title: LacQ140I 12 months Striatum female mRNA rep3

description:
Q140_12M_ALW_STR_222_F_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I 12 months Striatum female mRNA rep4

status: Public on Oct 14 2022

type: SRA

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

country: USA

institute: CHDI

description:
Q140_12M_ALW_STR_223_F_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt

library_source: transcriptomic

data_processing:
Libraries for RNA-seq were sequenced using an Illumina NovaSeq6000.
Sequenced reads were trimmed for adaptor sequence using Omitsoft aligner and then mapped to mouse genome Mouse.B38 (GeneModel Ensembl.R94).
a) Trimmed low-quality bases from the reads, aligned reads to the mouse genome GRCm38 with OmicSoft Aligner and quantitated the reads per gene with OmicSoft Quantitate. b) Fragments Per Kilobase of exon model per million reads mapped were calculated with OmicSoft. c) Generated the QC plots (PCA, Volcano, Bar charts of QC metrics).
Genome_build: Mouse.B38 (GeneModel Ensembl.R94)
Supplementary_files_format_and_content: Tab-delimited text files include Count values for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: Striatum

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen mRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: Corpus Striatum

tag: genotype

value: Hdh(LacO-140Q/+):beta-actin-LacIR tg

tag: strain/background

tag: age

value: 12 months

tag: Sex

value: Female

tag: treatment

tag: treatment initiation

tag: treatment withdrawal

tag: batch


title: LacQ140I 6 months Striatum female mRNA rep5

description:
Q140_6M_ALW_STR_68_F_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt

source_name: Right Striatum

value: 6 months


title: LacQ140I 12 months Striatum male mRNA rep1

description:
Q140_12M_ALW_STR_300_M_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt

value: Male


title: LacQ140I 12 months Striatum female mRNA rep2

description:
Q140_12M_ALW_STR_221_F_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I 12 months Striatum female mRNA rep1

description:
Q140_12M_ALW_STR_220_F_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I 12 months Cortex male mRNA rep4

description:
Q140_12M_ALW_COR_303_M_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt

source_name: Cortex

value: Cerebral Cortex


title: LacQ140I 12 months Cortex male mRNA rep5

description:
Q140_12M_ALW_COR_304_M_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I 12 months Cortex male mRNA rep3

description:
Q140_12M_ALW_COR_302_M_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I 12 months Cortex male mRNA rep2

description:
Q140_12M_ALW_COR_301_M_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I 6 months Cortex male mRNA rep1

description:
Q140_6M_ALW_COR_30_M_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt

source_name: Right Cortex


title: LacQ140I 12 months Cortex male mRNA rep1

description:
Q140_12M_ALW_COR_300_M_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I 12 months Cortex female mRNA rep5

description:
Q140_12M_ALW_COR_224_F_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 6 months IPTG Striatum male mRNA rep5

description:
Q140_6M_NEV_STR_116_M_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt

value: IPTG

value: 6 months (Never)


title: LacQ140I 12 months Cortex female mRNA rep3

description:
Q140_12M_ALW_COR_222_F_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I 12 months Cortex female mRNA rep2

description:
Q140_12M_ALW_COR_221_F_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 6 months IPTG Striatum male mRNA rep4

description:
Q140_6M_NEV_STR_115_M_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I 12 months Cortex female mRNA rep4

description:
Q140_12M_ALW_COR_223_F_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 6 months IPTG Striatum male mRNA rep2

description:
Q140_6M_NEV_STR_83_M_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG Striatum male mRNA rep1

description:
Q140_6M_NEV_STR_82_M_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG Striatum female mRNA rep5

description:
Q140_6M_NEV_STR_108_F_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG Striatum female mRNA rep3

description:
Q140_6M_NEV_STR_48_F_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG Striatum female mRNA rep2

description:
Q140_6M_NEV_STR_47_F_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG Cortex male mRNA rep5

description:
Q140_6M_NEV_COR_116_M_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG Cortex male mRNA rep3

description:
Q140_6M_NEV_COR_84_M_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG Cortex male mRNA rep1

description:
Q140_6M_NEV_COR_82_M_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG Cortex male mRNA rep2

description:
Q140_6M_NEV_COR_83_M_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG Cortex female mRNA rep3

description:
Q140_6M_NEV_COR_48_F_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG Cortex female mRNA rep5

description:
Q140_6M_NEV_COR_108_F_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG Cortex female mRNA rep4

description:
Q140_6M_NEV_COR_81_F_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG Cortex female mRNA rep2

description:
Q140_6M_NEV_COR_47_F_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG Cortex female mRNA rep1

description:
Q140_6M_NEV_COR_46_F_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Striatum male mRNA rep5

description:
Q140_6M_2M_STR_125_M_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt

value: 2 months


title: LacQ140I 12 months Cortex female mRNA rep1

description:
Q140_12M_ALW_COR_220_F_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 6 months IPTG to 2 months Striatum male mRNA rep1

description:
Q140_6M_2M_STR_43_M_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Striatum male mRNA rep3

description:
Q140_6M_2M_STR_45_M_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG Striatum male mRNA rep3

description:
Q140_6M_NEV_STR_84_M_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Striatum female mRNA rep3

description:
Q140_6M_2M_STR_59_F_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Striatum male mRNA rep4

description:
Q140_6M_2M_STR_96_M_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Striatum male mRNA rep2

description:
Q140_6M_2M_STR_44_M_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Striatum female mRNA rep1

description:
Q140_6M_2M_STR_57_F_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Striatum female mRNA rep2

description:
Q140_6M_2M_STR_58_F_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Striatum female mRNA rep5

description:
Q140_6M_2M_STR_121_F_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG Striatum female mRNA rep4

description:
Q140_6M_NEV_STR_81_F_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Cortex male mRNA rep4

description:
Q140_6M_2M_COR_96_M_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Cortex male mRNA rep5

description:
Q140_6M_2M_COR_125_M_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Striatum female mRNA rep4

description:
Q140_6M_2M_STR_120_F_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Cortex male mRNA rep2

description:
Q140_6M_2M_COR_44_M_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Cortex female mRNA rep5

description:
Q140_6M_2M_COR_121_F_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG Striatum female mRNA rep1

description:
Q140_6M_NEV_STR_46_F_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Cortex female mRNA rep4

description:
Q140_6M_2M_COR_120_F_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Cortex male mRNA rep3

description:
Q140_6M_2M_COR_45_M_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG Cortex male mRNA rep4

description:
Q140_6M_NEV_COR_115_M_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Cortex male mRNA rep1

description:
Q140_6M_2M_COR_43_M_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Cortex female mRNA rep1

description:
Q140_6M_2M_COR_57_F_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Cortex female mRNA rep3

description:
Q140_6M_2M_COR_59_F_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 6 months IPTG to 2 months Cortex female mRNA rep2

description:
Q140_6M_2M_COR_58_F_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco6m_counts.txt


title: LacQ140I (*) 12 months IPTG Striatum male mRNA rep3

description:
Q140_12M_NEV_STR_242_M_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt

value: 12 months (Never)


title: LacQ140I (*) 12 months IPTG Striatum male mRNA rep4

description:
Q140_12M_NEV_STR_243_M_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG Striatum male mRNA rep5

description:
Q140_12M_NEV_STR_320_M_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG Striatum female mRNA rep5

description:
Q140_12M_NEV_STR_367_F_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG Striatum female mRNA rep4

description:
Q140_12M_NEV_STR_363_F_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG Striatum male mRNA rep1

description:
Q140_12M_NEV_STR_236_M_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG Cortex male mRNA rep5

description:
Q140_12M_NEV_COR_320_M_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG Striatum female mRNA rep1

description:
Q140_12M_NEV_STR_270_F_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG Striatum female mRNA rep3

description:
Q140_12M_NEV_STR_275_F_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG Cortex male mRNA rep3

description:
Q140_12M_NEV_COR_242_M_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG Cortex male mRNA rep1

description:
Q140_12M_NEV_COR_236_M_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG Cortex male mRNA rep2

description:
Q140_12M_NEV_COR_239_M_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG Cortex female mRNA rep3

description:
Q140_12M_NEV_COR_275_F_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG Cortex female mRNA rep4

description:
Q140_12M_NEV_COR_363_F_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG Cortex male mRNA rep4

description:
Q140_12M_NEV_COR_243_M_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG Cortex female mRNA rep1

description:
Q140_12M_NEV_COR_270_F_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Striatum male mRNA rep3

description:
Q140_12M_8M_STR_299_M_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt

value: 8 months


title: LacQ140I (*) 12 months IPTG to 8 months Striatum male mRNA rep5

description:
Q140_12M_8M_STR_391_M_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Striatum male mRNA rep1

description:
Q140_12M_8M_STR_296_M_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Striatum female mRNA rep5

description:
Q140_12M_8M_STR_340_F_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Striatum male mRNA rep2

description:
Q140_12M_8M_STR_298_M_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Striatum female mRNA rep4

description:
Q140_12M_8M_STR_267_F_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Striatum female mRNA rep2

description:
Q140_12M_8M_STR_261_F_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG Striatum male mRNA rep2

description:
Q140_12M_NEV_STR_239_M_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Cortex male mRNA rep5

description:
Q140_12M_8M_COR_391_M_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Cortex male mRNA rep3

description:
Q140_12M_8M_COR_299_M_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Cortex male mRNA rep4

description:
Q140_12M_8M_COR_387_M_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Cortex male mRNA rep2

description:
Q140_12M_8M_COR_298_M_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Cortex female mRNA rep5

description:
Q140_12M_8M_COR_340_F_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG Cortex female mRNA rep5

description:
Q140_12M_NEV_COR_367_F_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Cortex female mRNA rep4

description:
Q140_12M_8M_COR_267_F_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Cortex female mRNA rep2

description:
Q140_12M_8M_COR_261_F_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Cortex female mRNA rep3

description:
Q140_12M_8M_COR_264_F_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Striatum male mRNA rep4

description:
Q140_12M_2M_STR_379_M_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Striatum male mRNA rep5

description:
Q140_12M_2M_STR_382_M_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Striatum male mRNA rep3

description:
Q140_12M_2M_STR_290_M_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Striatum male mRNA rep2

description:
Q140_12M_2M_STR_287_M_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Cortex female mRNA rep1

description:
Q140_12M_8M_COR_260_F_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Striatum female mRNA rep5

description:
Q140_12M_2M_STR_335_F_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Striatum male mRNA rep1

description:
Q140_12M_2M_STR_285_M_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Striatum male mRNA rep4

description:
Q140_12M_8M_STR_387_M_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG Cortex female mRNA rep2

description:
Q140_12M_NEV_COR_271_F_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Striatum female mRNA rep2

description:
Q140_12M_2M_STR_255_F_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Striatum female mRNA rep1

description:
Q140_12M_8M_STR_260_F_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Striatum female mRNA rep3

description:
Q140_12M_2M_STR_258_F_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Cortex male mRNA rep5

description:
Q140_12M_2M_COR_382_M_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Cortex male mRNA rep3

description:
Q140_12M_2M_COR_290_M_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Cortex male mRNA rep4

description:
Q140_12M_2M_COR_379_M_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Cortex male mRNA rep2

description:
Q140_12M_2M_COR_287_M_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Cortex male mRNA rep1

description:
Q140_12M_2M_COR_285_M_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Cortex female mRNA rep5

description:
Q140_12M_2M_COR_335_F_R5
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 8 months Cortex male mRNA rep1

description:
Q140_12M_8M_COR_296_M_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Striatum female mRNA rep1

description:
Q140_12M_2M_STR_253_F_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Cortex female mRNA rep4

description:
Q140_12M_2M_COR_334_F_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Cortex female mRNA rep2

description:
Q140_12M_2M_COR_255_F_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Striatum female mRNA rep4

description:
Q140_12M_2M_STR_334_F_R4
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: LacQ140I (*) 12 months IPTG to 2 months Cortex female mRNA rep1

description:
Q140_12M_2M_COR_253_F_R1
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt


title: tpst/psyr123 Root rep1

city: Nagoya

first: Yoshikatsu

last: Matsubayashi

state: Aichi

address: Chikusa

department: Graduate School of Science

country: Japan

institute: Nagoya University

data_processing:
RNA-seq data was mapped to Arabidopsis TAIR10 genome release using the bioinformatic pipeline of illumina Base Space Sequence Hub.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Arabidopsis thaliana

source_name: Root

extract_protocol:
Total RNA was prepared from roots and shoots of the plants using an RNeasy kit (Qiagen).
Total RNA (1 µg) was used to prepare RNA-seq libraries, using a TruSeq RNA Sample Prep Kit v2 (MiniSeq) and NEBNext Ultra II RNA Library Prep Kit (NextSeq550) (illumina) according to the manufacturer’s instructions.

value: Root

tag: developmental stage

value: 7 days


title: tpst+PSY5 Root rep2

value: 1uM PSY5 treatment


title: tpst/psyr123 Root rep3


title: tpst+PSY5 Root rep3


title: tpst-1 Root rep2


title: tpst-1 Root rep1


title: tpst-1 Root rep3


title: GvHD allogeneic PD-1+ CD8 T cells_spleen

city: Suwon-si

first: Se Jin

last: Im

state: Gyeonggi-do

address: 2066, Seobu-ro, Jangan-gu

department: Department of Immunology

country: South Korea

institute: Sungkyunkwan University School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequences were aligned to the mm10 mouse reference genome using the Cell Ranger (v.5.0.0, 10x Genomics).
Assembly: mm10
Supplementary files format and content: The cell ranger output filtered matrix files including barcodes.tsv, features.tsv and matrix.mtx were included as processed data files

source_name: Spleen

extract_protocol:
Freshly harvested spleens from GvHD B6 recipients of Balb/c T cells at 33-35 days post transplantation were dissociated mechanically using gentle force with iron strainer and 3ml syringe. Transfer the homogenized cell solution into the 50ml conical tube and spin down at 1500rpm for 5min at RT. Aspirate the supernatant, resuspend the pellet in 2ml ACK buffer, and incubate it for 5min at RT to lyse red blood cells. After the incubation, add 10ml of R2 (2%FBS in RPMI media) and pour the splenocytes into 70um cell strainer to filter the solution. After spinning down the tube at 1500rpm for 5min, cells were stained with CD8 APC, PD-1 BV421 antibodies, and Amcyan live/dead viability dye in FACS buffer (2% FBS and 2mM EDTA in PBS). Alive PD-1+ CD8 T cells were sorted using a FACS Aria II (BD Bioscience).
Use LUNA-FL™ Automated Fluorescence Cell Counter (logos biosystems) to consult the 10x Genomics Single Cell Protocols Cell Preparation Guide and the Guidelines for Optimal Sample Preparation flowchart (Documents CG00053 and CG000126 respectively) for more information on preparing cells. Libraries were prepared using the Chromium controller according to the 10x chromium Next GEM Single Cell 3’ v3.1 protocol(CG000315). Briefly, the cell suspensions were diluted in nuclease-free water to achieve a targeted cell count of 10,000. Cell suspension was mixed with master mix and loaded with Single Cell 3’V3.1 Gel Beads and Partitioning Oil into a chromium Next GEM chip G. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled and the cDNA pool then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide(KAPA) and qualified using the Agilent Technologies 4200 TapeStation(Agilent technologies). And then the libraries were sequenced using HiSeq platform(Illumina) according to the read length in the user guide.

value: Spleen

tag: cell type

value: CD8 T lymphocytes

tag: strain

value: BALB/c

value: 6-8 weeks old

tag: disease stage

value: GvHD Day33-35


title: tpst/psyr123 Root rep2


title: cortex.ko.3

city: Hangzhou

first: HONGWEI

last: OUYANG

state: Zhejiang

address: 866 Yu Hang Tang Road,Hangzhou, Zhejiang, P.R.China.

country: China

institute: Zhejiang University

data_processing:
Sequence reads were mapped to reference genome mm10 using Bowtie2 using default parameters and per gene counts were calculated using HTSeq
The reads were mapped to the mouse genome(mm10) using bowtie2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes count values for each sample

source_name: cortex-ko

extract_protocol:
Total RNA was extracted from tissue samples using Trizol reagent (TAKARA)
Reverse transcription was conducted by SuperScript II reverse transcriptase (Invitrogen), double strand cDNA was conducted using NEBNext mRNA second strand synthesis kit (NEB), double strand DNA was cleaned with AMPure XP beads (Beckman Coulter), sequencing library was constructed with Nextera XT kit(Illumina) and sequenced on Illumina X-Ten platform.

treatment_protocol: Sixteen tissues, including adipose, bladder, bone, cartilage, cortex, heart, hippocampus, intestine, kidney, liver, lung, muscle, rectum, spleen, stomach, and vascular from 3-week-old wild-type and Scx-/-mice were used in this study. At necropsy, whole organs were removed, quick-frozen in liquid N2 and stored at -80 °C for RNA extraction.

value: Scx-/-

value: cortex


title: tpst+PSY5 Root rep1


title: hippocampus.wt.1

source_name: hippocampus-wt

value: WT

value: hippocampus


title: cortex.wt.3

source_name: cortex-wt


title: hippocampus.ko.1

source_name: hippocampus-ko


title: hippocampus.wt.3


title: LacQ140I (*) 12 months IPTG to 2 months Cortex female mRNA rep3

description:
Q140_12M_2M_COR_258_F_R3
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt

value: Cerebral Cortex

value: Hdh(LacO-140Q/+):beta-actin-LacIR tg

value: 12 months

value: Female

value: IPTG


title: hippocampus.wt.2


title: hippocampus.ko.3


title: hippocampus.ko.2


title: cortex.wt.2


title: cortex.ko.2


title: cartilage.wt.2

source_name: cartilage-wt

value: cartilage


title: cartilage.wt.1


title: cartilage.ko.2

source_name: cartilage-ko


title: cartilage.ko.3


title: cartilage.ko.1


title: cartilage.wt.3


title: bone.ko.3

source_name: bone-ko

value: bone


title: cortex.wt.1


title: bone.ko.2


title: bone.wt.2

source_name: bone-wt


title: bone.ko.1


title: bone.wt.3


title: rectum.ko.3

source_name: rectum-ko

value: rectum


title: bone.wt.1


title: intestine.ko.3

source_name: intestine-ko

value: intestine


title: intestine.ko.2


title: cortex.ko.1


title: stomach.ko.3

source_name: stomach-ko

value: stomach


title: intestine.wt.1

source_name: intestine-wt


title: intestine.wt.2


title: rectum.ko.2


title: intestine.ko.1


title: rectum.wt.2

source_name: rectum-wt


title: stomach.ko.2


title: stomach.ko.1


title: kidney.ko.1

source_name: kidney-ko

value: kidney


title: stomach.wt.1

source_name: stomach-wt


title: rectum.ko.1


title: rectum.wt.1


title: stomach.wt.2


title: kidney.ko.2


title: kidney.wt.3

source_name: kidney-wt


title: kidney.wt.1


title: stomach.wt.3


title: muscle.wt.3

source_name: muscle-wt

value: muscle


title: vascular.ko.2

source_name: vascular-ko

value: vascular


title: muscle.ko.3

source_name: muscle-ko

value: Scx-/-


title: vascular.ko.1


title: vascular.wt.3

source_name: vascular-wt


title: rectum.wt.3


title: kidney.wt.2


title: vascular.wt.1


title: vascular.wt.2


title: intestine.wt.3


title: kidney.ko.3


title: muscle.wt.2


title: adipose.ko.3

source_name: adipose-ko

value: adipose


title: muscle.ko.2


title: adipose.ko.2


title: adipose.wt.3

source_name: adipose-wt

value: WT


title: adipose.ko.1


title: adipose.wt.2


title: adipose.wt.1


title: muscle.wt.1


title: bladder.ko.1

source_name: bladder-ko

value: bladder


title: muscle.ko.1


title: bladder.wt.2

source_name: bladder-wt


title: bladder.wt.3


title: bladder.ko.3


title: vascular.ko.3


title: bladder.wt.1


title: lung.wt.3

source_name: lung-wt

value: lung


title: spleen.ko.2

source_name: spleen-ko

value: spleen


title: spleen.ko.3


title: spleen.ko.1


title: spleen.wt.3

source_name: spleen-wt


title: spleen.wt.2


title: lung.ko.2

source_name: lung-ko


title: bladder.ko.2


title: lung.wt.2


title: lung.ko.3


title: liver.ko.2

source_name: liver-ko

value: liver


title: liver.ko.1


title: liver.wt.3

source_name: liver-wt


title: liver.wt.1


title: heart.ko.3

source_name: heart-ko

value: heart


title: lung.ko.1


title: heart.wt.3

source_name: heart-wt


title: heart.wt.1


title: spleen.wt.1


title: heart.wt.2


title: liver.wt.2


title: heart.ko.2


title: Limb cells, Scx_ko_97

data_processing:
Raw sequencing reads was processed with Perl scripts to ensure the quality of data used in further analysis. We first removed the adaptor-polluted reads (reads containing more than 5 adapter-polluted bases) and the low-quality reads (reads with the number of phred Quality value less than 19 accounting for more than 15% of total bases). And then discarded reads with number of N bases accounting for more than 5 %. The obtained clean data was mapped to the mm10 genome release with bowtie2 using default parameters. Reads count for each gene in each sample was counted by HTSeq.
The reads were mapped to the mouse genome (mm10) using bowtie2.
The mapped reads for genes were counted via featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes count values for each sample

source_name: Limb cells, Scx_ko

extract_protocol:
Single-cell capture, RNA extraction and cDNA synthesis were performed following the methods described in the Fluidigm protocol(PN 100-9886)
The cDNA reaction products were quantified using the Qubit and were then diluted to a final concentration of 0.2 ng/ μl using C1 Harvest Reagent. The diluted cDNA reaction products were then converted into mRNA-seq libraries using the Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1096, -2001 and -2002) following the manufacturer’s instructions.

treatment_protocol: In general, embryonic experiments were performed on pooled sibling limbs of one litter (three to five limbs per pool). Embryos were genotyped and wild-type and Scx-/- mice were dissected and limbs were isolated. We finely chopped the tissue with small scissors in a drop of DMEM, and then digested the tissues in type I Collagenase 0.1% / Trypsin 0.05% (Life Technologies) diluted in low-glucose Dulbecco’s modified Eagle’s (L-DMEM) medium (Gibco) solution at 37°C for 10 min. Then, we let tissues to settle down and collected the supernatant in a fresh 50 ml tube, before adding 10-20% of fetal bovine serum to quench trypsin (on ice to stop collagenase). We repeated digestion steps for 4 times or more till all tissues are digested. The supernatants were then pooled. We filtered the pooled supernatants through 70μ cell filters (Falcon BD), and centrifuge for 10 min at 1600 rpm, before re-suspending the pellet in DMEM containing 2% serum, and kept cell suspension on ice until load on chip.

value: limb cells


title: Limb cells, Scx_ko_99


title: Limb cells, Scx_ko_9


title: Limb cells, Scx_ko_98


title: liver.ko.3


title: Limb cells, Scx_ko_96


title: Limb cells, Scx_ko_92


title: Limb cells, Scx_ko_93


title: Limb cells, Scx_ko_8


title: Limb cells, Scx_ko_91


title: Limb cells, Scx_ko_89


title: Limb cells, Scx_ko_90


title: Limb cells, Scx_ko_95


title: Limb cells, Scx_ko_88


title: lung.wt.1


title: heart.ko.1


title: Limb cells, Scx_ko_85


title: Limb cells, Scx_ko_87


title: Limb cells, Scx_ko_86


title: Limb cells, Scx_ko_80


title: Limb cells, Scx_ko_82


title: Limb cells, Scx_ko_83


title: Limb cells, Scx_ko_84


title: Limb cells, Scx_ko_79


title: Limb cells, Scx_ko_78


title: Limb cells, Scx_ko_7


title: Limb cells, Scx_ko_94


title: Limb cells, Scx_ko_77


title: Limb cells, Scx_ko_75


title: Limb cells, Scx_ko_76


title: Limb cells, Scx_ko_72


title: Limb cells, Scx_ko_73


title: Limb cells, Scx_ko_71


title: Limb cells, Scx_ko_74


title: Limb cells, Scx_ko_70


title: Limb cells, Scx_ko_65


title: Limb cells, Scx_ko_69


title: Limb cells, Scx_ko_6


title: Limb cells, Scx_ko_62


title: Limb cells, Scx_ko_68


title: Limb cells, Scx_ko_67


title: Limb cells, Scx_ko_64


title: Limb cells, Scx_ko_66


title: Limb cells, Scx_ko_63


title: Limb cells, Scx_ko_59


title: Limb cells, Scx_ko_60


title: Limb cells, Scx_ko_61


title: Limb cells, Scx_ko_52


title: Limb cells, Scx_ko_58


title: Limb cells, Scx_ko_51


title: Limb cells, Scx_ko_4


title: Limb cells, Scx_ko_55


title: Limb cells, Scx_ko_54


title: Limb cells, Scx_ko_5


title: Limb cells, Scx_ko_50


title: Limb cells, Scx_ko_49


title: Limb cells, Scx_ko_42


title: Limb cells, Scx_ko_44


title: Limb cells, Scx_ko_46


title: Limb cells, Scx_ko_47


title: Limb cells, Scx_ko_48


title: Limb cells, Scx_ko_41


title: Limb cells, Scx_ko_57


title: Limb cells, Scx_ko_40


title: Limb cells, Scx_ko_3


title: Limb cells, Scx_ko_39


title: Limb cells, Scx_ko_393


title: Limb cells, Scx_ko_392


title: Limb cells, Scx_ko_391


title: Limb cells, Scx_ko_53


title: Limb cells, Scx_ko_390


title: Limb cells, Scx_ko_387


title: Limb cells, Scx_ko_388


title: Limb cells, Scx_ko_38


title: Limb cells, Scx_ko_386


title: Limb cells, Scx_ko_389


title: Limb cells, Scx_ko_384


title: Limb cells, Scx_ko_385


title: Limb cells, Scx_ko_45


title: Limb cells, Scx_ko_383


title: Limb cells, Scx_ko_381


title: Limb cells, Scx_ko_43


title: Limb cells, Scx_ko_382


title: Limb cells, Scx_ko_380


title: Limb cells, Scx_ko_378


title: Limb cells, Scx_ko_373


title: Limb cells, Scx_ko_374


title: Limb cells, Scx_ko_379


title: Limb cells, Scx_ko_376


title: Limb cells, Scx_ko_375


title: Limb cells, Scx_ko_37


title: Limb cells, Scx_ko_377


title: Limb cells, Scx_ko_368


title: Limb cells, Scx_ko_370


title: Limb cells, Scx_ko_369


title: Limb cells, Scx_ko_367


title: Limb cells, Scx_ko_364


title: Limb cells, Scx_ko_365


title: Limb cells, Scx_ko_361


title: Limb cells, Scx_ko_363


title: Limb cells, Scx_ko_366


title: Limb cells, Scx_ko_359


title: Limb cells, Scx_ko_362


title: Limb cells, Scx_ko_360


title: Limb cells, Scx_ko_35


title: Limb cells, Scx_ko_358


title: Limb cells, Scx_ko_356


title: Limb cells, Scx_ko_357


title: Limb cells, Scx_ko_372


title: Limb cells, Scx_ko_355


title: Limb cells, Scx_ko_354


title: Limb cells, Scx_ko_353


title: Limb cells, Scx_ko_352


title: Limb cells, Scx_ko_371


title: Limb cells, Scx_ko_351


title: Limb cells, Scx_ko_348


title: Limb cells, Scx_ko_36


title: Limb cells, Scx_ko_350


title: Limb cells, Scx_ko_347


title: Limb cells, Scx_ko_346


title: Limb cells, Scx_ko_345


title: Limb cells, Scx_ko_343


title: Limb cells, Scx_ko_344


title: Limb cells, Scx_ko_341


title: Limb cells, Scx_ko_33


title: Limb cells, Scx_ko_342


title: Limb cells, Scx_ko_339


title: Limb cells, Scx_ko_340


title: Limb cells, Scx_ko_337


title: Limb cells, Scx_ko_336


title: Limb cells, Scx_ko_338


title: Limb cells, Scx_ko_334


title: Limb cells, Scx_ko_333


title: Limb cells, Scx_ko_349


title: Limb cells, Scx_ko_332


title: Limb cells, Scx_ko_331


title: Limb cells, Scx_ko_34


title: Limb cells, Scx_ko_330


title: Limb cells, Scx_ko_328


title: Limb cells, Scx_ko_329


title: Limb cells, Scx_ko_327


title: Limb cells, Scx_ko_32


title: Limb cells, Scx_ko_325


title: Limb cells, Scx_ko_323


title: Limb cells, Scx_ko_322


title: Limb cells, Scx_ko_321


title: Limb cells, Scx_ko_320


title: Limb cells, Scx_ko_31


title: Limb cells, Scx_ko_335


title: Limb cells, Scx_ko_315


title: Limb cells, Scx_ko_317


title: Limb cells, Scx_ko_319


title: Limb cells, Scx_ko_316


title: Limb cells, Scx_ko_314


title: Limb cells, Scx_ko_313


title: Limb cells, Scx_ko_312


title: Limb cells, Scx_ko_311


title: Limb cells, Scx_ko_307


title: Limb cells, Scx_ko_310


title: Limb cells, Scx_ko_308


title: Limb cells, Scx_ko_309


title: Limb cells, Scx_ko_30


title: Limb cells, Scx_ko_326


title: Limb cells, Scx_ko_324


title: Limb cells, Scx_ko_306


title: Limb cells, Scx_ko_302


title: Limb cells, Scx_ko_305


title: Limb cells, Scx_ko_304


title: Limb cells, Scx_ko_303


title: Limb cells, Scx_ko_300


title: Limb cells, Scx_ko_301


title: Limb cells, Scx_ko_2


title: Limb cells, Scx_ko_299


title: Limb cells, Scx_ko_318


title: Limb cells, Scx_ko_298


title: Limb cells, Scx_ko_297


title: Limb cells, Scx_ko_296


title: Limb cells, Scx_ko_294


title: Limb cells, Scx_ko_293


title: Limb cells, Scx_ko_292


title: Limb cells, Scx_ko_291


title: Limb cells, Scx_ko_290


title: Limb cells, Scx_ko_288


title: Limb cells, Scx_ko_28


title: Limb cells, Scx_ko_289


title: Limb cells, Scx_ko_286


title: Limb cells, Scx_ko_281


title: Limb cells, Scx_ko_284


title: Limb cells, Scx_ko_283


title: Limb cells, Scx_ko_285


title: Limb cells, Scx_ko_282


title: Limb cells, Scx_ko_29


title: Limb cells, Scx_ko_277


title: Limb cells, Scx_ko_280


title: Limb cells, Scx_ko_27


title: Limb cells, Scx_ko_278


title: Limb cells, Scx_ko_275


title: Limb cells, Scx_ko_274


title: Limb cells, Scx_ko_273


title: Limb cells, Scx_ko_272


title: Limb cells, Scx_ko_295


title: Limb cells, Scx_ko_271


title: Limb cells, Scx_ko_26


title: Limb cells, Scx_ko_269


title: Limb cells, Scx_ko_268


title: Limb cells, Scx_ko_276


title: Limb cells, Scx_ko_287


title: Limb cells, Scx_ko_267


title: Limb cells, Scx_ko_266


title: Limb cells, Scx_ko_279


title: Limb cells, Scx_ko_264


title: Limb cells, Scx_ko_261


title: Limb cells, Scx_ko_259


title: Limb cells, Scx_ko_258


title: Limb cells, Scx_ko_263


title: Limb cells, Scx_ko_256


title: Limb cells, Scx_ko_262


title: Limb cells, Scx_ko_25


title: Limb cells, Scx_ko_260


title: Limb cells, Scx_ko_257


title: Limb cells, Scx_ko_81


title: Limb cells, Scx_ko_56


title: Limb cells, Scx_ko_254


title: Limb cells, Scx_ko_270


title: Limb cells, Scx_ko_253


title: Limb cells, Scx_ko_251


title: Limb cells, Scx_ko_252


title: Limb cells, Scx_ko_249


title: Limb cells, Scx_ko_255


title: Limb cells, Scx_ko_248


title: Limb cells, Scx_ko_265


title: Limb cells, Scx_ko_250


title: Limb cells, Scx_ko_24


title: Limb cells, Scx_ko_247


title: Limb cells, Scx_ko_246


title: Limb cells, Scx_ko_245


title: Limb cells, Scx_ko_244


title: Limb cells, Scx_ko_242


title: Limb cells, Scx_ko_243


title: Limb cells, Scx_ko_241


title: Limb cells, Scx_ko_23


title: Limb cells, Scx_ko_240


title: Limb cells, Scx_ko_237


title: Limb cells, Scx_ko_239


title: Limb cells, Scx_ko_234


title: Limb cells, Scx_ko_230


title: Limb cells, Scx_ko_236


title: Limb cells, Scx_ko_238


title: Limb cells, Scx_ko_231


title: Limb cells, Scx_ko_232


title: Limb cells, Scx_ko_233


title: Limb cells, Scx_ko_229


title: Limb cells, Scx_ko_22


title: Limb cells, Scx_ko_235


title: Limb cells, Scx_ko_226


title: Limb cells, Scx_ko_221


title: Limb cells, Scx_ko_222


title: Limb cells, Scx_ko_225


title: Limb cells, Scx_ko_224


title: Limb cells, Scx_ko_220


title: Limb cells, Scx_ko_217


title: Limb cells, Scx_ko_218


title: Limb cells, Scx_ko_219


title: Limb cells, Scx_ko_227


title: Limb cells, Scx_ko_228


title: Limb cells, Scx_ko_212


title: Limb cells, Scx_ko_214


title: Limb cells, Scx_ko_215


title: Limb cells, Scx_ko_216


title: Limb cells, Scx_ko_213


title: Limb cells, Scx_ko_211


title: Limb cells, Scx_ko_20


title: Limb cells, Scx_ko_209


title: Limb cells, Scx_ko_208


title: Limb cells, Scx_ko_210


title: Limb cells, Scx_ko_205


title: Limb cells, Scx_ko_206


title: Limb cells, Scx_ko_207


title: Limb cells, Scx_ko_204


title: Limb cells, Scx_ko_223


title: Limb cells, Scx_ko_203


title: Limb cells, Scx_ko_200


title: Limb cells, Scx_ko_202


title: Limb cells, Scx_ko_21


title: Limb cells, Scx_ko_198


title: Limb cells, Scx_ko_201


title: Limb cells, Scx_ko_1


title: Limb cells, Scx_ko_197


title: Limb cells, Scx_ko_199


title: Limb cells, Scx_ko_19


title: Limb cells, Scx_ko_195


title: Limb cells, Scx_ko_196


title: Limb cells, Scx_ko_194


title: Limb cells, Scx_ko_192


title: Limb cells, Scx_ko_190


title: Limb cells, Scx_ko_193


title: Limb cells, Scx_ko_191


title: Limb cells, Scx_ko_188


title: Limb cells, Scx_ko_18


title: Limb cells, Scx_ko_189


title: Limb cells, Scx_ko_186


title: Limb cells, Scx_ko_185


title: Limb cells, Scx_ko_184


title: Limb cells, Scx_ko_187


title: Limb cells, Scx_ko_181


title: Limb cells, Scx_ko_182


title: Limb cells, Scx_ko_17


title: Limb cells, Scx_ko_180


title: Limb cells, Scx_ko_176


title: Limb cells, Scx_ko_178


title: Limb cells, Scx_ko_177


title: Limb cells, Scx_ko_175


title: Limb cells, Scx_ko_179


title: Limb cells, Scx_ko_171


title: Limb cells, Scx_ko_172


title: Limb cells, Scx_ko_174


title: Limb cells, Scx_ko_16


title: Limb cells, Scx_ko_169


title: Limb cells, Scx_ko_167


title: Limb cells, Scx_ko_165


title: Limb cells, Scx_ko_183


title: Limb cells, Scx_ko_166


title: Limb cells, Scx_ko_163


title: Limb cells, Scx_ko_162


title: Limb cells, Scx_ko_164


title: Limb cells, Scx_ko_160


title: Limb cells, Scx_ko_158


title: Limb cells, Scx_ko_15


title: Limb cells, Scx_ko_157


title: Limb cells, Scx_ko_159


title: Limb cells, Scx_ko_156


title: Limb cells, Scx_ko_170


title: Limb cells, Scx_ko_155


title: Limb cells, Scx_ko_173


title: Limb cells, Scx_ko_151


title: Limb cells, Scx_ko_154


title: Limb cells, Scx_ko_152


title: Limb cells, Scx_ko_153


title: Limb cells, Scx_ko_149


title: Limb cells, Scx_ko_147


title: Limb cells, Scx_ko_148


title: Limb cells, Scx_ko_168


title: Limb cells, Scx_ko_150


title: Limb cells, Scx_ko_146


title: Limb cells, Scx_ko_14


title: Limb cells, Scx_ko_144


title: Limb cells, Scx_ko_145


title: Limb cells, Scx_ko_143


title: Limb cells, Scx_ko_161


title: Limb cells, Scx_ko_140


title: Limb cells, Scx_ko_13


title: Limb cells, Scx_ko_141


title: Limb cells, Scx_ko_142


title: Limb cells, Scx_ko_138


title: Limb cells, Scx_ko_139


title: Limb cells, Scx_ko_137


title: Limb cells, Scx_ko_136


title: Limb cells, Scx_ko_135


title: Limb cells, Scx_ko_134


title: Limb cells, Scx_ko_132


title: Limb cells, Scx_ko_129


title: Limb cells, Scx_ko_131


title: Limb cells, Scx_ko_130


title: Limb cells, Scx_ko_12


title: Limb cells, Scx_ko_133


title: Limb cells, Scx_ko_128


title: Limb cells, Scx_ko_116


title: Limb cells, Scx_ko_123


title: Limb cells, Scx_ko_11


title: Limb cells, Scx_ko_124


title: Limb cells, Scx_ko_122


title: Limb cells, Scx_ko_119


title: Limb cells, Scx_ko_118


title: Limb cells, Scx_ko_126


title: Limb cells, Scx_ko_125


title: Limb cells, Scx_ko_121


title: Limb cells, Scx_ko_114


title: Limb cells, Scx_ko_113


title: Limb cells, Scx_ko_115


title: Limb cells, Scx_ko_112


title: Limb cells, Scx_ko_111


title: Limb cells, Scx_ko_110


title: Limb cells, Scx_ko_108


title: Limb cells, Scx_ko_109


title: Limb cells, Scx_ko_107


title: Limb cells, Scx_ko_127


title: Limb cells, Scx_ko_120


title: Limb cells, Scx_ko_105


title: Limb cells, Scx_ko_106


title: Limb cells, Scx_ko_104


title: Limb cells, Scx_ko_103


title: Limb cells, Scx_ko_102


title: Limb cells, Scx_ko_117


title: Limb cells, Scx_ko_100


title: Limb cells, Scx_ko_101


title: Limb cells, WT_99

source_name: Limb cells, WT


title: Limb cells, WT_91


title: Limb cells, WT_93


title: Limb cells, WT_8


title: Limb cells, WT_92


title: Limb cells, WT_96


title: Limb cells, WT_97


title: Limb cells, WT_87


title: Limb cells, WT_88


title: Limb cells, WT_95


title: Limb cells, WT_94


title: Limb cells, Scx_ko_10


title: Limb cells, WT_90


title: Limb cells, WT_89


title: Limb cells, WT_98


title: Limb cells, WT_9


title: Limb cells, WT_86


title: Limb cells, WT_82


title: Limb cells, WT_80


title: Limb cells, WT_79


title: Limb cells, WT_7


title: Limb cells, WT_85


title: Limb cells, WT_77


title: Limb cells, WT_81


title: Limb cells, WT_75


title: Limb cells, WT_76


title: Limb cells, WT_68


title: Limb cells, WT_6


title: Limb cells, WT_71


title: Limb cells, WT_69


title: Limb cells, WT_72


title: Limb cells, WT_65


title: Limb cells, WT_83


title: Limb cells, WT_73


title: Limb cells, WT_66


title: Limb cells, WT_70


title: Limb cells, WT_63


title: Limb cells, WT_84


title: Limb cells, WT_60


title: Limb cells, WT_61


title: Limb cells, WT_64


title: Limb cells, WT_67


title: Limb cells, WT_59


title: Limb cells, WT_78


title: Limb cells, WT_58


title: Limb cells, WT_56


title: Limb cells, WT_57


title: Limb cells, WT_55


title: Limb cells, WT_53


title: Limb cells, WT_5


title: Limb cells, WT_52


title: Limb cells, WT_74


title: Limb cells, WT_62


title: Limb cells, WT_4


title: Limb cells, WT_47


title: Limb cells, WT_46


title: Limb cells, WT_54


title: Limb cells, WT_49


title: Limb cells, WT_50


title: Limb cells, WT_48


title: Limb cells, WT_45


title: Limb cells, WT_42


title: Limb cells, WT_43


title: Limb cells, WT_41


title: Limb cells, WT_51


title: NL, volunteer J20

type: RNA

city: Aulnay sous Bois

first: Emilie

last: Warrick

address: 1 avenue Eugène Schueller

country: France

institute: L'Oreal R&I

description:
non lesional adjacent skin
Affymetrix Human Genome U133 Plus 2.0 Array

hyb_protocol: Fragmented cRNA was hybridized to a human U133A 2.0 plus microarray (Affymetrix). Arrays were processed on a GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 (Affymetrix).

data_processing: Affymetrix RMA software was used to generate the CEL files. CEL files were imported into Array Studio and normalized using the RMA (Robust Multichip Average) method.

label: biotin

organism: Homo sapiens

source_name: non lesional skin

label_protocol: Biotinylated cRNA was produced using Affymetrix IVT labelling kit.

extract_protocol: Samples were homogenized in Qiagen lysis buffer. Total RNA was obtained using RNeasy Micro Kit according to the manufacturer’s instructions(Qiagen).

treatment_protocol: Lesions were selected through quantitative analysis of dermoscopic images obtained with Fotofinder® dermoscope

tag: anatomical site

value: hand

value: non lesional skin


title: AL, volunteer J9

description:
AL lesion
Affymetrix Human Genome U133 Plus 2.0 Array

source_name: actinic lentigine

value: actinic lentigine


title: AL, volunteer J20


title: AL, volunteer J18


title: Limb cells, WT_44


title: Limb cells, WT_3


title: NL, volunteer J9


title: AL, volunteer J19


title: NL, volunteer J17


title: NL, volunteer J18


title: NL, volunteer J16


title: AL, volunteer J16


title: NL, volunteer J15


title: NL, volunteer J19


title: AL, volunteer J17


title: Limb cells, WT_39


title: AL, volunteer J14


title: Limb cells, WT_395


title: Limb cells, WT_394


title: Limb cells, WT_40


title: Limb cells, WT_393


title: Limb cells, WT_392


title: Limb cells, WT_390


title: NL, volunteer J13


title: NL, volunteer J12


title: AL, volunteer J12


title: AL, volunteer J11


title: Limb cells, WT_38


title: Limb cells, WT_389


title: Limb cells, WT_388


title: Limb cells, WT_385


title: Limb cells, WT_387


title: Limb cells, WT_386


title: Limb cells, WT_384


title: Limb cells, WT_383


title: AL, volunteer J13


title: NL, volunteer J14


title: Limb cells, WT_391


title: Limb cells, WT_381


title: NL, volunteer J11


title: AL, volunteer E15, technical rep2

hyb_protocol: Fragmented cRNA (15 μg) was hybridized to a human U133A 2.0 plus microarray (Affymetrix). For each sample, two microarrays were hybridized with two independently synthetized sets of probes. Arrays were processed on a GeneChip Fluidics Station 450 (Affymetrix).

data_processing: Raw data were analyzed using a GeneChip Expression Consol (Affymetrix) and normalized using the robust multi‐array average (RMA) method.

label_protocol: Biotinylated cRNA was produced using the in vitro transcription Gene Chip IVT labelling kit (Affymetrix).


title: NL, volunteer J10


title: NL, volunteer E14, technical rep1


title: Limb cells, WT_379


title: Limb cells, WT_380


title: AL, volunteer J15


title: AL, volunteer J10


title: NL, volunteer E15, technical rep2


title: NL, volunteer E15, technical rep1


title: Limb cells, WT_377


title: NL, volunteer E14, technical rep2


title: NL, volunteer E13, technical rep2


title: Limb cells, WT_376


title: AL, volunteer E13, technical rep1


title: Limb cells, WT_375


title: AL, volunteer E13, technical rep2


title: AL, volunteer E14, technical rep2


title: Limb cells, WT_37


title: Limb cells, WT_374


title: Limb cells, WT_373


title: Limb cells, WT_370


title: Limb cells, WT_378


title: Limb cells, WT_372


title: Limb cells, WT_371


title: AL, volunteer E10, technical rep2


title: Limb cells, WT_36


title: Limb cells, WT_369


title: Limb cells, WT_368


title: NL, volunteer E13, technical rep1


title: AL, volunteer E10, technical rep1


title: Limb cells, WT_367


title: Limb cells, WT_366


title: NL, volunteer E8, technical rep2


title: NL, volunteer E9, technical rep1


title: NL, volunteer E10, technical rep2


title: NL, volunteer E8, technical rep1


title: AL, volunteer E9, technical rep2


title: NL, volunteer E9, technical rep2


title: Limb cells, WT_363


title: Limb cells, WT_365


title: Limb cells, WT_362


title: AL, volunteer E8, technical rep2


title: AL, volunteer E8, technical rep1


title: NL, volunteer E7, technical rep2


title: NL, volunteer E7, technical rep1


title: Limb cells, WT_361


title: AL, volunteer E15, technical rep1


title: Limb cells, WT_360


title: Limb cells, WT_35


title: NL, volunteer E10, technical rep1


title: Limb cells, WT_364


title: NL, volunteer E6, technical rep2


title: Limb cells, WT_359


title: Limb cells, WT_358


title: Limb cells, WT_357


title: NL, volunteer E6, technical rep1


title: AL, volunteer E7, technical rep2


title: AL, volunteer E6, technical rep1


title: Limb cells, WT_355


title: Limb cells, WT_356


title: AL, volunteer E6, technical rep2


title: Limb cells, WT_354


title: Limb cells, WT_353


title: AL, volunteer E5, technical rep2


title: Limb cells, WT_352


title: NL, volunteer E4, technical rep2


title: AL, volunteer E7, technical rep1


title: NL, volunteer E5, technical rep1


title: AL, volunteer E5, technical rep1


title: Limb cells, WT_351


title: Limb cells, WT_34


title: Limb cells, WT_350


title: Limb cells, WT_349


title: AL, volunteer E4, technical rep2


title: NL, volunteer E5, technical rep2


title: AL, volunteer E9, technical rep1


title: AL, volunteer E4, technical rep1


title: NL, volunteer E3, technical rep1


title: AL, volunteer E3, technical rep2


title: NL, volunteer E3, technical rep2


title: Limb cells, WT_346


title: Limb cells, WT_347


title: NL, volunteer E2, technical rep1


title: AL, volunteer E3, technical rep1


title: Limb cells, WT_344


title: Limb cells, WT_342


title: AL, volunteer E2, technical rep1


title: Limb cells, WT_341


title: AL, volunteer E14, technical rep1


title: Limb cells, WT_343


title: Limb cells, WT_340


title: Vial, Day0, S4 - Donor 2

city: Boston

first: Lorna

last: Ewart

state: MA

address: 27 Drydock Avenue

institute: Emulate Inc.

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted
Assembly: GRCh38
Supplementary files format and content: counts

source_name: Primary Human Hepatocytes

growth_protocol: Liver-Chips were seeded with primary human hepatocytes  (introduced in the top channel of an Organ-on-Chip) and human liver sinusoidal endothelial cells (LSECs),Kupffer cells and stallate cells (introduced into the bottom channel). Cryopreserved primary human hepatocytes, purchased from Gibco (Thermo Fisher Scientific), and cryopreserved primary human liver sinusoidal endothelial cells (LSECs), purchased from Cell Systems, were cultured according to their respective vendor/Emulate protocols. The LSECs were expanded at a 1:1 ratio in 10-15 T-75 flask (Corning) that were pre-treated with 5mL of Attachment Factor (Cell Systems). Complete LSEC medium includes Cell Systems medium with final concentrations of 1% Pen/Strep (Sigma), 2% CultureBoost (Cell Systems), and 10% Fetal Bovine Serum (FBS) (Sigma). Media was refreshed daily until cells were ready for use. Cryopreserved human Kupffer cells (Samsara Sciences) and human Stellate cells (IXCells) were thawed according to their respective vendor/Emulate protocols on the day of seeding.

extract_protocol:
RNA was extracted from chips using TRI Reagent (Sigma-Aldrich) according to the manufacturer’s guidelines
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: individual

value: Donor 2

value: Primary Human Hepatocytes

tag: air liquid interface

value: Vial, Day0


title: Vial, Day0, S2 - Donor 2


title: Vial, Day0, S3 - Donor 2


title: Limb cells, WT_339


title: Limb cells, WT_33


title: Limb cells, WT_345


title: Limb cells, WT_338


title: Vial, Day0, S1 - Donor 2


title: Vehicle, Day7, S3 (Liver-Chip) - Donor 2

value: Vehicle, Day7 (Liver-Chip)


title: NL, volunteer E2, technical rep2


title: Limb cells, WT_337


title: Vehicle, Day7, S2 (Liver-Chip) - Donor 2


title: Limb cells, WT_336


title: Vehicle, Day3, S3 (Liver-Chip) - Donor 2

value: Vehicle, Day3 (Liver-Chip)


title: Vehicle, Day3, S2 (Liver-Chip) - Donor 2


title: AL, volunteer E1, technical rep2


title: NL, volunteer E1, technical rep2


title: Vehicle, Day7, S1 (Liver-Chip) - Donor 2


title: Limb cells, WT_332


title: Limb cells, WT_333


title: Limb cells, WT_331


title: AL, volunteer E2, technical rep2


title: AL, volunteer E1, technical rep1


title: Vial, Day0, S4 - Donor 3

value: Donor 3


title: NL, volunteer E1, technical rep1


title: NL, volunteer E4, technical rep1


title: Vial, Day0, S2 - Donor 3


title: Limb cells, WT_32


title: Vial, Day0, S1 - Donor 3


title: Limb cells, WT_329


title: Vehicle, Day7, S4 (Liver-Chip) - Donor 3


title: Limb cells, WT_328


title: Limb cells, WT_335


title: Limb cells, WT_327


title: Limb cells, WT_334


title: Limb cells, WT_326


title: Vehicle, Day7, S3 (Liver-Chip) - Donor 3


title: Vehicle, Day3, S1 (Liver-Chip) - Donor 2


title: Vehicle, Day7, S2 (Liver-Chip) - Donor 3


title: Vehicle, Day7, S1 (Liver-Chip) - Donor 3


title: Limb cells, WT_325


title: Limb cells, WT_382


title: Limb cells, WT_323


title: Limb cells, WT_321


title: Vehicle, Day3, S4 (Liver-Chip) - Donor 3


title: Limb cells, WT_322


title: Limb cells, WT_330


title: Limb cells, WT_31


title: Vial, Day0, S3 - Donor 3


title: Limb cells, WT_319


title: Vehicle, Day3, S1 (Liver-Chip) - Donor 3


title: Limb cells, WT_318


title: Limb cells, WT_317


title: Limb cells, WT_315


title: Limb cells, WT_316


title: Limb cells, WT_313


title: Limb cells, WT_320


title: Limb cells, WT_312


title: Limb cells, WT_311


title: Limb cells, WT_324


title: Limb cells, WT_314


title: Limb cells, WT_310


title: Vehicle, Day3, S3 (Liver-Chip) - Donor 3


title: Human thyroid (1D cDNA)

city: Philadelphia

first: Yi

last: Xing

state: PA

address: 3501 Civic Center Blvd

department: Department of Pathology and Laboratory Medicine

institute: Children's Hospital of Philadelphia

description:
processed data file:
30ClontechTissue_1D_cDNA_N2_R0_abundance.esp
30ClontechTissue_1D_cDNA_N2_R0_updated.gtf

data_processing:
Basecalling was performed in fast mode with Guppy (version 3.6.0) for all Nanopore sequencing data in this study (https://community.nanoporetech.com/downloads). Basecalling of direct RNA and cDNA libraries were done using config files rna_r9.4.1_70bps_fast.cfg and dna_r9.4.1_450bps_fast.cfg respectively.
Consensus sequences from multiple copies of cDNA found in each long read of an LRCA library were obtained by running SPIRIT (https://github.com/Xinglab/SPIRIT). In brief, nhmmer is first used to find splint sequences from each read with the parameter ‘-T 8 --max’. Sequences with similar lengths separated by each pair of neighboring splint sequences were considered as copies of cDNA. If three or more copies of cDNA were identified, their consensus was obtained using abPOA (https://github.com/Xinglab/abPOA).
Reads were then mapped to either the SIRVome or hg19 reference genome using minimap2 (v2.17) with parameters “-ax splice --splice-flank=no -w 4 -k 14” and either SIRV transcript annotations or GENCODE v34 annotations (https://www.gencodegenes.org/human/release_34lift37.html).
Alignment files (SAM format) were next processed by ESPRESSO (https://github.com/Xinglab/espresso) using default settings and either SIRV transcript annotations or GENCODE v34 annotations. Reads that either map to the mitochondrial genome or contain large continuous insertions (≥20 nt) in the raw alignment were filtered out by ESPRESSO.
Genome_build: hg19, SIRVome
Supplementary_files_format_and_content: .esp files are tab-delimited matrices generated by ESPRESSO that contain read count estimates for all identified isoforms (rows) across all samples (columns); .gtf files generated by ESPRESSO are in GTF format and provide genomic coordinates for all identified transcript isoforms and their corresponding exons

molecule: polyA RNA

source_name: Human thyroid tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human thyroid were purchased from Clontech
50 ng of poly(A)+ RNA from human thyroid tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human thyroid

tag: nanopore library type

value: 1D cDNA


title: Ctrl_Lung2

city: ChangSha

first: Ke

last: Gong

address: 139 Renmin Middle road

department: cardiovascular surgery

institute: The Second Xiangya Hospital of Central South University

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Rnor_6.0
Assembly: gene expression text files include raw counts and FPKM values for each Sample

organism: Rattus norvegicus

source_name: Lung tissue of rats, control group

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

tag: tissue

value: Lung

value: control


title: Ctrl_Lung1


title: Vehicle, Day3, S2 (Liver-Chip) - Donor 3


title: Ctrl_Lung3


title: colon_DSS+PAMK_rep1

city: Nanjing

first: Lixin

last: Sun

address: 24 Tong Jia Xiang

institute: China Pharmaceutical University

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1×Agilent fragmentation buffer and 2×Agilent blocking agent following the manufacturers’ instructions. On completion of the fragmentation reaction, 55 μl of 2×Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse ceRNA Microarray 2019 (4×180K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4×180K array slides (Scan Area 61×21.6 mm, Scan resolution 3μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0 (Agilent). Probe that at least 1 out of 2 samples flagged as “Detected” were maintained.

source_name: colonic tissue of DSS+PAMK group

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1561) following the manufacturer’s instructions.

treatment_protocol: Mice were fed adaptively for 7 days before the experiment and randomly divided into three groups (Control, DSS, DSS+PAMK). Acute colitis was induced by distilled water containing 3% DSS for 7 days, and the Control group was only given distilled water. From day 8 to day 14, the mice in the five groups received one of the following treatments: Control group (1 ml/100 g normal saline, i.g.), DSS group (1 ml/100 g normal saline, i.g.), and DSS+PAMK (200 mg/kg PAMK, i.g.).

value: colon

tag: gender

value: male

value: 10 weeks

value: DSS+PAMK


title: Human stomach (1D cDNA)

source_name: Human stomach tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human stomach were purchased from Clontech
50 ng of poly(A)+ RNA from human stomach tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human stomach


title: Ctrl_Lung4


title: Limb cells, WT_308

tag: genotype

value: WT

value: limb cells


title: MCT_Lung4

source_name: Lung tissue of rats, MCT treatment

value: MCT


title: colon_DSS_rep2

source_name: colonic tissue of DSS group

tag: age

value: DSS


title: colon_DSS+PAMK_rep2


title: MCT_Lung3


title: Limb cells, WT_307


title: Limb cells, WT_306


title: Limb cells, WT_304


title: colon_DSS_rep1


title: Human small intestine (1D cDNA)

source_name: Human small intestine tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human small intestine were purchased from Clontech
50 ng of poly(A)+ RNA from human small intestine tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human small intestine


title: colon_DSS_rep3


title: Limb cells, WT_303


title: colon_Control_rep3

source_name: colonic tissue of Control group

value: Control


title: MCT_Lung2


title: Limb cells, WT_30


title: colon_DSS+PAMK_rep3


title: Limb cells, WT_309


title: Limb cells, WT_305


title: Human pancreas (1D cDNA)

source_name: Human pancreas tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human pancreas were purchased from Clontech
50 ng of poly(A)+ RNA from human pancreas tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human pancreas


title: Limb cells, WT_302


title: colon_Control_rep1


title: Human colon (1D cDNA)

source_name: Human colon tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human colon were purchased from Clontech
50 ng of poly(A)+ RNA from human colon tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human colon


title: Limb cells, WT_301


title: MCT_Lung1


title: Human bladder (1D cDNA)

source_name: Human bladder tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human bladder were purchased from Clontech
50 ng of poly(A)+ RNA from human bladder tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human bladder


title: Limb cells, WT_2


title: ir_P5

city: Cincinnati

first: Guolun

last: Wang

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

data_processing:
The standard celllranger mkfastq software version 3.0 used for basecalling.
The standard celllranger count software version 3.0 used to produced raw expression matrix.
The matrix were normalized and scaled by Seurat v4.0 in R4.0.0 environment.
Assembly: mm10 and rn6
Supplementary files format and content: Matrix

source_name: bone marrow

extract_protocol:
The bone marrow cell samples were harvested from tibia and femur of P5. The samples were dissociated into single cell suspension and were sorted by Flow cytometry for library preparation.
The libraries were prepared for sequencing using standard 10X 3'v3 protocols
10x 3'v3 single cell RNAseq

value: SD

tag: subset

value: stromal and hematopoietic cells


title: Limb cells, WT_29


title: Limb cells, WT_299


title: Limb cells, WT_297


title: Human blood (1D cDNA)

source_name: Human blood, peripheral leukocytes

extract_protocol:
Poly(A)+ RNA (5 μg) from human blood (peripheral leukocytes) were purchased from Clontech
50 ng of poly(A)+ RNA from human blood (peripheral leukocytes) were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human blood

value: 1D cDNA


title: Limb cells, WT_294

source_name: Limb cells, WT


title: Limb cells, WT_295


title: Limb cells, WT_298


title: Limb cells, WT_348


title: Human skeletal muscle (1D cDNA)

source_name: Human skeletal muscle tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human skeletal muscle were purchased from Clontech
50 ng of poly(A)+ RNA from human skeletal muscle tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human skeletal muscle


title: Limb cells, WT_293


title: mr

data_processing:
The standard celllranger mkfastq software version 3.0 used for basecalling.
The standard celllranger count software version 3.0 used to produced raw expression matrix.
The matrix were normalized and scaled by Seurat v4.0 in R4.0.0 environment.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix

extract_protocol:
The Bone marrow cell samples were harvested from tibia and femur of P10 interspecies or intraspecies. The samples were dissociated into single cell suspension. The GFP+ Lineage- (561317, BD) cells were sorted by Flow cytometry for library preparation.
The libraries were prepared for sequencing using standard 10X 3'v3 protocols
10x 3'v3 single cell RNAseq

value: GFP+ Lineage-


title: Human ovary (1D cDNA)

source_name: Human ovary tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human ovary were purchased from Clontech
50 ng of poly(A)+ RNA from human ovary tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human ovary


title: Limb cells, WT_291


title: Limb cells, WT_296


title: MRL-MpJ

city: Brisbane

first: Zewen Kelvin

last: Tuong

state: QLD

address: 62 Graham Street, Centre for Children's Health Research (CCHR), South Brisbane, QLD, 4101

country: Australia

institute: The University of Queensland

description:
10x Genomics single-cell 3′ v2 kit
F7_171121

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: cellranger processed filtered h5 formats.

source_name: Kidney

extract_protocol:
Fresh cells were flow-sorted from mouse kidneys based on differential F4/80 and CD11b expression and pooled, centrifuged at 1,300 rpm for 5 minutes. Supernatant was discarded and the pellet resuspended in PBS 0.05% BSA. Cells were loaded at an appropriate concentration to enable recovery of 10,000 cells. 10x single-cell 3’ v2 kit as per the manufacturer’s protocol. Libraries were produced using the manufacturer’s protocol and sequenced on a HiSeq 4000 (Illumina).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Kidney

value: mononuclear phagocytes

value: MRL-MpJ

value: 12 weeks

value: pooled male and female


title: colon_Control_rep2

value: colon

value: male

value: 10 weeks

tag: treatment


title: Limb cells, WT_28

extract_protocol:
Single-cell capture, RNA extraction and cDNA synthesis were performed following the methods described in the Fluidigm protocol(PN 100-9886)
The cDNA reaction products were quantified using the Qubit and were then diluted to a final concentration of 0.2 ng/ μl using C1 Harvest Reagent. The diluted cDNA reaction products were then converted into mRNA-seq libraries using the Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1096, -2001 and -2002) following the manufacturer’s instructions.

value: WT

value: limb cells


title: Limb cells, WT_290


title: Limb cells, WT_300


title: Human spleen (1D cDNA)

source_name: Human spleen tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human spleen were purchased from Clontech
50 ng of poly(A)+ RNA from human spleen tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human spleen


title: Limb cells, WT_289


title: cr_P5

value: SD

value: stromal and hematopoietic cells


title: Human prostate (1D cDNA)

source_name: Human prostate tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human prostate were purchased from Clontech
50 ng of poly(A)+ RNA from human prostate tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human prostate

value: 1D cDNA


title: Stim Day 5

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

data_processing:
Base calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation of mkfastq
Then aligned against the mm9 (mouse) genome using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample
Cell barcodes representative of quality cells were delineated from barcodes of apoptotic cells or background RNA based on a threshold of having at least 200 unique transcripts profiled, less than 10,000 total transcripts, and less than 10% of their transcriptome of mitochondrial origin.
Unique molecular identifiers (UMIs) from each cell barcode were retained for all downstream analysis.
Raw UMI counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1).
Highly variable genes were identified, and cells were scaled by regression to the fraction of mitochondrial transcripts. Aggregated data was then evaluated using uniform manifold approximation and projection (UMAP) analysis
Assembly: mm9 (mouse)

source_name: GFP+ murine cells from parabiomes treated with electrical stimulation, D5

growth_protocol: A GFP and non-GFP mouse were parabiomed. An excisional wound was created on the non-GFP mouse. E-stim treatment was applied daily until D5. Tissue was harvested for analysis.

extract_protocol:
Tissue was enzymatically digested, cells were collected and washed. These cellular suspensions were then submitted for droplet-based microfluidic single cell RNA sequencing (scRNA-seq) at the Stanford Functional Genomics Facility (SFGF) using the 10x Chromium Single Cell platform (Single Cell 3’ v3, 10x Genomics, USA).
cDNA was fragmented followed by end repair and A-tailing at 65°C for 30min. cDNA were double-sided size selected using SpriSelect beats. Sequencing adaptors were ligated to the cDNA at 20°C for 15min. cDNA was amplified using a sample-specific index oligo as primer, followed by another round of double-sided size selection using SpriSelect beads.
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA libraries were sequenced on a HiSeq 4000 Illumina platform aiming for 50,000 reads per cell.

treatment_protocol: Mice wounds were treated daily with e-stimulation until D5, at which point the tissue was collected.

tag: passages

value: Freshly isolated and submitted

value: skin

value: stimulation


title: Tregs, FS-KO2

city: Shanghai

first: Ju

last: Qiu

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: cells were isolated from steady state large intestine

data_processing:
Quality control was the first step for processing raw sequence reads by FastQC.
Then adapter sequences and poor-quality reads were removed.
Reads were mapped to Mouse Genome Assembly GRCm38 by STAR v2.5
Gene expression quantification was called by RSEM v1.2 with default parameters on GENCODE mouse M16 gene annotation file
Genome_build: mm10
Supplementary_files_format_and_content: csv, raw counts of sequencing reads from replicates samples with tracking ID, gene short name.

source_name: LI Tregs

extract_protocol:
Cells were lysed in Trizol (Invitrogen) and total RNA was extracted.
Library construction and sequencing was performed by BGI Genomics, BGI-Wuhan. RNA were treated with DNase I and purified with magnetic beads with Oligo (dT). RNA were mixed with the fragmentation buffer and were fragmented into short fragments. Then cDNA was synthesized using the mRNA fragments as templates. Short fragments were purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments were connected with adapters. Suitable fragments were selected for the PCR amplification as templates. Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used for quantification and qualification of the sample library. 150bp paired sequencing was performed using Illumina HiSeqTM4000.

value: large intestine

value: LI Tregs


title: Limb cells, WT_288


title: Human liver (1D cDNA)

source_name: Human liver tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human liver were purchased from Clontech
50 ng of poly(A)+ RNA from human liver tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human liver


title: Limb cells, WT_292


title: Tregs, FS-KO1


title: Limb cells, WT_287


title: Limb cells, WT_286


title: Limb cells, WT_284


title: Tregs, FS-WT2


title: Human testis (1D cDNA)

source_name: Human testis tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human testis were purchased from Clontech
50 ng of poly(A)+ RNA from human testis tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human testis


title: Human lung (1D cDNA)

source_name: Human lung tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human lung were purchased from Clontech
50 ng of poly(A)+ RNA from human lung tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human lung