title: Empty vector cell 8

city: Edinburgh

first: Poorya

last: Parvizi

address: 9 Little France Rd

institute: The University of Edinburgh

description:
Batch 3
CH_FY_FP_079_S79_R1_001

data_processing:
The quality of the single-cell mRNA sequencing data checked using FastQC tool
Overrepresented sequences and adaptors were removed using Trimmomatic software version 0.36
Reads aligned to the GRCm38 (mm10) mouse reference genome with STAR aligner version 2.5 (two-pass alignment option was used). Aligned reads were converted to gene counts using HTSeq version 0.9.1
Quality check and filtering of cells were done in Scater. 4 outliers were detected and removed from the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Text file includes read counts of every gene in each sample

source_name: Empty vector

growth_protocol: Neurons were seeded and cultured on microisland astrocyte feeder layers that were prepared 1–2 weeks before the neuronal culture preparation. Astrocytes derived from C57BLJ6/N mouse cortices (P0-P1) were plated on collagen/ poly-D-lysine microislands made on agarose-coated coverslips using a custom-built rubber stamp to achieve uniform size (200µm diameter). For all experiments, striatal neurons were then digested with papain (Worthington) and plated on astrocytes at a density of 3500 neurons per 35 mm dish and grown in a chemically defined medium (Neurobasal-A medium supplemented with Glutamax and B-27).

extract_protocol:
Following electrophysiological recording at DIV15, single striatal GABAergic neurons or astrocytes were collected immediately by applying light negative pressure through the same glass patch pipette. Following successful aspiration, the sample was transferred in a volume of <2 μl of internal patch solution into a RNase-free PCR tube containing 1 μl Lysis buffer, supplemented with RNAse inhibitor, according to SMARTer Ultra Low RNA Kit (Clontech, Germany). Collected single cells were immediately spun down at room temperature and put on dry ice until -80°C storage. SMARTer cDNA synthesis was performed using SMARTer Ultra Low RNA Kit according to manufacturer’s protocol.
Single-cell cDNA library preparation was performed using Nextera XT DNA Library Prep Kit (Illumina, Germany).

treatment_protocol: Cultures were chronically treated with RGFP109; a brain-penetrant inhibitor of histone deacetylase inhibitor (HDACi) specific for HDAC classes 1 and 3 (HDACs; IC50s = 60 and 50 nM; Kis = 32 and 5 nM for HDAC1 and HDAC3 in cell-free assays, respectively). RGFP109 was applied to culture medium of the autaptic neurons at DIV 6 and re-added every 3 days at 100 nM. The dose of RGFP109 used in this study was chosen after assessment of dose-dependent toxicity assays. Drug-untreated neurons were treated with equal amount of drug vehicle (DMSO) on the same days.

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

value: wild type

value: vehicle treated


title: Empty vector cell 6

status: Public on May 05 2021

type: SRA

country: United Kingdom

description:
Batch 3
CH_FY_FP_077_S77_R1_001

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: genotype

tag: treatment


title: Empty vector cell 7

description:
Batch 3
CH_FY_FP_078_S78_R1_001


title: Gata3_Day3.1.pTEICM_32

city: Exeter

first: Daniel

last: Spindlow

state: Devon

address: Stocker Road

department: Living Systems Institute

institute: University of Exeter

data_processing:
Trim-Galore
STAR
FeatureCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts_raw.txt: Raw counts text file.

organism: Homo sapiens

source_name: Blastoid

growth_protocol: Frozen human blastocysts (E5 or E6) were thawed and cultured in N2B27 medium under mineral oil. The majority of embryos were cultured for 24 hours for development to late blastocysts (E6 or E7). Human naïve pluripotent stem cells (HNES1-GATA3:mKO2) [Ge Guo et al., 2021] or niPSC [Bredenkamp Nicholas et al.,2019] were cultured in PXGL on MEF. Dissociated human naïve pluripotent stem cells were cultured in a low attachment 96-well plate in N2B27 supplemented with 1.5uMPD03 and 1uMA83 and 10uM Y-27632 for 44h. The formed aggregates were transferred in N2B27 supplemented with 0.5uM A83. After 18h, they were transferred to N2B27 to form blastocyst-like structure.

extract_protocol:
Dissociated single cells were transferred immediately into Smart-Seq2 single-cell lysis buffer and immediately frozen.
The Smart-Seq2 library was prepared as described in Picelli S et al. 2014.

treatment_protocol: The zona pellucida was removed using acid Tyrode’s solution. Human embryos and human blastocyst model were moved to filtered M2 drop and cut mTE manually using glass pipettes. mTE and the other part containing ICM and pTE were transferred to a drop of Accutase or TrypLE respectively using glass capillary or Pasteur pipette and incubated for 7-10 min at 37 oC or room temperature. Then mTE and ICM with pTE were transferred to a drop of filtered M2 respectively and dissociated by repetitive pipetting using a finely drawn Pasteur pipette or glass capillary of which diameter is just larger than a cell.

value: Blastoid

tag: lineage

value: Trophectoderm

value: polar

tag: time point

value: 3 days after stem cells seeded to form cell aggregates


title: F_P7_normal_CD31_1_DC21_C15

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

source_name: distal lung

extract_protocol:
no extraction
scRNA-Seq: plate-based illumina-compatible Tn5 transposase single cell RNA-Seq

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Early Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: Empty vector-transduced NK92 cells, biological rep2

type: RNA

city: İzmir

first: Can

last: Küçük

address: Dokuz Eylül University Health Campus, Mithatpaşa Avenue. No: 58/5

department: İzmir Biomedicine and Genome Center

country: Turkey

institute: Dokuz Eylül University

description: Total RNA was purified from empty vector transduced, GFP-sorted NK92 cells 48h post-transduction.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. The arrays were washed and stained in the Affymetrix Fluidics Station 400 using protocol EukGE-WS2v5-450.

scan_protocol: Scanning was performed by the Affymetrix 3000 Scanner based on the Affymetrix Scanning Protocol.

data_processing: MAS 5.0 Data Processing Protocol. BRB-Array Tools is used for data normalization and log transformation.

label: Biotin

source_name: NK92 cell line

label_protocol: Biotinylated cRNA samples was prepared from 60 ng total RNA according to the standard Affymetrix protocol based on the Expression Analysis Technical Manual (Affymetrix).

growth_protocol: KHYG1 and NK92 cell lines were cultured in the presence of RPMI 1640 medium supplemented with 10 or 20% FBS, penicillin G (100 units/ml), streptomycin (100 g/ml), and 2mM  L-glutamine at 37 °C in 5% CO2. Exogenous rhIL2 (5-7 ng/ml) was included to support growth of these malignant NK cell lines as they are IL2 dependent.

extract_protocol: Total RNA was extracted with TRIzol™ Reagent and further purified with RNeasy Mini Kit (Qiagen, Valencia, CA). The quality of total RNA samples was evaluated by measuring them with spectrophotometre at 260 and 280 nm and running RNA samples within 1X TAE gel.

treatment_protocol: The functional and full-length isoform of PRDM1 (i.e. PRDM1α) was ectopically expressed in NK92 or KHYG1 cells using the PRDM1α-FL-PMIG construct that was available from previous studies. Empty vector (i.e. PMIG) transduced cells were used as the negative controls. Retroviral transduction was performed as described earlier (Küçük et al. PNAS 2011) with the following modifications: 4 μg of empty vector or PRDM1α-FL was co-transfected with 4 μg of PCL-Ampho, the packaging vector, into the 293T cell line. GFP+ cells were FACS-sorted 48h post-transduction.

value: Lymphoid


title: Empty vector-transduced NK92 cells, biological rep1


title: Empty vector cell 4

description:
Batch 3
CH_FY_FP_075_S75_R1_001

tag: developmental stage


title: PRDM1α-transduced KHYG1 cells, biological rep2

description: Total RNA was purified from PRDM1α-transduced, GFP-sorted KHYG1 cells 48h post-transduction.

source_name: KHYG1 cell line


title: H9_OPC_VNP2_rep2

city: Seongbuk-gu

first: Gyu-Bum

last: Yeon

state: Seoul

address: 145, Anam-ro

department: Department of Biodtechnology

country: South Korea

institute: Korea University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw FASTQ files were trimmed for adapters using TrimGalore, and quntified their transcripts with Salmon using the reference transcript GENCODEV32 (GRCh38.p13)
Normalized abundance measurements was conducted with DESeq2 (1.27.12)
Genome_build: GENCODEV32

molecule: polyA RNA

source_name: H9 (hESC)

extract_protocol:
The total RNAs were extracted using TRIzol® (Thermo Fisher Scientific) according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: hESC derived OPCs were seeded at a density of 2.0 × 105 cells/cm2 on a culture plate pre-coated with various matrices in OPC medium.

value: Oligodendrocytes progenitor cells

tag: cell line

value: H9 (hESC)

tag: ecm


title: Empty vector-transduced KHYG1 cells, biological rep2

description: Total RNA was purified from empty vector transduced, GFP-sorted KHYG1 cells 48h post-transduction.

tag: tissue


title: H9_OPC_VNP2_rep1


title: Empty vector cell 5

description:
Batch 3
CH_FY_FP_076_S76_R1_001

tag: strain

tag: genotype

tag: treatment


title: F_P7_normal_CD31_1_DC21_O23

tag: sequencing run


title: H9_OPC_VN_rep2

value: VN


title: Gata3_Day3.1.pTEICM_30

tag: lineage

tag: time point


title: H9_OPC_VN_rep1


title: Empty vector cell 9

description:
Batch 3
CH_FY_FP_080_S80_R1_001

value: striatum


title: F_P7_normal_CD31_1_DC21_J5

tag: gender

tag: plate

tag: well

value: Arterial EC II


title: Empty vector cell 2

description:
Batch 3
CH_FY_FP_073_S73_R1_001

value: Newborn mice (P0-P1)

value: wild type


title: F_P7_normal_CD31_1_DC21_M1

tag: timepoint

tag: cell type

tag: cell subtype


title: H9_OPC_MG_rep3

value: Control (Matrigel®)


title: Empty vector-transduced KHYG1, biological rep1


title: Gata3_Day3.1.pTEICM_29

value: Blastoid

value: Trophectoderm


title: Gata3_Day3.1.pTEICM_28

value: Epiblast

value: polar

value: 3 days after stem cells seeded to form cell aggregates


title: H9_OPC_MG_rep2


title: F_P7_normal_CD31_1_DC21_D21

value: distal lung

value: F

value: endothelial

value: Car4+ capillaries

tag: mousename

tag: coverage

tag: number of genes


title: F_P7_normal_CD31_1_DC21_D4

value: Early Car4- capillaries

value: normal


title: Gata3_Day3.1.pTEICM_31


title: Gata3_Day3.1.pTEICM_27


title: F_P7_normal_CD31_1_DC21_O12


title: Astrocyte cell 14

description:
Batch 3
CH_FY_FP_014_S14_R1_001

source_name: Astrocytes

value: cortex

tag: developmental stage

value: untreated


title: Gata3_Day3.1.pTEICM_26

tag: tissue


title: Astrocyte cell 13

description:
Batch 3
CH_FY_FP_013_S13_R1_001

tag: strain


title: Astrocyte cell 12

description:
Batch 3
CH_FY_FP_012_S12_R1_001

tag: genotype


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-H07P2-Run1_S18_L002

city: West Windsor

first: Yanhua

last: Hu

state: NJ

address: 3551 Lawrenceville Princeton Rd

country: USA

institute: Bristol Myers Squibb

data_processing:
Data quality assessment and principal component analysis (PCA) were performed to understand the main source of variability.
Differential expression analysis was performed using the limma package (v3.42.2) in R (v3.6.1)  to identify differentially expressed genes (DEGs) across subgroups. Adjusted P_x0002_values were calculated using the Benjamini-Hochberg method; a gene was considered differentially expressed if the absolute fold change was >2 or <0.5 and the false discovery rate-adjusted P-value was <0.05.
Genome_build: GRCh37ERCC-ensembl75
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: labial gland

extract_protocol:
RNA was extracted from 11 formalin-fixed (4%), paraffin-embedded tissue sections (4μm) per biopsy. After scraping the tissue from the slides and deparaffinization, tissue was digested in buffer PKD (Qiagen, USA). RNA was extracted using the RNAeasy FFPE kit, according to manufacturer’s protocol (Qiagen, USA). For RNA extraction from PBMCs, 3x10^6 cells were thawed and rested for 1h in RPMI medium supplemented with 10%FBS and Antibiotic-Antimycotic (all from Gibco, UK) at 37°C. After resting, cell lysis and RNA isolation were performed using the RNAeasy Mini kit, according to manufacturer’s protocol (Qiagen, USA). RNA was immediately stored at -80°C until further use.
Complementary DNA library preparation was performed using TruSeq Stranded Total RNA Library Prep Gold (Illumina, USA, Cat#20020598), following manufacturer’s recommendations. Prepared libraries were sequenced on a HiSeq 2500 System (Illumina, USA)

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group III

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Positive

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: Gata3_Day3.1.pTEICM_25

tag: tissue

value: Blastoid

tag: lineage

tag: time point


title: F_P7_normal_CD31_1_DC21_D12

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes

tag: treatment


title: F_P7_normal_CD31_1_DC21_J4


title: H9_OPC_VNP2_rep3

value: Oligodendrocytes progenitor cells

tag: cell line

value: H9 (hESC)

tag: ecm


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-H05P2-Run1_S40_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

value: Group IV

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: Astrocyte cell 11

description:
Batch 3
CH_FY_FP_011_S11_R1_001

tag: strain

tag: tissue

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: wild type

tag: treatment


title: Gata3_Day3.1.pTEICM_24

tag: lineage

value: Trophectoderm

value: polar

tag: time point

value: 3 days after stem cells seeded to form cell aggregates


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-H06P2-Run1_S48_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

value: Negative


title: F_P7_normal_CD31_1_DC21_A18

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Early Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: F_P7_normal_CD31_1_DC21_O15

tag: tissue

tag: treatment


title: Astrocyte cell 10

description:
Batch 3
CH_FY_FP_010_S10_R1_001

tag: strain

value: cortex

tag: developmental stage

tag: genotype

value: untreated


title: Empty vector cell 1

description:
Batch 3
CH_FY_FP_072_S72_R1_001

value: striatum

value: vehicle treated


title: Gata3_Day3.1.pTEICM_22

value: Blastoid

tag: lineage

value: Epiblast

tag: time point


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-H03P2-Run1_S24_L001

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: negative

tag: parotid infiltration phenotype

value: lymph node present

tag: labial infiltration phenotype

value: Group I

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Positive

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: Astrocyte cell 9

description:
Batch 3
CH_FY_FP_009_S9_R1_001

tag: strain

tag: tissue

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: wild type

tag: treatment


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-H04P2-Run1_S32_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

value: positive

value: Group IV


title: Astrocyte cell 8

description:
Batch 3
CH_FY_FP_008_S8_R1_001


title: F_P7_normal_CD31_1_DC21_L5

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Early Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: Gata3_Day3.1.pTEICM_21

tag: tissue

value: Blastoid

tag: lineage

value: polar

tag: time point

value: 3 days after stem cells seeded to form cell aggregates


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-H02P2-Run1_S16_L001

value: labial gland

tag: acr eular

tag: parotid infiltration phenotype

value: Group III

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Negative

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: Gata3_Day3.1.pTEICM_20

value: Epiblast


title: Astrocyte cell 7

description:
Batch 3
CH_FY_FP_007_S7_R1_001

tag: strain

value: cortex

tag: developmental stage

tag: genotype

tag: treatment

value: untreated


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-H01P2-Run1_S8_L001

tag: tissue

tag: sjnumber

tag: parotid focus score

tag: labial focus score

value: Positive

value: Female


title: F_P7_normal_CD31_1_DC21_C4

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-G07P2-Run1_S17_L002

tag: acr eular

value: positive

tag: parotid infiltration phenotype

tag: labial infiltration phenotype

value: Group IV

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: F_P7_normal_CD31_1_DC21_N11

tag: tissue

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment


title: Gata3_Day3.1.pTEICM_18

tag: lineage

value: Trophectoderm

tag: time point


title: Empty vector cell 3

description:
Batch 3
CH_FY_FP_074_S74_R1_001

tag: strain

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: wild type

value: vehicle treated


title: Astrocyte cell 5

description:
Batch 3
CH_FY_FP_005_S5_R1_001


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-G06P2-Run1_S47_L002

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf


title: F_P7_normal_CD31_1_DC21_G9

tag: tissue

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Proliferative EC

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-G05P2-Run1_S39_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: negative

tag: parotid infiltration phenotype

value: Group I

value: Negative

tag: esspri

tag: age

tag: Sex

tag: essdai


title: Gata3_Day3.1.pTEICM_17

tag: tissue

value: Blastoid

tag: lineage

value: polar

tag: time point

value: 3 days after stem cells seeded to form cell aggregates


title: Astrocyte cell 4

description:
Batch 3
CH_FY_FP_004_S4_R1_001

tag: strain

value: cortex

tag: developmental stage

tag: genotype

tag: treatment

value: untreated


title: F_P7_normal_CD31_1_DC21_D13

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Early Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes


title: Gata3_Day3.1.pTEICM_19

tag: tissue

value: Trophectoderm


title: Astrocyte cell 6

description:
Batch 3
CH_FY_FP_006_S6_R1_001

value: Newborn mice (P0-P1)

value: wild type


title: Gata3_Day3.1.pTEICM_16

tag: lineage

value: Primitive Endoderm


title: F_P7_normal_CD31_1_DC21_A15

value: endothelial

value: Late Car4- capillaries


title: F_P7_normal_CD31_1_DC21_K8

value: normal


title: Gata3_Day3.9.mTE_4

value: mural

tag: time point


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-G04P2-Run1_S31_L002

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: lymph node present

tag: labial infiltration phenotype

value: Group IV

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Negative

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-G02P2-Run1_S15_L001

tag: tissue

value: Positive


title: Astrocyte cell 2

description:
Batch 3
CH_FY_FP_002_S2_R1_001

tag: strain

value: cortex

tag: developmental stage

tag: genotype

tag: treatment

value: untreated


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-G03P2-Run1_S23_L001

tag: sjnumber

tag: parotid focus score

tag: labial focus score

value: negative

value: Group I

value: Male


title: Astrocyte cell 3

description:
Batch 3
CH_FY_FP_003_S3_R1_001

value: Newborn mice (P0-P1)

value: wild type


title: F_P7_normal_CD31_1_DC21_K5

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Early Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes


title: F_P7_normal_CD31_1_DC21_C3

tag: tissue

value: normal


title: 97Q-Htt+RGFP109 cell 26

description:
Batch 3
CH_FY_FP_071_S71_R1_001

source_name: Cultured striatal neurons

tag: strain

value: striatum

tag: developmental stage

value: mutant

value: RGFP109 inhibitor treated


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-F07P2-Run1_S16_L002

value: labial gland

tag: acr eular

tag: parotid infiltration phenotype

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Negative

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: Gata3_Day3.9.mTE_2

value: Blastoid

tag: lineage

value: Trophectoderm

value: mural

tag: time point

value: 3 days after stem cells seeded to form cell aggregates


title: Astrocyte cell 1

description:
Batch 3
CH_FY_FP_001_S1_R1_001

value: cortex

value: Newborn mice (P0-P1)

tag: genotype

tag: treatment

value: untreated


title: Gata3_Day3.9.mTE_3

tag: tissue


title: F_P7_normal_CD31_1_DC21_D10

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-F06P2-Run1_S46_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: negative

tag: parotid infiltration phenotype

value: unclassified

tag: labial infiltration phenotype

value: Group I

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf

tag: esspri

tag: age

tag: Sex


title: Gata3_Day3.9.mTE_1

tag: tissue

tag: lineage

tag: time point


title: 97Q-Htt+RGFP109 cell 25

description:
Batch 3
CH_FY_FP_064_S64_R1_001

tag: strain

value: striatum

tag: developmental stage

tag: genotype

value: mutant

tag: treatment


title: F_P7_normal_CD31_1_DC21_P20

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Early Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: Gata3_Day3.9.mTE_5

tag: tissue

value: Blastoid


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-F05P2-Run1_S38_L002

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group III

tag: labial infiltration phenotype

value: Group IV

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Negative

tag: rf

value: Positive

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: F_P7_normal_CD31_1_DC21_H20

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

tag: mousename

tag: coverage

tag: treatment


title: Gata3_Day3.9.pTEICM_21

tag: tissue

tag: lineage

value: Primitive Endoderm

value: polar

tag: time point

value: 3 days after stem cells seeded to form cell aggregates


title: Gata3_Day3.9.pTEICM_20

value: Trophectoderm


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-F04P2-Run1_S30_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

value: unclassified

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf

tag: esspri


title: F_P7_normal_CD31_1_DC21_G5

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Proliferative EC

tag: mousename

tag: number of genes


title: 97Q-Htt+RGFP109 cell 23

description:
Batch 3
CH_FY_FP_062_S62_R1_001

tag: strain

tag: tissue

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: mutant

tag: treatment

value: RGFP109 inhibitor treated


title: 97Q-Htt+RGFP109 cell 21

description:
Batch 3
CH_FY_FP_060_S60_R1_001


title: Gata3_Day3.1.pTEICM_14

value: Blastoid

tag: lineage

value: Epiblast

tag: time point


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-F03P2-Run1_S22_L001

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group III

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Positive

tag: rf

value: Negative

tag: esspri

tag: age

tag: Sex

tag: essdai


title: 97Q-Htt+RGFP109 cell 22

description:
Batch 3
CH_FY_FP_061_S61_R1_001

tag: strain

tag: tissue

tag: developmental stage

tag: genotype

tag: treatment


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-F02P2-Run1_S14_L001

tag: sjnumber

tag: parotid focus score

tag: labial focus score

value: Group IV

value: Female


title: F_P7_normal_CD31_1_DC21_B11

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Late Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: F_P7_normal_CD31_1_DC21_A20

tag: tissue

value: endothelial

value: Early Car4- capillaries


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-G01P2-Run1_S7_L001

tag: acr eular

value: negative

tag: parotid infiltration phenotype

value: Group I

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: Gata3_Day3.1.pTEICM_15

value: Blastoid

tag: lineage

value: polar

tag: time point

value: 3 days after stem cells seeded to form cell aggregates


title: 97Q-Htt+RGFP109 cell 20

description:
Batch 3
CH_FY_FP_059_S59_R1_001

tag: strain

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: mutant

tag: treatment

value: RGFP109 inhibitor treated


title: Gata3_Day3.1.pTEICM_13

tag: tissue

value: Trophectoderm


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-E07P2-Run1_S15_L002

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group IV

value: Positive

value: Negative

value: Female


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-F01P2-Run1_S6_L001

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf


title: F_P7_normal_CD31_1_DC21_E20

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Early Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: 97Q-Htt+RGFP109 cell 19

description:
Batch 3
CH_FY_FP_058_S58_R1_001

tag: strain

tag: tissue

tag: developmental stage

tag: genotype

tag: treatment


title: 97Q-Htt+RGFP109 cell 24

description:
Batch 3
CH_FY_FP_063_S63_R1_001


title: F_P7_normal_CD31_1_DC21_K15


title: Gata3_Day3.1.pTEICM_11

value: Blastoid

tag: lineage

value: polar

tag: time point

value: 3 days after stem cells seeded to form cell aggregates


title: F_P7_normal_CD31_1_DC21_E16

tag: sequencing run


title: 97Q-Htt+RGFP109 cell 17

description:
Batch 3
CH_FY_FP_034_S34_R1_001

value: striatum

value: Newborn mice (P0-P1)

value: mutant


title: Gata3_Day3.1.pTEICM_10

value: Trophectoderm


title: F_P21_normal_mesench_1_DC21_B6

tag: gender

value: Late Car4- capillaries


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-E05P2-Run1_S37_L002

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group IV

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: 97Q-Htt+RGFP109 cell 16

description:
Batch 3
CH_FY_FP_033_S33_R1_001

tag: strain

tag: tissue

tag: developmental stage

tag: genotype

tag: treatment

value: RGFP109 inhibitor treated


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-E04P2-Run1_S29_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

value: negative

value: Group I

value: Negative

value: Female


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-E03P2-Run1_S21_L001

tag: acr eular

tag: parotid infiltration phenotype

tag: labial infiltration phenotype

value: Positive


title: 97Q-Htt+RGFP109 cell 15

description:
Batch 3
CH_FY_FP_032_S32_R1_001


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-E02P2-Run1_S13_L001

tag: parotid %cd45

tag: labial %cd45

tag: ssa


title: Gata3_Day3.1.pTEICM_9

value: Blastoid

tag: lineage

value: Epiblast

tag: time point


title: Gata3_Day3.9.pTEICM_19

value: polar

value: 3 days after stem cells seeded to form cell aggregates


title: Gata3_Day3.1.pTEICM_12


title: F_P21_normal_mesench_2_DC21_B2

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: Gata3_Day3.1.pTEICM_8.1

tag: tissue


title: F_P7_normal_CD31_1_DC21_H7

value: Car4+ capillaries

tag: treatment


title: F_P7_normal_CD31_1_DC21_M3

value: Venous EC


title: F_P7_normal_CD31_1_DC21_N8

value: Early Car4- capillaries


title: 97Q-Htt+RGFP109 cell 12

description:
Batch 2
6414_S16_L008_R1_001

tag: strain

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: mutant

value: RGFP109 inhibitor treated


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-E01P2-Run1_S5_L001

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group III

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf

value: Negative

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-E06P2-Run1_S45_L002

tag: tissue

value: Group IV

value: Positive


title: 97Q-Htt+RGFP109 cell 18

description:
Batch 3
CH_FY_FP_057_S57_R1_001

tag: strain

tag: developmental stage

tag: treatment


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-D07P2-Run1_S14_L002

tag: sjnumber

tag: parotid focus score

value: negative

value: Group I


title: Gata3_Day3.9.pTEICM_17

value: Blastoid

tag: lineage

value: Trophectoderm

value: polar

tag: time point

value: 3 days after stem cells seeded to form cell aggregates


title: Gata3_Day3.9.pTEICM_15


title: F_P7_normal_CD31_1_DC21_N2

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Early Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: 97Q-Htt+RGFP109 cell 10

description:
Batch 2
6412_S14_L008_R1_001

tag: strain

tag: tissue

value: striatum

value: Newborn mice (P0-P1)

tag: genotype

value: mutant

value: RGFP109 inhibitor treated


title: 97Q-Htt+RGFP109 cell 11

description:
Batch 2
6413_S15_L008_R1_001

tag: developmental stage

tag: treatment


title: Gata3_Day3.9.pTEICM_14

tag: lineage


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-D05P2-Run1_S36_L002

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group III

tag: labial infiltration phenotype

value: Group IV

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Negative

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: F_P7_normal_CD31_1_DC21_D1

tag: tissue

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Proliferative EC

tag: mousename

tag: coverage

tag: number of genes


title: 97Q-Htt+RGFP109 cell 14

description:
Batch 3
CH_FY_FP_031_S31_R1_001

tag: strain

tag: developmental stage

tag: genotype

tag: treatment


title: 97Q-Htt+RGFP109 cell 9

description:
Batch 2
6411_S13_L008_R1_001


title: 97Q-Htt+RGFP109 cell 13

description:
Batch 3
CH_FY_FP_030_S30_R1_001


title: F_P7_normal_CD31_1_DC21_G3


title: F_P7_normal_CD31_1_DC21_M15

value: Late Car4- capillaries


title: Gata3_Day3.9.pTEICM_16

value: Blastoid

tag: lineage

value: Trophectoderm

value: polar

tag: time point

value: 3 days after stem cells seeded to form cell aggregates


title: Gata3_Day3.9.pTEICM_12

tag: tissue


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-D04P2-Run1_S28_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Positive

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: 97Q-Htt+RGFP109 cell 7

description:
Batch 1
CHFY052_S17_L012_R1_001

tag: strain

value: striatum

tag: developmental stage

tag: genotype

tag: treatment


title: F_P7_normal_CD31_1_DC21_D18

tag: tissue

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: 97Q-Htt+RGFP109 cell 6

description:
Batch 1
CHFY051_S16_L012_R1_001

value: Newborn mice (P0-P1)

value: mutant

value: RGFP109 inhibitor treated


title: 97Q-Htt+RGFP109 cell 8

description:
Batch 1
CHFY053_S18_L012_R1_001


title: Gata3_Day3.1.pTEICM_8

tag: lineage

value: Primitive Endoderm

tag: time point


title: F_P7_normal_CD31_1_DC21_J2

value: Early Car4- capillaries


title: Gata3_Day3.1.pTEICM_7


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-D01P2-Run1_S4_L001

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: negative

tag: parotid infiltration phenotype

value: Group I

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Negative

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: Gata3_Day3.1.pTEICM_6

tag: tissue

value: Blastoid

value: Epiblast

value: polar

value: 3 days after stem cells seeded to form cell aggregates


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-D03P2-Run1_S20_L001

value: positive

value: Group III

value: Group IV

value: Positive


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-D02P2-Run1_S12_L001


title: 97Q-Htt+RGFP109 cell 5

description:
Batch 1
CHFY043_S8_L012_R1_001

tag: strain

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: mutant

tag: treatment


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-D06P2-Run1_S44_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score


title: F_P21_normal_mesench_2_DC21_C6

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Car4+ capillaries

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: Gata3_Day3.1.pTEICM_5

tag: tissue

tag: lineage

tag: time point


title: F_P21_normal_mesench_1_DC21_M22

value: Late Car4- capillaries

tag: treatment


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-C06P2-Run1_S43_L002

value: labial gland

tag: sjnumber

tag: acr eular

tag: parotid infiltration phenotype

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: 97Q-Htt+RGFP109 cell 4

description:
Batch 1
CHFY042_S7_L012_R1_001

tag: strain

tag: developmental stage

tag: genotype

value: RGFP109 inhibitor treated


title: F_P7_normal_CD31_1_DC21_F13

tag: tissue

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Early Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes


title: Gata3_Day3.9.pTEICM_13

value: Blastoid

tag: lineage

value: Trophectoderm

value: polar

tag: time point

value: 3 days after stem cells seeded to form cell aggregates


title: 97Q-Htt+RGFP109 cell 3

description:
Batch 1
CHFY041_S6_L012_R1_001

value: striatum

tag: treatment


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-C05P2-Run1_S35_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: negative

tag: parotid infiltration phenotype

value: Group I

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Negative

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: F_P7_normal_CD31_1_DC21_G8

tag: tissue

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-C04P2-Run1_S27_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group IV

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Positive


title: 97Q-Htt+RGFP109 cell 2

description:
Batch 1
CHFY031_S13_L012_R1_001

tag: strain

tag: tissue

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: mutant

tag: treatment


title: Gata3_Day3.1.pTEICM_3

tag: lineage

value: Epiblast

tag: time point


title: F_P7_normal_CD31_1_DC21_C22

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Early Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: H9_OPC_VN_rep3

value: Oligodendrocytes progenitor cells

tag: cell line

value: H9 (hESC)

tag: ecm

value: VN


title: 97Q-Htt+RGFP109 cell 1

description:
Batch 1
CHFY030_S12_L012_R1_001

tag: strain

tag: tissue

value: striatum

tag: developmental stage

value: RGFP109 inhibitor treated


title: Gata3_Day3.1.pTEICM_2

value: Blastoid

tag: lineage

value: polar

value: 3 days after stem cells seeded to form cell aggregates


title: F_P21_normal_mesench_2_DC21_F21

value: distal lung

value: F

value: Late Car4- capillaries

tag: treatment


title: 25Q-Htt+RGFP109 cell 23

description:
Batch 3
CH_FY_FP_069_S69_R1_001

value: Newborn mice (P0-P1)

tag: genotype

value: wild type


title: F_P7_normal_CD31_1_DC21_I19

tag: sequencing run

tag: gender


title: Gata3_Day3.1.pTEICM_1

value: Epiblast

tag: time point


title: 25Q-Htt+RGFP109 cell 22

description:
Batch 3
CH_FY_FP_068_S68_R1_001


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-C03P2-Run1_S19_L001

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: negative

tag: parotid infiltration phenotype

value: Group I

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Negative

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: F_P21_normal_mesench_2_DC21_E17

tag: tissue

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Car4+ capillaries

tag: mousename

tag: coverage

tag: number of genes

tag: treatment

value: normal


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-C02P2-Run1_S11_L001

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

value: Group II

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-C07P2-Run1_S13_L002

tag: tissue

value: positive

value: Group IV

value: Positive

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: Day5.8.pTEICM_30

source_name: Blastocyst

value: Blastocyst

tag: lineage

value: Trophectoderm

value: polar

tag: time point

value: Embryonic day 5


title: Day5.8.mTE_1

value: mural


title: 25Q-Htt+RGFP109 cell 21

description:
Batch 3
CH_FY_FP_067_S67_R1_001

tag: strain

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: wild type

tag: treatment

value: RGFP109 inhibitor treated


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-C01P2-Run1_S3_L001

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

value: Group III

value: Negative

value: Female


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-B07P2-Run1_S12_L002

tag: tissue

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa


title: 25Q-Htt+RGFP109 cell 20

description:
Batch 3
CH_FY_FP_066_S66_R1_001


title: Gata3_Day3.1.pTEICM_4

value: Blastoid

value: Epiblast

value: 3 days after stem cells seeded to form cell aggregates


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-B06P2-Run1_S42_L002

value: positive

value: Group IV

value: Positive

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: F_P7_normal_CD31_1_DC21_D20

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Late Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: F_P7_normal_CD31_1_DC21_J1

tag: tissue

value: Nonproliferative embryonic EC

tag: treatment


title: Day5.3.mTE_4

value: Blastocyst

tag: lineage

value: Early Trophectoderm

value: mural

tag: time point

value: Embryonic day 5


title: 25Q-Htt+RGFP109 cell 19

description:
Batch 3
CH_FY_FP_065_S65_R1_001

tag: strain

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: wild type

value: RGFP109 inhibitor treated


title: Day5.8.pTEICM_24

value: Inner Cell Mass

value: polar


title: 25Q-Htt+RGFP109 cell 18

description:
Batch 3
CH_FY_FP_041_S41_R1_001


title: F_P7_normal_CD31_1_DC21_O2

tag: sequencing run

value: Arterial EC I


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-B05P2-Run1_S34_L002

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: negative

tag: parotid infiltration phenotype

value: Group I

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Negative

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: F_P7_normal_CD31_1_DC21_M9

tag: tissue

value: distal lung

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Late Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes

tag: treatment

value: normal


title: F_P7_normal_CD31_1_DC21_H9

tag: sequencing run

value: Early Car4- capillaries


title: 25Q-Htt+RGFP109 cell 17

description:
Batch 3
CH_FY_FP_040_S40_R1_001

tag: strain

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-B02P2-Run1_S10_L001

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group IV

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Positive

tag: rf

tag: esspri

tag: age

tag: Sex


title: 25Q-Htt+RGFP109 cell 16

description:
Batch 3
CH_FY_FP_039_S39_R1_001

tag: tissue

value: wild type

tag: treatment

value: RGFP109 inhibitor treated


title: Day5.8.pTEICM_21

value: Blastocyst

tag: lineage

value: Early Trophectoderm

value: polar

tag: time point

value: Embryonic day 5


title: Day5.8.pTEICM_22


title: F_P7_normal_CD31_1_DC21_O16

value: distal lung

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Proliferative EC

tag: mousename

tag: coverage

tag: number of genes


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-B01P2-Run1_S2_L001

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: negative

tag: parotid infiltration phenotype

value: Group II

tag: labial infiltration phenotype

value: Group I

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Negative

tag: rf

tag: esspri

value: Female

tag: essdai


title: 25Q-Htt+RGFP109 cell 15

description:
Batch 3
CH_FY_FP_037_S37_R1_001

tag: strain

tag: tissue

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

tag: treatment


title: 25Q-Htt+RGFP109 cell 14

description:
Batch 3
CH_FY_FP_036_S36_R1_001


title: Day5.8.pTEICM_20

tag: lineage

value: Inner Cell Mass

tag: time point


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-A08P2-Run1_S10_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

value: positive

value: MALT

value: Group IV

value: Positive

tag: age

tag: Sex


title: Day6.5.mTE_2

value: Blastocyst

value: Trophectoderm

value: mural

value: Embryonic day 6


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-A07P2-Run1_S11_L002

value: labial gland

tag: acr eular

tag: parotid infiltration phenotype

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45


title: F_P21_normal_mesench_2_DC21_P12

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Late Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: F_P7_normal_CD31_1_DC21_I6

tag: tissue

value: Car4+ capillaries

tag: treatment


title: Day5.8.pTEICM_19

tag: lineage

value: polar

tag: time point

value: Embryonic day 5


title: Day5.8.pTEICM_18


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-B04P2-Run1_S26_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: negative

tag: parotid infiltration phenotype

value: Group I

tag: labial infiltration phenotype

value: Group II

tag: ssa

value: Negative

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: 25Q-Htt+RGFP109 cell 12

description:
Batch 2
6410_S12_L008_R1_001

tag: strain

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: wild type

value: RGFP109 inhibitor treated


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-A06P2-Run1_S41_L002

tag: tissue

value: labial gland

value: positive

value: Group III

tag: parotid %cd45

tag: labial %cd45

value: Positive


title: Day5.8.pTEICM_23

value: Blastocyst

tag: lineage

value: Inner Cell Mass

tag: time point


title: F_P7_normal_CD31_1_DC21_P8

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Early Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes

tag: treatment

value: normal


title: 25Q-Htt+RGFP109 cell 11

description:
Batch 2
6409_S11_L008_R1_001

tag: strain

tag: developmental stage

tag: genotype


title: Day5.8.pTEICM_17

tag: tissue

value: Trophectoderm

value: polar

value: Embryonic day 5


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-B03P2-Run1_S18_L001

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

value: Group IV

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-A05P2-Run1_S33_L002


title: F_P7_normal_CD31_1_DC21_D2

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes

tag: treatment


title: F_P7_normal_CD31_1_DC21_K11

tag: tissue

value: Proliferative EC


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-A04P2-Run1_S25_L002

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: negative

tag: parotid infiltration phenotype

value: Group I

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Negative

tag: rf


title: 25Q-Htt+RGFP109 cell 10

description:
Batch 2
6408_S10_L008_R1_001

tag: strain

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: wild type

value: RGFP109 inhibitor treated


title: F_P21_normal_mesench_2_DC21_B5

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Late Car4- capillaries

tag: mousename

tag: coverage


title: 25Q-Htt+RGFP109 cell 9

description:
Batch 2
6407_S9_L008_R1_001

tag: tissue

tag: treatment


title: Day5.3.pTEICM_16

value: Blastocyst

tag: lineage

value: Early Trophectoderm

value: polar

tag: time point


title: 25Q-Htt+RGFP109 cell 13

description:
Batch 3
CH_FY_FP_035_S35_R1_001


title: 25Q-Htt+RGFP109 cell 8

description:
Batch 1
CHFY050_S15_L012_R1_001


title: Day5.3.pTEICM_18

value: Inner Cell Mass-Trophectoderm Transition

value: Embryonic day 5


title: Day5.3.pTEICM_15


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-A03P2-Run1_S17_L001

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group IV

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Positive

tag: rf

tag: esspri

tag: age

tag: Sex

value: Male

tag: essdai


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-A02P2-Run1_S9_L001

tag: tissue

value: negative

value: Group I

value: Negative

value: Female


title: 25Q-Htt+RGFP109 cell 7

description:
Batch 1
CHFY049_S14_L012_R1_001

tag: strain

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: wild type

tag: treatment

value: RGFP109 inhibitor treated


title: F_P7_normal_CD31_1_DC21_I3

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Early Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: Day5.3.pTEICM_14

value: Blastocyst

tag: lineage

value: Early Trophectoderm

value: polar

tag: time point

value: Embryonic day 5


title: F_P7_normal_CD31_1_DC21_F1

tag: tissue

value: Arterial EC I


title: 25Q-Htt+RGFP109 cell 6

description:
Batch 1
CHFY045_S10_L012_R1_001

tag: strain


title: F_P7_normal_CD31_1_DC21_O20

value: Proliferative EC


title: Day5.3.pTEICM_12

value: Inner Cell Mass-Trophectoderm Transition


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-H08P1-Run1_S8_L001

source_name: parotid gland

value: parotid gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group III

tag: labial infiltration phenotype

value: Group IV

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Negative

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: F_P7_normal_mesench_2_DC20_H1

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes

tag: treatment


title: 25Q-Htt+RGFP109 cell 5

description:
Batch 1
CHFY029_S11_L012_R1_001

tag: strain

tag: tissue

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: wild type

value: RGFP109 inhibitor treated


title: Day5.3.pTEICM_11

value: Blastocyst

tag: lineage

value: polar

tag: time point


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-H07P1-Run1_S48_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Positive

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: 25Q-Htt+RGFP109 cell 4

description:
Batch 1
CHFY028_S10_L012_R1_001

tag: strain

tag: tissue

tag: developmental stage

tag: genotype

tag: treatment


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-H06P1-Run1_S40_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

value: negative

value: Group I


title: Day5.8.pTEICM_16

tag: lineage

value: Inner Cell Mass

tag: time point

value: Embryonic day 5


title: F_P7_normal_mesench_2_DC20_H2

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Early Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: 25Q-Htt+RGFP109 cell 3

description:
Batch 1
CHFY027_S9_L012_R1_001

tag: strain

tag: tissue

tag: developmental stage

tag: genotype


title: Day5.8.pTEICM_15


title: 25Q-Htt+RGFP109 cell 2

description:
Batch 1
CHFY026_S8_L012_R1_001

tag: treatment


title: Day5.8.pTEICM_14

tag: lineage


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-H04P1-Run1_S24_L001

value: parotid gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group III

tag: labial infiltration phenotype

value: Group IV

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Negative

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: F_P7_normal_mesench_1_DC20_H22

tag: tissue

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Arterial EC I

tag: mousename

tag: coverage

tag: number of genes


title: F_P7_normal_mesench_2_DC20_P16

value: Late Car4- capillaries

tag: treatment


title: GRCh37ERCC-ensembl75-genes-N-20180730MN1-A01P2-Run1_S1_L001

value: labial gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf


title: F_P7_normal_mesench_1_DC20_P5

tag: tissue

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint


title: 97Q-Htt cell 26

description:
Batch 3
CH_FY_FP_070_S70_R1_001

tag: strain

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: mutant

tag: treatment

value: vehicle treated


title: 25Q-Htt+RGFP109 cell 1

description:
Batch 1
CHFY025_S7_L012_R1_001

value: wild type

value: RGFP109 inhibitor treated


title: Day5.8.pTEICM_13

value: Blastocyst

tag: lineage

value: Inner Cell Mass

value: polar

tag: time point

value: Embryonic day 5


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-H01P1-Run1_S8_L001

value: parotid gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: negative

tag: parotid infiltration phenotype

value: Group II

tag: labial infiltration phenotype

value: Group I

value: Negative

tag: esspri

tag: age

tag: Sex

tag: essdai


title: F_P7_normal_mesench_1_DC20_M4

tag: tissue

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Proliferative EC

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: Day5.8.pTEICM_12

tag: lineage

tag: time point


title: 97Q-Htt cell 25

description:
Batch 3
CH_FY_FP_056_S56_R1_001

tag: strain

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: mutant

tag: treatment

value: vehicle treated


title: Day5.8.pTEICM_11

tag: tissue

value: Blastocyst

value: Inner Cell Mass


title: F_P7_normal_mesench_1_DC20_F22

tag: sequencing run

value: Early Car4- capillaries


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-G08P1-Run1_S7_L001

value: parotid gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group IV

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Positive

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: 97Q-Htt cell 24

description:
Batch 3
CH_FY_FP_055_S55_R1_001

tag: strain

tag: developmental stage

tag: genotype

tag: treatment


title: F_P7_normal_mesench_1_DC20_K17

tag: tissue

value: distal lung

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Venous EC

tag: mousename

tag: coverage

tag: number of genes


title: Day5.8.pTEICM_10

tag: lineage

value: polar

tag: time point

value: Embryonic day 5


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-G07P1-Run1_S47_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: F_P7_normal_mesench_2_DC20_I11

tag: tissue

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes

tag: treatment

value: normal


title: 97Q-Htt cell 23

description:
Batch 3
CH_FY_FP_054_S54_R1_001

tag: strain

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: mutant


title: Day5.8.pTEICM_9

value: Blastocyst

tag: lineage

value: Inner Cell Mass

tag: time point


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-G06P1-Run1_S39_L002

tag: tissue

value: parotid gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: F_P7_normal_mesench_1_DC20_J20

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Early Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes

tag: treatment


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-H05P1-Run1_S32_L002

tag: tissue

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group IV

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa


title: 97Q-Htt cell 22

description:
Batch 3
CH_FY_FP_053_S53_R1_001

tag: strain

tag: developmental stage

tag: genotype

value: vehicle treated


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-H02P1-Run1_S16_L001

value: Group III

value: Negative

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: F_P7_normal_mesench_2_DC20_B5

tag: tissue

value: distal lung

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Late Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes

tag: treatment


title: Day5.3.pTEICM_10

tag: lineage

value: Inner Cell Mass-Trophectoderm Transition

value: polar

tag: time point

value: Embryonic day 5


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-G05P1-Run1_S31_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Positive

tag: rf

tag: esspri

tag: age


title: 97Q-Htt cell 21

description:
Batch 3
CH_FY_FP_052_S52_R1_001

tag: strain

tag: tissue

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: mutant


title: Day5.3.pTEICM_9

value: Blastocyst

tag: lineage

tag: time point


title: F_P7_normal_mesench_2_DC20_G9

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Venous EC

tag: mousename

tag: coverage

tag: number of genes

tag: treatment

value: normal


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-G02P1-Run1_S15_L001

value: parotid gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group III

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: F_P7_normal_mesench_2_DC20_N5

tag: tissue

value: distal lung

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Proliferative EC

tag: mousename

tag: coverage


title: 97Q-Htt cell 19

description:
Batch 3
CH_FY_FP_050_S50_R1_001

tag: strain

tag: developmental stage

tag: genotype

tag: treatment

value: vehicle treated


title: 97Q-Htt cell 20

description:
Batch 3
CH_FY_FP_051_S51_R1_001


title: Day5.3.pTEICM_7

tag: lineage

value: Inner Cell Mass-Trophectoderm Transition

value: polar

tag: time point


title: F_P7_normal_mesench_1_DC20_C9

value: Early Car4- capillaries

tag: number of genes


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-G01P1-Run1_S7_L001

tag: tissue

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

value: Group IV

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Negative

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: 97Q-Htt cell 18

description:
Batch 3
CH_FY_FP_029_S29_R1_001

tag: strain

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: mutant

tag: treatment


title: 97Q-Htt cell 17

description:
Batch 3
CH_FY_FP_028_S28_R1_001

tag: tissue


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-F08P1-Run1_S6_L001

tag: sjnumber

tag: parotid focus score

tag: labial focus score

value: Positive


title: F_P7_normal_mesench_1_DC20_O23

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Car4+ capillaries

tag: mousename

tag: coverage

tag: number of genes

value: normal


title: Day5.8.pTEICM_7

value: Blastocyst

tag: lineage

value: Inner Cell Mass

tag: time point

value: Embryonic day 5


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-F07P1-Run1_S46_L002

value: parotid gland

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group III

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: Day5.8.pTEICM_8

tag: tissue

value: Early Trophectoderm

value: polar


title: Day5.3.pTEICM_8

value: Inner Cell Mass-Trophectoderm Transition


title: 97Q-Htt cell 16

description:
Batch 3
CH_FY_FP_027_S27_R1_001

tag: strain

value: striatum

tag: developmental stage

tag: genotype

tag: treatment

value: vehicle treated


title: F_P7_normal_mesench_2_DC20_F4

value: distal lung

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Proliferative EC

tag: mousename

tag: coverage

tag: number of genes


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-F06P1-Run1_S38_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: negative

tag: parotid infiltration phenotype

value: Group I

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Negative

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female


title: Day5.8.pTEICM_6

tag: tissue

value: Blastocyst

tag: lineage

tag: time point


title: F_P7_normal_mesench_1_DC20_P4

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes

tag: treatment

value: normal


title: 97Q-Htt cell 15

description:
Batch 3
CH_FY_FP_026_S26_R1_001

tag: strain

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: mutant


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-G04P1-Run1_S23_L001

tag: tissue

value: parotid gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group III

tag: labial infiltration phenotype

value: Group IV

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Positive

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: F_P7_normal_mesench_1_DC20_B7

value: distal lung

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Car4+ capillaries

tag: mousename

tag: coverage

tag: number of genes

tag: treatment


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-F05P1-Run1_S30_L002

tag: tissue

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-F04P1-Run1_S22_L001

value: negative

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: F_P7_normal_mesench_1_DC20_H18

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes


title: Day5.8.pTEICM_5

tag: tissue

tag: lineage

value: Inner Cell Mass

value: polar

tag: time point

value: Embryonic day 5


title: 97Q-Htt cell 13

description:
Batch 3
CH_FY_FP_024_S24_R1_001

tag: strain

value: striatum

tag: developmental stage

tag: genotype

tag: treatment

value: vehicle treated


title: Day5.8.pTEICM_4

value: Blastocyst


title: Day5.8.pTEICM_2


title: F_P7_normal_mesench_1_DC20_J4

tag: sequencing run

value: F

value: endothelial

value: Late Car4- capillaries

value: normal


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-F02P1-Run1_S14_L001

value: parotid gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

value: Group I

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Negative

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: 97Q-Htt cell 14

description:
Batch 3
CH_FY_FP_025_S25_R1_001

tag: strain

tag: tissue

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: mutant


title: 97Q-Htt cell 12

description:
Batch 3
CH_FY_FP_023_S23_R1_001

tag: treatment


title: F_P7_normal_mesench_1_DC20_P6

value: distal lung

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Car4+ capillaries

tag: mousename

tag: coverage

tag: number of genes


title: 97Q-Htt cell 11

description:
Batch 2
6406_S8_L008_R1_001


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-F01P1-Run1_S6_L001

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group IV

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Positive

tag: rf

tag: esspri

tag: age

tag: Sex


title: Day5.8.pTEICM_1

tag: tissue

tag: lineage

value: Inner Cell Mass

value: polar

tag: time point

value: Embryonic day 5


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-E08P1-Run1_S5_L001

tag: essdai


title: Day5.2.mTE_5

value: Blastocyst

value: Early Trophectoderm

value: mural


title: F_P7_normal_mesench_2_DC20_K9

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes

tag: treatment

value: normal


title: 97Q-Htt cell 10

description:
Batch 2
6405_S7_L008_R1_001

tag: strain

value: striatum

tag: developmental stage

tag: genotype

value: vehicle treated


title: Day5.5.mTE_5

tag: tissue

tag: lineage

value: Inner Cell Mass-Trophectoderm Transition


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-E07P1-Run1_S45_L002

value: parotid gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: negative

tag: parotid infiltration phenotype

value: Group I

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Negative

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female

tag: essdai


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-E06P1-Run1_S37_L002

value: positive

value: Group IV

value: Positive


title: Day5.5.mTE_4

value: Blastocyst

tag: time point

value: Embryonic day 5


title: F_P7_normal_mesench_2_DC20_K6

tag: tissue

value: distal lung

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Early Car4- capillaries

tag: mousename

tag: coverage

tag: number of genes

tag: treatment


title: Mouse_MT_MFlp_10

city: Detroit

first: Kay-Uwe

last: Wagner

state: MI

address: 421 East Canfield, EL01TM

department: Department of Oncology

institute: Barbara Ann Karmanos Cancer Institute  Wayne State University School of Medicine

data_processing:
Quality of the sequence reads was assured with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Standard parameters, as described by the packge user guide, were used.
Paired end sequences were aligned to the mm10 reference genome with the align function of Rsubread (Version 2.2.0+). Standard parameters, as described by the packge user guide, were used.
Aligned reads were quantified through featureCounts (part of the Rsubread package). Standard parameters, as described by the packge user guide, were used. The inbuilt mm10 reference genome was used.
Reads were subsequently filtered [genes with 0 counts per million (cpm) across all samples were filtered out], normalized, anotated and differential expression analysis on isogneic cell lines was performed with edgeR ( version 3.14.0). Differential expression alanlysis is based on paired samples. Gene count tables provided are in cpm and are based on the processed data. Standard parameters, as described by the packge user guide, were used.
Bam files of the primary mammary tumors, resulting from Rsubread alignment, were sorted and indexed with samtools (version 1.10). The sorted bam file was subsequently converted to a bigwig file using the bamCoverage tool from the deepTools package (version 2.0). Standard parameters, as described by the packge user guide, were used.
Genome_build: mm10
Supplementary_files_format_and_content: The bigWig files contain normalized reads that can be viewed with the Broad Institutes genome browser. The csv files contain a processed matrix with the gene names, entrez id and the coressponding gene counts (cpm) for the samples. The counts are filtered, normalized, and annotated with gene name and entrez id).

source_name: Mammary Tumor

growth_protocol: Mammary cancer cells were derived from enzymatically dissociated mammary tumors and cultured in Dulbecco-modified Eagle medium (DMEM/F12) supplemented with insulin, epidermal growth factor, tetracycline-free fetal bovine serum, penicillin/streptomycin, and gentamicin.

extract_protocol:
Total RNA was extracted from fresh or flash-frozen mammary tumors or cultured cancer cells using the RNeasy Mini Kit (QIAGEN). The protocol, provided by QIAGEN, was followed to extract the total RNA. The concentration of the RNA was determined on a NanoDrop spectrophotometer, and the integrity of the RNA was validated using gel electrophoresis. Quality and quantity of the total RNA was re-confirmed by Novogene. Only high quality RNA was used for library prepration.
Libreary construction was performed by Novogene (After the QC procedures, mRNA is enriched using oligo(dT) beads. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment. The quality of the library was confirmed via these three steps: (1) Qubit 2.0: tests the library concentration preliminarily. (2) Agilent 2100: tests the insert size. (3) Q-PCR: quantifies the library effective concentration precisely.

treatment_protocol: Primary mammary tumors and off_dox cell lines were untreated. For doxycycline (Dox) treatment, the cells were split into 10 cm cell culture dishes, and 20 µg Dox per 10ml of media was added to the cells at 0 hours. Cells were washed with 1x PBS and Dox-containing media was replaced after 48 hours. After 72 or 96 hours, the cells were washed and collected

value: Primary mammary tumor

value: Untreated


title: 97Q-Htt cell 8

description:
Batch 1
CHFY048_S13_L012_R1_001

tag: strain

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: mutant


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-E05P1-Run1_S29_L002

value: parotid gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

value: Group III

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: 97Q-Htt cell 9

description:
Batch 2
6404_S6_L008_R1_001

tag: strain

tag: tissue

tag: treatment

value: vehicle treated


title: Mouse_MT_MFlp_9


title: Day5.8.pTEICM_3

tag: lineage

value: Trophectoderm

value: polar

tag: time point


title: 97Q-Htt cell 7

description:
Batch 1
CHFY047_S12_L012_R1_001

tag: developmental stage

tag: genotype


title: Day5.5.mTE_3

value: Inner Cell Mass-Trophectoderm Transition

value: mural


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-E04P1-Run1_S21_L001

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

value: Group IV

value: Positive

value: Female


title: Day5.5.mTE_2

value: Blastocyst

value: Embryonic day 5


title: Mouse_MT_MFlp_8

value: Primary mammary tumor

value: Untreated


title: 97Q-Htt cell 6

description:
Batch 1
CHFY040_S5_L012_R1_001

value: striatum

value: Newborn mice (P0-P1)


title: 97Q-Htt cell 5

description:
Batch 1
CHFY039_S4_L012_R1_001

value: mutant


title: Day5.5.mTE_1


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-E01P1-Run1_S5_L001

value: parotid gland

value: Group III

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

tag: rf


title: 97Q-Htt cell 4

description:
Batch 1
CHFY035_S17_L012_R1_001

tag: strain

value: vehicle treated


title: Day5.5.pTEICM_9

tag: tissue

value: polar


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-D07P1-Run1_S44_L002

value: negative

value: Group I

value: Negative

tag: esspri

tag: age

tag: Sex

tag: essdai


title: Day5.5.pTEICM_8

tag: lineage

value: Inner Cell Mass-Trophectoderm Transition

tag: time point


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-D06P1-Run1_S36_L002

tag: sjnumber

tag: parotid focus score


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-D08P1-Run1_S4_L001

tag: labial focus score

tag: acr eular

value: lymph node present

value: Positive


title: 97Q-Htt cell 2

description:
Batch 1
CHFY023_S5_L012_R1_001

tag: developmental stage

tag: genotype

tag: treatment


title: 97Q-Htt cell 3

description:
Batch 1
CHFY024_S6_L012_R1_001


title: Mouse_MT_MFlp_5


title: Mouse_MT_MFlp_4


title: Day5.5.pTEICM_7

value: Blastocyst


title: 97Q-Htt cell 1

description:
Batch 1
CHFY022_S4_L012_R1_001


title: Mouse_MT_MFlp_3


title: Day5.2.pTEICM_4

value: Early Trophectoderm

value: Embryonic day 5


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-D05P1-Run1_S28_L002

tag: parotid infiltration phenotype

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

tag: ssa

value: Female


title: Day5.5.pTEICM_6

tag: tissue


title: Mouse_MT_MFlp_1

value: Primary mammary tumor

value: Untreated


title: Mouse_MT_MFlp_2


title: 25Q-Htt cell 28

description:
Batch 3
CH_FY_FP_048_S48_R1_001

tag: strain

value: striatum

value: Newborn mice (P0-P1)

value: wild type


title: Cell_line_3_on_dox

tag: cell line

value: Mammary tumor derived cell lines

value: Treated with Doxycycline


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-D04P1-Run1_S20_L001

value: parotid gland

value: positive

value: Group IV

tag: rf

tag: esspri

tag: age

tag: Sex

tag: essdai


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-E02P1-Run1_S13_L001

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: Group III

value: Negative


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-D01P1-Run1_S4_L001

value: negative

tag: parotid infiltration phenotype

value: Group I


title: Mouse_MT_MFlp_6

tag: treatment


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-D02P1-Run1_S12_L001

tag: labial infiltration phenotype

value: sclerosing sialoadenitis

tag: parotid %cd45


title: 25Q-Htt cell 27

description:
Batch 3
CH_FY_FP_047_S47_R1_001

tag: developmental stage

tag: genotype

value: vehicle treated


title: Day5.5.pTEICM_5

tag: tissue

value: Blastocyst

tag: lineage

value: Inner Cell Mass-Trophectoderm Transition

value: polar

tag: time point

value: Embryonic day 5


title: Mouse_MT_MFlp_7

value: Primary mammary tumor

value: Untreated


title: 25Q-Htt cell 29

description:
Batch 3
CH_FY_FP_049_S49_R1_001

tag: strain

value: striatum

value: Newborn mice (P0-P1)

value: wild type


title: 25Q-Htt cell 26

description:
Batch 3
CH_FY_FP_046_S46_R1_001


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-C08P1-Run1_S3_L001

value: parotid gland

value: positive

tag: labial %cd45

tag: ssa

value: Positive

tag: rf

tag: esspri

tag: age

value: Female


title: Cell_line_3_off_dox

tag: cell line

value: Mammary tumor derived cell lines


title: 25Q-Htt cell 25

description:
Batch 3
CH_FY_FP_045_S45_R1_001


title: Day5.5.pTEICM_3


title: Day5.5.pTEICM_2


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-C07P1-Run1_S43_L002

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: negative

value: Group I

value: Negative

tag: Sex

tag: essdai


title: Cell_line_2_on_dox

tag: treatment

value: Treated with Doxycycline


title: Day5.5.pTEICM_1

tag: tissue

value: Blastocyst

value: Inner Cell Mass-Trophectoderm Transition


title: Cell_line_1_on_dox


title: Cell_line_2_off_dox


title: 25Q-Htt cell 24

description:
Batch 3
CH_FY_FP_044_S44_R1_001

tag: developmental stage

tag: genotype

value: vehicle treated


title: 25Q-Htt cell 23

description:
Batch 3
CH_FY_FP_043_S43_R1_001

tag: strain


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-C05P1-Run1_S27_L002

tag: parotid infiltration phenotype

value: lymph node present

tag: labial infiltration phenotype

value: Group IV

tag: parotid %cd45

tag: labial %cd45


title: Day5.4.mTE_10

tag: lineage

value: Early Trophectoderm

value: mural

tag: time point

value: Embryonic day 5


title: Cell_line_1_off_dox

tag: cell line

value: Untreated


title: 25Q-Htt cell 22

description:
Batch 3
CH_FY_FP_042_S42_R1_001

value: striatum

value: Newborn mice (P0-P1)

value: wild type


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-C04P1-Run1_S19_L001

value: parotid gland

tag: sjnumber

tag: parotid focus score

value: positive

value: Group III

tag: ssa

value: Positive

tag: rf

tag: esspri

tag: age

value: Female


title: 25Q-Htt cell 21

description:
Batch 3
CH_FY_FP_021_S21_R1_001

tag: tissue

tag: treatment


title: Day5.5.pTEICM_4

value: Blastocyst

value: polar


title: Day5.4.mTE_9


title: Day5.4.mTE_6


title: NIH3T3_mNG_rep1

city: Rehovot

first: Anna

last: Uzonyi

address: 234 Herzl street

department: Department of Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: RNA amplicon

data_processing:
Fastq files of amplicon libraries were processed and analysed using a custom R script. During the filtering process, reads that don’t start or end at the proper position, don’t contain one of the planned barcodes or have non-A or G nucleotides at A positions were removed. Single-reads were assembled by truncating and matching read 1 and 2. Based on the barcodes, information about the variable strand was matched to each read. Editing percentage was determined as G/(A+G) at a given position. For the positive and negative control constructs sequenced as total, poly-A selected RNA, A to G mismatch rate was quantified with Jacusa (Piechotta et al., 2017).
Supplementary_files_format_and_content: Compressed folder containing csv and txt files. 24 file contains average editing at every position and single construct for the first arm samples (1-24). 2 files contain mismatch quantification of B2 and mNG positive control construct. 2 files contain merged, filtered reads of the variable strand libraries.

source_name: mouse cell line

growth_protocol: HEK293T, MCF7, A549 and NIH3T3 cells were cultured in DMEM (Gibco) supplemented with 10% FBS and 1% Penicillin and Streptomycin.

extract_protocol:
RNA was extracted with NucleoZOL (Macherey-Nagel)
RNA was poly-A selected with oligo dT-beads (Dynabeads® mRNA DIRECT™ Kit life tech). For the control constructs, poly-A selected libraries were prepared. Poly-A RNA from oligo-pool transfected cells was reverse transcribed to obtain the constant or variable fragments of the constructs with the matching 8 nt barcode. PCR amplicons of these fragments were generated.

treatment_protocol: 2 million cells were seeded on a 10 cm plate 24 hours prior to transfection. 5 µg DNA was transfected with PolyJet reagent (SignaGen Laboratories). Cells were harvested 24 hours after transfection. For the IFN-stimulated samples, HEK293T cells were seeded on a 10 cm plate and transfected with the plasmid construct as before. At the same time, 650 U/ml IFN-α (pbl assay science) was added. For the Adar knockdown samples, HEK293T cells were subjected to two rounds of Adar siRNA (Ambion #4427038) treatment using the Lipofectamine RNAiMAX (Thermo Fisher Scientific) reagent, and 15 pmol siRNA in a 6-well format, with 24 h interval. Cells were reseeded on 10 cm plates and transfected with the plasmid as before.

value: no treatment

tag: condition

value: mNG


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-C01P1-Run1_S3_L001

tag: labial focus score

tag: acr eular

value: Group IV

value: Negative

tag: Sex

tag: essdai


title: NIH3T3_mNG_rep2

description: RNA amplicon


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-C02P1-Run1_S11_L001

value: negative

tag: parotid infiltration phenotype

value: Group II

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45


title: Day5.4.mTE_5

tag: lineage

value: Early Trophectoderm

value: mural

tag: time point

value: Embryonic day 5


title: 25Q-Htt cell 19

description:
Batch 3
CH_FY_FP_019_S19_R1_001

tag: strain

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: wild type

value: vehicle treated


title: 25Q-Htt cell 20

description:
Batch 3
CH_FY_FP_020_S20_R1_001


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-C06P1-Run1_S35_L002

value: parotid gland

tag: sjnumber

tag: parotid focus score

value: positive

value: lymph node present

tag: ssa

value: Positive

tag: rf

tag: esspri

tag: age


title: Day5.4.mTE_4

tag: tissue

value: Blastocyst


title: Day5.4.mTE_3


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-B08P1-Run1_S2_L001

tag: labial focus score

tag: acr eular

tag: Sex

value: Female

tag: essdai


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-B07P1-Run1_S42_L002

tag: parotid infiltration phenotype

value: Group IV

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45


title: 25Q-Htt cell 18

description:
Batch 3
CH_FY_FP_018_S18_R1_001

tag: strain

tag: developmental stage

tag: treatment


title: Day5.4.mTE_2

tag: lineage

tag: time point


title: NIH3T3_B2_rep1

description: RNA amplicon

tag: cell line

value: no treatment

tag: condition


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-B06P1-Run1_S34_L002

tag: sjnumber

tag: parotid focus score

value: Group III

tag: ssa

tag: rf

value: Negative

tag: esspri

tag: age


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-B05P1-Run1_S26_L002

tag: tissue

tag: labial focus score

tag: acr eular

value: negative

tag: parotid infiltration phenotype

value: Group I

tag: Sex

tag: essdai


title: 25Q-Htt cell 17

description:
Batch 3
CH_FY_FP_017_S17_R1_001

tag: strain

tag: developmental stage

tag: genotype

tag: treatment


title: 25Q-Htt cell 16

description:
Batch 3
CH_FY_FP_016_S16_R1_001


title: Day5.4.mTE_1

tag: lineage

value: Early Trophectoderm

value: mural

tag: time point

value: Embryonic day 5


title: Day5.4.pTEICM_8

value: Inner Cell Mass-Trophectoderm Transition

value: polar


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-B04P1-Run1_S18_L001

value: parotid gland

tag: sjnumber

tag: parotid focus score

value: unclassified

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45


title: CW2.Gal-9-Treated.Xenograft.tissue4

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: microRNA

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: The human colon cancer cell lines CACO-2, CW-2, COLO-320, LoVo, and the colorectal cancer cell line WiDr were obtained from the Japanese Cancer Research Resources Bank (Tokyo, Japan). All the cell lines were certified by STRA and mycoplasma testing has been done for cell lines used in our experiments. The cells were cultured in RPMI-1640 (Gibco Invitrogen, Carlsbad, CA, USA) supplemented with 10% heat-inactivated FBS, and penicillin-streptomycin (100 μg/ml; Invitrogen) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: RNA samples were extracted from serum using 3D-Gene extraction reagent from liquid sample(Toray Industries Inc., Tokyo, Japan).

treatment_protocol: After incubation for 24 h, cells were treated with 0.01, 0.03, 0.1, and 0.3 μM of Gal-9 added to the culture medium and subsequently cultured for an additional 48 h.

tag: sample type

value: Colon cancer cell xenograft tumor

value: 30 ug galectin-9


title: NIH3T3_B2_rep2

description: RNA amplicon

tag: cell line

tag: condition


title: Day5.4.pTEICM_7

tag: tissue

value: Blastocyst

value: Inner Cell Mass


title: CW2.Control.Xenograft.tissue4

description: microRNA

value: control


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-B02P1-Run1_S10_L001

tag: labial focus score

tag: acr eular

value: positive

tag: parotid infiltration phenotype

tag: ssa

value: Positive

tag: rf

tag: esspri

tag: age

tag: Sex

value: Female


title: Day5.4.pTEICM_6

tag: lineage

tag: time point


title: CW2.Control.Xenograft.tissue3

description: microRNA

tag: treatment


title: CW2.Gal-9-Treated.Xenograft.tissue3

description: microRNA


title: 25Q-Htt cell 13

description:
Batch 2
6401_S3_L008_R1_001

tag: strain

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: wild type

value: vehicle treated


title: 25Q-Htt cell 12

description:
Batch 2
6400_S2_L008_R1_001


title: Day5.4.pTEICM_5

value: Embryonic day 5


title: Day5.4.pTEICM_4


title: CW2.Gal-9-Treated.Xenograft.tissue2

description: microRNA

tag: sample type


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-A08P1-Run1_S1_L001

tag: sjnumber

tag: parotid focus score

value: negative

value: Group I

tag: labial infiltration phenotype

tag: parotid %cd45

tag: labial %cd45

value: Negative

value: Male

tag: essdai


title: CW2.Control.Xenograft.tissue2

description: microRNA

value: Colon cancer cell xenograft tumor


title: 25Q-Htt cell 11

description:
Batch 2
6399_S1_L008_R1_001

tag: tissue


title: 25Q-Htt cell 10

description:
Batch 1
CHFY046_S11_L012_R1_001


title: 25Q-Htt cell 15

description:
Batch 3
CH_FY_FP_015_S15_R1_001


title: CW2.Gal-9-Treated.Xenograft.tissue1

description: microRNA

value: 30 ug galectin-9


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-A06P1-Run1_S33_L002

value: parotid gland

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

value: Group IV

tag: ssa

tag: rf

tag: esspri


title: 25Q-Htt cell 14

description:
Batch 2
6402_S4_L008_R1_001

tag: strain

tag: treatment


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-A05P1-Run1_S25_L002

value: Group II

tag: age

tag: Sex


title: CW2.Control.Xenograft.tissue1

description: microRNA

tag: sample type

value: control


title: Day5.4.pTEICM_2

value: Blastocyst

tag: lineage

value: Inner Cell Mass

value: polar

tag: time point


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-B01P1-Run1_S2_L001

tag: sjnumber

tag: parotid focus score

value: positive

tag: labial infiltration phenotype

tag: parotid %cd45

value: Positive

value: Female


title: Day7.6.pTEICM_18

tag: tissue

value: Trophectoderm

value: Embryonic day 7


title: Caco-2.Gal-9-Treated.Xenograft.tissue8

description: microRNA

value: 90ug of galectin-9


title: Caco-2.Control.Xenograft.tissue8

description: microRNA


title: 25Q-Htt cell 8

description:
Batch 1
CHFY037_S2_L012_R1_001

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

tag: genotype

value: wild type

value: vehicle treated


title: 25Q-Htt cell 7

description:
Batch 1
CHFY036_S1_L012_R1_001


title: Day7.6.pTEICM_17


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-A03P1-Run1_S9_L001

value: parotid gland

tag: labial focus score

tag: acr eular

tag: parotid infiltration phenotype

value: Group III

tag: labial %cd45

tag: ssa

value: Negative

tag: essdai


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-A07P1-Run1_S41_L002

value: Group IV

tag: rf

tag: esspri

tag: age

tag: Sex


title: 25Q-Htt cell 6

description:
Batch 1
CHFY034_S16_L012_R1_001

tag: strain

tag: treatment


title: Day5.4.pTEICM_3

value: Blastocyst

tag: lineage

tag: time point

value: Embryonic day 5


title: 25Q-Htt cell 9

description:
Batch 1
CHFY038_S3_L012_R1_001

tag: tissue


title: Caco-2.Control.Xenograft.tissue7

description: microRNA

tag: sample type

value: Colon cancer cell xenograft tumor

value: control


title: Caco-2.Gal-9-Treated.Xenograft.tissue7

description: microRNA


title: 25Q-Htt cell 5

description:
Batch 1
CHFY033_S15_L012_R1_001

tag: developmental stage

tag: genotype


title: Day7.6.pTEICM_14

value: polar


title: 25Q-Htt cell 4

description:
Batch 1
CHFY032_S14_L012_R1_001


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-A02P1-Run1_S9_L001

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

value: positive

tag: labial infiltration phenotype

tag: parotid %cd45

value: Positive

value: Female


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-A01P1-Run1_S1_L001

value: negative

tag: parotid infiltration phenotype

value: Group I

tag: labial %cd45

tag: ssa

tag: rf

tag: esspri

tag: essdai


title: s77a_3

city: Hangzhou

first: Huajun

last: Zhao

address: 548 Binwen Road

country: China

institute: Zhejiang Chinese Medical University

data_processing:
Quality control. Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010):  Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Genome_build: miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures.
Supplementary_files_format_and_content: readcount of different miRNA readcount in each sample replicate

source_name: MDA-MB-231_transfected with RARαS77A

extract_protocol:
RNA was extracted with Trizol reagent. RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer  (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: cell line

tag: cell type

value: triple negative breast cancer cell

tag: genotype/variation

value: transfected with RARalphaS77A


title: 25Q-Htt cell 3

description:
Batch 1
CHFY021_S3_L012_R1_001

tag: strain

tag: tissue

value: striatum

tag: developmental stage

value: Newborn mice (P0-P1)

value: wild type

tag: treatment

value: vehicle treated


title: Day7.6.pTEICM_13

tag: lineage

value: Epiblast

tag: time point

value: Embryonic day 7


title: GRCh37ERCC-ensembl75-genes-N-20180723MN1-A04P1-Run1_S17_L001

value: parotid gland

tag: sjnumber

tag: parotid focus score

tag: labial focus score

tag: acr eular

tag: labial infiltration phenotype

value: Negative

tag: age

tag: Sex


title: Caco-2.Gal-9-Treated.Xenograft.tissue6

description: microRNA

tag: sample type

value: Colon cancer cell xenograft tumor

value: 90ug of galectin-9


title: Caco-2.Control.Xenograft.tissue6

description: microRNA

value: control


title: 25Q-Htt cell 2

description:
Batch 1
CHFY020_S2_L012_R1_001

tag: genotype


title: s77a_2

tag: cell line

tag: cell type


title: Day7.6.pTEICM_12.1

value: Blastocyst

value: Trophectoderm

value: polar


title: s77a_1

tag: genotype/variation


title: Day7.6.pTEICM_16

tag: tissue


title: 25Q-Htt cell 1

description:
Batch 1
CHFY019_S1_L012_R1_001

tag: strain

tag: developmental stage


title: Caco-2.Control.Xenograft.tissue5

description: microRNA

tag: treatment


title: Caco-2.Gal-9-Treated.Xenograft.tissue5

description: microRNA


title: Day7.6.pTEICM_15

tag: lineage

tag: time point


title: con_3

value: non-transfected


title: Caco-2.Gal-9-Treated.Xenograft.tissue4

description: microRNA