title: Ph+ALL215

description: Ph+ALL215, processed data in the file titled "Ph+ALL-1 REPORT_ProbeBasedReport Part1&2&3"

value: F

value: Alive


title: ATAC day10 RFP-GFP- rep1

status: Public on Apr 29 2022

type: SRA

city: Shanghai

first: Tu

middle: zhi

last: fen

address: Tongji University Siping Road Campus

department: life science and technology

country: China

institute: Tongji University

description: ALPG-promoter-RFP/OCT4-ΔPE-GFP dual repoter

library_source: genomic

data_processing:
All sequenced reads were checked for quality control by using FastQC (v0.11.9) with default parameters.
Sequenced reads was removed adapters and low-quality sequence by using trim_galore (v0.6.6 )with the default parameters.
The processed RNA-Seq reads were mapped to hg38 genome using STAR (v2.5.2b). Refseq genes were quantified to FPKM using Stringtie.
The processed ATAC-Seq reads were mapped to hg38 genome using Bowtie2 (v2.4.1). MACS2(v2.2.7.1) was used to call peaks
Genome_build: hg38
Supplementary_files_format_and_content: text files of counts and FPKM values

molecule: genomic DNA

organism: Homo sapiens

source_name: pluripotent stem cells

growth_protocol: For primed-to-naive state transition and prolong culture , cells were cultured in 5iLAF medium containing DMEM/F12: Neurobasal (1:1) (ThermoFisher), 1% N2 supplement (ThermoFisher), 2% B27 supplement (ThermoFisher), 0.5% KnockOut SR (ThermoFisher), 1% nonessential amino acids (Millipore), 2mM GlutaMAX (Millipore), Penicillin Streptomycin (Millipore), 20 ng/ml human LIF (Milipore), 8 ng/ml bFGF (Peprotech), 50 mg/ml BSA (Sigma) and the following cytokines and small molecules: 1 mM PD0325901 (Selleck), 0.5 mM SB590885 (Selleck), 1 mM WH-4-023 (Selleck), 10 mM Y-27632 (Selleck), and 20 ng/ml Activin A (Peprotech). For TS induction, cells were cultured in TSC medium containing DMEM/F-12 supplemented with 0.3% BSA (Sigma), 0.2% FBS (ThermoFisher), 1% ITS-X supplement (ThermoFisher), 0.1 mM 2-mercaptoethanol (Millipore), 2mM GlutaMAX (Millipore), Penicillin Streptomycin (Millipore), 1.5 μg/ml l-ascorbic acid (Sigma), 5 μM Y27632 (Selleck), 2 μM CHIR99021 (Selleck), 0.5 μM A83-01 (Sigma), 1 μM SB431542 (Selleck), 50 ng/ml EGF (Peprotech) and 0.8 mM valproic acid (VPA) (Sigma). Medium were changed daily, and cells were passaged every 2-4 days using 0.5 mM EDTA (Invitrogen).

extract_protocol:
total RNAs were isolated from cells using TRizol (Invitrogen). To generate RNA sequencing libraries, KAPA Stranded mRNA-Seq Kit (KAPA) was used following the manufacturer’s instructions.
mRNA-seq and ATAC-seq libraries were prepared for sequencing using standard Illumina protocols
mRNA-seq and ATAC-seq

treatment_protocol: For primed-to-naive state transition, 2~3×105 dissociated single cells of RFP; GFP pESCs were seeded on the irradiated feeder layer in conventional ESC medium supplemented with Y-27632 (Selleck, 10 mM). Medium was then switched to 5iLAF medium on the second day, and was changed every day. Intermediate cells were collected at different time points during primed-to-naïve transition.

tag: source

value: H9 primed ESC

tag: library type

value: ATAC-seq

tag: condition

value: primed-to-naive transition


title: SG_GFP-_9m_1

city: Groningen

first: Rob

last: Coppes

address: Ant. Deusinglaan 1

department: Biomedical Sciences of Cells and Systems

country: Netherlands

institute: University Medical Center Groningen

library_source: transcriptomic

data_processing:
Base-calling: bcl2fastq software (Illumina Inc.) version 2.20.0.422.
QuantSeq 3′ mRNA-Seq analysis: Bluebee (Lexogen) version 015UG108V0311
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

organism: Mus musculus

source_name: freshly sorted GFP negative murine salivary gland cells from 9 month old H2B-GFP mice

extract_protocol:
RNA was isolated with the RNeasy Mini Kit (Qiagen, 74104) according to manufacturer’s instructions including DNase I treatment
QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen)

tag: cell type

value: Salivary gland cells

tag: gfp status

value: negative


title: Ph+ALL185

type: genomic

city: Suzhou

first: Wenzhi

last: Cai

address: 296 Shizi Street

institute: The First Affiliated Hospital of Soochow University

description: Ph+ALL185, processed data in the file titled "Ph+ALL-1 REPORT_ProbeBasedReport Part1&2&3"

hyb_protocol: Array hybridization was performed using Agilent Oligo aCGH Hybridization Kit (Cat#5188-5380, Agilent technologies, Santa Clara, CA, US)in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 65℃, 20rpm for 40 hours. Array wash was performed using Agilent Oligo aCGH Wash Buffer 1 and 2 set (Cat#5188-5226, Agilent technologies, Santa Clara, CA, US) in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) follow the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US),scan resolution=3μm, PMT 100% to generate tiff image.

data_processing:
Raw data was acquired and normalized(algorithm: LOWESS) using Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).Calculate Z-score for each CNV region using DNA Analytics 4.0.81 software (Agilent technologies, Santa Clara, CA, US), window size is set to 1M and Z-score threshold is set to 4.0.
value definition: Logarithm value(log2) of test/control ratios.

source_name: mononuclear cells of bone marrow at diagnosis

label_protocol: Experimental sample and control sample were labeled with Cy5 NHS ester (Cat#PA15100, GE healthcare Biosciences, Pittsburgh, PA, US) and Cy3 NHS ester (Cat#PA13105, GE healthcare Biosciences, Pittsburgh, PA, US) respectively, using Agilent Genomic DNA Labeling Kit PLUS (Cat#5188-5309, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions. Labeled DNA fragments were purified using Amicon Ultra-0.5, Ultracel-30 Membrane,30 kDa(Cat#UFC5030BK, Millipore, Billerica, MA, US). Measured the absorbance at A260nm (DNA),A550nm (Cyanine 3),and A650nm(Cyanine 5)of purified DNA fragments to calculate the Specific Activity.

growth_protocol: Mononuclear cells of fresh bone marrow from each patient were isolated with Ficoll following manufacturer's instructions. Cells were carefully frozen and stored in -80℃ and recovered when used.

extract_protocol: Total DNA were extracted from mononuclear cells with Invitrogen Genomic DNA Mini Kit following manufacturer's instructions. Genomic DNA was digested by two Restriction Enzymes AluI (Cat#R6281, Promega, Madison, WI, US) and RsaI (Cat#R6371, Promega, Madison, WI, US), follow the instructions provided by the manufacture.

tag: subject status

value: Ph+ALL

tag: gender

value: M

tag: age

tag: status

value: Dead

tag: months

source_name: mononuclear cells from pooled healthy donors

value: healthy donor

value: mononuclear cells


title: Thy_GFP-_9m_3

source_name: freshly sorted GFP negative murine thyroid gland cells from 9 month old H2B-GFP mice

value: Thyroid gland cells


title: SG_GFP-_9m_2


title: Ph+ALL193

description: Ph+ALL193, processed data in the file titled "Ph+ALL-1 REPORT_ProbeBasedReport Part1&2&3"

value: mononuclear cells of bone marrow at diagnosis


title: Thy_GFP-_9m_2


title: Ph+ALL180

description: Ph+ALL180, processed data in the file titled "Ph+ALL-1 REPORT_ProbeBasedReport Part1&2&3"


title: T-Ch-3

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.Only sequences at least 25 nt in length were considered for further analysis
Bowtie version 1.2.2 (parameters --chunkmbs 400 -m 1) was used for alignment on the reference genome.
Genes were counted using featureCounts version 1.4.6-p3 from the Subreads package (parameters: -t gene -g ID -s 1).
For statistical analysis of NGS data, count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0 16 . The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. For each virus, a generalized linear model including the replicate, beads and protein factors as well as the beads x protein interaction was set in order to test for the differential expression between the biological conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure 17 and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Supplementary_files_format_and_content: FeatureCounts output

molecule: total RNA

source_name: INPUT RNA extracted on Cherry protein

growth_protocol: Cells were maintained in DMEM-Glutamax (GIBCO, Thermo Fisher Scientific, Waltham, Massachusetts) supplemented with 10% heat-inactivated FCS (Invitrogen, Thermo Fisher Scientific, Waltham, Massachusetts),100 U/ml/100 mg/ml of Penicillin-Streptomycin (GIBCO), and G418 at 500 mg/ml (#G8168, SIGMA, St. Louis, Missouri).

extract_protocol:
Cells were washed twice with cold PBS and lysed in 6 mL of lysis buffer (20 mM MOPS-KOH [pH 7.4], 120 mM KCl, 0.5% Igepal, 2 mM b-mercaptoethanol), supplemented with 200 U/mL RNasin (Promega) and Complete Protease Inhibitor Cocktail (Roche). Cell lysates were incubated on ice for 20 min, with gentle mixing every 5 min, and then clarified by centrifugation at 16,0003g for 15 min at 4°C. A 250-mL aliquot of each cell lysate was used to perform total RNA purification using TRI Reagent LS [Sigma]). The remaining cell lysate was incubated for 2 hr on a spinning wheel at 4°C with 200 mL StrepTactin Sepharose High Performance beads (GE Healthcare). Beads were collected by centrifugation (1,600 g) for 5 min at 4°C) and washed twice for 5 min on a spinning wheel with 5 mL washing buffer (20mMMOPS-KOH [pH 7.4], 120mMKCl, 2mMb-mercaptoethanol) supplemented with 200 U/mL RNasin and complete protease inhibitor cocktail. Precipitates were eluted using biotin elution buffer (IBA Lifesciences). RNA purification was performed using TRI Reagent LS (T3934; Sigma). RNA was dissolved in 50 mL DNase-free and RNase-free ultrapure water. Extracted RNAs were analyzed using Nanovue (GE Healthcare) and the Bioanalyser RNA nano kit (Agilent Technologies).
Before RNA-seq analysis of total and RLR-bound RNA from virus- and mock-infected cells, depletion of ribosomal RNA was done using the riboZero reagents included in the TruSeq stranded total RNA library prep kit (#20020596, Illumina). NGS libraries were generated following the manufacturer’s protocol. The indexed samples were multiplexed per 4 and sequenced on a HiSeq2500 sequencer (Illumina) to produce single-ends 65 bases reads, bearing strand specificity.

treatment_protocol: no treatment

tag: cell line

tag: genotype/variation

value: Cherry protein tagged 1-STrEP tag

tag: infection

value: mock


title: T-Ch-1


title: T-MDA-1

source_name: INPUT RNA extracted on MDA5 protein

value: MDA5 protein tagged 1-STrEP tag


title: Ph+MPAL001

description: Ph+MPAL001, processed data in the file titled "Ph+MPAL-2 REPORT_ProbeBasedReport Part1&2"

value: Ph+MPAL

value: F

value: ND


title: Thy_GFP-_6m_3

source_name: freshly sorted GFP negative murine thyroid gland cells from 6 month old H2B-GFP mice


title: Thy_GFP-_9m_1


title: Ph+ALL175

description: Ph+ALL175, processed data in the file titled "Ph+ALL-2 REPORT_ProbeBasedReport Part1&2&3"


title: Ph+ALL177

description: Ph+ALL177, processed data in the file titled "Ph+ALL-1 REPORT_ProbeBasedReport Part1&2&3"


title: Ph+ALL167

description: Ph+ALL167, processed data in the file titled "Ph+ALL-2 REPORT_ProbeBasedReport Part1&2&3"


title: Thy_GFP-_6m_2


title: T-Ch-2


title: Thy_GFP-_6m_1


title: Thy_GFP-_3m_4

source_name: freshly sorted GFP negative murine thyroid gland cells from 3 month old H2B-GFP mice


title: Thy_GFP-_3m_2


title: Thy_GFP-_6m_4


title: B-RIG1-3

source_name: OUTPUT RNA extracted on RIG-I protein

value: RIG-I protein tagged 1-STrEP tag


title: Ph+ALL159

description: Ph+ALL159, processed data in the file titled "Ph+ALL-2 REPORT_ProbeBasedReport Part1&2&3"


title: B-RIGI-2


title: Ph+ALL173

description: Ph+ALL173, processed data in the file titled "Ph+ALL-1 REPORT_ProbeBasedReport Part1&2&3"

value: Alive


title: B-RIGI-1


title: Lnc473 exp 4

city: Heidelberg

first: Priit

last: Pruunsild

address: INF 364

department: Neurobiology

country: Germany

institute: University of Heidelberg

description:
rAAV infection on DIV3 (for expression of Lnc473 and EGFP).
Directional RNA-seq

data_processing:
Illumina Casava1.8 used for basecalling.
Reads were mapped to the mouse genome with HISAT2 (2.1.0).
Mapped reads per gene were counted with HTSeq-count (0.6.1).
DESeq2 (2.11.40.6) was used to determine differentially expressed genes.
Assembly: GRCm38/mm10
Supplementary files format and content: Tabular text files contain read counts per gene.

source_name: mouse hippocampal primary neurons

growth_protocol: Cells were plated with the density of ~80000/cm2 and were first kept in Neurobasal-A (Life Technologies) with B27 (Life Technologies), 0.5 mM L-glutamine and 1 % rat serum. On day in vitro (DIV) 8 the medium was changed to a salt-glucose-glycine solution [10 mM Hepes (pH 7.4), 1 mM glycine, 26.1 mM NaHCO3, 5.3 mM KCI, 1 mM MgCI2, 2 mM CaCI2, 30 mM glucose, 114 mM NaCI, 0.5 mM sodium pyruvate] and Eagle’s minimum essential medium (MEM) (vol:vol 9:1), with insulin, transferrin and sodium selenite (ITS, all 7.5 ng/mL, Sigma-Aldrich). RNA was extracted at DIV 10.

extract_protocol:
Poly(A)+ RNA was isolated from mouse hippocampal neuron total RNA (obtained with the RNeasy Mini Kit (Qiagen) and on-column DNase digestion) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
cDNA libraries were prepared with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). NEBNext Multiplex Oligos for Illumina (New England Biolabs) were used to provide adaptors and permit multiplexing.

treatment_protocol: Cells were infected at DIV 3. EGFP levels were used to titer ectopic expression. Infection rate was >90%.

tag: strain

value: Hippocampal primary neurons

tag: age at neuron preparation

tag: expression

value: Human lnc473 RNA and EGFP

tag: sample collection time


title: B-MDA-1

source_name: OUTPUT RNA extracted on MDA5 protein


title: Ph+ALL150

description: Ph+ALL150, processed data in the file titled "Ph+ALL-2 REPORT_ProbeBasedReport Part1&2&3"

value: Ph+ALL


title: Lnc473 exp 2


title: B-MDA-2


title: Thy_GFP-_3m_3

value: negative


title: Lnc473 exp 1


title: Thy_GFP-_3m_1


title: B-LGP-1

source_name: OUTPUT RNA extracted on LGP2 protein

value: LGP2 protein tagged 1-STrEP tag


title: B-LGP-3


title: Lnc473 exp 3


title: Ph+ALL128

description: Ph+ALL128, processed data in the file titled "Ph+ALL-3 REPORT_ProbeBasedReport Part1&2&3"

value: M

value: Dead

value: healthy donor


title: Ph+ALL151

description: Ph+ALL151, processed data in the file titled "Ph+ALL-1 REPORT_ProbeBasedReport Part1&2&3"

value: mononuclear cells of bone marrow at diagnosis

value: mononuclear cells


title: B-LGP-2

value: mock


title: Ph+ALL144

description: Ph+ALL144, processed data in the file titled "Ph+ALL-1 REPORT_ProbeBasedReport Part1&2&3"


title: Ph+ALL135

description: Ph+ALL135, processed data in the file titled "Ph+ALL-1 REPORT_ProbeBasedReport Part1&2&3"


title: B-MDA-3

value: MDA5 protein tagged 1-STrEP tag


title: B-Ch-3

source_name: OUTPUT RNA extracted on Cherry protein

value: Cherry protein tagged 1-STrEP tag


title: Ph+ALL124

description: Ph+ALL124, processed data in the file titled "Ph+ALL-1 REPORT_ProbeBasedReport Part1&2&3"


title: EGFP exp 2

description:
rAAV infection on DIV3 (for expression of EGFP).
Directional RNA-seq

value: EGFP


title: day6 SSEA4+ rep1

description: ALPG-promoter-RFP/OCT4-ΔPE-GFP dual repoter

tag: source

value: H9 primed ESC

value: mRNA-seq

value: primed-to-naive transition


title: EGFP exp 4

value: Hippocampal primary neurons


title: B-Ch-2


title: day6 SSEA4+ rep2

tag: library type


title: B-Ch-1


title: EGFP exp 1


title: Ph+ALL122

description: Ph+ALL122, processed data in the file titled "Ph+ALL-3 REPORT_ProbeBasedReport Part1&2&3"

value: F

value: Alive


title: EGFP exp 3


title: pAPL::3xYFP

city: Cambridge

first: Yrjö

last: Helariutta

address: 47 Bateman Street,

department: Sainsbury Laboratory

country: United Kingdom

institute: University of Cambridge

data_processing:
Quantification was performed using 10x Genomics Cell Ranger v3.1.0 using default options
Genome_build: Arabidopsis TAIR10 genome using the Araport11 gene annotation (Ensembl release 45)
Supplementary_files_format_and_content: HDF5 file with sparse matrix of raw counts output by the Cell Ranger software (the file by default named 'outs/raw_feature_bc_matrix.h5'). This can be imported into R, for example, using the DropleUtils::read10xCounts() function.

organism: Arabidopsis thaliana

source_name: root phloem tissue

growth_protocol: Seedlings were grown on plates containing 1x MS Media (1x MS Salts, 1% Difco agar,  1% sucrose) at 23ºC with 30% humidity and 188 μM of light for 5 days in long day conditions

extract_protocol:
Single-cell RNA-seq libraries were prepared in the Cancer Research UK Cambridge Institute Genomics Core Facility using the following: Chromium Single Cell 3′ Library & Gel Bead Kit v3, Chromium Chip B Kit and Chromium Single Cell 3' Reagent Kits v3 User Guide (Manual Part CG000183 Rev C; 10X Genomics). Cell suspensions were loaded on the Chromium instrument with the expectation of collecting gel-beads emulsions containing single cells. RNA from the barcoded cells for each sample was subsequently reverse-transcribed in a C1000 Touch Thermal cycler (Bio-Rad) and all subsequent steps to generate single-cell libraries were performed according to the manufacturer’s protocol with no modifications. cDNA quality and quantity was measured with Agilent TapeStation 4200 (High Sensitivity 5000 ScreenTape) after which 25% of material was used for gene expression library preparation.
Libraries were prepared according to instructions for 10x Genomics Single Cell 3’ Reagent Kit v3 protocol

treatment_protocol: Approximately one third of the root including the root tip was chopped with razor blades and the tissue transferred to the protoplasting solution B (containing pectolyase and cellulase)  for 1h. Protoplasts were washed and resuspended in solution A (as solution B, no enzymes), stained with DAPI and DRAQ5 and sorted using FACS selecting YFP/GFP positive cells, negative for DAPI and positive for DRAQ5. In the case of MAKR5_root_tip, roots were not chopped and tips were separated from the rest of the root by incubating them for 15 minutes in the protoplasting solution and discarding the rest of the root. Then root tips were treated as the other samples.

tag: developmental stage

value: elongation zone shootward

tag: cell types

value: Protophloem sieve element and later companion cells, metaphloem sieve element and phloem pole pericycle


title: day6 SSEA4- rep2

tag: condition


title: day6 SSEA4- rep1


title: div12_48_d-Rep2

city: Baltimore

first: Amit

middle: K

last: Singh

state: MD

address: 251 Bayview Blvd, BRC, NIA-NIH

department: LMBI

country: USA

institute: NIA-NIH

data_processing:
Reads were analyzed using online server Galaxy RNA-seq pipeline _usegalaxy.org_.
Adapter trimmed sequences were aligned to mouse genome _mm10_ using HISAT2.  and
Estimation of transcripts was done using Salmon algorithm _TPM_
featureCounts or htseq-count were used for differential gene expression analysis using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include TPM values form each Sample _both replicate_

source_name: mitogen-independent divided

growth_protocol: Two independent biological replicates each consisting pools of 4-5 mice were used for Phase-I _mitogen-dependnet proliferation_. For Phase-I consitits of naive B cells, pulse anti-IgM+anti-CD40 antibody activated B cells for 48h but not divided- div0 and activated for 48h and divided- div12. For Phase-II _mitogen-independent proliferation_, divided _div12_ B cells were further cultured in presence of 0.12 µg/ml of anti-CD40 antibody for next 48h and further FACS sorted in divided _div12_48_d_ and non-divided _div12_48_u_ cells.

extract_protocol:
Total RNA from 1x10^6 _Phase-I_ and 5x10^5 _Phase-II_ cells was isolated using Qiazol _Qiagen_ kit according to manufacturer’s protocol.
RNA-sequencing of total RNA was performed at the Johns Hopkins Deep Sequencing and Microarray Core facility using standard protocol for NextSeq 500 sequencer. Ribosomal RNA was depleted from 100ng of total RNA and barcoded library was made and 50bp single end reads were generated from each sample.

tag: treatment

value: low anti-CD40 for 48h


title: pPEAR1(del)::YFPer

value: meristematic

value: Protophloem sieve element,  metaphloem sieve element, procambial cell


title: div12_48_u-Rep2

source_name: mitogen-independent not-divided


title: div12_48_d-Rep1


title: pSAPL::YFPer

value: Companion cells and metaphloem sieve element


title: div12_48_u-Rep1


title: Ph+ALL108

description: Ph+ALL108, processed data in the file titled "Ph+ALL-3 REPORT_ProbeBasedReport Part1&2&3"

tag: subject status

value: Ph+ALL

tag: gender

value: M

tag: cell type

value: mononuclear cells of bone marrow at diagnosis

value: healthy donor

value: mononuclear cells


title: day14 RFP-GFP- rep2

source_name: pluripotent stem cells

value: H9 primed ESC


title: Ph+ALL107

description: Ph+ALL107, processed data in the file titled "Ph+ALL-2 REPORT_ProbeBasedReport Part1&2&3"

tag: age

tag: status

value: Dead

tag: months


title: day14 RFP+GFP+ rep2

value: mRNA-seq

value: primed-to-naive transition


title: Ph+ALL116

description: Ph+ALL116, processed data in the file titled "Ph+ALL-3 REPORT_ProbeBasedReport Part1&2&3"

value: F


title: Ph+ALL109

description: Ph+ALL109, processed data in the file titled "Ph+ALL-3 REPORT_ProbeBasedReport Part1&2&3"


title: pMAKR5::MAKR5-3xYFP_root_tip

value: All the cells around protophloem sieve element


title: Ph+ALL103

description: Ph+ALL103, processed data in the file titled "Ph+ALL-3 REPORT_ProbeBasedReport Part1&2&3"

value: Alive


title: day14 RFP+GFP- rep2


title: Ph+ALL111

description: Ph+ALL111, processed data in the file titled "Ph+ALL-3 REPORT_ProbeBasedReport Part1&2&3"


title: Ph+ALL118

description: Ph+ALL118, processed data in the file titled "Ph+ALL-3 REPORT_ProbeBasedReport Part1&2&3"


title: day14 RFP+GFP+ rep1


title: day14 RFP+GFP- rep1


title: div0-Rep1

source_name: 48h activated not-divided

value: pulse anti-IgM+antiCD40 for 48h


title: pMAKR5::MAKR5-3xYFP_whole_root


title: day12 RFP-GFP- rep2


title: Naïve-Rep2

source_name: B cell-Naïve

value: resting (no-activation)


title: day14 RFP-GFP- rep1


title: Ph+ALL095

description: Ph+ALL095, processed data in the file titled "Ph+ALL-3 REPORT_ProbeBasedReport Part1&2&3"

source_name: mononuclear cells of bone marrow at diagnosis

source_name: mononuclear cells from pooled healthy donors


title: PRMT1fl/fl; cx3r1cre-ert2 microglia normal diet_rep1

city: Montreal

first: Stephane

last: Richard

address: 3755 Côte Ste-Catherine Road

country: Canada

institute: McGill University

data_processing:
CLC Genomics Workbench v 11.0.1
Single-end reads of length 76 were first trimmed off the adapter sequence as well as the polyA tail and then mapped through the Bowtie2 short read aligner v2.4.1 to the hg19 reference genome from the University of California Santa Cruz (UCSC) (Lander et al., 2001; Langmead and Salzberg, 2012).
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Quality control checks on the raw sequence data were carried out through the FASTQC software v0.11.9. BAM files were sorted and indexed, and duplicate reads were removed through Samtools v0.1.19.
Gene expression was quantified for RNA-seq experiments using HOMER, and the differential expression relative to the control was computed by DESeq2 (Love et al., 2014). Upregulated or downregulated genes were defined as having a false discovery rate (FDR) smaller than 0.05 and absolute log fold change larger than one.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Brains were digested, and myelin were removed using 30% percoll gradient. Microglia was sorted using CD45 and CD11B surface markers. RNA in 2X SuperScript III buffer was incubated for 1 min at 50 C on a PCR cycler with 2.5 ul of the following mix: 1.5 ug Random Primer (Life Technologies 48190-011), 10 M Oligo d(T) (Life Technologies 18418020), 10 units SUPERase-In (Ambion AM2696), 4 mM dNTP mix (Life Technologies 18427088), in water. Samples were then immediately placed on ice for 5 min. First-strand synthesis was then performed by incubation at 25 C for 10 min and 50 C for 50 min on a PCR cycler with 7.6 ul of the following mix: 0.2 ug actinomycin (Sigma A1410), 13.15 mM DTT (Life Technologies), 0.026% Tween-20, 100 units SuperScript III (Life Technologies kit 18080-044), in water. After incubation, RNA/DNA complexes were isolated by adding 36 ul of Agencourt RNAClean XP beads (Beckman Coulter A63987) and incubated for 10 min at RT and then 10 min on ice. Samples were then placed on a magnet and beads were washed twice with 150 ul of 75% EtOH. Following washings, beads were air-dried for 10-12 min and eluted with 10 ul of water. Second-strand synthesis was then performed. RNA/DNA samples in 10 ul of water were incubated for 2.5 hours at 16 C with 5 ul of the following mix: 3x Blue Buffer (Enzymatics), 1.0 ul PCR mix (Affymetrix 77330), 2.0 mM dUTP (Affymetrix 77206), 1 unit RNAseH (Ezymatics Y9220L), 10 units DNA Polymerase I (Enzymatics P7050L), 0.03% Tween-20, in water). DNA was then purified by addition of 1.5 ul Sera-Mag SpeedBeads (Thermo Scientific, 651520505025), resuspended in 30 ul 20% PEG 8000/2.5 M NaCl, incubated at RT for 15 min and placed on a magnet for two rounds of bead washing with 80% EtOH. Beads were then air dried for 10-12 min and DNA was eluted from the beads by adding 40 ul of water. Supernatant was then collected on a magnet and placed on ice or stored at -20C until DNA blunting, poly(A)-tailing, and adapter ligation.
Ethanol-precipitated with glycogen and dissolved in water at 9 μM) were heat-denatured together with the RNA for 2 min at 70°C, and ligated with 100 U truncated T4 RNA ligase 2 K227Q (NEB) in 10 μl 1x T4 RNA ligase buffer without ATP, containing 10 U SUPERase-In and 15% PEG8000 for 2 hr at 16°C. To reduce adaptor dimer formation, 0.5 μl 10 μM MPX_ RT primer 5′-GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T-3′ (IDT, desalted) was added and annealed to the ligation product by incubating at 75°C for 2 min, then 37°C for 30 min, then 25°C for 15 min. Finally, 0.5 μl 5 μM hybrid DNA/RNA sRNA5′h adaptor 5′-GTT CAG AGT TCT ACA rGrUrC rCrGrA rCrGrA rUrC-3′ (IDT) were ligated to previously capped RNA 5′ ends by adding 2 μl T4 RNA ligase buffer, 6 μl 50% PEG8000 (15% final), 1 μl 10 mM ATP, 9.5 μl water and 0.5 μl (5 U) T4 RNA ligase 1 for 90 min at 20°C. To 15 μl ligation reaction, an additional 0.5 μl 10 μM MPX_ RT primer were added, reactions were denatured at to 70°C for 1 min, then placed on ice. RNA was reverse-transcribed by adding 3 μl 10x first strand buffer, 4.5 μl water, 1.5 μl 10 mM dNTP, 3 μl 0.1 M DTT, 1.5 μl RNaseOUT and 1 μl Superscript III reverse transcriptase (Invitrogen), and incubating for 30 min at 50°C. Complementary DNA was isolated with Sera-Mag SpeedBeads (Thermo Scientific, 6515205050250) in 20% PEG/2.5M NaCl. and dissolved in 40 μl TET. RNA-seq libraries were digested by 30 min of incubation at 37C with Uracil DNA Glycosylase (final concentration of 0.134 units per ul of library volume; UDG, Enzymatics G5010L) to generate strand-specific libraries. Libraries were PCR-amplified for 12-15 cycles and size selected for fragments (200-500 for RNA-seq) by gel extraction (10% TBE gels, Life Technologies EC62752BOX).  RNA-seq librairies were single-end sequenced for 76 cycles on an Illumina HiSeq 4000 (Illumina, San Diego, CA) according to manufacturer’s instruction.

treatment_protocol: 0.2% of Cuprizone diet was fed in 4-6 weeks-old wild-type (PRMT1Ifl/fl) and microglia specific knockout (PRMT1fl/fl; cx3r1cre-ert2) mice

tag: cell line

value: Microglia

tag: genotype

value: PRMT1fl/fl; cx3r1cre-ert2

value: Normal diet

tag: time

value: 11 weeks


title: PRMT1fl/fl; cx3r1cre-ert2 microglia CPZ diet_CD11c_low

value: 0.2% cuprizone diet

value: 5 weeks


title: PRMT1Ifl/fl microglia CPZ diet_CD11c_high


title: div12-Rep1

source_name: 48h activated divided

tag: strain


title: Ph+ALL094

description: Ph+ALL094, processed data in the file titled "Ph+ALL-3 REPORT_ProbeBasedReport Part1&2&3"

value: Ph+ALL

value: mononuclear cells of bone marrow at diagnosis

value: healthy donor


title: pS17::GFP

value: elongation zone shootward

value: Phloem pole pericycle


title: day12 RFP+GFP+ rep1

value: H9 primed ESC

value: mRNA-seq

value: primed-to-naive transition


title: PRMT1Ifl/fl microglia CPZ diet_CD11c_low


title: PRMT1fl/fl; cx3r1cre-ert2 microglia normal diet_rep2


title: Ph+ALL090

description: Ph+ALL090, processed data in the file titled "Ph+ALL-1 REPORT_ProbeBasedReport Part1&2&3"

value: F

value: Alive

value: mononuclear cells


title: day12 RFP-GFP- rep1


title: Ph+ALL089

description: Ph+ALL089, processed data in the file titled "Ph+ALL-3 REPORT_ProbeBasedReport Part1&2&3"

value: M

value: Dead


title: IgG

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
Library strategy: CUT&RUN
CUT&RUN data was aligned using bowtie against mm10 version of the mouse genome and HOMER was used to call significant peaks using “-histone” option.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *bw: Processed files contain the CUT&RUN signal in bigwig format.

source_name: ID8 cell line

extract_protocol:
Cells were harvested by trypsinization and gently washed twice using wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, and EDTA-free Protease Inhibitor Cocktail). Cells were then incubated with the antibody at 4 °C overnight in antibody buffer (wash buffer supplemented with 0.05% digitonin and 2 mM EDTA). The next day, supernatant was removed by centrifugation and cell pellets were washed once with Dig-wash buffer (Wash buffer containing 0.05% digitonin). Cell pellets were then incubated with Protein A MNase (700 ng/ml in Dig-wash buffer) for 1 h by rotation at 4 °C. After three times of washes, cell pellets were resuspended in 100 ul Dig-wash buffer with 2 ul 100 mM CaCl2 and incubated at 0 °C for 30 min; reactions were stopped by addition of 100 ul 2× STOP buffer (340 mM NaCl, 20 mM EDTA pH 8.0, 4 mM EGTA, 0.05% digitonin, 50 ug/ml RNase A, 50 ug/ml glycogen). The supernatant DNA was collected after centrifugation and further purified using phenol–chloroform–isoamyl alcohol (Sigma, Cat# p3803) extraction and ethanol precipitation.
Purified DNA was used for library construction using the NEBNext Ultra DNA Library Prep Kit (NEB, Cat# E7645) following the manufacturer’s instructions.

tag: kdm5a genotype

value: WT

tag: antibody

value: IgG

tag: replicate


title: div0-Rep2

value: pulse anti-IgM+antiCD40 for 48h


title: div12-Rep2


title: day12 RFP+GFP+ rep2

tag: source

tag: library type


title: Naïve-Rep1

value: resting (no-activation)


title: day12 RFP+GFP- rep1

tag: condition


title: Ph+ALL070

description: Ph+ALL070, processed data in the file titled "Ph+ALL-3 REPORT_ProbeBasedReport Part1&2&3"

value: Ph+ALL


title: Ph+ALL071

description: Ph+ALL071, processed data in the file titled "Ph+ALL-3 REPORT_ProbeBasedReport Part1&2&3"

value: mononuclear cells of bone marrow at diagnosis


title: PRMT1Ifl/fl microglia normal diet_rep3

value: Microglia

tag: treatment

value: Normal diet

value: 11 weeks


title: day12 RFP+GFP- rep2

value: H9 primed ESC


title: KDM5A KO cells, replicate 2

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and mm10 genome with ensemble transcriptome information.
DESeq2 was used for differential expression analysis.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: KDM5A_RNAseq.txt: Processed file contains the raw counts for each gene.

extract_protocol:
Total RNA of control ID8 and Kdm5a knockout ID8 cell lines was extracted using RNeasy mini Kit (Qiagen, Cat# 74106) and digested with DNase I (Qiagen, Cat# 79254).
RNA-seq libraries were constructed using ScriptSeq complete Gold kit (Epicentre, Cat# SCL24EP).

value: KO


title: papl1-1papl2(cog1-6cdf4)_rep3

data_processing:
map to a reference genome using TopHat2
HTSeq software was used to analyze the gene expression level using the union mode. FPKM value of 0.1 or 1 is set as the threshold to determine whether a gene is expressed or not
The differential gene exprsesion analysis consists on readcount normalization, model-dependent mean value stimation and FDR value estimation based on multiple hypotheses testing. DESeq was used for thtese steps
Genome_build: TAIR10 genome with Araport 11 gene annotation
Supplementary_files_format_and_content: CSV file with counts estimated by HTSeq. These can be imported into R, for example, using the `read.csv()` function and used in the DESeq2 differential expression analysis.

source_name: root meristems

growth_protocol: Seedlings were grown on plates containing 1/2 x MS Media (0.5 x MS Salts, 1% Difco agar,  1% sucrose) at 23ºC for 5 days in long day conditions

extract_protocol:
RNA was extracted using the RNA extraction kit from Qiagen and RNA integrity and concentration were checked using TapeStation and Qubit 2.0 fluorometer (Life Technologies) respectively. After quality control in Novogene company, the best 3 replicates for mutant and wild type were used for library construction and sequencing following the Novogene pipeline.
mRNA is enriched by using oligo dT, fragmented randomly followed by cDNA synthesis using random hexamers and reverse transcriptase. Second strand is synthesized by nick-translation. Library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment

treatment_protocol: meristems were manually dissected under the stereomicroscope, prserved with RNAlater and processed using the RNA Qiagen extraction kit

tag: developmental stage

value: 5 day old

tag: extraction

value: manually dissected under stereomicroscope

tag: tissue

value: root meristems


title: papl1-1papl2(cog1-6cdf4)_rep2


title: Ph+ALL055

description: Ph+ALL055, processed data in the file titled "Ph+ALL-2 REPORT_ProbeBasedReport Part1&2&3"

tag: subject status

tag: gender

tag: age

tag: cell type

value: healthy donor

value: mononuclear cells


title: Ph+ALL086

description: Ph+ALL086, processed data in the file titled "Ph+ALL-3 REPORT_ProbeBasedReport Part1&2&3"

value: F

tag: status

value: Dead

tag: months


title: Ph+ALL067

description: Ph+ALL067, processed data in the file titled "Ph+ALL-3 REPORT_ProbeBasedReport Part1&2&3"

value: M


title: PRMT1Ifl/fl microglia normal diet_rep2

tag: cell line

tag: genotype

tag: time


title: KDM5A KO cells, replicate 3

tag: kdm5a genotype

tag: replicate


title: KDM5A

value: WT

tag: antibody


title: day10 RFP-GFP- rep1

description: ALPG-promoter-RFP/OCT4-ΔPE-GFP dual repoter

tag: source

tag: library type

value: mRNA-seq

tag: condition

value: primed-to-naive transition


title: H3K4me3


title: Ph+ALL038

description: Ph+ALL038, processed data in the file titled "Ph+ALL-1 REPORT_ProbeBasedReport Part1&2&3"

value: Ph+ALL

value: mononuclear cells of bone marrow at diagnosis


title: wt_Col0_rep2

tag: developmental stage

tag: extraction


title: KDM5A WT cells, replicate 2


title: Ph+ALL042

description: Ph+ALL042, processed data in the file titled "Ph+ALL-2 REPORT_ProbeBasedReport Part1&2&3"

tag: subject status


title: KDM5A WT cells, replicate 3


title: KDM5A KO cells, replicate 1


title: day10 RFP-GFP- rep2


title: PRMT1Ifl/fl microglia normal diet_rep1

value: Microglia

tag: treatment

value: Normal diet


title: wt_Col0_rep3

tag: tissue


title: KDM5A WT cells, replicate 1


title: wt_Col0_rep1


title: Ph+ALL019

description: Ph+ALL019, processed data in the file titled "Ph+ALL-2 REPORT_ProbeBasedReport Part1&2&3"

tag: gender

tag: age

value: Alive

tag: cell type


title: papl1-1papl2(cog1-6cdf4)_rep1


title: Ph+ALL006

description: Ph+ALL006, processed data in the file titled "Ph+ALL-2 REPORT_ProbeBasedReport Part1&2&3"

tag: status

tag: months


title: KT2440_glc_2

status: Public on Apr 28 2022

city: San Diego

first: Bernhard

middle: O.

last: Palsson

state: California

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

description: Pseudomonas putida KT2440 grown in a minimal medium supplemented gluconate Replicate 2

data_processing:
Raw RNA-Seq reads were mapped to the original reference genome using Bowtie and transcript abundance was analyzed using summarizeOverlaps (Lawrence et al., 2013). Calculation of transcripts per million (TPM) and prediction of differentially expressed genes were conducted using DESeq2 (Love et al., 2014).
Assembly: AE015451.2
Supplementary files format and content: csv and log tpm

organism: Pseudomonas putida KT2440

growth_protocol: Shake flask experiments were performed by inoculating seed cultures from glycerol stocks into 5 mL of LB medium, incubating overnight at 30°C and 225 rpm. Overnight cultures were then used to inoculate a second seed culture in LB medium starting at an optical density of 0.2 measured at 600 nm (OD600) using a Beckman DU640 spectrophotometer (Beckman Coulter). The second seed cultures were incubated at 30°C at 225 rpm for 2–3 h until an OD600 of approximately 2 was reached. These seed cultures were centrifuged at 4500 rpm for 5 min, the pellets were resuspended in 1X M9 salts, and were used to inoculate the shake flasks containing modified M9 minimal media comprising 6.78 g/L Na2HPO4, 3 g/L KH2PO4, 0.5 g/L NaCl, 1 g/L NH4Cl, 2 mM MgSO4, 100 μM CaCl2, 18 μM FeSO4, and 25 mM or 30 mM glucose, as specified in text, to a starting OD600 of 0.1.

extract_protocol:
Cells pelleted from 15 mL of M9 minimal medium were flash frozen and stored at −80°C. Cells were resuspended in TRIzol (ThermoFisher-Invitrogen) and processed according to the manufacturer's protocol. The samples were then purified on an RNeasy column (Qiagen) with on-column DNase digestion. RNA was eluted off the column in 35 μL RNase free H2O (Qiagen). The RNA concentration was quantified using a Nanodrop 1000 (ThermoScientific) and RNA quality was verified by obtaining RNA Integrity Numbers (RIN) using an RNA 6000 Nanochip on an Agilent 2100 Bioanalyzer (Agilent).
Ribosomal RNA was depleted using a RiboZero rRNA Removal Kit for bacteria (Illumina). The depleted sample was purified on an RNA Clean & Concentrator-5 (Zymo Research), and then the depleted material was quantified using a Nanodrop 1000 and visualized on an Agilent 2100 Bioanalyzer instrument with an RNA 6000 Nanochip (Agilent). RNA depleted of ribosomal RNA was used as input material to synthesize cDNA libraries using a ScriptSeq v2 RNA-Seq Library Preparation Kit (Illumina) and TruSeq compatible barcodes. Pooled barcoded libraries were sequenced in one direction for 75 bases (SE75) on an Illumina NextSeq500 (Illumina) and de-multiplexed as a sequencing service provided by Vanderbilt 2.9 (VUMC VANTAGE Vanderbilt University Medical Center Technologies for Advanced Genomics).

tag: atcc catalog number

tag: genotype

value: KT2440 wildtype

tag: treatment (carbon sources)

value: gluconate

tag: treatment (supplements)


title: KT2440_glc_3

description: Pseudomonas putida KT2440 grown in a minimal medium supplemented gluconate Replicate 3


title: KT2440_glc_1

description: Pseudomonas putida KT2440 grown in a minimal medium supplemented gluconate Replicate 1


title: KT2440_gg_2

description: Pseudomonas putida KT2440 grown in a minimal medium supplemented glucose and gluconate Replicate 2

value: glucose and gluconate


title: KT2440_gg_3

description: Pseudomonas putida KT2440 grown in a minimal medium supplemented glucose and gluconate Replicate 3


title: KT2440_fg_3

description: Pseudomonas putida KT2440 grown in a minimal medium supplemented fructose and glucose Replicate 3

value: fructose and glucose


title: KT2440_gfg_3

description: Pseudomonas putida KT2440 grown in a minimal medium supplemented fructose, glucose, and gluconate Replicate 3

value: fructose, glucose, and gluconate


title: KT2440_gg_1

description: Pseudomonas putida KT2440 grown in a minimal medium supplemented glucose and gluconate Replicate 1


title: KT2440_gfg_2

description: Pseudomonas putida KT2440 grown in a minimal medium supplemented fructose, glucose, and gluconate Replicate 2


title: KT2440_gfg_1

description: Pseudomonas putida KT2440 grown in a minimal medium supplemented fructose, glucose, and gluconate Replicate 1


title: KT2440_f_3

description: Pseudomonas putida KT2440 grown in a minimal medium supplemented fructose Replicate 3

value: fructose


title: KT2440_f_2

description: Pseudomonas putida KT2440 grown in a minimal medium supplemented fructose Replicate 2


title: KT2440_f_1

description: Pseudomonas putida KT2440 grown in a minimal medium supplemented fructose Replicate 1


title: KT2440_fg_1

description: Pseudomonas putida KT2440 grown in a minimal medium supplemented fructose and glucose Replicate 1


title: GB062_gg_3

description: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented glucose and gluconate Replicate 3


title: GB062_glc_3

description: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented gluconate Replicate 3


title: GB062_glc_2

description: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented gluconate Replicate 2


title: GB062_gg_1

description: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented glucose and gluconate Replicate 1


title: GB062_glc_1

description: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented gluconate Replicate 1


title: GB062_gg_2

description: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented glucose and gluconate Replicate 2


title: GB062_gfg_3

description: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented fructose, glucose, and gluconate Replicate 3


title: GB062_gfg_2

description: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented fructose, glucose, and gluconate Replicate 2


title: GB062_f_2

description: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented fructose Replicate 2


title: GB062_f_3

description: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented fructose Replicate 3


title: GB062_fg_2

description: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented fructose and glucose Replicate 2


title: GB062_f_1

description: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented fructose Replicate 1


title: GB062_fg_1

description: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented fructose and glucose Replicate 1


title: GB062_gfg_1

description: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented fructose, glucose, and gluconate Replicate 1


title: GB045_glc_3

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented gluconate Replicate 3


title: GB045_glc_2

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented gluconate Replicate 2


title: GB045_glu_3

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented glucose Replicate 3

value: glucose


title: GB045_glu_2

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented glucose Replicate 2


title: GB045_glu_1

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented glucose Replicate 1


title: KT2440_fg_2

description: Pseudomonas putida KT2440 grown in a minimal medium supplemented fructose and glucose Replicate 2


title: GB045_glc_1

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented gluconate Replicate 1


title: GB045_gfg_3

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented fructose, glucose, and gluconate Replicate 3


title: GB045_gg_1

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented glucose and gluconate Replicate 1


title: GB045_gg_2

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented glucose and gluconate Replicate 2


title: GB045_gg_3

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented glucose and gluconate Replicate 3


title: GB045_gfg_2

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented fructose, glucose, and gluconate Replicate 2


title: GB062_fg_3

description: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented fructose and glucose Replicate 3


title: GB045_fg_2

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented fructose and glucose Replicate 2


title: GB045_gfg_1

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented fructose, glucose, and gluconate Replicate 1


title: GB045_fg_1

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented fructose and glucose Replicate 1


title: GB045_f_3

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented fructose Replicate 3


title: GB045_fg_3

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented fructose and glucose Replicate 3


title: GB032_glu_1

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented glucose Replicate 1


title: GB032_glc_3

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented gluconate Replicate 3


title: GB032_glu_3

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented glucose Replicate 3


title: GB032_glu_2

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented glucose Replicate 2


title: GB045_f_1

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented fructose Replicate 1


title: GB032_gg_3

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented glucose and gluconate Replicate 3


title: GB032_glc_1

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented gluconate Replicate 1


title: GB032_gg_2

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented glucose and gluconate Replicate 2


title: GB032_gfg_3

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented fructose, glucose, and gluconate Replicate 3


title: GB032_gfg_2

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented fructose, glucose, and gluconate Replicate 2


title: GB032_fg_3

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented fructose and glucose Replicate 3


title: GB032_fg_2

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented fructose and glucose Replicate 2


title: GB032_gg_1

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented glucose and gluconate Replicate 1


title: GB032_f_2

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented fructose Replicate 2


title: GB032_f_3

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented fructose Replicate 3


title: CJ522_glc_1

description: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented gluconate Replicate 1


title: GB032_gfg_1

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented fructose, glucose, and gluconate Replicate 1


title: GB032_glc_2

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented gluconate Replicate 2


title: GB032_fg_1

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented fructose and glucose Replicate 1


title: CJ522_gg_3

description: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented glucose and gluconate Replicate 3


title: GB045_f_2

description: Pseudomonas putida KT2440 GB045 grown in a minimal medium supplemented fructose Replicate 2


title: CJ522_gfg_1

description: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented fructose, glucose, and gluconate Replicate 1


title: CJ522_glc_2

description: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented gluconate Replicate 2


title: CJ522_glc_3

description: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented gluconate Replicate 3


title: CJ522_gg_2

description: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented glucose and gluconate Replicate 2


title: CJ522_fg_1

description: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented fructose and glucose Replicate 1


title: CJ522_gg_1

description: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented glucose and gluconate Replicate 1


title: CJ522_gfg_3

description: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented fructose, glucose, and gluconate Replicate 3


title: CJ522_fg_3

description: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented fructose and glucose Replicate 3


title: CJ522_f_3

description: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented fructose Replicate 3


title: CJ522_f_1

description: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented fructose Replicate 1


title: Aromatic_Wildtype_glc, rep3

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L glucose as a sole carbon source replicate 3

data_processing:
Raw RNA-Seq reads were mapped to the original reference genome using Bowtie and transcript abundance was analyzed using summarizeOverlaps (Lawrence et al., 2013). Calculation of transcripts per million (TPM) and prediction of differentially expressed genes were conducted using DESeq2 (Love et al., 2014).
Genome_build: AE015451.2
Supplementary_files_format_and_content: csv and log tpm

growth_protocol: All microbial cultures were conducted at 30 ˚C using the modified minimal M9 medium (4 g/L glucose, 2 g/L (NH4)2SO4, 6.8 g/L Na2HPO4, 3 g/L KH2PO4, 0.5 g/L NaCl, 2 mM MgSO4, 0.1 mM CaCl2, 500 μL/L 2000X trace element solution). The composition of the trace element solution is 4.5 g/L ZnSO4⋅7H2O, 0.7 g/L MnCl2⋅4H2O, 0.3 g/L CoCl2⋅6H2O, 0.2 g/L CuSO4⋅2H2O, 0.4 g/L Na2MoO4⋅2H2O, 4.5 g/L CaCl2⋅2H2O, 3.0 g/L FeSO4⋅7H2O, 1.0 g/L H3BO3, 0.1 g/L KI, 15 g/L disodium ethylenediaminetetraacetate. 2.5 g/L of a carbon source was used for the 12 samples used in the "Aromatic" project.

extract_protocol:
For transcriptomic analysis, cell cultures at the exponential phase (OD600 0.4-0.6) were mixed with two volumes of RNA protect Bacteria Reagent (Qiagen, Hilden, Germany) for stabilization and their total RNA was extracted by using Quick-RNA Fungal/Bacterial Miniprep Kit (Zymo Research). Residual genomic DNA was removed by incubating the samples with DNase I (RNase-free, NEB). Ribosomal RNA was removed by hybridizing with 30-bp oligonucleotides designed to bind the ribosomal RNA of KT2440 specifically and treating with Thermostable RNase H purchased from Lucigen (Middleton, WI, USA). The remaining oligonucleotides were removed by incubating the resulting samples with DNase I (NEB). The samples were purified by using an RNA Clean & Concentrator Kit (Zymo Research). The 12 samples for the “aromatic” project were prepared with several modifications. Collected cells were resuspended in TRIzolTM reagent (ThermoFisher Scientific, Waltham, MA, USA).  Total RNA was isolated using the RNeasy Mini Kit (Qiagen) by following the manufacturer’s instructions. Ribosomal RNA was removed from total RNA using the Ribo-Zero rRNA removal kit (illumina).
Paired-end RNA-Seq libraries were constructed using either KAPA RNA HyperPrep kit from Kapa Biosystems (Wilmington, MA, USA) or ScriptSeqTM Complete kit (illumina, CA, USA).

value: 2.5 g/L glucose


title: CJ522_gfg_2

description: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented fructose, glucose, and gluconate Replicate 2


title: CJ522_fg_2

description: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented fructose and glucose Replicate 2


title: Aromatic_Wildtype_glc, rep2

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L glucose as a sole carbon source replicate 2


title: CJ522_f_2

description: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented fructose Replicate 2


title: Aromatic_Wildtype_glc, rep1

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L glucose as a sole carbon source replicate 1


title: Aromatic_Wildtype_ferulate, rep2

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L ferulate as a sole carbon source replicate 2

value: 2.5 g/L ferulic acid


title: Aromatic_Wildtype_ferulate, rep1

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L ferulate as a sole carbon source replicate 1


title: GB032_f_1

description: Pseudomonas putida KT2440 GB032 grown in a minimal medium supplemented fructose Replicate 1


title: Aromatic_Wildtype_coum, rep2

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L coumarate as a sole carbon source replicate 2

value: 2.5 g/L p-coumaric acid


title: Aromatic_Wildtype_coum, rep3

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L coumarate as a sole carbon source replicate 3


title: Aromatic_Wildtype_coumferul, rep2

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L of a mixture of coumarate and ferulate as sole carbon sources replicate 2

value: 2.5 g/L p-coumaric acid and ferulic acid


title: Aromatic_Wildtype_ferulate, rep3

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L ferulate as a sole carbon source replicate 3


title: Aromatic_Wildtype_coumferul, rep3

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L of a mixture of coumarate and ferulate as sole carbon sources replicate 3


title: Aromatic_Wildtype_coumferul, rep1

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L of a mixture of coumarate and ferulate as sole carbon sources replicate 1


title: Aromatic_Wildtype_coum, rep1

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L coumarate as a sole carbon source replicate 1


title: GapmeR against ADIPINT 1 replicate4

type: RNA

city: Huddinge

first: hui

last: Gao

address: Novum

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

hyb_protocol: 5 ug fragmented and biotinylated ssDNA were hybridized for 16 hr at 45C to Affymetrix Clariom S human arrays according to standard protocol. Washing and staining were performed using Affymetrix Fluidics Station 450.

scan_protocol: The fluorescent intensities were determined with Affymetrix GeneChip Scanner 3000 7G

data_processing: Data were preprocessed and analyzed using the Affymetrix Expression Console (version 1.4.1) and standard SST-RMA method. Prior to further analysis, collapseRows R function (Miller et al., 2011) was used to convert and collapse the transcript abundance quantification detected by Affymetrix probe sets to mapped FANTOM-CAT IDs. Affymetrix probe IDs were mapped to the FANTOM-CAT gene model , 54,980 probe sets mapped to 40,590 unique gene IDs.

label: biotin

source_name: hADSC

label_protocol: Biotinylated cRNA was prepared using the GeneChip WT Plus Reagent Kit according to the standard Affymetrix protocol from 150ng total RNA.

growth_protocol: hADSC cells were plated at a cell density of 20 000 cells/cm2 and incubated at 37°C with 5% CO2. Adipogenesis was induced two days post confluence using DMEM/F12  as well as the adipogenic cocktail; 5 mg/mL insulin, 0.25 mmol/l dexamethasone, 0.5 mmol/l 3-isobutyl-1-methylxanthine (IBMX) and 10 mmol/l rosiglitazone for two days after which the dexamethasone and IBMX were removed and the cells were allowed to undergo full adipogenic differentiation.

extract_protocol: Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, cat. 740955.250) according to the manufacture's instructions. The concentration, purity and quality were measured using Nanodrop 2000 (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Antisense LNA GapmeRs (Qiagen) were introduced by electroporation using a Neon Transfection System (1300 V, 20 ms, 2 pulses) 100 µL Kit (Invitrogen) in human in vitro differentiated hADSCs at day eight of differentiation.

value: Adipose Derived Stem Cells (hADSC)

tag: group

value: GapmeR 1


title: Gapmer Negative Control A replicate6

value: GapmeR NC


title: Gapmer Negative Control A replicate7


title: GapmeR against ADIPINT 3 replicate3

value: GapmeR 3


title: Gapmer Negative Control A replicate4


title: GapmeR against ADIPINT 2 replicate1

value: GapmeR 2


title: GapmeR against ADIPINT 1 replicate2


title: Gapmer Negative Control A replicate1


title: GapmeR against ADIPINT 2 replicate4


title: GapmeR against ADIPINT 3 replicate2


title: GapmeR against ADIPINT 1 replicate1


title: D80_5_year

data_processing: These arrays were preprocessed using the Affymetrix Expression Console (version 1.4.1) and standard SST-RMA method, which includes normalization, summarization of probes to probesets, and background correction. Prior to further analysis, collapseRows R function (Miller et al., 2011) was used to convert and collapse the transcript abundance quantification detected by Affymetrix probe sets to mapped FANTOM-CAT IDs, 54,980 probe sets mapped to 40,590 unique gene IDs

source_name: Subcutaneous adipose tissue

extract_protocol: Total RNA was isolated using the RNeasy kit (cat no. 217004, Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Biopsies from the subcutaneous adipose tissue depot were obtained from the surgical incision. Samples were immediately frozen in liquid nitrogen and kept at -70C for subsequent DNA and RNA preparation.

value: Female

value: Adipose tissue


title: GapmeR against ADIPINT 3 replicate4


title: D78_5_year


title: Gapmer Negative Control A replicate2


title: Gapmer Negative Control A replicate5


title: GapmeR against ADIPINT 2 replicate2


title: D70_5_year


title: D72_5_year


title: GapmeR against ADIPINT 2 replicate3


title: D75_5_year


title: D65_5_year


title: D64_5_year


title: D71_5_year


title: GapmeR against ADIPINT 1 replicate3


title: GapmeR against ADIPINT 3 replicate1


title: Gapmer Negative Control A replicate3


title: D76_5_year


title: D66_5_year


title: D62_5_year


title: D56_5_year


title: D59_5_year


title: D49_5_year


title: D40_5_year


title: D38_5_year


title: D53_5_year


title: D47_5_year


title: D42_5_year


title: D33_5_year


title: D23_5_year


title: D31_5_year


title: D29_5_year


title: D58_5_year


title: D22_5_year


title: D11_5_year


title: D14_5_year


title: D8_5_year


title: D15_5_year


title: D67_5_year


title: D35_5_year


title: D6_5_year


title: D1_5_year


title: D79_2_year


title: D19_5_year


title: D72_2_year


title: D76_2_year


title: D69_2_year


title: D30_5_year


title: D67_2_year


title: D80_2_year


title: D7_5_year


title: D75_2_year


title: D74_2_year


title: D66_2_year


title: D65_2_year


title: D70_2_year


title: D59_2_year


title: D52_2_year


title: D62_2_year


title: D64_2_year


title: D78_2_year


title: D56_2_year


title: D47_2_year


title: D58_2_year


title: D4_5_year


title: D50_2_year


title: D73_2_year


title: D42_2_year


title: D49_2_year


title: D33_2_year


title: D31_2_year


title: D3_5_year


title: D40_2_year


title: D51_2_year


title: D36_2_year


title: D29_2_year


title: D30_2_year


title: D23_2_year


title: D27_2_year


title: D22_2_year


title: D35_2_year


title: D20_2_year


title: D21_2_year


title: D38_2_year


title: D19_2_year


title: D11_2_year


title: D15_2_year


title: D7_2_year


title: D9_2_year


title: D4_2_year


title: D6_2_year


title: D8_2_year


title: D3_2_year


title: K25_Control

value: Control


title: K30_Control


title: D1_2_year


title: K33_Control


title: K27_Control


title: D14_2_year


title: K20_Control


title: K16_Control


title: K28_Control


title: K19_Control


title: K7_Control


title: K31_Control


title: K32_Control


title: K15_Control


title: K9_Control


title: K26_Control


title: K12_Control


title: D71_2_year


title: K2_Control


title: K22_Control


title: K5_Control


title: K13_Control


title: K1_Control


title: K14_Control


title: K4_Control


title: K3_Control


title: K18_Control


title: D78_Baseline

value: Baseline


title: K29_Control


title: D75_Baseline


title: K23_Control


title: D76_Baseline


title: K24_Control


title: D79_Baseline


title: D74_Baseline


title: D72_Baseline


title: D70_Baseline


title: D80_Baseline


title: D66_Baseline


title: D73_Baseline


title: D69_Baseline


title: D67_Baseline


title: D71_Baseline


title: D56_Baseline


title: D58_Baseline


title: D53_Baseline


title: D65_Baseline


title: D52_Baseline


title: D50_Baseline


title: D64_Baseline


title: D59_Baseline


title: D62_Baseline


title: D35_Baseline


title: D51_Baseline


title: D36_Baseline


title: D33_Baseline


title: D42_Baseline


title: D29_Baseline


title: D49_Baseline


title: D38_Baseline


title: D47_Baseline


title: D40_Baseline


title: D31_Baseline


title: D20_Baseline


title: D15_Baseline


title: D8_Baseline


title: Non-IR_Z-Br-6h

city: Beijing

first: Zhang

middle: Xiao

last: Chang

address: Taiping 27 Road

institute: Beijing Institute of Radiation Medicine

description: This is a brain sample from an untreated wild mouse

hyb_protocol: Hybridization was performed by Bioassay Laboratory of CapitalBio Corporation，Beijing, following their standard operating protocol. See http:www.capitalbio.com.

scan_protocol: Scan  was performed by Bioassay Laboratory of CapitalBio Corporation，Beijing, following their standard operating protocol. See http:www.capitalbio.com.

data_processing:
After data correction, such as normalization of signal value with RMA, SAM4.0 software was used for analysis.
FDR was controlled within 5%, and differential expression genes were screened by 2 or 1.5 times standard.

source_name: C57BL/6J wild mice

label_protocol: Labeling was performed by Bioassay Laboratory of CapitalBio Corporation，Beijing, following their standard operating protocol. See http:www.capitalbio.com.

growth_protocol: Mice were divided into normal control group, drug control group, radiation control group, drug irradiation group, radiation control group. Mice in the radiation control group and drug irradiation group were given 6.5 Gy 60Co γ -ray 30 min after administration.

extract_protocol: Total RNA was extracted from tissues by appropriate methods and purified with NucleoSpin RNA clean-up Kit (Macherey-Nagel, Germany), quantified by spectrophotometer and inspected by formaldehyde denaturing gel electrophoresis.

treatment_protocol: Bone marrow and brain tissues of mice in each group were collected 6 h, 7 days and 14 days after irradiation

value: Brain

tag: treat

value: Non-IR

tag: time


title: Non-IR_Z-Bm-14d

description: This is a bone marrow sample from an untreated wild mouse

value: Bone marrow


title: Non-IR_Z-Br-7d


title: D11_Baseline


title: D1_Baseline


title: Non-IR_Z-Br-14d


title: IR_F-Bm-7d

description: Bone marrow samples were obtained from mice in the radiation control group 7 days after irradiation.

value: IR


title: IR_F-Br-7d

description: Brain samples were obtained from mice in the radiation control group 7 days after irradiation.


title: IR_F-Bm-14d

description: Bone marrow samples were obtained from mice in the radiation control group 14 days after irradiation.


title: D9_Baseline


title: D14_Baseline


title: IR_F-Br-14d

description: Brain samples were obtained from mice in the radiation control group 14 days after irradiation.


title: D4_Baseline


title: Non-IR_Z-Bm-6h


title: D27_Baseline


title: Non-IR_Z-Bm-7d


title: D3_Baseline


title: IR_F-Br-6h

description: Brain samples were obtained from mice in the radiation control group 6 hours after irradiation.


title: D23_Baseline


title: D22_Baseline


title: D7_Baseline


title: D19_Baseline


title: D6_Baseline


title: D21_Baseline


title: IR_F-Bm-6h

description: Bone marrow samples were obtained from mice in the radiation control group 6 hours after irradiation.


title: K6_Control


title: crossbred male, rep 3

city: Madrid

first: Cristina

last: Ovilo

address: Ctra Coruña km 7.5

country: Spain

institute: INIA-CSIC

data_processing:
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to assess the quality of raw sequencing data.
TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to quality trim data with default settings and to remove the sequencing adaptors and poly A and T tails (stringency of 6 bp, -s 6) keeping only paired-end reads where both pairs were longer than 40 bp.
Filtered reads were mapped against the pig reference genome (Sscrofa11.1) using HISAT2 applying default settings.
HTseq-count software was used to obtain information on number of reads per gene.
Differential expression was analysed with DESeq2 software in R environment.
Assembly: Sscrofa 11.1
Supplementary files format and content: processed_data.xlsx: Processed data file includes normalized expression values for all genes in all 20 samples.

organism: Sus scrofa

source_name: hypothalamus

growth_protocol: All tissues were collected within 15 min postmortem, snap-frozen in liquid nitrogen, and then stored at -80° C until processing.

extract_protocol:
Total RNA was extracted from 50-100mg samples of hypothalamus using the RiboPure TM of High Quality total RNA kit (Ambion, Austin, TX, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-100 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The quality of the RNA was evaluated using the RNA Integrity Number (RIN) value from the Agilent 2100 Bioanalyzer device (Agilent technologies, Santa Clara, CA, USA). The RIN values ranged from 7.8 to 9.8.
Sequencing libraries were made using the mRNA-Seq sample preparation kit (Illumina Inc., Cat. # RS-100-0801) according to manufacturer’s protocol. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired end mode with the read length 2x76bp on a on a HiSeq2000 sequence analyzer (Illumina, Inc). Images from the instrument were processed using the manufacturer’s software to generate FASTQ sequence files.

treatment_protocol: 50-100 mg samples of each tissue were ground in liquid nitrogen with mortar and pestle.

value: hypothalamus

value: 2 months

tag: Sex

value: male

tag: breed

value: Iberian x Large White


title: crossbred female, rep 5

value: female


title: Iberian male, rep 5

value: Iberian


title: Iberian male, rep 4


title: Iberian female, rep 5


title: crossbred male, rep 4


title: crossbred female, rep 4


title: Iberian male, rep 2


title: Iberian male, rep 3


title: crossbred male, rep 5


title: Iberian female, rep 4


title: Iberian female, rep 3


title: crossbred female, rep 3


title: crossbred male, rep 2


title: crossbred male, rep 1


title: Iberian male, rep 1


title: crossbred female, rep 2


title: Iberian female, rep 1


title: crossbred female, rep1


title: Adipocyte, Input, 4

city: Jinan

first: Junjun

last: Liu

address: 18877 Jingshi road

institute: Shandong First Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11)
Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the  reference genome using BWA mem ( v 0.7.12).
The MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets.
Assembly: mm10
Supplementary files format and content: narrowPeak (except for Input sample)

source_name: Adipocyte

extract_protocol:
the epididymal adipose tissues was removed at the 4th week after injection.
ChIP-seq libraries were purified, quantified, multiplexed and submitted to 75 bp single-end sequencing using the NextSeq® 500/550 High output Kit v2 (75 cycles) on a NextSeq® 500 sequencing system (Illumina), pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.  platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Mice were transfected with AAV2-Otud3-Flag by i.p. injection

tag: cell line

value: Adipocyte

tag: antibody

value: Genomic DNA


title: Iberian female, rep 2

tag: tissue


title: Engineered NK cells with CAR19

city: Houston

first: Katy

last: Rezvani

address: Zayed Building, 5th floor 6565 MD Anderson Blvd. Unit 1061 Houston, TX 77030

department: Stem Cell Transplantation & Cellular Therapy department

institute: MD Anderson Cancer Center

data_processing:
Cellranger mkfastq v3.01 to generate FASTQ
Cellranger count v3.01 to generate count matrix
Assembly: GRCh38
Supplementary files format and content: [Cellranger files] comprising a MatrixMarket file (matrix.mtx) and two tab separated metadata files (barcodes.tsv, features.tsv)

source_name: NK cells

growth_protocol: CD19+ cell lines of Raji were cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, and 1% GlutaMAX™.  For NK cells, cord blood (CB) units were provided by the MD Anderson Cord Blood Bank. CB-derived NK cells (CB-NK) were isolated and expanded. In brief, lymphocytes were collected by density-gradient centrifugation using Ficoll-Histopaque solution. CD56+CD3- NK cells were then purified using an NK negative isolation kit, and co-cultured with irradiated (100 Gy) uAPCs at a 2:1 ratio in complete stem cell growth medium (SCGM), supplemented with 200 U/ml recombinant human IL-2 (Proleukin). On Day 4 post uAPC stimulation, fresh NK cells were purified again and transduced with retroviral vectors expressing CAR-constructs. Irradiated uAPC were added weekly to the NK cell culture to support NK cell expansion.

extract_protocol:
By applying single-cell RNA sequencing, we first compared the genexpression profiles of CAR-engineered NK cells in the presence or absence of supplemental IL-15 signaling in vitro. We subsequently validated our findings in vivo in a non-curative lymphoma model by systematically tracking the evolution of both the tumor and CAR-NK cells collected from liver, spleen, blood, and bone marrow from animals in each of our treatment groups, NT-NK, CAR19 NK and Car19/IL-15 NK cells. Mouse-derived samples were collected serailly at different time point after CAR-NK cell infusion. Cryopreserved tumor and NK cells isolated from mouse tissues were thawed and stained with antibodies against human CD45 (Clone HI30: Biolegend), CD56 (Clone HCD56: Biolegend) and CD20 (Clone 2H7: Biolegend). NK cells (identified as hCD45+CD56+) and tumor cells (identified as hCD45+CD20+) were sorted into separate tubes containing cell culture medium and kept on ice. NK cells and tumor cells were mixed in one tube at 1:1 ratio before generating single cell libraries.
Single-cell libraries were prepared using the 10X Genomics Chromium 3’ scRNAseq according to manufacturer’s protocol. Briefly, single cells were partitioned into Gel beads in Emulsion (GEM) in the 10X Chromium Controller instrument followed by cell lysis, barcoded reverse transcription of RNA, and amplification.  Subsequent to 5’ adapter ligation, samples were indexed for sequencing. On average, 5000 cells were loaded on each channel, resulting in recovery of an average of 1200 cells/sample. Libraries were sequenced on Illumina (NovaSeq6000, SP flow cell -100 cycle kit per pool), Paired end reads: read 1, 28 bp, Read 2, 91 bp.

treatment_protocol: NOD/SCID IL-2Rγnull (NSG) mice grafted with aggressive, NK-resistant tumor cells CD19+ Raji lymphoma were used to examine the anti-tumor activity of CAR-NK populations. Seven-week-old female NSG mice (Jackson Laboratories) were irradiated (300 cGy) on Day -1. On Day 0 firefly luciferase-GFP labeled Raji cells were injected intravenously (i.v.) at the dose level of 0.2×10e5 Raji cells. The mice were then serially treated with 1×10e7 CAR-NK cell i.v. After CAR-NK cell infusion, cells were collected from different organs (blood, bone marrow, liver, and spleen) of mice at different time points.

tag: treatment

tag: strain

value: NSG


title: Adipocyte, Input, 1


title: Adipocyte, Input, 3


title: Engineered NK cells with IL-15


title: Adipocyte, Flag-OTUD3, CST, 4


title: Adipocyte, Flag-OTUD3, CST, 3


title: Non-transduced NK cells


title: Adipocyte, Flag-OTUD3, CST, 1


title: s1_1_hi

city: Dresden

first: Alexander

last: Gerbaulet

state: Saxony

address: Fetscherstr. 74

department: Institute for Immunology

institute: Medical Faculty TU Dresden

data_processing:
Basic quality control of the resulting sequencing reads was performed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and RNA-SeQC (version 1.1.8).
Reads were aligned to the mm10 reference genome using GSNAP (version 2020-12-16)
The Ensembl gene annotation version 98 was used for splice site detection.
Uniquely aligned reads per gene were counted using featureCounts (version 2.0.1) and the respective Ensembl annotation.
Normalisation of raw read counts based on library size, and testing for differential gene expression between conditions was performed using the DESeq2 R package (version 1.30.1, R version 3.5.1).
Supplementary_files_format_and_content: Excel

source_name: murine bone marrow

extract_protocol:
5000-20000 CD48hi  or CD48-/lo MkPs (lin- CD117+ Sca-1- CD150+ CD41+) were sorted using a BD ARIA II FACS sorter and RNA was isolated using the RNeasy Micro Kit (Qiagen). RNA quality was analysed using a Agilent 2100 Bioanalyzer (Agilent Technologies) and samples were frozen at ‑80°C.
Total RNA was desiccated to 3 µl and denatured for 3 minutes at 72 °C  in the presence of 2.4 mM dNTP (Invitrogen), 240 nM dT-primer (dT-primer: C6-aminolinker-AAGCAGTGGTATCAACGCAGAGTCGACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN, where N represents a random base and V any base beside thymidine) and 4 U RNase Inhibitor (NEB). The reverse transcription and addition of the template switch oligo is performed at 42°C for 90 min after filling up to 10 µl with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer (TSO-primer: AAGCAGTGGTATCAACGCAGAGTACATrGrGrG, where rG stands for ribo-guanosine;  UP-primer: AAGCAGTGGTATCAACGCAGAGT), 9 U RNase Inhibitor and 90 U Superscript II. The reverse transcriptase is inactivated at 70 °C for 15 min. The single stranded cDNA is subsequently amplified using Kapa HiFi HotStart Readymix (Roche) at a 1x concentration together with 0.1 µM UP-primer* under following cycling conditions: initial denaturation at 98°C for 3 min, 18 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 1x volume of Sera-Mag SpeedBeads (GE Healthcare) resuspended in a buffer consisting of 10 mM Tris, 20 mM EDTA, 18.5 % (w/v) PEG 8000 and 2 M sodium chloride solution. The cDNA quality and concentration is determined with the Fragment Analyzer (Agilent).  For library preparation 3 ng cDNA was tagmented using 0.5 µl TruePrep Tagment Enzyme V50 and 1x TruePrep Tagment Buffer L (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme), followed by an incubation step at 55 °C for 5 min. Next, Illumina indices are added during PCR (72 °C 3 min, 98 °C 30 sec, 12 cycles [98 °C 10 sec, 63 °C 20 sec, 72 °C 1 min], 72°C 5 min) with 1x concentrated KAPA Hifi HotStart Ready Mix and 300 nM dual indexing primers. After PCR, libraries are purified twice with 1x volume Sera-Mag SpeedBeads and quantified with the Fragment Analyzer, followed by paired-end sequencing of 60-83 million fragments on the Illumina NovaSeq 6000 platform in S4 PE mode

tag: cell type

value: CD48-high megakaryocyte progenitor cells

tag: cell number


title: s7_4_lo

value: CD48-low megakaryocyte progenitor cells


title: s5_1_lo


title: s2_3_hi


title: s6_3_lo


title: s3_4_hi


title: s4_5_hi


title: snATAC-Pitx2-PV-MUT

city: Cincinnati

first: Jeffrey

middle: D

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

description:
genomic DNA
Single Cell ATAC v1
snATAC_barcodes.tsv
snATAC_filtered_peak_bc_matrix.h5
snATAC_fragments.tsv.gz
snATAC_fragments.tsv.gz
snATAC_matrix.mtx
snATAC_peaks.bed
snATAC_singlecell.csv

data_processing:
Raw sequencing data was handled by the 10x Genomics Cell Ranger software (cellranger-3.0.1 and cellranger-atac-1.2.0) and mapped to the mouse mm10 genome.
For snRNA-seq, the gene counts were quantified using cellranger count to the mouse transcriptome including pre-mRNA (v3.0.0) and passed to Seurat for downstream analysis.
For snATAC-seq, samples were individually aligned using cellranger-atac count and aggregated using cellranger-atac aggr (--nosecondary --normalize=none) using the peak output from each individual sample.
Following initial clustering (see below for downstream analysis) and per cluster and per sample peak calling using MACS2 callpeak (v2.1.1.20160309) with parameters -f BAMPE -g mm -B -q 0.1 samples were re-aggregated using cellranger-atac aggr using a union set of peaks and passed to Seurat and Signac for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: The barcodes.tsv files contain the single cell barcodes present in the libraries. The features.tsv files contain the list of total features (for snRNA-seq = genes, for snATAC-seq = peaks). The matrix.mtx files contain the feature by barcode information in MEX formating. The singlecell.csv is the per barcode QC information from cellranger. The peaks.bed file is the feature peaks in bed format. The files snATAC_metatable.txt and snRNA_metatable.txt are the metatables used in Seurat/Signac.

source_name: pulmonary vein

extract_protocol:
Tissues were minced with sharp scissors in 250μl of HB++ (HB: 0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, pH 7.8; ++: 0.15mM spermine, 0.5mM spermidine, 1mM DTT) and centrifuged at 500g for 5 minutes to remove excess red blood cells and fat and replaced with 250μl of fresh HB++. Sample was transferred to a 2mL Dounce homogenizer and the tube washed with an additional 250μl of HB++ to collect any remaining sample and transferred. Tissue was homogenized 30 times with loose and tight pestle before adding 32μl of 5% NP40 (in HB) and Dounced with tight pestle an additional 75 times. Sample was strained through a 40μM strainer and washed with 9.5mL of NWB (PBS with 1% BSA and 0.2U RNAse inhibitor) and spun down at 500g at 4°C for 5 minutes. The supernatant removed and nuclei resuspended in 500μl of NWB and 900μl of SCB (90% Nuclei PURE 2M Sucrose Cushion Solution and 10% Nuclei PURE Sucrose Cushion Solution; Sigma NUC-201: S9308 and S9058). The 1400μl of nuclei suspension is layered on top of 500μl SCB in a 2mL LoBind Eppendorf tube and centrifuged at 13,000g at 4°C for 45 minutes. The supernatant removed leaving ~50μl of nuclei pellet, which is resuspended in 1mL of NWB. Pellet nuclei at 500g at 4°C for 5 minutes, remove supernatant leaving ~50μl of nuclei pellet.
The snRNA-seq libraries were generated using the 10x Chromium Single Cell 3’ v3 reagent kit and in parallel the snATAC-seq libraries were generated using the 10x Chromium Single Cell ATAC v1 with a target of 10,000 nuclei per library according to the manufacturer’s instructions.

tag: age

value: adult

value: Pitx2 mutant


title: snATAC-Pitx2-LA-WT

source_name: left atrium

value: Control


title: snATAC-Pitx2-PV-WT


title: Moc2 tumor, EphB4 sh C1M1

city: Aurora

first: Sana

last: Karam

state: CO

address: 1665 Aurora Court Suite 1032

institute: University of Colorado Denver Anschutz Medical Campus

description: EphB4_C1M1 (CPM.xlsx)

data_processing:
Illumina adapters and the first 12 base pairs of each read were trimmed using BBDuk (BBMap - Bushnell B.-sourceforge.net/projects/bbmap/), and reads <50bp post-trimming were discarded. Reads were aligned and quantified using STAR (2.6.0a) against the Ensembl mouse transcriptome (mg38.p6 genome (release 96)). Reads were normalized to CPM using the edgeR R package. Differential expression was calculated using the voom function in the limma R package. Gene set  enrichment analysis was performed using the list of genes by fold change for the indicated comparison and the fgsea R package using gene sets from the Molecular Signatures Database. Heat-maps were generated with the Complex Heatmap R package following z-score transformation
Assembly: Ensembl mouse transcriptome (mg38.p6 genome (release 96))
Supplementary files format and content: .xlsx file for each of the control sh and EphB4 sh samples showing CPM values

source_name: Moc2 EphB4 sh C1M1 tumor

growth_protocol: Moc2 control sh and EphB4 sh cell lines were maintained in DMEM F12: IMDM (1:2) supplemented with 10% FBS and 1% primocin/fungin, 1.75 μg EGF, 20 μg hydrocortisone, and 0.1% insulin solution at 37°C and 5% CO2.

extract_protocol:
Tumors for RNA-Seq analysis were harvested and immediately frozen in liquid nitrogen. Frozen tumors were stored at –80°C until time of analysis. RNA from tumors was harvested using an RNA miniprep kit (Zymo research, Irvine CA).
Sequencing and library prep were performed by The Genomics and Microarray Shared Resource at University of Colorado Denver Cancer Center. PolyA selection was used for library prep and sequencing was performed on an Illumina NovaSEQ 6000 with 2×150 paired end reads at a depth of 20 million reads per sample

treatment_protocol: Moc2 EphB4 sh cells were selected with 10 μg/ml dose of puromycin

value: Moc2 EphB4 sh C1M1 tumor

value: Moc2 EphB4 sh

value: Head and Neck Squamous cell carcinoma

value: EphB4 knockdown

tag: host strain

tag: gender

value: Female

value: EphB4 shRNA


title: Moc2 tumor, Control sh C2M3

description: CTRL_C2M3 (CPM.xlsx)

source_name: Moc2 Control sh C2M3 tumor

value: Moc2 Control sh C2M3 tumor

value: Moc2 Control sh

tag: genotype

value: Control shRNA


title: Moc2 tumor, EphB4 sh C1M2

description: EphB4_C1M2 (CPM.xlsx)

source_name: Moc2 EphB4 sh C1M2 tumor

value: Moc2 EphB4 sh C1M2 tumor


title: Moc2 tumor, EphB4 sh C2M2

description: EphB4_C2M2 (CPM.xlsx)

source_name: Moc2 EphB4 sh C2M2 tumor

value: Moc2 EphB4 sh C2M2 tumor


title: Moc2 tumor, Control sh C2M1

description: CTRL_C2M1 (CPM.xlsx)

source_name: Moc2 Control sh C2M1 tumor

value: Moc2 Control sh C2M1 tumor


title: snRNA-Pitx2-PV-MUT

description:
nuclear RNA
10x Chromium Single Cell 3’ v3
snRNA-Pitx2-PV-MUT_barcodes.tsv.gz
snRNA-Pitx2-PV-MUT_features.tsv.gz
snRNA-Pitx2-PV-MUT_matrix.mtx.gz


title: snRNA-Pitx2-PV-WT

description:
nuclear RNA
10x Chromium Single Cell 3’ v3
snRNA-Pitx2-PV-WT_barcodes.tsv.gz
snRNA-Pitx2-PV-WT_features.tsv.gz
snRNA-Pitx2-PV-WT_matrix.mtx.gz


title: D30_Baseline

value: Adipose tissue

value: Baseline


title: snRNA-Pitx2-LA-MUT

description:
nuclear RNA
10x Chromium Single Cell 3’ v3
snRNA-Pitx2-LA-MUT_barcodes.tsv.gz
snRNA-Pitx2-LA-MUT_features.tsv.gz
snRNA-Pitx2-LA-MUT_matrix.mtx.gz

value: adult


title: Megakaryocyte Progenitor (MkP) 189

data_processing:
Alignment of the samples with GSNAP (version 2018–07-04) to the mm10 reference, and using Ensembl 87 for the support of splicesite detection
featureCounts (version1.6.2) was used to assign the reads to genes with the help of Ensembl 87 annotation
Genome_build: mm10

source_name: bone marrow

extract_protocol:
Whole bone marrow cells were isolated by crushing long bones with mortar and pestle using PBS/2% FCS/2 mM EDTA and filtered through a 100 µm mesh. After erythrocyte lysis in hypotonic NH4Cl-buffer, cells were filtered through a 40 µm mesh. Hematopoietic lineage+ cells were removed with the lineage cell depletion kit (Miltenyi Biotec). Cells were incubated with antibodies in PBS / 2% FCS for 30 min, washed twice with PBS / 2% FCS. Single BM HSPC cells were sorted on an BD ARIA II SORP flow cytometer. Single hematopoietic stem and progenitor cells were index-sorted into 384 well plates containing 0.5 µl of nuclease free water with 0.2% Triton-X 100 and 4 U murine RNase Inhibitor (NEB), spun down and frozen at -80°C. After thawing, 0.5 µl of a primer mix were added (5 mM dNTP (Invitrogen), 0.5 µM dT-primer (C6 aminolinkerAAGCAGTGGTATCAACGCAGAGTCGACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN), 1 U RNase Inhibitor (NEB)). RNA was denatured for 3 minutes at 72°C and the reverse transcription (RT) was performed at 42°C for 90 min after filling up to 10 µl with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer (AAGCAGTGGTATCAACGCAGAGTACATrGrGrG), 9 U RNase Inhibitor and 90 U Superscript II. After synthesis, the reverse transcriptase was inactivated at 70°C for 15 min. The cDNA was amplified using Kapa HiFi HotStart Readymix (Peqlab) at a final 1x concentration and 0.1 µM UP-primer (AAGCAGTGGTATCAACGCAGAGT) under following cycling conditions: initial denaturation at 98°C for 3 min, 23 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA was purified using 1x volume of hydrophobic Sera-Mag SpeedBeads (GE Healthcare) resuspended in a buffer consisting of 10 mM Tris, 20 mM EDTA, 18.5 % (w/v) PEG 8000 and 2 M sodium chloride solution. The cDNA was eluted in 12 µl nuclease free water and the concentration of the samples was measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates (Corning) using AccuBlue Broad range chemistry (Biotium).
For library preparation up to 700 pg cDNA was desiccated and rehydrated in 1 µl Tagmentation mix (1x TruePrep Tagment Buffer L, 0.1 µl TruePrep Tagment Enzyme V50; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme) and tagmented at 55°C for 5 min. Subsequently, Illumina indices are added during PCR (72°C 3 min, 98°C 30 sec, 13 cycles [98°C 10 sec, 63°C 20 sec, 72°C 1 min], 72°C 5 min) with 1x concentrated KAPA Hifi HotStart Ready Mix and 300 nM dual indexing primers. After PCR, libraries are quantified with AccuBlue Broad range chemistry, equimolarly pooled and purified twice with 1x volume Sera-Mag SpeedBeads. This was followed by Illumina 50 bp paired-end sequencing on a Novaseq6000 aiming at an average sequencing depth of 0.5 mio reads per cell.

tag: col1a1 genotype

tag: rosa26 genotype

value: rtTA/rtTA

tag: doxycyclin induction

value: induced


title: Megakaryocyte Progenitor (MkP) 188


title: snRNA-Pitx2-LA-WT

description:
nuclear RNA
10x Chromium Single Cell 3’ v3
snRNA-Pitx2-LA-WT_barcodes.tsv.gz
snRNA-Pitx2-LA-WT_features.tsv.gz
snRNA-Pitx2-LA-WT_matrix.mtx.gz

value: Control


title: Megakaryocyte Progenitor (MkP) 186


title: Megakaryocyte Progenitor (MkP) 185

description:
raw_counts+metadata.csv
counts_filtered.csv
counts_filtered_normalized_log.csv
cell_metadata_filtered.csv


title: Megakaryocyte Progenitor (MkP) 187


title: Megakaryocyte Progenitor (MkP) 184


title: Megakaryocyte Progenitor (MkP) 183


title: Megakaryocyte Progenitor (MkP) 181


title: Megakaryocyte Progenitor (MkP) 182


title: Megakaryocyte Progenitor (MkP) 179


title: snATAC-Pitx2-LA-MUT

value: Pitx2 mutant


title: Megakaryocyte Progenitor (MkP) 180


title: Megakaryocyte Progenitor (MkP) 175


title: Multipotent Progenitor (MPP) 283


title: Multipotent Progenitor (MPP) 277


title: Multipotent Progenitor (MPP) 276


title: Multipotent Progenitor (MPP) 282


title: Megakaryocyte Progenitor (MkP) 176


title: Multipotent Progenitor (MPP) 285


title: Megakaryocyte Progenitor (MkP) 177


title: Megakaryocyte Progenitor (MkP) 174


title: Megakaryocyte Progenitor (MkP) 178


title: Multipotent Progenitor (MPP) 278


title: Multipotent Progenitor (MPP) 279


title: Multipotent Progenitor (MPP) 280


title: Multipotent Progenitor (MPP) 273


title: Multipotent Progenitor (MPP) 281


title: Multipotent Progenitor (MPP) 275


title: Multipotent Progenitor (MPP) 270


title: Multipotent Progenitor (MPP) 274


title: lineage- kit+ CD150+ cell 41


title: Multipotent Progenitor (MPP) 271


title: lineage- kit+ CD150+ cell 42


title: lineage- kit+ CD150+ cell 44


title: lineage- kit+ CD150+ cell 43


title: Multipotent Progenitor (MPP) 272


title: lineage- kit+ CD150+ cell 45


title: Multipotent Progenitor (MPP) 284


title: lineage- kit+ CD41- CD150- cell 47


title: lineage- kit+ CD150+ cell 39


title: lineage- kit+ CD150+ cell 40


title: lineage- kit+ CD41- CD150- cell 43


title: lineage- kit+ CD150+ cell 38


title: lineage- kit+ CD41- CD150- cell 45


title: lineage- kit+ CD41- CD150- cell 46


title: Hematopoietic stem cell (HSC) 320


title: lineage- kit+ CD41- CD150- cell 44


title: Hematopoietic stem cell (HSC) 318


title: Hematopoietic stem cell (HSC) 319


title: lineage- kit+ CD41- CD150- cell 50


title: lineage- kit+ CD41- CD150- cell 49


title: Hematopoietic stem cell (HSC) 315


title: Hematopoietic stem cell (HSC) 317


title: Hematopoietic stem cell (HSC) 312


title: Hematopoietic stem cell (HSC) 313


title: Hematopoietic stem cell (HSC) 314


title: Hematopoietic stem cell (HSC) 311


title: Hematopoietic stem cell (HSC) 309


title: Hematopoietic stem cell (HSC) 316


title: Hematopoietic stem cell (HSC) 306


title: Hematopoietic stem cell (HSC) 310


title: Hematopoietic stem cell (HSC) 305


title: Megakaryocyte Progenitor (MkP) 173


title: Megakaryocyte Progenitor (MkP) 172


title: Hematopoietic stem cell (HSC) 308


title: Megakaryocyte Progenitor (MkP) 171


title: lineage- kit+ CD41- CD150- cell 48


title: Megakaryocyte Progenitor (MkP) 170


title: Megakaryocyte Progenitor (MkP) 167


title: Megakaryocyte Progenitor (MkP) 169


title: Megakaryocyte Progenitor (MkP) 166


title: Megakaryocyte Progenitor (MkP) 161


title: Megakaryocyte Progenitor (MkP) 162


title: Megakaryocyte Progenitor (MkP) 168


title: Megakaryocyte Progenitor (MkP) 165


title: Megakaryocyte Progenitor (MkP) 160


title: Megakaryocyte Progenitor (MkP) 159


title: Megakaryocyte Progenitor (MkP) 158


title: Hematopoietic stem cell (HSC) 304


title: Hematopoietic stem cell (HSC) 303


title: Hematopoietic stem cell (HSC) 307


title: Hematopoietic stem cell (HSC) 301


title: Hematopoietic stem cell (HSC) 296


title: Hematopoietic stem cell (HSC) 298


title: Hematopoietic stem cell (HSC) 302


title: Hematopoietic stem cell (HSC) 295


title: Hematopoietic stem cell (HSC) 300


title: Hematopoietic stem cell (HSC) 292


title: Hematopoietic stem cell (HSC) 297


title: Hematopoietic stem cell (HSC) 290


title: Hematopoietic stem cell (HSC) 294


title: Hematopoietic stem cell (HSC) 291


title: Hematopoietic stem cell (HSC) 289


title: Hematopoietic stem cell (HSC) 293


title: E34 Hematopoietic Stem Cell (E34 HSC) 62


title: E34 Hematopoietic Stem Cell (E34 HSC) 64


title: E34 Hematopoietic Stem Cell (E34 HSC) 61


title: E34 Hematopoietic Stem Cell (E34 HSC) 63


title: E34 Hematopoietic Stem Cell (E34 HSC) 59


title: Megakaryocyte Progenitor (MkP) 163


title: Megakaryocyte Progenitor (MkP) 164


title: E34 Hematopoietic Stem Cell (E34 HSC) 58


title: E34 Hematopoietic Stem Cell (E34 HSC) 56


title: E34 Hematopoietic Stem Cell (E34 HSC) 55


title: E34 Hematopoietic Stem Cell (E34 HSC) 54


title: Hematopoietic stem cell (HSC) 299


title: E34 Hematopoietic Stem Cell (E34 HSC) 53


title: E34 Hematopoietic Stem Cell (E34 HSC) 52


title: E34 Hematopoietic Stem Cell (E34 HSC) 51


title: Restricted hematopoietic progenitor 1 (HPC-1) 190


title: Restricted hematopoietic progenitor 1 (HPC-1) 189


title: Restricted hematopoietic progenitor 1 (HPC-1) 187


title: E34 Hematopoietic Stem Cell (E34 HSC) 49


title: E34 Hematopoietic Stem Cell (E34 HSC) 50


title: Restricted hematopoietic progenitor 1 (HPC-1) 186


title: Restricted hematopoietic progenitor 1 (HPC-1) 191


title: Restricted hematopoietic progenitor 1 (HPC-1) 185


title: Restricted hematopoietic progenitor 1 (HPC-1) 183


title: Restricted hematopoietic progenitor 1 (HPC-1) 181


title: Restricted hematopoietic progenitor 1 (HPC-1) 182


title: Restricted hematopoietic progenitor 1 (HPC-1) 184


title: Restricted hematopoietic progenitor 1 (HPC-1) 178


title: E34 Hematopoietic Stem Cell (E34 HSC) 60


title: Restricted hematopoietic progenitor 1 (HPC-1) 180


title: Multipotent Progenitor (MPP) 268


title: Restricted hematopoietic progenitor 1 (HPC-1) 176


title: Multipotent Progenitor (MPP) 267


title: Multipotent Progenitor (MPP) 266


title: Multipotent Progenitor (MPP) 264


title: E34 Hematopoietic Stem Cell (E34 HSC) 57


title: Multipotent Progenitor (MPP) 263


title: Multipotent Progenitor (MPP) 262


title: Multipotent Progenitor (MPP) 261


title: Restricted hematopoietic progenitor 1 (HPC-1) 188


title: Multipotent Progenitor (MPP) 259


title: Multipotent Progenitor (MPP) 258


title: Hematopoietic stem cell (HSC) 288


title: Hematopoietic stem cell (HSC) 286


title: Multipotent Progenitor (MPP) 253


title: Restricted hematopoietic progenitor 1 (HPC-1) 179


title: Hematopoietic stem cell (HSC) 284


title: Hematopoietic stem cell (HSC) 282


title: Hematopoietic stem cell (HSC) 281


title: Hematopoietic stem cell (HSC) 287


title: Restricted hematopoietic progenitor 1 (HPC-1) 177


title: Hematopoietic stem cell (HSC) 279


title: Hematopoietic stem cell (HSC) 278


title: Multipotent Progenitor (MPP) 265


title: Hematopoietic stem cell (HSC) 275


title: Hematopoietic stem cell (HSC) 276


title: Hematopoietic stem cell (HSC) 273


title: Hematopoietic stem cell (HSC) 277


title: Restricted hematopoietic progenitor 1 (HPC-1) 175


title: Restricted hematopoietic progenitor 1 (HPC-1) 174


title: Restricted hematopoietic progenitor 1 (HPC-1) 173


title: Multipotent Progenitor (MPP) 260


title: Multipotent Progenitor (MPP) 257


title: Multipotent Progenitor (MPP) 256


title: Multipotent Progenitor (MPP) 255


title: Hematopoietic stem cell (HSC) 274


title: Restricted hematopoietic progenitor 1 (HPC-1) 172


title: Multipotent Progenitor (MPP) 254


title: Restricted hematopoietic progenitor 1 (HPC-1) 171


title: Hematopoietic stem cell (HSC) 285


title: Hematopoietic stem cell (HSC) 283


title: Restricted hematopoietic progenitor 1 (HPC-1) 169


title: Restricted hematopoietic progenitor 1 (HPC-1) 170


title: Restricted hematopoietic progenitor 1 (HPC-1) 167


title: Restricted hematopoietic progenitor 1 (HPC-1) 166


title: Hematopoietic stem cell (HSC) 280


title: Restricted hematopoietic progenitor 1 (HPC-1) 163


title: Restricted hematopoietic progenitor 1 (HPC-1) 162


title: Restricted hematopoietic progenitor 1 (HPC-1) 161


title: Restricted hematopoietic progenitor 1 (HPC-1) 165


title: Restricted hematopoietic progenitor 1 (HPC-1) 164


title: Multipotent Progenitor (MPP) 252


title: Restricted hematopoietic progenitor 1 (HPC-1) 160


title: Restricted hematopoietic progenitor 1 (HPC-1) 168


title: Multipotent Progenitor (MPP) 244


title: Multipotent Progenitor (MPP) 243


title: Multipotent Progenitor (MPP) 241


title: Multipotent Progenitor (MPP) 242


title: Multipotent Progenitor (MPP) 237


title: Multipotent Progenitor (MPP) 235


title: Multipotent Progenitor (MPP) 245


title: Multipotent Progenitor (MPP) 240


title: Multipotent Progenitor (MPP) 251


title: Multipotent Progenitor (MPP) 227


title: Multipotent Progenitor (MPP) 236


title: Multipotent Progenitor (MPP) 239


title: Multipotent Progenitor (MPP) 226


title: Multipotent Progenitor (MPP) 229


title: Multipotent Progenitor (MPP) 234


title: Multipotent Progenitor (MPP) 231


title: Multipotent Progenitor (MPP) 238


title: Multipotent Progenitor (MPP) 247


title: Multipotent Progenitor (MPP) 232


title: Multipotent Progenitor (MPP) 230


title: Multipotent Progenitor (MPP) 225


title: Multipotent Progenitor (MPP) 221


title: Restricted hematopoietic progenitor 1 (HPC-1) 159


title: Multipotent Progenitor (MPP) 224


title: Multipotent Progenitor (MPP) 250


title: Restricted hematopoietic progenitor 1 (HPC-1) 157


title: Multipotent Progenitor (MPP) 246


title: Multipotent Progenitor (MPP) 228


title: Multipotent Progenitor (MPP) 249


title: Restricted hematopoietic progenitor 1 (HPC-1) 158


title: Restricted hematopoietic progenitor 1 (HPC-1) 155


title: Restricted hematopoietic progenitor 1 (HPC-1) 156


title: Multipotent Progenitor (MPP) 248


title: Multipotent Progenitor (MPP) 222


title: Restricted hematopoietic progenitor 1 (HPC-1) 154


title: Restricted hematopoietic progenitor 1 (HPC-1) 148


title: Restricted hematopoietic progenitor 1 (HPC-1) 151


title: Restricted hematopoietic progenitor 1 (HPC-1) 149


title: Restricted hematopoietic progenitor 1 (HPC-1) 152


title: Restricted hematopoietic progenitor 1 (HPC-1) 153


title: Hematopoietic stem cell (HSC) 272


title: Hematopoietic stem cell (HSC) 269


title: Hematopoietic stem cell (HSC) 265


title: Hematopoietic stem cell (HSC) 271


title: Restricted hematopoietic progenitor 1 (HPC-1) 145


title: Hematopoietic stem cell (HSC) 270


title: Hematopoietic stem cell (HSC) 266


title: Restricted hematopoietic progenitor 1 (HPC-1) 150


title: Hematopoietic stem cell (HSC) 267


title: Multipotent Progenitor (MPP) 223


title: Hematopoietic stem cell (HSC) 268


title: Hematopoietic stem cell (HSC) 262


title: Hematopoietic stem cell (HSC) 263