title: BMF4_80M_C4T1.2_CM-3

first: Supriyo

last: De

institute: NIA-IRP, NIH

data_processing: Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

source_name: BM F4/80+monocyte, cultured in 4T1.2 cancer-conditioned media

growth_protocol: The animal protocol was approved and permission was granted to perform animal experiments by the ACUC committee of the National Institute on Aging (ASP 321-LMBI-2022) under the Guide for the Care and Use of Laboratory Animals (NIH Publication No. 86-23, 1985). The study used young (8-12 weeks old) female mice bred and housed in the same, specific pathogen-free environment at the National Institute on Aging (NIA). All experiments were performed together with randomized, age- and sex-matched control mice. BALB/CJ mice were purchased from the Jackson Laboratory (Bar Harbor, ME). Cancer conditioned (CM) media was collected from 4T1.2 cells, a subset of 4T1 cells, gifted by Dr. Robin L. Anderson (Peter McCallum Cancer Center, Melbourne, Australia), and cultured in cRPMI (RPMI1640 supplemented with 10% FBC, 1× HEPES, sodium pyruvate, nonessential amino acids solution, penicillin–streptomycin–glutamine (Gibco, Gaithersburg, MD), and 55 mmol/L beta-mercaptethanol).CM was collected the by 5 min centrifugation at 1500 rpm, filtered with 0.2µm filter, and stored at -80℃ as single use aliquots. B cell media was complete RPMI containing SCF(10ng/ml), IL7 (1ng/ml), Flt3L(25ng/ml) and BAFF(50ng/ml). Macrophage media was complete RPMI containing MCSF(10ng/ml). BM B cells and monocytes were isolated from BALB/CJ mice using FACSAriaTM Fusion sorter and cultured in 50% cancer CM in cRPMI for 7 days in Nunc™ Multidishes with UpCell™ Surface (Thermo Fisher) without changing media for 7 days. Adherent cells (macrophages) were harvested by detaching them at 4℃ for 15 mins in PBS.

extract_protocol: Total  RNA was isolated using RNeasy Plus Micro (Qiagen, Germantown, MD, USA).Total RNA quantity and quality were evaluated using the Bioanalyzer RNA 6000 Chip (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: In vitro pre B-cell to macrophage conversion (BMF) was performed using BM Lin- (TER119, CD11b, Gr-1, CD3ε, NK1.1 or CD49b, Ly6C, Ly6G, CD11c)- CD19+ B cells (pre Bisolated from young (8-12 weeks) C57BL/CJ or BALB/CJ mice using a FACSAriaTM Fusion sorter. Cells (106/ml) were then cultured in 50% cancer-conditioned media (CM) in cRPMI for 7 days in NuncTM Multidishes with UpCellTM Surface (Thermo Fisher, Waltham, MA, USA) to generate pre-B cell-derived macrophages (BMF) without changing media. On day 7, adherent cells (macrophages) were washed with 1×PBS and then incubated at 4°C for 15 mins to detach them from plastic. Then, after replenishing with fresh 50% cancer CM, the cells (at 105/ml concentration) cultured for additional 7 to 28 days.

value: Bone marrow (BM) monocyte

tag: final culture media

value: Cultured in 4T1.2 cancer-conditioned media (CM)

tag: days in final media

tag: Sex

value: 8-12 weeks

value: BALB/CJ


title: 45-yo Gastric ORGs MOCK [CoV_122020_10_S10]

status: Public on Sep 20 2021

type: SRA

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

library_source: transcriptomic

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Alignment was performed with STAR 2.6.0a on hg38 reference assembly obtained from cellRanger website (Ensembl 93)
The expression levels of genes were determined with RSEM 1.3.0 by using gencode pre-build genes annotations (hg38 primary assembly)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include expected counts for each sample as output from RSEM

molecule: total RNA

organism: Homo sapiens

source_name: 45-yo Gastric ORGs MOCK

growth_protocol: Fully grown gastric organoids at day 7 after single cell disaggregation were removed from surrounding extracellular matrix using a modified published protocol. Matrigel was dissolved with 60 min treatment of the droplets with Cell Recovery Solution (Corning) at 4°C. Organoids were retrieved from the plates using 1% BSA-coated cut-end tips and transferred to 1% BSA-coated 15 mL tubes. Cells were extensively washed with ice-cold PBS and centrifuged at 200 g for 5 min at 4°C. Supernatant was discarded, the pellet was resuspended in complete medium and transferred to non-tissue culture treated low-adhesive multiwell plates (pre-coated in 1% BSA). Organoids were cultured in suspension for 3 days to allow reversion of polarity, before use in infection experiments.

extract_protocol:
Pelletted organoids were extracted in RLT buffer
cDNA was synthesized using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, following manufacturer suggested protocol. cDNA generated with SMART-Seq v4 Kit were used for preparation of library with NEXTERA XT DNA Library Preparation kit, following the suggested protocol().

treatment_protocol: Reversed-polarity organoids were infected at a MOI of 1 by incubation with 250 µl of an expansion medium viral suspension for 2 hours. After infection, organoids were washed twice in DMEM to remove unbound virus. RP-GOs were dispersed in a 400 µl expansion medium at 37 °C with 5% CO2. For all organoid cultures 50 µl of supernatant were harvested at 0, 24, 48, and 72 hours post infection. An equal volume of expansion medium replaced the sampled supernatant at each collection time. An extra sample at 96 hours post infection was collected for the RP-GOs. Samples were stored at -80°C before titration through the FFA.

tag: cell type

value: Cultured organoid (RP-Gos) from adult stomach tissue (age 45 year)

tag: passage

tag: sars-cov-2 infection

value: negative paired control


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 4

city: MInneapolis

first: Michael

last: Farrar

state: MN

address: 2101 6th Street SE

department: Lab Medicine and Pathology

country: USA

institute: University of Minnesota

description:
SB-PE-4
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt

data_processing:
Reads were aligned with HiSat2 to the mouse genome (mm10) with the SB transposon sequence appended.
Counts were estimated using the Subread featureCounts tool.
FPKM data were generated using the detailed protocol described here: Sarver A. (2019) Identification of Cancer Genes Based on De Novo Transposon Insertion Site Analysis Using RNA and DNA Sequencing. In: Starr T. (eds) Cancer Driver Genes. Methods in Molecular Biology, vol 1907. Humana Press, New York, NY.
Genome_build: mm10 (GRCm38) + SB transposon sequence
Supplementary_files_format_and_content: Two processed data files (tab-delimited text) are provided: (1) counts_gsea_analysis.txt: subread counts txt file with gene counts for all samples, (2) fpkm_fusion_analysis.txt: Cufflinks FPKM values for all samples.

organism: Mus musculus

source_name: Lymph Node

growth_protocol: Mice were maintained according to IACUC protocols at the University of Minnesota.

extract_protocol:
RNA was isolated using a Qiagen Miniprep Kit.
TruSeq RNA v2 libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Single cell suspensions were created from the lymph nodes of leukemic mice, flash frozen and stored at -80 degrees Celsius. Progenitor B cells were purified from the bone marrow using column purification.

tag: strain

tag: genotype

value: Pax5+/- x Ebf1+/- x CD79a-Cre+ x SB1

value: Leukemic B Cells

tag: number of mice


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 3

description:
SB-PE-3
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: scRNAseq_Sp7_cKO

city: Dallas

first: Jialiang

last: Wang

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Raw reads obtained from scRNA-seq experiments were demultiplexed, aligned to the mouse genome, version mm10 (with tdTomato gene inserted), and collapsed into unique molecular identifiers (UMIs) with the Cellranger toolkit (version 3.1.0, 10X Genomics)
Libraries were batch-corrected to achieve a similar average read count using the CellRanger aggr function. Using a cutoff of 1000 UMIs, cell type annotation were performed iteratively through two rounds of dimensionality reduction, clustering, and removal of putative doublets across all cells.
Genome_build: mm10
Supplementary_files_format_and_content: gene-barcode matrices; genes; barcodes

source_name: tdTomato positve cells

extract_protocol:
4-week old mice were sacrificed and tibiae, femura, and calvariae were dissected. Soft tissue was removed through scraping, and the epiphysis was cut off. Bone marrow cells were flushed out with cold PBS using a syringe. Bones were cut into 1- to 2-mm lengths and subjected to 8 serial digestions of type I collagenase/EDTA. The final three collagenase fractions were collected by centrifuging the supernatant at 4ºC/300 rcf/8 min. Cell pellets were resuspended with 2% FACS buffer containing RNAse inhibitor and were filtered through a 100 µm cell strainer.
tdTomato+/DAPI- cells were sorted (Sony SH800s Cell Sorter) into a new PCR tube containing 2% FACS buffer. Single cells were encapsulated into emulsion droplets using Chromium Controller (10x Genomics). scRNA-seq libraries were constructed using Chromium Single Cell 3’ v3 Reagent Kit according to the manufacturer’s protocol. Briefly, ~ 15,000 cells were loaded in each channel with a target output of 2,000 cells. Reverse transcription and library preparation were performed on C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad). Amplified cDNA and final libraries were evaluated on an Agilent BioAnalyzer using a High Sensitivity DNA Kit (Agilent Technologies). Libraries were sequenced with PE100 on the DNBSEQTM NGS technology platform (BGI, China) to reach ~ 450 million reads.

value: Osteoblasts and osteocytes

tag: tissue

value: tdTomato positve cells

tag: age

value: post natal day 28

value: Sp7 cKO:Dmp1-Cre; Sp7 f/f; tdTm+


title: 45-yo Gastric ORGs MOCK [CoV_122020_9_S9]


title: Flank_CBT_2

city: CAMBRIDGE

first: Duncan

middle: Matthew

last: Morgan

state: MA

address: 500 Main St

department: Koch Institute

institute: MIT

data_processing:
Raw read processing of single-cell RNA sequencing reads was performed as previously described in Macosko et al. Briefly, reads were aligned to the mm10 reference genome and collapsed by cell barcode and unique molecular identifier (UMI).
Correction for ambient RNA contamination was performed using SoupX v1.2.1.
Data was further analyzed in Seurat v2.3.4.
Genome_build: mm10
Supplementary_files_format_and_content: DGE: single-cell genes/cell count matricies

source_name: Tumor

growth_protocol: Tumor cell lines were cultured at 37°C and 5% CO2 in DMEM (Gibco) supplemented with 10% 782 FBS (Atlanta Biologicals), 1% penicillin/streptomycin (Gibco), and 1X HEPES (Gibco). Tumor cells were harvested by trypsinization (Gibco) and washed 2 times with 1X PBS (Gibco). Cells were resuspended in PBS, and 2.5x105 tumor cells were injected subcutaneously into the flanks of mice, or intravenously via the tail vein.

extract_protocol:
Tumor-bearing mice were injected retro-orbitally with fluorescently-labeled anti-CD45 antibodies (CD45-IV) 3 minutes prior to euthanasia to differentiate tumor- and lung-infiltrating immune cells from circulating immune cells. Spleens and lymph nodes were dissected from mice and physically dissociated through a 70 µm filter to generate single cell suspensions. Splenocyte suspensions were lysed with ACK lysis buffer (Gibco) for 3 minutes to deplete red blood cells. Subcutaneous tumors and tumor-bearing lungs were dissected from mice, weighed, and collected in 5 mL DMEM (Gibco) containing the human tumor dissociation kit (Miltenyi) enzymes. Tumors were dissociated using the gentleMACS Octo Dissociator (Miltenyi). Following the digestion, tumor or lung pieces were mashed through a 70 µm filter with a 1 mL syringe plunger to generate a single cell suspension. The dissociated cells were washed 2 times with PBS and were layered over Ficoll (GE). Cells were spun over Ficoll at 450 g for 30 minutes with the lowest settings of acceleration and brakes. The layer at the interface of Ficoll and PBS, which contained the majority of the live immune cells, was collected and washed with PBS.
Cell suspensions were washed twice with cold PBS + 0.5% BSA + 2mM EDTA and then enriched for tumor-resident immune cells by performing negative selection with anti-PE microbeads (Miltenyi Biotec) followed by positive or negative selection with anti-CD45 microbeads (Miltenyi Biotec).
Seq-Well

treatment_protocol: Mice were injected intraperitoneally with anti-CTLA-4 (clone UC10-4F10-11, Bio X Cell) and anti-PD-L1 (clone 10F.9G2, Bio X Cell) antibodies on days 7, 10, 13, and 16 post-tumor inoculation. Each mouse received 100 µg of each antibody per treatment.

tag: treatment

value: Checkpoint blockade

tag: enrichment protocol

tag: mouse


title: scRNAseq_WT

value: WT:Dmp1-Cre; tdTm+


title: BMF4_80M_C4T1.2_CM-2

type: RNA

city: Baltimore

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were rinsed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 3 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cy3-labeled cRNA was prepared from 200 ng of total RNA using the Agilent Low-Input Quick Amp Labeling Kit and was purified and quantitated according to the manufacturer’s instructions.

value: F


title: Flank_CBT_1_CD45


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 2

description:
SB-PE-2
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: 45-yo Gastric ORGs HIGH dose [CoV_122020_8_S8]

source_name: 45-yo Gastric ORGs HIGH dose

value: infected at MOI 10


title: BMF4_80M_C4T1.2_CM-1


title: BMBCM_C4T1.2_CM-2

source_name: BM B cell, cultured in 4T1.2 cancer-conditioned media

value: Bone marrow (BM) B cell


title: BMF4_80M_MM-3

source_name: BM F4/80+ monocyte, cultured  in macrophage media

value: Bone marrow (BM) monocyte

value: Cultured  in macrophage media (MM)


title: Flank_CBT_1


title: BMBCM_C4T1.2_CM-1

value: Cultured in 4T1.2 cancer-conditioned media (CM)

value: 8-12 weeks


title: BMBC_BCM-2

source_name: BM B cell, cultured in B cell media

value: Cultured in B cell media (BCM)

value: BALB/CJ


title: Sample exposed to darkness – Replicate 3

city: Nice

first: Melanie

last: Pousse

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

country: France

institute: IRCAN

data_processing:
Paired-end sequencing (read length: 2x150bp) was performed by NovoGene compagny using HiSeq sequencer
Reads were trimmed using fastp software. Reads were mapped on the S.pistillata transcriptome using Salmon software (v0.11.4)
Differential expression analysis was performed using DESeq2 R package
Genome_build: S.pistillata NCBI transcriptome GCF_002571385.1
Supplementary_files_format_and_content: tab-delimited text files include Raw counts for each sample

organism: Stylophora pistillata

source_name: Subapical coral branch tissue

growth_protocol: Coral fragments (n=nubbins) were kept in aquaria supplied with Mediterranean seawater (exchange rate of 70% per hour) at a salinity of 38 g liter−1, temperature of 25°C, pHT 7.94 ± 0.02 and for the control condition at an irradiance of 230 μmol photons m−2s−1 on a 12:12 photoperiod. Both dark and control conditions corals were fed daily with frozen rotifers and twice a week with live artemia nauplii.

extract_protocol:
Samples were flash frozen in liquid nitrogen in WhirlPack bags, to be crushed in small pieces with a press. Fragments were put in 600uL of lysis buffer RLT in PowerBeads Glass 0.1mm (Qiagen), samples were lysed in CryoMill bead beating instrument (Retsch) for 4 minutes with a program of 30 cycles/s. Samples were spin at max speed for 3 minutes and the 600uL of supernatant was transferred to a fresh tube. A 600uL (1V) volume of cold EtOH 70% was added to the column (Qiagen, RNeasy Mini Kit), gently mixed by pipetting, and immediately applied on the column to be then centrifugde 15s at 8 000g (10 000 rpm). Flow-through was discarded and the step was repeated. A 350 uL volume of RWI buffer was applied to the column and centrifuge 15s at 8 000g (10 000 rpm). Flow-through was discarded and 70ul of RDD buffer was added to 10uL DNAse, Rnase free, (Qiagen, 79254) stored at -20°C, to be then applied to the column. Leave the column at RT for 15min before adding 350 uL of RWI buffer and centrifuge 15s at 8 000g (10 000 rpm), discard the flow-through and add 500uL of RPE buffer, repeat the centrifugation, add again 500uL of RPE buffer and make a 2min at 8 000g (10 000 rpm) centrifuge before discarding the flow-through and putting the column in a clean 1.5ml tube. Add 30ul of RNase free water to the column and centrifuge for 1min at 8 000g (10 000 rpm), keep the tube on ice for further experiment and store at -80°C
Libraries were prepared according to standards Illumina's instructions

treatment_protocol: Treated coral fragments (n=nubbins) were kept on a 0:24 photoperiod, complete darkness, and were experiencing a bleaching phenotype.

value: Subapical coral branch tissue

tag: photoperiod

value: Continuous darkness


title: BMF4_80M_MM-2


title: BMBCM_C4T1.2_CM-3


title: Sleeping Beauty Mutagenesis Pax5 x Ebf1 Leukemia Repeat 1

description:
SB-PE-1
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt

value: Pax5+/- x Ebf1+/- x CD79a-Cre+ x SB1

value: Leukemic B Cells


title: BMF4_80M_MM-1


title: 45-yo Gastric ORGs HIGH dose [CoV_122020_7_S7]

value: Cultured organoid (RP-Gos) from adult stomach tissue (age 45 year)


title: BMBC_BCM-3


title: BMBC_BCM-1


title: Pax5 x Ebf1 Leukemia Repeat 7

description:
PE-Leuk-7
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Sample exposed to darkness – Replicate 2


title: 45-yo Gastric ORGs HIGH dose [CoV_122020_6_S6]


title: Invivo-Tumor-rep3_scRNA

first: Bongsoo

last: Park

department: Translational Gerontology Branch

institute: National Institute on Aging

description: Invivo-tumor = Macrophage isolated from tumor samples

data_processing:
cutadapt
BWA-mem alignment
macs2 peak-calling
Cell ranger
STAR alignment
Genome_build: mm10
Supplementary_files_format_and_content: text file

source_name: Macrophage

extract_protocol:
The engineered hyperactive Tn5 transposase that is preloaded with DNA adapters thus removing the need for a separate annealing step. Chromium Genome Reagent Kit v2 for scRNA-seq
ATAC-seq and 10X scRNAseq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Csf1r +/- macrophages from Bone Marrow, and Spleen were treated with tn5 enzyme. cDNA library with reverse transcriptase treatment from invitro and invivo macrophage

value: Macrophage isolated from tumor samples


title: Invivo-Tumor-rep4_scRNA


title: Sample exposed to darkness – Replicate 1


title: 45-yo Gastric ORGs HIGH dose [CoV_122020_5_S5]


title: Control sample – Replicate 3

value: 12:12 photoperiod


title: 45-yo Gastric ORGs LOW dose [CoV_122020_4_S4]

source_name: 45-yo Gastric ORGs LOW dose

value: infected at MOI 1


title: Invivo-Tumor-rep2_scRNA


title: Pax5 x Ebf1 Leukemia Repeat 6

description:
PE-Leuk-6
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Pax5 x Ebf1 Leukemia Repeat 5

description:
PE-Leuk-5
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: 45-yo Gastric ORGs LOW dose [CoV_122020_3_S3]


title: Control sample – Replicate 2


title: Pax5 x Ebf1 Leukemia Repeat 3

description:
PE-Leuk-3
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Invivo-Tumor-rep1_scRNA


title: Invitro-Mo-MF-rep2_scRNA

description: Invitro-Mo-MF = Monocyte derived macrophage cultured in vitro environment


title: 45-yo Gastric ORGs LOW dose [CoV_122020_1_S1]


title: Pax5 x Ebf1 Leukemia Repeat 2

description:
PE-Leuk-2
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Control sample – Replicate 1


title: Pax5 x Ebf1 Leukemia Repeat 1

description:
PE-Leuk-1
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Pax5 x Ebf1 Leukemia Repeat 4

description:
PE-Leuk-4
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Invitro-Mo-MF-rep1_scRNA

value: Monocyte derived macrophage cultured in vitro environment


title: 45-yo Gastric ORGs LOW dose [CoV_122020_2_S2]


title: Invitro-B-MF-rep2_scRNA

description: Invitro: B-MF = B-cell derived macrophage cultured in vitro environment


title: Invitro-B-MF-rep1_scRNA

value: B-cell derived macrophage cultured in vitro environment


title: 0.1mM TA treated WT-1

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description: TA-mock.txt

data_processing:
RNA-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using TopHat (version 2.1.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using Cufflinks（version 2.2.0）.
Raw data were processed using the QIIME (v1.7.0) to get the OUT table.USEARCH software (v8.0.1) were used to generated the OUT table file by aligning the original reads back to the OTUs.
Genome_build: Pseudomonas sringae 1448A NC_005773.3
Supplementary_files_format_and_content: txt files were generated from RNA-seq/root metagenome

organism: Pseudomonas savastanoi pv. phaseolicola 1448A

source_name: liquid culture in minimal medium

growth_protocol: MM

extract_protocol:
Psph strains were grown, harvested and washed as above, then the bacteria were transferred to MM at 28 ℃ for 6 hours. Total RNA was extracted by using RNeasy Mini Kit (QIAGEN, USA). Genomic DNA was removed by using DNaseI (NEB, USA) for 30 min.
After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the NEBNext UltraTM II RNA Library Prep Kit protocol (NEB, USA), which was then sequenced using the HiSeq 2000 system (Illumina, USA). All RNA-seq samples have two biological replications.
NEBNext UltraTM II RNA Library Prep Kit protocol (NEB, USA)

treatment_protocol: Grow until mid-log phase in KB and transfer to  minimal medium with the presence of indicated drugs

tag: agent

value: 0.1mM TA

value: wildtype

tag: technology

value: RNA-seq


title: WT used for TA treated samples-1

description: TA-mock.txt


title: Pax5 x Ebf1 Repeat 4

description:
PE-4
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt

source_name: Bone Marrow

value: Progenitor B Cells


title: WT used for TA treated samples-2

description: TA-mock.txt


title: 0.1mM TA treated WT-2

description: TA-mock.txt


title: Pax5 x Ebf1 Repeat 3

description:
PE-3
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: MCF10A_H1047R_BYL_120h_rep3 [RM_24_1]

city: Dundee

first: Ralitsa

middle: Radostinova

last: Madsen

address: Dow Street

department: Medical Research Council Protein Phosphorylation and Ubiquitylation Unit

country: United Kingdom

institute: School of Life Sciences, University of Dundee

data_processing:
Raw read processing was performed with the Nextflow (version 20.07.1) nf-core RNAseq pipeline (version 1.4.2), with Spliced Transcripts Aligment to a Reference (STAR) for read alignment to the human genome (Homo_sapiens.GRCh38.96.gtf) and featureCounts for counting of mapped reads (multimapped reads were discarded).
All subsequent data processing was performed in R. Raw counts were converted to counts per million (cpm) using the cpm() function in the edgeR package, followed filtering of lowly expressed genes using the TCGAbiolinks package with quantile values 0.80 (chosen empirically based on the observed count distribution). Next, read count normalisation was performed with the trimmed mean of M (TMM) method. One sample ("EV_DMSO_48h_rep2") was removed due to a low total read count and outlier behaviour upon unsupervised dimensionality reduction (principal component analysis with the PCAtools package).
The mean-variance relationship was modelled with voom(), followed by linear modelling and computation of moderated t-statistics using the lmFit() and eBayes() functions in the limma package [73]. Experimental replicate was included as a batch effect term in the model. The associated p-values for assessment of differential gene expression were adjusted for multiple comparisons with the Benjamini-Hochberg method at false-discovery rate (FDR) = 0.05.
Genome_build: Homo_sapiens.GRCh38.96.gtf
Supplementary_files_format_and_content: raw count text file

growth_protocol: The generation of polyclonal non-transformed, immortalised breast epithelial MCF10A cells engineered either with empty vector (EV) or bovine PIK3CA-H1047R-expressing retrovirus was described previously [Lien, E. C. et al. (2017) Oncogenic PI3K promotes methionine dependency in breast cancer cells through the cystine-glutamate antiporter xCT. Sci. Signal. 10]. Cells were maintained in DMEM/F12 supplemented with the 5 % horse serum, 10 µg/ml insulin, 0.5 mg/ml hydrocortisone, 20 ng/ml hEGF, and 100 ng/ml cholera toxin.  Cells were subcultured for two weeks post-thawing to ensure adaptation and used for experiments at passage 6-7.

extract_protocol:
RNA extraction was performed with Takara’s Nucleospin RNA Plus (# 740984.50) according to the manufacturer’s instructions.
Samples were submitted to Novogene for quality control (Agilent 2100 analysis), mRNA library preparation (unstranded) and final paired-end sequencing on a NovaSeqS4 lane.

treatment_protocol: All treatments were performed according to a backwards design for simultaneous collection of all samples within a replicate run. Briefly, cells were seeded at 1500 cells/cm2 (14000 cells per 6-well) on day 1, followed by start of the 120 h DMSO or BYL719 (500 nM; Active Biochem #A-1214) on day 2, including full medium replacement for all cultures. Media replacement -/+ treatments was repeated on day 3 and 5. On day 5, 48 h treatments with DMSO or BYL719 were also initiated. On Day 7, cells were washed once with 2 ml ice-cold PBS, followed by snap-freezing on dry ice and storage at -80 C until further processing. All media replacements and the final collection were performed at the same time of day to minimise biological noise.

value: Female breast epithelial MCF10A cell line

tag: time


title: MCF10A_H1047R_DMSO_120h_rep3 [RM_23_1]

value: DMSO


title: Spinal cord Clp1R140H-_3_RNA

city: Farmington

first: Scott

last: Adamson

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
Spinal cord RNA-seq adaptors were trimmed with cutadapt (v1.18) with parameters -u 1 -U 1 --minimum-length 50 -a AGATCGGAAGAG -A AGATCGGAAGAG
Spinal cord RNA-seq was quantified using kallisto version 0.42.4 and psuedo-aligned to the Gencode vM24 transcript reference.
UMIs for 3'READS+ libraries were marked with UMItools (v1.0.1) and parameters --bc-pattern = NNN and --bc-pattern2 = NNN
3'READS+ adaptors were trimmed from reads using cutadapt (v1.18) with parameters -a NNNNTGGAATTCTCGGGTGCCAAGG -A NNNNGATCGTCGGACTGTAGAACTCTGAAC, then polyA tails were removed with cutadapt using parameters "A{100}"X --overlap 1 -m 20 -G X"T{100}" --overlap 2 -m 20.
Trimmed 3'READS+ reads were then mapped to mm10 using hisat2 (v2.1.0) with a gencode vM24 annotation.
PCR duplicated 3'READS + reads were then removed using UMItools dedup.
3'READS + reads with polyA tails trimmed were compared to the same reads without trimming and custom python scripts were used to identify reads with untemplated A's at the 3' end and considered poly adenylation sites.
Polyadenylation sites were clustered using bedtools (v2.29.2) cluster with paramters -d 25 and -s to establish PACs, and PACs with five or more total reads associated with them were retained.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include kallisto estimated counts and TPM values for each forebrain RNA-seq sample at the transcript level.
Supplementary_files_format_and_content: tab-delimited text files include read counts and genomic coordinates for poly-adenylation clusters (PACs) as well as overlapping gene features annotated.

molecule: polyA RNA

source_name: Spinal cord

extract_protocol:
For 3’READS+ libraries, spinal cords were dissociated and lightly fixed in preparation for cell sorting using protocol adapted from previous publications (M-J Beaudet et al., 2015 and ER Thomsen et al., 2015). These RNA samples were pooled so that the input for each library consisted of 175 ng of RNA derived from six spinal cords. For RNA-seq libraries, RNA was extracted from individual spinal cords using Trizol and miRNeasy Mini kit columns (Qiagen) with on-column DNase digestion.
3’READS+ libraries were prepared as described (D Zheng, X Liu, and B Tian 2016 and D Zheng and B Tian 2017), with some modifications: RNase III fragmentation was reduced to 5 min. and adapter and primer sequences came from the NEXTFLEX Small RNA-Seq Kit v3 (Bioo Scientific). 100-nt paired-end reads were generated on a HiSeq 4000. RNA-Seq libraries were made with the Kapa Stranded mRNA-Seq Kit in accordance with the manufacturer’s instructions. 100-nt paired-end reads were generated on a NovaSeq 6000.

value: Cerebellum


title: Spinal cord Clp1R140H-_2_RNA


title: PSPH-quadruple-mutant-MM-2

description: processed data file: quadruple-mutant-MM-rhpS.txt

tag: genotype/variation

tag: growth condition

value: liquid culture in minimal medium


title: MCF10A_H1047R_BYL_48h_rep3 [RM_20_1]

tag: cell type


title: Pax5 x Ebf1 Repeat 2

description:
PE-2
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: PSPH-quadruple-mutant-MM-1


title: MCF10A_H1047R_DMSO_48h_rep3 [RM_19_1]


title: PSPH-rhpS-mutant-MM-2

description: processed data file: rhpS-MM.txt

source_name: rhpS mutant

value: rhpS mutant


title: Spinal cord WT_3_RNA


title: Pax5 Repeat 4

description:
Pax5-4
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Pax5 Repeat 3

description:
Pax5-3
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Spinal cord WT_2_RNA


title: MCF10A_EV_DMSO_48h_rep3 [RM_17_1]

value: Empty Vector


title: PSPH-rhpS-mutant-MM-1

description: processed data file: rhpS-MM.txt


title: MCF10A_H1047R_BYL_120h_rep2 [RM_16_1]


title: PSPH-WT-MM_2

description: processed data file:

source_name: WT

value: wild type


title: PSPH-WT-MM_1

description: processed data file:


title: Spinal cord WT_1_RNA


title: a7_minus_minus_rep3

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

description:
Kpna6 (importin α7-/-)
Animal tissue

data_processing:
Raw sequence reads were pseudo aligned to the mouse transcriptome mm10 (Ensembl Build 100) using Kallisto (Version 0.45), Bray et al. Nat. Biotechnology 2016) runing 30 bootstrap rounds.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files per sample include effectice read counts and transcript per million (TPM) values for each transcript

source_name: Testis obtained from Importin α7-/-  mouse

growth_protocol: Importin α7-/- and α7ΔIBB/ΔIBB mice were generated as described previously (Rother et al., 2011).  α7ΔIBB/ΔIBB mice: exon 2 of the importin alpha7 gene is deleted which, results in a shortened mRNA containing a cryptic translational start site in exon 3 and  leads to a truncated protein lacking the importin ß binding domain. Importin α7-/- mice: a gene trap cassette is located in intron 1 of the importin α7 gene resulting in a complete loss of the protein.  Animals were backcrossed for 10 generations to C57Bl6/N background. If not stated otherwise, male mice aged 10-20 weeks were used for the analyses

extract_protocol:
Murine  testis were homogenized in trizol (FIRMA) and extracted with chloroform, subsequently precipitated in isopropanol and washed with 70% ethanol. The pellet was dried and resuspended in DEPC water. Then RNA was digested with DNAse I, and 2 g of digested RNA was subjected to reverse transcription using a standard protocol. RNAs quality was checked using a Bioanalyzer system (Agilent Genomics).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor- ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.
Libraries were sequenced on a Illumina NovaSeqas 150bp paired end

value: Testis

value: Kpna6 (importin alpha7-/-)

tag: Sex

value: male

value: 15 weeks

tag: replicate

value: replicate 3


title: MCF10A_EV_DMSO_120h_rep3 [RM_21_1]


title: MCF10A_H1047R_DMSO_120h_rep2 [RM_15_1]


title: Pax5 Repeat 2

description:
Pax5-2
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt

tag: strain


title: PSPH WT mock-2

description: processed data file:


title: Pax5 Repeat 1

description:
Pax5-1
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt

tag: genotype


title: MCF10A_EV_DMSO_120h_rep2 [RM_13_1]


title: MCF10A_H1047R_BYL_48h_rep2 [RM_12_1]


title: Ebf1 Repeat 4

description:
Ebf1-4
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt

tag: number of mice


title: a7_minus_minus_rep1

description:
Kpna6 (importin α7-/-)
Animal tissue

tag: tissue

value: replicate 1


title: Pax5 x Ebf1 Repeat 1

description:
PE-1
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: PSPH-WT-mock-1

description: processed data file:


title: Spinal cord Clp1R140H-_1_RNA

tag: age


title: Ebf1 Repeat 3

description:
Ebf1-3
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: MCF10A_H1047R_DMSO_48h_rep2 [RM_11_1]

tag: treatment


title: a7_dIBB_rep3

description:
Kpna6 (importin α7ΔIBB/ΔIBB)
Animal tissue

source_name: Testis obtained from importin α7ΔIBB/ΔIBB  mouse


title: PSPH-WT-EGCG-10-1

description: processed data file: psph-EGCG-MM.txt

source_name: 4mM EGCG treated WT

value: 4mM EGCG


title: MCF10A_EV_DMSO_48h_rep2 [RM_9_1]


title: a7_dIBB_rep2

value: replicate 2


title: Ebf1 Repeat 1

description:
Ebf1-1
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: Psph-wt-MM-2

description: processed data file: L13-NAR500-MM.txt


title: wt_rep3

description: Animal tissue

source_name: Testis obtained from C57Bl6/N  mouse

value: wildtype


title: a7_dIBB_rep1


title: MCF10A_EV_DMSO_120h_rep1 [RM_5_1]


title: Psph-wt-MM-1

description: processed data file: L13-NAR500-MM.txt


title: MCF10A_H1047R_DMSO_120h_rep1 [RM_7_1]


title: a7_minus_minus_rep2

description:
Kpna6 (importin α7-/-)
Animal tissue


title: WT Repeat 1

description:
WT1
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt

value: Wild Type

value: Progenitor B Cells


title: PSPH-WT-EGCG-10-2

description: processed data file: psph-EGCG-MM.txt


title: L13-NAR500-MM-1

description: processed data file: L13-NAR500-MM.txt

source_name: 0.5 mM PGG treated WT

value: 0.5 mM PGG


title: PBS_LSK_biological_rep4

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: P-K_LSK cells

data_processing:
Whole transcriptome sequencing was applied to the RNA samples with use of on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat ver. 2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 1.0.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: PBS injected bone marrow LSK cells

growth_protocol: 12-13 week-old C57BL/6 male mice were purchased from SLC. All mice were housed with free access to water under specific pathogen free condition and standard light/dark conditions (12/12 hours). Glucose (2g/kg) and/or lipid emulsion (Intralipid 20%; 6ml/kg) was injected intravenously for 7 days with overnight fasted (> 14 hours) C57BL/6 mice in the early morning. PBS injected mice were served as control. During daytime, all mice were allowed to access freely to food. On day 8, mice were euthanized and bone marrow cells were harvested from the femurs and tibias. For the study in which we examined the role of pyruvate dehydrogenase kinase, dichloacetate (DCA; 0.75 g/l, Sigma-Aldrich (17)) was added to the drinking water 3 days before starting intravenous injection of glucose or PBS. DCA treatment was continued during 7 days injection of glucose or PBS.

extract_protocol:
Total RNA was extracted from sorted LSK cells (approx. 10,000 cells) with miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
Each cDNA was generated using a Clontech SMART-Seq HT Kit (Takara Clontech, Mountain View, CA, USA). Each library was prepared using a Nextera XT DNA Library Prep Kit (Illumina, San Diego, USA) according to the manufacturer’s instructions.

treatment_protocol: Lineage- Sca-1+ c-Kit+ cells (LSK cells) were detected by FACS Calibur (BD) or sorted by FACS Aria III (BD). Lineage flow cytometric analysis data were plotted as the percentage of B220+ (BD), CD3+ (BD) or myeloid (Gr-1+ and/or Mac-1+) (BD) cells among total bone marrow cells.

value: Lineage- Sca-1+ c-Kit+ cells

value: PBS control


title: MCF10A_EV_DMSO_48h_rep1 [RM_1_1]

value: Female breast epithelial MCF10A cell line

value: DMSO


title: 2574_M13_CX: Cortex Tcf4 cKO rep2

city: Shanghai

first: Yunli

last: Xie

address: 131 Dong`an Road

department: Institutes of Brain Science

country: China

institute: Fudan University

data_processing:
Base calling was performed using bcl2fastq v1.8.4
Adapter trimming and quality filtering were performed using trim_gaplore v0.4.4
Alignment to the reference genome was performed using STAR v2.5.4b
Read counting was performed using featureCounts v1.6.1
Differential expression analysis was performed using R v3.4.1 and the R package DESeq2 v1.22.1
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited spreadsheet, FPKM values

source_name: neocortex

extract_protocol:
Cortex were removed on ice, and RNA was harvested using Trizol reagent
TruSeq RNA Library Prep Kit

tag: develpmental stage

value: postnatal stage 0 (P0)

value: Tcf4 f/f; Emx1Cre/+

value: neocortex


title: MCF10A_H1047R_DMSO_48h_rep1 [RM_3_1]


title: WT Repeat 4_2

description:
WT4_2
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: 2576_M15_CX: Cortex Tcf4 cKO rep3


title: Ebf1 Repeat 2

description:
Ebf1-2
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt


title: MCF10A_H1047R_BYL_120h_rep1 [RM_8_1]


title: L13-NAR500-MM-2

description: processed data file: L13-NAR500-MM.txt

value: wild type

value: liquid culture in minimal medium


title: PBS_LSK_biological_rep2

description: P-I_LSK cells


title: 2572_M8_CX: Cortex Tcf4 cKO rep1


title: PBS_LSK_biological_rep1

description: P-H_LSK cells


title: 2582_C12_CX: Cortex WT rep3

value: WT


title: glucose+lipid_LSK_biological_rep1

description: GL-H_LSK cells

source_name: glucose+lipid injected bone marrow LSK cells

value: glucose+lipid (G+L)


title: MCF10A_H1047R_BYL_48h_rep1 [RM_4_1]


title: glucose+lipid_LSK_biological_rep2

description: GL-I_LSK cells


title: 2580_C10_CX: Cortex WT rep2


title: Cluster_rep2

city: Stanford

first: Jin Billy

last: Li

state: CA California

address: 240 Pasteur Drive

department: Genetics Department

institute: Stanford University

data_processing:
We ran RSEM on the STAR-aligned reads to obtain read counts
We included all genes with TPM ≥ 2 (for both replicates)
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: read counts

source_name: HEK293FT cells

growth_protocol: HEK293DT cells were grown in T-75 flasks in DMEM+10%FBS

extract_protocol:
RNA was isolated with the RNeasy MinElute Kit (Qiagen, #74204), treated with DNase I (NEB, #M0303S), incubated with an RNA strand reverse complementary to the antisense part of the respective guide RNA, heated to 95 °C for 3 min and purified again with the RNeasy MinElute Kit.
Purified RNA was delivered to CeGaT (Germany) for poly(A)+ mRNA sequencing. The library was prepared from 200 ng RNA with the TruSeq Stranded mRNA Library Prep Kit (Illumina, USA)

treatment_protocol: The RNA editing experiment was done by transfection of 1200 ng guide RNA plasmid (NucleoSpin Plasmid Transfection‐grade, Macherey Nagel, #740490) into 6x104 HEK293FT cells 24h post seeding using a 1:3 ratio of FuGene6 (Promega, #E2691) in 24 cell format. 48h after transfection, cells were harvested. Overall, three settings were carried out, each with an independent duplicate. Those settings include (1) non‐targeting guide RNA (NT gRNA), (2) RAB7A 3’UTR 19‐11‐13‐20p8 CLUSTER guide RNA (Cluster gRNA), and (3) RAB7A 3’UTR 111p56 LEAPER guide RNA (Leaper gRNA).

tag: biological source

value: human kidney (embryonic)

tag: cell line/type

value: HEK293 FT cells

value: transfected with Cluster gRNA


title: Cluster_rep1


title: Leaper_rep2

value: transfected with Leaper gRNA


title: glucose_LSK_biological_rep2

description: G-B_LSK cells

source_name: glucose injected bone marrow LSK cells

value: glucose (G)


title: Leaper_rep1


title: 2578_C9_CX: Cortex WT rep1


title: Ocy454_Input_DNA

library_source: genomic

data_processing:
Sequencing read quality was evaluated using FastQC.
ChIP-seq reads were aligned to the mouse genome (mm9) using bowtie2.
Peaks were identified using MACS2 with default parameters except for the effective genome size set for mouse (mm9)
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file was generated by MACS2
Supplementary_files_format_and_content: bed file was generated by MACS2

molecule: genomic DNA

growth_protocol: Ocy454 cells were cultured for 10 days at 37°C

extract_protocol:
Lysates were clarified from sonicated nuclei and FLAG-Sp7-DNA complexes were isolated with antibody.
Libraries were prepared according to instructions accompanying the ThruPLEX®-FD Prep Kit (R40012, Rubicon Genomics). Libraries were sequenced on the Illumina HiSeq X platform.

tag: cell line

value: Osteocyte-like cell line

tag: chip antibody


title: glucose_LSK_biological_rep1

description: G-A_LSK cells

value: Lineage- Sca-1+ c-Kit+ cells


title: PBS_LSK_biological_rep3

description: P-J_LSK cells

value: PBS control


title: NT gRNA_rep2

value: transfected with NT gRNA


title: NT gRNA_rep1


title: wt_rep1

description: Animal tissue

source_name: Testis obtained from C57Bl6/N mouse

value: Testis

value: wildtype

value: male

value: 15 weeks

value: replicate 1


title: Ocy454_Sp7_ChIPseq

value: anti-FLAG M2 (Sigma Aldrich, lot F1804)


title: MEL Matr3KO day0 rep1

status: Public on Sep 19 2021

city: Boston

first: Hye Ji

last: Cha

address: 1 Blackfan Circle

institute: Boston Children’s Hospital

data_processing:
Paired-end 100bp reads were generated using Illumina HiSeq 2500 sequencing platform for MEL cells, and single-end 75bp reads were generated using Illumina NextSeq500.
Sequencing reads were mapped to the mm10 mouse reference genome using STAR (v2.5.4a) and/or HISAT2.
Raw counts were produced using Htseq and/or a Python script downloaded from https://ccb.jhu.edu/software/stringtie/dl/prepDE.py.
Genome_build: mm10
Supplementary_files_format_and_content: Raw gene counts for every gene and every sample

source_name: MEL cells

growth_protocol: MEL cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) with 10% fetal calf serum, 1% L-glutamine, and 2% penicillin/streptomycin at 37 °C in a humidified. atmosphere of 5% CO2. Mouse ES cells were maintained on mouse embryonic fibroblasts (Gibco MEFs) feeders in standard ES medium supplemented with 15% heat-inactivated fetal calf serum, 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acid, 1% of nucleoside mix, 50 U/ml Penicillin/Streptomycin, 1000U/ml recombinant leukemia inhibitory factor(LIF/ESGRO).

extract_protocol:
RNA was extracted using TRIzol reagent (Thermo Fisher) and the RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mouse ES cells were differentiated in Iscove’s Modified Dulbecco Media (IMDM) supplemented with 10% heat-inactivated fetal calf serum, 2mmol L-glutamine, 4.5x10-4mol/L monothioglycerol, 0.5 mmol/L ascorbic acid, 200 μg/mL transferrin, 5% protein free hybridoma media (PFHM-II) and 50 U/ml Penicillin/Streptomycin.

value: Erythroleukemia cells

value: Matr3 -/-

value: untreated


title: MEL Matr3KO day4 rep1

value: treated with 2%DMSO for 4 days


title: MEL Matr3KO day2 rep1

value: treated with 2%DMSO for 2 days


title: MEL Matr3KO day0 rep2


title: MEL Matr3KO day4 rep2


title: MEL parental day4 rep2

value: wild type


title: MEL parental day2 rep1


title: MEL parental day0 rep2


title: MEL parental day2 rep2


title: MEL parental day4 rep1


title: HiC MEL diff parental rep1

data_processing:
Fastq reads were mapped using bwa-mem, and then classified, de-duplicated.
Low-quality reads were filtered out using pairtools (phred score<30) to achieve valid pairs.
Valid pairs were binned at 1kb, 2kb, 5kb, 10kb, 25kb, 50kb, 100kb, 250kb, 500kb and 1Mb resolutions to generate interaction matrices.
A and B compartments were defined by eigen vector decomposition on 100kb binned Hi-C data using the call-compartments function of the cooltools.
Genome_build: mm10
Supplementary_files_format_and_content: PC1 value tsv file

growth_protocol: MEL cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) with 10% fetal calf serum, 1% L-glutamine, and 2% penicillin/streptomycin at 37 °C in a humidified. atmosphere of 5% CO2

extract_protocol:
5 million MEL cells were crosslinked with 1% formaldehyde for 10 minutes, quenched with glycine, and then lysed.
Illumina TruSeq adapted were ligated, cleaned-up and amplified using Illumina PCR master mix.

value: treated with 2%DMSO


title: MEL parental day0 rep1


title: HiC MEL diff Matr3KO rep1


title: MEL Matr3KO day2 rep2


title: HiC MEL unt parental rep1


title: MEL Matr3KO CTCF rep1

data_processing:
ChIP sequencing was performed using Illumina HiSeq2500 or NextSeq500.
Sequencing reads were aligned to the assembly of the mouse genome mm10 using Bowtie2 with the default parameters.
Duplicate reads were removed using Picard Tools (http://broadinstitute.github.io/picard/).
Peaks were called using Model-based Analysis of ChIP-Seq (MACS2).
Genome_build: mm10
Supplementary_files_format_and_content: peak files

extract_protocol:
Cells were crosslinked and nuclei were prepared using truChIP Chromatin Shearing Reagent Kit (Covaris).
Purified ChIP DNA was processed to generate libraries using the NEBNext ChIP-seq Library Prep Master Mix, NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs), ThruPLEX DNA-Seq Kit (Rubicon Genomics), or Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) according to the manufacturer’s instructions.


title: MEL parental H3K36me3


title: MEL Matr3KO H3K27Ac rep1


title: MEL parental H3K27Ac rep1


title: MEL Matr3KO H3K4me1


title: HiC MEL unt Matr3KO rep1


title: MEL parental Rad21 rep1


title: MEL Matr3KO H3K36me3


title: MEL Matr3KO Rad21 rep1


title: ATAC MEL Matr3KO rep2

data_processing:
Sequencing reads were trimmed for adapter sequences and low quality bases using Cutadapt.
Then reads were aligned to the assembly of the mouse genome mm10 using Bowtie2 with the parameter –X 2000 allowing fragment length up to 2 kb to aligned.
Reads were filtered for properly paired reads, and duplicates and reads mapped to the mitochondria were removed.
All reads aligned to the + strand were offset by + 4bp and reads aligned to the – strand were offset by –5 bp.
Peaks were called subsequently using MACS2 with following parameters (--nomodel --shift 37 --extsize 73).
Genome_build: mm10
Supplementary_files_format_and_content: peak files

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., 2015). Briefly, 50,000 cells were washed and lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). The pellet was then resuspended in the transposition reaction mix (25 μL 2× TD buffer, 2.5 μL Tn5 Transposes (Illumina) and 22.5 μL nuclease-free water) and purified using a Qiagen MinElute Kit.
Transposed DNA fragments were amplified by PCR and libraries were sequenced on Illumina HiSeq 2500 with paired-end reads.


title: MEL parental CTCF rep1


title: ATAC MEL Matr3KO rep1


title: ATAC MEL parental rep2


title: ATAC MEL parental rep1


title: MEL parental H3K4me1


title: wt_rep2

description: Animal tissue

value: replicate 2


title: PJ317_LacZ_Ci_S10

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

country: Sweden

institute: Lund University

description: iPS-derived human neural forebrain progenitors

data_processing:
RNA-seq: raw base call files were converted to fastq and demultiplexed using bcl2fastq. The fastq files were mapped to hg38 and pantro6 reference genomes using STAR/2.5.0a with parameter --outFilterMismatchNoverLmax 0.03 and --sjdbGTFfile gencode.v27.annotation.gtf. When mapping to pantro6, the gencode.v27.annotation.gtf were lifted from hg38 coordinates to pantro6. Gene counts were quantified using featurecounts from Subread/1.5.0-p1, with -s 2, -p and -t exon parameters.
single-cell RNA-seq: raw basecall files were converted to fastq and demultiplexed using cellranger/2.1 mkfastq. Gene counting was done with cellranger count.
Genome_build: hg38
Supplementary_files_format_and_content: counts and coverage tracks

growth_protocol: We used two human iPSC lines generated by mRNA transfection (RBRC-HPS0328 606A1 and RBRC-HPS0360 648A1, both from RIKEN; from here on referred to as HS1 and HS2, respectively). We used two chimpanzee iPSC lines: one generated by mRNA transfection (Sandra A, herein referred to as PT1) and the other with viral vector transduction (PR00818 PTCL-5, herein referred to as PT2) (Marchetto et al., 2013; Mora-Bermúdez et al., 2016). iPSCs were maintained on LN521-coated (0.7 µg/cm2; Biolamina) Nunc multidishes in iPS media (StemMACS iPS-Brew XF and 0.5% penicillin/streptomycin (Gibco)). Cells were passaged 1:2-1:6 every 2-4 days by being rinsed once with DPBS (Gibco) and dissociated using 0.5 mM EDTA (75 µl/cm2; Gibco) at 37 ºC for 7 minutes. Following incubation, EDTA was carefully aspirated from the well and the cells were washed off from the dish using washing medium (9.5 ml DMEM/F-12 (31330-038; Gibco) and 0.5 ml knockout serum replacement (Gibco)). The cells were then centrifuged at 400g for 5 minutes and resuspended in iPS brew medium supplemented with 10 µM Y27632 (Rock inhibitor; Miltenyi) for expansion.

extract_protocol: On the day of harvest, the cells were washed once with PBS and detached using accutase. GFP+/Drak7-  cells were collected using FACS Aria3. Cell pellets were snap frozen and kept at -80°C until RNA extraction.  RNA was extracted using the RNeasy mini kit (Qiagen) according to manufacturer’s protocol. The quality and concentration of the RNA was analyzed using 2100 Bioanalyzer (RNA nano; Agilent) and Qubit (RNA HS assay kit).

treatment_protocol: Differentiation to fbNPCs: iPSCs were grown to approximately 70-90% confluency and were then dissociated as usual for passaging. After centrifugation, the cells were resuspended in N2 medium (1:1 DMEM/F-12 (21331-020; Gibco) and Neurobasal (21103-049; Gibco) supplemented with 1% N2 (Gibco), 2 mM L-glutamine (Gibco), and 0.2% penicillin/streptomycin). The cells were manually counted twice and plated at a density of 10,000 cells/cm2 in 250 µl medium/cm2 on LN111 Nunc  multidishes (1.14 µg/cm2; Biolamina). 10 µM SB431542 (Axon) and 100 ng/ml noggin (Miltenyi) for dual SMAD inhibition, and 10 µM Y27632 was added to the medium. The medium was changed every 2-3 days (N2 medium with SB431542 and noggin) until day 9 of differentiation, when N2 medium without SMAD inhibitors was used. On day 11, the cells were replated by washing twice with DPBS followed by adding StemPro accutase (75 µl/cm2; Gibco) for 10-20 minutes at 37 ºC. The dissociated cells were washed off with 10 ml wash medium, centrifuged for 5 minutes at 400g and resuspended in B27 medium (Neurobasal supplemented with 1% B27 without vitamin A (Gibco), 2 mM L-glutamine and 0.2% penicillin/streptomycin Y27632 (10 µM), BDNF (20 ng/ml; R&D), and L-ascorbic acid (0.2 mM; Sigma). The cells were counted and replated at 800,000 cells/cm2 on LN111- coated plastic in B27 medium (600 µl medium/cm2). The cells were kept in the same medium until day 14, after which new B27 medium was added (Grassi et al., 2020).

value: human neural forebrain progenitor cells

tag: days in culture

tag: molecule subtype

value: polyA RNA


title: PJ308_LacZ_Ci_S9


title: PJ314_g3_Z558Ci_S17


title: PJ311_g2_Z558Ci_S13


title: PJ304_g3_Z558Ci_S16


title: PJ300_g2_Z558Ci_S12


title: PJ320_g2_Z558Ci_S14


title: PJ292_g3_Z558Ci_S15


title: PJ323_g3_Z558Ci_S18


title: PJ296_LacZ_Ci_S8


title: PJ288_g2_Z558Ci_S11


title: CR050_S4

data_processing:
Library strategy: CUT&RUN
RNA-seq: raw base call files were converted to fastq and demultiplexed using bcl2fastq. The fastq files were mapped to hg38 and pantro6 reference genomes using STAR/2.5.0a with parameter --outFilterMismatchNoverLmax 0.03 and --sjdbGTFfile gencode.v27.annotation.gtf. When mapping to pantro6, the gencode.v27.annotation.gtf were lifted from hg38 coordinates to pantro6. Gene counts were quantified using featurecounts from Subread/1.5.0-p1, with -s 2, -p and -t exon parameters.
single-cell RNA-seq: raw basecall files were converted to fastq and demultiplexed using cellranger/2.1 mkfastq. Gene counting was done with cellranger count.
Genome_build: hg38
Supplementary_files_format_and_content: counts and coverage tracks

extract_protocol: On the day of harvest, the cells were washed once with PBS, detached using Accutase, washed and resuspended in PBS. Briefly, 2x105 cells were washed twice (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1x Roche complete protease inhibitors) and attached to pre-activated ConA-coated magnetic beads (Bangs Laboratories). Bead-bound cells were resuspended in 50 µL buffer (20 mM HEPES pH 7.5, 0.15 M NaCl, 0.5 mM Spermidine, 1x Roche complete protease inhibitors, 0.02% w/v digitonin, 2 mM EDTA) containing primary antibody (H3K9me3 (Ab8898, Abcam 1:50); H3k4me3 (Cat #39159, Active Motif 1;50) or IgG control antibody  (Ab97047, Abcam 1:50) at 4 ºC over-night. Washed with digitonin buffer, pA-MNase was added and incubated with the cells at 4 ºC for 1 h. Bead-bound cells were washed, resuspended in 100 µL digitonin buffer, and chilled to 0-2 ºC. Genome cleavage was stimulated by addition of 2 mM CaCl2 at 0 ºC for 30 min. The reaction was quenched by addition of 100 µL 2x stop buffer. After 10 min incubation at 37 ºC to release genomic fragments, cells and beads were pelleted by centrifugation (16,000 g, 5 min, 4 ºC) and fragments from the supernatant purified.

value: IgG

value: DNA released by antibody-targeted MNase


title: CR051_S5


title: CR053_S7


title: CR048_S2


title: CR052_S6


title: PJ284_LacZ_Ci_S7


title: CR023_wo_S15


title: CR049_S3


title: CR012_S2


title: CR014_S4


title: CR013_S3


title: CR015_S5


title: hiPS_H6_d14_scRNA

extract_protocol: HS1 and PT1 were differentiated to day 14, washed twice with DPBS, and dissociated with Accutase for approximately 10 minutes, followed by centrifugation at 400 × g for 5 minutes in wash medium. All pipetting was done very gently to avoid cell death. The pellets were resuspended in 1 ml PBS with 0.04% BSA (Sigma) and filtered through 100 µm cell strainers (Falcon) twice. Cells were resuspended in order to yield a concentration of approximately 1000 cells/µl. The single-cell libraries were prepared with Chromium Single Cell A chip kit and Chromium Single Cell 3’ Library & Gel Bead kit v2 (10× Genomics), quality controlled, and quantified using Qubit ds DNA HS and Bioanalyzer High Sensitivity DNA Assay prior to sequencing. The samples were sequenced for 26 cycles on read 1 and 98 cycles on read 2 using the Illumina NextSeq 500.


title: CR025_wo_S17


title: CR026_wo_S2


title: CR028_wo_S4


title: hiPS_H6_d15_batch2

description:
iPS-derived human neural forebrain progenitors
RNAseq_H6_C6_map_hg38_pt6.tab
275

extract_protocol:
On the day of harvest, the cells were washed once with PBS and lysed with 350 µl RLT buffer with 1% mercaptoethanol (Thermo Fisher). RNA was extracted using the RNeasy mini kit (Qiagen) according to manufacturer’s protocol. The quality and concentration of the RNA was analyzed using 2100 Bioanalyzer (RNA nano; Agilent) and Qubit (RNA HS assay kit).
TruSeq RNA Library Prep kit v2 (Illumina)


title: hiPS_H6_d16_batch2

description:
iPS-derived human neural forebrain progenitors
RNAseq_H6_C6_map_hg38_pt6.tab
278


title: hiPS_h48_d14_s2

description:
iPS-derived human neural forebrain progenitors
Merged_MultiMapping_Hg38.PanTro6_allGenes_h48_cPT.txt
mRNA2


title: hiPS_H6_d13_batch2

description:
iPS-derived human neural forebrain progenitors
RNAseq_H6_C6_map_hg38_pt6.tab
269


title: hiPS_h48_d14_s1

description:
iPS-derived human neural forebrain progenitors
Merged_MultiMapping_Hg38.PanTro6_allGenes_h48_cPT.txt
mRNA1


title: WT Repeat 4

description:
WT4
processed data file: counts_gsea_analysis.txt
processed data file: fpkm_fusion_analysis.txt

data_processing:
Reads were aligned with HiSat2 to the mouse genome (mm10) with the SB transposon sequence appended.
Counts were estimated using the Subread featureCounts tool.
FPKM data were generated using the detailed protocol described here: Sarver A. (2019) Identification of Cancer Genes Based on De Novo Transposon Insertion Site Analysis Using RNA and DNA Sequencing. In: Starr T. (eds) Cancer Driver Genes. Methods in Molecular Biology, vol 1907. Humana Press, New York, NY.
Genome_build: mm10 (GRCm38) + SB transposon sequence
Supplementary_files_format_and_content: Two processed data files (tab-delimited text) are provided: (1) counts_gsea_analysis.txt: subread counts txt file with gene counts for all samples, (2) fpkm_fusion_analysis.txt: Cufflinks FPKM values for all samples.

extract_protocol:
RNA was isolated using a Qiagen Miniprep Kit.
TruSeq RNA v2 libraries were prepared for sequencing using standard Illumina protocols.

value: Wild Type

value: Progenitor B Cells


title: hiPS_H6_d14_batch2

description:
iPS-derived human neural forebrain progenitors
RNAseq_H6_C6_map_hg38_pt6.tab
272


title: hiPS_H6_d16_batch1

description:
iPS-derived human neural forebrain progenitors
RNAseq_H6_C6_map_hg38_pt6.tab
266


title: hiPS_H6_d14_batch1

description:
iPS-derived human neural forebrain progenitors
RNAseq_H6_C6_map_hg38_pt6.tab
260


title: T=1 hour at 37˚C_RepH

city: Northampton

first: Christine

middle: Ann

last: White-Ziegler

address: Clark Science Center

department: Biological Sciences

institute: Smith College

description: Analysis used 23˚C initial culture (T=0) RNA as control for comparison to the experimental samples taken at 0.5, 1, and 4 hours after a shift to 37˚C

hyb_protocol: Labelled cDNA was allowed to hybridize to slides containing full-length PCR products from all 4,290 annotated open reading frames (ORFs) in E. coli MG1655.  Each slide included three printings of the PCR products, yielding three technical replicates.  cDNA from each timepoint at 37˚C was cohybridized with the cDNA from the starting 23˚C T=0 culture.  The slides were submerged in a water bath at 60 °C for 72 h for the first hybridization.  Arrays were then washed in 2X SSC (+0.2 % SDS) at 42˚C for 10 minutes: the subsequent 2X SSC and 0.2X SSC washes were completed at room temperature for 10 minutes each.  A second hybridization to allow capture of the Cy3/Cy5 dyes was completed for 4 hours at 60˚C.  Arrays were then washed in 2X SSC (+0.2 % SDS) at 65˚C for 10 minutes: the subsequent 2X SSC and 0.2X SSC washes were completed at room temperature for 10 minutes each.

scan_protocol: Hybridized slides were scanned using GenePix Pro 4.1 software (Axon Instruments, Inc.).  Photomultiplier tube voltage was altered for the initial scanning to ensure proper channel balance and decrease background.  Any gene feature that had a signal-to-background noise ratio of <2.0 was rejected and not further analyzed.  Data was compiled from three biological replicates (D, E, H) at each timepoint (T=0.5, 1, 4) after a shift to 37˚C and compared to the control retained at 23˚C (T=0).

data_processing:
For each timepoint, the ratio of median value data set for each array was uploaded to Babelomics 4 gene expression and functional profiling analysis suite for normalization between arrays (printtiploess fit) and imputation of missing values (k-value=15).  On each array slide, the PCR products were printed three times (spots a, b, c) and three different arrays were completed for each timepoint (biological replicates D, E, H).  Thus, there are up to 9 independent datapoints that are included in the data matrix table for each timepoint.  These datapoints were used for differential gene expression analysis completed as a one-class response using Significance Analysis of Microarrays (SAM) with ∆=1.68 and a median false discovery rate ≤ 1% for all timepoints.
values: normalized log2 ratio (experiment/control)

organism: Escherichia coli

source_name: T=1 hours at 37˚C, exponential growth phase

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA 3DNA Array 350 RP Expression Array Detection Kit.  The dye was reversed for one array (of 3 total) for each timepoint.

growth_protocol: For each biological replicate, an initial 200 ml culture was grown to mid-exponential phase (A600= 0.2-0.6) with shaking at 225 rpm at 23˚C in M9 minimal medium containing glycerol as a carbon source.  Three biological replicates (D, E, H) were included in the experiment.

extract_protocol: Bacterial cultures were immediately iced.  Aliquots of cells were centrifuged, the supernatant removed, and pellets containing 5 x 10e8 cells were frozen at -80˚C.  Total RNA was isolated using phenol-chloroform extraction, followed by cleanup and concentration using QIAGEN RNEasy Mini columns.  DNAse digestion was completed twice in solution.

treatment_protocol: Aliquots (20 ml) from the 200 ml culture were shifted to 37˚C to allow harvest of cells at time points 0.5, 1, and 4 hours after a shift to 37˚C; the 23˚C culture harvested at T=0 was used as the control.  For 20 ml cultures to be harvested past T=0.5 hours at 37˚C, the aliquots were additionally diluted with M9 minimal glycerol medium to ensure collection of cells within the exponential phase.

source_name: T=0 hours at 23˚C (control), exponential phase growth


title: T=4 hours at 37˚C_Rep D

source_name: T=4 hours at 37˚C, exponential growth phase


title: hiPS_H6_d15_batch1

description:
iPS-derived human neural forebrain progenitors
RNAseq_H6_C6_map_hg38_pt6.tab
263


title: left ventricular non-compaction rep6

city: Nanchang

first: Qingshan

last: Tian

state: Jiangxi

address: 17 Yongwaizheng Street

department: Cardiology

institute: The First Affiliated Hospital of Nanchang University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: Peripheral Blood centrifuged at 1000 rpm for 10 minutes

label_protocol: LncRNA and mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

extract_protocol: Total RNA was isolated from LVNC patients and healthy volunteers using TRIzol reagent. RNA integrity was assessed by standard denaturing agarose gel electrophoresis. The RNA samples were labeled, purified and amplified. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner

treatment_protocol: Blood samples from each patient and healthy subject were centrifuged at 1000 rpm for 10 minutes to separate plasma from cells, then saved at -80 ℃.

tag: tissue source

value: whole blood

value: plasma

tag: patient diagnosis

value: left ventricular non-compaction


title: hiPS_H6_d13_batch1

description:
iPS-derived human neural forebrain progenitors
RNAseq_H6_C6_map_hg38_pt6.tab
257

tag: cell type


title: T=4 hours at 37˚C_Rep E


title: healthy group rep5

value: healthy


title: left ventricular non-compaction rep5


title: healthy group rep4


title: healthy group rep1


title: left ventricular non-compaction rep4


title: healthy group rep6


title: T=0.5 hours at 37˚C_RepH

source_name: T=0.5 hours at 37˚C, exponential growth phase


title: healthy group rep2


title: T=1 hour at 37˚C_RepE


title: T=4 hours at 37˚C_Rep H


title: T=0.5 hours at 37˚C_RepE


title: D78

city: SHANGHAI

first: XIANGYU

last: ZHOU

state: SHANGHAI

address: Shanghai First Maternity and Infant Hospital

institute: Tongji University

data_processing:
The expression level of each transcript was calculated according to fragments per kilobase of exon per million mapped reads (FPKM)
Genome_build: Mus_musculus.GRCm39.dna.primary_assembly.fa
Supplementary_files_format_and_content: xls (fpkm, reads count)

source_name: Lung tissues

growth_protocol: Lung tissues were collected from mice at the age of 2 months

extract_protocol:
RNA extracted from freshed lung tissues
Transcriptome libraries were prepared using a TruSeq RNA Sample Preparation kit (Illumina) and then sequenced using the Illumina HiSeq 2000
TruSeq RNA Sample Preparation kit (Illumina)

treatment_protocol: no additional treatment

value: Lung tissues

value: Dnah9 knockout


title: D77

value: Hez


title: T=0.5 hours at 37˚C_RepD


title: T=1 hour at 37˚C_RepD


title: D76


title: 72h NICD-OE single-cell RNA-Seq dataset

city: New Orleans

first: Wu-Min

last: Deng

state: LA

address: 1700 Tulane Avenue

department: School of Medicine, Department of Biochemistry

institute: Tulane University

data_processing:
Illumina Casava1.7 software used for base-calling
Single-ended fastq files for the whole-tissue RNA-Seq samples were aligned to Drosophila melanogaster Release 6 (Drosophila_melanogaster.BDGP6.28.100.chr_filtered.gtf) reference genome assembly using STAR (v2.7) aligner. featureCounts (Subread package) was run on individual bam files for the generation of count-matrix.
Genome index for single-cell analysis was built using the Drosophila melanogaster Release 6 (Drosophila_melanogaster.BDGP6.28.100.chr_filtered.gtf) reference genome assembly using 10X genomics cellranger (version 3.0.1) mkref pipeline. Sequenced reads were then mapped to this reference genome index. The cellranger count pipeline for alignment, filtering, barcode counting and UMI counting was used to generate the multidimensional feature-barcode matrix for single-cell RNA-Seq datasets.
Genome_build: dm6
Supplementary_files_format_and_content: csv files contain raw counts for each whole-genome RNA Seq sample.
Supplementary_files_format_and_content: 3 files were obtained after running cellranger pipeline (barcodes.tsv, features.tsv and matrix.mtx) on the single-cell RNA-Seq datasets. All these files are readable in R and were processed using the Seurat pipeline which resulted in the individual R object files for each corresponding dataset.

organism: Drosophila melanogaster

source_name: Whole ovarian tissue

growth_protocol: 100 adult ovaries from 50 female Drosophila melanogaster flies maintained at 25°C, with access to males and yeast supplements for 3 days

extract_protocol:
For bulk-RNA sequencing: Whole ovaries were extracted from 40 females in complete medium (Grace’s Insect Basal Medium supplemented with 15% FBS. The anterior part of the ovaries were carefully removed before stage 10 egg chambers. Samples were transferred to a steril Eppendorf tube and media was aspirated. Samples were flash frozen using liquid nitrogen and stored until day of the library preparation in -80°C. Total RNA was extracted using Trizol. For single-cell RNA sequencing: Whole ovaries were extracted from female flies that were dissected in complete medium (Grace’s Insect Basal Medium supplemented with 15% FBS) and were transferred to a tube containing 300 μL EBSS (no calcium, magnesium, and phenol red), followed by a gentle wash for 2 minutes. The EBSS was then removed and the tissue was dissociated in 100 μL Papain (50 U/mL in EBSS and previously heat activated in 37°C for 15 minutes) for 30 minutes. The suspension was mechanically dissociated every 3 minutes by gentle pipetting up and down. To quench the digestion, 500 μL complete medium was added to dissociated cells. The suspension was then passed through a 40 μL sterile cell strainer and centrifuged for 10 minutes at 700 RCF to remove large eggs with intact eggshell which cannot be dissociated and debris. Supernatant was removed and single cells were re-suspended in 100 μL. Cell viability was assayed using Trypan Blue and estimates of cell concentration were made using a hemocytometer. Cells were then further diluted to an approximate, final concentration of 2,000 cells/μL according to 10X Genomics recommendations.
Bulk sequencing libraries were made using the Ultra II Directional RNA library prep kit for Illumina using the protocol for NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB#E7490). Single-cell libraries were prepared using the Single Cell 3’ Library & Gel Bead Kit v2 and Chip Kit according to the recommended 10X Genomics protocol. Single cell suspension was loaded onto the Chromium Controller (10X Genomics). Library quantification assays and quality check analysis was performed using the 2100 Bioanalyzer instrument (Agilent Technologies). The library samples were then diluted to a 10nM concentration and loaded onto two lanes of the NovaSeq 6000 (Illumina) instrument flow cell for a 100-cycle sequencing run.

treatment_protocol: Flies were transferred to 29°C incubator for 1 (24h), 3 (72h) and 4 (96h) days depending on the dataset, and were subsequently dissected.

value: Ovary

value: 3 days after eclosion

value: tj>GAL4, UAS-Gal80TS>UAS-NICD

value: 3 day in 29°C


title: 72h lgl-KD single-cell RNA-Seq dataset


title: 96h NICD+lgl-KD replicate 2

value: tj>GAL4, UAS-Gal80TS>UAS-lglRNAi, UAS-NICD, UAS-Dcr2

value: 4 day in 29°C


title: WTC5

city: Montreal

first: Christian

middle: F

last: Deschepper

state: QC

address: 110 Pine Ave West

department: Institut de recherches cliniques de Montréal (IRCM)

country: Canada

institute: Université de Montréal

data_processing:
Basecalls performed using CASAVA version 1.4
Data were analysed using the Lexogen's proprietary Bluebee sequence analysis platform. Trimming using Bbduk and quality control with FASTQC. Alignment on the reference genome mm10 with STAR.
Raw counts for each feature from GRCm38 ENSEMBL v98 annotation file  including custom genes (AK142197, AK153586, Gm39552, C030026M15) were extracted using FeatureCounts v1.6.0
DESeq2 version 1.22.2 was used to normalize gene readcounts and compute differential expression between uty and b6 experimental conditions correctinf for batch effect.
Genome_build: GRCm38
Supplementary_files_format_and_content: excel file including normalized readcounts values for each sample from DESeq2 analysis

source_name: cardiac left ventricle

growth_protocol: adult male mice were used at 40 days of age to harvest cardiac tissues

extract_protocol:
Qiagen Rneasy microRNA kit with Dnase treatment
3′ end RNA sequencing libraries were prepared using the Lexogen QuantSeq 3′ mRNA-Seq   Library Prep Kit FWD library.

treatment_protocol: At about 10 days of age, the animals were either sham-operated (S) or castrated (C).

value: left ventricle


title: 96h NICD+lgl-KD replicate 1


title: w1118 single-cell RNA-Seq dataset

value: no treatment


title: 18 hours-old scl30a-1 seeds rep2

city: Cerdanyola del Vallès

first: Guiomar

last: Martín

state: Barcelona

address: Vall Moronta

institute: Centre for Research in Agricultural Genomics

data_processing:
Gene expression (GE) quantification is performed using vast-tools. vast-tools maps the first 50 nucleotides of the forward read (if longer and paired end) to a library with one reference transcript per gene, the *.1 transcript according to the TAIR 10 nomenclature or else that with the lowest suffix (33,602 genes in total). GE levels are provided using the cRPKM metric (corrected [for mappability] Reads Per Kilobasepair and Million mapped reads), as detailed in Labbé et al., Stem Cells 2012. cRPKM can be converted to TPMs applying the following formula: TPM = 10^6 * cRPKM/sum_all(cRPKM).
Supplementary_files_format_and_content: Tab-delimited files include cRPKM values (as defined above), as well as the total read count for each gene's canonical transcript

organism: Arabidopsis thaliana

source_name: germinating seed

growth_protocol: Stratified seeds were grown in continuous white light (100 µmol/m2) at 21 ºC for 18 h.

extract_protocol:
Total RNA was extracted from whole Arabidopsis seedlings using the innuPREP Plant RNA kit (Analytik Jena BioSolutions).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: 18 h after stratification

tag: growth conditions

value: continuous white light  (100 µmol/m2)

tag: genetic background

value: Columbia


title: WTC3


title: 18 hours-old scl30a-1 seeds rep3

tag: genotype


title: 72h lgl-KD+NICD-OE single-cell RNA-Seq dataset

tag: tissue


title: 18 hours-old scl30a-1 seeds rep1


title: WTC4


title: left ventricular non-compaction rep3

value: whole blood

value: plasma


title: healthy group rep3

value: healthy


title: left ventricular non-compaction rep1

value: left ventricular non-compaction


title: left ventricular non-compaction rep2


title: WTIR-

city: Beijing

first: Junyun

last: Wang

state: Beijing

address: NO.1 Beichen West Road, Chaoyang District

department: CAS Key Laboratory of Genomic and Precision Medicine

institute: Beijing Institute of Genomics

hyb_protocol: Amplified RNA was hybridized to Illumina HT-12 V4 beadchips following manufacturer's protocols

scan_protocol: Standard Illumina scanning protocol

data_processing: Data processing was completed using GenomeStudio version 2011.1 with the Gene Expression Module v1.9.0 (Illumina). After background subtraction the average normalization was conducted using GenomeStudio to rescale the difference in overall intensity to the mean average intensity for all samples across multiple chips.

label: biotin

source_name: MDA-MB-231 breast cancer cell

label_protocol: RNA was amplified and labeled using Illumina TotalprepTM -96 RNA Amplification Kit (Ambion, #4393543)

growth_protocol: Cells were cultured in DMEM containing 10% FBS  and 1% penicillin-streptomycin solution, and all cells maintained in a humidified 37 °C incubator with 5% carbon dioxide.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Illumina HumanHT-12 V4.0 expression beadchip.

treatment_protocol: MDA-MB-231 cells of WTIR- and WTIR+ groups were collected before and after radiotherapy (2 Gy). Cells of OE+IR- and OE+IR+ groups were transfected with LSD1 vector with or without 2 Gy of X-rays. Cells of ORY1001+IR- and ORY1001+IR+ groups were cultured with LSD1 inhibitor ORY1001 (10μm) 24 hours and then were collected before , at 4 h after the 2-Gy radiotherapy (2 Gy).

tag: ionizing radiation treatment

value: control

value: wild type


title: WTC6


title: OE+IR-

tag: treatment

value: LSD1 overexpression


title: ORY1001+IR-

value: LSD1 inhibitor ORY1001


title: OE+IR+

value: exposed to IR


title: ORY1001+IR+


title: WTIR+


title: D74

value: Lung tissues

tag: strain


title: WTC1


title: 18 hours-old WT seeds rep3


title: WTC7


title: KOC6


title: 24h NICD+lgl-KD replicate 1

value: Ovary

tag: age

value: 3 days after eclosion

value: tj>GAL4, UAS-Gal80TS>UAS-lglRNAi, UAS-NICD, UAS-Dcr2

value: 1 day in 29°C


title: 18 hours-old WT seeds rep2

value: 18 h after stratification


title: KOC3

value: left ventricle


title: WTC2


title: 18 hours-old WT seeds rep1

value: continuous white light  (100 µmol/m2)

value: Columbia


title: 96h lgl-KD replicate 1

value: 4 day in 29°C


title: KOC5


title: KOC1


title: WTS4


title: WTS6


title: WTS5


title: KOC2


title: KOC7


title: 96h control replicate 2

value: tj>GAL4, UAS-Gal80TS>UAS-GFP


title: 24h lgl-KD replicate 2


title: 96h control replicate 1


title: 24h lgl-KD replicate 1


title: Xr.h

city: Christchurch

first: Anna

last: Pilbrow

address: 2 Riccarton Avenue

country: New Zealand

institute: University of Otago, Christchurch

data_processing:
Individual libraries were separated from multiplexed sequencing data (total yield=93.9Gb), adapter- and quality-trimmed and converted to FASTQ format with fastq-mcf (https://expressionanalysis.github.io/ea-utils/).
Paired-end reads <50 nucleotides were removed with the SolexaQA package (Cox et al. BMC Bioinformatics 2010;11:485) and the quality of the remaining reads verified using fastqc tools (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequence reads for all samples were aligned to the Ovis aries genome using Bowtie 2 (Langmead et al. Nat Methods 2012;9:357-9) and TopHat2 (Kim et al. Genome Biol 2013;14:R36).
Read counts for each transcript based on RefSeq and Ensembl annotations were extracted with Bedtools (Quinlan et al. Bioinformatics 2010;26:41-2). Those mapping to different isoforms of the same gene were combined to provide gene-level counts for comparative analysis.
Genome_build: Ovis aries genome (assembly version-3.1, http://www.ncbi.nlm.nih.gov/genome/83)
Supplementary_files_format_and_content: Data for individual genes are provided as raw read counts (not normalised for library size)

source_name: heart failure_kidney

extract_protocol:
Serial kidney biopsies were performed in duplicate prior to pacing (Baseline), on Day-14 of pacing (HF), and after 25-days (non-pacing) recovery (6 sheep, 5 x Baseline, 6 x Heart Failure and 5 x Recovery serial samples). For the first two procedures, the sheep were anaesthetized (as described above) and 2 adjacent percutaneous kidney biopsies taken under ultrasonic guidance (Philips iE33; Philips Ultrasound, WA, USA) using a 14g spring-loaded automated biopsy gun (BARD Peripheral Vascular, Inc., Tempe, USA). Final kidney samples were collected at study-end immediately following euthanasia (IV Pentobarb300 100mg/kg). On each occasion, one of the biopsies was fixed in 10% formalin (4oC overnight) for histological analysis, and the other snap frozen in liquid nitrogen and stored at -80oC for subsequent RNA extraction and RNA-Seq analysis. To maximise statistical power, the 5 x Baseline, 6 x Heart Failure and 5 x Recovery serial samples were supplemented with kidney samples collected post-mortem from animals sacrificed before, during or after the same pacing protocol. This provided a total of 14 x Baseline, 13 x HF and 8 x Recovery samples for RNA-Seq analysis.
Total RNA was extracted from frozen kidney biopsy samples and purified with RNeasy Midi Columns (Qiagen, Hilden, Germany).  RNA-Seq libraries were prepared using total RNA (500 ng input) and TruSeq stranded mRNA library prep kits (Illumina, San Diego, CA).

treatment_protocol: Nine adult Coopworth ewes (4-6 yrs; 47-69 kg; Lincoln University Farm, Canterbury, New Zealand) were instrumented via a left lateral thoracotomy as previously described (Rademaker et al. Am J Physiol 2007;293:H1536-1544) under general anaesthesia (induced by intravenous (IV) diazepam [1x0.5mg/kg] / IV ketamine [1x4mg/kg]; maintained with 2% isoflurane / 2L/min nitrous oxide / 2L/min oxygen) and using approved peri-/post-operative analgesia (IV carprofen [4mg/kg QD for >3 days]; IV buprenorphine [0.005-0.01mg/kg QD for >3 days]; intercostal bupivacaine [1x25mg] / intercostal lignocaine [1x100mg]) and antibiotics (IV cephazolin [2x20mg/kg]; IV enrofloxacin [1x2.5mg/kg]). Briefly, catheters were placed via the jugular vein and in the left atrium for blood sampling and measurement of central venous and left atrial pressures (CVP and LAP, respectively); Konigsberg pressure-tip transducers inserted in the aorta to record mean arterial pressure (MAP) and into the apex of the left ventricle (LV) to obtain heart rate, LV pressures and derivatives of pressure over time (dP/dt(max)); a Swan-Ganz thermodilution catheter (American Edwards) was placed in the pulmonary artery for measurement of cardiac output (CO); and a 7-French His-bundle electrode was stitched sub-epicardially to the LV for subsequent cardiac pacing. A bladder catheter was inserted per urethra to allow timed urine collections. Adequacy of anaesthesia was monitored via serial measurement of  heart rate, blood pressure, capillary refill time, mucous membrane colour, palpable blink response, jaw tone, anesthetic gas analysis, oxygen saturation and end-tidal CO2 levels. Animals recovered for at least 14-days before commencing the study protocol, and throughout the study were held in metabolic cages receiving a diet of Lucerne chaff and food pellets (providing ~75mmol sodium/day; ~150mmol potassium/day) with free access to water. The study followed a longitudinal repeated-measures design, with sampling conducted over a 5-day baseline period (Days -4-0) followed by 14-days of rapid LV pacing @220bpm to induce ADHF (Days 1-14-Pace), and then termination of pacing and 25-days recovery (Days 1-25-Recovery).

value: kidney

tag: time point

value: heart failure


title: WTS2


title: Xr.b

value: baseline


title: WTS3


title: KOS5


title: KOS7


title: WTS1


title: Od.r

value: recovery


title: 96h lgl-KD replicate 2


title: KOS4


title: KOC4


title: 24h control replicate 2


title: Ec.b


title: KOS3


title: Ec.h


title: 24h control replicate 1


title: Od.h


title: Od.b


title: KOS2


title: KOS1


title: d7351.PR (PD+RAP rep3)

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing:
HiSeq2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNAseq reads were aligned to the mouse transcriptome prepared with the mm10 primary assembly and the Ensembl version 88 annotation using STAR version 2.5.3a (Dobin et al., 2013). Gene expression was summarized with RSEM version 1.3.0 (Li and Dewey, 2011) and samtools version 1.3 (Li et al., 2009).
Genome_build: mm10 with ensembl 88 annotation
Supplementary_files_format_and_content: ljette_treatment_counts.txt.gz is a tab separated text file of integer count data
Supplementary_files_format_and_content: ljette_treatment_l2tpm.txt.gz is a tab separated text file of log2 transcripts per million with a plus1 offset

source_name: Hematopoietic Stem Cells (HSCs)

growth_protocol: HSCs were isolated by harvesting bone marrow by flushing the long bones. Red blood cells were lysed in Ammonium-  Chloride-Potassium (ACK) buffer and samples were washed in Iscove’s Modified Dulbecco’s Medium  (IMDM) containing 2 % fetal bovine serum (FBS). Lineage positive cells were depleted using a mouse  lineage cell depletion kit (#130-090-858, Miltenyi Biotec) and the following antibodies from  BioLegend (CD150 [TC15-12F12.2] (PE/Cy7#115913, PE#115904), CD48 [HM48-1] (BV421#103427,  APC/Cy7(#103431), Sca-1 [D7] (PE/Cy7#108114), CD117 [2B8] (APC#105812)) and BD Biosciences  (CD150 [Q38-480] (PE#562651), Sca-1 [D7] (FITC #562058)) were used for staining. 7-AAD or  propidium Iodide was used for the identification of non-viable cells. Cells were sorted using an Aria I  cell sorter (Becton Dickinson).

extract_protocol:
For RNA isolation, 10,000 HSCs in G0/1 were isolated in the absence of FBS and HSCs were sorted into 750 μL TrizolLS. During the sort, the collection  sample was vortexed every 10 min. Post-sort, the samples were brought to a total volume of 1 mL  with DEPC treated water. Samples were stored at -80 °C or directly used for RNA extraction. To  extract RNA, 200 μL chloroform was added to the sample and briefly vortexed at medium speed.  After 2 min at RT, the sample was centrifuged at 12,000 x g for 15 min at 4 °C. 400 μL of aqueous  phase was removed and put into 1,400 μL RLT buffer (Qiagen) with 14 μL β-mercaptoethanol and  mixed vigorously. 1 mL 100 % ethanol was added to each sample, mixed by pipetting, then loaded  onto RNeasy Micro Kit (Qiagen) columns.
Clontech v4 Low-Input RNA Kit

value: Hematopoietic Stem Cells (HSCs)

value: Mice treated with PD (Palbociclib) at 30.4 mg/kg body weight and rapamycin at 6.4 mg/kg body weight in 20 % DMSO, 40 % PEG 400 in PBS by intraperitoneally injected at a volume of 100 μL every 48 h for 85 days.


title: d7352.PR (PD+RAP rep4)


title: Ind.r


title: Ind.b


title: Ind.h


title: d7349.PR (PD+RAP rep1)


title: d7350.PR (PD+RAP rep2)


title: d7347.R (RAP rep3)

value: Mice treated with rapamycin at 6.4 mg/kg body weight in 20 % DMSO, 40 % PEG 400 in PBS by intraperitoneally injected at a volume of 100 μL every 48 h for 85  days.


title: d7346.R (RAP rep2)


title: Hot.h


title: Hot.r


title: 24h lgl-KD replicate 2

data_processing:
Illumina Casava1.7 software used for base-calling
Single-ended fastq files for the whole-tissue RNA-Seq samples were aligned to Drosophila melanogaster Release 6 (Drosophila_melanogaster.BDGP6.28.100.chr_filtered.gtf) reference genome assembly using STAR (v2.7) aligner. featureCounts (Subread package) was run on individual bam files for the generation of count-matrix.
Genome index for single-cell analysis was built using the Drosophila melanogaster Release 6 (Drosophila_melanogaster.BDGP6.28.100.chr_filtered.gtf) reference genome assembly using 10X genomics cellranger (version 3.0.1) mkref pipeline. Sequenced reads were then mapped to this reference genome index. The cellranger count pipeline for alignment, filtering, barcode counting and UMI counting was used to generate the multidimensional feature-barcode matrix for w1118 single-cell RNA-Seq dataset. For 72h lgl-KD single-cell RNA-Seq dataset, the barcodes were further processed by the velocyto pipeline to include counts for the unspliced RNA molecules, which resulted in the loom file output.
Genome_build: dm6
Supplementary_files_format_and_content: csv files contain raw counts for each whole-genome RNA Seq sample.
Supplementary_files_format_and_content: 3 files were obtained after running cellranger pipeline (barcodes.tsv, features.tsv and matrix.mtx) on the single-cell RNA-Seq datasets. For 72h lgl-KD single-cell RNA-Seq dataset, loom file was obtained after running the velocyto pipeline. All these files are readable in R and were processed using the Seurat pipeline.

extract_protocol:
Whole ovaries were extracted from female flies that were dissected in complete medium (Grace’s Insect Basal Medium supplemented with 15% FBS) and were transferred to a tube containing 300 μL EBSS (no calcium, magnesium, and phenol red), followed by a gentle wash for 2 minutes. The EBSS was then removed and the tissue was dissociated in 100 μL Papain (50 U/mL in EBSS and previously heat activated in 37°C for 15 minutes) for 30 minutes. The suspension was mechanically dissociated every 3 minutes by gentle pipetting up and down. To quench the digestion, 500 μL complete medium was added to dissociated cells. The suspension was then passed through a 40 μL sterile cell strainer and centrifuged for 10 minutes at 700 RCF to remove large eggs with intact eggshell which cannot be dissociated and debris. Supernatant was removed and single cells were re-suspended in 100 μL. Cell viability was assayed using Trypan Blue and estimates of cell concentration were made using a hemocytometer. Cells were then further diluted to an approximate, final concentration of 2,000 cells/μL according to 10X Genomics recommendations.
Single-cell libraries were prepared using the Single Cell 3’ Library & Gel Bead Kit v2 and Chip Kit according to the recommended 10X Genomics protocol. Single cell suspension was loaded onto the Chromium Controller (10X Genomics). Library quantification assays and quality check analysis was performed using the 2100 Bioanalyzer instrument (Agilent Technologies). The library samples were then diluted to a 10nM concentration and loaded onto two lanes of the NovaSeq 6000 (Illumina) instrument flow cell for a 100-cycle sequencing run.

value: Ovary

value: 1 day

value: 34 degreeC


title: 96h lgl-KD replicate 2

value: 3 days after eclosion

value: 4 day

value: 36 degreeC


title: w1118 single-cell RNA-Seq dataset

value: no treatment


title: d7345.R (RAP rep1)


title: d7344.PD (PD rep4)

value: Mice treated with PD (Palbociclib) at 30.4 mg/kg body weight in 20 % DMSO, 40 % PEG 400 in PBS by intraperitoneally injected at a volume of 100 μL every 48h for 85  days.


title: D1-Tg P56 rep3

first: Lingfang

last: Zhuang

state: Shanghai

address: 197 Rui Jin Road II

department: Department of Vascular & Cardiology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Sequencing data were filtered with SOAPnuke (v1.5.2) to remove reads containing sequencing adapters and those with more than 1/5 low-quality base ratio. The resulting clean reads were saved in FASTQ format.
The transcriptional reads were mapped to the mm8 whole genome  using HISAT2 (v2.0.4) and STAR (v2.3.0).
fragments per kilobase million (FPKM) value using the DESeq2 were calculated.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: D1-Tg P56_heart

extract_protocol:
WT and DYRK1B-Transgenic hearts were collected at 3-day and 8-week old mice and immediately frozen in liquid nitrogen. Total RNA was extracted from above tissues using Trizol according to standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cDNA encoding the full-length mouse DYRK1B transcript was cloned into a plasmid containing a cardiac-specific α-myosin heavy chain (αMHC) promotor. Then the transgenic mice and their WT littermates were sacrificed at 3-days and 8-week old for RNA-sequencing analysis.

value: Heart

value: 8-week old


title: D1-Tg P56 rep2


title: 24h lgl-KD replicate 1

value: 33 degreeC


title: 72h lgl-KD single-cell RNA-Seq dataset

value: 3 day

value: 38 degreeC


title: D1-Tg P56 rep1


title: Hot.b

value: kidney

value: baseline


title: Go.r

value: recovery


title: 96h control replicate 2

value: tj>GAL4, UAS-Gal80TS>UAS-GFP

value: 32 degreeC


title: d7342.PD (PD rep2)

value: Hematopoietic Stem Cells (HSCs)


title: WT P56 rep3

source_name: WT P56_heart

value: WT


title: 96h lgl-KD replicate 1

value: Ovary

value: 3 days after eclosion

value: 35 degreeC


title: 96h control replicate 1

value: 4 day

value: 31 degreeC


title: d7348.R (RAP rep4)

value: Mice treated with rapamycin at 6.4 mg/kg body weight in 20 % DMSO, 40 % PEG 400 in PBS by intraperitoneally injected at a volume of 100 μL every 48 h for 85  days.


title: 24h control replicate 2

value: 1 day

value: 30 degreeC


title: WT P56 rep2

value: Heart

value: 8-week old


title: WT P56 rep1


title: Go.h

value: kidney

value: heart failure


title: d7341.PD (PD rep1)

value: Mice treated with PD (Palbociclib) at 30.4 mg/kg body weight in 20 % DMSO, 40 % PEG 400 in PBS by intraperitoneally injected at a volume of 100 μL every 48h for 85  days.


title: 24h control replicate 1

value: tj>GAL4, UAS-Gal80TS>UAS-GFP

value: 29 degreeC


title: Go.b

value: baseline


title: D1-Tg P3 rep3

source_name: D1-Tg P3_heart

value: 3-day old


title: Fo.h

value: recovery


title: d7340.V (Vehicle rep4)

value: Hematopoietic Stem Cells (HSCs)

value: Mice treated with 20 % DMSO, 40 % PEG 400 in PBS by intraperitoneally injected at a volume of 100 μL every 48 h for 85 days.


title: D1-Tg P3 rep2


title: P74-M

first: Yong-Bin

last: Yan

address: Tsinghua University

department: School of Life Sciences

institute: Tsinghua University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by Cutadapt , and discard low-quality sequence by Trimmomatic-0.36, then mapped to HG38 whole genome using STAR with parameters  --outSAMmapqUnique 255 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 21 --alignIntronMax 0 --alignMatesGapMax 0 --outFilterMultimapNmax 10 --outSAMprimaryFlag OneBestScore --outSAMstrandField intronMotif --outSAMattributes Standard --outSAMtype BAM SortedByCoordinate --chimSegmentMin 0 --outReadsUnmapped Fastx --outFilterIntronMotifs RemoveNoncanonical --outWigType bedGraph --outFilterMismatchNoverReadLmax 1 --outSJfilterReads All -outSJfilterIntronMaxVsReadN 5000 10000 20000 --outFilterMatchNmin 0 --outFilterMatchNminOverLread 0.66 --outFilterScoreMinOverLread 0.66
Cuffdiff were used for calculating differential expression between flag-C and flag-M,GFP-C and GFP-M, P74-C and P74-M, D28A-C and D28A-M,P74-C and flag-C, D28A-C and flag-C,P74-M and flag-M, D28A-M and flag-M
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: Renal epithelium cell

extract_protocol:
The cytosolic and ER fraction of each sample were prepared by sequential detergent extraction. Total RNAs were extracted using Trizol reagent.
RNA library was prepared for the total RNAs extracted from the cytosol and membrane fractions of HEK-293T cell by KAPA Stranded RNA-Seq Library Preparation Kit.

value: HEK-293T cell

value: PARN overexpressed

tag: fraction

value: ER


title: d7339.V (Vehicle rep3)


title: D28A-M

value: D28A overexpressed


title: Fo.r


title: D28A-C

value: cytosol


title: d7337.V (Vehicle rep1)


title: D1-Tg P3 rep1

value: Heart


title: d7338.V (Vehicle rep2)


title: WT P3 rep3

source_name: WT P3_heart

value: WT


title: Zo.r

value: kidney


title: Fo.b


title: P74-C