title: RNA-Seq for total RNA from U2OS treated with siCDK12+mock_150324_r2

description: FPKM RIP-Seq_eIF4G_IP.xlsx


title: RNA-Seq for eIF4G-IP RNA from U2OS treated with control siRNA+mock _150324_r3

status: Public on Jun 12 2019

type: SRA

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

country: USA

institute: Salk Institute for Biological Studies

description: FPKM RIP-Seq_eIF4G_IP.xlsx

library_source: transcriptomic

data_processing:
Sequenced reads were quality-tested using FASTQC.
Reads were aligned to the hg19 human genome using the STAR aligner version 2.4.0k. Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read). The genome index was constructed using the gene annotation supplied with the hg19 Illumina iGenomes collection and sjdbOverhang value of 100.
Raw gene expression was quantified across all gene exons (RNA-Seq) or across gene bodies (RIP-Seq), using the top-expressed isoform as proxy for gene expression and fragments per kilobase per million mapped reads (FPKM) values were calculated.
We then added a pseudocount of 1 and averaged the log2-transformed FPKM values to obtain average log-transformed expression values for Control, siCDK12, and Rapamycin treated conditions in both the RIP and Total RNA contexts.
We defined the relative change with siCDK12 and Rapamycin by subtracting the average log2 transformed values for those conditions from the control condition for the total RNA samples, and the relative RIP signal by subtracting the average log2-transformed RIP value for the corresponding average log2-transformed total RNA value for each gene.
We then filtered for genes for which the RIP signal was at least 0.5 lower in the siCDK12 vs control (CDK12-dependent), or for genes for which the RIP signal was at least 0.5 lower with Rapamycin treatment vs control (mTORc-dependent), or for genes for which both was true (CDK12- and mTORc-dependent), while simultaneously imposing that relative total RNA log2fold changes remain below 0.5 (not differentially expressed). This resulted in a list of 137 genes whose pulldown was sensitive to CDK12 depletion, 1992 genes whose pulldown was sensitive to mTORc inhibition and 181 genes whose pulldown was sensitive to both mTORc inhibition and CDK12 depletion, while maintaining approximately similar levels of overall abundance.
Genome_build: hg19
Supplementary_files_format_and_content: Excel table containing the FPKM expression values for all samples and the processing step results.

molecule: total RNA

organism: Homo sapiens

source_name: U2OS cells

growth_protocol: DMEM supplemeted with 10% (v/v) Fetal Bovine Serum, Glutamine, 5% CO2

extract_protocol:
Trizol extraction
Ribo-Zero Mammalian Kit (Illumina)
single-end RIP-Seq

treatment_protocol: Rapamycin 50 ng/ml for 24 hr, siRNA transfection for 48 hr

tag: cell line

value: U2OS cells

tag: replicate


title: RNA-Seq for eIF4G-IP RNA from U2OS treated with control siRNA+mock _150324_r1

description: FPKM RIP-Seq_eIF4G_IP.xlsx


title: RNA-Seq for eIF4G-IP RNA from U2OS treated with control siRNA+mock _150324_r2

description: FPKM RIP-Seq_eIF4G_IP.xlsx


title: RNA-Seq for eIF4G-IP RNA from U2OS treated with siCDK12+mock_150324_r3

description: FPKM RIP-Seq_eIF4G_IP.xlsx


title: RNA-Seq for total RNA from U2OS treated with control siRNA+mock_150324_r1

description: FPKM RIP-Seq_eIF4G_IP.xlsx


title: RNA-Seq for total RNA from U2OS treated with control siRNA+Rapamycin_150520_r2

description: FPKM RIP-Seq_eIF4G_IP.xlsx


title: RNA-Seq for total RNA from U2OS treated with siCDK12+mock_150324_r1

description: FPKM RIP-Seq_eIF4G_IP.xlsx


title: RNA-Seq for eIF4G-IP RNA from U2OS treated with control siRNA+Rapamycin _150520_r1

description: FPKM RIP-Seq_eIF4G_IP.xlsx


title: MLL_AF9_mock_2_bulk_RNA-seq

status: Public on Apr 16 2019

city: Milwaukee

last: Zhu

state: WI

address: 8733 W Watertown Plank Rd

institute: Versiti Blood Research Institute Milwaukee

data_processing:
Libraries were demultiplexed and and FastQ files were genereated using bcl2fastq v2.22.0.422
Reads were pseudoaligned to the mm10 genome using Salmon v0.13.0
Data was imported into R v3.5.3 using tximport v1.10.0 and summarized at the gene level
Gene level FPKM values were calculated using DESeq2 v1.22.1
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited Gene level FPKM

organism: Mus musculus

source_name: Mouse primary leukemia

growth_protocol: MLL-AF9 leukemia cells were cultured in RPMI media supplemented with 10% FBS 1% P/S and 10ng/ml mIL3.

extract_protocol:
Total RNA was extracted with TRIzol reagent (#15596018). mRNA was further extracted using NEBNext Poly(a) mRNA Magnetic Isolation Module (NEB #E7490).
cDNA Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit from Illumina.

tag: cell type

value: MLL-AF9 cas9 leukemia cells


title: RNA-Seq for total RNA from U2OS treated with control siRNA+Rapamycin_150520_r1

description: FPKM RIP-Seq_eIF4G_IP.xlsx


title: RNA-Seq for eIF4G-IP RNA from U2OS treated with siCDK12+mock_150324_r2

description: FPKM RIP-Seq_eIF4G_IP.xlsx


title: MLL_AF9_mock_1_bulk_RNA-seq


title: H3K9me1_3508_CRE_ChIP

status: Public on Apr 12 2019

library_source: genomic

data_processing:
Samples were demultiplexed and FastQ files were generated using Illumina BaseSpace
The BasePairTech.com ChIP-seq pipeline was used for analysis
Reads were trimmed using trim galore to remove adapters and read ends with phred quality scores < 15
Reads were aligned to the mm10 genome using bowtie2
Duplicate reads were removed using Picard tools and bigwig files were created representing coverage per million reads mapped
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files represent ChIP-seq coverage across the genome per one million reads mapped

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K36Me3, H3K27Me3, H3K9me3, or H3K9me1 antibody.
Libraries were prepared using standard NEBNext Ultra I/II DNA Library Prep Kit for Illumina (#E7370S) (#E7645S)

value: MLL-AF9 leukemia cells

tag: chip antibody


title: H3K9me1_3511_CRE_ChIP


title: Jumonji_scRNAseq

data_processing:
Raw Illumina sequencing data was demultiplexed and fastq files were generated using 10X Genomics Cellranger mkfastq v1.3.1
Fastq files were aligned to the mm10 genome and unique UMI sums per gene were calculated using 10X Genomics Cellranger count v1.3.1
Genome_build: mm10
Supplementary_files_format_and_content: The three files per sample are 10X cellranger count output from non-empty droplets.  Valid cell barcodes and analyzed genes are present as tab-delimited files.  Unique UMI sums per gene per cell are recorded in market exchange format.

extract_protocol:
For the single cell drop-seq RNA expression profiling, GEM (Gel bead-in-EMulsions) generation & barcoding, post GEM-RT cleanup & cDNA amplification and the library construction were done according to manufacture procedures using Chromium Single Cell 3’ Library & Gel Bead Kit v2 (PN-120237), Chromium Single Cell A Chip Kit (PN-1000009) and Chromium i7 Multiplex Kit (PN-120262) by 10x Genomics (Pleasanton, California, USA).
For the single cell drop-seq RNA expression profiling, GEM (Gel bead-in-EMulsions) generation & barcoding, post GEM-RT cleanup & cDNA amplification and the library construction were done according to manufacture procedures using Chromium Single Cell 3’ Library & Gel Bead Kit v2 (PN-120237), Chromium Single Cell A Chip Kit (PN-1000009) and Chromium i7 Multiplex Kit (PN-120262) by 10x Genomics (Pleasanton, California, USA).


title: Renilla_scRNAseq


title: H3K9me1_3511_MIT_ChIP


title: H3K9me1_3512_MIT_ChIP


title: H3K9me1_3512_CRE_ChIP


title: H3K9me1_3508_MIT_ChIP


title: H3K9me3_3512_MIT_ChIP


title: RNA-Seq for total RNA from U2OS treated with control siRNA+mock_150324_r2

description: FPKM RIP-Seq_eIF4G_IP.xlsx


title: H3K9me3_3512_CRE_ChIP


title: H3K27me3_3512_CRE_ChIP


title: H3K9me3_3508_MIT_ChIP


title: H3K9me3_3508_CRE_ChIP


title: H3K27me3_3511_CRE_ChIP


title: H3K27me3_3512_MIT_ChIP


title: H3K9me3_3511_CRE_ChIP


title: H3K27me3_3511_MIT_ChIP


title: H3K36me3_3512_CRE_ChIP


title: H3K36me3_3508_CRE_ChIP


title: H3K36me3_3511_MIT_ChIP


title: H3K27me3_3508_MIT_ChIP


title: H3K27me3_3508_CRE_ChIP


title: H3K9me3_3511_MIT_ChIP


title: H3K36me3_3508_MIT_ChIP


title: H3K36me3_3511_CRE_ChIP


title: H3K36me3_MLL_AF9_e12.4 1_ChIP


title: H3K36me3_MLL_AF9_e12.3 1_ChIP


title: H3K36me3_MLL_AF9_e21.1 1_ChIP


title: H3K36me3_MLL_AF9_e21.1 2_ChIP


title: H3K36me3_MLL_AF9_e20.1 1_ChIP


title: H3K36me3_MLL_AF9_e12.3 2_ChIP


title: H3K36me3_MLL_AF9_e20.1 2_ChIP


title: H3K36me3_MLL_AF9_Renilla 1_ChIP


title: H3K36me3_MLL_AF9_e12.4 2_ChIP


title: MLL_AF9_mock_3_bulk_RNA-seq


title: Microglia 3 days post LPC 2

status: Public on May 24 2019

city: Edinburgh

first: Veronique

last: Miron

address: 49 Little France Crescent

department: UK DRI

country: United Kingdom

institute: The University of Edinburgh

description:
100 paired end sequence reads
Sample 2

data_processing:
Alignment to mouse genome (GRCm38): STAR aligner v2.5.2a
Number of mapped read pairs/gene: GENCODE vM12
Normalization (TMM): R v3.3.2, edgeR v3.16.5
Transformation (VOOM): R v3.3.2, limma v3.30.8
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files with raw gene counts for each sample, and normalised data as log2 CPM

molecule: polyA RNA

source_name: Microglia

extract_protocol:
Mice were perfused with ice cold PBS with 10% sodium citrate. Lesions were isolated, manually dounced, and cells isolated by Percoll gradient. Microglia were FACS isolated, first excluding dead cells, then gating on Cd11b+ Ly6G- CD3- Cd45lo cells.
NuGEN Ovation RNAseq System v2 kit (NuGEN) by BGI (Hong Kong). End Repair Mix was added to the amplified cDNA and incubated at 20°C for 30 min. AxyPrep Mag PCR clean up kit (Axygen) was used to purify the end-repaired DNA, which was then combined with A-tailing Mix (Enzymatic) and incubated at 37°C for 30 min. Adaptors (Invitrogen) were ligated to the Adenylate 3’ ends DNA, and incubated at 16°C for 16 h. Insert size was used to select the adaptor-ligated DNA fragments. Several rounds of PCR amplification with PCR Primer cocktail (Invitrogen) and PCR Master Mix (New England Biolabs) were performed to enrich the adaptor-ligated DNA fragments to produce the final library, purified using AxyPrep Mag PCR clean up kit (Axygen). The final library average molecule length was determined using the Bioanalyser 2100 using the DNA 1000 kit (Agilent) and was quantified by real-time qPCR (TaqMan probe). cBot (Illumina) was used to amplify the libraries to generate the cluster on the Flow Cell (HiSeq 4000, Illumina).

treatment_protocol: LPC stereotaxic injection into the corpus callosum and sacrifice at 3 or 10 days post injection.

tag: strain

tag: Sex

value: male

tag: age

value: 10 weeks

value: Microglia

tag: time point

value: 3 days

tag: agent

value: LPC stereotaxic


title: H3K36me3_3512_MIT_ChIP


title: MLL_AF9_e21.1_2_bulk_RNAseq


title: MLL_AF9_e21.1_3_bulk_RNAseq


title: MLL_AF9_e12.4_2_bulk_RNAseq


title: MLL_AF9_e12.4_1_bulk_RNAseq


title: MLL_AF9_e12.3_3_bulk_RNAseq


title: H3K36me3_MLL_AF9_Renilla 2_ChIP


title: MLL_AF9_e12.3_1_bulk_RNAseq


title: MLL_AF9_Renilla_1_bulk_RNAseq


title: MLL_AF9_e20.1_3_bulk_RNAseq


title: MLL_AF9_e20.1_2_bulk_RNAseq


title: MLL_AF9_e12.4_3_bulk_RNAseq


title: MLL_AF9_Renilla_2_bulk_RNAseq


title: MLL_AF9_e21.1_1_bulk_RNAseq


title: MLL_AF9_e20.1_1_bulk_RNAseq


title: MLL_AF9_Renilla_3_bulk_RNAseq


title: mRNA_ColorectalCancer_rep58

status: Public on Feb 26 2019

type: RNA

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

country: Japan

institute: Japanese Foundation Cancer Research

hyb_protocol: After fragmentation, cRNA was hybridized with Affymetrix Hybridization, Wash, and Stain Kit on Affymetrix Human Genome GeneChip U133 Plus 2.0 array following manufacturer's instruction.

scan_protocol: GeneChip was scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data was processed with RMA using Affymetrix Expression Console software.

label: biotin

source_name: fresh frozen colorectal tumor tissue

label_protocol: Biotinylated cRNA was prepared with Affymetrix GeneChip 3'IVT Plus kit according to the manufacturer's instruction.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy mini kit following manufacturer's instruction.

tag: tissue

value: colorectal tumor

tag: gender

value: female


title: MLL_AF9_e12.3_2_bulk_RNAseq


title: mRNA_ColorectalCancer_rep59


title: mRNA_ColorectalCancer_rep52


title: mRNA_ColorectalCancer_rep54


title: mRNA_ColorectalCancer_rep50


title: mRNA_ColorectalCancer_rep51


title: mRNA_ColorectalCancer_rep60


title: mRNA_ColorectalCancer_rep53


title: mRNA_ColorectalCancer_rep55


title: mRNA_ColorectalCancer_rep45


title: mRNA_ColorectalCancer_rep42


title: mRNA_ColorectalCancer_rep44


title: mRNA_ColorectalCancer_rep46


title: mRNA_ColorectalCancer_rep38


title: mRNA_ColorectalCancer_rep39


title: mRNA_ColorectalCancer_rep57


title: mRNA_ColorectalCancer_rep48


title: mRNA_ColorectalCancer_rep41


title: mRNA_ColorectalCancer_rep47


title: mRNA_ColorectalCancer_rep40


title: mRNA_ColorectalCancer_rep56


title: mRNA_ColorectalCancer_rep37


title: mRNA_ColorectalCancer_rep49


title: mRNA_ColorectalCancer_rep35


title: V-RAS rep3

status: Public on Feb 12 2019

city: Madrid

first: Ignacio

last: Palmero

state: Madrid

address: Arturo Duperier, 4.

country: Spain

institute: CSIC

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software
Illumina BCL files were converted to bam format with Illumina2bam
Sequencing reads were aligned to the transcriptome with Tophat, and alignment data were quantitated with HTSeq
Differential gene expression analysis was performed with DESeq
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text file includes non-normalized read counts calculated with HTSeq and RPM (reads per million) for each sample.

source_name: fibroblast tumor

growth_protocol: Early passage wild-type Mouse Embryo Fibroblasts (MEF) were immortalized with shp53, then retrovirally transduced with a SIX1 expression vector and the corresponding empty vector, and finally infected with a vector expressing Ha-RASV12. Transformed fibroblasts with or without SIX1 overexpression (SIX1-RAS or V-RAS respectively) were injected subcutaneously in athymic nude (Foxn1nu/Foxn1nu) mice. Fourteen days after the injection (or when the tumors reached the maximum allowed size) the mice were euthanized and the tumors were excised, weighed and processed for RNA extraction. Total RNA from three tumors of each genotype was used for RNASeq analysis.

extract_protocol:
Tumors were removed, flash frozen on dry ice, and RNA was prepared using Trizol reagent. 1 ug of total RNA was used for construction of sequencing libraries.
PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments using Illumina's TruSeq Stranded Library Prep Kit. Adapter-ligated library was completed by PCR with Illumina PE primers.

value: fibroblast tumors

tag: genotype

value: control


title: SIX1-RAS rep2


title: SIX1-RAS rep3


title: V-RAS rep2


title: mRNA_ColorectalCancer_rep34


title: SIX1-RAS rep1


title: mRNA_ColorectalCancer_rep32


title: mRNA_ColorectalCancer_rep33


title: mRNA_ColorectalCancer_rep36


title: mRNA_ColorectalCancer_rep43


title: L-iAMPK_HFD_liver2

status: Public on Feb 05 2019

data_processing:
Sequenced reads were quality-tested using the FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were aligned to the  mouse mm10 genome using the STAR aligner version 2.4.0k (Dobin et al., 2013).
Raw gene expression was quantified across all annotated mm10 exons using HOMER (Heinz et al., 2010).
Differential expression analysis was carried out using the edgeR package version 3.6.8 using triplicates to compute within-group dispersion and correcting for batch effects (Robinson et al., 2010). Differentially expressed genes were defined as having a false discovery rate (FDR) <0.05.
The genes were then z-score normalized, clustered using a hierarchical clustering approach with Cluster 3 (de Hoon et al., 2004) and visualized by heat maps using Java TreeView (version 1.1.6r4) (Saldanha, 2004).
Functional pathway analysis of both upregulated and downregulated genes was done using Metascape (Tripathi et al., 2015).
Known motif enrichment analysis was carried out using HOMER findMotifs.pl.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files containing normalized read expression and differential expression analysis.

source_name: Liver

extract_protocol:
Livers were harvested and flash frozen in liquid nitrogen. RNA was isolated using Quick-RNA MiniPrep kit from Zymo Research.
Libraries were prepared using TruSeq stranded-mRNA RNA library preperation kit according to Illuminas instructions

value: liver

tag: diet

value: High fat diet

tag: ampk activation?

value: No


title: L-iAMPK_HFD+doxy_liver3

value: High fat diet with doxycycline

value: Yes


title: iAMPK_HFD_liver2


title: L-iAMPK_HFD+doxy_liver1


title: L-iAMPK_HFD_liver1


title: iAMPK_HFD+doxy_liver2


title: iAMPK_HFD_liver3


title: iAMPK_HFD+doxy_liver1


title: iAMPK_HFD+doxy_liver3


title: L-iAMPK_HFD+doxy_liver2


title: 26RH3_2

status: Public on Dec 15 2018

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

institute: University of Oxford

description: mRNA-seq

data_processing:
All reads containing unassigned nucleotides (Ns) were discarded.
The matching to the genome (Dme, v6.10) was done full length, with 0 mismatches and 0 gaps allowed.
The gene expression was calculated as indicated in Mortazavi et al. 2008.
The differential expression analysis was conducted using offset fold change, with an offset of 20.
Genome_build: Drosophila melanogaster v6.10 (FB2016_02, ftp://ftp.flybase.net/releases/FB2016_02/)
Supplementary_files_format_and_content: *csv: Comma-separated text files include gene expression levels.

organism: Drosophila melanogaster

source_name: head-thorax, exposed to rivals, 26h

growth_protocol: Dahomey wild type males were raised at a density of 100 larvae per vial on SYA medium.

extract_protocol:
Prior to RNA extraction, males were separated into abdomen and Head+Thorax body parts. RNA was extracted (MiRVana kit) from pools of n=40 male body parts.
Sequencing libraries were constructed using standard methods by the BaseClear provider.

treatment_protocol: Upon eclosion, males were stored 10 per vial and then at 1d old placed in individual vials for 5 days. The focal males were then snap frozen in liquid nitrogen.

tag: background/strain

value: Dahomey

tag: genotype/variation

value: wild type

value: head-thorax

tag: treatment

value: exposed to rivals

tag: time


title: 2RH2_2

description: mRNA-seq

source_name: head-thorax, exposed to rivals, 2h

value: male


title: 2RA3_2

description: mRNA-seq

source_name: abdomen, exposed to rivals, 2h

value: abdomen


title: V-RAS rep1


title: 26RH3_1

description: mRNA-seq


title: 2RH2_1

description: mRNA-seq


title: 2RA3_1

description: mRNA-seq


title: L-iAMPK_HFD_liver3


title: 201_6ys11mos_F_Unknown

status: Public on Nov 16 2018

description: fpkm.txt

data_processing:
Reads were aligned to the human genome (hg19) using STAR (version 2.5.1b)
Only reads that aligned uniquely to a single genomic location were used for downstream analysis (MAPQ > 10 ).
Gene expression (FPKM) values were calculated for annotated RefSeq genes using HOMER (V4.9.1) by counting reads found overlapping exons
The top expressed isoform was used as proxy for gene expression, resulting in 27,142  unique genes.
Age prediction models were fit to the FPKM data for all subjects using leave-one-out cross-validation.  Model performance is reported on the average error made on the held-out sample for each validation fold.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM expression table

source_name: Unknown

growth_protocol: Human dermal fibroblasts documented as ‘apparently healthy individuals’ deposited from the National Institute of Aging or the NIGMS Human Genetic Cell Repository were obtained or purchased from the Coriell Biobank Cell Repository (Camden, New Jersey, USA). The cells were cultured in high-glucose (4.5mg/ml) DMEM (Gibco) supplemented with 15% (vol/vol) fetal bovine serum (Gibco), 1X glutamax (Gibco), 1X non-essential amino acids (Gibco) and 1% (vol/vol) penicillin-streptomycin (Gibco). HGPS patient fibroblasts were obtained from the Progeria Research Foundation and were cultured in high-glucose (4.5mg/ml) DMEM (Gibco) supplemented with 20% (vol/vol) fetal bovine medium and 1% (vol/vol) penicillin-strepomycin. All fibroblasts were cultured in DMEM unless specified and were maintained at 37oC in a humidified incubator with 3% O2 and 7.5% CO2. Cells were passaged every 2 to 5 days at 85% confluence.

extract_protocol:
Total RNA was extracted using 1ml of TriZol reagent (Invitrogen) directly from the six-well plates or trypsinized and pelleted from 100mm dishes. RNA was purified with RNeasy Mini kits with 30 minutes of DNase I treatment to remove Genomic DNA in accordance to the manufacturer’s instructions (Qiagen).
mRNA sequence libraries were prepared using the Illumina TruSeq Stranded mRNA kit with 150ng-1ug of total RNA.

tag: cell id

tag: disease

value: HGPS

value: Female

tag: ethnicity

value: Unknown


title: 203_8yr10mos_M_Unknown

description: fpkm.txt

value: Male


title: 197_2yr3mos_F_Unknown

description: fpkm.txt


title: 141_8_Male-HGPS_Unknown

description: fpkm.txt


title: 200_8yr6mos_M_Unknown

description: fpkm.txt


title: 202_5yr0mos_F_Unknown

description: fpkm.txt


title: 139_8_Female-HGPS_Caucasian

description: fpkm.txt

source_name: Skin; Leg

value: Caucasian


title: 204_3yr0mos_F_Unknown

description: fpkm.txt


title: 199_4yr8mos_F_Unknown

description: fpkm.txt


title: iAMPK_HFD_liver1

tag: strain


title: 170_69yr_Male_Caucasian

description: fpkm.txt

source_name: Skin; Arm

value: Normal

tag: Sex


title: 198_3yr9mos_F_Unknown

description: fpkm.txt

tag: age


title: 165_68YR_Male_Unknown

description: fpkm.txt


title: 163_67YR_Female_Black

description: fpkm.txt

value: Black


title: 167_66yr_Male_Black

description: fpkm.txt

source_name: Skin; Thigh


title: 156_25yr_Female_Caucasian

description: fpkm.txt


title: 159_23YR_Male_AmericanIndian

description: fpkm.txt

value: American Indian


title: 164_67YR_Female_Filipino

description: fpkm.txt

value: Filipino


title: 166_82yr_Female_Caucasian

description: fpkm.txt


title: 160_26yr_Female_Asian

description: fpkm.txt

value: Asian


title: 162_21YR_Male_Caucasian

description: fpkm.txt

source_name: Skin;Neck


title: 169_70yr_Male_Caucasian

description: fpkm.txt


title: 136_87_Male_Caucasian

description: fpkm.txt


title: 157_29yr_Male_Unknown

description: fpkm.txt

source_name: Skin; Buttock


title: 133_89_Male_Caucasian

description: fpkm.txt


title: 168_68YR_Male_Caucasian

description: fpkm.txt


title: 131_87_Male_Caucasian

description: fpkm.txt


title: 134_86_Male_Caucasian

description: fpkm.txt


title: 127_78yr_Male_Caucasian

description: fpkm.txt

source_name: Skin; Unspecified


title: 135_92_Male_Caucasian

description: fpkm.txt


title: 155_22yr_Male_Caucasian

description: fpkm.txt


title: 123_57_male_Caucasian

description: fpkm.txt


title: 128_80yr_Female_Caucasian

description: fpkm.txt

source_name: Skin; Abdomen


title: 158_24YR_Male_Caucasian

description: fpkm.txt


title: 132_90_Male_Caucasian

description: fpkm.txt


title: 125_71yr_Female_Caucasian

description: fpkm.txt


title: 121_52yr_Male_Caucasian

description: fpkm.txt

source_name: skin; Unspecified


title: 129_94_Male_Caucasian

description: fpkm.txt

source_name: skin; Arm


title: 126_75_male_Caucasian

description: fpkm.txt


title: 124_60yr_Male_Caucasian

description: fpkm.txt


title: 122_55yr_Male_Caucasian

description: fpkm.txt


title: 112_33yr_Male_Caucasian

description: fpkm.txt


title: 117_37yr_Male_Caucasian

description: fpkm.txt


title: 120_51yr_Male_Caucasian

description: fpkm.txt


title: 118_39yr_Male_Caucasian

description: fpkm.txt


title: 110_32_female_BlackPuertoRican

description: fpkm.txt

value: female

value: Black/Puerto Rican


title: 114_37yr_Female_Unknown

description: fpkm.txt

source_name: Skin/Blood


title: 115_37yr_Female_Unknown

description: fpkm.txt


title: 105_20yr_Male_Caucasian

description: fpkm.txt


title: 104_19yr_Male_Caucasian

description: fpkm.txt


title: 107_31yr_Female_Caucasian

description: fpkm.txt


title: 109_32_male_Unknown

description: fpkm.txt


title: 108_31_female_Caucasian

description: fpkm.txt


title: 103_19yr_Male_Caucasian

description: fpkm.txt


title: 106_20yr_Female_Caucasian

description: fpkm.txt

source_name: skin; arm


title: 99_17yr_Male_Caucasian

description: fpkm.txt


title: 97_16yr_Female_Unknown

description: fpkm.txt


title: 101_19yr_Female_Caucasian

description: fpkm.txt


title: 102_19yr_Male_Caucasian

description: fpkm.txt


title: 130_89_Male_Caucasian

description: fpkm.txt


title: 98_17yr_Male_Caucasian

description: fpkm.txt


title: 111_33yr_Male_Caucasian

description: fpkm.txt


title: 76_91_Male_Caucasian

description: fpkm.txt


title: 73_88_Male_Caucasian

description: fpkm.txt


title: 88_8yr_Male_Caucasian

description: fpkm.txt

source_name: Skin; Inguinal area


title: 77_92_Female_Caucasian

description: fpkm.txt


title: 93_11_female_Caucasian

description: fpkm.txt


title: 83_5yr_Male_Black

description: fpkm.txt

source_name: Skin; Umbilical Cord Area


title: 81_3_male_LatinoHispanic

description: fpkm.txt

source_name: skin; Inguinal area

value: Latino/Hispanic


title: 80_2_female_Caucasian

description: fpkm.txt


title: 92_11_female_Caucasian

description: fpkm.txt


title: 70_87_Male_caucasian

description: fpkm.txt

value: caucasian


title: 86_7yr_Male_Caucasian

description: fpkm.txt


title: 82_3_male_Unknown

description: fpkm.txt


title: 89_9yr_Female_Black

description: fpkm.txt

source_name: Skin; unspecified


title: 75_90_Male_Caucasian

description: fpkm.txt


title: 78_96_Male_Caucasian

description: fpkm.txt


title: 94_12_male_Caucasian

description: fpkm.txt


title: 90_10yr_Male_Black

description: fpkm.txt


title: 79_1_male_Caucasian

description: fpkm.txt

source_name: skin; chet


title: 91_10yr_Male_Caucasian

description: fpkm.txt


title: 85_7yr_Male_Black

description: fpkm.txt

source_name: Skin; inguinal area


title: 87_8yr_Male_Caucasian

description: fpkm.txt


title: 72_87_Male_Black

description: fpkm.txt


title: 71_87_Male_caucasian

description: fpkm.txt


title: 95_13yr_Male_WhiTEEASTINDIAN

description: fpkm.txt

value: WhiTE/EAST INDIAN


title: 84_6yr_Male_Black

description: fpkm.txt


title: 66_86_Male_CaucasianSardinian

description: fpkm.txt

value: Caucasian/Sardinian


title: 69_87_Female_caucasian

description: fpkm.txt


title: 68_86_Male_caucasian

description: fpkm.txt


title: 74_89_Male_Caucasian

description: fpkm.txt


title: 67_86_Male_caucasian

description: fpkm.txt


title: 64_84_Male_Caucasian

description: fpkm.txt


title: 60_84_Male_Caucasian

description: fpkm.txt


title: 56_83_Male_Caucasian

description: fpkm.txt


title: 57_83_Male_Caucasian

description: fpkm.txt


title: 46_62YR_Female_Caucasian

description: fpkm.txt


title: 53_68YR_Male_Caucasian

description: fpkm.txt


title: 55_69YR_Female_Caucasian

description: fpkm.txt


title: 45_62YR_Female_Caucasian

description: fpkm.txt


title: 48_64YR_Male_Caucasian

description: fpkm.txt


title: 54_69YR_Male_Caucasian

description: fpkm.txt


title: 49_66YR_Male_Caucasian

description: fpkm.txt


title: 40_45yr_Male_Caucasian

description: fpkm.txt


title: 42_46yr_Male_Caucasian

description: fpkm.txt


title: 52_68YR_Male_Caucasian

description: fpkm.txt


title: 41_46yr_Male_Caucasian

description: fpkm.txt


title: 63_84_Male_Caucasian

description: fpkm.txt


title: 58_83_Male_Caucasian

description: fpkm.txt


title: 38_43yr_Male_Caucasian

description: fpkm.txt


title: 43_47yr_Male_Caucasian

description: fpkm.txt


title: 50_67YR_Male_Caucasian

description: fpkm.txt


title: 61_84_Female_Caucasian

description: fpkm.txt


title: 62_84_Male_Caucasian

description: fpkm.txt


title: 23_29YR_Male_Caucasian

description: fpkm.txt


title: 51_67YR_Male_Caucasian

description: fpkm.txt


title: 44_61YR_Male_Caucasian

description: fpkm.txt


title: 24_30YR_Male_Caucasian

description: fpkm.txt


title: 39_44yr_Male_Caucasian

description: fpkm.txt


title: 65_84_Male_Caucasian

description: fpkm.txt


title: 59_84_Female_Caucasian

description: fpkm.txt


title: 47_63YR_Male_Caucasian

description: fpkm.txt


title: 21_28YR_Male_Caucasian

description: fpkm.txt


title: 17_25YR_Male_caucasian

description: fpkm.txt


title: 16_24YR_Female_Caucasian

description: fpkm.txt


title: 18_25YR_Female_caucasian

description: fpkm.txt


title: 35_42yr_Female_Caucasian

description: fpkm.txt


title: 33_46yr_Male_Caucasian

description: fpkm.txt


title: 20_26YR_Female_Caucasian

description: fpkm.txt


title: 34_50yr_Male_Caucasian

description: fpkm.txt


title: 36_47yr_Male_Caucasian

description: fpkm.txt


title: 14_1yr_Male_Asian

description: fpkm.txt

source_name: Skin; Foreskin


title: 19_26YR_Male_Caucasian

description: fpkm.txt

source_name: Skin; Arm


title: 30_41yr_Male_Caucasian

description: fpkm.txt


title: 32_50yr_Female_Caucasian

description: fpkm.txt


title: 37_41yr_Female_Caucasian

description: fpkm.txt


title: 27_30YR_Male_Caucasian

description: fpkm.txt


title: 26_30YR_Male_Caucasian

description: fpkm.txt


title: 28_43yr_Female_Caucasian

description: fpkm.txt


title: 31_47yr_Male_Caucasian

description: fpkm.txt


title: 29_44yr_Male_Caucasian

description: fpkm.txt


title: 25_30YR_Female_Caucasian

description: fpkm.txt


title: 15_12yr_Male_Caucasian

description: fpkm.txt


title: GiWi_rep1

status: Public on Nov 14 2018

data_processing:
FastQC v0.11.5 with default parameter was used for quality test.
Reads were mapped to hg19 reference genome by STAR v2.5.1 with default parameters. Only uniquely mapped reads were considered for downstream analysis.
RNA-Seq gene expression was quantified by HOMER analyzeRepeats command, summing reads mapped across all gene exons of RefSeq genes.
RNA-Seq differential expression was carried out using edgeR v3.16.1 on the raw counts of replicates. FDR < 0.05 and abs(logFC) > 1 was used as cutoff to identify the DE genes.
Genome_build: hg19 (illumina iGenome)
Supplementary_files_format_and_content: Raw count table for gene expression in Excel spreadsheet.
Supplementary_files_format_and_content: FPKM normalized gene expression table in Excel spreadsheet.

growth_protocol: H1 hESCs grow in TeSR media

extract_protocol:
Quick RNA miniprep Plus from Zymo was used to extract the RNA for RNA-seq
RNA-seq libraries were performed using stranded  LT mRNA  kit from Illumina and sequenced in an Illumina HiSeq 4000 device.

treatment_protocol: H1 hESCs were grown in TeSR media.  For RNA-seq, H1 hESC were treated with the cytokines or molecules indicated (Activin, YAPi, GSK3i, or Wnt inhibitor) and samples were extracted at Day 30 after differentiation.

tag: cell line

tag: cell type

value: human embryonic stem cell (hESC) line

value: WT

value: GSK3i+Wnt/β-catenin inhibitor

tag: time point

value: Day 30 after differentiation.


title: YAPi_rep3

value: YAP inhibitor + Activin


title: YAPi_rep2


title: GiWi_rep2


title: YAPi_rep1


title: RGCtreat092016

status: Public on Oct 29 2018

data_processing:
Sequenced reads were quality-tested using FASTQC
Alingment to rn6 rat genome using the STAR aligner version 2.4.0k.
The genome index was constructed using the gene annotation supplied with rn6 Illumina iGenomes collection and sjdbOverhang value of 100.
Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read).
Normalized gene expression (Fragments per kilobase per million mapped reads, FPKM) was quantified with HOMER v4.8.3 across all gene exons using the top-expressed isoform as proxy for gene expression.
Genome_build: rn6
Supplementary_files_format_and_content: fpkm normalized expression table (text file)

organism: Rattus norvegicus

source_name: RGC culture

growth_protocol: RGCs were grown for 10 days maintained in a humidified incubator at 37°C and 10% CO2.

extract_protocol:
RNA was isolated from the visual cortex using the RNeasy mini kit QIAgen (74104).
RNA-Seq libraries were prepared using the Illumina TrueSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions

treatment_protocol: RGCs were treated for 12h with 1ug/ml of Chrdl1, or vehicle as a control.

value: Sprague Dawley

value: Chrdl1 1ug/ml

value: RGC


title: 22_29YR_Male_Caucasian

description: fpkm.txt

value: Normal

value: Male

value: Caucasian


title: RGCtreat052416


title: RGCtreat092716


title: RGCControl052416

value: Vehicle 0.1% BSA 4mM HCl


title: RGCControl092716


title: WT1013_1_1

data_processing:
Sequenced reads were quality-tested using FASTQC
Alingment to the mm10 mouse genome using the STAR aligner version 2.4.0k.
Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read)
Normalized gene expression (Fragments per kilobase per million mapped reads, FPKM) was quantified with HOMER v4.8.3 across all gene exons using the top-expressed isoform as proxy for gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: fpkm normalized expression table (text file)

source_name: WT_visual cortex

growth_protocol: 12 hour light/dark cycle with ad lib access to standard mouse chow

extract_protocol:
Mice were perfused with 4%PFA. Visual cortex isolated. RNA was isolated from the visual cortex using the RNeasy mini kit QIAgen (74104).
RNA-Seq libraries were prepared using the Illumina TrueSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions

tag: tissue

value: Visual cortex


title: WT1011_2_1

tag: genotype


title: KO1013_1_3

source_name: KO_visual cortex

value: Chrdl1 KO


title: RGCControl092016


title: WT1012_3_1


title: KO1012_3_3


title: KO1011_2_3


title: ASULi_UNINFECTED_1

status: Public on Sep 21 2018

data_processing:
Sequenced reads were quality-tested using FASTQC (Andrews, 2010)
Reads were aligned to the mm10 mouse genome using the STAR aligner (Dobin, 2013) version 2.4.0k. Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read). The genome index was constructed using the gene annotation supplied with the mm10 Illumina iGenomes collection (Illumina) and sjdbOverhang value of 100.
Uniquely mapped reads were quantified across all gene exons using the top-expressed isoform as proxy for gene expression with the HOMER (Heinz, 2010) analysis suite.
Differential gene expression was carried out with edgeR (Robinson, 2010) using triplicates to compute within-group dispersion. Differentially expressed genes were defined as having a false discovery rate (FDR) < 0.01 and a log2 fold change >1 when comparing two experimental conditions.
HOMER was used to test for overrepresentation of differentially expressed genes within KEGG (Kenehisa and Goto, 2000) pathways corrected for multiple testing using the Benjamini and Yekutieli general correction for multiple testing (Benjamini, 1995).
Heatmaps were constructed with JTreeView (Saldanha, 2004).
Genome_build: mm10
Supplementary_files_format_and_content: Excel worksheet containing an FPKM expression table and additional expression-based analyses

source_name: Liver

growth_protocol: 100 mls of sterile LB media was inoculated with a single colony of C. rodentium. Culture was grown overnight at 37 deg C

extract_protocol:
Upon harvest, livers were snap frozen and ground to a powder in liquid nitrogen. RNA was then extracted using the Life Technologies Paris extraction kit according to manufacturer's protocol
Libraries were prepared according to Illumina's instructions accompanying TruSeq Stranded mRNA Library Prep Kit. Briefly, total RNA (0.5µg) from each sample was used to isolate poly(A) mRNA. Steps involved in library preparation were mRNA fragmentation, first strand cDNA synthesis followed by second strand cDNA synthesis and adaptor ligation, cDNA fragments isolation and amplification.

treatment_protocol: Mice were orally infected with 1x10^6 CFU of C. rodentium

tag: survival

value: living

tag: agent

value: uninfected


title: ASULi_UNINFECTED_3


title: ASCLi_MORBID_1

value: morbid

value: infected with C. rodentium


title: ASCLi_LIVING_2


title: ASCLi_LIVING_1


title: ASCLi_MORBID_3


title: CRWT

data_processing:
Library strategy: Paired-End 150 bp shot-gun sequencing
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Sequencing libraries were mapped against the reference genome C. rodentium ICC168.
SNPs were identified using Snippy (Galaxy Version 0.2.0).
For whole-genome comparisons between C. rodentium ICC169, DBS100 and isolates, reads were assemblied de novo using SPAdes genome assembler (Galaxy version 3.11.1)
Contigs were reordered and aligned against the ICC168 chromosome using MAUVE genome aligment softare (version 2.4.0).
Genome_build: Citrobacter rodentium ICC168 (Assession: GCA_000027085.1)
Supplementary_files_format_and_content: fasta files containing scaffolds and vcf files containing SNPs.

organism: Citrobacter rodentium

source_name: bacteria

growth_protocol: Luria-Broth, 37°C

extract_protocol:
Genomic DNA was extracted from overnight cultures of bacteria by lysis and purification of DNA using the Qiagen Dneasy Blood and Tissue kit (Qiagen, 69506) according to manufacturer's instructions. DNA samples were submitted to The Sequencing Center (Fort Collins, CO) for library preparation.
Genomic DNA libraries were prepared using Illumina's Nextera XT DNA Library Preparation kit (Illumina).

tag: host

value: n/a (parental strain)


title: CR8

value: C3H/HeJ + iron diet, infection

value: feces of C3H/HeJ mice


title: CR50


title: CR46


title: CR32


title: CR39


title: CR42


title: CR38


title: CR25


title: CR20


title: CR15


title: ASULi_UNINFECTED_2


title: ASCLi_MORBID_2


title: ASCLi_LIVING_3


title: in vivo iSEPs from mouse2

status: Public on Jul 16 2018

data_processing:
Sequenced reads were quality-tested using FASTQC v0.11.5
Reads were aligned to the mm10 mouse genome using the STAR aligner version 2.5.1b. Mapping was carried out using default parameters, filtering non-canonical introns and allowing up to 10 mismatches per read and only keeping uniquely mapped reads. The genome index was constructed using the gene annotation supplied with the mm10 Illumina iGenomes collection and sjdbOverhang value of 100.
FPKM (fragments per kilobase per million mapped reads) gene expression was quantified across all gene exons with HOMER using the top-expressed isoform as proxy for gene expression.
Genes with FPKM values > 32 in at least one sample and at least a 2-fold difference between the minimum and maximum FPKM value were kept for clustering (leaving the top 2,380 expressed genes).
The log2 of FPKM +1 expression values were z-normalized and centered and hierarchically clustered using average linkage agglomeration and uncentered Pearson correlation as a distance measure (Cluster 3 v 1.5.2)
Data were visualized with TreeView version v1.1.6r4.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized gene expression table in tab-separated text format.

source_name: Mesenchymal-converted epithelial tissue

growth_protocol: DMEM+10%FBS cultures for ADSCs. Non-serum keratinocyte culture medium for in vitro iSEPs, in vivo iSEPs, and keratinocytes.

extract_protocol:
RNA was harvested using Quick-RNA MiniPrep Kit (Zymo Research).  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA

value: Pdgfra-creERxLSL-tdTomato

value: Primary cultured epithelial cells converted from Pdgfra (+) ADSCs in vivo


title: in vitro iSEPs from mouse1

source_name: Subcutaneous adipose tissue

value: Epithelial cells converted from Pdgfra (+) ADSCs in vitro


title: in vivo iSEPs from mouse1


title: Pdgfra (+) ADSCs from mouse3

value: Primary cultured cells from subcutaneous adipose tissue


title: Keratinocytes from mouse3

source_name: Back skin

value: Primary cultured keratinocytes from back skin


title: in vitro iSEPs from mouse2


title: in vitro iSEPs from mouse3


title: Pdgfra (+) ADSCs from mouse1


title: Keratinocytes from mouse2


title: ANCA Associated Vasculitis [B4_TI_AAV_57]

status: Public on May 17 2018

city: Ann Arbor

first: Sean

last: Eddy

state: MI

address: 1150 West Medical Center Drive

institute: University of Michigan

description: Gene expression data from the tubulointerstitial compartment of human ANCA Associated Vasculitis.

hyb_protocol: cRNA were hybridized to Affymetrix Human Gene 2.1 ST Arrays.

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing:
The data were analyzed using RMA method and Human Entrez Gene custom CDF annotation version 19.
Each of the hybridizations was normalized separately. Data was batch corrected using Combat.

source_name: Kidney Biopsy from Human ANCA Associated Vasculitis

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

extract_protocol: Total RNA was isolated using RNeasy kit (Qiagen) following manufacturer's protocol.

value: Tubulointerstitium from kidney biopsy


title: in vivo iSEPs from mouse3


title: Keratinocytes from mouse1


title: ANCA Associated Vasculitis [B4_TI_AAV_8]


title: ANCA Associated Vasculitis [B4_TI_AAV_56]


title: ANCA Associated Vasculitis [B4_TI_AAV_7]


title: ANCA Associated Vasculitis [B4_TI_AAV_9]


title: ANCA Associated Vasculitis [B4_TI_AAV_58]


title: ANCA Associated Vasculitis [B4_TI_AAV_6]


title: ANCA Associated Vasculitis [B4_TI_AAV_50]


title: ANCA Associated Vasculitis [B4_TI_AAV_54]


title: Pdgfra (+) ADSCs from mouse2


title: ANCA Associated Vasculitis [B4_TI_AAV_55]


title: ANCA Associated Vasculitis [B4_TI_AAV_51]


title: ANCA Associated Vasculitis [B4_TI_AAV_49]


title: ANCA Associated Vasculitis [B4_TI_AAV_5]


title: ANCA Associated Vasculitis [B4_TI_AAV_48]


title: ANCA Associated Vasculitis [B4_TI_AAV_45]


title: ANCA Associated Vasculitis [B4_TI_AAV_47]


title: ANCA Associated Vasculitis [B4_TI_AAV_42]


title: ANCA Associated Vasculitis [B4_TI_AAV_40]


title: ANCA Associated Vasculitis [B4_TI_AAV_41]


title: ANCA Associated Vasculitis [B4_TI_AAV_39]


title: ANCA Associated Vasculitis [B4_TI_AAV_4]


title: ANCA Associated Vasculitis [B4_TI_AAV_46]


title: ANCA Associated Vasculitis [B4_TI_AAV_43]


title: ANCA Associated Vasculitis [B4_TI_AAV_53]


title: ANCA Associated Vasculitis [B4_TI_AAV_36]


title: ANCA Associated Vasculitis [B4_TI_AAV_38]


title: ANCA Associated Vasculitis [B4_TI_AAV_37]


title: ANCA Associated Vasculitis [B4_TI_AAV_34]


title: ANCA Associated Vasculitis [B4_TI_AAV_32]


title: ANCA Associated Vasculitis [B4_TI_AAV_30]


title: ANCA Associated Vasculitis [B4_TI_AAV_31]


title: ANCA Associated Vasculitis [B4_TI_AAV_35]


title: ANCA Associated Vasculitis [B4_TI_AAV_33]


title: ANCA Associated Vasculitis [B4_TI_AAV_26]


title: ANCA Associated Vasculitis [B4_TI_AAV_28]


title: ANCA Associated Vasculitis [B4_TI_AAV_23]


title: ANCA Associated Vasculitis [B4_TI_AAV_25]


title: ANCA Associated Vasculitis [B4_TI_AAV_27]


title: ANCA Associated Vasculitis [B4_TI_AAV_29]


title: ANCA Associated Vasculitis [B4_TI_AAV_24]


title: ANCA Associated Vasculitis [B4_TI_AAV_44]


title: ANCA Associated Vasculitis [B4_TI_AAV_20]


title: ANCA Associated Vasculitis [B4_TI_AAV_21]


title: ANCA Associated Vasculitis [B4_TI_AAV_2]


title: ANCA Associated Vasculitis [B4_TI_AAV_22]


title: ANCA Associated Vasculitis [B4_TI_AAV_15]


title: ANCA Associated Vasculitis [B4_TI_AAV_18]


title: ANCA Associated Vasculitis [B4_TI_AAV_17]


title: ANCA Associated Vasculitis [B4_TI_AAV_12]


title: ANCA Associated Vasculitis [B4_TI_AAV_14]


title: ANCA Associated Vasculitis [B4_TI_AAV_16]


title: ANCA Associated Vasculitis [B4_TI_AAV_13]


title: ANCA Associated Vasculitis [B4_TI_AAV_11]


title: Membranous Nephropathy [B2_TI_MN_148]

description: Gene expression data from the tubulointerstitial compartment of human Membranous Nephropathy.

source_name: Kidney Biopsy from Human Membranous Nephropathy


title: Membranous Nephropathy [B2_TI_MN_118]


title: Membranous Nephropathy [B2_TI_MN_39]


title: Membranous Nephropathy [B2_TI_MN_146]


title: Membranous Nephropathy [B2_TI_MN_134]


title: ANCA Associated Vasculitis [B4_TI_AAV_10]


title: ANCA Associated Vasculitis [B4_TI_AAV_1]


title: Membranous Nephropathy [B2_TI_MN_37]


title: Membranous Nephropathy [B2_TI_MN_40]


title: Membranous Nephropathy [B2_TI_MN_152]


title: Membranous Nephropathy [B2_TI_MN_38]


title: Membranous Nephropathy [B2_TI_MN_99]


title: ANCA Associated Vasculitis [B4_TI_AAV_19]


title: Membranous Nephropathy [B2_TI_MN_123]


title: Membranous Nephropathy [B2_TI_MN_129]


title: Membranous Nephropathy [B2_TI_MN_110]


title: Minimal Change Disease [B2_TI_MCD_33]

description: Gene expression data from the tubulointerstitial compartment of human Minimal Change Disease.

source_name: Kidney Biopsy from Human Minimal Change Disease


title: Minimal Change Disease [B2_TI_MCD_150]


title: Minimal Change Disease [B2_TI_MCD_144]


title: Minimal Change Disease [B2_TI_MCD_160]


title: Membranous Nephropathy [B2_TI_MN_109]


title: Minimal Change Disease [B2_TI_MCD_157]


title: Minimal Change Disease [B2_TI_MCD_143]


title: Membranous Nephropathy [B2_TI_MN_135]


title: Membranous Nephropathy [B2_TI_MN_36]


title: Minimal Change Disease [B2_TI_MCD_140]


title: Minimal Change Disease [B2_TI_MCD_117]


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_72]

description: Gene expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis.

source_name: Kidney Biopsy from Human Focal and Segmental Glomerulosclerosis


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_69]


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_96]


title: Minimal Change Disease [B2_TI_MCD_130]


title: Minimal Change Disease [B2_TI_MCD_106]


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_29]


title: Minimal Change Disease [B2_TI_MCD_149]


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_31]


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_21]


title: Minimal Change Disease [B2_TI_MCD_126]


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_26]


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_67]


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_62]


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_66]


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_85]


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_112]


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_19]


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_142]


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_20]


title: Membranous Nephropathy [B1_TI_MN_97]


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_70]


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_80]


title: Membranous Nephropathy [B1_TI_MN_91]


title: Membranous Nephropathy [B1_TI_MN_159]


title: Focal and Segmental Glomerulosclerosis [B2_TI_FSGS_65]


title: Membranous Nephropathy [B1_TI_MN_156]


title: Membranous Nephropathy [B1_TI_MN_154]


title: Membranous Nephropathy [B1_TI_MN_94]


title: Membranous Nephropathy [B1_TI_MN_119]


title: Membranous Nephropathy [B1_TI_MN_127]


title: Membranous Nephropathy [B1_TI_MN_138]


title: Membranous Nephropathy [B1_TI_MN_125]


title: Membranous Nephropathy [B1_TI_MN_13]


title: Membranous Nephropathy [B1_TI_MN_14]


title: Membranous Nephropathy [B1_TI_MN_136]


title: Membranous Nephropathy [B1_TI_MN_133]


title: Membranous Nephropathy [B1_TI_MN_111]


title: Membranous Nephropathy [B1_TI_MN_124]


title: Membranous Nephropathy [B1_TI_MN_11]


title: ANCA Associated Vasculitis [B4_TI_AAV_3]


title: Membranous Nephropathy [B1_TI_MN_155]


title: Membranous Nephropathy [B1_TI_MN_107]


title: Membranous Nephropathy [B1_TI_MN_103]


title: Membranous Nephropathy [B1_TI_MN_102]


title: Membranous Nephropathy [B1_TI_MN_101]


title: Minimal Change Disease [B1_TI_MCD_145]


title: Membranous Nephropathy [B1_TI_MN_105]


title: Minimal Change Disease [B1_TI_MCD_95]


title: Membranous Nephropathy [B1_TI_MN_100]


title: Minimal Change Disease [B1_TI_MCD_158]


title: Membranous Nephropathy [B1_TI_MN_131]


title: Membranous Nephropathy [B1_TI_MN_113]


title: Membranous Nephropathy [B1_TI_MN_147]


title: Minimal Change Disease [B1_TI_MCD_128]


title: Minimal Change Disease [B1_TI_MCD_108]


title: Healthy Living Donor [B1_TI_LD_6]

description: Gene expression data from the tubulointerstitial compartment of human Healthy Living Donor.

source_name: Kidney Biopsy from Human Healthy Living Donor


title: Minimal Change Disease [B1_TI_MCD_6]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_92]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_68]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_88]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_83]


title: Healthy Living Donor [B1_TI_LD_3]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_75]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_82]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_87]


title: Healthy Living Donor [B1_TI_LD_7]


title: Healthy Living Donor [B1_TI_LD_2]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_77]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_78]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_81]


title: Healthy Living Donor [B1_TI_LD_1]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_71]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_51]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_153]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_49]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_50]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_47]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_132]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_4]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_5]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_2]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_121]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_122]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_151]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_120]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_104]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_114]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_1]


title: ANCA Associated Vasculitis [B4_Glom_AAV_4]

description: Gene expression data from human ANCA Associated Vasculitis.

data_processing:
The data were analyzed using a modified Affy package using the RMA method and Human Entrez Gene custom CDF annotation version 19.
Each of the hybridizations was normalized separately. Data was batch corrected using Combat.

value: Glomeruli from kidney biopsy


title: ANCA Associated Vasculitis [B4_Glom_AAV_2]


title: ANCA Associated Vasculitis [B4_Glom_AAV_7]


title: ANCA Associated Vasculitis [B4_Glom_AAV_8]


title: Focal and Segmental Glomerulosclerosis [B1_TI_FSGS_116]


title: ANCA Associated Vasculitis [B4_Glom_AAV_9]


title: ANCA Associated Vasculitis [B4_Glom_AAV_11]


title: ANCA Associated Vasculitis [B4_Glom_AAV_13]


title: ANCA Associated Vasculitis [B4_Glom_AAV_14]


title: ANCA Associated Vasculitis [B4_Glom_AAV_5]


title: ANCA Associated Vasculitis [B4_Glom_AAV_1]


title: Membranous Nephropathy [B2_Glom_MN_99]

description: Gene expression data from the glomerular compartment of human Membranous Nephropathy.


title: Membranous Nephropathy [B2_Glom_MN_98]


title: Membranous Nephropathy [B2_Glom_MN_38]


title: ANCA Associated Vasculitis [B4_Glom_AAV_10]


title: ANCA Associated Vasculitis [B4_Glom_AAV_6]


title: ANCA Associated Vasculitis [B4_Glom_AAV_15]


title: Membranous Nephropathy [B2_Glom_MN_39]


title: Membranous Nephropathy [B2_Glom_MN_40]


title: ANCA Associated Vasculitis [B4_Glom_AAV_3]


title: Membranous Nephropathy [B2_Glom_MN_90]


title: Membranous Nephropathy [B2_Glom_MN_152]


title: Membranous Nephropathy [B2_Glom_MN_93]


title: Membranous Nephropathy [B2_Glom_MN_36]


title: ANCA Associated Vasculitis [B4_Glom_AAV_12]


title: Membranous Nephropathy [B2_Glom_MN_37]


title: Membranous Nephropathy [B2_Glom_MN_146]


title: Membranous Nephropathy [B2_Glom_MN_141]


title: Membranous Nephropathy [B2_Glom_MN_135]


title: Membranous Nephropathy [B2_Glom_MN_134]


title: Membranous Nephropathy [B2_Glom_MN_129]


title: Membranous Nephropathy [B2_Glom_MN_115]


title: Membranous Nephropathy [B2_Glom_MN_118]


title: Membranous Nephropathy [B2_Glom_MN_110]


title: Membranous Nephropathy [B2_Glom_MN_109]


title: Minimal Change Disease [B2_Glom_MCD_157]

description: Gene expression data from the glomerular compartment of human Minimal Change Disease.


title: Minimal Change Disease [B2_Glom_MCD_150]


title: Minimal Change Disease [B2_Glom_MCD_139]


title: Minimal Change Disease [B2_Glom_MCD_140]


title: Minimal Change Disease [B2_Glom_MCD_160]


title: Minimal Change Disease [B2_Glom_MCD_144]


title: Minimal Change Disease [B2_Glom_MCD_126]


title: Minimal Change Disease [B2_Glom_MCD_143]


title: Minimal Change Disease [B2_Glom_MCD_117]


title: Minimal Change Disease [B2_Glom_MCD_149]


title: Membranous Nephropathy [B2_Glom_MN_148]


title: Focal and Segmental Glomerulosclerosis [B2_Glom_FSGS_80]

description: Gene expression data from the glomerular compartment of human Focal and Segmental Glomerulosclerosis.


title: Membranous Nephropathy [B2_Glom_MN_124]


title: Focal and Segmental Glomerulosclerosis [B2_Glom_FSGS_72]


title: Membranous Nephropathy [B2_Glom_MN_123]


title: Minimal Change Disease [B2_Glom_MCD_106]


title: Focal and Segmental Glomerulosclerosis [B2_Glom_FSGS_67]


title: Focal and Segmental Glomerulosclerosis [B2_Glom_FSGS_65]


title: Focal and Segmental Glomerulosclerosis [B2_Glom_FSGS_69]


title: Focal and Segmental Glomerulosclerosis [B2_Glom_FSGS_31]


title: Focal and Segmental Glomerulosclerosis [B2_Glom_FSGS_70]


title: Focal and Segmental Glomerulosclerosis [B2_Glom_FSGS_29]


title: Focal and Segmental Glomerulosclerosis [B2_Glom_FSGS_66]


title: Membranous Nephropathy [B1_Glom_MN_97]


title: Focal and Segmental Glomerulosclerosis [B2_Glom_FSGS_26]


title: Focal and Segmental Glomerulosclerosis [B2_Glom_FSGS_85]


title: Focal and Segmental Glomerulosclerosis [B2_Glom_FSGS_21]


title: Focal and Segmental Glomerulosclerosis [B2_Glom_FSGS_62]


title: Focal and Segmental Glomerulosclerosis [B2_Glom_FSGS_19]


title: Membranous Nephropathy [B1_Glom_MN_94]


title: Membranous Nephropathy [B1_Glom_MN_159]


title: Membranous Nephropathy [B1_Glom_MN_91]


title: Membranous Nephropathy [B1_Glom_MN_136]


title: Membranous Nephropathy [B1_Glom_MN_13]


title: Membranous Nephropathy [B1_Glom_MN_138]


title: Membranous Nephropathy [B1_Glom_MN_12]


title: Membranous Nephropathy [B1_Glom_MN_111]


title: Membranous Nephropathy [B1_Glom_MN_127]


title: Membranous Nephropathy [B1_Glom_MN_156]


title: Membranous Nephropathy [B1_Glom_MN_11]


title: Membranous Nephropathy [B1_Glom_MN_105]


title: Membranous Nephropathy [B1_Glom_MN_113]


title: Membranous Nephropathy [B1_Glom_MN_107]


title: Membranous Nephropathy [B1_Glom_MN_14]


title: Membranous Nephropathy [B1_Glom_MN_119]


title: Membranous Nephropathy [B1_Glom_MN_102]


title: Membranous Nephropathy [B1_Glom_MN_154]


title: Membranous Nephropathy [B1_Glom_MN_103]


title: Membranous Nephropathy [B1_Glom_MN_133]


title: Living donor [B1_Glom_LD_6]

description: Gene expression data from the glomerular compartment of human Living donor.

source_name: Kidney Biopsy from Human Living donor


title: Minimal Change Disease [B1_Glom_MCD_108]


title: Minimal Change Disease [B1_Glom_MCD_128]


title: Living donor [B1_Glom_LD_3]


title: Minimal Change Disease [B1_Glom_MCD_158]


title: Minimal Change Disease [B1_Glom_MCD_145]


title: Living donor [B1_Glom_LD_2]


title: Living donor [B1_Glom_LD_5]


title: Living donor [B1_Glom_LD_4]


title: Living donor [B1_Glom_LD_1]


title: Membranous Nephropathy [B1_Glom_MN_101]


title: Minimal Change Disease [B1_Glom_MCD_95]


title: Focal and Segmental Glomerulosclerosis [B1_Glom_FSGS_81]


title: Focal and Segmental Glomerulosclerosis [B1_Glom_FSGS_87]


title: Focal and Segmental Glomerulosclerosis [B1_Glom_FSGS_78]


title: Focal and Segmental Glomerulosclerosis [B1_Glom_FSGS_83]


title: Focal and Segmental Glomerulosclerosis [B1_Glom_FSGS_88]


title: Focal and Segmental Glomerulosclerosis [B1_Glom_FSGS_4]


title: Focal and Segmental Glomerulosclerosis [B1_Glom_FSGS_75]


title: Focal and Segmental Glomerulosclerosis [B1_Glom_FSGS_71]


title: Focal and Segmental Glomerulosclerosis [B1_Glom_FSGS_68]


title: Focal and Segmental Glomerulosclerosis [B1_Glom_FSGS_77]


title: Focal and Segmental Glomerulosclerosis [B1_Glom_FSGS_73]


title: Focal and Segmental Glomerulosclerosis [B1_Glom_FSGS_1]


title: Focal and Segmental Glomerulosclerosis [B1_Glom_FSGS_2]


title: Focal and Segmental Glomerulosclerosis [B1_Glom_FSGS_64]


title: Focal and Segmental Glomerulosclerosis [B1_Glom_FSGS_82]


title: Focal and Segmental Glomerulosclerosis [B1_Glom_FSGS_5]


title: B2_GlomAffyAnnot_FSGS_80

description: Gene Expression data from the glomerular compartment of human Focal and Segmental Glomerulosclerosis

hyb_protocol: According to manufacturer's protocols.

data_processing: Preprocessing, normalization with RMA, and batch correction performed in R.

extract_protocol: Total RNA was isolated using Rneasy kit (Qiagen) following manufacturer's protocol.

tag: diagnosis

value: Focal and Segmental Glomerulosclerosis


title: B2_GlomAffyAnnot_FSGS_63


title: B2_GlomAffyAnnot_FSGS_76


title: B2_GlomAffyAnnot_FSGS_86


title: B2_GlomAffyAnnot_FSGS_70


title: B2_GlomAffyAnnot_FSGS_72


title: B2_GlomAffyAnnot_FSGS_84


title: B2_GlomAffyAnnot_FSGS_62


title: B2_GlomAffyAnnot_FSGS_74


title: B2_GlomAffyAnnot_FSGS_85


title: B2_GlomAffyAnnot_FSGS_89


title: B2_GlomAffyAnnot_FSGS_69


title: B2_GlomAffyAnnot_FSGS_67


title: B2_GlomAffyAnnot_FSGS_61


title: B2_GlomAffyAnnot_FSGS_65


title: B2_GlomAffyAnnot_FSGS_27


title: B2_GlomAffyAnnot_FSGS_58


title: B2_GlomAffyAnnot_FSGS_29


title: B2_GlomAffyAnnot_FSGS_66


title: B2_GlomAffyAnnot_FSGS_30


title: B2_GlomAffyAnnot_FSGS_23


title: B2_GlomAffyAnnot_FSGS_21


title: B2_GlomAffyAnnot_FSGS_28


title: B2_GlomAffyAnnot_FSGS_60


title: B1_GlomAffyAnnot_LD_3

description: Gene Expression data from the glomerular compartment of human Living donor

value: Healthy


title: B1_GlomAffyAnnot_FSGS_88


title: B1_GlomAffyAnnot_LD_4


title: B2_GlomAffyAnnot_FSGS_26


title: B1_GlomAffyAnnot_LD_1


title: B1_GlomAffyAnnot_FSGS_79


title: B2_GlomAffyAnnot_FSGS_59


title: B1_GlomAffyAnnot_LD_2


title: B1_GlomAffyAnnot_LD_6


title: B1_GlomAffyAnnot_FSGS_87


title: B2_GlomAffyAnnot_FSGS_24


title: B2_GlomAffyAnnot_FSGS_22


title: B1_GlomAffyAnnot_LD_5


title: B2_GlomAffyAnnot_FSGS_31


title: B1_GlomAffyAnnot_FSGS_81


title: B1_GlomAffyAnnot_FSGS_82


title: B2_GlomAffyAnnot_FSGS_19


title: B1_GlomAffyAnnot_FSGS_78


title: B1_GlomAffyAnnot_FSGS_83


title: B1_GlomAffyAnnot_FSGS_71


title: T03 pH 6

status: Public on May 12 2018

city: Fuzhou

first: Chen

last: Lisong

address: Shangdian street NO.15

country: China

institute: Fujian Agriculture and Forestry University

data_processing:
Illumina HiSeq xten software used for basecalling.
Clean reads were obtained by removing low quality sequences, reads containing adapter and reads containing ploy-N.
These clean reads were mapped to the sweet orange reference sequences (Xu et al., 2013) and maintained in the Citrus sinensis Genome Annotation Project (http://citrus.hzau.edu.cn/) using TopHat2 (Kim et al., 2013). The gene expression level was calculated by FPKM (Fragments Per Kilobase of transcript per Million mapped reads) by Cufflinks (Ghosh et al., 2016).Differential expression analysis was performed using the DESeq R package (Anders et al., 2010). Genes with an FDR (Benjamini-Hochberg adjusted p-value) ≤0.05 and fold changes ≥ 2 were assigned as differentially expressed genes.
Supplementary_files_format_and_content: Excel files include FPKM values.

organism: Citrus sinensis

source_name: citrus leaf

extract_protocol:
Equal amounts of frozen leaves from four seedlings (one seedling per pot) were pooled as one biological replicate. There were two-three biological replicates for each treatment. Total RNA was independently extracted twice from ca. 100 - 200 mg frozen control and +Al roots of C. sinensis and C. grandis seedlings using Recalcirtant Plant Total RNA Extraction Kit (Centrifugal column type, Bioteke Corporation, China) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: control with pH 6.0, low-pH with pH 2.5

tag: category

value: seedling

value: leaves

value: treatment for 9 monthes


title: T01 pH 2.5

extract_protocol:
Equal amounts of sample from four seedlings (one seedling per pot) were mixed as a biological replicate. There were 2-3 biological replicates per treatment. Frozen leaves samples were send to Biomarker Technologies, in Beijing, China, for RNA extraction.A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina®(NEB, CA,USA) following manufacturer’s recommendations
RNA libraries were prepared for sequencing using standard Illumina protocols


title: T10 pH 2.5

extract_protocol:
Equal amounts of sample from four seedlings (one seedling per pot) were mixed as a biological replicate. There were 2-3 biological replicates per treatment. Frozen leaves samples were send to Biomarker Technologies, in Beijing, China, for RNA Equal amounts of frozen leaves from four seedlings (one seedling per pot) were pooled as one biological replicate. There were two-three biological replicates for each treatment. Total RNA was independently extracted twice from ca. 100 - 200 mg frozen control and +Al roots of C. sinensis and C. grandis seedlings using Recalcirtant Plant Total RNA Extraction Kit (Centrifugal column type, Bioteke Corporation, China) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: T04 pH 6

extract_protocol:
EEqual amounts of frozen leaves from four seedlings (one seedling per pot) were pooled as one biological replicate. There were two-three biological replicates for each treatment. Total RNA was independently extracted twice from ca. 100 - 200 mg frozen control and +Al roots of C. sinensis and C. grandis seedlings using Recalcirtant Plant Total RNA Extraction Kit (Centrifugal column type, Bioteke Corporation, China) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: T02 pH 6


title: B1_GlomAffyAnnot_FSGS_75


title: Cell_TTGCTCGGCCATGAG

status: Public on May 02 2018

data_processing:
The second read was used to assign the first read to a cell index and unique molecular indentifier according to the suggested protocol from Illumina which includes error correction and filtering of unassignable reads.
Cells with fewer than 14,000 assigned reads were filtered out as artifacts.
Reads were mapped to the hg19 genome using the STAR aligner version 2.5.1b using the default parameters and --outFilterIntronMotifs RemoveNoncanonical.
Mapped reads were deduplicated by removing all but one read with the same unique molecular identifier mapping to the same position.
Raw read expression was quantified across exons for all genes with the top-expressed isoform taken as proxy for gene expression resulting in a raw count table for 507 cells and all genes.
Genome_build: hg19
Supplementary_files_format_and_content: Tab separated raw count table

source_name: hCA3 neurons from huES6 derived NPCs

growth_protocol: huES6 derived NPCs were differentiated to hCA3 neurons for 14 days in vitro

extract_protocol:
Differentiating hCA3 population were dissociated into a single cell suspension by enzymatic dissociation by treating with Accutase (Stem cell technologies). Cells were collected in PBS containing 0.1%BSA on ice. The cell suspension obtained was filtered with 22µm filter (Millipore) and kept in cold PBS-BSA solution. Before counting, trypan blue was added to the cell suspension and the viability, cell density and presence of clumps were assayed on a TC20™ Automated Cell Counter. Cell suspension at a final dilution of 2500 cells/µL and containing no less than 85% live cells were taken for the encapsulation and later steps. All reagents for encapsulation, cDNA synthesis, library preparation and sequencing were from Illumina inc. Cell suspensions were loaded into a ddSEQ catridge in a ratio of 21.5 µL Cell enzyme mix to every 4.5 µL cell suspension. 60ul of 3’ barcode suspension mix and encapsulation oil were also loaded on the ddSEQ cartridge. The chip was then processed on a ddSEQ™ Single-Cell Isolator for about 5 minutes to generate single cell droplets.
Encapsulated samples were transferred to a 96 well plate and reverse transcription mix was added and followed by reverse transcription on a thermal cycler. When the reverse transcription was done droplet disruptor was added to the product. This was followed by the first strand purification using magnetic beads. The beads were immobilized using magnetic peg stand and dynamag and supernatant was discarded. The beads were washed twice with 80% EtOH. 30uls of resuspension buffer was added for elution and supernatant was transferred to a new tube. The purified first strand was used to synthesize the second strand to generate the double strand cDNA. Again the cDNA was purified using magnetic beads, followed by 80% EtOH wash and elution. Amplified cDNA was simultaneously fragmented and barcoded by tagmentation using Tagment enzyme on thermal cycler. DNA adapters were added for cluster formation. Followed by the index addition, libraries were cleaned up using magnetic beads as before. Purified libraries were eluted with 20ul resuspension buffer. 1ul of eluted product was assessed on an Agilent BioAnalyzer. Library size was about 500bp.
Sequencing was performed on an Illumina HiSeq 2500 instrument using surecell-sequencing primers.

value: hCA3 neuron


title: Cell_TTGGATCGTTATCTA


title: Cell_TTTGGGGAAGGGCCA


title: B1_GlomAffyAnnot_FSGS_73


title: Cell_TTGCTCTTCTTGCTT


title: Cell_TTTGGGCGAGCAATC


title: Cell_TTTGGGGAGGCCGAG


title: B1_GlomAffyAnnot_FSGS_4


title: Cell_TTTGGGTCTAGCTAT


title: B1_GlomAffyAnnot_FSGS_68


title: Cell_TTTGGGAATTGGCAG


title: Cell_TTCTTGTTGGATTGT


title: Cell_TTTGGGCTTACGGCC


title: B1_GlomAffyAnnot_FSGS_77


title: Cell_TTCGCAGTTTCAGCT


title: B1_GlomAffyAnnot_FSGS_2


title: Cell_TTAAGATTGGATTTG


title: B1_GlomAffyAnnot_FSGS_64


title: Cell_TTAAGATGCGGTAAG


title: Cell_TGTTCGGTCGGCTTG


title: Cell_TTAAGAGTCCTACGG


title: B1_GlomAffyAnnot_FSGS_1


title: Cell_TTAAGACGAAAGATT


title: Cell_TTAAGAGCCAGACAA


title: Cell_TGTTCGAGTAAAGAC


title: Cell_TGTTCGTCGCCTGCC


title: Cell_TGTGTAAACGTGCAC


title: Cell_TGCTAACAGACTAGA


title: B1_GlomAffyAnnot_FSGS_5


title: Cell_TGTGTAGCCGTTAGT


title: B1_GlomAffyAnnot_FSGS_3


title: Cell_TGCGGTTAATAGCAG


title: Cell_TGTGTACGTTATAGA


title: Cell_TGCGGTTCGGGACGT


title: Cell_TGTGTACTATTACGA


title: Cell_TGCGGTTTGGATAGA


title: Cell_TGCGGTGGTAGGGTT


title: Cell_TGCTAACGCATATGA


title: Cell_TGAGACCTTGAACAG


title: Cell_TGCGGTTAAGCTAGG


title: Cell_TGCGGTACCCAAGTG


title: Cell_TGCGGTTCAGTGACC


title: Cell_TGAATTGTACAGCGG


title: Cell_TGAGACCACCACGAG


title: Cell_TGAGACAAAGAAAGA


title: Cell_TCTAGCCTTACGACC


title: Cell_TCGGGATCATCACGG


title: Cell_TGAATTATGAAGTCA


title: Cell_TCGGGACGCATATCG


title: Cell_TGAATTAAGTATCCG


title: Cell_TCTAGCAAAGAATCA


title: Cell_TCGCCTGATCAACGC


title: Cell_TGTTCGCTCAATTGC


title: Cell_TCGCCTGAAATATGC


title: Cell_TCGCCTTTAAGATGT


title: Cell_TCGGGACACCACGAG


title: Cell_TCCAAGCGAGCACTG


title: Cell_TCCAAGCCGTAAGTT


title: Cell_TCGCCTAATTGGACG


title: Cell_TCGCCTCACTGTAAG


title: Cell_TCAGTGGCGCGGTTA


title: Cell_TCAGTGTTTGGGCGT


title: Cell_TCATCAACCCAACAA


title: Cell_TCAGTGCACCACTAG


title: Cell_TCATCAATGAAGCCT


title: Cell_TAGAGGGTACAGATA


title: Cell_TAGAGGCAACCGGCT


title: Cell_TACCGAGACTCGAGA


title: Cell_TACCGATTAAGAACT


title: Cell_TACCGACCACGCGCT


title: Cell_TAATAGGCTTGTGCC


title: Cell_TAAGCTTAATAGTGT


title: Cell_TAATAGACAAGGCTA


title: Cell_GTTAACGTGGTGCAG


title: Cell_TAAGCTCCGTAACAG


title: Cell_TAAGCTGCTTGTATA


title: Cell_TAAGCTTATTTCACC


title: Cell_GTTAACGCGCGGGCG


title: Cell_GTTAACATGAAGCAC


title: Cell_GTGGTGCTTACGATG


title: Cell_GTCGGCCCTCTACGA


title: Cell_GTCGGCCTAGGTGCC


title: Cell_GTACAGATTAGTTCC


title: Cell_TCATCAAGACCCCAG


title: Cell_GGTGCTTTCTTGAAT


title: Cell_GTCGGCCACTGTGGT


title: Cell_TCAGTGGACTCGACC


title: Cell_GTACAGAGCACGCCG


title: Cell_GTACAGACAAGGTCA


title: Cell_GGTAGGGGGATCACT


title: Cell_TCAGTGCAAGTCGGT


title: Cell_GTCGGCACCTTCGGG


title: Cell_GGTGCTCTATTACTA


title: Cell_GGTGCTGGACGAGTT


title: Cell_GGTAGGCTAGGTATC


title: Cell_GGGATCGCGCGGACT


title: Cell_GGGATCTAATAGGTT


title: Cell_GGGATCCGTTATAAC


title: Cell_GGGATCAATTGGGCT


title: Cell_GGGATCAGTAAATCG


title: Cell_GGCCATTGCTAATCC


title: Cell_GGGATCTTGGATCAG


title: Cell_GGCCATGCTTGTAAG


title: Cell_GGCCATCTATTAGTT


title: Cell_GTCGGCTTGGATAGA


title: Cell_GGATTGTTAAGAGTT


title: Cell_GGATTGCTCAATCTA


title: Cell_GGATTGACGGACTGT


title: Cell_GGATTGACCCAAATA


title: Cell_GGTGCTTAATAGCAA


title: Cell_GGACGATCGCCTCAA


title: Cell_GGACGATCATCAAGA


title: Cell_GGACGATCAGTGGCT


title: Cell_GGACGACAGACTGTT


title: Cell_GGACGATTCTTGCAA


title: Cell_GGTGCTAAGTATAGA


title: Cell_GGACGATTTGGGACC


title: Cell_GGACGACAACCGGCC


title: Cell_GGACGAAAGTATTCC


title: Cell_GGACGACGCATATAT


title: Cell_GGACGAACTGCATCA


title: Cell_GCTTGTGCGAATGGT


title: Cell_GCTTGTACTGCACGC


title: Cell_GCTGAGTCTAGCATG


title: Cell_GCTTGTAAAGAATCC


title: Cell_GGCCATGCTTGTCGC


title: Cell_GCTGAGCCGTAACAG


title: Cell_GCTGAGTAATAGATA


title: Cell_GCTGAGGCGCGGTAT


title: Cell_GGCCATGCTTGTACC


title: Cell_GCTGAGCACTGTGCG


title: Cell_GCTGAGAGATGTGTT


title: Cell_GCTGAGAGGTTAATA


title: Cell_GCTCCCTCCAAGGCT


title: Cell_GCTCCCTACCGAAAT


title: Cell_GCTCCCGTTAACGCT


title: Cell_GGACGACTTGAATTG


title: Cell_GCTCCCGTGGTGGCC


title: Cell_GCTCCCCAGACTGAT


title: Cell_GCTTGTGTTTCAAGT


title: Cell_GCTCCCAGGTTACAT


title: Cell_GCGCGGTAGAGGATT


title: Cell_GCTCCCACCTTCAAG


title: Cell_GCGCGGCATAGATAA


title: Cell_GCGCGGGAGTGAGTT


title: Cell_GCGCGGTTGGATAGG


title: Cell_GCGCGGATGAAGCAG


title: Cell_GCGAATTGAATTGGA


title: Cell_GCGCGGTAGAGGGCG


title: Cell_GCGAATTCTAGCTAG


title: Cell_GCGAATATAGCGCTT


title: Cell_GCGAATATACTTTAC


title: Cell_GCGAATTCCAAGGTT


title: Cell_GCCAGATTTGGGCAG


title: Cell_GCGAATGCTTGTGAG


title: Cell_GCCGTTAGTCTGGTC


title: Cell_GCTGAGGGACGAAGG


title: Cell_GCCGTTCTATTATTG


title: Cell_GCCAGACTTACGAGA


title: Cell_GCCGTTATATACGCT


title: Cell_GCCAGAAAGCCATAG


title: Cell_GCCAGATAAGCTTAC


title: Cell_GCTCCCTCCAAGTAG


title: Cell_GATCAATTTGGGAAT


title: Cell_GATCAATTGCTCGAG


title: Cell_GATCAAGACTCGTCC


title: Cell_GATCAATGCGGTTCG


title: Cell_GATCAACTATTAAAG


title: Cell_GATCAACGTTATAGT


title: Cell_GATCAACCACGCGTC


title: Cell_GAGTGATTCTTGTGA


title: Cell_GAGTGATTGGATTCA


title: Cell_GAGTGATCAGTGTGT


title: Cell_GAGTGAGAGCTTAAC


title: Cell_GAGTGACTTACGCGA


title: Cell_GAGTGATCGCCTTGA


title: Cell_GAGGCCTAATAGTAT


title: Cell_GAGTGACAGGAGTGC


title: Cell_GAGGCCCACTGTCGG


title: Cell_GAGGCCCTTACGCAA


title: Cell_GAGGCCATACTTGCT


title: Cell_GAGCTTTTTGGGGAC


title: Cell_GAGCTTGTGGTGATG


title: Cell_GAGCTTGGGATCGAG


title: Cell_GAGCTTGCGAATCTT


title: Cell_GAGCTTGGATTGAAC


title: Cell_GAGTGAAGACCCTAA


title: Cell_GAGCTTTACCGAGGT


title: Cell_GAGCTTCTATTAATA


title: Cell_GAGCTTGTCCTACTT


title: Cell_GAGCTTGGGATCTTG


title: Cell_GAGCTTCGGCGTCGA


title: Cell_GAGCTTCCTCTACAG


title: Cell_GACTCGTCATCAAAG


title: Cell_GAGCTTAGATGTGCC


title: Cell_GACTCGCGTTATGGA


title: Cell_GACTCGAGATGTGGA


title: Cell_GACTCGAAGCCAACA


title: Cell_GAAGGGTCCAAGGGG


title: Cell_GAAGGGTTCTTGATC


title: Cell_GAAGGGTCGGGAGGC


title: Cell_GAGTGACGGTCCAGT


title: Cell_GAAGGGGCTCCCACG


title: Cell_GAAGGGACAAGGGCC


title: Cell_GAAGGGGCCAGACAG


title: Cell_GAAGGGCTCAATTCA


title: Cell_GAAATATTGCTCCAG


title: Cell_GAAGGGATCCGGATA


title: Cell_GAAATACGTTATTTA


title: Cell_GAAATAGAAATATGT


title: Cell_GAAATACGAAAGCTA


title: Cell_GAAATAACCCAAAGG


title: Cell_GAGCTTGAGCTTTGG


title: Cell_CTTGAATATTTCAGA


title: Cell_CTTGAAGCGCGGCTA


title: Cell_CTTGAAGCTTGTCTT


title: Cell_CTTGAACGAAAGAGA


title: Cell_CTTGAACAACCGATA


title: Cell_CTTGAAATACTTAAC


title: Cell_GACTCGCTGTGGAAT


title: Cell_CTTACGTTCTTGCGT


title: Cell_CTTACGTTCTTGTAT


title: Cell_CTTGAAAGCACGGCC


title: Cell_CTTACGGCTTGTTGA


title: Cell_CTTACGTCGCCTTAT


title: Cell_CTTACGTGGCAGGAG


title: Cell_CTTACGATCCGGAAC


title: Cell_CTGTGGTTCTTGTGA


title: Cell_CTGTGGGCTCCCAGA


title: Cell_CTGTGGTCATCAGCT


title: Cell_CTGTGGGTCGGCCTA


title: Cell_CTGTGGCTAGGTGGT


title: Cell_CTGTGGACTGCAGTT


title: Cell_GAAATAGTTTCATCT


title: Cell_CTGTGGCCGATGTGC


title: Cell_CTCAATGAGTGAATG


title: Cell_CTGTGGAAGTATACT


title: Cell_CTCAATGAAATACCA


title: Cell_CTTGAATTCTTGATA


title: Cell_CTCAATCGGCGTACG


title: Cell_CTCAATATGAAGCAC


title: Cell_CTCAATATACTTGCC


title: Cell_CTTGAACCTCTATCA


title: Cell_CTATTATTCTTGCAC


title: Cell_CTTGAAATTAGTTCT


title: Cell_CTCAATCTAGGTCCG


title: Cell_CTATTATGCTAATTG


title: Cell_CTATTAGTTTCAAAT


title: Cell_CTATTAGCCAGAAGA


title: Cell_CTATTACTCAATAAC


title: Cell_CTGTGGTTTGGGTAA


title: Cell_CTATTACTTGAAGGA


title: Cell_CTATTAACCCAAAGG


title: Cell_CTTACGGACTCGTAA


title: Cell_CTATTAAAGCCAACT


title: Cell_CTATTACGAGCAGGA


title: Cell_CTAGGTGTTAACCAT


title: Cell_CTAGGTGTGGTGGTA


title: Cell_CTAGGTGACTCGCCG


title: Cell_CTAGGTGACTCGATA


title: Cell_CTAGGTGTACAGAAC


title: Cell_CTAGGTGGGATCGCT


title: Cell_CGTTATTGGCAGCCT


title: Cell_CTAGGTAGACCCTGA


title: Cell_CTAGGTGAAGGGCGG


title: Cell_CGTTATGCGCGGCAC


title: Cell_CGTTATTCGGGATGT


title: Cell_CGTTATGCCAGATCA


title: Cell_CGTTATGCCAGATAA


title: Cell_CGTTATCCACGCATG


title: Cell_CGTTATCAGGAGGGC


title: Cell_CGTTATCATAGAGGT


title: Cell_CGTTATCAGGAGACC


title: Cell_CGGTCCTCGCCTTGG


title: Cell_CGGTCCCTCAATGTC


title: Cell_CGGTCCTATTTCTAA


title: Cell_CGGTCCCGTTATATA


title: Cell_CGGTCCCAAGTCCCG


title: Cell_CGGCGTTTTGGGTCA


title: Cell_CGGTCCCGGTCCTCG


title: Cell_CGGTCCAGTCTGCTT


title: Cell_CGGCGTATCCGGCAG


title: Cell_CTATTACAGGAGCTG


title: Cell_CGCATAGTCGGCGGA


title: Cell_CGGCGTAAAGAAGAT


title: Cell_CGCATACGAAAGGTC


title: Cell_CGAGCATTTGGGTGT


title: Cell_CGAGCATGCTAACAC


title: Cell_CTAGGTCAACCGGGT


title: Cell_CGAGCAGGGATCAGA


title: Cell_CGAGCAGCTTGTACT


title: Cell_CGAGCAAAGTATTCG


title: Cell_CGAGCACGTTATTGC


title: Cell_CGAAAGTGCGGTTGA


title: Cell_CGAAAGTCCAAGCAA


title: Cell_CGAAAGTTGGATTCG


title: Cell_CGAAAGGGCCATGAC


title: Cell_CGAAAGCGCATACAG


title: Cell_CGAAAGACCTTCGCT


title: Cell_CCTCTATGGCAGACG


title: Cell_CCTCTAGTACAGAAT


title: Cell_CCTCTAGAGTGACTA


title: Cell_CCTCTACCACGCAGG


title: Cell_CCGTAATCATCATGT


title: Cell_CGAAAGCTTGAAGCG


title: Cell_CCGTAAGCTCCCGTC


title: Cell_CGCATATACCGAAAA


title: Cell_CCGTAAGAGTGAGGG


title: Cell_CCGTAACAGACTATA


title: Cell_CCGTAACAGGAGCTG


title: Cell_CGCATACTTACGCAA


title: Cell_CCGATGTAAGCTCGG


title: Cell_CCGATGTGAATTACG


title: Cell_CCGATGGACTCGCAG


title: Cell_CCGATGCGAGCAGGA


title: Cell_CCGTAACAAGTCTTA


title: Cell_CCGATGTTCTTGTAA


title: Cell_CCACGCGTACAGGAG


title: Cell_CCACGCGCTCCCATA


title: Cell_CCACGCTTGGATGTC


title: Cell_CCACGCGTCCTAGGA


title: Cell_CATAGATCGGGATTC


title: Cell_CCACGCTAATAGTTA


title: Cell_CCACGCGCGAATGGA


title: Cell_CCACGCCTATTATAG


title: Cell_CCACGCATAGCGGCC


title: Cell_CGAAAGGTACAGATC


title: Cell_CATAGACATAGAACC


title: Cell_CATAGATAATAGAGT


title: Cell_CATAGATCCAAGCGT


title: Cell_CCTCTAATACTTGGT


title: Cell_CATAGACTAGGTTCC


title: Cell_CATAGAAAAGAACAC


title: Cell_CAGGAGCCGATGTTA


title: Cell_CAGGAGGAAGGGCGG


title: Cell_CAGGAGTGAATTGGT


title: Cell_CAGGAGGAGTGAAAT


title: Cell_CAGGAGGTTTCAACT


title: Cell_CAGGAGGCGCGGCAG


title: Cell_CAGACTTCGCCTTCA


title: Cell_CAGGAGCTAGGTTCA


title: Cell_CCGATGACCTTCTTG


title: Cell_CACTGTGGACGATGC


title: Cell_CAGGAGATATACCTT


title: Cell_CAGACTACTGCACTG


title: Cell_CACTGTGGACGAGGA


title: Cell_CAGGAGAGTAAACCG


title: Cell_CACCACGGTAGGACC


title: Cell_CACCACCAACCGTGT


title: Cell_CACCACATGAAGAGT


title: Cell_CACCACAGGTTAGAA


title: Cell_CAAGTCGTGGTGGAT


title: Cell_CAAGTCTGTTCGGAA


title: Cell_CAAGTCATTAGTTTT


title: Cell_CAAGTCCTTGAATTT


title: Cell_CAAGTCCGCATACAC


title: Cell_CAAGTCAACAGCACG


title: Cell_CAACCGTGAGACAGT


title: Cell_CAACCGTCGCCTTTC


title: Cell_CAGGAGTGGCAGCTA


title: Cell_CAACCGGTTTCAGGG


title: Cell_CAACCGGCTCCCGGA


title: Cell_CAACCGCGAAAGCAG


title: Cell_CAACCGCGAAAGAAG


title: Cell_ATTAGTCTCAATTCG


title: Cell_CAACCGACCTTCGCC


title: Cell_ATTAGTCATAGATTC


title: Cell_CAGGAGATCCGGGTC


title: Cell_ATTAGTCAACCGCTT


title: Cell_ATTAGTACAAGGCAA


title: Cell_ATGAAGGTACAGAAT


title: Cell_ATGAAGTATTTCAAT


title: Cell_ATGAAGTGAGACGGT


title: Cell_ATGAAGGAGTGACCT


title: Cell_ATTAGTACGGACGCC


title: Cell_CACTGTCTTGAAACA


title: Cell_ATGAAGCCACGCCAT


title: Cell_ATGAAGGAGTGAGAT


title: Cell_ATGAAGAACGTGTTC


title: Cell_ATCCGGGGATTGCAG


title: Cell_ATCCGGGAAGGGGGA


title: Cell_ATCCGGCGGCGTATA


title: Cell_ATCCGGAGTCTGTTC


title: Cell_ATATACTCAGTGTGC


title: Cell_ATATACGATCAATAA


title: Cell_ATCCGGTCATCACAA


title: Cell_ATGAAGCACCACGTA


title: Cell_ATATACGAAGGGATA


title: Cell_ATCCGGCTAGGTTGC


title: Cell_ATATACATCCGGATG


title: Cell_ATCCGGACTGCACTT


title: Cell_ATATACCAAGTCCGG


title: Cell_ATAGCGTATTTCTAT


title: Cell_ATATACAGACCCCAA


title: Cell_ATAGCGTCGGGAAGT


title: Cell_ATAGCGCGAGCACGT


title: Cell_ATAGCGAGGTTAAGC


title: Cell_ATACTTTTCGCATAA


title: Cell_ATACTTATTAGTGTT


title: Cell_ATACTTCTAGGTTTC


title: Cell_ATACTTCCGATGAAG


title: Cell_ATACTTAACGTGATA


title: Cell_ATACTTAACGTGTTG


title: Cell_AGTCTGATTAGTCCG


title: Cell_AGTCTGATGAAGTCT


title: Cell_AGTAAATCATCAGGT


title: Cell_AGTAAATAATAGTTG


title: Cell_AGTAAACCGTAAGGG


title: Cell_AGTAAAGTTTCATAA


title: Cell_AGTAAAATATACGTC


title: Cell_AGGTTAGGCCATGAG


title: Cell_AGGTTAGCTGAGGGT


title: Cell_AGGTTAGAGTGAGCC


title: Cell_AGGTTACTCAATACC


title: Cell_AGGTTAATCCGGCAA


title: Cell_AGCACGTAGAGGGAA


title: Cell_ATATACCTTACGTCG


title: Cell_AGCACGGATCAATGC


title: Cell_AGCACGATAGCGGGC


title: Cell_AGATGTTCTAGCGAG


title: Cell_ATAGCGGCGAATAAG


title: Cell_AGCACGCGTTATAGG


title: Cell_AGATGTGTTTCATGT


title: Cell_AGATGTGGGATCATA


title: Cell_AGATGTGTACAGCCG


title: Cell_ATACTTCGTTATCTA


title: Cell_AGATGTGTTTCATAA


title: Cell_AGATGTGCGAATAAA


title: Cell_AGATGTGAAGGGGAG


title: Cell_AGATGTCCACGCAGG


title: Cell_AGTCTGGGACGAATA


title: Cell_AGACCCTTCGCATGA


title: Cell_AGACCCTGGCAGCAA


title: Cell_AGACCCGGCCATGAA


title: Cell_AGACCCGAGCTTGAA


title: Cell_AGACCCGAAGGGTGC


title: Cell_ACTGCAGACTCGCAG


title: Cell_AGACCCAACGTGCAC


title: Cell_AGTAAAACGGACGGC


title: Cell_ACTGCACTCAATGTT


title: Cell_ACTGCAAGTAAAGTT


title: Cell_ACGGACTGAGACCCA


title: Cell_ACGGACGATCAAACT


title: Cell_ACGGACAGTAAATGG


title: Cell_AGATGTTAATAGTGC


title: Cell_AGCACGGCTGAGGTT


title: Cell_ACGGACGTACAGTGA


title: Cell_ACGGACACGGACGCC


title: Cell_ACCTTCGAGCTTCTT


title: Cell_ACCTTCGAGCTTTAA


title: Cell_ACCCAATTCTTGAAC


title: Cell_ACCTTCCTCAATCCG


title: Cell_ACCTTCCAACCGGCT


title: Cell_ACCTTCTGCTAAGCC


title: Cell_ACCCAACTATTACCG


title: Cell_ACCCAATGCGGTTGT


title: Cell_ACCCAACCGATGGAA


title: Cell_ACCTTCCATAGACCG


title: Cell_ACCCAACGCATACGT


title: Cell_ACCCAAAAAGAAGCT


title: Cell_ACAAGGTCCAAGCAC


title: Cell_ACAAGGTCTAGCTGG


title: Cell_ACAAGGCGGCGTAAC


title: Cell_ACAAGGGCTTGTATC


title: Cell_ACAAGGCATAGAACC


title: Cell_ACAAGGACCTTCCAC


title: Cell_ACAAGGAATTGGGCG


title: Cell_AGACCCGCTCCCTGT


title: Cell_ACGGACGTGGTGATA


title: Cell_ACCTTCTACCGAGCC


title: Cell_AATTGGTTAAGAATG


title: Cell_AATTGGCTTGAATTT


title: Cell_AATTGGCGTTATGAA


title: Cell_ACCCAAGGATTGTCA


title: Cell_AATTGGTAAGCTCTG


title: Cell_AATTGGCTTACGACC


title: Cell_AATTGGGACTCGTAC


title: Cell_AATTGGAAAGAACGC


title: Cell_AATTGGGAAGGGATC


title: Cell_AATTGGCGCATAGCT


title: Cell_AAGCCAGTACAGCGT


title: Cell_AAGTATTGAATTGTT


title: Cell_AAGTATAGACCCGTT


title: Cell_AAGTATACAAGGCGT


title: Cell_AAGCCATGTGTACGT


title: Cell_AATTGGCGAAAGTGA


title: Cell_ACCCAAAATTGGCTG


title: Cell_AAGTATCAGGAGAAA


title: Cell_AAGCCACTGTGGTAT


title: Cell_AACGTGTTTGGGCAC


title: Cell_AAGCCACGCATACGA


title: Cell_AACGTGCCGTAAACG


title: Cell_AACGTGGCTTGTTGC


title: Cell_AACGTGTTCTTGACA


title: Cell_AACGTGACGGACCTA


title: Cell_AACGTGAGTCTGCAC


title: Cell_AAGCCACGGTCCGTT


title: Cell_AACAGCTTGGATTGT


title: Cell_AACAGCTGCGGTGAC


title: Cell_AACAGCGTGGTGCAA


title: Cell_AACAGCGGCCATATG


title: Cell_AACAGCGAGGCCCGT


title: Cell_AACAGCAGTAAATAT


title: Cell_AACAGCCAACCGGGT


title: Cell_AACAGCATATACGGG


title: Cell_AAAGAAGTTTCATCA


title: Cell_AAAGAATTTGGGCAG


title: Cell_AAAGAACTATTAATC


title: Cell_AAAGAATAGAGGGCT


title: Cell_AAAGAACTAGGTCTT


title: Cell_AAAGAACCGTAAAGT


title: Cell_AAAGAAACCTTCCTT


title: Cell_AAAGAACGTTATTTG


title: Cell_AAAGAAAAAGAATGC


title: panNPC_1

data_processing:
Sequenced reads were quality-tested using FASTQC.
Adapters and low-quality sequence ends were trimmed with cutadapt.
Reads were aligned to the hg38 human genome using the STAR[2] version 2.5.2a using default parameters.
The genome index was constructed using the hg38 genome build downloaded from UCSC.
Raw gene expression was quantified at the gene level across all exons, using htseq-count, and differential gene expression was carried out using the DESeq2[4] package version 1.12 using replicates to compute within-group dispersion. Differentially expressed genes were defined as having a false discovery rate (FDR) <0.05.
Genome_build: hg38
Supplementary_files_format_and_content: Raw count expression tables in csv format

source_name: panNPC 1

growth_protocol: Differentiation of hCA3 neuron protocol was followed for obtaining hCA3 neurons; hpNPCs were obtained as described in DX Yu et al, Stem Cell Reports 2014; Pan NPCs were generated follwing the protocol described in Marchetto, M.C.,et al  Mol Psychiatry. 2016

extract_protocol:
Total cellular RNA was extracted from 3-5X 106 cells using the RNA-BEE (QIAGEN), according to the manufacturer’s instructions, and reverse transcribed using the high-capacity cDNA synthesis kit from AB Biosystems.
Poly(A)+ RNA was selected and fragmented to prepare sequencing libraries using the Illumina TruSeq Stranded RNA sample preparation kit.
Single-end stranded

tag: human es line

tag: time


title: panNPC_3

source_name: panNPC 3


title: hpNPC_3

source_name: hpNPC 3


title: panNPC_2

source_name: panNPC 2


title: hpNPC_2

source_name: hpNPC 2


title: hCA3_6wk_3

source_name: hCA3 6wk 3

value: 6 week


title: hCA3_4wk_3

source_name: hCA3 4wk 3

value: 4 week


title: hCA3_5wk_2

source_name: hCA3 5wk 2

value: 5 week


title: hpNPC_1

source_name: hpNPC 1


title: hCA3_6wk_1

source_name: hCA3 6wk 1


title: hCA3_4wk_2

source_name: hCA3 4wk 2


title: hCA3_4wk_1

source_name: hCA3 4wk 1


title: hCA3_3wk_3

source_name: hCA3 3wk 3

value: 3 week


title: hCa3_3wk_1

source_name: hCa3 3wk 1


title: hCA3_1wk_1

source_name: hCA3 1wk 1

value: 1 week


title: hCA3_2wk_1

source_name: hCA3 2wk 1

value: 2 week


title: hCA3_2wk_2

source_name: hCA3 2wk 2


title: Cell_AACAGCCAAGTCATT

source_name: hCA3 neurons from huES6 derived NPCs


title: hCA3_1wk_2

source_name: hCA3 1wk 2


title: Cell_AAAGAATTCGCAGGT


title: hCA3_1wk_3

source_name: hCA3 1wk 3


title: hCA3_3wk_2

source_name: hCA3 3wk 2


title: Nup98 ChIPseq in HPCs immortalized with Nup98-Nsd1 (antibody only recognized WT Nup98)

status: Public on Apr 11 2018

description:
Wild-type Nup98 ChIP-Nup98-Nsd1 Immortalized HPCs
Franks et al. 2017 WTNup98 and FlagNup98-Nsd1 Peaks

data_processing:
Reads were aligned to mouse genome (hg19, GRCh37) using STAR
Reads were aligned to the mouse (mm10, GRCm38) (Figures 1-5) using bwa (version 0.7.12) (Li and Durbin, 2009).
Only reads that aligned uniquely to a single genomic location (MAPQ > 10) were used for downstream analysis.
ChIP-Seq peaks and normalized bedGraph files were generated using HOMER using an FDR or 0.1% and fold-enrichment over input of at least 4-fold (2-fold with Nup98 ChIP) (Heinz et al., 2010)
Genome_build: mm10, GRCm38)
Supplementary_files_format_and_content: Excel spreadsheets with peak locations and identities

source_name: Mouse HPCs

growth_protocol:
RPMI, 10% FBS, 1X GMCSF (HPCs) or (1X Stem Cell Factor in Flag-Nup98-Nsd1 cells only)
DMEM 15% + amino acids for IMR90

extract_protocol:
Fix 1% paraformaldehyde, nuclear purification with 0.5% NP40, DNA solubilization and sonication in 1% SDS followed by Co-IP with antibody of interest
Illumina Truseq LT

treatment_protocol: siRNA transfection with RNAimax (Biorad)

value: Hematopoietic System

tag: antibody


title: H3K4me3 ChIPseq in HPCs

description:
H3K4me3 ChIPseq in HPCs (HoxA9 Immortalized)
Franks et al. 2017_H3K4me3 Peaks


title: ORG14_POS

status: Public on Apr 25 2018

description: organoid 14

data_processing:
Sequenced reads were quality-tested using FASTQC v0.11.5
Reads were aligned to the hg19 human genome using the STAR aligner version 2.5.1b. Mapping was carried out using default parameters, filtering non-canonical introns and allowing up to 10 mismatches per read and only keeping uniquely mapped reads.
The genome index was constructed using the gene annotation supplied with the hg19 Illumina iGenomes colelction and sjdbOverhang value of 100.
FPKM (fragments per kilobase per million mapped reads) gene expression was quantified across all gene exons with HOMER (Shienz et. al, 2010), using the top-expressed isoform as proxy for gene expression.
Subtype-specific gene signature centroids were obtained and k-means clustering was used (Cluster 3 v 1.5.2) to identify sets of genes upregulated or depleted in neural, proneural, mesenchymal, or classical GBM subtypes. The log-normalized FPKM expression values from  data were z-normalized across tdTomato positive (POS) and negative (NON) samples, centered, and visualized with TreeView v1.1.6r4. The log-normalized FPKM values for each of the 8 gene signature sets were tested for differences in mean between POS and NON samples (Welches 2-tailed t-test) to show altered expression of signature genes between NON and POS samples. All subtype signature genes were then pooled and their log-normalized  expression values were k-means clustered (Cluster 3) to find if these genes were either up in POS organoids, down in POS organoids, or part of an ambiguous set. Then for each of the 8 sets of marker genes, the proportion belonging to the up in POS cluster compared to the proportion that are in the down in POS cluster were plotted, and significance was evaluated with a binomial test.
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet containing FPKM, ln(FPKM), and results from overlapping RNA-Seq with a previously published microarray dataset

source_name: human cerebral organoid

growth_protocol: Human cerebral organoids were generated from the human Embryonic Stem (ES) cell line H9 using the protocol previously described by Lancaster et. al., (Lancaster, M.A., and Knoblich, J.A. (2014). Nat. Protoc. 9, 2329–2340.)

extract_protocol:
About 16 weeks after the electroporation, the transduced organoids were dissociated in Accutase then passed through a mesh filter to create a single-cell suspension. Cells were collected by centrifugation and resuspended in cerebral organoid differentiation medium and FACS sorted into TRI-zol LE and RNA was purified by Direct-zol™ RNA MicroPrep.
cDNA libraries were prepared using the TruSeq RNA Sample Prep kit (Illumina). RNA sequencing was performed using a HiSeq 2500 Sequencing System (Illumina).

treatment_protocol: A CRISPR-CAS9 TP53 gRNA construct, and a donor construct CMV H-RAS G12V tdTomato with homology arms targeting the TP53 locus,  were co- electroporated into 4 month old cerebral organoids.

value: human cerebral organoid

value: human Embryonic Stem (ES) cell line H9

tag: cell population

value: tdTomato fraction


title: ORG2_POS

description: organoid 2


title: ORG3_NON

description: organoid 3

value: no tdTomato fraction


title: ORG3_POS

description: organoid 3


title: ORG2_NON

description: organoid 2


title: 1202_POS

description: organoid 1202


description:
H3K4me3 ChIPseq in HPCs depleted of Nup98  (HoxA9 Immortalized)
Franks et al. 2017_H3K4me3 Peaks


title: SET1A ChIPseq in HPCs

description:
Set1A ChIP - HPCs (HoxA9 immortalized)
Franks et al. 2017_Set1A promoters +/- Nup98 knockdown


title: Nup98 ChIPseq in HPCs

description:
Nup98 ChIP-HPCs (HoxA9 immortalized)
Franks et al. 2017 WTNup98 and FlagNup98-Nsd1 Peaks


title: Flag ChIPseq in HPCs expressing Flag-Nup98-Nsd1

description:
Flag ChIP - Flag-Nup98-Nsd1 immortalized cells
Franks et al. 2017 WTNup98 and FlagNup98-Nsd1 Peaks

value: Flag


title: hCA3_5wk_1

source_name: hCA3 5wk 1


title: SET1A ChIPseq in HPCs depleted of Nup98

description:
Set1A ChIP - HPCs depleted of Nup98 (HoxA9 immortalized)
Franks et al. 2017_Set1A promoters +/- Nup98 knockdown


title: IgG ChIPseq in HPCs

description: IgG ChIP-Set1a experiment (HoxA9 Immortalized)

value: IgG


title: ORG14_NON

description: organoid 14


title: 1202_NON

description: organoid 1202


title: RfxCasR NT array rep 2

status: Public on Mar 21 2018

description:
stranded mRNA
fpkm.txt
ANXA4_array_CasR_vs_NT_array_CasR.xlsx

data_processing:
Sequenced reads were quality-tested using FASTQC (Andrews, 2010)
Reads were aligned to the hg19 human genome using the 2.5.1b STAR aligner (Dobin, 2013). Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read). The genome index was constructed using the  gene annotation supplied with the hg19 Illumina iGenomes collection (Illumina) and sjdbOverhang value of 100.
Uniquely mapped reads were quantified across all gene exons using the top-expressed isoform as proxy for gene expression with the HOMER (Heinz, 2010) analysis suite
differential gene expression was carried out with DESeq2 v 1.14.1(Love, 2014) using triplicates to compute within-group dispersion and contrasts to compare between targeting and non-targeting conditions. Differentially expressed genes were defined as having a false discovery rate (FDR) <0.05 and a log2 fold change >1.
Volcano plots were generated in R 3.3.2 using included plotting libraries and the alpha() color function from the scales 0.5.0 package.
Genome_build: hg19
Supplementary_files_format_and_content: .txt normalized expression table and differential expression tables.

source_name: RfxCasR NT array, 293FT kidney cell line

growth_protocol: HEK 293FT cells were grown in DMEM media supplemented with 10% FBS and 1% HEPES and passaged at 1:2 ratio daily using TrypLE reagent.

extract_protocol:
48h after transfection, total RNA was extracted using the Rneasy plus kit from Qiagen.
Stranded mRNA libraries were prepared using the NEBNext II Ultra Directional RNA Library Prep Kit from New England Biolabs (Cat# E7760S)

treatment_protocol: Plasmid constructs expressing either shRNAs or RfxCasR plus guide RNAs were transfected using Lipofectamine 2000 reagent.

value: 293FT kidney cell line

tag: passages

tag: treatment

value: RfxCasR NT array


title: RfxCasR B4GALNT1 gRNA rep 3

description:
stranded mRNA
fpkm.txt
B4GALNT1_CasR_vs_NT_CasR.xlsx

source_name: RfxCasR B4GALNT1 gRNA, 293FT kidney cell line

value: RfxCasR B4GALNT1 gRNA


title: RfxCasR ANXA4 array rep 3

source_name: RfxCasR ANXA4 array, 293FT kidney cell line

value: RfxCasR ANXA4 array


title: RfxCasR ANXA4 array rep 1


title: RfxCasR B4GALNT1 gRNA rep 2


title: RfxCasR ANXA4 array rep 2


title: IgG ChIPseq in HPCs (HoxA9 cells)

description: IgG ChIP (HoxA9 Immortalized)


title: RfxCasR B4GALNT1 gRNA rep 1


description:
H3K4me3 ChIPseq in HPCs depleted of Wdr82  (HoxA9 Immortalized)
Franks et al. 2017_H3K4me3 Peaks


title: RfxCasR NT array rep 3


title: RfxCasR NT array rep 1


title: RfxCasR NT gRNA rep 2

source_name: RfxCasR NT gRNA, 293FT kidney cell line

value: RfxCasR NT gRNA


title: IgG ChIPseq_H3K4me3 experiment

description: IgG ChIP_H3K4me3 experiment  (HoxA9 Immortalized)


title: RfxCasR NT gRNA rep 3


title: shRNA ANXA4 rep 2

description:
stranded mRNA
fpkm.txt
ANXA_shRNA_vs_NT_shRNA.xlsx

source_name: shRNA ANXA4, 293FT kidney cell line

value: shRNA ANXA4


title: shRNA NT rep 2

description:
stranded mRNA
fpkm.txt
B4GALNT1_shRNA_vs_NT_shRNA.xlsx
ANXA_shRNA_vs_NT_shRNA.xlsx

source_name: shRNA NT, 293FT kidney cell line

value: shRNA NT


title: shRNA B4GALNT1 rep 3

description:
stranded mRNA
fpkm.txt
B4GALNT1_shRNA_vs_NT_shRNA.xlsx

source_name: shRNA B4GALNT1, 293FT kidney cell line

value: shRNA B4GALNT1


title: shRNA NT rep 1


title: shRNA ANXA4 rep1


title: shRNA B4GALNT1 rep 1


title: shRNA NT rep 3


title: shRNA B4GALNT1 rep 2


title: shRNA ANXA4 rep 3


title: H1-Glom-TMD2

status: Public on Jan 24 2018

description: Gene Expression data from the glomerular compartment of human Membranous Nephropathy

data_processing: Each batch and platform was processed individually with its corresponding BrainArray CDF and normalized by RMA. After individual batch and platform processing, samples were merged by common EntrezGeneIDs, and finally batch corrected using Combat.

source_name: Kidney Biopsy from Human H1-Glom-TMD2

value: Glomeruli from kidney biopsy

value: Thin Membrande Disease


title: H1-Glom-MCD5

source_name: Kidney Biopsy from Human H1-Glom-MCD5

value: Minimal Change Disease


title: H1-Glom-MCD2

source_name: Kidney Biopsy from Human H1-Glom-MCD2


title: H1-Glom-TMD1

source_name: Kidney Biopsy from Human H1-Glom-TMD1


title: RfxCasR NT gRNA rep 1


title: H1-Glom-MCD3

source_name: Kidney Biopsy from Human H1-Glom-MCD3


title: H5-Tub-LD374

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-LD374

source_name: Kidney biopsy from human H5-Tub-LD374

value: Tubulointerstitium from kidney biopsy


title: H1-Glom-DN1

description: Gene Expression data from the glomerular compartment of human H1-Glom-DN1

source_name: Kidney Biopsy from Human H1-Glom-DN1

value: Diabetic Nephropathy


title: H1-Glom-MCD1

source_name: Kidney Biopsy from Human H1-Glom-MCD1


title: H5-Tub-LD375

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-LD375

source_name: Kidney biopsy from human H5-Tub-LD375


title: H5-Tub-LD373

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-LD373

source_name: Kidney biopsy from human H5-Tub-LD373


title: H1-Glom-DN10

description: Gene Expression data from the glomerular compartment of human H1-Glom-DN10

source_name: Kidney Biopsy from Human H1-Glom-DN10


title: H5-Tub-SLE362

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE362

source_name: Kidney biopsy from human H5-Tub-SLE362

value: Systemic lupus erythematosus


title: H1-Glom-DN5

source_name: Kidney Biopsy from Human H1-Glom-DN5


title: H1-Glom-DN2

source_name: Kidney Biopsy from Human H1-Glom-DN2


title: H1-Glom-DN8

source_name: Kidney Biopsy from Human H1-Glom-DN8


title: H5-Tub-SLE361

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE361

source_name: Kidney biopsy from human H5-Tub-SLE361


title: H5-Tub-SLE352

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE352

source_name: Kidney biopsy from human H5-Tub-SLE352


title: H5-Tub-SLE359

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE359

source_name: Kidney biopsy from human H5-Tub-SLE359


title: H5-Tub-SLE358

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE358

source_name: Kidney biopsy from human H5-Tub-SLE358


title: H5-Tub-SLE360

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE360

source_name: Kidney biopsy from human H5-Tub-SLE360


title: H5-Tub-SLE348

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE348

source_name: Kidney biopsy from human H5-Tub-SLE348


title: H5-Tub-MGN355

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN355

source_name: Kidney biopsy from human H5-Tub-MGN355

value: Membranous glomerulonephropathy


title: H5-Tub-MGN354

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN354

source_name: Kidney biopsy from human H5-Tub-MGN354


title: H5-Tub-SLE349

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE349

source_name: Kidney biopsy from human H5-Tub-SLE349