title: Basophils from Nb infected mice (hashtag library)

description:
hashtag index A0312: skin basophils during second Nb infection,  hashtag index A0313: bone marrow basophils during second Nb infection,  hashtag index A0314: spleenbone marrow basophils during second Nb infection,  hashtag index A0315: whole skin cells during second Nb infection
hashtag index A0312: skin basophils during second Nb infection,
hashtag index A0313: bone marrow basophils during second Nb infection,
hashtag index A0314: spleenbone marrow basophils during second Nb infection,
hashtag index A0315: whole skin cells during second Nb infection

data_processing:
After adaptor removal and quality filtering of sequencing data by Cutadapt-2.10, cDNA reads were mapped to murine reference RNA sequences (GRCm38.p6, release-101) by Bowtie2-2.3.4.1, and count matrices were generated using the modified python script of BD Rhapsody workflow. Identification of valid cell barcodes were conducted by utilizing the DropletUtils package as previously described (Shichino et al. bioRxiv 2022). Each sample origin and doublets were identified based on fold-change of the normalized read counts of Hashtag antibodies. Distribution-based error correction (DBEC) was performed for subtracting background read counts of each gene derived from RNA diffusion during the lysis step within the BD Rhapsody cartridge and reverse transcription, as described previously (Shichino et al. bioRxiv 2022).
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files

source_name: Mixed (bone marrow, spleen and skin)

extract_protocol:
Single-cell suspensions were prepared from the bone marrow, spleen and infected skin and subjected to positive selection of CD49b-positive cells by using biotinylated anti-CD49b antibody (DX5) and EasySep mouse Biotin Positive Selection Kit II (Stemcell Technologies), followed by the isolation of CD200R3+cKit- cells by cell sorting.
Library construction was conducted according to the TAS-seq protocol reported in the report by Shichino et al. bioRxiv 2022. Briefly, cells were indexed with Totalseq anti-mouse Hashtag antibody (BioLegend) for multiplexing. Reverse-transcription was conducted by using the BD Rhapsody according to the manufacturer’s instruction. Preparation of cDNA library and hashtag library was performed as described previously (Chen CY et al. Cancer Immunol Res 2021). Sequencing librarie were prepared by utilizing NEBNext UltraII FS Library Prep Kit (New England BioLabs, USA).

treatment_protocol: Mice were subcutaneously infected once or twice with third-stage larvae (L3) of Nippostrongylus brasiliensis (Nb). Mice were first injected with 500 L3 in the tail base, and infected mice were injected again with 500 L3 in the flank 18 days after the first infection. Two days after the secondary Nb infection, the bone marrow, spleen and skin inoculation site were harvested.

value: Mixed (bone marrow, spleen and skin)

value: basophil and mixed skin cells

value: Nb larvae were infected twice with WT mice


title: Basophils from Nb infected mice (cDNA library)

status: Public on Mar 21 2023

type: SRA

city: Bunkyo-ku

first: Kensuke

last: Miyake

state: Tokyo

address: 1-5-45, Yushima

department: Institute of Integrated Research

country: Japan

institute: Institute of Science Tokyo

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype

value: C57BL/6J WT

tag: treatment


title: MBH_P90_control_4

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

library_source: transcriptomic

data_processing:
Basecalling performed using Illumina bcl2fastq v2.20
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were processed for mapping and quantification using nf-core rnaseq pipeline v1.4.2 (https://nf-co.re/rnaseq/1.4.2/usage) and using Gene set from Ensembl.org release 102.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text file include raw counts for annotations for all Sample

organism: Rattus norvegicus

source_name: medio-basal hypothalamus

extract_protocol:
At PND22, PND42 and PND90,  the pre-optic area (POA) and the mediobasal hypothalamus (MBH) were dissected and frozen. Total RNA was extracted from the MBH and POA using Universal RNA mini kit (Qiagen,Venlo, Netherlands) following the manufacturer’s instructions.
Libraries were prepared using Truseq® stranded mRNA Sample Preparation Kits (Illumina, CA, USA) following manufacturer’s instructions. Libraries were validated using QIAxcel Advanced System and quantified by qPCR using the KAPA library quantification kit. Libraries were multiplexed and sequenced on an Illumina NovaSeq6000 sequencer to generate more than ~25,000,000 paired-end reads (2 × 150 bases) per library.

treatment_protocol: Dams were exposed by oral gavage with either chemical or vehicle (corn oil) once daily from GD 7 until birth and from the day after birth until postnatal (PND) 22. Doses for DES were 0; 3; 6; 12 µg/kg bw/day and doses for KTZ were 0; 3; 6; 12 mg/kg bw/day.

tag: strain

value: Sprague-Dawley

tag: Sex

value: female

value: medio-basal hypothalamus

tag: age

value: vehicle


title: MBH_P90_KTZ 3_4

value: KTZ 3 mg/kg bw/day


title: MBH_P90_DES 3_3

value: DES 3 ug/kg bw/day


title: Old_MSC_scRNAseq_39

city: Tokyo

first: Keiyo

last: Takubo

address: 1-21-1 Toyama Shinjuku-ku

department: Department of Stem Cell Biology

institute: National Center for Global Health and Medicine

description: Single cell RNA-seq of bone marrow CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell from old mice

data_processing:
Sequencing was performed using an Illumina HiSeq2000 system. Sequence reads were aligned to the murine genome mm9 using RNA-seq Unified Mapper (RUM) version 2.0.4, and transcripts were assembled using Cufflinks version 2.1.1.
Assembly: mm9
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

source_name: Bone marrow

extract_protocol:
Young and old MSCs (CD45-Ter119-CD31-CD140a+LepR+) were isolated with a FACSAria II cell sorter from 10-week-old and 2-year-old mice, respectively. Single-cell cDNA synthesis was performed with a C1 Single-Cell Auto Prep System (Fluidigm)
Reverse transcription and preamplification were performed according to the manufacturer’s instructions using a SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (Clontech) and a C1 Single-Cell Auto Prep Reagent Kit for mRNA Seq (Fluidigm). For RNA controls, tubes #1, #4, and #7 of ArrayControl RNA Spikes (Thermo Fisher Scientific) were mixed at a ratio of 100:10:1, and the RNA Spikes mixture was diluted 1:10000 in C1 Loading Reagent (Fluidigm). Sorted MSCs were diluted in Suspension Reagent to ~1000 cells/µL and loaded into a C1-Single-Cell Auto Prep IFC for mRNA-seq (5-10 μm). After loading the cells, the integrated fluidic circuit (IFC) was observed microscopically using an IN Cell Analyzer 6000 (GE Healthcare) to ensure that single cells were captured in each well. Wells with 0, >1, or shrunken cells were excluded. A total of 83 of the 96 wells for young MSCs and 79 of the 96 wells for old MSCs were considered valid. The thermal cycling conditions for cell lysis, reverse transcription, and preamplification were as follows: 72°C for 3 min, 4°C for 10 min, and 25°C for 10 min for cell lysis; 42°C for 90 min and 70°C for 10 min for reverse transcription; 95°C for 1 min and 5 cycles at 95°C for 20 s, 58°C for 4 min, and 68°C for 6 min, 9 cycles at 95°C for 20 s, 64°C for 30 s, and 68°C for 6 min, 7 cycles at 95°C for 30 s, 64°C for 30 s, and 68°C for 7 min, and 1 cycle at 72°C for 10 min for preamplification; and holding at 4°C until harvest. Amplified cDNA (approximately 3.5 μL) from each well was diluted with 10 μL of C1 DNA Dilution Reagent (Fluidigm) and frozen at -30°C until use. The sample in each well was further diluted 1:2 with C1 Harvest Reagent and subjected to tagmentation and Illumina sequencing library preparation using a Nextera XT DNA Sample Preparation Kit (Illumina) and a Nextera XT DNA Sample Preparation Index Kit (96 indices, Illumina). Then, 2.5 μL of Tagment DNA Buffer, 1.25 μL of Amplification Tagment Mix and 1.25 μL of the diluted cDNA sample were mixed and incubated at 55°C for 10 min in a thermal cycler. The tagmentation reaction was then stopped by adding 1.25 μL of neutralizing buffer (NT buffer). Next, the samples were subjected to PCR amplification. A 6.25 μL aliquot of each sample was mixed with NPM buffer, and 1.25 μL each of Index Primer 1 and Index Primer 2. The thermal cycling conditions were as follows: 72°C for 3 min, 95°C for 30 s, 12 cycles at 95°C for 10 s, 55°C for 30 s, and 72°C for 1 min, and 1 cycle at 72°C for 5 min. A 1 μL aliquot from each well of amplified DNA was processed by two rounds of mixing and cleanup with AMPure XP beads (Beckman Coulter), and DNA was then eluted with 144 μL of DNA suspension buffer.

value: Bone marrow

value: 24 month old


title: Old_MSC_scRNAseq_40

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell


title: Old_MSC_scRNAseq_37


title: Bortezomib-treated Atg5-/- replicate 2 [ATG_BZ2]

city: La Jolla

first: Robert

last: Signer

state: California

address: 3855 Health Sciences Drive

department: Division of Regenerative Medicine

country: USA

institute: UCSD

description: Mx1-Cre;Atg5fl/fl mice treated with bortezomib; freshly isolated

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were against the GRCh38 reference genome and Gencode v27 annotations using STAR v2.6.1 (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Assembly: GRCm38.p4.gencode.rM9
Supplementary files format and content: read count matrix with rows as genes and columns as cells

growth_protocol: Not applicable

extract_protocol:
RNA was extrated using the Rneasy Plus Micro Kit
Illumina mRNA libarries were prepared using the SMARTseq2 protocol

treatment_protocol: For mice that received control DMSO, 10% DMSO was injected retro-orbitally 48h and 24h before analysis. For mice that received bortezomib, 10mg/kg bortezomib was injected retro-orbitally 48h and 24h before analysis.

value: Mx1-Cre; Atgfl/fl

value: Bortezomib

tag: cell subset

value: HSC (CD48- LSK CD150+)


title: Bortezomib-treated Atg5-/- replicate 3 [ATG_BZ3]


title: Bortezomib-treated Atg5-/- replicate 1 [ATG_BZ1]


title: BMBAs and basophils under homeostatic conditions (hashtag library)

description:
hashtag index A0302: Spleen basophils from Mcpt8-GFP Tg mice,
hashtag index A0301: Bone marrow basophils from Mcpt8-GFP Tg mice,
hashtag index A0302: Spleen basophils from Mcpt8-GFP Tg mice,
hashtag index A0303: Bone marrow cells cultured with IL-3 for 3 days,
hashtag index A0306: Bone marrow cells cultured with IL-3 for 7 days

source_name: Mixed (bone marrow-derived basophils, bone marrow basophils and splenic basophils)

extract_protocol:
For scRNA-seq of bone marrow-derived basophils (BMBAs), bone marrow cells cultured in the presence of IL-3 (0.3 ng/mL: BioLegend) for 3 or 7 days were subjected to scRNA-seq analysis. For scRNA-seq of basophils under homeostatic conditions, single cell samples were prepared from the bone marrow and spleen of Mcpt8GFP transgenic mice and depleted of lineage-positive cells by using biotinylated lineage antibodies (anti-CD4, anti-CD8a, anti-CD19, anti-B220, anti-Gr-1 and anti-TER-119) and EasySep Mouse Streptavidin RapidSpheres Isolation Kit (Stemcell Technologies). GFP-positive cells were sort-purified from lineage-negative cells and subjected to scRNA-seq analysis
Library construction was conducted according to the TAS-seq protocol reported in previous report (Shichino et al. bioRxiv 2022). Briefly, cells were indexed with Totalseq anti-mouse Hashtag antibody (BioLegend) for multiplexing. Reverse-transcription was conducted by using the BD Rhapsody system according to the manufacturer’s instruction. Preparation of cDNA library and hashtag library was performed as described previously (Chen CY et al. Cancer Immunol Res 2021). Sequencing libraries were prepared by utilizing NEBNext UltraII FS Library Prep Kit (New England BioLabs, USA).

value: basophil

value: Mixed (C57BL/6J and Mcpt8-GFP Tg)

value: Mixed (IL-3-cultured cells and homeostatic condition)


title: DMSO-treated Atg5-/- replicate 2 [ATG_DMSO2]

description: Mx1-Cre;Atg5fl/fl mice treated with control DMSO; freshly isolated

value: DMSO


title: MBH_P90_DES 12_4

value: DES 12 ug/kg bw/day


title: MBH_P90_KTZ 3_3

value: Sprague-Dawley


title: MBH_P90_DES 12_2

value: female


title: Old_MSC_scRNAseq_38


title: DMSO-treated Atg5-/- replicate 1 [ATG_DMSO1]


title: BMBAs and basophils under homeostatic conditions (cDNA library)

description:
hashtag index A0301: Bone marrow basophils from Mcpt8-GFP Tg mice,
hashtag index A0301: Bone marrow basophils from Mcpt8-GFP Tg mice,
hashtag index A0302: Spleen basophils from Mcpt8-GFP Tg mice,
hashtag index A0303: Bone marrow cells cultured with IL-3 for 3 days,
hashtag index A0306: Bone marrow cells cultured with IL-3 for 7 days

value: Mixed (bone marrow-derived basophils, bone marrow basophils and splenic basophils)


title: MBH_P90_DES 6_4

value: medio-basal hypothalamus

value: DES 6 ug/kg bw/day


title: MBH_P90_control_3

value: vehicle


title: Old_MSC_scRNAseq_36

value: Bone marrow


title: RNAseq.mouse.CD8.Positive.Tcells.Day9.Treatment.FHT1015.Rep1

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

institute: Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the mm10 and hg19 transcriptomes with STAR v2.5.2b with default parameters and tracks were generated using the deepTools v2.5.3 bamCoverage function.
Assembly:hg19, mm10
Supplementary files format and content: tab-delimited text files include raw gene count values for each sample

source_name: CD8 Positive T-Cells

growth_protocol: Human and mouse T cells were maintained in RPMI media supplemented with 10% FBS, 1% Pen/Strep, 1X GlutaMAX, 1X Non-essential Amino Acids, 1X Sodium Pyruvate and 10mM 2-Mercaptoethanol, and 30U/ml human IL2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB Next mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Human cells were activated with Human T-Activator CD3/CD28 Dynabeads (Thermo Fisher Scientific, Cat# 11132D) at 1:1 beads-to-cells ratio on Day 0, 3 and 6.Mouse cells were activated with Mouse T-Activator CD3/CD28 Dynabeads (Thermo Fisher Scientific, Cat#11453D) at 1:1 beads-to-cells ratio on Day 0, 3 and 6.
Cells were treated with inhibitors (Compound 14 and FHT1015) on Day 3 and Day 6 and taken down for one timepoint at Day9.  Cells were treated with degraders (ACBI1 and AU-15330, 100nM) on Day 3 and Day 6 and taken down for one timepoint at Day9.

tag: cell line

value: CD8 Positive T-Cells

value: Primary T cells

tag: sample type

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from mouse 1 treated with FHT1015 100 nM replicate 1

tag: time

value: Day 9


title: MBH_P90_KTZ 12_4

value: KTZ 12 mg/kg bw/day


title: BM BaP_02

data_processing:
Sequencing data generated by Illumina Novaseq 6000 (Illumina, USA) was subjected to adaptor trimming by Cutadapt-3.4.
Trimmed reads were aligned against murine reference RNA sequences (GRCm39 RefSeq RNA) by utilizing bowtie2-2.4.2 .
Supplementary files format and content: mm39
Supplementary files format and content: Tab-separated values files

source_name: bone marrow

extract_protocol:
Basophil progenitors, immature basophils and mature basophils were isolated from the bone marrow and mature basophils were isolated from the spleen by FACS sorting.
Library construction for bulk-RNA sequencing was conducted according to the previous study (Ogawa et al. Biochem Biophys Res Commun. 2022). Briefly, 100ng of amplified cDNA libraries were subjected to Illumina library construction by using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs). Fragmentation, end-repair, dA-tailing, adaptor ligation, and barcoding PCR were sequentially conducted according to the manufacturer’s instruction.

value: bone marrow

value: basophil

value: C57BL/6J WT


title: Bortezomib-treated WT replicate 3 [WT_BZ3]

description: WT mice treated with bortezomib; freshly isolated

value: Wildtype

value: Bortezomib

value: HSC (CD48- LSK CD150+)


title: Old_MSC_scRNAseq_35

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell

value: 24 month old


title: RNAseq.mouse.CD8.Positive.Tcells.Day9.Transient.Rep2

treatment_protocol:
Human cells were activated with Human T-Activator CD3/CD28 Dynabeads (Thermo Fisher Scientific, Cat# 11132D) at 1:1 beads-to-cells ratio on Day 0, 3 and 6. Mouse cells were activated with Mouse T-Activator CD3/CD28 Dynabeads (Thermo Fisher Scientific, Cat#11453D) at 1:1 beads-to-cells ratio on Day 0, 3 and 6.
Cells were treated with inhibitors (Compound 14 and FHT1015) on Day 3 and Day 6 and taken down for one timepoint at Day9.  Cells were treated with degraders (ACBI1 and AU-15330, 100nM) on Day 3 and Day 6 and taken down for one timepoint at Day9.

value: 9 day transient CD3/CD28 activated CD8 Positive T cell from mouse 1 replicate 2


title: MBH_P22_DES 12_2

value: Sprague-Dawley

value: female

value: medio-basal hypothalamus

value: DES 12 ug/kg bw/day


title: Old_MSC_scRNAseq_29

value: Bone marrow


title: Bortezomib-treated WT replicate 1 [WT_BZ1]


title: RNAseq.mouse.CD8.Positive.Tcells.Day9.Transient.Rep1

value: CD8 Positive T-Cells

value: Primary T cells

value: 9 day transient CD3/CD28 activated CD8 Positive T cell from mouse 1 replicate 1


title: MBH_P90_DES 3_2

value: DES 3 ug/kg bw/day


title: MBH_P90_DES 12_1


title: RNAseq.mouse.CD8.Positive.Tcells.Day9.Treatment.Compound14.Rep2

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from mouse 1 treated with compound 14 100 nM replicate 2

value: compound 14

value: Day 9


title: Old_MSC_scRNAseq_34


title: Old_MSC_scRNAseq_28


title: DMSO-treated Atg5-/- replicate 3 [ATG_DMSO3]

value: Mx1-Cre; Atgfl/fl

value: DMSO


title: RNAseq.mouse.CD8.Positive.Tcells.Day9.Treatment.FHT1015.Rep2

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from mouse 1 treated with FHT1015 100 nM replicate 2


title: MBH_P90_KTZ 12_3

value: KTZ 12 mg/kg bw/day


title: MBH_P90_DES 6_3

value: DES 6 ug/kg bw/day


title: Old_MSC_scRNAseq_33

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell

value: 24 month old


title: Old_MSC_scRNAseq_27


title: RNAseq.mouse.CD8.Positive.Tcells.Day9.Chronic.Rep2

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from mouse 1 replicate 2


title: Old_MSC_scRNAseq_32


title: Old_MSC_scRNAseq_31


title: RNAseq.mouse.CD8.Positive.Tcells.Day9.Treatment.Compound14.Rep1

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from mouse 1 treated with compound 14 100 nM replicate 1


title: MBH_P22_DES 12_1

value: Sprague-Dawley

value: female

value: medio-basal hypothalamus

value: DES 12 ug/kg bw/day


title: Old_MSC_scRNAseq_30

value: Bone marrow


title: Bortezomib-treated WT replicate 2 [WT_BZ2]

value: Wildtype

value: Bortezomib

value: HSC (CD48- LSK CD150+)


title: RNAseq.mouse.CD8.Positive.Tcells.48HR.Rep2

value: CD8 Positive T-Cells

value: Primary T cells

value: 48 hour CD3/CD28 activated CD8 Positive T cell from mouse 1 replicate 2

value: 48 hour


title: MBH_P90_KTZ 3_2

value: KTZ 3 mg/kg bw/day


title: DMSO-treated WT replicate 3 [WT_DMSO3]

description: WT mice treated with control DMSO; freshly isolated

value: DMSO


title: RNAseq.mouse.CD8.Positive.Tcells.Day9.Chronic.Rep1

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from mouse 1 replicate 1

value: Day 9


title: Old_MSC_scRNAseq_23

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell

value: 24 month old


title: MBH_P90_KTZ 6_2

value: Sprague-Dawley

value: female

value: KTZ 6 mg/kg bw/day


title: RNAseq.mouse.CD8.Positive.Tcells.48HR.Rep1

value: 48 hour CD3/CD28 activated CD8 Positive T cell from mouse 1 replicate 1


title: RNAseq.mouse.CD8.Positive.Tcells.0HR.Rep2

value: Naïve CD8 Positive T cells from mouse 4 replicate 2

value: 0 hour


title: MBH_P90_KTZ 12_2

value: medio-basal hypothalamus

value: KTZ 12 mg/kg bw/day


title: Old_MSC_scRNAseq_26

value: Bone marrow


title: RNAseq.mouse.CD8.Positive.Tcells.72HR.Rep2

value: CD8 Positive T-Cells

value: Primary T cells

value: 72 hour CD3/CD28 activated CD8 Positive T cell from mouse 1 replicate 2

value: 72 hour


title: MBH_P90_KTZ 6_3


title: DMSO-treated WT replicate 2 [WT_DMSO2]

value: Wildtype

value: DMSO

value: HSC (CD48- LSK CD150+)


title: DMSO-treated WT replicate 1 [WT_DMSO1]


title: RNAseq.mouse.CD8.Positive.Tcells.0HR.Rep1

value: Naïve CD8 Positive T cells from mouse 4 replicate 1


title: RFP GFP double negative replicate 2 [DN2]

description: RFP EGFP double negative subset from RFP-EGFP-LC3 autophagy reporter mice; freshly isolated


title: Old_MSC_scRNAseq_25

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell

value: 24 month old


title: MBH_P90_KTZ 12_1

value: Sprague-Dawley

value: female


title: Old_MSC_scRNAseq_24


title: CutAndTag.mouse.CD8.Positive.Tcells.Day9.Transient.SS18

library_source: genomic

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
For Cut and Tag libraries, the CutRunTools pipeline (Zhu et al. 2020) was leveraged to perform read trimming, quality filtering, alignment, peak calling, and track building using default parameters
Assembly: hg19, mm10
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

growth_protocol: Human T cells were maintained in RPMI media supplemented with 10% FBS, 1% Pen/Strep, 1X GlutaMAX, 1X Non-essential Amino Acids, 1X Sodium Pyruvate and 10mM 2-Mercaptoethanol, and 30U/ml human IL2

extract_protocol:
Epicypher's CUT&Tag protocol was used for nuclear extraction and probing chromatin localization.
Epicypher's CUT&Tag protocol was used to ampllify tagmented DNA from isolated genomic DNA with 14 PCR cycles. DNA purification was completed  using AMPure beads (1.3X). Library size distribution was determined using TapeStation D1000.

treatment_protocol: Cells were activated with Human T-Activator CD3/CD28 Dynabeads (Thermo Fisher Scientific, Cat# 11132D) at 1:1 beads-to-cells ratio on Day 0, 3 and 6.

tag: chip antibody

value: 9 day transient CD3/CD28 activated CD8 Positive T cell from mouse 1


title: MBH_P90_DES 6_2

value: DES 6 ug/kg bw/day


title: RFP GFP double negative replicate 3 [DN3]


title: RFP GFP double negative replicate 1 [DN1]


title: RFP single positive replicate 3 [RFP3]

description: RFP single positive subset from RFP-EGFP-LC3 autophagy reporter mice; freshly isolated


title: RFP single positive replicate 2 [RFP2]


title: RFP GFP double positive replicate 3 [RFP_GFP3]

description: RFP EGFP double positive subset from RFP-EGFP-LC3 autophagy reporter mice; freshly isolated


title: RFP GFP double positive replicate 2 [RFP_GFP2]


title: Old_MSC_scRNAseq_20


title: MBH_P90_KTZ 3_1

value: medio-basal hypothalamus

value: KTZ 3 mg/kg bw/day


title: RNAseq.mouse.CD8.Positive.Tcells.72HR.Rep1

value: 72 hour CD3/CD28 activated CD8 Positive T cell from mouse 1 replicate 1


title: MBH_P22_KTZ 12_1

value: KTZ 12 mg/kg bw/day


title: CutAndTag.mouse.CD8.Positive.Tcells.Day9.Transient.IgG

value: CD8 Positive T-Cells

value: Primary T cells


title: Old_MSC_scRNAseq_21

value: Bone marrow


title: RFP GFP double positive replicate 1 [RFP_GFP1]


title: Old_MSC_scRNAseq_15


title: Old_MSC_scRNAseq_22


title: CutAndTag.mouse.CD8.Positive.Tcells.Day9.Transient.H3K27ac


title: Old_MSC_scRNAseq_19


title: CutAndTag.mouse.CD8.Positive.Tcells.Day9.Transient.SMARCA4

value: SMARCA4 (CST, #49360S)


title: Old_MSC_scRNAseq_18


title: MBH_P90_control_2

value: vehicle


title: MBH_P22_DES 6_1


title: Old_MSC_scRNAseq_14


title: CutAndTag.mouse.CD8.Positive.Tcells.Day9.Chronic.SMARCA4

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from mouse 1


title: MBH_P90_KTZ 6_1

value: KTZ 6 mg/kg bw/day


title: Old_MSC_scRNAseq_17

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell


title: RFP single positive replicate 1 [RFP1]

value: HSC (CD48- LSK CD150+)


title: CutAndTag.mouse.CD8.Positive.Tcells.Day9.Transient.PBRM1


title: ELAC2-/- TRAMP +/- 30weeks rep 3

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

data_processing:
Sequenced reads were trimmed with Trim Galore (0.4.1) using cutadapt (1.18) (with parameters: --paired --fastqc).
Trimmed reads were aligned to the mouse genome downloaded from GENCODE (GRCm38.p6, primary assembly) masked for nuclear mitochondrial sequences with the vM24 GENCODE mouse gene annotation using STAR (v2.7.3a) and a customised mitochondrial annotation.
The transcriptome alignments produced by STAR were quantified with Salmon(-l ISR --seqBias --gcBias) against a transcriptome FASTA file produced from the GENCODE gene annotation and genome sequence with gffread.
The output files were imported into R (3.6.3) (https://www.R-project.org) with tximport (1.14) 50 and were analysed for differential expression against wild types with DESeq2 (1.26) using apeglm (1.8.0) for effect size shrinkage estimation.
Assembly: GRCm38 (mm10)

source_name: ventral and lateral prostate lobes

growth_protocol: ELAC2 Pb-Cre (KO) and ELAC2 Ala537Thr (A537T) mice on a C56NL/6N background were generated by the Australian Phenomics Network (APN; Monash University, Melbourne, Australia) and breed with homozygous TRAMP mice to generate homozygous KO/heterozygous TRAMP and homozygous A537T/heterozygous TRAMP mice. Male age- and littermate-matched (10-week-old and 30-week-old) WT, WT-TRAMP, knockout (KO/KO-TRAMP) and point mutation (A537T/A537T-TRAMP) mice were housed in standard cages (45 cm x 29 cm x 12 cm) under a 12-hour light/dark schedule (lights on 7 a.m. to 7 p.m.) in controlled environmental conditions of 22± 2°C and 50 + 10% relative humidity. Mice were fed a normal chow diet (Rat and Mouse Chow, Specialty Feeds, Perth, Australia). Food and water were available ad libitum.

extract_protocol:
Individual prostate lobes were dissected as described previously by Zingiryan et al., 2017. Briefly, an OPMI 6-SFC Universal Microscope (Zeiss) was used to remove each prostate lobe to isolate high quality and pure tissue. Upon removal of the urogenital system from the sacrificed animal, all tissue was completely submerged in PBS. The seminal vesicles, bladder, urethra and surrounding connective or adipose tissue were removed and then the individual ventral, lateral, anterior and dorsal lobes were dissected and frozen in liquid nitrogen.
RNA was isolated from the ventral and lateral prostate lobes as recommended by Zingiryan et al., 2017, using the miRNeasy Mini kit (Qiagen) incorporating an on-column RNase-free DNase digestion to remove all DNA. RNA sequencing was performed on total prostate RNA from three of each control (WT or TRAMP) and the four mutant mouse lines by the Australian Genomic Research Facility (Melbourne, Australia). Sequencing was performed using the Illumina NovaSeq platform, according to the Illumina TruSeq RNA-Seq protocol and as we have done previously (Rudler et al., 2019).

value: ventral and lateral prostate lobes

value: 30 weeks

value: ELAC2-/- / TRAMP +/-


title: MBH_P22_KTZ 6_2

value: Sprague-Dawley

value: female


title: CutAndTag.mouse.CD8.Positive.Tcells.Day9.Chronic.IgG


title: ELAC2A537T TRAMP +/- 30weeks rep 3

value: ELAC2A537T / TRAMP +/-


title: MBH_P90_DES 3_1

value: medio-basal hypothalamus

value: DES 3 ug/kg bw/day


title: MBH_P22_KTZ 3_3

value: KTZ 3 mg/kg bw/day


title: Old_MSC_scRNAseq_11

value: 24 month old


title: ELAC2A537T TRAMP +/- 30weeks rep 2


title: ELAC2A537T TRAMP +/- 30weeks rep 1


title: CutAndTag.mouse.CD8.Positive.Tcells.Day9.Chronic.SS18

value: CD8 Positive T-Cells

value: Primary T cells


title: ELAC2-/- TRAMP +/- 30weeks rep 1


title: MBH_P22_KTZ 6_1


title: MBH_P90_DES 6_1

value: DES 6 ug/kg bw/day


title: Old_MSC_scRNAseq_10

value: Bone marrow


title: Old_MSC_scRNAseq_9


title: Old_MSC_scRNAseq_16


title: CutAndTag.mouse.CD8.Positive.Tcells.72HR.SMARCA4

value: SMARCA4 (CST, #49360S)

value: 72 hour CD3/CD28 activated CD8 Positive T cell from mouse 1


title: ELAC2+/+ TRAMP +/- 30weeks rep 3

value: ELAC2+/+ / TRAMP +/-


title: Old_MSC_scRNAseq_13

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell


title: CutAndTag.mouse.CD8.Positive.Tcells.Day9.Chronic.H3K27ac

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from mouse 1


title: CutAndTag.mouse.CD8.Positive.Tcells.Day9.Chronic.PBRM1


title: ELAC2+/+ TRAMP +/- 30weeks rep 1

value: ventral and lateral prostate lobes

value: 30 weeks


title: ELAC2-/- TRAMP +/- 10weeks rep 3

value: 10 weeks

value: ELAC2-/- / TRAMP +/-


title: ELAC2-/- TRAMP +/- 30weeks rep 2


title: Old_MSC_scRNAseq_12


title: CutAndTag.mouse.CD8.Positive.Tcells.72HR.SS18


title: MBH_P22_KTZ 3_1

value: Sprague-Dawley

value: female

value: medio-basal hypothalamus


title: MBH_P22_KTZ 3_2

value: KTZ 3 mg/kg bw/day


title: ELAC2+/+ TRAMP +/- 30weeks rep 2


title: MBH_P90_control_1

value: vehicle


title: 120hpf WT sibling Clutch 6

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing quality was assessed by using MultiQC v1.7 (https://multiqc.info)
Quality trimmed reads were aligned to the D. rerio GRCz10 reference genome using HISAT2 with default parameters
Quantfication were assessed using HTSeq
The resulting raw counts were used for differential gene expression analysis performend using DEseq2
Assembly: GRCz10
Supplementary files format and content: .txt file containing raw counts for each gene

organism: Danio rerio

source_name: liver, pooled

growth_protocol: Zebrafish larvae derived from incross of Tg(fabp10a:hUHRF1-EGFP)high+/- adults were kept in 10 cm petri dish at a density of 60 larvae/plate (30ml) in a 10:14 light/dark cycle.

extract_protocol:
Livers from between 20-30 larvae at  120 hpf were manually dissected and put in 500 ul of Trizol. RNA was extracted the same day of the liver dissection. Total RNA was treated by DNAseI (Thermo Scientific) for 30 minutes at 37C followed by RNA purification (RapidOut  DNA Removal Kit–Thermo Fisher Scientific). 80-120ng of total RNA was used for libarary prep. Samples were collected from pools of 5 independent clutches
RNA quantitiy and quality was assesed by Qbit. 80-120ng of total RNA was used for libarary prep. RiboZero was  used to remove ribosomal RNA and the remaining sample  was used for library preparation according to manufacturer’s  instructions (Illumina). Libraries were  sequenced on HiSeq 2500 (Illumina) to obtain 150 bp paired end  reads.

treatment_protocol: Zebrafish larvae were anethetized in tricane and the liver was dissected out between 120 and 122 hpf.

value: 120 hpf

value: 120hpf WT sibling of Tg(hUHRF1-EGF)high Clutch 6

value: 20 livers


title: 120hpf_WT_Clutch9

value: wild type sibling of Tg(hUHRF1-EGF)high_9


title: 120hpf_WT_ Clutch 8

value: wild type sibling of Tg(hUHRF1-EGF)high_8


title: Old_MSC_scRNAseq_8

value: Bone marrow

value: 24 month old


title: CutAndTag.mouse.CD8.Positive.Tcells.72HR.PBRM1

value: CD8 Positive T-Cells

value: Primary T cells

value: 72 hour CD3/CD28 activated CD8 Positive T cell from mouse 1


title: CutAndTag.mouse.CD8.Positive.Tcells.72HR.IgG


title: ELAC2-/- TRAMP +/- 10weeks rep 2

value: ventral and lateral prostate lobes

value: 10 weeks


title: Old_MSC_scRNAseq_6

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell


title: 120hpf WT sibling Clutch 4

value: 120hpf WT sibling of Tg(hUHRF1-EGF)high Clutch 4


title: CutAndTag.mouse.CD8.Positive.Tcells.72HR.H3K27ac


title: 120hpf_WT_Clutch 7

value: wild type sibling of Tg(hUHRF1-EGF)high_7


title: ELAC2-/- TRAMP +/- 10weeks rep 1

value: ELAC2-/- / TRAMP +/-


title: Old_MSC_scRNAseq_3


title: Old_MSC_scRNAseq_2


title: CutAndTag.mouse.CD8.Positive.Tcells.48HR.SS18

value: 48 hour CD3/CD28 activated CD8 Positive T cell from mouse 1


title: Old_MSC_scRNAseq_1


title: Old_MSC_scRNAseq_5


title: Old_MSC_scRNAseq_4


title: CutAndTag.mouse.CD8.Positive.Tcells.48HR.SMARCA4

value: SMARCA4 (CST, #49360S)


title: 120hpf WT sibling Clutch 5

value: 120 hpf

value: 120hpf WT sibling of Tg(hUHRF1-EGF)high Clutch 5


title: ELAC2+/+ TRAMP +/- 10weeks rep 2

value: ELAC2+/+ / TRAMP +/-


title: ELAC2A537T TRAMP +/- 10weeks rep 3

value: ELAC2A537T / TRAMP +/-


title: Young_MSC_scRNAseq_82

description: Single cell RNA-seq of bone marrow CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell from young mice

value: Bone marrow

value: 9 week old


title: ELAC2+/+ TRAMP +/- 10weeks rep 3


title: ELAC2A537T TRAMP +/- 10weeks rep 2


title: 120hpf_hUHRF1-high_Clutch 7

value: EGFP positive from Tg(hUHRF1-EGFP)high incross_7

value: 30 livers


title: Old_MSC_scRNAseq_7

value: 24 month old


title: ELAC2A537T TRAMP +/- 10weeks rep 1

value: ventral and lateral prostate lobes


title: CutAndTag.mouse.CD8.Positive.Tcells.48HR.IgG

value: CD8 Positive T-Cells

value: Primary T cells


title: CutAndTag.mouse.CD8.Positive.Tcells.48HR.PBRM1


title: CutAndTag.mouse.CD8.Positive.Tcells.0HR.SMARCA4

value: Naïve CD8 Positive T cells from mouse 3


title: Young_MSC_scRNAseq_81

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell


title: CutAndTag.mouse.CD8.Positive.Tcells.0HR.PBRM1


title: 120hpf_hUHRF1-high_Clutch 9

value: EGFP positive from Tg(hUHRF1-EGFP)high incross_9


title: CutAndTag.mouse.CD8.Positive.Tcells.48HR.H3K27ac

value: 48 hour CD3/CD28 activated CD8 Positive T cell from mouse 1


title: 120hpf hUHRF1-high Clutch 4

value: 120hpf EGFP positive from Tg(hUHRF1-EGF)high Clutch 4


title: ELAC2+/+ TRAMP +/- 10weeks rep 1

value: 10 weeks


title: ELAC2A537T 10weeks rep 2


title: Young_MSC_scRNAseq_80


title: CutAndTag.mouse.CD8.Positive.Tcells.0HR.IgG


title: Young_MSC_scRNAseq_78


title: ELAC2A537T 10weeks rep 1


title: ELAC2A537T 10weeks rep 3


title: Young_MSC_scRNAseq_79


title: CutAndTag.mouse.CD8.Positive.Tcells.0HR.H3K27ac


title: ATACseq.mouse.CD8.Positive.Tcells.Day9.Treatment.FHT1015

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
For the ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
Output BAM files were converted into BigWig track files using MACS2 and UCSC utilities in order to display coverage throughout the genome (in RPM).
Assembly: hg19, mm10
Supplementary files format and content: bigWig, broadPeak

extract_protocol:
Regions of tagmented genomic DNA were purified Qiagen's MinElute DNA purification Kit.
Custom PCR primers were used to amplify tagmented DNA for a total of 7 cycles to prevent over amplification.

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from mouse 1 treated with FHT1015 100 nM


title: Total_RNAseq_22Rv1_WildType_DMSO_4hours_Replicate1

first: Garrett

middle: Lee

last: Lindsey

state: CA

address: 10650 N Torrey Pines Rd

department: Chemistry

institute: Scripps Research

data_processing:
RNA-seq reads were mapped to hg38 using STAR Aligner
Alternative splicing (AS) analysis was completed using rMATs (v3.2.5)
genome build: HG19
processed data files format and content: rMATs table was used for splicing analysis

organism: Homo sapiens

source_name: Prostate carcinoma

growth_protocol: Cells were grown in vitro under standard culture conditions

extract_protocol:
QIAGEN Rneasy Plus mini
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: Samples were treated in biological triplicate in the presence of small molecules, as indicated, for 4 hours prior to collection.

value: Prostate carcinoma

value: 22Rv1 cells overexpressing Wild type NONO

tag: timepoint

value: 4 hours

value: DMSO


title: Total_RNAseq_22Rv1_WildType_DMSO_4hours_Replicate3


title: Total_RNAseq_22Rv1_WildType_10S_4hours_Replicate3

value: SKBG-1 (S), 20µM


title: ELAC2-/- 10weeks rep 1


title: Young_MSC_scRNAseq_76

value: Bone marrow

value: 9 week old


title: Total_RNAseq_22Rv1_WildType_DMSO_4hours_Replicate2


title: Young_MSC_scRNAseq_77


title: Total_RNAseq_22Rv1_WildType_10S_4hours_Replicate1


title: ATACseq.mouse.CD8.Positive.Tcells.72HR

value: 72 hour CD3/CD28 activated CD8 Positive T cell from mouse 1


title: ATACseq.mouse.CD8.Positive.Tcells.Day9.Transient.Rep2

value: CD8 Positive T-Cells

value: 9 day transient CD3/CD28 activated CD8 Positive T cell from mouse 1 replicate 2


title: Total_RNAseq_22Rv1_WildType_10S_4hours_Replicate2


title: Young_MSC_scRNAseq_75


title: ATACseq.mouse.CD8.Positive.Tcells.Day9.Chronic

value: Primary T cells

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from mouse 1


title: ELAC2+/+ 10weeks rep 3

value: ventral and lateral prostate lobes


title: ELAC2+/+ 10weeks rep 2


title: Total_RNAseq_22Rv1_WildType_10R_4hours_Replicate3

value: SKBG-1 (R), 20µM


title: ATACseq.mouse.CD8.Positive.Tcells.0HR

value: Naive CD8 Positive T cells from mouse 4


title: ATACseq.mouse.CD8.Positive.Tcells.48HR

value: 48 hour CD3/CD28 activated CD8 Positive T cell from mouse 1


title: Young_MSC_scRNAseq_72

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell


title: ATACseq.mouse.CD8.Positive.Tcells.Day9.Treatment.Compound14

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from mouse 1 treated with compound 14 100 nM


title: ELAC2-/- 10weeks rep 2

value: 10 weeks


title: Young_MSC_scRNAseq_71


title: Total_RNAseq_22Rv1_EmptyVector_DMSO_4hours_Replicate3

value: Prostate carcinoma

value: 22Rv1 cells overexpressing Empty Vector

value: 4 hours


title: GSK3368715-3

first: Chen

last: Chu

state: MA

address: 450 Brookline Ave, Smith 914

institute: Dana-Farber Cancer Institute

description:
DEG_GSKvsCtrl.csv
normalized_counts_PRMT1i.csv

data_processing:
The data were aligned to mm10 using Salmon 1.4.0 (using the default parameters)
The DEGs were calculated using DESeq2.
Assembly: mm10
Supplementary files format and content: csv files containing normalized counts and DEGs

source_name: cultured cells

extract_protocol:
Total RNAs were extracted using QIAsheredder (Qiagen, #79656) and Qiagen RNeasy mini kit (Qiagen. #74106).
Library preparation (Roche, Kapa mRNAseq Hyper prep) and sequencing analysis (Illumina NextSeq 500 Paired-end 2 x 150 bp) were performed at the Molecular Biology Core facility in Dana-Farber Cancer Institute.

value: cultured cells

value: mouse colon tumor cells

value: WT


title: Young_MSC_scRNAseq_74

value: Bone marrow

value: 9 week old


title: GSK3368715-2


title: CutAndTag.mouse.CD8.Positive.Tcells.0HR.SS18

value: CD8 Positive T-Cells

value: Primary T cells

value: Naïve CD8 Positive T cells from mouse 3


title: GSK3368715-1


title: Young_MSC_scRNAseq_73


title: ELAC2A537T 30weeks rep 3

value: ventral and lateral prostate lobes

value: 30 weeks


title: Total_RNAseq_22Rv1_WildType_10R_4hours_Replicate1

value: 22Rv1 cells overexpressing Wild type NONO

value: SKBG-1 (R), 20µM


title: ELAC2A537T 30weeks rep 2


title: Total_RNAseq_22Rv1_WildType_10R_4hours_Replicate2


title: ELAC2A537T 30weeks rep 1


title: Young_MSC_scRNAseq_69

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell


title: Young_MSC_scRNAseq_70


title: 120hpf hUHRF1-high Clutch 6

value: 120 hpf

value: 120hpf EGFP positive from Tg(hUHRF1-EGF)high Clutch 6

value: 27 livers


title: ELAC2-/- 30weeks rep 3


title: ELAC2-/- 30weeks rep 2


title: Total_RNAseq_22Rv1_EmptyVector_DMSO_4hours_Replicate2

value: Prostate carcinoma

value: 22Rv1 cells overexpressing Empty Vector

value: 4 hours

value: DMSO


title: 120hpf_hUHRF1-high_Clutch 8

value: EGFP positive from Tg(hUHRF1-EGFP)high incross_8

value: 30 livers


title: ELAC2+/+ 10weeks rep 1

value: 10 weeks


title: Young_MSC_scRNAseq_66

value: Bone marrow

value: 9 week old


title: ELAC2-/- 30weeks rep 1

value: ventral and lateral prostate lobes


title: MS023-2

description:
DEG_MS023vsCtrl.csv
normalized_counts_PRMT1i.csv

value: cultured cells

value: mouse colon tumor cells

value: WT


title: Young_MSC_scRNAseq_68

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell


title: Total_RNAseq_22Rv1_EmptyVector_DMSO_4hours_Replicate1


title: MS023-3


title: Total_RNAseq_22Rv1_EmptyVector_10S_4hours_Replicate3

value: SKBG-1 (S), 20µM


title: ELAC2+/+ 30weeks rep 3

value: 30 weeks


title: MS023-1


title: Total_RNAseq_22Rv1_EmptyVector_10S_4hours_Replicate1


title: Total_RNAseq_22Rv1_EmptyVector_10S_4hours_Replicate2


title: Young_MSC_scRNAseq_64


title: Control-3

description:
DEG_GSKvsCtrl.csv
DEG_MS023vsCtrl.csv
normalized_counts_PRMT1i.csv

value: Vehicle


title: Total_RNAseq_22Rv1_EmptyVector_10R_4hours_Replicate3

value: Prostate carcinoma

value: SKBG-1 (R), 20µM


title: ELAC2+/+ 30weeks rep 2


title: Control-2


title: Young_MSC_scRNAseq_67


title: ELAC2+/+ 30weeks rep 1


title: Control-1


title: Young_MSC_scRNAseq_63


title: ELAC2A537T 10weeks miRNA rep 3

data_processing:
Paired-end sequenced reads were merged, removing adapters, with BBMerge (adapter=default mininsert=18 mininsert0=18 k=31 ecct).
Merged reads were mapped (-e -h -I -j -m -q) and quantified (-W) with mirDeep2 v0.1.3 against the GRCm38 mouse genome and mirBase mouse release 22.1 mature and precursor miRNA sequences.
Duplicate entries in the miRNA count table were summed and miRNAs with unique names but identical sequences were also summed under a merged miRNA name, to ensure that each unique miRNA sequence was represented only once in the count table.
Differential expression changes were tested with DESeq2, using the apeglm shrinkage estimator.
Assembly: GRCm38 (mm10)

extract_protocol:
Individual prostate lobes were dissected as described previously by Zingiryan et al., 2017. Briefly, an OPMI 6-SFC Universal Microscope (Zeiss) was used to remove each prostate lobe to isolate high quality and pure tissue. Upon removal of the urogenital system from the sacrificed animal, all tissue was completely submerged in PBS. The seminal vesicles, bladder, urethra and surrounding connective or adipose tissue were removed and then the individual ventral, lateral, anterior and dorsal lobes were dissected and frozen in liquid nitrogen.
Sequencing was performed using the Illumina NovaSeq platform, prepared with the Illumina TruSeq Small RNA-Seq library prep kit according to manufacturers instructions.


title: Young_MSC_scRNAseq_61


title: Young_MSC_scRNAseq_62


title: Total_RNAseq_22Rv1_EmptyVector_10R_4hours_Replicate1

value: 22Rv1 cells overexpressing Empty Vector

value: 4 hours


title: ELAC2A537T 10weeks miRNA rep 2


title: Total_RNAseq_22Rv1_C145S_DMSO_4hours_Replicate3

value: 22Rv1 cells overexpressing NONO C145S

value: DMSO


title: Young_MSC_scRNAseq_60


title: Young_MSC_scRNAseq_65


title: Total_RNAseq_22Rv1_EmptyVector_10R_4hours_Replicate2


title: shPRM1-3

description:
DEG_shPRMT1vsCtrl.csv
normalized_counts_PRMT1kd

value: Prmt1 knockdown


title: shPRM1-1


title: ELAC2-/- 10weeks miRNA rep 3

value: 10 weeks


title: shControl-3

value: Ctrl knockdown


title: shPRM1-2


title: ELAC2A537T 10weeks miRNA rep 1

value: ventral and lateral prostate lobes


title: Total_RNAseq_22Rv1_C145S_DMSO_4hours_Replicate1


title: Young_MSC_scRNAseq_57

value: Bone marrow

value: 9 week old


title: Young_MSC_scRNAseq_59


title: ELAC2-/- 10weeks miRNA rep 2


title: shControl-2

value: cultured cells

value: mouse colon tumor cells


title: ELAC2-/- 10weeks miRNA rep 1


title: ELAC2+/+ 10weeks miRNA rep 3


title: shControl-1


title: Total_RNAseq_22Rv1_C145S_10S_4hours_Replicate2

value: SKBG-1 (S), 20µM


title: Young_MSC_scRNAseq_55

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell


title: Total_RNAseq_22Rv1_C145S_10S_4hours_Replicate1


title: Total_RNAseq_22Rv1_C145S_10R_4hours_Replicate3


title: Young_MSC_scRNAseq_56


title: NHD13 HSPC shSF3B1 RNA-seq #3

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

data_processing:
RNA-seq datasets were aligned to the mm10 mouse genome using STAR  with the parameter outFilterMultimapNmax set to 1.
Bioconductor package DESeq2 was used to analyze differential gene expression.
Assembly: mm10
Supplementary files format and content: bigwig files

source_name: NHD13 HSPCs

growth_protocol: Primary cKIT-enriched hematopoietic stem and progenitor cells (HSPCs) from pre-leukemic NUP98-HOXD13 mice were cultured in SFEM medium with cyotkines (Flt-3, TPO, IL3) + 1% Penicilin/Streptomycin under standard conditions (5% CO2 humified chamber).

extract_protocol:
Total RNA from the cells was prepared using the Direct-zol™ RNA MicroPrep (Zymo Research Corporation) according to manufacturer's protocol. DNAse in column treatment was performed according to guidelines of the producer. Integrity and quantity of the resulting RNA was confirmed by RNA Nano LabChip Bioanalyzer run (Agilent).
Libraries were constructed from 300 ng of total RNA using the TruSeq Stranded Total RNA LT Sample Prep (with  Ribo-Zero treatment and single indexing). Quality of libraries was ensured with Bioanalyzer High Sensitivity DNA kit (Agilent). Sequencing was performed using the NextSeq 500 High Output v2 kit (75 cycles) Illumina platform.

treatment_protocol: cKIT enriched NHD-13-derived HSPCs were transduced with lentiviral vectors harboring shCTR or shSf3b1 on retronectin coated plates at 2mln/condition. Afterwards, cells were washed with PBS, spun down and lysed in Trizol reagent.

tag: source

value: transgenic mice


title: Total_RNAseq_22Rv1_C145S_DMSO_4hours_Replicate2

value: Prostate carcinoma


title: ELAC2+/+ 10weeks miRNA rep 1


title: ELAC2-/- 10weeks rep 3


title: NHD13 HSPC shSF3B1 RNA-seq #2


title: Young_MSC_scRNAseq_53


title: Total_RNAseq_22Rv1_C145S_10R_4hours_Replicate2

value: SKBG-1 (R), 20µM


title: Young_MSC_scRNAseq_54


title: ELAC2A537T 30weeks miRNA rep 3

value: 30 weeks


title: Total_RNAseq_22Rv1_C145S_10S_4hours_Replicate3

value: 4 hours


title: NHD13 HSPC shSF3B1 RNA-seq #1


title: Total_RNAseq_22Rv1_C145S_10R_4hours_Replicate1

value: 22Rv1 cells overexpressing NONO C145S


title: Young_MSC_scRNAseq_58


title: ELAC2A537T 30weeks miRNA rep 2


title: NHD13 HSPC WT RNA-seq #2

value: shCTR


title: Total_RNAseq_22Rv1_sgNONO_sgSFPQ_72 hours_Replicate3

data_processing:
Transcript abundance was quantified using Salmon [v1.3.0] with GENCODE v37 annotation.
Gene level quantification was performed using tximeta [v1.8.4].
Differential gene expression was analyzed by DESeq2 [v1.30.1]
genome build: HG19
processed data files format and content: gene counts

treatment_protocol: Samples were treated in biological triplicate in the presence of sgRNA targeting Control, PSPC1, or SFPQ for 72 hours prior to collection.

value: sgNONO 22Rv1 cells

value: 72 hours

value: sgSFPQ


title: Young_MSC_scRNAseq_52


title: Young_MSC_scRNAseq_51


title: NHD13 HSPC WT RNA-seq #3

value: shSTR


title: ELAC2A537T 30weeks miRNA rep 1

value: ventral and lateral prostate lobes


title: ELAC2+/+ 10weeks miRNA rep 2

value: 10 weeks


title: NHD13 HSPC WT RNA-seq #1


title: Total_RNAseq_22Rv1_sgNONO_sgSFPQ_72 hours_Replicate2


title: Young_MSC_scRNAseq_50

value: Bone marrow

value: 9 week old


title: ELAC2-/- 30weeks miRNA rep 2


title: Total_RNAseq_22Rv1_sgNONO_sgPSPC1_72 hours_Replicate3


title: ELAC2-/- 30weeks miRNA rep 3


title: aHSPC_Tompos_transplant

first: Anna

last: Konturek-Ciesla

state: Skane

address: Klinikgatan 26, BMC B12

department: Laboratory Medicine

description:
scRNA-seq
3' RNA

data_processing:
scRNAseq dataset processing: Libraries were processed using Cellranger version 3 pipeline, demultiplexed based on 10x Chromium and HTO UMIs and aligned to custom reference genome. Dataset filtering was performed in R, v. 4.0.2 with the following parameters: percent.mt < 5%, nFeature_RNA > 200, nFeature_RNA < 6000 and nCount_RNA < 1000, nCount_RNA > 40000. For the HTO libraries, separate Seurat object containing HTO data was generated and normalized using parameters assay=”HTO” and normalization.method=”CLR” (centred log-ratio transformation). The cells were then demultiplexed based on HTO UMIs and assigned for singlets. The normalization was done across RNA counts for each cell using Seurat package v3.2.3. Libraries were normalized to 10,000 reads, natural log-normalised and scaled to unit variance with zero mean for downstream analyses.
scRNAseq dataset integration: Dataset integration and batch correction were performed using the BBKNN v1.4.0 algorithm. For that, files in the phyton loom format were created for each dataset of all experiments and concatenated to generate the integrated data object. The raw read counts of the integrated dataset were next normalised with Scanpy toolkit, using scanpy.pp.normalize_per_cell and scanpy.pp.log1p functions and variable genes were detected and regressed out for ’n_counts’, with scanpy.pp.regress_out function. Last, the data was re-scaled and the BBKNN batch correction was applied for batch_key Experiment using function scanpy.external.pp.bbknn.
scRNAseq dimensionality reduction, clustering and marker detection: Dimensionality reduction was implemented using the UMAP algorithm with the scanpy.tl.umap function. All generated UMAPs use log10-normalised raw data. Next, Louvain clustering was applied with scanpy.tl.louvain using default parameters. Two clusters were further sub-clustered using Kmeans function implemented in the sklearn package. Individual cluster markers were identified using the FindMarkers function in Seurat, applying the logistic regression model.
CITEseq dataset processing: After the cDNA and HTO libraries from CITEseq experiment (Sca1pos_CITEseq and Sca1neg_CITEseq samples) were demultiplexed using Cellranger pipeline, the Undetermined fastq files from each library were used as input for the CITE-seq-count v1.4.4 tool to quantify the ADTs. The antibody specific TotalSeqA barcodes were used as the reference and additional parameters were set for the last nucleotide of the cell barcode, first and last nucleotides of the UMI in the read 1 (-cbl 16 -umif 17 -umil 28).
Genome_build: Reference genome was generated using the GRCm38.p6 (mm10) mouse genome and a custom fasta sequence for the tdTomato-labelled marker gene.
Supplementary_files_format_and_content: cellranger output raw_feature_bc_matrix

source_name: Aged Bone Marrow

extract_protocol:
For scRNAseq; cells were FACS sorted and directly subjected to 10x genomics 3' RNA sequencing library preparation. For CITEseq; cell were stained with CITEseq antibodies, FACS sorted and subjected to 10x genomics 3' RNA sequencing library preparation.
For scRNAseq; libraries were generated accoring to 10x genomics 3’ v3 or v2 kit. For CITEseq; libraries were generated accoring to 10x genomics 3’ v3 kit with the addition of CITEseq protocol. All libraries were sequenced on the Illumina NextSeq 500 following the manufacturer's protocol.

treatment_protocol: FACS sorted

value: Aged Bone Marrow

tag: population


title: ELAC2-/- 30weeks miRNA rep 1


title: Young_MSC_scRNAseq_48

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell


title: Total_RNAseq_22Rv1_sgNONO_sgPSPC1_72 hours_Replicate1


title: Young_MSC_scRNAseq_47


title: aHSPC_Tompos

description:
scRNA-seq
3' RNA


title: yHSPC_Tompos_transplant

description:
scRNA-seq
3' RNA

source_name: Young Bone Marrow

value: Young Bone Marrow


title: Young_MSC_scRNAseq_49


title: ELAC2+/+ 30weeks miRNA rep 3


title: aHSPC_Tomneg

description:
scRNA-seq
3' RNA


title: Young_MSC_scRNAseq_46


title: ELAC2+/+ 30weeks miRNA rep 2


title: Young_MSC_scRNAseq_45


title: Total_RNAseq_22Rv1_sgNONO_sgCtrl_72 hours_Replicate3

value: Prostate carcinoma

value: sgCtrl


title: Total_RNAseq_22Rv1_sgNONO_sgCtrl_72 hours_Replicate2


title: ELAC2+/+ 30weeks miRNA rep 1

value: 30 weeks


title: Young_MSC_scRNAseq_44


title: Total_RNAseq_22Rv1_sgNONO_sgPSPC1_72 hours_Replicate2


title: yHSPC_Tompos

description:
scRNA-seq
3' RNA


title: Sca1neg_scRNAseq

description:
scRNA-seq
3' RNA

source_name: Bone Marrow

value: Bone Marrow


title: Total_RNAseq_22Rv1_sgNONO_sgSFPQ_72 hours_Replicate1


title: ELAC2-/- TRAMP +/- 30weeks miRNA rep 3

value: ELAC2-/- / TRAMP +/-


title: Young_MSC_scRNAseq_43


title: ELAC2-/- TRAMP +/- 30weeks miRNA rep 2


title: Sca1pos_scRNAseq

description:
scRNA-seq
3' RNA


title: Total_RNAseq_22Rv1_sgControl_sgSFPQ_72 hours_Replicate3

value: sgControl 22Rv1 cells


title: ELAC2-/- TRAMP +/- 30weeks miRNA rep 1


title: Sca1pos_CITEseq

description:
CITEseq
3' RNA+epitope

data_processing:
Library strategy: CITE-seq
scRNAseq dataset processing: Libraries were processed using Cellranger version 3 pipeline, demultiplexed based on 10x Chromium and HTO UMIs and aligned to custom reference genome. Dataset filtering was performed in R, v. 4.0.2 with the following parameters: percent.mt < 5%, nFeature_RNA > 200, nFeature_RNA < 6000 and nCount_RNA < 1000, nCount_RNA > 40000. For the HTO libraries, separate Seurat object containing HTO data was generated and normalized using parameters assay=”HTO” and normalization.method=”CLR” (centred log-ratio transformation). The cells were then demultiplexed based on HTO UMIs and assigned for singlets. The normalization was done across RNA counts for each cell using Seurat package v3.2.3. Libraries were normalized to 10,000 reads, natural log-normalised and scaled to unit variance with zero mean for downstream analyses.
scRNAseq dataset integration: Dataset integration and batch correction were performed using the BBKNN v1.4.0 algorithm. For that, files in the phyton loom format were created for each dataset of all experiments and concatenated to generate the integrated data object. The raw read counts of the integrated dataset were next normalised with Scanpy toolkit, using scanpy.pp.normalize_per_cell and scanpy.pp.log1p functions and variable genes were detected and regressed out for ’n_counts’, with scanpy.pp.regress_out function. Last, the data was re-scaled and the BBKNN batch correction was applied for batch_key Experiment using function scanpy.external.pp.bbknn.
scRNAseq dimensionality reduction, clustering and marker detection: Dimensionality reduction was implemented using the UMAP algorithm with the scanpy.tl.umap function. All generated UMAPs use log10-normalised raw data. Next, Louvain clustering was applied with scanpy.tl.louvain using default parameters. Two clusters were further sub-clustered using Kmeans function implemented in the sklearn package. Individual cluster markers were identified using the FindMarkers function in Seurat, applying the logistic regression model.
CITEseq dataset processing: After the cDNA and HTO libraries from CITEseq experiment (Sca1pos_CITEseq and Sca1neg_CITEseq samples) were demultiplexed using Cellranger pipeline, the Undetermined fastq files from each library were used as input for the CITE-seq-count v1.4.4 tool to quantify the ADTs. The antibody specific TotalSeqA barcodes were used as the reference and additional parameters were set for the last nucleotide of the cell barcode, first and last nucleotides of the UMI in the read 1 (-cbl 16 -umif 17 -umil 28).
Genome_build: Reference genome was generated using the GRCm38.p6 (mm10) mouse genome and a custom fasta sequence for the tdTomato-labelled marker gene.
Supplementary_files_format_and_content: cellranger output raw_feature_bc_matrix


title: ELAC2A537T TRAMP +/- 30weeks miRNA rep 3

value: ELAC2A537T / TRAMP +/-


title: Total_RNAseq_22Rv1_sgControl_sgPSPC1_72 hours_Replicate3

value: 72 hours


title: Sca1neg_CITEseq

description:
CITEseq
3' RNA+epitope


title: Total_RNAseq_22Rv1_sgControl_sgSFPQ_72 hours_Replicate1

value: sgSFPQ


title: Total_RNAseq_22Rv1_sgControl_sgPSPC1_72 hours_Replicate2


title: Young_MSC_scRNAseq_41


title: Young_MSC_scRNAseq_39


title: ELAC2A537T TRAMP +/- 30weeks miRNA rep 1


title: Young_MSC_scRNAseq_38


title: phot_HL rep 3

city: Grenoble

first: Dimitris

last: Petroutsos

address: 17 rue des Martyrs

country: France

institute: 4University of Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV

data_processing:
Reads were mapped to the C. reinhardtii reference genome (JGI v.5.5) using the STAR aligner v.2.5.3a with default parameters.
The obtained BAM files were analyzed using HTSseq-count v.0.6.p1 to generate raw count files.
Assembly: C. reinhardtii JGI v5.5
Supplementary files format and content: Tab-seperated text file with raw counts from HTSseq output. Library names as column names and gene locus IDs as row names.

organism: Chlamydomonas reinhardtii

source_name: phot

growth_protocol: C. reinhardtii strain CC-125 and the mutant strain phot were grown under 15 µmol photons m-2 s-1 in Tris-acetate-phosphate (TAP) media at 23 oC in Erlenmeyer flasks shaken at 125 rpm.

extract_protocol:
Freshly obtained samples were lysed using Tri-reagent (Sigma). After double chloroform extraction the aqueous phase was transferred to a RNeasy Mini-Kit column (Quiagen) and processed according to the manufacturers guide.
TruSeq LT libraires stranded mRNA

treatment_protocol: For RNA sampling cells were transferred to Sueoka's high salt medium (HSM) at 1 million cells mL-1, 5 µmol photons m-2 s-1. Part of the culture was subjected to high light irradiance (300µmol  photons m-2 s-1) . RNA samples were taken before high light treatment and after 60 min of high light irradiance.

value: phot

tag: culture media

value: HSM

value: PHOT KO

tag: light irradiance_(photons_m^-2_s-^1)


title: phot_HL rep 1


title: Total_RNAseq_22Rv1_sgControl_sgPSPC1_72 hours_Replicate1

tag: tissue


title: wt_HL rep 3

value: wt


title: ELAC2+/+ TRAMP +/- 30weeks miRNA rep 3

value: ventral and lateral prostate lobes

value: ELAC2+/+ / TRAMP +/-


title: phot_HL rep 2


title: Total_RNAseq_22Rv1_sgControl_sgCtrl_72 hours_Replicate3

tag: cell type


title: ELAC2A537T TRAMP +/- 30weeks miRNA rep 2

tag: genotype


title: Young_MSC_scRNAseq_42

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell

value: Bone marrow

value: 9 week old


title: ELAC2+/+ TRAMP +/- 30weeks miRNA rep 2


title: Young_MSC_scRNAseq_36


title: Total_RNAseq_22Rv1_sgControl_sgCtrl_72 hours_Replicate2

value: Prostate carcinoma

tag: treatment

value: sgCtrl


title: wt_HL rep 2


title: Total_RNAseq_22Rv1_sgControl_sgSFPQ_72 hours_Replicate2


title: Total_RNAseq_22Rv1_sgNONO_sgCtrl_72 hours_Replicate1

value: sgNONO 22Rv1 cells


title: wt_HL rep 1


title: Young_MSC_scRNAseq_40

tag: strain


title: Total_RNAseq_22Rv1_sgControl_sgCtrl_72 hours_Replicate1


title: ELAC2-/- TRAMP +/- 10weeks miRNA rep 2

value: 10 weeks

value: ELAC2-/- / TRAMP +/-


title: Total_RNAseq_MCF7_sgNONO_4hours_SKBG1-S_Replicate3

data_processing:
For differential expression:
Transcript abundance was quantified using Salmon [v1.3.0] with GENCODE v37 annotation.
Gene level quantification was performed using tximeta [v1.8.4].
Differential gene expression was analyzed by DESeq2 [v1.30.1].
For splicing analysis, 22Rv1 data only:
RNA-seq reads were mapped to hg38 using STAR Aligner.
Alternative splicing (AS) analysis was completed using rMATs (v3.2.5).
Assembly: hg19
Supplementary files format and content: *.csv: Gene counts were used for differential expression.
Supplementary files format and content: *.xlsx: rMATs table was used for splicing analysis.

source_name: Breast carcinoma

growth_protocol: Cells were grown in vitro under standard culture conditions.

extract_protocol:
QIAGEN RNeasy Plus mini.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

tag: sg

value: sgNONO

tag: treatment+dose

value: SKBG-1 (S), 5uM

value: 4 hours

tag: rna library prep

value: Total mRNA


title: phot_LL rep 2

tag: cell line

value: phot

value: HSM


title: Young_MSC_scRNAseq_37

data_processing:
Sequencing was performed using an Illumina HiSeq2000 system. Sequence reads were aligned to the murine genome mm9 using RNA-seq Unified Mapper (RUM) version 2.0.4, and transcripts were assembled using Cufflinks version 2.1.1.
Assembly: mm9
Supplementary files format and content: Tab-separated values files and matrix files

tag: age


title: Young_MSC_scRNAseq_34


title: Total_RNAseq_MCF7_sgNONO_4hours_SKBG1-S_Replicate2


title: ELAC2-/- TRAMP +/- 10weeks miRNA rep 1


title: phot_LL rep 1

value: PHOT KO


title: Total_RNAseq_MCF7_sgNONO_4hours_SKBG1-S_Replicate1


title: ELAC2A537T TRAMP +/- 10weeks miRNA rep 3

value: ventral and lateral prostate lobes

value: ELAC2A537T / TRAMP +/-


title: ELAC2+/+ TRAMP +/- 30weeks miRNA rep 1

value: 30 weeks

value: ELAC2+/+ / TRAMP +/-


title: wt_LL rep 2

value: wt


title: Young_MSC_scRNAseq_32

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell

value: Bone marrow

value: 9 week old


title: Young_MSC_scRNAseq_30


title: Total_RNAseq_MCF7_sgNONO_4hours_SKBG1-R_Replicate2

value: SKBG-1 (R), 5uM


title: ELAC2A537T TRAMP +/- 10weeks miRNA rep 2

value: 10 weeks


title: ELAC2A537T TRAMP +/- 10weeks miRNA rep 1


title: Young_MSC_scRNAseq_35


title: Total_RNAseq_MCF7_sgNONO_4hours_SKBG1-R_Replicate3

value: sgNONO


title: wt_LL rep 1


title: Young_MSC_scRNAseq_29


title: phot_LL rep 3


title: Total_RNAseq_MCF7_sgNONO_4hours_SKBG1-R_Replicate1


title: Young_MSC_scRNAseq_33


title: ELAC2+/+ TRAMP +/- 10weeks miRNA rep 3


title: Total_RNAseq_MCF7_sgNONO_4hours_DMSO_Replicate3

value: DMSO


title: ELAC2-/- TRAMP +/- 10weeks miRNA rep 3

value: ELAC2-/- / TRAMP +/-


title: ELAC2+/+ TRAMP +/- 10weeks miRNA rep 2


title: Young_MSC_scRNAseq_28


title: Young_MSC_scRNAseq_27


title: Total_RNAseq_MCF7_sgNONO_4hours_DMSO_Replicate2

value: 4 hours

value: Total mRNA


title: ELAC2+/+ TRAMP +/- 10weeks miRNA rep 1


title: wt_LL rep 3

value: HSM


title: Young_MSC_scRNAseq_31


title: Young_MSC_scRNAseq_26


title: Total_RNAseq_MCF7_sgNONO_4hours_DMSO_Replicate1


title: Young_MSC_scRNAseq_25


title: Total_RNAseq_MCF7_sgControl_4hours_SKBG1-S_Replicate3

value: sgControl

value: SKBG-1 (S), 5uM


title: Young_MSC_scRNAseq_24


title: Young_MSC_scRNAseq_23


title: Total_RNAseq_MCF7_sgControl_4hours_SKBG1-R_Replicate3


title: Young_MSC_scRNAseq_22


title: Total_RNAseq_MCF7_sgControl_4hours_SKBG1-S_Replicate1


title: Young_MSC_scRNAseq_21


title: Total_RNAseq_MCF7_sgControl_4hours_SKBG1-R_Replicate2


title: Young_MSC_scRNAseq_20


title: Total_RNAseq_MCF7_sgControl_4hours_SKBG1-R_Replicate1


title: Young_MSC_scRNAseq_19


title: Total_RNAseq_MCF7_sgControl_4hours_DMSO_Replicate3


title: Total_RNAseq_MCF7_sgControl_4hours_DMSO_Replicate2


title: Young_MSC_scRNAseq_17


title: Total_RNAseq_MCF7_sgControl_4hours_SKBG1-S_Replicate2


title: Young_MSC_scRNAseq_16


title: Total_RNAseq_22Rv1_sgNONO_4hours_SKBG1-S_Replicate3

value: SKBG-1 (S), 20uM


title: Young_MSC_scRNAseq_15


title: P11

city: Shanghai

first: Shaocong

last: Mo

address: 12th Urumqi middle road

country: China

institute: Huashan Hospital, Fudan University

description: Colonic mucosa

data_processing:
fastqc was used for quanlity control
Trim-galore was used for filtering
Hisat2 was used for blasting to GRh38
samtools was used for sorting
featurecount was used for counting
Assembly: GRh38.release105
Supplementary files format and content: counts

source_name: Colon

extract_protocol:
total RNA was extracted by Trizol
Poly (A) RNA from 1 mg total mRNA were used to generate the cDNA libraries, respectively, according to TruSeq RNA Sample Prep Kit protocol.

value: Colon


title: P9

description: Colonic mucosa


title: Young_MSC_scRNAseq_18

extract_protocol:
Young and old MSCs (CD45-Ter119-CD31-CD140a+LepR+) were isolated with a FACSAria II cell sorter from 10-week-old and 2-year-old mice, respectively. Single-cell cDNA synthesis was performed with a C1 Single-Cell Auto Prep System (Fluidigm)
Reverse transcription and preamplification were performed according to the manufacturer’s instructions using a SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (Clontech) and a C1 Single-Cell Auto Prep Reagent Kit for mRNA Seq (Fluidigm). For RNA controls, tubes #1, #4, and #7 of ArrayControl RNA Spikes (Thermo Fisher Scientific) were mixed at a ratio of 100:10:1, and the RNA Spikes mixture was diluted 1:10000 in C1 Loading Reagent (Fluidigm). Sorted MSCs were diluted in Suspension Reagent to ~1000 cells/µL and loaded into a C1-Single-Cell Auto Prep IFC for mRNA-seq (5-10 μm). After loading the cells, the integrated fluidic circuit (IFC) was observed microscopically using an IN Cell Analyzer 6000 (GE Healthcare) to ensure that single cells were captured in each well. Wells with 0, >1, or shrunken cells were excluded. A total of 83 of the 96 wells for young MSCs and 79 of the 96 wells for old MSCs were considered valid. The thermal cycling conditions for cell lysis, reverse transcription, and preamplification were as follows: 72°C for 3 min, 4°C for 10 min, and 25°C for 10 min for cell lysis; 42°C for 90 min and 70°C for 10 min for reverse transcription; 95°C for 1 min and 5 cycles at 95°C for 20 s, 58°C for 4 min, and 68°C for 6 min, 9 cycles at 95°C for 20 s, 64°C for 30 s, and 68°C for 6 min, 7 cycles at 95°C for 30 s, 64°C for 30 s, and 68°C for 7 min, and 1 cycle at 72°C for 10 min for preamplification; and holding at 4°C until harvest. Amplified cDNA (approximately 3.5 μL) from each well was diluted with 10 μL of C1 DNA Dilution Reagent (Fluidigm) and frozen at -30°C until use. The sample in each well was further diluted 1:2 with C1 Harvest Reagent and subjected to tagmentation and Illumina sequencing library preparation using a Nextera XT DNA Sample Preparation Kit (Illumina) and a Nextera XT DNA Sample Preparation Index Kit (96 indices, Illumina). Then, 2.5 μL of Tagment DNA Buffer, 1.25 μL of Amplification Tagment Mix and 1.25 μL of the diluted cDNA sample were mixed and incubated at 55°C for 10 min in a thermal cycler. The tagmentation reaction was then stopped by adding 1.25 μL of neutralizing buffer (NT buffer). Next, the samples were subjected to PCR amplification. A 6.25 μL aliquot of each sample was mixed with NPM buffer, and 1.25 μL each of Index Primer 1 and Index Primer 2. The thermal cycling conditions were as follows: 72°C for 3 min, 95°C for 30 s, 12 cycles at 95°C for 10 s, 55°C for 30 s, and 72°C for 1 min, and 1 cycle at 72°C for 5 min. A 1 μL aliquot from each well of amplified DNA was processed by two rounds of mixing and cleanup with AMPure XP beads (Beckman Coulter), and DNA was then eluted with 144 μL of DNA suspension buffer.


title: P12

description: Colonic mucosa


title: P10

description: Colonic mucosa


title: P8

description: Colonic mucosa


title: Young_MSC_scRNAseq_13


title: Total_RNAseq_22Rv1_sgNONO_4hours_SKBG1-S_Replicate1


title: Total_RNAseq_22Rv1_sgNONO_4hours_SKBG1-R_Replicate3

value: SKBG-1 (R), 20uM


title: Total_RNAseq_22Rv1_sgNONO_4hours_SKBG1-R_Replicate2


title: 26_30_100-53_v1

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Reads were aligned to the Human Reference Genome Sequence and transcripts annotated with  Genome Reference Consortium Build 38 (GRCh38) using STAR software (v2·5·2b).
Unsorted bam files were sorted and indexed using samtools and converted to HTSeq-count format.
Estimates of gene-wise and isoform-wise expression levels for individual genes were performed using the R package DESeq2 with R version 3.5.0
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: rectal pinch biopsy

growth_protocol: Rectal mucosal tissue biopsies were obtained via rigid sigmoidoscopy

extract_protocol:
After thaw and wash, cell pellets were resuspended in RNAzolRT prior to RNA extraction. Purified RNA was used for transcriptome analysis. Polyadenylated transcripts were purified on oligo-dT magnetic beads, fragmented, reverse transcribed using random hexamers and incorporated into barcoded cDNA libraries based on the Illumina TruSeq platform.
Libraries were sequenced on an Illumina HiSeq 3000 system in 101-base single-read

treatment_protocol: Biopsies were stored at -80deg in RNAlater media before extraction.

value: rectal mucosa

tag: donor id

tag: treatmentgroup

value: exp

tag: alttreatmentgroup

value: CRAI


title: 27_36_100-59_v1


title: Young_MSC_scRNAseq_11

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell

value: Bone marrow

value: 9 week old


title: 28_37_100-57_v1


title: 29_44_100-63_v1

value: con

value: control


title: 25_29_100-55_v1


title: binding mRNAs of QKI, siNC

type: RNA

city: Zunyi

first: Handong

last: Huang

state: 贵州

address: 149 Dalian Road

institute: Affiliated Hospital of Zunyi Medical University

description: Gene expression data from SW480 cells in negative control group

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

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: SW480 cells, negative control group

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: SW480 cells were kept at 37°C in an air incubator and cultured until 70-80% confluence.

extract_protocol: SW480 cells treated with siRNA were lysed with RIP lysis buffer. Anti-QKI antibody or IgG from rabbit serum were pre-bound to Protein A Magnetic Beads and then incubated with cell lysate at 4°C overnight with rotation. The magnetic bead-antibody-QKI complex was washed and resuspended with RIP wash buffer. RNA was recovered using TRI Reagent according to the manufacturer's instructions.

treatment_protocol: siRNA transfection of cells was performed with 100 pmol siRNAs using Lipofectamine 3000 Transfection Reagent. At 48 hours after transfection, cells were collected for subsequent experiments.

value: Negative control group


title: binding mRNAs of QKI, siLnc

description: Gene expression data from SW480 cells after silencing NONHSAT136151

source_name: SW480 cells, NONHSAT136151 silenced

value: NONHSAT136151 silenced


title: Total_RNAseq_22Rv1_sgNONO_4hours_SKBG1-R_Replicate1

value: sgNONO

tag: timepoint

value: 4 hours

value: Total mRNA


title: Young_MSC_scRNAseq_10

source_name: Bone marrow


title: 24_26_100-45_v1


title: Total_RNAseq_22Rv1_sgNONO_4hours_DMSO_Replicate3

value: DMSO


title: Young_MSC_scRNAseq_9


title: Total_RNAseq_22Rv1_sgNONO_4hours_SKBG1-S_Replicate2

value: SKBG-1 (S), 20uM


title: Total_RNAseq_22Rv1_sgNONO_4hours_DMSO_Replicate1


title: Young_MSC_scRNAseq_14


title: 22_22_100-37_v1


title: Young_MSC_scRNAseq_6


title: 21_15_100-25_v1


title: 20_14_100-19_v1


title: Young_MSC_scRNAseq_12


title: Young_MSC_scRNAseq_8


title: 23_23_100-39_v1


title: Young_MSC_scRNAseq_7


title: Total_RNAseq_22Rv1_sgControl_4hours_SKBG1-S_Replicate2

value: sgControl


title: Young_MSC_scRNAseq_5


title: 18_41_100-61_v1


title: Total_RNAseq_22Rv1_sgControl_4hours_SKBG1-S_Replicate1


title: 19_11_100-17_v1


title: Total_RNAseq_22Rv1_sgNONO_4hours_DMSO_Replicate2


title: 17_21_100-35_v1


title: Young_MSC_scRNAseq_4


title: Young_MSC_scRNAseq_3


title: 16_20_100-29_v1


title: Total_RNAseq_22Rv1_sgControl_4hours_SKBG1-S_Replicate3


title: Total_RNAseq_22Rv1_sgControl_4hours_SKBG1-R_Replicate3

value: SKBG-1 (R), 20uM


title: Total_RNAseq_22Rv1_sgControl_4hours_SKBG1-R_Replicate2


title: Young_MSC_scRNAseq_2


title: Total_RNAseq_22Rv1_sgControl_4hours_SKBG1-R_Replicate1


title: 15_19_100-33_v1

value: rectal mucosa


title: Total_RNAseq_22Rv1_sgControl_4hours_DMSO_Replicate3


title: 14_18_100-27_v1


title: Total_RNAseq_22Rv1_sgControl_4hours_DMSO_Replicate1


title: 21433-3

city: changsha

first: FENG

middle: zhan

last: Gao

state: hunan

address: no

department: College of Biology

institute: Hunan university

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts
Data mapping to the reference genome of S. meliloti (http://www.microbesonline.org/cgi-bin/genomeInfo.cgi?tId=266834).
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Sinorhizobium meliloti 1021

growth_protocol: Medicago incubated with S. meliloti Rm1021 nifH::GUS for 12 days

extract_protocol:
Total symbiosome RNA was isolated isolated using RNAprep Pure Cell/Bacteria Kit (TIANGEN, China)
Total RNA was used as input material for the RNA sample preparations. For prokaryotic samples, mRNA was purified from total RNA by using probes to remove rRNA. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. And in the DNA polymerase I system, use dUTP to replace the dNTP of dTTP as the raw material to synthesize the second strand of cDNA. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. Then USER Enzyme was used to degrade the second strand of cDNA containing U, In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

treatment_protocol: Symbiosome isolated form Medicago nodule cells using sucrose buffer (0.5 M sucrose with 50 mM Tris-HCl, 10 mM DTT, pH 7.4)

tag: host

value: debino1 mutant medicago


title: 12_16_100-30_v1


title: 13_17_100-21_v1


title: Total_RNAseq_22Rv1_sgControl_4hours_DMSO_Replicate2


title: 21433-2


title: 11_13_100-13_v1


title: frozen rumen wall tissue from TMR+30% green feed fed animal  [G_VERDE_-_8]

city: Barcelona

first: Riccardo

last: Aiese Cigliano

address: Calle Comte D'Urgell 240

country: Spain

institute: Sequentia Biotech SL

data_processing:
Bioinformatic analysis were carried out by Sequentia Biotech (Barcelona, Spain). The quality of raw RNA-seq reads was assessed with the software FastQC v0.11.5. Adapters and lowquality bases were then removed using Trimmomatic v0.39 setting a minimum base quality of 25, minimum length of 35 bp and leaving the other options as default
Trimmed reads were then aligned to the buffalo genome (Bubalus bubalis, version UOA_WB_1 from NCBI) with STAR aligner v2.5.2b. Read summarization to produce gene counts matrix was performed with featureCounts v2.0.0  with the following parameters: -Q 30 -s 2 -p.
FPKM values were produced with the edgeR package.
Assembly: Bubalus bubalis, version UOA_WB_1
Supplementary files format and content: tab delimited text with the FPKM values of all the samples

organism: Bubalus bubalis

source_name: rumen wall

extract_protocol:
Total RNA was isolated from 100-200 mg of frozen rumen wall tissue using the EuroGold TriFast (EuroClone, Pero, Milano, Italy) reagent, according to the manufacturer's instructions.
RNA-seq libraries were prepared using TruSeq Stranded Total RNA Sample Prep kit (Illumina, San Diego, CA) according to the manufacturer’s recommendations, using 1-2 micrograms of total RNA as input.

value: rumen wall

tag: diet

value: total mixed ration (TMR) + 30% green feed


title: frozen rumen wall tissue from TMR+30% green feed fed animal  [G_VERDE_-_7]


title: 21433-1


title: 10_12_100-11_v1


title: frozen rumen wall tissue from TMR+30% green feed fed animal  [G_VERDE_-_6]


title: WT-2

description: WT

value: wild type medicago


title: WT-3

description: WT


title: 9_9-CFAR_14-83527-0016

value: new

value: TGW


title: frozen rumen wall tissue from TMR+30% green feed fed animal  [G_VERDE_-_4]


title: C2_3 neurons, tauP301L, 25d, sample4

city: Leuven

first: Patrik

last: Verstreken

address: Herestraat 49

institute: VIB-KU Leuven

description:
adapted Smart-seq3
C2_3_FACS_25d_counts.tsv
C2_3_25d_tauP301L_sample4

data_processing:
Pooled sequencing data from 10x libraries was demultiplexed and index-hopping-filter v1.0.1 (10x Genomics) applied. Feature-barcode matrices were computed with Cell Ranger (v4.0.0, 10x Genomics). The fraction of contaminating ambient RNA was automatically determined and corrected with soupX (v1.5.2). Subsequently, individual ambient RNA corrected matrices were loaded into scanpy (v1.8.1) and concatenated into one dataset. Quality control steps included filtering of cells from 5 day old animals at a minimum of 800, 25/45 day old animals 600 detected genes as well as a maximum of 20 000 counts and 15% mitochondrial content.
Reads from the adapted Smart-seq3 libraries were preprocessed with fastp (v0.20.0) followed by alignment and counting with STARsolo (STAR v2.7.9).
Assembly: 4th 2020 FlyBase Drosophila melanogaster release (r6.35)
Supplementary files format and content: tab-delim text and matrix files

organism: Drosophila melanogaster

source_name: C2_3 neurons

growth_protocol: light-controlled incubator at 25°C and 12-hour light-dark cycle, standard corn meal and molasses food

extract_protocol:
For 10x library preparation cells were first counted with the FLUNA-FL Dual Fluorescence Cell Counter and viability determined with Acridine Orange/Propidium Iodide dyes (Logos biosystems), which was >93% for all samples, typically 98-100%. We targeted 10 000 captured cells per genotype and sample with Chromium v3.1 chemistry (10x Genomics). For adapted Smart-seq3, 400 GFP+ C2_3 neurons were FAC-sorted for each sample.
For the 5d and 25d 10x datasets, single-cell encapsulation was carried out with the 10x Chromium Next GEM chip; for the 45d 10x dataset with a custom HyDrop chip. Library preparation followed the 10x Single cell 3’ reagent kit v3.1 user guide (CG000204 Rev D). Briefly, reverse transcription was performed on a C1000 Touch Thermal Cycler (Bio Rad) at 53°C 45 min and 85°C 5 min with a 4°C hold, followed by breakage of the single-cell emulsion, Dynabeads MyOne SILAN clean-up and cDNA amplification at 98°C 3 min, 13 cycles of 98°C 3 min - 63°C 20 s - 72°C 1 min, with a final 72°C 1 min extension and 4°C hold. Amplified cDNA was cleaned with SPRIselect (Beckman Coulter). Thereafter cDNA was enzymatically fragmented, followed by end-repair, A-tailing, SPRIselect clean-up, adapter ligation and another SPRIselect clean-up was carried out prior to PCR amplification of the ligation products incorporating unique sample indices at 98°C 45 s, 15 cycles 98°C 20 s - 54°C 30 s - 72°C 20 s - with a final 72°C 1 min extension and 4°C hold. SPRIselect clean-up of the amplified libraries was carried out. At different check points the quality of cDNA and final sequencing library was evaluated using Qubit (ThermoFisher) and Bioanalyzer (Agilent). Libraries were first sequenced shallow to determine library complexity and subsequently sequenced deeper to achieve ~80% sequencing saturation. For the FAC-sorted bulk RNAseq of C2_3 neurons we followed the Smart-seq3 protocol with increased lysis buffer to 7.5 µl including the sorted cell volume, the RT mix volume to 2.5 µl and the final cDNA amplified product to 25 µl in total. Tn5 concentration increased to the Smart-seq2 protocol.
10x Genomics v3.1 scRNAseq and adapted Smart-seq3 for bulk RNAseq

value: C2_3 neurons


title: frozen rumen wall tissue from TMR+30% green feed fed animal  [G_VERDE_-_5]


title: 8_8-CFAR_14-83527-0012


title: WT-1

description: WT


title: C2_3 neurons, tauP301L, 25d, sample3

description:
adapted Smart-seq3
C2_3_FACS_25d_counts.tsv
C2_3_25d_tauP301L_sample3


title: frozen rumen wall tissue from TMR+30% green feed fed animal  [G_VERDE_-_2]


title: Young_MSC_scRNAseq_1

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell

value: Bone marrow

value: 9 week old


title: C2_3 neurons, tauP301L, 25d, sample2

description:
adapted Smart-seq3
C2_3_FACS_25d_counts.tsv
C2_3_25d_tauP301L_sample2


title: 7_7-CFAR_14-83527-0011


title: 6_6-CFAR_14-83527-006


title: frozen rumen wall tissue from TMR fed animal  [G_secco_-_7]

value: total mixed ration (TMR)


title: C2_3 neurons, tauP301L, 25d, sample1

description:
adapted Smart-seq3
C2_3_FACS_25d_counts.tsv
C2_3_25d_tauP301L_sample1


title: C2_3 neurons, asynA53T, 25d, sample4

description:
adapted Smart-seq3
C2_3_FACS_25d_counts.tsv
C2_3_25d_asynA53T_sample4

value: C2_3 > asyn[A53T], CD8::GFP


title: frozen rumen wall tissue from TMR fed animal  [G_secco_-_4]


title: 5_5-CFAR_14-83527-005


title: frozen rumen wall tissue from TMR fed animal  [G_secco_-_5]


title: C2_3 neurons, asynA53T, 25d, sample3

description:
adapted Smart-seq3
C2_3_FACS_25d_counts.tsv
C2_3_25d_asynA53T_sample3


title: 4_4-CFAR_14-83527-004


title: 3_3-CFAR_14-83527-003


title: C2_3 neurons, asynA53T, 25d, sample 2

description:
adapted Smart-seq3
C2_3_FACS_25d_counts.tsv
C2_3_25d_asynA53T_sample2


title: frozen rumen wall tissue from TMR fed animal  [G_secco_-_3]


title: frozen rumen wall tissue from TMR fed animal  [G_secco_-_2]


title: frozen rumen wall tissue from TMR fed animal  [G_secco_-_1]


title: 1_1-CFAR_14-83527-001


title: HK-2-overexpressed NK-1R cells+SP replicate1

status: Public on Mar 20 2023

city: Shenzhen

first: Enyi

last: Zhu

state: Guangdong

address: no.628 Zhenyuan Road

institute: the Seventh Affiliated Hospital,Sun yat-sen university

data_processing:
Sequencing was performed on the DNBSEQ platform.
Raw reads were aligned to the human genome using hierarchical indexing for spliced alignment of transcripts 2 (HISAT2) and Bowtie2.
Assembly: GCF_000001405.39_GRCh38.p13
hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HK-2 cells

growth_protocol: S) under 5% CO2 and 37 °C conditions.

extract_protocol:
RNA was harvested using Trizol reagent (ThermoFisher Scientific, Darmstadt, Germany) and was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: We added 20 μM SP or PBS to NK-1R-overexpressed HK-2 cells for a 48-h incubation period, followed by harvesting for RNA isolation using Trizol reagent.

value: HK-2 cells

value: renal proximal epithelial tubular cells

value: NK-1R overexpressed

value: SP


title: HK-2-overexpressed NK-1R cells+SP replicate3


title: HK-2-overexpressed NK-1R cells+SP replicate2


title: HK-2-overexpressed NK-1R cells+PBS replicate1

value: PBS


title: HK-2-overexpressed NK-1R cells+PBS replicate2


title: SC_FL_3

city: Chicago

first: Md. Wasim

last: Khan

state: IL

address: 835 S Wolcott Ave

department: Medicine

institute: University of Illinois at Chicago

description: HKDC1-knockout; KO rep3

data_processing:
RNA integrity was assessed with Agilent Bioanalyzer 2100 to select RNA samples with RIN >7.3 to 9.3. Two hundred fifty to 300 base pair insert cDNA libraries, non–strand-specific, were prepared with New England Biolabs (Ipswich, MA) Next Ultra RNA Library Prep and sequenced with Illumina (San Diego, CA) HiSeq PE150 Platform ∼6G/sample Q30 >90%.
The reads were mapped to the human reference genome sequence using STAR v2.5 and v2.6.1, with a total mapping rate >90%/sample.
For gene expression level analysis and to calculate the fragments per kilobase of transcript per million mapped reads, HTSeq v0.6.1 was used.
The differential expression analysis between 2 different groups was done with DESeq2 R package v2_1.6.3.
The P values were adjusted using the Benjamini-Hochberg approach for controlling the false discovery rate, adjusted P <.05. TFCat and Cosmic databases were used to annotate the differential expressed gene.

source_name: Subcutaneous fat

extract_protocol:
RNA was extracted using RNAeasy kit (Bio-Rad)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatement

value: Overexpression


title: SC_FL_2

description: HKDC1-knockout; KO rep2


title: L_FL_3

description: HKDC1-knockout; KO rep3

source_name: Liver


title: SC_Nu_2

description: Null; sample 2

value: Control


title: SC_Nu_3

description: Null; sample 3


title: L_FL_1

description: HKDC1-overexpression; sample 1


title: L_Nu_1

description: Null; sample 1


title: b.NOTCH4KO2

city: New York

first: Richard

middle: A

last: Friedman

state: NY

address: 1130 St. Nicholas Av

institute: Columbia University Irving  Medical Center

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Reads were mapped to the genome with bowtie version 0.12.7 and featureCounts.
Reads in each gene were counted with featureCounts.
Genome_build: mm9
Supplementary_files_format_and_content: text file with read counts per gene

source_name: N4-/-PKC (Notch4 -/-; p16fl/fl;LSL-KrasG12D;p48-Cre mouse pancreatic tumor cell lines

growth_protocol:
Freshly isolated murine tumor specimens were minced with sterile razor blades,
digested with 0.5% trypsin for 15 minutes at 37°C,
resuspended in DMEM and 15% fetal bovine serum (FBS), and seeded in 10 cm dishes.
All genetic analyses were performed on cells cultivated for less than 7 passages

extract_protocol:
Total RNA of PKC and N4-/-PKC pancreatic tumor cell lines were extracted using the miRNeasy Mini kit (Qiagen, Venlo, Netherlands),
quantified by spectrophotometry (Ultraspec2100; Amersham Pharmacia Biotech, Cambridge, UK)
and reversed-transcribed with SuperScriptⅢ Reverse Transcriptase (Invitrogen, MA, USA) according to the manufacturer's protocol.
The quality of purified RNA samples was determined using a
Bioanalyzer 2100 (Agilent) with an RNA Pico kit. RNAs with RNA Integrity Number (RIN)
values greater than 8.0 were used to generate sequencing libraries.
Illumina Truseq RNA Sample Prep v2 using the LT protocol.

tag: cell-type

value: mouse pancreatic tumor cell lines


title: b.NOTCH4KO1

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Reads were mapped to the genome with bowtie version 0.12.7 and Tophat .
Reads in each gene were counted with featureCounts .
Genome_build: mm9
Supplementary_files_format_and_content: text file with read counts per gene


title: C2_3 neurons, asynA53T, 25d, sample1

description:
adapted Smart-seq3
C2_3_FACS_25d_counts.tsv
C2_3_25d_asynA53T_sample1

tag: tissue


title: L_Nu_2

description: Null; sample 2


title: a.WT3

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Reads were mapped to the genome with bowtie version 0.12.7 and Tophat.
Reads in each gene were counted with featureCounts .
Genome_build: mm9
Supplementary_files_format_and_content: text file with read counts per gene

source_name: PKC ( p16fl/fl; LSL-KrasG12D;p48-Cre) mouse pancreatic tumor cell lines

value: PKC


title: L_Nu_3

description: Null; sample 3


title: O DNA methylation replicate 4

city: Palo Alto

first: Jamie

middle: O.

last: Brett

address: 3801 Miranda Avenue, Building 100, Room E4-216

department: Neurology and Neurological Sciences

institute: Stanford University

description:
processed data file: oldCpGmethylratios.bedGraph
processed data file: Aging_MuSC_WGBS.txt

data_processing:
Reads were adapter- and quality-trimmed with trim_galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore) (quality cutoff 20, adapter stringency 1, final length filter 50) and then deduplicated, mapped to the mm10 version of the mouse genome, and called for methylation using Bismark (Krueger et al. 2011) (seedmms 1, maxins 1000, ignore_r2 2). Bisulfite conversion efficiency (as assessed by conversion of non-CpG cytosines) was >99.5%.
Genes lacking an Entrez ID and ERCC reads were filtered out. Raw count data were then normalized using edgeR with the TMM method (Robinson et al. 2010).
DSS (Wu et al. 2012) was used to estimate CpG methylation means, dispersions, and significance across the two age groups (default parameters).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Aging_MuSC_WGBS.txt: Tab-delimited text file containing CpGs profiled in both age groups, with genome (mm10) position (0-based coordinate) and methylation means, dispersions, p-values, and FDR (BH correction) values from DSS.
Supplementary_files_format_and_content: bedGraph files: bedGraph format for genome browsers of the mean methylation ratios of each CpG estimated by DSS, each age group in a separate bedGraph file.

source_name: Skeletal muscle stem cells

extract_protocol:
FACS-isolated MuSCs were snap-frozen. Genomic DNA was extracted using the QIAamp Micro DNA extraction kit (Qiagen).
DNA (150 ng) was sheared with a Bioruptor 300 (Diagenode) and then end-repaired and A-tailed with the NEBNext DNA Library Prep kit (NEB). Methylated Illumina adapters were ligated with LigaFast (Promega), and size selection was performed with AMPure XP beads (Beckman Coulter). Bisulfite conversion was performed with the EZ DNA Methylation Direct kit (Zymo) and amplified with 14 cycles with PfuTurbo Cx Hotstart DNA Polymerase (Agilent) followed by final size selection with the AMPure XP beads. Libraries underwent paired-end 101-bp sequencing at the Stanford Genome Sequencing Service Center with an Illumina HiSeq 2000 at low cluster density with PhiX spike-in to a depth of 115-200 million reads.

tag: Sex

value: Male

value: 22 months

tag: cell type

value: Skeletal muscle stem cells


title: a.WT1

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Reads were mapped to the genome with bowtie version 0.12.7 and Tophat
Reads in each gene were counted with featureCounts
Genome_build: mm9
Supplementary_files_format_and_content: text file with read counts per gene

tag: strain


title: O DNA methylation replicate 3


title: SC_FL_1

description: HKDC1-overexpression; sample 1


title: O DNA methylation replicate 2


title: O DNA methylation replicate 1


title: Y DNA methylation replicate 2

description:
processed data file: youngCpGmethylratios.bedGraph
processed data file: Aging_MuSC_WGBS.txt

value: 4 months


title: HK-2-overexpressed NK-1R cells+PBS replicate3

tag: genotype

tag: treatment


title: Y DNA methylation replicate 3


title: SC_Nu_1

description: Null; sample 1


title: Y DNA methylation replicate 4


title: 2_2-CFAR_14-83527-002

value: rectal mucosa

value: new

value: TGW


title: O RNA-Seq replicate 4

description:
O4
PolyA-selected RNA
processed data file: Aging_MuSC_RNASeq.txt

data_processing:
Reads were adapter- and quality-trimmed with trim_galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore) (quality cutoff 20, adapter stringency 1, final length filter 50). Trimmed reads were mapped to mm10 (Ensembl release 89, no patches) using transcript annotations from Ensembl with STAR (Dobin et al. 2013) along with the ERCC RNA sequences (mismatch cutoff 4% of read length, no non-canonical junction alignments). Exonic reads that mapped uniquely were summarized over genes with the featureCounts module of the Subread package (Liao et al. 2014).
Genes lacking an Entrez ID and ERCC reads were filtered out. Raw count data were then normalized using edgeR with the TMM method (Robinson et al. 2010).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Aging_MuSC_RNASeq.txt: Tab-delimited text file containing normalized FPKMs for each gene.

extract_protocol:
FACS-isolated MuSCs were snap-frozen. ERCC RNA (Invitrogen 4456740) was spiked in proportional to cell number: 10 mcL of 1:10,000 diluted ERCC RNA per 122,000 cells. RNA was extracted using the Nucleospin RNA XS kit (Machery-Nagel).
RNA (10 ng) was reverse-transcribed using oligo(dT) priming with the SMARTer Ultra Low Input system (Takara). The cDNA then sheared with a Covaris S2 ultrasonicator. End repair, multiplexed adapter ligation, and 6-9 cycles of library amplification were performed using the Ovation Ultralow Multiplex system (NuGEN). Libraries underwent paired-end 101-bp sequencing at the Stanford Genome Sequencing Service Center with an Illumina HiSeq 2000 to a depth of 26-37 million reads.


title: L_FL_2

description: HKDC1-knockout; KO rep2


title: Y DNA methylation replicate 1


title: a.WT2

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Reads were mapped to the genome with bowtie version 0.12.7 and Tophat.
Reads in each gene were counted with featureCounts.
Genome_build: mm9
Supplementary_files_format_and_content: text file with read counts per gene


title: O RNA-Seq replicate 1

description:
O1
PolyA-selected RNA
processed data file: Aging_MuSC_RNASeq.txt


title: Y RNA-Seq replicate 3

description:
Y3
PolyA-selected RNA
processed data file: Aging_MuSC_RNASeq.txt


title: Y RNA-Seq replicate 1

description:
Y1
PolyA-selected RNA
processed data file: Aging_MuSC_RNASeq.txt


title: O RNA-Seq replicate 3

description:
O3
PolyA-selected RNA
processed data file: Aging_MuSC_RNASeq.txt


title: Y RNA-Seq replicate 2

description:
Y2
PolyA-selected RNA
processed data file: Aging_MuSC_RNASeq.txt


title: Y RNA-Seq replicate 4

description:
Y4
PolyA-selected RNA
processed data file: Aging_MuSC_RNASeq.txt


title: OL-RL_WT_HC-2

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Paired-end sequencing (101 x 2) was performed using a Hiseq (Illumina).
Illumina Casava1.7 software used for basecalling.
mapped to mm10 whole genome using STAR v2.5.1.
Gene expression levels were calculated count-per-million (CPM) values normalized with trimmed mean of M-values (TMM) using an edgeR v.3.12.1. The CPM values are on log2 scale.
Heat map was constructed using Mev (v. 4.9.0). Statistical analyses were performed using R (v. 3.3.0) and PYTHON (v. 2.7.6).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

source_name: Hippocampus from wild-type mouse after Morris water maze original and reversal learning

growth_protocol: Mice were bred and maintained at the SPF facility in the Korea Institute of Science and Technology (KIST).

extract_protocol:
Total RNA was isolated from the hippocampal tissues using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit (Illumina).
The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.

treatment_protocol: Morris water maze original and reversal learning tasks were applied to wild-type and Ccny knockout mice. All experimental protocols were approved by the KIST Institutional Animal Care and Use Committee (approval number 2018-048)

value: Mouse Hippocampal tissue

value: 8-10 weeks old


title: Basal_KO_HC-2

source_name: Hippocampus from Ccny knockout mouse


title: OL_KO_HC-2

source_name: Hippocampus from Ccnyknockout mouse after Morris water maze original learning


title: Basal_WT_HC-1

source_name: Hippocampus from wild-type mouse


title: OL-RL_KO_HC-2

source_name: Hippocampus from Ccny knockout mouse after Morris water maze original and reversal learning


title: OL-RL_WT_HC-1


title: OL_KO_HC-3


title: OL_KO_HC-1


title: OL-RL_KO_HC-1


title: Basal_WT_HC-3


title: OL-RL_WT_HC-3


title: OL_WT_HC-2

source_name: Hippocampus from wild-type mouse after Morris water maze original learning


title: OL_WT_HC-1


title: Basal_KO_HC-1


title: OL-RL_KO_HC-3


title: Basal_KO_HC-3


title: OL_WT_HC-3