title: RPMI + galactose_50354

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900618545.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2
Supplementary_files_format_and_content: genome annotations


title: Pooled sera_50337

status: Public on Jul 01 2021

type: SRA

city: Sydney

first: Antibiotic Resistant Sepsis Pathogens Framework Initiative

last: Bioplatforms Australia

state: NSW

address: Level 4, Building 4WW, Research Park Drive, Macquarie University

country: Australia

institute: Bioplatforms Australia

description: Additional information about the bacterial cultures is available from the Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Initiative website. https://data.bioplatforms.com/organization/about/bpa-sepsis

library_source: transcriptomic

molecule: total RNA

organism: Streptococcus pneumoniae

source_name: Bacteria in growth media

growth_protocol: Complete information about the bacterial cultures is available from the Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Initiative website. https://data.bioplatforms.com/organization/about/bpa-sepsis

extract_protocol: Bacterial rRNA depletion with Illumina Ribo-Zero rRNA Removal Kit (Bacteria) followed by strand RNAseq sample preparation with Illumina TruSeq Stranded mRNA Library Prep Kit

tag: growth media

value: Pooled sera

tag: strain

tag: growth time

value: 2 hrs exposure to sera

tag: growth phase

tag: od600 reading

tag: temperature

tag: bpa identifier

tag: serovar


title: RPMI + galactose_50339

value: RPMI + galactose

value: Mid log phase


title: Pooled sera_50286

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900618575.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2
Supplementary_files_format_and_content: genome annotations


title: Developing mouse embryo sections D09E08_S45

city: Seattle

first: Sanjay

middle: R

last: Srivatsan

state: WA

address: 3720 15TH Ave NE Genome Sciences S Foefe Bldg

department: Genome Sciences

country: USA

institute: University of Washington

description:
Developing mouse embryo sections
sci-Space Slides 7-14
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell

data_processing:
Basecalls performed using bcl2fastq version 2.20
Poly-dT adapters were trimmed using Trimmomatic and aligned to mm10 using STAR. Mapped reads were then deduplicated and assigned to a gene (GENCODE vM15 - mouse). UMIs were enumerated for each cell/gene combination and finally a count matrix was made.
Count matrix was loaded into Monocle3 for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: Count Matrix (matrix marker file- .mtx), Cell Metadata (tab separated values- .tsv), Gene Metadata (tab separated values- .tsv)

molecule: polyA RNA

organism: Mus musculus

source_name: E14 saggital sections 8-10um thick

extract_protocol:
Nuclei were extracted with a permeabilization buffer, sonicated and fixed. cDNA molecules within nuclei are extracted after tagmentation through the use of denaturants.
3' end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis, tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it, a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.

tag: genotype

tag: tissue

value: E14 Mouse Embryo

tag: sample type

value: Sagigital section


title: RPMI + galactose_50309


title: Developing mouse embryo sections D10E09_S142


title: RPMI + glucose_50308

value: RPMI + glucose


title: Pooled sera_50352


title: RPMI + galactose_50273


title: RPMI + glucose_50302


title: RPMI + galactose_50324


title: Developing mouse embryo sections D03E09_S135


title: RPMI + galactose_50294


title: RPMI + glucose_50353


title: Developing mouse embryo sections D03E08_S39


title: Developing mouse embryo sections D07E09_S139


title: Developing mouse embryo sections D02E09_S134


title: Developing mouse embryo sections D07E08_S43


title: RPMI + galactose_50279


title: Developing mouse embryo sections D06E09_S138


title: Developing mouse embryo sections D06E08_S42


title: Pooled sera_50307


title: Developing mouse embryo sections D08E08_S44


title: Developing mouse embryo sections D04E09_S136


title: Developing mouse embryo sections D04E08_S40


title: RPMI + galactose_50342

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900622505.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2
Supplementary_files_format_and_content: genome annotations


title: Developing mouse embryo sections D01E08_S37


title: Developing mouse embryo sections C12E09_S132


title: Pooled sera_50277


title: RPMI + glucose_50338


title: RPMI + glucose_50341


title: Developing mouse embryo sections D05E09_S137


title: Pooled sera_50322


title: Developing mouse embryo sections D01E09_S133


title: RPMI + glucose_50326


title: RPMI + galactose_50312


title: Developing mouse embryo sections C12E08_S36


title: Pooled sera_50292


title: RPMI + galactose_50297


title: RPMI + glucose_50293


title: Pooled sera_50295


title: Developing mouse embryo sections C10E09_S130


title: Developing mouse embryo sections D02E08_S38


title: RPMI + glucose_50323


title: RPMI + galactose_50327


title: Developing mouse embryo sections C05E09_S125


title: Developing mouse embryo sections D05E08_S41


title: Developing mouse embryo sections C11E08_S35


title: Developing mouse embryo sections C09E08_S33


title: Developing mouse embryo sections C09E09_S129


title: Developing mouse embryo sections C08E09_S128


title: Developing mouse embryo sections C07E08_S31


title: RPMI + glucose_50311


title: Pooled sera_50325


title: Developing mouse embryo sections C10E08_S34


title: Developing mouse embryo sections C07E09_S127


title: RPMI + galactose_50267


title: RPMI + glucose_50266


title: Developing mouse embryo sections C05E08_S29


title: RPMI + glucose_50296


title: RPMI + glucose_50278


title: Developing mouse embryo sections C06E09_S126


title: Developing mouse embryo sections C08E08_S32


title: Developing mouse embryo sections C03E09_S123


title: RPMI + glucose_50281


title: Pooled sera_50340


title: Developing mouse embryo sections C03E08_S27


title: Jmonkey IL-4_3

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
Fastq files were generated from bcl2 files using bcl2fastq v2.20.0.422
Quality check and trimming of adaptor sequences were performed using trim_galore version 0.6.4.
Genes were counted using kalisto version 0.44.0.
Genome_build: mmul10
Supplementary_files_format_and_content: plain text

organism: Macaca fuscata

source_name: transcripts from JM intestinal organoid

growth_protocol: Cells were grown in standard condition for primate epitherial cells

extract_protocol: mRNA is isolated from approximately 300 ng of the total RNA using the Dynabeads mRNA Purification Kit. The sequencing library was prepared using the MGIEasy RNA Directional Library Prep Kit.

treatment_protocol: Cell were stimulated by IL4.

tag: animal id

tag: cell type

value: intestinal organoid

tag: medium

value: DI medium with IL4


title: Developing mouse embryo sections C06E08_S30


title: Developing mouse embryo sections C02E08_S26


title: Developing mouse embryo sections B12E09_S120


title: RPMI + galactose_50282


title: Pooled sera_50310


title: Developing mouse embryo sections B12E08_S24


title: Pooled sera_50265


title: Developing mouse embryo sections C11E09_S131


title: Pooled sera_50280


title: Jmonkey IL-4_2


title: Developing mouse embryo sections C01E09_S121


title: Developing mouse embryo sections B09E09_S117


title: Developing mouse embryo sections C02E09_S122


title: Developing mouse embryo sections C04E09_S124


title: Developing mouse embryo sections C04E08_S28


title: Jmonkey DI_3

value: DI medium w/o IL4


title: 18_DQ17A_Emanual_9-12-19_(Clariom_S_Mouse)

type: RNA

city: Philadelphia

first: Emanuel

middle: José

last: Novais

state: PA

address: 1025 Walnut St., Suite 511 College Bldg.

department: Department of Orthopaedic Surgery

institute: Thomas Jefferson

description: Gene expression data from  23-month-old annulus fibrosus C57BL/6 mouse treated with Dasatinib and Quercetin combination.

hyb_protocol: Gene chips (Mouse Clariom S) were hybridized with fragmented and biotin-labeled cDNA. Arrays were washed and stained with GeneChip hybridization wash & stain kit

scan_protocol: scanned on an Affymetrix Gene Chip Scanner 3000 7G, using Command Console Software.

data_processing: Chp files were generated by sst-rma normalization from Affymetrix cel file using Expression Console Software. Experimental group was compared with control group by using Transcriptome array console 4.0 software. The SST-RMA algorithm was used for data normalization.

label: biotin

source_name: AF D+Q

label_protocol: Fragmented biotin labeled cDNA was synthesized using the GeneChip WT Plus kit according to ABI protocol (Thermo Fisher Scientific).

growth_protocol: NP and AF tissues were dissected from lumbar discs of 23M Veh (n=5) and D+Q (n=4) BL6 mice.

extract_protocol: Pooled tissue from single animal served as an individual sample. Samples were homogenized and total RNA was extracted using RNeasy® Mini kit (Qiagen).

value: Annulus Fibrosus

tag: age


title: Jmonkey IF_1

value: Prolifereation medium (IGF-1 and FGF-2)


title: Jmonkey DI_2


title: Jmonkey DI_1


title: 16_DQ11A_Emanual_9-12-19_(Clariom_S_Mouse)


title: 15_DQ8A_Emanual_9-12-19_(Clariom_S_Mouse)


title: Developing mouse embryo sections C01E08_S25


title: Jmonkey IF_3


title: 14_CT15A_Emanual_9-12-19_(Clariom_S_Mouse)

description: Gene expression data from  23-month-old annulus fibrosus C57BL/6 mouse Vehicle

source_name: AF Veh


title: Jmonkey IF_2


title: Developing mouse embryo sections B11E08_S23


title: Developing mouse embryo sections B08E09_S116


title: Developing mouse embryo sections B08E08_S20


title: Jmonkey IL-4_1


title: Developing mouse embryo sections B09E08_S21


title: 11_CT5A_Emanual_9-12-19_(Clariom_S_Mouse)


title: Developing mouse embryo sections B05E09_S113


title: Developing mouse embryo sections B11E09_S119


title: Developing mouse embryo sections B10E09_S118


title: Developing mouse embryo sections B04E09_S112


title: 10_CT4A_Emanual_9-12-19_(Clariom_S_Mouse)


title: 17_DQ16A_Emanual_9-12-19_(Clariom_S_Mouse)


title: Developing mouse embryo sections B06E08_S18


title: 13_CT7A_Emanual_9-12-19_(Clariom_S_Mouse)


title: 12_CT6A_Emanual_9-12-19_(Clariom_S_Mouse)


title: Developing mouse embryo sections B07E09_S115


title: Developing mouse embryo sections B05E08_S17


title: Developing mouse embryo sections B04E08_S16


title: Developing mouse embryo sections B03E08_S15


title: Developing mouse embryo sections B07E08_S19


title: Developing mouse embryo sections B10E08_S22


title: Developing mouse embryo sections B02E09_S110


title: 05_CT15N_Emanual_9-12-19_(Clariom_S_Mouse)

description: Gene expression data from  23-month-old nucleus pulposus C57BL/6 mouse Vehicle

source_name: NP Veh

value: Nucleus Pulposus


title: Developing mouse embryo sections B06E09_S114


title: 03_CT6N_Emanual_9-12-19_(Clariom_S_Mouse)


title: Developing mouse embryo sections B02E08_S14


title: 08_DQ16N_Emanual_9-12-19_(Clariom_S_Mouse)

description: Gene expression data from  23-month-old nucleus pulposus C57BL/6 mouse treated with Dasatinib and Quercetin combination.

source_name: NP D+Q


title: 06_DQ8N_Emanual_9-12-19_(Clariom_S_Mouse)


title: Developing mouse embryo sections B03E09_S111


title: Developing mouse embryo sections B01E09_S109


title: 04_CT7N_Emanual_9-12-19_(Clariom_S_Mouse)


title: Developing mouse embryo sections A11E09_S107


title: 07_DQ11N_Emanual_9-12-19_(Clariom_S_Mouse)


title: high groups High_Q9G

city: Nanjing

first: Chengyu

last: Li

address: College of Animal Science and Technology, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, China.

country: China

institute: Nanjing Agricultural University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Sus scrofa

source_name: ovarian granulosa cells

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately, The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ovary

value: granulosa cells

tag: difference

value: high G0/G1 distribution


title: Pooled sera_51458

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900622585.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2

organism: Klebsiella variicola


title: low groups Low_S9G

department: College of Animal Science and Technology

value: low G0/G1 distribution


title: Pooled sera_51457

value: Pooled sera


title: Pooled sera_51455

value: 2 hrs exposure to sera


title: 09_DQ17N_Emanual_9-12-19_(Clariom_S_Mouse)


title: RPMI_51454

value: RPMI

value: 1 hr


title: low groups Low_W7G


title: Developing mouse embryo sections B01E08_S13

value: E14 Mouse Embryo


title: Developing mouse embryo sections A10E08_S10

value: Sagigital section


title: Developing mouse embryo sections A09E08_S9


title: Developing mouse embryo sections A12E09_S108


title: Developing mouse embryo sections A11E08_S11


title: RPMI_51452

value: Mid log phase


title: high groups High_W8G


title: Developing mouse embryo sections A08E09_S104


title: Pooled sera_51460


title: Pooled sera_51456


title: 02_CT5N_Emanual_9-12-19_(Clariom_S_Mouse)


title: Developing mouse embryo sections A09E09_S105


title: Developing mouse embryo sections A07E09_S103


title: Developing mouse embryo sections A10E09_S106


title: Developing mouse embryo sections A06E09_S102


title: RPMI_51453


title: Developing mouse embryo sections A08E08_S8


title: Pooled sera_51505

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900622625.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2


title: Developing mouse embryo sections A06E08_S6


title: 01_CT4N_Emanual_9-12-19_(Clariom_S_Mouse)


title: Pooled sera_51504


title: Developing mouse embryo sections A12E08_S12


title: RPMI_51451


title: Developing mouse embryo sections A03E08_S3


title: RPMI_51502


title: RPMI_51501


title: Developing mouse embryo sections A05E09_S101


title: Pooled sera_51508


title: RPMI_51500


title: Developing mouse embryo sections A02E09_S98


title: RPMI_51450


title: RPMI_51497


title: Developing mouse embryo sections A07E08_S7


title: Developing mouse embryo sections A03E09_S99


title: Developing mouse embryo sections A04E09_S100


title: Pooled sera_51519

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900622615.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2


title: RPMI_51449


title: Pooled sera_51507


title: Pooled sera_51459


title: Pooled sera_51517


title: Developing mouse embryo sections H10D11_S190


title: Developing mouse embryo sections H11D11_S191


title: RPMI_51499


title: Pooled sera_51518


title: Developing mouse embryo sections A01E09_S97


title: Pooled sera_51506


title: Developing mouse embryo sections A05E08_S5


title: Developing mouse embryo sections A02E08_S2


title: Developing mouse embryo sections H12D11_S192


title: Pooled sera_51516


title: Developing mouse embryo sections H11D10_S95


title: Developing mouse embryo sections H10D10_S94


title: Pooled sera_51503


title: Pooled sera_51520


title: RPMI_51513


title: Developing mouse embryo sections A04E08_S4


title: Developing mouse embryo sections A01E08_S1


title: Developing mouse embryo sections H07D11_S187


title: Developing mouse embryo sections H08D10_S92


title: RPMI_51512


title: Pooled sera_51483

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900622595.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2


title: RPMI_51498


title: RPMI_51511


title: RPMI_51510


title: RPMI_51514


title: Pooled sera_51515


title: RPMI_51509


title: Developing mouse embryo sections H06D11_S186


title: Developing mouse embryo sections H04D11_S184


title: Developing mouse embryo sections H09D10_S93


title: Pooled sera_51481


title: Developing mouse embryo sections H12D10_S96


title: Developing mouse embryo sections H05D10_S89


title: Developing mouse embryo sections H07D10_S91


title: Pooled sera_51480


title: Developing mouse embryo sections H06D10_S90


title: Developing mouse embryo sections H09D11_S189


title: Developing mouse embryo sections H03D11_S183


title: Developing mouse embryo sections H05D11_S185


title: Pooled sera_51484


title: RPMI_51478


title: Developing mouse embryo sections H02D11_S182


title: Developing mouse embryo sections H08D11_S188


title: Pooled sera_51482


title: Developing mouse embryo sections G12D11_S180


title: RPMI_51475


title: RPMI_51477


title: Developing mouse embryo sections G11D11_S179


title: Pooled sera_51479


title: ODS2

city: Pittsburgh

first: Sruthi

last: Sivakumar

address: 450 Technology drive

institute: University of Pittsburgh

data_processing:
Raw fastq files were pre-processed and aligned using PartekFlow Software version 10.0
FastQC was applied to check the quality of the sequences
STAR alignment was done with reference genome mm10 downloaded from UCSC browser, and gene ID type ENSEMBL transcriptome ID.
ENSEMBL IDs were converted to ENTREZ IDs using biomaRt for downstream analysis
deseq2 was used on raw read tables for differential gene expression analysis
Functional enrichment was performed using EnrichR and clusterprofiler
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Tibialis anterior

extract_protocol:
Supplemetal methods-EV injection, Animal injury model, RNA seq analysis
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: injection

value: Depleted young serum

value: 21-24 months


title: ODS3


title: Developing mouse embryo sections H01D11_S181


title: ODS4


title: Developing mouse embryo sections H02D10_S86


title: RPMI_51476

tag: growth media


title: RPMI_51473

tag: strain


title: Developing mouse embryo sections H01D10_S85


title: RPMI_51474

tag: growth time


title: Developing mouse embryo sections H04D10_S88


title: Developing mouse embryo sections G10D11_S178


title: Developing mouse embryo sections G12D10_S84


title: Developing mouse embryo sections G09D11_S177


title: Developing mouse embryo sections H03D10_S87


title: OYS3

value: Young serum


title: Developing mouse embryo sections G10D10_S82


title: Developing mouse embryo sections G09D10_S81


title: OYS1


title: Developing mouse embryo sections G08D11_S176


title: Developing mouse embryo sections G11D10_S83


title: OSH6

value: Saline


title: OSH4


title: OSH2


title: Developing mouse embryo sections G06D11_S174


title: Developing mouse embryo sections G06D10_S78


title: OYS4


title: OSH3


title: Developing mouse embryo sections G07D11_S175


title: Developing mouse embryo sections G08D10_S80


title: Developing mouse embryo sections G05D11_S173


title: Developing mouse embryo sections G05D10_S77


title: ciCPCs at Passage 20 (replicate 3)

city: Guangzhou

first: tao

last: xu

state: Guangdong

address: North Campus, Sun Yat-*Sen University, No. 74, 2nd Yat-*Sen Road/Street，Yuexiu District, Guangzhou City, Guangdong Province

department: ZHONGSHAN SCHOOL OF MEDICINE

institute: SUN YAT-SEN UNIVERSITY

description: The ciCPCs were collected at late passage

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using hisat2 version 2.0.5 with parameters -p 10 -x  -5 15 -3 5 -1 *.fq -2 *.fq -S *.sam
aligned BAM files were indexed and sorted with SAMtools for downstream convenience, and PCR duplicates were removed using Samtools command rmdup –S.
HTSeq was used for counting reads with parameters "-t exon –i gene_id -r name -s no".
Samples in this work and three previous studies were normalized and batch removed using the DEseq2
Genome_build: grcm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: ciCPCs at Late Passage

growth_protocol: ciCPCs were cultured in ciCPC basal medium supplemented with BMP4, Activin A, CHIR99021, and SU5402 (BACS)

extract_protocol:
Total RNA was prepared using the RNeasy Plus Mini Kit with Qiashredder columns  (Qiagen). Potentially residual DNA was removed by on-column DNase digestion with  RNase-free DNase (Qiagen). Total RNA was quantified on Nanodrop and quality was checked by electropherogram.
Total RNA (10 μg) was used as input material for  preparing the RNA sequencing (RNA-seq) libraries following the standard Illumina RNASeq  protocol as previously described (Wamstad et al., 2012)

treatment_protocol: ciCPCs were cultured for passages after colony picking on day 14 of cardiac reprogramming

value: cardiac progenitors

value: mixed background of C57BL/6 and 129J/SvE

value: Wildtype (WT)

tag: passages


title: Developing mouse embryo sections G04D10_S76


title: Developing mouse embryo sections G02D11_S170


title: ciCPCs at Passage 20 (replicate 2)


title: Developing mouse embryo sections G04D11_S172


title: Developing mouse embryo sections G07D10_S79


title: OYS2


title: Developing mouse embryo sections G01D11_S169


title: ciCPCs at Passage 3 (replicate 3)

description: The ciCPCs were collected at early passage

source_name: ciCPCs at Early Passage


title: Developing mouse embryo sections G02D10_S74


title: AAV-shPhpt1-2 [PHP_1_2]

city: Beijing

first: Anjian

last: Xu

address: No. 95 Yong'an road, Xicheng District, Beijing

institute: Capital medical university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CCl4-treated shPhpt1 liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 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: For the CCl4 injection model, C57BL/6J mice were treated with 12.5 ml/kg body weight CCl4 (Sigma-Aldrich, St. Louis, MO) diluted in olive oil (Sigma-Aldrich, St. Louis, MO) by intraperitoneal injection twice weekly. Mice were sacrificed and tissues were harvested 48 h after the final CCl4 injection. AAV-shRNA was intravenously injected into C57BL/6 mice (n = 5 per group) after 1 week of CCl4 treatment.

tag: strain background

tag: genotype/variation

tag: treatment/condition

value: liver


title: ciCPCs at Passage 3 (replicate 2)


title: Developing mouse embryo sections G03D11_S171


title: Developing mouse embryo sections G03D10_S75


title: AAV-shPhpt1-1 [PHP_1_1]


title: ciCPCs at Passage 3 (replicate 1)


title: Developing mouse embryo sections G01D10_S73


title: ciCPCs at Passage 20 (replicate 1)


title: AAV-Ctrl-2 [MC_1_2]

source_name: CCl4-treated AAV-control liver

value: AAV-control


title: Developing mouse embryo sections F12D11_S168


title: Developing mouse embryo sections F12D10_S72


title: AAV-Ctrl-1 [MC_1_1]


title: Normal-2 [C_2]

source_name: normal liver

value: normal


title: Developing mouse embryo sections F11D11_S167


title: Developing mouse embryo sections F11D10_S71


title: Normal-1 [C_1]


title: Developing mouse embryo sections F10D11_S166


title: Non Stimulated 5 [S28]

city: Bern

first: Britta

last: Engelhardt

address: Freiestrasse 1

department: Theodor Kocher Institute

country: Switzerland

institute: University of Bern

data_processing:
Ilumina 1.9
FASTQ files were checked for quality control metrics using FastQC (version 0.11.2) and Qualimap (version 2.2)
Post-Quality control, raw reads were mapped to the reference genome using TopHat2 (version 2.0.13) proceeded by exon-counting using HTSeq-count (version 0.6.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimeted files containing the Ensembl gene id and the RLE normalized counts

source_name: pMBMECs_Non Stimulated

growth_protocol: pMBMECs isolated and cultured as described before (Coisne et al, Lab. Invest., 2005)

extract_protocol:
RNA was extracted from pMBMECs with the High Pure RNA Isolation Kit (Hoffman-La Roche, Basel, Switzerland).
According to the manufacturer’s instruction using TruSeq stranded mRNA Library Prep Kit (Illumina, San Diego, USA) with polyA selection.

treatment_protocol: Non stimulated condition consisted of medium change only. TNFalpha and IL-1beta conditions consisted of medium change cointaining 10 ng/ml TNFalpha or 20 ng/ml IL-1beta, respectevely. Stimulation was performed for 4 hours prior RNA extraction

tag: gender

value: female

value: 7 weeks

value: Primary Mouse Brain Microvascular Endothelial Cells (pMBMECs)

tag: treatment

value: Non Stimulated


title: Developing mouse embryo sections F09D10_S69

tag: genotype

tag: tissue

value: E14 Mouse Embryo


title: Developing mouse embryo sections F10D10_S70

tag: sample type

value: Sagigital section


title: Developing mouse embryo sections F08D11_S164


title: Non Stimulated 4 [S25]

tag: cell type


title: TNF alpha Stimulated 4 [S26]

source_name: pMBMECs_TNF alpha Stimulated

value: TNF alpha Stimulated


title: IL1 Beta Stimulated 5 [S27]

source_name: pMBMECs_IL1 Beta stimulated

value: IL1 Beta stimulated


title: Developing mouse embryo sections F09D11_S165


title: IL1 Beta Stimulated 4 [S24]


title: Non Stimulated 3 [S22]


title: Developing mouse embryo sections F06D11_S162


title: Developing mouse embryo sections F07D11_S163


title: TNF alpha Stimulated 2 [S20]


title: Developing mouse embryo sections F08D10_S68


title: Developing mouse embryo sections F07D10_S67


title: Developing mouse embryo sections F05D11_S161


title: Non Stimulated 2 [S19]


title: Developing mouse embryo sections F06D10_S66


title: Developing mouse embryo sections F05D10_S65


title: IL1 Beta Stimulated 2 [S18]


title: Developing mouse embryo sections F04D11_S160


title: TNF alpha Stimulated 1 [S17]


title: Developing mouse embryo sections F04D10_S64


title: IL1 Beta Stimulated 1 [S15]


title: TNF alpha Stimulated 3 [S23]


title: Developing mouse embryo sections F03D11_S159


title: Developing mouse embryo sections F02D10_S62


title: EKHT1_ROW40_9

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

institute: University of Geneva

data_processing:
read1 containing umi sequences are appended at the end of the headers of read2
read2 are mapped with tophat v2.0.13 on the mouse genome GRCm38 considering Ensembl78 genes annotations
bam files are processed with umi_tools to deduplicate reads with identical UMI sequence
gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification and this includes 5' and 3' UTRs.
Genome_build: GRCm38
Supplementary_files_format_and_content: retrobeads.tsv.gz contains the result of gene expression quantification by summarizeOverlaps() for each cell. The integers values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contains information about the genes that are quantified.

source_name: primary somatosensory cortex

extract_protocol:
The primary somatosensory cortex was microdissected as aforementioned. Cells were further dissociated by incubating micro-dissected samples in 0.5 mg/mL pronase (Sigma, #P5147) at 37°C for 10 minutes, followed by incubation in 5% bovine serum albumin for 3 minutes and manual trituration in ACSF using pulled glass pipettes. Cells were then centrifuged for 10 minutes at 600 rpm and resuspended before filtration using a 70 mm cell strainer (ClearLine, # 141379C). Cells were then incubated for 10 minutes at 37°C with Hoechst (0.1 mg/mL) and isolated using a Beckman Coulter Moflo Astrios FAC-sorter. Singlet Hoechst+cells were sorted according to their Forward and Side scattering properties (FSC and SSC), and their negativity for Draq7TM (Viability dye, Far red DNA intercalating agent, Beckman Coulter, #B25595). 5000 to 10 000 cells were FACsorted for each experiment. Three microliters of C1 Suspension Reagent (Fluidigm) was added to 10 ml of FAC-sorted cells GFP+ cells, yielding a 300-500 cells / ml suspension. 12 ml of this suspension mix were loaded on a C1 Single-Cell AutoPrep integrated fluidic circuit (IFC) designed for 10 to 17 mm diameter-cells (Fluidigm, #100-5780). RNA was extracted using an RNeasy kit (Qiagen, #74034), and quality control was done using 2001 Bioanalyzer from Agilent. cDNA libraries were obtained using SMARTseq v4 kit (Clontech, # 634888) and sequenced using HiSeq 2500 sequencer.
SMARTseq v4 kit (Clontech, # 634888)


title: EKHT1_ROW39_9


title: IL1 Beta Stimulated 3 [S21]


title: Non Stimulated 1 [S16]


title: Developing mouse embryo sections F03D10_S63

source_name: E14 saggital sections 8-10um thick


title: Developing mouse embryo sections F02D11_S158


title: EKHT1_ROW35_9


title: Developing mouse embryo sections F01D10_S61


title: EKHT1_ROW34_9


title: EKHT1_ROW32_9


title: Developing mouse embryo sections F01D11_S157


title: Developing mouse embryo sections E12D10_S60


title: Developing mouse embryo sections E12D11_S156


title: EKHT1_ROW28_9


title: EKHT1_ROW31_9


title: Developing mouse embryo sections E11D10_S59


title: Developing mouse embryo sections E11D11_S155


title: Developing mouse embryo sections E10D11_S154


title: TNF alpha Stimulated 5 [S29]


title: EKHT1_ROW22_9


title: EKHT1_ROW18_9


title: EKHT1_ROW14_9


title: EKHT1_ROW27_9


title: EKHT1_ROW17_9


title: EKHT1_ROW20_9


title: Developing mouse embryo sections E09D11_S153


title: Developing mouse embryo sections E10D10_S58


title: EKHT1_ROW11_9


title: EKHT1_ROW02_9


title: EKHT1_ROW10_9


title: EKHT1_ROW09_9


title: Developing mouse embryo sections E08D10_S56


title: Developing mouse embryo sections E08D11_S152


title: Developing mouse embryo sections E09D10_S57


title: Developing mouse embryo sections E05D11_S149


title: Developing mouse embryo sections E07D11_S151


title: EKHT1_ROW37_8


title: Developing mouse embryo sections E07D10_S55


title: Developing mouse embryo sections E05D10_S53


title: EKHT1_ROW34_8


title: Developing mouse embryo sections E04D11_S148


title: Developing mouse embryo sections E02D11_S146


title: Developing mouse embryo sections E06D11_S150


title: EKHT1_ROW05_8


title: EKHT1_ROW40_7


title: Developing mouse embryo sections E01D11_S145


title: Developing mouse embryo sections E04D10_S52


title: Developing mouse embryo sections E01D10_S49


title: EKHT1_ROW23_8


title: EKHT1_ROW29_7


title: Developing mouse embryo sections D11D10_S47


title: Developing mouse embryo sections E06D10_S54


title: EKHT1_ROW32_8


title: EKHT1_ROW39_8


title: EKHT1_ROW36_8


title: EKHT1_ROW10_8


title: Developing mouse embryo sections E03D10_S51


title: Developing mouse embryo sections D12D11_S144


title: EKHT1_ROW28_8


title: Developing mouse embryo sections E03D11_S147


title: EKHT1_ROW20_7


title: EKHT1_ROW18_7


title: MA-10 Leydig cells transfected with siRNA targeting COUP-TFII, biological replicate 2

city: Québec City

first: Jacques J.

last: Tremblay

state: Quebec

address: 2705 Laurier Blvd.

department: Reproduction, Mother and Child Health

country: Canada

institute: Centre de recherche du CHU de Québec

description: gene expression data from siRNA COUP-TFII transfected cells

hyb_protocol: The labeled cDNA mixes were hybridized for 16 hr at 45C on Affymetrix Mouse Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix GeneChip fluidics station 450.

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

data_processing: The data was analyzed using Partek genomics suite 7.0 (Partek, Inc. St. Louis, MO, USA) according to the manufacturer’s instructions.

label_protocol: Biotinylated cDNA mixes were prepared according to the standard Affymetrix protocol from 200 ng total RNA.

growth_protocol: MA-10 Leydig cells were grown in DMEM/F12 medium supplemented with 2.438 g/L sodium bicarbonate, 3.57 g/L HEPES, 15% horse serum, 50 mg/L penicillin and streptomycin sulphate on plates coated with 0.1% gelatin at 37 Celsius (C) and 5% CO2.

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

treatment_protocol: Cells were transiently transfected with siRNAs as indicated above for 48 hours.

tag: cell line

value: MA-10 Leydig cells


title: Developing mouse embryo sections D11D11_S143


title: MA-10 Leydig cells transfected with siRNA control, biological replicate 2

description: gene expression data from siRNA control transfected cells


title: Developing mouse embryo sections E02D10_S50


title: EKHT1_ROW29_8


title: Developing mouse embryo sections D12D10_S48


title: EKHT1_ROW28_7


title: EKHT1_ROW31_7


title: EKHT1_ROW36_7


title: MA-10 Leydig cells transfected with siRNA targeting COUP-TFII, biological replicate 1


title: Developing mouse embryo sections D10D10_S46


title: EKHT1_ROW19_7


title: EKHT1_ROW23_7


title: EKHT1_ROW38_7


title: Developing mouse embryo sections D09D11_S141


title: Developing mouse embryo sections D08D11_S140


title: Developing mouse embryo sections D09D10_S45


title: EKHT1_ROW06_7


title: HD3 NKp65-

city: Frankfurt am Main

first: Alexander

last: Steinle

address: Theodor-Stern-Kai 7

department: Institute for Molecular Medicine

country: Germany

institute: Goethe-University Frankfurt am Main

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
Unsupported Human Gene 1.0 ST Array CDF Files
HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

organism: Homo sapiens

source_name: HD3 NKp65-

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

growth_protocol: Peripheral blood lymphocytes of 4 healthy donors were enriched for NK cell like cells (MACS technology)

extract_protocol: RNA was extracted with the RNeasy Micro Kit from Qiagen. 40ng of the total RNA was amplified using the Ovation Pico WTA System V2 from NUGEN.

treatment_protocol: Stimulation with IL-2/-12/-18 for 4 days followed by FACSorting


title: EKHT1_ROW01_7


title: MA-10 Leydig cells transfected with siRNA targeting COUP-TFIIs, biological replicate 3


title: Developing mouse embryo sections D10D11_S142


title: EKHT1_ROW39_6


title: HD4 NKp65+

source_name: HD4 NKp65+


title: Developing mouse embryo sections D08D10_S44


title: MA-10 Leydig cells transfected with siRNA control, biological replicate 1


title: neonate fibroblast-induced pluripotent stem cell (OCT4, SOX2, MYC and KLF4), biological replicate 2

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

hyb_protocol: In accordance with manufacturer's protocols

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

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm and baseline transformation to the median of all samples using Partek GeneSuite v6 software.

growth_protocol: Human embryonic stem cell (hESC) research received Canadian Stem Cell Oversight Committee (SCOC; Canadian Institutes of Health Research, CIHR) approval, and Research Ethics and Biohazard Utilization Protocols approval at McMaster University, following the principles of the 2016 ISSCR Guidelines for Stem Cell Research and Clinical Applications of Stem Cells. Human iPSC and ESC were cultured in feeder-free conditions in mouse embryonic feeder-conditioned media with 8 ng/mL basic fibroblast growth factor, with daily media changes. Cells were passaged as clumps every seven days on to matrigel-coated tissue culture plates.

extract_protocol: Extraction of total RNA using total RNA purification kit (QIAGEN) was performed according to the manufacturer's instructions. Total RNA was amplified following the standard protocol at London Regional Genomics Centre.


title: EKHT1_ROW10_7


title: Developing mouse embryo sections D06D11_S138

data_processing:
Basecalls performed using bcl2fastq version 2.20
Poly-dT adapters were trimmed using Trimmomatic and aligned to mm10 using STAR. Mapped reads were then deduplicated and assigned to a gene (GENCODE vM15 - mouse). UMIs were enumerated for each cell/gene combination and finally a count matrix was made.
Count matrix was loaded into Monocle3 for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: Count Matrix (matrix marker file- .mtx), Cell Metadata (tab separated values- .tsv), Gene Metadata (tab separated values- .tsv)


title: MA-10 Leydig cells transfected with siRNA control, biological replicate 3


title: EKHT1_ROW03_7


title: HD2 NKp65+

source_name: HD2 NKp65+


title: Developing mouse embryo sections D07D11_S139


title: CA2 embryonic stem cells, presence of trisomy 12 confirmed by Cytoscan HD array, biological replicate 2

label_protocol: In accordance with manufacturer's protocols


title: HD4 NKp65-

source_name: HD4 NKp65-


title: Developing mouse embryo sections D07D10_S43


title: HD3 NKp65+

source_name: HD3 NKp65+


title: EKHT1_ROW35_6


title: neonate fibroblast-induced pluripotent stem cell (OCT4, SOX2, MYC and KLF4), biological replicate 1


title: Developing mouse embryo sections D05D10_S41


title: EKHT1_ROW08_7


title: Developing mouse embryo sections D05D11_S137


title: Developing mouse embryo sections D04D10_S40


title: CA2 embryonic stem cells, presence of trisomy 12 confirmed by Cytoscan HD array, biological replicate 3


title: Developing mouse embryo sections D06D10_S42


title: 4188 cells MYC OFF 4 hours

city: Portland

first: Daniel

last: Liefwalker

state: Oregon

address: 2730 SW Moody Ave

department: Molecular and Medical Genetics

institute: Oregon Health and Science University

data_processing:
BWA to map clean reads to genome reference and Bowtie to gene reference
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: 100 X 10^6 cells were seeded in uncoated T175 flasks in fresh media and timepoint samples began 24hr post seeding.

extract_protocol:
RNA extraction included QIA shredder step, RNEasy kit, and on column DNA digestion (all reagents from Qiagen).
Beijing Genomics Institute (BGI) for the RNA-seq QC and sequencing pipeline and read analysis

treatment_protocol: Cells were dosed with 20ng/ml doxycycline and samples collected at the indicated time-points

tag: cell line origin

value: E{mu}-tTA/Tet-O-MYC primary model of T-ALL

tag: culture condition

value: dox 4 hrs, MYC OFF

tag: background strain

value: FVBN


title: 4188 cells MYC on

value: no dox, MYC ON


title: 4188 cells MYC OFF 8 hours

value: dox 8 hrs, MYC OFF


title: HD2 NKp65-

source_name: HD2 NKp65-


title: 4188 cells MYC OFF 24 hours

value: dox 24 hrs, MYC OFF


title: 4188 cells MYC OFF 48 hours

value: dox 48 hrs, MYC OFF


title: EKHT1_ROW29_6


title: EKHT1_ROW31_6


title: cord blood-induced pluripotent stem cell (OCT4, SOX2, MYC and KLF4), biological replicate 1


title: H9 embryonic stem cells, biological replicate 2

source_name: H9 embryonic stem cells

value: H9 embryonic stem cells


title: Developing mouse embryo sections D03D10_S39


title: H9 embryonic stem cells, biological replicate 1


title: HD1 NKp65+

source_name: HD1 NKp65+


title: ID3954_G9aKOPDXCre_Rep2

city: Milwaukee

first: Gwen

last: Lomberk

state: WI

address: 8701 W Watertown Plank Rd

department: Surgery

institute: Medical College of Wisconsin

data_processing:
Sequencing reads were processed through the MAP-Rseq version 3.0.0 workflow
Differential Expression Analysis using GLM model in edgeR (version 3.28.1)
Pathway analysis of DEGs using RITAN , R package
Genome_build: Gencode vM23 (GRCm38.p6)
Supplementary_files_format_and_content: tab-delimited text files include RAW and RPKM values for each Sample

growth_protocol: Standard mouse housing with controlled temperature, humidity and light cycles and provided with ad libitum standard rodent chow and water.

extract_protocol:
Pancreas was taken at time of euthanasia, minced in RNAlater and snap frozen with liquid nitrogen. RNA extraction was completed with ToTALLY RNA Kit (Ambion, Cat# AM1910) according to manufacturer’s protocols.  Precipitated RNA was cleaned up according to Qiagen’s protocol on the miRNeasy column (Qiagen, Cat# 217004), with an on-column DNA digestion and RNaseOUT (Invitrogen, Cat# 10777019) added to final elution to reduce degradation during storage at -80°C.
Illumina TruSeq RNA v2 library preparation kit

treatment_protocol: To induce chronic pancreatitis and accelerate the progression of PDAC, caerulein was administered via IP injection to 4-week-old mice once a day, 5 times a week, for a total of 4 weeks at a dose of 50μg/kg. Animals were given 7 days with no treatment before sacrifice to allow recovery.

value: pancreas

value: EHMT2 flox/flox; Pdx1-Cre+

tag: age

value: 4 weeks

value: No treatment


title: CA2 embryonic stem cells, presence of trisomy 12 confirmed by Cytoscan HD array, biological replicate 1


title: cord blood-induced pluripotent stem cell (OCT4, SOX2, MYC and KLF4), biological replicate 3


title: HD1 NKp65-

source_name: HD1 NKp65-


title: cord blood-induced pluripotent stem cell (OCT4, SOX2, MYC and KLF4), biological replicate 2


title: EKHT1_ROW32_6

tag: strain


title: EKHT1_ROW34_6


title: EKHT1_ROW38_6


title: Developing mouse embryo sections D04D11_S136

value: E14 Mouse Embryo


title: ID3978_G9aKOPDXCre_Rep3


title: 4188 cells MYC OFF 12 hours

value: dox 12 hrs, MYC OFF


title: Developing mouse embryo sections D03D11_S135

value: Sagigital section


title: ID4015-PDXCre_Rep2

source_name: PDXCre


title: Developing mouse embryo sections D01D10_S37


title: ID3982_G9aKOKRASPDXCre_Rep2

value: EHMT2 flox/flox; LSL-KrasG12D+; Pdx1-Cre+

value: 8 weeks


title: EKHT1_ROW25_6


title: ID3817_KRASPDXCre_Rep1

source_name: KRASPDXCre

value: LSL-KrasG12D+; Pdx1-Cre+


title: ID3951_G9aKOPDXCre_Rep1


title: ID4020_KRASPDXCre_Rep3


title: EKHT1_ROW21_6


title: 5853_G9aKOKRASPDXCRE_AccePDAC_Rep4

value: chronic pancreatitis by caerulein treatment


title: 5528_KRASPDXCre_AccePDAC_Rep2

source_name: KRASCreAP


title: Developing mouse embryo sections C12D10_S36


title: ID4061_G9aKOKRASPDXCre_Rep3


title: EKHT1_ROW08_6


title: Developing mouse embryo sections D02D11_S134


title: ID4069_G9aKOKRASPDXCre_Rep4


title: Developing mouse embryo sections D02D10_S38


title: ID3888_KRASPDXCre_Rep2


title: ID3999-PDXCre_Rep1


title: 5533_KRASPDXCre_AccePDAC_Rep3


title: Developing mouse embryo sections D01D11_S133


title: EKHT1_ROW19_6


title: EKHT1_ROW14_6


title: 5539_G9aKOKRASPDXCRE_AccePDAC_Rep1


title: Developing mouse embryo sections C11D10_S35


title: EKHT1_ROW03_6


title: 5588_KRASPDXCre_AccePDAC_Rep4


title: EKHT1_ROW20_6


title: EKHT1_ROW01_6


title: EKHT1_ROW40_5


title: Developing mouse embryo sections C12D11_S132


title: EKHT1_ROW39_5


title: Developing mouse embryo sections C11D11_S131


title: EKHT1_ROW06_6


title: PH_131

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

data_processing:
fastq files were aligned to the mouse reference genome with Hisat
sam files were sorted and converted to bam files with SAMtools
reads were counted with featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: read count matrix

source_name: 48h regenerating liver tissue of CLDN3+/+ mouse

extract_protocol:
total RNA was extracted with Trizol from whole liver tissue
Libraries were constructed using IlluminaTruSeq Stranded mRNA Prep kit according to the manufacture's protocol.

treatment_protocol: Mice underwent a standard two-thirds surgical hepatectomy. The resected liver tissue served as the baseline, non-regenerating control. The regeneratng liver tissue was harvested 48 hours post resection.

tag: Sex

value: female

value: liver

tag: sample group

value: 48 hours  post two-thirds hepatectomy


title: CTRL_6

source_name: baseline liver tissue of CLDN3+/+ mouse

tag: strain background

value: baseline; no surgery


title: PH_123

tag: genotype/variation


title: PH_124


title: Developing mouse embryo sections C10D11_S130


title: PH_127

source_name: 48h regenerating liver tissue of CLDN3-/- mouse


title: CTRL_7


title: 5598_G9aKOKRASPDXCRE_AccePDAC_Rep2


title: Developing mouse embryo sections C09D11_S129


title: PH_126


title: PH_128


title: EKHT1_ROW38_5

source_name: primary somatosensory cortex


title: CTRL_3

source_name: baseline liver tissue of CLDN3-/- mouse


title: Developing mouse embryo sections C09D10_S33

source_name: E14 saggital sections 8-10um thick


title: CTRL_2


title: EKHT1_ROW35_5


title: CTRL_5


title: CTRL_1


title: mouse liver Adult

first: Zhang

last: Yin

address: Xin Gang West 135

institute: Sun Yat-sen University

data_processing:
5' barcode sequences and 3' Adapters (CTGTAGGCACCATCAATCGTATGCCGTCTTCTGCTTG) were removed using FASTX-Toolkit
Reads were mapped into mm9 using bowtie ---best --strata
Overlapping reads were grouped to identify Clusters. The clusters were then annotated according to UCSC refgene and ensembl annotations
The clusters sequence of mRNA were scanned to identify miRNAs-target interaction by matching the seed sequences of all known mouse miRNAs
Genome_build: mm10

source_name: mouse liver

extract_protocol:
The embryonic or adult mouse liver were washed dissected, homogenized and crosslinked 3 times using 254 nm UV light (0.2 J/cm2 ) in cold PBS. Then the tissue were lysed and incubated with Ago antibodies and sperated by SDS-PAGE and transfer to nitrocellulose.membrane. The RNA were isolated by phenol chloroform extraction
RNA were ligated with adapters and reversed tanscipted into cDNA and PCR amplification.
HITS-CLIP

tag: antibody

value: Ago2 and Ago1(MBL  RN028PW )

value: Ago binding RNAs


title: mouse liver e18.5 rep2


title: Developing mouse embryo sections C10D10_S34


title: EKHT1_ROW33_5


title: Developing mouse embryo sections C08D10_S32


title: EKHT1_ROW31_5


title: mouse liver P7


title: mouse liver e18.5


title: mouse liver e15.5


title: EKHT1_ROW29_5


title: mouse liver e12.5


title: Developing mouse embryo sections C07D10_S31


title: IM2-5Con-3

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

description: The group information is prefixed with Con_3 in the column of processed data file

data_processing: The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.

extract_protocol:
Testis samples were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

value: ICR

value: Testis

value: Con (No treatment)


title: Developing mouse embryo sections C07D11_S127

last: Srivatsan

address: 3720 15TH Ave NE Genome Sciences S Foefe Bldg

extract_protocol:
Nuclei were extracted with a permeabilization buffer, sonicated and fixed. cDNA molecules within nuclei are extracted after tagmentation through the use of denaturants.
3' end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis, tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it, a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.


title: EKHT1_ROW26_5


title: IM2-5Con-1

description: The group information is prefixed with Con_1 in the column of processed data file


title: Developing mouse embryo sections C08D11_S128


title: EKHT1_ROW23_5


title: IM2-5Sa-3

description: The group information is prefixed with Sa_3 in the column of processed data file

value: Sa (Busulfan treatment then Treated with saline)


title: Developing mouse embryo sections C06D10_S30

value: E14 Mouse Embryo


title: IM2-5Sa-1

description: The group information is prefixed with Sa_1 in the column of processed data file


title: EKHT1_ROW18_5


title: EKHT1_ROW22_5


title: IM2-5Con-2

description: The group information is prefixed with Con_2 in the column of processed data file


title: IM2-5C-3

description: The group information is prefixed with IMC_3 in the column of processed data file

value: IMC (Busulfan treatment then Treated with gut microbiota from ddH2O treated mice)


title: EKHT1_ROW17_5


title: IM2-5C-1

description: The group information is prefixed with IMC_1 in the column of processed data file


title: Developing mouse embryo sections C04D11_S124

value: Sagigital section


title: IM2-5A10-3

description: The group information is prefixed with IMA10_3 in the column of processed data file

value: IMA10 (Busulfan treatment then Treated with gut microbiota from Aligina Oligosaccharide  (10mg/kg body weight)  treated mice)


title: IM2-5C-2

description: The group information is prefixed with IMC_2 in the column of processed data file


title: Developing mouse embryo sections C05D11_S125

description:
Developing mouse embryo sections
sci-Space Slides 7-14
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell


title: Developing mouse embryo sections C06D11_S126


title: IM2-5A10-2

description: The group information is prefixed with IMA10_2 in the column of processed data file


title: EKHT1_ROW16_5


title: IM2-5A10-1

description: The group information is prefixed with IMA10_1 in the column of processed data file

value: IMA10 (Busulfan treatment then Treated with gut microbiota from Aligina Oligosaccharide (10mg/kg body weight) treated mice)


title: EKHT1_ROW13_5


title: Oligodendrocyte specific, TDP-43 homozygous conditional knockout mouse ID 637, P60 [RMS637]

city: Singapore

first: Shuo-Chien

last: Ling

state: Singapore

address: 12 Science Drive 2, MD1, 16-03-H

department: Physiology

country: Singapore

institute: National University of Singapore

description:
processed data file:
samples_normScaledReadsPerBase.csv

data_processing:
Sequenced reads filtered for low quality reads with skewer 0.2.2 (-Q 5)
RNA-seq read quantification was performed using Kallisto 0.43.0 (-b 50 –single -l 200 -s 20)
DEG calling was performed using Sleuth 0.28.1 (Control contrast)
Genome_build: GRCm38
Supplementary_files_format_and_content: tsv file with gene abundance for all samples
samples_normScaledReadsPerBase.csv: csv (Normalized scaled reads per base for each sample)

source_name: Oligodendrocyte specific, TDP-43 homozygous conditional knockout mouse_spinal cord

extract_protocol:
Spinal cords were removed, flash frozen under liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA-Seq libraries were constructed using either Illumina TruSeq Sample Prep Kit or the NEXTflex Rapid Directional RNA-Seq Kit as per manufacturer's directions. The subset of samples for which each protocol was used is mentioned against each sample in the SAMPLES section

tag: gender

value: Male

tag: genotype/variatation

value: Cnp-Cre; Tardbp-fl/fl

value: Spinal Cord

tag: library preparation

value: NEXTflex Rapid Directional RNA-Seq Kit


title: Oligodendrocyte specific, TDP-43 homozygous conditional knockout mouse ID 636, P60 [RMS636]

tag: tissue


title: Developing mouse embryo sections C04D10_S28

first: Sanjay

institute: University of Washington

tag: genotype

tag: sample type


title: EKHT1_ROW09_5


title: IM2-5Sa-2

description: The group information is prefixed with Sa_2 in the column of processed data file

tag: treatment


title: Developing mouse embryo sections C03D10_S27


title: Developing mouse embryo sections C05D10_S29


title: Oligodendrocyte specific, TDP-43 homozygous conditional knockout mouse ID 635, P60 [RMS635]


title: Developing mouse embryo sections C03D11_S123


title: Oligodendrocyte specific, TDP-43 heterozygous conditional knockout mouse ID 633, P60 [RMS633]

source_name: Oligodendrocyte specific, TDP-43 heterozygous conditional knockout mouse_spinal cord

value: Cnp-Cre; Tardbp-fl/+


title: Oligodendrocyte specific, TDP-43 heterozygous conditional knockout mouse ID 634, P60 [RMS634]


title: EKHT1_ROW05_5


title: Oligodendrocyte specific, TDP-43 heterozygous conditional knockout mouse ID 632, P60 [RMS632]


title: Developing mouse embryo sections C02D11_S122


title: Developing mouse embryo sections C02D10_S26


title: Control- TDP-43 floxed mouse ID 631, P60 [RMS631]

data_processing:
Sequenced reads filtered for low quality reads with skewer 0.2.2 (-Q 5)
RNA-seq read quantification was performed using Kallisto 0.43.0 (-b 50 –single -l 200 -s 20)
DEG calling was performed using Sleuth 0.28.1 (Control contrast)
Genome_build: GRCm38
Supplementary_files_format_and_content: tsv file with gene abundance for all samples
samples_normScaledReadsPerBase.csv: csv (Normalized scaled reads per base for each sample)
p21-double-ko_vs_control.tsv: tsv (DE calls for Cnp-Cre; Tardbp-fl/fl vs Tardbp-fl/fl mice at 21 days)
p21-double-ko_vs_single-ko.tsv: tsv (DE calls for Cnp-Cre; Tardbp-fl/fl vs Cnp-Cre;Tardbp-fl/+ mice at 21 days)
p21-single-ko_vs_control.tsv: tsv (DE calls for Cnp-Cre; Tardbp-fl/+ vs Tardbp-fl/fl mice at 21 days)
p60-double-ko_vs_control.tsv: tsv (DE calls for Cnp-Cre; Tardbp-fl/fl vs Tardbp-fl/fl mice at 60 days)
p60-double-ko_vs_single-ko.tsv: tsv (DE calls for Cnp-Cre; Tardbp-fl/fl vs Cnp-Cre;Tardbp-fl/fl mice at 60 days)
p60-single-ko_vs_control.tsv: tsv (DE calls for Cnp-Cre; Tardbp-fl/+ vs Tardbp-fl/fl mice at 60 days)

source_name: Control TDP-43 floxed mouse_spinal cord

value: Female

value: Tardbp-fl/fl


title: Control- TDP-43 floxed mouse ID 630, P60 [RMS630]


title: Control- TDP-43 floxed mouse ID 629, P60 [RMS629]


title: Developing mouse embryo sections C01D11_S121


title: EKHT1_ROW01_5


title: EKHT1_ROW06_5


title: H2D (for small RNA-seq)

city: Wuhan

first: Yu

last: Sun

address: Luojiashan Street

institute: Wuhan University

data_processing:
Quality control: Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
Transcriptome assembly: The mapped reads of each sample were assembled by both Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010) in a reference-based approach. Both methods use spliced reads to determine exons connectivity, but with two different approaches. Scripture uses a statistical segmentation model to distinguish expressed loci from experimental noise and uses spliced reads to assemble expressed segments. It reports all statistically expressed isoforms in a given locus. Cufflinks uses a probabilistic model to simultaneously assemble and quantify the expression level of a minimal set of isoforms that provides a maximum likelihood explanation of the expression data in a given locus (Cabili et al. 2011). Scripture was run with default parameters, Cufflinks was run with ‘min-frags-per-transfrag=0’ and ‘--library-type’, other parameters were set as default.
Conservative analysis: Phast (v1.3) is a software package contains much of statistical programs, most used in phylogenetic analysis (Siepel, et al. 2005), and phastCons is a conservation scoring and identificating program of conserved elements. We used phyloFit to compute phylogenetic models for conserved and non-conserved regions among species and then gave the model and HMM transition parameters to phyloP to compute a set of conservation scores of lncRNA and coding genes.
Quantification of gene expression level: Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Differential expression analysis: Cuffdiff provides statistical routines for determining differential expression in digital transcript or gene expression data using a model based on the negative binomial distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned as differentially expressed.
GO and KEGG enrichment analysis: Gene Ontology (GO) enrichment analysis of differentially expressed genes or lncRNA target genes were implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used KOBAS software to test the statistical enrichment of differential expression genes or lncRNA target genes in KEGG pathways
PPI analysis: PPI analysis of differentially expressed genes was based on the STRING database, which known and predicted Protein-Protein Interactions. For the species existing in the database, we construct the networks by extract the target gene list from the database; Otherwise, Blastx (v2.2.28) was used to align the target gene sequences to the selected reference protein sequences, and then the networks was built according to the known interaction of selected reference species.
Alternative splicing analysis: Alternative splicing events were classified to 12 basic types by the software Asprofile v1.0. The number of AS events in each sample was estimated, separately.
SNP analysis: Picard-tools v1.96 and samtools v0.1.18 were used to sort, mark duplicated reads and reorder the bam alignment results of each sample. GATK2 software was used to perform SNP calling.
Genome_build: Mus_musculus, GRCm38, ensembl 79
Supplementary_files_format_and_content: Zip files of all processed data of lncRNA and small RNA for samples including Nor, NCD, H1D, H2D, H3D

source_name: Liver

growth_protocol: C57BL/6 breeding pairs were housed at a controlled temperature with a 12 hr/12 hr light/dark cycle, with free access to water and food. Animals were handled according to the Guidelines of the China Animal Welfare Legislation and approved by the Committee on Ethics in the Care and Use of Laboratory Animals of College of Life Sciences, Wuhan University.

extract_protocol:
Total RNA from liver samples was extracted individually using RNAiso Plus (Takara Biotechnology, Dalian, China). An equal amount of RNA (n = 4-8) from the same group was combined into 2 samples/group for lncRNA sequencing and 1 sample/group for small RNA sequencing as described previously (Ding et al., 2014). Sequencing was performed by Novogene (Beijing, China).
For lncRNA sequencing, briefly, ribosomal RNA was removed by Ribo-zero rRNA Removal Kit (Epicentre, USA), and sequencing libraries were generated. The clustering of the index-coded samples was performed using TruSeq PE Cluster Kit v3-cBot-HS (Illumina). After cluster generation, the libraries were sequenced on an Illumina Hiseq 2500 platform and 125 bp paired-end reads were generated. For small RNA sequencing, briefly, sequencing libraries were generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed, after which the library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated.
lncRNA RNA-Seq and small RNA RNA-seq

treatment_protocol: C57BL/6 female mice (F0 generation) were fed with either normal chow (NC) or HFD (60% kcal fat) from 1-month to 3-month old, and mated with NC-fed male mice to produce F1 generation. The F2 generation was similarly created. Male offspring of the F0, F1 and F2 generations were intraperitoneally injected with DEN at 2-weeks-old, and kept inmaintained on HFD and named as H1D, H2D and H3D groups, respectively. Male offspring of the F0 generation injected with PBS (Nor group) or DEN (NCD group) at the same age and kept inmaintained on NC. All groups were sacrificed at 40-weeks-old.

value: high fat

value: liver

value: wild type


title: H3D (for small RNA-seq)


title: Developing mouse embryo sections B12D11_S120

city: Seattle


title: EKHT1_ROW40_4


title: H1D (for small RNA-seq)


title: Developing mouse embryo sections C01D10_S25


title: H3D rep2 (for LncRNA-seq)

description:
Annotated_lncRNA_FPKM.xls
Novel_lncRNA_FPKM.xls
mRNA_FPKM.xls
TUCP_FPKM.xls


title: Developing mouse embryo sections B12D10_S24


title: H2D rep2 (for LncRNA-seq)


title: EKHT1_ROW38_4


title: NCD (for small RNA-seq)

value: normal chow


title: Developing mouse embryo sections B11D11_S119


title: H1D rep1 (for LncRNA-seq)


title: H3D rep1 (for LncRNA-seq)


title: Developing mouse embryo sections B11D10_S23


title: H1D rep2 (for LncRNA-seq)


title: NCD rep1 (for LncRNA-seq)


title: Nor (for small RNA-seq)

value: PBS


title: EKHT1_ROW04_5


title: EKHT1_ROW34_4


title: NCD rep2 (for LncRNA-seq)


title: EKHT1_ROW20_4


title: EKHT1_ROW21_4


title: Nor rep2 (for LncRNA-seq)


title: Nor rep1 (for LncRNA-seq)


title: Developing mouse embryo sections B10D10_S22

value: E14 Mouse Embryo


title: EKHT1_ROW36_4


title: H2D rep1 (for LncRNA-seq)


title: EKHT1_ROW19_4


title: Developing mouse embryo sections B09D11_S117


title: EKHT1_ROW13_4


title: DMSO treated HD patient-derived B-lymphocytes, replicate 3, Ampliseq

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

data_processing:
For data analysis, Ampliseq reads (Fastq format) were mapped to human genome (hg19) using TopHat2 which allows identification of both known and novel splice junctions.
For each one of the 66 introns of the HTT gene, we calculated a Junction Expression Index (JEI) using the percent of read supporting the splicing of the exact annotated intron among all reads supporting the splicing isoforms using either the 5’ss or/and 3’ss of that intron. A JEI value of 100% indicates full splicing of the intron. A JEI value <100% indicates alternative splicing paths (eg inclusion of a cryptic exon or use of alternative 5’ or 3’ss).
Genome_build: hg19
Supplementary_files_format_and_content: "AmpliSeq_HTT_Counts_JEI.xlsx" is an Excel spreadsheet file. Each row is an intron of HTT gene. 5' and 3' splice sites (ss) coordinates are based on human genome version hg19. "num_", total read counts for all junction reads using either the 5'ss or the 3'ss of the intron. "JEI_", the Junction Expression Index for a particular intron. "JEI_average", the average JEI for the three replicates of a treatment. "JEI_sd_", the standard deviation of JEI of  the three replicates of a treatment. "delta-JEI_(Cpd vs. Ctl)", the change of JEI between compound-treated samples and control (DMSO). "P value (T-test)", the P-value using the Student's t-test.

source_name: HD patient-derived B-lymphocytes

growth_protocol: GM04856 cells were plated in 6-well plates at 5e5 cells/well in 2 mL of 10% FBS, DMEM and incubated for 6 hours (37ºC, 5% CO2, 100% relative humidity) before treatment.

extract_protocol:
RNA was purified with the RNeasy Mini Kit (Qiagen) using the manufacturer’s protocol.
The Ion AmpliSeq technology (Thermo Fisher Scientific), which is a PCR-based target enrichment and next-generation sequencing platform, was used as a targeted measure of exons across the entire HTT transcript with the goal of monitoring the presence of any (and all) novel splice variants in the presence of compound. PCR enrichment of HTT exon targets was accomplished by applying a custom HTT AmpliSeq panel (PTC proprietary primer set). The panel consisted of two separate PCR primer pools, each producing 33 amplicons. The complete HTT assay has 66 amplicons (mean size, 135 bp) covering all 67 exons. The Ampliseq workflow included: a) RNA reverse transcription, b) target amplification, c) partial primer digestion, d) adapter ligation, e) library amplification, f) sequencing reaction, g) sequencing data analysis.
RNA-Ampliseq

treatment_protocol: treated with 125 nM HTT-C1 (in 0.5% DMSO) in triplicate for 24 hours

tag: cell type

value: HD patient-derived B-lymphocytes

value: DMSO

tag: replicate


title: EKHT1_ROW12_4


title: DMSO treated HD patient-derived B-lymphocytes, replicate 1, Ampliseq


title: DMSO treated HD patient-derived B-lymphocytes, replicate 2, Ampliseq


title: 125nM HTT-C1 treated HD patient-derived B-lymphocytes, replicate 2, Ampliseq

value: 125nM HTT-C1


title: Developing mouse embryo sections B10D11_S118

value: Sagigital section


title: 125nM HTT-C1 treated HD patient-derived B-lymphocytes, replicate 3, Ampliseq


title: EKHT1_ROW09_4


title: EKHT1_ROW08_4


title: Developing mouse embryo sections B08D11_S116


title: 125nM HTT-C1 treated HD patient-derived B-lymphocytes, replicate 1, Ampliseq


title: Developing mouse embryo sections B07D11_S115


title: EKHT1_ROW06_4


title: Developing mouse embryo sections B08D10_S20


title: Developing mouse embryo sections B07D10_S19


title: EKHT1_ROW04_4


title: Developing mouse embryo sections B09D10_S21


title: EKHT1_ROW01_4


title: Developing mouse embryo sections B06D11_S114


title: Developing mouse embryo sections B06D10_S18


title: Developing mouse embryo sections B05D11_S113


title: Developing mouse embryo sections B05D10_S17


title: EKHT1_ROW40_3


title: EKHT1_ROW39_3


title: Developing mouse embryo sections B04D11_S112


title: WT_Liver_replicate_4

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Five micrograms of cDNA was hybridized for 16h at 45C on a Rat Gene 2.0 ST GeneChip array.

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console v1.1 software

label: Biotin

organism: Rattus norvegicus

label_protocol: Sense target cDNA was prepared from 125ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671).

growth_protocol: Tissues were collected from 10 week old male rats. Liver tissue was snap frozen and maintained at -80°C until RNA extraction. Brain frontal cortex and kidney tissues were stored in RNAlaterTM (ThermoFisher P/N AM7020) following the manufacturer’s instructions until RNA extraction.

extract_protocol: Total RNA was extracted from tissues using TRIzolTM Reagent (ThermoFisher P/N 15596018) according to the manufacturer's recommended procedures.

value: Abcg2+/+ Abcb1a+/+

value: Male

value: Sprague-Dawley

value: 10 weeks

tag: animal id

value: Liver


title: WT_Liver_replicate_2

tag: age


title: dKO_Liver_replicate_5

value: Abcg2-/- Abcb1a-/-

tag: strain


title: WT_Liver_replicate_3


title: WT_Liver_replicate_5


title: dKO_Liver_replicate_1


title: dKO_Liver_replicate_3


title: dKO_Liver_replicate_4


title: WT_Liver_replicate_1


title: dKO_Liver_replicate_2


title: WT_Kidney_replicate_5

source_name: Kidney

value: Kidney


title: dKO_Kidney_replicate_5


title: WT_Kidney_replicate_2


title: Developing mouse embryo sections B03D11_S111


title: WT_Kidney_replicate_3


title: WT_Kidney_replicate_1


title: EKHT1_ROW38_3


title: EKHT1_ROW37_3


title: WT_Kidney_replicate_4


title: Developing mouse embryo sections B03D10_S15


title: EKHT1_ROW34_3


title: Developing mouse embryo sections B04D10_S16


title: EKHT1_ROW19_3


title: EKHT1_ROW20_3


title: dKO_Kidney_replicate_2


title: Developing mouse embryo sections B02D10_S14


title: Developing mouse embryo sections B01D11_S109


title: Developing mouse embryo sections B01D10_S13


title: EKHT1_ROW26_3


title: WT_Brain_replicate_5

source_name: Frontal cortex of brain

value: Frontal cortex of brain


title: EKHT1_ROW21_3


title: Developing mouse embryo sections A12D10_S12


title: Developing mouse embryo sections B02D11_S110


title: EKHT1_ROW11_3


title: EKHT1_ROW18_3


title: Developing mouse embryo sections A10D11_S106


title: EKHT1_ROW15_3


title: Developing mouse embryo sections A12D11_S108


title: WT_Brain_replicate_1


title: EKHT1_ROW01_3


title: Developing mouse embryo sections A10D10_S10


title: EKHT1_ROW40_20


title: dKO_Kidney_replicate_1


title: Developing mouse embryo sections A11D11_S107


title: dKO_Brain_replicate_5


title: dKO_Brain_replicate_3


title: EKHT1_ROW10_3


title: WT_Brain_replicate_3


title: Developing mouse embryo sections A11D10_S11


title: EKHT1_ROW39_20


title: dKO_Brain_replicate_1


title: Developing mouse embryo sections A09D10_S9


title: EKHT1_ROW06_3


title: WT_Brain_replicate_2


title: dKO_Brain_replicate_2


title: WT_Brain_replicate_4


title: Developing mouse embryo sections A07D11_S103


title: EKHT1_ROW35_20


title: Developing mouse embryo sections A06D11_S102


title: dKO_Kidney_replicate_4


title: EKHT1_ROW23_20


title: dKO_Brain_replicate_4


title: dKO_Kidney_replicate_3


title: Developing mouse embryo sections A09D11_S105


title: REB212: CFT073 delta hsdSMR log rep 3

first: Swaine

middle: L

last: Chen

address: 60 Biopolis Street, Genome, #02-01

department: Medicine

institute: National University of Singapore and Genome Institute of Singapore

data_processing:
Raw sequencing reads were mapped to their respective reference genomes: RefSeq accession GCF_000013265.1 for E. coli UTI89, GCF_000005845.2 for E. coli MG1655 and GCF_000007445.1 for E. coli CFT073 using BWA-MEM (version 0.7.10) with default parameters, then the resulting bam files were sorted and deduplicated using PicardTools v.2.2.2
HTseq was used to quantify sequencing reads mapping to predicted open reading frames (ORFs)
Ribosomal RNA (rRNA) and transfer RNA (tRNA) sequences (based on the corresponding Genbank RefSeq annotation) were filtered out of the data set.
R (version 2.15.1) was used for differential expression analysis, using the edgeR package (samples were normalized by TMM (trimmed median of means), common and tagwise dispersion factors were estimated using a negative binomial model, and then fold change values were calculated from these normalized counts)
Genome_build: RefSeq accession GCF_000013265.1 for E. coli UTI89, GCF_000005845.2 for E. coli MG1655 and GCF_000007445.1 for E. coli CFT073
Supplementary_files_format_and_content: Tab-delimited text files with normalized expression values, fold change, P-values, and FDR values.

organism: Escherichia coli CFT073

source_name: CFT073 delta hsdSMR

growth_protocol: Stationary phase cells were obtained by propagating strains statically for two serial 24 hour passages at 37°C, with a 1:1000 dilution between passages (identical to the inoculum used for mouse infections). Log phase cells were obtained by diluting overnight cultures 1:100 in LB and growing to log phase (OD600 = 0.4 – 0.5) at 37°C with shaking.

extract_protocol:
RNA extraction with the Qiagen RNAEasy Mini Kit; ribosomal depletion with the Ribo Zero rRNA removal kit
RNA libraries were prepared using the ScriptSeq v2 RNA-seq library preparation kit

tag: growth condition

value: log phase

value: delta hsdSMR


title: Developing mouse embryo sections A08D11_S104

department: Genome Sciences


title: EKHT1_ROW33_20


title: Developing mouse embryo sections A05D10_S5


title: Developing mouse embryo sections A08D10_S8


title: EKHT1_ROW32_20


title: EKHT1_ROW12_3


title: REB216: CFT073 delta hsdSMR stat rep 2

value: stationary phase


title: EKHT1_ROW31_20


title: Developing mouse embryo sections A07D10_S7


title: REB218: CFT073 delta hsdSMR stat rep 3


title: REB214: CFT073 delta hsdSMR stat rep 1


title: REB210: CFT073 delta hsdSMR log rep 2


title: Developing mouse embryo sections A06D10_S6


title: EKHT1_ROW18_20


title: EKHT1_ROW19_20


title: EKHT1_ROW17_20


title: REB213: CFT073 wt stat rep 1

source_name: CFT073 wt

value: wt


title: EKHT1_ROW07_20


title: REB208: CFT073 delta hsdSMR log rep 1


title: Developing mouse embryo sections A04D11_S100

value: E14 Mouse Embryo


title: EKHT1_ROW14_20


title: EKHT1_ROW04_20


title: REB209: CFT073 wt log rep 2


title: REB217: CFT073 wt stat rep 3


title: EKHT1_ROW30_2


title: Developing mouse embryo sections A05D11_S101


title: EKHT1_ROW40_19


title: EKHT1_ROW39_19


title: REB211: CFT073 wt log rep 3


title: EKHT1_ROW08_20


title: Developing mouse embryo sections A03D11_S99


title: Developing mouse embryo sections A02D11_S98


title: Developing mouse embryo sections A04D10_S4


title: REB207: CFT073 wt log rep 1


title: REB038: UTI89 hsdS-UTI89 stat rep 1

organism: Escherichia coli UTI89

source_name: UTI89 hsdS-UTI89


title: REB056: UTI89 hsdS-UTI89 stat rep 3


title: REB053: UTI89 delta hsdSMR stat rep 3

source_name: UTI89 delta hsdSMR


title: EKHT1_ROW12_20


title: REB044: UTI89 delta hsdSMR stat rep 2


title: EKHT1_ROW36_19


title: Developing mouse embryo sections H12A04_S96


title: REB047: UTI89 hsdS-UTI89 stat rep 2


title: Developing mouse embryo sections H11H06_S191


title: REB215: CFT073 wt stat rep 2


title: REB035: UTI89 delta hsdSMR stat rep 1


title: REB052: UTI89 wt stat rep 3

source_name: UTI89 wt


title: Developing mouse embryo sections H12H06_S192


title: EKHT1_ROW37_19


title: EKHT1_ROW29_19


title: Developing mouse embryo sections A01D10_S1


title: Developing mouse embryo sections A03D10_S3


title: EKHT1_ROW38_19


title: Developing mouse embryo sections H11A04_S95


title: Developing mouse embryo sections A02D10_S2


title: Developing mouse embryo sections H10A04_S94


title: Developing mouse embryo sections A01D11_S97


title: EKHT1_ROW33_19


title: EKHT1_ROW25_19


title: EKHT1_ROW34_19


title: EKHT1_ROW21_19


title: EKHT1_ROW19_19


title: Developing mouse embryo sections H09A04_S93


title: RBB239: UTI89 hsdSMR-CFT073 stat rep 2

source_name: UTI89 hsdSMR-CFT073


title: Developing mouse embryo sections H08H06_S188


title: RBB237: UTI89 hsdSMR-CFT073 stat rep 1


title: RBB241: UTI89 hsdSMR-CFT073 stat rep 3


title: EKHT1_ROW28_19

source_name: primary somatosensory cortex


title: Developing mouse embryo sections H10H06_S190


title: Developing mouse embryo sections H09H06_S189


title: Developing mouse embryo sections H07A04_S91


title: EKHT1_ROW14_19


title: REB043: UTI89 wt stat rep 2


title: EKHT1_ROW13_19


title: REB034: UTI89 wt stat rep 1


title: EKHT1_ROW18_19


title: EKHT1_ROW12_19


title: Developing mouse embryo sections H07H06_S187


title: EKHT1_ROW16_19


title: Developing mouse embryo sections H05H06_S185


title: WEB127: UTI89 delta hsdSMR log rep 3


title: EKHT1_ROW08_19


title: RBB235: UTI89 hsdSMR-CFT073 log rep 3


title: RBB233: UTI89 hsdSMR-CFT073 log rep 2


title: Developing mouse embryo sections H06H06_S186


title: RBB231: UTI89 hsdSMR-CFT073 log rep 1


title: EKHT1_ROW07_19


title: Developing mouse embryo sections H06A04_S90


title: RBB240: UTI89 wt stat rep 6


title: WEB129: UTI89 hsdS-UTI89 log rep 3


title: Developing mouse embryo sections H05A04_S89


title: Developing mouse embryo sections H08A04_S92


title: RBB238: UTI89 wt stat rep 5


title: Developing mouse embryo sections H03A04_S87


title: Developing mouse embryo sections H04A04_S88


title: RBB232: UTI89 wt log rep 5


title: EKHT1_ROW04_19


title: EKHT1_ROW39_18


title: RBB234: UTI89 wt log rep 6


title: EKHT1_ROW03_19


title: EKHT1_ROW36_18


title: REB086: UTI89 hsdS-UTI89 log rep 2


title: EKHT1_ROW31_18


title: Developing mouse embryo sections H02A04_S86


title: WEB126: UTI89 wt log rep 3


title: Developing mouse embryo sections H02H06_S182


title: RBB230: UTI89 wt log rep 4


title: Developing mouse embryo sections H04H06_S184


title: Developing mouse embryo sections H01A04_S85


title: Developing mouse embryo sections H01H06_S181


title: REB077: UTI89 hsdS-UTI89 log rep 1


title: RBB236: UTI89 wt stat rep 4


title: REB083: UTI89 delta hsdSMR log rep 2


title: EKHT1_ROW35_18


title: Developing mouse embryo sections H03H06_S183


title: Developing mouse embryo sections G12H06_S180


title: EKHT1_ROW28_18


title: EKHT1_ROW37_18


title: Developing mouse embryo sections G12A04_S84


title: EKHT1_ROW29_18


title: Developing mouse embryo sections G11H06_S179


title: REB082: UTI89 wt log rep 2


title: EKHT1_ROW27_18


title: REB073: UTI89 wt log rep 1


title: REB074: UTI89 delta hsdSMR log rep 1


title: EKHT1_ROW22_18


title: Developing mouse embryo sections G11A04_S83


title: EKHT1_ROW18_18


title: Root Tips (RT), Root cap (RC)_2

city: New York

first: Kenneth

middle: David

last: Birnbaum

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

description:
replicate 2: dissected root cap
collumela_2

data_processing:
Sequenced reads were trimmed for adaptor sequences using trimmomatic and trancript abundances were map to Zea mays ssp mays B73 v4 Reference Genome and quatified using Kallisto version 0.43 in paired end mode .
DeSeq2 was used for count normalization using median of ratios method.
Genome_build: Zea mays ssp mays B73 v4
Supplementary_files_format_and_content: Matrix table with normalized counts for every sample (column) and gene (rows)

organism: Zea mays

source_name: Root Cap

growth_protocol: Growth chamber: 26 oC, 12h light/12 h dark

extract_protocol:
Protoplasts were collected collected using FACS directly in Qiagen RTL buffer and flash frozen in liquid nitrogen. RNA was extracted using Qiagen RNeasy Micro Kit (Cat No./ID: 74004).
Libraries were prepared using Ovation® RNA-Seq System V2

treatment_protocol: Stained samples where incubated for 15 min with syto 40 and syto 81 cell fluorescent dyes

tag: cultivar

value: Root Cap

value: wild type

value: 7 DAG

value: dissected root cap


title: EKHT1_ROW20_18

data_processing:
read1 containing umi sequences are appended at the end of the headers of read2
read2 are mapped with tophat v2.0.13 on the mouse genome GRCm38 considering Ensembl78 genes annotations
bam files are processed with umi_tools to deduplicate reads with identical UMI sequence
gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification and this includes 5' and 3' UTRs.
Genome_build: GRCm38
Supplementary_files_format_and_content: retrobeads.tsv.gz contains the result of gene expression quantification by summarizeOverlaps() for each cell. The integers values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contains information about the genes that are quantified.


title: EKHT1_ROW17_18


title: Developing mouse embryo sections G10A04_S82

source_name: E14 saggital sections 8-10um thick

value: Sagigital section


title: Developing mouse embryo sections G09H06_S177


title: Root Tips (RT), Root cap (RC)_1

description:
replicate 1: dissected root cap
collumela_1


title: EKHT1_ROW06_18


title: Root Tip Protoplast (RP), QC (QC)_3

description:
replicate 3: zmWOX5::RFP sorted QC cells
qc_3

source_name: Quiescent center

value: Quiescent center

value: zmWOX5::RFP sorted QC cells


title: EKHT1_ROW15_18


title: EKHT1_ROW05_18


title: Root Tip Protoplast (RP), QC (QC)_1

description:
replicate 1: zmWOX5::RFP sorted QC cells
qc_1


title: Developing mouse embryo sections G06H06_S174


title: Developing mouse embryo sections G08H06_S176


title: Developing mouse embryo sections G08A04_S80


title: Developing mouse embryo sections G07A04_S79


title: EKHT1_ROW37_17


title: Root Tips Without Cap (RTW), Control (C)_1

description:
replicate 1: whole root meristems with root cap removed
rootips_withoutCap_1

source_name: Root Tips Without Cap

value: Root Tips Without Cap


title: Root Tips Without Cap (RTW), Control (C)_2

description:
replicate 2: whole root meristems with root cap removed
rootips_withoutCap_2


title: Developing mouse embryo sections G06A04_S78


title: Root Tip Protoplast Without Cap (RPW), Control (C)_3

description:
replicate 3: all protoplasts from the root meristem but without root cap cells
protoplast_withoutCap_3

source_name: Root Tip Protoplast Without Cap

value: Root Tip Protoplast Without Cap


title: EKHT1_ROW36_17


title: Developing mouse embryo sections G10H06_S178


title: Root Tip Protoplast Without Cap (RPW), Control (C)_1

description:
replicate 1: all protoplasts from the root meristem but without root cap cells
protoplast_withoutCap_1


title: Root Tips (RT), Root cap (RC)_3

description:
replicate 3: dissected root cap
collumela_3


title: EKHT1_ROW29_17


title: Developing mouse embryo sections G09A04_S81


title: EKHT1_ROW34_17


title: Developing mouse embryo sections G05A04_S77


title: Developing mouse embryo sections G07H06_S175


title: Root Tip Protoplast (RP), QC (QC)_2

description:
replicate 2: zmWOX5::RFP sorted QC cells
qc_2


title: EKHT1_ROW03_18


title: EKHT1_ROW38_17


title: Developing mouse embryo sections G04H06_S172


title: Root Tips Without Cap (RTW), Control (C)_3

description:
replicate 3: whole root meristems with root cap removed
rootips_withoutCap_3


title: Root Tip Protoplast (RP), Endodermis (ED)_3

description:
replicate 3: zmSCR::RFP sorted endodermal cells
Endodermis_3

source_name: Endodermis

value: Endodermis

value: zmSCR::RFP sorted endodermal cells


title: Root Tip Protoplast Without Cap (RPW), Control (C)_2

description:
replicate 2: all protoplasts from the root meristem but without root cap cells
protoplast_withoutCap_2


title: Root Tip Protoplast (RP), Endodermis (ED)_2

description:
replicate 2: zmSCR::RFP sorted endodermal cells
Endodermis_2


title: EKHT1_ROW28_17


title: EKHT1_ROW39_17


title: Developing mouse embryo sections G05H06_S173

description:
Developing mouse embryo sections
sci-Space Slides 7-14
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell


title: Developing mouse embryo sections G03H06_S171


title: Developing mouse embryo sections G04A04_S76


title: Root Tip Protoplast Stained (RPS), Cortex (CO)_3

description:
replicate 2: dye sorted cortex layer
cortex_3

source_name: Cortex

value: Cortex

value: dye sorted cortex layer


title: EKHT1_ROW27_17


title: EKHT1_ROW25_17


title: Developing mouse embryo sections G02A04_S74


title: Root Tip Protoplast (RP), Endodermis (ED)_1

description:
replicate 1: zmSCR::RFP sorted endodermal cells
Endodermis_1


title: Root Tip Protoplast Stained (RPS), Cortex (CO)_2

description:
replicate 2: dye sorted cortex layer
cortex_2


title: EKHT1_ROW17_17


title: Developing mouse embryo sections G02H06_S170


title: Developing mouse embryo sections G03A04_S75


title: EKHT1_ROW15_17


title: Developing mouse embryo sections G01A04_S73


title: Root Tip Protoplast Stained (RPS), Cortex (CO)_1

description:
replicate 1: dye sorted cortex layer
cortex_1


title: Root Tip Protoplast Stained (RPS), Stele (S)_3

description:
replicate 2: dye sorted stele layer
stele_3

source_name: Stele

value: Stele

value: dye sorted stele layer


title: Root Tip Protoplast Stained (RPS), Stele (S)_1

description:
replicate 1: dye sorted stele layer
stele_1


title: Developing mouse embryo sections F12H06_S168


title: EKHT1_ROW09_17


title: Developing mouse embryo sections G01H06_S169


title: EKHT1_ROW11_17


title: EKHT1_ROW04_17


title: Root Tip Protoplast Stained (RPS), Stele (S)_2

description:
replicate 2: dye sorted stele layer
stele_2


title: Root Tip Protoplast Stained (RPS), Epidermis (E)_3

description:
replicate 2: dye sorted epidermal layer
epidermis_3

source_name: Epidermis

value: Epidermis

value: dye sorted epidermal layer


title: EKHT1_ROW06_17


title: Root Tip Protoplast Stained (RPS), Epidermis (E)_2

description:
replicate 2: dye sorted epidermal layer
epidermis_2


title: Developing mouse embryo sections F12A04_S72

value: E14 Mouse Embryo


title: Developing mouse embryo sections F11H06_S167


title: Developing mouse embryo sections F10A04_S70


title: Root Tip Protoplast Stained (RPS), Epidermis (E)_1

description:
replicate 1: dye sorted epidermal layer
epidermis_1

value: wild type


title: EKHT1_ROW14_17


title: Developing mouse embryo sections F10H06_S166


title: EKHT1_ROW40_16


title: EKHT1_ROW31_16


title: EKHT1_ROW30_16


title: EKHT1_ROW28_16


title: EKHT1_ROW38_16


title: Developing mouse embryo sections F09A04_S69


title: Developing mouse embryo sections F08H06_S164


title: EKHT1_ROW01_17


title: EKHT1_ROW24_16


title: Developing mouse embryo sections F11A04_S71


title: EKHT1_ROW02_17


title: EKHT1_ROW21_16


title: Developing mouse embryo sections F07H06_S163


title: Developing mouse embryo sections F07A04_S67


title: Developing mouse embryo sections F08A04_S68


title: EKHT1_ROW20_16


title: EKHT1_ROW18_16


title: Developing mouse embryo sections F09H06_S165


title: Patient 4 Ca4

first: Xiaohua

address: Fuyudong Road 8，Qiaonan street，Panyu

institute: Panyu Central Hospital

description:
Ca4
Tissues obtained from the patients by esophagoscopy or surgery.
Moderately differentiated squamous esophageal carcinoma.

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K, Arraystar).

scan_protocol: The hybridized arrays were scanned using the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package.

source_name: primary esophageal tissue, carcinoma

label_protocol: Circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

growth_protocol: Esophageal carcinoma tissues and normal adjacent tissue were excised and stored at -80°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions. RNA quality and quantity were measured by using NanoDrop spectrophotometer (ND-1000, NanoDrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: After grinded under the ice, the tissues were collected for further total RNA extraction.

tag: disease status

value: esophageal carcinoma

value: esophageal carcinoma tumor tissue

value: male

tag: patient


title: Patient 5 Ca5

description:
Ca5
Tissues obtained from the patients by esophagoscopy or surgery.
High differentiated squamous esophageal carcinoma.


title: Patient 2 N2

description:
N2
Tissues obtained from the patients by esophagoscopy or surgery.
Matched normal adjacent tissue of Ca2.

source_name: primary esophageal tissue, normal

value: normal adjacent tissue