title: Kidney CC049 F

value: CC049 F


title: Kidney CC046 F

status: Public on Feb 05 2023

type: SRA

city: Bar Harbor

first: Kristen

last: O'Connell

state: ME

address: 600 Main St

country: USA

institute: The Jackson Laboratory

library_source: transcriptomic

data_processing:
Reads were aligned to the pooled transcriptomes (mm10) of the eight founder strains using bowtie v1.0.0 with parameters -q -p 8 -a --best --strata --sam -v 3 -m 100.
Aligned reads were input into the Genotype recontruction by RNA-Seq (GBRS) software which estimated total gene counts using the Expectation-Maximization for Allele Specific Expression (EMASE) software.
Filtered out genes for which > 50% of samples had no expression.
Assembly: mm10

molecule: total RNA

organism: Mus musculus

source_name: Kidney tissue

extract_protocol:
Hearts, livers, and kidneys were removed, flash frozen, and RNA was harvested using Trizol reagent. KAPA mRNA HyperPrep Kit (Roche) was used with total RNA for the construction of sequencing libraries.
Pooled libraries were sequenced on the NovaSeq 6000 platform (Illumina) using the S1 Reagent Kit v1, yielding 20-40M (target 30M) 1 x 1000bp single-end reads per sample.

tag: mouse

value: CC046 F

tag: strain

tag: Sex

value: female

tag: tissue

value: kidney


title: Kidney CC039 F

value: CC039 F


title: Kidney CC037 F

value: CC037 F


title: Kidney CC038 F

value: CC038 F


title: Kidney CC035 M

value: CC035 M

value: male


title: Kidney CC033 F

value: CC033 F


title: Kidney CC036 F

value: CC036 F


title: Kidney CC035 F

value: CC035 F


title: Kidney CC027 M

value: CC027 M


title: Kidney CC029 M

value: CC029 M


title: Kidney CC030 F

value: CC030 F


title: Kidney CC030 M

value: CC030 M


title: Kidney CC027 F

value: CC027 F


title: Kidney CC032 M

value: CC032 M


title: Kidney CC029 F

value: CC029 F


title: Kidney CC026 M

value: CC026 M


title: Kidney CC032 F

value: CC032 F

value: female

value: kidney


title: Kidney CC025 M

value: CC025 M


title: Kidney CC025 F

value: CC025 F


title: Kidney CC024 M

value: CC024 M

value: male


title: Kidney CC026 F

value: CC026 F


title: Kidney CC037 M

value: CC037 M


title: Kidney CC024 F

value: CC024 F


title: Kidney CC038 M

value: CC038 M


title: Kidney CC033 M

value: CC033 M


title: Kidney CC036 M

value: CC036 M


title: Kidney CC031 F

value: CC031 F


title: Kidney CC023 F

value: CC023 F


title: Kidney CC019 M

value: CC019 M


title: Kidney CC023 M

value: CC023 M


title: Kidney CC031 M

value: CC031 M


title: Kidney CC017 M

value: CC017 M


title: Kidney CC021 M

value: CC021 M

value: kidney


title: Kidney CC017 F

value: CC017 F

value: female


title: Kidney CC019 F

value: CC019 F


title: Kidney CC016 M

value: CC016 M

value: male


title: Kidney CC016 F

value: CC016 F


title: Kidney CC015 F

value: CC015 F


title: Kidney CC013 F

value: CC013 F


title: Kidney CC015 M

value: CC015 M


title: Kidney CC012 F

value: CC012 F


title: Kidney CC012 M

value: CC012 M


title: Kidney CC013 M

value: CC013 M


title: Kidney CC011 M

value: CC011 M


title: Kidney CC010 M

value: CC010 M


title: Kidney CC011 F

value: CC011 F


title: Kidney CC010 F

value: CC010 F


title: Kidney CC008 F

value: CC008 F

value: kidney


title: Kidney CC009 F

value: CC009 F

value: female


title: Kidney CC021 F

value: CC021 F


title: Kidney CC007 F

value: CC007 F


title: Kidney CC007 M

value: CC007 M

value: male


title: Kidney CC008 M

value: CC008 M


title: Kidney CC009 M

value: CC009 M


title: Kidney CC006 M

value: CC006 M


title: Kidney CC004 M

value: CC004 M


title: Kidney CC005 M

value: CC005 M


title: Kidney CC004 F

value: CC004 F


title: Kidney CC006 F

value: CC006 F


title: Kidney CC005 F

value: CC005 F


title: Shutdown knockdown small RNA-seq-5

city: Nijmegen

first: Jieqiong

last: Qu

address: Geert Grooteplein Zuid 28

department: Department of Medical Microbiology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences, Radboud University Medical Center

description:
small RNA-seq
dsShutdown_5

data_processing:
initial quality check with FastQC
raw sequence reads were first trimmed with Cutadapt
mapping with Bowtie
Reads in the size range from 21 to 24 bp were mapped to the pre-miRNA sequences of Ae. aegypti from miRBase database and annotated as miRNA. Reads in the size range from 25 to 30 bp were regarded as piRNAs. piRNA reads counts were compared to the luciferase control knockdown after normalization to the total mapped miRNAs.
piRNA clusters are annotated with published pipeline (Crava,CM, et al. Molecular ecology, 2021), and piRNA cluster expression is determined with samtools
Ae. aegypti LVP, vectorbase release 56
chromosome coordinates and expression of piRNA clusters

organism: Aedes aegypti

source_name: Aag2 cell line is an embryonic-derived cell line

extract_protocol:
Three days post-transfection, Aag2 cells were lysed in 1 mL RNA-Solv reagent (Omega Bio-tek), followed by RNA extraction through phase separation and isopropanol precipitation. RNA integrity was evaluated on EtBr stained agarose gels, and RNA concentration was determined using the Nanodrop ND-1000.
Small RNA deep sequencing libraries were generated using the NEBNext Small RNA Library Prep Set for Illumina (E7560, New England Biolabs), using 1 µg RNA as input. Library preparation was performed in accordance with the manufacturer’s instructions except for 3’ adapter ligation, which was performed for 18 h at 16°C to enhance the ligation efficiency of 2'-O-methylated small RNAs. Libraries were sequenced on an Illumina Hiseq4000 machine by the GenomEast Platform (Strasbourg, France).

treatment_protocol: For dsRNA knockdown of target genes, Aag2 cells were seeded at a density of 1.5x105 cells/well in a 24-well plate, 24 h prior to the dsRNA transfection in triplicates. For each target gene, transfection mix containing 300 μl non-supplemented L-15 medium, 500 ng dsRNA and 1.3 μl X-treme GENE HP DNA transfection reagent (Sigma) was prepared according to the manufacturer’s instructions. Per 24-well, 100 μl of the transfection mix was added in a dropwise manner.

tag: cell line

value: Aag2 cell line

tag: passages

tag: antibody

tag: treatment

value: Shutdown knockdown


title: Shutdown knockdown small RNA-seq-4

description:
small RNA-seq
dsShutdown_4


title: Kidney CC003 M

value: CC003 M

value: kidney


title: Kidney CC002 F

value: CC002 F

value: female


title: Kidney CC003 F

value: CC003 F


title: Kidney CC002 M

value: CC002 M


title: Kidney CC001 M

value: CC001 M

value: male


title: Yb knockdown small RNA-seq-5

description:
small RNA-seq
dsYb_5

value: Yb knockdown


title: Heart CC082 M

source_name: Heart tissue

value: CC082 M

value: heart


title: Yb knockdown small RNA-seq-4

description:
small RNA-seq
dsYb_4


title: Heart CC082 F

value: CC082 F


title: Heart CC081 M

value: CC081 M


title: Heart CC081 F

value: CC081 F


title: Tejas knockdown small RNA-seq-4

description:
small RNA-seq
dsTejas_4

value: Tejas knockdown


title: Vreteno knockdown small RNA-seq-5

description:
small RNA-seq
dsVreteno_5

value: Aag2 cell line

value: Vreteno knockdown


title: Heart CC080 M

value: CC080 M


title: Heart CC080 F

value: CC080 F


title: Heart CC079 M

value: CC079 M


title: Luc knockdown small RNA-seq-5

description:
small RNA-seq
dsLuc_5

value: control Luciferase knockdown


title: Topo-Seq, E. coli DY330 parC-SPA gyrA-S83L strain, no Cfx treatment, mock sample, replicate 3

city: Seattle

first: Dmitry

last: Sutormin

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Exponentially growing culture (OD600=0.6, 50 mL, 37C) in LB was harvested by centrifugation (3000 g, 5 min, 4C), and cells were washed twice with TES buffer (10 mM Tris–HCl pH 7.5, 1 mM EDTA, 250 mM NaCl). Then, cells were resuspended in 1 mL of TES and disrupted by sonication (DNA fragmentation range 200-800 bp). Lysate was cleared by centrifugation, and DNA was extracted from 100 µL of it using the GeneJET DNA purification kit (Thermo Scientific). NGS libraries were prepared using Accel NGS 1S kit (Swift Bioscience). DNA sequencing was performed with Illumina HiSeq 4000 in a 150+150 bp paired-end mode. Biological replicate 3.

library_source: genomic

data_processing:
Raw reads were trimmed and filtered using Trimmomatic (ILLUMINACLIP:2:30:10 LEADING:0 TRAILING:0 SLIDINGWINDOW:4:0 MINLEN:30).
Processed reads were aligned to the E. coli w3110 MuSGS genome with BWA MEM (default settings).
Coverage depth and N3E tracks were obtained based on read alignments stored in SAM files using custom script (see https://github.com/sutormin94/https://github.com/sutormin94/Topo IV_Topo-Seq_experiment).
Topo IV cleavage sites (TCSs) were called based on N3E values using custom script (https://github.com/sutormin94/https://github.com/sutormin94/Topo IV_Topo-Seq_experiment). File with TCSs coordinates, enrichment and motif score is provided as a supplementary file.
Assembly: NC_007779.1_w3110_Mu (custom build, fasta is provided as a supplementary file)
Supplementary files format and content: wig files with coverage depth and N3E (number of DNA fragments' 3'-ends per genomic position).
Library strategy: Topo-Seq

molecule: genomic DNA

organism: Escherichia coli

source_name: Escherichia coli DY330 parC-SPA gyrA-S83L

growth_protocol: For starter culture, a single colony of E. coli DY330 parC-SPA or E. coli DY330 parC-SPA gyrA-S83L was inoculated in 5 mL of LB. The starter was grown overnight at 37C with shaking 180 rpm. 1 mL of the starter was inoculated in 100 mL of fresh LB, and the culture was cultivated at 37C with shaking 180 rpm until reaching OD600=0.6.

extract_protocol:
For Input DNA (mock samples, treated and non-treated with Cfx) 100 µl of the lysates were treated with proteinase K (Thermo-Fisher Scientific) for 2 h at 55C and DNA was purified using GeneJET DNA purification kit (Thermo Scientific). DNA fragmentation range was assessed by electrophoresis. For cleavage complexes immunoprecipitation (IP samples, treated and non-treated with Cfx), 900 µl of the remaining lysates were incubated with 100 µL of the ANTI-FLAG M2 affinity gel (Sigma-Aldrich). After immunoprecipitation, the resin was treated with Proteinase K (Sigma-Aldrich) in 200 µL of TES and DNA fragments were purified with AMPure XP magnetic beads from the supernatant (Beckman Coulter).
NGS libraries were prepared using Accel NGS 1S kit (Swift Bioscience). DNA sequencing was performed with Illumina HiSeq 4000 in a 150+150 bp paired-end mode. Libraries preparation and sequencing were performed at Skoltech Sequencing Core Facilities. Topo-Seq experiments were performed in triplicate.

treatment_protocol: When OD600 of the culture reached 0.6, the 100 mL culture was bisected and ciprofloxacin (Cfx) was added (final concentration 10 mkM) to one half (50 mL) to stabilize Topo IV cleavage complexes with DNA. Then, cultivation proceeded for 15 min, and cells from the treated and non-treated samples were harvested by centrifugation (3000 g, 5 min, 4C) and washed twice with TES buffer (10 mM Tris–HCl pH 7.5, 1 mM EDTA, 250 mM NaCl). Finally, cells were resuspended in 1 mL of TES and disrupted by sonication (DNA fragmentation range 200-800 bp). Lysate was cleared by centrifugation (8000 g, 5 min, 4C).

value: DY330 parC-SPA gyrA-S83L

tag: growth phase

value: Exponential phase

tag: optical density at 600 nm

tag: treatment with ciprofloxacin

tag: ip or control

value: Mock control


title: Vreteno knockdown small RNA-seq-4

description:
small RNA-seq
dsVreteno_4


title: Topo-Seq, E. coli DY330 parC-SPA gyrA-S83L strain, no Cfx treatment, mock sample, replicate 2

description: Exponentially growing culture (OD600=0.6, 50 mL, 37C) in LB was harvested by centrifugation (3000 g, 5 min, 4C), and cells were washed twice with TES buffer (10 mM Tris–HCl pH 7.5, 1 mM EDTA, 250 mM NaCl). Then, cells were resuspended in 1 mL of TES and disrupted by sonication (DNA fragmentation range 200-800 bp). Lysate was cleared by centrifugation, and DNA was extracted from 100 µL of it using the GeneJET DNA purification kit (Thermo Scientific). NGS libraries were prepared using Accel NGS 1S kit (Swift Bioscience). DNA sequencing was performed with Illumina HiSeq 4000 in a 150+150 bp paired-end mode. Biological replicate 2.


title: Luc knockdown small RNA-seq-4

description:
small RNA-seq
dsLuc_4


title: Topo-Seq, E. coli DY330 parC-SPA gyrA-S83L strain, no Cfx treatment, mock sample, replicate 1

description: Exponentially growing culture (OD600=0.6, 50 mL, 37C) in LB was harvested by centrifugation (3000 g, 5 min, 4C), and cells were washed twice with TES buffer (10 mM Tris–HCl pH 7.5, 1 mM EDTA, 250 mM NaCl). Then, cells were resuspended in 1 mL of TES and disrupted by sonication (DNA fragmentation range 200-800 bp). Lysate was cleared by centrifugation, and DNA was extracted from 100 µL of it using the GeneJET DNA purification kit (Thermo Scientific). NGS libraries were prepared using Accel NGS 1S kit (Swift Bioscience). DNA sequencing was performed with Illumina HiSeq 4000 in a 150+150 bp paired-end mode. Biological replicate 1.


title: Kidney CC001 F

value: CC001 F

value: female

value: kidney


title: Heart CC078 M

value: CC078 M

value: male

value: heart


title: UAP56 knockdown small RNA-seq-3

description:
small RNA-seq
dsUAP56_3

value: UAP56 knockdown


title: Heart CC079 F

value: CC079 F


title: Topo-Seq, E. coli DY330 parC-SPA gyrA-S83L strain, 10 mkM Cfx, mock sample, replicate 3

description: Exponentially growing culture (OD600=0.6, 50 mL, 37C) in LB was treated with 10 mkM ciprofloxacin for 15 min. Cells were harvested by centrifugation (3000 g, 5 min, 4C) and washed twice with TES buffer (10 mM Tris–HCl pH 7.5, 1 mM EDTA, 250 mM NaCl). Then, cells were resuspended in 1 mL of TES and disrupted by sonication (DNA fragmentation range 200-800 bp). Lysate was cleared by centrifugation, and DNA was extracted from 100 µL of it using the GeneJET DNA purification kit (Thermo Scientific). NGS libraries were prepared using Accel NGS 1S kit (Swift Bioscience). DNA sequencing was performed with Illumina HiSeq 4000 in a 150+150 bp paired-end mode. Biological replicate 3.

value: Treatment with 10 mkM Cfx for 15 min


title: Tejas knockdown small RNA-seq-5

description:
small RNA-seq
dsTejas_5

value: Aag2 cell line

value: Tejas knockdown


title: Topo-Seq, E. coli DY330 parC-SPA gyrA-S83L strain, 10 mkM Cfx, mock sample, replicate 1

description: Exponentially growing culture (OD600=0.6, 50 mL, 37C) in LB was treated with 10 mkM ciprofloxacin for 15 min. Cells were harvested by centrifugation (3000 g, 5 min, 4C) and washed twice with TES buffer (10 mM Tris–HCl pH 7.5, 1 mM EDTA, 250 mM NaCl). Then, cells were resuspended in 1 mL of TES and disrupted by sonication (DNA fragmentation range 200-800 bp). Lysate was cleared by centrifugation, and DNA was extracted from 100 µL of it using the GeneJET DNA purification kit (Thermo Scientific). NGS libraries were prepared using Accel NGS 1S kit (Swift Bioscience). DNA sequencing was performed with Illumina HiSeq 4000 in a 150+150 bp paired-end mode. Biological replicate 1.


title: Nxf1 knockdown small RNA-seq-3

description:
small RNA-seq
dsNxf1_3

value: Nxf1 knockdown


title: Topo-Seq, E. coli DY330 parC-SPA gyrA-S83L strain, no Cfx treatment, immunoprecipitation, replicate 1

description: Exponentially growing culture (OD600=0.6, 50 mL, 37C) in LB was harvested by centrifugation (3000 g, 5 min, 4C), and cells were washed twice with TES buffer (10 mM Tris–HCl pH 7.5, 1 mM EDTA, 250 mM NaCl). Then, cells were resuspended in 1 mL of TES and disrupted by sonication (DNA fragmentation range 200-800 bp). Lysate was cleared by centrifugation and incubated with 100 µL of ANTI-FLAG M2 affinity gel (Sigma-Aldrich). After immunoprecipitation, the resin was treated with Proteinase K (Sigma-Aldrich) in 200 µL of TES and DNA fragments were purified with AMPure XP magnetic beads from the supernatant (Beckman Coulter). NGS libraries were prepared using Accel NGS 1S kit (Swift Bioscience). DNA sequencing was performed with Illumina HiSeq 4000 in a 150+150 bp paired-end mode. Biological replicate 1.

value: IP


title: Heart CC078 F

value: CC078 F


title: UAP56 knockdown small RNA-seq-1

description:
small RNA-seq
dsUAP56_1


title: Heart CC075 M

value: CC075 M


title: Topo-Seq, E. coli DY330 parC-SPA gyrA-S83L strain, no Cfx treatment, immunoprecipitation, replicate 2

description: Exponentially growing culture (OD600=0.6, 50 mL, 37C) in LB was harvested by centrifugation (3000 g, 5 min, 4C), and cells were washed twice with TES buffer (10 mM Tris–HCl pH 7.5, 1 mM EDTA, 250 mM NaCl). Then, cells were resuspended in 1 mL of TES and disrupted by sonication (DNA fragmentation range 200-800 bp). Lysate was cleared by centrifugation and incubated with 100 µL of ANTI-FLAG M2 affinity gel (Sigma-Aldrich). After immunoprecipitation, the resin was treated with Proteinase K (Sigma-Aldrich) in 200 µL of TES and DNA fragments were purified with AMPure XP magnetic beads from the supernatant (Beckman Coulter). NGS libraries were prepared using Accel NGS 1S kit (Swift Bioscience). DNA sequencing was performed with Illumina HiSeq 4000 in a 150+150 bp paired-end mode. Biological replicate 2.

value: DY330 parC-SPA gyrA-S83L

value: Exponential phase


title: Nxf1 knockdown small RNA-seq-2

description:
small RNA-seq
dsNxf1_2


title: Heart CC075 F

value: CC075 F


title: Topo-Seq, E. coli DY330 parC-SPA gyrA-S83L strain, 10 mkM Cfx, immunoprecipitation, replicate 2

description: Exponentially growing culture (OD600=0.6, 50 mL, 37C) in LB was treated with 10 mkM ciprofloxacin for 15 min. Cells were harvested by centrifugation (3000 g, 5 min, 4C) and washed twice with TES buffer (10 mM Tris–HCl pH 7.5, 1 mM EDTA, 250 mM NaCl). Then, cells were resuspended in 1 mL of TES and disrupted by sonication (DNA fragmentation range 200-800 bp). Lysate was cleared by centrifugation and incubated with 100 µL of ANTI-FLAG M2 affinity gel (Sigma-Aldrich). After immunoprecipitation, the resin was treated with Proteinase K (Sigma-Aldrich) in 200 µL of TES and DNA fragments were purified with AMPure XP magnetic beads from the supernatant (Beckman Coulter). NGS libraries were prepared using Accel NGS 1S kit (Swift Bioscience). DNA sequencing was performed with Illumina HiSeq 4000 in a 150+150 bp paired-end mode. Biological replicate 2.


title: Heart CC072 M

value: CC072 M


title: Topo-Seq, E. coli DY330 parC-SPA gyrA-S83L strain, 10 mkM Cfx, immunoprecipitation, replicate 1

description: Exponentially growing culture (OD600=0.6, 50 mL, 37C) in LB was treated with 10 mkM ciprofloxacin for 15 min. Cells were harvested by centrifugation (3000 g, 5 min, 4C) and washed twice with TES buffer (10 mM Tris–HCl pH 7.5, 1 mM EDTA, 250 mM NaCl). Then, cells were resuspended in 1 mL of TES and disrupted by sonication (DNA fragmentation range 200-800 bp). Lysate was cleared by centrifugation and incubated with 100 µL of ANTI-FLAG M2 affinity gel (Sigma-Aldrich). After immunoprecipitation, the resin was treated with Proteinase K (Sigma-Aldrich) in 200 µL of TES and DNA fragments were purified with AMPure XP magnetic beads from the supernatant (Beckman Coulter). NGS libraries were prepared using Accel NGS 1S kit (Swift Bioscience). DNA sequencing was performed with Illumina HiSeq 4000 in a 150+150 bp paired-end mode. Biological replicate 1.


title: Topo-Seq, E. coli DY330 parC-SPA gyrA-S83L strain, 10 mkM Cfx, immunoprecipitation, replicate 3

description: Exponentially growing culture (OD600=0.6, 50 mL, 37C) in LB was treated with 10 mkM ciprofloxacin for 15 min. Cells were harvested by centrifugation (3000 g, 5 min, 4C) and washed twice with TES buffer (10 mM Tris–HCl pH 7.5, 1 mM EDTA, 250 mM NaCl). Then, cells were resuspended in 1 mL of TES and disrupted by sonication (DNA fragmentation range 200-800 bp). Lysate was cleared by centrifugation and incubated with 100 µL of ANTI-FLAG M2 affinity gel (Sigma-Aldrich). After immunoprecipitation, the resin was treated with Proteinase K (Sigma-Aldrich) in 200 µL of TES and DNA fragments were purified with AMPure XP magnetic beads from the supernatant (Beckman Coulter). NGS libraries were prepared using Accel NGS 1S kit (Swift Bioscience). DNA sequencing was performed with Illumina HiSeq 4000 in a 150+150 bp paired-end mode. Biological replicate 3.


title: Nxf1 knockdown small RNA-seq-1

description:
small RNA-seq
dsNxf1_1


title: Heart CC072 F

value: CC072 F

value: female


title: Topo-Seq, E. coli DY330 parC-SPA strain, no Cfx treatment, mock sample, replicate 3

source_name: Escherichia coli DY330 parC-SPA

value: DY330 parC-SPA

value: Mock control


title: Topo-Seq, E. coli DY330 parC-SPA strain, no Cfx treatment, mock sample, replicate 1


title: Topo-Seq, E. coli DY330 parC-SPA strain, no Cfx treatment, mock sample, replicate 2


title: UAP56 knockdown small RNA-seq-2

description:
small RNA-seq
dsUAP56_2

value: UAP56 knockdown


title: Heart CC071 M

value: CC071 M

value: male

value: heart


title: Luc knockdown small RNA-seq-3

description:
small RNA-seq
dsLuc_3

value: Aag2 cell line

value: control Luciferase knockdown


title: Topo-Seq, E. coli DY330 parC-SPA gyrA-S83L strain, no Cfx treatment, immunoprecipitation, replicate 3

description: Exponentially growing culture (OD600=0.6, 50 mL, 37C) in LB was harvested by centrifugation (3000 g, 5 min, 4C), and cells were washed twice with TES buffer (10 mM Tris–HCl pH 7.5, 1 mM EDTA, 250 mM NaCl). Then, cells were resuspended in 1 mL of TES and disrupted by sonication (DNA fragmentation range 200-800 bp). Lysate was cleared by centrifugation and incubated with 100 µL of ANTI-FLAG M2 affinity gel (Sigma-Aldrich). After immunoprecipitation, the resin was treated with Proteinase K (Sigma-Aldrich) in 200 µL of TES and DNA fragments were purified with AMPure XP magnetic beads from the supernatant (Beckman Coulter). NGS libraries were prepared using Accel NGS 1S kit (Swift Bioscience). DNA sequencing was performed with Illumina HiSeq 4000 in a 150+150 bp paired-end mode. Biological replicate 3.

value: IP


title: Topo-Seq, E. coli DY330 parC-SPA gyrA-S83L strain, 10 mkM Cfx, mock sample, replicate 2

description: Exponentially growing culture (OD600=0.6, 50 mL, 37C) in LB was treated with 10 mkM ciprofloxacin for 15 min. Cells were harvested by centrifugation (3000 g, 5 min, 4C) and washed twice with TES buffer (10 mM Tris–HCl pH 7.5, 1 mM EDTA, 250 mM NaCl). Then, cells were resuspended in 1 mL of TES and disrupted by sonication (DNA fragmentation range 200-800 bp). Lysate was cleared by centrifugation, and DNA was extracted from 100 µL of it using the GeneJET DNA purification kit (Thermo Scientific). NGS libraries were prepared using Accel NGS 1S kit (Swift Bioscience). DNA sequencing was performed with Illumina HiSeq 4000 in a 150+150 bp paired-end mode. Biological replicate 2.

value: Treatment with 10 mkM Cfx for 15 min


title: Topo-Seq, E. coli DY330 parC-SPA strain, 10 mkM Cfx, mock sample, replicate 2


title: Luc knockdown small RNA-seq-2

description:
small RNA-seq
dsLuc_2


title: Topo-Seq, E. coli DY330 parC-SPA strain, 10 mkM Cfx, mock sample, replicate 3


title: Topo-Seq, E. coli DY330 parC-SPA strain, 10 mkM Cfx, mock sample, replicate 1


title: Luc knockdown small RNA-seq-1

description:
small RNA-seq
dsLuc_1


title: Topo-Seq, E. coli DY330 parC-SPA strain, no Cfx treatment, immunoprecipitation, replicate 2


title: Topo-Seq, E. coli DY330 parC-SPA strain, 10 mkM Cfx, immunoprecipitation, replicate 3


title: Topo-Seq, E. coli DY330 parC-SPA strain, no Cfx treatment, immunoprecipitation, replicate 3


title: Topo-Seq, E. coli DY330 parC-SPA strain, 10 mkM Cfx, immunoprecipitation, replicate 2


title: Heart CC062 F

value: CC062 F


title: Topo-Seq, E. coli DY330 parC-SPA strain, no Cfx treatment, immunoprecipitation, replicate 1


title: E11AGMWT31n117n45nNG2nRbetan (I15-1451-03)

city: Edinburgh

first: Mihaela

last: Crisan

address: 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

data_processing:
The reads were aligned using Tophat2  2.0.10 36 to align the reads to the mouse reference genome (mm10).
Read counts on GENCODE annotation version MM19 were computed using the union mode from the Bioconductor Genomic Alignments package (v1.18.1).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes Ensembl Gene Id, annotation and TPM values

molecule: polyA RNA

source_name: E11 AGM cells

extract_protocol:
Cells were sorted and collected directly into 20μl of lysis buffer containing Nuclease-free water (Ambion AM9930) 0.2% Triton and 1/20 RNAse inhibitor.
RNA libraries were prepared for sequencing using Smarter 2 protocol

tag: age

tag: region

value: AGM

tag: cell type

value: Stroma (NG2- PDGFRb- CD31- CD45- cKit-)


title: Heart CC061 M

value: CC061 M


title: E11AGMWT31n117n45nNG2nRbetap (I15-1451-04)

value: sub-vSMCs (NG2- PDGFRb+ CD31- CD45- cKit-)


title: E11AGMWT31n117n45nNG2pRbetap (I15-1451-02)

value: vSMCs (NG2+ PDGFRb+ CD31- CD45- cKit-)


title: PT06D14 (M10)

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

description:
AML patient
M10

data_processing:
Cellranger 10X demultiplexing (mkfastq)
Cellranger 10X quantification (counts)
Cellranger 10X quantification (alignment possorted files)
Seurat data analysis workflow
Genome_build: refdata-cellranger-GRCh38-3.0.0
Supplementary_files_format_and_content: matrix, barcodes, features
Full_Patient_metadata.rds (Complete metadata (NPM1 annotation) - Full dataset)
AML_metadata.rds (single-cell metadata (clustering + signatures + annotation) - AML dataset)

organism: Homo sapiens

source_name: BMMC (Bone marrow mononuclear cells)

growth_protocol: no growth

extract_protocol:
Freshly thawed BM or PB cells were sorted for population of interest as detailed for each sample. If cell recovery was > 10'000 cells then cells were washed and counted, prior to chip loading, otherwise total recovered cells were loaded on the 10x genomics chip.
Chromium(TM) Single Cell 3' Library & Gel Bead Kit v2 or v3 (10xGENOMICS) according to manufacturer’s instructions.

treatment_protocol: lineage negative transduced cells transplant

tag: disease state

value: acute myeloid leukemia (AML)

tag: patient id

tag: timepoint

value: Live CD34+


title: PT06D14 (M09)

description:
AML patient
M09

value: Live CD117+


title: Heart CC061 F

tag: mouse

value: CC061 F

tag: strain

value: female


title: PT06DX (M07)

description:
AML patient
M07

source_name: PBMC (Peripheral blood mononuclear cells)

value: DX (Diagnosis)


title: Heart CC060 M

value: CC060 M

tag: Sex

value: male

tag: tissue

value: heart


title: Colon_02

city: Rotterdam

first: Maria

last: Alves

address: Doctor Molewaterplein 40

department: Clinical Genetics

institute: Erasmus MC

description:
10x Genomics
ENS_counts.tsv.gz
ENS_metadata.tsv.gz

library_source: transcriptomic single cell

data_processing:
Cellranger count (v 4.0.0) was employed for demultiplexing, barcode processing, gene counting and aggregation of the samples
Downstream analysis was performed in Seurat (v 4.1.1)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files, including counts of the merged data set as well as associated meta data

source_name: colon

extract_protocol:
Cryopreserved tissue was rapidly thawed in a 37°C water bath and processed to yield high viablity single cells. Cells were stained with fluorescent antibodies and ENS cells were enriched by FACS. Cells were then loaded onto the 10X platform for single-cell RNA sequencing.
Libraries were made according to the manufacter’s instructions (Single Cell 3' v3 chemistry, 10x Genomics)

value: Enteric nervous system cells

value: colon

tag: gender

value: 4 months old


title: Heart CC071 F

value: CC071 F


title: Colon_01

value: 5 months old


title: PT06DX (M08)

description:
AML patient
M08


title: PT01D14 (M05)

description:
AML patient
M05


title: PT01D14 (M06)

description:
AML patient
M06


title: PT01DX (M04)

description:
AML patient
M04


title: Heart CC062 M

value: CC062 M


title: Ileum_04

source_name: small intestine

value: small intestine

value: 2 months old


title: Heart CC059 M

value: CC059 M


title: PT01DX (M03)

description:
AML patient
M03

value: acute myeloid leukemia (AML)


title: Heart CC060 F

value: CC060 F


title: Ileum_01

value: 3 months old


title: minusD Ileum Rep3

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

description:
FPKM_VDR_Christakos_MinusDvs3xD_Ileum.txt
FPKM_VDR_Christakos_MinusDvs3xD_Ileum_Without4thVeh.txt

data_processing:
Alignment: RNA-seq: Kallisto v0.45.0.
RNA-seq Transcript Import: tximport 1.26.0
DESeq 1.14.0
Genome_build: mm9
Supplementary_files_format_and_content: RNA-Seq: fpkm table outputted by DESeq2 for fragment counts normalized per kilobase of feature length per million mapped fragments

source_name: minusD Ileum

extract_protocol:
Total RNA was isolated from mouse tissues, isolated mouse villus and crypt epithelium and human organoids using RiboZol RNA extraction reagent (Amresco, Solon, OH) or TRIzol reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions and subsequently purified with RNeasy Plus Universal Kit (Qiagen, Hilden, Germany) using on column DNAse digestion (Qiagen, Hilden, Germany). RNA concentration was measured with a NanoDrop spectrophotometer ND-1000 (Isogen Life Science, Utrecht, The Netherlands). RNA integrity was assessed using a denaturing agarose gel stained with ethidium bromide (EtBr) or by using an Agilent (Agilent Technologies, Santa Clara, CA) Bioanalyzer nanochip. For quantitative real time PCR (qRT-PCR), 2 µg of total RNA were used to synthesize complementary DNA using Superscript III First Strand synthesis system (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions. Relative quantification of target gene expression was performed using Taqman analyses. Taqman Gene Expression Probes (Applied Biosystems, Foster City, CA) used for qRT-PCR are the following: Cyp24a1 (Mm00487244-m1), S100g (Mm00486654-m1), Slc30a10 (Mm00437377-m1), Slc37a2 (Mm00451435_m1), Trpv5 (Mm01166037_m1), Trpv6 (Mm00499069-m1). Reactions were performed in a 7500 Real-Time PCR System (Applied Biosystems, Foster City, CA). The cycle steps as follow: an initial 3-min incubation at 95 °C, followed by 40 cycles of 95 °C for 10?s, 60 °C for 30?s, and 72 °C for 30?s. Expressions of gene of interest were normalized to Gapdh (Mm999999-g1). The 2-??Ct method was used to calculate relative gene expression.
The kit used to prepare the library include the following: NEBNext Ultra II RNA Library Prep with Sample Purification Beads Cat# E7775L, NEBNext Poly(A) mRNA Magnetic Isolation Module Cat# E7490L, and NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) Cat# E7600S. CLC genomics workbench from Qiagen was utilized to map samples to the mouse genome, create transcript IDs, count reads, and normalization. For global assessment of mouse RNA levels, total RNA was subjected to ribosomal RNA (rRNA) depletion using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, Ipswich, MA, USA). Libraries were constructed using the TruSeqRNA Sample Prep Kit (Illumina Inc, San Diego, CA) according to the manufacturer’s instructions. rRNA depletion and library quality were assessed using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). The prepared libraries were sequenced on an Illumina NextSeq 500 instrument. (Illumina, San Diego, CA). Over 60 M reads per sample were obtained. The raw reads were aligned to the Mus musculus reference genome build 9 (mm9) using Kallisto. Differential gene expression was assessed using DESeq2 in R and transcript levels were obtained using a false discovery rate of 0.05.

treatment_protocol: 3-time injection of 1,25D3 (1 ng/g bw, 48h, 24h, 6h injection before termination)

tag: genotype

value: wild type

tag: background strain


title: minusD Ileum Rep4

value: female

tag: treatment


title: Topo-Seq, E. coli DY330 parC-SPA strain, 10 mkM Cfx, immunoprecipitation, replicate 1

value: DY330 parC-SPA

tag: growth phase

value: Exponential phase

tag: optical density at 600 nm

value: Treatment with 10 mkM Cfx for 15 min

value: IP


title: Heart CC059 F

value: CC059 F

value: heart


title: minusD Ileum Rep2

value: male


title: Heart CC058 M

value: CC058 M


title: ME111A

city: Milan

first: Pasquale

last: Tomaiuolo

state: Milan

address: via Balzaretti n.9

department: Department of Pharmacologic Sciences

institute: University of Milan

data_processing:
Reads were aligned to the Human reference genome (GRCh37) using STAR v2.5.3a
The featureCounts 1.6.2  from the Subread package v1.4.6 was next used to summarize and quantify the mapped reads
Gene expression differential analyses between proband and sibling were conducted by means of the R package DESeq2 v1.24.0 using both unpaired and paired models
Assembly: homosapiens.grch37.75
Supplementary files format and content: Count matrix of gene counts per sample.

source_name: peripheral blood

extract_protocol:
RNA was extracted using TempusTM Spin RNA Isolation Kit following the manufacturer’s instructions.
Sequencing libraries were prepared with 250 ng of total RNA using TruSeq Stranded mRNA (Illumina, Inc.) following the manufacturer’s protocol. This approach delineates the coding transcriptome using Oligo-dT beads to capture polyA mRNA tails

value: M

value: peripheral blood

value: ASD

tag: family

value: no

tag: puberty

value: pre


title: ME111S

value: SIB


title: Heart CC058 F

value: CC058 F


title: 3xD Ileum Rep3

source_name: 3xD Ileum

value: wild type

tag: age

value: 3-time injection of 1,25D3 (1 ng/g bw, 48h, 24h, 6h injection before termination)


title: ME23S

tag: cell type


title: 3xD Ileum Rep4


title: 3xD Ileum Rep2

value: female


title: 3xD Ileum Rep1


title: Heart CC057 F

value: CC057 F


title: ME89S1


title: minusD Duodenum Rep3

description:
FPKM_VDR_Christakos_MinusDvs3xD_Duodenum.txt
FPKM_VDR_Christakos_MinusDvs3xD_Duodenum_Without4thVeh.txt

source_name: minusD Duodenum


title: minusD Duodenum Rep4


title: ME23A


title: minusD Duodenum Rep2


title: minusD Duodenum Rep1


title: ME89A


title: Heart CC055 F

value: CC055 F


title: 3xD Duodenum Rep4

source_name: 3xD Duodenum


title: Heart CC055 M

value: CC055 M


title: ME77S3

value: post


title: 3xD Duodenum Rep2


title: minusD Ileum Rep1


title: 3xD Duodenum Rep1


title: Heart CC053 M

value: CC053 M

value: heart


title: ME77A


title: minusD Colon Rep4

description:
FPKM_VDR_Christakos_MinusDvs3xD_Colon.txt
FPKM_VDR_Christakos_MinusDvs3xD_Colon_Without4thVeh.txt

source_name: minusD Colon


title: Heart CC053 F

value: CC053 F


title: minusD Colon Rep3

value: male


title: Heart CC051 M

value: CC051 M


title: CA180S

value: M

value: peripheral blood


title: Heart CC057 M

value: CC057 M


title: CA180A

value: ASD

value: yes


title: Heart CC051 F

value: CC051 F


title: minusD Colon Rep1

value: wild type


title: 3xD Colon Rep4

source_name: 3xD Colon

value: 3-time injection of 1,25D3 (1 ng/g bw, 48h, 24h, 6h injection before termination)


title: 3xD Colon Rep2


title: minusD Colon Rep2


title: 3xD Colon Rep1

value: female


title: Heart CC049 M

value: CC049 M


title: CA176S

value: SIB

value: no

value: pre


title: 3xD Duodenum Rep3


title: 3xD Colon Rep3


title: CA176A


title: Heart CC046 M

value: CC046 M

value: heart


title: Heart CC049 F

value: CC049 F


title: M6124

value: post


title: M6122

value: M


title: tdTomato injected blastocyst-17

city: Guangzhou

first: Shixue

last: Gou

address: No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou

country: China

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

data_processing:
Quality control was performed to remove adapter sequences and low complexity reads using Fastp (version 0.23.2).
Salmon (version 0.8.2) was used to align clean reads to Sus scrofa transcriptome (NCBI version GCF_000003025.6) for generating gene expression matrix.
DESeq and vst (variance stabilizing transformation), functions of DESeq2 package (version 1.20.0) was used to normalize and transform data.
The vst transformed data was used as input to perform the weighted gene co-expression network analysis (WGCNA) using WGCNA packages (version 1.69).
The KEGG pathway enrichment analysis of the genes in the module was performed using clusterProfiler (version 3.10.1).
Assembly: GCF_000003025.6
Supplementary files format and content: tab-delimited text files include RawCount and TPM values for each Sample

organism: Sus scrofa

source_name: parthenogenetic activated (PA) porcine embryos

growth_protocol: After the maturation period, the cumulus cells were removed by oocyte-denuding medium containing 0.1mg/mL hyaluronidase. The denuded oocytes were washed twice by oocyte manipulation medium. The matured oocytes were collected and activated by electro cell manipulator as 1 DC pulses, 120V and 30μs pulse length. After activation, the oocytes were washed twice and cultured in porcine zygote medium-3 (PZM-3) at 38.5℃ in 5% CO2 humidified air.

extract_protocol:
RNA was harvested using Rneasy MiniElute Cleanup kit (50) was used for the extraction of mRNA.
The TruSeq RNA Sample Preparation kit (Illumina) was used to construct RNA-seq libraries.

tag: cell line

value: blastocyst

value: WT

value: tdTomato injected


title: tdTomato injected blastocyst-19

value: parthenogenetic activated (PA) porcine embryos


title: M0224

value: peripheral blood


title: tdTomato injected blastocyst-14


title: tdTomato injected blastocyst-16


title: tdTomato injected blastocyst-18


title: tdTomato injected blastocyst-20


title: Heart CC046 F

value: CC046 F


title: tdTomato injected blastocyst-13


title: tdTomato injected blastocyst-12


title: Heart CC045 M

value: CC045 M

value: male


title: tdTomato injected blastocyst-11


title: tdTomato injected blastocyst-15


title: M0225

value: ASD

value: yes


title: Heart CC045 F

value: CC045 F

value: female


title: CA177S1

value: F

value: SIB

value: no

value: pre


title: Heart CC044 F

value: CC044 F

value: heart


title: Heart CC044 M

value: CC044 M


title: tdTomato injected blastocyst-6

value: blastocyst

value: WT

value: tdTomato injected


title: M0191

value: M

value: peripheral blood

value: post


title: tdTomato injected blastocyst-9

value: parthenogenetic activated (PA) porcine embryos


title: tdTomato injected blastocyst-7


title: tdTomato injected blastocyst-5


title: tdTomato injected blastocyst-10


title: Heart CC043 M

value: CC043 M

value: male


title: CA177A

value: ASD

value: yes


title: M0188


title: tdTomato injected blastocyst-4


title: tdTomato injected blastocyst-3


title: Heart CC043 F

value: CC043 F

value: female


title: M2099

value: pre


title: M2198

value: SIB

value: no


title: Heart CC042 M

value: CC042 M

value: heart


title: Cas9 injected blastocyst-37

value: blastocyst

value: WT

value: Cas9 injected


title: Cas9 injected blastocyst-36


title: tdTomato injected blastocyst-2

value: tdTomato injected


title: tdTomato injected blastocyst-1


title: Cas9 injected blastocyst-35


title: Cas9 injected blastocyst-33


title: M4255

value: M

value: peripheral blood

value: post


title: Heart CC041 M

value: CC041 M

value: male


title: tdTomato injected blastocyst-8

value: parthenogenetic activated (PA) porcine embryos


title: Cas9 injected blastocyst-34


title: M4256


title: Heart CC041 F

value: CC041 F


title: Cas9 injected blastocyst-31


title: M4754


title: Cas9 injected blastocyst-30


title: Cas9 injected blastocyst-29


title: Cas9 injected blastocyst-28


title: Heart CC040 M

value: CC040 M


title: Cas9 injected blastocyst-27


title: M3068

value: pre


title: Heart CC039 M

value: CC039 M


title: Heart CC040 F

value: CC040 F

value: female


title: Cas9 injected blastocyst-26


title: Heart CC042 F

value: CC042 F

value: heart


title: M3061

value: ASD

value: no


title: Cas9 injected blastocyst-25

value: blastocyst

value: WT

value: Cas9 injected


title: Heart CC039 F

value: CC039 F


title: Heart CC038 M

value: CC038 M


title: Cas9 injected blastocyst-24


title: Cas9 injected blastocyst-22


title: M7805

value: M

value: peripheral blood

value: SIB

value: post


title: Cas9 injected blastocyst-23

value: parthenogenetic activated (PA) porcine embryos


title: M763

value: yes


title: Cas9 injected blastocyst-32


title: M7292


title: Cas9 injected blastocyst-18


title: M4751


title: Cas9 injected blastocyst-19


title: Heart CC038 F

value: CC038 F


title: Cas9 injected blastocyst-17


title: Heart CC037 M

value: CC037 M

value: male


title: M2391


title: Heart CC037 F

value: CC037 F

value: female

value: heart


title: Cas9 injected blastocyst-15

value: blastocyst


title: Cas9 injected blastocyst-14

value: WT


title: M099

value: ASD


title: Cas9 injected blastocyst-20

value: Cas9 injected


title: Heart CC036 M

value: CC036 M


title: Heart CC036 F

value: CC036 F


title: M6904

value: M

value: peripheral blood

value: no


title: Cas9 injected blastocyst-13

value: parthenogenetic activated (PA) porcine embryos


title: Cas9 injected blastocyst-10


title: Cas9 injected blastocyst-11


title: Cas9 injected blastocyst-9


title: M6906

value: post


title: Cas9 injected blastocyst-12


title: Cas9 injected blastocyst-21


title: Heart CC033 M

value: CC033 M


title: M4637


title: Heart CC035 M

value: CC035 M


title: Cas9 injected blastocyst-4


title: Heart CC035 F

value: CC035 F


title: Heart CC033 F

value: CC033 F


title: M089

value: SIB


title: Cas9 injected blastocyst-5


title: M4636


title: F2659

value: F


title: Cas9 injected blastocyst-6

value: blastocyst


title: Cas9 injected blastocyst-3

value: WT


title: Cas9 injected blastocyst-2


title: Cas9 injected blastocyst-1


title: F4384

value: ASD


title: Heart CC032 F

value: CC032 F

value: female

value: heart


title: Heart CC031 M

value: CC031 M

value: male


title: Cas9 injected blastocyst-8

value: Cas9 injected


title: PT20REL

description:
AML_patient
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: refdata-cellranger-GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

value: Live CD34+ and or CD117+ and CD3- CD19- CD235a-

tag: patientid

value: REL


title: PT19REL

description:
AML_patient
10x Genomics

tag: timepoint


title: Heart CC031 F

tag: mouse

value: CC031 F


title: Cas9 injected blastocyst-7

value: parthenogenetic activated (PA) porcine embryos


title: Heart CC029 M

value: CC029 M

tag: strain


title: Heart CC032 M

value: CC032 M

tag: Sex


title: PT18DX

description:
AML_patient_Del7
10x Genomics

value: DX


title: Heart CC030 F

value: CC030 F

tag: tissue


title: PT17D14

description:
AML_patient_Del7
10x Genomics


title: PT16_Control_GFP_L_5

data_processing:
FastQC + Trimming (cutadapt)
STAR alignment
featurecounts (min overlap 10 + nochimera + uniquely mapping)
Genome_build: refdata-cellranger-GRCh38-3.0.0
Supplementary_files_format_and_content: counts_raw.txt

source_name: BMMC (Bone Marrow Monoclear Cells)

extract_protocol:
BM cells were sorted for human AML blasts and split in the top and bottom 20% GFP expressing populations (GFPlow/miR-126high) and (GFPhigh/miR-126low) gates respectively. After sorting cells were washed and counted. RNA was extracted with the miRNEasy Micro Kit (Qiagen) with on column DNAse digestion.
Sequencing libraries were produced with SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Mountain View, CA, USA), as per manufacturer’s instructions

treatment_protocol: Xenografted mice were treated with combination chemotherapy of 1.5 mg/kg Daunorubicin hydrochloride (Pfizer) by tail vein injection on days 1, 2 and 3. Cytarabine (Hospira) was administered at a dose of 60 mg/kg by subcutaneous injection on days 1 to 5 of the treatment regimen. Cells were recovered at day 8 from start of treatment.

tag: disease state

value: acute myeloid leukemia (AML)

tag: patient id

tag: cell population

value: Control

value: Xenograft AML blasts


title: Heart CC029 F

source_name: Heart tissue

value: CC029 F


title: PBMC_H2-10X5

city: WuHan

first: Tang

last: ZhaoHui

state: HuBei

address: Qiaokou No.1095, Jiefang Avenue

department: Department of Emergency, Division of Surgical Critical Care

institute: TongJi hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
PBMC were isolation by using sodium heparin as an anti-coagulant. Mix thoroughly. Process within 24 hours, with best results obtained by prompt processing. If storing is needed before processing, store the blood at room temperature in the dark and on a rocker. Always keep cells at 20-37ºC. Pool the heparinized blood of individual donor and dilute blood 1:1 with Ca2+-free PBS (e.g., add 15ml PBS to 15ml blood). PBS should be at room temperature (20-37ºC). Gently mix by inverting the tubes/flasks two times. In a sterile, 50ml conical tube, add 15ml of Ficoll®. To avoid mixing the two phases, gently overlay the Ficoll® with 30ml of the diluted blood using a sterile serological pipette. Centrifuge the samples at 740g for 30 minutes at room temperature. After the centrifuge stops, immediately collect the mononuclear cells from the plasma/Ficoll® interphase and transfer into a sterile 50ml conical tube. Fill the tube to the 45ml mark with 37ºC CTL-Wash™ Medium. Centrifuge cells again, this time at 330g for ten minutes at room temperature. As soon as centrifugation is complete, cautiously decant the supernatant and discard it. Resuspend the cell pellet by tapping the tube until no clumps are visible. Pool cells of the same donor and count the cells (see Cell Counting above). The cell yield should be one-two million PBMC for each ml of blood drawn. Fill tubes to the 45ml mark with warm CTL-Wash™ (or CTL-Test™) Medium, and spin at 330g for ten minutes with the break on. RNA extraction was identified using TRIZOL RNA kits. Rinse cell monolayer with ice cold PBS once. Lyse cells directly in a culture dish by adding 1 ml of TRIZOL Reagent per 3.5 cm diameter dish and scraping with cell scraper. Pass the cell lysate several times through a pipette. Vortex thoroughly. The amount of TRIZOL reagent added is based on the area of the culture dish (1 ml per 10 cm2) and not on the number of cells present. An insufficient amount of TRIZOL Reagent may result in DNA contamination of the isolated RNA. Add 0.2 ml of chloroform per 1 ml of TRIZOL Reagent. Cap sample tubes securely. Vortex samples vigorously for 15 seconds and incubate them at room temperature for 2 to 3 minutes. Centrifuge the samples at no more than 12,000 x g for 15 minutes at 2 to 80C. Following centrifugation, the mixture separates into lower red, phenolchloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. Transfer upper aqueous phase carefully without disturbing the interphase into fresh tube. Measure the volume of the aqueous phase (The volume of the aqueous phase is about 60% of the volume of TRIZOL Reagent used for homogenization). Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIZOL Reagent used for the initial homogenization.  Incubate samples at 15 to 30oC for 10 minutes and centrifuge at not more than 12,000 x g for 10 minutes at 2 to 4oC. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube. Remove the supernatant completely. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIZOL Reagent used for the initial homogenization. Mix the samples by vortexing and centrifuge at no more than 7,500 x g for 5 minutes at 2 to 8 oC. Repeat above washing procedure once. Remove all leftover ethanol. Air-dry or vacuum dry RNA pellet for 5-10 minutes. Do not dry the RNA pellet by centrifuge under vacuum. It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility. Partially dissolved RNA samples have an A260/A280 ratio < 1.6. Dissolve RNA in DEPC-treated water by passing solution a few times through a pipette tip.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: PBMC

tag: subject status

value: healthy controls and patients with confirmed sepsis


title: PT16_Control_GFP_H_5

tag: treatment


title: Missense mutation p.A312V [Fibpat 48]

type: RNA

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

description: Gene expression data from human fibroblasts

hyb_protocol: ssDNA molecules were heat fragmented and applied to the HTA2  GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

label: biotin

source_name: Missense mutation p.A312V

label_protocol: Biotinylation of cDNA carried out according to Affymetrix protocol for the HTA2 arrAYS

extract_protocol:
Fibroblast cell cultures were established in minimal cell culture medium (Lonza) supplemented with 10% foetal calf serum (Labtech), 2 mM glutamine, 50 mg/ml uridine, vitamins, amino acids and 1 mM sodium pyruvate in humid incubators at 37°C with 5% CO2
Total RNA was extracted from pelleted fibroblasts using the Trizol method (Invitrogen), following manufacturer’s instructions. The RNA quality and quantity was established using the Agilent Bioanalyser (Agilent) and the Nanodrop 1000 (Thermo Fisher).

value: Female

value: 40 years old at time of skin biopsy


title: PT16_Control_GFP_L_4


title: PT17DX

description:
AML_patient_Del7
10x Genomics


title: Heart CC027 M

value: CC027 M

value: male

value: heart


title: PT16_Control_GFP_H_4


title: PT11D30

description:
AML_patient_Del7
10x Genomics

value: Live CD34+ and or CD117+ and CD3- CD19- CD235a-


title: Heart CC030 M

value: CC030 M


title: Missense mutation p.M337V [Fibpat 51]

source_name: Missense mutation p.M337V

value: Male

value: 62 years old at time of skin biopsy


title: Missense mutation p.G287S [Fibpat 55]

source_name: Missense mutation p.G287S

value: 56 years old at time of skin biopsy


title: Truncation mutation p.Y374X [Fibpat 193]

source_name: Truncation mutation p.Y374X

value: 53 years old at time of skin biiopsy


title: Neurologically normal control [Fibcom 2303]

source_name: Neurologically normal control


title: Truncation mutation p.Y374X [Fibpat 192]

value: 41 years old at time of skin biopsy


title: Neurologically normal control [Fibcon 155]


title: Truncation mutation p.Y374X [Fibpat194]

value: 68 years old at time of skin biopsy


title: PT16_Treated_GFP_L_7

value: acute myeloid leukemia (AML)

value: Treated

value: Xenograft AML blasts


title: Neurologically normal control [Fibcon 170]

value: 63 years old at time of skin biopsy


title: PT18D14

description:
AML_patient_Del7
10x Genomics

source_name: BMMC (Bone marrow mononuclear cells)


title: PT17D30

description:
AML_patient_Del7
10x Genomics


title: PBMC_H1-10X5

description: 10x Genomics

value: PBMC

value: healthy controls and patients with confirmed sepsis


title: PT16_Control_GFP_L_3

value: Control


title: PT16_Treated_GFP_H_7


title: PT16_Control_GFP_H_3


title: PT16_Treated_GFP_L_6


title: Heart CC026 F

value: CC026 F

value: female


title: PT16_Treated_GFP_H_6


title: PT16_Treated_GFP_L_5


title: T-cell depleted bone marrow Rep2 Multiome (ATAC)

first: Manu

last: Setty

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

data_processing:
Count matrices for the two samples were generated using CellRanger ARC 2.0
Starting with the filtered barcode matrices from CellRanger ARC, barcodes from the bottom and top 2.5th percentile in molecule counts were excluded. Further cells with less than 0.4 fraction of reads in peaks in ATAC modality and greater than 20% of reads from mitochondria from the RNA modality were excluded from downstream analysis.
For each sample, scrublet [ref] was used to remove doublet scores using default parameters and a cluster of cells with high doublet scores were removed from downstream analysis.
RNA analysis was performed using scanpy. Following the filtering steps, normalized for molecule counts dy dividing the raw data by the total counts per cell. The normalized data was multiplied by the median of total counts across cells to avoid numerical issues and log transformed with a pseudo-count of 0.1. Feature selection was then performed to select the top 2500 most highly variable genes (using scanpy.pp.highly_variable_genes) which was then used as input for principal component analysis with 50 components.
Analysis of the ATAC modality was undertaken using the ArchR pipeline [ref] using the subset of cells post-filtering from the RNA modality. 100k features were used instead of the default 25k features for ArchR processing. Using ArchR, data was normalized using IterativeLSI and SVD used to determine a lower dimensional representation of the sparse data. The first SVD component showed a greater than 0.97 correlation with log library size and was excluded from downstream analysis. SVD was used as input to cluster the data using phenograph and visualize using umaps. Peak calling was performed using fragments < 147 length.
Assembly: GRCh38
Supplementary files format and content: Scanpy anndata objects for both RNA and ATAC containing counts, normalized data and cell-types

source_name: T-cell depleted cells from bone marrow

growth_protocol: Cryopreserved bone marrow stem/progenitor CD34+ cells from a healthy donor were purchased from AllCells, LLC.  and stored in vapor phase nitrogen.

extract_protocol:
Vial was removed from the storage and immediately thawed at 37 °C in a water bath for 2 min while gently shaking. Next, vial content (1 mL) was transferred to a 50-mL conical tube. To prevent osmotic lysis and ensure gradual loss of cryoprotectant, 1 mL of warm medium (IMDM with 10% FBS supplement) was added dropwise after washing the storage vial, while gently shaking the tube.
ingle Cell Multiome ATAC + Gene Expression was performed with a 10X genomics system using Chromium Next GEM Single Cell Multiome Reagent Kit A (catalog no. 1000282) and ATAC Kit A (catalog no. 1000280) following Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide and demonstrated protocol - Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing. Briefly, 200k-300k cells (viability 95%) were lysed for 4min and resuspended in Diluted Nuclei Buffer (10x Genomics, PN- 2000207). Lysis efficiency and nuclei concentration was evaluated on Countess II automatic cell counter by trypan blue staining.  9,660 and 16,100 nuclei were loaded per transposition reaction for CD34+ and T-cell depleted marrow, targeting recovery of 6,000 and 10,000 nuclei after encapsulation. After transposition reaction nuclei were encapsulated and barcoded.
Next-generation sequencing libraries were constructed following the User Guide, which were sequenced on an Illumina NovaSeq 6000 system.

treatment_protocol: The cell suspension was dropwise diluted to 15 mL by addition of warm complete growth medium. The final 15 mL volume of cell suspension was pelleted at room temperature, 400g for 5 min. After removing supernatant, cells were washed once with 1 mL of Cell Staining Buffer (CSB), Biolegend (420201), cells were centrifuged again at 400g for 5 minutes 4 °C and resuspended in 100 uL of CSB. Concentration and viability were determined with a Countess II automated cell counter using 0.4% trypan blue staining method. Cells were incubated with Human TruStain FcX™ (Fc Receptor Blocking Solution), Biolegend (422301), for 10min at 4 °C. After blocking, bone marrow cells were stained with CD3 Monoclonal Antibody (UCHT1), PE-Cyanine7, eBioscience™ (25-0038-42) 1:100 for 20 minutes at 4 °C. Cells were washed 2 times with CSB before Fluorescence-activated cell sorting (FACSymphony S6, BD Biosciences) where CD3 negative cells were collected. Sorted cells were concentrated, count and viability was determined with a Countess II automated cell counter using trypan blue staining.

value: Bone marrow

tag: sorting

tag: system

value: Hematopoietic differentiation

tag: catalog

value: AllCells, LLC (ABM007F)


title: PT11DX

description:
AML_patient_Del7
10x Genomics

value: Live CD34+ and or CD117+ and CD3- CD19- CD235a-

value: DX


title: Heart CC025 M

value: CC025 M

value: male

value: heart


title: Cas9 injected blastocyst-16

value: parthenogenetic activated (PA) porcine embryos

value: blastocyst

tag: genotype

value: WT

value: Cas9 injected


title: PT16_Treated_GFP_H_5

value: acute myeloid leukemia (AML)

value: Treated

tag: cell type

value: Xenograft AML blasts


title: PT16_Control_GFP_L_2

value: Control


title: Heart CC025 F

value: CC025 F

value: female


title: Heart CC024 M

value: CC024 M


title: PT16_Treated_GFP_L_4


title: PT16_Treated_GFP_H_4


title: Heart CC026 M

value: CC026 M


title: PT16_Treated_GFP_L_3


title: PT16_Control_GFP_H_2


title: T-cell depleted bone marrow Rep2 Multiome (RNA)

value: Bone marrow

value: Hematopoietic differentiation

value: AllCells, LLC (ABM007F)


title: CD34 Rep2 Multiome (ATAC)

source_name: CD34+ hematopoietic stem and progenitor cells

treatment_protocol: The cell suspension was serially diluted 5 times with 1:1 volume additions of warm complete growth medium with 2-min wait between additions. The final ~32-mL volume of cell suspension was pelleted at 300g for 5 min. After removing supernatant, cells were washed once with 10-mL of warm media and twice in ice-cold 1× PBS with 0.04% (wt/vol) BSA supplement to remove traces of medium. Cell concentration and viability were determined with a Countess II automatic cell counter using 0.4% trypan blue staining method.

value: AllCells, LLC (ABM022F)


title: PT16_Treated_GFP_H_3


title: T-cell depleted bone marrow Rep1 Multiome (RNA)


title: PT16_Treated_GFP_L_2


title: CD34 Rep2 Multiome (RNA)


title: Neurologically normal control [Fibcon 159]

value: Female

tag: age

value: 62 years old at time of skin biopsy


title: PT16_Treated_GFP_H_2


title: PT16_Treated_GFP_L_1


title: Heart CC023 F

value: CC023 F

value: heart


title: Heart CC023 M

value: CC023 M

value: male


title: CD34 Rep1 Multiome (ATAC)


title: PT16_Treated_GFP_H_1

value: acute myeloid leukemia (AML)

value: Treated


title: T-cell depleted bone marrow Rep1 Multiome (ATAC)


title: Heart CC021 M

value: CC021 M


title: PT16_Control_GFP_H_1

value: Control

value: Xenograft AML blasts


title: PT09_PT13D30 (M50)

description:
AML patient
M50

value: Live CD34+ and or CD117+ and CD3- CD19- CD235a-


title: CD34 Rep1 Multiome (RNA)


title: Heart CC024 F

value: CC024 F

value: female


title: PT03_Treated_GFP_L_3


title: Heart CC021 F

value: CC021 F


title: Sox10Cre_BtR_IOM_3dplt_Red, scRNAseq

city: New York

first: Joanna

last: Smeeton

state: NY

address: 650 W 168TH ST, ROOM 1103A, William Black Building

department: Rehabilitation and Regenerative Medicine

institute: Columbia University Irving Medical Center

description: 10X Genomics

data_processing:
Fastq files were aligned to GRCz11 using CellRanger v3.0.0 from 10X Genomics.
Assembly: GRCz11.fa
Supplementary files format and content: Processed data for each sample includes CellRanger outputs: barcode, features, and matrix files in tsv format.

organism: Danio rerio

source_name: jaw joint

extract_protocol:
Microdissected joints were mechanically and enzymatically dissociated prior to FACS sorting with either enrichment for DsRed+ cranial neural crest (CNCC) lineage cells or no enrichment in BFP+ libraries. FACS-sorted cells were processed using the 10X Chromium controller for single cell profiling.
Barcoded single cell cDNA library constuction performed as per manufacturer's instructions using the 10X scRNAseq Kit v2.

treatment_protocol: IOM transection surgery was performed on adult zebrafish and collected at 1 and 3 days post-injury for 24hplt and 3dplt samples. Controls include uninjured samples and SHAM injury samples. For SHAM, fish were anaesthetized as per experimental samples but only the skin overlying the IOM ligament was lightly nicked. Joints were collected 1 and 3 days post surgery for 24hSHAM and 3dSHAM samples.

value: jaw joint

value: 3-5mpf adult

value: CNCC enriched

value: ligament transection


title: PT03_Treated_GFP_H_3


title: PT15REL (M49)

description:
AML patient
M49

value: REL (Relapse)


title: Sox10Cre_BtR_IOM_3dplt_Blue, scRNAseq

description: 10X Genomics

value: no enrichment


title: PT15DX (M48)

description:
AML patient
M48

value: DX (Diagnosis)


title: Heart CC019 F

value: CC019 F

value: heart


title: PT03_Control_GFP_L_2

value: acute myeloid leukemia (AML)


title: PT12D30 (M45)

description:
AML patient
M45


title: Sox10Cre_BtR_IOM_24hplt_Red, scRNAseq

description: 10X Genomics


title: PT16_Control_GFP_L_1


title: PT03_Treated_GFP_L_2

value: Treated


title: PT03_Control_GFP_H_2

value: Control


title: Heart CC017 F

value: CC017 F


title: PT01_PT10D30 (M43)

description:
AML patient
M43

value: Live CD34+ and or CD117+ and CD3- CD19- CD235a-


title: Sox10Cre_BtR_IOM_24hplt_Blue, scRNAseq

description: 10X Genomics


title: Sox10Cre_BtR_IOM_3dSHAM_Red, scRNAseq

description: 10X Genomics

value: SHAM injury


title: PT12_PT13D14 (M44)

description:
AML patient
M44


title: Heart CC017 M

value: CC017 M

value: male


title: Heart CC016 M

value: CC016 M


title: Sox10Cre_BtR_IOM_3dSHAM_Blue, scRNAseq

description: 10X Genomics

value: jaw joint

value: 3-5mpf adult


title: PT10REL (M42)

description:
AML patient
M42


title: Heart CC019 M

value: CC019 M


title: PT13DX (M41)

description:
AML patient
M41


title: Heart CC015 M

value: CC015 M


title: Sox10Cre_BtR_IOM_24hSHAM_Blue, scRNAseq

description: 10X Genomics

value: no enrichment


title: PT03_Treated_GFP_L_1

value: Xenograft AML blasts


title: Heart CC015 F

value: CC015 F

value: female


title: Sox10Cre_BtR_IOM_uninjured_Red, scRNAseq

description: 10X Genomics

value: CNCC enriched

value: uninjured


title: PT12DX (M40)

description:
AML patient
M40

value: acute myeloid leukemia (AML)

value: DX (Diagnosis)


title: PT08D30 (M39)

description:
AML patient
M39

value: Live CD34+ and or CD117+ and CD3- CD19- CD235a-


title: PT03_Control_GFP_H_1

value: Control


title: Sox10Cre_BtR_IOM_uninjured_Blue, scRNAseq

description: 10X Genomics


title: PT03_Treated_GFP_H_2

value: Treated


title: PT02_Control_GFP_L_5


title: Heart CC013 M

value: CC013 M

value: male

value: heart


title: PT02_Control_GFP_H_5


title: PT09D14 (M34)

description:
AML patient
M34


title: Heart CC013 F

value: CC013 F


title: PT03_Treated_GFP_H_1


title: Heart CC012 M

value: CC012 M


title: PT10DX (M33)

description:
AML patient
M33


title: PT10D14 (M35)

description:
AML patient
M35


title: Heart CC016 F

value: CC016 F


title: TSA_rep2

city: Moscow

first: Victoria

last: Kobets

state: Moscow Oblast

address: Bolshoy Bulvar, 30. 1

country: Russia

institute: Skolkovo University of Science and Technology

data_processing:
Hi-C reads were mapped with distiller version 0.3.3 with default parameters to genome assembly dm3.
Pairs were filtered with mapping quality larger than 30.
The maps were iteratively corrected with default parameters with pairtools
Replicates were mapped independently.
Hi-C observed contacts were normalized by the expected for each genomic distance with cooltools
Assembly: dm3
Supplementary files format and content: .mcool

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: S2 cells were obtained from the collection of IMG. Cells were grown at 25°C in Schneider’s Drosophila Medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco), 50 units/mL penicillin, and 50 μg/mL streptomycin.

extract_protocol:
For each treatment condition, a separate Hi-C experiment was performed for two replicates of treated cells and two replicates of control cells using the HindIII-HF restriction endonuclease according to a previously published protocol (Belton et al. 2012)
DNA libraries were prepared during Hi-C experiment according to a previously published protocol (Belton et al. 2012)

treatment_protocol: S2 cells were incubated with 50 ng/ml TSA (dissolved in dimethyl sulfoxide (DMSO); T8552, Sigma-Aldrich) or with 50 µM curcumin (dissolved in DMSO; C1386, Sigma-Aldrich) for 24 h. Control cells were treated with 6 µl/ml DMSO (D2650, Sigma-Aldrich). Treatment of S2 cells with dsRNA was performed over four days using a previously described protocol (Clemens et al. 2000). dsRNA against lacZ (control) was prepared as previously described (Shevelyov et al. 2009). dsRNA against HDAC1 was prepared in the same fashion using Drosophila genome DNA as a template for PCR amplification with 5’- GAATTAATACGACTCACTATAGGGAGAGCAGCGTTTCAATGTCGGCGAAGATT and 5’- GAATTAATACGACTCACTATAGGGAGATCATCGTTGATGGCATCCTCGGGAA primers.

value: embryo

tag: cell line

value: Schneider-2 (S2) cells

value: trichostatin A


title: TSA_control_rep1

value: DMSO


title: PT03_Control_GFP_L_1

value: Xenograft AML blasts


title: Sox10Cre_BtR_IOM_24hSHAM_Red, scRNAseq

description: 10X Genomics

value: jaw joint

value: 3-5mpf adult

value: CNCC enriched

value: SHAM injury


title: PT02_Treated_GFP_L_4

value: acute myeloid leukemia (AML)


title: PT09DX (M32)

description:
AML patient
M32

tag: timepoint

value: DX (Diagnosis)

value: Live CD34+ and or CD117+ and CD3- CD19- CD235a-


title: Heart CC011 M

tag: mouse

value: CC011 M

value: male


title: TSA_rep1


title: HDAC_control_rep2

value: dsRNA against lacZ


title: PT08REL (M31)

description:
AML patient
M31

value: REL (Relapse)


title: TSA_control_rep2


title: PT02_Control_GFP_L_4

value: Control


title: Heart CC011 F

value: CC011 F

tag: strain

value: female

value: heart


title: Heart CC027 F

value: CC027 F

tag: Sex


title: PT08REL (M30)

description:
AML patient
M30


title: Heart CC012 F

value: CC012 F

tag: tissue


title: Heart CC010 M

value: CC010 M


title: Heart CC010 F

value: CC010 F


title: PT02_Treated_GFP_H_3

tag: disease state

value: Treated

value: Xenograft AML blasts


title: PT08D14 (M29)

description:
AML patient
M29

value: acute myeloid leukemia (AML)

tag: patient id


title: HDAC1_depl_rep2

value: embryo

value: Schneider-2 (S2) cells

value: dsRNA against HDAC1


title: PT02_Treated_GFP_L_3

tag: cell population


title: HDAC1_depl_rep1


title: PT02_Control_GFP_L_3


title: PT02_Control_GFP_H_4


title: Cur_control_rep2

value: DMSO


title: Heart CC009 M

value: CC009 M

value: male


title: Heart CC009 F

value: CC009 F


title: PT02D30 (M26)

description:
AML patient
M26

value: Live CD34+ and or CD117+ and CD3- CD19- CD235a-


title: PT01D30 (M27)

description:
AML patient
M27


title: Cur_control_rep1


title: PT02_Control_GFP_H_3

value: Control


title: HDAC_control_rep1

value: dsRNA against lacZ


title: PT02_Treated_GFP_H_4


title: Heart CC008 M

value: CC008 M

value: heart


title: Heart CC008 F

value: CC008 F

value: female


title: Cur_rep2

value: curcumin


title: PT02DX (M25)

description:
AML patient
M25

value: DX (Diagnosis)


title: PT02_Control_GFP_L_2

value: acute myeloid leukemia (AML)

value: Xenograft AML blasts


title: PT07D14 (M24)

description:
AML patient
M24


title: PT02_Control_GFP_H_2


title: Heart CC007 M

value: CC007 M


title: Cur_rep1

value: embryo

value: Schneider-2 (S2) cells


title: Heart CC007 F

value: CC007 F


title: ATAC-seq 3

data_processing:
initial quality check with FastQC
mapping with BWA
Potential PCR duplicates were removed using Picard MarkDuplicates option.
The filtered BAM files were used as input in MACS2 for peak calling with standard settings and a q value of 0.05
Ae. aegypti LVP, vectorbase release 56
peak file

source_name: Aag2 cell line is an embryonic-derived cell line

extract_protocol:
Aag2 cells were trypsinized on plates and resuspended into single cells. Cells were pelleted by spinning at 500 × g for 5 min at 4°C and then washed twice with ice-cold 1× PBS buffer. 50,000 cells were counted and suspended in ice-cold 1× PBS. The same volume of 2× lysis buffer (20 mM Tris-HCl, 20 mM NaCl, 30 mM MgCl2, 0.5% IGEPAL) was added to 50,000 cells and pipetted up and down for 20 times to lyse the cells. Cells were pelleted at 500 × g for 30 min at 4°C and suspended in 25 µL of digestion buffer (10 mM Tris pH 7.6, 5 mM MgCl2, 10% DMF, 1U Tn5 transposase), followed by tagmentation in 37°C incubator for 1 h at 650 rpm. After tagmentation, 9 µL of clean-up buffer (0.5 M NaCl, 150 mM EDTA, 1% SDS, 2 mg/mL Protease K) was added for incubation at 40°C for 30 min with 650 rpm shaking. Normal phase 2× AMPure XP beads (68 µL) purification was performed to remove small fragments (<100 bp). Purified DNA was used for a first PCR amplification (Nextera Index Kit) with KAPA HiFi HotStart ReadyMix (Roche) for seven cycles. Reverse phase 0.55× SPRI bead (27.5 µL) purification was performed to remove large fragments (>300 bp), followed by purification with QIAquick PCR Purification Kit (Qiagen). Purified DNA was used for a second PCR amplification (Nextera Index Kit) with KAPA HiFi HotStart ReadyMix (Roche) for another seven cycles. The PCR product was purified again with QIAquick PCR Purification Kit (Qiagen). DNA amounts were determined with Qubit fluorometric quantification (ThermoFisher Scientific) and analyzed for fragment size distribution with a DNA 1000 Chip on a Bioanalyzer 2100 system (Agilent).
Prepared libraries can be directly loaded to sequencer

value: Aag2 cell line

tag: passages

tag: antibody


title: PT07D14 (M23)

description:
AML patient
M23


title: PT07DX (M22)

description:
AML patient
M22


title: PT02_Control_GFP_L_1

tag: treatment


title: Heart CC006 M

data_processing:
Reads were aligned to the pooled transcriptomes (mm10) of the eight founder strains using bowtie v1.0.0 with parameters -q -p 8 -a --best --strata --sam -v 3 -m 100.
Aligned reads were input into the Genotype recontruction by RNA-Seq (GBRS) software which estimated total gene counts using the Expectation-Maximization for Allele Specific Expression (EMASE) software.
Filtered out genes for which > 50% of samples had no expression.
Assembly: mm10

value: CC006 M

value: male


title: Heart CC006 F

value: CC006 F


title: PT02_Treated_GFP_L_2

value: Treated


title: PT02_Control_GFP_H_1

value: Control


title: Heart CC005 M

value: CC005 M

value: heart


title: PT01_DX_Control_2

description:
Xenografted AML
M79

data_processing:
Cellranger 10X demultiplexing (mkfastq)
Cellranger 10X quantification (counts)
Oligo Hash Tag processing (Seurat) custom - refined
Seurat data analysis workflow
Genome_build: refdata-cellranger-GRCh38-3.0.0
Supplementary_files_format_and_content: matrix, barcodes, features, rds

source_name: Xenograft BMMC

extract_protocol:
BM cells were sorted for live human CD45+ AML blasts and split in either total AML blasts or further sorted for the bottom 20% GFP expressing blasts (GFPlow/miR-126high gate). After sorting cells were washed and counted , stained with relevant TotalSeq-B (BioLegend) Hashtag antibodies following manufacturer's instructions, and pooled for chip loading.
Chromium(TM) Single Cell 3' Library & Feature Barcode (10xGENOMICS) according to manufacturer’s instructions.

value: DX

value: Live human CD45+ or Live human CD45+GFPlow


title: RNA pol II ser2p ChIP-seq 1

description: RNA pol II ser2p ChIP-seq p35

data_processing:
initial quality check with FastQC
mapping with BWA
Peak calling was performed with the MACS2 against input sample with standard settings and a q value of 0.05, with the option of broad peak calling for H3K36me3 and H3K9me3
Ae. aegypti LVP, vectorbase release 56
peak file

growth_protocol: Aag2 cells were grown in Leibovitz’s L-15 medium (Invitrogen) supplemented with 10% fetal bovine serum (Gibco), 50 U/ml Penicillin, 50 μg/mL Streptomycin (Invitrogen), 1x Non-essential Amino Acids (Invitrogen) and 2% Tryptose phosphate broth solution (Sigma) at 28°C in a humidified atmosphere without CO2. Cell lines were maintained by splitting twice weekly according to confluency.

extract_protocol:
Aag2 cells were cross-linked with 1% formaldehyde for 10 min at room temperature with gentle shaking. Cross-linking was quenched with the addition of 1/10 volume 1.25 M glycine. Cells were washed with 1× PBS, then harvested by scraping in Buffer B (20 mM HEPES, 0.25% Triton X-100, 10 mM EDTA, and 0.5 mM EGTA). Cells were then pelleted by spinning at 600 × g for 5 min at 4 °C. Cell pellet was resuspended in Buffer C (150 mM NaCl, 50 mM HEPES, 1 mM EDTA, and 0.5 mM EGTA) and rotated for 10 min at 4 °C. Cells were again pelleted by spinning at 600 × g for 5 min at 4 °C. The cell pellet was resuspended in 1× incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES) at 15 million cells/mL. Cells were sheared with a Bioruptor Pico sonicator (Diagenode) at 4 °C using 6 cycles of 30 s on, 30 s off. Sonicated chromatin was spun at 18,000 × g for 5 min at 4 °C. Chromatin in the upper supernatant was aliquoted, immediately frozen in liquid nitrogen, and stored in -80°C.  Sonicated chromatin from 2 million cells were used for each ChIP experiment. Chromatin was incubated in 1× incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES) supplemented with 1× protease inhibitors, 0.1% BSA, and a 50:50 mix of Protein A and G Dynabeads (Invitrogen), with agitation overnight at 4 °C. Generally, 1 µg antibody was used for each ChIP (H3K4me3, Diagenode, C15410003; H3K27ac, Diagenode, C15410196; H3K36me3, Diagenode, C15410058; H3K9me3, Diagenode, C15410193; RNA pol II, Santa cruz, sc-56767; RNA pol II ser5p, Abcam, ab5131; RNA pol II ser2p, Chromotek, 3E10). As a control, no antibody was added to ChIP input sample (sonicated chromatin). The beads were washed twice with wash buffer 1 (0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES), once with wash buffer 2 (wash buffer 1 with 500 mM NaCl), once with wash buffer 3 (250 mM LiCl, 0.5% sodium deoxycholate, 0.5% NP-50, 1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES), and twice with wash buffer 4 (1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES). After the washing steps, beads were rotated for 20 min at room temperature in elution buffer (1% SDS and 0.1 M NaHCO3). The supernatant was de-cross-linked with 200 mM NaCl and 100 μg/mL proteinase K for 4 h at 65 °C. De-cross-linked DNA was purified with MinElute PCR Purification columns (Qiagen). DNA concentrations were determined by Qubit fluorometric quantification (ThermoFisher Scientific).
Libraries were prepared with the Kapa Hyper Prep Kit for Illumina sequencing (Kapa Biosystems) according to the manufacturer's protocol with the following modifications. 3 ng DNA was used as input, with NEXTflex adapters (Bioo Scientific) and ten cycles of PCR amplification. Post-amplification cleanup and size selection was performed with dual AMPure XP beads selection (0.6× and 0.8×). Size-selected samples were analyzed for purity with a High Sensitivity DNA Chip on a Bioanalyzer 2100 system (Agilent), with an average size between 300 and 500 bp.

value: Chromotek #3E10


title: PT01_DX_Control_1

description:
Xenografted AML
M78

value: acute myeloid leukemia (AML)


title: PT02_Treated_GFP_L_1

value: Xenograft AML blasts


title: PT07DX (M21)

description:
AML patient
M21

value: DX (Diagnosis)

value: Live CD34+ and or CD117+ and CD3- CD19- CD235a-


title: RNA pol II ser2p ChIP-seq 2

description: RNA pol II ser2p ChIP-seq p36


title: ATAC-seq 1


title: Heart CC004 M

extract_protocol:
Hearts, livers, and kidneys were removed, flash frozen, and RNA was harvested using Trizol reagent. KAPA mRNA HyperPrep Kit (Roche) was used with total RNA for the construction of sequencing libraries.
Pooled libraries were sequenced on the NovaSeq 6000 platform (Illumina) using the S1 Reagent Kit v1, yielding 20-40M (target 30M) 1 x 1000bp single-end reads per sample.

value: CC004 M


title: PT02_Treated_GFP_H_2


title: PT01_DX_Treated_2

description:
Xenografted AML
M77


title: Heart CC005 F

value: CC005 F

value: female


title: RNA pol II ser5p ChIP-seq 1

description: RNA pol II ser5p ChIP-seq p35

value: Aag2 cell line

value: Abcam #ab5131


title: RNA pol II ser5p ChIP-seq 2

description: RNA pol II ser5p ChIP-seq p36


title: Heart CC004 F

value: CC004 F


title: PT02_Treated_GFP_H_1

value: Treated


title: ATAC-seq 2


title: PT01_DX_Treated_1

description:
Xenografted AML
M76


title: RNA pol II ChIP-seq 2

description: RNA pol II ChIP-seq p36

value: Santa cruz #sc-56767


title: PT15_DX_Treated_2

description:
Xenografted AML
M71


title: PT01_Treated_GFP_H_3


title: Heart CC003 M

value: CC003 M

value: male


title: PT15_DX_Treated_1

description:
Xenografted AML
M70

value: DX


title: Heart CC003 F

value: CC003 F

value: heart


title: RNA pol II ChIP-seq 1

description: RNA pol II ChIP-seq p35


title: PT01_Control_GFP_L_3

value: acute myeloid leukemia (AML)

value: Control


title: PT15_DX_Control_2

description:
Xenografted AML
M69

value: Live human CD45+ or Live human CD45+GFPlow


title: PT01_Control_GFP_H_3

value: Xenograft AML blasts


title: Heart CC002 M

value: CC002 M


title: ChIP-seq input DNA 2

description: ChIP-seq input p36


title: PT15_DX_Control_1

description:
Xenografted AML
M68


title: PT01_Control_GFP_L_2


title: ChIP-seq input DNA 1

description: ChIP-seq input p35


title: Heart CC002 F

value: CC002 F


title: PT03_REL_Control_2

description:
Xenografted AML
M63

value: REL


title: Heart CC001 M

value: CC001 M


title: H3K9me3 ChIP-seq 2

description: H3K9me3 ChIP-seq p36

value: Aag2 cell line

value: Diagenode #C15410193


title: PT01_Treated_GFP_L_3

value: Treated


title: H3K9me3 ChIP-seq 1

description: H3K9me3 ChIP-seq p35


title: Heart CC001 F

value: CC001 F

value: female


title: PT01_Treated_GFP_L_2


title: PT03_REL_Control_1

description:
Xenografted AML
M62


title: PT01_Control_GFP_H_2


title: PT03_REL_Treated_2

description:
Xenografted AML
M61


title: H3K36me3 ChIP-seq 2

description: H3K36me3 ChIP-seq p36

value: Diagenode #C15410058


title: H3K36me3 ChIP-seq 1

description: H3K36me3 ChIP-seq p35


title: PT01_Treated_GFP_L_1


title: PT03_REL_Treated_1

description:
Xenografted AML
M60


title: PT16_DX_Treated_2

description:
Xenografted AML
M55

value: DX


title: H3K27ac ChIP-seq 2

description: H3K27ac ChIP-seq p36

value: Diagenode #C15410196


title: PT01_Treated_GFP_H_1


title: Heterochronic graft (HH8-HH4), 3 hours, replicate 1

city: Cambridge

first: Ben

middle: John

last: Steventon

state: Cambridgeshire

address: Downing Street

institute: University of Cambridge

data_processing:
Data was processed using CellRanger (10X Genomics) to align reads to a reference transcriptome (produced using the galGal6 genome assembly published by Genome Reference Consortium) and produce matrices of gene expression. Note that the eGFP transcript and annotation was added manually to this transcriptome. CellRanger count performs alignment, filtering, barcode counting, and UMI counting.
Supplementary files format and content: Outputs from CellRanger count (Filtered_feature_bc_matrix) are provided for each sample. This encompasses three files for each sample: barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz.

organism: Gallus gallus

source_name: Gastrula tissue incl. primitive streak, epiblast, mesendoderm

growth_protocol: Chicken embryos incubated at 37 degrees Celsius for 20 hours (HH4) or 30 hours (HH8). Host embryos were cultured in New Culture and stored in a humidified chamber during their incubation period.

extract_protocol:
Samples were prepared for single-cell RNA sequencing as follows: tissue was dissected in cold PBS and washed thrice in cold PBS. PBS was replaced with dissociation solution (Trypsin + 0.05% EDTA, Gibco) and samples were incubated at 37ºC for 15 minutes, with trituration every 5 minutes. The dissociation reaction was terminated by addition of 10% Foetal Bovine Serum (FBS). Samples were spun down at 4ºC for 5 minutes and the supernatant discarded. Each cell pellet was resuspended in PBS + 0.25% BSA and passed through a 40μm pluriStrainer cell strainer (pluriSelect).
cDNA libraries were prepared using the 10X Genomics 3’mRNA-seq workflow (10X Genomics) and sequenced using a NovaSeq instrument (Illumina).

treatment_protocol: Transplants of somite progenitors (90% region of the primitive streak) were performed from GFP expressing donor embryos into the corresponding location in wild-type host embryos.

tag: time

value: 3 hours

tag: graft type

value: Heterochronic graft (HH8-HH4)

value: HH8 donor cells express eGFP

value: Graft of HH8 eGFP expressing somitic progenitors to HH4 WT embryo


title: Heterochronic graft (HH8-HH4), 0 hours, replicate 1

value: Gastrula tissue incl. primitive streak, epiblast, mesendoderm

value: 0 hours

tag: genotype


title: Homochronic graft (HH4-HH4), 3 hours, replicate 1

value: Homochronic graft (HH4-HH4)

value: HH4 donor cells express eGFP

value: Graft of HH4 eGFP expressing somitic progenitors to HH4 WT embryo


title: PT16_DX_Treated_1

description:
Xenografted AML
M54

value: acute myeloid leukemia (AML)

tag: cell type

value: Live human CD45+ or Live human CD45+GFPlow


title: H3K27ac ChIP-seq 1

description: H3K27ac ChIP-seq p35

value: Aag2 cell line


title: PT01_Treated_GFP_H_2

value: Treated

value: Xenograft AML blasts


title: PT01_Control_GFP_L_1

value: Control


title: Homochronic graft (HH4-HH4), 0 hours, replicate 2


title: PT16_DX_Control_2

description:
Xenografted AML
M53

value: DX


title: H3K4me3 ChIP-seq 1

description: H3K4me3 ChIP-seq p35

value: Diagenode #C15410003


title: PT16_DX_Control_1

description:
Xenografted AML
M52


title: Homochronic graft (HH4-HH4), 0 hours, replicate 1


title: H3K4me3 ChIP-seq 2

description: H3K4me3 ChIP-seq p36


title: PT01_Control_GFP_H_1


title: Leaf, control, biol rep2 [BOM2]

status: Public on Feb 04 2023

city: Vancouver

first: Keith

middle: L.

last: Adams

state: BC

address: 3156-6270 University Blvd.

department: Botany

country: Canada

institute: The University of British Columbia

data_processing:
genome build/assembly: Brassica oleracea TO1000
Basecalling was performed using NovaSeq 6000's RTA3 software.
Trimmomatic v0.32 was used for adapter trimming and quality filtering, retaining reads with average quality >Q20 that exceeded 50 bases following a 6 base headcrop.
STAR v2.7 was used for alignment of trimmed reads to their respective genomes (parameters:--outFilterMultimapScoreRange 0, --outFilterMultimapNmax 1, --outSAMprimaryFlag AllBestScore).
Constitutive gene expression was quantified using featureCounts v1.5.2 from the Subread package such that only exon-spanning fragments were counted (parameters: -p)
Raw counts were normalized using edgeR v3.20.9 to perform weighted TMM normalization.
Supplementary files format and content: tab-delimited text files contain counts of exon-spanning fragments aligned to species reference.
Supplementary files format and content: tab-delimited text files contain counts of exon-spanning fragments of natural B. napus aligned to pangenomes.

organism: Brassica oleracea

source_name: Leaf

growth_protocol: Seeds were surface sterilized with Plant Preservative Mixture and sandwiched in distilled water-saturated Miracloth for 24 hours in the dark, then transferred to individual seed-starting pots filled with soil. Plants were grown at 20 degrees C and with 16:8 hour photoperiod (200 E/m^2/s) for three weeks prior to treatment.

extract_protocol:
RNA was extracted using the Invitrogen RNAqueous Total RNA Isolation Kit with supplementary Plant RNA Isolation Aid.
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Ascospores of Sclerotinia sclerotiorum (5x10^5 spores/50 ml) were pipeted onto potato dextrose agar and incubated in low light at 20 degrees C for 48 hours. Mycelial plugs (7 mm diameter) were taken from the growing margin and brushed with 2% agar solution prior to placing the plugs on healthy leaves and securing with sterilized needles to simulate wounding. Mock-infected plants were handled similarly, but with potato dextrose agar without the the pathogen. Plants were placed in plastic bags in an 18 degree C chamber for 24 hours before tissue collection.

value: Leaf

tag: line

value: Brassica oleracea

value: B. oleracea

value: Mock-infected


title: Leaf, infected, biol rep1 [BOI1]

value: Sclerotinia sclerotiorum-infected


title: Leaf, infected, biol rep3 [BOI3]


title: Leaf, control, biol rep1 [BOM1]


title: Horse smRNA-seq Rep #2

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
DESeq_breastCancer_normalized_counts.csv
Horse2_S12_L002_R1_001

data_processing:
Small RNA-seq samples were processed using miRquant2.0 (https://github.com/Sethupathy-Lab/miRquant) using default settings
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: bosTauMd3, canFam3, equCab2, rn6, susScr10, and hg19 for cow, dog, horse, rat, pig and human small RNA-seq, canFam3 and equCab2 for the dog and horse RNA-seq
Supplementary_files_format_and_content: Normalized counts files are comma separated value matrices containing the DESeq2 normalized counts for each of the samples.

organism: Equus caballus

source_name: mammosphere-derived epithelial cells

extract_protocol: Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol

value: mammary gland

value: mammosphere-derived epithelial cells

tag: breast cancer susceptibility

value: resistant


title: Leaf, infected, biol rep2 [BOI2]


title: Leaf, control, biol rep3 [BOM3]


title: Horse smRNA-seq Rep #3

description:
DESeq_breastCancer_normalized_counts.csv
Horse3_S18_L002_R1_001


title: muscle tissue-3, 21 salinity

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

institute: School of Pharmaceutical Sciences, Jilin University

data_processing:
Sequencing was performed on an Illumina HiSeq X Ten platform, generating 150 bp paired-end reads.
Using Trimmomatic 0.39, low-quality and poly-N reads were trimmed to obtain clean data.
For subsequent analyses, clean data were retained for each sample. The M. nipponense genome (cngb_100843) was utilized to map to the clean data by the approach of HISAT2
Bowtie2 (Langmead and Salzberg, 2012) was applied to calculate the FPKM of each gene
eXpress was used to determine the read counts of each gene.
Assembly: The M. nipponense genome (cngb_100843)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Macrobrachium nipponense

source_name: muscle

growth_protocol: The gills, hepatopancreas and muscle of 30 M. nipponense were used from the control (0 ppt) and other (7, 14, and 21 ppt) groups for long term salinity exposure

extract_protocol:
total RNA extraction
libraries were prepared for each group with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, CA, USA).

value: muscle

tag: cell line

value: tissue

value: different salinity exposure


title: in cell transcribed SINEUP

city: Yokohama

first: Harshita

last: Sharma

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN IMS

description: Full-length RNA

library_source: other

data_processing:
library strategy: Direct-RNA sequencing
fast5 files basecalled using Guppy
Basecalled data mapped to reference (SINEUP sequence) using minimap2
Raw signal-level data realigned to kmers of reference with Nanopolish, with output collapsed by kmer using NanopolishComp
Nanocompore SampComp used to compare signal of 2 experimental conditions (20% IVT and ICT), with statistical analyses performed using SampCompDB
Output was filtered by p-value (0.05) and log odds ratio (absolute value > 1), and a peak-calling algorithm (https://gist.github.com/tleonardi/0bb31e6a380e5766f04f4e197d36b38e) was run to further merge kmers into significantly modified regions
Assembly: mIVT.SINEUP: AATACAAGCTACTTGTTCTTTTTGCAGGATCCCATCGATTCGAATTCAAGGCTAGACTCGAGCCATGGTGGCGACCGGTAGCGCTAGCGGATCTGACGGTTCACTAGATGCGGCCGCCACTGTGCTGGATATCTGCAGAATTCGCCCTTCAGTGCTAGAGGAGGTCAGAAGAGGGCATTGGATCCCCCAGAACTGGAGTTATACGGTAACCTCGTGGTGGTTGTGAACCACCATGTGGATGGATATTGAGTTCCAAACACTGGTCCTGTGCAAGAGCATCCAGTGCTCTTAAGTGCTGAGCCATCTCTTTAGCTCCAGTCTCTTAAAAAACAAACAAACGAACGAACAGCAAGGGAGCTGGGTATGACAACACATACTATAATTCTAGTACTCAGGATGCTGAAACAGGAGGATTGCCTGACTGGGAGATATAAGGAGAATCTGTTGTCACCCCCACCCCTCCCCATAAAGGCAGAATAAAAGAACGTCCTATAAACAAATAAACAAACAACCCAATAAAACAAAACCAAGATCTCTCCACCTTTTCTTTGCTTTTTCAGACTTTGTAATAAGGCCCTTTGGAGTGCAGGATATTCGGCAGGACAAGCAGAGAGGGAGACCATCAGTTCTTTCTTTGATCAAGAAGACTATGTTCCTTAGCAAACTGGTGTGTATTATCTCTTATGCAATGAGCCTGGAAAGAGGGCACAGCCACCGAGGATGGTACAGCATGGATGGATGGTACGCTACAGAGACTCGGGAGCCCAACTGTGAGTGGCTGACTGGCATGGTAGGTTCAGGGAAGAATTGGCCTGTGAAGAAAATGTTCTTGAAAAGTGAACAAGGTGCAGGAGGTAGGAGTGGGTCCTGGGCAAAGCAGGGGGTGCATCCCAGCCTCAGGGAATAGCACAGCAGAGGTCTGTTGATGCATGCGAGTGCATGACCTGCTTGCCAATAGACGATCAAGAATGGGCAAAGCATCATGGGTGATGAGTGGGAGAGGGGATGAGACATTCCTTTCTCCCTGCTGAGACTTCCATTGAACCGATGAGTTCTGAATAGAAGATGCCCCCCCACCCCCCCACCAGTGTAGAATCTGAAGGGAGGCATATATTACCCTATATTACTCTGTGTTGGCGGCGAGCTATCTGACAGCCAACCTTCCCATACATTTCATTGGGCATACACTAATGACAGGAAGTTCCTTTTGCTTGTATGCAAGAGATGGCTCACACGATGGAGAATTTAATCTTGAAGGGCGAATTCCACCACACTGGACTAGTGGATCCGAGCTCGCCTCTCGAGCCT
Supplementary files format and content: nanocompore_GMMlogit_sig_LORfilt_peakfilt.txt

molecule: other

growth_protocol: 0.5 X 10^7 cells seeded on a 10 cm plate in DMEM Glutamax+10% FBS+1% P/S (penicillin/streptomycin) at 37°C, 5% CO2.

extract_protocol:
In case of ICT SINEUP RNA, after 24 h of transfection, ~20 million cells were harvested by Trizol/chloroform extraction, and total RNA containing SINEUP-GFP RNAs at the aqueous phase was extracted by RNeasy mini kit (Qiagen) followed by DNase treatment. The purified RNA was hybridized with SINEUP RNA-specific biotinylated probes described by Toki et al. (Nucleic Acids Research, 2020) and pulled down twice followed by extraction by Trizol/chloroform method and purification by miRNeasy mini column (Qiagen).
All IVT and ICT direct SINEUP-GFP RNA-seq libraries were prepared with SQK-RNA002 (Oxford Nanopore Technology) kit following the manufacturer’s protocol. The original reverse transcription adapter (RTA) and four barcoded RTA, which are described by Leger et al. (2021), were used for IVT and ICT SINEUP-GFP RNAs respectively. The libraries were applied to MinION Mk1C sequencer and sequenced for 72 h.

treatment_protocol: The in vitro transcribed (IVT) SINEUP-GFP RNA were synthesized as described by Toki et al. (FEBS Lett. 2020). The in vitro transcribed SINEUP-GFP RNA was modified by following the protocol by Mandal and Rossi (Nat Protoc. 2013). For 20% Ψ modification condition, UTP was replaced with 20% pseudouridine-5ʹ-triphosphate (Ψ). In case of in-cell transcribed (ICT) SINEUP RNA, HEK293T/17 cells were plated on a 10 cm dish and SINEUP-GFP and sense GFP plasmids were transfected after 24 h.

value: Human embryonic kidney

value: SINEUP-GFP and sense EGFP co-transfected

tag: molecule type

value: in-cell transcribed (ICT) SINEUP RNA


title: in vitro transcribed SINEUP, 0% pseudouridine

description: Full-length RNA

source_name: N/A, in vitro

value: N/A, in vitro

value: in vitro transcribed (IVT) SINEUP-GFP RNA


title: muscle tissue-3, 14 salinity

treatment_protocol: The gills, hepatopancreas and muscle of 30 M. nipponense were used from the control (0 ppt) and other (7, 14, and 21 ppt) groups


title: muscle tissue-1, 14 salinity


title: muscle tissue-1, 21 salinity


title: Leaf, infected, biol rep3 [BRI3]

data_processing:
genome build/assembly: Brassica rapa v3
Basecalling was performed using NovaSeq 6000's RTA3 software.
Trimmomatic v0.32 was used for adapter trimming and quality filtering, retaining reads with average quality >Q20 that exceeded 50 bases following a 6 base headcrop.
STAR v2.7 was used for alignment of trimmed reads to their respective genomes (parameters:--outFilterMultimapScoreRange 0, --outFilterMultimapNmax 1, --outSAMprimaryFlag AllBestScore).
Constitutive gene expression was quantified using featureCounts v1.5.2 from the Subread package such that only exon-spanning fragments were counted (parameters: -p)
Raw counts were normalized using edgeR v3.20.9 to perform weighted TMM normalization.
Supplementary files format and content: tab-delimited text files contain counts of exon-spanning fragments aligned to species reference.
Supplementary files format and content: tab-delimited text files contain counts of exon-spanning fragments of natural B. napus aligned to pangenomes.

organism: Brassica rapa

value: Brassica rapa

value: B. rapa


title: Leaf, control, biol rep3 [BRM3]

value: Leaf


title: muscle tissue-2, 21 salinity


title: Leaf, control, biol rep2 [BRM2]


title: Leaf, infected, biol rep1 [BRI1]


title: Leaf, infected, biol rep2 [BRI2]


title: muscle tissue-1, 7 salinity


title: muscle tissue-3, 7 salinity


title: Leaf, control, biol rep1 [BRM1]


title: muscle tissue-2, 7 salinity


title: in vitro transcribed SINEUP, 20% pseudouridine

description: Full-length RNA


title: muscle tissue-3, 0 salinity


title: muscle tissue-2, 14 salinity


title: ATAC hMSCs, Flat Surface, Osteogenic Medium (bio rep 3)

city: Chicago

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

data_processing:
Reads trimmed using trimmomatic/0.39 using the following parameters: ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:5:20 MINLEN:30;
Reads aligned with Bowtie2  to hg38 using the following parameters: bowtie2 -X 2000 --very-sensitive -q --local and converted to BAMs using SAMtools folllowed by duplicate removal with Picard
Peaks were called on BAMs using MACS2/2.1.0 using the following parameters: macs2 callpeak -t $sortedBAM -f BAMPE -n $FILENew -g hs --nomodel --keep-dup all
Peaks were counted against BAMs using the Genomic Ranges package in R to generate a counts table
Differential accesibility analysis was carried out using DESeq2 and the counts table
Assembly: hg38
Supplementary files format and content: Tab-delimited csv count file annotated with HGNC Gene IDs/other metadata and narrowPeak files

source_name: hMSCs

growth_protocol: Human mesenchymal stromal cells (hMSCs, PCS-500-012) were purchased from the American Type Culture Collection (ATCC) and sub-cultured using a growth medium acquired from the same company. hMSCs (P4) were seeded onto the flat mPOC substrates and the mPOC micropillars

extract_protocol: Nextera DNA Library Prep kit (Illumina) was utilized for Tagmentation and the ATAC-Seq library preparation protocol was utilized as previoulsy published by Buenrostro et al (2015).

value: hMSCs

value: mesenchymal stem cells

value: WT

tag: substrate

value: osteogenic differentiation

value: Day 1


title: muscle tissue-1, 0 salinity


title: ATAC hMSCs, Flat Surface, Osteogenic Medium (bio rep 2)


title: Horse smRNA-seq Rep #1

description:
DESeq_breastCancer_normalized_counts.csv
Horse1_S5_L001_R1_001

value: mammary gland

value: mammosphere-derived epithelial cells

value: resistant


title: ATAC hMSCs, Flat Surface, Osteogenic Medium (bio rep 1)


title: hepatopancreas tissue-3, 21 salinity

source_name: hepatopancreas

value: hepatopancreas

value: tissue

value: different salinity exposure


title: ATAC hMSCs, Pillar Surface, Osteogenic Medium (bio rep 2)


title: hepatopancreas tissue-2, 21 salinity


title: ATAC hMSCs, Pillar Surface, Osteogenic Medium (bio rep 1)


title: hepatopancreas tissue-1, 21 salinity


title: ATAC hMSCs, Pillar Surface, Growth Medium (bio rep 3)

value: growth medium


title: ATAC hMSCs, Pillar Surface, Growth Medium (bio rep 1)


title: hepatopancreas tissue-3, 7 salinity


title: ATAC hMSCs, Flat Surface, Growth Medium (bio rep 3)


title: hepatopancreas tissue-2, 7 salinity


title: hepatopancreas tissue-3, 0 salinity


title: hepatopancreas tissue-1, 7 salinity


title: ATAC hMSCs, Pillar Surface, Growth Medium (bio rep 2)


title: hepatopancreas tissue-2, 0 salinity


title: hepatopancreas tissue-2, 14 salinity