title: A2.1001200107


title: C8.1001200108

status: Public on Dec 31 2018

type: SRA

city: Stanford

first: Qingyun

last: Li

state: CA

address: 299 Campus Drive

department: Neurobiology

country: USA

institute: Stanford University

description: Single_myeloid_1922_cells_processed_data.csv

library_source: transcriptomic

data_processing:
Prinseq (version 0.20.4) was first used to filter sequencing reads shorter than 30 bp (-min_len 30), trim the first 10 bp at the 5’-end (-trim_left 10) of the reads, trim reads with low quality from the 3’-end (-trim_qual_right 25) and remove low complexity reads (-lc_method entropy, -lc_threshold 65).
Trim Galore (version 0.4.3) was applied to trimmed the Nextera adapters (--stringency 1).
The remaining reads were aligned to the mm10 genome by calling STAR (version 2.5.3a) with the following options: --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMstrandField intronMotif.
Picard was then used to remove the duplicate reads (VALIDATION_STRINGENCY=LENIENT, REMOVE_DUPLICATES=true).
The aligned reads were converted to counts for each gene by using HTSeq (-m intersection-nonempty, -s no)
To filter out cells with low sequencing quality, three criteria, namely the number of total reads, the number of total detected genes and correlation coefficient between ERCC spike-ins input and corresponding read counts, were each evaluated based on the distributions of the data. The distribution of the total reads (in logarithmic scale) was fitted by a truncated Cauchy distribution, and data points in two tails of the estimated distribution were considered as outliers and eliminated. Fitting and elimination were then applied to the remaining data. This process was run iteratively until the estimated distribution became stable. The threshold was set to the value where the cumulative distribution function of the estimated distribution reaches 0.05. Similarly, cells with small numbers of detected genes, and poor correlation coefficients for ERCC (low sequencing accuracy) were dropped. After filtering, 1816 cells, out of 1922, were retained.
Genome_build: mm10
Supplementary_files_format_and_content: Common delimited file (csv) containing all 1922 cells and mapped gene counts (including counts for ERCC spike-ins)

molecule: total RNA

organism: Mus musculus

source_name: Brain myeloid cell

extract_protocol:
For the E14.5 stage, whole brains were dissected out from timed embryos, and collected into 1ml PBS with 1% fetal bovine serum (added 10ul Ambion DNase I, 2ul RNase inhibitor) on ice. The sample was passed through a 26G needle 5-10 times to create single cell suspension. Cells were spun down (500g) at 4˚C for 5min, and suspended in 1ml PBS for FACS staining. Single live cells in the cKit-CD45+ gate were sorted into 96-well plates for library preparation.  For P7 and P60 stages, cortex (CTX), cerebellum (CB), hippocampus (HIP), striatum (STR), olfactory bulb (OB) and choroid plexus (CP) were dissected out. Tissues from the same region were pooled from multiple mice (3-8 depending on the ages and regions) into a 6cm petri dish with 200ul cold medium A on ice (15mM HEPES, 0.5% glucose in 1 X Hanks' Balanced Salt Solution (HBSS without phenol red)). Microglia (myeloid cells) extraction was carried out on ice following a published protocol (Bennett et al. PNAS. 2016) through douncing, MACS myelin removal and FACS staining. Single live cells in the CD45lowCD11b+ (microglia) or CD45hiCD11b+ (myeloid cells) gate were sorted into 96-well plates for library preparation.
Sequencing libraries were prepared following the published Smart-seq2 protocol with the aid of liquid handling robotics (Picelli et al. Nature Protocols. 2014). Briefly, plates with sorted cells were thawed on ice and incubated at 72˚C for 3 min in order to anneal RNAs to the Oligo-dT30VN primer. After that, 6ul reverse transcription mixture (95U SMARTScribe™ Reverse Transcriptase (100U/ul, Clontech 639538), 10U RNase inhibitor (40U/ul), 1XFirst-Strand buffer, 5mM DTT, 1M Betaine, 6mM MgCl2, 1uM TSO (Exiqon, Rnase free HPLC purified)) was added into each well, and RT was performed at 42˚C for 90 min, followed by 70˚C, 5 min. To amplify cDNA, 15ul PCR amplification mix (1X KAPA HIFI Hotstart Master Mix (Kapa Biosciences KK2602), 0.1uM ISPCR Oligo (AAGCAGTGGTATCAACGCAGAGT), 0.56U Lambda Exonuclease (5U/ul, New England BioLabs M0262S)) was added, and the following PCR program was used: (1) 37˚C 30 min; (2)95˚C 3 min; (3) 21 cycles of 98˚C 20 sec, 67˚C 15 sec, 72˚C 4 min; (4) 72˚C 5 min. Amplified cDNA samples were then purified with PCRClean DX beads (0.7:1 ratio, Aline C-1003-50), and resuspended in 20ul EB buffer. cDNA quality was examined with a Fragment Analyzer (AATI, High Sensitivity NGS Fragment Analysis Kit:1 bp - 6000 bp) following the manufacture’s instruction. Samples with sufficient amount of cDNA content (>0.05ng/ul) and normal peaks on the quantification graphs were retained for library preparation. To make libraries, all samples were first diluted down to 0.15ng/ul (only if higher than 0.15ng/ul) in 384-well plates using Mantis Liquid Handler (Formulatrix) and Mosquito X1 (TTP Labtech) with customized scripts. Nextera XT DNA Sample Prep Kit (Illumina FC-131-1096) was used at 1/10 of recommendation volume, with the help of a Mosquito HTS robot for liquid transfer. Specifically, tagmentation was done in 1.6ul (1.2ul Tagment enzyme mix, 0.4ul diluted cDNA) at 55˚C, 10 min. Neutralization buffer was added 0.4ul per well and incubated at room temperature for 5 min to stop the reaction. Then 0.8ul Illumina Nextera XT 384 Indexes (0.4ul each, 5uM from 4 sets of 96 indexes) and 1.2ul PCR master mix were added to amplify whole transcriptomes using the following program: (1) 72˚C 3 min; (2) 95˚C 30 sec; (3) 10 cycles of 95˚C 10 sec, 55˚C 30 sec, 72˚C 1 min; (4) 72˚C 5 min. Libraries from a single 384 plate were pooled together in an Eppendorf tube and purified twice with PCRClean DX beads. The quality and concentrations of the final mixed libraries were measured with Bioanalyzer and Qubit, respectively, before Illumina Nextseq sequencing.

tag: strain

tag: genotype

value: wild type

tag: tissue

value: OB

tag: age

tag: gate

value: Y


title: G3.1001200106


title: B4.1001200106


title: D5.1001200109

value: CB


title: G8.1001200109


title: H5.1001200106


title: F2.1001200106


title: C9.1001200107

value: HIP


title: B12.1001200106


title: D11.1001200109


title: C7.1001200107


title: A2.1001200106


title: B6.1001200107


title: B10.1001200106


title: C11.1001200108


title: B4.1001200108


title: H9.1001200146

description: Gpnmb_Clec7a_143_Microglia_processed_data.csv

data_processing:
Prinseq (version 0.20.4) was first used to filter sequencing reads shorter than 30 bp (-min_len 30), trim the first 10 bp at the 5’-end (-trim_left 10) of the reads, trim reads with low quality from the 3’-end (-trim_qual_right 25) and remove low complexity reads (-lc_method entropy, -lc_threshold 65).
Trim Galore (version 0.4.3) was applied to trimmed the Nextera adapters (--stringency 1).
The remaining reads were aligned to the mm10 genome by calling STAR (version 2.5.3a) with the following options: --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMstrandField intronMotif.
Picard was then used to remove the duplicate reads (VALIDATION_STRINGENCY=LENIENT, REMOVE_DUPLICATES=true).
The aligned reads were converted to counts for each gene by using HTSeq (-m intersection-nonempty, -s no)
To filter out cells with low sequencing quality, three criteria, namely the number of total reads, the number of total detected genes and correlation coefficient between ERCC spike-ins input and corresponding read counts, were each evaluated based on the distributions of the data. The distribution of the total reads (in logarithmic scale) was fitted by a truncated Cauchy distribution, and data points in two tails of the estimated distribution were considered as outliers and eliminated. Fitting and elimination were then applied to the remaining data. This process was run iteratively until the estimated distribution became stable. The threshold was set to the value where the cumulative distribution function of the estimated distribution reaches 0.05. Similarly, cells with small numbers of detected genes, and poor correlation coefficients for ERCC (low sequencing accuracy) were dropped. After filtering, 1816 cells, out of 1922, were retained.
Genome_build: mm10
Supplementary_files_format_and_content: Common delimited file (csv) containing 143 microglia (enriched for P7 PAM) and mapped gene counts (including counts for ERCC spike-ins).

source_name: Microglia

extract_protocol:
Cerebella (CB) were dissected out and put into a 6cm petri dish with 200ul cold medium A on ice (15mM HEPES, 0.5% glucose in 1 X Hanks' Balanced Salt Solution (HBSS without phenol red)). Microglia (enriched for PAM with Gpnmb and Clec7a surface markers) extraction was carried out on ice following a published protocol (Bennett et al. PNAS. 2016) through douncing, MACS myelin removal and FACS staining. Single live cells in the CD45lowCD11b+Gpnmb+Clec7a+ gate were sorted into 96-well plates for library preparation.
Sequencing libraries were prepared following the published Smart-seq2 protocol with the aid of liquid handling robotics (Picelli et al. Nature Protocols. 2014). Briefly, plates with sorted cells were thawed on ice and incubated at 72˚C for 3 min in order to anneal RNAs to the Oligo-dT30VN primer. After that, 6ul reverse transcription mixture (95U SMARTScribe™ Reverse Transcriptase (100U/ul, Clontech 639538), 10U RNase inhibitor (40U/ul), 1XFirst-Strand buffer, 5mM DTT, 1M Betaine, 6mM MgCl2, 1uM TSO (Exiqon, Rnase free HPLC purified)) was added into each well, and RT was performed at 42˚C for 90 min, followed by 70˚C, 5 min. To amplify cDNA, 15ul PCR amplification mix (1X KAPA HIFI Hotstart Master Mix (Kapa Biosciences KK2602), 0.1uM ISPCR Oligo (AAGCAGTGGTATCAACGCAGAGT), 0.56U Lambda Exonuclease (5U/ul, New England BioLabs M0262S)) was added, and the following PCR program was used: (1) 37˚C 30 min; (2)95˚C 3 min; (3) 21 cycles of 98˚C 20 sec, 67˚C 15 sec, 72˚C 4 min; (4) 72˚C 5 min. Amplified cDNA samples were then purified with PCRClean DX beads (0.7:1 ratio, Aline C-1003-50), and resuspended in 20ul EB buffer. cDNA quality was examined with a Fragment Analyzer (AATI, High Sensitivity NGS Fragment Analysis Kit:1 bp - 6000 bp) following the manufacture’s instruction. Samples with sufficient amount of cDNA content (>0.05ng/ul) and normal peaks on the quantification graphs were retained for library preparation. To make libraries, all samples were first diluted down to 0.15ng/ul (only if higher than 0.15ng/ul) in 384-well plates using Mantis Liquid Handler (Formulatrix) and Mosquito X1 (TTP Labtech) with customized scripts. Nextera XT DNA Sample Prep Kit (Illumina FC-131-1096) was used at 1/10 of recommendation volume, with the help of a Mosquito HTS robot for liquid transfer. Specifically, tagmentation was done in 1.6ul (1.2ul Tagment enzyme mix, 0.4ul diluted cDNA) at 55˚C, 10 min. Neutralization buffer was added 0.4ul per well and incubated at room temperature for 5 min to stop the reaction. Then 0.8ul Illumina Nextera XT 384 Indexes (0.4ul each, 5uM from 4 sets of 96 indexes) and 1.2ul PCR master mix were added to amplify whole transcriptomes using the following program: (1) 72˚C 3 min; (2) 95˚C 30 sec; (3) 10 cycles of 95˚C 10 sec, 55˚C 30 sec, 72˚C 1 min; (4) 72˚C 5 min. Libraries from a single 384 plate were pooled together in an Eppendorf tube and purified twice with PCRClean DX beads. The quality and concentrations of the final mixed libraries were measured with Bioanalyzer and Qubit, respectively, before Illumina Nextseq sequencing.


title: H8.1001200146


title: H6.1001200146


title: H5.1001200146


title: A8.1001200106


title: D6.1001200107


title: B1.1001200108


title: H11.1001200146


title: H7.1001200146


title: H4.1001200146


title: G8.1001200146


title: H10.1001200146


title: H1.1001200146


title: G7.1001200146


title: G5.1001200146


title: G6.1001200146


title: H2.1001200146


title: G4.1001200146


title: G11.1001200146


title: G2.1001200146


title: G10.1001200146


title: G1.1001200146


title: F9.1001200146


title: G12.1001200146


title: F7.1001200146


title: G3.1001200146


title: F8.1001200146


title: F5.1001200146


title: H3.1001200146


title: F6.1001200146


title: G9.1001200146


title: F4.1001200146


title: F2.1001200146


title: F3.1001200146


title: F12.1001200146


title: F10.1001200146


title: F11.1001200146


title: E7.1001200146


title: E6.1001200146


title: E9.1001200146


title: E4.1001200146


title: E5.1001200146


title: E8.1001200146


title: E11.1001200146


title: E10.1001200146


title: D9.1001200147


title: E1.1001200146


title: D8.1001200147


title: D9.1001200146


title: D7.1001200147


title: D6.1001200147


title: D7.1001200146


title: D6.1001200146


title: D5.1001200146


title: D5.1001200147


title: D4.1001200147


title: D4.1001200146


title: F1.1001200146


title: D3.1001200147


title: E3.1001200146


title: D2.1001200147


title: D12.1001200147


title: D11.1001200147


title: D2.1001200146


title: D12.1001200146


title: D3.1001200146


title: D10.1001200146


title: E12.1001200146


title: D1.1001200146


title: E2.1001200146


title: D1.1001200147


title: D8.1001200146


title: C8.1001200146


title: C7.1001200147


title: D11.1001200146


title: C9.1001200146


title: C9.1001200147


title: D10.1001200147


title: C7.1001200146


title: C6.1001200147


title: C8.1001200147


title: C5.1001200147


title: C6.1001200146


title: C5.1001200146


title: Dnmt1cKO_urogenital epithelium_8

city: Madison

first: Chad

middle: Michael

last: Vezina

state: WI

address: 1656 Linden Drive

department: Comparative Biosciences

institute: University of Wisconsin-Madison

description:
mUGE_b7_rep3
jat_063824_0100656__S33_L005
jat_063824_0100698__S33_L004

data_processing:
Basecalls/demuxxing performed using Illumina bcl2fastq, v2.17.1.14
Reads were filtered and trimmed for adapters and quality.
Expression estimates were calculated using RSEM v1.2.3 with alignments by bowtie v0.12.9
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file with a table of Expected Counts expression estimates from the RSEM application

source_name: E15.5 Urogenital epithelium

growth_protocol: Embryos generated by timed matings

extract_protocol:
Urogenital epithelium separated from stroma by trypsin digestion. Dissected tissues were placed directly into RLT Plus lysis buffer (Qiagen) for later processing. For each batch of harvest, dissected tissues from multiple embryos were pooled into one lysate. Total RNA was purified from the RLT Plus lysates using the RNeasy Plus Micro Kit (Qiagen) according to manufacturer’s instructions.
The following is an excerpt from Hou et al, Sci Rep. 2015; 5:9570, the manuscript that details the protocol employed. Poly-A-tailed mRNA is isolated from total RNA using oligo-dT beads. Purified mRNA is then fragmented with heat in fragmentation buffer. First strand cDNA is then synthesized using random hexamer oligos containing partial Illumina 3′ adaptor sequence. After RNA removal, a modified oligo containing partial Illumina's 5′ adaptor is then ligated to the 5′ of the single stranded cDNA. The library is then amplified by PCR using oligos that contain full Illumina adaptor sequences and our in-house index sequences.

tag: tissue type

value: Urogenital epithelium

tag: genotype (experimental group)


title: C3.1001200147


title: C4.1001200146


title: C4.1001200147


title: Dnmt1cKO_urogenital epithelium_7

description:
mUGE_b7_rep2
jat_063823_0100655__S32_L005
jat_063823_0100697__S32_L004


title: C3.1001200146


title: C2.1001200147


title: C2.1001200146


title: C12.1001200147


title: Dnmt1cKO_urogenital epithelium_6

description:
mUGE_b7_rep1
jat_063822_0100654__S31_L005
jat_063822_0100696__S31_L004


title: Dnmt1cKO_urogenital epithelium_4

description:
mUGE_b5_rep1
jat_063820_0100652__S29_L005
jat_063820_0100694__S29_L004


title: Dnmt1cKO_urogenital epithelium_5

description:
mUGE_b6_rep1
jat_063821_0100653__S30_L005
jat_063821_0100695__S30_L004


title: C11.1001200147


title: C12.1001200146


title: Dnmt1cKO_urogenital epithelium_1

description:
mUGE_b2_rep1
jat_063817_0100649__S26_L005
jat_063817_0100691__S26_L004


title: Control_urogenital epithelium_4

description:
UGE_b7_rep3
jat_063803_0100635__S12_L005
jat_063803_0100677__S12_L004

value: Control


title: C10.1001200147


title: C11.1001200146


title: C10.1001200146


title: C1.1001200147


title: Control_urogenital epithelium_3

description:
UGE_b6_rep2
jat_063800_0100632__S9_L005
jat_063800_0100674__S9_L004


title: B9.1001200147


title: C1.1001200146


title: stroke1

city: Los Angeles

first: Zhifei

last: Luo

address: 1450 Biggy Street, NRT 6514

institute: University of Southern California

data_processing:
RNA-seq data was inspected by FastQC. Using default settings, STAR version 2.5.2b were used to map reads to mouse genome GRCm38.
Alignment results were processed for gene quantification using featureCounts version 1.5.1 with the strand-specific option
Differentially expressed genes were determined using DESeq2 version 1.14.1
Genome_build: GRCm38

source_name: C57BL/6J mice

growth_protocol: Mice were housed in plastic cages on a 12h light cycle, with ad libitum access to water, with a standard laboratory diet, and in a specific pathogen-free facility. The Institutional Animal Care and Use Committee at the University of Southern California approved all procedures per the National Institutes of Health guidelines.

extract_protocol:
RNA was prepared using TRIzol Reagent (Thermo Fisher Scientific, catalog # 15596018) followed by RNeasy Mini Kit (Qiagen, catalog # 74104).
The libraries were made using KAPA stranded mRNA-seq kits (KAPA Biosystems, catalog # kk8421) according to manufacturer’s protocol.

treatment_protocol: Using a 27-½ gauge needle, mice were anesthetized with 100 mg/kg Ketamine intraperitoneally (IP) and 10 mg/kg IP xylazine. Rectal temperature was maintained at 37°C using a feedback-controlled heating system. MCA was occluded for 30 minutes using a silicon-coated nylon monofilament (DOCCOL, CO) as we previously described. Cerebral blood flow was monitored by laser Doppler flowmetry (Transonic Systems). Mice with an adequacy of MCAO as evidenced by ≥80% drop in the cerebral blood flow were included in the study. Motor neurological examination was determined after 24 hours, using the following criteria: no neurological deficit, 0; failure to extend left forepaw fully, 1; turning to left, 2; circling to left, 3; unable to walk spontaneously, 4; and stroke-related death, 5.

tag: treatment

value: stroke


title: B9.1001200146


title: stroke3


title: Control_urogenital epithelium_1

description:
UGE_b4_rep1
jat_063796_0100628__S5_L005
jat_063796_0100670__S5_L004


title: stroke2


title: Dnmt1cKO_urogenital epithelium_2

description:
mUGE_b3_rep1
jat_063818_0100650__S27_L005
jat_063818_0100692__S27_L004


title: B8.1001200146


title: B8.1001200147


title: sham2

value: sham


title: sham1


title: B7.1001200147


title: Dnmt1cKO_urogenital epithelium_3

description:
mUGE_b4_rep1
jat_063819_0100651__S28_L005
jat_063819_0100693__S28_L004


title: B7.1001200146


title: B6.1001200147


title: Control_urogenital epithelium_2

description:
UGE_b5_rep2
jat_063798_0100630__S7_L005
jat_063798_0100672__S7_L004


title: B5.1001200147


title: B4.1001200147


title: B5.1001200146


title: B3.1001200146


title: B3.1001200147


title: B2.1001200147


title: B12.1001200146


title: B12.1001200147


title: B11.1001200147


title: B4.1001200146


title: Patient_13_cancer_rep1_HG-U133A

type: RNA

city: Athens

first: Aristotelis

last: Chatziioannou

state: Not in US

address: 48 Vassileos Constantinou Avenue

department: Institute of Biology, Medicinal Chemistry and Biotechnology

country: Greece

institute: National Hellenic Research Foundation

description:
Patient13.2
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

hyb_protocol: Affymetrix HG-U133A GeneChip arrays hybridization was performed using Affymetrix standard protocols (Affymetrix, Santa Clara, CA).

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

data_processing: The data were analyzed with Rstudio console using the affy R package and RMA as the normalization method.

label: biotin

organism: Homo sapiens

source_name: Patient 13 primary colorectal adenocarcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted by Rneasy kit (Qiagen , Inc)

value: primary colorectal adenocarcinoma

tag: anatomic location

value: sigmoid

tag: presence of synchronous distant metastasis

value: Yes

tag: suv pet variable values

tag: vb pet variable values

tag: k1 pet variable values

tag: k2 pet variable values

tag: k3 pet variable values

tag: k4 pet variable values

tag: fd pet variable values

tag: inf pet variable values


title: Patient_12_normal_rep1_HG-U133A

description:
Patient12.1
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 12 normal adjacent sample

value: normal adjacent

value: left colic flexure


title: Patient_13_normal_rep1_HG-U133A

description:
Patient13.1
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 13 normal adjacent sample


title: B11.1001200146

tag: strain

tag: genotype


title: B6.1001200146

tag: tissue

tag: age


title: Patient_9_cancer_rep1_HG-U133A

description:
Patient9.2
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 9 primary colorectal adenocarcinoma

value: coecum


title: Patient_6_cancer_rep1_HG-U133A

description:
Patient6.2
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 6 primary colorectal adenocarcinoma

value: rectum


title: Patient_11_normal_rep1_HG-U133A

description:
Patient11.1
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 11 normal adjacent sample


title: Patient_10_normal_rep1_HG-U133A

description:
Patient10.1
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 10 normal adjacent sample

value: right colic flexure


title: Patient_7_cancer_rep1_HG-U133A

description:
Patient7.2
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 7primary colorectal adenocarcinoma

value: No


title: Patient_11_cancer_rep1_HG-U133A

description:
Patient11.2
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 11 primary colorectal adenocarcinoma


title: Patient_7_normal_rep1_HG-U133A

description:
Patient7.1
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 7 normal adjacent sample


title: Patient_10_cancer_rep1_HG-U133A

description:
Patient10.2
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 10 primary colorectal adenocarcinoma


title: Patient_9_normal_rep1_HG-U133A

description:
Patient9.1
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 9 normal adjacent sample


title: Patient_6_normal_rep1_HG-U133A

description:
Patient6.1
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 6 normal adjacent sample


title: B2.1001200146

description: Gpnmb_Clec7a_143_Microglia_processed_data.csv

value: wild type

tag: gate


title: B1.1001200147

value: Y


title: B10.1001200146

value: CB


title: Patient_5_cancer_rep1_HG-U133A

description:
Patient5.2
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 5 primary colorectal adenocarcinoma


title: A9.1001200147

source_name: Microglia


title: A8.1001200147


title: B10.1001200147


title: B1.1001200146


title: A9.1001200146


title: A8.1001200146


title: A7.1001200147


title: A7.1001200146


title: Patient_12_cancer_rep1_HG-U133A

description:
Patient12.2
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 12 primary colorectal adenocarcinoma


title: Patient_1_cancer_rep1_HG-U133A

description:
Patient1.2
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 1 primary colorectal adenocarcinoma


title: Patient_4_cancer_rep1_HG-U133A

description:
Patient4.2
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 4 primary colorectal adenocarcinoma


title: Patient_4_normal_rep1_HG-U133A

description:
Patient4.1
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 4 normal adjacent sample


title: Patient_1_normal_rep1_HG-U133A

description:
Patient1.1
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 1 normal adjacent sample


title: Patient_8_normal_rep1_HG-U133A

description:
Patient8.1
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 8 normal adjacent sample


title: Patient_5_normal_rep1_HG-U133A

description:
Patient5.1
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 5 normal adjacent sample


title: Patient_3_cancer_rep1_HG-U133A

description:
Patient3.2
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 3 primary colorectal adenocarcinoma


title: Patient_2_normal_rep1_HG-U133A

description:
Patient2.1
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 2 normal adjacent sample

value: rectosigmoid


title: H8.1001200141

description: Single_myeloid_1922_cells_processed_data.csv

source_name: Brain myeloid cell

value: CP


title: H8.1001200140


title: H7.1001200139


title: H7.1001200140


title: H9.1001200136


title: H9.1001200141


title: H9.1001200140


title: H8.1001200136


title: H6.1001200141

value: N


title: H6.1001200140


title: H6.1001200136


title: Patient_3_normal_rep1_HG-U133A

description:
Patient3.1
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 3 normal adjacent sample


title: H5.1001200141


title: H5.1001200140


title: H4.1001200140


title: H3.1001200140


title: Patient_2_cancer_rep1_HG-U133A

description:
Patient2.2
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 2 primary colorectal adenocarcinoma


title: H5.1001200139


title: H4.1001200139


title: H5.1001200136


title: Patient_8_cancer_rep1_HG-U133A

description:
Patient8.2
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

source_name: Patient 8 primary colorectal adenocarcinoma


title: H4.1001200136


title: H2.1001200140


title: 33_3_CD4+CD25highCD127low Treg

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in R

source_name: buffy coats of peripheral blood

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

growth_protocol: Freshly isolated CD4+ T cells and CD4+ T cells separated into CD25 negativ and positiv subpopulation activated with variuos conditions

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with NanoDrop ThermoScientific.

treatment_protocol: Immediately after isolation, cells were lysed in Trizol reagent or activated with CD3CD28 and either TGFb1 or PGE2

tag: cell type

value: CD4+CD25high-CD127 low

tag: treatment protocol

value: freshly isolated


title: H11.1001200141


title: H2.1001200139


title: 5_1_PGE2

description: replicate 1

value: CD4+ T cell

value: activated via CD3CD28 and treated with PGE2


title: 5_3_PGE2

description: replicate 3


title: H2.1001200136


title: 2_3_TGF_3

description: replicate 3

value: activated via CD3CD28 and treated with TGFb1


title: 28_3_CD4+CD25low

description: replicate 3


title: 33_1_CD4+CD25highCD127low Treg

description: replicate 1


title: 28_2_CD4+CD25low

description: replicate 2


title: 28_1_CD4+CD25low

description: replicate 1


title: 33_2_CD4+CD25highCD127low Treg

description: replicate 2


title: 5_2_PGE2

description: replicate 2


title: H11.1001200136


title: H11.1001200139


title: 4_3_IL10

description: replicate 3

growth_protocol: freshly isolated CD4+ T cells were treated either immediately after isolation or after 12 hrs of cell culture with the indicated conditions

treatment_protocol: immediately after isolation, cells were lysed in Trizol reagent.

value: 8 hrs culture with IL10


title: 2_1_TGF_1

description: replicate 1


title: 4_1_IL10

description: replicate 1


title: 2_2_TGF_2

description: replicate 2


title: 41_2_expTreg + RAPA +CD3/28

description: replicate 2

source_name: expanded CD4+CD25+ Treg cell (isolated from peripheral blood)

growth_protocol: freshly isolated CD4+ T cells, CD4+CD25- as well as CD4+CD25+ Treg cells were treated as indicated.

treatment_protocol: immediately after described treatment, cells were lysed in Trizol reagent.

tag: cell type subpopulation

value: CD25+ Treg

value: expanded in cell culture with Rapamycin with short-term CD3CD28 stimulation


title: H10.1001200141


title: H10.1001200136


title: H1.1001200141


title: H10.1001200140


title: 41_3_expTreg + RAPA +CD3/28

description: replicate 3


title: 18_1_Tconv_18h

description: replicate 1

growth_protocol: freshly isolated CD4+ T cells were treated either immediately after isolation or after 18 hrs of cell culture with the indicated conditions

value: 18 hrs culture


title: H1.1001200140


title: G9.1001200141


title: 41_1_expTreg + RAPA +CD3/28

description: replicate 1


title: 16_1_CD4 T cells

description: replicate 1

value: 8 hrs culture


title: 16_3_CD4 T cells

description: replicate 3


title: G9.1001200140


title: 18_3_Tconv_18h

description: replicate 3


title: 18_2_Tconv_18h

description: replicate 2


title: G8.1001200139


title: G9.1001200136


title: G8.1001200140


title: 4_2_IL10

description: replicate 2


title: 16_2_CD4 T cells

description: replicate 2


title: G6.1001200141


title: 17_2_Tconv_12h

description: replicate 2

source_name: peripheral blood

value: 12 hrs culture


title: 14_3_20h+10ng TGF

description: replicate 3

value: 20 hrs culture with TGFb1


title: 17_1_Tconv_12h

description: replicate 1


title: G7.1001200141

value: wild type

value: Y


title: G8.1001200136


title: G7.1001200139


title: 14_1_20h+10ng TGF

description: replicate 1


title: 3_2_VEGF

description: replicate 2

value: 8 hrs CD3CD28 activation + VEGF


title: 14_2_20h+10ng TGF

description: replicate 2


title: 9_1_aCD4+CD25-

description: replicate 1

value: CD4+CD25- Tconv cell

value: 24 hrs culture with CD3 and IL2


title: 39_2_expTreg + RAPA

description: replicate 2

value: expanded in cell culture with Rapamycin


title: 3_1_VEGF

description: replicate 1


title: 39_1_expTreg + RAPA

description: replicate 1


title: 9_2_aCD4+CD25-

description: replicate 2


title: G7.1001200136

value: CP


title: G6.1001200140


title: 17_3_Tconv_12h

description: replicate 3

value: CD4+ T cell


title: 39_3_expTreg + RAPA

description: replicate 3


title: 9_3_aCD4+CD25-

description: replicate 3


title: 26_2_CD4+CD25- Tconv 6h

description: replicate 2

source_name: CD4+CD25- T cell (isolated from peripheral blood)

value: cultured for 6 hrs


title: 3_3_VEGF

description: replicate 3


title: G4.1001200140


title: G4.1001200139

value: N


title: G4.1001200136


title: 26_1_CD4+CD25- Tconv 6h

description: replicate 1


title: G3.1001200139


title: 7_3_CTLA4

description: replicate 3

source_name: CD4+ T cell (isolated from peripheral blood)

value: activated via 8 hrs CD3CD28 + CTLA4


title: G2.1001200140


title: 7_2_CTLA4

description: replicate 2


title: G2.1001200139


title: G2.1001200141


title: G6.1001200139


title: G5.1001200140


title: G6.1001200136


title: G2.1001200136


title: 25_1_CD4+CD25- Tconv

description: replicate 1

source_name: 25_1_CD4+CD25- Tconv (isolated from buffy coats of peripheral blood)

growth_protocol: freshly isolated CD4+ T cells and CD4+ T cells separated into CD25 negativ and positiv subpopulation activated with variuos conditions

treatment_protocol: immediately after isolation, cells were lysed in Trizol reagent or activated with CD3, Cd3CD28, CD3IL2

value: CD25- non-Treg


title: 25_2_CD4+CD25- Tconv

description: replicate 2

source_name: CD4+CD25- Tconv cell (isolated from buffy coats of peripheral blood)


title: G5.1001200139


title: G3.1001200136


title: 1_3_CD3CD28

description: replicate 3

source_name: activated CD4+ T cell (isolated from buffy coats of peripheral blood)

value: activated via CD3CD28


title: 24_2_CD4+CD25- Tconv

description: replicate 2

source_name: CD4+CD25- T cell (isolated from buffy coats of peripheral blood)


title: 1_2_CD3CD28

description: replicate 2


title: 1_1_CD3CD28

description: replicate 1


title: 24_1_CD4+CD25- Tconv

description: replicate 1


title: 8_2_CD3

description: replicate 2

value: activated via CD3


title: G5.1001200136


title: G11.1001200141


title: G12.1001200136


title: G12.1001200139


title: G12.1001200140


title: 13_2_20h+1ng TGF

description: replicate 2

value: activated via TGFb1, cultured for 20 hrs


title: G11.1001200140


title: 13_3_20h+1ng TGF

description: replicate 3


title: 38_2_expTreg

description: replicate 2

growth_protocol: Freshly isolated CD4+CD25low/intCD127+ T cells; CD4+ T cells were cultured for 12 hrs followed by 8 hrs treatment as indicated. CD4+CD25+ Treg cells were expanded in cell culture.

treatment_protocol: Immediately after isolation or after described treatment, cells were lysed in Trizol reagent.

value: expanded CD4+CD25+ Treg

value: expanded in cell culture


title: 26_3_CD4+CD25- Tconv 6h

description: replicate 3


title: 8_3_CD3

description: replicate 3


title: G11.1001200139

value: wild type


title: G11.1001200136

value: Y


title: 8_1_CD3

description: replicate 1


title: G1.1001200140


title: G1.1001200136


title: G1.1001200139


title: G10.1001200139


title: 20_2_Tconv 20h

description: replicate 2

value: 20 hrs culture


title: G3.1001200140


title: F8.1001200141


title: 6_2_PD1

description: replicate 2

value: 8 hrs CD3CD28 activation + PD1


title: F9.1001200139


title: 38_3_expTreg

description: replicate 3


title: 7_1_CTLA4

description: replicate 1


title: F9.1001200136


title: F8.1001200139


title: 30_3_CD4+CD25low-int

description: replicate 3


title: 20_3_Tconv 20h

description: replicate 3


title: 30_1_CD4+CD25low-int

description: replicate 1


title: F9.1001200140


title: 6_3_PD1

description: replicate 3


title: F8.1001200140


title: F7.1001200141


title: 30_2_CD4+CD25low-int

description: replicate 2


title: 13_1_20h+1ng TGF

description: replicate 1


title: 35_2_CD4+CD25+ 6h Treg

description: replicate 2

growth_protocol: Freshly isolated CD4+CD25intCD127+ T cellls; CD4+ T cells were cultured for 12 hrs followed by 8 hrs treatment as indicated. CD4+CD25+ Treg cells were cultured for 6 hrs.

value: CD4+CD25+ Treg cell

value: 6 hrs culture


title: F7.1001200139

value: CP


title: 20_1_Tconv 20h

description: replicate 1

value: CD4+ T cell


title: 6_1_PD1

description: replicate 1

growth_protocol: Freshly isolated CD4+CD25low/intCD127+ T cells; CD4+ T cells were cultured as indicated. CD4+CD25+ Treg cells were expanded in cell culture.


title: 35_1_CD4+CD25+ 6h Treg

description: replicate 1


title: 29_2_CD4+CD25int

description: replicate 2

value: CD4+CD25intCD127+ T cell


title: 29_3_CD4+CD25int

description: replicate 3


title: F6.1001200139


title: F6.1001200141


title: F6.1001200140


title: F7.1001200136


title: F5.1001200141


title: F6.1001200136


title: G1.1001200141


title: 29_1_CD4+CD25int

description: replicate 1


title: 12_3_Tconv 18+8hrs TGF

description: replicate 3

growth_protocol: CD4+ T cells were cultured for 18 hrs followed by 8 hrs treatment as indicated.

value: 18 hrs culture, then 8 hrs treatment with TGFb1


title: F5.1001200140


title: 11_3_Tconv 18+2hrs TGF

description: replicate 3

growth_protocol: CD4+ T cells were cultured for 18 hrs followed by 2 hrs treatment as indicated.

value: 18 hrs culture, then 2 hrs TGFb1


title: 11_2_Tconv 18+2hrs TGF

description: replicate 2


title: F4.1001200141


title: 11_1_Tconv 18+2hrs TGF

description: replicate 1


title: F5.1001200139


title: 12_2_Tconv 18+8hrs TGF

description: replicate 2


title: F4.1001200140


title: F4.1001200139


title: F3.1001200141


title: F3.1001200140


title: F3.1001200139

value: N


title: F2.1001200141


title: F2.1001200140


title: F12.1001200140


title: F2.1001200139


title: F12.1001200139


title: F12.1001200136


title: MM231 cells transfected with eGFP/Flag vector, biological rep3

city: Pittsburgh

first: Yi

last: Huang

state: Pennsylvania

address: 204 Craft Ave

department: Pharmacology & Chemical Biology

institute: University of Pittsburgh Cancer Institute

description: control

hyb_protocol: cRNA was hybridized to U133A 2.0 arrays (Affymetrix, Santa Clara, CA)

scan_protocol: cRNA synthesis and labeling, hybridization, and scanning were performed by the University of Pittsburgh Cancer Biomarkers Facility

data_processing: The data were processed as RMA files (Affymetrix Robust Multi-Array Average) in which the raw intensity data were background corrected, log2 transformed, and then quantile normalized according to Affymetrix recommendations. The Student’s t-test was used to determine the statistical differences between various experimental and control groups. Microarray statistical tests were performed using Significance Analysis of Microarrays software (SAM version 3.09c), which is designed to reduce the risk of Type 1 errors due to multiple testing.

source_name: Breast cancer cell line

label_protocol: cRNA synthesis and labeling was performed using the Ambion MessageAmp Premier Kit (Life Technologies)

growth_protocol: normal culturing conditions for MDA-MB-231; 800ug/ml G-418 was added to medium to kill untransfected cells.

extract_protocol: QIAgen RNeasy Mini (Animal Cells Spin protocol, w/DNase I digest performed on homogenized lysate prior to applying lysate to column for purification)

tag: cell line

tag: genotype/variation

value: eGFP/Flag vector


title: MM231 cells transfected with LSD2 shRNA, biological rep2

description: modified

value: LSD2 shRNA knockdown


title: F11.1001200139


title: MM231 cells transfected with LSD2 shRNA, biological rep3

description: modified


title: 12_1_Tconv 18+8hrs TGF

description: replicate 1


title: MM231 cells transfected with eGFP/Flag vector, biological rep2

description: control


title: MM231 cells transfected with LSD2/eGFP/Flag vector, biological rep3

description: modified

value: LSD2/eGFP/Flag vector overexpression


title: F10.1001200139


title: MM231 cells transfected with LSD2/eGFP/Flag vector, biological rep2

description: modified


title: MM231 cells transfected with Scramble shRNA, biological rep1

description: control

value: Scramble shRNA


title: MM231 cells transfected with Scramble shRNA, biological rep3

description: control


title: F10.1001200136


title: MM231 cells transfected with LSD2/eGFP/Flag vector, biological rep1

description: modified


title: MM231 cells transfected with eGFP/Flag vector, biological rep1

description: control


title: MM231 cells transfected with LSD2 shRNA, biological rep1

description: modified


title: F1.1001200141


title: KL_3_Namalwa_scr_1

city: Ulm

first: Alexey

last: Ushmorov

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

institute: Ulm University

description: Namalwa transduced with a lentiviral vector expressing scrambled shRNA

hyb_protocol: Labeled ssDNA was hybridized to Human Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA).

scan_protocol: The chips were scanned with a Affymetrix GeneChip Scanner 3000 according to the Affimetrix protocol.

data_processing: The microarray data were processed using GeneSifter software (http://www.geospiza.com) using RMA normalization protocol.

source_name: Namalwa scr-1

label_protocol: The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com).

growth_protocol: BL41 and Namalwa BL cells were grown in RPMI1640 medium with addition of 15 % FBS, glutamine and antibiotics at 37 ºC, 5% CO2.

extract_protocol: Total RNA was isolated with RNeasy mini kit (QIAGEN) according to the manufacturers instruction.

treatment_protocol: BL41 and Namalwa BL cells were transduced with a lentiviral vector expressing scrambled shRNA of shRNA tageting human FOXO1 mRNA. The infected cells were sorted on day 4 after transduction.  The experiment was done in duplicate.  Total RNA was isolated with RNeasy mini kit (QIAGEN).

value: Namalwa

value: Burkitt's lymphoma


title: KL_3_Namalwa_scr_2

source_name: Namalwa scr-2


title: KL_4_Namalwa_F1sh81_2

description: Namalwa transduced with a lentiviral vector expressing FOXO1 shRNA

source_name: Namalwa shFOXO1-2


title: F11.1001200141

source_name: Brain myeloid cell

value: wild type

value: Y


title: MM231 cells transfected with Scramble shRNA, biological rep2

description: control


title: KL_4_Namalwa_F1sh81_1

source_name: Namalwa shFOXO1-1


title: KL_2_BL41_F1sh81_2

description: BL41 transduced with a lentiviral vector expressing FOXO1 shRNA

source_name: BL41 shFOXO1-2


title: KL_2_BL41_F1sh81_1

source_name: BL41 shFOXO1-1


title: F1.1001200140


title: E9.1001200141


title: E9.1001200140


title: E9.1001200139


title: E9.1001200136


title: E8.1001200141


title: KL_1_BL41_scr_2

description: BL41 transduced with a lentiviral vector expressing scrambled shRNA

source_name: BL41 scr-2


title: E8.1001200140


title: E7.1001200141


title: KL_1_BL41_scr_1

source_name: BL41 scr-1


title: E7.1001200140


title: E7.1001200139


title: E7.1001200136


title: E6.1001200141


title: E6.1001200139


title: HBL-1 C D2

city: CABA

first: Stella

last: Ranuncolo

state: Buenos Aires

address: Potosí 4240

country: Argentina

institute: Instituto Universitario del Hospital Italiano (IUHI)

hyb_protocol: Sense strand DNA was fragmented and labeled using Affymetrix WT terminal labeling kit. Four replicates of each group were hybridized to Affymetrix mouse (human) Gene ST 1.0 GeneChip in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs. Wash and stain were performed on Affymetrix Fluidics Station 450.

scan_protocol: Scanned on Affymetrix GeneChip scanner 3000.  Data were collected using Affymetrix AGCC software.

data_processing: Statistical and clustering analysis was performed with Partek Genomics Suite software using RMA normalization algorithm.  Differentially expressed genes were identified with ANOVA analysis.

label: Biotin

source_name: HBL-1 ABC-Like DLBCL cell line

label_protocol: biotin

growth_protocol: U-H01 HL cell line growths in RPM1 + ATB + 20% FBS and HBL-1 cells growth in RPMI + ATB +10% FBS

extract_protocol: Total RNA was isolated using RNAeasy kit from QUIAGEN. ARN quality was checked on Agilent Bioanalyzer. All samples used for microarray analysis have high quality score (RIN >9). 100 ng of RNA was reverse transcribed and amplified using Ambion WT expression kit following manufacturer’s suggested protocol.

treatment_protocol: U-H01 and HBL-1 cells were infected with an shRNA for Rel-B and a shRNA for cRel (two different sequences were applied in ech case). Half of the trasnduced population was induced with doxycylin to allow the hairpin expression and half was uninduced. Two time point were tried.

value: HBL-1 ABC-Like DLBCL

tag: treatment

value: knock-down Day2 treated


title: HBL-1 C Un1

value: shRNA infected not treated


title: HBL-1 C Un2


title: E5.1001200141

value: CP


title: HBL-1 C D1

value: knock-down Day1 treated


title: U-H01 B2 D2

source_name: U-H01 HL cell line

value: U-H01 HL

value: knock-down Seq2 D2 treated


title: U-H01 B2 Un2


title: U-H01 B2 D1

value: knock-down Seq2 D1 treated


title: U-H01 B2 Un1


title: E5.1001200140


title: E5.1001200139

value: N


title: U-H01 B1 Un1


title: E5.1001200136


title: ApcMin QKO adenomas rep 2

city: Cambridge

first: Laurens

middle: Moore

last: van Tienen

state: Cambridgeshire

address: Francis Crick Avenue

department: PNAC

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description:
replicate 2
SAMPLE 31

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Sample and control probe profiles were exported from Illumina GenomeStudio software v2011.1 without background correction or normalization, and subsequently loaded into the R environment. Relevant subsets of the data were imported separately for each comparison into a LumiBatch object, and filtered by keeping probes that were detected in at least one sample (using a detection p-value < 0.01). The data were then quality-controlled, transformed (Variance Stabilizing Transformation, VST) and quantile-normalized with the lumi v2.30.0 package, and non-biological experimental variation between the two microarray sample batches was eliminated with the ComBat function from the SVA v3.26.0 package. Differentially expressed genes were identified with the limma v3.34.9 package, and p-values were corrected for using the Benjamini & Hochberg False Discovery Rate.

source_name: inestinal adenomas

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit.

extract_protocol: Tissue was flash-frozen in liquid nitrogen and stored at -80 °C for for <24 months. Frozen samples were thawed on ice in RLT buffer containing 1% Beta-mercaptoethanol, and homogenized with a Qiagen TissueRuptor followed by QIAshredder columns according to the manufacturer's instructions. RNA was extracted from tissue lysates with the RNeasy Kit, and treated with RNase-free DNase I. The concentration and quality was determined with a NanoDrop 2000 and a 2100-Bioanalyzer. RNA was linearly amplified with the Illumina Totalprep RNA Amplification Kit, and the resulting cRNA was hybridized to the MouseWG-6 v2.0 Expression BeadChip overnight; subsequently, the BeadChip was washed, stained, and scanned with the Illumina BeadArray Reader.

value: ApcMin/+, Bcl9 LoxP/LoxP, B9l LoxP/LoxP, Pygo1-/-, Pygo2 LoxP/LoxP, villin.Cre/+

value: 120 days

value: intestinal adenoma

tag: tissue extraction method

value: excision

tag: batch number


title: U-H01 B1 Un2


title: U-H01 B1 D1

value: shRNA Knock-down D1 treated


title: E4.1001200139


title: ApcMin Bcl9/B9l DKO adenomas rep 3

description:
replicate 3
SAMPLE 29

value: ApcMin/+, Bcl9 LoxP/LoxP, B9l LoxP/LoxP, villin.Cre/+


title: ApcMin QKO adenomas rep 1

description:
replicate 1
SAMPLE 30


title: E4.1001200141

value: wild type


title: E6.1001200136

value: Y


title: E6.1001200140


title: E3.1001200141


title: ApcMin QKO adenomas rep 3

description:
replicate 3
SAMPLE 32


title: E3.1001200139


title: ApcMin Bcl9/B9l DKO adenomas rep 1

description:
replicate 1
SAMPLE 27


title: ApcMin Pygo1/2 DKO adenomas rep 5

description:
replicate 5
SAMPLE 26

value: ApcMin/+, Pygo1-/-, Pygo2 LoxP/LoxP, villin.Cre/+


title: E3.1001200136


title: U-H01 B1 D2

value: Knock-down D2 treated


title: E2.1001200141


title: ApcMin Pygo1/2 DKO adenomas rep 2

description:
replicate 2
SAMPLE 23


title: E2.1001200140


title: ApcMin Pygo1/2 DKO adenomas rep 3

description:
replicate 3
SAMPLE 24


title: E4.1001200136


title: E2.1001200139


title: E2.1001200136


title: E12.1001200141


title: ApcMin Bcl9/B9l DKO adenomas rep 2

description:
replicate 2
SAMPLE 28


title: ApcMin Pygo1/2 DKO adenomas rep 1

description:
replicate 1
SAMPLE 22


title: ApcMin adenomas rep 9

description:
replicate 9
SAMPLE 21

value: ApcMin/+


title: ApcMin adenomas rep 8

description:
replicate 8
SAMPLE 20


title: ApcMin adenomas rep 7

description:
replicate 7
SAMPLE 19


title: ApcMin Pygo1/2 DKO adenomas rep 4

description:
replicate 4
SAMPLE 25


title: E11.1001200141

value: CP


title: ApcMin adenomas rep 6

description:
replicate 6
SAMPLE 18


title: E12.1001200139


title: E3.1001200140


title: ApcMin adenomas rep 5

description:
replicate 5
SAMPLE 17


title: E11.1001200136


title: E11.1001200140


title: ApcMin adenomas rep 4

description:
replicate 4
SAMPLE 16


title: ApcMin adenomas rep 2

description:
replicate 2
SAMPLE 14


title: E11.1001200139


title: E10.1001200141


title: E10.1001200140


title: ApcMin adenomas rep 1

description:
replicate 1
SAMPLE 13


title: E10.1001200139


title: Bcl9/B9l DKO crypt rep 1

description:
replicate 1
SAMPLE 10

source_name: EDTA dissociated intestinal epithelial tissue

value: Bcl9LoxP/LoxP, B9l LoxP/LoxP, villin.Cre/+

value: intestinal epithelium

value: EDTA dissociation


title: E1.1001200141


title: Bcl9/B9l DKO crypt rep 2

description:
replicate 2
SAMPLE 11


title: E1.1001200139


title: Bcl9/B9l DKO crypt rep 3

description:
replicate 3
SAMPLE 12


title: E1.1001200136


title: D9.1001200141


title: D9.1001200139


title: D9.1001200136


title: D8.1001200139


title: D8.1001200141


title: ApcMin adenomas rep 3

description:
replicate 3
SAMPLE 15


title: Pygo1/2 DKO crypt rep 1

description:
replicate 1
SAMPLE 7

value: Pygo1-/-, Pygo2 LoxP/LoxP, villin.Cre/+


title: D8.1001200136


title: wt crypt (villin.Cre/+) rep 1

description:
replicate 1
SAMPLE 4

value: wt (villin.Cre/+)


title: wt crypt rep 3

description:
replicate 3
SAMPLE 3

value: wt


title: Pygo1/2 DKO crypt rep 3

description:
replicate 3
SAMPLE 9

value: 120 days


title: wt crypt (villin.Cre/+) rep 3

description:
replicate 3
SAMPLE 6


title: wt crypt rep 1

description:
replicate 1
SAMPLE 1


title: wt crypt rep 2

description:
replicate 2
SAMPLE 2


title: D7.1001200139


title: wt crypt (villin.Cre/+) rep 2

description:
replicate 2
SAMPLE 5


title: D7.1001200136


title: D6.1001200141


title: D7.1001200141


title: D6.1001200140


title: D7.1001200140


title: D6.1001200139


title: Pygo1/2 DKO crypt rep 2

description:
replicate 2
SAMPLE 8


title: VEGFR1 del + AAV-VEGF-B 3

city: Helsinki

first: Riikka

last: Kivelä

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki and Wihuri Research Institute

description: SAMPLE 11

data_processing: The data were normalised using quantile normalisation with Chipster software (www.chipster.csc.fi)

source_name: Heart

extract_protocol: Total RNA was isolated from the heart with TRIsure reagent (Bioline) and further purified with NucleoSpin RNA II (Macherey-Nagel). Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cdh5-Cre-ERT2; Flt1 flox/flox adult male mice were treated with tamoxifen to delete VEGFR1 in endothelial cells. AAV-VEGF-B was injected i.p. to induce overexpression of VEGF-B in the heart.

tag: Sex

value: male

value: VEGFR1 del + AAV-VEGF-B


title: D6.1001200136


title: VEGFR1 del + AAV-VEGF-B 4

description: SAMPLE 12


title: VEGFR1 del + AAV-Scramble 3

description: SAMPLE 6

value: VEGFR1 del + AAV-Scramble


title: D5.1001200141


title: WT heart + AAV-VEGF-B 1

description: SAMPLE 7

value: WT + AAV-VEGF-B


title: VEGFR1 del + AAV-Scramble 2

description: SAMPLE 5


title: VEGFR1 del + AAV-VEGF-B 2

description: SAMPLE 10


title: WT heart + AAV-VEGF-B 2

description: SAMPLE 8


title: VEGFR1 del + AAV-VEGF-B 1

description: SAMPLE 9


title: WT heart + AAV-Scramble 2

description: SAMPLE 2

value: WT + AAV-Scramble


title: VEGFR1 del + AAV-Scramble 1

description: SAMPLE 4


title: WT heart + AAV-Scramble 3

description: SAMPLE 3


title: D5.1001200140

value: wild type

value: Y

value: N


title: D5.1001200139


title: D4.1001200141


title: D3.1001200136


title: D2.1001200141


title: D3.1001200141


title: D2.1001200140


title: D2.1001200139


title: D2.1001200136


title: D12.1001200141


title: D12.1001200139


title: D12.1001200136


title: D12.1001200140


title: D11.1001200141


title: D11.1001200140


title: D10.1001200141


title: D11.1001200139


title: D10.1001200140


title: WT1 LSC

city: Houston

first: Toni-Ann

last: Mistretta

state: TX

address: 1 Baylor Plaza, BCM 315

department: Pathology

institute: Baylor College of Medicine

description: Wild Type 1

hyb_protocol: Asuragen Inc. performed target preparation and quality control measures for hybridization, scanning, and image analysis of Illumina arrays

scan_protocol: Illumina Scanner by Asuragen, Inc.

data_processing: The image signal quantitation results are generated by Illumina BeadStudio Software and are background-subtracted.

organism: Mus

source_name: CML bone marrow

tag: tumor type

value: WT LSC

tag: gender

value: 14 days post BMT


title: WT heart + AAV-Scramble 1

description: SAMPLE 1


title: Wildtype_β-Catenin_(Tamoxifen treated)_rep 1 [induced post-injury]

city: Toronto

first: Benjamin

last: Alman

state: Ontario

address: TMDT, 101 College Street

department: Developmental and Stem Cell Biology

country: Canada

institute: Hospital for Sick Children

description:
sample name: 4
biological replicate 1

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: The data was normalized using the neqc function in R (v 2.14) limma package.

source_name: Wildtype_β-Catenin_(Tamoxifen treated)

label_protocol: Ambion - Illumina TotalPrep-96 RNA Amplification Kit

extract_protocol: Total RNA was extracted from full thickness cutaneous wounds using the Qiagen Rneasy Mini Kit (Qiagen Inc., Mississauga, ON, Canada), following the manufacturer's instructions.  RNA quality and integrity was checked by Bioanalyzer (Agilent Technologies).

tag: strain background

value: β-Catenin flox/flox (exons 2-6)

value: 4 months

tag: time-point

value: wound eight days post injury

value: Dorsal full thickness wound (skin)


title: D10.1001200136

tag: strain

tag: genotype

value: CP


title: KO1 LSC

description: Knock Out 1

label_protocol: Asuragen Inc. performed target preparation and quality control measures for hybridization, scanning, and image analysis of Illumina arrays

value: KLF4-deficient LSC


title: Adenovirus-CRE_treated_Stabilized_β-Catenin_rep 1 [induced post-injury]

description:
sample name: 10 Cre
biological replicate 1

value: β-Catenin flox/flox (exon 3)

tag: age

value: 2 months

tag: tissue


title: KO3 LSC

description: Knock Out 3

extract_protocol: Asuragen Inc. performed target preparation and quality control measures for hybridization, scanning, and image analysis of Illumina arrays

tag: cell type


title: D1.1001200141

tag: gate


title: KO2 LSC

description: Knock Out 2

treatment_protocol: Asuragen Inc. performed target preparation and quality control measures for hybridization, scanning, and image analysis of Illumina arrays


title: D1.1001200140


title: β-Catenin_Knockdown_(Tamoxifen Treated)_rep 2 [induced post-injury]

description:
sample name: 5
biological replicate 2

source_name: β-Catenin_Knockdown_(Tamoxifen Treated)

value: β-Catenin flox/flox (exons 2-6);Cre-Esr1

value: 5 months


title: WT3 LSC

description: Wild Type 3


title: β-Catenin_Knockdown_(Tamoxifen Treated)_Replicate_2

description:
sample name: H
biological replicate 2

data_processing: The data was normalized using the neqc function in R (v 2.14) 1limma package.

value: eight days post injury


title: WT2 LSC

description: Wild Type 2


title: Wildtype_β-Catenin_(Tamoxifen treated)_rep 2 [induced post-injury]

description:
sample name: 6
biological replicate 2


title: Adenovirus-GFP_treated_Wildtype_β-Catenin_rep 1 [induced post-injury]

description:
sample name: 3 GFP
biological replicate 1


title: Adenovirus-CRE_treated_Stabilized_β-Catenin_Replicate_1

description:
sample name: CRE Stab
biological replicate 1

data_processing: The data was normalized using the neqc function in R (v 2.14) 1limma package


title: β-Catenin_Knockdown_(Tamoxifen_Treated)_rep 1 [induced post-injury]

description:
sample name: 1
biological replicate 1


title: β-Catenin_Knockdown_(Tamoxifen_Treated)_Replicate_1

description:
sample name: A
biological replicate 1


title: Control_β-Catenin_(Tamoxifen treated)_Replicate_1

description:
sample name: B
biological replicate 1

source_name: Control_β-Catenin_(Tamoxifen treated)


title: Control_β-Catenin_(Tamoxifen treated)_Replicate_2

description:
sample name: F
biological replicate 2


title: C9.1001200141


title: C9.1001200140


title: D1.1001200139


title: C8.1001200141


title: C9.1001200139


title: C9.1001200136


title: 836MS0218-20110324

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

description: TotalEmbryoContro

hyb_protocol: Following fragmentation, the RNA was loaded on to the Affymetrix Mouse-1_0-st-v1 GeneChip as directed (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G

data_processing: The primary microarray data was normalized using RMA method in Affymetrix Expression Console 1.1.

source_name: Total Embryo

label_protocol: The RNA was labeled with GeneChipR One-Cycle Target Labeling and Control Reagents.

extract_protocol: H2BVenus+ cells were directly FACS'd into Trisol-LS for extraction of RNA following procedures modified from the vendor's instructions (detailed protocol posted at www.gudmap.org).  All samples were DNAse treated, assayed on Agilent Bioanalyzer to assess integrity and quantified by Ribogreen assay prior to microarray hybridization.

treatment_protocol: The lower urogenital tract comprising of the bladder, flanking blood vessels, pelvic ganglia and urethra at the level of the pelvic ganglia are sub-dissected from Sox10-H2BVenus transgenic mice. Cells are isolated from the dissected tissue by dissociation in Accumax, filtration and fluorescence activated cell sorting for YFP positive cells.

value: Total Embryo


title: C8.1001200140

value: wild type


title: C8.1001200139

value: Y


title: C8.1001200136


title: C7.1001200140


title: C7.1001200139


title: C7.1001200136


title: 2090MS0001-20130729

description: TotalEmbryoContro


title: Adenovirus-GFP_treated_Control_β-Catenin_replicate_1

description:
sample name: GFP Stab
biological replicate 1


title: 836MS218-20091015

description: TotalEmbryoContro


title: C6.1001200141


title: 836MS0218-20091130

description: TotalEmbryoContro


title: 836MS0218-20110112

description: TotalEmbryoContro


title: 2090MS0003-20120126

source_name: Sox10-H2BVenus+ sacral neural crest (NC) progenitors


title: 2090MS0001-20120126

description: TotalEmbryoContro


title: 2090MS0001-20120510

description: TotalEmbryoContro


title: C6.1001200139

source_name: Brain myeloid cell


title: 2090MS0004-20120126

value: Sox10-H2BVenus+ sacral neural crest (NC) progenitors


title: 2090MS0002-20120126


title: Maf control #3

city: Heidelberg

first: Hagen

last: Wende

address: Im Neuenheimer Feld 366

department: Institute of Pharmacology

institute: Heidelberg University

description: replicate 1

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were normalised using RMA normalisation with Partek Genomic Suite 6.5, batch effects between strains were removed

source_name: sciatic nerve

label_protocol: cDNA was prepared with the GeneChipTM WT PLUS Reagent Kit

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: C57/BL6;129Ola mixed

tag: genotype c-maf

value: Maf flox/flox

value: sciatic nerve


title: Maf control #1

description: replicate 1


title: Maf control #5

description: replicate 1


title: Maf mutant #5

description: replicate 1

value: Egr2-Cre; Maf -/flox


title: Maf control #2

description: replicate 1


title: Maf control #4

description: replicate 1


title: C5.1001200140

data_processing:
Prinseq (version 0.20.4) was first used to filter sequencing reads shorter than 30 bp (-min_len 30), trim the first 10 bp at the 5’-end (-trim_left 10) of the reads, trim reads with low quality from the 3’-end (-trim_qual_right 25) and remove low complexity reads (-lc_method entropy, -lc_threshold 65).
Trim Galore (version 0.4.3) was applied to trimmed the Nextera adapters (--stringency 1).
The remaining reads were aligned to the mm10 genome by calling STAR (version 2.5.3a) with the following options: --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMstrandField intronMotif.
Picard was then used to remove the duplicate reads (VALIDATION_STRINGENCY=LENIENT, REMOVE_DUPLICATES=true).
The aligned reads were converted to counts for each gene by using HTSeq (-m intersection-nonempty, -s no)
To filter out cells with low sequencing quality, three criteria, namely the number of total reads, the number of total detected genes and correlation coefficient between ERCC spike-ins input and corresponding read counts, were each evaluated based on the distributions of the data. The distribution of the total reads (in logarithmic scale) was fitted by a truncated Cauchy distribution, and data points in two tails of the estimated distribution were considered as outliers and eliminated. Fitting and elimination were then applied to the remaining data. This process was run iteratively until the estimated distribution became stable. The threshold was set to the value where the cumulative distribution function of the estimated distribution reaches 0.05. Similarly, cells with small numbers of detected genes, and poor correlation coefficients for ERCC (low sequencing accuracy) were dropped. After filtering, 1816 cells, out of 1922, were retained.
Genome_build: mm10
Supplementary_files_format_and_content: Common delimited file (csv) containing all 1922 cells and mapped gene counts (including counts for ERCC spike-ins)


title: C5.1001200139

value: N


title: C4.1001200141


title: Maf mutant #4

description: replicate 1

value: Egr2-Cre; Maf flox/flox


title: C4.1001200139

value: CP


title: C4.1001200140


title: C4.1001200136


title: C3.1001200141


title: C3.1001200139


title: Maf mutant #3

description: replicate 1


title: Maf mutant #2

description: replicate 1


title: C2.1001200141


title: Maf mutant #1

description: replicate 1


title: C2.1001200136


title: C12.1001200141


title: C12.1001200139


title: C12.1001200140


title: C11.1001200141


title: C12.1001200136


title: ErbB2 control #5

description: replicate 1

value: ErbB2 flox/flox


title: ErbB2 control #4

description: replicate 1


title: C11.1001200140


title: ErbB2 control #3

description: replicate 1


title: ErbB2 control #2

description: replicate 1


title: ErbB2 mutant #3

description: replicate 1

value: Egr2-Cre; ErbB2 flox/flox


title: C11.1001200139


title: ErbB2 mutant #5

description: replicate 1


title: ErbB2 mutant #4

description: replicate 1

value: Egr2-Cre; ErbB2 -/flox


title: ErbB2 control #1

description: replicate 1


title: ErbB2 mutant #1

description: replicate 1


title: ErbB2 mutant #2

description: replicate 1


title: C10.1001200141


title: C10.1001200139


title: C10.1001200136


title: C1.1001200141


title: C1.1001200140


title: C1.1001200139


title: C11.1001200136


title: RPE/choroid_WT_IFNg-infusion_rep1

city: Copenhagen

first: Carsten

last: Faber

address: Blegdamsvej 3

department: Fac. of Health Science, ISIM

country: Denmark

institute: University of Copenhagen

hyb_protocol: Standard protocol

scan_protocol: Standard protocol

data_processing: Expression Console 1.1 (Affymetrix)

source_name: RPE/choroid

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

extract_protocol: Nucleospin RNA XS (Macherey-Nagel, Düren, Germany)

value: WT

tag: infection

value: IFNg-infusion


title: RPE/choroid_WT_unstimulated_rep8

tag: genotype/variation

value: unstimulated


title: RPE/choroid_WT_PBS-infusion_rep4

value: PBS-infusion


title: RPE/choroid_WT_PBS-infusion_rep1


title: RPE/choroid_WT_IFNg-infusion_rep2


title: RPE/choroid_WT_IFNg-infusion_rep4


title: RPE/choroid_WT_PBS-infusion_rep3


title: RPE/choroid_WT_IFNg-infusion_rep3


title: B9.1001200139

value: wild type


title: B9.1001200140

value: Y


title: C10.1001200140


title: B9.1001200141


title: B9.1001200136


title: RPE/choroid_WT_unstimulated_rep6


title: RPE/choroid_WT_PBS-infusion_rep2


title: RPE/choroid_WT_unstimulated_rep7


title: RPE/choroid_WT_unstimulated_rep5


title: B8.1001200141


title: RPE/choroid_IFNg-KO_LCMV_day 8_rep4

tag: genotype/variaion

value: IFNg-KO

value: LCMV day 8


title: RPE/choroid_IFNg-KO_LCMV_day 8_rep3


title: B8.1001200140


title: RPE/choroid_WT_LCMV_day 8_rep4


title: RPE/choroid_WT_LCMV_day 8_rep3


title: RPE/choroid_IFNg-KO_LCMV_day 8_rep1


title: RPE/choroid_WT_LCMV_day 8_rep2


title: RPE/choroid_IFNg-KO_LCMV_day 8_rep2


title: B7.1001200140


title: RPE/choroid_WT_LCMV_day 8_rep1


title: B7.1001200141


title: B6.1001200141


title: B6.1001200139


title: B6.1001200140


title: B7.1001200139


title: B4.1001200141


title: B5.1001200141


title: B6.1001200136


title: B8.1001200139


title: B5.1001200139


title: B4.1001200140


title: RPE/choroid_WT_LCMV_day 3_rep4

value: LCMV day 3


title: RPE/choroid_IFNAR-KO_LCMV_day 3_rep4

value: IFNAR-KO


title: RPE/choroid_IFNAR-KO_LCMV_day 3_rep3


title: RPE/choroid_IFNAR-KO_LCMV_day 3_rep2


title: RPE/choroid_WT_LCMV_day 3_rep2


title: B5.1001200140


title: B4.1001200139


title: RPE/choroid_WT_LCMV_day 3_rep3


title: RPE/choroid_WT_unstimulated_rep1


title: RPE/choroid_WT_unstimulated_rep2


title: 38_1_expTreg

description: replicate 1

source_name: peripheral blood

value: expanded CD4+CD25+ Treg

tag: treatment protocol

value: expanded in cell culture


title: RPE/choroid_WT_unstimulated_rep4


title: RPE/choroid_WT_LCMV_day 3_rep1


title: RPE/choroid_IFNAR-KO_LCMV_day 3_rep1


title: B3.1001200139


title: B3.1001200141


title: B3.1001200140


title: B3.1001200136


title: B2.1001200140


title: RPE/choroid_WT_unstimulated_rep3


title: B11.1001200140


title: B2.1001200141


title: B12.1001200140


title: B2.1001200139


title: B11.1001200139


title: eWAT KO4

city: Slat Lake City

first: Sihem

last: Boudina

institute: University of Utah

data_processing:
De-mulitplexed fastq files were aligned to the genome containing using Novocraft Novoalign (version 2.8.1). The index contained all known and theoretical splice juctions prepared using USeq MakeTranscriptome (version 8.5.4). Up to 50 alignments are allowed. Alignments to splices are converted to genomic alignments using USeq SamTranscriptomeParser (version 8.5.4), allowing for one alignment per read, and converted to Bam files.
RNA quality metrics was evaluated  with Picard CollectRnaSeqMetrics.
Gene counts were generated for Ensembl genes (multiple genic transcripts collapsed into a single, merged transcript) using USeq DefinedRegionDifferentialSeq (version 8.5.4). FPKM expression values were generated based on the counts.
Genome_build: mm10
Supplementary_files_format_and_content: File containing gene identifiers (Ensembl identifier plus common name), raw gene counts, and FPKM normalized expression values.

molecule: polyA RNA

source_name: epididymal adipose tissue

extract_protocol:
Intact poly(A) RNA was purified from total RNA samples (100-500 ng) with oligo(dT) magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit (RS-122-2101, RS-122-2102).  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 10 nM and equal volumes were pooled in preparation for Illumina sequence analysis.
HiSeq 50 Cycle Single-Read Sequencing v3  Sequencing libraries (18 pM) were chemically denatured and applied to an Illumina TruSeq v3 single read flowcell using an Illumina cBot.  Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina TruSeq SR Cluster Kit v3-cBot-HS (GD-401-3001).   Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCS v2.0.12 and RTA v1.17.21.3), a 50 cycle single read sequence run was performed using TruSeq SBS v3 sequencing reagents (FC-401-3002).

treatment_protocol: Mice were treated with Tamoxifen

value: Epididymal adipose tissue

value: Adiponectin-Cre ERT2-Atg3 flox/flox


title: B11.1001200141

extract_protocol:
For the E14.5 stage, whole brains were dissected out from timed embryos, and collected into 1ml PBS with 1% fetal bovine serum (added 10ul Ambion DNase I, 2ul RNase inhibitor) on ice. The sample was passed through a 26G needle 5-10 times to create single cell suspension. Cells were spun down (500g) at 4˚C for 5min, and suspended in 1ml PBS for FACS staining. Single live cells in the cKit-CD45+ gate were sorted into 96-well plates for library preparation.  For P7 and P60 stages, cortex (CTX), cerebellum (CB), hippocampus (HIP), striatum (STR), olfactory bulb (OB) and choroid plexus (CP) were dissected out. Tissues from the same region were pooled from multiple mice (3-8 depending on the ages and regions) into a 6cm petri dish with 200ul cold medium A on ice (15mM HEPES, 0.5% glucose in 1 X Hanks' Balanced Salt Solution (HBSS without phenol red)). Microglia (myeloid cells) extraction was carried out on ice following a published protocol (Bennett et al. PNAS. 2016) through douncing, MACS myelin removal and FACS staining. Single live cells in the CD45lowCD11b+ (microglia) or CD45hiCD11b+ (myeloid cells) gate were sorted into 96-well plates for library preparation.
Sequencing libraries were prepared following the published Smart-seq2 protocol with the aid of liquid handling robotics (Picelli et al. Nature Protocols. 2014). Briefly, plates with sorted cells were thawed on ice and incubated at 72˚C for 3 min in order to anneal RNAs to the Oligo-dT30VN primer. After that, 6ul reverse transcription mixture (95U SMARTScribe™ Reverse Transcriptase (100U/ul, Clontech 639538), 10U RNase inhibitor (40U/ul), 1XFirst-Strand buffer, 5mM DTT, 1M Betaine, 6mM MgCl2, 1uM TSO (Exiqon, Rnase free HPLC purified)) was added into each well, and RT was performed at 42˚C for 90 min, followed by 70˚C, 5 min. To amplify cDNA, 15ul PCR amplification mix (1X KAPA HIFI Hotstart Master Mix (Kapa Biosciences KK2602), 0.1uM ISPCR Oligo (AAGCAGTGGTATCAACGCAGAGT), 0.56U Lambda Exonuclease (5U/ul, New England BioLabs M0262S)) was added, and the following PCR program was used: (1) 37˚C 30 min; (2)95˚C 3 min; (3) 21 cycles of 98˚C 20 sec, 67˚C 15 sec, 72˚C 4 min; (4) 72˚C 5 min. Amplified cDNA samples were then purified with PCRClean DX beads (0.7:1 ratio, Aline C-1003-50), and resuspended in 20ul EB buffer. cDNA quality was examined with a Fragment Analyzer (AATI, High Sensitivity NGS Fragment Analysis Kit:1 bp - 6000 bp) following the manufacture’s instruction. Samples with sufficient amount of cDNA content (>0.05ng/ul) and normal peaks on the quantification graphs were retained for library preparation. To make libraries, all samples were first diluted down to 0.15ng/ul (only if higher than 0.15ng/ul) in 384-well plates using Mantis Liquid Handler (Formulatrix) and Mosquito X1 (TTP Labtech) with customized scripts. Nextera XT DNA Sample Prep Kit (Illumina FC-131-1096) was used at 1/10 of recommendation volume, with the help of a Mosquito HTS robot for liquid transfer. Specifically, tagmentation was done in 1.6ul (1.2ul Tagment enzyme mix, 0.4ul diluted cDNA) at 55˚C, 10 min. Neutralization buffer was added 0.4ul per well and incubated at room temperature for 5 min to stop the reaction. Then 0.8ul Illumina Nextera XT 384 Indexes (0.4ul each, 5uM from 4 sets of 96 indexes) and 1.2ul PCR master mix were added to amplify whole transcriptomes using the following program: (1) 72˚C 3 min; (2) 95˚C 30 sec; (3) 10 cycles of 95˚C 10 sec, 55˚C 30 sec, 72˚C 1 min; (4) 72˚C 5 min. Libraries from a single 384 plate were pooled together in an Eppendorf tube and purified twice with PCRClean DX beads. The quality and concentrations of the final mixed libraries were measured with Bioanalyzer and Qubit, respectively, before Illumina Nextseq sequencing.

value: CP


title: B11.1001200136


title: B10.1001200141


title: eWAT KO3


title: eWAT WT3


title: eWAT WT2


title: B10.1001200136


title: B10.1001200139


title: eWAT KO1


title: B12.1001200141


title: B1.1001200140


title: eWAT WT4


title: A9.1001200141


title: 20160118_C88_170330_8

city: Ramat Gan

first: Isabelle

last: Stévant

address: Institute of Nanotechnology and Advanced Materials, Building 206

country: Israel

institute: University of Bar Ilan

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Some libraries were sequenced twice because of a technical issue and the Fastq files of the two runs were merged and are annotated as « merged » in the sample and fastq file name.
FastQ files were mapped with GemTools (version 1.7.1) to the mouse reference genome (GRCm38.p3) and the genome annotation (version M4) downloaded from GENCODE, with an extra fake “Z” chromosome  with the GFP sequence.
RPKM (Reads Per Kilobase of exon per Million reads mapped) were computed with an in house pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each sample

source_name: XX gonad

extract_protocol:
XX gonads were collected in PBS at room temperature. PBS was removed and tissues were digested 10 minutes at 37°C with trypsin/EDTA 0.05% and filtered through a 40µm cell strainer to obtain single cell suspension. Nr5a1-eGFP+ cells were then sorted by fluorescent-active cell sorting (BD FACSARIA II) with Draq7TM dye to exclude dead cells and collected in PBS for the single-cell capture. Cells were centrifuged at low speed to be concentrated at an average of 400 million cells per mL prior cell capture. Single cells were capture on small size IFC microfluidic chips using the C1 Single-Cell Auto Prep System (Fluidigm) following the manufacturer recommended protocol. Reverse-transcription and pre-amplification of the single-cell cDNAs were achieved within the IFC chip using the SMARTer Ultra Low RNA kit for Illumina (Clontech) according to the C1 protocol.
RNA-sequencing libraries of the single-cell cDNA were prepared using the Illumina Nextera XT DNA Sample Preparation kit using the modified protocol described in the C1 documentation.

value: Mixed background

value: NR5A1-eGFP positive cells

tag: c1 ifc size

value: small

tag: sequencing depth

value: 10M reads 100bp p-e


title: 20160118_C95_170330_8


title: 20160118_C93_170330_8


title: A9.1001200136

city: Stanford

first: Qingyun

last: Li

institute: Stanford University


title: eWAT WT1

value: WT


title: B1.1001200141


title: B1.1001200136


title: 20160118_C87_170330_7


title: A7.1001200141


title: A8.1001200136


title: A8.1001200141


title: 20160118_C82_170330_7


title: eWAT KO2


title: 20160118_C84_170330_7


title: 20160118_C83_170330_7


title: 20160118_C81_170330_6


title: A7.1001200139


title: B10.1001200140


title: A7.1001200136


title: A6.1001200140


title: A5.1001200140


title: A4.1001200141


title: A4.1001200140


title: 20160118_C77_170330_6


title: 20160118_C74_170330_5


title: A3.1001200139

value: N


title: 20160118_C70_170330_5


title: 20160118_C72_170330_5


title: 20160118_C86_170330_7


title: A4.1001200136

value: wild type


title: A3.1001200140

value: Y


title: A3.1001200136


title: 20160118_C68_170330_4


title: A2.1001200141


title: A2.1001200140


title: 20160118_C67_170330_4


title: 20160118_C80_170330_6


title: 20160118_C66_170330_4


title: 20160118_C65_170330_4


title: A2.1001200139


title: 20160118_C62_170330_3


title: A2.1001200136


title: A12.1001200140


title: A12.1001200139


title: A11.1001200141


title: 20160118_C60_170330_3


title: 20160118_C75_170330_5


title: A11.1001200139


title: 20160118_C56_170330_2


title: A10.1001200141


title: 20160118_C73_170330_5


title: 20160118_C55_170330_2


title: A10.1001200140


title: A1.1001200140


title: A1.1001200136


title: 20160118_C47_170330_8


title: 20160118_C48_170330_8


title: 20160118_C46_170330_8


title: 20160118_C45_170330_8


title: 20160118_C61_170330_3


title: 20160118_C43_170330_8


title: F6.1001200132

value: CTX


title: 20160118_C44_170330_8


title: D7.1001200134

value: HIP


title: D1.1001200133

value: STR


title: 20160118_C42_170330_7


title: 20160118_C41_170330_7


title: A9.1001200125

value: CB


title: 20160118_C58_170330_2


title: C8.1001200130


title: A4.1001200129


title: 20160118_C37_170330_7


title: F5.1001200129


title: 20160118_C34_170330_6


title: C3.1001200131

value: OB


title: 20160118_C52_170330_1


title: A10.1001200136


title: 20160118_C32_170330_6


title: E12.1001200130


title: 20160118_C36_170330_6


title: A5.1001200132


title: 20160118_C31_170330_6