1, scRNAseq

description:
10x Genomics
TY-1_4months

value: 4 months after tamoxifen

value: 6 months old


title: 200s_H5

description: Mouse non-parenchymal single cells


title: TY-3_4months, replicate 3, scRNAseq

description:
10x Genomics
TY-3_4months


title: 200s_I16

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1062


title: TY-1_2week, replicate 1, scRNAseq

description:
10x Genomics
TY-1_2week


title: 200s_H15

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1061


title: 200s_H12

description: Mouse non-parenchymal single cells


title: EWT-3_2week, replicate 3, scRNAseq

description:
10x Genomics
EWT-3_2week


title: 200s_H14

description: Mouse non-parenchymal single cells


title: EWT-3_4months, replicate 3, scRNAseq

description:
10x Genomics
EWT-3_4months


title: 200s_H16

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1060


title: MGE_B_15pcw_1065


title: TY-2_4months, replicate 2, scRNAseq

description:
10x Genomics
TY-2_4months


title: MGE_B_10pcw_1066


title: MGE_B_15pcw_1059


title: 200s_G8

description: Mouse non-parenchymal single cells


title: 200s_G7

description: Mouse non-parenchymal single cells


title: TY-2_2week, replicate 2, scRNAseq

description:
10x Genomics
TY-2_2week


title: EWT-2_4months, replicate 2, scRNAseq

description:
10x Genomics
EWT-2_4months


title: EWT-2_2week, replicate 2, scRNAseq

description:
10x Genomics
EWT-2_2week


title: MGE_B_10pcw_1058


title: 200s_G5

description: Mouse non-parenchymal single cells


title: 200s_G4

description: Mouse non-parenchymal single cells


title: 200s_G24

description: Mouse non-parenchymal single cells


title: EWT-1_4months, replicate 1, scRNAseq

description:
10x Genomics
EWT-1_4months


title: 200s_G2

description: Mouse non-parenchymal single cells


title: EWT-1_2week, replicate 1, scRNAseq

description:
10x Genomics
EWT-1_2week


title: 200s_G19

description: Mouse non-parenchymal single cells


title: 200s_G18

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1055


title: E4Ap53-3_4months, replicate 3, scRNAseq

description:
10x Genomics
E4Ap53-3_4months


title: 200s_H1

description: Mouse non-parenchymal single cells


title: 200s_G14

description: Mouse non-parenchymal single cells


title: 200s_G17

description: Mouse non-parenchymal single cells


title: 200s_G15

description: Mouse non-parenchymal single cells


title: 200s_G16

description: Mouse non-parenchymal single cells


title: 200s_G10

description: Mouse non-parenchymal single cells


title: E4Ap53-2_4months, replicate 2, scRNAseq

description:
10x Genomics
E4Ap53-2_4months


title: MGE_B_12pcw_1051


title: E4Ap53-2_2week, replicate 2, scRNAseq

description:
10x Genomics
E4Ap53-2_2week


title: E4Ap53-3_2week, replicate 3, scRNAseq

description:
10x Genomics
E4Ap53-3_2week


title: MGE_B_12pcw_1047


title: 200s_G1

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1053


title: 200s_G11

description: Mouse non-parenchymal single cells


title: 200s_F9

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1049


title: 200s_F8

description: Mouse non-parenchymal single cells


title: E4Ap53-1_4months, replicate 1, scRNAseq

description:
10x Genomics
E4Ap53-1_4months


title: MGE_B_12pcw_1057


title: MGE_B_12pcw_1045


title: 200s_F3

description: Mouse non-parenchymal single cells


title: 200s_F7

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1044


title: 200s_F21

description: Mouse non-parenchymal single cells


title: E4A-3_4months, replicate 3, scRNAseq

description:
10x Genomics
E4A-3_4months


title: 200s_F23

description: Mouse non-parenchymal single cells


title: 200s_F14

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1043


title: E4A-3_2week, replicate 3, scRNAseq

description:
10x Genomics
E4A-3_2week


title: 200s_F13

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1042


title: 200s_F12

description: Mouse non-parenchymal single cells


title: E4A-2_4months, replicate 2, scRNAseq

description:
10x Genomics
E4A-2_4months


title: MGE_B_12pcw_1041


title: 200s_F10

description: Mouse non-parenchymal single cells


title: 200s_E9

description: Mouse non-parenchymal single cells


title: 200s_E7

description: Mouse non-parenchymal single cells


title: 200s_E8

description: Mouse non-parenchymal single cells


title: E4A-1_4months, replicate 1, scRNAseq

description:
10x Genomics
E4A-1_4months


title: 200s_E5

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1039


title: E4A-2_2week, replicate 2, scRNAseq

description:
10x Genomics
E4A-2_2week


title: 200s_E4

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1040


title: MGE_B_12pcw_1038


title: E4A-1_2week, replicate 1, scRNAseq

description:
10x Genomics
E4A-1_2week


title: E4Ap53-1_2week, replicate 1, scRNAseq

description:
10x Genomics
E4Ap53-1_2week


title: 200s_E22

description: Mouse non-parenchymal single cells


title: 200s_E21

description: Mouse non-parenchymal single cells


title: 200s_E3

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1037


title: 200s_E14

description: Mouse non-parenchymal single cells


title: 200s_E16

description: Mouse non-parenchymal single cells


title: 200s_E19

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1036


title: MGE_B_12pcw_1035


title: 200s_E13

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1033


title: 200s_E12

description: Mouse non-parenchymal single cells


title: 200s_E10

description: Mouse non-parenchymal single cells


title: 200s_E11

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1034


title: 200s_D9

description: Mouse non-parenchymal single cells


title: 200s_D7

description: Mouse non-parenchymal single cells


title: 200s_E1

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1031


title: 200s_D21

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1030


title: 200s_D5

description: Mouse non-parenchymal single cells


title: 200s_D8

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1029


title: 200s_D20

description: Mouse non-parenchymal single cells


title: 200s_E17

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1027


title: Sample 26

city: Oviedo

first: Guillermo

middle: M

last: Albaiceta

address: Avenida de Roma s/n

country: Spain

institute: Instituto de Investigación Sanitaria del Principado de Asturias

library_source: transcriptomic

data_processing:
Basecalling was performed using the default Ion Torrent software
trimming was performed using the fastp software v0.20.1 and the parameters -f 3, -r, -M 15
Counts were calculated using the pseudoalignment tool salmon v1.4.0 with the default parameters for mapping-based quantification and the hg38 salmon partial index
Reads were loaded in R using the tximport library
Assembly: hg38
Supplementary files format and content: the csv file was generated based on the txi matrix imported in R.
Supplementary files format and content: Raw counts

source_name: blood sample

extract_protocol:
Venous blood samples were extracted in TEMPUS tubes (Thermo Fisher). After centrifugation, pellets were homogeneized in Trizol and total RNA was extracted by isopropanol precipitation.
Libraries were prepared using the Ion Ampliseq Trascriptome Human Gene Expression Kit (Ion Torrent)
Amplification of known human transcripts

value: blood

tag: cluster

tag: agent

value: steroid

tag: disease


title: Sample 25


title: 200s_D3

description: Mouse non-parenchymal single cells


title: 200s_D19

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1026


title: Sample 24


title: 200s_D2

description: Mouse non-parenchymal single cells


title: Sample 23


title: MGE_B_12pcw_1025


title: 200s_D17

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1028


title: MGE_B_12pcw_1032


title: Sample 22


title: Sample 21


title: MGE_B_12pcw_1024


title: Sample 27


title: MGE_B_12pcw_1023


title: 200s_D15

description: Mouse non-parenchymal single cells


title: 200s_D13

description: Mouse non-parenchymal single cells


title: 200s_D12

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1022


title: Sample 20


title: Sample 19


title: MGE_B_12pcw_1021


title: 200s_D1

description: Mouse non-parenchymal single cells


title: 200s_D10

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1020


title: 200s_C9

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1019


title: 200s_C8

description: Mouse non-parenchymal single cells


title: Sample 17


title: Sample 16


title: Sample 15


title: 200s_C7

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1017


title: Sample 14


title: 200s_C6

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1016


title: 200s_C5

description: Mouse non-parenchymal single cells


title: Sample 13


title: 200s_C3

description: Mouse non-parenchymal single cells


title: Sample 11


title: MGE_B_12pcw_1015


title: 200s_C24

description: Mouse non-parenchymal single cells


title: Sample 12


title: MGE_B_12pcw_1014


title: Sample 18


title: MGE_B_12pcw_1012


title: MGE_B_12pcw_1013


title: 200s_C20

description: Mouse non-parenchymal single cells


title: 200s_C23

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1011


title: Sample 9


title: Sample 10


title: Sample 8


title: MGE_B_12pcw_1010


title: 200s_C2

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1018


title: Sample 7


title: MGE_B_12pcw_1009


title: 200s_C18

description: Mouse non-parenchymal single cells


title: Sample 6


title: Sample 5


title: MGE_B_12pcw_1008


title: MGE_B_12pcw_1007


title: 200s_C16

description: Mouse non-parenchymal single cells


title: Sample 4


title: MGE_B_12pcw_1006


title: Sample 3


title: 200s_C15

description: Mouse non-parenchymal single cells


title: 200s_C14

description: Mouse non-parenchymal single cells


title: 200s_C21

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1004


title: 200s_C12

description: Mouse non-parenchymal single cells


title: Sample 1


title: MGE_B_12pcw_1003


title: MGE_B_12pcw_1002


title: 200s_C11

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1001


title: 200s_C10

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_1000


title: 200s_C1

description: Mouse non-parenchymal single cells


title: 200s_C17

description: Mouse non-parenchymal single cells


title: 200s_B8

description: Mouse non-parenchymal single cells


title: 200s_B7

description: Mouse non-parenchymal single cells


title: arrayCGH data from patient 1446

type: genomic

city: Utrecht

first: Rico

last: Hagelaar

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

hyb_protocol: The hybridization mixtures were denatured at 95°C for 3 minutes, preincubated at 37°C for 30 minutes, and hybridized to the array in a microarray hybridization chamber (Agilent Technologies) for 14 to 18 hours at 65°C in a rotating oven (Robbins Scientific, Mountain View, CA). The array slides were washed in 0.5x SSC/0.005% Triton X-102 at room temperature for 5 minutes, followed by 5 minutes at 37°C in 0.1x SSC/0.005% Triton X-102.

scan_protocol: TIF images were obtained using Agilent scanner (model B and C)

data_processing: Images were analyzed using Cytogenomics v.50.0.38 software with the default analysis method: CGH v2 (ADM-2 algortihm). Threshold of 6.0, with a minimum of 3 consecutive aberrant probes and a minimum absolute amplification/deletion average of 0.25 log2ratio

source_name: pediatric patient samples

label_protocol: Labeling reactions with Cy5-dUTP and Cy3-dUTP (PerkinElmer, Wellesley, MA) were performed with 5 μg purified restricted DNA using the Bioprime labeling kit (Invitrogen, Paisley, United Kingdom) according to the manufacturer's instructions. Experimental and reference targets for each hybridization were pooled and mixed with 50 μg human Cot-1 DNA (Invitrogen), 100 μg yeast tRNA (Invitrogen), and 1x hybridization control targets (SP310; Operon Technologies, Alameda, CA) in a final volume of 500 μL in situ hybridization buffer (Agilent Technologies).

extract_protocol: 10 μg genomic reference or patient DNA was digested with AluI (20 U) and RsaI (20 U) (Invitrogen) overnight at 37°C. Patient genomic DNA (2 μg) and male/female reference DNA (2 μg; Promega) were fragmented by sonification (VibraCell Model VC130; Sonics & Materials, Newtown, CT). DNA fragmentation was verified by agarose gel electrophoresis. Individual reference and experimental samples were then purified using the QIAQuick polymerase chain reaction (PCR) clean-up kit (Qiagen, Valencia, CA).

tag: subject

value: patient 1446

value: control


title: 200s_B23

description: Mouse non-parenchymal single cells


title: NSC, AMFR KO, B2

city: Rotterdam

first: Tahsin Stefan

last: Barakat

state: South Holland

address: Dr. Molewaterplein 40

department: Clinical Genetics

institute: The Erasmus University Medical Center

data_processing:
RNA-seq reads were trimmed by Trim Galore! (version 0.6.6)
Trimmed reads were aligned to the GRCh38 genome assembly using STAR (version 2.7.7)
Technical replicates bam files were merged as one biological sample by samtools merge (version 1.9)
Count table were generated by featureCount (version 2.0.1)
bigwig files were  were converted to bigwig format using bamCoverage (-bs 10 –normalizeUsing RPKM) via deepTools (version 3.4.3)
Assembly: GRCh38
Supplementary files format and content: raw counts, bigwig

source_name: H9 human embryonic stem cells

growth_protocol: Human embryonic stem cells were maintained on feeder free conditions in mTeSR1 medium (STEMCELL technologies) on Matrigel (Corning) coated culture dishes, as previously described (Barakat et al Cell Stem Cell 2019, PMID: 30033119). For NSC differentiation, modified dual SMAD inhibition protocol was used, as described previously (Perenthaler et al Acta Neuropathologica 2020, PMID: 31820119) and in our accompanying publication on AMFR

extract_protocol:
RNA was isolated using TRI reagent (Invitrogen) following manufacturer’s instructions from six-wells. Obtained RNA was purified using column purification (Qiagen, #74204)
Libraries were prepared with the Illumina TruSeq Stranded mRNA Library Prep Kit. The resulting libraries were sequenced according to the Illumina TruSeq Rapid  v2 protocol on an Illumina HiSeq2500 sequencer.

value: AMFR knock-out

tag: cell line

value: H9 human embryonic stem cells

value: Neural Stem Cells


title: 200s_B22

description: Mouse non-parenchymal single cells


title: Sample 2


title: MGE_B_12pcw_1005


title: NSC, AMFR KO, B1


title: NSC, AMFR WT, B2

value: Wild type


title: 200s_B19

description: Mouse non-parenchymal single cells


title: NSC, AMFR WT, B1


title: 200s_B15

description: Mouse non-parenchymal single cells


title: 200s_B13

description: Mouse non-parenchymal single cells


title: 200s_B17

description: Mouse non-parenchymal single cells


title: 200s_B12

description: Mouse non-parenchymal single cells


title: 200s_B11

description: Mouse non-parenchymal single cells


title: 200s_A5

description: Mouse non-parenchymal single cells


title: 200s_A8

description: Mouse non-parenchymal single cells


title: 200s_B5

description: Mouse non-parenchymal single cells


title: 200s_B3

description: Mouse non-parenchymal single cells


title: 200s_A3

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_LigNull_Act_4h_r3

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

country: Australia

institute: SAiGENCI

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing samples generated by Illumina HiSeq sequencing. Illumina RTA 3.4.4 and bcl2fastq2 v2.20 was used for basecalling and demultiplexing samples generated by Illumina NovaSeq sequencing. RNA-seq reads were mapped to mm10 using STAR aligner (Dobin et al, Bioinformatics 2013).
Assembly: mm10
Supplementary files format and content: Alignments overlapping the exon of a gene (gene annotation from the GENCODE release M25) were counted using the featureCounts function from the Rsubread Bioconductor package by gene_name (Liao et al, Nucleic Acids Research, 2019) with default parameters. Only protein coding genes were retained and excluding predicted genes (beginning Gm#####).  Count matrixes were generated and TMM-normalized by the DGEList and calcNormFactors functions from the edgeR (Robinson et al, Bioinformatics, 2010), and finally, counts per million (CPM) were generated using the cpm function from edgeR and adding a pseudocount of 8 and log2 transforming the data.

source_name: embryonic stem cells

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma).

extract_protocol:
RNA for RNA-seq was isolated using Direct-zol RNA Purification Kit (Zymo), following the manufacturer’s instructions.
Sequencing libraries were prepared from 100ng of purified total RNA for biological replicates using TruSeq stranded Total RNA Library Prep (Illumina).

treatment_protocol: Cells (0.25x10^6) were seeded into 6-well plates the day before the experiment. Doxorubicin (1uM) or dTAG13 (500nM) compound were added to specific samples to activate p53 or degrade degron tagged alleles.

value: embryonic stem cells

value: degron-tagged Trim24

tag: treatment condition

value: activated p53 - 4 hours


title: RNAseq_ESC_LigNull_Act_4h_r4

tag: cell type


title: RNAseq_ESC_LigNull_Act_4h_r2

tag: genotype


title: NSC, AMFR KO, B3


title: 200s_A22

description: Mouse non-parenchymal single cells

tag: tissue

value: Liver


title: 200s_A21

description: Mouse non-parenchymal single cells

tag: disease state


title: RNAseq_ESC_dTrim24_DegrAct_4h_r7

value: degraded Trim24; activated p53 - 4 hours


title: RNAseq_ESC_dTrim24_DegrAct_4h_r6


title: 200s_A16

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_DegrAct_4h_r5


title: RNAseq_ESC_dTrim24_DegrAct_4h_r4


title: 200s_A17

description: Mouse non-parenchymal single cells


title: 200s_A2

description: Mouse non-parenchymal single cells


title: 200s_A14

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_Act_4h_r6


title: 6

type: RNA

city: Fuzhou

first: LH

last: Xie

address: 282hao,Wusi Road ,Gulou distract

country: China

institute: Fujian Academy of Traditional Chinese Medicine

hyb_protocol: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Agilent Microarray Scanner (Agilent p/n G2565BA),Scan region Scan Area (61 x 21.6 mm),Scan resolution:5μm,scanning mode Single Pass.Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing:
Add the images (.tif) to be extracted to the Agilent Feature Extraction (FE) software Project. Select Project > Start Extracting and export data to txt.Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1, and low intensity genes were filtered (Genes that at least 5 out of 15 samples have flags in Detected were chosen for further analysis).
To identify differentially expressed genes, we performed a Volcano Plot filtering between the two compared samples from the experiment. The threshold is Fold Change >= 2, P-value <= 0.05.

source_name: human bone

label_protocol: if the yield is <1.65μg and the specific activity is <9.0 pmol Cy3 or Cy5 per μg cRNA do not proceed to the hybridization step. Repeat cRNA preparation.

extract_protocol: the femur (1g) was collected from each patient during hip arthroplasty and stored in liquid nitrogen as soon as possible.The femur stored in liquid nitrogen was ground into a powder and add 1ml Trizol lysate.

tag: subjet status

value: postmenopausal osteoporosis

tag: Sex

value: Female

value: femur


title: 22


title: 21


title: 18


title: RNAseq_ESC_LigNull_Act_4h_r1


title: 25


title: 200s_A13

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_Act_4h_r5


title: 16


title: 14


title: 17


title: RNAseq_ESC_dTrim24_Act_4h_r4


title: RNAseq_ESC_dTrim24_Act_4h_r7


title: 200s_A15

description: Mouse non-parenchymal single cells


title: Male 3 weeks 01

status: Public on Apr 28 2023

city: Tallahassee

first: Mohamed

last: Kabbaj

state: Florida

address: 1115 W Call St

department: Biomedical Sciences

institute: Florida State University

data_processing:
Basecalling and demultiplexing was done using Illumina bcl2fastq2 v2.20.0.422
Raw reads were first processed for quality filtering and adapter trimming with fastp (v0.14.1) with adapter trimming, base correction (-p option), and polyX tail trimming (-x option). The final quality of reads was then verified using FastQC (v0.11.7).
Filtered reads were then pseudo-aligned and quantified using Salmon (v0.12) with -g, --numBootstraps 500, --validateMappings, --rangeFactorizationBins 4, --seqBias, and --gcBias parameters.
Genome_build: MicOch1.0 Ensembl Release 93 + GenBank #AF069304.2
Supplementary_files_format_and_content: Matrix of normalized counts for each gene in each sample as computed by DESeq2 (tab-delimited txt file).

organism: Microtus ochrogaster

source_name: Nucleus accumbens

extract_protocol:
Brains were dissected out, flash frozen, and stored at -80C until sectioning on a cryostat at -20C for tissue-punching of the nucleus accumbens. Total RNA was then extracted using TRI-Reagent according to the manufacturer's protocol (Molecular Research Center, #TR 118), followed by DNAse I treatment to remove any eventual DNA contamination and clean-up (RNA Clean & Concentrator, Zymo Research, Irvine, CA, USA) .
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina with poly(A) mRNA purification from 300 ng of total RNA based on magnetic beads, cDNA synthesis using random hexamers, and final amplification using barcoded primers following the manufacturer’s protocol (#E7530, New England Biolabs, Ipswich, MA, USA). In order to determine the lower limit of detection and verify the linearity of quantification during the statistical analysis of the sequencing data, synthetic RNA Spike-Ins (#4456739, ERCC ExFold RNA Spike-In Mixes, Life technologies, Carlsbad, CA) were added to each sample prior to poly(A) mRNA purification following the recommended dilutions (6 µL of a 1:1000 dilution). Of note, Mix 1 and Mix 2 of the ERCC ExFold RNA Spike-Ins were equally distributed among samples in an exclusive manner. The resulting barcoded and unstranded libraries were quantified using a KAPA qPCR library quantification kit (KAPA Biosystems, Boston, MA, USA) with three serial dilutions ran in duplicates on a CFX384 real-time PCR instrument (Bio-Rad). Finally, the absence of adapters or primers contamination was verified on a Bioanalyzer using a DNA High Sensitivity chip (Agilent Technologies, Santa Clara, CA, USA).

value: male


title: Male 3 weeks 05


title: Male 3 weeks 02


title: Male 3 weeks 04


title: Male 3 weeks 03


title: 10


title: Male 24hrs 06


title: 200s_A12

description: Mouse non-parenchymal single cells


title: 23


title: 7


title: 5


title: Male 24hrs 02


title: Male Sexually-Naïve 05


title: Male Sexually-Naïve 04


title: Male Sexually-Naïve 03


title: Male 24hrs 01


title: 9

value: healthy postmenopausal women; control group


title: Male 24hrs 04


title: Male Sexually-Naïve 06


title: Male 24hrs 05


title: 8


title: Female 3 weeks 09

value: female


title: Male Sexually-Naïve 01


title: Male Sexually-Naïve 02


title: Female 3 weeks 08


title: 11


title: Female 3 weeks 07


title: Female 3 weeks 06


title: Female 3 weeks 05


title: Female 3 weeks 03


title: Female 3 weeks 02


title: Female 24hrs 10


title: Male 24hrs 03


title: Female 3 weeks 01


title: Female 24hrs 09


title: Female 24hrs 08


title: Female 24hrs 04


title: Female 24hrs 05


title: Female 24hrs 01


title: Female 24hrs 02


title: Female 24hrs 06


title: Female 24hrs 03


title: Female Sexually-Naïve 06


title: Female 24hrs 07


title: Female Sexually-Naïve 03


title: Female Sexually-Naïve 07


title: Female Sexually-Naïve 04


title: Female Sexually-Naïve 08


title: Female Sexually-Naïve 05


title: Female Sexually-Naïve 10


title: Female Sexually-Naïve 09


title: Female Sexually-Naïve 02


title: 200s_A1

description: Mouse non-parenchymal single cells


title: Female 3 weeks 04


title: Input_2

city: London

first: Athanasia

last: Stathopoulou

address: 30 Guilford Street

institute: University College London

data_processing:
Data were UDI demultiplexed using BCL Convert (v03.75) before pre-processing with fastp (v0.20.1) to remove Illumina adapter, polyG+ sequences and trim low-quality bases. Processed reads were aligned to the mouse genome (UCSC mm10) with bwa (v 0.7.17.4) before being UMI deduplicated with JE-Suite (v1.2.1). Peaks were called by MACS2 (v2.1.2) for each sample with IgG as controls and overlapping peaks in at least two replicates were used as the final peaks.
Deeptools (v3.1.0) was used to compute read coverage across the peaks and generate heatmap for comparing the coverage across samples.
Assembly: UCSC mm10
Supplementary files format and content: tab-delimited text files including peak Chd7 co-ordinates
Library strategy: CUT&RUN-seq

source_name: Cardiac Progenitor cells

extract_protocol:
CUT&RUN was performed using 0.5x10^6 cells with the CUT&RUN assay kit (CST, 86652), according to the manufacturer’s protocol. DNA fragments were purified using DNA Purification kit (CST, 14209).
Library preparation was performed with the NEB DNA Ultra II assay

value: Cardiac Progenitor cells

value: WT

tag: cut&run antibody


title: IgG_3


title: IgG_2


title: Input_1


title: CHD7_2


title: Input_3


title: CHD7_3


title: CHD7_1


title: IgG_1


title: JM8, IgG, mitosis, rep1

city: Vancouver

first: Sheila

last: Teves

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry

country: Canada

institute: Life Science Institute

description: JM8-M-IgG-biol rep1

data_processing:
library strategy: CUT&Tag
Quality Assurance was done using FastQC to check metrics
CUT&Tag reads were aligned to the mouse mm10 or fly dm6 genome using bowtie2 with parameters: --no-unal –local –very-sensitive-local –no-discordant –no-mixed –contain –overlap –dovetail –phred33 -I 10 -X 9999 with PCR duplicates being kept
bigwig generation was done using the D.melanogaster normalization factor determined from Bowtie2 mapping of dm6
Heatmaps, IGV tracks, and other downstream analysis were generated from bigwig files using Deeptools/ComputeMatrix
Read counts were generated using multiBigwigSummary
Peak calling was performing uising SECAR v1.3 software using --stringent and --non options
Called beaks were merged for peaks present in both biol. replicates using bedtools intersect -wa option
Assembly: mm10 and dm6
Supplementary files format and content: bigWig, peaks coordinates as bed files (except IgG, HA-tag), readcounts as .tab file

growth_protocol: Cells were cultured on gelatin-coated plates in ESC media (Knockout DMEM, 15% FBS, 0.1mM MEM non essential amino acids, 2mM GlutaMAX, 0.1mM 2-mercaptoethanol and 1000 units/ml of ESGRO. ES cells are fed daily, cultured at 37C in a 5% CO2 incubator and passaged every two days via trypsinization.)

extract_protocol:
Extract protocol was done following the CUT&Tag published protocol where cells and DNA were sheared using 10uL 0.5M EDTA, 3uL 10% SDS, 2.5uL 20mg/mL Proteinase followed by phenol chloroform isoamyl extracted
Librarires were prepared following the CUT&Tag protocol. Briefly 21uL(out of 30uL) was used with 2uL Universal i5 primer (10uM) +2uL uniquely barcoded i7 primers (10uM) using a different unique barcode for each sample. 25UL of NEBNext HiFi 2x PCR Master mix (NEB M0541L) was used for the PCR reaction following the PCR protocol for CUT&Tag using 12 cycles. Library was cleaned up using Ampure XP beads using 1.1x volume and samples were pooled by volume and bead cleaned again before sequencing

treatment_protocol: mESCs were treated with 50 ng/mL nocodazole (Sigma) at 37 °C in a 5% CO2 incubator for 6 hours. After nocodazole removal, cells were washed with 1X PBS and mitotic cells were collected via shake-off.

value: embryonic stem cell

tag: antibody

value: IgG, Antibodies-Online

value: 50 ng/ml Nocodazole for 6h


title: JM8, IgG, mitosis, rep2

description: JM8-M-IgG-biol rep2

tag: treatment


title: JM8, HA ctrl, asynchronous, rep2

value: HA-tag, Epicypher


title: Female Sexually-Naïve 01


title: JM8, IgG, asynchronous, rep1

description: JM8-A-IgG-biol rep1


title: JM8, HSF2 KO, asynchronous, rep2

source_name: Jm8, HSF2 KO

value: Jm8, HSF2 KO


title: JM8, HSF2 KO, asynchronous, rep1


title: JM8, HSF2, asynchronous, 5% WT cells, rep2

description:
JM8-H2-peaks.bed
JM8-A-5%Wt_rep2


title: JM8, HSF2, asynchronous, 5% WT cells, rep1

description:
JM8-H2-peaks.bed
JM8-A-5%Wt_rep1


title: JM8, HSF2 KO, mitosis, rep2


title: JM8, HSF2 KO, mitosis, rep1


title: JM8, HSF2, asynchronous, 10% WT cells, rep1

description:
JM8-H2-peaks.bed
JM8-A-10%Wt_rep1


title: JM8, HSF2 DBD, HA tag, asynchronous, rep2

description:
JM8-H2-peaks.bed
HSF2-mean-scores.tab
JM8-A-HA-DBD_HSF2_rep2


title: JM8, HSF2 DBD, HA tag, mitosis, rep1

description:
JM8-H2-peaks.bed
HSF2-mean-scores.tab
JM8-M-HA-DBD_HSF2_rep1


title: JM8, HSF2 DBD, HA tag, mitosis, rep2

description:
JM8-H2-peaks.bed
HSF2-mean-scores.tab
JM8-M-HA-DBD_HSF2_rep2


title: JM8, HSF2 DBD, HA tag, asynchronous, rep1

description:
JM8-H2-peaks.bed
HSF2-mean-scores.tab
JM8-A-HA-DBD_HSF2_rep1


title: JM8, HSF2 Full_Length, HA tag, mitosis, rep1

description:
JM8-H2-peaks.bed
HSF2-mean-scores.tab
JM8-M-HA-FullLenght_HSF2_rep1


title: JM8, IgG, asynchronous, rep2

description: JM8-A-IgG-biol rep2


title: JM8, HA ctrl, asynchronous, rep1


title: JM8, HSF2 Full_Length, HA tag, asynchronous, rep1

description:
JM8-H2-peaks.bed
HSF2-mean-scores.tab
JM8-A-HA-FullLength_HSF2_rep1


title: JM8, HSF2-OE, mitosis, rep1

description:
JM8-H2-peaks.bed
HSF2-mean-scores.tab
JM8-M-HSF2-OE-in_KO_rep1


title: JM8, Sox2, mitosis, rep2

description:
SOX2_peaks_mm10.bed
JM8-Sox2-scores.tab
JM8-M-Sox2-biol rep2

value: Sox2, ActiveMotif


title: JM8, HSF2-OE, asynchronous, rep1

description:
JM8-H2-peaks.bed
HSF2-mean-scores.tab
JM8-A-HSF2-OE-in_KO_rep1


title: JM8, HSF2-OE, asynchronous, rep2

description:
JM8-H2-peaks.bed
HSF2-mean-scores.tab
JM8-A-HSF2-OE-in_KO_rep2


title: JM8, HSF2, mitosis, rep1

description:
JM8-H2-peaks.bed
HSF2-mean-scores.tab
JM8-M-H2-biol rep1


title: JM8, Sox2, mitosis, rep1

description:
SOX2_peaks_mm10.bed
JM8-Sox2-scores.tab
JM8-M-Sox2-biol rep1


title: JM8, HSF2 Full_Length, HA_tag, asynchronous, rep2

description:
JM8-H2-peaks.bed
HSF2-mean-scores.tab
JM8-A-HA-FullLength_HSF2_rep2


title: JM8, Sox2, asynchronous, rep1

description:
SOX2_peaks_mm10.bed
JM8-Sox2-scores.tab
JM8-A-Sox2-biol rep1


title: JM8, HSF2, mitosis, rep2

description:
JM8-H2-peaks.bed
HSF2-mean-scores.tab
JM8-M-H2-biol rep2


title: JM8, HSF2, asynchronous, rep2

description:
JM8-H2-peaks.bed
HSF2-mean-scores.tab
JM8-A-H2-biol rep2


title: JM8, HSF2, asynchronous, 10% WT cells, rep2

description:
JM8-H2-peaks.bed
JM8-A-10%Wt_rep2


title: JM8, HSF1, mitosis, rep2

description:
JM8-H1_peaks.bed
JM8-H1-scores.tab
JM8-M-H1-biol rep2

value: HSF1, ENZO


title: JM8, HSF1, asynchronous, rep1

description:
JM8-H1_peaks.bed
JM8-H1-scores.tab
JM8-A-H1-biol rep1


title: JM8, HSF1, asynchronous, rep2

description:
JM8-H1_peaks.bed
JM8-H1-scores.tab
JM8-A-H1-biol rep2


title: JM8, HSF1, mitosis, rep1

description:
JM8-H1_peaks.bed
JM8-H1-scores.tab
JM8-M-H1-biol rep1


title: JM8, HSF2 Full_Length, HA tag, mitosis, rep2

description:
JM8-H2-peaks.bed
HSF2-mean-scores.tab
JM8-M-HA-FullLength_HSF2_rep2


title: Pristina leidyi, whole-body, scRNA-seq, batch 3, library 30

city: Exeter

first: Jordi

last: Solana

address: Northcote House

department: Health and Life Sciences

institute: University of Exeter

description: SPLiT-seq

data_processing:
Barcode processing and adapter trimming were made using SPLiT-seq toolbox (https://github.com/RebekkaWegmann/splitseq_toolbox), CutAdapt  v2.8 (https://github.com/marcelm/cutadapt), pairfq makepairs (https://github.com/sestaton/Pairfq) and Picard v2.21.1-SNAPSHOT (https://github.com/broadinstitute/picard)
Transcriptome mapping was made with STAR-2.7.3a (https://github.com/alexdobin/STAR/releases/tag/2.7.3a)
Pristina.fasta is the "flattened" (i.e. headers tidied, shorter transcript forms removed) transcriptome that was used for SPLiTseq analysis.
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Consensus fasta file transcriptome after processing with EvidentialGene (https://www.biorxiv.org/content/10.1101/829184v1)
Supplementary files format and content: hq_transcripts.fasta: raw fasta output by the PacBio CCS processing pipeline https://github.com/ben-lerch/IsoSeq-3.0/blob/master/README.md#output-files
Supplementary files format and content: Transcriptome reads obtained from the Isoseq3 pipeline were combined with a previously published transcriptome (https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-13-287)

organism: Pristina leidyi

source_name: Whole-body

extract_protocol:
We used ACME dissociation to dissociate whole animals into fixed and permeable cell suspensions. Dissociated cells were proccessed using a SPLiT-seq protocol (we sorted singlets by FACS during SPLiT-seq, right before the cell lysis step).
We followed the SPLiT-seq library construction pipeline (Dynabeads cDNA purification, template switching, PCR amplification, size selection, tagmentation, indexed-PCR amplification and second size selection). Size selection was performed using Roche KAPA Pure Beads at 0.6X-0.8X ratios. Tagmentation was performed using the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer´s instructions.

value: Whole-body


title: VR_SD21_3

city: Brookings

first: Anne

middle: Y

last: Fennell

state: South Dakota

address: North Campus Drive

department: Department of Plant Science

institute: South Dakota State University

data_processing:
Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.3).
Filtered adaptor and poor quality sequences respectively, using cutadapt (v. 1.8.1) and prinseq-lite (v 0.20.4).
The reference genome based alignment and assembly of clean reads were performed using tuxedo pipeline (Trapnell et al., 2012). The Vitis vinifera reference genome (Genome12X, V1) was indexed using Bowtie2 (v.2.2.4).
Quality reads were aligned using tophat (v2.0.13) to the indexed reference genome and guided using gene model available for V. vinifera (V1.phase.gff3).
Mapped reads in each library were assembled into transcripts using cufflinks (v. 2.2.1).
Genome_build: V. vinifera reference genome (Genome12X, V1 ).
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

organism: Vitis riparia

source_name: Shoot tip

growth_protocol: Potted, spur-pruned six-year-old V. riparia ecodormant grapevines were removed from cold storage, repotted and grown under a long photoperiod (LD, 15 h) with 25/20°C + 3°C day/night temperatures and 600 to 1400 μmolm-2s-1 photosynthetic photon flux (PPF) in a climate-controlled, un-shaded glass greenhouse (En Tech Control Systems Inc., Montrose, MN) in Brookings, SD, USA (44.3°N).

extract_protocol:
Total RNA was extracted from shoot tips using the Qiagen RNeasy Midi RNA isolation kit according to manufacture protocol and as described by Mathiason et al 54, DNAased and stored at -80°C. DNA was removed by incubation with 1 unit per microgram (μg) RNase-free DNase (Promega, Madison WI) at 37°C for 30 min. RNA was purified using RNeasy plant mini columns (Qiagen, Valencia CA). RNA quality and quantity were verified with an Agilent (Santa Clara, CA) 243 Bioanalyzer RNA 6000 nano chip.
RNA seq libraries for LD and SD shoot transcriptome at 7 and 21 days were prepared and sequenced by Illumina HiScanSQ (43bp, single strand) at the Cornell University, Institute of Biotechnology Genome Facility (Ithaca, NY, USA).

treatment_protocol: After 30 days, when grapevines reached 12-15 nodes, pots were randomized into two treatment groups. Five days after randomization, differential photoperiod treatments began with one treatment group continuing in LD and the other receiving a short photoperiod (SD, 13 h). The SD was imposed using an automated, white covered black-out system (Van Rijn Enterprises LTD, Grassie, Ontario, Canada). At 7 and 21 days of differential photoperiod treatment, four node shoot tips were collected between 8:30 and 10:30 AM, immediately frozen in liquid nitrogen, and placed at -80°C for future RNA extraction. Three replications (5 vines/replicate) were harvested.

value: shoot tip

value: Short day

tag: days of treatment

value: 21 day of SD photoperiod

value: V. riparia PI588259


title: VR_SD21_2


title: VR_SD21_1


title: VR_LD21_1

value: Long day

value: Continued LD photoperiod


title: VR_LD21_3


title: VR_LD21_2


title: JM8, HSF2-OE, mitosis, rep2

description:
JM8-H2-peaks.bed
HSF2-mean-scores.tab
JM8-M-HSF2-OE-in_KO_rep2


title: Pristina leidyi, whole-body, scRNA-seq, batch 2, library 21

description: SPLiT-seq


title: JM8, Sox2, asynchronous, rep2

description:
SOX2_peaks_mm10.bed
JM8-Sox2-scores.tab
JM8-A-Sox2-biol rep2


title: VR_SD7_3

value: 7 day of SD photoperiod


title: JM8, HSF2, asynchronous, rep1

description:
JM8-H2-peaks.bed
HSF2-mean-scores.tab
JM8-A-H2-biol rep1


title: VR_SD7_2


title: VR_LD7_2


title: VR_SD7_1


title: acomys DM

city: UTRECHT

first: PHILIP

last: LIJNZAAD

state: Utrecht

address: HEIDELBERGLAAN 25

department: Single Cell Facility

institute: Princess Maxima Center for Pediatric Oncology

data_processing:
10x genomics cellranger version 6.1.1  was used for all the analysis steps from fastq.gz to count tables
Assembly: For the mouse samples, the 10x genomics genome refdata-gex-mm10-2020-A (which is Mus musculus, GRCm38, patchlevel 6 and gencode version M23). For the Acomys samples, a custom genome was used.
Supplementary files format and content: 10x genomics cellranger 6.1.1 hdf5 file. For details see https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices

organism: Acomys cahirinus

source_name: ear pinna skin

extract_protocol:
Tissue was dissociated into single cell suspension using Protease from B. Licheniformis and Dounce homogenizer. Red blood cells were removed with RBC lysis buffer. Centrifugation steps were performed at 300g 5min. Cells were resuspended in PBS/BSA 0.04%
The barcoding of individual transcripts from single cells, followed by cDNA amplification and library construction, were performed using 10X Genomics reagents and 10X Chromium Controller, according to the manufacturer’s user guide nr. CG000315 (“Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index), RevC”).

treatment_protocol: pERK, FGFR and ErbB2 inhibitors were injected from D12 to D15, similarly to DMSO control;  micro-beads soaked with either PBS, recombinant FGF-2/NRG-1 were implanted locally at D10.

value: healing ear punch

tag: strain

value: wild-type

value: DMSO


title: VR_LD7_1


title: acomys AZD

value: FGFR1/2/3 inhibitor


title: Pristina leidyi, whole-body, Iso-seq

description:
Iso-seq
PacBio Iso-Seq sequencing, used for native full-length sequencing (i.e. full 5' to 3' sequence without the need for assembly). This was done on a single mixed sample, and no quantitative analysis is intended from this sample.

value: WT


title: acomys TAK

value: ErbB2 inhibitor


title: acomys PD

value: ERK inhibitor


title: HUDEP2_Hemi_175_186_LDB1

city: Memphis

first: Jonanthan

last: Yen

state: TN

address: 262 Danny Thomas Pl

department: Hematology

institute: St. Jude Children's Research Hospital

description: CUT&RUN

data_processing:
BWA mem mapping to hg19
normalized signal (bw file) was generated using s3norm_pipeline.py -r mean
Assembly: hg19
Supplementary files format and content: bigwiggle and bedgraph
Library strategy: CUT&RUN

growth_protocol: HUDEP-2 cells were cultured at a density of 0.3-0.5x10e6/mL in StemSpan serum-free expansion medium (SFEM; Stemcell Technologies) supplemented with 1 μM dexamethasone, 1 μg/mL doxycycline, 50 ng/ml human SCF (R&D Systems), 3 U/mL EPO (Amgen), and 1% penicillin/streptomycin. Erythroid differentiation of CD34+ cells was performed using a three-phase culture protocol. For phase 1 (days 0-7), cells were maintained at a density of 1-4 × 105 /mL in IMDM supplemented with 2% human AB plasma, 3% human AB serum, 1% penicillin-streptomycin, 3 IU/mL heparin, 10 μg/mL insulin, 200 μg/mL holo-transferrin, 1 IU erythropoietin, 10 ng/mL SCF, and 1 ng/mL interleukin-3 (IL-3). For phase 2 (days 8-12), IL-3 was omitted from the medium. Cells were maintained at a density of 0.2-0.8 × 106/mL. For phase 3 (days 12-18), IL-3 and SCF were omitted, the holo-transferrin concentration was increased to 1 mg/mL, and the cells were maintained at a density of 1-2 × 106/mL.

extract_protocol: Library construction for DNA sequencing was performed using a NEBNext UltraII DNA Library Prep Kit from NEB (E7645S). Indexed samples were analyzed by paired-end NGS using an Illumina NextSeq Mid-Output (150 cycles) Kit.

treatment_protocol: HUDEP2 cells were eletroporated with NT or -175 sgRNA RNP complex.


title: HUDEP2_Hemi_175_LMO2

description: CUT&RUN


title: HUDEP2_Hemi_175_186_LMO2

description: CUT&RUN


title: HUDEP2_Hemi_175_186_TAL1

description: CUT&RUN


title: HUDEP2_Hemi_175_TAL1

description: CUT&RUN


title: iPSC_F37 OBs

city: Houston

first: Mo-Fan

last: Huang

state: TX

address: 6431 Fannin Street

department: Integrative Biology and Pharmacology

institute: University of Texas Health science center

data_processing:
The first tool of this workflow is FastQC and file was trimmed using Cutadapt. This tool trimmed the sequence with high uncertainty (i.e. low quality bases) at the reads ends.
 After groomed and trimmed, the reads were assembled using RNA STAR with human reference genome (hg19).
The output of RNA STAR was BAM file containing information for all our reads which can be inspected by the Integrative Genomics Viewer(IGV).
The aligned reads from RNA STAR output were assembled by featureCounts to count reads per genes. This process produced tabular files showing table with the counts, i.e. the number of reads mapped to each gene (in rows, with their ID in the first column) in the provided annotation.
The expression level of each transcript was stated in term of Fragments Per Kilobase of exon per Million fragments (FPKM).
Analysis of the differential gene expression was performed by DESeq2.
Assembly: hg19
Supplementary files format and content: Excel files reporting readcounts or FPKMs

growth_protocol: The MSCs were maintained in aMEM medium. Then the MSCs were cultured in ostegenic differentiation medium (ODM) for osteoblast differentiation.

extract_protocol:
Whole RNA extraction using Trizol.
Libraries were prepared according to Illumina's instructions.

treatment_protocol:
(S1-S44) MSCs were cultured in osteogenic differentiation medium. Cells were collected for whole RNA extraction at different differentiation stages.
(S45-S48) We prepared lentivirus expressing system to overexpress SDC1 in H9 MSCs. And cultured the H9 MSCs in osteogenic differentiation medium. After 24 days, cells were collected for whole RNA extraction.
(S49-S52) We prepared lentivirus expressing system to knockout CEBPD in H9 MSCs. And cultured the H9 MSCs in osteogenic differentiation medium. After 24 days, cells were collected for whole RNA extraction.
(S53-S56) We prepared lentivirus expressing system to knockout IL1R1 in H9 MSCs. And cultured the H9 MSCs in osteogenic differentiation medium. After 24 days, cells were collected for whole RNA extraction.
(S55-S58) We prepared lentivirus expressing system to knockdown CORIN in H9 MSCs. And cultured the H9 MSCs in osteogenic differentiation medium. After 24 days, cells were collected for whole RNA extraction.

value: iPSC_F37 osteoblasts

value: no


title: p19 WT 2

city: Ottawa

first: John

middle: Paul

last: Pezacki

state: Ontario

address: 140 Louis Pasteur Private

department: Chemistry and Biomolecular Sciences

institute: University of Ottawa

hyb_protocol: Hybridization of Fluorescent reporter and capture probes was performed according to Nanostring ncounter plateform and human v3 miRNA panel

scan_protocol: NanoString Flex system

data_processing: Extraction of raw reads and analysis of individual datasets was carried out using nSolver analysis software. From each miRNA the mean of negative control from all counts was subtracted.

label: Biotin and colour coded tag

source_name: small RNA extracted from huh7 cells and treated with p19 WT

label_protocol: Nanostring human v3 miRNA panel (50 ng of RNA was hybridized to the Reporter and Capture probes for 16 hours at 65 oC.

growth_protocol: Huh7 cells were seeded in a 6-well plate at 500,000 cells/ well. Forty-eight hours post seeding, the cells were lysed using ML lysis buffer. Small RNA fractions were isolated using NucleoSpin miRNA (Macherey-Nagel).

treatment_protocol: 900 ng RNA was then treated with 5 µM protein (p19 WT or T111BpyAla), 10 µM CuSO4, 2.5 mM β-mercaptopropionic acid and allowed to incubate for 4 hours at 37oC. 100 attomoles of Cel-miR248 was used as a spike-in oligo control (IDT technologies), serving as an internal monitor to account for any changes caused during RNA purification. RNA was then further purified and concentrated using RNA concentrator kit t remove any protein complexes, according to the manufacturer’s protocol (Zymo Research)

tag: cell lilne

value: p19 WT

tag: molecule subtype

value: small RNA; miRNAs


title: p19 T111BpyAla 2

source_name: small RNA extracted from huh7 cells and treated with p19 T111BpyAla

extract_protocol: Small RNA fractions were isolated using NucleoSpin miRNA (Macherey-Nagel).

value: p19 T111BpyAla


title: p19 WT 1


title: p19 T111BpyAla 1


title: HUDEP2_Hemi_175_186_GATA1

description: CUT&RUN


title: HUDEP2_Hemi_175_LDB1

description: CUT&RUN


title: No treatment 2

source_name: small RNA extracted from huh7 cells

value: No treatment


title: No treatment 1


title: Pristina leidyi, whole-body, scRNA-seq, batch 1, library 12

description: SPLiT-seq

value: Whole-body


title: iPSC_F37 Mat-OBs


title: iPSC_F37 Pre-OBs


title: HUDEP2_Hemi_175_GATA1

description: CUT&RUN


title: VR_LD7_3

value: shoot tip

value: Long day

value: V. riparia PI588259


title: HUDEP2_Hemi_LMO2

description: CUT&RUN


title: iPSC_F37 MSCs


title: HUDEP2_Hemi_LDB1

description: CUT&RUN


title: HUDEP2_Hemi_TAL1

description: CUT&RUN


title: iPSC_F6 OBs

value: iPSC_F6 osteoblasts


title: iPSC_F6 Pre-OBs


title: iPSC_F6 Mat-OBs


title: HUDEP2_175_TAL1

description: CUT&RUN


title: HUDEP2_Hemi_GATA1

description: CUT&RUN


title: iPSC_F6 MSCs


title: HUDEP2_175_LMO2

description: CUT&RUN


title: HUDEP2_175_LDB1

description: CUT&RUN


title: iPSC_1J OBs

value: iPSC_1J osteoblasts


title: iPSC_1J Mat-OBs


title: HUDEP2_LMO2

description: CUT&RUN


title: HUDEP2_175_GATA1

description: CUT&RUN


title: HUDEP2_GATA1

description: CUT&RUN


title: iPSC_1H OBs

value: iPSC_1H osteoblasts


title: HUDEP2_LDB1

description: CUT&RUN


title: iPSC_1H Pre-OBs


title: iPSC_1J Pre-OBs


title: HUDEP2_TAL1

description: CUT&RUN


title: iPSC_1G OBs

value: iPSC_1G osteoblasts


title: iPSC_1J MSCs


title: iPSC_1H Mat-OBs


title: iPSC_1H MSCs


title: iPSC_1G Pre-OBs


title: iPSC_1G MSCs


title: iPSC_1G Mat-OBs


title: hFoB OBs

source_name: hFoB

value: hFoB

value: hFoB osteoblasts


title: CS14_B_3_12

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

country: Italy

institute: University of Verona

data_processing:
The reads were aligned onto the grapevine 12x reference genome PN40024 using TopHat v2.0.6 with default parameters
Mapped reads were used to reconstruct the transcripts using Cufflinks v2.0.2 and the reference genome annotation V1
The normalized expression of each transcript was calculated as RPKM (Reads Per Kilobase per Million mapped reads) for each sample.
Genome_build: 12X reference genome PN400024
Supplementary_files_format_and_content: tab delimited text file containing the normalized reads counts RPKM  for all the samples.

organism: Vitis vinifera

source_name: Cabernet Sauvignon berry sample collected at time point 12 (replicate 3) over ripening season 2014 - Crop thinned 50%

growth_protocol: Vineyard Features: Vitis vinifera cultivar Cabernet Sauvignon (clone FPS 8 grafted on 5C rootstock and planted in 1997) was grown nearby Modesto (USA, CA) in sandy clay loam in an east-west orientation with 10 foot row spacing and 5 foot vine spacing.

extract_protocol:
Total RNA was isolated using the Spectrum Plant Total RNA kit (Sigma-Aldrich) following the manufacturer’s instructions with some modifications (Fasoli et al., 2012). RNA quality and quantity were determined using a Nanodrop 2000 spectrophotometer (Thermo Scientific) and a Bioanalyzer Chip RNA 7500 series II (Agilent).
206 non-directional cDNA libraries were prepared from 2.5 μg of total RNA using the Illumina TruSeq RNA Sample preparation protocol (Illumina Inc., San Diego, CA, USA). Library quality was determined using the Agilent High Sensitivity DNA kit on the Agilent 2100 bioanalyzer, and the quantity was determined by quantitative PCR using the KAPA Library Quantification kit (KapaBiosystems).

treatment_protocol: Cluster thinning treatments: Moderate thinning (50% crop load reduction) was achieved removing clusters to maintain one cluster per shoot; severe thinning (75% crop load reduction) consisted in mantaining one cluster every other shoot; control (0% crop load reduction) was unthinned vines.

tag: cultivar

value: Cabernet Sauvignon

value: grape berry pericarp

tag: year

tag: time point

tag: time point replicate

tag: day after veraison

tag: sugar content (g/100ml)

tag: treatment (cluster thinning)

value: Crop thinned 50%


title: CS14_C_2_12

source_name: Cabernet Sauvignon berry sample collected at time point 12 (replicate 2) over ripening season 2014 - Crop thinned 75%

tag: tissue

value: Crop thinned 75%


title: CS14_C_3_11

source_name: Cabernet Sauvignon berry sample collected at time point 11 (replicate 3) over ripening season 2014 - Crop thinned 75%


title: CS14_B_1_12

source_name: Cabernet Sauvignon berry sample collected at time point 12 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: CS14_C_1_12

source_name: Cabernet Sauvignon berry sample collected at time point 12 (replicate 1) over ripening season 2014 - Crop thinned 75%


title: CS14_B_2_12

source_name: Cabernet Sauvignon berry sample collected at time point 12 (replicate 2) over ripening season 2014 - Crop thinned 50%


title: CS14_C_3_12

source_name: Cabernet Sauvignon berry sample collected at time point 12 (replicate 3) over ripening season 2014 - Crop thinned 75%


title: hFoB Pre-OBs

tag: cell line

tag: cell type

value: no


title: CS14_C_2_11

source_name: Cabernet Sauvignon berry sample collected at time point 11 (replicate 2) over ripening season 2014 - Crop thinned 75%


title: hFoB Mat-OBs


title: CS14_C_1_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 1) over ripening season 2014 - Crop thinned 75%


title: CS14_C_2_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 2) over ripening season 2014 - Crop thinned 75%


title: CS14_C_3_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 3) over ripening season 2014 - Crop thinned 75%


title: CS14_B_1_11

source_name: Cabernet Sauvignon berry sample collected at time point 11 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: hESC_RUES2 Mat-OBs

value: RUES2 osteoblasts


title: hESC_RUES2_4


title: CS14_C_1_11

source_name: Cabernet Sauvignon berry sample collected at time point 11 (replicate 1) over ripening season 2014 - Crop thinned 75%


title: hFoB MSCs


title: CS14_B_3_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 3) over ripening season 2014 - Crop thinned 50%


title: CS14_B_3_11

source_name: Cabernet Sauvignon berry sample collected at time point 11 (replicate 3) over ripening season 2014 - Crop thinned 50%


title: hESC_RUES2 MSCs


title: hESC_H9_4

value: H9 osteoblasts


title: hESC_H9 MSCs


title: CS14_B_1_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: CS14_B_2_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 2) over ripening season 2014 - Crop thinned 50%


title: hESC_H9 Pre-OBs


title: hESC_H1 OBs

value: H1 osteoblasts


title: CS14_B_2_11

source_name: Cabernet Sauvignon berry sample collected at time point 11 (replicate 2) over ripening season 2014 - Crop thinned 50%


title: hESC_H1 Mat-Obs


title: CS14_C_1_9

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 1) over ripening season 2014 - Crop thinned 75%


title: hESC_H9 Mat-OBs


title: CS14_C_2_9

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 2) over ripening season 2014 - Crop thinned 75%


title: hESC_H1 Pre-OBs


title: CS14_B_3_9

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 3) over ripening season 2014 - Crop thinned 50%


title: hESC_H1 MSCs


title: bm_HMSC OBs

source_name: bm-HMSC

value: bm_HMSC osteoblasts


title: CS14_B_2_9

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 2) over ripening season 2014 - Crop thinned 50%


title: CS14_C_3_9

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 3) over ripening season 2014 - Crop thinned 75%


title: bm_HMSC Mat-OBs


title: bm_HMSC Pre-OBs


title: ad_HMSC OBs

source_name: ad-HMSC

value: ad_HMSC osteoblasts


title: CS14_C_2_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 2) over ripening season 2014 - Crop thinned 75%


title: bm_HMSC MSCs


title: CS14_C_1_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 1) over ripening season 2014 - Crop thinned 75%


title: ad_HMSC Mat-OBs


title: CS14_B_1_9

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: CS14_B_2_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 2) over ripening season 2014 - Crop thinned 50%


title: CS14_C_3_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 3) over ripening season 2014 - Crop thinned 75%


title: CS14_B_3_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 3) over ripening season 2014 - Crop thinned 50%


title: CS14_B_1_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: CS14_C_3_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 3) over ripening season 2014 - Crop thinned 75%


title: ChIP CEBPD-1

data_processing:
The quality control of the sequencing reads was done by FASTQ.
The clean reads were aligned to the human reference genome (hg19) using STAR v2.6.0 with parameters of – genomeSAindexNbases 14 – outFilterMultimapNmax 10 –outFilterMismatchNmax 10.
Duplicated reads were removed, and only unique aligned reads were considered for later visualization and quantification.
The unique aligned reads were converted to bigWig format with a fragment length of 75 on IGV browser55.
Peak-calling of ChIP-Seq data was performed by MACS2 with default parameters.
The genomic annotations and motif analyses were performed with HOMER.
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: H9 MSCs were seeded onto 100 mm dishes at 14.7X10^4 cells/dish and cultured in Osteogenic Differentiation Medium (α-MEM supplemented with 10% FBS, 10 mM β-glycerol phosphate, 200 μM ascorbic acid, and 0.1 μM dexamethasone) at the indicated differentiation time points (day 0 to day 30) to induce osteogenic differentiation.

extract_protocol:
For ChIP of CEBPD, we pre-fixed cells in 1.5 mM disuccinimidylglutarate (DSG; Thermo Fisher Scientific, 20593) for 30 minutes and treated by 4% paraformaldehyde (Thermo Fisher Scientific, 28906) for fixation for 10 minutes at room temperature. Then cells were crosslinked in 1% formaldehyde for 10 min at room temperature. Cell pellets were lysed and collected after glycine quenching followed by sonication using a Branson Sonifier 450 (sonication conditions: 200 cycles, power 10%, 10s on and 10s off for IgG or CEBPD). We used the same sonication buffer to dilute the supernatant and then subjected to immunoprecipitation with corresponding antibodies at 4°C overnight. Beads were washed and DNA was then reverse-crosslinked and purified.
Libraries were prepared according to Illumina's instructions. The CEBPD antibody is from Santa Cruz. Cat # sc-365546x. The IgG antibody is from Vector Laboratory. Cat # BA-9200.
ChIP-seq.  We used BGIseq 500 platform.

treatment_protocol: no treatment

value: H9 derived osteoblasts

value: NO

tag: chip antibody

value: CEBPD (Santa Cruz. sc-365546X)


title: ad_HMSC Pre-OBs


title: hESC_RUES2 Pre-OBs


title: ChIP CEBPD-2


title: CS14_C_2_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 2) over ripening season 2014 - Crop thinned 75%


title: ChIP CEBPD Input-2

value: IgG control (Vector Laboratory. Cat # BA-9200)


title: CS14_C_1_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 1) over ripening season 2014 - Crop thinned 75%


title: ChIP CEBPD Input-1


title: CS14_B_3_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 3) over ripening season 2014 - Crop thinned 50%


title: CS14_B_2_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 2) over ripening season 2014 - Crop thinned 50%


title: CS14_C_3_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 3) over ripening season 2014 - Crop thinned 75%


title: Top1-AID_Top2-AID_OsTIR1_IAA_MNase_3_rep2

city: Amsterdam

first: Tineke

middle: L

last: Lenstra

state: North Holland

address: Plesmanlaan 121

department: Division of Gene Regulation

institute: Netherlands Cancer Institute

data_processing:
Paired-end 2x75 bp reads were aligned to the reference genome SacCer3 (January 2015) using bowtie2 (Langmead and Salzberg, 2012) with the settings --sensitive --end-to-end -3 15 -5 5 -X 1980 --no-contain --no-discordant -p 40 -x.
aligned reads were filtered for length and only reads between 95 and 225 bp were retained for analysis
read coverage was determined on a chromosome-by-chromosome basis by counting the number of reads covering each base, and the normalized coverage was determined by normalizing the read coverage to the total coverage on the chromosome
coverage was smoothed with a 31bp window
Genome_build: sacCer3
Supplementary_files_format_and_content: paired-end sequencing reads aligned to reference sequence and filtered for length to retain reads between 95-225 bp

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae BY4742

growth_protocol: Cultures were inoculated and grown overnight in synthetic complete media with 2%  galactose. The following day, overnight cultures for YTL245 was diluted in 125mL SC media and YTL1290 was diluted in 250 ml of SC media such that the starting OD600=0.30. The cultures were grown in a shaker. The 100mL culture was grown OD600 = 1.0. When the 250mL culture reached OD600 = 0.75, it was split into 2 seperate 100 ml cultures, each of which was one was either untreated or treated for 60 minutes with 500uM auxin.

extract_protocol:
Preparation and analysis of mono-nucleosomal DNA was performed as described previously (Donovan et al., 2019; Jonge et al., 2017) with minor modifications. Briefly, cells were grown in  synthetic complete media + 2% galactose from OD 0.3 to OD 0.75 and then either untreated or treated with 500 uM auxin for 60 min. Then, cells were fixed in 1% PFA, washed with 1 M sorbitol, treated with spheroplasting buffer (1M sorbitol, 1 mM β-mercaptoethanol, 10 mg/ml zymolyase 100T (US biological, Z1004.250)) and washed twice with 1 M sorbitol. Spheroplasted cells were treated with 0.01171875 U (low MNase) or 0.1875 U (high MNase) micrococcal nuclease (Sigma-Aldrich, N5386-200UN) in digestion buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris pH7.4, 5 mM MgCl2, 0.075% NP-40, 1 mM β-mercaptoethanol, 0.5 mM spermidine) at 37°C. After 45 min, reactions were terminated on ice with 25 mM EDTA and 0.5% SDS. Samples were treated with proteinase K for 1 h at 37°C and decrosslinked overnight at 65°C. Digested DNA was extracted with phenol/chloroform (PCI 15:14:1), precipitated with NH4-Ac, and treated with 0.1 mg/ml RNaseA/T1. The extent of digestion was checked on a 3% agarose gel.
Sequencing libraries were prepared using the KAPA HTP Library Preparation Kit (07961901001, KAPA Biosystems) using 1 ug of input DNA, 5 uL of 10 uM adapter, double-sided size selection before and after amplification using 10 cycles. Libraries were checked on Bioanalyzer High Sensitivity DNA kit (agilent).

treatment_protocol: Untreated or 60 min treatment with 500 uM auxin.

tag: condition

value: galactose; 500 uM auxin

tag: mnase concentration


title: Top1-AID_Top2-AID_OsTIR1_MNase_3_rep2

value: galactose


title: CS14_B_1_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: Top1-AID_Top2-AID_OsTIR1_IAA_MNase_1_rep1


title: CS14_C_2_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 2) over ripening season 2014 - Crop thinned 75%


title: Top1-AID_Top2-AID_OsTIR1_IAA_MNase_3_rep1


title: ad_HMSC MSCs

source_name: ad-HMSC

tag: treatment


title: CS14_C_1_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 1) over ripening season 2014 - Crop thinned 75%


title: Top1-AID_Top2-AID_OsTIR1_MNase_1_rep2

tag: strain


title: Top1-AID_Top2-AID_OsTIR1_MNase_3_rep1


title: Top1-AID_Top2-AID_MNase_1_rep2

value: yTL1245:Top1-AID, Top2-AID


title: CS14_B_1_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 1) over ripening season 2014 - Crop thinned 50%

value: Cabernet Sauvignon


title: CS14_B_3_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 3) over ripening season 2014 - Crop thinned 50%

value: grape berry pericarp


title: CS14_C_2_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 2) over ripening season 2014 - Crop thinned 75%


title: Top1-AID_Top2-AID_MNase_1_rep1


title: Top1-AID_Top2-AID_OsTIR1_MNase_1_rep1


title: CS14_B_3_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 3) over ripening season 2014 - Crop thinned 50%

value: Crop thinned 50%


title: CS14_C_1_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 1) over ripening season 2014 - Crop thinned 75%

value: Crop thinned 75%


title: CS14_B_2_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 2) over ripening season 2014 - Crop thinned 50%


title: Top1-AID_Top2-AID_MNase_3_rep1


title: Top1-AID_Top2-AID_MNase_3_rep2


title: CS14_B_1_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: CS14_C_1_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 1) over ripening season 2014 - Crop thinned 75%


title: CS14_C_3_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 3) over ripening season 2014 - Crop thinned 75%


title: CS14_B_2_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 2) over ripening season 2014 - Crop thinned 50%


title: CS14_B_3_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 3) over ripening season 2014 - Crop thinned 50%


title: CS14_B_2_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 2) over ripening season 2014 - Crop thinned 50%


title: CS14_C_3_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 3) over ripening season 2014 - Crop thinned 75%


title: CS14_B_1_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: CS14_C_3_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 3) over ripening season 2014 - Crop thinned 75%


title: CS14_C_2_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 2) over ripening season 2014 - Crop thinned 75%


title: CS14_C_1_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 1) over ripening season 2014 - Crop thinned 75%


title: CS14_B_3_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 3) over ripening season 2014 - Crop thinned 50%


title: CS14_B_2_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 2) over ripening season 2014 - Crop thinned 50%


title: CS14_C_2_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 2) over ripening season 2014 - Crop thinned 75%


title: CS14_B_1_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: CS14_C_2_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 2) over ripening season 2014 - Crop thinned 75%


title: CS14_C_1_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 1) over ripening season 2014 - Crop thinned 75%


title: pals-17(*) pals-20(*) mutant Replicate 2

city: La Jolla

first: Emily

last: Troemel

state: California

address: 4202 Bonner Hall, 9500 Gilman #0349

department: Cell and Developmental Biology

institute: University of California, San Diego

description:
ERT999
p17p20_R2

data_processing:
Reads were aligned to WS235 using Rsubreads in R studio
Reads were counted using Featurecounts in Galaxy
Differential expression analyses were performed using limma-voom in Galaxy
Assembly: Wormbase Release WS235
Supplementary files format and content: Matrix table of normalized counts from lima-voom

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Synchronized animals were grown on OP-50 bacterial food source for 48 h at 20C from L1 stage.

extract_protocol:
Total RNA was extracted using TriReagent(Sigma-Aldrich)and cleaned using RNAeasy (Qiagen) column purification. RNA quality was assesed using Tapestation analysis.
TruSeq Stranded mRNA (Illumina) prep kit

value: Whole animal

tag: genotype


title: pals-17(*) pals-20(*) mutant Replicate 3

description:
ERT999
p17p20_R3


title: CS14_B_3_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 3) over ripening season 2014 - Crop thinned 50%


title: pals-17(*) pals-20(*) mutant Replicate 4

description:
ERT999
p17p20_R4


title: pals-16(Δ) pals-17(*) pals-20(*) mutant Replicate 4

description:
ERT1074
p17p20p16_R4


title: pals-16(Δ) pals-17(*) pals-20(*) mutant Replicate 2

description:
ERT1074
p17p20p16_R2


title: Wild type Replicate_ 1

description:
N2
N2_R1

value: Wild type


title: pals-16(Δ) pals-17(*) mutant Replicate 1

description:
ERT1082
p17p16_R1


title: pals-16(Δ) pals-17(*) mutant Replicate 2

description:
ERT1082
p17p16_R2


title: pals-16(Δ) pals-17(*) pals-20(*) mutant Replicate 1

description:
ERT1074
p17p20p16_R1


title: pals-16(Δ) pals-17(*) pals-20(*) mutant Replicate 3

description:
ERT1074
p17p20p16_R3


title: Wild type Replicate_ 3

description:
N2
N2_R3


title: pals-17(*) pals-20(*) mutant Replicate 1

description:
ERT999
p17p20_R1


title: pals-16(Δ) pals-17(*) mutant Replicate 4

description:
ERT1082
p17p16_R4


title: Wild type Replicate_ 2

description:
N2
N2_R2


title: pals-16(Δ) pals-17(*) mutant Replicate 3

description:
ERT1082
p17p16_R3


title: Wild type Replicate_ 4

description:
N2
N2_R4


title: pals-17(*) mutant Replicate 2

description:
p17_R2
ERT994

growth_protocol: Synchronized wild-type animals were grown on OP-50 bacterial food source for 48 h at 20C from L1 stage. Synchronized pals-17 mutant animals were grown on OP-50 bacterial food source for 72 h at 20C from L1 stage. pals-17 mutants grow slower than the wild type.


title: pals-17(*) mutant Replicate 3

description:
p17_R3
ERT994


title: Wild type Replicate 4

description:
N2_R4
N2


title: pals-17(*) mutant Replicate 4

description:
p17_R4
ERT994


title: pals-17(*) mutant Replicate 1

description:
p17_R1
ERT994


title: CS14_B_1_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: Wild type Replicate 3

description:
N2_R3
N2


title: Wild type Replicate 2

description:
N2_R2
N2


title: CS14_C_3_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 3) over ripening season 2014 - Crop thinned 75%


title: CS14_C_3_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 3) over ripening season 2014 - Crop thinned 75%


title: CS14_B_2_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 2) over ripening season 2014 - Crop thinned 50%


title: CS14_C_2_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 2) over ripening season 2014 - Crop thinned 75%


title: Wild type Replicate 1

description:
N2_R1
N2


title: CS14_B_3_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 3) over ripening season 2014 - Crop thinned 50%


title: CS14_B_1_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 1) over ripening season 2014 - Crop thinned 50%


title: CS13_C_3_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 3) over ripening season 2013 - Crop thinned 75%


title: control fat tissue

city: Daejeon

first: Kyu-Sun

last: Lee

address: 125 Gwahak-ro

country: South Korea

institute: KRIBB

data_processing:
Alignment: Transcriptome with novel splices
Quality Trimming: >average Q20
Normalization Method: Global normalization(RC)
Assembly: dm6 (UCSC)
Supplementary files format and content: tab-delimited text files include RC values for each Sample ...

organism: Drosophila melanogaster

source_name: Drosophila larval fat tissue

extract_protocol:
To extract total RNAs for RNA sequencing (RNA-seq) experiments, 30 adult heads were dissected and isolated with easy-BLUE™ reagent (iNtRON biotechnology). RNA quality control and data analyses were performed by ebiogen (ebiogen.com).
RNA libraries were constructed by Lexogen Quant-Seq Library Preparation Kit

value: Dcg/+


title: CS14_C_1_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 1) over ripening season 2014 - Crop thinned 75%


title: CS14_B_2_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 2) over ripening season 2014 - Crop thinned 50%


title: CS13_C_1_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 1) over ripening season 2013 - Crop thinned 75%


title: CS13_B_1_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 1) over ripening season 2013 - Crop thinned 50%


title: CS13_C_2_9

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 2) over ripening season 2013 - Crop thinned 75%


title: Hpo knockdown fat tissue

value: Dcg>Hpo-Ri


title: Hpo overexpression fat tissue

value: Dcg>Hpo


title: CS13_C_2_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 2) over ripening season 2013 - Crop thinned 75%


title: CS13_C_1_9

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 1) over ripening season 2013 - Crop thinned 75%


title: CS13_B_2_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 2) over ripening season 2013 - Crop thinned 50%


title: CS13_B_3_9

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 3) over ripening season 2013 - Crop thinned 50%


title: CGN, DMSO_DIV3, RNA-seq, Rep 3

city: Durham

middle: E

last: West

state: NC

address: 311 Research Dr

department: Neurobiology

institute: Duke University

data_processing:
RNA-seq raw fastq read files were analyzed with FastQC and processed with Trimmomatic 0.38 for quality control and adapter trimming
Trimmed reads were then aligned to the mm10 reference genome using STAR 2.7.2b. Duplicates were filtered from the resulting alignments with macs2 2.1 filterdup keeping only one duplicate
Read counts for genes were generated using the count command of the HTseq2 package, with feature type set to ‘exon’, and the Gencode mm10 GTF annotation file
DESeq2 was used for read-count normalization and differential expression analysis.
Assembly: mm10
Supplementary files format and content: exon.reads

source_name: Cerebellum

extract_protocol:
Cerebellar tissue was lysed in Trizol reagent, after which chloroform was added and phase separation was performed. The resulting aqueous layer was further processed using the Zymo Direct-zol RNA miniprep kit (Zymo #R2052). RNA purity was then measured to make sure samples had A260/280 and A260/230 values > 1.9.
Novogene mRNA library preparation
poly A enrichment

value: Cerebellum

tag: agent

value: DMSO

tag: time


title: CGN, DMSO_DIV3, RNA-seq, Rep 1


title: CGN, GSK-126_DIV3, RNA-seq, Rep 3


title: CGN, GSK-126_DIV3, RNA-seq, Rep 2


title: WT Stomach Corpus Rep4

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

institute: CRUK Scotland Institute

description: G12a_EKDL210002225-1a-AK5396-AK6727_H3VG7DSX2_L1

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts

source_name: Stomach Corpus

extract_protocol:
RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina TruSeq Stranded mRNA kit, then run on an Illumina Novaseq 6000 (2x150 cycles, paired end, dual index).

treatment_protocol: Mice were treated with a single i.p. injection of 3mg tamoxifen to induce floxing of the Apc allele in the whole body via the ROSACreER allele. Tissues were harvested on Day4.

tag: Sex

value: Male

value: Stomach Corpus

value: WT

value: Day 4


title: WT Stomach Corpus Rep1

description: A03a_EKDL210002225-1a-AK5159-AK6654_H3VG7DSX2_L1


title: WT Stomach Corpus Rep2

description: B05d_EKDL210002228-1a-AK6507-AK6667_H3VG7DSX2_L4

value: Female


title: WT Stomach Corpus Rep3

description: D05c_EKDL210002227-1a-AK6518-AK6688_H3VG7DSX2_L3


title: WT Stomach Antrum Rep4

description: H08a_EKDL210002225-1a-AK6544-AK6735_H3VG7DSX2_L1

source_name: Stomach Antrum

value: Stomach Antrum


title: CGN, GSK-126_DIV3, RNA-seq, Rep 1


title: CGN, DMSO_DIV3, RNA-seq, Rep 2


title: CS13_B_3_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 3) over ripening season 2013 - Crop thinned 50%

tag: cultivar

value: Cabernet Sauvignon

tag: year

tag: time point


title: CS13_B_2_9

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 2) over ripening season 2013 - Crop thinned 50%

value: grape berry pericarp

tag: time point replicate

tag: day after veraison

tag: sugar content (g/100ml)


title: CS13_C_3_9

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 3) over ripening season 2013 - Crop thinned 75%

tag: tissue

tag: treatment (cluster thinning)


title: WT Stomach Antrum Rep3

description: E01c_EKDL210002227-1a-AK5146-AK6696_H3VG7DSX2_L3


title: WT Stomach Antrum Rep2

description: B06d_EKDL210002228-1a-AK6508-AK6668_H3VG7DSX2_L4


title: CS13_C_1_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 1) over ripening season 2013 - Crop thinned 75%


title: WT Spleen Rep4

description: H04a_EKDL210002225-1a-AK6540-AK6731_H3VG7DSX2_L1

source_name: Spleen

value: Spleen


title: CS13_C_3_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 3) over ripening season 2013 - Crop thinned 75%

value: Crop thinned 75%


title: CS13_C_2_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 2) over ripening season 2013 - Crop thinned 75%


title: WT Spleen Rep3

description: F05d_EKDL210002228-1a-AK6530-AK6709_H3VG7DSX2_L4


title: CS13_B_3_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 3) over ripening season 2013 - Crop thinned 50%

value: Crop thinned 50%


title: WT Spleen Rep2

description: D09c_EKDL210002227-1a-AK6522-AK6692_H3VG7DSX2_L3


title: CS13_B_1_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 1) over ripening season 2013 - Crop thinned 50%


title: CS13_B_2_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 2) over ripening season 2013 - Crop thinned 50%


title: WT Proximal SI Rep3

description: H04d_EKDL210002228-1a-AK6540-AK6731_H3VG7DSX2_L4

source_name: Proximal SI

value: Proximal SI


title: CS13_C_3_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 3) over ripening season 2013 - Crop thinned 75%


title: WT Proximal SI Rep2

description: D03c_EKDL210002227-1a-AK4639-AK6604_H3VG7DSX2_L3


title: CS13_C_1_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 1) over ripening season 2013 - Crop thinned 75%


title: CS13_C_2_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 2) over ripening season 2013 - Crop thinned 75%


title: WT Proximal SI Rep1

description: A01a_EKDL210002225-1a-AK5140-AK242_H3VG7DSX2_L1


title: WT Mid Colon Rep4

description: G11a_EKDL210002225-1a-AK4938-AK6726_H3VG7DSX2_L1

source_name: Mid Colon

value: Mid Colon


title: CS13_B_3_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 3) over ripening season 2013 - Crop thinned 50%


title: WT Mid Colon Rep3

description: D04c_EKDL210002227-1a-AK6517-AK6687_H3VG7DSX2_L3