title: MPH-SHCTRL

city: Orlando

first: Manuel

last: Roqueta-Rivera

state: FL

address: 6400 Sanger Rd

institute: Sanford Burnham Preby Medical Research Institute

description: shControl

data_processing:
Base-calling was performed on Hiseq1500 using Real-Time Analysis (RTA) version 1.18.64
BCL to Fastq files, De-multiplexing and adapetr trimming was done using Illumina's Basespace.
RNA-seq reads were aligned to mm10 genome assembly using TOPHAT Version 2.0.12 with the default parameters 'tophat <mm10 index> <read1_1,..><read1_2,…>'
Use Cufflinks Version 2.2.1  to get the differentially expressed genes based on the .bam files from TOPHAT results.
Genome_build: mm10
Supplementary_files_format_and_content: XLSX file includes RPKM values for shCTRL, shSETDB2 and Cufflink analysis results.

source_name: primary hepatocytes

growth_protocol: Isolated mouse primary hepatocytes were maintained overnight in dexamethasone (Dex) and serum free Medium199 prior to adenoviral infection (MOI=40). Infection was for 48hr in Medium199(2%FBS,10nMDex), followed by 24hr in serum free Medium 199 prior to a 4h 1uM Dex treatment.

extract_protocol:
Total RNA was harvested using Trizol reagent and the Directzol RNA miniprep kit (Cat#11-331) for the construction of sequencing libraries.
1ug of Total RNA was used to construct multiplexed Libraries using Illumina's Truseq Stranded Total RNA Kit. First, the Total RNA was subjected to ribodepletion process to remove rRNA. The remaining RNA is purified, fragmented, Reverse transcribed, adapter ligated and finally PCR amplified to enrich the DNA fragments.

treatment_protocol: 1uM Dex 4hours

value: mouse primary hepatocytes (MPH)

value: shControl


title: MPH-SHSETDB2

status: Public on Aug 28 2016

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: cell type

tag: infected with


title: Ad/NICD WAT Replicate3

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

description:
Biological replicate 3 of 4. Ad/NICD White adipose tissue
Ad/NICD WAT08

data_processing:
Paired-end reads from lanes L004 and L005 were concatenated and processed using Trimmomatic for quality (Phred <20) from both 5' and 3' ends. After trimming, reads of 30 nt or less were removed.  Trimming generated some unpaired reads.
Both paired and unpaired reads were aligned against the mouse GRCm38 genome assembly using iGenomes genome fasta file and iGenomes Bowtie2 small index files using TopHat 2.1.0
TopHat 2.1.0; command_line; -a 20 -m 1 -I 100000 -g 9 -N 3 --read-gap-length 1 --read-edit-dist 4 --read-realign-edit-dist 0; Data_input paired and unpaired fastq for each sample; Data_output accepted_hits.bam for each sample.
cufflinks 2.2.1; command_line; -G GRCm38_iGenome.gtf -b GRCm38_iGenome/genome.fa -u -N -F 0.05; Data_input accepted_hits.bam for each sample; Data_output annotation gtf files for each sample.
cuffmerge 2.2.1; command_line;  -g GRCm38_iGenome.gtf -s GRCm38_iGenome/genome.fa; Data_input path/sample.gtf; Data_output merged.gtf
cuffquant 2.2.1; command_line; -u -b GRCm38_iGenome/genome.fa -max-bundle-frags 10000000; Data_input merged.gtf, accepted_hits.bam for each sample; Data_output abundances.cxb for each sample.
cuffdiff 2.2.1; command_line; -u  -c 12 -FDR 0.05 -b GRCm38_iGenome/genome.fa --max-bundle-frags 10000000 -L Tumor,IngWAT --compatible-hits-norm; Data_input merged.gtf abundances.cxb files grouped by treatment Data_output 23 data and summary files, two are provided
Genome_build: GRCm38; ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/Ensembl/GRCm38/Mus_musculus_Ensembl_GRCm38.tar.gz
Supplementary_files_format_and_content: genes_FPKM_table.txt.gz; This file contains the cuffdiff genes.read_group_tracking FPKM data reformated from long to wide format.  The FPKM values for each sample are in columns. Rows contain FPKM data by gene_names and locus
Supplementary_files_format_and_content: gene_exp.dif.gzf; This file contains the statistical comparisons between tumor (liposarcoma) and WAT groups generated by cuffdiff 2.2.1.

source_name: White adipose tissue

extract_protocol:
WAT and LPS were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
Total RNA was depleted of rRNA using the Illumina Ribo-Zero Gold kit. Libraries were made from the depleted RNA using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

tag: tissue

value: white adipose

tag: age

value: Three-week old


title: rST rep1

city: Beijing

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

country: China

institute: Chinese Academy of Sciences

description: Sample 7

data_processing:
RNA-seq reads generated from 4 types of SPCs were aligned to the mouse genome (UCSC mm9) with Tophat-2.0.6.
Mapped reads were subsequently assembled into transcripts guided by reference annotation (mm9, USCS gene annotation) with Cufflink-2.0.2.
Differential gene and expression analysis was conducted by using cuffdiff.
RNA-seq reads generated from SSCs (with and without RNase R treatment ) were aligned to the mouse genome (UCSC mm9) with BWA-MEM.
circRNAs were identified using the CIRI program.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: bigWig files were generated using bam2wig; The bigWig format is for display of dense, continuous data that will be displayed in the Genome Browser as a graph

source_name: rST

growth_protocol: Mouse spermatogonial stem cells(SSCs) were cultured by following a protocol described in one of our previous study (PMID: 25356638).

extract_protocol:
RNA extraction followed standard protocol using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Spermatogenic cells were freshly isolated by using the STAPUT method and cultured spermatogonial stem cells were harvested directly without special treatment.

value: F1 pups of DBA/2 and C57BL6

tag: gender

value: male

tag: development stage

value: 60 dpp

tag: tissue/cell type

value: testes

tag: spermatogenic cell subtypes

value: round spermatids (rST)


title: Ad/NICD WAT Replicate2

description:
Biological replicate 2 of 4. Ad/NICD White adipose tissue
Ad/NICD WAT07


title: rST rep2

description: Sample 8


title: pacSC rep1

description: Sample 5

source_name: pacSC

value: 17 dpp

value: pachytene spermatocytes (pacSC)


title: 1772099-104_F07

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Read processing was performed as described (Islam et al., Nat Methods (2014) 11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis. We rejected cells that had less than 2000 mRNA molecules,  more than 26,000 mRNA molecules (putative doublets) as well as cells that formed a separate cluster with no specific gene expression (putative damaged or dead cells). Genes that were detected at less than 4 molecules in the whole datasets were eliminated.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited table of total number of detected mRNA molecules from each gene in each cell identified by the "Title" field in Samples list.

molecule: polyA RNA

source_name: thoracic ganglion

growth_protocol: R26R-Tomato (Jackson Laboratory) mice were crossed to the Wnt1-Cre (PS Danelian et at., Current biology (1998) 8:1323-1326) to allow delineation of sympathetic ganglia against surronding tissue. Animals were kept in cages in groups, with food and water ad libitum, under 12-h light-dark cycle conditions.

extract_protocol:
Sympathetic ganglia (SG) were collected in freshly oxygenated artificial cerebral spinal fluid (ASCF) kept on ice. SG were transferred into a 3cm plastic  dish  containing  2.7mL of 37°C digestion solution (500μL TrypLE™  Express (Life  Technologies), 2000μL Papain solution (Worthington Biochemical, 25U/ml), 100 μL DNAseI (Worthington  Biochemical, 1  mM) and 100 μL Collagenase/Dispase (Roche) 20 mg/ml). SGs were mechanically triturated  every 30 min  using glass  pasteur pipettes. After 1h incubation at 37°C, 100 μL fresh Collagenase/Dispase (20mg/mL) solution was added and SGs  were ripped open by using fine forceps. The solution was filtered using a 40μm cell strainer (FALCON) and collected in a 15 ml plastic tube. The digestion solution was diluted in 3ml ACSF and centrifuged at 100xg for 4 min at 4°C. The supernatant was removed and the pellet resuspended in 0.5 mL ASCF and 0.5 mL Neurobasal-A medium (Gibco). The cell suspension was transferred onto 80μl of Optiprep Density Solution (Sigma), 460 μL of ACSF and 460 μL Neurobasal media with supplements, and centrifuged at 100xg for 10min at 4°C and the solution concentrated to 100 μL by removing the supernatant. 10μL DNaseI was added to avoid cell clustering.  Cell density wasa djusted to 400-500 cells/μL.
The Fluidigm C1 Autoprep System microfluidic chip (medium size) was used to capture cells (Zeisel et al., Science (2015) 6;347(6226):1138-42). Cells at the capture sites were visually inspected and only single healthy cells were selected for library preparation. Cell barcoding and fragmentation were performed in a single step using Tn5 DNA transposase as described previously (ibid.) but using a different Binding and Blocking buffer (10mM Tris, 250mM NalCl, 5mM EDTA, 0.5% SDS).

value: sympathetic neuronal cells

tag: Sex

value: F

tag: celltype identifier


title: plpSC rep1

description: Sample 3

source_name: plpSC

value: preleptotene spermatocytes (plpSC)


title: 1772099-104_A10


title: SSC Rnase R-treated rep1

source_name: SSC Rnase R-treated

value: 5 dpp

value: spermatogonial stem cells (SSCs)


title: Ad/NICD WAT Replicate1

description:
Biological replicate 1 of 4. Ad/NICD White adipose tissue
Ad/NICD WAT02


title: pacSC rep2

description: Sample 6


title: 1772099-104_A01


title: plpSC rep2

description: Sample 4


title: 1772099-220_C07


title: priSG-A rep1

description: Sample 1

source_name: priSG-A

value: 7 dpp

value: primitive type A spermatogonia (priSG-A)


title: priSG-A rep2

description: Sample 2


title: SOMD1

status: Public on Aug 27 2016

city: Berkeley

first: Richard

last: Harland

state: CA

address: 571 Life Sciences Addition #3200

department: Department of Molecular and Cell Biology

institute: UC Berkeley

data_processing:
RNA-seq reads were aligned to mm10 mouse genome annotation using Tophat v2.0.9
Paired end reads were aligned using the annotation as a guide, thus allowing for novel junctions to be discovered.
all reads were realigned to mm10 using a junction annotation containing the novel junctions. After the second alignment novel transcripts were assembled to generate an augmented annotation using Cufflinks/Cuffmerge v2.1.1
HTSeq v0.6 was used to generate gene counts and DESeq2 v1.10 1 was used for differential gene expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: Files are tab delineated text (.txt) and contain the features in column A and normalized counts in column B.

source_name: E9.0 mouse paraxial mesoderm

growth_protocol: Explants of E9.0 Dll1-YFP mouse embryos were isolated.

extract_protocol:
RNA was extracted using Trizol according to the manufacturer's instructions
Sequencing libraries were made using the TruSeq RNA Library Preparation Kit V2 with 11 rounds of PCR.

treatment_protocol: RNA was directly extraced from WT and MUT samples.  SOM samples were disociated and YFP+ Dll1 lineages cells collected by FACS.  CTRL and DIR sampels were cultured without or with the sclerotome-inducing molecules LDN and SAG, respectively.

value: SOMD contained somites 10 to 13

tag: passages

value: FACS collected Dll1 lineage cells


title: SOMC1

value: SOMC contained somites 6 to 9.


title: SOMC4


title: SOMC2


title: SOMD4

value: SOMD contained somites 10 to 16


title: SOMD2

value: SOMD contained somites 10 to 14


title: SOMB3

value: SOMB contained somites 2 to 5.


title: SOMB2


title: SOMC3


title: RBBP4-K9Ac ChIPSeq

city: Rochester

first: Jeff

last: Nie

state: MN

address: 200 First St. SW

institute: Mayo Clinic

library_source: genomic

data_processing:
bcl2fastq 2.15.0 is used for basecalling.
Data was processed with Mayo chip-seq pipeline-- HiChIP (http://www.biomedcentral.com/1471-2105/15/280).
Paired_end reads are aligned to genome with BWA. Duplicated reads are filtered out with picard. Peak calling is performed with Sicer.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Peak file is in bed format with header of chr, peak_start, peak_end, peak_raw_count, INPUT_raw_count, raw_p_value and FDR.

molecule: genomic DNA

organism: Homo sapiens

source_name: T98G GBM cells, shRBBP4, H3K9Ac ChIP

growth_protocol: T98G cells were grown in DMEM supplemented with 10% FBS at 37 degree Celsius in humidified incubators.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation, DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: Cells were transduced with lentivirus constructs carrying control NT shRNA or RBBP4 shRNA.

tag: cell line

value: glioblastoma cell line

tag: passage

tag: shRNA

tag: chip antibody

value: H3K9Ac Rabbit mAb (Cell Signaling #9649)


title: NT-K9Ac ChIPSeq

source_name: T98G GBM cells, shNT, H3K9Ac ChIP

value: shNT


title: T98G-shRBBP4 RNA-seq

description:
T98G-shRBBP4
RBBP4-
Processed data file: GeneCount.txt

data_processing:
Illumina Casava1.9 software used for basecalling.
Paired-end reads are aligned by TopHat 2.0.6 (3) against the hg19 genome build using the bowtie1 aligner option.
Gene counts are generated using HTseq software (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) and gene annotation files are obtained from Illumina.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text file includes raw tag count and RPKM values for each Sample.

source_name: T98G, shRBBP4

growth_protocol: Cells were grown in standard culture conditions in DMEM media supplemented with 10% FBS and 1% penicillin and streptomycin.

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: SOMA3

source_name: E9.0 mouse presomitic mesoderm

value: SOMA included PSM and the non-committed most recently formed somite


title: SOMB1


title: T98G-shNT RNA-seq

description:
T98G-shNT
RBBP4+
Processed data file: GeneCount.txt

source_name: T98G, shNT


title: SOMD3

value: SOMD contained somites 10 to 15


title: DIR4

value: LDN+SAG treated, sclerotome-induced Dll1-lineage cells


title: SOMA4


title: DIR3


title: 1772099-226_D10

value: sympathetic neuronal cells

value: F


title: SOMA1


title: Escherichia WT Lysate

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

description: Total RNA

data_processing:
Demultiplexing
Fastq quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt (via READemption)
Read mapping using segemehl (via READemption)
Coverage calculation and normalisation (via READemption)
Genome_build: NC_007779.1
Supplementary_files_format_and_content: wiggle

organism: Escherichia coli

source_name: bacterial cells

extract_protocol:
The equivalent of 5 OD600 was saved for RNA extraction with TriZOL before adding antibodies (lysate RNA sample). For coIP samples, beads were resuspended in the lysis buffer, mixed with an equal volume of phenol:chloroform:isopropanol (25:24:1, pH4.5, Roth) for 20 s and incubated at room temperature for 3 min. After centrifugation, the aqueous phase was precipitated with isopropanol (coIP RNA sample). The purified RNA coIP sample was treated with DNase I (Thermo Scientific) to remove the residual DNA and reisolated with phenol:chloroform:isopropanol. The spike-in RNA (5’P-CUCGUCCGACGUCACCUAGA, IBA) had been added to 40 pg/µl for coIP samples and to 1.6 ng/µl for lysate samples.
RNA-seq libraries were prepared by Vertis AG (Freising-Weihenstephan, Germany). Briefly, RNA was polyadenylated with poly(A) polymerase, 5’-triphosphates were removed with tobacco acid pyrophosphatase followed by ligation of a 5’-adapter. First-strand cDNA synthesis was performed with the use of an oligo(dT) barcoded adapter primer and the M-MVL reverse transcriptase. The resulting cDNA was PCR-amplified with a high fidelity DNA polymerase. cDNA was purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics).

treatment_protocol: 50 OD600 of bacteria have been grown to the desired growth stage and harvested by centrifugation. They were lysed in 500 µl of the lysis buffer (20 mM Tris-HCl, pH7.5, 150 mM KCl, 1 mM MgCl2, 1 mM DTT, 1 mM PMSF, 0.2% Triton X100, 20 U/ml DNase I, Thermo Scientific, 200 U/ml SUPERase-IN, Life Technologies). Lysis was carried out on a Retsch MM400 machine at 30 Hz for 10 min in the presence of 750 µl 0.1 mm glass beads. The lysate was cleared by centrifugation at 14,000 g  at 4°C for 10 min.  The lysate was added 35 µl of monoclonal anti-FLAG M2 antibody (Sigma, #F1804) and rocked for 30 min at 4°C. Then 75 µl of pre-washed Protein A sepharose (Sigma, #P6649) were added and the mixture was rocked for additional 30 min. Afterwards, beads were washed extensively with the lysis buffer, and similar flow-through and wash protein and RNA samples were collected.

tag: rip antibody

value: Monoclonal ANTI-FLAG^=AE M2 antibody produced in mouse, Sigma, F1804-200UG,SLBG5673V


title: Escherichia ProQ coIP

description: ProQ-bound RNA

tag: strain


title: RBBP4-Input DNA

source_name: T98G GBM cells, shRBBP4, input

tag: cell type


title: SOMB4


title: Escherichia ProQ Lysate

description: Total RNA


title: DIR1


title: Fc silicic acid-limited B

city: Seattle

first: E. Virginia

last: Armbrust

state: WA

department: School of Oceanography

institute: University of Washington

description: processed data file: Fc_Si_expression.txt

data_processing:
Sequence reads were converted from raw color-space into fastq format and then trimmed based on quality score using trimfastq (Iverson et al., 2012; SEAStAR, http://armbrustlab.ocean.washington.edu/seastar). The appropriate read error probability cutoff (Ò-pÓ) was determined based on a subsample of reads trimmed at 10 equally spaced cutoff values. The cutoff value that yielded the highest number of bases aligned was chosen. Trimmed reads with a length shorter than 30 colorspace transitions (Ò-lÓ) or an entropy value less than 3.0 (Ò-eÓ) were discarded.
Trimmed reads were aligned with BWA (v.0.5.9) to predicted genes for Thalassiosira pseudonana (http://genome.jgi.doe.gov/Thaps3/Thaps3.home.html), Fragilariopsis cylindrus (http://genome.jgi.doe.gov/Fracy1/Fracy1.home.html) or Pseudo-nitzschia multiseries (http://genome.jgi.doe.gov/Psemu1/Psemu1.home.html). Parameters for Òbwa alnÓ were Ò-n .001 -c -l 18 -k 2Ó, and parameters for Òbwa samseÓ were Ò-n 500000Ó (Li and Durbin, 2009).
Counts, the number of sequence reads that aligned to predicted genes, were calculated from the resulting SAM alignment files using ref_select as part of the SEAStAR package. Only those sequences that aligned to predicted genes were used for subsequent analyses.
Transcriptomes from biological triplicates for each condition and species (N=27) were analyzed with the R software package edgeR from Bioconductor (Robinson et al., 2010). Alignment counts generated from ref_select in the SEAStAR package were normalized to library size for each replicate in edgeR. Then, an estimate of common dispersion of normalized counts for the three biological replicates within each treatment was calculated so that triplicates could be pooled for further analyses (Robinson and Smyth, 2007). Pairwise comparisons of pooled counts (i.e. transcript abundances) between treatments (nitrate-limited versus nutrient-replete or silicic acid-limited versus nutrient replete) were made with the exactTest function. A false discovery rate (fdr) of 0.01 was used to account for Type I errors; all p values provided have been fdr-corrected. P-values < 0.01 reflect statistically significant differences between nutrient-limited and nutrient-replete gene transcription. Up-regulated genes exhibit greater transcript abundances in response to nutrient-limited growth and down-regulated genes exhibit lower transcript abundances under nutrient-limited growth. For each diatom, the nutrient-limited transcript abundances were normalized to the nutrient-replete "control" abundances to give a log fold-change value, also referred to as the expression ratio.
Genome_build: Thalassiosira pseudonana (http://genome.jgi.doe.gov/Thaps3/Thaps3.home.html)
Genome_build: Fragilariopsis cylindrus (http://genome.jgi.doe.gov/Fracy1/Fracy1.home.html)
Genome_build: Pseudo-nitzschia multiseries (http://genome.jgi.doe.gov/Psemu1/Psemu1.home.html)
Supplementary_files_format_and_content: *_Si_expression.txt - tab delimited text files generated from edgeR that contain log fold change, log abundance, p-values, and fdr-corrected p-values for 3 biological replicates per condition; protein identification is also given

organism: Fragilariopsis cylindrus

source_name: Fc silicic acid-limited

growth_protocol: Thalassiosira pseudonana (Hustedt) Hasle et Heimdal (Provasoli-Guillard National Center for Marine Algae and Microbiota, Maine, USA; CCMP 1335), Fragilariopsis cylindrus (Provasoli-Guillard National Center for Marine Algae and Microbiota, CCMP 1102), and Pseudo-nitzschia multiseries (S. Bates, Fisheries and Oceans Canada; CLNN-17) were maintained at their optimum growth temperatures without bubbling in semi-continuous batch cultures under continuous light (100 μmol photons m−2 s−1) in modified artificial seawater with f/2 concentrations of nutrients (882 μM NaNO3, 106 μM Na2SiO3, 36.2 μM NaH2PO4; Guillard and Ryther, 1962). Growth of non-axenic triplicate cultures of T. pseudonana at 20oC, F. cylindrus at 4°C and P. multiseries at 13°C were monitored with a 10-AU fluorometer (Turner, California, USA). Cultures were considered acclimated to these growth conditions when the growth rates of three consecutive transfers were not significantly different from one another (ANCOVA). Each acclimated diatom culture was then transferred into a batch culture with nutrient-replete media (882 μM NaNO3, 106 μM Na2SiO3, 36.2 μM NaH2PO4) and a batch culture with low nitrate media (55 μM NaNO3, 212 μM Na2SiO3, 72.4 μM NaH2PO4) and a batch culture with low silicic acid media (1764 μM NaNO3, 53 μM Na2SiO3, 72.4 μM NaH2PO4) in artificial seawater, maintaining three biological replicates per condition and per diatom. The reduced amount of nitrate relative to other nutrients, including a doubling of Na2SiO3 and NaH2PO4 concentrations, ensured  that the onset of stationary phase in the low nitrate media was caused by availability of nitrate.  Similarly, the reduced amount of silicic acid relative to other nutrients ensured that the onset of stationary phase in low silicic acid media was caused by availability of silicic acid.  In total, there were triplicate biological replicates of low nitrate, low silicic acid, and the replete-media conditions for each diatom (N=27). Experiments were conducted in 10 L (T. pseudonana and F. cylindrus) or 4 L (P. multiseries) bottles; all cultures were bubbled with sterile filtered air. Pseudo-nitzschia multiseries was also stirred continuously. Photosynthetic yield of photosystem II (Fv/Fm) was monitored with a PhytoPAM fluorometer (Walz, Germany). The onset of stationary phase was defined by when chlorophyll a fluorescence of a culture no longer increased exponentially and Fv/Fm values decreased. Silicic acid limitation of growth in the low silicic acid media was confirmed by removing two 50 mL aliquots from the remaining cultures and adding 212 μM Na2SiO3 to aliquot one, no nutrients to aliquot two, and 212 μM Na2SiO3 to the remaining post-harvest large-volume cultures. All samples were monitored for at least two more days to confirm that chlorophyll a fluorescence and Fv/Fm increased after the addition of silicic acid to aliquot one and the large-volume cultures.

extract_protocol:
RNA was extracted from frozen cells on filters using the Totally RNA extraction kit (Life Technologies, New York, USA). The RNA was incubated with DNase I (Ambion, New York, USA) at 37°C for 2 hr and purified by DNase inactivation reagent (Ambion). Messenger RNA was polyA-selected from total RNA using the Ambion Micro Poly(A)Purist Kit (Life Technologies, New York, USA) to minimize bacterial RNA sequencing.
The mRNA was prepared for sequencing according to the SOLiD Total RNA-Seq Kit protocol. For each sample, 700 million beads were loaded onto a slide and run on a Life Technologies (New York, USA) SOLiD sequencer version 4.

treatment_protocol: Between 4.5 and 1.5 L of the experimental cultures (approximately half of the volume of each culture) were filtered onto 0.8 mm polycarbonate filters (Millipore, Massachusetts, USA) during mid-exponential growth (nutrient-replete) or at the onset of stationary phase due to nitrate limitation or silicic acid limitation. Filtered cells were immediately flash frozen in liquid nitrogen and stored at 80°C until later RNA extraction.

value: CCMP 1102

tag: nutrient condition

value: silicic acid-limited


title: Fc silicic acid-limited C


title: NT-Input DNA

source_name: T98G GBM cells, shNT, input


title: CTRL3

value: Control cultured Dll1-lineage cells


title: Fc silicic acid-limited A


title: Tp silicic acid-limited A

description: processed data file: Tp_Si_expression.txt

organism: Thalassiosira pseudonana

source_name: Tp silicic acid-limited

value: CCMP 1335


title: CTRL4

value: FACS collected Dll1 lineage cells


title: CRTL2


title: Tp silicic acid-limited C


title: Gradient fraction 20

data_processing:
Demultiplexing
Fastq quality trimming using a cut-off value of 20 (via READemption)
Fastq to fasta conversion (via READemption)
Size filtering: discarding reads shorter than 12 nt (via READemption)
Read mapping using segemehl (via READemption)
Coverage calculation and normalisation (via READemption)
Genome_build: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1
Supplementary_files_format_and_content: wiggle

organism: Salmonella enterica subsp. enterica serovar Typhimurium

extract_protocol:
Each fraction was deproteinized by addition of 1% SDS and 1 volume of hot phenol and shaking at 1,500 rpm at 55°C for 5 min. Phases were separated by centrifugation at 12,000 g for 15 min at 4°C. The aqueous phases were added glycogen to 50 µg/ml and RNA was precipitated with 60% isopropanol. The RNA pellets were dissolved in 35 µl of DEPC-treated sterile MilliQ water and stored at -80°C. Each fraction sample was added 85 pg/µl of the spike-in RNA (5’P-CUCGUCCGACGUCACCUAGA, IBA).
RNA-seq libraries were prepared by Vertis AG (Freising-Weihenstephan, Germany). Briefly, RNA was polyadenylated with poly(A) polymerase, 5’-triphosphates were removed with tobacco acid pyrophosphatase followed by ligation of a 5’-adapter. First-strand cDNA synthesis was performed with the use of an oligo(dT) barcoded adapter primer and the M-MVL reverse transcriptase. The resulting cDNA was PCR-amplified with a high fidelity DNA polymerase. cDNA was purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics).

treatment_protocol: For lysis, ~200  OD600 of bacterial culture were harvested by centrifugation at 4000 g at 4°C for 15 min, washed thrice with ice-cold 1×TBS and resuspended in 500 µl of the lysis buffer (20 mM Tris-HCl, pH7.5, 150 mM KCl, 1 mM MgCl2, 1 mM DTT, 1 mM PMSF, 0.2% Triton X100, 20 U/ml DNase I, Thermo Scientific, 200 U/ml SUPERase-IN, Life Technologies). Lysis was carried out on a Retsch MM400 machine at 30 Hz for 10 min in the presence of 750 µl 0.1 mm glass beads. The lysate was cleared by centrifugation at 14,000 g  at 4°C for 10 min and layered on a linear 10%-40% (w/v) glycerol gradient in the same buffer without DNase I nor SUPERase-IN, formed in a Beckman SW40Ti tube. The gradient was centrifuged at 100,000 g (23,700 rpm) for 17 h at 4°C and fractionated in 20 equal fractions by pipetting. OD260 for each fraction was measured with Nanodrop.


title: CTRL1


title: Gradient fraction 19


title: Gradient fraction 18


title: Escherichia WT coIP

description: Bead-bound RNA


title: Gradient fraction 17


title: Gradient fraction 16


title: DIR2


title: Soft tissue sarcoma 1

city: Toronto

first: Benjamin

last: Alman

state: Ontario

address: PGCRL 16th Floor, 686 Bay Street

department: Developmental and Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

data_processing:
Raw read data was first extracted from the BAM files and then processed using the TrimGalore toolkit which employs Cutadapt and FastQC to trim low quality bases and Illumina sequencing adapters from the 3' end of the reads. Only pairs where both reads were 35nt or longer were kept for further analysis.
Reads were mapped to the GRCm38.73 version of the mouse genome and transcriptome using the STAR RNA-seq alignment tool. Reads were kept for subsequent analysis if they mapped to a single genomic location.
Gene counts were compiled using the HTSeq tool. Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression was carried out using the DESeq2 Bioconductor package with the R statistical programming environment. A negative binomial generalized linear model was employed to identify differentially expressed genes across sample types.
The false discovery rate was calculated to control for multiple hypothesis testing.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated text file that contains the raw read counts as calculated by HTSeq

source_name: Primary tumor

extract_protocol:
Total RNA was extracted using Trizol reagent. Quality control was performed with Bioanalyser.
For each sample, approximately 10ng of total RNA was processed using the SMART(TM) cDNA synthesis protocol including SMARTScribe Reverse Transcriptase. This method deploys a modified oligo(dT) primer to prime the first strand synthesis reaction and a template switching mechanism to generate full-length single-stranded cDNAs containing the complete 5’ end of the mRNA as well as universal priming sequences for end-to-end amplification during 20 cycles of PCR. The amplified cDNA was subject to Illumina paired-end library construction using NEBNext paired-end DNA sample Prep Kit.

value: NG2-Cre;p53flox/flox (Mixed background)

tag: anatomic site

value: Subcutaneous tissue

tag: tissue type

value: Malignant


title: Soft tissue sarcoma 2


title: Gradient fraction 13


title: Gradient fraction 14


title: Gradient fraction 12


title: Osteosarcoma 1

value: Right tibia


title: Tp silicic acid-limited B


title: Gradient fraction 10


title: Gradient fraction 11


title: Gradient fraction 09


title: Osteosarcoma 2

value: Lumber spine


title: Gradient fraction 15


title: Gradient fraction 08


title: NG2 expressing cells 1

source_name: Perivascular cells of skeletal muscle tissue

value: Normal


title: NG2 expressing cells 2


title: Gradient fraction 04


title: Gradient fraction 05


title: Gradient fraction 07


title: Gradient fraction 02


title: WT3

value: Trunk tissue from E9.0 embryos


title: Gradient fraction 03


title: Gradient fraction 01


title: IEL.SP_3

city: New York

first: Luka

last: Mesin

state: NY

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
The samples were sequenced on HiSeq 2500. Image analysis and base calling was done in real time by the instrument using default parameters.
40-bp single-end reads were aligned to the mouse reference genome (mm10) using TopHat. Gene read count was performed using HTseq-count with Refseq mm10 annotation.
Supplementary_files_format_and_content: Normalized gene counts

source_name: Small intestine

extract_protocol:
Sorted cells were lysed in a guanidine thiocyanate buffer (Qiagen) supplemented with 1% β-mercaptoethanol. RNA isolated by SPRI bead cleanup (Agencourt RNAClean XP Kit) was reversely transcribed into cDNA.
Nextera XT (Illumina) was used to prepare a pooled library of fragmented and uniquely indexed samples, totaling six independent conditions in three biological replicates. 18 samples were multiplexed using 6 Index1 adapters (N701, N702, N703, N704, N705, N706) and 3 Index 2 adapters (S517, S502, S503).

tag: host strain

value: C57BL/6 TCRa-/- TCRb-/-

value: Intraepithelial T lymphocyte

tag: cell phenotye

tag: donor strain

value: C57BL/6 TNa TNb RAG1-/- Foxp3GFP


title: IEL.SP_2


title: IEL.SP_1


title: WT2


title: MUT3


title: WT1


title: LP.SP_3

value: Lamina propria T lymphocyte


title: MUT2


title: LP.SP_2


title: IEL.TR_3


title: Pm silicic acid-limited B

description: processed data file: Pm_Si_expression.txt

organism: Pseudo-nitzschia multiseries

source_name: Pm silicic acid-limited


title: MUT1


title: IEl.TR_2


title: LP.SP_1


title: Gradient fraction 06


title: LP.TR_1


title: LP.TR_2


title: Pm silicic acid-limited A


title: IEL.DP_3


title: LP.TR_3


title: IEL.DP_1


title: LP.DP_3


title: IEL.DP_2


title: LP.DP_2


title: LP.DP_1


title: Homozygous Stage6-7 Rep2

city: Santiago

first: Christian

middle: E

last: Hodar

state: Santiago

address: Av. El Libano 5524

department: INTA

country: Chile

institute: Universidad de Chile

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were received already filtered by quality and mapped using STAR alignment.
Counts were extracted from BAM files using htseq-count
Genome_build: D. Melanogaster r6.04 (Flybase)
Supplementary_files_format_and_content: tab-delimited text files include counts each Sample.

organism: Drosophila melanogaster

source_name: Whole embryo

extract_protocol:
For RNA extractions, extracts of homozygous (zen[7]) and heterozygous (zen[7]/TM3, ftz-lacZ) staged embryos, previously preserved in RNAWIZ reagent (N = 100) were pooled, then samples were carefully homogenized in a 1.5 mL Eppendorf tube on ice with the aid of RNAse-free polypropylene pellet pestle. After homogenization, RNA extraction was performed using standard protocols. RNA was quantified using Qubit RNA HS Assay Kit (Thermo Fisher) and the integrity was assayed in a Tape station 2200 (Agilent Technologies). Samples were treated with Turbo DNA-free DNase (Ambion) to remove contaminating DNA.
Transcriptome sequencing was performed at the Duke Center for Genomic and Computational Biology in a Hiseq2000 platform (Illumina) with a 100 bp pair end library and 200 bp insert size

treatment_protocol: zen[7] homozygous embryos were selected using a genotyping procedure described by Ghanim and White (2006). In our case, both the absence of lacZ specific band together with the presence of a control band (non-coding region of gene Dtg) were indicators of homozygous lethal embryos.

tag: developmental stage

value: Gastrula

tag: genotype

value: zen[7] homozygous

tag: embryonic stage

value: stage 6-7


title: Homozygous Stage6-7 Rep1


title: Heterozygous Stage5 Rep2

value: Cellular blastoderm

value: zen[7]/TM3, ftz-lacZ

value: stage 5


title: Heterozygous Stage5 Rep1


title: Homozygous Stage5 Rep1


title: Homozygous Stage5 Rep2


title: Pm silicic acid-limited C

value: silicic acid-limited


title: minus-CHIR 8D

status: Public on Aug 26 2016

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

description: CHIR99021 removed from culture medium for 8 days

source_name: Kidney

growth_protocol: For cultured NPC lines, they are cultured in NPSR medium as 3D aggregates. Medium were freshed every two days and cells were passaged every 4 days at the ratio of 1:30.

extract_protocol:
30,000 to 100,000 primary NPCs and 200,000 cultured NPC lines were havested. Trizol was used to extract total RNA from samples, following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Not applicable

value: C57BL/6 and 129 hybrid

tag: age

tag: genotyping

value: Six2-GCE (JAX Stock ID #009600)


title: minus-LIF 8D

description: LIF removed from culture medium for 8 days


title: minus-BMP7 8D

description: BMP7 removed from culture medium for 8 days


title: minus-Y27632 4D

description: Y27632 removed from culture medium for 4 days


title: xl_st10.5_MethylC-seq

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
MethylC-seq libraries were sequenced in single-end mode on the Illumina HiSeq 1500 platform. The sequenced reads in FASTQ format were mapped to the in silico bisulfite-converted reference genome (Xenopus laevis: J-Strain v9.1) using the Bowtie alignment algorithm with the following parameters: -e 120 -l 20 -n 0 as described before (Lister et al, 2009; Nature).
Genome_build: Xenopus laevis genome (J-Strain v9.1)
Supplementary_files_format_and_content: .txt file reports DNA methylation calls (CG context)
col1: chromosome name, col2: sequence start, col3: sequence end, col4: C calls, col5: coverage

organism: Xenopus laevis

source_name: whole embryos

extract_protocol:
Embryos were homogenized in 3 volumes STOP buffer (15 mM EDTA, 10 mM Tris-HCl pH7.5, 1% SDS, 0.5 mg/mL proteinase K) after which two phenol:chloroform:isoamylalcohol (PCI, 25:24:1) extractions were performed. DNA was then precipitated in 1/5 volume NH4AC 4M and 3 volumes EtOH and dissolved in 100 uL, treated with RNase and purified by a PCI extraction. The precipitation was done with EtOH and the DNA was resuspended in 50 uL H2O.
MethylC-seq library generation was performed as described previously (Ulrich et al, 2015; Nature Protocols). Briefly, the genomic DNA was sonicated to an average size of 200 bp using a Covaris sonicator. Sonicated DNA was then purified and end-repaired followed by the ligation of methylated Illumina TruSeq sequencing adapters. Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA), using 6 cycles of amplification.

value: gastrula (st10.5) embryo

tag: tissue

value: whole embryo


title: IEL.TR_1


title: minus-Y27632 8D

description: Y27632 removed from culture medium for 8 days


title: minus-Heparin 8D

description: Heparin removed from culture medium for 8 days


title: minus-CHIR 4D

description: CHIR99021 removed from culture medium for 4 days


title: Heterozygous Stage6-7 Rep2


title: Gfi1-/- Irf8-/- GMP cell H7

city: Cincinnati

first: H. Leighton

last: Grimes

state: OH

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

institute: Cincinnati Childrens Hospital Medical Center

description: Lin- CD117+ Sca1- CD16/32+ CD34+

data_processing:
RNA reads were aligned to the reference mm9 mouse genome using Bowtie2.
Single-cell and matched bulk sorted RNA-Seq were analyzed using RSEM to estimate transcripts per million mapped reads (TPM) for all genes.
Differentially expressed genes were identified using AltAnalyze using a FDR adjusted empirical Bayes moderated t-test p<0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file of log2 (incremented by 1 before log2) TPM RSEM expression values

source_name: Bone Marrow

extract_protocol:
Cells were harvested from bone marrow. Femurs, tibias and iliac crest were harvested immediately after euthanasia and put in cold PBS+2%FBS. Bones were crushed with mortar and pestle, filtered and washed in cold PBS+2%FBS, then enriched using CD117 MicroBeads on a Automacs Pro separator (Miltenyi, San Diego, CA). CD117+ cells were stained with CD16/32-PerCp-ef710 (clone 93), CD3-biotin (clone 145-2C11), CD4-biotin (clone RM4-5), CD8-biotin (clone 53-6.7), CD11b-biotin (clone M1/70), CD19-biotin (clone 6D5), Gr1-biotin (clone RB6-8C5), Ter119-biotin (clone Ter-119) CD45R-biotin (clone RA3-6B2), CD117-APC (clone 2B8), Sca-1-Pe-Cy7 (clone D7), CD34-BV421 (clone RAM34), CD115-BV605 (clone TR15-12F1 2.2), CD135-PE (A2F10.1), CCR3-FITC (clone 83101), SiglecF (clone E50-2440) and Gr1-FITC (clone RB6-8C5).  Cell sorting was performed on MoFloXDP (Beckman Coulter, Brea, CA) or BD FACSAria II with a 100μm nozzleand subjected to flow cytrometric sorting of Lin- CD117+ Sca1- CD16/32+ CD34+ cells (GMP).
cDNA was made with Clontech SMARTer® Kit “the mRNA Seq: RT + Amp (1771x), Libraries were constructed using Nextera XT DNA Library Preparation Kit
Single cells were separated using Fluidigm C1 system

value: GMP Progenitors

tag: cdna synthesis

value: Fluidigm C1 protocol

tag: library prep

value: Nextera XT DNA Library Preparation Kit (Illumina Inc, Santa Clara, CA)


title: Gfi1-/- Irf8-/- GMP cell H6

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: minus-BMP7 4D

description: BMP7 removed from culture medium for 4 days


title: Heterozygous Stage6-7 Rep1


title: minus-Heparin 4D

description: Heparin removed from culture medium for 4 days


title: Gfi1-/- Irf8-/- GMP cell H4

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell H3

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell H5

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell G16

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell H1

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell G15

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell G12

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell G11

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell F7

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell F5

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell F3

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell E8

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell E6

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell E5

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell E2-60

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell E2-59

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell E7

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell D7

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell E3

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell G17

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell C8

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell E1

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell D1

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell C6

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell G13

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell C2

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell C7

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell D4

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell C1

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell D2

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell F6

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell B3

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell B2

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell F4

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell B1

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell C5

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell A8

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell A7

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell A6

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell A4

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell A5

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell B4

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- Irf8-/- GMP cell A2

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: P1 NPC line (P20)

data_processing:
read alignment with STAR
expression quantification with Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: expression matrix with FPKM values

value: NPC


title: E16.5 NPC line (P20)


title: E16.5 NPC line (P80)


title: P1 NPC line (P80)


title: E13.5 NPC line (P20)


title: Six2-negative #1


title: Six2-negative #2


title: E13.5 NPC line (P80)


title: E16.5 NPCs #2


title: Gfi1-/- Irf8-/- GMP cell A3

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: E11.5 NPC line (P80)


title: P1 NPCs #1


title: E13.5 NPCs #2


title: E16.5 NPCs #1


title: P1 NPCs #2


title: E13.5 NPCs #1


title: E11.5 NPC line (P20)


title: E11.5 NPCs #2


title: Gfi1-/- Irf8-/- GMP cell B7

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: LSK cell 96

description: Lin- CD117+ Sca1+

extract_protocol:
Cells were harvested from bone marrow. Femurs, tibias and iliac crest were harvested immediately after euthanasia and put in cold PBS+2%FBS. Bones were crushed with mortar and pestle, filtered and washed in cold PBS+2%FBS, then enriched using CD117 MicroBeads on a Automacs Pro separator (Miltenyi, San Diego, CA). CD117+ cells were stained with CD16/32-PerCp-ef710 (clone 93), CD3-biotin (clone 145-2C11), CD4-biotin (clone RM4-5), CD8-biotin (clone 53-6.7), CD11b-biotin (clone M1/70), CD19-biotin (clone 6D5), Gr1-biotin (clone RB6-8C5), Ter119-biotin (clone Ter-119) CD45R-biotin (clone RA3-6B2), CD117-APC (clone 2B8), Sca-1-Pe-Cy7 (clone D7), CD34-BV421 (clone RAM34), CD115-BV605 (clone TR15-12F1 2.2), CD135-PE (A2F10.1), CCR3-FITC (clone 83101), SiglecF (clone E50-2440) and Gr1-FITC (clone RB6-8C5). Cell sorting was performed on MoFloXDP (Beckman Coulter, Brea, CA) or BD FACSAria II with a 100μm nozzleand subjected to flow cytrometric sorting of bone marrow lineage-negative Sca1+ CD117+ cells (LSK).
cDNA was made with Clontech SMARTer® Kit “the mRNA Seq: RT + Amp (1771x), Libraries were constructed using Nextera XT DNA Library Preparation Kit
Single cells were separated using Fluidigm C1 system

value: LSK Stem cells


title: LSK cell 95

description: Lin- CD117+ Sca1+


title: LSK cell 94

description: Lin- CD117+ Sca1+


title: LSK cell 93

description: Lin- CD117+ Sca1+


title: LSK cell 91

description: Lin- CD117+ Sca1+


title: LSK cell 92

description: Lin- CD117+ Sca1+


title: LSK cell 88

description: Lin- CD117+ Sca1+


title: LSK cell 84

description: Lin- CD117+ Sca1+


title: LSK cell 87

description: Lin- CD117+ Sca1+


title: LSK cell 90

description: Lin- CD117+ Sca1+


title: E12.5 NPCs #1


title: LSK cell 86

description: Lin- CD117+ Sca1+


title: LSK cell 78

description: Lin- CD117+ Sca1+


title: LSK cell 89

description: Lin- CD117+ Sca1+


title: E12.5 NPCs #2


title: LSK cell 77

description: Lin- CD117+ Sca1+


title: LSK cell 79

description: Lin- CD117+ Sca1+


title: LSK cell 75

description: Lin- CD117+ Sca1+


title: LSK cell 83

description: Lin- CD117+ Sca1+


title: E11.5 NPCs #1


title: LSK cell 70

description: Lin- CD117+ Sca1+


title: LSK cell 82

description: Lin- CD117+ Sca1+


title: LSK cell 80

description: Lin- CD117+ Sca1+


title: LSK cell 81

description: Lin- CD117+ Sca1+


title: LSK cell 69

description: Lin- CD117+ Sca1+


title: LSK cell 85

description: Lin- CD117+ Sca1+


title: LSK cell 72

description: Lin- CD117+ Sca1+


title: LSK cell 71

description: Lin- CD117+ Sca1+


title: LSK cell 66

description: Lin- CD117+ Sca1+


title: LSK cell 73

description: Lin- CD117+ Sca1+


title: LSK cell 74

description: Lin- CD117+ Sca1+


title: LSK cell 65

description: Lin- CD117+ Sca1+


title: LSK cell 64

description: Lin- CD117+ Sca1+


title: LSK cell 67

description: Lin- CD117+ Sca1+


title: LSK cell 63

description: Lin- CD117+ Sca1+


title: LSK cell 76

description: Lin- CD117+ Sca1+


title: LSK cell 60

description: Lin- CD117+ Sca1+


title: LSK cell 62

description: Lin- CD117+ Sca1+


title: LSK cell 61

description: Lin- CD117+ Sca1+


title: LSK cell 59

description: Lin- CD117+ Sca1+


title: LSK cell 58

description: Lin- CD117+ Sca1+


title: LSK cell 56 (poor quality)

description: Lin- CD117+ Sca1+


title: LSK cell 57

description: Lin- CD117+ Sca1+


title: LSK cell 53

description: Lin- CD117+ Sca1+


title: LSK cell 51

description: Lin- CD117+ Sca1+


title: LSK cell 52

description: Lin- CD117+ Sca1+


title: LSK cell 50

description: Lin- CD117+ Sca1+


title: LSK cell 54

description: Lin- CD117+ Sca1+


title: LSK cell 48

description: Lin- CD117+ Sca1+


title: LSK cell 49

description: Lin- CD117+ Sca1+


title: LSK cell 46

description: Lin- CD117+ Sca1+


title: LSK cell 44

description: Lin- CD117+ Sca1+


title: LSK cell 55

description: Lin- CD117+ Sca1+


title: LSK cell 43

description: Lin- CD117+ Sca1+


title: LSK cell 42

description: Lin- CD117+ Sca1+


title: LSK cell 41

description: Lin- CD117+ Sca1+


title: LSK cell 40

description: Lin- CD117+ Sca1+


title: LSK cell 47

description: Lin- CD117+ Sca1+


title: LSK cell 39

description: Lin- CD117+ Sca1+


title: LSK cell 37

description: Lin- CD117+ Sca1+


title: LSK cell 36

description: Lin- CD117+ Sca1+


title: LSK cell 35

description: Lin- CD117+ Sca1+


title: LSK cell 34

description: Lin- CD117+ Sca1+


title: LSK cell 45

description: Lin- CD117+ Sca1+


title: LSK cell 31

description: Lin- CD117+ Sca1+


title: LSK cell 33

description: Lin- CD117+ Sca1+


title: LSK cell 30

description: Lin- CD117+ Sca1+


title: LSK cell 28

description: Lin- CD117+ Sca1+


title: LSK cell 32

description: Lin- CD117+ Sca1+


title: LSK cell 27

description: Lin- CD117+ Sca1+


title: LSK cell 23

description: Lin- CD117+ Sca1+


title: LSK cell 25 (poor quality)

description: Lin- CD117+ Sca1+


title: LSK cell 24

description: Lin- CD117+ Sca1+


title: LSK cell 22

description: Lin- CD117+ Sca1+


title: LSK cell 26

description: Lin- CD117+ Sca1+


title: LSK cell 18

description: Lin- CD117+ Sca1+


title: LSK cell 20

description: Lin- CD117+ Sca1+


title: LSK cell 19

description: Lin- CD117+ Sca1+


title: LSK cell 17

description: Lin- CD117+ Sca1+


title: LSK cell 14

description: Lin- CD117+ Sca1+


title: LSK cell 13

description: Lin- CD117+ Sca1+


title: LSK cell 15

description: Lin- CD117+ Sca1+


title: LSK cell 12

description: Lin- CD117+ Sca1+


title: LSK cell 11

description: Lin- CD117+ Sca1+


title: LSK cell 9

description: Lin- CD117+ Sca1+


title: LSK cell 29

description: Lin- CD117+ Sca1+


title: LSK cell 8

description: Lin- CD117+ Sca1+


title: LSK cell 21

description: Lin- CD117+ Sca1+


title: LSK cell 7

description: Lin- CD117+ Sca1+


title: LSK cell 10

description: Lin- CD117+ Sca1+


title: LSK cell 38

description: Lin- CD117+ Sca1+


title: LSK cell 2

description: Lin- CD117+ Sca1+


title: LSK cell 4

description: Lin- CD117+ Sca1+


title: LSK cell 1

description: Lin- CD117+ Sca1+


title: LK CD34 cell 64

description: Lin- CD117+ CD34+

extract_protocol:
Cells were harvested from bone marrow. Femurs, tibias and iliac crest were harvested immediately after euthanasia and put in cold PBS+2%FBS. Bones were crushed with mortar and pestle, filtered and washed in cold PBS+2%FBS, then enriched using CD117 MicroBeads on a Automacs Pro separator (Miltenyi, San Diego, CA). CD117+ cells were stained with CD16/32-PerCp-ef710 (clone 93), CD3-biotin (clone 145-2C11), CD4-biotin (clone RM4-5), CD8-biotin (clone 53-6.7), CD11b-biotin (clone M1/70), CD19-biotin (clone 6D5), Gr1-biotin (clone RB6-8C5), Ter119-biotin (clone Ter-119) CD45R-biotin (clone RA3-6B2), CD117-APC (clone 2B8), Sca-1-Pe-Cy7 (clone D7), CD34-BV421 (clone RAM34), CD115-BV605 (clone TR15-12F1 2.2), CD135-PE (A2F10.1), CCR3-FITC (clone 83101), SiglecF (clone E50-2440) and Gr1-FITC (clone RB6-8C5). Cell sorting was performed on MoFloXDP (Beckman Coulter, Brea, CA) or BD FACSAria II with a 100μm nozzleand subjected to flow cytrometric sorting of bone marrow lineage-negative CD117+ CD34+ cells (a broad gate inclusive of most hematopoietic stem and progenitors, as well as myelocytes and metamyelocytes).
cDNA was made with Clontech SMARTer® Kit “the mRNA Seq: RT + Amp (1771x), Libraries were constructed using Nextera XT DNA Library Preparation Kit
Single cells were separated using Fluidigm C1 system

value: Myeloid progenitors


title: LSK cell 5

description: Lin- CD117+ Sca1+


title: LK CD34 cell 63

description: Lin- CD117+ CD34+


title: LK CD34 cell 61

description: Lin- CD117+ CD34+


title: LK CD34 cell 65

description: Lin- CD117+ CD34+


title: LK CD34 cell 62

description: Lin- CD117+ CD34+


title: LSK cell 16

description: Lin- CD117+ Sca1+


title: LK CD34 cell 58

description: Lin- CD117+ CD34+


title: LK CD34 cell 57

description: Lin- CD117+ CD34+


title: LK CD34 cell 56

description: Lin- CD117+ CD34+


title: LK CD34 cell 55

description: Lin- CD117+ CD34+


title: LK CD34 cell 52

description: Lin- CD117+ CD34+


title: LK CD34 cell 60

description: Lin- CD117+ CD34+


title: LK CD34 cell 54

description: Lin- CD117+ CD34+


title: LK CD34 cell 53

description: Lin- CD117+ CD34+


title: LK CD34 cell 49

description: Lin- CD117+ CD34+


title: LK CD34 cell 51

description: Lin- CD117+ CD34+


title: LK CD34 cell 50

description: Lin- CD117+ CD34+


title: LK CD34 cell 47

description: Lin- CD117+ CD34+


title: LK CD34 cell 46

description: Lin- CD117+ CD34+


title: LK CD34 cell 48

description: Lin- CD117+ CD34+


title: LK CD34 cell 66

description: Lin- CD117+ CD34+


title: LK CD34 cell 44

description: Lin- CD117+ CD34+


title: LK CD34 cell 43

description: Lin- CD117+ CD34+


title: LK CD34 cell 42

description: Lin- CD117+ CD34+


title: LK CD34 cell 41

description: Lin- CD117+ CD34+


title: LK CD34 cell 59

description: Lin- CD117+ CD34+


title: LK CD34 cell 40

description: Lin- CD117+ CD34+


title: LK CD34 cell 37

description: Lin- CD117+ CD34+


title: LK CD34 cell 38

description: Lin- CD117+ CD34+


title: LK CD34 cell 36

description: Lin- CD117+ CD34+


title: LK CD34 cell 35

description: Lin- CD117+ CD34+


title: LK CD34 cell 34

description: Lin- CD117+ CD34+


title: LK CD34 cell 32

description: Lin- CD117+ CD34+


title: LK CD34 cell 33

description: Lin- CD117+ CD34+


title: LK CD34 cell 45

description: Lin- CD117+ CD34+


title: LK CD34 cell 28

description: Lin- CD117+ CD34+


title: LK CD34 cell 26

description: Lin- CD117+ CD34+


title: LK CD34 cell 24

description: Lin- CD117+ CD34+


title: LK CD34 cell 27

description: Lin- CD117+ CD34+


title: LK CD34 cell 21

description: Lin- CD117+ CD34+


title: LK CD34 cell 23

description: Lin- CD117+ CD34+


title: LK CD34 cell 20

description: Lin- CD117+ CD34+


title: LK CD34 cell 19

description: Lin- CD117+ CD34+


title: LK CD34 cell 31

description: Lin- CD117+ CD34+


title: LK CD34 cell 39

description: Lin- CD117+ CD34+


title: LSK cell 3

description: Lin- CD117+ Sca1+


title: LK CD34 cell 17

description: Lin- CD117+ CD34+


title: LK CD34 cell 15

description: Lin- CD117+ CD34+


title: LK CD34 cell 13

description: Lin- CD117+ CD34+


title: LK CD34 cell 10

description: Lin- CD117+ CD34+


title: LK CD34 cell 14

description: Lin- CD117+ CD34+


title: LK CD34 cell 9

description: Lin- CD117+ CD34+


title: LK CD34 cell 29

description: Lin- CD117+ CD34+


title: LK CD34 cell 30

description: Lin- CD117+ CD34+


title: LK CD34 cell 18

description: Lin- CD117+ CD34+


title: LK CD34 cell 16

description: Lin- CD117+ CD34+


title: LSK cell 68 (poor quality)

description: Lin- CD117+ Sca1+


title: LK CD34 cell 11 (poor quality)

description: Lin- CD117+ CD34+


title: LK CD34 cell 25

description: Lin- CD117+ CD34+


title: LK CD34 cell 7

description: Lin- CD117+ CD34+


title: LK CD34 cell 8 (poor quality)

description: Lin- CD117+ CD34+


title: LK CD34 cell 22

description: Lin- CD117+ CD34+


title: LK CD34 cell 6

description: Lin- CD117+ CD34+


title: LK CD34 cell 5

description: Lin- CD117+ CD34+


title: LK CD34 cell 2

description: Lin- CD117+ CD34+


title: LK CD34 cell 3 (poor quality)

description: Lin- CD117+ CD34+


title: Irf8-/- GMP cell 62

description: Lin- CD117+ Sca1- CD16/32+ CD34+

extract_protocol:
Cells were harvested from bone marrow.  Femurs, tibias and iliac crest were harvested immediately after euthanasia and put in cold PBS+2%FBS. Bones were crushed with mortar and pestle, filtered and washed in cold PBS+2%FBS, then enriched using CD117 MicroBeads on a Automacs Pro separator (Miltenyi, San Diego, CA). CD117+ cells were stained with CD16/32-PerCp-ef710 (clone 93), CD3-biotin (clone 145-2C11), CD4-biotin (clone RM4-5), CD8-biotin (clone 53-6.7), CD11b-biotin (clone M1/70), CD19-biotin (clone 6D5), Gr1-biotin (clone RB6-8C5), Ter119-biotin (clone Ter-119) CD45R-biotin (clone RA3-6B2), CD117-APC (clone 2B8), Sca-1-Pe-Cy7 (clone D7), CD34-BV421 (clone RAM34), CD115-BV605 (clone TR15-12F1 2.2), CD135-PE (A2F10.1), CCR3-FITC (clone 83101), SiglecF (clone E50-2440) and Gr1-FITC (clone RB6-8C5). Cell sorting was performed on MoFloXDP (Beckman Coulter, Brea, CA) or BD FACSAria II with a 100μm nozzleand subjected to flow cytrometric sorting of Lin- CD117+ Sca1- CD16/32+ CD34+ (GMP).
cDNA was made with Clontech SMARTer® Kit “the mRNA Seq: RT + Amp (1771x), Libraries were constructed using Nextera XT DNA Library Preparation Kit
Single cells were separated using Fluidigm C1 system


title: LK CD34 cell 1

description: Lin- CD117+ CD34+


title: Irf8-/- GMP cell 63

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 61

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 60

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: LK CD34 cell 12

description: Lin- CD117+ CD34+


title: Irf8-/- GMP cell 58

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 59

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 56

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 51

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 50

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 48

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 55

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 52

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 54

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 44

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 47

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 42

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 49

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 46

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 45

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 43

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 41

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 37

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 38

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 40

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 39

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 34

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 35

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 36

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 33

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 53

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 57

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 32

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: LK CD34 cell 4

description: Lin- CD117+ CD34+


title: Irf8-/- GMP cell 31

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 30

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 29

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 26

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 24

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 27

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 22

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 25

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 28

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 21

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 18

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 19

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 20

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 23 (poor quality)

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 12

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 13

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 15

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 14

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 17

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 11

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 9

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 2

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 3

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 6

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 5

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 7

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-GFP GMP cell 37 (poor quality)

description: Lin- CD117+ Sca1- CD16/32+ CD34+ CD115- Irf8-GFP dim

extract_protocol:
Cells were harvested from bone marrow. Mice were euthanized with carbon dioxide and cervical dislocation. Femurs, tibias and iliac crest were harvested immediately after euthanasia and put in cold PBS+2%FBS. Bones were crushed with mortar and pestle, filtered and washed in cold PBS+2%FBS, then enriched using CD117 MicroBeads on a Automacs Pro separator (Miltenyi, San Diego, CA). CD117+ cells were stained with CD16/32-PerCp-ef710 (clone 93), CD3-biotin (clone 145-2C11), CD4-biotin (clone RM4-5), CD8-biotin (clone 53-6.7), CD11b-biotin (clone M1/70), CD19-biotin (clone 6D5), Gr1-biotin (clone RB6-8C5), Ter119-biotin (clone Ter-119) CD45R-biotin (clone RA3-6B2), CD117-APC (clone 2B8), Sca-1-Pe-Cy7 (clone D7), CD34-BV421 (clone RAM34), CD115-BV605 (clone TR15-12F1 2.2), CD135-PE (A2F10.1), CCR3-FITC (clone 83101), SiglecF (clone E50-2440) and Gr1-FITC (clone RB6-8C5). Cell sorting was performed on MoFloXDP (Beckman Coulter, Brea, CA) or BD FACSAria II with a 100μm nozzleand subjected to flow cytrometric sorting of Lin- CD117+ Sca1- CD16/32+ CD34+ CD115-intermediate Irf8-GFP-intermediate GMP .
cDNA was made with Clontech SMARTer® Kit “the mRNA Seq: RT + Amp (1771x), Libraries were constructed using Nextera XT DNA Library Preparation Kit
Single cells were separated using Fluidigm C1 system

value: Irf8-GFP dim Csf1r- GMP Progenitors


title: Irf8-/- GMP cell 1

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-GFP GMP cell 35


title: Irf8-/- GMP cell 4

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-GFP GMP cell 34


title: Irf8-GFP GMP cell 36


title: Irf8-GFP GMP cell 32


title: Irf8-GFP GMP cell 33 (poor quality)


title: Irf8-GFP GMP cell 31


title: Irf8-/- GMP cell 16

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-GFP GMP cell 27


title: Irf8-GFP GMP cell 28


title: Irf8-GFP GMP cell 26


title: Irf8-/- GMP cell 8

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-/- GMP cell 10

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: LSK cell 6

description: Lin- CD117+ Sca1+


title: Irf8-GFP GMP cell 25


title: Irf8-GFP GMP cell 24


title: Irf8-GFP GMP cell 21


title: Irf8-GFP GMP cell 14


title: Irf8-GFP GMP cell 18


title: Irf8-GFP GMP cell 16


title: Irf8-GFP GMP cell 13


title: Irf8-GFP GMP cell 23


title: Irf8-GFP GMP cell 19


title: Irf8-GFP GMP cell 12 (poor quality)


title: Irf8-GFP GMP cell 3


title: Irf8-GFP GMP cell 4


title: Irf8-GFP GMP cell 9


title: Irf8-GFP GMP cell 10


title: Irf8-GFP GMP cell 30


title: Irf8-GFP GMP cell 15


title: Irf8-GFP GMP cell 22


title: Irf8-GFP GMP cell 29 (poor quality)


title: Irf8-GFP GMP cell 7


title: Irf8-GFP GMP cell 6


title: Irf8-GFP GMP cell 11


title: GMP cell R3.68

description: Lin- CD117+ Sca1- CD16/32+ CD34+

extract_protocol:
Cells were harvested from bone marrow.  Femurs, tibias and iliac crest were harvested immediately after euthanasia and put in cold PBS+2%FBS. Bones were crushed with mortar and pestle, filtered and washed in cold PBS+2%FBS, then enriched using CD117 MicroBeads on a Automacs Pro separator (Miltenyi, San Diego, CA). CD117+ cells were stained with CD16/32-PerCp-ef710 (clone 93), CD3-biotin (clone 145-2C11), CD4-biotin (clone RM4-5), CD8-biotin (clone 53-6.7), CD11b-biotin (clone M1/70), CD19-biotin (clone 6D5), Gr1-biotin (clone RB6-8C5), Ter119-biotin (clone Ter-119) CD45R-biotin (clone RA3-6B2), CD117-APC (clone 2B8), Sca-1-Pe-Cy7 (clone D7), CD34-BV421 (clone RAM34), CD115-BV605 (clone TR15-12F1 2.2), CD135-PE (A2F10.1), CCR3-FITC (clone 83101), SiglecF (clone E50-2440) and Gr1-FITC (clone RB6-8C5). Cell sorting was performed on MoFloXDP (Beckman Coulter, Brea, CA) or BD FACSAria II with a 100μm nozzleand subjected to flow cytrometric sorting of Lin- CD117+ Sca1- CD16/32+ CD34+ cells (GMP).
cDNA was made with Clontech SMARTer® Kit “the mRNA Seq: RT + Amp (1771x), Libraries were constructed using Nextera XT DNA Library Preparation Kit
Single cells were separated using Fluidigm C1 system


title: GMP cell R3.64

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.67

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-GFP GMP cell 8


title: Irf8-GFP GMP cell 5


title: GMP cell R3.59

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-GFP GMP cell 2


title: Irf8-GFP GMP cell 1


title: GMP cell R3.61

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.58

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-GFP GMP cell 20


title: GMP cell R3.66

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.63

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.54

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.53

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.56

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.60

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.57

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.49

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Irf8-GFP GMP cell 17


title: GMP cell R3.48

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.55

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.51

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.50

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.52

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.62

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.65

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.47

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.46

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.45

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.41

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.39

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.43

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.44

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.40

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.42

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.36

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.35

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.32

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.33

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.28

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.29

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.34

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.37

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.27

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.31

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.20

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.25

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.21

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.30

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.26

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.24

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.23

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.19

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.22

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.18

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.15

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.38

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.12

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.11

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.14

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.13

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.10

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.9

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.8

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.7

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.6

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.4

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.3

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.2

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.1

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.66

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.17

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.67

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.64

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.65

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.58

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.57

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.5

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.62 (poor quality)

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.63

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.54

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.51

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.55

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.61

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R3.16

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.50

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.52

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.59

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.53 (poor quality)

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.68

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.56

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.60

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.49

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.47

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.45

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.46

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.41

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.40

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.44

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.43

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.42

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.38

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.39

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.35

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.37

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.36

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.32

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.48

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.30

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.34

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.33

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.25 (poor quality)

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.29

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.26

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.24

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.28

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.23

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.21

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.27

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.22

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.20

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.19

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.17

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.16

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.18

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.15

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.11

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.10

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.12

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.5

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.9

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.8

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.13

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.14

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.6

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.4

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.2

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.7

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.1

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 82

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 81

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 78

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 83

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 76

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 84

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 79

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 80

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 75

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 77

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 74

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.31 (poor quality)

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 72

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 73

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: GMP cell R2.3

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 68

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 70

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 64

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 67

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 71

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 63

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 65

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 62

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 59

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 66

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 61

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 60

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 58

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 56

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 54

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 69

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 55

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 53

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 52

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 51

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 50

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 48

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 47

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 49

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 57

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 41

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 46

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 38

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 44

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 45

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 43

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 34

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 32

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 37

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 33

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 30

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 29

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 39

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 42

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 27

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 24

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 25

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 21

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 23

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 19

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 18

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 36

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 16

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 20

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 35

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 15

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 14

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 31

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 12

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 13

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 8

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 9

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 11 (poor quality)

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 7

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 6

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 5

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 4

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 1

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-/- GMP cell 26

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-GFP GMP cell R2.47

description: Lin- CD117+ Sca1- CD16/32+ CD34+ CD115- Gfi1-GFP dim

extract_protocol:
Cells were harvested from bone marrow.  Femurs, tibias and iliac crest were harvested immediately after euthanasia and put in cold PBS+2%FBS. Bones were crushed with mortar and pestle, filtered and washed in cold PBS+2%FBS, then enriched using CD117 MicroBeads on a Automacs Pro separator (Miltenyi, San Diego, CA). CD117+ cells were stained with CD16/32-PerCp-ef710 (clone 93), CD3-biotin (clone 145-2C11), CD4-biotin (clone RM4-5), CD8-biotin (clone 53-6.7), CD11b-biotin (clone M1/70), CD19-biotin (clone 6D5), Gr1-biotin (clone RB6-8C5), Ter119-biotin (clone Ter-119) CD45R-biotin (clone RA3-6B2), CD117-APC (clone 2B8), Sca-1-Pe-Cy7 (clone D7), CD34-BV421 (clone RAM34), CD115-BV605 (clone TR15-12F1 2.2), CD135-PE (A2F10.1), CCR3-FITC (clone 83101), SiglecF (clone E50-2440) and Gr1-FITC (clone RB6-8C5). Cell sorting was performed on MoFloXDP (Beckman Coulter, Brea, CA) or BD FACSAria II with a 100μm nozzleand subjected to flow cytrometric sorting of Lin- CD117+ Sca1- CD16/32+ CD34+ CD115- Gfi1-GFP-intermediate cells (the GG1 gate subset of GMP).
cDNA was made with Clontech SMARTer® Kit “the mRNA Seq: RT + Amp (1771x), Libraries were constructed using Nextera XT DNA Library Preparation Kit
Single cells were separated using Fluidigm C1 system

value: Gfi1-GFP dim Csf1r- GMP Progenitors


title: Gfi1-GFP GMP cell R2.46


title: Gfi1-/- GMP cell 3

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-GFP GMP cell R2.44


title: Gfi1-GFP GMP cell R2.45


title: Gfi1-GFP GMP cell R2.43


title: Gfi1-GFP GMP cell R2.42


title: Gfi1-/- GMP cell 17

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-GFP GMP cell R2.41


title: Gfi1-/- GMP cell 10

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Gfi1-GFP GMP cell R2.40


title: Gfi1-GFP GMP cell R2.39


title: Gfi1-GFP GMP cell R2.38


title: Gfi1-GFP GMP cell 96


title: Gfi1-GFP GMP cell 95


title: Gfi1-GFP GMP cell 93


title: Gfi1-GFP GMP cell 94


title: Gfi1-GFP GMP cell 92


title: Gfi1-GFP GMP cell 86


title: Gfi1-GFP GMP cell 85


title: Gfi1-GFP GMP cell 91


title: Gfi1-GFP GMP cell 87


title: Gfi1-GFP GMP cell 83 (poor quality)


title: Gfi1-GFP GMP cell 84


title: Gfi1-GFP GMP cell 88


title: Gfi1-GFP GMP cell R2.48


title: Gfi1-GFP GMP cell 82


title: Gfi1-GFP GMP cell 80


title: Gfi1-GFP GMP cell 81


title: Gfi1-GFP GMP cell 79


title: Gfi1-GFP GMP cell 73


title: Gfi1-GFP GMP cell 78 (poor quality)


title: Gfi1-GFP GMP cell 77


title: Gfi1-GFP GMP cell 74


title: Gfi1-GFP GMP cell 76


title: Gfi1-GFP GMP cell 75


title: Gfi1-GFP GMP cell 72


title: Gfi1-GFP GMP cell 70


title: Gfi1-GFP GMP cell 69


title: Gfi1-GFP GMP cell 71


title: Gfi1-GFP GMP cell 90


title: Gfi1-GFP GMP cell 89


title: CMP cell 96

description: Lin- CD117+ Sca1- CD16/32 dim CD34+

extract_protocol:
Cells were harvested from bone marrow. Femurs, tibias and iliac crest were harvested immediately after euthanasia and put in cold PBS+2%FBS. Bones were crushed with mortar and pestle, filtered and washed in cold PBS+2%FBS, then enriched using CD117 MicroBeads on a Automacs Pro separator (Miltenyi, San Diego, CA). CD117+ cells were stained with CD16/32-PerCp-ef710 (clone 93), CD3-biotin (clone 145-2C11), CD4-biotin (clone RM4-5), CD8-biotin (clone 53-6.7), CD11b-biotin (clone M1/70), CD19-biotin (clone 6D5), Gr1-biotin (clone RB6-8C5), Ter119-biotin (clone Ter-119) CD45R-biotin (clone RA3-6B2), CD117-APC (clone 2B8), Sca-1-Pe-Cy7 (clone D7), CD34-BV421 (clone RAM34), CD115-BV605 (clone TR15-12F1 2.2), CD135-PE (A2F10.1), CCR3-FITC (clone 83101), SiglecF (clone E50-2440) and Gr1-FITC (clone RB6-8C5). Cell sorting was performed on MoFloXDP (Beckman Coulter, Brea, CA) or BD FACSAria II with a 100μm nozzleand subjected to flow cytrometric sorting of Lin- CD117+ Sca1- CD16/32-intermediate CD34-intermediate cells (CMP).
cDNA was made with Clontech SMARTer® Kit “the mRNA Seq: RT + Amp (1771x), Libraries were constructed using Nextera XT DNA Library Preparation Kit
Single cells were separated using Fluidigm C1 system

value: CMP Progenitors


title: CMP cell 93

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: H3K4me2 ChIP-Seq Gfi1-/- ChIP-seq

data_processing:
ChIP-seq reads were aligned to the reference mm9 mouse genome using Bowtie2.
ChIP-seq peaks were called using the software Homer. Gene assignment was performed using the software GREAT (version 3.0.0), with the association rule of basal+extension: 5000 bp upstream, 1000 bp downstream, 100000 bp max extension, curated regulatory domains excluded.
Genome_build: mm9
Supplementary_files_format_and_content: Peak calling using HOMER in bed format. All parameters and commands are included (text file)
Supplementary_files_format_and_content: Tag statistics per chromosome

growth_protocol: Cells were harvested from bone marrow. Femurs, tibias and iliac crest were harvested immediately after euthanasia and put in cold PBS+2%FBS. Bones were crushed with mortar and pestle, filtered and washed in cold PBS+2%FBS, then enriched using CD117 MicroBeads on a Automacs Pro separator (Miltenyi, San Diego, CA). CD117+ cells were stained with CD16/32-PerCp-ef710 (clone 93), CD3-biotin (clone 145-2C11), CD4-biotin (clone RM4-5), CD8-biotin (clone 53-6.7), CD11b-biotin (clone M1/70), CD19-biotin (clone 6D5), Gr1-biotin (clone RB6-8C5), Ter119-biotin (clone Ter-119) CD45R-biotin (clone RA3-6B2), CD117-APC (clone 2B8), Sca-1-Pe-Cy7 (clone D7), CD34-BV421 (clone RAM34), CD115-BV605 (clone TR15-12F1 2.2), CD135-PE (A2F10.1), CCR3-FITC (clone 83101), SiglecF (clone E50-2440) and Gr1-FITC (clone RB6-8C5). Cell sorting was performed on MoFloXDP (Beckman Coulter, Brea, CA) or BD FACSAria II with a 100μm nozzleand subjected to flow cytrometric sorting of Lin- CD117+ Sca1- CD16/32+ CD34+ cells (GMP).

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on HiSeq 2500.

value: Lineage Negative Cells

value: ChIP Seq

tag: chip antibody

value: H3K4me2 Diagenode pAb-035-050


title: CMP cell 92

description: Lin- CD117+ Sca1- CD16/32 dim CD34+

tag: strain


title: CMP cell 88

description: Lin- CD117+ Sca1- CD16/32 dim CD34+

tag: cell type


title: CMP cell 91

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 89

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 90

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 94

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 87

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 86

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: Input GMP ChIP-Seq

description: Lin- CD117+ Sca1- CD16/32+ CD34+

value: Granulocyte Macrophage Progenitors


title: CMP cell 85

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: Gfi1 GMP ChIP-Seq

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: H3K4me2 ChIP-Seq wt ChIP-seq


title: CMP cell 81

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 79

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 82

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 78

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 77

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 80

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: Irf8 GMP ChIP-Seq

description: Lin- CD117+ Sca1- CD16/32+ CD34+

value: Irf8 antibody Santa Cruz sc-6058


title: CMP cell 83

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 75

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 74

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 72

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 95

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 73

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 66

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 64

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 63

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 65

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 69

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 67

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 71

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 68

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 59

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 84

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 62

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 58

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 57

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 60

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 61

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 55

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 53

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 76

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 51

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 49

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 47

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 50

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 48

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 70

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 46

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 45

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 44

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 38

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 41 (poor quality)

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 43

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 37

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 33

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 34

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 52

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 31

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 29

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 30

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 40

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 39

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 35

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 27

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 54

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 28

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 26

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 56

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 24

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 23

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 20

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 22

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 21

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 18

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 19

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 42

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 17

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 36

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 16

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 15

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 14

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 32

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 13

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 25

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 8

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 11

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 10

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 5

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 7

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 6

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 12

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 9

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: CMP cell 4

description: Lin- CD117+ Sca1- CD16/32 dim CD34+