title: RNAseq_48 h_Rep1

data_processing:
RNA-seq reads were first aligned to human transcriptome annotations and genome assembly (hg38) using Bowtie2.
Reads mapped to the bodies of RefSeq genes were obtained using Bioconductor (Gentleman et al., 2004).
Numbers of reads mapped to each gene were further converted to TPM (transcripts per million) values as previously described (Li and Dewey, 2011).
Genome_build: hg38
Supplementary_files_format_and_content: The proceesed data file "Differentiation_RNA-seq.txt". Columns 1 to 7 are Refseq ID, Gene name, chromosome, start, end, strand and TSS. Remaining columns are TPM values for each differentiation state.

extract_protocol:
Total RNA was harvested and purified with Qiagen’s RNeasy (74104) mini kit.
Poly-A RNA was sequenced by Hudson Alpha using Illumina HiSeq v4.

treatment_protocol: Differentiation towards Definitive Endoderm for 6, 12, 24 and 48 h time-points were carried out after adapting protocol from Schulz et al., 2012 to adherent culture. Briefly, hESC cultures at ~70% confluency were washed 2x with cold PBS and stimulated to differentiate by the addition of RPMI (Invitrogen), 50ng/ml Wnt (CellGS, GFM77), 100ng/ml Activin A (CellGS, GFH6). 24 hours after stimulation, media was replaced with RPMI containing 0.2% FBS, and 100 ng/ml Activin A.


title: H9 ESC_Rep1_Early

status: Public on Jun 20 2019

type: SRA

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

country: USA

institute: Florida State University

library_source: genomic

data_processing:
Reads were mapped on mm10 using bowtie2.
Reads were converted to reads per million.
Coverage data in 10 kb bins are calculated from mapped reads using samtools and bedtools.
Replication timing score is calculated as base 2 log of early to late coverage ratio in 10 kb windows.
Genome_build: hg38
Supplementary_files_format_and_content: The proceesed data file ("Differentiation_Repli-seq.txt") is the replication timing caluclated as the base 2 log ratio between early and late S fraction. Column 1 and 2 are CHR and POS. Remaining columns are scaled , smoothed quantile normalized replication timing score.

molecule: genomic DNA

organism: Homo sapiens

source_name: human ESC (H9)

growth_protocol: H9 hESCs were cultured under feeder-free conditions on Geltrex (Thermo Fisher, A14133) coated dishes, and maintained in StemPro (Thermo Fisher, A100701) culture media per manufacture’s specifications.

extract_protocol:
Genome-wide replication timing profiles were constructed as previously described (Marchal et al., 2018). Briefly, cells were pulse labeled with BrdU and separated into early and late S-phase fractions by flow cytometry and processed by NGS.
Sequencing libraries of BrdU-substituted DNA from early and late fractions were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina (E7370).

treatment_protocol: Differentiation towards Definitive Endoderm for 24 h and 48 h time-points were carried out after adapting protocol from Schulz et al., 2012 to adherent culture. Briefly, hESC cultures at ~70% confluency were washed 2x with cold PBS and stimulated to differentiate by the addition of RPMI (Invitrogen), 50ng/ml Wnt (CellGS, GFM77), 100ng/ml Activin A (CellGS, GFH6). 24 hours after stimulation, media was replaced with RPMI containing 0.2% FBS, and 100 ng/ml Activin A. Definitive Endoderm, Pancreatic Progenitor, Poly-Hormonal cells and Pancreatic Beta-like cells were made from hESCs as previously described in Pagliuca et al., 2014 with modifications. H9 hESC aggregates were made by seeding cells at 1 million/ml in 5.5-6ml HAIF with 10M ROCK-inhibitor (Y27632) per well in a 6-well plate. Cells were incubated on rotator (97 rpm) at 37oC with 5% CO2 overnight.  Aggregates were washed 3x with MCDB 131 media and re-suspend in DE media with 3uM CHIR and 10M Y27632. On day 1 and 2, the media was replaced with DE media (MCB131, 1% Probumin (10% stock made in MCB131), 1x NEAA, 2mM Glutagro, 1x Trace Elements A, B, & C, 10ug/ml Human Transferrin, 50ug/ml L- Ascorbic acid, 100ng/ml Activin, 8ng/ml bFGF.). On Day 3 Definitive Endoderm cells were collected. From day 3 onwards the method in Pagliuca et al., 2014 was followed to collect Pancreatic Progenitor, Poly-Hormonal cells and Pancreatic Beta-like cells.

tag: s-phase fraction

value: Early S fraction

tag: replicate

tag: differentiation state

value: ESC


title: SS2_17_449_star_mm10_J3

city: Solna

first: Chris

middle: Andrew

last: Tibbitt

state: non-US

address: Biomedicum C7,, Tomtebodavägen 16

country: Sweden

institute: KI

description:
Lung
Day 10 Lymph node and MLN mouse 1

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the NCBI Build 37 (UCSC mm9) of the mouse genome using TopHat (Trapnell et al., 2009). The resulting alignments were processed by Cufflinks to evaluate the expression of transcripts from RefSeq.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file

molecule: total RNA

organism: Mus musculus

source_name: Day 10 Lymph node and MLN mouse 1

extract_protocol:
Single memory T helper cells (CD4+CD3+CD44+) sorted directly inflammed tissues (either BAL, lung or mLN) into 2% titron.
SMART-SEQ2 (see Picelli et al 2014)
Single cell RNA-Seq

tag: tissue

value: Lymph Node

tag: model

value: HDM


title: H9 ESC_Rep1_Late

value: Late S fraction


title: SS2_17_449_star_mm10_J18

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_J15

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: RNAseq_24 h_Rep2

molecule: polyA RNA

value: 24 hours


title: RNAseq_24 h_Rep1


title: SS2_17_449_star_mm10_J16

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_J13

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: RNAseq_12 h_Rep1

value: 12 hours


title: SS2_17_449_star_mm10_J20

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: RNAseq_12 h_Rep2


title: SS2_17_449_star_mm10_J14

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_J12

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_J11

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: RNAseq_6 h_Rep2

value: 6 hours


title: RNAseq_6 h_Rep1


title: SS2_17_449_star_mm10_J10

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I9

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: RNAseq_H9 ESC_Rep1


title: RNAseq_H9 ESC_Rep2


title: SS2_17_449_star_mm10_I7

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: RNAseq_48 h_Rep2

value: 48 hours


title: Hi-C_Beta-Like_4bp

data_processing:
Hi-C paired-end reads were aligned using Bowtie 2 and processed using Homer software package.
PC1 values were calculated using the software package Homer with at 50 Kb bins (Homer parameter res= 50 kb and super res= 500 Kb).
Sex chromosomes (X, Y) were removed from further analysis. Chromosome 19 and 4 were removed from further analysis since PC1 values did not reflect A/B compartmentalization for certain datasets.
Genome_build: hg38
Supplementary_files_format_and_content: The proceesed data file "Differentiation_Hi-C_A/B compartment.txt". Column 1 and 2 are CHR and POS. Remianing columns are A/B comparment scores (scaled, quantile normalized PC1 values) for each sample.

extract_protocol:
Hi-C libraries were created using HindIII 6bp restriction enzyme based on Dixon et al., 2015 protocol or using DpnII 4bp restriction enzyme based on Rao et al., 2014 in-situ Hi-C protocol
Final libraries were sequenced by Hudosn Alpha Sequencing facility on Illumina-HiSeq 2500

treatment_protocol: Differentiation towards Definitive Endoderm for  24 and 48 h time-points were carried out after adapting protocol from Schulz et al., 2012 to adherent culture. Briefly, hESC cultures at ~70% confluency were washed 2x with cold PBS and stimulated to differentiate by the addition of RPMI (Invitrogen), 50ng/ml Wnt (CellGS, GFM77), 100ng/ml Activin A (CellGS, GFH6). 24 hours after stimulation, media was replaced with RPMI containing 0.2% FBS, and 100 ng/ml Activin A. Definitive Endoderm, Pancreatic Progenitor, Poly-Hormonal cells and Pancreatic Beta-like cells were made from hESCs as previously described in Pagliuca et al., 2014 with modifications. H9 hESC aggregates were made by seeding cells at 1 million/ml in 5.5-6ml HAIF with 10M ROCK-inhibitor (Y27632) per well in a 6-well plate. Cells were incubated on rotator (97 rpm) at 37oC with 5% CO2 overnight.  Aggregates were washed 3x with MCDB 131 media and re-suspend in DE media with 3uM CHIR and 10M Y27632. On day 1 and 2, the media was replaced with DE media (MCB131, 1% Probumin (10% stock made in MCB131), 1x NEAA, 2mM Glutagro, 1x Trace Elements A, B, & C, 10ug/ml Human Transferrin, 50ug/ml L- Ascorbic acid, 100ng/ml Activin, 8ng/ml bFGF.). On Day 3 Definitive Endoderm cells were collected. From day 3 onwards the method in Pagliuca et al., 2014 was followed to collect Pancreatic Progenitor, Poly-Hormonal cells and Pancreatic Beta-like cells.

value: Beta-Like


title: SS2_17_449_star_mm10_I8

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I6

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: Hi-C_Poly_hormonal_4bp


title: Hi-C_Pancreatic Progenitor_4bp

value: Pancreatic Projenitor


title: Hi-C_Definitve Endoderm_4bp

value: Definitive Endoderm


title: Hi-C_48hr_6bp_Rep2


title: Hi-C_48hr_6bp_Rep1


title: Hi-C_24hr_6bp_Rep2


title: SS2_17_449_star_mm10_I3

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I24

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I4

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I5

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I2

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: Hi-C_24hr_6bp_Rep1


title: SS2_17_449_star_mm10_I22

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: Hi-C_H9_ESC_6bp


title: SS2_17_449_star_mm10_I23

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: Hi-C_H9_ESC_4bp


title: SS2_17_449_star_mm10_I20

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I21

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I17

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I18

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I15

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I13

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I12

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I16

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I1

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I11

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I10

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_H9

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I14

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_H8

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_H7

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_H6

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_H5

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_H2

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: JeDa_Rady_87_SpeA_S504_N710

city: San Diego

first: Jennifer

last: Dan

state: CA

address: 9420 Athena Cir

institute: La Jolla Institute of Immunology

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the human hg19 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Transcript per million(TPM) normalization is done to the count matrix
Genome_build: hg19
Supplementary_files_format_and_content: TPM matrix with rows as genes and columns as samples

extract_protocol:
Sorted cells were lysed in Trizol LS (ThermoFisher), RNA was prepared using miRNeasy micro kit from Qiagen and quantified using real-time PCR
Adapted from the Smart-seq2 protocol, an oligo-based capture of Poly-A tailed mRNA was carried out followed by a high-fidelity reverse transcription using locked nucleic acids (LNA)-oligos to obtain full-length transcripts. mRNA complementary (c)DNA strands were then amplified using a PCR-based method and sequencing adaptors incorporated into the cDNA fragments in a single step using Tn5 transposase technology (Nextera XT reagents and barcoded adaptors kits).

tag: subject group

value: recurrent Group A Streptococcus (GAS) tonsillitis (RT)

tag: cell type

value: Tonsillar cells

tag: treatment

value: SpeA

tag: cell subtype/sorted fraction

value: AIM+ GC Tfh cells (CD25+OX40+ of CXCR5hi PD-1hi of CD45RA-CD4+ T cells)


title: SS2_17_449_star_mm10_H24

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: JeDa_Rady_003_Strep_S507_N706

value: Strep


title: JeDa_Navy_27_Strep_S506_N707


title: SS2_17_449_star_mm10_H4

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_I19

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: JeDa_Navy_34_SpeA_S505_N708

value: non-RT (sleep apnea)


title: JeDa_Navy_43_None_S508_N705

value: Unstim

value: AIM- GC Tfh cells (CD25-OX40- of CXCR5hi PD-1hi of CD45RA-CD4+ T cells)


title: SS2_17_449_star_mm10_H22

description:
Lung
Day 10 Lymph node and MLN mouse 1

value: Lymph Node

value: HDM


title: JeDa_Navy_32_SpeA_S517_N709


title: SS2_17_449_star_mm10_H23

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_H21

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: JeDa_Rady_87_Strep_S503_N710


title: SS2_17_449_star_mm10_H20

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: JeDa_Navy_44_SpeA_S507_N710


title: JeDa_Navy_60_Strep_S502_N709


title: JeDa_Rady_1054_None_S502_N707

description: JeDa_Rady_1054_None_S502_N707(Unstim/1054)


title: JeDa_Rady_87_None_S502_N710


title: SS2_17_449_star_mm10_H1

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_H19

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_H17

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_H16

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_H18

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_H3

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_H15

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: JeDa_Rady_003_None_S506_N708


title: JeDa_Navy_34_None_S503_N708


title: JeDa_Navy_32_Strep_S508_N709


title: SS2_17_449_star_mm10_H14

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: JeDa_Navy_32_None_S507_N709


title: SS2_17_449_star_mm10_H13

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: JeDa_Navy_27_SpeA_S507_N705


title: SS2_17_449_star_mm10_H12

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: JeDa_Navy_27_None_S505_N707


title: JeDa_Navy_44_None_S505_N710


title: SS2_17_449_star_mm10_G9

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: JeDa_Navy_16_SpeA_S506_N709


title: SS2_17_449_star_mm10_G7

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: JeDa_Navy_16_None_S504_N709


title: SS2_17_449_star_mm10_H11

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_H10

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_G6

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_G5

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: JeDa_Rady_1054_SpeA_S504_N707

description: JeDa_Rady_1054_SpeA_S504_N707(SpeA/1054)


title: SS2_17_449_star_mm10_G4

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: JeDa_Navy_44_Strep_S506_N710


title: JeDa_Navy_34_Strep_S504_N708


title: JeDa_Navy_16_Strep_S505_N709


title: SS2_17_449_star_mm10_G3

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: JeDa_Navy_60_None_S517_N706


title: SS2_17_449_star_mm10_G23

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: JeDa_Rady_1054_Strep_S503_N707

description: JeDa_Rady_1054_Strep_S503_N707(Strep/1054)


title: SS2_17_449_star_mm10_G21

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_K20

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_G24

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: JeDa_Navy_43_Strep_S517_N705


title: JeDa_Navy_43_SpeA_S502_N708


title: SS2_17_449_star_mm10_G2

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: JeDa_Navy_60_SpeA_S503_N709


title: SS2_17_449_star_mm10_G8

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_H11

city: WAUWATOSA

first: ZIQING

last: LIU

state: WI

address: 8701 W Watertown Plank Rd, BSB 5320

institute: Medical College of Wisconsin

description:
processed data file:
SCnorm_337cells_d3579_d3UN

data_processing:
QC: Qualities of de-barcoded raw sequence reads were checked by fastqc.
Mapping: Mapping to the merged genome of hg19 and ERCC was performed with Tophat2 using default settings.
Counting and outlier removal: Gene expression was counted with Htseq-count (0.6.1p1) using the union mode and no-feature and ambiguous counts were excluded for downstream analysis. Outliers showing high ratios of % reads mapped to spike-in to % reads mapped to human genome were removed.
Normalization: SCnorm was used to correct the dependence of read counts on sequencing depth (FilterCellProportion = .1, 1 condition). This normalization step considered only human genes not ERCC spike-in. Plate D0hCF, D3M1, D3M2, and D3UN were normalized together (329 cells, K = 7) and plate D3M3, D5M1, D7M1, and D9M1 were normalized together (346 cells, K=9).
Removal of additional outliers: Additional outliers were removed at the default outlier removal step during analysis using the “SINGuLAR Analysis Toolset” R package. A total of 23 additional outliers were removed based on median gene expression or PCA, resulting 652 high-quality single cells for analysis including 85 original hCFs (D0hCF), 14 uninfected hCFs (D3UN), 54  day 3 DsRed- and EV-transduced hCFs (D3UN), 14, 21, 18, and 18 Tdtomato- and EV-transduced hCFs collected on day 3 (D3M3), 5 (D5M1), 7 (D7M1), and 9 (D9M1), and 248, 54, 64, and 62  hMGT-  and miR-133-transduced hCFs collected at day 3 (D3M1, D3M2, and D3M3), 5 (D5M1), 7 (D7M1) and 9 (D9M1).
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file containing the normalized counts for each gene in each cell.

source_name: Cardiac fibroblasts

growth_protocol: Human cardiac fibroblasts (hCF) were derived from heart tissue by explant culture. The heart tissue was firstly minced into small aggregates, then plated onto one gelatin coated 10 cm dish for explant culture with fibroblast media (IMDM + 20% FBS). After 7 days of migration, fibroblasts were trypsinized and dissociated into single cells. Then, hCFs were seeded onto SureCoat (Celltron) pre-coated wells of 24 well plate at a cell density of 20,000 per well one day before infection.

extract_protocol:
On day of collection, the cells were trypsinized, stained with NearIR live/dead dye (Thermo Fisher Scientific), and FACS-sorted for live cells (negative for the live/dead dye). The sorted single cell suspension (~2000 cells/µl) was loaded on a large-sized (17-25 µm) microfluidic RNA-seq chip and single cells were captured with the C1 system. Bright field images were taken for captured cells. For the next step, cDNAs were prepared on chip using the SMARTer Ultra Low RNA kit from Illumina (Clontech). Judged by cell number and morphology in the microscopic images, only cDNA libraries from single healthy cells were selected for Illumina library preparation.
The libraries were prepared using the Nextera XT DNA Sample Preparation kit according to Fluidigm’s standard protocol except that 13 cycles of amplification was used instead of 12 cycles.

treatment_protocol: Retroviruses based on pMXs backbone expressing polycistronic human MEF2C, GATA4, TBX5 (puro-hMGT)/puro-DsRed/Tdtomato and retroviruses based on pBabeX backbone encoding miR-133/empty vector (EV) were packged separately with pUMVC and pCMV-VSV-G by transfecting 293T cells with lipofectamine 2000. Viruses collected from one 10-cm dish were resuspended in 100 µl DMEM media. Day 0 hCFs were collected before infection. Uninfected hCFs cultured in iCM media (10% FBS/20% M199/DMEM) were harvest at day 3. For day 3, 5, 7and 9 reprogrammin samples, hCFs were infected with 10 µl each of puro-hMGT and miR-133, or 10 µl each of puro-DsRed and EV, or 10 µl each of Tdtomato and EV with iCM media supplemented with 8 µg/ml polybrene. Forty-eight hours post infection, viral medium was replaced with regular iCM medium.

value: Heart


title: D9M1_H10


title: SS2_17_449_star_mm10_G1

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_G19

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_H09


title: SS2_17_449_star_mm10_G18

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_H08


title: JeDa_Rady_003_SpeA_S508_N706


title: D9M1_H07


title: SS2_17_449_star_mm10_G16

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_H05


title: SS2_17_449_star_mm10_G14

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_G13

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_H04


title: SS2_17_449_star_mm10_G15

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_H03


title: D9M1_H06


title: SS2_17_449_star_mm10_G22

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_G12

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_G20

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_G11

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_G10

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_F9

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_H01


title: D9M1_H02


title: D9M1_G10


title: D9M1_G11


title: SS2_17_449_star_mm10_F8

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_G08


title: SS2_17_449_star_mm10_G17

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_G07


title: SS2_17_449_star_mm10_F7

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_G06


title: SS2_17_449_star_mm10_F5

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_G05


title: SS2_17_449_star_mm10_F4

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_F6

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_G04


title: SS2_17_449_star_mm10_F24

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_G03


title: SS2_17_449_star_mm10_F3

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_F23

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_F2

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_G01


title: D9M1_F11


title: D9M1_G09


title: D9M1_F08


title: D9M1_G02


title: SS2_17_449_star_mm10_F22

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_F10


title: SS2_17_449_star_mm10_F20

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_F19

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_F18

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_F1

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_F06


title: SS2_17_449_star_mm10_F21

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_F05


title: SS2_17_449_star_mm10_F17

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_F15

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_F14

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_F02


title: D9M1_F03


title: SS2_17_449_star_mm10_F13

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_F09


title: D9M1_E11


title: D9M1_E12


title: D9M1_E10


title: SS2_17_449_star_mm10_F12

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_F07


title: SS2_17_449_star_mm10_E9

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_E8

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_E07


title: SS2_17_449_star_mm10_E7

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_E09


title: D9M1_F04


title: D9M1_E05


title: SS2_17_449_star_mm10_E5

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_F16

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_E08


title: D9M1_E03


title: D9M1_E04


title: SS2_17_449_star_mm10_E4

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_E3

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_E6

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_E06


title: D9M1_F01


title: D9M1_E02


title: D9M1_E01


title: SS2_17_449_star_mm10_F10

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_D12


title: SS2_17_449_star_mm10_F11

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_E23

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_E2

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_D11


title: D9M1_D10


title: SS2_17_449_star_mm10_E21

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_E20

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_D09


title: SS2_17_449_star_mm10_E19

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_E1

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_E18

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_E17

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_D05


title: D9M1_D08


title: D9M1_D03


title: D9M1_D02


title: SS2_17_449_star_mm10_E14

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_E24

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_D04


title: SS2_17_449_star_mm10_E15

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_D06


title: SS2_17_449_star_mm10_E16

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_C12


title: SS2_17_449_star_mm10_E12

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_E13

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_E22

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_C11


title: D9M1_C09


title: D9M1_C10


title: SS2_17_449_star_mm10_D9

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_E10

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_D8

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_C08


title: SS2_17_449_star_mm10_E11

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_C07


title: D9M1_D07


title: SS2_17_449_star_mm10_D7

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_D01


title: SS2_17_449_star_mm10_D6

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_D5

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_C05


title: D9M1_C04


title: SS2_17_449_star_mm10_D4

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_C03


title: SS2_17_449_star_mm10_D3

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_D2

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_C01


title: SS2_17_449_star_mm10_D23

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_B12


title: D9M1_B11


title: SS2_17_449_star_mm10_D24

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_D22

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_D21

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_B10


title: D9M1_B09


title: SS2_17_449_star_mm10_D1

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_D20

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_D19

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_B05


title: D9M1_C06


title: SS2_17_449_star_mm10_D17

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_C02


title: D9M1_B08


title: D9M1_B06


title: SS2_17_449_star_mm10_D16

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_B07


title: SS2_17_449_star_mm10_D18

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_D15

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_B03


title: D9M1_B02


title: D9M1_B04


title: D9M1_B01


title: SS2_17_449_star_mm10_D12

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_A11


title: D9M1_A09


title: SS2_17_449_star_mm10_D10

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_C9

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_A12


title: SS2_17_449_star_mm10_D14

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_A08


title: D9M1_A10


title: SS2_17_449_star_mm10_C8

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_A07


title: D9M1_A06


title: SS2_17_449_star_mm10_C5

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_A03


title: D9M1_A04


title: SS2_17_449_star_mm10_C2

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_D13

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_A05


title: SS2_17_449_star_mm10_C4

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D9M1_A02


title: SS2_17_449_star_mm10_C24

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_C23

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_H10


title: D7M1_H11


title: SS2_17_449_star_mm10_C22

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_D11

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_C21

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_H09


title: D7M1_H08


title: SS2_17_449_star_mm10_C20

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_C1

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_C7

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_C18

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_H05


title: SS2_17_449_star_mm10_C6

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_C17

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_C3

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_C19

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_H04


title: D9M1_A01


title: D7M1_H03


title: D7M1_H01


title: D7M1_H02


title: SS2_17_449_star_mm10_C16

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_C15

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_H07


title: SS2_17_449_star_mm10_C10

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_C13

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_C14

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_H06


title: SS2_17_449_star_mm10_C12

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_B8

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_G11


title: SS2_17_449_star_mm10_B9

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_C11

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_B7

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_G09


title: D7M1_G10


title: SS2_17_449_star_mm10_B6

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_G06


title: D7M1_G07


title: D7M1_G05


title: D7M1_G04


title: SS2_17_449_star_mm10_B5

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_B4

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_G02


title: D7M1_G01


title: D7M1_G03


title: SS2_17_449_star_mm10_B3

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_F11


title: D7M1_G08


title: SS2_17_449_star_mm10_B24

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_F10


title: SS2_17_449_star_mm10_B2

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_F08


title: D7M1_F09


title: SS2_17_449_star_mm10_B22

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_B23

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_F07


title: D7M1_F06


title: SS2_17_449_star_mm10_B21

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_B19

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_B1

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_F05


title: D7M1_F03


title: D7M1_F04


title: SS2_17_449_star_mm10_B18

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_F02


title: SS2_17_449_star_mm10_B15

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_B17

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_B16

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_E11


title: SS2_17_449_star_mm10_B14

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_B13

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_E08


title: D7M1_F01


title: D7M1_E09


title: D7M1_E07


title: SS2_17_449_star_mm10_B10

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_B20

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_A9

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_B12

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_B11

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_E05


title: SS2_17_449_star_mm10_A8

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_A7

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_E06


title: D7M1_E02


title: D7M1_E04


title: D7M1_E03


title: SS2_17_449_star_mm10_A6

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_E01


title: D7M1_D12


title: SS2_17_449_star_mm10_A4

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_A3

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_A5

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_D09


title: D7M1_D10


title: SS2_17_449_star_mm10_A24

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_A2

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_D11


title: SS2_17_449_star_mm10_A23

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_D08


title: D7M1_D06


title: D7M1_D07


title: SS2_17_449_star_mm10_A21

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_D05


title: SS2_17_449_star_mm10_A1

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_A19

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_D04


title: D7M1_D03


title: SS2_17_449_star_mm10_A20

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_D02


title: D7M1_D01


title: SS2_17_449_star_mm10_A17

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_A15

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_C12


title: D7M1_C11


title: D7M1_C10


title: SS2_17_449_star_mm10_A14

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_A16

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_C09


title: SS2_17_449_star_mm10_A22

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_A11

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_C06


title: D7M1_C07


title: D7M1_C08


title: SS2_17_449_star_mm10_A10

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_C05


title: SS2_17_218_star_mm10_P8

description:
airways
Day 15 BAL T helper cells mouse 2

source_name: Day 15 BAL T helper cells mouse 2

value: BAL


title: D7M1_C04


title: SS2_17_449_star_mm10_A18

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_218_star_mm10_P9


title: D7M1_C03


title: SS2_17_218_star_mm10_P7


title: D7M1_C02


title: SS2_17_218_star_mm10_P6


title: D7M1_C01


title: SS2_17_218_star_mm10_P5


title: SS2_17_218_star_mm10_P4


title: D7M1_B11


title: D7M1_B12


title: SS2_17_218_star_mm10_P3


title: SS2_17_218_star_mm10_P2


title: D7M1_B09


title: D7M1_B10


title: D7M1_B08


title: SS2_17_449_star_mm10_A13

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_218_star_mm10_P23


title: SS2_17_449_star_mm10_A12

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: D7M1_B07


title: D7M1_B06


title: SS2_17_218_star_mm10_P20


title: SS2_17_218_star_mm10_P21


title: D7M1_B03


title: D7M1_B04


title: D7M1_E10


title: SS2_17_218_star_mm10_P1


title: SS2_17_218_star_mm10_P18


title: D7M1_B02


title: SS2_17_218_star_mm10_P17


title: SS2_17_218_star_mm10_P19


title: D7M1_B01


title: SS2_17_218_star_mm10_P16


title: SS2_17_218_star_mm10_P14


title: SS2_17_218_star_mm10_P13


title: D7M1_A11


title: D7M1_A09


title: D7M1_A08


title: SS2_17_218_star_mm10_P15


title: SS2_17_218_star_mm10_P24


title: D7M1_A12


title: D7M1_B05


title: D7M1_A10


title: D7M1_A06


title: SS2_17_218_star_mm10_P22


title: SS2_17_218_star_mm10_P11


title: SS2_17_218_star_mm10_P10


title: SS2_17_218_star_mm10_O9


title: SS2_17_218_star_mm10_P12


title: D7M1_A05


title: D7M1_A04


title: D7M1_A03


title: SS2_17_218_star_mm10_O8


title: D7M1_A02


title: SS2_17_218_star_mm10_O6


title: D5M1_H10


title: SS2_17_218_star_mm10_O4


title: D5M1_H09


title: SS2_17_218_star_mm10_O5


title: SS2_17_218_star_mm10_O7


title: D7M1_A01


title: SS2_17_218_star_mm10_O3


title: D7M1_A07


title: D5M1_H07


title: D5M1_H08


title: SS2_17_218_star_mm10_O24


title: SS2_17_218_star_mm10_O2


title: D5M1_H05


title: SS2_17_218_star_mm10_O23


title: D5M1_H04


title: SS2_17_218_star_mm10_O21


title: SS2_17_218_star_mm10_O20


title: D5M1_H02


title: SS2_17_218_star_mm10_O1


title: SS2_17_218_star_mm10_O19


title: D5M1_G10


title: D5M1_G09


title: SS2_17_218_star_mm10_O18


title: D5M1_G08


title: SS2_17_218_star_mm10_O16


title: D5M1_G07


title: SS2_17_218_star_mm10_O15


title: D5M1_G06


title: D5M1_H06


title: SS2_17_218_star_mm10_O13


title: SS2_17_218_star_mm10_O22


title: D5M1_G05


title: SS2_17_218_star_mm10_O10


title: SS2_17_218_star_mm10_O12


title: D5M1_G03


title: D5M1_G01


title: SS2_17_218_star_mm10_N9


title: SS2_17_218_star_mm10_O11


title: D5M1_H01


title: SS2_17_218_star_mm10_N8


title: D5M1_F10


title: SS2_17_218_star_mm10_N7


title: SS2_17_218_star_mm10_O17


title: D5M1_F09


title: D5M1_F07


title: SS2_17_218_star_mm10_N5


title: SS2_17_218_star_mm10_N6


title: D5M1_H03


title: D5M1_F06


title: SS2_17_218_star_mm10_N4


title: D5M1_G04


title: SS2_17_218_star_mm10_O14


title: D5M1_F05


title: D5M1_F08


title: D5M1_F04


title: SS2_17_218_star_mm10_N2


title: SS2_17_218_star_mm10_N24


title: D5M1_F02


title: D5M1_F03


title: SS2_17_218_star_mm10_N3


title: D5M1_F01


title: D5M1_G02


title: SS2_17_218_star_mm10_N23


title: SS2_17_218_star_mm10_N22


title: SS2_17_218_star_mm10_N21


title: D5M1_E10


title: SS2_17_218_star_mm10_N20


title: D5M1_E07


title: SS2_17_218_star_mm10_N1


title: D5M1_E05


title: SS2_17_218_star_mm10_N19


title: SS2_17_218_star_mm10_N18


title: D5M1_E08


title: SS2_17_218_star_mm10_N16


title: D5M1_E06


title: D5M1_E03


title: SS2_17_218_star_mm10_N17


title: SS2_17_218_star_mm10_N15


title: SS2_17_218_star_mm10_N14


title: D5M1_E02


title: SS2_17_218_star_mm10_N13


title: D5M1_E01


title: D5M1_D11


title: D5M1_D10


title: D5M1_E09


title: D5M1_D09


title: SS2_17_218_star_mm10_N10


title: SS2_17_218_star_mm10_N11


title: SS2_17_218_star_mm10_M7


title: SS2_17_218_star_mm10_M8


title: SS2_17_218_star_mm10_M9


title: D5M1_D06


title: D5M1_D05


title: D5M1_D08


title: D5M1_D07


title: SS2_17_218_star_mm10_M6


title: D5M1_D04


title: D5M1_D03


title: D5M1_D02


title: D5M1_E04


title: SS2_17_218_star_mm10_M5


title: SS2_17_218_star_mm10_M3


title: SS2_17_218_star_mm10_M4


title: SS2_17_218_star_mm10_M2


title: D5M1_C11


title: SS2_17_218_star_mm10_N12


title: D5M1_D01


title: SS2_17_218_star_mm10_M24


title: D5M1_C10


title: SS2_17_218_star_mm10_M23


title: SS2_17_218_star_mm10_M20


title: D5M1_C07


title: SS2_17_218_star_mm10_M22


title: D5M1_C09


title: SS2_17_218_star_mm10_M19


title: D5M1_C08


title: SS2_17_218_star_mm10_M1


title: SS2_17_218_star_mm10_M16


title: D5M1_C05


title: D5M1_C04


title: D5M1_C03


title: D5M1_C01


title: D5M1_C02


title: SS2_17_218_star_mm10_M18


title: D5M1_B11


title: SS2_17_218_star_mm10_M14


title: D5M1_B10


title: SS2_17_218_star_mm10_M13


title: D5M1_B09


title: D5M1_B07


title: SS2_17_218_star_mm10_M11


title: SS2_17_218_star_mm10_M21


title: D5M1_B06


title: D5M1_C06


title: SS2_17_218_star_mm10_L9


title: SS2_17_218_star_mm10_M17


title: D5M1_B04


title: D5M1_B05


title: SS2_17_218_star_mm10_L8


title: D5M1_B02


title: SS2_17_218_star_mm10_L6


title: D5M1_B03


title: SS2_17_218_star_mm10_L7


title: D5M1_B01


title: SS2_17_218_star_mm10_M15


title: SS2_17_218_star_mm10_L5


title: SS2_17_218_star_mm10_M12


title: SS2_17_218_star_mm10_L2


title: SS2_17_218_star_mm10_L24


title: D5M1_A09


title: SS2_17_218_star_mm10_M10


title: SS2_17_218_star_mm10_L4


title: D5M1_A07


title: D5M1_B08


title: SS2_17_218_star_mm10_L23


title: D5M1_A08


title: SS2_17_218_star_mm10_L21


title: SS2_17_218_star_mm10_L22


title: D5M1_A06


title: D5M1_A05


title: SS2_17_218_star_mm10_L19


title: D5M1_A02


title: D5M1_A04


title: SS2_17_218_star_mm10_L20


title: D5M1_A11


title: SS2_17_218_star_mm10_L1


title: D5M1_A10


title: D5M1_A01


title: D3M3_H11


title: SS2_17_218_star_mm10_L17


title: SS2_17_218_star_mm10_L15


title: SS2_17_218_star_mm10_L16


title: SS2_17_218_star_mm10_L3


title: D3M3_H10


title: SS2_17_218_star_mm10_L13


title: D3M3_H08


title: D3M3_H06


title: D3M3_H07


title: SS2_17_218_star_mm10_L14


title: D3M3_H09


title: SS2_17_218_star_mm10_L18


title: D3M3_H04


title: D3M3_H05


title: SS2_17_218_star_mm10_L10


title: SS2_17_218_star_mm10_L11


title: D5M1_A03


title: SS2_17_218_star_mm10_L12


title: SS2_17_218_star_mm10_K8


title: D3M3_H02


title: SS2_17_218_star_mm10_K6


title: SS2_17_218_star_mm10_K9


title: SS2_17_218_star_mm10_K7


title: D3M3_H03


title: D3M3_G11


title: D3M3_G09


title: SS2_17_218_star_mm10_K4


title: SS2_17_218_star_mm10_K5


title: D3M3_G08


title: D3M3_G10


title: D3M3_H01


title: SS2_17_218_star_mm10_K3


title: D3M3_G03


title: D3M3_G06


title: SS2_17_218_star_mm10_K23


title: D3M3_G07


title: SS2_17_218_star_mm10_K24


title: D3M3_G05


title: D3M3_G01


title: D3M3_G02


title: SS2_17_218_star_mm10_K19


title: SS2_17_218_star_mm10_K1


title: SS2_17_218_star_mm10_K22


title: D3M3_F11


title: SS2_17_218_star_mm10_K20


title: SS2_17_218_star_mm10_K16


title: D3M3_F10


title: SS2_17_218_star_mm10_K17


title: SS2_17_218_star_mm10_K18


title: D3M3_F07


title: SS2_17_218_star_mm10_K2


title: SS2_17_218_star_mm10_K15


title: D3M3_F09


title: SS2_17_218_star_mm10_K13


title: SS2_17_218_star_mm10_K12


title: D3M3_F08


title: D3M3_F05


title: D3M3_F06


title: SS2_17_218_star_mm10_K14


title: D3M3_F04


title: SS2_17_218_star_mm10_K11


title: D3M3_F03


title: SS2_17_218_star_mm10_K10


title: SS2_17_218_star_mm10_J9


title: D3M3_F01


title: SS2_17_218_star_mm10_J8


title: D3M3_F02


title: D3M3_E11


title: SS2_17_218_star_mm10_J7


title: SS2_17_218_star_mm10_J6


title: D3M3_E09


title: SS2_17_218_star_mm10_J5


title: SS2_17_218_star_mm10_J4


title: SS2_17_218_star_mm10_J3


title: SS2_17_218_star_mm10_J2


title: D3M3_E07


title: D3M3_E08


title: D3M3_E06


title: SS2_17_218_star_mm10_J23


title: SS2_17_218_star_mm10_J24


title: SS2_17_218_star_mm10_J22


title: D3M3_E03


title: D3M3_E05


title: D3M3_E02


title: D3M3_E04


title: SS2_17_218_star_mm10_J20


title: D3M3_E01


title: D3M3_D11


title: SS2_17_218_star_mm10_J1


title: D3M3_D10


title: SS2_17_218_star_mm10_J17


title: D3M3_D09


title: D3M3_E10


title: D3M3_D08


title: SS2_17_218_star_mm10_J16


title: SS2_17_218_star_mm10_J18


title: D3M3_D06


title: D3M3_D07


title: SS2_17_218_star_mm10_J15


title: SS2_17_218_star_mm10_J14


title: D3M3_D04


title: SS2_17_218_star_mm10_J21


title: SS2_17_218_star_mm10_J13


title: D3M3_D05


title: SS2_17_218_star_mm10_J10


title: SS2_17_218_star_mm10_J11


title: SS2_17_218_star_mm10_J19


title: D3M3_C10


title: D3M3_D01


title: D3M3_D02


title: SS2_17_218_star_mm10_J12


title: SS2_17_218_star_mm10_I8


title: SS2_17_218_star_mm10_I7


title: D3M3_C09


title: SS2_17_218_star_mm10_I6


title: D3M3_C08


title: D3M3_C11


title: D3M3_C06


title: SS2_17_218_star_mm10_I5


title: D3M3_D03


title: D3M3_C05


title: SS2_17_218_star_mm10_I4


title: SS2_17_218_star_mm10_I3


title: D3M3_C04


title: SS2_17_218_star_mm10_I9


title: D3M3_C03


title: SS2_17_218_star_mm10_I2


title: SS2_17_218_star_mm10_I22


title: SS2_17_218_star_mm10_I23


title: D3M3_B11


title: D3M3_C07


title: D3M3_B10


title: SS2_17_218_star_mm10_I24


title: SS2_17_218_star_mm10_I20


title: D3M3_B09


title: SS2_17_218_star_mm10_I1


title: D3M3_C02


title: D3M3_C01


title: D3M3_B06


title: SS2_17_218_star_mm10_I19


title: SS2_17_218_star_mm10_I18


title: SS2_17_218_star_mm10_I17


title: D3M3_B05


title: D3M3_B07


title: D3M3_B03


title: D3M3_B04


title: SS2_17_218_star_mm10_I14


title: SS2_17_218_star_mm10_I16


title: SS2_17_218_star_mm10_I21


title: D3M3_B02


title: D3M3_B01


title: D3M3_A11


title: SS2_17_218_star_mm10_I13


title: SS2_17_218_star_mm10_I10


title: SS2_17_218_star_mm10_I11


title: D3M3_A10


title: SS2_17_218_star_mm10_I15


title: SS2_17_218_star_mm10_H9


title: D3M3_B08


title: SS2_17_218_star_mm10_H7


title: D3M3_A07


title: D3M3_A08


title: D3M3_A06


title: SS2_17_218_star_mm10_H8


title: SS2_17_218_star_mm10_H6


title: D3M3_A04


title: SS2_17_218_star_mm10_H5


title: D3M3_A01


title: D3M3_A05


title: SS2_17_218_star_mm10_H3


title: SS2_17_218_star_mm10_I12


title: D3M3_A02


title: SS2_17_218_star_mm10_H24


title: SS2_17_218_star_mm10_H2


title: D3M3_A09


title: SS2_17_218_star_mm10_H23


title: D3UN_H09

data_processing:
QC: Qualities of de-barcoded raw sequence reads were checked by fastqc.
Mapping: Mapping to the merged genome of hg19 and ERCC was performed with Tophat2 using default settings.
Counting and outlier removal: Gene expression was counted with Htseq-count (0.6.1p1) using the union mode and no-feature and ambiguous counts were excluded for downstream analysis. Outliers showing high ratios of % reads mapped to spike-in to % reads mapped to human genome were removed.
Normalization: SCnorm was used to correct the dependence of read counts on sequencing depth (FilterCellProportion = .1, 1 condition). This normalization step considered only human genes not ERCC spike-in. Plate D0hCF, D3M1, D3M2, and D3UN were normalized together (329 cells, K = 7) and plate D3M3, D5M1, D7M1, and D9M1 were normalized together (346 cells, K=9).
Removal of additional outliers:  Additional outliers were removed at the default outlier removal step during analysis using the "SINGuLAR Analysis Toolset" R package. A total of 23 additional outliers were removed based on median gene expression or PCA, resulting 652 high-quality single cells for analysis including 85 original hCFs (D0hCF), 14 uninfected hCFs (D3UN), 54  day 3 DsRed- and EV-transduced hCFs (D3UN), 14, 21, 18, and 18 Tdtomato- and EV-transduced hCFs collected on day 3 (D3M3), 5 (D5M1), 7 (D7M1), and 9 (D9M1), and 248, 54, 64, and 62  hMGT-  and miR-133-transduced hCFs collected at day 3 (D3M1, D3M2, and D3M3), 5 (D5M1), 7 (D7M1) and 9 (D9M1).
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file containing the normalized counts for each gene in each cell.

treatment_protocol: Retroviruses based on pMXs backbone expressing polycistronic human MEF2C, GATA4, TBX5 (puro-hMGT)/puro-DsRed/Tdtomato and retroviruses based on pBabeX backbone encoding miR-133/empty vector (EV) were packaged separately with pUMVC and pCMV-VSV-G by transfecting 293T cells with lipofectamine 2000. Viruses collected from one 10-cm dish were resuspended in 100 µl DMEM media. Day 0 hCFs were collected before infection. Uninfected hCFs cultured in iCM media (10% FBS/20% M199/DMEM) were harvest at day 3. For day 3,5,7 and 9 reprogramming samples, hCFs were infected with 10 µl each of puro-hMGT and miR-133, or 10 µl each of puro-DsRed and EV, or 10 µl each of Tdtomato and EV with iCM media  supplemented with 8 µg/ml polybrene. Forty-eight hours post infection, viral medium was replaced with regular iCM medium.


title: D3UN_H08


title: SS2_17_218_star_mm10_H21


title: SS2_17_218_star_mm10_H20


title: SS2_17_218_star_mm10_H1


title: D3UN_H05


title: D3UN_H07


title: D3UN_H06


title: SS2_17_218_star_mm10_H4


title: D3UN_H03


title: SS2_17_218_star_mm10_H22


title: D3UN_H04


title: SS2_17_218_star_mm10_H17


title: D3M3_A03


title: D3UN_H01


title: D3UN_G09


title: SS2_17_218_star_mm10_H14


title: SS2_17_218_star_mm10_H13


title: SS2_17_218_star_mm10_H15


title: D3UN_G07


title: D3UN_G06


title: SS2_17_218_star_mm10_H12


title: SS2_17_218_star_mm10_H11


title: SS2_17_218_star_mm10_H19


title: SS2_17_218_star_mm10_G9


title: D3UN_H02


title: SS2_17_218_star_mm10_H18


title: SS2_17_218_star_mm10_G8


title: SS2_17_218_star_mm10_K21


title: SS2_17_218_star_mm10_G7


title: D3UN_G04


title: D3UN_F09


title: D3UN_G01


title: D3UN_G03


title: SS2_17_218_star_mm10_G6


title: D3UN_G05


title: D3UN_F08


title: SS2_17_218_star_mm10_G5


title: D3UN_F07


title: D3UN_G08


title: SS2_17_218_star_mm10_G3


title: SS2_17_218_star_mm10_H16


title: SS2_17_218_star_mm10_G4


title: SS2_17_218_star_mm10_H10


title: D3UN_F06


title: D3UN_F05


title: D3UN_F04


title: SS2_17_218_star_mm10_G23


title: D3UN_G02


title: SS2_17_218_star_mm10_G24


title: SS2_17_218_star_mm10_G21


title: D3UN_F03


title: SS2_17_218_star_mm10_G22


title: D3UN_F01


title: D3UN_F02


title: SS2_17_218_star_mm10_G20


title: D3UN_E09


title: SS2_17_218_star_mm10_G19


title: SS2_17_218_star_mm10_G18


title: SS2_17_218_star_mm10_G17


title: D3UN_E08


title: SS2_17_218_star_mm10_G1


title: D3UN_E05


title: D3UN_E04


title: D3UN_E06


title: D3UN_E03


title: SS2_17_218_star_mm10_G16


title: SS2_17_218_star_mm10_G2


title: SS2_17_218_star_mm10_G15


title: SS2_17_218_star_mm10_G14


title: SS2_17_218_star_mm10_G12


title: SS2_17_218_star_mm10_G11


title: D3UN_E01


title: D3UN_D09


title: D3UN_D08


title: D3M3_G04


title: SS2_17_218_star_mm10_G10


title: D3UN_E02


title: SS2_17_218_star_mm10_F8


title: D3UN_D06


title: SS2_17_218_star_mm10_F9


title: SS2_17_218_star_mm10_G13


title: D3UN_E07


title: D3UN_D05


title: SS2_17_218_star_mm10_F7


title: D3UN_D04


title: SS2_17_218_star_mm10_F5


title: SS2_17_218_star_mm10_F6


title: SS2_17_218_star_mm10_F3


title: D3UN_D02


title: D3UN_D03


title: SS2_17_218_star_mm10_F2


title: SS2_17_218_star_mm10_F4


title: SS2_17_218_star_mm10_F24


title: SS2_17_218_star_mm10_F22


title: D3UN_D01


title: D3UN_C08


title: D3UN_C07


title: D3UN_C04


title: SS2_17_218_star_mm10_F23


title: SS2_17_218_star_mm10_F20


title: D3UN_D07


title: D3UN_C02


title: D3UN_C03


title: SS2_17_218_star_mm10_F1


title: D3UN_C06


title: D3UN_C09


title: D3UN_C01


title: SS2_17_218_star_mm10_F19


title: D3UN_B09


title: D3UN_B10


title: SS2_17_218_star_mm10_F15


title: D3UN_B08


title: SS2_17_218_star_mm10_F21


title: SS2_17_218_star_mm10_F16


title: D3UN_C05


title: D3UN_B04


title: D3UN_B07


title: D3UN_B02


title: SS2_17_218_star_mm10_F12


title: SS2_17_218_star_mm10_F11


title: SS2_17_218_star_mm10_F13


title: D3UN_B06


title: SS2_17_218_star_mm10_F10


title: SS2_17_218_star_mm10_F17


title: SS2_17_218_star_mm10_E9


title: D3UN_B01


title: SS2_17_218_star_mm10_E7


title: D3UN_A10


title: D3UN_A09


title: SS2_17_218_star_mm10_E8


title: SS2_17_218_star_mm10_F14


title: D3UN_A08


title: SS2_17_218_star_mm10_F18


title: D3UN_A06


title: SS2_17_218_star_mm10_E6


title: SS2_17_218_star_mm10_E5


title: SS2_17_218_star_mm10_E4


title: SS2_17_218_star_mm10_E3


title: SS2_17_218_star_mm10_E2


title: SS2_17_218_star_mm10_E24


title: D3UN_A04


title: SS2_17_218_star_mm10_E23


title: D3UN_A03


title: D3UN_A02


title: SS2_17_218_star_mm10_E21


title: SS2_17_218_star_mm10_E22


title: D3M2_H11


title: D3UN_B03


title: SS2_17_218_star_mm10_E20


title: D3UN_A07


title: D3M2_H10


title: D3M2_H09


title: D3M2_H08


title: SS2_17_218_star_mm10_E17


title: D3M2_H06


title: SS2_17_218_star_mm10_E19


title: D3M2_H05


title: D3UN_A05


title: D3M2_H04


title: SS2_17_218_star_mm10_E15


title: SS2_17_218_star_mm10_E16


title: D3M2_H03


title: D3M2_H01


title: D3M2_G11


title: D3M2_H02


title: SS2_17_218_star_mm10_E11


title: SS2_17_218_star_mm10_E12


title: SS2_17_218_star_mm10_E14


title: SS2_17_218_star_mm10_E10


title: SS2_17_218_star_mm10_E13


title: SS2_17_218_star_mm10_D8


title: SS2_17_218_star_mm10_D7


title: D3M2_G08


title: D3M2_G10


title: D3M2_H07


title: D3M2_G07


title: SS2_17_218_star_mm10_E18


title: D3M2_G06


title: SS2_17_218_star_mm10_D6


title: SS2_17_218_star_mm10_D5


title: D3M2_G05


title: SS2_17_218_star_mm10_D4


title: D3M2_G02


title: D3M2_G03


title: D3M2_G04


title: SS2_17_218_star_mm10_D3


title: D3M2_G09


title: D3M2_G01


title: SS2_17_218_star_mm10_D24


title: SS2_17_218_star_mm10_D2


title: SS2_17_218_star_mm10_D23


title: D3M2_F11


title: D3M2_F10


title: SS2_17_218_star_mm10_D22


title: D3M2_F07


title: D3M2_F09


title: SS2_17_218_star_mm10_D21


title: SS2_17_218_star_mm10_D19


title: D3M2_F06


title: SS2_17_218_star_mm10_D20


title: D3M2_F05


title: SS2_17_218_star_mm10_D1


title: SS2_17_218_star_mm10_D18


title: D3M2_F08


title: D3M2_F04


title: SS2_17_218_star_mm10_D9


title: D3M2_F03


title: SS2_17_218_star_mm10_D17


title: SS2_17_218_star_mm10_D16


title: SS2_17_218_star_mm10_D15


title: D3M2_F01


title: D3M2_F02


title: SS2_17_218_star_mm10_D14


title: D3M2_E11


title: D3M2_E10


title: SS2_17_218_star_mm10_D13


title: D3M2_E08


title: SS2_17_218_star_mm10_D11


title: D3M2_E07


title: D3M2_E09


title: SS2_17_218_star_mm10_D10


title: SS2_17_218_star_mm10_C8


title: D3M2_E05


title: D3M2_E03


title: D3M2_E04


title: SS2_17_218_star_mm10_C9


title: SS2_17_218_star_mm10_C7


title: D3M2_E02


title: D3M2_D11


title: D3M2_E01


title: D3M2_E06


title: SS2_17_218_star_mm10_C4


title: SS2_17_218_star_mm10_C2


title: SS2_17_218_star_mm10_C3


title: SS2_17_218_star_mm10_C5


title: D3M2_D10


title: D3M2_D09


title: SS2_17_218_star_mm10_D12


title: SS2_17_218_star_mm10_C23


title: SS2_17_218_star_mm10_C22


title: D3M2_D08


title: D3M2_D07


title: SS2_17_218_star_mm10_C21


title: D3M2_D05


title: SS2_17_218_star_mm10_C6


title: D3M2_D06


title: SS2_17_218_star_mm10_C24


title: SS2_17_218_star_mm10_C19


title: D3M2_D04


title: D3M2_D03


title: SS2_17_218_star_mm10_C17


title: D3M2_D01


title: D3UN_B05


title: D3M2_C12


title: SS2_17_218_star_mm10_C16


title: D3M2_C11


title: SS2_17_218_star_mm10_C18


title: SS2_17_218_star_mm10_C14


title: D3M2_D02


title: D3M2_C10


title: SS2_17_218_star_mm10_C15


title: SS2_17_218_star_mm10_C13


title: SS2_17_218_star_mm10_C12


title: D3M2_C08


title: SS2_17_218_star_mm10_C11


title: SS2_17_218_star_mm10_C1


title: SS2_17_218_star_mm10_C20


title: D3M2_C07


title: D3M2_C05


title: SS2_17_218_star_mm10_C10


title: D3M2_C06


title: SS2_17_218_star_mm10_B8


title: D3M2_C04


title: SS2_17_218_star_mm10_B7


title: D3M2_C03


title: SS2_17_218_star_mm10_B6


title: D3M2_C02


title: SS2_17_218_star_mm10_B5


title: D3M2_C01


title: D3M2_B12


title: D3M2_C09


title: D3M2_B11


title: D3M2_B10


title: SS2_17_218_star_mm10_B24


title: D3M2_B09


title: SS2_17_218_star_mm10_B3


title: SS2_17_218_star_mm10_B23


title: D3M2_B08


title: SS2_17_218_star_mm10_B22


title: SS2_17_218_star_mm10_B9


title: D3M2_B06


title: SS2_17_218_star_mm10_B20


title: D3M2_B07


title: D3M2_B05


title: SS2_17_218_star_mm10_E1


title: D3M2_B03


title: SS2_17_218_star_mm10_B19


title: SS2_17_218_star_mm10_B4


title: D3M2_B02


title: SS2_17_218_star_mm10_B17


title: SS2_17_218_star_mm10_B16


title: D3M2_A12


title: SS2_17_218_star_mm10_B2


title: SS2_17_218_star_mm10_B14


title: SS2_17_218_star_mm10_B12


title: D3M2_A08


title: D3M2_A09


title: D3M2_B01


title: SS2_17_218_star_mm10_B11


title: D3M2_A07


title: SS2_17_218_star_mm10_B10


title: D3M2_A05


title: D3M2_A06


title: D3M2_B04


title: SS2_17_218_star_mm10_B18


title: SS2_17_218_star_mm10_A9


title: SS2_17_218_star_mm10_A8


title: D3UN_A01


title: D3M2_A02


title: D3M2_A04


title: D3M2_A03


title: SS2_17_218_star_mm10_A5


title: D3M2_A10


title: D3M2_A01


title: SS2_17_218_star_mm10_A4


title: SS2_17_218_star_mm10_A6


title: SS2_17_218_star_mm10_B13


title: D3M1_H10


title: SS2_17_218_star_mm10_A2


title: D3M1_H09


title: SS2_17_218_star_mm10_A24


title: D3M1_H11


title: SS2_17_218_star_mm10_A23


title: SS2_17_218_star_mm10_A7


title: D3M1_H08


title: SS2_17_218_star_mm10_A22


title: SS2_17_218_star_mm10_A21


title: D3M1_H07


title: D3M1_H05


title: SS2_17_218_star_mm10_A20


title: D3M1_H06


title: SS2_17_218_star_mm10_A1


title: SS2_17_218_star_mm10_A19


title: D3M1_H04


title: D3M1_H02


title: SS2_17_218_star_mm10_A3


title: D3M1_H03


title: D3M1_H01


title: SS2_17_218_star_mm10_A16


title: SS2_17_218_star_mm10_A17


title: D3M1_G11


title: D3M1_G10


title: D3M1_G09


title: SS2_17_218_star_mm10_A13


title: SS2_17_218_star_mm10_A14


title: D3M1_G08


title: D3M1_G07


title: SS2_17_218_star_mm10_A15


title: SS2_17_218_star_mm10_A12


title: D3M1_G06


title: SS2_17_218_star_mm10_A10


title: SS2_17_218_star_mm10_A11


title: SS2_15_0160_star_mm10_P9

description:
airways
Day 15 BAL T helper cells mouse 1

source_name: Day 15 BAL T helper cells mouse 1


title: D3M1_G05


title: D3M1_G04


title: SS2_15_0160_star_mm10_P8


title: D3M1_G03


title: SS2_15_0160_star_mm10_P7


title: SS2_15_0160_star_mm10_P6


title: D3M1_F12


title: SS2_15_0160_star_mm10_P5


title: D3M1_G01


title: SS2_15_0160_star_mm10_P4


title: D3M1_F11


title: SS2_15_0160_star_mm10_P3


title: D3M1_F10


title: SS2_15_0160_star_mm10_P2


title: D3M1_F09


title: 982_16

city: Warsaw

first: Mateusz

last: Bujko

address: Roentgena 5

department: Molecular Oncology Department

country: Poland

institute: Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology

data_processing:
1. Creating read count matrix with summarizeOverlaps function from Genomic Alignments BioconductoR package.
2. Calculation differential expression with DESeq and results function from DESeq2 BioconductoR package.
Genome_build: hg18
Supplementary_files_format_and_content: normalized_read_counts_USP8_Cushing_and_SCA.csv containing raw normalized readcounts for the whole dataset.

source_name: FFPE sections of pituitary tumors obtained during transsphenoidal surgery

extract_protocol:
RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE [Ambion]
Ion AmpliSeq™ Library Kit 2.0 [Thermo Fisher Scientific]

tag: usp8 mutation status

value: wt

tag: silent (=sca) or functioning (=cushing_disease)


title: 18843_15


title: D3M1_G02


title: SS2_15_0160_star_mm10_P22


title: D3M1_F08


title: SS2_15_0160_star_mm10_P1


title: SS2_15_0160_star_mm10_P20


title: D3M1_F06


title: 10613_11


title: SS2_15_0160_star_mm10_P19


title: 5389_16


title: SS2_15_0160_star_mm10_P18


title: D3M1_F05


title: SS2_17_218_star_mm10_A18


title: 16_16300


title: 18827_15


title: SS2_15_0160_star_mm10_P16


title: D3M1_F04


title: SS2_15_0160_star_mm10_P15


title: SS2_15_0160_star_mm10_P23


title: SS2_15_0160_star_mm10_P24


title: SS2_15_0160_star_mm10_P14


title: D3M1_F07


title: SS2_15_0160_star_mm10_P21


title: SS2_15_0160_star_mm10_P13


title: D3M1_F03


title: D3M1_F01


title: 789_17


title: SS2_15_0160_star_mm10_P10


title: SS2_15_0160_star_mm10_P12


title: D3M1_F02


title: 10610_17

value: mut


title: SS2_15_0160_star_mm10_P17


title: 10447_16


title: SS2_15_0160_star_mm10_O9


title: SS2_15_0160_star_mm10_O8


title: SS2_15_0160_star_mm10_O5


title: SS2_15_0160_star_mm10_O6


title: 9438_15


title: SS2_15_0160_star_mm10_O7


title: D3M1_E12


title: SS2_15_0160_star_mm10_O4


title: D3M1_E11


title: D3M1_E10


title: 1327_16

value: SCA


title: SS2_15_0160_star_mm10_O2


title: D3M1_E09


title: SS2_15_0160_star_mm10_O22


title: SS2_15_0160_star_mm10_O23


title: 6307_17


title: SS2_15_0160_star_mm10_O21


title: SS2_15_0160_star_mm10_O3


title: H17-12553


title: D3M1_E08


title: SS2_15_0160_star_mm10_O24


title: 17225_15


title: D3M1_E07


title: SS2_15_0160_star_mm10_O20


title: 12280_13


title: 17226


title: SS2_15_0160_star_mm10_O19


title: 3855_13


title: D3M1_E06


title: D3M1_E05


title: SS2_15_0160_star_mm10_O18


title: SS2_15_0160_star_mm10_O17


title: SS2_15_0160_star_mm10_O16


title: 11963_15


title: SS2_17_218_star_mm10_B1


title: SS2_17_218_star_mm10_B15


title: D3M2_A11


title: SS2_15_0160_star_mm10_O15


title: H17_14385


title: H16_17015


title: D3M1_E04


title: D3M1_E02


title: SS2_15_0160_star_mm10_O13


title: D3M1_E03


title: SS2_15_0160_star_mm10_O14


title: SS2_15_0160_star_mm10_O10


title: SS2_15_0160_star_mm10_O11


title: D3M1_E01


title: SS2_17_218_star_mm10_B21


title: SS2_15_0160_star_mm10_N9


title: D3M1_D12


title: SS2_15_0160_star_mm10_N7


title: SS2_15_0160_star_mm10_N5


title: SS2_15_0160_star_mm10_N8


title: MCF-7_H3K27ac_ChIPSeq_EPZ-6438

city: Shanghai

first: Yafang

last: Wang

state: Shanghai

address: 555 Zuchongzhi R.D

department: Division of Anti-Tumor Pharmacology

country: China

institute: Shanghai Institute of Materia Medica

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the human/mouse genome (hg19) using the BWA algorithm (v0.7.12, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1e-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations"
Genome_build: hg19
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)

growth_protocol: MCF-7 cells were grown in DMEM + 10%FBS at 37°C and 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation."
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500

treatment_protocol: MCF-7 cells were treated with 1 μM EPZ-6438 or DMSO for 6 days

tag: cell line

tag: chip antibody


title: MCF-7_H3K27ac_ChIPSeq_DMSO

value: DMSO


title: SS2_15_0160_star_mm10_N4


title: D3M1_D11


title: SS2_15_0160_star_mm10_N6


title: SS2_15_0160_star_mm10_O1


title: S004739.l.rs.lib_re-analyzed

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

institute: Lund University, Sweden

description: re-analysis of GSM2693060

data_processing:
Base-calling using manufacturer's on-instrument software.
Demultiplexing was done with Picard.
Alignment was done against hg38 using Novoalign with settings -a TGGAATTCTCGGGTGCCAAGG -l 14 -h -1 -1 -t 90 -g 50 -x 15 -o SAM -o FullNW -r All 51 -e 51
MicroRNA expression was analyzed using custom Perl scripts and calculated as counts per million miRNA reads (cpm).
Genome_build: hg38, mirbase 22 release
Supplementary_files_format_and_content: counts

source_name: Primary breast tumour

extract_protocol:
TRIZOL LS
Small RNA sequencing libraries were prepared from 500 ng total RNA using a protocol analogous with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs), but with custom adapters to incorporate dual indexes. Pooled libraries were sequenced on a NextSeq 500 with High Output v2 75 cycle-kits (Illumina)

tag: scan-b external id

tag: sample fullname

value: Primary breast tumour

value: Basal

value: ERneg

value: PRneg

value: High

tag: grade


title: D3M1_D10


title: SS2_15_0160_star_mm10_N3


title: pooled_MCF-7_Input DNA


title: S004724.l.rs.lib_re-analyzed

description: re-analysis of GSM2692908


title: SS2_15_0160_star_mm10_O12


title: D3M1_D09


title: SS2_15_0160_star_mm10_N24


title: S004562.l.rs.lib_re-analyzed

description: re-analysis of GSM2693003

value: LumA

value: Low


title: D3M1_D08


title: SS2_15_0160_star_mm10_N23


title: SS2_15_0160_star_mm10_N21


title: S004512.l.rs.lib_re-analyzed

description: re-analysis of GSM2692907


title: SS2_15_0160_star_mm10_N2


title: SS2_15_0160_star_mm10_P11


title: SS2_15_0160_star_mm10_N22


title: SS2_15_0160_star_mm10_N20


title: D3M1_D07


title: S004462.l.rs.lib_re-analyzed

description: re-analysis of GSM2693030

value: ERpos

value: PRpos


title: SS2_15_0160_star_mm10_N1


title: SS2_15_0160_star_mm10_N19


title: S004450.l.rs.lib_re-analyzed

description: re-analysis of GSM2693059


title: SS2_15_0160_star_mm10_N18


title: D3M1_D05


title: SS2_15_0160_star_mm10_N17


title: SS2_15_0160_star_mm10_N15


title: D3M1_D04


title: S004446.l.rs.lib_re-analyzed

description: re-analysis of GSM2693029

value: LumB


title: S004386.l.rs.lib_re-analyzed

description: re-analysis of GSM2693058


title: D3M1_D03


title: SS2_15_0160_star_mm10_N13

value: HDM


title: S004350.l.rs.lib_re-analyzed

description: re-analysis of GSM2692955


title: SS2_15_0160_star_mm10_N12


title: SS2_15_0160_star_mm10_N11


title: D3M1_D01

value: Heart


title: D3M1_D02


title: S004321.l.rs.lib_re-analyzed

description: re-analysis of GSM2693002


title: SS2_15_0160_star_mm10_M9

value: BAL


title: SS2_15_0160_star_mm10_N10


title: SS2_15_0160_star_mm10_M8


title: SS2_15_0160_star_mm10_M7


title: D3M1_C12


title: SS2_15_0160_star_mm10_M5


title: S004239.l.rs.lib_re-analyzed

description: re-analysis of GSM2693056


title: SS2_15_0160_star_mm10_M6


title: D3M1_C11


title: D3M1_C10


title: S004268.l.rs.lib_re-analyzed

description: re-analysis of GSM2693057


title: SS2_15_0160_star_mm10_M4


title: S004225.l.rs.lib_re-analyzed

description: re-analysis of GSM2693000


title: SS2_15_0160_star_mm10_N16


title: SS2_15_0160_star_mm10_M24


title: D3M1_C09


title: D3M1_D06


title: S002712.l.rs.lib_re-analyzed

description: re-analysis of GSM2692998


title: SS2_15_0160_star_mm10_N14


title: SS2_15_0160_star_mm10_M2


title: SS2_15_0160_star_mm10_M23


title: D3M1_C08


title: S004308.l.rs.lib_re-analyzed

description: re-analysis of GSM2693001


title: SS2_15_0160_star_mm10_M22


title: S002706.l.rs.lib_re-analyzed

description: re-analysis of GSM2693055


title: D3M1_C07


title: D3M1_C06


title: SS2_15_0160_star_mm10_M19


title: SS2_15_0160_star_mm10_M1


title: S002657.l.rs.lib_re-analyzed

description: re-analysis of GSM2692954


title: SS2_15_0160_star_mm10_M21


title: D3M1_C05


title: SS2_15_0160_star_mm10_M20


title: SS2_15_0160_star_mm10_M3


title: SS2_15_0160_star_mm10_M17


title: S002637.l.rs.lib_re-analyzed

description: re-analysis of GSM2692905


title: D3M1_C04


title: SS2_15_0160_star_mm10_M16


title: SS2_15_0160_star_mm10_M15


title: SS2_15_0160_star_mm10_M18


title: SS2_15_0160_star_mm10_M14


title: D3M1_C03


title: SS2_15_0160_star_mm10_M13


title: D3M1_C02


title: SS2_15_0160_star_mm10_M12


title: S002607.l.rs.lib_re-analyzed

description: re-analysis of GSM2692997


title: S002573.l.rs.lib_re-analyzed

description: re-analysis of GSM2692996


title: SS2_15_0160_star_mm10_M11


title: S002559.l.rs.lib_re-analyzed

description: re-analysis of GSM2692999


title: D3M1_C01


title: SS2_15_0160_star_mm10_L9


title: SS2_15_0160_star_mm10_L8


title: SS2_15_0160_star_mm10_L6


title: S002634.l.rs.lib_re-analyzed

description: re-analysis of GSM2693054


title: SS2_15_0160_star_mm10_L7


title: D3M1_B12


title: S002498.l.rs.lib_re-analyzed

description: re-analysis of GSM2692952


title: D3M1_B11


title: S002493.l.rs.lib_re-analyzed

description: re-analysis of GSM2692995


title: SS2_15_0160_star_mm10_L3


title: SS2_15_0160_star_mm10_L4


title: D3M1_B10


title: SS2_15_0160_star_mm10_L24


title: SS2_15_0160_star_mm10_L2


title: D3M1_B09


title: D3M1_B08


title: SS2_15_0160_star_mm10_L23


title: SS2_15_0160_star_mm10_M10


title: S002470.l.rs.lib_re-analyzed

description: re-analysis of GSM2692896


title: SS2_15_0160_star_mm10_L21


title: SS2_15_0160_star_mm10_L20


title: S002554.l.rs.lib_re-analyzed

description: re-analysis of GSM2692953


title: SS2_15_0160_star_mm10_L1


title: D3M1_B07


title: S002463.l.rs.lib_re-analyzed

description: re-analysis of GSM2692994


title: SS2_15_0160_star_mm10_L19


title: D3M1_B06


title: S002451.l.rs.lib_re-analyzed

description: re-analysis of GSM2692906


title: SS2_15_0160_star_mm10_L5


title: SS2_15_0160_star_mm10_L18


title: SS2_15_0160_star_mm10_L17


title: D3M1_B05


title: SS2_15_0160_star_mm10_L16


title: D3M1_B04


title: S002473.l.rs.lib_re-analyzed

description: re-analysis of GSM2692951


title: SS2_15_0160_star_mm10_L15


title: S002373.l.rs.lib_re-analyzed

description: re-analysis of GSM2692964


title: SS2_15_0160_star_mm10_L22


title: D3M1_B03


title: SS2_15_0160_star_mm10_L13


title: SS2_15_0160_star_mm10_L12


title: S002353.l.rs.lib_re-analyzed

description: re-analysis of GSM2692992


title: S002338.l.rs.lib_re-analyzed

description: re-analysis of GSM2692902


title: D3M1_B02


title: D3M1_B01


title: S002322.l.rs.lib_re-analyzed

description: re-analysis of GSM2692903


title: SS2_15_0160_star_mm10_L10


title: SS2_15_0160_star_mm10_K8


title: D3M1_A12


title: S002296.l.rs.lib_re-analyzed

description: re-analysis of GSM2692950


title: SS2_15_0160_star_mm10_K6


title: SS2_15_0160_star_mm10_K7


title: D3M1_A11


title: SS2_15_0160_star_mm10_K5


title: S002448.l.rs.lib_re-analyzed

description: re-analysis of GSM2692993


title: S002276.l.rs.lib_re-analyzed

description: re-analysis of GSM2692991


title: D3M1_A10


title: SS2_15_0160_star_mm10_L14


title: S002245.l.rs.lib_re-analyzed

description: re-analysis of GSM2692949


title: SS2_15_0160_star_mm10_K2


title: SS2_15_0160_star_mm10_K3


title: SS2_15_0160_star_mm10_L11


title: SS2_15_0160_star_mm10_K24


title: SS2_15_0160_star_mm10_K9


title: D3M1_A08


title: S002210.l.rs.lib_re-analyzed

description: re-analysis of GSM2693052


title: SS2_15_0160_star_mm10_K21


title: SS2_15_0160_star_mm10_K23


title: SS2_15_0160_star_mm10_K22


title: S002193.l.rs.lib_re-analyzed

description: re-analysis of GSM2693028


title: SS2_15_0160_star_mm10_K20


title: S002131.l.rs.lib_re-analyzed

description: re-analysis of GSM2693051


title: D3M1_A07


title: SS2_15_0160_star_mm10_K19


title: SS2_15_0160_star_mm10_K18


title: D3M1_A06


title: SS2_15_0160_star_mm10_K4


title: SS2_15_0160_star_mm10_K16


title: D3M1_A05


title: SS2_15_0160_star_mm10_K17


title: S002130.l.rs.lib_re-analyzed

description: re-analysis of GSM2693050


title: S002117.l.rs.lib_re-analyzed

description: re-analysis of GSM2692948


title: D3M1_A09


title: SS2_15_0160_star_mm10_K1


title: D3M1_A04


title: SS2_15_0160_star_mm10_K15


title: D3M1_A03


title: S002116.l.rs.lib_re-analyzed

description: re-analysis of GSM2692947


title: S002102.l.rs.lib_re-analyzed

description: re-analysis of GSM2692904


title: SS2_15_0160_star_mm10_K12


title: SS2_15_0160_star_mm10_K11


title: D3M1_A02


title: S002065.l.rs.lib_re-analyzed

description: re-analysis of GSM2692990


title: SS2_15_0160_star_mm10_K10


title: D3M1_A01


title: SS2_15_0160_star_mm10_J8


title: S001609.l.rs.lib_re-analyzed

description: re-analysis of GSM2693027


title: D0HCF_H11


title: SS2_15_0160_star_mm10_J9


title: SS2_15_0160_star_mm10_J7


title: SS2_15_0160_star_mm10_J6


title: S001587.l.rs.lib_re-analyzed

description: re-analysis of GSM2693049


title: D0HCF_H10


title: SS2_15_0160_star_mm10_J5


title: D0HCF_H09


title: SS2_15_0160_star_mm10_J4


title: SS2_15_0160_star_mm10_J3


title: S001570.l.rs.lib_re-analyzed2

description: re-analysis of GSM2692901


title: SS2_15_0160_star_mm10_J2


title: S001570.l.rs.lib_re-analyzed

description: re-analysis of GSM2692900


title: SS2_15_0160_star_mm10_J24


title: D0HCF_H08


title: SS2_15_0160_star_mm10_J23


title: D0HCF_H07


title: S001564.l.rs.lib_re-analyzed

description: re-analysis of GSM2692899


title: SS2_15_0160_star_mm10_J22


title: S001555.l.rs.lib_re-analyzed

description: re-analysis of GSM2692946


title: D0HCF_H06


title: SS2_15_0160_star_mm10_J21


title: SS2_15_0160_star_mm10_J1


title: D0HCF_H05


title: SS2_15_0160_star_mm10_J20


title: S001554.l.rs.lib_re-analyzed

description: re-analysis of GSM2692945


title: S001544.l.rs.lib_re-analyzed

description: re-analysis of GSM2692989


title: SS2_15_0160_star_mm10_J17


title: SS2_15_0160_star_mm10_J16


title: D0HCF_H03


title: D0HCF_H04


title: SS2_15_0160_star_mm10_J18


title: SS2_15_0160_star_mm10_J19


title: SS2_15_0160_star_mm10_J13


title: SS2_15_0160_star_mm10_J15


title: SS2_15_0160_star_mm10_J14


title: D0HCF_H02


title: SS2_15_0160_star_mm10_J12


title: S001505.l.rs.lib_re-analyzed

description: re-analysis of GSM2692944


title: S001524.l.rs.lib_re-analyzed

description: re-analysis of GSM2692898


title: SS2_15_0160_star_mm10_J11


title: S001485.l.rs.lib_re-analyzed

description: re-analysis of GSM2692894


title: SS2_15_0160_star_mm10_J10


title: D0HCF_G11


title: S001473.l.rs.lib_re-analyzed

description: re-analysis of GSM2693046


title: D0HCF_G10


title: S001532.l.rs.lib_re-analyzed

description: re-analysis of GSM2693048


title: S001471.l.rs.lib_re-analyzed

description: re-analysis of GSM2693026


title: D0HCF_G09


title: SS2_15_0160_star_mm10_I6


title: SS2_15_0160_star_mm10_I5


title: S001467.l.rs.lib_re-analyzed

description: re-analysis of GSM2692943


title: SS2_15_0160_star_mm10_I4


title: D0HCF_H01


title: D0HCF_G08


title: SS2_15_0160_star_mm10_I3


title: S001459.l.rs.lib_re-analyzed

description: re-analysis of GSM2692963


title: SS2_15_0160_star_mm10_I2


title: D0HCF_G07


title: S001455.l.rs.lib_re-analyzed

description: re-analysis of GSM2693047


title: SS2_15_0160_star_mm10_I24


title: SS2_15_0160_star_mm10_I22


title: S001444.l.rs.lib_re-analyzed

description: re-analysis of GSM2692893


title: SS2_15_0160_star_mm10_I9


title: SS2_15_0160_star_mm10_I21


title: SS2_15_0160_star_mm10_I8


title: D0HCF_G06


title: SS2_15_0160_star_mm10_I7


title: D0HCF_G05


title: SS2_15_0160_star_mm10_I1


title: SS2_15_0160_star_mm10_I20


title: S001437.l.rs.lib_re-analyzed

description: re-analysis of GSM2692942


title: D0HCF_G04


title: SS2_15_0160_star_mm10_I19


title: SS2_15_0160_star_mm10_I18


title: SS2_15_0160_star_mm10_I17


title: D0HCF_G03


title: D0HCF_G02


title: SS2_15_0160_star_mm10_I23


title: SS2_15_0160_star_mm10_I14


title: SS2_15_0160_star_mm10_I13


title: D0HCF_G01


title: SS2_15_0160_star_mm10_I12


title: D0HCF_F11


title: S001419.l.rs.lib_re-analyzed

description: re-analysis of GSM2692890


title: SS2_15_0160_star_mm10_I11


title: SS2_15_0160_star_mm10_I10


title: SS2_15_0160_star_mm10_H9


title: SS2_15_0160_star_mm10_H8


title: D0HCF_F10


title: S001380.l.rs.lib_re-analyzed

description: re-analysis of GSM2692941


title: S001421.l.rs.lib_re-analyzed

description: re-analysis of GSM2692895


title: D0HCF_F09


title: SS2_15_0160_star_mm10_H7


title: S001394.l.rs.lib_re-analyzed

description: re-analysis of GSM2693015


title: SS2_15_0160_star_mm10_H6


title: S001224.l.rs.lib_re-analyzed

description: re-analysis of GSM2693025


title: SS2_15_0160_star_mm10_I15


title: D0HCF_F08


title: S001394.l.rs.lib_re-analyzed2

description: re-analysis of GSM2693016


title: SS2_15_0160_star_mm10_I16


title: D0HCF_F07


title: S001207.l.rs.lib_re-analyzed

description: re-analysis of GSM2692940


title: D0HCF_F06


title: SS2_15_0160_star_mm10_H3


title: SS2_15_0160_star_mm10_H24


title: SS2_15_0160_star_mm10_H4


title: S001206.l.rs.lib_re-analyzed

description: re-analysis of GSM2692939


title: SS2_15_0160_star_mm10_H22


title: SS2_15_0160_star_mm10_H23


title: SS2_15_0160_star_mm10_H21


title: S001205.l.rs.lib_re-analyzed

description: re-analysis of GSM2692891


title: SS2_15_0160_star_mm10_H20


title: D0HCF_F04


title: D0HCF_F03


title: SS2_15_0160_star_mm10_H5


title: S001200.l.rs.lib_re-analyzed

description: re-analysis of GSM2693014


title: SS2_15_0160_star_mm10_H19


title: S001197.l.rs.lib_re-analyzed

description: re-analysis of GSM2693013


title: SS2_15_0160_star_mm10_H18


title: D0HCF_F02


title: S001210.l.rs.lib_re-analyzed

description: re-analysis of GSM2693024


title: S001192.l.rs.lib_re-analyzed

description: re-analysis of GSM2692938


title: SS2_15_0160_star_mm10_H2


title: SS2_15_0160_star_mm10_H15


title: D0HCF_E11


title: SS2_15_0160_star_mm10_H13


title: S001168.l.rs.lib_re-analyzed

description: re-analysis of GSM2692986


title: D0HCF_F01


title: SS2_15_0160_star_mm10_H1


title: S001167.l.rs.lib_re-analyzed

description: re-analysis of GSM2692983


title: SS2_15_0160_star_mm10_H16


title: SS2_15_0160_star_mm10_H14


title: SS2_15_0160_star_mm10_H10


title: SS2_15_0160_star_mm10_H12


title: SS2_15_0160_star_mm10_K14


title: S001164.l.rs.lib_re-analyzed

description: re-analysis of GSM2692897


title: D0HCF_E10


title: D0HCF_E09


title: SS2_15_0160_star_mm10_K13


title: S001152.l.rs.lib_re-analyzed

description: re-analysis of GSM2692987


title: SS2_15_0160_star_mm10_H17


title: SS2_15_0160_star_mm10_G7


title: SS2_15_0160_star_mm10_H11


title: SS2_15_0160_star_mm10_G8


title: SS2_15_0160_star_mm10_G9


title: SS2_15_0160_star_mm10_G6


title: D0HCF_E08


title: D0HCF_E07


title: SS2_15_0160_star_mm10_G5


title: S001151.l.rs.lib_re-analyzed

description: re-analysis of GSM2692985


title: SS2_15_0160_star_mm10_G3


title: SS2_15_0160_star_mm10_G2


title: D0HCF_E05


title: SS2_15_0160_star_mm10_G24


title: D0HCF_E06


title: D0HCF_F05


title: S001135.l.rs.lib_re-analyzed

description: re-analysis of GSM2693045


title: SS2_15_0160_star_mm10_G23


title: SS2_15_0160_star_mm10_G22


title: D0HCF_E04


title: SS2_15_0160_star_mm10_G21


title: SS2_15_0160_star_mm10_G1


title: SS2_15_0160_star_mm10_G20


title: S001130.l.rs.lib_re-analyzed

description: re-analysis of GSM2692962


title: S001144.l.rs.lib_re-analyzed

description: re-analysis of GSM2692886


title: S001122.l.rs.lib_re-analyzed

description: re-analysis of GSM2692936


title: D0HCF_E02


title: SS2_15_0160_star_mm10_G17


title: D0HCF_E01


title: S001118.l.rs.lib_re-analyzed

description: re-analysis of GSM2692984


title: SS2_15_0160_star_mm10_G16


title: S001105.l.rs.lib_re-analyzed

description: re-analysis of GSM2692892


title: SS2_15_0160_star_mm10_G18


title: S001146.l.rs.lib_re-analyzed

description: re-analysis of GSM2692937


title: SS2_15_0160_star_mm10_G4


title: D0HCF_D11


title: SS2_15_0160_star_mm10_G15


title: SS2_15_0160_star_mm10_G14


title: S001095.l.rs.lib_re-analyzed

description: re-analysis of GSM2692961


title: D0HCF_D10


title: SS2_15_0160_star_mm10_G13


title: SS2_15_0160_star_mm10_G12


title: S001090.l.rs.lib_re-analyzed

description: re-analysis of GSM2693043


title: S001080.l.rs.lib_re-analyzed

description: re-analysis of GSM2692935


title: SS2_15_0160_star_mm10_G19


title: D0HCF_E03


title: SS2_15_0160_star_mm10_G10


title: SS2_15_0160_star_mm10_F7


title: SS2_15_0160_star_mm10_F8


title: D0HCF_D07


title: D0HCF_D08


title: S001056.l.rs.lib_re-analyzed

description: re-analysis of GSM2692934


title: S001054.l.rs.lib_re-analyzed

description: re-analysis of GSM2693023


title: D0HCF_D06


title: S001051.l.rs.lib_re-analyzed

description: re-analysis of GSM2692933


title: SS2_15_0160_star_mm10_F6


title: SS2_15_0160_star_mm10_F5


title: S002480.l.rs.lib_re-analyzed

description: re-analysis of GSM2693053


title: SS2_15_0160_star_mm10_F4


title: D0HCF_D05


title: SS2_15_0160_star_mm10_F2


title: D0HCF_D09


title: SS2_15_0160_star_mm10_F24


title: SS2_15_0160_star_mm10_F3


title: D0HCF_D04


title: S001032.l.rs.lib_re-analyzed

description: re-analysis of GSM2692930


title: S001040.l.rs.lib_re-analyzed

description: re-analysis of GSM2693044


title: SS2_15_0160_star_mm10_G11


title: SS2_15_0160_star_mm10_F21


title: SS2_15_0160_star_mm10_F23


title: SS2_15_0160_star_mm10_F9


title: SS2_15_0160_star_mm10_F22


title: D0HCF_D02


title: S001031.l.rs.lib_re-analyzed

description: re-analysis of GSM2692932


title: SS2_15_0160_star_mm10_F19


title: S001385.l.rs.lib_re-analyzed

description: re-analysis of GSM2692988


title: SS2_15_0160_star_mm10_F1


title: SS2_15_0160_star_mm10_F18


title: SS2_15_0160_star_mm10_F17


title: SS2_15_0160_star_mm10_F16


title: S001028.l.rs.lib_re-analyzed

description: re-analysis of GSM2692889


title: S001045.l.rs.lib_re-analyzed

description: re-analysis of GSM2692931


title: S000980.l.rs.lib_re-analyzed

description: re-analysis of GSM2693042


title: D0HCF_C10


title: SS2_15_0160_star_mm10_F15


title: D0HCF_D01


title: S000969.l.rs.lib_re-analyzed

description: re-analysis of GSM2692980


title: SS2_15_0160_star_mm10_F14


title: D0HCF_D03


title: D0HCF_C08


title: SS2_15_0160_star_mm10_F12


title: SS2_15_0160_star_mm10_F13


title: SS2_15_0160_star_mm10_F11


title: SS2_15_0160_star_mm10_E9


title: D0HCF_C09


title: SS2_15_0160_star_mm10_F10


title: SS2_15_0160_star_mm10_E8


title: SS2_15_0160_star_mm10_F20


title: S000950.l.rs.lib_re-analyzed

description: re-analysis of GSM2692960


title: S000965.l.rs.lib_re-analyzed

description: re-analysis of GSM2692929


title: S000948.l.rs.lib_re-analyzed

description: re-analysis of GSM2692928


title: D0HCF_C07


title: S000928.l.rs.lib_re-analyzed

description: re-analysis of GSM2693022


title: D0HCF_C06


title: SS2_15_0160_star_mm10_E5


title: D0HCF_C11


title: SS2_15_0160_star_mm10_E7


title: D0HCF_C05


title: S000927.l.rs.lib_re-analyzed2

description: re-analysis of GSM2692982


title: S000927.l.rs.lib_re-analyzed

description: re-analysis of GSM2692981


title: SS2_15_0160_star_mm10_E2


title: D0HCF_C04


title: SS2_15_0160_star_mm10_E3


title: SS2_15_0160_star_mm10_E4


title: SS2_15_0160_star_mm10_E24


title: SS2_15_0160_star_mm10_E23


title: SS2_15_0160_star_mm10_E21


title: SS2_15_0160_star_mm10_E22


title: S000901.l.rs.lib_re-analyzed

description: re-analysis of GSM2692926


title: D0HCF_B11


title: D0HCF_C01


title: SS2_15_0160_star_mm10_E20


title: D0HCF_C02


title: SS2_15_0160_star_mm10_E6


title: SS2_15_0160_star_mm10_E1


title: SS2_15_0160_star_mm10_E19


title: S000893.l.rs.lib_re-analyzed

description: re-analysis of GSM2692979


title: SS2_15_0160_star_mm10_E17


title: SS2_15_0160_star_mm10_E16


title: D0HCF_B09


title: S000869.l.rs.lib_re-analyzed

description: re-analysis of GSM2692925


title: SS2_15_0160_star_mm10_E18


title: S000861.l.rs.lib_re-analyzed

description: re-analysis of GSM2692978


title: SS2_15_0160_star_mm10_E15


title: SS2_15_0160_star_mm10_E14


title: S000925.l.rs.lib_re-analyzed

description: re-analysis of GSM2692927


title: D0HCF_B08


title: SS2_15_0160_star_mm10_E12


title: D0HCF_C03


title: D0HCF_B07


title: SS2_15_0160_star_mm10_E11


title: SS2_15_0160_star_mm10_E13


title: S000913.l.rs.lib_re-analyzed

description: re-analysis of GSM2692887


title: S000832.l.rs.lib_re-analyzed

description: re-analysis of GSM2692977


title: SS2_15_0160_star_mm10_E10


title: S000824.l.rs.lib_re-analyzed

description: re-analysis of GSM2693041


title: D0HCF_B10


title: D0HCF_B06


title: SS2_15_0160_star_mm10_D8


title: D0HCF_B05


title: S000802.l.rs.lib_re-analyzed

description: re-analysis of GSM2692976


title: SS2_15_0160_star_mm10_D9


title: S000800.l.rs.lib_re-analyzed

description: re-analysis of GSM2692888


title: SS2_15_0160_star_mm10_D7


title: D0HCF_B04


title: S000792.l.rs.lib_re-analyzed

description: re-analysis of GSM2692924

value: NX


title: SS2_15_0160_star_mm10_D5


title: SS2_15_0160_star_mm10_D2


title: SS2_15_0160_star_mm10_D4


title: D0HCF_B03


title: SS2_15_0160_star_mm10_D6


title: SS2_15_0160_star_mm10_D3


title: S000666.l.rs.lib_re-analyzed

description: re-analysis of GSM2692923


title: SS2_15_0160_star_mm10_D24


title: S000695.l.rs.lib_re-analyzed

description: re-analysis of GSM2693012


title: SS2_15_0160_star_mm10_D22


title: D0HCF_B02


title: SS2_15_0160_star_mm10_D21


title: D0HCF_B01


title: D0HCF_A11


title: SS2_15_0160_star_mm10_D20


title: S000651.l.rs.lib_re-analyzed

description: re-analysis of GSM2692921


title: S000658.l.rs.lib_re-analyzed

description: re-analysis of GSM2692922


title: SS2_15_0160_star_mm10_D1


title: D0HCF_A10


title: SS2_15_0160_star_mm10_D19


title: S000642.l.rs.lib_re-analyzed

description: re-analysis of GSM2693040


title: SS2_15_0160_star_mm10_D18


title: D0HCF_A09


title: SS2_15_0160_star_mm10_D17


title: SS2_15_0160_star_mm10_D16


title: S000633.l.rs.lib_re-analyzed

description: re-analysis of GSM2692959


title: D0HCF_A08


title: SS2_15_0160_star_mm10_D15


title: S000629.l.rs.lib_re-analyzed

description: re-analysis of GSM2692975


title: SS2_15_0160_star_mm10_D23


title: SS2_15_0160_star_mm10_D14


title: SS2_15_0160_star_mm10_D13


title: S000628.l.rs.lib_re-analyzed

description: re-analysis of GSM2692885


title: D0HCF_A06


title: SS2_15_0160_star_mm10_D12


title: S000618.l.rs.lib_re-analyzed

description: re-analysis of GSM2692883


title: SS2_15_0160_star_mm10_D10


title: SS2_15_0160_star_mm10_C9


title: SS2_15_0160_star_mm10_D11


title: SS2_15_0160_star_mm10_C8


title: SS2_15_0160_star_mm10_C7


title: D0HCF_A05


title: S000617.l.rs.lib_re-analyzed

description: re-analysis of GSM2692876


title: SS2_15_0160_star_mm10_C6


title: D0HCF_A03


title: S000606.l.rs.lib_re-analyzed

description: re-analysis of GSM2692974


title: D0HCF_A04


title: SS2_15_0160_star_mm10_C5


title: S000602.l.rs.lib_re-analyzed

description: re-analysis of GSM2692884


title: D0HCF_A02


title: SS2_15_0160_star_mm10_C3


title: S000590.l.rs.lib_re-analyzed

description: re-analysis of GSM2692973


title: D0HCF_A01


title: SS2_15_0160_star_mm10_C2


title: S000573.l.rs.lib_re-analyzed

description: re-analysis of GSM2692920


title: D0HCF_A07


title: SS2_15_0160_star_mm10_C23


title: SS2_15_0160_star_mm10_C22


title: SS2_15_0160_star_mm10_C21


title: FGF1 variant rep1

city: Wenzhou

first: Dezhong

address: Chashan town

department: ILS

institute: Wenzhou Univsersity

description:
T1_1
Cells were a gift from Dr. Stuart Shankland (University of Washington).
processed data file: 4_genes_fpkm_expression.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps: Prior to assembly, the low quality reads (1, reads containing sequencing adaptors; 2, reads containing sequencing primer; 3, nucleotide with q quality score lower than 20) were removed. Software CutAdapter, parameters -o 5 -p 100
Read alignment software, software HISAT, version 2.0, parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Perform expression level for mRNAs by calculating FPKM. Estimate the expression levels of all transcripts. Software StringTie, version 1.3.0, parameters -b dta -q phred33-quals
Genome_build: mm8 (MGSCv36)
Supplementary_files_format_and_content: 4_genes_fpkm_expression.txt Tab-delimited text file includes FPKM values for each Sample.

source_name: mouse podocytes cells

growth_protocol: The cells were grown in collagen I (BD Biosciences) pre-coated plates with RPMI-1640 (5.5 mM D-glucose, Gibco) medium containing 10% FBS (Gibco) and interferon gamma (50 U/mL, Sigma) at 33 ℃. Cell differentiation was induced by incubation without interferon gamma for 10 days at 37 ℃.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific renal type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were starved for 12 hrs in serum-free RPMI-1640 medium and pretreated with serum-free medium containing rFGF1△HBS (100 ng/ml) or rFGF1WT (100 ng/ml) for 1 hr. For HG treatment, cells were not pretreated. Then, the cells were incubated in high glucose (HG) (25 mM) (with D-mannitol as an osmotic control) for 12 hrs.

value: Murine Podocyte Cell Line

tag: passages

tag: pre-treatment

value: FGF1 <delta>HBS

value: High glucose


title: S000561.l.rs.lib_re-analyzed

description: re-analysis of GSM2692958

value: Primary breast tumour


title: SS2_15_0160_star_mm10_C1


title: SS2_15_0160_star_mm10_C20


title: SS2_15_0160_star_mm10_C18


title: SS2_15_0160_star_mm10_C17


title: S000559.l.rs.lib_re-analyzed

description: re-analysis of GSM2692918


title: S000553.l.rs.lib_re-analyzed2

description: re-analysis of GSM2692875


title: SS2_15_0160_star_mm10_C19


title: SS2_15_0160_star_mm10_C4


title: FGF1 WT rep1

description:
T2_1
Cells were a gift from Dr. Stuart Shankland (University of Washington).
processed data file: 4_genes_fpkm_expression.txt

value: FGF1 WT


title: FGF1 variant rep2

description:
T1_2
Cells were a gift from Dr. Stuart Shankland (University of Washington).
processed data file: 4_genes_fpkm_expression.txt


title: FGF1 WT rep2

description:
T2_2
Cells were a gift from Dr. Stuart Shankland (University of Washington).
processed data file: 4_genes_fpkm_expression.txt


title: SS2_15_0160_star_mm10_C15


title: Model rep2

description:
HG2
Cells were a gift from Dr. Stuart Shankland (University of Washington).
processed data file: 4_genes_fpkm_expression.txt


title: Model rep1

description:
HG1
Cells were a gift from Dr. Stuart Shankland (University of Washington).
processed data file: 4_genes_fpkm_expression.txt


title: SS2_15_0160_star_mm10_C24


title: SS2_15_0160_star_mm10_C14


title: SS2_15_0160_star_mm10_C11


title: S000553.l.rs.lib_re-analyzed

description: re-analysis of GSM2692874

value: ERneg


title: SS2_15_0160_star_mm10_C12


title: SS2_15_0160_star_mm10_C13


title: S000572.l.rs.lib_re-analyzed

description: re-analysis of GSM2692919


title: S000544.l.rs.lib_re-analyzed

description: re-analysis of GSM2693020


title: S000525.l.rs.lib_re-analyzed

description: re-analysis of GSM2692882


title: SS2_15_0160_star_mm10_B8


title: SS2_15_0160_star_mm10_B9


title: CFIm68KD DRB Input

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

data_processing:
Adapters were trimmed with Cutadapt v. 1.9.1 with the following parameters: --minimum-length 10 -e 0.05 --times 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -q 15,10
Alignment was done with Bowtie2 v. 2.2.5 to hg19.
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v. 1.3.1
Mapped reads were de-duplicated with Picard
BigWig files were generated with deepTools2 v.2.2.4 with bamCoverage tool and the following parameters: -bs 10 --normalizeUsingRPKM -e -p max
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: CFIm68KD DRB

growth_protocol: 293 cells were maintained in DMEM with 10% fetal bovine serum and antibiotics.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using Illumina's TruSeq ChIP library Preparation Kit according to Illumina's instructions.

value: 293 Flp-In

value: DRB


title: 293 Flp-In DRB Pol II

source_name: 293 Flp-In DRB

value: Pol II (N-20) X Antibody (Santa Cruz Biotechnology; sc-899X)


title: CFIm68KD DRB Pol II


title: SS2_15_0160_star_mm10_B7


title: SS2_15_0160_star_mm10_B6


title: S000416.l.rs.lib_re-analyzed

description: re-analysis of GSM2693038

value: LumA

value: Low


title: S000520.l.rs.lib_re-analyzed

description: re-analysis of GSM2692972

value: ERpos

value: PRpos

value: High


title: SS2_15_0160_star_mm10_C16

value: HDM


title: S000524.l.rs.lib_re-analyzed

description: re-analysis of GSM2693021


title: 293 Flp-In DRB Input


title: SS2_15_0160_star_mm10_B4

value: BAL


title: SS2_15_0160_star_mm10_B24


title: SS2_15_0160_star_mm10_C10


title: SS2_15_0160_star_mm10_B3


title: SS2_15_0160_star_mm10_B2