title: In-vitro TGF-beta treated sample [TGF3-B-BR3_S3]

city: Stanford

first: Daniel

last: Richard

address: 290 Jane Stanford Way

department: Genetics

institute: Stanford University

data_processing:
alignment to hg19; Bowtie2 version 2.3.2;default parameters for hg19 alignment;
filter for duplicates; picard;default parameters;
peak calling; MACS2 version 2.1.1.2;macs2 bampe -f BAMPE --nolambda;
peak filtering ; IDR https://github.com/nboley/idr;idr --samples rep1file rep2file --peak-list pooled_peaks --input-file-type narrowPeak --output-file IDR_output --rank p.value --soft-idr-threshold 0.05 –plot;MACS2 .narrowPeak output was cut using the number of peaks below the IDR threshold, sorting by MACS2 reported p-value
RNA-seq read mapping; Salmon version 0.14.0;salmon -l A --numBootstraps 100 --gcBias –validateMappings;
Read abundance normalization ; DESeq2 version 1.26.0
Genome_build: hg19
Supplementary_files_format_and_content:
BMP_pool_merge_bampe_call_peaks_replicate_consolidated_IDR_threshold0.01_clean.bed: bed format; contains the coordinates of the peaks called and filtered as described for the BMP-treated ATAC-seq experiment
TGF_pool_merge_bampe_call_peaks_replicate_consolidated_IDR_threshold0.05.clean.bed: bed format; contains the coordinates of the peaks called and filtered as described for the TGF-treated ATAC-seq experiment
BMP1-1-BR2_S6_bowtie2_mapping_dupremove_bampe_call_peaks.narrowPeak: bed format; contains the coordinates of the peaks called and filtered as described for the BMP-treated ATAC-seq experiment
BMP3-1-BR1_S3_bowtie2_mapping_dupremove_bampe_call_peaks.narrowPeak: bed format; contains the coordinates of the peaks called and filtered as described for the BMP-treated ATAC-seq experiment
BMP3-A-BR3_S4_bowtie2_mapping_dupremove_bampe_call_peaks.narrowPeak: bed format; contains the coordinates of the peaks called and filtered as described for the BMP-treated ATAC-seq experiment
TGF3-1-BR2_S2_bowtie2_mapping_dupremove_bampe_call_peaks.narrowPeak: bed format; contains the coordinates of the peaks called and filtered as described for the TGF-treated ATAC-seq experiment
TGF3-1-BR1_S1_bowtie2_mapping_dupremove_bampe_call_peaks.narrowPeak: bed format; contains the coordinates of the peaks called and filtered as described for the TGF-treated ATAC-seq experiment
TGF3-B-BR3_S3_bowtie2_mapping_dupremove_bampe_call_peaks.narrowPeak: bed format; contains the coordinates of the peaks called and filtered as described for the TGF-treated ATAC-seq experiment
chondrocyte_read_abundances_and_DEG_statistics.xlsx: Normalized abundance counts, along with differential-expression statistics, across all primary and in-vitro RNA-seq datasets generated

source_name: HESC-derived chondrocytes

growth_protocol: A detailed description of the protocol for generating chondrogenic cells and tissues from human pluripotent stem cells has been published (PMID: 25961409).

extract_protocol: Samples were subjected to PCR amplification and barcoding following Buenrostro et al., 2015. 10 ul of transposed DNA was then placed in a reaction containing NEBNext High-Fidelity PCR Master Mix, ddH20, and primers. After amplification, samples were transferred to micro-centrifuge tubes and subjected to the OMEGA Bead Purification Protocol following manufacturers protocol. The samples were eluted in 30 ul of TE, run on a nanodrop, diluted to 5 ng/ul and run on a bioanalyzer. Prior to sequencing sample concentrations were determined using the KAPA Library Quantification Complete Kit (KK4824). Samples were then sent out to the Harvard University Bauer Core Facility for sequencing on one lane of the Illumina NextSeq 500, for three rounds, after which raw reads for each sample were pooled.

treatment_protocol: Collagenase digestion, followed by nuclei isolation

value: chondrocytes

value: In-vitro TGF-beta treated sample

value: tn5 transposase


title: Replicate 1, GFP high

status: Public on Apr 03 2023

type: SRA

city: London

first: Gordon

last: Beattie

address: Gower Street

country: United Kingdom

institute: UCL

library_source: transcriptomic single cell

data_processing:
A FASTA and GTF file of mm10 was modified to contain eGFP, Tdtomato and EDGFR  sequences (complete with associated UTRs), raw reads were then mapped to this reference using cellranger count (v5.0.1)
Assembly: mm10
Supplementary files format and content: filtered (for cells) h5 matrix files of raw counts

molecule: total RNA

organism: Mus musculus

source_name: Brain (GBM tumour)

extract_protocol:
Tumours were dissociated using papain and cells sorted based on tdTomato and GFP fluorescence into 0.04% BSA in PBS.
Cells were processed according to 10X Genomics User Guide (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index)). Cells were resuspended with RT Master Mix and loaded onto Chip G along with the barcoded gel beads and partitioning oil in order to generate the gel bead-in-emulsion (GEM) on the Chromium Controller. Once complete, the GEMS are loaded onto a thermocycler to complete the RT inside each GEM to produce cDNA, which contain Illumina R1 primer sequence primer sequence, Unique Molecular Identifier (UMI) and the 10X Barcode. Silane Dynabeads are used to clean up the pooled barcoded cDNA. The cDNA is then amplified and a quick QC is conducted to look at the fragment sizes. 10ul of the amplified cDNA is taken forward for the library construction which involves 3 steps of fragmentation (to obtain fragments around 450bp), ligation (to add the Illumina p5 and p7 primers) and Indexing (to add unique sample index to each sample). These steps are always followed by a SPRI Select bead purification. Once Indexing is complete the libraries were pooled and submitted for sequencing.

tag: tissue

value: Brain (GBM tumour)

tag: Sex

value: Male

tag: cell fraction

value: GFP high


title: Adipose visceral_2e29b1fc-76ef-45bd-8e5e-2ee1139ba59e at day D8

city: Cambridge

first: Melina

last: Claussnitzer

state: MA

address: 75 Ames Street

country: USA

institute: Broad Institute of MIT and Harvard

library_source: transcriptomic

data_processing:
Generating count tables using featureCounts function (Liao, Smyth, and Shi 2013) in the Rsubread package
Normalization using DESeq2
Analysis of variance (ANOVA) in R
Genome_build: hg19
Supplementary_files_format_and_content: normalized count

organism: Homo sapiens

source_name: Adipose visceral

growth_protocol: For RNAseq, cells were seeded at 40K cells/well in 12-well dishes (Corning). Before Induction cells were cultured in proliferation medium (Basic medium consisting of DMEM-F12 1% Penicillin - Streptomycin, 33µM Biotin and 17µM Pantothenate supplemented with 0.13µM Insulin, 0.01ug/ml EGF, 0.001ug/ml FGF, 2.5%FCS). Adipogenic differentiation was induced by changing culture medium to induction medium. (Basic medium supplemented with 0.861μM Insulin, 1nM T3, 0.1μM Cortisol, 0.01mg/ml Transferrin, 1μM Rosiglitazone, 25nM Dexamethasone, 2.5nM IBMX). On day 3 of adipogenic differentiation culture medium was changed to differentiation medium (Basic medium supplemented with 0.861μM Insulin, 1nM T3, 0.1μM Cortisol, 0.01mg/ml Transferrin). Medium was changed every 3 days. Visceral-derived AMSCs were differentiated by further adding 2% FBS as well as 0.1mM oleic and linoleic acid to the induction and differentiation media.

extract_protocol: Library preparation, sequencing and reference genome alignment was carried out by the Genomics Platform at the Broad Institute. After final quality control samples were sequenced generating 50 million paired end reads per sample

treatment_protocol: We used the same differentiation media to investigate different days of differentiation under the same conditions.

value: adipose

tag: depot

value: visceral

tag: differentation day


title: In-vitro TGF-beta treated sample [TGF3-1-BR1_S1]

state: CA

library_source: genomic

molecule: genomic DNA

tag: cell type

tag: treatment


title: In-vitro TGF-beta treated sample [TGF1-1-BR2_S4]


title: Adipose visceral_2e29b1fc-76ef-45bd-8e5e-2ee1139ba59e at day D3


title: SW_3min

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

data_processing:
Single end reads were first stripped of 3' ligated adapter using a custom python script.
Adapter stripped reads were then aligned to rRNA using bowtie 0.12.8 to remove remaining rRNA reads.  Reads that did not align to rRNA were then aligned to the full C. crescentus NA1000 genome using bowtie 0.12.8.
mRNA levels were then calcualted by normalizing using the reads per kilobase per million mapped reads (RPKM).  The relative mRNA levels over time were then calculated using the rifcorrect software [Aretakis et al. BioRxiv 2022].
Assembly: NA1000 operon annotation (Bharmal et al. MRA 2020)
Supplementary files format and content: tab delimited text

organism: Caulobacter vibrioides

growth_protocol: WT(Caulobacter crescentus NA1000) cells, were grown in M2G media overnight at 28 C. The next day, the cells were diluted and grown until midlog-phase  (0.3 to 0.5 OD600) which were used for mRNA half-life profiling.

extract_protocol:
The cells were pelleted at 20,000 x g for 1 min in 1.5 mL eppendorf tubes to prepare for RNA extraction.Pelleted cells were resuspended in 1mL of pre-warmed (to 65 0C) TRizol Reagent (Ambion) and incubated for 10 min at 65 0C in a heat block. 200 mL of chloroform were added to the samples and tubes were gently inverted a few times. Then samples were incubated at room temperature for 5 min and spun at 20,000 x g for 10 min. The supernatant was moved to siliconized tubes and 500 mL of chloroform was added, vortexed, and spun at 20,000 x g for 10 minutes. RNA samples were precipitated using isopropanol (1x volume isopropanol, 0.1X volume 5M NaOAc pH 5.2) overnight at – 80 0C. The RNA samples were spun at 20,000 x g at 4 0C for 1 hour. Pellets were washed with cold 80% ethanol and spun for 10 min at 20,000 x g, air-dried, and resuspended in 10 mM Tris-HCl (pH 7.0). The RNA-Seq libraries were made using 5µg of total RNA of each sample. Ribosomal RNAs were removed by ribozero gram negative kit and library construction was performed according to the protocol in (Aretakis et al., 2018).
mRNA fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)].  Updated adapter oligos that are compatible with the novaseq were used from [Aretakis et al. Methods in Enzymology (2019)].

treatment_protocol: The cells were treated with 100µg/mL rifampicin and placed immediately in RNAprotect bacterial reagent (QIAGEN) at the indicated timepoint (0,1,2,4,8,and 15 min).  0 minute time-points were collected just prior to rifampicin addition.

tag: cell line

value: C. crescentus cells

tag: genotype

value: WT


title: 4.Crym IP

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description:
Crym IP replicate 4
MO_2147_IP

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with GRCm38 as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: mm10
Supplementary files format and content: Counts

source_name: Striatum, brain

extract_protocol:
Brain was extracted and striatum was dissected.Tissue was immunoprecipitated with HA antibodies, with some tissue left as is for input. All tissue RNA extracted with Qiagen micro kit
Library constructed with TruSeq library prep RNA kit from Illumina

value: Striatum, brain

tag: condition

value: IP

tag: mouse

value: Crym KO


title: SW_0min


title: Adipose visceral_2e29b1fc-76ef-45bd-8e5e-2ee1139ba59e at day D14


title: In-vitro BMP treated sample [BMP3-A-BR3_S4]

value: In-vitro BMP treated sample


title: RppH 9 min rep 2

growth_protocol: WT(Caulobacter crescentus NA1000) cells, delta rhlB(∆rhlB) and delta rppH (∆rppH cells) were grown in M2G media overnight at 28 C. The next day, the cells were diluted and grown until midlog-phase  (0.3 to 0.5 OD600) which were used for mRNA half-life profiling.

extract_protocol:
The cells were pelleted at 20,000 x g for 1 min in 1.5 mL eppendorf tubes to prepare for RNA extraction.Pelleted cells were resuspended in 1mL of pre-warmed (to 65 0C) TRizol Reagent (Ambion) and incubated for 10 min at 65 0C in a heat block. 200 mL of chloroform were added to the samples and tubes were gently inverted a few times. Then samples were incubated at room temperature for 5 min and spun at 20,000 x g for 10 min. The supernatant was moved to siliconized tubes and 500 mL of chloroform was added, vortexed, and spun at 20,000 x g for 10 minutes. RNA samples were precipitated using isopropanol (1x volume isopropanol, 0.1X volume 5M NaOAc pH 5.2) overnight at – 80 0C. The RNA samples were spun at 20,000 x g at 4 0C for 1 hour. Pellets were washed with cold 80% ethanol and spun for 10 min at 20,000 x g, air-dried, and resuspended in 10 mM Tris-HCl (pH 7.0). The RNA-Seq libraries were made using 5µg of total RNA of each sample. Ribosomal RNAs were removed by riboPOOLs (oligos designed for removal of Caulobacter crescentus rRNAs from siTOOLs Biotech) and library construction was performed according to the protocol in (Aretakis et al., 2018).
mRNA fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)].  Updated adapter oligos that are compatible with the novaseq were used from [Aretakis et al. Methods in Enzymology (2019)].

treatment_protocol: The cells were treated with 200µg/mL rifampicin and placed immediately in RNAprotect bacterial reagent (QIAGEN) at the indicated timepoint (0,1,3,9 min).  0 minute time-points were collected just prior to rifampicin addition.

value: RppH deletion


title: Adipose visceral_2e29b1fc-76ef-45bd-8e5e-2ee1139ba59e at day D0


title: 4.Crym Input

description:
Crym Input replicate 4
MO_2147_Input

value: Input


title: 3.Crym IP

description:
Crym IP replicate 3
MO_2146_IP


title: In-vitro BMP treated sample [BMP3-1-BR1_S3]


title: RppH 3 min rep 2


title: 3.Crym Input

description:
Crym Input replicate 3
MO_2146_Input


title: Adipose visceral_37be71a4-3248-4605-a65b-43f0dd318360 at day D8


title: In-vitro BMP treated sample [BMP1-1-BR2_S6]


title: RppH 1 min rep 2


title: Adipose subcutaneous_536e8e82-761b-453a-ad72-1c925afb6d04 at day D14

source_name: Adipose subcutaneous

value: subcutaneous


title: CT32-2 [bulk ATAC-seq]

city: Chicago

first: Benjamin

middle: J

last: Weidemann

state: IL

address: 303 E. Superior St.

department: Medicine

institute: NORTHWESTERN UNIVERSITY

data_processing:
Alignment using bowtie2 (ChIP), ENCODE Pipeline (ATAC), Cellranger mkfastq and count (snATAC), STAR (RNA)
Quantification and annotation using HOMER (ChIP, ATAC), Cellranger count (snATAC), RSEM (RNA)
Differential analysis, QC, and visualization using R v4.1.0 (DESeq2, ChIPpeakAnno, Seurat, Signac, ggplot2, rtracklayer)
Rhythmic analysis of synchronized human ATAC-seq data (eJTK_Cycle)
Assembly: mm10, hg38
Supplementary files format and content: Comma-delimited normalized mouse Bulk ATAC-Seq counts file and P-values: Mm_norm_counts_ATAC.csv
Supplementary files format and content: Tab-delimited eJTK_cycle output from synchronized human Bulk ATAC-Seq: Hs_eJTK_cycle_ATAC.txt

source_name: pancreatic islet

growth_protocol: DMEM + 15% FBS (cells), RPMI + 10% FBS or human AB serum (islets)

extract_protocol:
Omni-ATAC protocol for bulk ATAC-seq, 10X Protocol for snATAC-seq, DirectZol MicroPrep (Zymo) for RNA, AQuA HiChIP for HiChIP
10X Protocol for snATAC-seq. NEBNext Ultra II for RNA, ChIP, and HiChIP-seq. Nextera (Tn5) for ATAC-Seq

treatment_protocol: Cells synchronized using 1 hour 10 micromolar forskolin pulse

value: pancreatic islet

value: Donor 5

value: 32 hours post-synchronization


title: Replicate 1, GFP low

value: Brain (GBM tumour)

value: GFP low


title: Adipose visceral_37be71a4-3248-4605-a65b-43f0dd318360 at day D3

description: Low quality sample removed from the analysis


title: RppH 0 min rep 2


title: SW_1min


title: 2.Crym IP

description:
Crym IP replicate 2
MO_2142_IP


title: 2.Crym Input

description:
Crym Input replicate 2
MO_2142_Input


title: In-vitro TGF-beta treated sample [SP46-T3]

molecule: polyA RNA

extract_protocol: Samples were prepared using Tru-Seq Illumina library preparation

treatment_protocol: Collagenase digestion

value: chondrocytes

value: In-vitro TGF-beta treated sample


title: Adipose visceral_37be71a4-3248-4605-a65b-43f0dd318360 at day D14

value: adipose

value: visceral


title: Adipose visceral_773424b4-483e-4618-b51c-8f7643097fbd at day D3


title: In-vitro BMP treated sample [SP46-B1]


title: 1.Crym IP

description:
Crym IP replicate 1
MO_2141_IP


title: RppH 3 min rep 1

value: C. crescentus cells


title: RppH 9 min rep 1


title: 1.Crym Input

description:
Crym Input replicate 1
MO_2141_Input

value: Striatum, brain


title: In-vivo growth plate chondrocytes [28743-GP-Right2]

source_name: Human fetal donor samples

growth_protocol: in vivo collected growth plate / epiphyseal chondrocytes

treatment_protocol: Human products of conception were collected from late first-trimester and early second-trimester terminations through the Laboratory of Developmental Biology in full compliance with the ethical guidelines of the National Institutes of Health and with the approval of the University of Washington Institutional Review Boards for the collection and distribution of human tissues for research, and Harvard University for the receipt and use of such materials. The Laboratory of Developmental Biology obtained written consent from all tissue donors.

value: In-vivo growth plate chondrocytes


title: RppH 1 min rep 1


title: 4.WT Input

description:
Wild type Input replicate 4
MO_2149_Input

value: WT


title: Adipose subcutaneous_37be71a4-3248-4605-a65b-43f0dd318360 at day D3


title: RppH 0 min rep 1


title: In-vivo epiphyseal chondrocytes [28743-EP-Right2]

value: In-vivo epiphyseal chondrocytes


title: Adipose subcutaneous_37be71a4-3248-4605-a65b-43f0dd318360 at day D14


title: In-vivo growth plate chondrocytes [28743-GP-Left2]


title: In-vivo growth plate chondrocytes [28743-GP-Right1]


title: Adipose subcutaneous_37be71a4-3248-4605-a65b-43f0dd318360 at day D8


title: RhlB 9 min rep 2

value: RhlB deletion


title: 3.WT IP

description:
Wild type IP replicate 3
MO_2148_IP

value: IP


title: Adipose visceral_99b56b6f-c3cd-4d24-8635-bd62742a2f42 at day D8


title: 4.WT IP

description:
Wild type IP replicate 4
MO_2149_IP


title: In-vivo epiphyseal chondrocytes [28743-EP-Right1]


title: RhlB 3 min rep 2


title: Adipose visceral_99b56b6f-c3cd-4d24-8635-bd62742a2f42 at day D3


title: RhlB 1 min rep 2


title: 3.WT Input

description:
Wild type Input replicate 3
MO_2148_Input

value: Input


title: Adipose visceral_37be71a4-3248-4605-a65b-43f0dd318360 at day D0


title: In-vivo epiphyseal chondrocytes [28743-EP-Left2]


title: In-vivo epiphyseal chondrocytes [28743-EP-Left1]


title: RhlB 0 min rep 2


title: Adipose visceral_99b56b6f-c3cd-4d24-8635-bd62742a2f42 at day D14


title: Adipose visceral_99b56b6f-c3cd-4d24-8635-bd62742a2f42 at day D0


title: 2.WT Input

description:
Wild type Input  replicate 2
MO_2145_Input


title: In-vitro BMP treated sample [H9_B_30_rep1]

extract_protocol: Samples were prepared using Kappa (Roche) library preparation

treatment_protocol: Direct Trizol extraction

value: In-vitro BMP treated sample


title: RhlB 9 min rep 1


title: 2.WT IP

description:
Wild type IP replicate 2
MO_2145_IP


title: 1.WT IP

description:
Wild type IP replicate 1
MO_2144_IP


title: Adipose subcutaneous_99b56b6f-c3cd-4d24-8635-bd62742a2f42 at day D8

value: subcutaneous


title: In-vitro TGF-beta treated sample [H9_T_30_rep1]


title: Adipose subcutaneous_99b56b6f-c3cd-4d24-8635-bd62742a2f42 at day D3


title: 1.WT Input

description:
Wild type Input replicate 1
MO_2144_Input


title: RhlB 3 min rep 1


title: In-vitro BMP treated sample [H9_B_28_rep1]


title: RhlB 1 min rep 1


title: Adipose subcutaneous_99b56b6f-c3cd-4d24-8635-bd62742a2f42 at day D14


title: In-vitro TGF-beta treated sample [H9_T_28_rep1]


title: RhlB 0 min rep 1


title: WT 9 min rep 2


title: PSGL-1-/- OT-I, tumor, scRNAseq

city: La Jolla

first: Jennifer

last: Hope

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

description: 10x Genomics

data_processing:
Data was collected using an Illumina HiSeq400 (PE50) and fastq files were demultiplexed, aligned, counted, and aggregated using Cell Ranger software v2.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Further data analysis was completed using Seurat (v4.1.1) following "IntegrateData" to downsample to 2500 cells in each sample.
SeqGeq (FlowJo, BD) was used to visualize gene expression changes in subsets of cells.
Assembly: mm10
Supplementary files format and content: Tab-separate value files,  matrix files, h5 files

source_name: Lymphocyte

extract_protocol: Library generation was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, T cells were loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA cell lysate in each GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and a 10x Barcode. Barcoded and pooled cDNA was cleaned up with DynaBeads, amplified by PCR and the appropriate size fragments were selected using SPRIselect beads for downstream library construction. During  library construction, Ilumina primer sequences and a sample index were added for paired-end sequencing.

value: Lymphocyte

value: CD8 T cell


title: Adipose subcutaneous_99b56b6f-c3cd-4d24-8635-bd62742a2f42 at day D0


title: WT OT-I, tumor, scRNAseq

description: 10x Genomics


title: Adipose visceral_45adb24f-23b7-43f8-9612-0a7ecaa22ada at day D3


title: WT 3 min rep 2


title: Adipose visceral_45adb24f-23b7-43f8-9612-0a7ecaa22ada at day D14


title: In-vitro TGF-beta treated sample [H9_T_25_rep1]


title: WT 1 min rep 2


title: In-vitro BMP treated sample [H9_B_44_rep3]


title: Adipose visceral_45adb24f-23b7-43f8-9612-0a7ecaa22ada at day D0


title: In-vitro BMP treated sample [H9_B_44_rep1]


title: Adipose subcutaneous_45adb24f-23b7-43f8-9612-0a7ecaa22ada at day D3


title: In-vitro BMP treated sample [H9_B_44_rep2]


title: H1299 miR411ED 2

type: RNA

city: Richmond

first: Mario

last: Acunzo

state: Virginia

address: 1220 East Broad Street

department: Internal Medicine

institute: VCU

description: Gene expression of H1299 transfected with edited miR411

hyb_protocol: 100 nanograms of total RNA were hybridized overnight with nCounter Reporter (20 μL) probes in hybridization buffer and excess of nCounter Capture probes (5 μL) at 65 °C for over night. After overnight hybridization, excess probes were removed using two-step magnetic beads-based purification on an automated fluidic handling system (nCounter Prep Station). Biotinylated capture probe-bound samples were immobilized and recovered on a streptavidin-coated cartridge. The abundance of specific target molecules was then quantified using the nCounter digital analyzer. Individual fluorescent barcodes and target molecules present in each sample were recorded with a CCD camera by performing a high-density scan (600 fields of view).

data_processing:
Normalization was performed using the nSolver Analysis Software (Version 4.0; NanoString Technologies), applying the geometric mean of the negative controls for negative background subtraction; the positive controls for the technical normalization; and the housekeeping genes for the biological normalization in all samples, as recommended by NanoString.
P values were calculated using the limma package (v3.48.3) from the Bioconductor R project.
P values were used to rank all genes, retaining those under a significant threshold of 0.01 and with a geometric mean expression of > 20 counts (in at least one condition) after negative background subtraction and a |linear fold-change| > 1.25.

label: color-coded digital barcodes

source_name: Lung Cancer Cell Line

label_protocol: All sample preparations were performed according to the manufacturer’s instructions (NanoString Technologies).

extract_protocol: Cell lines were transfected at 60% confluence in OPTIMEM® (ThermoFisher) without antibiotics and then transfected with 100 nmol of custom-made ed.miR-411-5p oligonucleotides, miR-411-5p WT or negative control using lipofectamine 3000 ( ThermoFischer)  for 48h.   Total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA, USA) and purified using RNA Cleanup and Concentration kit (Norgen, Thorold, ON, Canada). RNA quantification was performed using Nanodrop 2000 (Thermo-Scientific, Waltham, MA, USA). gene expression profile was performed using the nCounter PanCancer Pathways Panel and nCounter Nanostring platform according to the manufacturer’s protocol (NanoString Technologies).


title: H1299 miR411ED 1

scan_protocol: Individual fluorescent barcodes and target molecules present in each sample were recorded with a CCD camera by performing a high-density scan (600 fields of view).


title: H1299 miR411ED 3


title: WT 9 min rep 1


title: H1299 Scamble 2

description: Gene expression of H1299 transfected with Scr as control

value: SCR


title: In-vitro BMP treated sample [H9_B_25_rep1]

value: chondrocytes


title: Adipose subcutaneous_45adb24f-23b7-43f8-9612-0a7ecaa22ada at day D14


title: Adipose subcutaneous_45adb24f-23b7-43f8-9612-0a7ecaa22ada at day D0


title: WT 3 min rep 1


title: H1299 Scamble 3


title: In-vitro TGF-beta treated sample [H9_T_44_rep3]

value: In-vitro TGF-beta treated sample


title: Adipose visceral_3d591a9f-64e9-4308-8814-2b8b662b8833 at day D8

value: adipose


title: H520 miR411ED 3

description: Gene expression of H520 transfected with edited miR411


title: Adipose visceral_3d591a9f-64e9-4308-8814-2b8b662b8833 at day D3

value: visceral


title: H1299 Scamble 1


title: WT 0 min rep 1

value: C. crescentus cells


title: WT 0 min rep 2


title: Retap rep 2 time 15


title: Retap rep 2 time 8


title: N91_dis50mM_4

city: Montréal

first: Noel

last: Raynal

state: QC

address: 3175, Chemin de la Côte-Sainte-Catherine

department: Pharmacologie et physiologie

country: Canada

institute: Université de Montréal

data_processing:
Raw reads were aligned to the hg19 genome reference using STAR v2.4.2.
Expression counts were obtained using htseq-count v0.6.1p1 on the Ensembl Homo_sapiens.GRCh37.75.gtf.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw gene expression counts for each sample

growth_protocol: Neuroblastoma cell line N91, was obtained from ATCC (Manassas, VA) and grown in EMEM. Cell culture media was supplemented with 10 % foetal bovine serum (Wisent, Saint-Jean-Baptiste, QC). Cells were maintained in log phase growth and passaged twice a week.

extract_protocol:
Mini AllPrep DNA/RNA kits from Qiagen
Ribo-Zero Gold Kit according to Illumina's protocol
Strand specific total RNA-seq

treatment_protocol: Disulfiram was dissolved in DMSO and replaced after 24h. Treatment was 50 nM for 448 hours.

value: Neuroblastoma cell line

value: Disulfiram 50 nM, 48h


title: H520 miR411ED 2


title: H520 miR411ED 1


title: Adipose visceral_3d591a9f-64e9-4308-8814-2b8b662b8833 at day D0


title: N91_dis50mM_2


title: Adipose subcutaneous_3d591a9f-64e9-4308-8814-2b8b662b8833 at day D8


title: Retap rep 2 time 4

value: WT


title: In-vitro TGF-beta treated sample [H9_T_44_rep2]


title: H520 Scamble 3

description: Gene expression of H520 transfected with Scr as control


title: WT 1 min rep 1


title: In-vitro TGF-beta treated sample [H9_T_44_rep1]


title: Retap rep 2 time 2


title: Adipose subcutaneous_3d591a9f-64e9-4308-8814-2b8b662b8833 at day D3


title: H520 Scamble 2


title: Adipose visceral_3d591a9f-64e9-4308-8814-2b8b662b8833 at day D14


title: N91_ctl_3

value: Untreated


title: Retap rep 2 time 1


title: Adipose subcutaneous_3d591a9f-64e9-4308-8814-2b8b662b8833 at day D14


title: Zebrafish heart , 7dpa, DN, H3K4me3

city: Beijing

first: Jing-Wei

last: Xiong

address: Peking University, No.5 Yiheyuan Road Haidian District

country: China

institute: Institute of Molecular Medicine, Peking University

data_processing:
The libraries were loaded for pair-end sequencing using Illumina Novaseq 6000.
We used the same number of reads (17.5 million pairs) randomly selected from samples of each condition for downstream analysis. Trimmomatic tool (Version: 0.39) was used to trim reads with a quality drop below a mean of Q15 in a window of 5 nucleotides and reads with length below 15 nucleotides were filtered out.
After the quality control step, the trimmed and filtered reads were aligned to the Zebrafish reference genome GRCz11 using STAR (Version: 2.7.8a) with the parameters “--outFilterMismatchNoverLmax 0.2-outFilterMatchNmin 20 --alignIntronMax 1 --outFilterMultimapNmax 1” to retain only unique alignments.
Reads were deduplicated using Picard (Version: 2.25.0) to remove PCR artefacts.
The MACS2 peak caller (Version: 2.2.7.1) was employed for each condition with parameters “-q 0.0001 -broad -nomodel -nolambda”. Peaks not located in defined chromosomes were further removed. The filtered peaks were used to do the downstream analysis.
Intersection between peaks in CtrlK and DNK conditions was performed with Bedtools toolkit (Version: 2.30.0). Normalized read coverages and subtraction of read coverage were calculated with deeptools toolkit (Version: 2.5.3). ChIPseeker was performed to display the genomic distribution of H3K4me3 peaks based on the matching gene annotation (v. 103) from Ensembl. The H3K4me3 ChIP-seq traces were represented in IGV (Integrative Genomics Viewer) browser.
Assembly: GRCz11
Supplementary files format and content: BROADPEAK files include broad peaks for each sample

organism: Danio rerio

source_name: heart

extract_protocol:
About 25 zebrafish hearts were pooled for each ChIP experiment. The hearts were dissected from adult zebrafish, and the outflow tract and atrium were removed. Chromatin isolation and ChIP assays were performed using a Pierce Magnetic ChIP Kit (Pierce). Anti-H3K4me3 (Abcam) antibodies were used for the ChIP assays. The DNA bound by ChIP was used for ChIP-seq library construction.
ChIP-seq libraries were prepared using the VAHTS Universal Pro DNA Library Prep Kit (Vazyme) for Illumina. 5 nanogram of DNA was used as starting material for input and IP samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit (Agilent).

treatment_protocol: Adult zebrafish were treated with 4-HT for 3days before ventricles amputation. The adult zebrafish hearts were then amputated. The whole ventricles at 7 dpa were subjected to ChIP-seq analysis using H3K4me3 antibody.

value: heart

value: 4-HT for 3days

value: whole heart cells


title: H520 Scamble 1


title: N91_dis50mM_3


title: N91_ctl_2


title: Adipose subcutaneous_3d591a9f-64e9-4308-8814-2b8b662b8833 at day D0


title: Adipose visceral_1602e628-4243-4c33-ab30-b774f1db0740 at day D3


title: Zebrafish heart , 7dpa, Ctrl, input

description: Ctrl-input

treatment_protocol: Adult zebrafish were treated with 4-HT for 3days before ventricles amputation. The adult zebrafish hearts were then amputated.


title: Retap rep 2 time 0


title: Adipose visceral_1602e628-4243-4c33-ab30-b774f1db0740 at day D14


title: ATAC-seq_shCEBPA 2

city: paris

first: Jerome

last: Tamburini

address: 22 rue mechain

country: France

institute: Cochin Institute

data_processing: Adapter trimming and quality controls were performed using Trimgalore v0.6.5. and FastQC v0.11.7. Reads were aligned to the hg38 reference genome by using Bowtie2 v2.2.9. with the splicing alignment feature switched off. The chromatin-accessible peaks were called using Macs2 callpeaks v2.2.7.1 (q-value <0.01). The CHIPIN method and bedtools suite were used for normalisation and comparision.

source_name: hematopoietic

extract_protocol: shCTL and shC/EBPα MOLM14 cells (in biological duplicates) were FACS-sorted, and ATAC-seq was performed as previously described (94) with minor modifications. Briefly, 50 000 cells were lysed in ice-cold lysis buffer and the transposition reaction was performed using the Tn5 transposase at 37°C for 30 min. DNA was purified using the QIAGEN MinElute kit (QIAGEN). The libraries were prepared using Tagment DNA Enzyme and Buffer kits (Illumina), NEBNext High-Fidelity 2X PCR Master Mix (NEB, catalog # M0541S) with custom sequencing primers (95–98). The libraries were purified twice using AMPure XP beads (Beckman) following a double-sided protocol to remove primer dimers and large fragments. Libraries quality was assessed using the NGS High Sensitivity Kit on the Fragment Analyzer (Agilent Technologies, Santa Clara, USA). Only high-quality libraries were subsequently equimolarly pooled and sequencing was performed at the Pôle Technologique du CRCT – Plateau de Génomique et Transcriptomique (Inserm-UMR1037, Toulouse, France). The pool of libraries was quantified by qPCR using the KAPA Library Quantification Kit (Roche, Basel, Switzerland) to obtain an accurate quantification. Sequencing was then performed on one flowcell of the Illumina NextSeq 550 instrument (Illumina, San Diego, USA), using the NextSeq 500/550 High Output Kit v2.5 (150 Cycles), and a paired-end 2 x 75 pb strategy. A minimum of 2x80 million raw reads were produced per sample.

tag: disease state

value: acute myeloid leukemia

value: hematopoietic

value: shCEBPA


title: ATAC-seq_shCTL 2

value: shCTL


title: Retap rep 1 time 4


title: Retap rep 1 time 8


title: Retap rep 1 time 15


title: Adipose visceral_1602e628-4243-4c33-ab30-b774f1db0740 at day D0


title: ATAC-seq_shCTL 1


title: N91_ctl_4


title: Zebrafish heart , 7dpa, DN, input

description: DN-input


title: Retap rep 1 time 2


title: EOC733_pPer_scRNAre-analyzed

city: Helsinki

first: Matías

last: M. Falco

address: Biomedicum Helsinki 1, Haartmaninkatu 8

department: Faculty of Medicine

country: Finland

institute: University of Helsinki

data_processing:
de-multiplexing, alignment, barcode processing and unique molecular identifier (UM)I quantification were performed using the Cell Ranger Software Suite (Version 6.0.1)
cell quality control was performed using Seurat v4
Assembly: GRCh38.d1.vd1
Supplementary files format and content: Matrix table with raw UMI counts

source_name: Peritoneum

extract_protocol:
Tumor samples were dissected and enzymatically digested in a mixture of collagenase and hyaluronidase to obtain single-cell suspensions. Resulting cell suspensions were used without any selection/enrichment to create single-cell RNA sequencing libraries
Chromium Single Cell 3′ Reagent Kit v. 3.1 (10x Genomics)

value: high-grade serous ovarian cancer (HGSOC)

tag: individual

tag: treatment phase

value: Treatment-naive

value: Peritoneum


title: EOC883_pAdn_scRNAre-analyzed

source_name: Adnexa

value: Adnexa


title: Adipose subcutaneous_1602e628-4243-4c33-ab30-b774f1db0740 at day D3

value: adipose

value: subcutaneous


title: ATAC-seq_shCEBPA 1


title: In-vitro TGF-beta treated sample [RR22-12wT]

data_processing:
alignment to hg19: Star align version 2.7.3, default parameters for hg19 alignment
RNA-seq read mapping: Salmon version 1.2.1, salmon -l A --numBootstraps 100 --gcBias –validateMappings
Read abundance normalization: DESeq2 version 1.36.0
Assembly: hg19
Supplementary files format and content: batch5RR4812samples_normalized_counts.txt: Normalized abundance counts across  primary RNA-seq datasets generated

extract_protocol: NEBNext Ultra II RNA Library Prep Kit

value: chondrocytes

value: In-vitro TGF-beta treated sample


title: Retap rep 1 time 0

value: C. crescentus cells

value: WT


title: H3A31S-GFP Replicate 3

city: Baltimore

last: Urban

state: MD

address: 3400 N. Charles Street

department: Biology Department

institute: Johns Hopkins University

description:
rc_HMM_9states.txt
H3mutant_combined_dm6_mapq10_noDup.graph.sort.bw

data_processing:
Basecalls performed
Reads from  ChIC-seq were mapped to drosophila genome (dm6) using Bowtie2. Reads with MAPQ ≤ 10 or redundant reads that mapped to the same location and orientation were removed
Assembly: dm6
Supplementary files format and content: rc_HMM_9states.txt number of reads were measured at each region indluded in the file named "9_State_HMM_prediction_v2.txt". Each column refer to the 12 samples and the number refer to readcount
Supplementary files format and content: H3_combined_dm6_mapq10_noDup.graph.sort.bw normlized by the library size and using a window size of 20bp
Supplementary files format and content: H3mutant_combined_dm6_mapq10_noDup.graph.sort.bw normlized by the library size and using a window size of 20bp
Supplementary files format and content: H3p3_combined_dm6_mapq10_noDup.graph.sort.bw normlized by the library size and using a window size of 20bp
Supplementary files format and content: H3p3mutant_combined_dm6_mapq10_noDup.graph.sort.bw normlized by the library size and using a window size of 20bp
Supplementary files format and content: 9_State_HMM_prediction_v2.txt the DNA Rregions refer to 9 chromatin states first column is for chromsome, second column is for start site, and third column is for end site, the forth column is for one of the nine state

organism: Drosophila melanogaster

source_name: Testis

growth_protocol: Fly stocks were maintained in bottles containing a standard molassas recipe from the Bloomington Stock Center. Crosses to combine the nanos driver with the combined Unpaired and GFP-tagged histone transgenes were prepared in bottles and maintained at 25°C. Upon eclosion, male progenies of the appropriate genotype were allowed to age for ~2 days prior to sample preparation.

extract_protocol:
Resuspended cells were fixed for 5 minutes upon the addition of formaldehyde to a final concentration of 1%. The reaction was quenched by adding 1/10 the volume of 1.25M glycine, followed by end-over-end rotation for 5 minutes. Next, the fixation solution was removed by pelleting cells at 1,320rpm for 7 minutes at 4°C. The cell pellet was washed with 500uL cold 1XPBS, followed by centrifugation and wash removal. This was repeated once. After the last wash, cells were resuspended in 20uL 1XPBS and 1uL of cells was removed for cell count with Trypan Blue.    The cleaved DNA was purified from the cell lysate following the manufacturer's recommendations in the MinElute Reaction Cleanup Kit. The DNA was eluted in 10uL of sterile 10mM Tris, pH8.0.      For a single biological replicate, the ProteinA-MNase and antibody complex was prepared by combining 1uL anti-GFP antibody (Abcam ab290), 3uL PA-MNase enzyme, and 4uL antibody binding buffer (1X Tris EDTA, pH7.5, 150mM NaCl, 0.1% Triton-X 100). The mixture was incubated on ice for 30 minutes. Meanwhile, the cell pellet was resuspended in 500uL RIPA buffer (1X Tris, EDTA pH7.5, 150mM NaCl, 0.2% SDS, 0.1% Sodium Deoxycholate, 1% Triton-X 100)  and incubated at room temperature for 10 minutes. Next, the cells were pelleted by spinning at room temperature for 5 minutes at 3,000 rpm. The cells were washed once with 500uL antibody binding buffer after RIPA removal. The cells werecentrifuged again and the pellet resuspended gently in 100uL antibody binding buffer. The 100uL of cells were gently added to the tubes containing 8uL of the antibody-MNase enzyme complex before incubating on ice for 1hour.    Following incubation, the cells were washed several times to remove excess antibody-enzyme complex. All centrifugation steps were done at 3,000 rpm for 5 minutes at 4°C. First, the cells were spun down to remove the antibody binding buffer. They were then washed in 500uL high salt wash (1X Tris, EDTA pH 7.5, 400mM NaCl, 1% Triton-X 100), with a 1 minute room temperature incubation prior to centrifugation. The high salt wash was repeated a total of three times. After the third wash, the cells were washed in 200uL rinsing buffer (10mM Tris pH7.5, 10mM NaCl, 0.1% Triton-X 100) followed by immediate centrifugation.     After removing the rinsing buffer, the cell pellet was resuspended in 40uL RSB (20mM Tris pH7.5, 10mM NaCl, 2mM CaCl2, 0.1% Triton-X 100). Next, the cells were incubated in a 37°C waterbath for precisely 3 minutes to perform the MNase digestion. To stop the digestion, 80uL of stop buffer (20mM Tris pH8, 10mM EGTA, 20mM NaCl, 0.2% SDS) was added to the reaction. Finally, 1uL of 19mg/mL Proteinase K was added and the solution incubated overnight at 65°C.
Library construction was performed by following the manufacturer's recommendations in the NEBNext DNA UltraII kit.

treatment_protocol: Male flies of the correct genotype were first briefly rinsed in 74% ethanol before proceeding to dissection. Testis tumors were dissected in freshly prepared and filter sterilized Schneider's media containing 10% FBS. At this point, a quality control check of testis tumor condition was performed. Only very large testes with minimal differentiating germline were used in the sample preparation. The biological replicates for each histone type contain an equivalent number of testis pairs (ranging from 18-20). Following dissection, testes were digested in 200-300uL tissue digestion buffer composed of 2mg/mL collagenase disolved in TrypLE Express. The tissue was digested to completion in a 37°C water bath for 10-15 with agitation every 2-3 minutes. The suspended cells were next filtered sequentially first with a 40um nylon mesh cell stainer, followed by at 10um cell strainer. Cells were pelleted in 10 minute intervals at 1,200rpm  until all digestion buffer was removed. The cell pellets were gently resuspended in 400uL Schnieder's media with 10% FBS.

value: Testis

value: germcell

value: nanos > Unpaired, H3A31S-GFP

tag: antibody

value: ChIC antibody, ABCAM ab290


title: In-vitro TGF-beta treated sample [RR22-8wT]


title: Chlor rep 2 time 15


title: In-vitro BMP4 treated sample [RR22-12wB]

value: In-vitro BMP4 treated sample


title: Adipose subcutaneous_1602e628-4243-4c33-ab30-b774f1db0740 at day D0


title: Chlor rep 2 time 4


title: Zebrafish heart , 7dpa, Ctrl, H3K4me3

value: heart

value: 4-HT for 3days

value: whole heart cells


title: H3A31S-GFP Replicate 1


title: H3A31S-GFP Replicate 2


title: Adipose visceral_04555ceb-a655-4306-a122-02ef5bd2564d at day D14

value: visceral


title: Adipose visceral_04555ceb-a655-4306-a122-02ef5bd2564d at day D3


title: Human melanocyte, UV-irradiated, 1 [scRNA-seq]

city: Suwon

first: Jin Cheol

last: Kim

address: 206, World cup-ro, Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

data_processing:
Single cell gene expression data was analyzed using Cell Ranger v6.1.2 (10x Genomics; https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Briefly, raw BCL files from Illumina sequencing instrument were demultiplexed to generate FASTQ files using ‘cellranger mkfastq’. Then, these raw FASTQ files were analyzed using ‘cellranger count’. The ‘cellranger count’ step includes mapping to the human reference genome (GRCh38-2020-A), measuring gene expression with unique molecular identifier (UMI) and cell barcode, determining cell clusters, and conducting differential gene expression analysis.
Assembly: hg19
Supplementary files format and content: tav and mtx files contating cell barcodes and gene count  matrix

source_name: Primary normal human melanocytes (HEMn-MP, Gibco, C1025C)

extract_protocol:
Chromium Single Cell 3' Protocol of 10x genomics to profile 3' digital gene expression of 500-10,000 individual cells per sample.
Libraries were prepared using the Chromium controller according to the 10x chromium Next GEM Single Cell 3’ v3.1 protocol(CG000315). Briefly, the cell suspensions were diluted in nuclease-free water to achieve a targeted cell count of 10,000. Cell suspension was mixed with master mix and loaded with Single Cell 3’V3.1 Gel Beads and Partitioning Oil into a chromium Next GEM chip G. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled and the cDNA pool then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide(KAPA) and qualified using the Agilent Technologies 4200 TapeStation(Agilent technologies). And then the libraries were sequenced using HiSeq X Ten(Illumina) according to the read length in the user guide.

value: Melanocyte

value: Ultraviolet (UV)


title: H3.3S31A-GFP Replicate 3

description:
rc_HMM_9states.txt
H3p3mutant_combined_dm6_mapq10_noDup.graph.sort.bw

value: nanos > Unpaired, H3.3S31A-GFP


title: In-vitro BMP4 treated sample [RR22-8wB]


title: In-vitro BMP4 treated sample [RR22-4wB]


title: Chlor rep 2 time 1


title: Retap rep 1 time 1


title: Adipose visceral_04555ceb-a655-4306-a122-02ef5bd2564d at day D0

value: adipose


title: Chlor rep 2 time 2


title: Adipose subcutaneous_04555ceb-a655-4306-a122-02ef5bd2564d at day D3

value: subcutaneous


title: H3.3S31A-GFP Replicate 2


title: In-vitro TGF-beta treated sample [RR4-8wT]

value: chondrocytes

value: In-vitro TGF-beta treated sample


title: Adipose subcutaneous_1602e628-4243-4c33-ab30-b774f1db0740 at day D14


title: H3.3S31A-GFP Replicate 1


title: H3.3-GFP Replicate 3

description:
rc_HMM_9states.txt
H3p3_combined_dm6_mapq10_noDup.graph.sort.bw

value: nanos > Unpaired, H3.3-GFP


title: Chlor rep 2 time 0

value: C. crescentus cells

value: WT


title: In-vitro TGF-beta treated sample [RR4-4wT]


title: Chlor rep 2 time 8


title: In-vitro TGF-beta treated sample [RR22-4wT]


title: Adipose subcutaneous_04555ceb-a655-4306-a122-02ef5bd2564d at day D0


title: Chlor rep 1 time 15


title: H3.3-GFP Replicate 2

value: Testis

value: germcell


title: Adipose visceral_04e9a263-be56-4ee1-b497-2a4afc3750ae at day D3


title: Chlor rep 1 time 8


title: Adipose visceral_04e9a263-be56-4ee1-b497-2a4afc3750ae at day D14


title: In-vitro BMP4 treated sample [RR4-8wB]

value: In-vitro BMP4 treated sample


title: Chlor rep 1 time 4


title: In-vitro BMP4 treated sample [RR4-4wB]


title: H3.3-GFP Replicate 1

value: ChIC antibody, ABCAM ab290


title: H3-GFP Replicate 3

description:
rc_HMM_9states.txt
H3_combined_dm6_mapq10_noDup.graph.sort.bw

value: nanos > Unpaired, H3-GFP


title: H3-GFP Replicate 2


title: Adipose visceral_66b82cc1-412a-4f50-9281-734f34bcf645 at day D8


title: H3-GFP Replicate 1


title: Chlor rep 1 time 2


title: In-vitro TGF-beta treated sample [RR2-12wT]


title: Adipose visceral_66b82cc1-412a-4f50-9281-734f34bcf645 at day D3


title: Adipose subcutaneous_04555ceb-a655-4306-a122-02ef5bd2564d at day D14


title: In-vitro TGF-beta treated sample [RR2-4wT]


title: In-vitro TGF-beta treated sample [RR2-8wT]


title: 13d41

city: Madison

last: Ortega

state: Wisconsin

address: 1675 Observatory Drive

department: Department of Animal and DairySciences

institute: University of Wisconsin

description: RNA from individual embryo outgrowths

data_processing:
The quality of fastq files of sequences data was checked with a FastQC tool
Illumina adapters were trimmed
Reads were mapped to the bovine reference genome using the Hisat2
Read counts were determined using FeatureCounts program
Differentially expressed genes (DEGs) between sample groups were determined by edgeR-robust
Assembly: Bos_taurus.ARS-UCD1.2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: Trophectoderm

growth_protocol: Hatched embryos were plated in collagen IV plates, at day 10 and kept in trophectoderm growth media.

extract_protocol:
Cells were collected in Trizol reagent, flash frozen on liquid nitrogen, and RNA was harvested using manufacter protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Trophectoderm cells outgrowths from two different days in culture, day 35 and day 41.

value: In vitro produced embryos

value: Trophectoderm cells


title: Adipose visceral_66b82cc1-412a-4f50-9281-734f34bcf645 at day D14

extract_protocol: Library preparation, sequencing and reference genome alignment was carried out by the Genomics Platform at the Broad Institute. After final quality control samples were sequenced generating 50 million paired end reads per sample

value: visceral


title: 7d41

description: RNA from individual embryo outgrowths


title: Chlor rep 1 time 0

extract_protocol:
The cells were pelleted at 20,000 x g for 1 min in 1.5 mL eppendorf tubes to prepare for RNA extraction.Pelleted cells were resuspended in 1mL of pre-warmed (to 65 0C) TRizol Reagent (Ambion) and incubated for 10 min at 65 0C in a heat block. 200 mL of chloroform were added to the samples and tubes were gently inverted a few times. Then samples were incubated at room temperature for 5 min and spun at 20,000 x g for 10 min. The supernatant was moved to siliconized tubes and 500 mL of chloroform was added, vortexed, and spun at 20,000 x g for 10 minutes. RNA samples were precipitated using isopropanol (1x volume isopropanol, 0.1X volume 5M NaOAc pH 5.2) overnight at – 80 0C. The RNA samples were spun at 20,000 x g at 4 0C for 1 hour. Pellets were washed with cold 80% ethanol and spun for 10 min at 20,000 x g, air-dried, and resuspended in 10 mM Tris-HCl (pH 7.0). The RNA-Seq libraries were made using 5µg of total RNA of each sample. Ribosomal RNAs were removed by ribozero gram negative kit and library construction was performed according to the protocol in (Aretakis et al., 2018).
mRNA fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)].  Updated adapter oligos that are compatible with the novaseq were used from [Aretakis et al. Methods in Enzymology (2019)].


title: DENV4 ex virion RNA DMSO

city: Chapel Hill

first: Mark

middle: A

last: Boerneke

state: NC

address: Campus Box 3290

department: Chemistry

institute: University of North Carolina

description:
reverse transcribed RNA
dengue virus 4
SHAPE-MaP

data_processing:
Adduct locations identified by Shapemapper2 software
RNA structure models were generated from SHAPE data using SuperFold software
RNP-MaP analysis was generated with in-house software from shapemapper outputs
Supplementary files format and content: filename_shapemapper.txt; shapemapper output text file
Supplementary files format and content: filename_SHAPE-MaP.shape; shapemapper output shape file

organism: dengue virus type 4

source_name: kidney

extract_protocol:
RNA gently extracted from purified virus particles
Nextera XT workflow
SHAPE-MaP and RNP-MaP

value: kidney

value: Vero

value: epithelial

value: DMSO


title: In-vitro BMP4 treated sample [RR2-12wB]

source_name: HESC-derived chondrocytes

value: chondrocytes


title: Adipose visceral_66b82cc1-412a-4f50-9281-734f34bcf645 at day D0

value: adipose


title: DENV4 ex virion RNA 1M7


title: In-vitro BMP4 treated sample [RR4-12wB]


title: Adipose visceral_04e9a263-be56-4ee1-b497-2a4afc3750ae at day D0


title: Chlor rep 1 time 1


title: DENV3 ex virion RNA DMSO

description:
reverse transcribed RNA
dengue virus 3
SHAPE-MaP

organism: dengue virus type 3


title: 1d41

description: RNA from individual embryo outgrowths


title: Adipose subcutaneous_66b82cc1-412a-4f50-9281-734f34bcf645 at day D8

value: subcutaneous


title: In-vitro BMP4 treated sample [RR2-4wB]


title: 8d35

description: RNA from individual embryo outgrowths


title: EOC883_pAdn_scRNA

value: high-grade serous ovarian cancer (HGSOC)

value: Treatment-naive

value: Adnexa


title: Adipose subcutaneous_66b82cc1-412a-4f50-9281-734f34bcf645 at day D3


title: Adipose subcutaneous_66b82cc1-412a-4f50-9281-734f34bcf645 at day D14


title: DENV3 ex virion RNA 1M7


title: 4d35

description: RNA from individual embryo outgrowths


title: 5d35

description: RNA from individual embryo outgrowths


title: DENV2 8500 Lock Mutant in cell RNA DMSO

description:
reverse transcribed RNA
dengue virus 2
RNP-MaP

organism: dengue virus type 2

value: fibroblast


title: Adipose subcutaneous_66b82cc1-412a-4f50-9281-734f34bcf645 at day D0


title: EOC733_pPer_scRNA

value: Peritoneum


title: DENV2 8500 Lock Mutant in cell RNA SDA

value: 3J-UV and 10mM SDA


title: Adipose visceral_d2a02910-676b-4642-b935-eeb655587eb0 at day D8


title: 1d35

description: RNA from individual embryo outgrowths


title: Adipose visceral_d2a02910-676b-4642-b935-eeb655587eb0 at day D3


title: In-vitro BMP4 treated sample [RR2-8wB]

value: In-vitro BMP4 treated sample


title: 3d41

description: RNA from individual embryo outgrowths

value: In vitro produced embryos


title: DENV2 8500 WT in cell RNA DMSO


title: DENV2 8500 WT in cell RNA SDA


title: Human menstrual bloodderived endometrial stem cells-conditioned medium2

type: protein

city: Xinxiang

first: Han

last: Li

address: 601 Jinsui Road, Hongqi District, Xinxiang City, Henan Province

institute: Xinxiang Medical University

description: Secreted proteins

hyb_protocol: 5-fold diluted culture supernatant was added to each well. After overnight incubation at 4°C and extensive washing, the biotin-labeled detection antibody was added for 2 hours and then washed away. AlexaFluor 555-conjugated streptavidin was then added and incubated for 1 hour at room temperature.

scan_protocol: The signals (532 nm excitation, 635 nm emission) were scanned and extracted using an InnoScan 300 scanner (Innopsys, Carbonne, France).

data_processing:
Individual array spots were background subtracted locally by subtracting the median background across spot replicated in each sample, and then normalized using two positive controls.
GSH-CAA-X00 software was used to analyze the data

label: AlexaFluor 555

molecule: protein

label_protocol: AlexaFluor 555-conjugated streptavidin

extract_protocol: When MenSCs were 70%–80% sub-confluent,  the growth medium was replaced with 20 mL serum-free DMEM-HG medium (containing 100 m/mL penicillin, 100 mg/mL streptomycin). Culture medium was collected  after  48 h incubation, centrifuged at 600 g for 5 min and passed through a 0.22 mm filter, which was termed  as MenSCs-CM.

value: mesenchymal stem cells derived from menstrual blood

tag: passage


title: Adipose visceral_d2a02910-676b-4642-b935-eeb655587eb0 at day D14

value: visceral


title: DENV2 ex virion RNA DMSO

description:
reverse transcribed RNA
dengue virus 2
SHAPE-MaP

value: kidney


title: Human menstrual bloodderived endometrial stem cells-conditioned medium1

description: Secreted proteins


title: RNAseq.ScapKO.KC.ZT22.rep2

city: Houston

first: Dongyin

last: Guan

state: TX

address: 1 Baylor Plaza, ABBR

institute: Baylor College of Medicine

data_processing:
RNA-seq reads were aligned to the University of California, Santa Cruz (UCSC) mm9 genome browser using STAR. The tag directories were established and normalized read counts were measured with RefSeq genes using Homer.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include tag counts for each Sample.

source_name: liver

extract_protocol:
Total RNA was extracted from liver tissue or isolated endothelial cells and Liver macrophages using Trizol reagent followed by RNeasy Mini Kit (#74104).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: liver

tag: stain

value: male

value: Liver macrophage

value: ScaphKO

tag: diet

value: 4-week high fat and sucrose diet, D12492i


title: ZH112

city: Guangzhou

first: Limin

last: Wang

address: zhongkai road 501

institute: Zhongkai University of Agriculture and Engineering

data_processing:
In order to gain clean reads, the raw reads were filtered using Fastp by removing low-quality reads.
We used the Bowtie 2 to remove the read of the rRNA on the comparison without mismatch, and used the retained unmapped read for subsequent transcriptome analysis.
The resulting high-quality clean reads were mapped to Nipponbare (http://plants.ensembl.org/Oryza_sativa/Info/Index) reference genome using HISAT 2.
The resulting alignment was used Stringtie to reconstruct transcripts.
The fragment counts of each gene were normalized by kb of transcript per million mapped reads to obtain the fragment per kilobase million (FPKM).
Assembly: Nipponbare (http://plants.ensembl.org/Oryza_sativa/Info/Index) reference genome
Supplementary files format and content: Gene expression levels were estimated using FPKM values by the RSEM.

organism: Oryza sativa

source_name: Fresh leaves

extract_protocol:
RNA-seq analysis was conducted using total RNA extracted from leaves of Dap1 mutant and WT plants at the booting stage with three biological replicates. Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) Beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

tag: tissue

value: Fresh leaves

value: wildtype


title: ZH113


title: RNAseq.ScapKO.KC.ZT22.rep1

tag: Sex


title: DENV2 ex virion RNA 1M7

value: Vero

value: epithelial


title: Adipose visceral_d2a02910-676b-4642-b935-eeb655587eb0 at day D0

city: Cambridge

last: Claussnitzer

address: 75 Ames Street

institute: Broad Institute of MIT and Harvard

data_processing:
Generating count tables using featureCounts function (Liao, Smyth, and Shi 2013) in the Rsubread package
Normalization using DESeq2
Analysis of variance (ANOVA) in R
Genome_build: hg19
Supplementary_files_format_and_content: normalized count

source_name: Adipose visceral

value: adipose

tag: depot


title: RNAseq.ScapKO.KC.ZT16.rep3


title: ZH111


title: Adipose subcutaneous_d2a02910-676b-4642-b935-eeb655587eb0 at day D8

source_name: Adipose subcutaneous

value: subcutaneous

tag: differentation day


title: Dap3

value: Dap


title: DENV1 ex virion RNA DMSO

description:
reverse transcribed RNA
dengue virus 1
SHAPE-MaP

organism: dengue virus type 1

tag: cell type

value: DMSO


title: Dap2


title: Adipose subcutaneous_d2a02910-676b-4642-b935-eeb655587eb0 at day D3


title: RNAseq.ScapKO.KC.ZT16.rep1


title: Δslf1 transcriptomic treated rep 2

city: Manchester

first: Graham

middle: D

last: Pavitt

address: Dover Street

department: MCF/SBS/FBMH

institute: University of Manchester

description: Transcriptomics

data_processing:
PAR-CLIP - adapters (TGGAATTCTCGG and CCACGTTCCCGTGG) were trimmed using Trim Galore!
PAR-CLIP - reads longer than 10nt were aligned to Saccharomyces cerevisiae S288C reference genome R64-1-1 (sacCer3) downloaded from yeastgenome.org using Bowtie v 1.2.0 (-n 2 -v 2 -m 10 -- best -- strata).
PAR-CLIP - reads were processed for binding sites using PARalyzer v1.5 - with standard settings.
Total RNA - Trimmed using Trim Galore! - automatic adaptor detection, filtering for reads over 20.
Total RNA - Mapped with Bowtie - default settings.
Transcriptomic read counts were identified using featureCounts.
Genome_build: R64-1-1 (sacCer3)
Supplementary_files_format_and_content: PARalyzer binding site coordinates and read count in csv file.
Supplementary_files_format_and_content: Transcript read counts in csv file.

organism: Saccharomyces cerevisiae

source_name: Δslf1 transcriptomic treated

growth_protocol: Cells grown until OD600 of 0.6 before splitting into treated versus untreated.

extract_protocol:
Extraction using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Addition of 0.4 mM Hydrogen peroxide for 15 min.

tag: genotype/variation

tag: strain name

tag: treatment

value: Hydrogen peroxide treated - 0.4mM, 15 min

tag: rna extracted

value: Total RNA followed by rRNA depletion


title: RNAseq.ScapKO.KC.ZT22.rep3

tag: genotype


title: DENV1 ex virion RNA 1M7

tag: cell line


title: RNAseq.ScapKO.KC.ZT16.rep2


title: Dap1


title: Adipose subcutaneous_d2a02910-676b-4642-b935-eeb655587eb0 at day D0


title: RNAseq.ScapKO.KC.ZT10.rep3


title: Δslf1 transcriptomic treated rep 1

description: Transcriptomics


title: Adipose visceral_d6d94a18-d93f-436c-b6f1-5ae2ca42b032 at day D3

value: visceral


title: RNAseq.ScapKO.KC.ZT10.rep2


title: Adipose visceral_d6d94a18-d93f-436c-b6f1-5ae2ca42b032 at day D14


title: Rep2 CUT&Tag, rsc2 trunc, replicate 2

city: Austin

first: Vishy

last: Iyer

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Basecalls were performed using BCL2FASTQ version 2.20
ChIP-seq reads were aligned to the sacCer3 reference genome using Bowtie version 1.2.3 using default parameters. CUT&Tag reads were aligned using Bowtie version 1.2.3 with parameters '--end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700'
Aligned reads were processed using MACS version 2.1.4 to generate signal density tracks (bigWig files) after combining biological replicates. For ChIP-seq, tracks were generated by comparing ChIP to input samples. For CUT&Tag (lacking inputs), each sample was processed on its own.
Assembly: sacCer3
Supplementary files format and content: bigWig (except for input samples)
Library strategy: CUT&Tag

growth_protocol: Cells were grown in yeast extract + peptone + raffinose (YPR) medium

extract_protocol:
For ChIP-seq, cells were fixed with 1% formaldehyde for 30 minutes, then quenched with glycine (125 mM) for 5 minutes. After cell lysis, chromatin was sonicated using an immersion tip sonicator. For CUT&Tag, cells were spheroplasted using Zymolase. Nuclei were processed using the CUT&Tag-IT Assay Kit from Active Motif using the manufacturer's instructions.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA kit (NEB, product number E7645). The CUT&Tag protocol results in ready to sequence libraries after the final PCR amplication step and cleanup.

treatment_protocol: Cells were induced with 2% galactose for 2 hours at 30°C

tag: strain

value: MATa ade2-1 his3-11::GAL10-3HA-REP1-GAL1-REP2-10Myc::HIS3  leu2-3,112  trp1 ura3-1 truncated rsc2 [Cir0]

tag: chip antibody

value: EZview Red Anti-c-Myc Affinity Gel (Sigma-Aldrich Cat# E6654)


title: Rep2 CUT&Tag, rsc2 trunc, replicate 1


title: RNAseq.ScapKO.KC.ZT10.rep1

value: liver

value: male


title: Adipose subcutaneous_d2a02910-676b-4642-b935-eeb655587eb0 at day D14

first: Melina


title: Rep2 CUT&Tag, rsc2 delta, replicate 2

value: MATa ade2-1 his3-11::GAL10-3HA-REP1-GAL1-REP2-10Myc::HIS3  leu2-3,112  trp1  ura3-1 rsc2d::URA3  [Cir0]


title: Adipose visceral_d6d94a18-d93f-436c-b6f1-5ae2ca42b032 at day D0


title: Δslf1 transcriptomic untreated rep 1

description: Transcriptomics

source_name: Δslf1 transcriptomic untreated

value: Untreated


title: Δslf1 transcriptomic untreated rep 2

description: Transcriptomics


title: Δsro9 transcriptomic treated rep 2

description: Transcriptomics

source_name: Δsro9 transcriptomic treated


title: RNAseq.ScapKO.KC.ZT4.rep3

value: Liver macrophage

value: ScaphKO

value: 4-week high fat and sucrose diet, D12492i


title: Adipose subcutaneous_d6d94a18-d93f-436c-b6f1-5ae2ca42b032 at day D0

description: Low quality sample removed from the analysis


title: Rep2 CUT&Tag, rsc2 delta, replicate 1


title: Rep1 CUT&Tag, rsc2 trunc, replicate 2

value: MATa ade2-1 his3-11::GAL10-REP1-10Myc-GAL1-3HA-REP2::HIS3  leu2-3,112  trp1  ura3-1 truncated rsc2  [Cir0]


title: Δsro9 transcriptomic treated rep 1

description: Transcriptomics


title: RNAseq.ScapKO.KC.ZT4.rep1


title: Rep1 CUT&Tag, rsc2 trunc, replicate 1


title: RNAseq.ScapKO.Hep.ZT22.rep3


title: Adipose visceral_054d67b1-4922-4344-9f66-eedb238355d2 at day D3

value: adipose


title: Δsro9 transcriptomic untreated rep 1

description: Transcriptomics

source_name: Δsro9 transcriptomic untreated


title: RNAseq.ScapKO.KC.ZT4.rep2


title: RNAseq.ScapKO.Hep.ZT22.rep2


title: Δsro9 transcriptomic untreated rep 2

description: Transcriptomics


title: WT transcriptomic treated rep 2

description: Transcriptomics

source_name: WT transcriptomic treated

value: WT


title: Adipose visceral_054d67b1-4922-4344-9f66-eedb238355d2 at day D14


title: Adipose visceral_054d67b1-4922-4344-9f66-eedb238355d2 at day D0


title: RNAseq.ScapKO.Hep.ZT22.rep1


title: Flp CUT&Tag, wt, replicate 2


title: WT transcriptomic treated rep 1

description: Transcriptomics


title: RNAseq.ScapKO.Hep.ZT16.rep2


title: Flp CUT&Tag, wt, replicate 1


title: RNAseq.ScapKO.Hep.ZT16.rep3


title: Rep1 CUT&Tag, rsc2 delta, replicate 1

value: MATa ade2-1 his3-11::GAL10-REP1-10Myc-GAL1-3HA-REP2::HIS3  leu2-3,112  trp1  ura3-1 rsc2d::URA3  [Cir0]


title: Rep1 CUT&Tag, rsc2 delta, replicate 2


title: Rep2 CUT&Tag, wt, replicate 2

value: MATa ade2-1 his3-11::GAL10-3HA-REP1-GAL1-REP2-10Myc::HIS3  leu2-3,112  trp1 ura3-1  [Cir0]


title: Adipose subcutaneous_054d67b1-4922-4344-9f66-eedb238355d2 at day D14

value: subcutaneous


title: RNAseq.ScapKO.Hep.ZT16.rep1


title: Adipose subcutaneous_054d67b1-4922-4344-9f66-eedb238355d2 at day D0


title: WT transcriptomic untreated rep 1

description: Transcriptomics

source_name: WT transcriptomic untreated

value: Total RNA followed by rRNA depletion


title: Adipose visceral_054d67b1-4922-4344-9f66-eedb238355d2 at day D8

value: visceral


title: Adipose subcutaneous_054d67b1-4922-4344-9f66-eedb238355d2 at day D3


title: Adipose visceral_00247bee-1cb5-4e24-92d5-1c0661a9584e at day D3


title: RNAseq.ScapKO.Hep.ZT10.rep3


title: RNAseq.ScapKO.Hep.ZT10.rep2


title: Slf1-TAP transcriptomic peroxide treated rep 2

description: Transcriptomics

value: Hydrogen peroxide treated - 0.4mM, 15 min


title: Rep1 CUT&Tag, wt, replicate 2

value: MATa ade2-1 his3-11::GAL10-REP1-10Myc-GAL1-3HA-REP2::HIS3  leu2-3,112  trp1 ura3-1  [Cir0]

value: EZview Red Anti-c-Myc Affinity Gel (Sigma-Aldrich Cat# E6654)


title: Rep1 No Ab CUT&Tag, wt


title: Adipose subcutaneous_054d67b1-4922-4344-9f66-eedb238355d2 at day D8


title: Adipose visceral_00247bee-1cb5-4e24-92d5-1c0661a9584e at day D0


title: Rep1 CUT&Tag, wt, replicate 1


title: Adipose visceral_00247bee-1cb5-4e24-92d5-1c0661a9584e at day D14


title: RNAseq.ScapKO.Hep.ZT10.rep1

value: liver

value: male


title: Slf1-TAP transcriptomic untreated rep 2

description: Transcriptomics

source_name: Slf1-TAP transcriptomic untreated

value: Untreated


title: Sl1f-TAP transcriptomic peroxide treated rep 1

description: Transcriptomics


title: RNAseq.ScapKO.Hep.ZT4.rep3

value: Liver macrophage


title: Slf1-TAP transcriptomic untreated rep 1

description: Transcriptomics


title: Sro9-TAP transcriptomic peroxide treated rep 2

description: Transcriptomics


title: Rep2 ChIP, rsc2 trunc, replicate 2

data_processing:
Basecalls were performed using BCL2FASTQ version 2.20
ChIP-seq reads were aligned to the sacCer3 reference genome using Bowtie version 1.2.3 using default parameters. CUT&Tag reads were aligned using Bowtie version 1.2.3 with parameters '--end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700'
Aligned reads were processed using MACS version 2.1.4 to generate signal density tracks (bigWig files) after combining biological replicates. For ChIP-seq, tracks were generated by comparing ChIP to input samples. For CUT&Tag (lacking inputs), each sample was processed on its own.
Assembly: sacCer3
Supplementary files format and content: bigWig (except for input samples)

value: MATa ade2-1 his3-11::GAL10-3HA-REP1-GAL1-REP2-10Myc::HIS3  leu2-3,112  trp1 ura3-1 truncated rsc2 [Cir0]


title: Rep2 input, rsc2 trunc, replicate 2


title: Rep2 ChIP, rsc2 trunc, replicate 1


title: Rep2 CUT&Tag, wt, replicate 1


title: Adipose subcutaneous_00247bee-1cb5-4e24-92d5-1c0661a9584e at day D3


title: Sro9-TAP transcriptomic peroxide treated rep 1

description: Transcriptomics


title: RNAseq.ScapKO.Hep.ZT4.rep2

value: ScaphKO

value: 4-week high fat and sucrose diet, D12492i


title: RNAseq.ScapKO.Hep.ZT4.rep1


title: AOM/DSS Normal2

city: BOSTON

first: Nilay

last: Sethi

state: Massachusetts

address: 450 Brookline Ave

institute: DANA-FARBER CANCER INSTITUTE

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Pre-processing, alignment and gene counts: De-multiplexing, alignment to the transcriptome, and unique molecular identifier (UMI) collapsing were performed using the Cellranger toolkit provided by 10X Genomics.
General Clustering: Standard procedures for QC filtering, data scaling and normalization, detection of highly variable genes, and hashtag oligo (HTO) demultiplexing were followed using the Seurat v3 in RStudio. Cells with unique feature counts lower than 100 and greater than 25,000 as well as cells with greater than 25% mitochondrial DNA were excluded. Counts were log-normalized and scaled by a factor of 10,000 according to the default parameters when using the Seurat LogNormalize function. Variable features were identified, and the data were scaled using the default parameters (Ngenes = 2000) of the FindVariableFeatures FIG. caleData Seurat functions, respectively. HTOs were demultiplexed using the HTODemux function, and cells were identified as containing HTO-1 or HTO-2 based on their maximal HTO-ID signal. The cell population was filtered to contain only HTO-positive, singlet cells for further analysis.
HASHING CONDITIONS:72 day induced samples:  - HTO-1 = ApcKO, Sox9WT (mouse 2792)  - HTO-2 = ApcKO, Sox9 F/+ (mouse 3012)  30 day induced sample:  - HTO-3 = ApcKO, Sox9 F/+ (mouse 3047)
Note: The Day 28: WT and Sox9KO and Day 10 data were done using 5' kit with single index, while the rest of the samples were done with 5' v2 kit with dual index.
Assembly: mm10,hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Distal colon

extract_protocol:
Isolated intestines from euthanized mice were washed with ice-cold PBS; villi were scraped using glass slides and dissociated in 5mM EDTA in PBS at 4ºC for 20 minutes, shaking every 5-7 minutes for about 30 seconds. The epithelial fraction was collected by centrifugation and incubated at 37ºC for 30 minutes in pre-warmed 4x TrypLE. Single cells filtered through 70um filter post trypsinization, washed with complete media, and collected in FACS buffer.
About 17,000 viable cells were loaded onto a 10X Genomics ChromiumTM instrument (10× Genomics) according to the manufacturer’s recommendations.  The scRNAseq libraries were processed using ChromiumTM single cell 5’ or 3' library & gel bead kit (10× Genomics). Matched cell hashing libraries were prepared using single cell 5’ feature barcode library kit. Quality controls for amplified cDNA libraries, cell hashing libraries, and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). The sequencing libraries for scRNAseq and scTCRseq were normalized to 4nM concentration and pooled using a volume ratio of 4:1. The pooled sequencing libraries were sequenced on Illumina NovaSeq S4 300 cycle platform. The sequencing parameters were: Read 1 of 150bp, Read 2 of 150bp and Index 1 of 8bp. The sequencing data were demultiplexed and aligned to mm10 or hg19-3.0.0 using cell ranger version 3.1.0 pipeline (10× Genomics).

value: Microdissected Lesion

value: Distal colon

tag: age

value: 23 weeks


title: Sro9-TAP transcriptomic untreated rep 1

description: Transcriptomics

source_name: Sro9-TAP transcriptomic untreated


title: Rep2 input, rsc2 trunc, replicate 1


title: Adipose subcutaneous_00247bee-1cb5-4e24-92d5-1c0661a9584e at day D14

value: adipose


title: Adipose subcutaneous_00247bee-1cb5-4e24-92d5-1c0661a9584e at day D0

value: subcutaneous


title: WT transcriptomic untreated rep 2

description: Transcriptomics

value: WT

value: Total RNA followed by rRNA depletion


title: Slf1-TAP PAR-CLIP peroxide treated rep 2

description: PAR-CLIP

source_name: Slf1-TAP PAR-CLIP peroxide treated

value: Hydrogen peroxide treated - 0.4mM, 15 min

tag: antibody

value: anti-TAP

value: Slf1-TAP crosslinked and RNase trimmed RNA


title: Adipose visceral_abfd88f9-47a0-4161-9333-a848451ea880 at day D3

value: visceral


title: AOM/DSS Normal1

description: 10x Genomics


title: AOM/DSS lesion2

description: 10x Genomics


title: Sl1f-TAP PAR-CLIP peroxide treated rep 1

description: PAR-CLIP

source_name: Sl1f-TAP PAR-CLIP peroxide treated


title: Rep2 ChIP, rsc2 delta, replicate 2

value: MATa ade2-1 his3-11::GAL10-3HA-REP1-GAL1-REP2-10Myc::HIS3  leu2-3,112  trp1  ura3-1 rsc2d::URA3  [Cir0]

value: EZview Red Anti-c-Myc Affinity Gel (Sigma-Aldrich Cat# E6654)


title: Adipose visceral_abfd88f9-47a0-4161-9333-a848451ea880 at day D14


title: Rep2 ChIP, rsc2 delta, replicate 1


title: Rep2 input, rsc2 delta, replicate 2


title: AOM/DSS lesion1

description: 10x Genomics


title: Adipose subcutaneous_abfd88f9-47a0-4161-9333-a848451ea880 at day D3


title: Slf1-TAP PAR-CLIP untreated rep 1

description: PAR-CLIP

source_name: Slf1-TAP PAR-CLIP untreated

value: Untreated


title: Sro9-TAP transcriptomic untreated rep 2

description: Transcriptomics


title: Rep2 input, rsc2 delta, replicate 1


title: Day 10

description: 10x Genomics

source_name: Intestine

value: TdT+

value: Intestine

value: 6-8 weeks old


title: Adipose subcutaneous_abfd88f9-47a0-4161-9333-a848451ea880 at day D14


title: Sox9 HET

description: 10x Genomics


title: Day 28: WT & SOX9KO

description: 10x Genomics


title: Rep1 ChIP, rsc2 trunc, replicate 2

value: MATa ade2-1 his3-11::GAL10-REP1-10Myc-GAL1-3HA-REP2::HIS3  leu2-3,112  trp1  ura3-1 truncated rsc2  [Cir0]


title: Rep1 ChIP, rsc2 trunc, replicate 1


title: Adipose visceral_78ca8a24-4069-41bb-84a4-ad7a4fadd048 at day D3


title: Sro9-TAP PAR-CLIP peroxide treated rep 1

description: PAR-CLIP

source_name: Sro9-TAP PAR-CLIP peroxide treated

value: Sro9-TAP crosslinked and RNase trimmed RNA


title: Adipose subcutaneous_abfd88f9-47a0-4161-9333-a848451ea880 at day D0


title: SN_9_Sham-HFD

city: Oxford

first: Thomas

last: Monfeuga

address: Innovation Building, Old Road Campus, Roosevelt Drive

institute: Novo Nordisk Research Centre Oxford

data_processing:
Adaptor trimming with Trim Galore! (v. 0.6.4_dev)
Alignement with Salmon (v. 1.9.0) (with --noLengthCorrection argument)
Abundance data imported with Tximeta (v. 1.10) (with countsFromAbundance = "no" argument)
Assembly: GRCm38, release M23

source_name: Microdissected hypothalami from Aldh1l1 eGFP-L10a mice

extract_protocol:
Dynabeads mRNA DIRECT Kit
QuantSeq 3’mRNA-Seq Library Prep Kit-FWD

treatment_protocol: Aldh1l1eGFP-L10a mice were fed for 4 weeks with either a chow diet or a high-fat diet (HFD), and a subset of mice were subjected to an orchiectomy ORX. TRAP-seq was performed on micro-dissected hypothalami from mice under three experimental conditions: sham-chow, sham-HFD, and ORX-HFD

tag: fraction

value: Supernatant

value: HFD

value: Sham

tag: group


title: Rep1 input, rsc2 trunc, replicate 2


title: Adipose visceral_abfd88f9-47a0-4161-9333-a848451ea880 at day D0

source_name: Adipose visceral

tag: tissue

value: adipose


title: Sro9-TAP PAR-CLIP untreated rep 2

description: PAR-CLIP

source_name: Sro9-TAP PAR-CLIP untreated


title: Adipose visceral_78ca8a24-4069-41bb-84a4-ad7a4fadd048 at day D14


title: Rep1 input, rsc2 trunc, replicate 1


title: Slf1-TAP PAR-CLIP untreated rep 2

description: PAR-CLIP


title: Zebrafish heart endothelial cells, 7dpa, DNK1

data_processing:
The libraries were loaded for 2 × 150 bp pair-end sequencing using Illumina Hiseq2500.
Raw reads were pre-processed and quality controlled with FastQC (Version: 0.11.9).
Reads for each library were mapped using HISAT2 (Version: 2.2.1) against the zebrafish reference genome assembly GRCz11 with default parameters.
Uniquely mapped reads were extracted to calculate the read counts of each gene, using the matching gene Annotation (v. 103) from Ensembl with featureCounts (Version: 2.0.1).
Genes were further filtered, and those with low expression in all samples (FPKM < 0.5 in all samples) were removed from differential gene expression analysis. Differential analysis was conducted with DEseq2.
Genes with an adjusted P-value <0.05 were taken as significantly differentially expressed genes in the DNK condition compared with CtrlK. FPKM values were calculated with Stringtie (Version: 2.1.5) and Normalized Z-score values were used to draw heatmaps using the ComplexHeatmap R package.
Assembly: GRCz11
Supplementary files format and content: Text files include raw counts for each sample

source_name: heart

extract_protocol:
The total RNA of heart endothelial cells from CtrlK sibling and DNK mutant ventricles at 7 dpa was purified using a Magen RNA Nano Kit (Magen). 30 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using EBNext Ultra DNA Library Prep Kit for Illumina (NEB) following manufacturer's protocols.

value: heart

value: 4-HT for 3days

value: endothelial cells


title: SN_8_Sham-Chow

tag: diet

value: Chow


title: IP_9_Sham-HFD

value: Immunoprecipitate


title: IP_8_Sham-Chow


title: Adipose visceral_78ca8a24-4069-41bb-84a4-ad7a4fadd048 at day D0

tag: depot

value: visceral


title: Rep1 ChIP, rsc2 delta, replicate 1

value: MATa ade2-1 his3-11::GAL10-REP1-10Myc-GAL1-3HA-REP2::HIS3  leu2-3,112  trp1  ura3-1 rsc2d::URA3  [Cir0]

value: EZview Red Anti-c-Myc Affinity Gel (Sigma-Aldrich Cat# E6654)


title: Rep1 ChIP, rsc2 delta, replicate 2


title: Zebrafish heart endothelial cells, 7dpa, DNK2


title: Sro9-TAP PAR-CLIP peroxide treated rep 2

description: PAR-CLIP

value: Hydrogen peroxide treated - 0.4mM, 15 min

value: anti-TAP


title: Adipose subcutaneous_78ca8a24-4069-41bb-84a4-ad7a4fadd048 at day D14

source_name: Adipose subcutaneous

value: subcutaneous

tag: differentation day


title: Zebrafish heart endothelial cells, 7dpa, CtrlK2

tag: cell type


title: SN_7_Sham-Chow


title: IP_7_Sham-Chow


title: Adipose subcutaneous_78ca8a24-4069-41bb-84a4-ad7a4fadd048 at day D0


title: Adipose subcutaneous_27fb8066-80b4-4f0a-be77-e8614d5aaa2e at day D8


title: Rep1 input, rsc2 delta, replicate 1


title: SN_6_GDX-HFD

value: GDX


title: Flp ChIP, wt, replicate 2


title: Zebrafish heart endothelial cells, 7dpa, CtrlK1

treatment_protocol: Adult zebrafish were treated with 4-HT for 3days before ventricles amputation. The adult zebrafish hearts were then amputated. The kdrl:eGFP endothelial cells, which were sorted by FACS (fluorescence-activated cell sorting) from CtrlK and DNK hearts at 7 dpa.


title: Adipose subcutaneous_27fb8066-80b4-4f0a-be77-e8614d5aaa2e at day D14


title: LN naïve

first: Nir

last: Hacohen

address: 415 Main St

data_processing:
cellranger-3.1.0, force-cells=10000
Assembly: mm10
Supplementary files format and content: Cellranger filtered expression h5 format

source_name: Lymph node

extract_protocol:
We isolated lymph nodes from mice that were either untreated or 6 hours after subcutaneous/intradermal vaccination with 200 mg of ovalbumin peptide and 20 mg CpG 1826 adjuvant. Lymph nodes were dissociated using Collagenase IV, 0.8 mg/ml Dispase, and Dnase I in RPMI at 37°C and cells using a protocol that is optimized for myeloid and stromal cell recovery (Fletecher et al., 2011). After harvesting, cells were put on ice, washed with PBS/2mM EDTA/0.5% biotin-free bovine serum albumin, and filtered through a 70µm cell strainer. T and B cells were isolated with MACS columns using biotinylated anti-CD3 and anti-CD19 antibodies. A small fraction of the CD3+ or CD19+ cells was pooled with CD3-/CD19- cells for more balanced representation of immune lineages prior to performing scRNA-seq (10X genomics).
10X Genomics 3' v2 was performed according to the manufacturer’s instructions

value: Lymph node

value: untreated


title: SN_23_Sham-Chow

value: Supernatant


title: LN 6 hours post-vaccination

value: vaccination with 200 mg of ovalbumin peptide and 20 mg CpG 1826 adjuvant


title: Adipose subcutaneous_27fb8066-80b4-4f0a-be77-e8614d5aaa2e at day D3

value: adipose


title: Adipose subcutaneous_78ca8a24-4069-41bb-84a4-ad7a4fadd048 at day D3


title: Flp input, wt, replicate 2


title: IP_6_GDX-HFD

value: HFD


title: IP_23_Sham-Chow

value: Sham


title: Adipose subcutaneous_df6de9df-1da3-4cc2-813c-447e652f4eaa at day D8


title: Adipose subcutaneous_27fb8066-80b4-4f0a-be77-e8614d5aaa2e at day D0


title: Control3

city: Harbin

first: Yang

last: Chong

state: Heilongjiang

address: 23, YouZheng Street, Nangang District

department: Critical Care Medicine

institute: The First Affiliated Hospital of Harbin Medical University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
The clean reads were mapped to the reference genome using HISAT2 2 . FPKM 3 of each gene was calculated andthe read counts of each gene were obtained by HTSeq-count 4 . PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).
After reads ressembled by StringTie2, gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using Cuffcompare software.
ASprofile was used to analyse the alternatively splicing of differentially regulated transcripts isoforms or exons. SNPs and InDels were called using SAMtools and BCFtools.
Assembly: mm12
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: kidney

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: kidney

value: WT

value: PBS intraperitoneal injection

tag: time

value: Day 1


title: Adipose subcutaneous_df6de9df-1da3-4cc2-813c-447e652f4eaa at day D3


title: Rep2 ChIP, wt, replicate 2

value: MATa ade2-1 his3-11::GAL10-3HA-REP1-GAL1-REP2-10Myc::HIS3  leu2-3,112  trp1 ura3-1  [Cir0]


title: Control1


title: IP_22_GDX-HFD

value: Immunoprecipitate


title: Control2


title: LPS3

value: LPS intraperitoneal injection


title: Flp ChIP, wt, replicate 1

value: EZview Red Anti-c-Myc Affinity Gel (Sigma-Aldrich Cat# E6654)


title: Flp input, wt, replicate 1


title: SN_22_GDX-HFD


title: SN_21_Sham-Chow

value: Chow


title: Rep2 ChIP, wt, replicate 1


title: IP_21_Sham-Chow


title: Rep2 input, wt, replicate 2


title: LPS2


title: Adipose subcutaneous_df6de9df-1da3-4cc2-813c-447e652f4eaa at day D0

value: subcutaneous


title: Adipose subcutaneous_df6de9df-1da3-4cc2-813c-447e652f4eaa at day D14


title: SN_20_Sham-HFD


title: Rep2 input, wt, replicate 1


title: Adipose subcutaneous_a5eaebf8-0843-48c2-885f-31295ad25afc at day D8


title: KO OT-I, replicate 5, ATACseq

city: La Jolla

first: Jennifer

last: Hope

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

description: KO

data_processing:
Data was processed using Cutadapt, and data quality was assessed using Fastqc and MutliQC. STAR and Homer were used for mapping, alignment and peak calling.
Data was visualized using IGV Genome Browser.
Differential peak analysis and gene annotation was completed using DESeq2 and Homer. Reproducible peaks were compared with public datasets using BEDTools.
Assembly: Mouse Genome B38, Ensembl v84
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: bigBed (.bb) files for graphing tracks

source_name: Lymphocyte

extract_protocol:
50K cells per sample were lysed in digitonin-containing buffer and nuclei were extracted following centrifugation.
Extracted nuclei were resuspended in transposition mix and incubated at 37 degrees C for 30 minutes before DNA extranction. Libraries were prepared using KAPA HiFi High sensitivity Real-time PCR master mix.

value: Lymphocyte

value: CD8 T cell


title: Rep1 ChIP, wt, replicate 2

value: MATa ade2-1 his3-11::GAL10-REP1-10Myc-GAL1-3HA-REP2::HIS3  leu2-3,112  trp1 ura3-1  [Cir0]


title: Adipose subcutaneous_a5eaebf8-0843-48c2-885f-31295ad25afc at day D3


title: LPS1


title: Rep1 ChIP, wt, replicate 1


title: Adipose subcutaneous_a5eaebf8-0843-48c2-885f-31295ad25afc at day D0


title: KO OT-I, replicate 3, ATACseq

description: KO


title: KO OT-I, replicate 4, ATACseq

description: KO


title: SN_2_GDX-HFD

value: Supernatant

value: GDX


title: Adipose visceral_9a7f34af-b22d-47d0-9b39-8213f867b828 at day D3

value: adipose

value: visceral


title: IP_2_GDX-HFD

value: HFD


title: Rep1 input, wt, replicate 2


title: KO OT-I, replicate 2, ATACseq

description: KO


title: SN_19_Sham-Chow

value: Sham


title: Sro9-TAP PAR-CLIP untreated rep 1

description: PAR-CLIP

tag: genotype/variation

tag: strain name

value: Untreated

value: anti-TAP

value: Sro9-TAP crosslinked and RNase trimmed RNA


title: Rep1 input, wt, replicate 1


title: IP_20_Sham-HFD

value: Immunoprecipitate

tag: treatment


title: KO OT-I, replicate 1, ATACseq

description: KO

tag: genotype


title: SN_18_Sham-HFD


title: Adipose visceral_4a6702b0-15c3-4572-b740-a34828815149 at day D3


title: No tag ChIP, wt, replicate 2

value: MATa ade2-1 his3-11::GAL10-REP1-GAL1-REP2::HIS3  leu2-3,112  trp1 ura3-1  [Cir0]


title: No tag ChIP, wt, replicate 1

value: EZview Red Anti-c-Myc Affinity Gel (Sigma-Aldrich Cat# E6654)


title: WT OT-I, replicate 5, ATACseq

description: WT


title: WT OT-I, replicate 4, ATACseq

description: WT


title: No tag input, wt, replicate 1


title: No tag input, wt, replicate 2


title: IP_18_Sham-HFD


title: WT OT-I, replicate 3, ATACseq

description: WT


title: Adipose visceral_4a6702b0-15c3-4572-b740-a34828815149 at day D14


title: Adipose visceral_4a6702b0-15c3-4572-b740-a34828815149 at day D0


title: SN_17_GDX-HFD


title: IP_17_GDX-HFD


title: WT OT-I, replicate 2, ATACseq

description: WT


title: Adipose visceral_1d84b0be-4512-4f24-837c-972d8908af5a at day D14


title: WT OT-I, replicate 1, ATACseq

description: WT


title: Adipose visceral_9a7f34af-b22d-47d0-9b39-8213f867b828 at day D14


title: Adipose visceral_1d84b0be-4512-4f24-837c-972d8908af5a at day D0


title: WCE-SL369_S32_L004_R1_001.fastq.gz

city: San Francisco

first: Sujin

last: Lee

institute: University of California San Francisco

description: Whole Cell Extract (WCE)

data_processing:
ChIP-seq
Illumina adaptor removed from read 3' ends using Cutadapt
Reads were aligned to the genome with bowtie.
Analysis performed using custom scripts
Genome_build: C. neoformans CNA3
Supplementary_files_format_and_content: .bedgraph: Signal of H3K27me3 ChIP-seq of the sample normalized to the corresponding whole cell extract (WCE).

organism: Cryptococcus neoformans

source_name: Yeast

growth_protocol: Samples were inoculated from saturated starter cultures in YPAD at 30C until reaching OD 1.0 then harvested by centrifugation at 2000xg for 5 minutes.

extract_protocol:
ChIP DNA was extracted by bead beater with 0.5mm zirconia beads.  ChIP DNA was isolated by an antibody against H3K27me3 (described in PubMed ID 25533783). DNA was then isolated by incubation with SDS/proteinase K followed by column purification (Macherey-Nagel Nucleospin Gel Cleanup Columns).
NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads (E7103, NEB) was used according to the product manual.

value: none (WCE)


title: WCE-SL367_S38_L004_R1_001.fastq.gz

description: Whole Cell Extract (WCE)


title: Adipose visceral_9a7f34af-b22d-47d0-9b39-8213f867b828 at day D0


title: WCE-SL366_S37_L004_R1_001.fastq.gz

description: Whole Cell Extract (WCE)


title: IP_19_Sham-Chow

value: Chow


title: Adipose visceral_f67c7d4c-53a2-4d98-8015-5984bddc70fd at day D3


title: SN_15_Sham-Chow


title: WCE-SL364_S35_L004_R1_001.fastq.gz

description: Whole Cell Extract (WCE)


title: 20077X33 Male, Adrenal Gland, 9-week, SF1-Cre+;Znrf3Fx/Fx, Sham surgical procedure at week-4, biol rep 1

city: Salt Lake City

first: Kaitlin

last: Basham

state: UT

address: 2000 Circle of Hope Dr.

department: Oncological Sciences

institute: Huntsman Cancer Institute, University of Utah

data_processing:
Mouse FASTA and GTF files were downloaded from Ensembl release 102 and a reference database was created using STAR version 2.7.6a.
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16.
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using RSEM version 1.6.3.
Expected gene counts were filtered to remove features with zero counts and features with fewer than 10 reads in any sample.
Assembly: Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.30.1.
Supplementary files format and content: GRCm38
Supplementary files format and content: raw counts from featureCounts combined into a single tab-delimited matrix

source_name: Adrenal Gland

growth_protocol: Adrenal glands were obtained from mice following rapid decapitation to mimize stress. Adrenals were places in ice-cold phosphate buffered saline, cleaned of excess fat and snap frozen in liquid nitrogen.

extract_protocol:
RLT lysis buffer (Qiagen, 74104) containing 1% B-mercaptoethanol was added to thawed adrenal tissue in high impact zirconium 1.5mm bead tubes (Benchmark Scientific, D1032-15). Samples were homogenized for 30 seconds using the Beadbug™ 3 (Benchmark Scientific, D1030), returned to ice, and homogenized for an additional 30 seconds. Total RNA isolation was completed using the RNeasy® Kit (Qiagen, 74104) according to manufacturer guidelines. DNases were removed using the RNase-Free DNase Set (Qiagen, 79254) and subsequently purified using the RNeasy MinElute Cleanup Kit (Qiagen, 74204) according to manufacturer guidelines
NEBNext Ultra II Directional RNA Library Prep with poly(A)mRNA Isolation

value: Adrenal Gland

tag: Sex

value: Male

value: SF1-Cre+; Znrf3 Fx/Fx; R26eYFP/WT


title: 20077X16 Male, Adrenal Gland, 9-week, SF1-Cre+;Znrf3Fx/Fx, Castrated at week-4, biol rep 4

tag: strain

value: SF1-Cre+; Znrf3 Fx/Fx; R26mTmG/mTmG


title: Adipose visceral_1d84b0be-4512-4f24-837c-972d8908af5a at day D3


title: 20077X15 Male, Adrenal Gland, 9-week, SF1-Cre+;Znrf3Fx/Fx, Castrated at week-4, biol rep 3


title: SN_16_Sham-HFD

value: Supernatant


title: Adipose visceral_f67c7d4c-53a2-4d98-8015-5984bddc70fd at day D0

value: adipose


title: IP_16_Sham-HFD


title: Adipose subcutaneous_f67c7d4c-53a2-4d98-8015-5984bddc70fd at day D3

value: subcutaneous


title: WCE-SL362_S33_L004_R1_001.fastq.gz

description: Whole Cell Extract (WCE)


title: WCE-SL363_S34_L004_R1_001.fastq.gz

description: Whole Cell Extract (WCE)


title: WCE-CK6644_S27_L004_R1_001.fastq.gz

description: Whole Cell Extract (WCE)


title: 20077X13 Male, Adrenal Gland, 9-week, SF1-Cre+;Znrf3Fx/Fx, Castrated at week-4, biol rep 1


title: Adipose subcutaneous_f67c7d4c-53a2-4d98-8015-5984bddc70fd at day D14


title: 20077X29 Male, Adrenal Gland, 9-week, SF1-Cre+;Znrf3Fx/Fx, Sham surgical procedure at week-4, biol rep 1

value: SF1-Cre+; Znrf3 Fx/Fx


title: SN_13_Sham-HFD

value: HFD

value: Sham


title: 20077X12 Male, Adrenal Gland, 9-week, SF1-Cre+;Znrf3Fx/Fx, Sham surgical procedure at week-4, biol rep 1

value: SF1-Cre+; Znrf3 Fx/Fx; R26mTmG/WT


title: WCE-SL365_S36_L004_R1_001.fastq.gz

description: Whole Cell Extract (WCE)


title: Adipose subcutaneous_f67c7d4c-53a2-4d98-8015-5984bddc70fd at day D0


title: WCE-CK2308_S28_L004_R1_001.fastq.gz

description: Whole Cell Extract (WCE)


title: 20077X10 Male, Adrenal Gland, 9-week, SF1-Cre+;Znrf3Fx/Fx, Sham surgical procedure at week-4, biol rep 1


title: Adipose visceral_4ca0419d-a567-4f62-b0c1-b66654b5a13b at day D3

value: visceral


title: WCE-SL372_S29_L004_R1_001.fastq.gz

description: Whole Cell Extract (WCE)


title: IP_15_Sham-Chow

value: Immunoprecipitate


title: E4

city: Lexington

first: Lance

last: Johnson

state: KY

address: 760 Press Ave, HKRB 135

department: Physiology/Sanders-Brown Center on Aging

institute: University of Kentucky

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

source_name: Brain

extract_protocol:
Following perfusion, brains were quickly removed, and the whole right hemispheres sans brainstem and cerebellum were quickly minced using forceps on top of an ice-chilled petri dish. Minced tissue from the 3 pooled hemispheres per genotype was immediately transferred into a gentle MACS C-tube (Miltenyi #130-93-237) containing Adult Brain Dissociation Kit (ADBK) enzymatic digest reagents (Miltenyi #130–107-677) prepared according to manufacturer’s protocol. Tissues were dissociated using the “37C_ABDK” protocol on the gentle-MACS Octo Dissociator instrument (Miltenyi #130-095-937) with heaters attached. After tissue digestion, cell suspensions were processed for debris removal and filtered through 70μm mesh cell filters following the manufacturer’s suggested ABDK protocol. The resultant suspension was filtered sequentially two more times using fresh 30μm mesh filters. Cell viability was checked using AO/PI viability kit (Logos Biosystems # LGBD10012). Both cell suspensions were determined to have > 88% viable cells. Following viability and counting, cells were diluted to achieve a concentration of ~ 1000 cells/100uL.
The diluted cell suspensions were loaded onto the 10x Genomics Chromium Controller. Each sample was loaded into a separate channel on the Single Cell 3′ Chip, and libraries were prepared using the Chromium v3 Single Cell 3′ Library and Gel Bead Kit (10x Genomics). Final library quantification and quality check were performed using BioAnalyzer (Agilent), and sequencing was performed on a NovaSeq 6000 S4 flow cell, 150 bp Paired-End sequencing (Novogene).

value: Brain

tag: cell line

value: non-neuronal brain cells

value: Brain cells


title: Adipose visceral_f67c7d4c-53a2-4d98-8015-5984bddc70fd at day D14

extract_protocol: Library preparation, sequencing and reference genome alignment was carried out by the Genomics Platform at the Broad Institute. After final quality control samples were sequenced generating 50 million paired end reads per sample


title: SN_14_GDX-HFD

value: GDX


title: K27-ccc1-CC∆-2

description:
Affinity purified DNA
WCE raw file used for normalization:
WCE-SL369_S32_L004_R1_001.fastq.gz


title: IP_12_Sham-Chow

value: Chow


title: 20077X14 Male, Adrenal Gland, 9-week, SF1-Cre+;Znrf3Fx/Fx, Castrated at week-4, biol rep 2

value: Adrenal Gland

value: Male


title: Adipose visceral_4ca0419d-a567-4f62-b0c1-b66654b5a13b at day D14


title: IP_14_GDX-HFD


title: E3


title: Adipose visceral_4ca0419d-a567-4f62-b0c1-b66654b5a13b at day D0


title: K27-ccc1(9DEA)-2

description:
Affinity purified DNA
WCE raw file used for normalization:
WCE-SL367_S38_L004_R1_001.fastq.gz