title: TAP Input

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

data_processing:
Sequencing data were mapped to the S. cerevisiae reference genome sacCer3, using bowtie2 with the default settings.
PCR duplicates were removed using the samtools rmdup software.
Reads were size selected, and those longer than 300bp were discarded.
Genome-wide coverage profiles were computed in MATLAB, and they were normalized such that the average coverage for every chromosome is 1.
IGV tracks (tdf files) were generated using igvtools.
Genome_build: sacCer3
Supplementary_files_format_and_content: tdf files containing the normalized occupancy profiles, for the IGV browser

source_name: TAP Input

growth_protocol: Myc and TAP-tagged Mediator strains were grown in synthetic complete medium with 2% Glucose till they reached a mid-log phase.

extract_protocol:
Mid-log phase cells were fixed with 0.6% formaldehyde to crosslink mediator to chromatin. Fixed cells were lysed, chromatin was sheared and immunoprecipitated with anti-Myc and anti-TAP antibody (See paper for details)
The DNA was end repaired and ligated with adapters using the KAPA Hyper Prep Kit to prepare libraries for Illumina sequencing.

tag: strain name

value: MATa his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0


title: CycC-TAP IP

status: Public on May 23 2017

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: CycC-TAP IP

tag: genotype

value: MATa SSN8- TAP-HIS3MX his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0


title: input_untreated

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
ChIP-Seq reads were mapped to S. cerevisiae reference genome R64-2-1 using Bowtie 2 (v2.2.5). Peaks were called using MACS2 (-g 12e6 --nomodel --extsize 250 --keep-dup all), artifactual peaks containing a single mis-mapped read were manually removed, and only peaks with a 2-fold or greater enrichment were considered.
RNA-Seq reads were mapped to genome R64-2-1 using HISAT2 v2.0.5 (parameters: --sp 1000,1000 ). BAM files were imported into Seqmonk v0.34.1 and Log2 read counts were performed for each annotated CDS and normalised for CDS length.
Genome_build: R64-2-1
Supplementary_files_format_and_content: ChIP-Seq: Filtered output of MACS2, format as given (https://github.com/taoliu/MACS/)
Supplementary_files_format_and_content: RNA-Seq: Quantitated RNA-Seq data files are tab delimited SeqMonk reports containing the following relevant columns: (1) CDS name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (8) Description (Ensembl); (12-13) log2 RPKM value

growth_protocol: Cells were grown in YPD to mid-log (0.5-0.7 cells/ml)

extract_protocol:
ChIP-Seq: Cells were fixed for 15 min in 1% formaldehyde and quenched with 150mM glycine. Cells were washed 2x with cold PBS then re-suspended in 600µl lysis buffer (50mM HEPES pH7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, 1x Roche Complete Protease Inhibitors), broken with 500µl zirconium beads  in an MP Biomedical Fast Prep (6 cycles 30s), then the lysate was separated from the beads and diluted to 1ml final volume in lysis buffer. Samples were sonicated 19x 30s in a Diagenode Bioruptor on High and cleared by centrifugation at 20,000g, 4°C for 5 min. 1µl anti-γH2A (Millipore 07-745-I) was added to 100µl lysate and incubated overnight at 4°C before addition of 15µl Gammabind beads (GE) in 25µl lysis buffer (pre-blocked with 1% BSA) and incubation for 2 hr at 4°C. Beads were washed 5 min each with lysis buffer, 0.5M salt lysis buffer, wash buffer (10mM Tris pH8.0, 0.25M LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1mM EDTA) and TE, then DNA eluted overnight at 65° in 200µl 50mM Tris pH8.0, 10mM EDTA, 1% SDS.  DNA was purified by phenol:chloroform extraction, ethanol precipitated and eluted in 50µl TE.
mRNA-Seq: Total RNA was extracted using a mirVANA kit (Thermo Fisher) according to manufacturer’s instructions, with glass bead lysis as described in Cruz and Houseley 2014
ChIP-Seq: Indexed ChIP-Seq libraries were generated from 5ng ChIP/input with the NEBNext DNA Ultra kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB).
mRNA-Seq: Indexed mRNA-Seq libraries were constructed from 500ng total RNA using the NEBNext Ultra Directional RNA Library Prep Kit (NEB), with poly(A) selection using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB)

treatment_protocol: With or without 4 hours 1mM CuSO4

tag: strain

tag: copper treatment


title: GAD_anterior_cell_1

city: Seattle

first: Thuc Nghi

last: Nguyen

state: WA

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

library_source: transcriptomic

data_processing:
Adapter sequences were clipped from 100  or 75 base-pair single-end reads in FASTQ format using the ea-utils application fastq-mcf with settings -C 200000 to filter against Nextera adapter sequences.
Trimmed reads were aligned to GRCm38 (mm10) using the RefSeq annotation gff file downloaded on 6/1/2013. Transcriptome alignment files in BAM format were generated with RSEM v1.2.4 and Bowtie v1.1.0 using the program rsem-calculate-expression with settings --keep-intermediate-files --bowtie-chunkmbs 2000 --output-genome-bam --bowtie-e 500 --bowtie-m 100.
Reads that did not map to the RefSeq annotations were aligned to ERCC sequences, tdTomato sequence, and nls-YFP-WPRE sequence using Bowtie v1.1.0 with settings -S --chunkmbs 2000.
Genome_build: mm10
Supplementary_files_format_and_content: CSV: Comma-separated tables of data values; Columns are samples and Rows are genes or ERCC/tdTomato. Column names correspond to sample Titles; Row names correspond to RefSeq Gene Symbols, ERCC symbols, or tdTomato.

molecule: total RNA

organism: Mus musculus

source_name: preopic area neuron

growth_protocol: Animals were provided food and water ad libitum and were maintained at a regular 12 h day/night cycle at no more than 5 adult animals per cage. Animals were maintained on the C57BL/6J background.

extract_protocol:
Individual adult male mice (P47-66) were anesthetized in an isoflurane chamber, decapitated, and the brain was immediately removed and submerged in fresh ice-cold artificial cerebrospinal fluid (ACSF). The brain was sectioned on a vibratome (Leica VT1000S) on ice, and each slice (300-400 µm) was immediately transferred to an ACSF bath at room temperature. After the brain slicing is complete (not more than 15 minutes), individual slices of interest were transferred to a small Petri dish containing bubbled room temperature ACSF. The regions of interest were microdissected under a fluorescence dissecting microscope. The dissected tissue pieces were transferred to a microcentrifuge tube and treated with 1 mg/ml pronase in carbogen-bubbled ACSF for 70 minutes at room temperature without mixing in a closed tube. After incubation, with the tissue pieces sitting at the bottom of the tube, the pronase solution was pipetted out of the tube and exchanged with cold ACSF containing 1% fetal bovine serum. The tissue pieces were dissociated into single cells by gentle trituration through Pasteur pipettes with polished tips of 600, 300, and 150-µm diameter. Single cells were isolated by FACS into individual wells of 96-well plates or 8-well PCR strips containing 2.275 µl of Dilution Buffer (SMARTer Ultra Low RNA Kit for Illumina Sequencing, Clontech Cat#634936), 0.125 µl RNase inhibitor (SMARTer kit), and 0.1 µl of 1:1,000,000 diluted RNA spike-in RNAs (ERCC RNA Spike-In Mix 1, Life Technologies Cat#4456740). Sorting was performed on a BD FACSAriaII SORP using a 130um nozzle, a sheath pressure of 10psi, and in the single cell sorting mode. To exclude dead cells, DAPI (DAPI*2HCl, Life Technologies Cat#D1306) was added to the single cell suspension to the final concentration of 2 ng/ml. FACS populations were chosen to select cells with low DAPI and high YFP fluorescence (for SADB-rEIAV-tloop-DIO-nls-YFP injected animals) or  tdTomato (tdT) fluorescence (for Chat-IRES-Cre;Ai14 animals). Sorted cells were frozen immediately on dry ice and stored at -80°C.
We used the SMARTer kit from Clontech (SMARTer Ultra Low RNA Kit for Illumina Sequencing, Clontech Cat#634936)  to reverse transcribe single cell RNA, and amplify the cDNA for 19 PCR cycles. To stabilize the RNA after quickly thawing the cells on ice, we immediately added to each sample an additional 0.125 µl of RNase inhibitor mixed with SMART CDS Primer II A. All steps downstream were carried out according to the manufacturer’s instructions. Each amplification experiment included a set of controls: 10 pg cortex RNA (isolated from Rbp4-Cre;Ai14, P57 male) as positive control for amplification, ERCC-only control to demonstrate the absence of RNases throughout the sorting process, and water-only control, to control for specificity of amplification/absence of contamination. cDNA concentration was quantified using Agilent Bioanalyzer High Sensitivity DNA chips. For most samples, 1 ng of amplified cDNA was used as input to make sequencing libraries with Nextera XT DNA kit (Illumina Cat#FC-131-1096).  We stopped the procedure after PCR clean-up and did not perform library normalization or library pooling. Individual libraries were quantified using Agilent Bioanalyzer DNA 7500 chips. In order to assess sample quality and adjust the concentrations of libraries for multiplexing on HiSeq or NextSeq. Libraries were sequenced on Illumina HiSeq single end 100-bp or NextSeq single end 75-bp.

treatment_protocol: We injected SADB-rEIAV-tloop-DIO-nls-YFP into brains of Gad2-IRES-Cre or Slc32a1-IRES-Cre mice. Briefly, mice were anesthetized with 5% isoflurane and then placed into a stereotaxic alignment instrument (Kopf, model 1900). Anesthesia was maintained for the duration of the surgery by administering isoflurane at 1-2% through a nose cone. The skin along the midline of the skull was opened using a scalpel, and a surgical drill was used to create a small hole in the skull. A pulled glass pipette prefilled with virus solution was lowered into the brain, and 500-700 nl of the virus solution was delivered to the targeted brain area using a pressure injection system (NanoJect II, Drummond Scientific Company, Catalog# 3-000-204). Stereotaxic coordinates were obtained from Paxinos adult mouse brain atlas for tuberomammillary nucleus (TMN, AP -2.45 mm, ML 1 mm, DV 5-5.2 mm). After the delivery of virus solution into the brain, the glass pipette was retracted and the incision in the scalp was closed using sutures. The animal was removed from the stereotaxic frame and allowed to recover from anesthesia. Mice were sacrificed 15−28 days after surgery for single cell isolation. YFP+ single cells were isolated from the preoptic area.

tag: mouse line abbreviation

tag: cre driver

tag: reporter

value: SADB-rEIAV-tloop-DIO-nls-YFP

tag: brain region

value: preoptic area

tag: dissection

value: anterior

tag: input material

value: single cell

tag: tdtomato labeling

tag: yfp labeling

value: Y

tag: passes qc checks

tag: animal id


title: Med19-TAP IP

source_name: Med19-TAP IP

value: MATa MED19- TAP-HIS3MX his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0


title: WT2_RPF

city: Muenster

first: Benedikt

middle: Sebastian

last: Nilges

address: Von-Esmarch-Straße 54

department: RNA Biology Group

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: mRNA - ribosome footprints

data_processing:
Library strategy: ribosome profiling
for fooprints: linkers were removed from reads using the fastx_clipper and randomized sequences removed  using the fastx_trimmer (FASTX Toolkit). Already performed for uploaded files.
Data was mapped to the hg38 transcriptome (UCSC knownCanonical) with bowtie (-m 1 -v1 -l 25 --best --strata) and counts generated using a custom script.
Genome_build: hg38
Supplementary_files_format_and_content: Count table showing the raw counts of ribosome profiling and RNAseq data for detected GENCODE v24_knownCanonical transcipts (available from the UCSC table browser for hg38)

molecule: polyA RNA

organism: Homo sapiens

source_name: Flp-In T-REx-293 wild-type_ribosomal profiling

growth_protocol: Wild type and EEF1AKMT4-deficient HAP-1 cells were cultured  in IMDM GlutaMAX™, 10 % FBS and 100 U/ml penicillin-streptomycin.

extract_protocol:
Cell lysates were incubated with RNAseI and subjected to sucrose gradient centrifugation. Monosomes were isolated and used for library preparation.
Libraries were prepared by isolating ribosome prorotected fragments, 3' linker ligation, reverse transcription with an RT primer complementary to the linker, cicularization of the resulting ssDNA and a final PCR to attach illumina index primers and amplify the library.

treatment_protocol: Cells were treated with 100 µg/ml cycloheximide (CHX) for 1 min, washed with ice cold PBS containing 100 µg/ml CHX and subsequently lysed in lysis buffer (10 mM Tris pH 7.5, 100 mM NaCl, 10 mM MgCl2, 1 % Triton X-100, 0.5 mM DTT, 100 µg/ml CHX).

tag: cell line

value: Flp-In T-REx-293

value: wildtype


title: WT1_RPF

description: mRNA - ribosome footprints


title: Med17-TAP IP

source_name: Med17-TAP IP

value: MATa MED17- TAP-HIS3MX his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0


title: GAD_posterior_cell_13

value: posterior


title: yH2A_Cu

value: 4 hours 1mM CuSO4

tag: chip antibody

value: anti-γH2A (Millipore 07-745-I)


title: yH2A_untreated


title: GAD_posterior_cell_12


title: Med14-TAP IP

source_name: Med14-TAP IP

value: MATa MED14- TAP-HIS3MX his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0


title: Med15-TAP IP

source_name: Med15-TAP IP

value: MATa MED15- TAP-HIS3MX his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0


title: GAD_posterior_cell_9


title: o_exp_1

city: Chendu

first: Maosen

last: Ye

address: Huiming road

country: China

institute: Sichuan Agriculture University

data_processing:
Illumina Hiseq 4000 was used to generate 120bp/150bp paired-end reads
The raw data of fastq format were first subjected to FastaQC program to remove reads containing adapter, containing poly-N and low quality reads to obtain clean reads
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3
paired-end clean reads were aligned to the reference genome using TopHat v2.0.12
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene and generate counts table for further analysis
Genome_build: gga5.0
Supplementary_files_format_and_content: counts table for each gene in each sample.

organism: Gallus gallus

source_name: CEFs

growth_protocol: Primary chicken embryonic fibroblasts were obtained from 9-day-old SPF (special pathogen free) chicken embryo. Fertilized SPF chicken eggs were purchased from Meili Breeding Corporation (Beijing, China). After separated at 9th day from embryo, CEFs were cultured in Dulbecco’s Modified Eagle’s Medium (Thermo Scientific, USA) added with 10% fetal bovine serum (Thermo Scientific, USA) that was filtered with 20nm filters before use. 100µg/mL streptomycin and 100U/mL penicillin (Thermo Scientific, USA) were also added to the cell culture supplement. Cell were cultured in 12 wells plates at 37℃ in a humified incubator (Thermo Fisher Scientific, USA) with CO2 concentration set to 5%.

extract_protocol:
The total RNA was extracted using Triol reagent and then diluted with RNase-free H2O
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: tranfected with Myoz3 siRNA and Myoz3 overexpresion vecteors respectively

tag: breed

value: Avian(broiler)

tag: treatment

value: Myoz3 overexpression


title: Med3-TAP IP

source_name: Med3-TAP IP

tag: strain name

tag: genotype

value: MATa MED3- TAP-HIS3MX his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0


title: o_exp_2


title: NC_3

value: control


title: Myc Input

source_name: Myc Input

value: S288c prototroph

value: MATa prototroph


title: Untagged, TAP IP

source_name: Untagged, TAP IP

value: MATa his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0


title: o_exp_3


title: CycC-Myc IP

source_name: CycC-Myc IP

value: MATa SSN8-8xGLY13xMYC-KANMX


title: NC_2


title: Med19-Myc IP

source_name: Med19-Myc IP

value: MATa MED19-8xGLY-13xMYC-KANMX


title: GAD_posterior_cell_7

value: SADB-rEIAV-tloop-DIO-nls-YFP

value: preoptic area

value: single cell

value: Y


title: NC_1


title: Med17-Myc IP

source_name: Med17-Myc IP

value: MATa MED17-8xGLY-13xMYC-KANMX


title: GAD_posterior_cell_6

value: posterior


title: inter_3

value: Myoz3 siRNA


title: 150 mM salt replicate 3

city: Boulder

first: Roy

middle: Robert

last: Parker

state: CO

address: 3415 Colorado Ave

department: Chemistry and Biochemistry

institute: University of Colorado at Boulder

description:
phase-separated RNA
ribosome depleted
Assemblies from BY4741 yeast RNA

data_processing:
Read quality was assessed using fastqc
Illumina adaptors were trimmed using Trimmomatic 0.32 in paired end (PE) mode
Reads mapping to each gene were counted using HTSeq with parameters –t gene –I Name –f sam –s reverse, using the R64-1-1 annotation file (SGD)
Reads were aligned using Bowtie 0.12.7 using the following parameters: -S -v 2 -m 3 –best.
Normalization and differential expression analysis were then performed using DESeq 1.22.1
Genome_build: An index genome was built with Bowtie 0.12.7 using the build command and the S288C reference genome version (R64-1-1.fasta file), which was acquired through Saccharomyces Genome Database (SGD)
Supplementary_files_format_and_content: The processed data file 'NormalizedData.xls' contains normalized seads for all replicates, average seads of replicates, foldchange values (phase-separated reads/ totalRNA reads), and p-values obtained from DESeq

source_name: Phase-separated RNA at 150mM salt

growth_protocol: RNA used for these experiments was phenol/chloroform extracted and EtOH precipitated from BY4741 yeast

extract_protocol:
Phenol chloroform extractiong followed by EtOH precipitation.
Library construction done by Sequencing Core facility at the Biofrontiers Institute at CU-Boulder. Samples were treated, with Ribozero, and paired end libraries were constructed using the Illumina Nextera kit.

treatment_protocol: No treatment to yeast before RNA isolation from BY4741 yeast in log phase.  Extracted RNA was placed in 150mM NaCl, 10% PEG, 1mM MgCl2.

value: RNA placed in 150mM NaCl, 10% PEG, 1mM MgCl2.  RNA self-assemblies were pelleted by centrifugation, resuspended, ribozero treated and sequenced (see methods)

tag: strain


title: inter_2

value: Avian(broiler)


title: Med15-Myc IP

source_name: Med15-Myc IP

value: MATa MED15-8xGLY-13xMYC-KANMX


title: GAD_posterior_cell_5

tag: mouse line abbreviation


title: 150 mM salt replicate 2


title: inter_1


title: GAD_posterior_cell_4

tag: cre driver


title: GAD_posterior_cell_11

tag: reporter


title: GAD_posterior_cell_10

tag: brain region


title: Med14-Myc IP

source_name: Med14-Myc IP

value: MATa MED14-8xGLY-13xMYC-KANMX


title: Med7-Myc IP

source_name: Med7-Myc IP

value: MATa MED7-8xGLY-13xMYC-KANMX


title: Med3-Myc IP

source_name: Med3-Myc IP

value: S288c prototroph

value: MATa MED3-8xGLY-13xMYC-KANMX


title: GAD_posterior_cell_8

source_name: preopic area neuron

tag: dissection


title: con_3

value: control


title: con_2


title: GAD_posterior_cell_2

tag: input material


title: Total RNA replicate 2

description:
total RNA
ribosome depleted
BY4741 total yeast RNA

source_name: Total yeast RNA

value: Ribozero treated


title: mRNA_Cu

tag: copper treatment

value: 4 hours 1mM CuSO4


title: GAD_posterior_cell_1

value: SADB-rEIAV-tloop-DIO-nls-YFP

tag: tdtomato labeling

tag: yfp labeling


title: mRNA_untreated


title: WT_ds1

status: Public on May 22 2017

city: Pittsburgh

first: Maria

last: Chikina

state: PA

address: 3501 5th ave

institute: University of Pittsburgh

description:
CountsLoggedNormedFiltered.txt
Counts.txt

data_processing:
adapter trimmed
aligned with STAR
quantified featureCounts
counts processed by limma voom
normalized counts produces by limma voom
Genome_build: mm10
Supplementary_files_format_and_content: all counts and normalized counts filtered for low expression and corrected for GC content and 3 prime bias

source_name: Treg

growth_protocol: Tregs (5x10 3 ) were either single (n=3) or double sorted (n=2) and cDNAs were prepared using the SMARTer®

extract_protocol:
Ultra TM Low Input RNA Kit for Sequencing - v3  (Clontech Laboratories).
Sequencing libraries were prepared using Nextera XT DNA Library Preparation kit(Illumina), normalized at 2nM using Tris-HCl (10mM, pH 8.5) with 0.1% Tween20, diluted and denatured to afinal concentration of 1.8nM using the Illumina Denaturing and Diluting libraries for the NextSeq 500 protocol

value: WT

tag: tissue

value: Tumor

tag: replicate


title: con_1


title: WT_3


title: Total RNA replicate1


title: WT_rep4


title: WT_ds2


title: WN_rep4

value: NDLN


title: WT_2


title: WN_ds1


title: WN_3


title: WN_2


title: TE_rep4

source_name: Teffector


title: TE_ds2


title: 150 mM salt replicate 1


title: WN_ds2


title: GAD_posterior_cell_3

value: preoptic area

value: single cell

value: Y

tag: passes qc checks

tag: animal id


title: TE_ds1


title: Total RNA replicate 3

tag: treatment


title: TE_3


title: NT_rep4


title: NT_ds2


title: NT_ds1


title: NT_2


title: NT_3


title: NN_3


title: NN_ds2


title: NN_rep4


title: NN_ds1


title: NN_2


title: HTY_3


title: HTY_2


title: HTY_ds1


title: HTG_rep4


title: HTY_rep4


title: HTG_ds1


title: HTG_ds2


title: HTG_3


title: HNY_ds2


title: HNY_ds1


title: HNY_rep4


title: HNY_3


title: HNY_2


title: HTG_2


title: HNG_rep4


title: TE_2


title: HNG_ds2


title: HNG_3


title: HNG_ds1


title: HNG_2


title: WT-Day-0_1

city: Pohang

first: Yoontae

last: Lee

state: Gyeongbuk

address: 77 Cheongam-Ro, Nam-Gu

department: Life Science

country: South Korea

institute: POSTECH

data_processing:
Illumina Casava software used for basecalling.
Sequencing reads were mapped to the mouse reference genome (mm9 RefSeq) using Tophat (v 2.0.10) followed by Cufflinks (v 2.1.1) for transcript assembly and identification of gene expression.
Results: Total reads: 60~80 million, Average Read Length (bp): 126~129, We mapped 25~39 million sequence reads per each group which result in 70~82% of mapped percentage.
Genome_build: mm9
Supplementary_files_format_and_content: [.xlsx] FPKMs, identification of differentially expressed genes (DEGs, Fold change (log2)>1.5 and P value<0.05), GO analysis

source_name: WT-Day-0, CD4 T cells

growth_protocol: Naïve CD4 T (CD4+CD25-CD44hiCD62Llo) cells were purified from spleen tissue.

extract_protocol:
Total RNA was extracted from naïve CD4+ or activated CD4+ T cells using Trizol reagent.
Libraries were prepared according to Illumina TruSeq RNA-seq Preparatino Kits.

treatment_protocol: Cells were activated with plate-bound a-CD3 (2 μg/ml) and plate-bound a-CD28 (2 μg/ml) for 3 days.

value: Spleen

tag: cell type

value: CD4 T cell

tag: age

value: 10-12 weeks old

tag: activation

value: naïve

value: Cic f/f


title: HTY_ds2

tag: genotype


title: cKO-Day-3_1

source_name: cKO-Day-3, CD4 T cells

tag: strain

value: a-CD3/CD28; 3 days

value: Cic f/f; Cd4-Cre


title: cKO-Day-0_1

source_name: cKO-Day-0, CD4 T cells


title: OS12h_2

city: La Jolla

first: Shu

last: Chien

state: CA

address: 9500 Gilman Drive

department: Institute of Engineering In Medicine

institute: University of California, San Diego

description: HUVECs subjected to oscillatory flow for 12 hr, batch 2

data_processing:
Fastq reads were aligned to human transcriptome (hg19 with Gencode v19 annotation)wth STAR aligner
Counts per feature were calculated by HTSeq-count with Gencode v19 annotations
DESeq2 were used to calculate the raw and normalized (variance stabilizing transformation) counts. Genes with low supporting reads were removed from the resulting RawCounts and VarStabTrf files.
Genome_build: hg19
Supplementary_files_format_and_content: The RawCounts and VarStabTrf are tab separated text files that contains Ensemble Gene ID, associated gene names and values of 24 samples

growth_protocol: HUVECs were seeded to glass slides coated with Collagen I, and maintained in medium M199 supplemented with 10% Endothelial Cell Growth Medium (Cell Application), 10% FBS, 1% sodium pyruvate, 1% L-glutamine, and 1% penicillin-streptomycin

extract_protocol:
Illumina TruSeq kits were used to contruct libraries
illumina unstranded
Total RNA were extracted with TRIZol

treatment_protocol: HUVECs were subject to PS (12±4 dyn/cm2), OS (0.5±4 dyn/cm2), or kept as static control (ST) for four time periods (1, 4, 12 and 24 hours)

value: HUVEC

tag: flow pattern

value: Oscillatory

tag: duration

value: 12 hr

tag: batch


title: OS24h_2

description: HUVECs subjected to oscillatory flow for 24 hr, batch 2

value: 24 hr


title: OS4h_2

description: HUVECs subjected to oscillatory flow for 4 hr, batch 2

value: 4 hr


title: WT-Day-3_1

source_name: WT-Day-3, CD4 T cells


title: OS1h_2

description: HUVECs subjected to oscillatory flow for 1 hr, batch 2

value: 1 hr


title: PS12h_2

description: HUVECs subjected to pulsatile flow for 12 hr, batch 2

value: Pulsatile


title: ST12h_2

description: HUVECs, static control, 12 hr, batch 2

value: Static


title: ST24h_2

description: HUVECs, static control, 24 hr, batch 2


title: PS4h_2

description: HUVECs subjected to pulsatile flow for 4 hr, batch 2


title: PS1h_2

description: HUVECs subjected to pulsatile flow for 1 hr, batch 2


title: ST1h_2

description: HUVECs, static control, 1 hr, batch 2


title: PS24h_2

description: HUVECs subjected to pulsatile flow for 24 hr, batch 2


title: OS24h_1

description: HUVECs subjected to oscillatory flow for 24 hr, batch 1

extract_protocol:
Illumina TruSeq kits were used to contruct libraries
polyA RNA
Total RNA were extracted with TRIZol


title: OS4h_1

description: HUVECs subjected to oscillatory flow for 4 hr, batch 1


title: OS1h_1

description: HUVECs subjected to oscillatory flow for 1 hr, batch 1


title: ST4h_2

description: HUVECs, static control, 4 hr, batch 2


title: PS12h_1

description: HUVECs subjected to pulsatile flow for 12 hr, batch 1


title: PS1h_1

description: HUVECs subjected to pulsatile flow for 1 hr, batch 1


title: PS4h_1

description: HUVECs subjected to pulsatile flow for 4 hr, batch 1


title: PS24h_1

description: HUVECs subjected to pulsatile flow for 24 hr, batch 1


title: ST4h_1

description: HUVECs, static control, 4 hr, batch 1


title: ST24h_1

description: HUVECs, static control, 24 hr, batch 1


title: ST1h_1

description: HUVECs, static control, 1 hr, batch 1

data_processing:
Fastq reads were aligned to human transcriptome (hg19 with Gencode v19 annotation) with STAR aligner
Counts per feature were calculated by HTSeq-count with Gencode v19 annotations
DESeq2 were used to calculate the raw and normalized (variance stabilizing transformation) counts. Genes with low supporting reads were removed from the resulting RawCounts and VarStabTrf files.
Genome_build: hg19
Supplementary_files_format_and_content: The RawCounts and VarStabTrf are tab separated text files that contains Ensemble Gene ID, associated gene names and values of 24 samples

extract_protocol:
Illumina TruSeq kits were used to contruct libraries
polyA RNA
Total RNA were extracted with TRIzol


title: ST12h_1

description: HUVECs, static control, 12 hr, batch 1


title: Pax7_ko_RNA-seq

city: Shenzhen

first: Kun

last: Sun

address: Rm B505, No. 9 Duxue Road, Nanshan District

department: Cancer Research

institute: Shenzhen Bay Laboratory

description: PolyA+ selected

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were first aligned to the mm9 genome using TopHat (v2.0.9). Then expression quantification was conducted using Cufflinks (v2.1.1).
Differentially expression between ko and wt was conducted using Cuffdiff (v2.1.1) against RefSeq genes.
Genome_build: mm9
Supplementary_files_format_and_content: Differentially expressed genes analysis result in EXCEL XLS format.

source_name: Activated skeletal muscle satellite cells isolated from Pax7 KO neonatal mouse muscle

growth_protocol: Mice were sacrificed by cervical dislocation. Skeletal muscles from hind limbs and back were dissected out and minced into small pieces. Muscles were then digested by 1 mg/ml Pronase (Calbiochem, San Diego, CA) in DMEM at 37ºC for 1 hour to dissociate MuSC from myofibers. The dissociated MuSC in the supernatant were passed through 40 μm cell sieves (BD Biosciences, Franklin Lakes, NJ). MuSC were collected by centrifugation, resuspended in culture medium and enriched by differential sedimentation. Primary myoblasts were cultured on Matrigel (Clontech, Mountain View, CA)-coated plates in the satellite cell growth medium (Ham’s F-10 medium containing 20% FBS, 10% horse serum, 0.5% chick embryo extract, 2.5 ng/ml bFGF, 100 u/ml penicillin and 100 μg/ml streptomycin)

extract_protocol:
Purified RNA was fragmented and the cDNA was synthesized by reverse transcription. The resulting double-stranded DNA fragments were end-repaired and A-nucleotide overhangs were added.
After the attachment of anchor sequences, fragments were PCR-amplified using Illumina primers.

treatment_protocol: Pax7CreER/+ (Stock No: 012476), Pax7flox/flox (Stock No: 012653) mice were from the Jackson Laboratory (Bar Harbor, ME, USA).  To induce Pax7 deletion in neonatal mice (day 5), 75µg of tamoxifen (in corn oil)/g of body weight were subcutaneously or intraperitoneally injected into mice of different ages for 5 consecutive days.

tag: developmental stage

value: neonate

tag: genotype/variation

value: Pax7 KO


title: Pax7_wt_RNA-seq

description: PolyA+ selected

source_name: Activated skeletal muscle satellite cells isolated from wt neonatal mouse muscle

value: WT


title: GBML8 DN sample 2

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the human genome (build hg19/GRCh37) using the splice-aware STAR aligner.
The htseq-count program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Technical replicates were merged so we ended up with 8 samples (4 cell populations of 2 biological replicates). Data for 8 samples are available in the processed data files.
Genome_build: hg19
Supplementary_files_format_and_content:
counts.norm.csv: normalized counts
counts.raw.csv: raw counts
gsea_report_for_CD133hi.p010.txt: CD133hi enriched gene sets for significant genes
gsea_report_for_CD133hi.preranked.txt: CD133hi enriched gene sets for ranked genes
gsea_report_for_Notchhi.p010.txt: Notchhi enriched gene sets for significant genes
gsea_report_for_Notchhi.preranked.txt: Notchhi enriched gene sets for ranked genes

source_name: Double negative (DN) cells

growth_protocol: Established tumorsphere cultures were maintained in Neural Stem Cell media, supplemented with 20 ng/ml EGF and FGF2.

extract_protocol:
Total RNA was extracted using RNeasy Qiagen extraction kit according to the manufacturer's instructions.
Libraries were prepared using the mammalian RiboZero magnetic rRNA depletion kit (Epicenter, Madison, WI) following the manufacturer’s protocol.  Five nanograms of RiboZero-treated RNA were used to construct a library using Epicenter’s ScriptSeq v2 RNASeq Library Preparation Kit.

treatment_protocol: FACS isolation for CD133hi, Notchhi, DP and DN cells

tag: cancer type

value: Glioblastoma multiforme

value: Double negative (DN) cells


title: GBML8 Notchhi sample 2

source_name: Notchhi cells

value: Notchhi cells


title: GBML8 Notchhi sample 1


title: GBML8 CD133hi sample 2

source_name: CD133hi cells

value: CD133hi cells


title: GBML8 CD133hi sample 1


title: GBML8 DN sample 1


title: GBML8 DP sample 2

source_name: Double positive (DP) cells

value: Double positive (DP) cells


title: GBML20 Notchhi sample 1


title: OS12h_1

description: HUVECs subjected to oscillatory flow for 12 hr, batch 1


title: GBML20 DP sample 1


title: GBML20 DN sample 1


title: GBML20 CD133hi sample 1


title: Calu3 H3K36me3 ChIP-seq

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Ave

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
DNase-seq: Bowtie v 1.0.0 used for alignment after removing first 20 bases of each read.
DNase-seq: Sequences are mapped to hg19 reference genome with parameters:  -q -m 1 -l 20 -n 3 --best --strata -p 10.
DNase-seq: The peak calls for the DNase-seq data were performed with homer software using default parameters. False discovery rate of 0.1% was used for all samples.
ChIP-seq: Fastq files were aligned to the hg19 version of the human genome using Bowtie (v 1.0.0) with a seed length of 40 and a maximum number of 3 mismatches allowed in the seed. Only unique reads were used.
ChIP-seq: Using Homer (v 1.2) software, tag directories were created using the makeTagDirectory command with default settings.
ChIP-seq: Using Homer (v 1.2) peaks were called using the findPeaks command with an FDR of 0.1%, factor style, input tag directory as the control library, and all other settings as default.
Genome_build: hg19
Supplementary_files_format_and_content: BED files containing DNase hypersensitive sites or ChIP peaks

source_name: Lung adenocarcinoma cells

growth_protocol: 16HBE14o- and Calu3 cells were grown in DMEM low glucose with 10% FBS. Primary HBE cells were grown in bronchial epithelial cell grown medium (BEGM).

extract_protocol:
DNase-seq: genomic DNA was digested with different concentrations of DNaseI (NEB) and purified for library construction (Boyle et al. Cell, 2008). ChIP-seq: Cells were lysed in lysis buffer (5mM PIPES pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protese Inhibitor Cocktail (Roche)). Nuclei were isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with the histone antibodies.
DNase-seq: libraries were prepared by Drs A. Safa and G. Crawford. ChIP-seq: DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. Next, DNA was incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were then ligated to the ends and converted to dsDNA using 5 cycles of PCR. DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles. DNA was purified with 1.2x AMPsureXP beads. Sequencing was preformed on an Illumina Hi-Seq.

tag: antibody


title: HBE H3K9me2 ChIP-seq

source_name: Primary human bronchial epithelial cells

value: HBE

value: H3K9me2 (Abcam 1220)


title: HBE H3K36me3 ChIP-seq


title: HBE H3K9me3 ChIP-seq

value: H3K9me3 (Abcam 8898)


title: Calu3 H3K9me3 ChIP-seq


title: HBE H3K4me3 ChIP-seq

value: H3K4me3 (Millipore 07-743)


title: Calu3 H3K27me3 ChIP-seq

value: H3K27me3 (Millipore 07-449)


title: Calu3 H3K9me2 ChIP-seq


title: HBE H3K27me3 ChIP-seq


title: pre-iPSC_XPC_MeDIP

city: Berkeley

first: Robert

last: Tjian

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

data_processing:
Base-calling performed with CASAVA by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley
Reads quality control performed with FastQC (version 0.10.1)
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie (version 0.12.8) with the following configurations: -n 2 -m 1
ChIP-Seq peaks were called using MACS2 (version 2.1.0.20140616) with the following configurations: -t <sample.bam>  -c <input.bam> -f BAM -g hs --nomodel. --extsize was set to 160 for HDFs and to 250 for pre-iPSCs.
bigWig coverage files, input subtracted, were generated with deepTools (version 2.4.1) with the following configurations: bamCompare -b1 <sample.bam> -b2 <input.bam> -of bigwig --binSize 50 --ratio subtract --normalizeTo1x 2451960000 --ignoreDuplicates. --extendReads was set to 160 for HDFs and to 250 for pre-iPSCs.
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing ChIP-Seq peak genomic coordinates (hg19), length, summit, pileup, pvalue, qvalue and fold enrichment over input as determined by MACS2
Supplementary_files_format_and_content: bigWig files containing the number of reads per 50 bp bins normalized to 1x sequencing depth (Reads Per Genomic Content) after input subtraction

growth_protocol: HDFs were cultured in DMEM high glucose with GlutaMAX (Life Technologies) supplemented with 10% fetal bovine serum (FBS; HyClone) and non-essential amino acids (Life Technologies).

extract_protocol:
Genomic DNA was obtained was using the DNeasy Blood & Tissue Kit (Qiagen).
Genomic DNA from HDFs (10 μg/sample) or pre-iPSCs (1.5 μg/sample) was sheared using the Covaris S2 Focused Ultrasonicator (10.0 duty power, 175 peak power, 200 cycles/burst, 430s in 130 μl AE Buffer). Size selection was performed using the Agencourt AMPure XP beads (Beckman Coulter) to obtain DNA fragments averaging 150-250bp in length. End repair was performed using the NEBNext End Repair Module (NEB) followed by A-tailing with Klenow (NEB). Annealed TruSeq adapters were ligated to the sample DNA and subjected to another round of size selection to remove adapter dimers. DNA was denatured at 95°C for 10 min then quickly spun down and placed on ice. An adapter blocking oligo (5’-AGATCGGAAGAGCGTC- 3’) was added to the sample to prevent adapters from annealing to each other and increasing background in the subsequent immunoprecipitation (IP). Denatured sample DNA and anti-5mC antibody (clone 33D3, Diagenode) or mouse IgG (015-000- 003, Jackson) were incubated together at 4°C, overnight in MeDIP buffer (1mM EDTA, 0.05% TritonX-100, in PBS). Input DNA was kept as a control and processed along side the samples. The IP was added to pre-cleared, equilibrated M-280 anti-mouse IgG Dynabeads (Life Technologies) for 2 hr at 4°C. The IPs were washes 6 times in MeDIP wash buffer and eluted from the beads with proteinase K. Following the IP, recovered ssDNA was converted to dsDNA with KAPA HiFi HotStart Polymerase (Kapa Biosystems) for 4 cycles. No sample DNA was recovered for IgG IPs, indicating very little background binding was occurring. Sample DNA was subsequently subjected to another round of size selection to obtain fragment sizes averaging 200-400bp in length suitable for sequencing. Libraries were amplified using KAPA HiFi HotStart Polymerase (Kapa Biosystems) for a final 10 cycles. Size, purity, and concentration of the libraries were checked by Agilent Technologies 2100 Bioanalyzer.

treatment_protocol: HDFs were transduced with control or XPC-expressing lentiviruses at a MOI of 5 in the presence of 4 μg/ml polybrene (Millipore), and replaced with fresh medium without polybrene after 24 hr. Following selection and expansion of the infected HDFs, we induced reprogramming via episomal vectors expressing OCT4, SOX2, KLF4, L-MYC, LIN28A, GFP, and a shRNA against p53. Sequencing libraries were made from either uninduced HDFs or FACS-sorted, GFP-positive pre-iPSCs, 7 days into reprogramming.

value: human induced pluripotent stem cells

tag: reprogramming stage

value: early-reprogramming (7 days post-induction)

value: XPC over-expressed


title: pre-iPSC_XPC_input


title: 16HBE14o- DNase-seq

source_name: Transformed human bronchial epithelial cells


title: Calu3 H3K4me3 ChIP-seq


title: pre-iPSC_WT_input

value: wild type


title: GBML8 DP sample 1


title: HDF_XPC_MeDIP

value: human dermal fibroblasts


title: pre-iPSC_WT_MeDIP


title: HDF_XPC_input


title: HDF_WT_MeDIP


title: HDF_WT_input


title: HBE EHF siRNA rep 5

city: Chicago

state: IL

address: 2430 N Halsted Street  Box 211

department: Human Molecular Genetics

institute: Lurie Children's Hospital of Chicago Research Center

data_processing:
Paired-end reads (100bp) in fastq format were mapped to the reference human genome (hg19) and the UCSC hg19 human gene annotations with TopHat (v2.0.9)
The aligned reads were then processed by Cufflinks (v2.1.1) to assemble expressed genes and transcripts against the UCSC hg19 gene structure annotation, and estimate expression levels for each transcript.
The assembly files for each of the samples (10 for EHF knockdown) were then merged to create a single transcriptome annotation and differentially expressed genes identified by Cuffdiff.
Samples were then normalized and expressed as fragments per kilobase of transcript per million fragments mapped (FPKM) and both a test statistic (p-value) and an adjusted p-value (q-value) were calculated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene and fold difference between control and EHF siRNA samples

source_name: HBE EHF siRNA

growth_protocol: HBE cells were grown in BEGM media (Lonza) on collagen-coated plastic.

extract_protocol:
TRIzol® (Life Technologies) used for RNA extraction.
RNA libraries were prepared from 2 μg of total RNA using TruSeqTM RNA sample preparation kit v2 as per the manufacturer’s low-throughput protocol (Illumina).

treatment_protocol: Cells at 70-80% confluence were transfected with negative control or EHF siRNA using RNAiMax transfection reagent reagent at a final concentration of 30 nM.  At 48h post transfection, the cells were washed in PBS and immediately harvested for RNA extraction using TRIzol® (Life Technologies).

tag: cell line

value: HBE cells

value: Primary human bronchial epithelial cells

tag: treated with

value: Silencer select EHF siRNA (s25399, Ambion)


title: HBE EHF siRNA rep 4


title: HBE EHF siRNA rep 3


title: HBE negative control siRNA rep 5

source_name: HBE negative control siRNA

value: Silencer select negative control siRNA #2 (Ambion)


title: HBE EHF siRNA rep 1


title: HBE negative control siRNA rep 4


title: HBE negative control siRNA rep 3


title: HBE negative control siRNA rep 2


title: HBE negative control siRNA rep 1


title: Calu-3_JunD ChIP-seq replicate 1

description: processed data file: AH201-282_Calu3-JunD_IDR_Peaks.bed

data_processing:
Fastq files were aligned to the hg19 version of the human genome using Bowtie (v 1.0.0) with a seed length of 40 and a maximum number of 3 mismatches allowed in the seed. Only unique reads were used. The --best argument was used.
Using Homer (v 1.2) software, tag directories were created using the makeTagDirectory command with default settings.
The HOMER-IDR protocol was used to call peaks with both replicates of ChIP-seq and an IDR <0.05, with one input sample.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq: BED files containing locations of EHF binding peaks. For histone modifications: bedgraph.

source_name: JunD ChIP-seq

growth_protocol: HBE cells were grown in BEGM media (Lonza) on collagen-coated plastic. Calu-3 cells were grown in DMEM/Low glucose supplemented with 10% FBS.

extract_protocol:
Cells were lysed in lysis buffer (5mM PIPEs pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protese Inhibitor Cocktail (Roche)).  Nuclear preparation was isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with antibody.
DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. DNA was then incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were ligated to the ends and converted to dsDNA using 5 cycles of PCR.  DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles.  DNA was purified with 1.2x AMPusreXP beads. Sequencing was performed on an Illumina Hi-Seq.

value: Calu-3 cells

value: Lung adenocarcinoma cells

tag: chip antibody

value: JunD (sc-74)

tag: input used for homer peak calling

value: Calu-3 Input


title: Calu-3_JunD ChIP-seq replicate 2

tag: cell type


title: Calu-3 Input

source_name: Calu-3 Input


title: Calu-3_c-Jun ChIP-seq replicate 2

description: processed data file: AH198-281_Calu3-cJun_IDR_peaks.bed

source_name: c-Jun ChIP-seq


title: Calu-3_c-Jun ChIP-seq replicate 1


title: HBE_H3K27ac ChIP-seq

source_name: H3K27ac ChIP-seq

value: H3K27ac (ab4729, Abcam)

value: HBE input


title: HBE_H3K4me1 ChIP-seq

source_name: H3K4me1 ChIP-seq

value: H3K4Me1 (ab8895, Abcam)


title: HBE_H3K4me3 ChIP-seq

source_name: H3K4me3 ChIP-seq

value: H3K4me3 (07-0473, Millipore)


title: HBE Input

description: processed data file: AH137-249_EHF-HBE-IDR_Peaks.bed

source_name: HBE Input


title: HBE_EHF ChIP-seq replicate 2

source_name: EHF ChIP-seq

value: EHF (Clone 5A.5)


title: HBE_EHF ChIP-seq replicate 1


title: shPHF20_rep1

city: Smithville

first: Yue

last: Lu

state: TX

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (hg19) by TopHat (version 2.0.10)
The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser on June 02, 2014) was enumerated using htseq-count from HTSeq package (version 0.6.0)
Genome_build: hg19
Supplementary_files_format_and_content: Number of fragments in each gene

source_name: H1792 human lung cancer cells

growth_protocol: Cells were cultured in RPMI with 10% FBS.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen, Gaithersburg, MD).
Samples were prepared as instructed using the TruSeq mRNA Sample Preparation Kit v2 (Illumina, San Diego, CA) in accordance with the manufacturer's instructions. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles, DNA fragments were sequenced using single-end sequencing technology on Illumina NextSeq 500 platform (for MOLM13 cells) or paried-end on Illumina HiSeq2000 (for MV4-11 cells) .

treatment_protocol: Cells were transduced with shRNA and selectd with puromycin for 4-6 days before RNA collection

tag: vector


title: shPHF20_rep2


title: shNT_rep3

value: pLKO-shNT none targeting control


title: shPHF20_rep3


title: shNT_rep1


title: CD3CD28_Floxed_rep3

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
FastQ files for each sample were obtained using CASAVA v1.8 software
Reads were pre-processed with Cutadapt (Criscuolo & Brisse, 2014) to trim sequencing reads, eliminating Illumina adaptor remains, and to discard reads that were shorter than 30 bp.
Reads were mapped against the mouse transcriptome (GRCm38, release 76; aug2014 archive) and quantified using RSEM v1.17 (Li & Dewey, 2011).
Data were then processed with a diferential expression analysis pipeline that used Bioconductor packages ComBat (Johnson et al, 2007), for correction of batch effects, and EdgeR (Robinson et al, 2010) for normalization and differential expression testing
Genome_build: GRCm38, release 76; aug2014 archive
Supplementary_files_format_and_content: Batch-corrected, TMM-normalized counts per million

source_name: Floxed - co-cultured with T cells stimulated with anti-CD3 and anti-CD28

growth_protocol: Resting B cells were isolated from the spleen of 8-12 week-old mice with anti-CD43 Microbeads (anti-Ly48; Miltenyi Biotech) and were cultured for 48 h with LPS (50 μg/ml) and IL-4 (5 ng/ml) or co-cultured with T cells stimulated with anti-CD3 (5μg/ml) and anti-CD28 (1μg/ml). Samples from each of the treatment groups were processed as separate batches.

extract_protocol:
Total RNA was purified using the Qiagen Rneasy kit following the manufacturer's protocol.
For RNAseq library preparation, 500 ng of total RNA were used to generate barcoded RNAseq libraries using the TruSeq RNA sample preparation kit v2 (Illumina). Briefly, poly A+ RNA was purified using poly-T oligo- attached magnetic beads using two rounds of purification followed by fragmentation and first and second cDNA strand synthesis. Next, cDNA 3’ ends were adenylated and the adapters were ligated followed by PCR library amplification. Finally, the size of the libraries was checked using the Agilent 2100 Bioanalyzer DNA 1000 chip and their concentration was determined using the Qubit® fluorometer (Life Technologies). Libraries were sequenced on a HiSeq2500 (Illumina) to generate 61 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina).

treatment_protocol: hCD2+ B cells were sorted from pooled CTCFfl/+; AID-CRETG/+   or CTCFfl/fl; AID-CRETG/+ cultures after 48h stimulation of CD3/CD28 or LPS/IL4 cultures (2-3 mice/sample)

value: Activated B cells

tag: tissue

value: Spleen

value: CTCFfl/fl; AID-CRETG/+


title: CD3CD28_Control_rep2

description: co-cultured with T cells stimulated with anti-CD3 (5μg/ml) and anti-CD28 (1μg/ml)

source_name: control - co-cultured with T cells stimulated with anti-CD3 and anti-CD28

tag: genotype

value: CTCFfl/+; AID-CRETG/+


title: LPSIL4_Floxed_rep3

description: cultured for 48 h with LPS (50 μg/ml) and IL-4 (5 ng/ml)

source_name: Floxed - cultured for 48 h with LPS and IL-4


title: CD3CD28_Control_rep1


title: HBE EHF siRNA rep 2

value: HBE cells

value: Primary human bronchial epithelial cells


title: LPSIL4_Floxed_rep2


title: LPSIL4_Floxed_rep1


title: CD3CD28_Floxed_rep1


title: LPSIL4_Control_rep2

source_name: control - cultured for 48 h with LPS and IL-4


title: LPSIL4_Control_rep1


title: SLX-13219.N712_N508

first: Anthony

last: Green

state: Cambridgeshire

address: Hills Road

department: Department of heamatology

institute: University of Cambridge

description: 12 Months HSC JAK2 HOM

data_processing:
Illumina basecalling
Reads mapped to Mouse GRC38-77 reference genome from ENSEMBL plus ERCC92 spike-in controls with tophat 2.0.13 and bowtie 2.2.3
Gene expression count matrix was calculated with htseq-count
Genome_build: GRC38 release 77
Supplementary_files_format_and_content: Tabular separated raw counts. First column is the genes, second column is the counts.

source_name: Hematopoietic Stem Cell

growth_protocol: not applicable

extract_protocol:
hematopoietic stem cells were isolated from whole bone marrow using ESLAM markers foir FACS sorting
The libraries were constructed according to Picelli et al 2014 using Nextera Illumina Kit

treatment_protocol: not applicable

value: whole bone marrow

value: Hematopoietic Stem Cell

tag: age

value: 12 Months

value: JAK2 V617F Homozygous


title: SLX-13219.N712_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N712_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N712_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N712_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N712_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N711_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N711_N507

description: 12 Months HSC JAK2 HOM


title: shNT_rep2


title: SLX-13219.N711_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N712_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N711_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N711_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N711_N504

description: 12 Months HSC JAK2 HOM


title: CD3CD28_Floxed_rep2


title: SLX-13219.N711_N503

description: 12 Months HSC JAK2 HOM


title: CD3CD28_Control_rep3


title: SLX-13219.N711_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N710_N508

description: 12 Months HSC JAK2 HOM


title: LPSIL4_Control_rep3


title: SLX-13219.N710_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N712_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N710_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N710_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N710_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N710_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N710_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N709_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N709_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N708_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N708_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N708_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N708_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N708_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N708_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N707_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N708_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N710_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N707_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N707_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N707_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N707_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N707_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N707_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N709_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N709_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N709_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N709_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N709_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N706_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N707_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N706_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N706_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N709_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N706_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N706_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N708_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N705_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N705_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N705_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N705_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N705_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N706_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N705_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N704_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N704_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N704_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N706_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N705_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N704_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N704_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N704_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N705_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N703_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N703_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N704_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N704_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N703_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N706_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N703_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N703_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N703_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N703_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N703_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N702_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N702_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N702_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N701_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N702_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N701_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N701_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N702_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N701_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N702_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N702_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N701_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N701_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13219.N701_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13215.N712_N507

description: 12 Months HSC JAK2 WT

value: Wild Type


title: SLX-13219.N701_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13215.N712_N508

description: 12 Months HSC JAK2 WT


title: SLX-13219.N702_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13215.N712_N506

description: 12 Months HSC JAK2 WT


title: SLX-13215.N712_N505

description: 12 Months HSC JAK2 WT


title: SLX-13215.N712_N504

description: 12 Months HSC JAK2 WT


title: SLX-13215.N711_N506

description: 12 Months HSC JAK2 WT


title: SLX-13215.N712_N502

description: 12 Months HSC JAK2 WT


title: SLX-13215.N711_N517

description: 12 Months HSC JAK2 WT


title: SLX-13215.N711_N505

description: 12 Months HSC JAK2 WT


title: SLX-13215.N711_N502

description: 12 Months HSC JAK2 WT


title: SLX-13215.N711_N507

description: 12 Months HSC JAK2 WT


title: SLX-13215.N711_N508

description: 12 Months HSC JAK2 WT


title: SLX-13215.N711_N503

description: 12 Months HSC JAK2 WT


title: SLX-13215.N711_N504

description: 12 Months HSC JAK2 WT


title: SLX-13215.N710_N517

description: 12 Months HSC JAK2 WT


title: SLX-13215.N712_N517

description: 12 Months HSC JAK2 WT


title: SLX-13215.N710_N508

description: 12 Months HSC JAK2 WT


title: SLX-13215.N710_N506

description: 12 Months HSC JAK2 WT


title: SLX-13215.N709_N508

description: 12 Months HSC JAK2 WT


title: SLX-13215.N710_N502

description: 12 Months HSC JAK2 WT


title: SLX-13215.N709_N507

description: 12 Months HSC JAK2 WT


title: SLX-13215.N709_N506

description: 12 Months HSC JAK2 WT


title: SLX-13215.N710_N505

description: 12 Months HSC JAK2 WT


title: SLX-13215.N709_N505

description: 12 Months HSC JAK2 WT


title: SLX-13215.N710_N503

description: 12 Months HSC JAK2 WT


title: SLX-13215.N709_N504

description: 12 Months HSC JAK2 WT


title: SLX-13215.N710_N504

description: 12 Months HSC JAK2 WT


title: SLX-13215.N709_N503

description: 12 Months HSC JAK2 WT


title: SLX-13215.N708_N517

description: 12 Months HSC JAK2 WT


title: SLX-13215.N709_N502

description: 12 Months HSC JAK2 WT


title: SLX-13215.N712_N503

description: 12 Months HSC JAK2 WT


title: SLX-13215.N708_N507

description: 12 Months HSC JAK2 WT


title: SLX-13215.N708_N506

description: 12 Months HSC JAK2 WT


title: SLX-13215.N708_N505

description: 12 Months HSC JAK2 WT


title: SLX-13215.N708_N504

description: 12 Months HSC JAK2 WT


title: SLX-13215.N708_N502

description: 12 Months HSC JAK2 WT


title: SLX-13215.N708_N503

description: 12 Months HSC JAK2 WT


title: SLX-13215.N707_N517

description: 12 Months HSC JAK2 WT


title: SLX-13215.N707_N507

description: 12 Months HSC JAK2 WT


title: SLX-13215.N707_N508

description: 12 Months HSC JAK2 WT


title: SLX-13215.N710_N507

description: 12 Months HSC JAK2 WT


title: SLX-13215.N709_N517

description: 12 Months HSC JAK2 WT


title: SLX-13215.N707_N506

description: 12 Months HSC JAK2 WT


title: SLX-13215.N707_N505

description: 12 Months HSC JAK2 WT


title: SLX-13215.N707_N503

description: 12 Months HSC JAK2 WT


title: SLX-13215.N707_N504

description: 12 Months HSC JAK2 WT


title: SLX-13215.N706_N517

description: 12 Months HSC JAK2 WT


title: SLX-13215.N705_N508

description: 12 Months HSC JAK2 WT


title: SLX-13215.N706_N502

description: 12 Months HSC JAK2 WT


title: SLX-13215.N706_N503

description: 12 Months HSC JAK2 WT


title: SLX-13215.N705_N517

description: 12 Months HSC JAK2 WT


title: SLX-13215.N706_N505

description: 12 Months HSC JAK2 WT


title: SLX-13215.N706_N506

description: 12 Months HSC JAK2 WT


title: SLX-13215.N706_N504

description: 12 Months HSC JAK2 WT


title: SLX-13215.N706_N507

description: 12 Months HSC JAK2 WT


title: SLX-13215.N708_N508

description: 12 Months HSC JAK2 WT


title: SLX-13215.N705_N506

description: 12 Months HSC JAK2 WT


title: SLX-13215.N705_N504

description: 12 Months HSC JAK2 WT


title: SLX-13215.N705_N507

description: 12 Months HSC JAK2 WT


title: SLX-13215.N705_N505

description: 12 Months HSC JAK2 WT


title: SLX-13215.N705_N503

description: 12 Months HSC JAK2 WT


title: SLX-13215.N704_N506

description: 12 Months HSC JAK2 WT


title: SLX-13215.N704_N507

description: 12 Months HSC JAK2 WT


title: SLX-13215.N705_N502

description: 12 Months HSC JAK2 WT


title: SLX-13215.N704_N517

description: 12 Months HSC JAK2 WT


title: SLX-13215.N704_N508

description: 12 Months HSC JAK2 WT


title: SLX-13215.N704_N502

description: 12 Months HSC JAK2 WT


title: SLX-13215.N704_N503

description: 12 Months HSC JAK2 WT


title: SLX-13215.N704_N504

description: 12 Months HSC JAK2 WT


title: SLX-13215.N703_N517

description: 12 Months HSC JAK2 WT


title: SLX-13215.N703_N508

description: 12 Months HSC JAK2 WT


title: SLX-13215.N707_N502

description: 12 Months HSC JAK2 WT


title: SLX-13215.N706_N508

description: 12 Months HSC JAK2 WT


title: SLX-13215.N703_N506

description: 12 Months HSC JAK2 WT


title: SLX-13215.N702_N517

description: 12 Months HSC JAK2 WT


title: SLX-13215.N703_N503

description: 12 Months HSC JAK2 WT


title: SLX-13215.N703_N502

description: 12 Months HSC JAK2 WT


title: SLX-13215.N703_N504

description: 12 Months HSC JAK2 WT


title: SLX-13215.N702_N507

description: 12 Months HSC JAK2 WT


title: SLX-13215.N702_N508

description: 12 Months HSC JAK2 WT


title: SLX-13215.N702_N505

description: 12 Months HSC JAK2 WT


title: SLX-13215.N702_N503

description: 12 Months HSC JAK2 WT


title: SLX-13215.N702_N504

description: 12 Months HSC JAK2 WT


title: SLX-13215.N701_N508

description: 12 Months HSC JAK2 WT


title: SLX-13215.N701_N517

description: 12 Months HSC JAK2 WT


title: SLX-13215.N702_N502

description: 12 Months HSC JAK2 WT


title: SLX-13215.N701_N507

description: 12 Months HSC JAK2 WT


title: SLX-13215.N701_N502

description: 12 Months HSC JAK2 WT


title: SLX-13215.N701_N506

description: 12 Months HSC JAK2 WT


title: SLX-13215.N704_N505

description: 12 Months HSC JAK2 WT


title: SLX-13214.N712_N506

description: 12 Months HSC JAK2 WT


title: SLX-13214.N712_N507

description: 12 Months HSC JAK2 WT


title: SLX-13215.N701_N505

description: 12 Months HSC JAK2 WT


title: SLX-13215.N703_N507

description: 12 Months HSC JAK2 WT


title: SLX-13215.N701_N504

description: 12 Months HSC JAK2 WT


title: SLX-13215.N701_N503

description: 12 Months HSC JAK2 WT


title: SLX-13214.N712_N508

description: 12 Months HSC JAK2 WT


title: SLX-13214.N712_N517

description: 12 Months HSC JAK2 WT


title: SLX-13215.N703_N505

description: 12 Months HSC JAK2 WT


title: SLX-13214.N712_N504

description: 12 Months HSC JAK2 WT


title: SLX-13214.N712_N502

description: 12 Months HSC JAK2 WT


title: SLX-13214.N711_N504

description: 12 Months HSC JAK2 WT


title: SLX-13214.N712_N505

description: 12 Months HSC JAK2 WT


title: SLX-13214.N711_N506

description: 12 Months HSC JAK2 WT


title: SLX-13214.N712_N503

description: 12 Months HSC JAK2 WT


title: SLX-13214.N711_N508

description: 12 Months HSC JAK2 WT


title: SLX-13214.N711_N503

description: 12 Months HSC JAK2 WT


title: SLX-13214.N710_N517

description: 12 Months HSC JAK2 WT


title: SLX-13214.N711_N505

description: 12 Months HSC JAK2 WT


title: SLX-13214.N711_N507

description: 12 Months HSC JAK2 WT


title: SLX-13214.N711_N502

description: 12 Months HSC JAK2 WT


title: SLX-13214.N710_N506

description: 12 Months HSC JAK2 WT


title: SLX-13214.N710_N508

description: 12 Months HSC JAK2 WT


title: SLX-13215.N702_N506

description: 12 Months HSC JAK2 WT


title: SLX-13214.N710_N505

description: 12 Months HSC JAK2 WT


title: SLX-13214.N710_N507

description: 12 Months HSC JAK2 WT


title: SLX-13214.N710_N504

description: 12 Months HSC JAK2 WT


title: SLX-13214.N709_N517

description: 12 Months HSC JAK2 WT


title: SLX-13214.N710_N502

description: 12 Months HSC JAK2 WT


title: SLX-13214.N709_N505

description: 12 Months HSC JAK2 WT


title: SLX-13214.N711_N517

description: 12 Months HSC JAK2 WT


title: SLX-13214.N709_N507

description: 12 Months HSC JAK2 WT


title: SLX-13214.N709_N503

description: 12 Months HSC JAK2 WT


title: SLX-13214.N709_N502

description: 12 Months HSC JAK2 WT


title: SLX-13214.N709_N506

description: 12 Months HSC JAK2 WT


title: SLX-13214.N709_N504

description: 12 Months HSC JAK2 WT


title: SLX-13214.N709_N508

description: 12 Months HSC JAK2 WT


title: SLX-13214.N708_N517

description: 12 Months HSC JAK2 WT


title: SLX-13214.N708_N508

description: 12 Months HSC JAK2 WT


title: SLX-13214.N708_N502

description: 12 Months HSC JAK2 WT


title: SLX-13214.N708_N503

description: 12 Months HSC JAK2 WT


title: SLX-13214.N708_N507

description: 12 Months HSC JAK2 WT


title: SLX-13214.N707_N502

description: 12 Months HSC JAK2 WT


title: SLX-13214.N710_N503

description: 12 Months HSC JAK2 WT


title: SLX-13214.N706_N506

description: 12 Months HSC JAK2 WT


title: SLX-13214.N708_N506

description: 12 Months HSC JAK2 WT


title: SLX-13214.N706_N505

description: 12 Months HSC JAK2 WT


title: SLX-13214.N706_N503

description: 12 Months HSC JAK2 WT


title: SLX-13214.N705_N508

description: 12 Months HSC JAK2 WT


title: SLX-13214.N706_N502

description: 12 Months HSC JAK2 WT


title: SLX-13214.N708_N505

description: 12 Months HSC JAK2 WT


title: SLX-13214.N707_N517

description: 12 Months HSC JAK2 WT


title: SLX-13214.N707_N508

description: 12 Months HSC JAK2 WT


title: SLX-13214.N707_N507

description: 12 Months HSC JAK2 WT


title: SLX-13214.N707_N506

description: 12 Months HSC JAK2 WT


title: SLX-13214.N708_N504

description: 12 Months HSC JAK2 WT


title: SLX-13214.N707_N503

description: 12 Months HSC JAK2 WT


title: SLX-13214.N707_N504

description: 12 Months HSC JAK2 WT


title: SLX-13214.N707_N505

description: 12 Months HSC JAK2 WT


title: SLX-13214.N706_N517

description: 12 Months HSC JAK2 WT


title: SLX-13214.N705_N503

description: 12 Months HSC JAK2 WT


title: SLX-13214.N706_N508

description: 12 Months HSC JAK2 WT


title: SLX-13214.N706_N507

description: 12 Months HSC JAK2 WT


title: SLX-13214.N705_N502

description: 12 Months HSC JAK2 WT


title: SLX-13214.N704_N507

description: 12 Months HSC JAK2 WT


title: SLX-13214.N704_N517

description: 12 Months HSC JAK2 WT


title: SLX-13214.N704_N505

description: 12 Months HSC JAK2 WT


title: SLX-13214.N706_N504

description: 12 Months HSC JAK2 WT


title: SLX-13214.N705_N517

description: 12 Months HSC JAK2 WT


title: SLX-13214.N705_N506

description: 12 Months HSC JAK2 WT


title: SLX-13214.N705_N507

description: 12 Months HSC JAK2 WT


title: SLX-13214.N705_N504

description: 12 Months HSC JAK2 WT


title: SLX-13214.N705_N505

description: 12 Months HSC JAK2 WT


title: SLX-13214.N703_N508

description: 12 Months HSC JAK2 WT


title: SLX-13214.N703_N506

description: 12 Months HSC JAK2 WT


title: SLX-13214.N703_N502

description: 12 Months HSC JAK2 WT


title: SLX-13214.N703_N504

description: 12 Months HSC JAK2 WT


title: SLX-13214.N704_N506

description: 12 Months HSC JAK2 WT


title: SLX-13214.N702_N517

description: 12 Months HSC JAK2 WT


title: SLX-13214.N704_N508

description: 12 Months HSC JAK2 WT


title: SLX-13214.N702_N506

description: 12 Months HSC JAK2 WT


title: SLX-13214.N704_N503

description: 12 Months HSC JAK2 WT


title: SLX-13214.N703_N517

description: 12 Months HSC JAK2 WT


title: SLX-13214.N703_N507

description: 12 Months HSC JAK2 WT


title: SLX-13214.N702_N504

description: 12 Months HSC JAK2 WT


title: SLX-13214.N704_N502

description: 12 Months HSC JAK2 WT


title: SLX-13214.N703_N505

description: 12 Months HSC JAK2 WT


title: SLX-13214.N703_N503

description: 12 Months HSC JAK2 WT


title: SLX-13214.N702_N503

description: 12 Months HSC JAK2 WT


title: SLX-13214.N701_N508

description: 12 Months HSC JAK2 WT


title: SLX-13214.N701_N504

description: 12 Months HSC JAK2 WT


title: SLX-13214.N701_N503

description: 12 Months HSC JAK2 WT


title: SLX-13212.N712_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13214.N701_N502

description: 12 Months HSC JAK2 WT


title: SLX-13214.N702_N507

description: 12 Months HSC JAK2 WT


title: SLX-13214.N702_N505

description: 12 Months HSC JAK2 WT


title: SLX-13214.N702_N508

description: 12 Months HSC JAK2 WT


title: SLX-13214.N704_N504

description: 12 Months HSC JAK2 WT


title: SLX-13214.N702_N502

description: 12 Months HSC JAK2 WT


title: SLX-13214.N701_N517

description: 12 Months HSC JAK2 WT


title: SLX-13212.N712_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N712_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13214.N701_N507

description: 12 Months HSC JAK2 WT


title: SLX-13212.N711_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N711_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N711_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N711_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13214.N701_N506

description: 12 Months HSC JAK2 WT


title: SLX-13214.N701_N505

description: 12 Months HSC JAK2 WT


title: SLX-13212.N712_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N712_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N712_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N712_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N710_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N710_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N710_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N712_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N710_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N711_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N709_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N709_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N711_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N709_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N711_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N711_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N710_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N710_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N708_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N708_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N707_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N708_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N707_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N707_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N710_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N709_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N707_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N709_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N709_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N709_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N706_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N706_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N710_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N708_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N708_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N706_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N706_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N708_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N705_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N708_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N707_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N705_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N705_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N704_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N707_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N707_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N706_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N706_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N707_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N709_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N704_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N706_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N706_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N704_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N703_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N703_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N705_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N705_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N708_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N705_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N703_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N705_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N705_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N704_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N703_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N704_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N704_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N704_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N703_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N702_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N703_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N702_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N702_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N702_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N702_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N701_N508

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N704_N502

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N703_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N702_N517

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N702_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N701_N506

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N701_N507

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N701_N504

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N703_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N701_N503

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N701_N505

description: 12 Months HSC JAK2 HOM


title: SLX-13212.N701_N517

description: 12 Months HSC JAK2 HOM


title: Naive B cells replicate1

first: Ángel

middle: F

last: Álvarez-Prado

institute: Centro Nacional de Investigaciones Cardiovasculares

data_processing:
Basecalls and demultiplexing were performed using CASAVA v1.8
Quality parameters of the raw sequences were calculated by FASTQC version
Sequencing adaptors were removed by cutadapt version 1.9
Reads were aligned and quantified to the mouse transcriptome using RSEM version 1.2.25
Data were processed by a differential expression analysis pipeline that used Bioconductor package EdgeR for normalization and differential expression testing
Genome_build: NCBIm38 v75
Supplementary_files_format_and_content: Tab delimited text file contains FPKM values summarized at gene level for all the analyzed samples

source_name: Peyer’s patch naive B cells

extract_protocol:
Peyer’s patches were isolated from the ileon of WT mice. Cells were sorted and lysed and total RNA was purified using Trizol reagent. Sequencing libraries were prepared from 100ng total RNA per sample using NEB NEXT Ultra RNAseq Library Prep Kit.
Sequencing libraries were prepared from 100ng total RNA per sample using NEB NEXT Ultra RNAseq Library Prep Kit.

tag: strain

value: ileum

tag: tissue compartment

value: Peyer’s patches

value: naive B cells

tag: Sex

value: female

value: 12 weeks


title: Naive B cells replicate2


title: SLX-13212.N701_N502

description: 12 Months HSC JAK2 HOM


title: GC B cells replicate2

source_name: Peyer’s patch germinal center B cells

value: germinal center B cells


title: SLX-9785.N712_N506

description: Old HSC WT

data_processing:
Illumina basecalling
Reads mapped to Mouse GRC38-77 reference genome from ENSEMBL plus ERCC92 spike-in controls with tophat 2.0.13 and bowtie 2.2.3
Gene expression count matrix was calculated with htseq
Genome_build: GRC38 release 77
Supplementary_files_format_and_content: Tabular separated raw counts. First column is the genes, second column is the counts.

value: 18 Months (Old)


title: GC B cells replicate3


title: SLX-9785.N712_N502

description: Old HSC WT


title: SLX-9785.N711_N508

description: Old HSC WT


title: SLX-9785.N711_N517

description: Old HSC WT


title: SLX-13212.N702_N508

description: 12 Months HSC JAK2 HOM


title: GC B cells replicate1


title: SLX-9785.N712_N517

description: Old HSC WT


title: SLX-9785.N711_N507

description: Old HSC WT


title: SLX-9785.N712_N508

description: Old HSC WT


title: SLX-9785.N712_N503

description: Old HSC WT


title: Naive B cells replicate3


title: SLX-9785.N712_N507

description: Old HSC WT


title: SLX-9785.N711_N504

description: Old HSC WT


title: SLX-9785.N711_N505

description: Old HSC WT


title: SLX-9785.N711_N503

description: Old HSC WT


title: SLX-9785.N711_N502

description: Old HSC WT


title: SLX-9785.N711_N506

description: Old HSC WT


title: SLX-9785.N710_N517

description: Old HSC WT


title: SLX-9785.N710_N505

description: Old HSC WT


title: SLX-9785.N710_N507

description: Old HSC WT


title: SLX-9785.N710_N502

description: Old HSC WT


title: SLX-9785.N712_N505

description: Old HSC WT


title: SLX-9785.N710_N506

description: Old HSC WT


title: SLX-9785.N710_N508

description: Old HSC WT


title: SLX-9785.N710_N503

description: Old HSC WT


title: SLX-9785.N709_N517

description: Old HSC WT


title: SLX-9785.N710_N504

description: Old HSC WT


title: SLX-9785.N712_N504

description: Old HSC WT


title: SLX-9785.N709_N508

description: Old HSC WT


title: SLX-9785.N708_N517

description: Old HSC WT


title: SLX-9785.N708_N507

description: Old HSC WT


title: SLX-9785.N709_N504

description: Old HSC WT


title: SLX-9785.N708_N508

description: Old HSC WT


title: SLX-9785.N709_N506

description: Old HSC WT


title: SLX-9785.N709_N505

description: Old HSC WT


title: SLX-9785.N709_N507

description: Old HSC WT


title: SLX-9785.N708_N505

description: Old HSC WT


title: SLX-9785.N709_N503

description: Old HSC WT


title: SLX-9785.N709_N502

description: Old HSC WT


title: SLX-9785.N708_N506

description: Old HSC WT


title: SLX-9785.N707_N517

description: Old HSC WT


title: SLX-9785.N708_N503

description: Old HSC WT


title: SLX-9785.N708_N504

description: Old HSC WT


title: SLX-9785.N708_N502

description: Old HSC WT


title: SLX-9785.N707_N507

description: Old HSC WT


title: SLX-9785.N707_N506

description: Old HSC WT


title: SLX-9785.N707_N505

description: Old HSC WT


title: SLX-9785.N706_N507

description: Old HSC WT


title: SLX-9785.N706_N508

description: Old HSC WT


title: SLX-9785.N707_N508

description: Old HSC WT


title: SLX-9785.N707_N503

description: Old HSC WT


title: SLX-9785.N706_N517

description: Old HSC WT


title: SLX-9785.N706_N505

description: Old HSC WT


title: SLX-9785.N707_N502

description: Old HSC WT


title: SLX-9785.N706_N504

description: Old HSC WT


title: SLX-9785.N706_N503

description: Old HSC WT


title: SLX-9785.N706_N502

description: Old HSC WT


title: SLX-9785.N705_N517

description: Old HSC WT


title: SLX-9785.N705_N507

description: Old HSC WT


title: SLX-9785.N705_N508

description: Old HSC WT


title: SLX-9785.N705_N505

description: Old HSC WT


title: SLX-9785.N705_N504

description: Old HSC WT


title: SLX-9785.N705_N503

description: Old HSC WT


title: SLX-9785.N704_N508

description: Old HSC WT


title: SLX-9785.N704_N517

description: Old HSC WT


title: SLX-9785.N705_N502

description: Old HSC WT


title: SLX-9785.N704_N504

description: Old HSC WT


title: SLX-9785.N707_N504

description: Old HSC WT


title: SLX-9785.N704_N506

description: Old HSC WT


title: SLX-9785.N703_N517

description: Old HSC WT


title: SLX-9785.N706_N506

description: Old HSC WT


title: SLX-9785.N704_N503

description: Old HSC WT


title: SLX-9785.N704_N502

description: Old HSC WT


title: SLX-9785.N703_N508

description: Old HSC WT


title: SLX-9785.N703_N507

description: Old HSC WT


title: SLX-9785.N703_N506

description: Old HSC WT


title: SLX-9785.N703_N503

description: Old HSC WT


title: SLX-9785.N703_N504

description: Old HSC WT


title: SLX-9785.N703_N505

description: Old HSC WT


title: SLX-9785.N704_N505

description: Old HSC WT


title: SLX-9785.N702_N507

description: Old HSC WT


title: SLX-9785.N703_N502

description: Old HSC WT


title: SLX-9785.N702_N508

description: Old HSC WT


title: SLX-9785.N702_N517

description: Old HSC WT


title: SLX-9785.N702_N504

description: Old HSC WT


title: SLX-9785.N704_N507

description: Old HSC WT


title: SLX-9785.N705_N506

description: Old HSC WT


title: SLX-9785.N702_N506

description: Old HSC WT


title: SLX-9785.N702_N502

description: Old HSC WT


title: SLX-9785.N701_N517

description: Old HSC WT


title: SLX-9785.N702_N505

description: Old HSC WT


title: SLX-9785.N701_N504

description: Old HSC WT


title: SLX-9785.N701_N508

description: Old HSC WT


title: SLX-9785.N701_N506

description: Old HSC WT


title: SLX-9785.N701_N503

description: Old HSC WT


title: SLX-9783.N712_N517

description: Old HSC JAK2 HOM


title: SLX-9785.N701_N505

description: Old HSC WT


title: SLX-9783.N712_N504

description: Old HSC JAK2 HOM


title: SLX-9783.N712_N507

description: Old HSC JAK2 HOM


title: SLX-9783.N712_N503

description: Old HSC JAK2 HOM


title: SLX-9783.N712_N502

description: Old HSC JAK2 HOM


title: SLX-9783.N712_N508

description: Old HSC JAK2 HOM


title: SLX-9783.N711_N508

description: Old HSC JAK2 HOM


title: SLX-9783.N711_N517

description: Old HSC JAK2 HOM


title: SLX-9783.N712_N505

description: Old HSC JAK2 HOM


title: SLX-9783.N711_N506

description: Old HSC JAK2 HOM


title: SLX-9783.N711_N507

description: Old HSC JAK2 HOM


title: SLX-9785.N702_N503

description: Old HSC WT


title: SLX-9783.N711_N505

description: Old HSC JAK2 HOM


title: SLX-9783.N711_N502

description: Old HSC JAK2 HOM


title: SLX-9785.N701_N507

description: Old HSC WT


title: SLX-9785.N701_N502

description: Old HSC WT


title: SLX-9783.N710_N507

description: Old HSC JAK2 HOM


title: SLX-9783.N710_N517

description: Old HSC JAK2 HOM


title: SLX-9783.N710_N504

description: Old HSC JAK2 HOM


title: SLX-9783.N710_N506

description: Old HSC JAK2 HOM


title: SLX-9783.N712_N506

description: Old HSC JAK2 HOM


title: SLX-9783.N709_N517

description: Old HSC JAK2 HOM


title: SLX-9783.N710_N508

description: Old HSC JAK2 HOM


title: SLX-9783.N709_N508

description: Old HSC JAK2 HOM


title: SLX-9783.N709_N507

description: Old HSC JAK2 HOM


title: SLX-9783.N710_N503

description: Old HSC JAK2 HOM


title: SLX-9783.N709_N505

description: Old HSC JAK2 HOM


title: SLX-9783.N709_N504

description: Old HSC JAK2 HOM


title: SLX-9783.N711_N504

description: Old HSC JAK2 HOM


title: SLX-9783.N708_N505

description: Old HSC JAK2 HOM


title: SLX-9783.N711_N503

description: Old HSC JAK2 HOM


title: SLX-9783.N709_N503

description: Old HSC JAK2 HOM


title: SLX-9783.N709_N502

description: Old HSC JAK2 HOM


title: SLX-9783.N708_N504

description: Old HSC JAK2 HOM


title: SLX-9783.N708_N517

description: Old HSC JAK2 HOM


title: SLX-9783.N708_N508

description: Old HSC JAK2 HOM


title: SLX-9783.N708_N502

description: Old HSC JAK2 HOM


title: SLX-9783.N708_N506

description: Old HSC JAK2 HOM


title: SLX-9783.N708_N507

description: Old HSC JAK2 HOM


title: SLX-9783.N708_N503

description: Old HSC JAK2 HOM


title: SLX-9783.N710_N505

description: Old HSC JAK2 HOM


title: SLX-9783.N707_N508

description: Old HSC JAK2 HOM


title: SLX-9783.N707_N507

description: Old HSC JAK2 HOM


title: SLX-9783.N710_N502

description: Old HSC JAK2 HOM


title: SLX-9783.N707_N503

description: Old HSC JAK2 HOM


title: SLX-9783.N709_N506

description: Old HSC JAK2 HOM


title: SLX-9783.N707_N505

description: Old HSC JAK2 HOM


title: SLX-9783.N707_N504

description: Old HSC JAK2 HOM


title: SLX-9783.N707_N502

description: Old HSC JAK2 HOM


title: SLX-9783.N706_N504

description: Old HSC JAK2 HOM


title: SLX-9783.N706_N517

description: Old HSC JAK2 HOM


title: SLX-9783.N706_N508

description: Old HSC JAK2 HOM


title: SLX-9783.N706_N506

description: Old HSC JAK2 HOM


title: SLX-9783.N706_N507

description: Old HSC JAK2 HOM


title: SLX-9783.N706_N502

description: Old HSC JAK2 HOM


title: SLX-9783.N706_N505

description: Old HSC JAK2 HOM


title: SLX-9783.N705_N507

description: Old HSC JAK2 HOM


title: SLX-9783.N707_N517

description: Old HSC JAK2 HOM


title: SLX-9783.N706_N503

description: Old HSC JAK2 HOM


title: SLX-9783.N705_N506

description: Old HSC JAK2 HOM


title: SLX-9783.N705_N504

description: Old HSC JAK2 HOM


title: SLX-9783.N707_N506

description: Old HSC JAK2 HOM


title: SLX-9783.N705_N502

description: Old HSC JAK2 HOM


title: SLX-9783.N705_N517

description: Old HSC JAK2 HOM


title: SLX-9783.N704_N507

description: Old HSC JAK2 HOM


title: SLX-9783.N705_N508

description: Old HSC JAK2 HOM


title: SLX-9783.N704_N504

description: Old HSC JAK2 HOM


title: SLX-9783.N705_N503

description: Old HSC JAK2 HOM


title: SLX-9783.N705_N505

description: Old HSC JAK2 HOM


title: SLX-9783.N704_N517

description: Old HSC JAK2 HOM


title: SLX-9783.N704_N506

description: Old HSC JAK2 HOM


title: SLX-9783.N704_N508

description: Old HSC JAK2 HOM


title: SLX-9783.N703_N517

description: Old HSC JAK2 HOM


title: SLX-9783.N704_N502

description: Old HSC JAK2 HOM


title: SLX-9783.N704_N503

description: Old HSC JAK2 HOM


title: SLX-9783.N704_N505

description: Old HSC JAK2 HOM


title: SLX-9783.N703_N505

description: Old HSC JAK2 HOM


title: SLX-9783.N703_N503

description: Old HSC JAK2 HOM


title: SLX-9783.N703_N508

description: Old HSC JAK2 HOM


title: SLX-9783.N702_N508

description: Old HSC JAK2 HOM


title: SLX-9783.N703_N504

description: Old HSC JAK2 HOM


title: SLX-9783.N702_N517

description: Old HSC JAK2 HOM


title: SLX-9783.N703_N506

description: Old HSC JAK2 HOM


title: SLX-9783.N702_N506

description: Old HSC JAK2 HOM


title: SLX-9783.N703_N507

description: Old HSC JAK2 HOM


title: SLX-9783.N702_N507

description: Old HSC JAK2 HOM


title: SLX-9783.N702_N505

description: Old HSC JAK2 HOM


title: SLX-9783.N703_N502

description: Old HSC JAK2 HOM


title: SLX-9783.N702_N503

description: Old HSC JAK2 HOM


title: SLX-9783.N701_N508

description: Old HSC JAK2 HOM


title: SLX-9783.N702_N504

description: Old HSC JAK2 HOM


title: SLX-9783.N701_N505

description: Old HSC JAK2 HOM


title: SLX-9783.N701_N504

description: Old HSC JAK2 HOM


title: SLX-9783.N701_N502

description: Old HSC JAK2 HOM


title: SLX-9782.N712_N508

description: Young HSC JAK2 HOM

value: 4 Months (young)


title: SLX-9782.N712_N517

description: Young HSC JAK2 HOM


title: SLX-9783.N702_N502

description: Old HSC JAK2 HOM


title: SLX-9783.N701_N517

description: Old HSC JAK2 HOM


title: SLX-9783.N701_N507

description: Old HSC JAK2 HOM


title: SLX-9783.N701_N506

description: Old HSC JAK2 HOM


title: SLX-9782.N712_N507

description: Young HSC JAK2 HOM


title: SLX-9782.N712_N504

description: Young HSC JAK2 HOM


title: SLX-9782.N712_N502

description: Young HSC JAK2 HOM


title: SLX-9782.N712_N503

description: Young HSC JAK2 HOM


title: SLX-9782.N711_N508

description: Young HSC JAK2 HOM


title: SLX-9782.N711_N504

description: Young HSC JAK2 HOM


title: SLX-9782.N710_N517

description: Young HSC JAK2 HOM


title: SLX-9782.N711_N507

description: Young HSC JAK2 HOM


title: SLX-9782.N711_N502

description: Young HSC JAK2 HOM


title: SLX-9782.N710_N506

description: Young HSC JAK2 HOM


title: SLX-9782.N710_N505

description: Young HSC JAK2 HOM


title: SLX-9783.N701_N503

description: Old HSC JAK2 HOM


title: SLX-9782.N712_N506

description: Young HSC JAK2 HOM


title: SLX-9782.N710_N502

description: Young HSC JAK2 HOM


title: SLX-9782.N712_N505

description: Young HSC JAK2 HOM


title: SLX-9782.N709_N504

description: Young HSC JAK2 HOM


title: SLX-9782.N711_N506

description: Young HSC JAK2 HOM


title: SLX-9782.N709_N507

description: Young HSC JAK2 HOM


title: SLX-9782.N711_N503

description: Young HSC JAK2 HOM


title: SLX-9782.N710_N508

description: Young HSC JAK2 HOM


title: SLX-9782.N710_N507

description: Young HSC JAK2 HOM


title: SLX-9782.N711_N517

description: Young HSC JAK2 HOM


title: SLX-9782.N709_N502

description: Young HSC JAK2 HOM


title: SLX-9782.N711_N505

description: Young HSC JAK2 HOM


title: SLX-9782.N710_N503

description: Young HSC JAK2 HOM


title: SLX-9782.N709_N517

description: Young HSC JAK2 HOM


title: SLX-9782.N709_N508

description: Young HSC JAK2 HOM


title: SLX-9782.N709_N506

description: Young HSC JAK2 HOM


title: SLX-9782.N708_N503

description: Young HSC JAK2 HOM


title: SLX-9782.N709_N503

description: Young HSC JAK2 HOM


title: SLX-9782.N708_N505

description: Young HSC JAK2 HOM


title: SLX-9782.N708_N517

description: Young HSC JAK2 HOM


title: SLX-9782.N708_N508

description: Young HSC JAK2 HOM


title: SLX-9782.N708_N506

description: Young HSC JAK2 HOM


title: SLX-9782.N708_N504

description: Young HSC JAK2 HOM


title: SLX-9782.N708_N507

description: Young HSC JAK2 HOM


title: SLX-9782.N710_N504

description: Young HSC JAK2 HOM


title: SLX-9782.N707_N503

description: Young HSC JAK2 HOM


title: SLX-9782.N707_N502

description: Young HSC JAK2 HOM


title: SLX-9782.N707_N508

description: Young HSC JAK2 HOM


title: SLX-9782.N706_N506

description: Young HSC JAK2 HOM


title: SLX-9782.N707_N507

description: Young HSC JAK2 HOM


title: SLX-9782.N707_N506

description: Young HSC JAK2 HOM


title: SLX-9782.N706_N507

description: Young HSC JAK2 HOM


title: SLX-9782.N707_N505

description: Young HSC JAK2 HOM


title: SLX-9782.N707_N517

description: Young HSC JAK2 HOM


title: SLX-9782.N707_N504

description: Young HSC JAK2 HOM


title: SLX-9782.N706_N508

description: Young HSC JAK2 HOM


title: SLX-9782.N706_N505

description: Young HSC JAK2 HOM


title: SLX-9782.N706_N503

description: Young HSC JAK2 HOM


title: SLX-9782.N705_N517

description: Young HSC JAK2 HOM


title: SLX-9782.N706_N504

description: Young HSC JAK2 HOM


title: SLX-9782.N708_N502

description: Young HSC JAK2 HOM


title: SLX-9782.N705_N508

description: Young HSC JAK2 HOM


title: SLX-9782.N705_N507

description: Young HSC JAK2 HOM


title: SLX-9782.N706_N502

description: Young HSC JAK2 HOM


title: SLX-9782.N705_N506

description: Young HSC JAK2 HOM


title: SLX-9782.N705_N504

description: Young HSC JAK2 HOM


title: SLX-9782.N705_N505

description: Young HSC JAK2 HOM


title: SLX-9782.N705_N503

description: Young HSC JAK2 HOM


title: SLX-9782.N704_N507

description: Young HSC JAK2 HOM


title: SLX-9782.N706_N517

description: Young HSC JAK2 HOM


title: SLX-9782.N704_N517

description: Young HSC JAK2 HOM


title: SLX-9782.N704_N506

description: Young HSC JAK2 HOM


title: SLX-9782.N704_N508

description: Young HSC JAK2 HOM


title: SLX-9782.N704_N505

description: Young HSC JAK2 HOM


title: SLX-9782.N704_N502

description: Young HSC JAK2 HOM


title: SLX-9782.N703_N517

description: Young HSC JAK2 HOM


title: SLX-9782.N703_N507

description: Young HSC JAK2 HOM


title: SLX-9782.N703_N506

description: Young HSC JAK2 HOM


title: SLX-9782.N703_N505

description: Young HSC JAK2 HOM


title: SLX-9782.N703_N504

description: Young HSC JAK2 HOM


title: SLX-9782.N709_N505

description: Young HSC JAK2 HOM


title: SLX-9782.N703_N508

description: Young HSC JAK2 HOM


title: SLX-9782.N702_N506

description: Young HSC JAK2 HOM


title: SLX-9782.N702_N507

description: Young HSC JAK2 HOM


title: SLX-9782.N702_N505

description: Young HSC JAK2 HOM


title: SLX-9782.N703_N502

description: Young HSC JAK2 HOM


title: SLX-9782.N702_N504

description: Young HSC JAK2 HOM


title: SLX-9782.N702_N503

description: Young HSC JAK2 HOM


title: SLX-9782.N702_N517

description: Young HSC JAK2 HOM


title: SLX-9782.N705_N502

description: Young HSC JAK2 HOM


title: SLX-9782.N702_N502

description: Young HSC JAK2 HOM


title: SLX-9782.N701_N517

description: Young HSC JAK2 HOM


title: SLX-9782.N701_N508

description: Young HSC JAK2 HOM


title: SLX-9782.N701_N507

description: Young HSC JAK2 HOM


title: SLX-9782.N701_N505

description: Young HSC JAK2 HOM


title: SLX-9782.N701_N506

description: Young HSC JAK2 HOM


title: SLX-9782.N701_N504

description: Young HSC JAK2 HOM


title: SLX-9782.N704_N503

description: Young HSC JAK2 HOM


title: SLX-9782.N701_N503

description: Young HSC JAK2 HOM


title: SLX-9782.N704_N504

description: Young HSC JAK2 HOM


title: SLX-9780.N712_N517

description: Young HSC WT


title: SLX-9780.N712_N506

description: Young HSC WT


title: SLX-9780.N712_N505

description: Young HSC WT


title: SLX-9782.N701_N502

description: Young HSC JAK2 HOM


title: SLX-9780.N712_N504

description: Young HSC WT


title: SLX-9780.N712_N502

description: Young HSC WT


title: SLX-9782.N703_N503

description: Young HSC JAK2 HOM


title: SLX-9780.N711_N517

description: Young HSC WT


title: SLX-9782.N702_N508

description: Young HSC JAK2 HOM


title: SLX-9780.N711_N508

description: Young HSC WT


title: SLX-9780.N711_N506

description: Young HSC WT


title: SLX-9780.N711_N505

description: Young HSC WT


title: SLX-9780.N711_N502

description: Young HSC WT


title: SLX-9780.N711_N503

description: Young HSC WT


title: SLX-9780.N710_N517

description: Young HSC WT


title: SLX-9780.N711_N504

description: Young HSC WT


title: SLX-9780.N710_N508

description: Young HSC WT


title: SLX-9780.N710_N503

description: Young HSC WT


title: SLX-9780.N709_N517

description: Young HSC WT


title: SLX-9780.N710_N502

description: Young HSC WT


title: SLX-9780.N710_N505

description: Young HSC WT


title: SLX-9780.N710_N507

description: Young HSC WT


title: SLX-9780.N710_N506

description: Young HSC WT


title: SLX-9780.N712_N508

description: Young HSC WT


title: SLX-9780.N710_N504

description: Young HSC WT


title: SLX-9780.N712_N507

description: Young HSC WT


title: SLX-9780.N712_N503

description: Young HSC WT


title: SLX-9780.N709_N508

description: Young HSC WT


title: SLX-9780.N709_N507

description: Young HSC WT


title: SLX-9780.N709_N505

description: Young HSC WT


title: SLX-9780.N708_N517

description: Young HSC WT


title: SLX-9780.N711_N507

description: Young HSC WT


title: SLX-9780.N709_N504

description: Young HSC WT


title: SLX-9780.N708_N507

description: Young HSC WT


title: SLX-9780.N708_N503

description: Young HSC WT


title: SLX-9780.N708_N508

description: Young HSC WT


title: SLX-9780.N708_N505

description: Young HSC WT


title: SLX-9780.N708_N504

description: Young HSC WT


title: SLX-9780.N708_N502

description: Young HSC WT


title: SLX-9780.N707_N507

description: Young HSC WT


title: SLX-9780.N709_N506

description: Young HSC WT


title: SLX-9780.N707_N508

description: Young HSC WT


title: SLX-9780.N707_N517

description: Young HSC WT


title: SLX-9780.N707_N506

description: Young HSC WT


title: SLX-9780.N706_N517

description: Young HSC WT


title: SLX-9780.N707_N503

description: Young HSC WT


title: SLX-9780.N706_N508

description: Young HSC WT


title: SLX-9780.N707_N502

description: Young HSC WT


title: SLX-9780.N707_N504

description: Young HSC WT


title: SLX-9780.N709_N503

description: Young HSC WT


title: SLX-9780.N706_N507

description: Young HSC WT


title: SLX-9780.N709_N502

description: Young HSC WT


title: SLX-9780.N708_N506

description: Young HSC WT


title: SLX-9780.N706_N505

description: Young HSC WT


title: SLX-9780.N706_N504

description: Young HSC WT


title: SLX-9780.N706_N503

description: Young HSC WT


title: SLX-9780.N706_N502

description: Young HSC WT


title: SLX-9780.N705_N517

description: Young HSC WT


title: SLX-9780.N706_N506

description: Young HSC WT


title: SLX-9780.N705_N508

description: Young HSC WT


title: SLX-9780.N705_N507

description: Young HSC WT


title: SLX-9780.N705_N506

description: Young HSC WT


title: SLX-9780.N705_N505

description: Young HSC WT


title: SLX-9780.N705_N504

description: Young HSC WT


title: SLX-9780.N705_N503

description: Young HSC WT


title: SLX-9780.N705_N502

description: Young HSC WT


title: SLX-9780.N704_N508

description: Young HSC WT


title: SLX-9780.N707_N505

description: Young HSC WT


title: SLX-9780.N704_N517

description: Young HSC WT


title: SLX-9780.N704_N507

description: Young HSC WT


title: SLX-9780.N704_N506

description: Young HSC WT


title: SLX-9780.N704_N505

description: Young HSC WT


title: SLX-9780.N703_N506

description: Young HSC WT


title: SLX-9780.N704_N504

description: Young HSC WT


title: SLX-9780.N703_N508

description: Young HSC WT


title: SLX-9780.N704_N503

description: Young HSC WT


title: SLX-9780.N703_N507

description: Young HSC WT


title: SLX-9780.N703_N504

description: Young HSC WT


title: SLX-9780.N703_N502

description: Young HSC WT


title: SLX-9780.N702_N508

description: Young HSC WT


title: SLX-9780.N704_N502

description: Young HSC WT


title: SLX-9780.N702_N505

description: Young HSC WT


title: SLX-9780.N702_N504

description: Young HSC WT


title: SLX-9780.N703_N505

description: Young HSC WT


title: SLX-9780.N702_N517

description: Young HSC WT


title: SLX-9780.N703_N517

description: Young HSC WT


title: SLX-9780.N703_N503

description: Young HSC WT


title: SLX-9780.N702_N506

description: Young HSC WT


title: SLX-9780.N702_N502

description: Young HSC WT