title: 313491_1-Sample1_Mock

city: Zuerich

first: Lennart

last: Opitz

address: Winterthurerstr. 190

country: Switzerland

institute: FGCZ Zuerich

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
As reference we used GRCh38.p13 with GENCODE gene model annotations based on Release 42. Further data processing was performed with Seurat v4.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Primary human airway epithelial cultures

extract_protocol:
Differentiated primary human bronchial epithelial cells (BEpC) were washed with PBS three times to remove mucus on the apical side of the insert. Basal media was removed  and basal side was washed once with PBS. Cells were then trypsinized by adding 0.25% Trypsin-EDTA (Thermo Fisher Scientific) on the basal and apical side of the insert for a total of 10 min at 37°C and resuspended in warm DMEM/F12 (Thermo Fisher Scientific) supplemented with 5% fetal bovine serum (FBS) (Thermo Fisher Scientific). Cells were centrifuged at 400*g (4°C) for 5 min and subsequently washed once in cold PBS supplemented with 0.04% bovine serum albumin (BSA) (Sigma-Aldrich). Finally, cells were resuspended in cold PBS + 0.04% BSA and filtered through a 40 μm Flowmi® filter (Merck) to produce a single cell suspension. The final cell concentration was around 600-1200 cells/ul, calculated with the Countess II Automated Cell Counter (ThermoFisher) using Trypan Blue Solution. The Gel Bead-in-emulsion (GEM) generation up to the 3’ gene expression library construction was done following the ‘Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index)’ protocol (10x Genomics) and using the Chromium Controller (10x Genomics).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: Bronchi epithelial cells

value: unknown

tag: age

value: donor age 62y


title: GM12878 0 uM EBndG 4h 100 uM control Replicate 5

status: Public on Jun 17 2024

type: SRA

city: Hershey

first: Thomas

middle: E

last: Spratt

state: PA

address: 500 University Dr

department: Biochemistry and Molecular Biology

country: USA

institute: Pennsylvania State University

description:
EBndG_100_100bp.bw
EBndG_100.50K.bw
EBndG_100.50K.txt
EBndG_100_Rep5.log2.bw

library_source: genomic

data_processing:
Base calls were performed and adapters trimmedusing bcl2fastq (v 2.20.0) from Novaseq output.
POLK-seq reads were aligned to USSC hg38 genome using Bowtie version 2.5.2.  Proper pairs were retained.
Log2 bigwig files were generated using Deeptools bamCompare (v 2.30.0) using a 100 bp window and DNA from EBndG-treated and untreated cells.
EBndG_20.50K.txt and EBndG_100.50K.txt files generated with deeptools (v 3.5.1) mutibamsummary function
EBndG_20.50K.bw and EBndG_100.50K.bw files generted by averaging the values in the txt files and converted to the bigwig files using bedGraphToBigWig (v 385) program
Assembly: hg38
Supplementary files format and content: Bigwig
Library strategy: POLK-seq

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: RPMI, 15% FBS, 2 mM glutamine,1x penicillin/streptomycin, 5% CO2, 37°C

extract_protocol:
Cells were lysed, DNA isolated by phenol/CHCl3/i-amyl alcohol.  DNA was sonicated with a Covaris E220 focued ultrasonicator to 200-400 bp size
EBndG-DNA was isolated by biotinylation using Click reaaction
Libraries were prepared with NEB Ultra IOI Library preparation kit.  3-8 ng DNA was used.  Libraries were amplified with 13 cycles on a thermocycle.  The libraries were sized selected from 250-450 using Agencourt AMPure XP beads from Beckman.  Libraries were validated using the Agilent 2100 Bioanalyzer.

treatment_protocol: Cells treated with 0, 20 100 uM EBndG for 4 h.

tag: cell line

tag: cell type

value: fibroblast

tag: genotype

value: wild-type

tag: treatment

value: 0 uM EBndG


title: at-aerial_part-BS_TEmob_replicate2

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description: Arabidopsis thaliana aerial part of TEmob (Columbia-0) T4

data_processing:
150-bp PE reads were trimmed by removing the first 5 bases from the 5’ end and the last 20 bases from the 3’ end. Reads were mapped to the Arabidopsis TAIR10 in PE mode (--score_min L,0,-0.6) genome using Bismark (Krueger & Andrews, 2011). Duplicated reads were eliminated and cytosine methylation values calculated using the Bismark Methylation Extractor.
Assembly: Arabidopis thaliana TAIR10
Supplementary files format and content: Three genome-wide cytosine methylation reports (for CG, CHG, CHH) per sample were created. These reports have the  following format:<chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Seeds were surface sterilized with 70% ethanol and washed three times with sterile water. Sterilized seeds were sown on 1⁄2MS plates containing 0.5% sucrose and 0.8% agar, stratified for 2 days at 4°C and germinated under long-day conditions (16h light/8h darkness) at 21°C. Seedlings were transferred to soil after 10–12 days and grown in phytotrons under long day conditions (day 21°C, night 20°C 70% humidity, 150μE light intensity).

extract_protocol:
DNA was extracted from 100 mg of ground flash-frozen aerial tissue pooled from three 4-week-old TEmob plants using the MagMAXTM Plant DNA Isolation Kit
Kit for ultra-low input library Accel-NGS Methyl-Seq DNA Library Kit for illumina (Cat No. 30096)

treatment_protocol: TEmob (Cm) line was generated as follows: Seeds were germinated in 1⁄2MS agar plates supplemented with 5,44μM α-amanitin (Sigma Cat. No. A2263) and 40μM zebularine (Sigma Cat. No.Z4775) and incubated at 4°C degrees for 24h and subsequently at 37°C in the dark. Line was cross to cenh3 CENH3-TAILSWAPplants (Ravi & Chan, 2010) and offspring haploids were grown and treated with colchicine; a diploid line was identified (TEmob).

tag: tissue

value: leaves

value: AT aerial part TEmob

value: TEmob (Col-0)


title: Olfactory mucosa, IAV, 8dpi, gene expression

city: Boston

first: Jose

last: Ordovas-Montanes

state: MA

address: 300 Longwood Ave

department: Gastroenterology, Hepatology and Nutrition Research

institute: Boston Children's Hospital

description: GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 contains transcript

library_source: transcriptomic single cell

data_processing:
FASTQs, cell count matrices, and hashtag oligo counts were generated using cellranger v6.0.1 through cumulus tools (https://cumulus.readthedocs.io/en/stable/)
Cellbender was then applied to the raw h5 output files to correct for transcript spill-over with the following parameters: expected_cells=30000, fpr=0.01, total_droplets_included=50000
Cellbender corrected cells were then filtered based on Unique Molecular Identifiers (UMI) count (>750 & <10000), number of detected genes (>500), and percentage of mitochondrial genes (<15%). Finally, cells labeled as doublets by demultiplexing were removed
Downstream clustering analysis was performed using Seurat (v.4.2.1) using scTransform normalization and corrected counts.
Remaining doublets were removed by inspection upon subclustering routines by identifying clusters expressing mutually exclusive cell type lineage markers
Assembly: GRCm39 + custom IAV PR8 genome (NCBI Taxonomy ID #211044; segment sequences: NC_002023.1, NC_002022.1, NC_002021.1, NC_002020.1, NC_00219.1, NC_2018.1, NC_002017.1, and NC_002016.1)
Supplementary files format and content: Cellranger output files: XXX.h5 contains the raw unfiltered cell count matrix
Supplementary files format and content: Cellranger output files: XXX.csv contains the hashtag oligo counts; feature_barcodes.csv contains the TotalSeqB Hashtag antibody oligo sequences used for every sample

molecule: polyA RNA

organism: Mus musculus

source_name: Nasal mucosa, olfactory mucosa

extract_protocol:
Tissue was harvested by microdissection and digested in RPMI (w/ FBS, HEPES, and P/S) for 20 min (LNG) or 30 min (RM/OM). Following enzyme inactivation with EDTA and filtration through a 70 µm membrane, ACK lysis was performed on ice for 1min. Epithelial cells were partially depleted using Biotin Binder Dynabeads pre-loaded with anti-biotin anti-EpCAM antibody during a 20min incubation on ice. Following bead removal, cells were stained with TotalSeqB Hashtag antibodies for 20 minutes before washing, counting, and combining. Finally, cells were captured and processed on either a 10x Chromium or X controller using the 3' transcriptome v3.1 kit and feature barcoding kits.
Libraries were constructed as outlined in the 10x Genomics guide for Dual-indexed 3' transcriptomics v3.1 with Feature Barcoding.

treatment_protocol: Mice were infected intranasally with a low volume of IAV PR8 (5 µl/nostril) while awake to restrict infection to the nasal mucosa.

value: Nasal mucosa, olfactory mucosa

value: IAV PR8

tag: timepoint

tag: Sex

value: female

tag: disease state

value: primary infection

tag: library type

value: mRNA


title: GM12878 0 uM EBndG 4h 100 uM control Replicate 6

description:
EBndG_100_100bp.bw
EBndG_100.50K.bw
EBndG_100.50K.txt
EBndG_100_Rep6.log2.bw


title: G1E-ER4_lateG1_YY1_ChIPseq_rep2

city: Philadelphia

first: Jessica

last: Lam

address: 3615 Civic Center Blvd

department: Perelman School of Medicine

institute: University of Pennsylvania

description:
YY1_lateG1_chip.bw
YY1_lateg1-emergent_peaks.bed

data_processing:
Fastq files were generated with Bclfastq2 v2.15.04
For Micro-C, we generated .mcool files with the distiller pipeline (v3.3)
Micro-C analysis was performed with cooltools (v0.5.0) and rGMAP
For ChIP-seq, alignment was performed with bowtie2 default settings, de-duplicated, and filtered for MAPQ>20
To generate bigwig files, we used deeptools (v3.5.1) bamCoverage (binSize=20, smoothLength=60, normalizeUsing=BPM)
To generate peak calls, we used macs2 (v2.2.7) with matched input and q=0.05
Assembly: mm9
Supplementary files format and content: mcool: Micro-C contact map. bw: tracks of processed ChIP-seq or Micro-C signals. bedpe: list of Micro-C loop coordinates. bed: list of ChIP-seq peak coordinates.

extract_protocol:
For ChIP-seq, DNA from lysed cells was sonicated, immunoprecipitated, and then extracted using the QIAquick PCR Purification kit (Qiagen 28106). For Micro-C, DNA was digested with MNase, proximity-ligated, and extracted using phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation. Gel extraction was used to select for fragments between 250-400bp. DNA was purified with Zymoclean Gel DNA Recovery kit (D4007).
We used the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7635) with unique dual-indexed primers (NEB E6440).

value: ES-derived erythroid progenitor cells

value: G1E-ER4 MD-mCherry subline

tag: chipantibody

value: anti-YY1 Active Motif 61980


title: at-aerial_part-BS_TEmob_replicate1


title: Respiratory mucosa, IAV, 8dpi, hashtag oligo

description: HTO library: read1 file contains cell barcode and UMI; read2 file contains antibody derived Tag reads

library_source: other

molecule: protein

source_name: Nasal mucosa, respiratory mucosa

value: Nasal mucosa, respiratory mucosa

value: HTO

tag: hto

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 12


title: G1E-ER4_lateG1_YY1_ChIPseq_rep1


title: GM12878 0 uM EBndG 4h 100 uM control Replicate 3

description:
EBndG_100_100bp.bw
EBndG_100.50K.bw
EBndG_100.50K.txt
EBndG_100_Rep3.log2.bw

value: fibroblast


title: GM12878 0 uM EBndG 4h 100 uM control Replicate 4

description:
EBndG_100_100bp.bw
EBndG_100.50K.bw
EBndG_100.50K.txt
EBndG_100_Rep4.log2.bw

value: wild-type


title: at-endosperm-BS_replicate2_ler_x_col_C

description: Arabidopsis thaliana F1-endosperm of Landsberg-erecta pi-1 (female) crossed with Columbia-0 INT (male)

source_name: endosperm

value: endosperm

value: AT F1-Endosperm Landsberg x Columbia WT

value: Ler (maternal) x Col (paternal)


title: G1E-ER4_earlyg1_YY1_ChIPseq_rep3

description:
YY1_earlyG1_chip.bw
YY1_earlyg1-emergent_peaks.bed


title: Lateral nasal gland, IAV, 5dpi, hashtag oligo

source_name: Nasal mucosa, lateral nasal gland

value: Nasal mucosa, lateral nasal gland

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 11


title: G1E-ER4_earlyG1_YY1_ChIPseq_rep2


title: GM12878 0 uM EBndG 4h 100 uM control Replicate 2

description:
EBndG_100_100bp.bw
EBndG_100.50K.bw
EBndG_100.50K.txt
EBndG_100_Rep2.log2.bw

value: 0 uM EBndG


title: at-endosperm-BS_replicate1_ler_x_col_C


title: G1E-ER4_earlyG1_YY1_ChIPseq_rep1


title: GM12878 0 uM EBndG 4h 100 uM control Replicate 1

description:
EBndG_100_100bp.bw
EBndG_100.50K.bw
EBndG_100.50K.txt
EBndG_100_Rep1.log2.bw


title: GM12878 0 uM EBndG 4h 20 uM control Replicate 3

description:
EBndG_20_100bp.bw
EBndG_20.50K.bw
EBndG_20.50K.txt
EBndG_20_Rep3.log2.bw


title: at-endosperm-BS_replicate2_ler_x_col_Cm

description: Arabidopsis thaliana F1-endosperm of Landsberg-erecta pi-1 (female) crossed with TEmob Columbia-0 INT (male)

value: AT F1-Endosperm Landsberg x Columbia TEmob

value: Ler (maternal) x TEmob Col (paternal)


title: Olfactory mucosa, IAV, 5dpi, hashtag oligo

value: Nasal mucosa, olfactory mucosa

value: IAV PR8

value: female

value: primary infection

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 10


title: G1E-ER4_async_YY1_ChIPseq_rep2

value: ES-derived erythroid progenitor cells

value: G1E-ER4 MD-mCherry subline

value: anti-YY1 Active Motif 61980

value: async


title: at-endosperm-BS_replicate1_ler_x_col_Cm

value: endosperm


title: GM12878 0 uM EBndG 4h 20 uM control Replicate 1

description:
EBndG_20_100bp.bw
EBndG_20.50K.bw
EBndG_20.50K.txt
EBndG_20_Rep1.log2.bw

value: fibroblast

value: wild-type


title: at-endosperm-BS_replicate2_col_C_x_ler

description: Arabidopsis thaliana F1-endosperm of Columbia-0 INT (female) crossed with Landsberg-erecta (male)

value: AT F1-Endosperm Columbia WT x Landsberg

value: Col (maternal) x Ler (paternal)


title: at-endosperm-BS_replicate1_col_C_x_ler


title: G1E-ER4_anatelo_YY1_ChIPseq_rep3

description:
YY1_anatelo_chip.bw
YY1_anatelo-emergent_peaks.bed

value: anatelo


title: Olfactory mucosa, IAV, 5dpi, gene expression

value: mRNA


title: Respiratory mucosa, IAV, 5dpi, hashtag oligo

value: Nasal mucosa, respiratory mucosa

value: HTO

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 9


title: Respiratory mucosa, IAV, 8dpi, gene expression

value: IAV PR8

value: female


title: GM12878 100 uM EBndG 4h Replicate 6

value: EBndG 100 uM


title: G1E-ER4_anatelo_YY1_ChIPseq_rep2

value: ES-derived erythroid progenitor cells


title: Respiratory mucosa, IAV, 5dpi, gene expression

value: primary infection


title: at-endosperm-BS_replicate1_col_Cm_x_ler

description: Arabidopsis thaliana F1-endosperm of TEmob Columbia-0 INT (female) crossed with Landsberg-erecta (male)

value: AT F1-Endosperm Columbia TEmob x Landsberg

value: TEmob Col (maternal) x Ler (paternal)


title: G1E-ER4_anatelo_YY1_ChIPseq_rep1

value: G1E-ER4 MD-mCherry subline

value: anti-YY1 Active Motif 61980


title: GM12878 100 uM EBndG 4h Replicate 5

description:
EBndG_100_100bp.bw
EBndG_100.50K.bw
EBndG_100.50K.txt
EBndG_100_Rep5.log2.bw

value: fibroblast

value: wild-type


title: GM12878 100 uM EBndG 4h Replicate 4


title: Lateral nasal gland, IAV, 2dpi, hashtag oligo

value: Nasal mucosa, lateral nasal gland

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 8


title: Plasmid library_STARRTYC10

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description:
Plasmid DNA, stranded library
G170M6

data_processing:
READ MAPPING: reads were aligned to the mm9 mouse genome using Bowtie2 (Langmead et al 2009, Genome Biology) with default settings. Reads were filtered so that only uniquely-aligned reads were used for downstream analysis.
PEAK CALLING: 117,122 merged peaks were called using MACS2 (Zhang et al 2008, Genome Biology) from the associated plasmid, DNA, RNA libraries with default parameters without filtering for PCR duplicates. Peaks were filtered to remove ENCODE blacklisted regions (www.sites.google.com/site/anshulkundaje/projects/blacklists) and also regions called as peaks by MACS2 but contain only PCR duplicated reads. 50,332 MACS2 regions with more than 40 normalized squence reads in plasmid library (G170M6) were considered as qualified regions with reliable readout for in vivo STARR-seq assay.
READ COUNTING: Reads within 50,332 qualified genomic regions (>40 normalized sequence reads in plasmid library) were counted using the bedtools coverage option without filtering for PCR duplicates.
Assembly: mm9
Supplementary files format and content: G187_global_processed_dataset.xlsx. In vivo global STARR-seq assay of 50,322 qualified open chromatin (DHS) regions. These 50,322 qualified DHS sites are a subset of regions with more than 40 normalized reads from a 117,122 MACS2 peak list. Columns E-S show the raw normalized reads per 10 million mapped reads in the STARR-seq plasmid library, each DNA library extracted from each liver, and each RNA library prepared from each liver after HDI.  Columns V-AA show the number of liver samples in the biological condition with at least 20 normalized RNA reads, and the averaged RNA counts in those qualified liver samples. For each biological condition (CTRL_M, CTRL_F and TCPO_M; columns AC-AE), we defined a set of active regions (regions with at least 20 sequence reads per 10 million mapped RNA reads in at least 3 out of 4 male livers, 3 out of 4 TCPOBOP-treated male livers, or 3 out of 3 female livers and a set of stringently inactive regions (regions with no more than 20 sequence reads per 10 million mapped RNA reads in 4 out of 4 male livers, 4 out of 4 TCPOBOP-treated male livers, or 3 out of 3 female livers) for the corresponding biological condition. "NA" in columns AB-AE indicate others.
Library strategy: STARR-seq

molecule: other

organism: synthetic construct

growth_protocol: Male and female CD1 mice (ICR strain), approx. 7 weeks old, were purchased from Charles River Laboratories (Wilmington, MA) and kept on a 12-hour light/dark cycle with food and water without restriction.

extract_protocol:
The extraction methods, adapted from the published STARR-seq protocol (Neumayr, Pagani et al. 2019), were used in a nested PCR amplification protocol to characterize the transcriptional activity of each DHS sequence (putative regulatory region) to be assayed by HDI-STARR-seq: 1) a library prepared from DNA extracted from flash frozen liver tissue collected 7 d after in vivo transfection by HDI (primers ON8381, ON8382); and 2) a library prepared from the transcribed RNA (reporter sequences) extracted from each HDI-transfected liver (primers ON8379, ON8380; see STARR_seq_primer.txt). STARR-seq reporter plasmid DNA remaining in the liver 7 d after HDI was extracted using a commercial QIAprep spin miniprep kit (QIAgen, cat. # 27106). Liver tissue (200 mg frozen liver) was initially homogenized in 750 ul of QIAgen Buffer P1 using a rubber-tipped micropestle and passed through a 20G needle 3 times to homogenize large tissue pieces. The extracted plasmid DNA was bound to a QIAprep spin column, eluted in EB buffer and used as a PCR template in a subsequent nested PCR reaction using primers ON8381 and ON8382 (see STARR_seq_primer.txt). To extract transcribed reporter RNA, 120 ug of total liver RNA was isolated from 60-100 mg liver tissue from each mouse by TRIzol guanidinium thiocyanate-phenol-chloroform extraction then purified by polyA selection using oligo(dT) beads (New England Biolabs, cat. #E7490L). The transcribed RNA was digested with Turbo DNase I (Ambion, cat. # AM2238) at 37°C for 30 min, reverse transcribed using primer ON8731 (see STARR_seq_primer.txt) for STARR-seq RNA first strand synthesis and Superscript III first-strand synthesis supermix (Invitrogen, cat. # 18080-400) and treated with 10 mg RNase A per ml (Fermentas, cat. # EN0531) for 1 h at 37 Celsius. The cDNA obtained was purified using 1.8x SPRI beads then used as a PCR template in the nested PCR reaction.
The nested PCR reaction requires a set of primers that specifically targets DNA or RNA derived from a STARR-seq reporter, after which the sequences are amplified using Illumina dual index primers. A primer set, primers ON8381 and ON8382 (see STARR_seq_primer.txt) was designed to amplify the STARR-seq plasmid DNA libraries by specifically targeting the unspliced intron incorporated into the original plasmid and present in the plasmid and DNA libraries, but that is spliced out of the reporter RNA sequences. Another primer set, primers ON8379 and ON8380 (see STARR_seq_primer.txt) straddles the splice junction and was designed to specifically amplify only the transcribed and spliced RNA molecules. Subsequently, nested PCR was completed using NEBNext® Multiplex Oligos for Illumina (#E7600S) for all three library types (plasmid, DNA and RNA) to further amplify the material and attach Illumina i5 and i7 barcoded sequences used for multiplex sequencing on an Illumina sequencer.

treatment_protocol: In vivo transfection: Plasmid DNA to be delivered to each mouse was resuspended in TransIT-EE delivery solution (MIR 5340, Mirus, Inc, Madison, WI) in a final volume of ~3 ml, equivalent to 10% of the mouse body weight (vol/weight). Each mouse was injected with a volume corresponding to ~10% of the body weight, up a maximum of 3 ml (for mice > 30 g weight) and delivered within 5-8 seconds without appreciable resistance. Hydrodynamic injection was largely ineffective, as judged by Renilla luciferase activity assayed in liver extracts, when resistance to injection precluded delivery of the full volume or when the total time of injection exceeded 10 seconds. For STARR-seq studies, 15 ug of STARR-seq library plasmid DNA was mixed with 3 ug of Renilla reporter plasmid DNA was injected per mouse. TCPOBOP (1,4-bis(2-(3,5-dichloropyridyloxy))benzene) (Chem Cruze, cat. #SC-203291) was delivered to mice at 6 days after HDI using Low Corn Oil regimen. Low Corn Oil regimen: TCPOBOP was dissolved in DMSO at 7.5 mg/ml, and then diluted 10-fold into corn oil, followed by IP injection at 4 µl per g body weight (final dose: 3 mg TCPOBOP and 4 µl of 10% DMSO in corn oil, per kg body weight). Mice were euthanized 1 day after TCPOBOP or corn oil vehicle treatment for the groups.  TCPOBOP or Vehicle injections were performed in the morning, and mice were euthanized between 10:30 AM and 12 noon under CO2 followed by cervical dislocation (Boston University animal facility light cycle: 7:30 AM to 7:30 PM). Livers were excised and flash frozen in liquid nitrogen then stored at -80° C.

tag: strain

tag: age at_euthanasia

tag: dosing regimen


title: Lateral nasal gland, IAV, 2dpi, gene expression

description: GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 contains transcript

value: mRNA


title: GM12878 100 uM EBndG 4h Replicate 3


title: at-endosperm-RNAseq_replicate3_ler_x_col_Cm

library_source: transcriptomic

data_processing:
The 150 bp reads were trimmed and mapped in single-end mode to the Arabidopsis (TAIR10) genome masked for rRNA genes using TopHat v2.1.0 (Trapnell et al., 2009) (parameters adjusted as -g 1 -a 10 -i 40 -I 5000 F 0 r 130). Transcript counts and RPKM values were calculated using GFOLD.
Assembly: The 150 bp reads were trimmed and mapped in single-end mode to the Arabidopsis (TAIR10) genome masked for rRNA genes using TopHat v2.1.0 (Trapnell et al., 2009) (parameters adjusted as -g 1 -a 10 -i 40 -I 5000 F 0 r 130). Transcript counts and RPKM values were calculated using GFOLD.
Supplementary files format and content: Expression levels (RPKM) are shown for genes in the genome annotation for Arabidopis thaliana TAIR10  at each condition and replicate.

molecule: total RNA

extract_protocol:
RNA was extracted from INTACT isolated endosperm nuclei using the mirVana kit.
NEBNext Poly(A) mRNA Magnetic Isolation kit, NEBNext® Ultra II RNA Library Prep Kit for Illumina® ,NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1)

treatment_protocol: Material was generated by manually crossing of pistillata (Ler) mutants with pollen of INT TEmob line (Col) and the INT TEmob line pollinated with Ler.  TEmob (Cm) line was generated as follows: Seeds were germinated in 1⁄2MS agar plates supplemented with 5,44μM α-amanitin (Sigma Cat. No. A2263) and 40μM zebularine (Sigma Cat. No.Z4775) and incubated at 4°C degrees for 24h and subsequently at 37°C in the dark. Line was cross to cenh3 CENH3-TAILSWAPplants (Ravi & Chan, 2010) and offspring haploids were grown and treated with colchicine; a diploid line was identified (TEmob).

value: endosperm

value: AT F1-Endosperm Landsberg x Columbia TEmob

value: Ler (maternal) x TEmob Col (paternal)


title: Lateral nasal gland, IAV, 5dpi, gene expression

value: IAV PR8


title: GM12878 0 uM EBndG 4h 20 uM control Replicate 2

description:
EBndG_20_100bp.bw
EBndG_20.50K.bw
EBndG_20.50K.txt
EBndG_20_Rep2.log2.bw

value: 0 uM EBndG


title: Olfactory mucosa, IAV, 2dpi, hashtag oligo

value: Nasal mucosa, olfactory mucosa

value: female

value: HTO

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 7


title: GM12878 100 uM EBndG 4h Replicate 2

value: EBndG 100 uM


title: STARRTYC3/7_plasmid_replicate1

description: plasmid DNA, stranded library

data_processing:
READ MAPPING: reads were aligned to the mm9 mouse genome using Bowtie2 (Langmead et al 2009, Genome Biology) with default settings. Reads were filtered so that only uniquely-aligned reads were used for downstream analysis.
PEAK CALLING: A set of 1,673 merged MACS2 peak regions were identified by MACS2 (Zhang et al 2008, Genome Biology) analysis of the associated plasmid, DNA, RNA libraries with default parameters without filtering for PCR duplicates. Peaks were filtered to remove ENCODE blacklisted regions (www.sites.google.com/site/anshulkundaje/projects/blacklists) and also regions called as peaks that contain only PCR duplicated reads.
READ COUNTING: Reads within the set of 1,673 MACS2 peak regions were counted using bedtools coverage option without filtering for PCR duplicates.
Assembly: mm9
Supplementary files format and content: G187_focus_processed_dataset.xlxs.  In vivo STARR-seq activity for the 1,673 MACS2 regions identified in the focused STARR-seq plasmid library. Columns F and G indicate the 100 genomic DNA PCR-amplified regions used to prepare the STARR-seq plasmid library. Columns H-O show the raw sequencing reads in each STARR-seq RNA library, prepared from each liver after HDI, and Columns P-S show the raw sequencing reads obtained from the DNA library extracted from each liver, and from the original focused plasmid library. Columns T-AF show raw normalized reads per 10 million mapped reads, obtained by dividing the raw reads (columns) by the total number of sequencing reads in the corresponding sample. Columns AG-AN show the calculated enhancer activity of each region, based on the ratio of reads between the individual RNA library and the DNA library under the same condition. Columns AO-AQ indicate the average enhancer activity across the biological replicates for each condition.
Library strategy: STARR-seq


title: at-endosperm-RNAseq_replicate2_ler_x_col_Cm


title: DPF2_D274A-R300A

city: Tianjin

first: 爱源

last: 王

state: —Please choose an option—

address: No. 22, Meteorological Observatory Road, Heping District, Tianjin

department: Department of Biochemistry and Molecular Biology

country: China

institute: TianjinMedical University

data_processing:
Raw reads were mapped to the human reference genome (hg19) and transcriptome using the RNA-Seq unified mapper. Read counts for each transcript were calculated using HTseq v0.6.1 using default parameters54. Differential gene expression analyses were performed using the “exactTest” function in edgeR v3.055
Assembly: hg19
Supplementary files format and content: rawcounts ; FPKM

source_name: Hela cells

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Briefly, mRNA was purified from total RNA using poly-T  oligo-attached magnetic beads. Fragmentation was carried out using  divalent cations under elevated temperature in First Strand Synthesis  Reaction Buffer(5X). First strand cDNA was synthesized using random  hexamer primer and M-MuLV ReverseTranscriptase(RNase H-).Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were  ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were  purified with AMPure XP system. Then PCR was performed with  Phusion High-Fidelity DNA polymerase, Universal PCR primers and  Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer  2100 system.

value: Hela cells


title: Olfactory mucosa, IAV, 2dpi, gene expression

value: primary infection


title: G1E-ER4_async_YY1_ChIPseq_rep1

value: ES-derived erythroid progenitor cells

value: G1E-ER4 MD-mCherry subline

value: anti-YY1 Active Motif 61980

value: async


title: GM12878 100 uM EBndG 4h Replicate 1

value: fibroblast

value: wild-type


title: DPF2_wt


title: TSP1 Knockout Replicate 3

city: Bethesda

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

description: Lineage depleted mouse B6H12 mice spleen cells.

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Downstream analysis, filtering, and visualization used the Seurat workflow as implemented on the National Institutes of Health Data Analysis Platform (NIDAP) and R scripts written by CCBR.
Assembly: mm10 3.0.0 using cellranger 3.0.2
Supplementary files format and content: 10x Genomics filtered h5 files

source_name: spleen

growth_protocol: WT, cd47−/− (B6.129S7-Cd47tm1Fpl/J), and thbs1−/− (B6.129S2-Thbs1tm1Hyn/J) mice were obtained from The Jackson Laboratory, backcrossed on the C57BL/6 background, and maintained under specific pathogen free conditions.

extract_protocol:
Spleens were removed from the mice and homogenized in HBSS and passed through a 70 µm mesh (Sigma, CLS431751) to remove debris. The cell suspension was treated with ACK lysis buffer for 4 minutes to lyse the RBC. The suspensions were centrifuged and washed twice with cold HBSS. Aliquots of single cell suspensions were stained using trypan blue and counted to assess viability.
Samples were loaded according to the 10x 3’ v3 User guide with a single capture lane per sample targeting a recovery of 6,000 cells per lane. Cell partitioning completed successfully with uniform emulsion consistency and the reverse transcription PCR was run overnight. All subsequent steps of library preparation and Quality Control were performed as described in the 10X Genomics 3’ v3 Single Cell User Guide.

value: spleen

value: RBC progenitors

value: TSP1 Knockout


title: at-endosperm-BS_replicate2_col_Cm_x_ler

value: endosperm

value: AT F1-Endosperm Columbia TEmob x Landsberg

value: TEmob Col (maternal) x Ler (paternal)


title: at-endosperm-RNAseq_replicate3_col_Cm_x_ler


title: Respiratory mucosa, IAV, 2dpi, gene expression

value: Nasal mucosa, respiratory mucosa

value: IAV PR8

value: female

value: mRNA


title: at-endosperm-RNAseq_replicate1_ler_x_col_Cm

value: AT F1-Endosperm Landsberg x Columbia TEmob

value: Ler (maternal) x TEmob Col (paternal)


title: GM12878 20 uM EBndG 4h Replicate 3

value: EBndG 20 uM


title: GM12878 20 uM EBndG 4h Replicate 2


title: at-endosperm-RNAseq_replicate1_col_Cm_x_ler


title: GM12878 20 uM EBndG 4h Replicate 1


title: VH-12_S43_AMKO-LPS

city: Houston

first: Amrit

last: Koirala

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Samples were trimmed using TrimGalore!
After trimming samples were aligned to mm10 using HISAT2
Features were quantified using featureCounts
Assembly: mm10
Supplementary files format and content: tab delimited, feature counts

source_name: lung

extract_protocol:
At postnatal day 5, 6 hours after the third dose of PBS or LPS, we extracted lung tissue from the study animals, immediately snap-froze it in liquid nitrogen, and stored it at − 80°C for subsequent RNA isolation.  Total lung RNA was isolated from the lung tissues of mice exposed to PBS or LPS (n=3/genotype/exposure) and purified using the Direct-zol RNA MiniPrep kit (Zymo Research, Irvine, CA; R2052).
RNA-seq libraries were next generated using the NEBNext Ultra II Directional RNA-Seq kit (p/n E7760) with rRNA depletion (p/n E7400), according to the manufacturer’s instructions.

treatment_protocol: Intraperitoneal injections of 6 mg/kg of Escherichia coli O55:B5 LPS (Sigma-Aldrich, St. Louis, MO; L2880) or an equivalent volume of PBS to both Adm+/+ and Adm+/- mice once daily for three days on postnatal days 3-5

value: lung

tag: mouse strain

value: postnatal day 5

value: Adm+/-

value: LPS (6 mg/kg of Escherichia coli O55:B5 lipopolysaccharide)


title: TSP1 Knockout Replicate 2

value: spleen


title: VH-11_S42_WT-LPS

value: Adm+/+


title: TSP1 Knockout Replicate 1

value: RBC progenitors

value: TSP1 Knockout


title: CD47 Knockout Replicate 3

value: CD47 Knockout


title: Pat_19_V_1_17

city: Columbus

first: Rodney

last: Britt

state: Oh

address: 575 Childrens Crossroad

department: Center for Perinatal Research

institute: Nationwide Children's Hospital

description:
Pat_19
DuplicateIDsMerged

data_processing:
fastq files were trimmed using default setting with the bbtools tool bbduk, and checked before and after with FastQC
Fastq files were aligned to the GRHh38 genome using Hisat2 --very sensitive, -k 2
sam files were converted to bam files, sorted, indexed, flagstats collected, and limited to only the 24 human chromosome with samtools
counts files were created with HTSeq2, -r pos,-t gene,-I gene_name, -s no, -m intersection strict, and collected into a single file with duplicate ENSMBL ID's merged with a custom Python script
differential expression was performed in EdgeR. 10 hemoglobin genes were removed from the counts matrix before analysis was performed ("HBA1","HBA2",'HBB','HBBP1','HBD','HBE1','HBG1','HBG2','HBM','HBQ1','HBZ','HBZP1')
Assembly: genome and annotation both from gencode.org release 33, GRCh38 primary assembly
Supplementary files format and content: Counts.csv

source_name: Blood

extract_protocol:
RNA was extracted from whole blood following the standard Invitrogen Tempus RNA Isolation protocol. 1ug RNA was used for library preparation.
Illumina Stranded mRNA Prep, Ligation
bulk-RNAseq

value: Blood

value: Pat

value: F


title: TCPOBOP_1d_Male_STARR_TYC6 (Alb promoter)_DNA_replicate1

description: extracted plasmid DNA, stranded library

data_processing:
READ MAPPING: reads were aligned to the mm9 mouse genome using Bowtie2 (Langmead et al 2009, Genome Biology) with default settings. Reads were filtered so that only uniquely-aligned reads were used for downstream analysis.
Assembly: mm9
Supplementary files format and content: STARR_seq_primer.txt    Excel workbook presenting the number of mapped reads from the DNA and RNA STARR-seq libraries prepared for each of the 3 STARR-seq promoters.
Library strategy: STARR-seq

source_name: liver

extract_protocol:
The extraction methods, adapted from the published STARR-seq protocol (Neumayr, Pagani et al. 2019), were used in a nested PCR amplification protocol to characterize the transcriptional activity of each DHS sequence (putative regulatory region) to be assayed by HDI-STARR-seq: 1) a library prepared from DNA extracted from flash frozen liver tissue collected 7 d after in vivo transfection by HDI (primers ON8381, ON8382); and 2) a library prepared from the transcribed RNA (reporter sequences) extracted from each HDI-transfected liver (primers ON8379, ON8380; see STARR_seq_primer.txt). STARR-seq reporter plasmid DNA remaining in the liver 7 d after HDI was extracted using a commercial QIAprep spin miniprep kit (QIAgen, cat. # 27106). Liver tissue (200 mg frozen liver) was initially homogenized in 750 ul of QIAgen Buffer P1 using a rubber-tipped micropestle and passed through a 20G needle 3 times to homogenize large tissue pieces. The extracted plasmid DNA was bound to a QIAprep spin column, eluted in EB buffer and used as a PCR template in a subsequent nested PCR reaction using primers ON8381 and ON8382 (see STARR_seq_primer.txt). To extract transcribed reporter RNA, 120 ug of total liver RNA was isolated from 60-100 mg liver tissue from each mouse by TRIzol guanidinium thiocyanate-phenol-chloroform extraction then purified by polyA selection using oligo(dT) beads (New England Biolabs, cat. #E7490L). The transcribed RNA was digested with Turbo DNase I (Ambion, cat. # AM2238) at 37°C for 30 min, reverse transcribed using primer ON8731 (see STARR_seq_primer.txt) for STARR-seq RNA first strand synthesis and Superscript III first-strand synthesis supermix (Invitrogen, cat. # 18080-400) and treated with 10 mg RNase A per ml (Fermentas, cat. # EN0531) for 1 h at 37 Celsius. The cDNA obtained was purified using 1.8x SPRI beads then used as a PCR template in the nested PCR reaction.
The nested PCR reaction requires a set of primers that specifically targets DNA or RNA derived from a STARR-seq reporter, after which the sequences are amplified using Illumina dual index primers. A primer set, primers ON8381 and ON8382 (see STARR_seq_primer.txt) was designed to amplify the STARR-seq plasmid DNA libraries by specifically targeting the unspliced intron incorporated into the original plasmid and present in the plasmid and DNA libraries, but that is spliced out of the reporter RNA sequences. Another primer set, primers ON8379 and ON8380 (see STARR_seq_primer.txt) straddles the splice junction and was designed to specifically amplify only the transcribed and spliced RNA molecules. Subsequently, nested PCR was completed using NEBNext® Multiplex Oligos for Illumina (#E7600S) for all three library types (plasmid, DNA and RNA) to further amplify the material and attach Illumina i5 and i7 barcoded sequences used for multiplex sequencing on an Illumina sequencer

value: liver

value: 8-9 weeks

value: Male

value: TCPOBOP, 3 mg/kg, i.p., 1 d exposure

value: Low Corn Oil


title: Pat_20_V_1_34

description:
Pat_20
DuplicateIDsMerged


title: CD47 Knockout Replicate 2


title: TCPOBOP_1d_Male_STARR_TYC6 (Alb promoter)_DNA_replicate2

description: extracted plasmid DNA, stranded library


title: VH-09_S40_WT-LPS

value: lung


title: TCPOBOP_1d_Male_STARR-TYC5 (ORI promoter)_DNA_replicate1

description: extracted plasmid DNA, stranded library


title: VH-08_S39_AMKO-PBS

value: postnatal day 5

value: PBS


title: VH-10_S41_WT-LPS

value: LPS (6 mg/kg of Escherichia coli O55:B5 lipopolysaccharide)


title: CD47 Knockout Replicate 1

value: spleen


title: Pat_18_V_1_16

description:
Pat_18
DuplicateIDsMerged

value: M


title: Respiratory mucosa, IAV, 2dpi, hashtag oligo

description: HTO library: read1 file contains cell barcode and UMI; read2 file contains antibody derived Tag reads

value: Nasal mucosa, respiratory mucosa

value: IAV PR8

value: female

value: primary infection

value: HTO

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, Totalseq-B0303 anti-mouse Hashtag 6


title: at-endosperm-RNAseq_replicate2_col_Cm_x_ler

value: endosperm

value: AT F1-Endosperm Columbia TEmob x Landsberg

value: TEmob Col (maternal) x Ler (paternal)


title: Pat_17_V_1_15

description:
Pat_17
DuplicateIDsMerged

value: Blood

value: Pat


title: Wild Type Replicate 3

value: RBC progenitors

value: WT

value: Wild Type


title: Wild Type Replicate 2


title: TCPOBOP_1d_Male_STARR-TYC4 (SCP1 promoter)_DNA_replicate2

description: extracted plasmid DNA, stranded library

value: liver

value: 8-9 weeks

value: Male

value: TCPOBOP, 3 mg/kg, i.p., 1 d exposure

value: Low Corn Oil


title: Pat_16_V_1_14

description:
Pat_16
DuplicateIDsMerged

value: M


title: TCPOBOP_1d_Male_STARR-TYC4 (SCP1 promoter)_DNA_replicate1

description: extracted plasmid DNA, stranded library


title: VH-07_S38_AMKO-PBS

value: lung

value: postnatal day 5

value: Adm+/-

value: PBS


title: Pat_15_V_1_13

description:
Pat_15
DuplicateIDsMerged

value: F


title: Wild Type Replicate 1

value: spleen


title: VH-05_S36_WT-PBS

value: Adm+/+


title: TCPOBOP_1d_Male_STARR-TYC5 (ORI promoter)_DNA_replicate2

description: extracted plasmid DNA, stranded library


title: Pat_14_V_1_12

description:
Pat_14
DuplicateIDsMerged

value: Blood

value: Pat


title: TCPOBOP_1d_Male_STARR_TYC6 (Alb promoter)_RNA_replicate2

description: polyA-selected RNA, stranded library


title: VH-04_S35_WT-PBS


title: Pat_13_V_1_11

description:
Pat_13
DuplicateIDsMerged


title: TCPOBOP_1d_Male_STARR_TYC6 (Alb promoter)_RNA_replicate1

description: polyA-selected RNA, stranded library


title: SpIB2 lager yeast, day 5, rep3

city: San Nicolás de los Garza

first: Benito

last: Pereyra Alférez

state: Nuevo León

address: Av. Pedro de Alba S/N

department: Instituto de Biotecnología

country: Mexico

institute: Universidad Autónoma de Nuevo León

data_processing:
Transcriptomic paired-end reads for both yeast strains were quality-trimmed using Trimmomatic version 0.38 with the parameters LEADING:5 TRAILING:5 MINLEN:50 and Sortmerna for contaminant RNA removal
Trimmed sequence reads were mapped to Saccharomyces pastorianus CBS1418 GCA_011022315.1 refernece genome with STAR software version 2.7.3a with the default parameters
Raw read count calculation was done with HTSeq-count version 0.11.1
The differential gene expression analyisis was done with edgeR version 3.34.0
Assembly: GCA_011022315.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Saccharomyces pastorianus

source_name: SpIB2 lager yeast

growth_protocol: Both strains were inoculated in standar brewing wort and Fermentation proceeded for five days at 16°C.

extract_protocol:
For total RNA extraction, the hot phenol protocol was performed. the RNA integrity number (RIN) above 8 was used for the preparation of sequencing libraries.
RNA libraries was prepared at GENEWIZ and the Poly-A selection was done to capture only mRNA species.

value: SpIB2 lager yeast

tag: time

value: Day 5


title: TCPOBOP_1d_Male_STARR-TYC5 (ORI promoter)_RNA_replicate2

description: polyA-selected RNA, stranded library

value: liver


title: Pat_12_V_1_10

description:
Pat_12
DuplicateIDsMerged

tag: age


title: VH-02_S33_AMKO-LPS

value: LPS (6 mg/kg of Escherichia coli O55:B5 lipopolysaccharide)


title: TCPOBOP_1d_Male_STARR-TYC5 (ORI promoter)_RNA_replicate1

description: polyA-selected RNA, stranded library

value: 8-9 weeks

value: Male


title: Dorsal skin leopard Gecko at E35

city: Pamplona

first: Asier

last: Ullate-Agote

state: Navarra

address: Av. de Pío XII, 55

department: Hemato-Oncology

country: Spain

institute: CIMA

data_processing:
Alignment to the Eublepharis macularius (MPM_Emac_v1) genome and quantification was performed using 10x Genomics Cell Ranger (v7.2.0)
Downstream analysis steps (quality control filtering, normalization, clustering and differential expression) were performed using the R package Seurat (v4.2.0) and doublet detection with scDblFinder v1.12.0
Assembly: MPM_Emac_v1
Supplementary files format and content: HDF5 Feature Barcode Matrix containing a Gene x Cells UMI count matrix

organism: Eublepharis macularius

source_name: embryonic dorsal skin

extract_protocol:
10X Chromium Single Cell 3ʹ v.3
Chromium Next GEM Single Cell 3p RNA library v3.1

value: embryonic dorsal skin

value: Wild type

tag: developmental stage


title: Pat_11_V_1_9

description:
Pat_11
DuplicateIDsMerged

value: M


title: SpIB2 lager yeast, day 5, rep1


title: SpIB2 lager yeast, day 5, rep2


title: VH-01_S32_AMKO-LPS

value: lung

value: postnatal day 5


title: VH-06_S37_AMKO-PBS

value: Adm+/-

value: PBS


title: TCPOBOP_1d_Male_STARR-TYC4 (SCP1 promoter)_RNA_replicate2

description: polyA-selected RNA, stranded library

value: TCPOBOP, 3 mg/kg, i.p., 1 d exposure

value: Low Corn Oil


title: Pat_10_V_1_8

description:
Pat_10
DuplicateIDsMerged

value: Blood

value: F


title: Pat_09_V_1_7

description:
Pat_9
DuplicateIDsMerged

value: Pat


title: TCPOBOP_1d_Male_STARR-TYC4 (SCP1 promoter)_RNA_replicate1

description: polyA-selected RNA, stranded library


title: SpIB2 lager yeast, day 2, rep3

value: SpIB2 lager yeast

value: Day 2


title: SpIB2 lager yeast, day 2, rep2


title: Pat_08_V_1_6

description:
Pat_8
DuplicateIDsMerged


title: corn oil_1d_Female_STARRTYC6_DNA

description:
extracted plasmid DNA, stranded library
G187M30

value: liver

value: Female

value: corn oil, 1d


title: Periosteal Cells, HIF1A, Chip

city: Bunkyo-ku

first: Masayuki

last: Tsukasaki

state: Tokyo

department: Department of Immunology Graduate School of Medicine and Faculty of Medicine

country: Japan

institute: The University of Tokyo

data_processing:
ChIP-seq data were processed using Galaxy server https://usegalaxy.org. (The Galaxy Community. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update, Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W345-W351, doi:10.1093/nar/gkac247). For mapping and visualization, paired-end FASTQ reads were mapped to mouse genome mm10 using Bowtie2 (v 2.5.0) with default filtering criteria. Resulted BAM files were converted to BED format using bedtools (v2.30.0). Peak calling of the Lys4 ChIP, Lys27 and HIF-1α and its corresponding Input was performed using MACS2 (v 2.2.9.1) with the --nomodel option and a p-value cutoff of 0.01 with the narrow peak option was used. The generated BedGraph files were converted to Bigwig format and visualized using IGV v2.13.0.
Assembly: Mouse genome build GRCm38/mm10
Supplementary files format and content: bigwig

source_name: Periosteum

extract_protocol: Primary periosteal cells (Ter119-CD45-CD31-PDPN+ PDGFRα+ cells) were isolated from the tumor-excised calvarial tissues from the scratch-negative groups one week after the implantation of HNM007 cell. Chromatin immunoprecipitation on 100,000 periosteal cells was performed with CUT&RUN Assay Kit (CST, #86652) using antibodies to acetylated histone H3 Lys27 (H3K27ac) (CST,#8173s), H3K4me3 (CST,#9751) and HIF-1α (CST,#36169). Illumina sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat No. 7645) according to the manufacturer's instructions. Barcoded libraries were run on the NovaSeq 6000 in a PE150 run, and an average of 40 million paired reads were generated per sample.

value: Periosteum

tag: chip antibody


title: Periosteal Cells, Lys27, Chip

value: Acetyl-Histone H3 (Lys27) (CST,#8173s)


title: SpIB2 lager yeast, day 2, rep1


title: corn oil_1d_Male_STARRTYC6_DNA

description:
extracted plasmid DNA, stranded library
G187M26

value: 8-9 weeks

value: Male


title: VH-03_S34_WT-PBS

value: lung

value: postnatal day 5

tag: genotype

value: Adm+/+


title: Pat_07_V_1_5

description:
Pat_7
DuplicateIDsMerged

tag: treatment

value: M


title: Periosteal Cells, Lys4, Chip

tag: tissue

value: Tri-Methyl-Histone H3 (Lys4)  (CST,#9751)


title: SpIB1 lager yeast, day 5, rep3

source_name: SpIB1 lager yeast

value: SpIB1 lager yeast

value: Day 5


title: SpIB1 lager yeast, day 5, rep2


title: corn oil_1d_Female_STARRTYC6_RNA_replicate3

description:
polyA-selected RNA, stranded library
G187M19

value: Low Corn Oil


title: Pat_04_V_1_3

description:
Pat_4
DuplicateIDsMerged

value: Blood

value: Pat

value: F


title: Pat_05_V_1_4

description:
Pat_5
DuplicateIDsMerged


title: SpIB1 lager yeast, day 5, rep1


title: Periosteal Cells, input


title: Whole-exome sequencing analysis of HNM007 cells

data_processing:
The quality of the raw paired-end sequence reads was assessed with FastQC (Version0.11.7). Low quality (< 20) bases and adapter sequences were trimmed by Trimmomaticsoftware (Version 0.38) with following parameters: ILLUMINACLIP:path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36.The trimmed reads were mapped to reference genome C57BL/6J based on GRCm39(mm39) using bwa-mem(v0.7.17-r1188). SAM files were converted into BAM files and sorted using Picard SortSam (Version2.18.11 ). The number of duplicates was calculated using Picard MarkDuplicates. After removing the duplicates, single nucleotide variants (SNVs) and short indels were called using freebayes (Version 1.3.4).
Assembly: GRCm39/mm39
Supplementary files format and content: Aggregated VCF file for all samples
Library strategy: WES

source_name: Epithelial tissue

extract_protocol: Genomic DNA was extracted from HNM007, AKR and NOOC1 cells by phenol–chloroform extraction and then purified with TIANamp Genomic DNA Kit (Spin Column). DNA concentrations were quantified using Qubit and quality was confirmed by gel electrophoresis. Whole-exome libraries were constructed with the Agilent SureSelectXT Mouse All Exon Kit. Libraries were constructed using 600 ng of DNA and were sequenced on Illumina NovaSeq 6000 platform using 150 bp paired-end reads at the Rhelixa Inc, Tokyo, Japan.

value: Epithelial tissue

tag: cell line

tag: cell type

value: squamous cell carcinoma


title: Whole-exome sequencing analysis of AKR cells

value: AKR


title: Pat_02_V_1_37

description:
Pat_2
DuplicateIDsMerged

tag: Sex


title: Pat_03_V_1_2

description:
Pat_3
DuplicateIDsMerged


title: SpIB1 lager yeast, day 2, rep3

value: Day 2


title: corn oil_1d_Female_STARRTYC6_RNA_replicate2

description:
polyA-selected RNA, stranded library
G187M18

value: liver

value: 8-9 weeks

value: Female

value: corn oil, 1d


title: corn oil_1d_Female_STARRTYC6_RNA_replicate1

description:
polyA-selected RNA, stranded library
G187M17


title: SpIB1 lager yeast, day 2, rep2


title: corn oil_1d_Male_STARRTYC6_RNA_replicate4

description:
polyA-selected RNA, stranded library
G187M08

value: Male


title: Pat_01_V_1_36

description:
Pat_1
DuplicateIDsMerged


title: Ptf1aERT;K*;Pdx1f/f, replicate 3

city: Detroit

first: Simone

last: Benitz

address: 2799 W Grand Blvd

institute: Henry Ford Health System

data_processing:
Sequencing reads were assessed for quality metrics using FastQC and multiQC. Reads were aligned to the mouse reference genome (GRCm38/mm10 Ensembl release 98) using Salmon.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Pancreatic acinar cells

extract_protocol:
For acinar cell isolation, pancreas tissue was washed three times in Hank’s Balanced Salt Solution (HBSS) (SH3026801, Thermo Fisher Scientific), minced and digested in HBSS containing 0.5mg/ml Collagenase P (Roche, 11249002001) for 15 minutes at 37°C. Digestion reaction was stopped by washing the tissue three times in HBSS with 5% FBS. Acinar cells were isolated by straining the tissue through 500µm and 100µm filter meshes and centrifugating the cells through a gradient of 30% FBS in HBSS. For total RNA extraction, the RNeasy® Plus Mini Kit (74134, Qiagen) was used following manufacturer’s instructions.
Library preparation and sequencing was performed at the Advanced Genomics Core of the University of Michigan. Library was constructed using standard Illumina protocols.

treatment_protocol: To induce Ptf1aCreERT-dependent recombination, animals were treated with Tamoxifen (T5648, Sigma). Tamoxifen was dissolved in corn oil and administered by oral gavage, 5mg daily for a total of five days.

value: Pancreatic acinar cells

value: 2 weeks after Tamoxifen

tag: gender


title: Cont_14_V_1_25

description:
Cont_14
DuplicateIDsMerged

value: Cont

value: M


title: Ptf1aERT;K*;Pdx1f/f, replicate 1


title: Cont_13_V_1_24

description:
Cont_13
DuplicateIDsMerged


title: corn oil_1d_Male_STARRTYC6_RNA_replicate2

description:
polyA-selected RNA, stranded library
G187M06

value: Low Corn Oil


title: Whole-exome sequencing analysis of NOOC1 cells


title: tumor-excised calvarial tissues from the scratch-negative (pre-invasive stage) group

description: 10x Genomics

data_processing:
Alignment, quantitation and aggregation of sample count matrices were performed using the 10x Genomics Cell Ranger pipeline as the manufacturer’s protocol (Azenta Japan Corp.)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor-excised calvarial tissue

extract_protocol:
Single-cell RNA-sequencing was performed on live cells, mixed CD45+ and CD45– cells in a 1:1 ratio, derived from calvarial tissues of tumor-free control mice and tumor-excised scratch-negative (pre-invasive stage) and scratch-positive (invasive stage) mice 1 week after the implantation of HNM007 cells.
The sequencing library was generated using the 10x Genomics Single Cell 3′ v3.1 and subjected to DNBSEQ-G400.

value: tumor-excised calvarial tissue

tag: group

value: 8 weeks old


title: tumor-excised calvarial tissues from the  scratch-positive (invasive stage) group

description: 10x Genomics

value: scratch-positive (invasive stage) group


title: corn oil_1d_Male_STARRTYC6_RNA_replicate1

description:
polyA-selected RNA, stranded library
G187M05


title: Ptf1aERT;Pdx1f/f, replicate 3


title: Cont_12_V_1_23

description:
Cont_12
DuplicateIDsMerged

value: Blood

value: F


title: Cont_11_V_1_22

description:
Cont_11
DuplicateIDsMerged


title: Ptf1aERT;Pdx1f/f, replicate 2


title: TCPOBOP_1d_Male_STARRTYC6_RNA_replicate4

description:
polyA-selected RNA, stranded library
G187M04

value: TCPOBOP, 1d


title: Aaus Development ATACseq Rep1

city: Stanford

first: Anne

last: Brunet

state: California

address: 290 Jane Stanford Way

department: Genetics

institute: Stanford University

description:
Aaus_consensusPeaks_rpkm.txt
Aaus_Dev_1

data_processing:
Fastq filles underwent read trimming using Trimgalore (v0.4.1)
Fastq files were mapped using --very-sensitve parameter on Bowtie2 (v2.2.5)
Duplicate reads were flagged and removes with Picard tools (v2.22.1) and SAMtools (v1.5)
Tn5 base shifting corrected by alignmentSieve in deepTools (version 3.2.1)
Peaks called using MACS2 (version 2.1.1.20160309)
Genome_build: Genomes used: African Turqouise Killifish: GCA_001465895.2 ; Red-Striped & Lyretail Killifish: GCA_006937985.1 MPIBA_Aaus_1.0 scaffolds: 12,236 contigs: 30,782 N50: 119,465 L50: 1,783 ; South American Killifish: GCA_001266775.1
Supplementary_files_format_and_content: Concensus Peak files across replicates and timepoints. Columns 1-11 are Bed format entries and all following are RPKM-normalized readcounts within each sample.

organism: Aphyosemion australe

source_name: Dissected Embryo (Whole Body)

growth_protocol: Synchronized killifish embryos for African turquoise and South American killifish were collected within a tight (~5 hour) breeding window. Most collected embryos were at the 1-2 cell stage upon collection. We monitored embryos every day post-collection to observe the visual markers of diapause and development as previously described. Briefly, we used Kupffer’s vesicle (KV), which is a transient embryonic organ present from early to middle somitogenesis as a marker to stage embryos that are about to reach diapause. KV-positive embryos reach the end of somitogenesis in 1-2 days and the loss of KV roughly coincides with the onset of heartbeat in killifish, followed by either diapause or continue development. We counted the number of somites in KV-positive embryos and designated KV-positive embryos at 15-22 somites as our “pre-diapause (Pre-Dia) stage”. Embryo morphology for all the killifish species was similar at this stage. This mid-somitogenesis time point also coincides with the vertebrate phylotypic period (the period of the most conserved gene expression pattern during vertebrate development) with available gene expression and chromatin accessibility data from multiple other fish species. we next monitored the onset of heartbeat, and stage diapause embryos at 6 days (Dia 6d) and 1 month of diapause (Dia 1m) as exhibiting a continuously decreasing heartbeat rate since diapause onset (<45 beat-per-minute (BPM)) as described in Hu et al. For embryos in 1 month diapause (Dia 1m), we additionally made sure that there was no heartbeat by monitoring them for 5 minutes under a stereoscope to verify that they were not prematurely exiting the diapause state. For embryos in development, embryos that had an increase in heartbeat rate 1 day after heartbeat onset (>45 BPM), but before the visual pigmentation in eyes was developed (i.e. before pharyngula stage) were designated as developing embryos (Dev). All the diapause and development stages stage are identical to our previous study, except Pre-Dia stage which is a day before the onset of heartbeat.

extract_protocol:
To generate nuclei-suspension for ATAC-seq libraries, snap frozen embryo samples (~10 embryos per sample) were thawed for 1 minute and resuspended at 4oC in 200ml EZ-lysis buffer (Sigma Aldritch No. 3408). Samples were then transferred to 250 ml mini-douncers (DWK (Kimble) 885300-0000) and dounced 25 times with pestle A and B respectively. After a 2 minute incubation following douncing, samples were spun at 500g for 5 minutes to precipitate nuclei, and the EZ-lysis supernatant was removed. Nuclei were then resuspended in 250ml PBS (ThermoFisher No. AM9624) and an aliquot of 5µl of nuclei was incubated with 5ml of 0.4% trypan blue stain (ThermoFisher No. 15250061) for counting the total intact nuclei counts.
Samples of ~25,000 nuclei were then suspended in a Tn5 transposition mix (65ml of tagmentation DNA buffer (Illumina No. 20034197), 63ml of nuclease-free water, and 2.5ml of tagmentation DNA enzyme I (e.g Tn5 transposase) (Illumina No. 20034197) for 20 minutes at 37oC. Following incubation, the mix was purified using the Qiagen mini-elute kit (Qiagen No. 28206) to isolate tagmented DNA. PCR amplification and subsequent qPCR monitoring was performed as described in the original ATAC-seq protocol (~14-18 cycles of PCR). Amplified DNA from the PCR reaction was purified using the Qiagen mini-elute kit (Qiagen No. 28206), as recommended by the manufacturer. Samples were subsequently pooled and sequenced using next-generation short-read sequencing on an Illumina NEXTseq 550.

treatment_protocol: All collected embryos were wildtype and untrated for the duration of their development.

value: Dissected Embryo (Whole body)

tag: Stage

value: Development

tag: time point

value: Development (>60BPM)


title: Cont_10_V_1_1

description:
Cont_10
DuplicateIDsMerged


title: Cont_09_V_1_32

description:
Cont_9
DuplicateIDsMerged


title: TCPOBOP_1d_Male_STARRTYC6_RNA_replicate2

description:
polyA-selected RNA, stranded library
G187M02

value: liver

tag: strain

tag: age at_euthanasia

value: 8-9 weeks


title: Ptf1aERT;K*;Pdx1f/f, replicate 2

value: Male


title: Ptf1aERT;K*, replicate 2

value: Pancreatic acinar cells


title: Aaus Pre-Diapause ATACseq Rep3

description:
Aaus_consensusPeaks_rpkm.txt
Aaus_preDia_3

value: Pre-Diapause (K-vesicle)


title: SpIB1 lager yeast, day 2, rep1

value: SpIB1 lager yeast

value: Day 2


title: Ptf1aERT;K*, replicate 3

value: 2 weeks after Tamoxifen


title: corn oil_1d_Male_STARRTYC6_RNA_replicate3

description:
polyA-selected RNA, stranded library
G187M07

value: corn oil, 1d

tag: dosing regimen

value: Low Corn Oil


title: Aaus Pre-Diapause ATACseq Rep2

description:
Aaus_consensusPeaks_rpkm.txt
Aaus_preDia_2


title: TCPOBOP_1d_Male_STARRTYC6_RNA_replicate1

description:
polyA-selected RNA, stranded library
G187M01


title: Cont_08_V_1_31

description:
Cont_8
DuplicateIDsMerged

value: Cont


title: TCPOBOP_1d_Male_STARRTYC6_DNA

description:
extracted plasmid DNA, stranded library
G187M25


title: corn oil_1d_Female_STARRTYC3/7_DNA_replicate1

description: extracted plasmid DNA, stranded library

value: 7-8 weeks

value: Female


title: Cont_07_V_1_30

description:
Cont_7
DuplicateIDsMerged

value: Blood

value: M


title: Nfur Diapause 1 Month ATACseq Rep3

description:
Nfur_consensusPeaks_rpkm.txt
Nfur_1M_3

organism: Nothobranchius furzeri

value: Dissected Embryo (Whole body)

value: Diapause

value: Diapause 1 Month


title: Ptf1aERT, replicate 3

tag: time


title: Nfur Diapause 1 Month ATACseq Rep2

description:
Nfur_consensusPeaks_rpkm.txt
Nfur_1M_2


title: calvaria of tumor-free control mice

description: 10x Genomics

source_name: control calvarial tissue

value: control calvarial tissue

value: control group

tag: age

value: 8 weeks old


title: Ptf1aERT;Pdx1f/f, replicate 1

value: Pancreatic acinar cells


title: corn oil_1d_Male_STARRTYC3/7_DNA_replicate1

description: extracted plasmid DNA, stranded library

value: liver

value: Male


title: TCPOBOP_1d_Male_STARRTYC3/7_DNA_replicate1

description: extracted plasmid DNA, stranded library

value: TCPOBOP (3mg/kg), 1d


title: Ptf1aERT, replicate 2

value: 2 weeks after Tamoxifen


title: Ptf1aERT, replicate 1


title: TCPOBOP_1d_Male_STARRTYC6_RNA_replicate3

description:
polyA-selected RNA, stranded library
G187M03

value: 8-9 weeks

value: TCPOBOP, 1d

value: Low Corn Oil


title: Nfur Diapause 1 Month ATACseq Rep1

description:
Nfur_consensusPeaks_rpkm.txt
Nfur_1M_1


title: Cont_04_V_1_27

description:
Cont_4
DuplicateIDsMerged

value: Cont

value: F


title: corn oil_1d_Female_STARRTYC3/7_RNA_replicate4

description: polyA-selected RNA, stranded library

value: 7-8 weeks

value: Female

value: corn oil, 1d


title: corn oil_1d_Female_STARRTYC3/7_RNA_replicate2

description: polyA-selected RNA, stranded library


title: Cont_03_V_1_26

description:
Cont_3
DuplicateIDsMerged

value: Blood

value: M


title: Ptf1aERT;K*;Pdx1f/f, 10 weeks, replicate 2

description: 10x Genomics, Sequencing Batch 2

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate demultiplexed fastq files.
Raw sequencing data was processed using cellranger-atac-2.0.0 (10X Genomics).
Assembly: mm10
Supplementary files format and content: Fragment files, peak data in bed format and barcode information (singlecell.csv)

source_name: Pancreas

extract_protocol:
Frozen tissue was pulverized by using the CP02 pulverizer (Covaris). Pulver was washed with PBS containing 0.04% BSA and 1X protease inhibitor and centrifuged (5 min, 500 g, 4 °C). Supernatant was discarded, pellet was resuspended in 0.1 U/μl DNase solution (EN0521, Thermo Fisher Scientific) and incubated on ice for 5 minutes. Tissue was washed twice with PBS containing 0.04% BSA and 1X protease inhibitor. After the last centrifugation step (5 min, 500 g, 4 °C), supernatant was discarded, pellet was resuspended in freshly prepared lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonident P40, 0.01% Digitonin (BN2006, Thermo Fisher Scientific), 1% BSA and 1X protease inhibitor) and incubated on ice for 10 minutes. Nuclei were isolated by using a 2 ml Dounce homogenizer. Sample was filtrated through a 70 μm cell strainer, followed by centrifugation (1 min, 100 g, 4 °C). Supernatant was transferred to a new tube and washed with wash buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA and 1X protease inhibitor) followed by centrifugation (5 min, 500 g, 4°C) for three times. Before the final washing step, suspension was filtered through a 40 μm Flowmi cell strainer. Nuclei were resuspended in Nuclei Buffer (10X Genomics).
Library preparation and sequencing was performed at the Advanced Genomics Core of the University of Michigan. Single nucleus suspensions were counted on the LUNA Fx7 Automated Cell Counter (Logos Biosystems) and snATAC libraries were generated using the 10x Genomics Chromium instrument following the manufacturer’s protocol. Final library quality was assessed using the LabChip GX (PerkinElmer).

value: Pancreas

value: 10 weeks after Tamoxifen


title: Cont_01_V_1_33

description:
Cont_1
DuplicateIDsMerged


title: Nfur Diapause Day 6 ATACseq Rep2

description:
Nfur_consensusPeaks_rpkm.txt
Nfur_6D_2

value: Dissected Embryo (Whole body)

value: Diapause

value: Diapause Day 6


title: corn oil_1d_Female_STARRTYC3/7_RNA_replicate3

description: polyA-selected RNA, stranded library

value: liver


title: Nfur Diapause Day 6 ATACseq Rep1

description:
Nfur_consensusPeaks_rpkm.txt
Nfur_6D_1


title: Ptf1aERT;K*, replicate 1

value: Pancreatic acinar cells

value: 2 weeks after Tamoxifen


title: Aaus Pre-Diapause ATACseq Rep1

description:
Aaus_consensusPeaks_rpkm.txt
Aaus_preDia_1

value: Development

value: Pre-Diapause (K-vesicle)


title: Ptf1aERT;K*, 10 weeks, replicate 2

description: 10x Genomics, Sequencing Batch 2

value: Male


title: corn oil_1d_Female_STARRTYC3/7_RNA_replicate1

description: polyA-selected RNA, stranded library

value: Low Corn Oil


title: Cont_05_V_1_28

description:
Cont_5
DuplicateIDsMerged

value: Cont

value: F


title: Nfur Development ATACseq Rep1

description:
Nfur_consensusPeaks_rpkm.txt
Nfur_Dev_1

value: Development (>60BPM)


title: Ptf1aERT;K*, 10 weeks, replicate 1

description: 10x Genomics, Sequencing Batch 2

value: Female


title: MDA-MB-231, selected on stiff, rep 4 (RNA-seq)

city: College Station

first: Ting-Ching

last: Wang

address: 101 Bizzell St

institute: Texas A&M University

data_processing:
The sequenced reads were trimmed and aligned to the human genome (hg19) using a RNA-seq aligner, Spliced Transcripts Alignment to a Reference (STAR)
Assembly: hg19
Supplementary files format and content: Fragments Per Kilobase of transcript per Million mapped reads (FPKM) as a txt file

growth_protocol: Cells were maintained in a humidified incubator at 37 °C and 5% CO2. Human breast carcinoma cells MDA-MB-231 (ATCC) were cultured in Dulbecco’s Modified Eagle’s Medium with 4.5 g/l glucose (Corning), supplemented with 10% v/v donor bovine serum (Gibco) and 1% v/v penicillin/streptomycin (Corning).

extract_protocol:
Total RNA was extracted with the Direct-zolTM RNA MiniPrep Plus Kit (Zymo Research Corp).
Library preparation was performed by the University of Florida (UF) Interdisciplinary Center for Biotechnology Research (ICBR) using an Illumina RNAseq library prep kit with ribodepletion.

treatment_protocol: Selection of MDA-MB-231 were initiated by plating 20,000 cells on polyacrylamide gels of Young’s modulus E = 1 kPa (soft) and 308 kPa (stiff) conjugated with type I collagen. Cell populations were allowed to grow for approximately seven days, and then 20,000 cells were passaged onto fresh substrates of the same (corresponding) stiffness. This procedure was carried out for 75 days.

value: Breast adenocarcinoma cells

value: WT

value: selected on stiff


title: Nfur Pre-Diapause ATACseq Rep2

description:
Nfur_consensusPeaks_rpkm.txt
Nfur_preDia_2

value: Dissected Embryo (Whole body)


title: MDA-MB-231, selected on stiff, rep 3 (RNA-seq)


title: MDA-MB-231, selected on stiff, rep 2 (RNA-seq)


title: Nfur Pre-Diapause ATACseq Rep1

description:
Nfur_consensusPeaks_rpkm.txt
Nfur_preDia_1


title: Ptf1aERT;K*;Pdx1f/f, 2 weeks, replicate 2

description: 10x Genomics, Sequencing Batch 1

value: Pancreas


title: Ptf1aERT;K*;Pdx1f/f, 2 weeks, replicate 1

description: 10x Genomics, Sequencing Batch 1


title: TCPOBOP_1d_Male_STARRTYC3/7_RNA_replicate2

description: polyA-selected RNA, stranded library

value: 7-8 weeks

value: TCPOBOP (3mg/kg), 1d


title: Ptf1aERT;K*;Pdx1f/f, 10 weeks, replicate 1

description: 10x Genomics, Sequencing Batch 2

value: 10 weeks after Tamoxifen


title: Cont_02_V_1_38

description:
Cont_2
DuplicateIDsMerged

value: Blood

value: M


title: Nfur Development ATACseq Rep2

description:
Nfur_consensusPeaks_rpkm.txt
Nfur_Dev_2

value: Development


title: MDA-MB-231, selected on soft, rep 4 (RNA-seq)

value: selected on soft


title: Ptf1aERT;Pdx1f/f, 2 weeks, replicate 2

description: 10x Genomics, Sequencing Batch1

value: 2 weeks after Tamoxifen

value: Male


title: TCPOBOP_1d_Male_STARRTYC3/7_RNA_replicate1

description: polyA-selected RNA, stranded library

value: liver

value: Low Corn Oil


title: PD_4

type: protein

city: Freiburg

first: Robert

last: Zeiser

address: Hugstetter Strasse 53

department: Inner Medicine 1

country: Germany

description:
Protein lysates with still active kinases, phosphorylation of spotted peptides on chip detected with FITC labeled anti-phospho antibody
180-205_PD_4

hyb_protocol: 5 μg of protein per well was loaded onto the PamChip and the assay was run on a PamStation96 (PamGene International).

scan_protocol: The degree of phosphorylation was measured in real time via the kinetic image capture program, Evolve (PamGene International), which captures FITC-labeled anti-phosphotyrosine antibody binding to each phosphorylated peptide substrate.   Following 60 min incubation, the signal intensities for each peptide were analyzed using BioNavigator Software (PamGene International).

data_processing: Only peptides that showed kinetics (increase of signal in time) on at least 25 % of the arrays were included in the analysis. Nominal coefficient of variation (CV) was calculated per peptide using a 2-component error fit model using overall mean as input and was used as a filter to remove low-intensity spots. Only peptides that showed nominal CV <0.5 were included in the analysis. For kinase interpretation, a ranked list of putative kinases responsible for differences in the peptide phosphorylation was generated by upstream kinase analysis (UKA, PamGene International).

label: PY20 FITC

source_name: Microglia isolated from anti-PD-1+ melanoma bearing group

label_protocol: We used the PTK PamGene Array according to instructions

growth_protocol: B16F10 Melanoma cells were maintainted in DMEM complete media with 10%FCS and Penstrip.

extract_protocol: PamGene lysates were prepared according to manufacturers instructions with M-PER Mammalian Protein Extraction Reagent (ThermoFisher) containing Halt phosphatase and Halt protease inhibitor cocktails (ThermoFisher). Total protein was quantified using the Pierce BCA Protein Assay Kit (ThermoFisher).

treatment_protocol: 10,000 B16F10 cells were injected and mice were treated with either Isotype or anti-PD-1 on day1,4,8,16 and 22. The mice were sacrificed on day 23 and FACS sorted for CD45lo And CD11b Microglia cells.

value: Microglia

value: Brain

tag: sample group

value: anti-PD-1+ melanoma bearing group

tag: pamchip number


title: MDA-MB-231, selected on soft, rep 3 (RNA-seq)

value: Breast adenocarcinoma cells

tag: genotype

value: WT


title: Ptf1aERT;Pdx1f/f, 2 weeks, replicate 1

description: 10x Genomics, Sequencing Batch 2

value: Pancreas

value: Female


title: Ptf1aERT;K*, 2 weeks, replicate 2

description: 10x Genomics, Sequencing Batch 1


title: PCBP2KO  β cells, 16.7mM G, rep 4

first: Doris

middle: A

last: Stoffers

address: 3400 Civic Center Blvd

department: IDOM

data_processing:
Reads were aligned to mm39 with Kallisto
Gene level counts were determined wth tximport and processed for differential expression using EdgeR
Assembly: mm39
Supplementary files format and content: Kallisto output count abundance for each samples as  tab-separated values

source_name: Islet

extract_protocol:
Samples in  TRIzol (Invitrogen)  were sent to Genewiz for RNA extraction, library preperation, and sequencing.
RNAseq libraries were prepared using Illumina Ultra Low Input RNA kit.

treatment_protocol: Islets from Tdtomato and RIPCre+;Pcbp2Fl/Fl;Tdtomato mice were incubated in 2.8mM or 16.7mM glucose for 3 days then β cells were FACS-sorted for sequencing.

value: Islet

value: male

value: Beta cell

tag: treatment

value: 16.7mM Glucose


title: MDA-MB-231, selected on soft, rep 2 (RNA-seq)


title: corn oil_1d_Male_STARRTYC3/7_RNA_replicate1

description: polyA-selected RNA, stranded library

data_processing:
READ MAPPING: reads were aligned to the mm9 mouse genome using Bowtie2 (Langmead et al 2009, Genome Biology) with default settings. Reads were filtered so that only uniquely-aligned reads were used for downstream analysis.
PEAK CALLING: A set of 1,673 merged MACS2 peak regions were identified by MACS2 (Zhang et al 2008, Genome Biology) analysis of the associated plasmid, DNA, RNA libraries with default parameters without filtering for PCR duplicates. Peaks were filtered to remove ENCODE blacklisted regions (www.sites.google.com/site/anshulkundaje/projects/blacklists) and also regions called as peaks that contain only PCR duplicated reads.
READ COUNTING: Reads within the set of 1,673 MACS2 peak regions were counted using bedtools coverage option without filtering for PCR duplicates.
Assembly: mm9
Supplementary files format and content: G187_focus_processed_dataset.xlxs.  In vivo STARR-seq activity for the 1,673 MACS2 regions identified in the focused STARR-seq plasmid library. Columns F and G indicate the 100 genomic DNA PCR-amplified regions used to prepare the STARR-seq plasmid library. Columns H-O show the raw sequencing reads in each STARR-seq RNA library, prepared from each liver after HDI, and Columns P-S show the raw sequencing reads obtained from the DNA library extracted from each liver, and from the original focused plasmid library. Columns T-AF show raw normalized reads per 10 million mapped reads, obtained by dividing the raw reads (columns) by the total number of sequencing reads in the corresponding sample. Columns AG-AN show the calculated enhancer activity of each region, based on the ratio of reads between the individual RNA library and the DNA library under the same condition. Columns AO-AQ indicate the average enhancer activity across the biological replicates for each condition.
Library strategy: STARR-seq

extract_protocol:
The extraction methods, adapted from the published STARR-seq protocol (Neumayr, Pagani et al. 2019), were used in a nested PCR amplification protocol to characterize the transcriptional activity of each DHS sequence (putative regulatory region) to be assayed by HDI-STARR-seq: 1) a library prepared from DNA extracted from flash frozen liver tissue collected 7 d after in vivo transfection by HDI (primers ON8381, ON8382); and 2) a library prepared from the transcribed RNA (reporter sequences) extracted from each HDI-transfected liver (primers ON8379, ON8380; see STARR_seq_primer.txt). STARR-seq reporter plasmid DNA remaining in the liver 7 d after HDI was extracted using a commercial QIAprep spin miniprep kit (QIAgen, cat. # 27106). Liver tissue (200 mg frozen liver) was initially homogenized in 750 ul of QIAgen Buffer P1 using a rubber-tipped micropestle and passed through a 20G needle 3 times to homogenize large tissue pieces. The extracted plasmid DNA was bound to a QIAprep spin column, eluted in EB buffer and used as a PCR template in a subsequent nested PCR reaction using primers ON8381 and ON8382 (see STARR_seq_primer.txt). To extract transcribed reporter RNA, 120 ug of total liver RNA was isolated from 60-100 mg liver tissue from each mouse by TRIzol guanidinium thiocyanate-phenol-chloroform extraction then purified by polyA selection using oligo(dT) beads (New England Biolabs, cat. #E7490L). The transcribed RNA was digested with Turbo DNase I (Ambion, cat. # AM2238) at 37°C for 30 min, reverse transcribed using primer ON8731 (see STARR_seq_primer.txt) for STARR-seq RNA first strand synthesis and Superscript III first-strand synthesis supermix (Invitrogen, cat. # 18080-400) and treated with 10 mg RNase A per ml (Fermentas, cat. # EN0531) for 1 h at 37 Celsius. The cDNA obtained was purified using 1.8x SPRI beads then used as a PCR template in the nested PCR reaction.
The nested PCR reaction requires a set of primers that specifically targets DNA or RNA derived from a STARR-seq reporter, after which the sequences are amplified using Illumina dual index primers. A primer set, primers ON8381 and ON8382 (see STARR_seq_primer.txt) was designed to amplify the STARR-seq plasmid DNA libraries by specifically targeting the unspliced intron incorporated into the original plasmid and present in the plasmid and DNA libraries, but that is spliced out of the reporter RNA sequences. Another primer set, primers ON8379 and ON8380 (see STARR_seq_primer.txt) straddles the splice junction and was designed to specifically amplify only the transcribed and spliced RNA molecules. Subsequently, nested PCR was completed using NEBNext® Multiplex Oligos for Illumina (#E7600S) for all three library types (plasmid, DNA and RNA) to further amplify the material and attach Illumina i5 and i7 barcoded sequences used for multiplex sequencing on an Illumina sequencer.

tag: tissue

value: 7-8 weeks

value: corn oil, 1d


title: corn oil_1d_Male_STARRTYC3/7_RNA_replicate2

description: polyA-selected RNA, stranded library


title: MDA-MB-231, selected on soft, rep 1 (RNA-seq)

tag: cell line

value: selected on soft


title: PCBP2KO  β cells, 16.7mM G, rep 3

tag: cell type


title: PD_1

description:
Protein lysates with still active kinases, phosphorylation of spotted peptides on chip detected with FITC labeled anti-phospho antibody
180-205_PD_1


title: PD_7

description:
Protein lysates with still active kinases, phosphorylation of spotted peptides on chip detected with FITC labeled anti-phospho antibody
180-205_PD_7


title: PD_9

description:
Protein lysates with still active kinases, phosphorylation of spotted peptides on chip detected with FITC labeled anti-phospho antibody
180-205_PD_9


title: Ptf1aERT;K*, 2 weeks, replicate 1

description: 10x Genomics, Sequencing Batch 1

value: 2 weeks after Tamoxifen


title: Ptf1aERT, 2 weeks, replicate 2

description: 10x Genomics, Sequencing Batch 1

value: Male


title: PD_3

description:
Protein lysates with still active kinases, phosphorylation of spotted peptides on chip detected with FITC labeled anti-phospho antibody
180-205_PD_3


title: MDA-MB-231, ancestral on stiff, rep 4 (RNA-seq)

value: ancestral on stiff


title: MDA-MB-231, ancestral on stiff, rep 3 (RNA-seq)


title: MDA-MB-231, selected on stiff, rep 1 (RNA-seq)

value: selected on stiff


title: PCBP2KO  β cells, 16.7mM G, rep 2

tag: Sex


title: Ptf1aERT, 2 weeks, replicate 1

description: 10x Genomics, Sequencing Batch 1

tag: gender


title: PCBP2KO  β cells, 16.7mM G, rep 1


title: PCBP2KO  β cells, 2.8mM G, rep 4

value: 2.8mM Glucose


title: PCBP2KO  β cells, 16.7mM G, rep 5


title: ISO_1

description:
Protein lysates with still active kinases, phosphorylation of spotted peptides on chip detected with FITC labeled anti-phospho antibody
180-205_ISO_1

source_name: Microglia isolated from Isotype+ melanoma bearing group

value: Microglia

value: Brain

value: Iso+ melanoma bearing group


title: RCA

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

description: 10xGenomics 3’scRNAseq protocol

data_processing:
Samples were prepared in two independent batches. The first batch included barcoded TGFbR-KO (RKO) and TGFbR-WT (WT1) TH17 cells, while the second batch was comprised of TGFbR-CA (RCA) and TGFbR-WT (WT2) cells. . Illumina bcl files were basecalled, demultiplexed and aligned to the mouse mm10 genome using the cellranger software (version 3.1.0, 10xGenomics)
The output of cellranger was used to run the python package velocyto and produce loom files for each sample with RNA velocity estimations (La Manno et al., 2018). Loom files from two independent sequencing runs were imported into R and single cell data was analyzed with the 'Seurat' package (Stuart et al., 2019). Integration of these two datasets followed the “Fast integration using reciprocal PCA (RPCA)” protocol.
After filtering for library size and mitochondrial gene expression, pre-processing was performed using Seurat functions for counts normalization (SCT), dimension reduction with principal component analysis (PCA) (RunPCA with default parameters), construction of a Shared Nearest Neighbor (SNN) graph and clustering.
Assembly: mm10
Supplementary files format and content: csv files containing normalized expression matrices. Suggested cell identities have been added to the first row (rowname = “Identity”)
Supplementary files format and content: filtered feature matrices (output of cellranger count on the raw fastq files)

source_name: Th17 cells

extract_protocol:
After tissue dissection and dissociation, FACS purified suspended cells were partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs) with the Chromium Single Cell Controller (10XGenomics) at the CRCL Single Cell Platform.
Cell encapsulation and barcoding was followed by the standard scRNAseq protocol comprising reverse transcription, amplification, and indexing (10xGenomics).

treatment_protocol: We bred Il-17a-CRE mice (Hirota et al., 2011) with mice bearing either floxed alleles of TgfbR2 (Levéen et al., 2005), (TGFbR-KO, or RKO) or a constitutively active (CA, or RCA) form of TgfbR1 placed after a floxed stop cassette (TGFbR-CA) (Bartholin et al., 2008).

value: RCA


title: WT2

description: 10xGenomics 3’scRNAseq protocol

value: WT


title: ISO_5

description:
Protein lysates with still active kinases, phosphorylation of spotted peptides on chip detected with FITC labeled anti-phospho antibody
180-205_ISO_5


title: RKO

description: 10xGenomics 3’scRNAseq protocol

value: TGFbR-KO


title: MDA-MB-231, ancestral on stiff, rep 2 (RNA-seq)

value: Breast adenocarcinoma cells


title: Nfur Wildtype Development RNAseq Rep18

description:
Nfur_Wildtype_Dev_18
Nfur_KO_Readcounts.csv

data_processing:
read trimming with Trim Galore (version 0.4.5)
Genome Alignment using STAR (version 2.7.1a) No reference genome is available for the red-striped killifish, so the reads from red-striped killifish RNA-seq libraries were aligned to the genome of its close relative, lyretail killifish.
Keep only uniquely mapped reads using samtools (version 1.5) samtools view -q255
Readcounts obtained using feature counts function from Subread package (version 2.0.1)
Normalized expression using DESeq2 (version1.30.1)
Assembly: Genomes used: African Turqouise Killifish: GCA_001465895.2 ; Red-Striped & Lyretail Killifish: GCA_006937985.1 MPIBA_Aaus_1.0 scaffolds: 12,236 contigs: 30,782 N50: 119,465 L50: 1,783
Supplementary files format and content: Read counts files for each speacies from featurecount of Subread package

growth_protocol: Animals were housed in automated circulating water system with pH maintained at 6-7.5 and conductivity maintained between 3500 and 4500μS/cm with a 10% system water exchange every day by reverse osmosis treated water. Adult fish were manually fed Otohime fish diet (Reed Mariculture, Otohime C1 [Ep1 for the South American killifish]) twice a day during weekdays and once a day during weekends.

extract_protocol:
For each stage in each species, roughly 8-30 embryos were carefully dissected in ice-cold PBS using biological-grade tweezers (Electron Microscopy Sciences, 72700-D) to carefully remove the chorion, the enveloping layer, and the yolk without damaging the embryo body. Freshly dissected embryos were then quickly rinsed with ice-cold PBS, and all the PBS was carefully removed. Embryo bodies were then snap-frozen in liquid nitrogen and stored at -80°C. We used 8-10 snap-frozen embryos for RNA-seq. Snap frozen embryos at -80°C were thawed on ice for 1 minute and washed with 200µl ice-cold PBS. The embryos were then dissociated and homogenized with ~25 Zirconia/Silicon 0.5mm glass beads (RPI, Research Products International Corp, 9834) using FastPrep® -24 homogenizer (MB Biomedicals, 116004500) for 20 seconds, followed by centrifugation (17000g for 3 minutes). After centrifugation, 10.5µl of the supernatant was used as input to the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara, 634890) for the cDNA synthesis followed by amplification with 12 cDNA amplification cycles. Amplified cDNA was validated with Agilent 2100 Bioanalyzer using Agilent’s High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626).
The DNA libraries were then generated using the Nextera XT DNA Library Prep Kit (Illumina, FC-131-1096). Library quality and concentration were assessed by the Agilent 2100 Bioanalyzer and Agilent’s High Sensitivity DNA Kit (Agilent Technologies, Cat. No. 5067-4626), followed by high throughput sequencing on Illumina HiSeq platform with 2 x 150bp paired end reads.

treatment_protocol: Synchronized killifish embryos for African turquoise and South American killifish were collected within a tight (~5 hour) breeding window. Most collected embryos were at the 1-2 cell stage upon collection. We monitored embryos every day post-collection to observe the visual markers of diapause and development as previously described (12). Briefly, we used Kupffer’s vesicle (KV), which is a transient embryonic organ present from early to middle somitogenesis as a marker to stage embryos that are about to reach diapause. KV-positive embryos reach the end of somitogenesis in 1-2 days and the loss of KV roughly coincides with the onset of heartbeat in killifish, followed by either diapause or continue development (12, 17). We counted the number of somites in KV-positive embryos and designated KV-positive embryos at 15-22 somites as our “pre-diapause (Pre-Dia) stage”. Embryo morphology for all the killifish species was similar at this stage. This mid-somitogenesis time point also coincides with the vertebrate phylotypic period (the period of the most conserved gene expression pattern during vertebrate development) with available gene expression and chromatin accessibility data from multiple other fish species

value: Dissected Embryo (Whole body)

value: Development

tag: timing

value: Diapause-Escape


title: ISO_6

description:
Protein lysates with still active kinases, phosphorylation of spotted peptides on chip detected with FITC labeled anti-phospho antibody
180-205_ISO_6


title: MDA-MB-231, ancestral on stiff, rep 1 (RNA-seq)


title: SMA mouse Smn1_KO DUET treated Rep3

city: La Jolla

first: Jingting

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Sequenced reads were quality-tested using FASTQC and adapters were trimmed using Cutadapt with parameters `-j 8 -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC`.
Paired reads after trimming were aligned to custom mouse transcriptome and quantified at transcript level using Kallisto with arguments `quant -b 30`.
The custom transcriptome index was built with `kallisto index` by merging the cDNA FASTA files of mm10 mouse transcriptomes and three genome-editing conditions of gene Smn1 (including cDNA, HITI and Gene-DUET).
Raw gene expression was estimated and summarized from transcript-level abundance with tximport. Differential gene expression was performed on the raw gene counts with DESeq2.
Assembly: custome genome including mm10 mouse genome and three genome-editing conditions of gene Smn1 (including cDNA, HITI and Gene-DUET)
Supplementary files format and content: tab-delimited text file including raw transcript-level expression estimated from Kallisto

source_name: Spinal cord

extract_protocol:
RNA was extraxcted from the spinal cord at P14 by using Trizol and RNAeasy kit
RNA libraries for RNA-seq were prepared using TruSeq  mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: AAVs were delivered by intravenous injection into SMA mice at P0.5

value: Spinal cord

value: Whole tissue

value: DUET


title: PCBP2KO  β cells, 2.8mM G, rep 3

value: Islet

value: male

value: Beta cell


title: MDA-MB-231, ancestral on soft, rep 4 (RNA-seq)

value: ancestral on soft


title: WT1

description: 10xGenomics 3’scRNAseq protocol


title: PCBP2KO  β cells, 2.8mM G, rep 5

value: 2.8mM Glucose


title: Nfur Wildtype Development RNAseq Rep16

description:
Nfur_Wildtype_Dev_16
Nfur_KO_Readcounts.csv

tag: Stage


title: WT β cells, 16.7 mM G, rep 4

value: 16.7mM Glucose


title: PCBP2KO  β cells, 2.8mM G, rep 2


title: MDA-MB-231, ancestral on soft, rep 3 (RNA-seq)


title: Nfur Wildtype Development RNAseq Rep14

description:
Nfur_Wildtype_Dev_14
Nfur_KO_Readcounts.csv


title: MDA-MB-231, ancestral on soft, rep 2 (RNA-seq)


title: PCBP2KO  β cells, 2.8mM G, rep 1


title: SMA mouse Smn1_KO DUET treated Rep1


title: Nfur Wildtype Development RNAseq Rep13

description:
Nfur_Wildtype_Dev_13
Nfur_KO_Readcounts.csv


title: SMA mouse Smn1_KO DUET treated Rep2


title: UM5, siROR2, replicate 3

data_processing:
Adapter trimming and removal of ribosomal and mitochondrial genome was carried out with fastq-mcf, cutadapt and Bowtie2, respectively. Reads were mapped to the hg19 genome using STAR and raw read counts were estimated with HTSeq (v0.11.2) and normalized with DESeq2.
Assembly: hg19
Supplementary files format and content: RawNormCounts_siROR2.txt

growth_protocol: PANC1 were cultivated in Dulbecco’s Modified Eagle Medium (DMEM), supplemented with 10% fetal bovine serum (FBS) and 0.5% Gentamicin. UM5 were cultivated in RPMI 1640 with 10% FBS and 0.5% Gentamicin.

extract_protocol:
For total RNA extraction, the RNeasy® Plus Mini Kit (74134, Qiagen) was used following manufacturer’s instructions. Genomic DNA was digested on column by using the RNase-Free DNase Set (79254, Qiagen).
Library preparation and sequencing was performed at MedGenome Inc.. RNA-seq library preparation was performed by using the Illumina TruSeq stranded mRNA kit.

value: Pancreatic cancer cell line


title: Nfur Wildtype Development RNAseq Rep11

description:
Nfur_Wildtype_Dev_11
Nfur_KO_Readcounts.csv


title: UM5, siROR2, replicate 2


title: SMA mouse Smn1_KO cDNA treated Rep4

value: cDNA


title: Nfur Wildtype Development RNAseq Rep12

description:
Nfur_Wildtype_Dev_12
Nfur_KO_Readcounts.csv


title: MDA-MB-231, ancestral on soft, rep 1 (RNA-seq)

value: WT


title: UM5, siROR2, replicate 1


title: WT β cells, 16.7 mM G, rep 2


title: Nfur Wildtype Development RNAseq Rep10

description:
Nfur_Wildtype_Dev_10
Nfur_KO_Readcounts.csv


title: WT β cells, 16.7 mM G, rep 3


title: SMA mouse Smn1_KO cDNA treated Rep3


title: Nfur Wildtype Development RNAseq Rep9

description:
Nfur_Wildtype_Dev_9
Nfur_KO_Readcounts.csv


title: SMA mouse Smn1_KO cDNA treated Rep5


title: WT β cells, 2.8mM G, rep 3


title: Nfur Wildtype Development RNAseq Rep8

description:
Nfur_Wildtype_Dev_8
Nfur_KO_Readcounts.csv


title: UM5, sicontrol, replicate 3


title: WT β cells, 16.7 mM G, rep1


title: Nfur Wildtype Development RNAseq Rep7

description:
Nfur_Wildtype_Dev_7
Nfur_KO_Readcounts.csv


title: SMA mouse Smn1_KO cDNA treated Rep2


title: WT β cells, 2.8mM G, rep 2


title: UM5, sicontrol, replicate 2


title: UM5, sicontrol, replicate 1


title: SMA mouse Smn1_KO HITI treated Rep3

value: HITI


title: YFP-positive neural stem cells, Opa1KO2

city: Ottawa

first: Ruth

last: Slack

state: Ontario

address: 451 Smyth Road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

data_processing:
HISAT2 was used to align the reads.
Aligned reads was sorted using samtools to generate BAM files.
FeatureCounts was applied to the BAM files.
Differentially expressed genes were calculated with DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary cell

extract_protocol:
RNA was harvested using PicoPure (Applied Biosystems). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by TCAG The Centre for Applied Genomics – Next Generation Sequencing Facility

value: primary cell

value: neural stem cell

value: Opa1 knockout


title: WT β cells, 2.8mM G, rep 1


title: Nfur Wildtype Development RNAseq Rep6

description:
Nfur_Wildtype_Dev_6
Nfur_KO_Readcounts.csv

value: Dissected Embryo (Whole body)

value: Development

value: Diapause-Escape


title: SMA mouse Smn1_KO HITI treated Rep2

value: Spinal cord

value: Whole tissue


title: Nfur Wildtype Development RNAseq Rep5

description:
Nfur_Wildtype_Dev_5
Nfur_KO_Readcounts.csv


title: YFP-positive neural stem cells, Opa1KO1


title: Nfur Wildtype Development RNAseq Rep3

description:
Nfur_Wildtype_Dev_3
Nfur_KO_Readcounts.csv


title: PANC1, siROR2, replicate 2


title: SMA mouse Smn1_KO HITI treated Rep1


title: YFP-positive neural stem cells, WT2


title: PANC1, siROR2, replicate 1


title: Nfur Wildtype Development RNAseq Rep2

description:
Nfur_Wildtype_Dev_2
Nfur_KO_Readcounts.csv


title: YFP-positive neural stem cells, WT1


title: SMA mouse Smn1_KO Rep3

value: No treatment


title: SMA mouse Smn1_KO Rep1


title: Nfur Wildtype 6-Day Diapause RNAseq Rep20

description:
Nfur_Wildtype_6D_20
Nfur_KO_Readcounts.csv

value: Diapause

value: 6-Day Diapause


title: SMA mouse Smn1_KO cDNA treated Rep1


title: Nfur Wildtype Development RNAseq Rep1

description:
Nfur_Wildtype_Dev_1
Nfur_KO_Readcounts.csv


title: SMA mouse Smn1_KO Rep2


title: Nfur Wildtype 6-Day Diapause RNAseq Rep19

description:
Nfur_Wildtype_6D_19
Nfur_KO_Readcounts.csv


title: PANC1, sicontrol, replicate 3


title: Male Myf5 low  2

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

institute: Nestle Institute Of Health Sciences

data_processing:
Sequencing raw data (bcl) were demultiplexed and transformed in fastq files using cassava v1.8.2.
The fastq files were aligned against the reference genome by RNAstar v2.5.3a.
The raw sequencing counts per gene were generated using htseq_count v2.16.2 using Mus_musculus.GRCm38.93_proteinCoding_lincRNA.gtf
Assembly: GRCm38
Supplementary files format and content: htseq_summary_20220628.tsv
Supplementary files format and content: tab-separated file containing count data per gene (row) per cells derived from pool of mice (column)

source_name: Skeletal muscle

extract_protocol:
RNA was extracted using RNAdvance Tissue Kit (Beckman Coulter). Quality control was performed with Fragment Analyzer (Advanced Analytical).
Libraries were quantified with the Quant-iT Picogreen (Invitrogen, 10545213) on a FilterMax F3 (Molecular Devices, F3). Size pattern was assessed with Fragment Analyzer-96 with the DNF-474-0500 High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies, DNF-474-0500).
Libraries (Average size: 295 bp) were pooled at an equimolar ratio and clustered at a concentration of 9 pM on a single read sequencing flow cell.

value: Skeletal muscle

value: Muscle stem cells

value: Low Myf5 expression

value: male

tag: pool


title: Nfur Wildtype 6-Day Diapause RNAseq Rep18

description:
Nfur_Wildtype_6D_18
Nfur_KO_Readcounts.csv


title: SMA mouse Smn1_Hetero Rep2


title: UM32, ROR2, replicate 2

data_processing:
Adapter trimming and removal of ribosomal and mitochondrial genome was carried out with fastq-mcf, cutadapt and Bowtie2, respectively. Reads were mapped to the hg19 genome using STAR and raw read counts were estimated with HTSeq (v0.11.2) and normalized with DESeq2.
Assembly: hg19
Supplementary files format and content: RawNormCounts_ROR2.txt

growth_protocol: HPAF-II cells were cultured in Minimum Essential Medium containing 1% sodium pyruvate , 1% non-essential amino acids, 10% FBS and 0.5% Gentamicin. UM32 were cultivated in RPMI 1640 supplemented with 10% FBS and 0.5% Gentamicin.

value: Pancreatic cancer cell line


title: Female Myf5 high  1

tag: strain

value: High Myf5 expression

value: female


title: PANC1, sicontrol, replicate 2


title: PANC1, siROR2, replicate 3


title: Male Myf5 high  1


title: Male Myf5 high  2


title: PANC1, sicontrol, replicate 1


title: Nfur Wildtype 6-Day Diapause RNAseq Rep15

description:
Nfur_Wildtype_6D_15
Nfur_KO_Readcounts.csv


title: UM32, ROR2, replicate 1


title: Male Myf5 low  1


title: Female Myf5 high  2