title: P6-Id4GFP-Seq5_C91

description:
single-cell
P6-Id4GFP-C1_GEmatrix

source_name: Post-natal day 6 testis

extract_protocol:
Testes from 6-day postpartum (P6) mice were used to generate suspensions of cells following enzymatic digestion as described previously (Ogawa et al., 1997; Nagano et al., 2003; Oatley and Brinster, 2006). Briefly, testicular parenchyma from at least two pups were pooled and digested with 0.25% trypsin/EDTA (ThermoFisher Scientific) for ~6-8 minutes at 37oC, quenched with 10% FBS (v/v, Sigma). Testis cell suspensions were used for FACS to enrich spermatogonia essentially as described (Hermann et al., 2015). Briefly, cells were suspended (5-20 x 106 cells/ml) in ice-cold Dulbecco’s phosphate-buffered saline (DPBS) containing 10% FBS (DPBS+S), and subjected to FACS using  a FACS Aria (BD). ID4-EGFP+ spermatogonia from P6 mice were used for single-cell RNA-seq facilitated by the Fluidigm C1 instrument essentially as described (Hermann et al., 2015; Wu et al., 2014). Briefly, single cells were captured on 10-17µm integrated fluidic circuit chips using the C1 Single-Cell Autoprep System (Fluidigm), stained with ethidium homodimer, and imaged on an AxioImager M1 (Zeiss), and used to prepare cDNA with SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (v2 chemistry; Takara). Dead cells (ethidium+), multiplets and cells contaminated with debris were excluded from further analysis. Mouse ID4-EGFP+ spermatogonia were stratified based on the EGFP epifluorescence intensity using the interactive measurement module of AxioVision 4.8.2 (Zeiss) and images taken of each cell. The densitometric mean value of the EGFP channel for each cell was normalized on a scale from 0 to 1 (1 representing the brightest EGFP+ cell) and cells were ranked. ID4-EGFPbright and ID4-EGFPdim spermatogonia were defined as the upper (Q1) or lower (Q2) quartiles (25%) of ranked EGFP+ cells, respectively.
Amplified cDNA was quantified with PicoGreen fluorometry (ThermoFisher Scientific) on a Synergy II (Biotek) based on manufacturer recommendations and normalized cDNA mass from each cell was used for Nextera XT dual-index library preparation (Illumina) with modifications from manufacturer recommendations essentially as described (Mutoji et al., 2016). Single-cell libraries were pooled, qualified for fragment size and distribution on a 2100 Bioanalyzer (Agilent) and quantified.


title: P6-Id4GFP-Seq5_C95

status: Public on Nov 06 2018

type: SRA

city: San Antonio

first: Brian

middle: P.

last: Hermann

state: TX

address: 1 UTSA Circle

department: Department of Biology

country: USA

institute: University of Texas at San Antonio

description:
single-cell
P6-Id4GFP-C1_GEmatrix

library_source: transcriptomic

data_processing:
Illumina base-calling (PE100) and demultiplexing with BCL-2-Fastq
Paired FASTQ files from each sample trimmed and the quality confirmed using FASTQC
Aligned to the mouse genome (mm10)  with TopHat (Galaxy v0.9)
Transcript abundance (FPKM) determined with Cufflinks (Galaxy v.2.2.1.0)
Quality control with the Picard tool Collectrnaseqmetrics was used to eliminate poorly performing cell samples
Genome_build: Mouse reference genome NCBI build 38, GRCm38 (mm10)
Supplementary_files_format_and_content: A single matrix file CSV containing columns of FPKM values for each cell. Rows are FPKM values for each gene in the reference annotation. First column is gene ID, first row is sample name.

molecule: polyA RNA

organism: Mus musculus

growth_protocol: Normal mouse husbandry with ad libitum food and water.

treatment_protocol: Animal were untreated.

tag: egfp epifluorescence quartile

tag: cell type

value: Spermatogonium


title: P6-Id4GFP-Seq5_C94

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C92

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C82

data_processing:
Illumina base-calling (PE100) and demultiplexing with BCL-2-Fastq
Paired FASTQ files from each sample trimmed and the quality confirmed using FASTQC
Aligned to the human genome (hg19)  with TopHat (Galaxy v0.9)
Transcript abundance (FPKM) determined with Cufflinks (Galaxy v.2.2.1.0)
Quality control with the Picard tool Collectrnaseqmetrics was used to eliminate poorly performing cell samples
Genome_build: Human reference genome NCBI build 37, GRCh37 (hg19)
Supplementary_files_format_and_content: A single matrix file CSV containing columns of FPKM values for each cell. Rows are FPKM values for each gene in the reference annotation. First column is gene ID, first row is sample name.

organism: Homo sapiens

source_name: Adult testis

extract_protocol:
Suspensions of human seminiferous tubule cells were prepared from adult testicular tissue parenchyma by a two-step enzymatic digestion was as described previously (Hermann et al., 2007b; Hermann et al., 2009; Dovey et al., 2013). Briefly, testis tissue was digested with 2mg/ml collagenase type IV at 37oC with vigorous agitation, washed with HBSS to remove interstitial cells, followed by digestion with 0.25% trypsin/EDTA containing 1.4mg/ml DNase I for 15 minutes at 37oC with trituration every 5 minutes, and quenched with 10% FBS. In all cases, cell suspensions were strained (40um pore size for mouse, 70um pore size for humans) and suspended in MEMα containing 10% FBS. Testis cell suspensions were used for FACS to enrich spermatogonia essentially as described (Hermann et al., 2015). Briefly, cells were suspended (5-20 x 106 cells/ml) in ice-cold Dulbecco’s phosphate-buffered saline (DPBS) containing 10% FBS (DPBS+S), labeled with antibodies (see Key Resources Table), and subjected to FACS using  a FACS Aria (BD). Positive antibody labeling was determined by comparison to staining with isotype control antibodies. Human spermatogonia were isolated by sorting cells with the phenotype HLA-ABCnegative / CD49enegative / THY1dim / ITGA6+ / EpCAMdim dim (see Fig. 2C). These markers were chosen because previous results indicate they specifically label undifferentiated spermatogonia, including some with colonization potential based on xenotransplantation (Dovey et al., 2013; Altman et al., 2014; Smith et al., 2014; Valli et al., 2014). Human spermatogonia were used for single-cell RNA-seq facilitated by the Fluidigm C1 instrument essentially as described (Hermann et al., 2015; Wu et al., 2014). Briefly, single cells were captured on 10-17µm integrated fluidic circuit chips using the C1 Single-Cell Autoprep System (Fluidigm), stained with ethidium homodimer, and imaged on an AxioImager M1 (Zeiss), and used to prepare cDNA with SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (v2 chemistry; Takara). Dead cells (ethidium+), multiplets and cells contaminated with debris were excluded from further analysis. Human spermatogonia were stratified post-hoc based on the levels of D4 mRNA to match EGFP epifluorescence intensity stratification used for cognate moues cells. ID4 mRNA levels were normalized on a scale from 0 to 1 (1 representing the greatest amount of ID4mRNA) and cells were ranked. ID4-high and ID4-low spermatogonia were defined as the upper (Q1) or lower (Q2) quartiles (25%) of ranked cells, respectively.
Amplified cDNA was quantified with PicoGreen fluorometry (ThermoFisher Scientific) on a Synergy II (Biotek) based on manufacturer recommendations and normalized cDNA mass from each cell was used for Nextera XT dual-index library preparation (Illumina) with modifications from manufacturer recommendations essentially as described (Mutoji et al., 2016). Single-cell libraries were pooled, qualified for fragment size and distribution on a 2100 Bioanalyzer (Agilent) and quantified.

treatment_protocol: De-identified, surgical excess normal adult human testicular tissue was obtained through the Infertility Center of St. Louis from patients undergoing a diagnostic testicular biopsy (n=28) in preparation for microscopic vasectomy reversal (MVR) or testicular sperm extraction (TESE) for obstructive azoospermia with the informed consent of patients (see Supplemental Table 2). Testicular tissue was also recovered from male organ donors (n=2) through the Texas Organ Sharing Alliance and the University of Texas Transplant Center with informed consent of the next of kin. The University of Texas at San Antonio IRB determined that research on these tissues did not constitute human subjects research (IRB #12-098N and #17-074N). The age of the individuals was recorded (median = 42yr, mean = 41.6 ± 1.3yr), and while organ donors tended to be younger (34.3 ± 7.2yr) than biopsy patients (42.4 ± 1.2yr), the difference was not significant (p=0.32). Procured tissue was transported to the laboratory on ice in either Lactated Ringer’s solution or minimal essential medium alpha (MEMα) containing 10% fetal bovine serum. The amount of time tissues were exposed to cold ischemia prior to processing was recorded (median = 18.7hr; mean = 24.7 ± 3.8 hr).

tag: id4 mrna quartile


title: HumanSpg-Seq3_C81


title: Ad-Id4GFP-Seq1_C08

extract_protocol:
Single-cell suspensions of seminiferous tubules were generated from adult mouse testes using a two-step enzymatic digestion approach. Briefly, testicular parenchyma from 2 or more adult mice were digested with 1mg/ml Collagenase Type IV (Worthington Biochemicals) for 2-3 minutes at 37oC, washed with Hank’s Buffered Salt Solution (HBSS) to remove interstitial cells, digested with 0.25% trypsin/EDTA containing 1.4mg/ml DNase I (Sigma) for 7-9 minutes at 37oC, and quenched with 10% FBS. Testis cell suspensions were used for FACS to enrich spermatogonia essentially as described (Hermann et al., 2015). Briefly, cells were suspended (5-20 x 10^6 cells/ml) in ice-cold Dulbecco’s phosphate-buffered saline (DPBS) containing 10% FBS (DPBS+S). Cells were pre-enriched for spermatogonia by density centrifugation in DPBS+S over a 30% Percoll cushion (Sigma) for 8 minutes at 600xg without braking. Pelleted cells were subjected to FACS and spermatogonia isolated based on gating CD9-bright and ID4-EGFP double-positive cells using  a FACS Aria (BD). CD9bright/ID4-EGFP+ spermatogonia adult mice were used for single-cell RNA-seq facilitated by the Fluidigm C1 instrument essentially as described (Hermann et al., 2015; Wu et al., 2014). Briefly, single cells were captured on 10-17µm integrated fluidic circuit chips using the C1 Single-Cell Autoprep System (Fluidigm), stained with ethidium homodimer, and imaged on an AxioImager M1 (Zeiss), and used to prepare cDNA with SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (v2 chemistry; Takara). Dead cells (ethidium+), multiplets and cells contaminated with debris were excluded from further analysis. Mouse ID4-EGFP+ spermatogonia were stratified based on the EGFP epifluorescence intensity using the interactive measurement module of AxioVision 4.8.2 (Zeiss) and images taken of each cell. The densitometric mean value of the EGFP channel for each cell was normalized on a scale from 0 to 1 (1 representing the brightest EGFP+ cell) and cells were ranked. ID4-EGFPbright and ID4-EGFPdim spermatogonia were defined as the upper (Q1) or lower (Q2) quartiles (25%) of ranked EGFP+ cells, respectively.
Amplified cDNA was quantified with PicoGreen fluorometry (ThermoFisher Scientific) on a Synergy II (Biotek) based on manufacturer recommendations and normalized cDNA mass from each cell was used for Nextera XT dual-index library preparation (Illumina) with modifications from manufacturer recommendations essentially as described (Mutoji et al., 2016). Single-cell libraries were pooled, qualified for fragment size and distribution on a 2100 Bioanalyzer (Agilent) and quantified.


title: HumanSpg-Seq3_C88


title: HumanSpg-Seq3_C86


title: P6-Id4GFP-Seq5_C89

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C80


title: HumanSpg-Seq3_C78


title: HumanSpg-Seq3_C90


title: P6-Id4GFP-Seq5_C84

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C85

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C83

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C86

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C77


title: P6-Id4GFP-Seq5_C81

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C76


title: P6-Id4GFP-Seq5_C79

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C93

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C96

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C75


title: HumanSpg-Seq3_C73


title: P6-Id4GFP-Seq5_C88

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C78

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C76

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C74


title: HumanSpg-Seq3_C71


title: P6-Id4GFP-Seq5_C75

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C72


title: P6-Id4GFP-Seq5_C77

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C69


title: HumanSpg-Seq3_C79


title: P6-Id4GFP-Seq5_C74

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C70


title: P6-Id4GFP-Seq5_C73

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C72

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C68


title: P6-Id4GFP-Seq5_C70

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C66


title: HumanSpg-Seq3_C67


title: P6-Id4GFP-Seq5_C71

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C65


title: P6-Id4GFP-Seq5_C68

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C64


title: P6-Id4GFP-Seq5_C69

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C63


title: P6-Id4GFP-Seq5_C67

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C66

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C62


title: P6-Id4GFP-Seq5_C65

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C64

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C61


title: HumanSpg-Seq3_C59


title: HumanSpg-Seq3_C60


title: P6-Id4GFP-Seq5_C63

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C61

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C58


title: P6-Id4GFP-Seq5_C62

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C56


title: P6-Id4GFP-Seq5_C59

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C60

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C54


title: P6-Id4GFP-Seq5_C57

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C53


title: HumanSpg-Seq3_C52


title: P6-Id4GFP-Seq5_C55

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C51


title: P6-Id4GFP-Seq5_C54

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C50


title: P6-Id4GFP-Seq5_C56

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C55


title: P6-Id4GFP-Seq5_C52

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C46


title: P6-Id4GFP-Seq5_C87

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C51

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C50

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C57


title: HumanSpg-Seq3_C40


title: HumanSpg-Seq3_C39


title: P6-Id4GFP-Seq5_C49

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C42


title: P6-Id4GFP-Seq5_C40

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C39

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C36

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C38


title: P6-Id4GFP-Seq5_C35

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C36


title: HumanSpg-Seq3_C37


title: HumanSpg-Seq3_C35


title: P6-Id4GFP-Seq5_C58

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C34


title: HumanSpg-Seq3_C49


title: P6-Id4GFP-Seq5_C53

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C33


title: P6-Id4GFP-Seq5_C31

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C32

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C31


title: P6-Id4GFP-Seq5_C33

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C30


title: P6-Id4GFP-Seq5_C29

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C28

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C29


title: P6-Id4GFP-Seq5_C27

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C28


title: P6-Id4GFP-Seq5_C26

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C25

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C27


title: HumanSpg-Seq3_C26


title: P6-Id4GFP-Seq5_C24

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C25


title: P6-Id4GFP-Seq5_C23

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C24


title: P6-Id4GFP-Seq5_C34

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C32


title: HumanSpg-Seq3_C23


title: P6-Id4GFP-Seq5_C21

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C20

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C19


title: HumanSpg-Seq3_C21


title: P6-Id4GFP-Seq5_C19

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C18


title: P6-Id4GFP-Seq5_C16

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C17


title: P6-Id4GFP-Seq5_C14

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C13

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C22


title: HumanSpg-Seq3_C16


title: HumanSpg-Seq3_C20


title: P6-Id4GFP-Seq5_C22

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C12

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C11

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C14


title: P6-Id4GFP-Seq5_C09

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C08

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C07

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C11


title: HumanSpg-Seq3_C12


title: P6-Id4GFP-Seq5_C06

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C09


title: P6-Id4GFP-Seq5_C05

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq5_C04

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C08


title: HumanSpg-Seq3_C05


title: HumanSpg-Seq3_C03


title: HumanSpg-Seq3_C06


title: P6-Id4GFP-Seq5_C02

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C02


title: HumanSpg-Seq3_C01


title: P6-Id4GFP-Seq4_C91

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C90

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C91


title: HumanSpg-Seq2_C93


title: P6-Id4GFP-Seq4_C88

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C89


title: HumanSpg-Seq2_C95


title: HumanSpg-Seq2_C88


title: P6-Id4GFP-Seq4_C86

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C87

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C87


title: P6-Id4GFP-Seq4_C93

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C86


title: HumanSpg-Seq3_C13


title: HumanSpg-Seq2_C85


title: P6-Id4GFP-Seq4_C85

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C84


title: P6-Id4GFP-Seq5_C03

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C96

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C82

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C80

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C83


title: P6-Id4GFP-Seq4_C79

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C83

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C82


title: P6-Id4GFP-Seq4_C78

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C81


title: P6-Id4GFP-Seq4_C92

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C77

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C74

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C73

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C79


title: HumanSpg-Seq2_C77


title: P6-Id4GFP-Seq4_C72

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C76


title: P6-Id4GFP-Seq4_C70

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C75


title: HumanSpg-Seq2_C74


title: P6-Id4GFP-Seq4_C69

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C73


title: P6-Id4GFP-Seq4_C67

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C66

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C65

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C71


title: HumanSpg-Seq2_C69


title: P6-Id4GFP-Seq4_C64

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C63

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C66


title: P6-Id4GFP-Seq4_C62

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C65


title: HumanSpg-Seq2_C80


title: HumanSpg-Seq2_C64


title: P6-Id4GFP-Seq4_C61

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C60

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C63


title: P6-Id4GFP-Seq4_C59

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C58

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C60


title: HumanSpg-Seq2_C62


title: P6-Id4GFP-Seq4_C53

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C52

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C55


title: P6-Id4GFP-Seq4_C68

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C58


title: P6-Id4GFP-Seq4_C56

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C53


title: HumanSpg-Seq2_C72


title: HumanSpg-Seq2_C50


title: P6-Id4GFP-Seq4_C50

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C67


title: P6-Id4GFP-Seq4_C51

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C49


title: HumanSpg-Seq2_C46


title: P6-Id4GFP-Seq4_C46

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C45


title: P6-Id4GFP-Seq4_C41

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C43


title: P6-Id4GFP-Seq5_C18

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C44


title: P6-Id4GFP-Seq4_C43

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C45

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C40

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C41


title: P6-Id4GFP-Seq4_C39

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C39


title: HumanSpg-Seq2_C38


title: P6-Id4GFP-Seq4_C38

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C36

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C35

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C37


title: P6-Id4GFP-Seq4_C49

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C34


title: HumanSpg-Seq2_C35


title: P6-Id4GFP-Seq4_C34

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C47


title: HumanSpg-Seq2_C33


title: P6-Id4GFP-Seq4_C47

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C31

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C33

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C32


title: P6-Id4GFP-Seq4_C29

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C27


title: HumanSpg-Seq2_C30


title: HumanSpg-Seq2_C28


title: HumanSpg-Seq2_C26


title: P6-Id4GFP-Seq4_C25

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C42


title: P6-Id4GFP-Seq4_C26

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C28

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C24


title: P6-Id4GFP-Seq4_C23

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C23


title: P6-Id4GFP-Seq4_C24

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C25


title: P6-Id4GFP-Seq4_C20

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C15

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C16

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C17

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C18


title: P6-Id4GFP-Seq4_C14

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C21


title: HumanSpg-Seq2_C16


title: HumanSpg-Seq2_C13


title: HumanSpg-Seq2_C14


title: P6-Id4GFP-Seq4_C13

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C12

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C17


title: P6-Id4GFP-Seq4_C11

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C10


title: HumanSpg-Seq2_C11


title: HumanSpg-Seq2_C09


title: P6-Id4GFP-Seq4_C08

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C12


title: HumanSpg-Seq2_C07


title: P6-Id4GFP-Seq4_C19

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C18

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq2_C06


title: HumanSpg-Seq2_C05


title: HumanSpg-Seq2_C19


title: P6-Id4GFP-Seq4_C05

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C04

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C96


title: P6-Id4GFP-Seq4_C02

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C01

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq3_C73

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C09

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C95


title: HumanSpg-Seq2_C04


title: HumanSpg-Seq2_C01


title: P6-Id4GFP-Seq3_C70

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C93


title: HumanSpg-Seq10_C92


title: P6-Id4GFP-Seq4_C06

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C03

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq3_C71

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq4_C07

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq3_C69

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq3_C15


title: HumanSpg-Seq10_C87


title: P6-Id4GFP-Seq3_C67

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C84


title: P6-Id4GFP-Seq3_C65

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C86


title: HumanSpg-Seq10_C91


title: P6-Id4GFP-Seq3_C62

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq3_C60

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C82


title: P6-Id4GFP-Seq3_C55

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C79


title: P6-Id4GFP-Seq3_C54

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq3_C58

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C80


title: P6-Id4GFP-Seq3_C57

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C90


title: P6-Id4GFP-Seq3_C68

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C73


title: HumanSpg-Seq10_C72


title: HumanSpg-Seq10_C77


title: HumanSpg-Seq10_C71


title: P6-Id4GFP-Seq3_C51

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq3_C52

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq3_C26

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C69


title: HumanSpg-Seq10_C68


title: HumanSpg-Seq10_C70


title: P6-Id4GFP-Seq3_C24

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C75


title: P6-Id4GFP-Seq3_C53

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq3_C25

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq3_C64

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq3_C23

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C83


title: P6-Id4GFP-Seq3_C49

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C67


title: P6-Id4GFP-Seq3_C22

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C66


title: HumanSpg-Seq10_C74


title: P6-Id4GFP-Seq3_C20

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C65


title: P6-Id4GFP-Seq3_C17

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq3_C19

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq3_C18

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C64


title: P6-Id4GFP-Seq3_C16

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C61


title: HumanSpg-Seq10_C62


title: HumanSpg-Seq10_C81


title: HumanSpg-Seq10_C63


title: P6-Id4GFP-Seq3_C10

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C58


title: HumanSpg-Seq10_C56


title: P6-Id4GFP-Seq3_C07

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq3_C09

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq3_C13

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C60


title: P6-Id4GFP-Seq3_C04

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq3_C03

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C54


title: HumanSpg-Seq10_C57


title: P6-Id4GFP-Seq3_C02

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C53


title: P6-Id4GFP-Seq3_C12

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq3_C01

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C55


title: HumanSpg-Seq10_C51


title: HumanSpg-Seq10_C50


title: P6-Id4GFP-Seq2_C94

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C95

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C88

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C39


title: P6-Id4GFP-Seq2_C93

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C87

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C38


title: HumanSpg-Seq10_C40


title: P6-Id4GFP-Seq2_C85

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C49


title: HumanSpg-Seq10_C36


title: HumanSpg-Seq10_C52


title: P6-Id4GFP-Seq2_C79

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C83

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C35


title: P6-Id4GFP-Seq2_C77

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C34


title: HumanSpg-Seq10_C37


title: P6-Id4GFP-Seq2_C75

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C30


title: HumanSpg-Seq10_C33


title: P6-Id4GFP-Seq2_C74

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C31


title: P6-Id4GFP-Seq2_C78

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C28


title: HumanSpg-Seq10_C27


title: P6-Id4GFP-Seq2_C73

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C72

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C26


title: HumanSpg-Seq10_C25


title: HumanSpg-Seq10_C23


title: P6-Id4GFP-Seq2_C69

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C21


title: P6-Id4GFP-Seq2_C68

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C18


title: P6-Id4GFP-Seq2_C76

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C67

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C24


title: HumanSpg-Seq10_C19


title: P6-Id4GFP-Seq2_C65

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C71

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C16


title: P6-Id4GFP-Seq2_C66

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C14


title: P6-Id4GFP-Seq2_C82

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C63

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C62

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C17


title: HumanSpg-Seq10_C15


title: P6-Id4GFP-Seq2_C60

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C61

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C13


title: HumanSpg-Seq10_C12


title: P6-Id4GFP-Seq2_C59

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C10


title: P6-Id4GFP-Seq2_C58

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C70

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C09


title: P6-Id4GFP-Seq2_C57

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C56

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C64

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq10_C08


title: HumanSpg-Seq10_C07


title: HumanSpg-Seq10_C05


title: HumanSpg-Seq10_C04


title: HumanSpg-Seq10_C03


title: HumanSpg-Seq10_C11


title: HumanSpg-Seq10_C06


title: HumanSpg-Seq10_C01


title: HumanSpg-Seq10_C02


title: P6-Id4GFP-Seq2_C55

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C53

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C46

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C44

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C54

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C43

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C49

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C39

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C38

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C37

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C90


title: HumanSpg-Seq1_C91


title: HumanSpg-Seq1_C81


title: HumanSpg-Seq1_C83


title: HumanSpg-Seq1_C80


title: P6-Id4GFP-Seq2_C33

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C29

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C77


title: P6-Id4GFP-Seq2_C28

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C27

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C70


title: P6-Id4GFP-Seq2_C24

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C20

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C67


title: P6-Id4GFP-Seq2_C18

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C66


title: P6-Id4GFP-Seq2_C19

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C16

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C63


title: P6-Id4GFP-Seq2_C14

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C62


title: HumanSpg-Seq1_C58


title: P6-Id4GFP-Seq2_C12

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C13

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C11

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C61


title: HumanSpg-Seq1_C53


title: P6-Id4GFP-Seq2_C10

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C54


title: P6-Id4GFP-Seq2_C07

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C08

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C52


title: P6-Id4GFP-Seq2_C05

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C74


title: HumanSpg-Seq1_C51


title: HumanSpg-Seq1_C73


title: HumanSpg-Seq1_C50


title: P6-Id4GFP-Seq2_C04

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C46


title: P6-Id4GFP-Seq2_C01

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C44


title: HumanSpg-Seq1_C42


title: HumanSpg-Seq1_C55


title: P6-Id4GFP-Seq1_C63

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq2_C02

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq1_C61

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq1_C60

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C64


title: P6-Id4GFP-Seq1_C55

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C37


title: HumanSpg-Seq1_C40


title: HumanSpg-Seq1_C34


title: HumanSpg-Seq1_C32


title: P6-Id4GFP-Seq1_C53

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C35


title: P6-Id4GFP-Seq1_C54

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C31


title: HumanSpg-Seq1_C30


title: P6-Id4GFP-Seq1_C20

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq1_C49

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C28


title: HumanSpg-Seq1_C27


title: P6-Id4GFP-Seq1_C19

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq1_C17

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C25


title: P6-Id4GFP-Seq1_C15

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq1_C14

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C23


title: HumanSpg-Seq1_C39


title: HumanSpg-Seq1_C22


title: P6-Id4GFP-Seq1_C13

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq1_C52

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq1_C12

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4-EGFP-bright

description: single-cell

data_processing:
Illumina base-calling and demultiplexing with BCL-2-Fastq. Trimmed FASTQ files (26bp Cell barcode and UMI Read1, 8bp i7 index, and 100bp Read2), were generated using the CellRanger mkfastq command (a 10X Genomics wrapper around BCL2Fastq).
Paired FASTQ files from each sample trimmed and the quality confirmed using FASTQC
Primary data analysis (alignment, filtering, and UMI counting) to determine gene transcript counts per cell (producing a gene-barcode matrix), quality control, clustering and statistical analysis were performed using CellRanger count (10X Genomics) and the mm10 (mouse) genome assembly/annotation references
Outputs from multiple independent samples of single-cells were combined using CellRanger aggr (10X Genomics) based on mapped read counts to normalize sequencing depth and produce aggregated gene-barcode matrices and clustering models.
Genome_build: Mouse reference genome NCBI build 38, GRCm38 (mm10)
Supplementary_files_format_and_content: A single gene x. cell-barcode matrix file (MTX). Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively.

extract_protocol:
Testes from 6-day postpartum (P6) mice were used to generate suspensions of cells following enzymatic digestion as described previously (Ogawa et al., 1997; Nagano et al., 2003; Oatley and Brinster, 2006). Briefly, testicular parenchyma from at least two pups were pooled and digested with 0.25% trypsin/EDTA (ThermoFisher Scientific) for ~6-8 minutes at 37oC, quenched with 10% FBS (v/v, Sigma). Testis cell suspensions were used for FACS to enrich spermatogonia essentially as described (Hermann et al., 2015). Briefly, cells were suspended (5-20 x 106 cells/ml) in ice-cold Dulbecco’s phosphate-buffered saline (DPBS) containing 10% FBS (DPBS+S), and subjected to FACS using  a FACS Aria (BD). ID4-EGFP-bright and ID4-EGFP-dim spermatogonia from P6 mice were sorted and, along with unselected cells, used for single-cell RNA-seq facilitated by the 10X Genomics Chromium Drop-Seq approach. Briefly, Cell suspensions were loaded into Chromium microfluidic chips with 3’ v2 chemistry and used to generate single-cell gelbead emulsions (GEMs) with using the Chromium controller (10X Genomics) per manufacturer recommendations (Zheng et al., 2017). In all cases, suspensions containing ~8700 cells were loaded on the instrument with the expectation of collecting up to 5,000 GEMs containing single cells. For the multiplet test (Fig. S1), equal numbers of mouse and human cells were loaded. GEM-RT was performed in a T100 Thermal cycler (Bio-Rad) and all subsequent steps to generate single-cell libraries were performed according to manufacturer recommendations.
Single-cell 3' libraries were prepared according to manufacturer recommendations (v2 chemistry).

tag: number of cells


title: HumanSpg-Seq1_C21


title: P6-Id4GFP-Seq1_C10

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4-EGFP-unselected

description: single-cell

value: Mixed


title: HumanSpg-Seq1_C20


title: P6-Id4-EGFP-dim

description: single-cell


title: P6-Id4GFP-Seq1_C11

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq1_C21

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C18


title: P6-Id4GFP-Seq1_C08

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C24


title: AdultMouse-Rep3

description: single-cell

extract_protocol:
Single-cell suspensions of seminiferous tubules were generated from adult mouse testes using a two-step enzymatic digestion approach. Briefly, testicular parenchyma from 2 or more adult mice were digested with 1mg/ml Collagenase Type IV (Worthington Biochemicals) for 2-3 minutes at 37oC, washed with Hank’s Buffered Salt Solution (HBSS) to remove interstitial cells, digested with 0.25% trypsin/EDTA containing 1.4mg/ml DNase I (Sigma) for 7-9 minutes at 37oC, and quenched with 10% FBS. Testis cell suspensions were used for FACS to enrich spermatogonia essentially as described (Hermann et al., 2015). Briefly, cells were suspended (5-20 x 10^6 cells/ml) in ice-cold Dulbecco’s phosphate-buffered saline (DPBS) containing 10% FBS (DPBS+S). Cells were pre-enriched for spermatogonia by density centrifugation in DPBS+S over a 30% Percoll cushion (Sigma) for 8 minutes at 600xg without braking. Pelleted cells were subjected to FACS and spermatogonia isolated based on gating CD9-bright and ID4-EGFP double-positive cells using  a FACS Aria (BD). Cells from adult Adult Id4-eGfp+ mouse were also enriched for spermatocytes and spermatids based on sedimentation velocity at unit gravity (Romrell et al., 1976; Bellve et al., 1977). Briefly, testis cells (10^6-10^7) suspended in 2 ml of buffer plus 0.5% BSA were loaded onto a 50 ml gradient of 2-4% BSA (McCarrey et al., 1992) and allowed to sediment for 2.5 hr at 4°C. Approximately one hundred 0.5 ml fractions were then collected in microcentrifuge tubes and analyzed for content of spermatocytes or spermatids on the basis of morphology under phase contrast optics (which typically yields ≥85% purity). Fractions containing spermatocytes or spermatids were pooled separately, concentrated (to ~2 x106 cells/ml) and stored in buffer containing FBS on ice until use. Ultimately, CD9bright/ID4-EGFP-birght,CD9bright/ID4-EGFP-dim spermatogonia, Sta-Put-enrichedspermatocytes and spermatids, or CD9-bright testis cells fromadult mice were used for single-cell RNA-seq facilitated by the 10X Genomics Chromium Drop-Seq approach. Briefly, Cell suspensions were loaded into Chromium microfluidic chips with 3’ v2 chemistry and used to generate single-cell gelbead emulsions (GEMs) with using the Chromium controller (10X Genomics) per manufacturer recommendations (Zheng et al., 2017). In all cases, suspensions containing ~8700 cells were loaded on the instrument with the expectation of collecting up to 5,000 GEMs containing single cells. For the multiplet test (Fig. S1), equal numbers of mouse and human cells were loaded. GEM-RT was performed in a T100 Thermal cycler (Bio-Rad) and all subsequent steps to generate single-cell libraries were performed according to manufacturer recommendations.
Single-cell 3' libraries were prepared according to manufacturer recommendations (v2 chemistry).

value: Steady-state Spermatogenic cells


title: HumanSpg-Seq1_C16


title: Ad-Id4-EGFP-dim

description: single-cell


title: Ad-Id4-EGFP-unselected

description: single-cell


title: Ad-Id4-EGFP-bright

description: single-cell


title: P6-Id4GFP-Seq1_C07

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: AdultMouse-Rep1

description: single-cell


title: AdultMouse-Rep2

description: single-cell


title: HumanSpg-Seq1_C15


title: P6-Id4GFP-Seq1_C04

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq1_C05

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C14


title: P6-Id4GFP-Seq1_C09

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C17


title: HumanSpg-Seq1_C12


title: P6-Id4GFP-Seq1_C03

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: P6-Id4GFP-Seq1_C02

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C13


title: HumanSpg-Seq1_C11


title: P6-Id4GFP-Seq1_C01

description:
single-cell
P6-Id4GFP-C1_GEmatrix


title: HumanSpg-Seq1_C10


title: HumanSpg-Seq1_C09


title: HumanSpg-Seq1_C04


title: HumanSpg-Seq1_C06


title: HCT116_Cu_4h_rep2

type: RNA

city: Buenos Aires

first: Christian

middle: Martin

last: Saporito-Magriña

state: Buenos Aires

address: Junin 956

department: Fisicoquímica y Química Analítica

country: Argentina

institute: Facultad de Farmacia y Bioquimica UBA

description:
replicate 2
SAMPLE 34

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were extracted using the Illumina BeadStudio software. Quantile normalization was applied to normalize the data (preprocessCore R package).

label: biotin

molecule: total RNA

source_name: colorectal carcinoma

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Cells were grown using DMEM as culture medium at 37 degrees for the times given.

extract_protocol: RNA was extracted with the QIAGEN RNeasy Plus Mini Kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: The BEAS-2B cells and HCT116 cells were expossed to 800 µM CuSO4 and 1400 µM CuSO4 respectively,  dissolved in the culture medium.

tag: cell line


title: HCT116_Cu_6h_rep1

description:
replicate 1
SAMPLE 36


title: HCT116_not_Cu_4h_rep1

description:
replicate 1
SAMPLE 32


title: HCT116_Cu_2h_rep1

description:
replicate 1
SAMPLE 30


title: HCT116_Cu_18h_rep2

description:
replicate 2
SAMPLE 25


title: HCT116_Cu_12h_rep2

description:
replicate 2
SAMPLE 22


title: HumanSpg-Seq1_C01


title: HCT116_not_Cu_2h_rep1

description:
replicate 1
SAMPLE 31


title: HCT116_Cu_6h_rep2

description:
replicate 2
SAMPLE 35


title: HCT116_Cu_4h_rep1

description:
replicate 1
SAMPLE 33


title: HumanSpg-Seq1_C07


title: HCT116_Cu_18h_rep1

description:
replicate 1
SAMPLE 24


title: HCT116_not_Cu_0h_rep1

description:
replicate 1
SAMPLE 27


title: HCT116_not_Cu_12h_rep1

description:
replicate 1
SAMPLE 23


title: HCT116_not_Cu_18h_rep1

description:
replicate 1
SAMPLE 26


title: HCT116_Cu_2h_rep2

description:
replicate 2
SAMPLE 29


title: HCT116_not_Cu_6h_rep2

description:
replicate 2
SAMPLE 19


title: BEAS-2B_Cu_6h_rep2

description:
replicate 2
SAMPLE 17

source_name: lung bronchus


title: HCT116_not_Cu_6h_rep1

description:
replicate 1
SAMPLE 20


title: BEAS-2B_Cu_6h_rep1

description:
replicate 1
SAMPLE 18


title: HCT116_Cu_12h_rep1

description:
replicate 1
SAMPLE 21


title: BEAS-2B_Cu_2h_rep1

description:
replicate 1
SAMPLE 12


title: BEAS-2B_Cu_2h_rep2

description:
replicate 2
SAMPLE 11


title: AAA0500991_a

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description: G5_Intestinal samples from Non-Responders (NR) patients collected on the 3rd day

data_processing: The data were normalised using quantile normalisation with lumi in R

label: Biotin

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Epicentre)

extract_protocol: RNA was extracted from the described tissues using miRNeasy Mini Kit (QIAGEN)

tag: tissue

value: intestine

tag: disease state

value: ulcerative colitis

tag: individual


title: KRAS G12V-3

city: Cambridge

first: Diana

last: Cai

state: MA

address: Massachusetts Hall

institute: Harvard University

data_processing:
Sequencing reads were aligned to the GRCm38 genome using the STAR aligner.
Reads were counted using HTSeq.
Supplementary_files_format_and_content: htseq_count.txt

growth_protocol: Cells were grown in DMEM, 10% FBS, and anti-mycotic/anti-biotic

extract_protocol:
RNA was extracted using the RNeasy kit from Qiagen
Sequencing libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina from NEB

tag: passages

tag: genotype/variation

value: KRAS G12V


title: KRAS G12V-2


title: BEAS-2B_not_Cu_2h_rep1

description:
replicate 1
SAMPLE 13


title: AAA0500990

description: G4_intestinal samples collected on the third day of treatment in treatment-responders (R) patients


title: AAA0500985_a

description: G1_healthy controls

value: healthy control

value: healthy controls


title: BEAS-2B_not_Cu_0h_rep2

description:
replicate 2
SAMPLE 10


title: AAA0500989_a

value: Non-Responders (NR) patients collected on the 3rd day


title: BEAS-2B_not_Cu_4h_rep1

description:
replicate 1
SAMPLE 16


title: BEAS-2B_Cu_4h_rep1

description:
replicate 1
SAMPLE 15


title: AAA0500988


title: AAA0500987


title: BEAS-2B_Cu_18h_rep2

description:
replicate 2
SAMPLE 8


title: BEAS-2B_not_Cu_0h_rep1

description:
replicate 1
SAMPLE 9


title: BEAS-2B_Cu_4h_rep2

description:
replicate 2
SAMPLE 14


title: BEAS-2B_Cu_18h_rep1

description:
replicate 1
SAMPLE 6


title: HCT116_not_Cu_0h_rep2

description:
replicate 2
SAMPLE 28


title: BEAS-2B_Cu_12h_rep2

description:
replicate 2
SAMPLE 4


title: AAA0500976

value: collected on the third day of treatment in treatment-responders (R) patients


title: AAA0500978

description: G2_intestinal samples from patients with active ulcerative colitis before receiving glucocorticoids tand who have a good response to treatment (responders, R)


title: BEAS-2B_Cu_12h_rep1

description:
replicate 1
SAMPLE 3


title: SOS1 N233Y-3

value: SOS1 N233Y


title: AAA0500977

description: G3_intestinal samples from patients with active ulcerative colitis before receiving glucocorticoids and who will have a poor response to treatment (non-responders, NR)


title: BEAS-2B_not_Cu_18h_rep1

description:
replicate 1
SAMPLE 7


title: SOS1 N233Y-1


title: BEAS-2B_not_Cu_6h_rep2

description:
replicate 2
SAMPLE 1


title: SOS1 N233Y-2


title: SOS1 WT-3

value: SOS1 WT


title: BEAS-2B_not_Cu_12h_rep1

description:
replicate 1
SAMPLE 5


title: vector-3

value: vector


title: SOS1 WT-1


title: SOS1 WT-2


title: vector-2


title: BEAS-2B_not_Cu_6h_rep1

description:
replicate 1
SAMPLE 2


title: vector-1


title: H3K4me3 ChIP-seq p63KO Day 7 - Replicate 1

city: Stanford

first: Anthony

middle: E

last: Oro

state: CA

address: 269 Campus Dr, CCSR 2140

institute: Stanford University

description: narrowPeak file generated using IDR 0.1

library_source: genomic

data_processing:
Quality control of Fastq files was assessed by Fastqc
Bowtie was used for read mapping and the parameters were as follows: -p 24 -S -a -m 1 --best --strata
Aligned reads were  processed to remove PCR duplicates using samtools
For peak calling using MACS2, default settings were specified with a p-value of 0.05.
IDR (specifying FDR of 1% for p63 and 5%-10% for broadPeak histone marks) was run on replicates to generate a final peak list.
DESeq2 was performed on the chromatin marks (specifying adjusted p-value < 0.05 and 2 fold change) comparing WT d7 to p63KO d7.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited broadpeak and narrowpeak files containing the high quality, hiqh confidence peaks called for the ChIP-seq experiment

molecule: genomic DNA

source_name: Surface Ectoderm Cells

growth_protocol: hESCs were cultured on Vitronectin Recombinant Human Protein in Essential 8 medium. Surface ectoderm differentiation 6.2x103 cells/cm2 were plated as colonies on Vitronectin coated plates. Next day, media was changed to Essential 6 supplemented media with 1 uM RA and 5 ng/mL Recombinant Human BMP-4, and replaced every two days for seven days.

extract_protocol:
Cells were fixed in 1% formaldehyde, chromatin lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with the indicated antibody. 60x10^6 and 10x10^6 cross-linked cells were used per assay for p63 or histone marks, respectively.
DNA was quantified using Qubit (Invitrogen). Between 5 and 10 ng of pooled DNA were used for library preparation using the NEBNext kit (New England Biolabs) and Agencourt AMPure XP beads (Beckman), both according to the manufacturer’s protocol.

treatment_protocol: For surface ectoderm differentiation, 6.2x10^3 cells/cm2 were plated as colonies on Vitronectin coated plates. Next day, media was changed to Essential 6 media supplemented with 1 uM RA and 5 ng/ml Recombinant Human BMP4, and replaced every two days for seven days. For p63GOF line, cells were treated with 2 ug/ml Doxycycline for two days to induce p63 expression.

tag: genotype

tag: treatment strategy

value: Day 7 of differentiation with RA/BMP4 (surface ectoderm)

tag: chip-seq antibody

value: H3K4me3 (Abcam ab8580)


title: H3K4me3 ChIP-seq p63KO Day 7 - Replicate 2

description: differential peaks between WT and KO


title: Input

value: wild-type


title: AAA0500975

value: patients with active ulcerative colitis before receiving glucocorticoids and who will have a poor response to treatment (non-responders, NR)


title: H3K4me3 ChIP-seq WT Day 7 - Replicate 2

description: differential peaks between WT and KO


title: H3K4me1 ChIP-seq p63KO Day 7 - Replicate 2

description: differential peaks between WT and KO

value: H3K4me1 (Abcam ab8895)


title: H3K4me1 ChIP-seq p63KO Day 7 - Replicate 1

description: broadPeak file generated using IDR 0.1


title: H3K4me3 ChIP-seq WT Day 7 - Replicate 1

description: narrowPeak file generated using IDR 0.1


title: AAA0500967


title: H3K4me1 ChIP-seq WT Day 7 - Replicate 1

description: broadPeak file generated using IDR 0.1


title: H3K27ac ChIP-seq p63KO Day 7 - Replicate 2

description: differential peaks between WT and KO

value: H3K27ac (Abcam ab4629)


title: AAA0500966


title: AAA0500961_a

description: G1_healthy controls


title: AAA0500973

description: G1_healthy controls


title: H3K27ac ChIP-seq p63KO Day 7 - Replicate 1

description: broadPeak file generated using IDR 0.1


title: H3K27ac ChIP-seq WT Day 7 - Replicate 2

description: differential peaks between WT and KO


title: H3K4me1 ChIP-seq WT Day 7 - Replicate 2

description: differential peaks between WT and KO


title: AAA0500953_a


title: AAA0500955

description: G2_intestinal samples from patients with active ulcerative colitis before receiving glucocorticoids and who have a good response to treatment (responders, R)


title: AAA0500964


title: H3K27ac ChIP-seq WT Day 7 - Replicate 1

description: broadPeak file generated using IDR 0.1


title: H3K27me3 ChIP-seq p63KO Day 7 - Replicate 2

description: differential peaks between WT and KO

value: H3K27me3 (Millipore 07-449)


title: ITP16-090_4003: methylenedianiline_100mg/kg_4003

city: North Chicago

first: Rita

last: Ciurlionis

state: IL

address: 1 North Waukegan Road

institute: Abbvie

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Omicsoft ArrayStudio using RMA;  trimmed mean target intensity of each array was set to 150.

organism: Rattus norvegicus

source_name: liver, left lateral lobe

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Qiazol extraction of total RNA with subsequent DNase treatment was performed according to the manufacturer's instructions.

tag: strain

value: Sprague Dawley

tag: Sex

value: male

value: liver, left lateral lobe


title: AAA0500954_a

value: intestine

value: ulcerative colitis

value: patients with active ulcerative colitis before receiving glucocorticoids and who have a good response to treatment (responders, R)


title: ITP16-090_1005: 35% ethanol_2ml/kg_1005


title: AAA0500965_a

value: Non-Responders (NR) patients collected on the 3rd day


title: ITP16-090_4001: methylenedianiline_100mg/kg_4001


title: AAA0500949

description: G1_healthy controls

value: healthy control

value: healthy controls


title: AAA0500943

value: collected on the third day of treatment in treatment-responders (R) patients


title: ITP16-041_4005: diclofenac_10mg/kg_4005


title: ITP16-090_1003: 35% ethanol_2ml/kg_1003


title: AAA0500942


title: AAA0500941


title: H3K27me3 ChIP-seq p63KO Day 7 - Replicate 1

description: broadPeak file generated using IDR 0.1

value: Day 7 of differentiation with RA/BMP4 (surface ectoderm)


title: ITP16-041_3005: acetaminophen_1000mg/kg_3005


title: ITP16-041_4001: diclofenac_10mg/kg_4001


title: AAA0500952


title: ITP16-090_4005: methylenedianiline_100mg/kg_4005


title: H3K27me3 ChIP-seq WT Day 7 - Replicate 2

description: differential peaks between WT and KO


title: ITP16-041_3001: acetaminophen_1000mg/kg_3001


title: ITP16-090_1001: 35% ethanol_2ml/kg_1001


title: H3K27me3 ChIP-seq WT Day 7 - Replicate 1

description: broadPeak file generated using IDR 0.1


title: H3K27me3 ChIP-seq p63GOF Day 0 - Replicate 2

source_name: human Embyronic Stem Cells

value: Doxycycline for 2 days (hESCs)


title: ITP16-041_3003: acetaminophen_1000mg/kg_3003


title: ITP16-041_2003: corn oil_2ml/kg_2003


title: ITP16-041_4003: diclofenac_10mg/kg_4003


title: AAA0500940


title: ITP16-041_2005: corn oil_2ml/kg_2005


title: AAA0500931


title: ITP16-041_2001: corn oil_2ml/kg_2001


title: ITP16-041_1003: water_10ml/kg_1003


title: AAA0500930


title: H3K27me3 ChIP-seq p63GOF Day 0 - Replicate 1

description: broadPeak file generated using IDR 0.05


title: ITP16-041_1001: water_10ml/kg_1001


title: CMET11-104_4003: CCl4_1582mg/kg_4003


title: CMET11-104_4005: CCl4_1582mg/kg_4005


title: CMET11-104_4001: CCl4_1582mg/kg_4001


title: AAA0500929


title: AAA0500928


title: H3K27me3 ChIP-seq WT Day 0 - Replicate 1

description: broadPeak file generated using IDR 0.05

value: wild-type

value: Day 0 of differentiation (hESCs)


title: AAA0500926


title: p63 ChIP-seq KC - Replicate 2

source_name: human Keratinocytes

value: Day 0 of epidermal differentiation (epidermal keratinocyte)

value: p63 (Active Motif 39739)


title: H3K27me3 ChIP-seq WT Day 0 - Replicate 2

value: H3K27me3 (Millipore 07-449)


title: p63 ChIP-seq KC - Replicate 1

description: narrowPeak file generated using IDR 0.01


title: CMET11-104_3005: ANIT_100mg/kg_3005

value: Sprague Dawley


title: p63 ChIP-seq WT Day 7 - Replicate 2

description: bed file containing all day 7 p63 peaks


title: CMET11-104_3003: ANIT_100mg/kg_3003

value: male


title: p63 ChIP-seq p63GOF Day 0 - Replicate 2


title: p63 ChIP-seq WT Day 7 - Replicate 1


title: AAA0500919


title: CMET11-104_1003: corn oil_5ml/kg_1001

value: liver, left lateral lobe


title: CMET11-104_1005: corn oil_5ml/kg_1001


title: CMET11-104_3001: ANIT_100mg/kg_3001


title: Hepatocytes 30 hrs after donor death, biological rep 1

city: Bronx

first: Sanjeev

last: Gupta

state: NY

address: 1300 Morris Park Ave.

department: Medicine

institute: Albert Einstein College of Medicine

description: Gene expression data from  hepatocytes of nonheart-beating donors

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Rat Genome 230 2.0  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affy Gene Chip Scanner 3000 7G.

data_processing: The probe level intensities were adjusted by quantile normalization and gene expression measures were summarized by the robust multi-array analysis (RMA) approach with Bioconductor software.  Statistical analysis of gene expression data used the LIMMA package for R. Genes for further investigation were identified by adjusted P values ≤0.01 (controlling expected false-discovery rates to not more than 1%) and fold difference in mean expression ≥|2.0|.

source_name: Liver from nonheart-beating rat

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: isolated hepatocytes were not cultured

extract_protocol: Hepatocytes were isolated by two-step collagenase perfusion. Total cellular RNA was extracted by Rneasy mini kit (Qiagen Inc., Valencia, CA)

value: Fischer 334

value: liver

value: Hepatocytes


title: Hepatocytes 16 hrs after donor death, biological rep 2


title: Hepatocytes 16 hrs after donor death, biological rep 1


title: Hepatocytes 30 hrs after donor death, biological rep 2


title: Hepatocytes 16 hrs after donor death, biological rep 3


title: Hepatocytes 30 hrs after donor death, biological rep 3


title: Hepatocytes 4 hrs after donor death, biological rep 3


title: AAA0500916

value: intestine

value: ulcerative colitis

value: Non-Responders (NR) patients collected on the 3rd day


title: CMET11-104_1001: corn oil_5ml/kg_1001


title: p63 ChIP-seq p63GOF Day 0 - Replicate 1


title: RNA-seq p63KO Day 7 - Replicate 2

data_processing:
Quality reads assessed by Fastqc
Sequence alignment performed using tophat
Aligned reads were processed to remove PCR duplicates using samtools
Raw reads on reference genes were recovered using HOMER (analyzeRepeats.pl command, using either -rpkm or -noadj parameters)
Genome_build: hg19
Supplementary_files_format_and_content: tab-deliminted text files containing either the raw signal for each replicate and sample, or the FPKM value for each replicate and sample

source_name: RNA-seq p63KO Day 7

growth_protocol: hESCs were cultured on Vitronectin Recombinant Human Protein in Essential 8 medium. Surface ectoderm differentiation 6.2x103 cells/cm2 were plated as colonies on Vitronectin coated  plates. Next day, media was changed to Essential 6 supplemented media with 1 uM RA and 5 ng/mL Recombinant Human BMP-4, and replaced every two days for seven days.

extract_protocol:
Cells were lysed in Trizol (Invitrogen) and run through Rneasy columns (Qiagen) for RNA purification.
Libraries were prepared using TrueSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer’s protocol. Real time PCR was performed with SYBR Green PCR master mix (Life Technologies) and in a Stratagene real time PCR machine.

treatment_protocol: For p63GOF line, cells were treated with 2 ug/ml Doxycycline for two days to induce p63 expression.

value: Surface Ectoderm cells


title: AAA0500907

value: patients with active ulcerative colitis before receiving glucocorticoids and who have a good response to treatment (responders, R)


title: Hepatocytes 4 hrs after donor death, biological rep 1


title: AAA0500905

value: patients with active ulcerative colitis before receiving glucocorticoids and who will have a poor response to treatment (non-responders, NR)


title: Hepatocytes 4 hrs after donor death, biological rep 2


title: AAA0500917


title: KRAS G12V-1

value: KRAS G12V


title: AAA0500914

description: G1_healthy controls

value: healthy control

value: healthy controls


title: AAA0500904


title: RNA-seq p63KO Day 7 - Replicate 1


title: Hepatocytes from heart-beating donor, biological rep2

description: Gene expression data from  hepatocytes of heart-beating donors

source_name: Liver from heart-beating rat


title: RNA-seq WT Day 7 - Replicate 2

source_name: RNA-seq WT Day 7

value: wild-type


title: Hepatocytes from heart-beating donor, biological rep1


title: RNA-seq WT Day 7 - Replicate 1


title: Hepatocytes from heart-beating donor, biological rep3


title: SKOV3_RBMS3 KO_2

city: Guangzhou

first: Geyan

last: Wu

state: Guangdong

address: Zhongshan Er Road

country: China

institute: Sun Yet-sen universtiy

description: gene expression in ovarian cancer cell line SKOV3/RBMS3 KO cells, rep 2

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded and data was processed further by quantile normalization.

source_name: SKOV3_RBMS3 KO

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The ovarian cancer cell line SKOV3 were cultured with DMEM medium supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA from cultured cells  was extracted using TRIzol (Life Technologies) according to the manufacturer’s instructions.

treatment_protocol: RBMS3 were knockout in SKOV3/RBMS3 KO cells in compared with SKOV3/Control cells

value: ovarian cancer cell line

value: RBMS3 KO


title: RNA-seq p63GOF Day 0 NoDox - Replicate 2

source_name: RNA-seq p63GOF Day 0 NoDox

value: human Embyronic Stem Cells


title: RNA-seq p63GOF Day 0 NoDox - Replicate 1


title: RNA-seq p63GOF Day 0 - Replicate 2

source_name: RNA-seq p63GOF Day 0


title: RNA-seq p63GOF Day 0 - Replicate 1


title: Sample_264BC8LPM

city: Pullman

first: Devendra

middle: H

last: Shah

state: Washington

address: #402, Bustad Hall

department: Veterinary Microbiology and Pathology

institute: Washington State University

description: Cultured in LPM (low phosphate, low magnesium)  at 42C

data_processing:
Demultiplexing and base calling were performed using CASAVA 1.8
Casava 1.8-quality filtered reads were paired (QC>30), trimmed and aligned to S. Enteritidis strain P125109 reference sequence using Geneious V11.15 (Biomatters Ltd, New Zealand). Alignment was performed with a minimum of 65bp, allowing up to two mismatches and >90% of the each reads length had to map to the reference sequence to be considered as mapped reads.Read counts were adjusted to RPKM (Reads per kilobase per million).
Genes with zero reads were removed from analysis and total raw read counts were adjusted to RPKM values (Reads per kilobase per million) using Geneious V11.15. RPKM values below 10 were excluded from analysis.
Processed data files in txt format are summarized to include raw reads and RPKM values
Genome_build: NCBI: NC_011294

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: poultry-associated field strains of S. Enteritidis grown in LPM media at avian body temperature (42C)

growth_protocol: A single colony of an overnight culture was inoculated onto Luria Bertani broth (LB) and incubated at 42C for 16 hours and 200 rpm shaking. These overnight cultures were diluted 1:100 into LB-salt (300mM NaCl) or LPM broth and incubated at 42C for 4 hours with shaking at 180 rpm. Cell pellets were obtained for total RNA extraction.

extract_protocol:
RNA extraction and DNAse treatment were performed with RiboPure Bacterial RNA Kit (Ambion, USA) following manufacter's instructions. For each strain in both conditions, a pool containing equimolar amounts of total RNA from 3 independent replicates was submitted for RNA-Seq.
Libraries were prepared by Illumina, Inc. (San Diego, CA) using TruSeq RNA sample Prep Kit following manufacturer's instructions (Illumina, Inc).
Libraries were sequenced on a HiSeq 2000 instrument using version 3 chemistry (75bp paired-end reads)

treatment_protocol: No special treatment

tag: phenotype

value: High-pathogenic


title: Sample_264UKLPM

value: UK


title: CD56 dull 13

city: Genova

first: annalisa

last: barla

state: GE

address: via Dodecaneso 35

department: DIBRIS

country: Italy

institute: Università degli Studi di Genova

hyb_protocol: The hybridization procedure was performed according to the “miRNA Complete Labeling and Hyb Kit” protocol (version 2.4, part number G4170-90011) using the miRNA Complete Labeling and Hyb Kit (Agilent Technologies). Briefly, Cy3-labeled RNA in hybridization buffer was hybridized overnight (20 hours, 55 °C) to Agilent Human microRNA Microarrays 8x60K v19 (Design ID 046064) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 5 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 5 min

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: CD56dull  (CD16+) NK cells

label_protocol: Sample labeling was performed as detailed in the “miRNA Microarray System with miRNA Complete Labeling and Hyb Kit” protocol (version 2.4, part number G4170-90011). Briefly, 100 ng of each total RNA sample was used for the labeling step using the miRNA Complete Labeling and Hyb Kit (Agilent Technologies).

growth_protocol: Pure populations of NK cells were obtained from peripheral blood mononuclear cells (PBMC) using the NK cell isolation kit (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturer’s instruction. Freshly purified NK cells were then sorted based on the expression of CD56 and CD16 molecules to collect the different NK cell subsets

extract_protocol: RNA was extracted using the miRNeasy mini Kit (Qiagen) following manufacturer's instructions

treatment_protocol: Sorted NK cells were washed in PBS and the pellet freeze-dried (20 sec in liquid nitrogen and then stored at -80°C)

tag: subject status/id

value: healthy donor 13

tag: cell subtype

value: CD56dull  (CD16+) NK cells


title: CD56 dull 12

value: healthy donor 12

tag: cell type

value: peripheral blood mononuclear cells (PBMC)


title: HFD+M-Replicate2

city: La Jolla

first: Vandana

last: Sharma

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

hyb_protocol: The labeled cDNA was hybridized to the Sentrix ® MouseWG-6 Expression BeadChip (Illumina) according to the manufacturer's instructions.

scan_protocol: BeadChips were scanned with an Illumina BeadArray Reader.

data_processing: Data processing was done using GenomeStudio software from Illumina.

label: streptavidin- Cy3

source_name: HFD+M_Epididymal fat

label_protocol: cDNA was labeled with Biotin NTP mix.

extract_protocol: RNA from epididymal tissue was extracted using RNeasy Lipd Tissue mini kit from Qiagen.

treatment_protocol: Mice were weaned on ND or HFD or HFD and 2% mannose in drinking water.

tag: age

value: 16 weeks

tag: diet

value: High fat diet with mannose

value: Epididymal fat


title: RNA-seq WT Day 0 - Replicate 2

source_name: RNA-seq WT Day 0

tag: cell line


title: HFD+M-Replicate3

tag: tissue


title: HFD-Replicate1

source_name: HFD_Epididymal fat

value: High fat diet


title: Sample_264BC8LB300

description: Cultured in Luria Bertani (LB) 300mM NaCl at 42C

source_name: poultry-associated field strains of S. Enteritidis grown in LB-salt media (300mM NaCl) at avian body temperature (42C)


title: Huh-7 cells transfected DEPDC1 siRNA, biological rep1

city: Chongqing

first: Wubin

last: Guo

address: Friendship Road No. 1

department: Department of Gastrointestinal Surgery

institute: First Affiliated Hospital of Chongqing Medical University

hyb_protocol: Following fragmentation, labeled ss-cDNA were hybridized for 16 hr at 45C on the Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The differentially expressed genes were analyzed using the Expression Console and Transcriptome Analysis Console v3.0 (Affymetrix).

source_name: Huh-7 cells transfected with DEPDC1 siRNA for 72 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Affymetrix).

growth_protocol: Huh-7 cells were transfected with DEPDC1 siRNA or NC and further cultured for 72 h. After incubation, Huh-7 cells transfected with DEPDC1 siRNA or NC were collected.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Remove the medium from the Huh-7 cells, and add TRIzol Reagent (Invitrogen).

tag: transfection

value: DEPDC1 siRNA for 72 h


title: HFD+M-Replicate1


title: Huh-7 cells transfected NC, biological rep1

source_name: Huh-7 cells transfected with NC for 72 h

value: control


title: HFD-Replicate3


title: ND-Replicate3

source_name: ND_Epididymal fat

value: Normal Diet


title: ND-Replicate2


title: ND-Replicate1


title: HFD-Replicate2


title: SKOV3_RBMS3 KO_1

description: gene expression in ovarian cancer cell line SKOV3/RBMS3 KO cells, rep 1


title: SKOV3_Control_1

description: gene expression in ovarian cancer cell line SKOV3/control cells, rep 1


title: Sample_264UKLB300


title: Sample_264G1LPM


title: SKOV3_Control_2

description: gene expression in ovarian cancer cell line SKOV3/control cells, rep 2


title: Sample_264G1LB300


title: RNA-seq WT Day 0 - Replicate 1

value: wild-type


title: MEL_WT_WGBS

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

country: Canada

institute: Memorial University of Newfoundland

data_processing:
Raw datasets underwent read quality check by FastQC, as well as quality and adapter trimming using Trim Galore.
Short reads in high quality were aligned to mm10 with Bismark using Bowtie2 and the default parameters
Methylation states in CpG context were extracted by Bismark methylation extractor module
Genome_build: mm10

source_name: MEL cell line

growth_protocol: MEL cells were grown in RPMI 1640 medium with L-glutamine supplemented, 10% heat-inactivated FBS and 1% Pen-strep.

extract_protocol:
The DNA was extracted using Qiagen DNeasy Blood & Tissue Kits.
After samples DNA testing, negative control DNAs were added into the initial DNA pool, and then fragmented into a 200-300bp range using Covaris S220. Next, terminal repairing, A-ligation, methylation sequencing adapters ligation were performed to DNA fragments. Then, DNA fragments undergone a bisulfite treatment using the EZ DNA Methylation Gold Kit from Zymo Research. Library concentration was firstly quantified by Qubit 2.0, and then is diluted to 1 ng/ul before an insert size verification using the Agilent Bioanalyzer 2100 and followed by Q-PCR. Finally, the library was paired-end sequenced using the Illumina HiSeq 4000.

treatment_protocol: No treatment

value: spleen

value: MEL


title: CD56 dull 8

value: healthy donor 8


title: HML_AM_Naive_02

city: Chicago

first: Ziyou

last: Ren

address: 303 E Chicago Ave

institute: Northwestern University

data_processing:
Reads were demultiplexed using bcl2fastq (version 2.17.1.14).
Quality was assessed with FastQC. Reads were then trimmed and aligned to the Homo sapiens reference genome (with hg19 assembly) using TopHat2 (version 2.1.0).
Read counts were associated with genes using HTSeq.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including raw htseq count.

source_name: Human alveolar macrophages grown in humanized MISTRG mice

growth_protocol: Two-week old MISTRG mice were given a retro-orbital injection of 5x104 hematopoietic CD34+ stem cells isolated from human cord blood (single donor, single batch) obtained from a commercial vendor (StemCell Technologies). Engraftment of the stem cells and development of the alveolar macrophages was verified via immunohistochemistry and flow cytometry 8 weeks later.

extract_protocol:
Total RNA from alveolar macrophages was extracted (MagMax 96, Thermofisher Scientific) and quality and quantity were assessed (4200 TapeStation, Agilent)
RNA-Seq libraries were prepared using a full-length transcript coverage kit (NEBNext Ultra RNA kit with rRNA depletion, New England Biolabs).

treatment_protocol: Low virulence (PABL065) and high virulence (PABL012) clinical isolates of P. aeruginosa were grown to log phase and diluted to OD600 0.002. Fourteen- week-old mice were anesthetized and intratracheally inoculated with 50 μl of bacterial suspension (9.2 x 106 CFU bacteria in phosphate-buffered saline). Four hours after infection, mice were anesthetized and both lungs were harvested for flow-sorting of alveolar macrophages

tag: virulence

value: Naïve

value: flow-sorted alveolar macrophages

tag: organ

value: Lung


title: HML_AM_Naive_01


title: CD56 dull 6

value: healthy donor 6

value: CD56dull  (CD16+) NK cells


title: CD56 dull 7

value: healthy donor 7

value: peripheral blood mononuclear cells (PBMC)


title: CD56 dull 5

value: healthy donor 5


title: CD56 dull 4

value: healthy donor 4


title: AAA0500902

description: G1_healthy controls

value: intestine

tag: disease state

value: healthy control

tag: individual

value: healthy controls


title: HRECs-48hr-normal glucose treatment-rep2

city: London

first: Saumik

last: Biswas

state: Ontario

address: 1151 Richmond Street

department: Pathology and Laboratory Medicine

institute: University of Western Ontario

description: Gene expression after 48 hours of normal glucose (5 mM/L) culture

hyb_protocol: Hybridization was performed in Agilent's SureHyb Hybridization Chambers and the labeled cRNAs were hybridized onto the Human LncRNA Array v3.0 (8 x 60K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs that at least 4 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.
Differentially expressed LncRNAs with statistical significance between two groups were identified through Volcano Plot filtering and differentially expressed lncRNAs between two samples were identified through Fold Change filtering.

source_name: Human retinal endothelial cells_normal glucose

label_protocol: For microarray analysis, Agilent Array platform was employed. The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The Agilet Quick Amp Labeling Kit was used for sample labeling.

growth_protocol: HRECs (Olaf Pharmaceuticals; Worcester, MA, USA) were grown in endothelial basal media-2 (EBM-2) supplemented with 10% fetal bovine serum. Cells were plated at a density of 4.3 x105 cells/mL and used between passages 5-6 to reduce variability in the subsequent experiments. HRECs were grown to 80-90% confluency post-seeding.

extract_protocol: At the 48-hour timepoint, total RNA was isolated from HRECs using a commercial RNA isolation kit (Ambion, Carlsbad, CA, USA). Total RNA from each sample was then quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Prior to experimentation, HRECs were incubated with serum free EBM-2 media for 24 hours, and then treated with either NG (5 mM/L) or HG (25 mM/L) for 48 hours.

value: retinal endothelial cells


title: HML_AM_Low_02

value: Low virulence (PABL065)


title: HRECs-48hr-high glucose treatment-rep1

description: Gene expression after 48 hours of high glucose (25 mM/L) culture

source_name: Human retinal endothelial cells_high glucose


title: HRECs-48hr-high glucose treatment-rep2


title: HML_AM_Naive_03


title: HML_AM_Low_01


title: HRECs-48hr-normal glucose treatment-rep1


title: CD56 dull 3

value: healthy donor 3


title: HML_AM_High_03

value: high virulence (PABL012)


title: CD56 dull 2

value: healthy donor 2


title: HML_AM_High_02


title: CD56 dull 1

value: healthy donor 1


title: HML_AM_High_01

value: flow-sorted alveolar macrophages


title: CD56 bright 13

source_name: CD56bright (CD16-) NK cells

value: healthy donor 13

value: CD56bright (CD16-) NK cells


title: ATAC-seq p63KO Day 7 - Replicate 1

description: processed data file: ATAC_sites_6037_morphogens_open_p63_closes.bed

data_processing:
Quality control of fastq files was done with FASTQC.
Bowtie2 was used for read mapping and the parameters were as follows: -p 24 -S -m 1 -X 2000
Aligned reads were processed to remove PCR duplicates and mitochondrial DNA using samtools.
For peak calling using MACS2, default settings were specified with a p-value of 0.05.
IDR (specifying FDR of 5%) was run on replicates to generate a final peak list.
DESeq2 was performed (specifying adjusted p-value < 0.05 and 2 fold change) comparing WT d0 to WT d7, and WT d7 to p63KO d7. Differential peaks that also passed IDR were processed into the following bed files.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.bed: Tab-delimited bed files containing the high quality, hiqh confidence, differential peaks from DESeq2 comparisons of the ATAC-seq experiment.

source_name: Surface Ectoderm cells

growth_protocol: hESCs were cultured on Vitronectin Recombinant Human Protein in Essential 8 medium.

extract_protocol:
After treatment with Accutase, 7x10^4 cells were washed with cold PBS and lysed using 0.1% NP40 in RSB buffer. Nuclei were then isolated by centrifugation.
Nuclei pellets were Tn5 transposed using the DNA Sample Preparation Kit from Nextera®. Libraries were amplified for 9-15 total cycles using the Ad1 and Ad 2.1-2.16 barcodes. Libraries were purified using the Min-Elute columns (Qiagen) and eluted with 10 μL of buffer EB. Library DNA concentrations were determined with Bioanalyzer High-Sensitivity DNA analysis kit (Agilent). Paired-end libraries were sequenced initially on a MiSeq sequencer and analyzed using a custom script to determine the signal enrichment over background at TSSs over a 2 kb window. Only libraries that had enrichment scores above 6 were sequenced deeper in a NextSeq Illumina sequencer.

tag: genotype/variation

tag: treatment

value: Day 7 of differentiation with RA/BMP4

value: Surface Ectoderm cells


title: ATAC-seq p63KO Day 7 - Replicate 2


title: CD56 bright 7

value: healthy donor 7

value: peripheral blood mononuclear cells (PBMC)


title: CD56 bright 8

value: healthy donor 8


title: CD56 bright 6

value: healthy donor 6


title: ATAC-seq WT Day 7 - Replicate 2

description:
processed data file: ATAC_sites_6037_morphogens_open_p63_closes.bed
processed data file: ATAC_sites_8154_morphogens_open.bed

value: wild-type


title: WBS_186_30_07

city: Kyoto

first: Ryo

last: Kimura

address: Yoshida-Konoe-cho

department: Anatomy and Developmental Biology

country: Japan

institute: Kyoto University Graduate School of Medicine

hyb_protocol: 600 ng of Cy3-labeled cRNA was fragmented and hybridized at 65 °C for 17 hours according to the manufacturer's instructions.

scan_protocol: Slides were scanned on the Agilent Microarray scanner (G2565CA).

data_processing: Data were extracted with Agilent Feature Extraction software version 11.0.1.1 (Agilent Technologies). Raw gene expression data were background corrected using the normexp method and normalized by the quantile method in Limma R package (Smyth et al.).

source_name: Peripheral blood from WBS patient

label_protocol: Total RNA (100 ng) was labeled with Cy3 using Low Input Quick Amp RNA Labeling kit, One-Color (Agilent Technologies) according to the manufacturer's instructions. Labelled cRNA were purified using an RNeasy mini kit (QIAGEN)..  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted from peripheral blood of participants by using the Paxgene Blood RNA System (QIAGEN, Tokyo, Japan) following the manufacture’s protocol with on-column DNase digestion.RNA quantity was measured using a Nano-drop ND-2000 spectrophotometer (Thermo Fisher Scientific, Yokohama, Japan). Qualities of RNA was determined by the Agilent 2100 Bioanalyzer (Agilent Technologies, Tokyo, Japan). RNA integrity number (RIN) values greater than 8 were used for subsequent analyses.

tag: diagnosis

value: Williams Syndrome (WS)

value: whole blood

tag: gender

value: male


title: WBS_135_19re_04


title: CD56 bright 12

value: healthy donor 12


title: WBS_103_15_07


title: WBS_127_27_05

value: female


title: WBS_183_30_06


title: WBS_181_27_08


title: WBS_173_20_07


title: WBS_138_21_07


title: WBS_134_19re_03


title: WBS_180_27_07


title: WBS_150_21_08


title: WBS_178_20_08


title: WBS_126_20_06


title: WBS_122_19re_02


title: CD56 bright 5

value: healthy donor 5


title: WBS_102_15_06


title: Neurons_WT_ZIKV_24h_rep3

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description: gene expression after 24h in cultured neurons

hyb_protocol: For each sample, 3 ug of Cy3 labeled cDNA was hybridized for 17 at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters. The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise. The resulting data were processed using OmicSoft Array Studio (Version 9.0) software. Raw feature extraction (FA) files were loaded in R (3.5.1) using limma (3.36.1). FA files were background corrected, control probes removed , and quantile normalized using limma.

source_name: Neurons, WT, ZIKV, 24 hours, replicate 3

label_protocol: Fifty nanograms (50 ng) of total RNA was amplified as directed in the NuGEN Ovation Pico WTA System and 5 ug of amplified cDNA was enzymatically labeled using the Agilent SureTag DNA Labeling Kit.

growth_protocol: Cortical neurons were isolated from E14.5 mouse embryos and cultured for

extract_protocol: RNA was extracted using a Qiagen Rneasy Kit according to manufacturer's instructions.

value: cortical neurons

value: wild type

tag: infection

value: Zika virus (ZIKV) strain MR766 at an MOI of 0.1


title: WBS_101_14_08


title: WBS_106_11_03


title: Neurons_WT_ZIKV_24h_rep1

source_name: Neurons, WT, ZIKV, 24 hours, replicate 1


title: Neurons_WT_ZIKV_24h_rep2

source_name: Neurons, WT, ZIKV, 24 hours, replicate 2


title: ATAC-seq WT Day 7 - Replicate 1


title: WBS_099_14_06


title: ATAC-seq p63GOF Day 0 - Replicate 1

description: processed data file:

source_name: human Embryonic Stem Cells

value: Doxycycline for 2 days

value: Embryonic Stem Cells


title: ATAC-seq WT Day 0 - Replicate 2

description: processed data file: ATAC_sites_8154_morphogens_open.bed

value: Day 0 of differentiation


title: ATAC-seq p63GOF Day 0 - Replicate 2

description: processed data file:


title: Neurons_WT_WNV_24h_rep3

source_name: Neurons, WT, WNV, 24 hours, replicate 3

value: West Nile virus (WNV) strain TX 2002-HC at an MOI of 0.001


title: ATAC-seq WT Day 0 - Replicate 1


title: CD56 bright 3

tag: subject status/id

value: healthy donor 3

value: peripheral blood mononuclear cells (PBMC)

value: CD56bright (CD16-) NK cells


title: CD56 bright 2

value: healthy donor 2

tag: cell subtype


title: CD56 bright 4

value: healthy donor 4

tag: cell type


title: UMI-4C p63KO Day 7 - Replicate 2

data_processing:
Library strategy: UMI-4C
Reads were processed using HiC-Pro, which performed Bowtie alignment, removal of PCR duplicates, assignment to MboI restriction fragments, and filtering for valid long-range contacts.
Binned 5 kb resolution interaction matrix files were converted to tab-delimited bed files.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *matrix.bed: Tab-delimited bed files of HiC-Pro filtered read counts from 5 kb contact matrix file.

source_name: Surface Ectoderm Cells

extract_protocol:
After treatment with Accutase, cells were fixed in 1% formaldehyde. After crosslinking, 1x10^7 cells were pelleted for isolating nuclei and digesting with DpnII overnight. Proximity ligations were generated and DNA was purified through a phenol/chloroform extraction and ethanol precipitation.
After Qubit quantification, 10 ug of 4C library was sonicated and used for library preparation using NEBNext kit (New England Biolabs) and Agencourt AMPure XP beads (Beckman) according to the manufacturer’s protocol. Two rounds of PCR were performed using custom bait primers at the TFAP2C locus along with the UMI-4C universal adapter. Library concentration was determined via Bioanalyzer (Agilent) and duplicates were sequenced paired-end on Illumina NextSeq sequencer.

treatment_protocol: For surface ectoderm differentiation, 6.2x10^3 cells/cm2 were plated as colonies on Vitronectin coated plates. Next day, media was changed to Essential 6 media supplemented with 1 uM RA and 5 ng/ml Recombinant Human BMP4, and replaced every two days for seven days.

value: Day 7 of differentiation with RA/BMP4

value: Surface Ectoderm Cells


title: control low density, 57 dpw, fish 5

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol for 4x44k microarrays

scan_protocol: Arrays were scanned with Agilent microarray scanner

data_processing: Global normalization was performed by equalizing the mean intensities of all microarrays. The individual values for each feature were divided to the mean value of all samples and expression ratios (ER) were calculated. Log2-ER were normalized with the locally weighted non-linear regression (Lowess)

organism: Salmo salar

source_name: low density_57 dpw_skin

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon was fed with commercial feed

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

tag: FISH id

value: fish 5

tag: stocking density

value: control low fish density (20 kg/m3)

tag: time point

value: 57 dpw

value: skin


title: control low density, 57 dpw, fish 4

value: fish 4

tag: tissue