title: TGTT_0001

tag: organ

value: Bone

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: metastatic spread

value: Bone only:no

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

value: no

tag: chemotherapy? yes vs not

tag: immunotherapy

value: POS

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: PR1729_378-L1-3

status: Public on May 28 2021

type: RNA

city: Philadelphia

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1020 Locust St, 314C

department: Pathology

country: USA

institute: Jefferson University

description:
Single Neuron excised from Right Atrial Ganglionic Plexus (RAGP) of the heart
Neuron Identified using Cresyl violet flourescent signal collected using Laser Capture microdissection
BioMark-qRTPCR

data_processing: none provided by the submitter

label: EvaGreen

molecule: total RNA

organism: Sus scrofa

source_name: RAGP of Pig Heart

label_protocol: none provided by the submitter

extract_protocol: Cell Lysates were directly processed for Reverse Transcription

tag: gender

value: female

tag: breed

value: Yucatan mini pig

tag: animal id

tag: sample flourecent label

value: Cresyl violet

tag: sample san (sino-atrial node) projecting/san non-projecting


title: PPZ_BR rep3

type: SRA

city: Fuzhou

first: wenfei

last: Wang

state: Fujian

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

department: Haixia Institute of Science and Technology

country: China

institute: Fujian Agriculture and Forestry University

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data filtering steps contain removing reads containing adapter, reads containing ploy-N and low quality reads to obtain clean reads. Meanwhile, Q20, Q30 and GC content the clean data were calculated.
Paired-end clean reads were aligned to Glycine max whole genome using Hisat2 v2.0.5 software.
FeatureCounts v1.5.0-p3 was used to calculate the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was used by DESeq2 software.
Genome_build: Glycine_max_Wm82.a4.v1.gtf
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Glycine max

source_name: 0.1 μM PPZ after 0.01 nM BL treatment_Root

growth_protocol: Soybean seeds for RNA-seq were germinated in vermiculite for 3 days. Then seedlings were transferred into modified half-strength Hoagland's nutrient solution under long-day conditions (16 h light / 8 h dark) at 24 °C for 7 and a half days

extract_protocol:
Total RNA  isolated of soybean seedlings root tips(1 cm) by using RNAprep pure Plant Kit (TIANGEN, China).
RNA degradation and contamination was detection on 1% agarose gels. The purity of RNA was checked by the NanoPhotometer spectrophotometer (IMPLEN, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system. RNA libraries were constructed by 1 μg total RNA per sample.

treatment_protocol: 3-day-old soybean seedlings were transferred to hydroponics medium for 5 days, then treated with 0.1 μM PPZ and mock for another 2.5 days. Meanwhile, 3-day-old soybean seedlings were transferred to hydroponics medium for 7 days, then treated with 0.01 nM BL and mock for another 0.5 days.

tag: cultivar

tag: age

value: ten and a half days seedlings

tag: treatment

value: 0.1 μM PPZ after 0.01 nM BL treatment

tag: tissue

value: 1 cm of the root tip


title: PR1729_366-L1-2


title: PR1729_366-L1-1


title: PR1729_358-L1-9


title: PR1729_358-L1-7


title: PR1729_358-L1-6


title: PR1729_358-L1-5


title: PR1729_346-L1-9


title: PR1729_358-L1-10


title: PR1729_346-L1-7


title: PR1729_346-L1-2


title: PR1729_346-L1-3


title: PR1729_358-L1-1


title: PR1729_338-L1-5


title: PR1729_346-L1-11


title: PR1729_346-L1-1


title: PR1729_338-L1-6


title: PR1729_338-L1-4


title: PR1729_358-L1-2


title: PR1729_338-L1-7


title: PR1729_358-L1-8


title: PR1729_338-L1-2


title: PR1729_338-L1-3


title: PR1729_338-L1-1


title: PR1729_326-L1-3


title: PR1729_326-L1-2


title: PR1729_314-L1-4


title: PR1729_358-L1-3


title: PR1729_314-L1-2


title: PR1729_314-L1-3


title: PR1729_314-L1-1


title: PR1729_326-L1-1


title: PR1729_306-L1-4


title: PR1729_306-L1-3


title: PR1729_358-L1-4


title: PR1729_346-L1-5


title: PR1729_286-L1-2


title: PR1729_286-L1-6


title: PR1729_278-L1-3


title: PR1729_278-L1-5


title: PR1729_278-L1-2


title: PR1729_278-L1-6


title: PR1729_266-L1-5


title: PR1729_258-L1-8


title: PR1729_258-L1-7


title: PR1729_286-L1-4


title: PR1729_258-L1-3


title: PR1729_266-L1-4


title: PR1729_278-L1-10


title: PR1729_258-L1-10


title: PR1729_258-L1-5


title: PR1729_266-L1-3


title: PR1729_250-L1-3


title: PR1729_258-L1-6


title: PR1729_278-L1-8


title: PR1729_258-L1-2


title: PR1729_266-L1-1


title: PR1729_250-L1-1


title: PR1729_240-L1-9


title: PR1729_250-L1-9


title: PR1729_258-L1-1


title: PR1729_240-L1-7


title: PR1729_250-L1-7


title: PR1729_240-L1-4


title: PR1729_220-L1-3


title: PR1729_240-L1-3


title: PR1729_240-L1-2


title: PR1729_220-L1-2


title: PR1729_240-L1-8


title: PR1729_240-L1-1


title: PR1729_220-L1-1


title: PR1729_190-L1-2


title: PR1705_258-L1-4

value: male

value: Non-SAN projecting


title: PR1705_399-L1-3


title: PR1705_258-L1-1


title: PR1705_375-L1-4


title: PR1705_201-S1-1


title: PR1705_375-L1-3


title: PR1705_258-L1-2


title: PR1705_463-L1-1

value: Fast Blue and Cresyl violet

value: SAN projecting


title: PR1705_201-S2-1


title: PR1729_240-L1-6


title: PR1705_84-S1-2


title: PR1705_84-S1-1


title: PR1705_531-S1-5


title: PR1729_190-L1-1


title: PR1705_84-L1-3


title: PR1705_84-L1-2


title: PR1729_240-L1-5


title: PR1705_531-S1-3


title: PR1705_531-S1-4


title: PR1729_266-L1-2


title: PR1705_201-S1-2


title: PR1705_531-S1-1


title: PR1705_479-L1-5


title: PR1705_531-L1-2


title: PR1705_479-L1-4


title: PR1705_479-L1-1


title: PR1705_463-L1-6


title: PR1705_431-L1-4


title: PR1705_431-L1-7


title: PR1705_463-L1-2


title: PR1705_399-L1-2


title: PR1705_463-L1-5


title: PR1705_431-L1-6


title: PR1705_399-L2-2


title: PR1705_431-L1-1


title: PR1705_431-L1-3


title: PR1705_399-L2-1


title: PR1705_531-S1-2


title: PR1705_479-L1-3


title: PR1705_431-L1-2


title: PR1705_375-S1-1


title: PR1705_399-L1-1


title: PR1705_375-S1-2


title: PR1705_479-S2-1


title: PR1705_375-L2-2


title: PR1705_375-L2-1


title: PR1705_479-L1-2


title: PR1705_375-L1-5


title: PR1705_463-L1-3


title: PR1705_375-L1-1


title: PR1705_360-S1-1


title: PR1705_330-L1-4


title: PR1705_330-S1-4


title: PR1705_360-L1-4


title: PR1705_360-L1-3


title: PR1705_360-L1-1


title: PR1705_360-L1-2


title: PR1705_330-L2-1


title: PR1705_330-S1-2


title: PR1705_294-S1-3


title: PR1705_330-S1-3


title: PR1705_330-L1-3


title: PR1705_360-L1-5


title: PR1705_360-L1-6


title: PR1705_431-L1-5


title: PR1705_330-S1-1


title: PR1705_360-S1-2


title: PR1705_375-L1-2


title: PR1705_294-S1-2


title: PR1705_294-S1-1


title: Small Intestine Multiplets

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

data_processing:
Illumina HiSeq2500 used for basecalling.
CellRanger 4.0.0 software package used for alignment, filtering and barcode reading, with default parameters.
Genome_build: mm10 (refdata-gex-mm10-2020-A)
Supplementary_files_format_and_content: counts.tsv: Tab-separated text files include transcript counts from CellRanger 4.0.0.
Supplementary_files_format_and_content: Annotation.csv: Comma-separated text files include annotation.

organism: Mus musculus

source_name: Small Intestinal Epithelium

extract_protocol:
Tissues were removed from mice, and cell suspensions were obtained through mechanical and enzymatic dissociation.
scRNA-seq libraries were constructed using Chromium Single Cell 3′ v3 Reagent Kit according to the manufacturer’s protocol.

tag: strain

value: Multiplet

value: Small Intestine


title: Lung Multiplets

source_name: Whole Lung

value: Lung


title: Small Intestine Singlets

value: Singlet


title: PR1705_294-L1-3


title: Lung Singlets


title: PR1705_294-L1-4


title: PR1705_294-L1-2


title: PR1705_294-L1-1


title: PR1705_531-L1-1


title: PR1705_330-L1-1


title: PR1705_258-S1-2


title: RAGP neuronal cell [PR1643_852.G.5]

description:
PR1643_852.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt

data_processing:
Single cell scale RNA-seq libraries from SMART-3Seq protocol were sequenced using an Illumina.
Raw sequencing data (Illumina sequencer’s base call files (BCLs)) was converted to fastq files using the Illumina bcl2fastq program.
The reads from Fastq files were trimmed to remove poly A tail and G overhang and the 5 base umi was extracted.
The trimmed reads were aligned, using STAR-2.7.2a (Dobin et al. 2013) to the Sus scrofa reference genome sequence version Sus_scrofa.Sscrofa11.1.fasta, available in the Ensembl database. Sus_scrofa.Sscrofa11.1.95.gtf was used as a reference transcriptome. Aligned files from reads from 4 lanes are merged by MergeSamfiles from picard.
Feature count algorithm, Subread R (featureCounts) package (Liao et al. 2013) was used to count genomic features genes and exons. A digital gene expression matrix was created from this data.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: PR1643-142-samples-raw-gene-counts.txt: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: PR1643-normalized-gene-counts.txt: Matrix table with normalized counts.

source_name: RAGP of pig heart

extract_protocol:
Single neuronal clusters were collected using Laser Capture Microdissection (LCM) from Right Atrial Ganglionic Plexus (RAGP) of the pig heart.
RNA libraries were prepared using Smart-3Seq protocol.

value: Yucatan minipig

value: Female

value: Right atrial ganglionic plexus (RAGP)


title: RAGP neuronal cell [PR1643_852.G.1]

description:
PR1643_852.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_852.G.4]

description:
PR1643_852.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_832.G.3]

description:
PR1643_832.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_808.G.3]

description:
PR1643_808.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1705_258-S1-1


title: RAGP neuronal cell [PR1643_832.G.2]

description:
PR1643_832.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_808.G.2]

description:
PR1643_808.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1705_258-L2-1


title: RAGP neuronal cell [PR1643_804.G.5]

description:
PR1643_804.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1705_222-L1-2


title: PR1705_222-L1-3


title: PR1705_201-L1-1


title: PR1705_180-S1-3


title: RAGP neuronal cell [PR1643_832.G.4]

description:
PR1643_832.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_852.G.6]

description:
PR1643_852.G.6
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_804.G.4]

description:
PR1643_804.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_784.G.5]

description:
PR1643_784.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1705_180-S1-2


title: PR1705_156-S2-1


title: PR1705_156-S2-3


title: PR1705_180-S1-1


title: PR1705_156-S1-1


title: PR1705_258-L1-3


title: PR1705_156-S2-2


title: RAGP neuronal cell [PR1643_784.G.6]

description:
PR1643_784.G.6
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1705_222-L1-1


title: RAGP neuronal cell [PR1643_808.G.1]

description:
PR1643_808.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_784.G.2]

description:
PR1643_784.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1705_156-L1-3


title: RAGP neuronal cell [PR1643_776.G.3]

description:
PR1643_776.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_784.G.1]

description:
PR1643_784.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_776.G.1]

description:
PR1643_776.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1705_156-L1-2

description:
Single Neuron excised from Right Atrial Ganglionic Plexus (RAGP) of the heart
Neuron Identified using Cresyl violet flourescent signal collected using Laser Capture microdissection
BioMark-qRTPCR


title: RAGP neuronal cell [PR1643_764.G.2]

description:
PR1643_764.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1705_156-L1-1


title: PR1705_132-L1-1


title: PR1705_108-L1-2


title: RAGP neuronal cell [PR1643_764.G.1]

description:
PR1643_764.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_848-L1-6

value: female


title: PR1705_108-L1-1

value: Yucatan mini pig


title: RAGP neuronal cell [PR1643_756.G.3]

description:
PR1643_756.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_848-L1-4


title: PR1643_848-L1-5

value: Cresyl violet


title: PR1643_848-L1-2


title: RAGP neuronal cell [PR1643_756.G.1]

description:
PR1643_756.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_744.G.4]

description:
PR1643_744.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_820-L1-6


title: RAGP neuronal cell [PR1643_744.G.1]

description:
PR1643_744.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_744.G.2]

description:
PR1643_744.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_736.G.5]

description:
PR1643_736.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_820-L1-5


title: RAGP neuronal cell [PR1643_776.G.2]

description:
PR1643_776.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_796-L1-9


title: PR1643_820-L1-4


title: RAGP neuronal cell [PR1643_764.G.3]

description:
PR1643_764.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_820-L1-2


title: PR1643_820-L1-3


title: RAGP neuronal cell [PR1643_756.G.2]

description:
PR1643_756.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_796-L1-8


title: RAGP neuronal cell [PR1643_728.G.2]

description:
PR1643_728.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_728.G.3]

description:
PR1643_728.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_736.G.4]

description:
PR1643_736.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_728.G.1]

description:
PR1643_728.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_796-L1-7


title: RAGP neuronal cell [PR1643_744.G.3]

description:
PR1643_744.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_796-L1-5

description:
Single Neuron excised from Right Atrial Ganglionic Plexus (RAGP) of the heart
Neuron Identified using Cresyl violet flourescent signal collected using Laser Capture microdissection
BioMark-qRTPCR


title: RAGP neuronal cell [PR1643_720.G.3]

description:
PR1643_720.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_796-L1-3


title: PR1643_796-L1-4


title: PR1643_796-L1-6


title: RAGP neuronal cell [PR1643_720.G.1]

description:
PR1643_720.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_720.G.4]

description:
PR1643_720.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_820-L1-1


title: RAGP neuronal cell [PR1643_712.G.5]

description:
PR1643_712.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_796-L1-10


title: PR1643_796-L1-1


title: PR1643_772-L1-6


title: RAGP neuronal cell [PR1643_712.G.2]

description:
PR1643_712.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_728.G.4]

description:
PR1643_728.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_804.G.3]

description:
PR1643_804.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_712.G.1]

description:
PR1643_712.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_704.G.4]

description:
PR1643_704.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_736.G.3]

description:
PR1643_736.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_772-L1-5


title: RAGP neuronal cell [PR1643_704.G.2]

description:
PR1643_704.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_704.G.1]

description:
PR1643_704.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_704.G.5]

description:
PR1643_704.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_732-L1-8


title: PR1643_748-L1-4


title: PR1643_748-L1-1


title: RAGP neuronal cell [PR1643_696.G.2]

description:
PR1643_696.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_748-L1-2


title: RAGP neuronal cell [PR1643_696.G.3]

description:
PR1643_696.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_696.G.1]

description:
PR1643_696.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_704.G.3]

description:
PR1643_704.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_748-L1-3

description:
Single Neuron excised from Right Atrial Ganglionic Plexus (RAGP) of the heart
Neuron Identified using Cresyl violet flourescent signal collected using Laser Capture microdissection
BioMark-qRTPCR


title: RAGP neuronal cell [PR1643_684.G.4]

description:
PR1643_684.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_732-L1-6


title: PR1643_732-L1-7


title: RAGP neuronal cell [PR1643_684.G.3]

description:
PR1643_684.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_684.G.2]

description:
PR1643_684.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_732-L1-5


title: RAGP neuronal cell [PR1643_684.G.1]

description:
PR1643_684.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_772-L1-3


title: RAGP neuronal cell [PR1643_672.G.5]

description:
PR1643_672.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_732-L1-4


title: PR1643_732-L1-3


title: PR1643_732-L1-2


title: PR1643_732-L1-1


title: PR1643_724-L1-4


title: RAGP neuronal cell [PR1643_672.G.1]

description:
PR1643_672.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_724-L1-2


title: RAGP neuronal cell [PR1643_672.G.4]

description:
PR1643_672.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_724-L1-3


title: RAGP neuronal cell [PR1643_664.G.5]

description:
PR1643_664.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_724-L1-1


title: RAGP neuronal cell [PR1643_664.G.4]

description:
PR1643_664.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_717-L1-6


title: RAGP neuronal cell [PR1643_664.G.1]

description:
PR1643_664.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_656.G.3]

description:
PR1643_656.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_717-L1-5


title: PR1643_717-L1-4


title: RAGP neuronal cell [PR1643_656.G.2]

description:
PR1643_656.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_717-L1-3


title: RAGP neuronal cell [PR1643_656.G.4]

description:
PR1643_656.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_656.G.1]

description:
PR1643_656.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_717-L1-2


title: PR1643_700-L1-9


title: PR1643_717-L1-1


title: RAGP neuronal cell [PR1643_646.G.2]

description:
PR1643_646.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_646.G.1]

description:
PR1643_646.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_700-L1-8

description:
Single Neuron excised from Right Atrial Ganglionic Plexus (RAGP) of the heart
Neuron Identified using Cresyl violet flourescent signal collected using Laser Capture microdissection
BioMark-qRTPCR


title: PR1643_700-L1-6


title: RAGP neuronal cell [PR1643_638.G.2]

description:
PR1643_638.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_638.G.1]

description:
PR1643_638.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_700-L1-2


title: PR1643_700-L1-4


title: RAGP neuronal cell [PR1643_618.G.4]

description:
PR1643_618.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_692-L1-4


title: RAGP neuronal cell [PR1643_618.G.5]

description:
PR1643_618.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_692-L1-5


title: RAGP neuronal cell [PR1643_646.G.3]

description:
PR1643_646.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_594.G.4]

description:
PR1643_594.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_594.G.5]

description:
PR1643_594.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_594.G.3]

description:
PR1643_594.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_692-L1-2


title: PR1643_692-L1-1


title: RAGP neuronal cell [PR1643_638.G.4]

description:
PR1643_638.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_578.G.6]

description:
PR1643_578.G.6
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_578.G.5]

description:
PR1643_578.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_676-L1-9


title: PR1643_676-L1-8


title: PR1643_700-L1-7


title: RAGP neuronal cell [PR1643_578.G.4]

description:
PR1643_578.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_570.G.5]

description:
PR1643_570.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_700-L1-1


title: RAGP neuronal cell [PR1643_570.G.4]

description:
PR1643_570.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_578.G.3]

description:
PR1643_578.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_676-L1-7


title: RAGP neuronal cell [PR1643_618.G.3]

description:
PR1643_618.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_570.G.3]

description:
PR1643_570.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_534.G.4]

description:
PR1643_534.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_676-L1-6

description:
Single Neuron excised from Right Atrial Ganglionic Plexus (RAGP) of the heart
Neuron Identified using Cresyl violet flourescent signal collected using Laser Capture microdissection
BioMark-qRTPCR


title: PR1643_676-L1-2


title: PR1643_676-L1-3


title: PR1643_692-L1-3


title: PR1643_676-L1-14


title: RAGP neuronal cell [PR1643_534.G.3]

description:
PR1643_534.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_514.G.4]

description:
PR1643_514.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_514.G.5]

description:
PR1643_514.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_676-L1-15


title: PR1643_676-L1-12


title: RAGP neuronal cell [PR1643_514.G.1]

description:
PR1643_514.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_676-L1-11


title: RAGP neuronal cell [PR1643_502.G.6]

description:
PR1643_502.G.6
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_676-L1-10


title: PR1643_676-L1-1


title: RAGP neuronal cell [PR1643_502.G.5]

description:
PR1643_502.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_668-L1-7


title: RAGP neuronal cell [PR1643_502.G.4]

description:
PR1643_502.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_502.G.3]

description:
PR1643_502.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_502.G.1]

description:
PR1643_502.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_502.G.2]

description:
PR1643_502.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_668-L1-3


title: RAGP neuronal cell [PR1643_630.G.1]

description:
PR1643_630.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_668-L1-11


title: PR1643_668-L1-8


title: PR1643_668-L1-12


title: RAGP neuronal cell [PR1643_618.G.2]

description:
PR1643_618.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_618.G.1]

description:
PR1643_618.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_676-L1-13


title: PR1643_660-L1-9


title: PR1643_668-L1-10


title: RAGP neuronal cell [PR1643_720.G.2]

description:
PR1643_720.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_660-L1-8


title: RAGP neuronal cell [PR1643_808.G.5]

description:
PR1643_808.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_720.G.5]

description:
PR1643_720.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_660-L1-6

description:
Single Neuron excised from Right Atrial Ganglionic Plexus (RAGP) of the heart
Neuron Identified using Cresyl violet flourescent signal collected using Laser Capture microdissection
BioMark-qRTPCR


title: PR1643_660-L1-7


title: PR1643_668-L1-9


title: PR1643_660-L1-5


title: PR1643_660-L1-3


title: RAGP neuronal cell [PR1643_776.G.4]

description:
PR1643_776.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_728.G.7]

description:
PR1643_728.G.7
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_660-L1-2


title: RAGP neuronal cell [PR1643_728.G.6]

description:
PR1643_728.G.6
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_776.G.5]

description:
PR1643_776.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_660-L1-10


title: RAGP neuronal cell [PR1643_664.G.2]

description:
PR1643_664.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_664.G.3]

description:
PR1643_664.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_638.G.5]

description:
PR1643_638.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_638.G.3]

description:
PR1643_638.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_578.G.2]

description:
PR1643_578.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_646.G.5]

description:
PR1643_646.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_578.G.1]

description:
PR1643_578.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_646.G.4]

description:
PR1643_646.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_808.G.4]

description:
PR1643_808.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_570.G.1]

description:
PR1643_570.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_744.G.5]

description:
PR1643_744.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_744.G.6]

description:
PR1643_744.G.6
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_570.G.2]

description:
PR1643_570.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_712.G.3]

description:
PR1643_712.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_514.G.2]

description:
PR1643_514.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_804.G.2]

description:
PR1643_804.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_852.G.3]

description:
PR1643_852.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_712.G.4]

description:
PR1643_712.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_514.G.3]

description:
PR1643_514.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_804.G.1]

description:
PR1643_804.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_594.G.1]

description:
PR1643_594.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_832.G.5]

description:
PR1643_832.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_672.G.2]

description:
PR1643_672.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_634-L1-3

description:
Single Neuron excised from Right Atrial Ganglionic Plexus (RAGP) of the heart
Neuron Identified using Cresyl violet flourescent signal collected using Laser Capture microdissection
BioMark-qRTPCR


title: PR1643_642-L1-6


title: PR1643_634-L1-7


title: PR1643_650-L1-9


title: PR1643_642-L1-5


title: PR1643_634-L1-9


title: PR1643_650-L1-10


title: PR1643_660-L1-1


title: PR1643_650-L1-7


title: PR1643_642-L1-8


title: PR1643_642-L1-1


title: PR1643_650-L1-13


title: PR1643_642-L1-3


title: PR1643_650-L1-15


title: PR1643_642-L1-7


title: PR1643_642-L1-2


title: PR1643_650-L1-11


title: PR1643_650-L1-8


title: PR1643_642-L1-9


title: PR1643_650-L1-1


title: PR1643_650-L1-12


title: PR1643_650-L1-14


title: PR1643_650-L1-2


title: PR1643_642-L1-4


title: RAGP neuronal cell [PR1643_832.G.1]

description:
PR1643_832.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_736.G.2]

description:
PR1643_736.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_672.G.3]

description:
PR1643_672.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_594.G.2]

description:
PR1643_594.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_634-L1-6


title: PR1643_634-L1-1


title: PR1643_634-L1-10


title: RAGP neuronal cell [PR1643_736.G.1]

description:
PR1643_736.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_630.G.2]

description:
PR1643_630.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_696.G.4]

description:
PR1643_696.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_534.G.1]

description:
PR1643_534.G.1
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_764.G.4]

description:
PR1643_764.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_784.G.4]

description:
PR1643_784.G.4
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_784.G.3]

description:
PR1643_784.G.3
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_696.G.5]

description:
PR1643_696.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: RAGP neuronal cell [PR1643_534.G.2]

description:
PR1643_534.G.2
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_610-L1-6


title: PR1643_610-L1-7


title: PR1643_626-L1-1


title: PR1643_626-L1-3


title: PR1643_610-L1-5


title: PR1643_610-L1-4


title: PR1643_626-L1-2


title: PR1643_626-L1-7


title: PR1643_626-L1-4


title: PR1643_626-L1-8


title: PR1643_610-L1-2


title: PR1643_610-L1-1


title: PR1643_610-L1-3


title: PR1643_626-L1-6


title: RAGP neuronal cell [PR1643_764.G.5]

description:
PR1643_764.G.5
Regional neurons
Smart-3SEQ from fresh frozen LCM, 22 PCR cycles.
processed data file: PR1643-142-samples-raw-gene-counts.txt
processed data file: PR1643-normalized-gene-counts.txt


title: PR1643_602-L1-9


title: Male 3

city: hangzhou

first: chengchao

last: zhang

address: Xuelin Street No.16

institute: Hangzhou Normal University

data_processing:
Determination of taxoid contents
Transcriptomic profiling
Bioinformatics of the transcriptomic datasets
Genome_build: FASTA file is available on series record.

organism: Taxus x media

source_name: male tree

growth_protocol: The growth conditions were set at 25 ± 1°C with a light/dark cycle of 12/12 h and a 60%–70% relative humidity

extract_protocol:
Fresh twigs were harvested from both of three independent female and male trees. After dried and grounded into fine powder, samples were used to prepare crude extracts according to a classic method
RNA extraction was performed using an RNeasy plant mini kit (Qiagen, Hilden,Germany). The mRNAs were purified by oligo (dT) attached magnetic beads and fragmented into small fragments. The fragmented mRNAs were reverse-transcribed to create cDNA libraries using a sample preparation kit (Illumina, San Diego, USA).
Sequencing was carried out using an Illumina Hiseq 4000 platform (LC-Bio, Hangzhou, China) to produce raw 100/50-bp paried/single-end reads according to the manufacturer’s protocol.

treatment_protocol: Independent twigs of female and male trees were harvested for metabolomic analysis (25 mg each, N = 10) and transcriptomic analysis (25 mg each, N = 3). All the samples were ground in liquid nitrogen and kept in -80℃ until used.

value: twigs

tag: Sex


title: Male 2


title: Male 1


title: Female 3

source_name: female tree


title: Female 2


title: Female 1


title: PR1643_602-L1-8


title: MOLM13_polysomalRNA_YBX1-sg1_14d_rep4

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

country: Germany

institute: Hannover Medical School

description:
mRNA
polysome_sgYBX1-4
DEGs_polysome_sgYBX1_vs_sgLuci.xlsx
Molm13_YBX1-ko_2weeks_counts.xlsx

data_processing:
Reads (paired-end) in fastq files were adapter-trimmed and quality-trimmed using Trimmomatic (v0.36.5, Galaxy).
Trimmed reads were aligned to the human (Gencode GRCh38/hg38) genome using STAR (v2.7.8a, Galaxy).
A count matrix was generated from mapped .bam files using featureCounts (v2.0.1, Galaxy).
Differential RNA-seq expression was calculated from raw counts using the BioConductor DESeq2 package (v1.30.0).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Molm13_YBX1-ko_2weeks_counts.xlsx: Raw deduplicated gene counts.
Supplementary_files_format_and_content: DEGs_input_sgYBX1_vs_sgLuci.xlsx: DESeq2 differentially expressed gene summary for total RNA (sgYBX1 vs. sgLUC) in MOLM13 cells 14d after transduction.
Supplementary_files_format_and_content: DEGs_polysome_sgYBX1_vs_sgLuci.xlsx: DESeq2 differentially expressed gene summary for polysomal RNA fractions (sgYBX1 vs. sgLUC) in MOLM13 cells 14d after transduction.

organism: Homo sapiens

source_name: MOLM13+Cas9 cultured cells

growth_protocol: MOLM13 cells were cultured in PRMI1640 media supplemented with 10% Fetal bovine serum (v/v) (Gibco), 1x penicillin/streptomycin (Gibco), plasmocin (ThermoFisher). MOLM13 cells were stably transduced with Cas9 (Lenti‐Cas9‐2A‐Blast, Addgene: #73310) and selected with Blasticidine (5ug/ml). After Lentiviral transduction with 2 different guide RNAs targeting YBX1 or non-targeting control (pUSEPR-vector, Puromycine+RFP) cells were cultured in Puromycine (1ug/ml).

extract_protocol:
For RNA isolation total RNA lysates or polysomal fractions were purified using Trizol-reagent and subsequent RNA purification according to the manufacturers instructions.
Poly-A tail selection and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA).
Sequencing was done using the Illumina Next Gen Sequencing HiSeq platform (Illumina, San Diego, CA) with 150bp, paired-end reads.

treatment_protocol: Molm13 cells were lentivirally transduced with Cas9 and YBX1-targeting or non-targeting guide RNAs and selected with Puromycine and Blasticidine for 14 days before cell lysis and sucrose gradient fractionation of polysomes.

tag: cell line

tag: timepoint

value: 14 days post transduction

tag: sgrna

value: CRISPR-Cas9 mediated knockout of YBX1 (sgRNA1)

tag: rna fraction

value: polysomal


title: MOLM13_polysomalRNA_YBX1-sg1_14d_rep2

description:
mRNA
polysome_sgYBX1-2
DEGs_polysome_sgYBX1_vs_sgLuci.xlsx
Molm13_YBX1-ko_2weeks_counts.xlsx


title: MOLM13_polysomalRNA_sgLUC_14d_rep4

description:
mRNA
polysome_sgLUC-4
DEGs_polysome_sgYBX1_vs_sgLuci.xlsx
Molm13_YBX1-ko_2weeks_counts.xlsx

value: non-targeting sgRNA


title: MOLM13_polysomalRNA_sgLUC_14d_rep1

description:
mRNA
polysome_sgLUC-1
DEGs_polysome_sgYBX1_vs_sgLuci.xlsx
Molm13_YBX1-ko_2weeks_counts.xlsx


title: MOLM13_polysomalRNA_sgLUC_14d_rep2

description:
mRNA
polysome_sgLUC-2
DEGs_polysome_sgYBX1_vs_sgLuci.xlsx
Molm13_YBX1-ko_2weeks_counts.xlsx


title: MOLM13_polysomalRNA_YBX1-sg1_14d_rep1

description:
mRNA
polysome_sgYBX1-1
DEGs_polysome_sgYBX1_vs_sgLuci.xlsx
Molm13_YBX1-ko_2weeks_counts.xlsx


title: MOLM13_polysomalRNA_sgLUC_14d_rep3

description:
mRNA
polysome_sgLUC-3
DEGs_polysome_sgYBX1_vs_sgLuci.xlsx
Molm13_YBX1-ko_2weeks_counts.xlsx


title: MOLM13_totalRNA_YBX1-sg1_14d_rep4

description:
mRNA
input_sgYBX1-4
DEGs_input_sgYBX1_vs_sgLuci.xlsx
Molm13_YBX1-ko_2weeks_counts.xlsx

value: total


title: MOLM13_totalRNA_YBX1-sg1_14d_rep3

description:
mRNA
input_sgYBX1-3
DEGs_input_sgYBX1_vs_sgLuci.xlsx
Molm13_YBX1-ko_2weeks_counts.xlsx


title: MOLM13_totalRNA_YBX1-sg1_14d_rep2

description:
mRNA
input_sgYBX1-2
DEGs_input_sgYBX1_vs_sgLuci.xlsx
Molm13_YBX1-ko_2weeks_counts.xlsx


title: MOLM13_totalRNA_YBX1-sg1_14d_rep1

description:
mRNA
input_sgYBX1-1
DEGs_input_sgYBX1_vs_sgLuci.xlsx
Molm13_YBX1-ko_2weeks_counts.xlsx


title: PR1643_602-L1-7

description:
Single Neuron excised from Right Atrial Ganglionic Plexus (RAGP) of the heart
Neuron Identified using Cresyl violet flourescent signal collected using Laser Capture microdissection
BioMark-qRTPCR

value: Non-SAN projecting


title: MOLM13_totalRNA_sgLUC_14d_rep3

description:
mRNA
input_sgLUC-3
DEGs_input_sgYBX1_vs_sgLuci.xlsx
Molm13_YBX1-ko_2weeks_counts.xlsx


title: MOLM13_totalRNA_sgLUC_14d_rep4

description:
mRNA
input_sgLUC-4
DEGs_input_sgYBX1_vs_sgLuci.xlsx
Molm13_YBX1-ko_2weeks_counts.xlsx


title: MOLM13_polysomalRNA_YBX1-sg1_14d_rep3

description:
mRNA
polysome_sgYBX1-3
DEGs_polysome_sgYBX1_vs_sgLuci.xlsx
Molm13_YBX1-ko_2weeks_counts.xlsx


title: MOLM13_totalRNA_sgLUC_14d_rep1

description:
mRNA
input_sgLUC-1
DEGs_input_sgYBX1_vs_sgLuci.xlsx
Molm13_YBX1-ko_2weeks_counts.xlsx


title: PR1643_566-L1-4


title: PR1643_574-L1-1

value: Fast Blue and Cresyl violet

value: SAN projecting


title: MOLM13_totalRNA_sgLUC_14d_rep2

description:
mRNA
input_sgLUC-2
DEGs_input_sgYBX1_vs_sgLuci.xlsx
Molm13_YBX1-ko_2weeks_counts.xlsx


title: HEK293T IgG GO-CaRT Rep2

city: San Francisco

first: Tomasz

last: Nowakowski

state: Ca

institute: UCSF

library_source: genomic

data_processing:
Library strategy: GO-CaRT
150bp paired-end sequencing of GO-CaRT libraries was performed on the Illumina HiSeq 4000. Low quality reads and adaptors were removed with BBduk (http://jgi.doe.gov/data-and-tools/bb-tools/), and resulting reads were aligned to the mouse (UCSC mm10), macaque (USCS rheMac8) or human (UCSC hg38) genome using bowtie2 and the following settings: --local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700. Duplicate reads were removed with Picard tools

molecule: genomic DNA

growth_protocol: Cells were cultured in DMEM with 10% FBS

extract_protocol:
75,000-100,000 acutely isolated cells from mouse, macaque, and human forebrain (or cultured 3T3 and HEK293T cells) were used for each experiment. Cells were resuspended in 500 mL ice cold Nuclei Isolation Buffer (NIB) (10 mM HEPES-KOH, Ph 7.9. 10 mM KCl, 0.1% NP40, 0.5 mM Spermidine and 1X Halt protease inhibitor cocktail) and incubated for 10 min in ice. Nuclear pellet was collected by centrifuging at 600xg for 3 min at 40C and again washed with 500 mL NIB. Nuclear pellet was collected by centrifugation at 600xg for 3 and resuspended in 100 mL of NIB. Successful nuclei isolation was confirmed by visual inspection under a phase contrast microscope. Next, 10 mL Concanavalin A lectin beads (Bio-Mag Plus) washed and resuspended in Binding Buffer (BiB) (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 1 mM CaCl2 and 1 mM MnCl2) were added to each sample and rotated for 10 min at room temperature. Nuclei bound Concanavalin A beads were pulled by placing the tubes on a magnetic stand to remove the supernatant. For LaminB GO-CaRT, anti LaminB1 antibody (Abcam# ab16048) was used and for SON GO-CaRT, anti-SON antibody (Atlas antibodies #HPA031755) was used at 1:100 dilution in Blocking Buffer (BlocB) (Wash buffer containing 2mM EDTA). Same steps were followed for histone marks using anti-H3K9me2 (Active Motif #39239, 1:100), anti-H3K9me3 (Abcam# ab8898; 1:100), anti-H3K27me3 (Cell signaling technologies #9733; 1:100). An IgG control was run in parallel for all experiments (Cell signaling technologies #2729; 1:100). To each sample 50 mL of BlocB containing primary antibody was added and incubated overnight on a rotator at 40C. Next day, samples were briefly spun and placed on magnetic stand to clear off the liquid. Samples were washed twice with 1mL Wash Buffer (WaB) (20 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 0.1% BSA, 0.5 mM Spermidine and 1X Halt protease inhibitor cocktail). At the end of two washing steps, Concanavalin A bound nuclei were resuspended in 50 mL of WaB and gently mixed. To each tube, 2.5 mL of pA-MNase (diluted 1:10 in WaB from 140 mg/mL stock) kindly provided by Steven Henikoff (Fred Hutchison Cancer Research Center) was added and rotated for 1 hour at 40C. Samples were briefly spun and placed on magnetic stand to remove the liquid. Samples were washed twice with 1mL WaB. At the end of two washing steps, Concanavalin A bound nuclei were resuspended in 100 mL of WaB and gently mixed. The tubes were placed in pre-chilled metal blocks sitting in ice. While gently vortexing, 2 mL of 100 mM CaCl2 was added to initiate MNase digestion and returned to pre-chilled metal blocks. Digestion was carried out for 30 min and stopped by adding 100 mL of 2XSTOP (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 mg/mL RNAseA, 40 mg/mL Glycogen and 10 pg/mL of heterologous DNA) while gently vortexing. To release pA-MNase cleaved fragments, samples were incubated at 370C for 15 min. DNA was extracted using Phenol: Chloroform extraction method. We considered the possibility that the pA-MNase cleaved DNA-protein complexes might be too large to diffuse out of the nucleus and enter the “soluble” fraction.  To test this, we recovered DNA from both soluble and total fractions (soluble + insoluble).  LaminB profiles were highly similar (Pearson= 0.94) between soluble and total fractions, indicating that DNA-protein complexes released by LaminB GO-CaRT can readily diffuse out of the nucleus.
Sequencing libraries were prepared from GO-CaRT DNA fragments using KAPA HyperPlus with amplification DNA library preparation kit (#KK8512) following manufacturer instructions. The library was amplified for 13-15 PCR cycles and larger DNA fragments were depleted by doing a 0.55X size selection using Agencourt AMPure XP beads (Beckman #A63881).


title: PR1643_582-L1-1


title: PR1643_590-L1-4


title: PR1643_590-L1-7


title: PR1643_590-L1-6


title: PR1643_582-L1-3


title: PR1643_590-L1-2


title: PR1643_574-L1-4


title: PR1643_602-L1-6


title: PR1643_590-L1-5


title: PR1643_590-L1-1


title: PR1643_602-L1-4


title: PR1643_602-L1-10


title: PR1643_602-L1-1


title: PR1643_602-L1-3


title: PR1643_566-L1-2


title: PR1643_558-L1-4


title: HEK293T IgG GO-CaRT Rep1


title: PR1643_566-L1-1


title: PR1643_574-L1-3


title: PR1643_574-L1-2


title: RNAseq rep1

city: nanjing

first: Aiping

last: Duan

address: zhongshan east road 305

institute: Jinling hospital

description: mRNA

data_processing:
ChIPseq: The adaptors were trimmed with cutadapt, then used Bowtie2 with default parameters to align the trimmed reads to the hg19, and called peaks using MACS2.
RNAseq: We used HISAT2 with default parameters to align reads to hg38. Transcript assembly was used Stringtie. Fragments per kilobase of transcript sequence per million mapped fragments (FPKM) was reported as expression level estimation.
Genome_build: ChIPseq: hg19 (GRCh37), RNAseq: hg38 (GRCh38)
Supplementary_files_format_and_content: ChIP-seq: peaks.bed files, bigWig files
Supplementary_files_format_and_content: RNA-seq: gtf files

source_name: kidney tubule HK2 cells

growth_protocol: Immortalized human renal proximal tubular cell line HK2 cells were cultured in DMEM-F12 medium with 10% FBS (Gibco), 1% penicillin-streptomycin at 37°C in a 5% (v/v) CO2 humidified incubator. FG-4592 was dissolved in DMSO and added to DMEM/F12 medium to the final concentration of 50μM for HK2 treatment.

extract_protocol:
The harvested HK2 cells were fixed with 1% formaldehyde for ChIPseq and harvested in Trizol for RNAseq.
Genomic DNA was extracted with DNA Clean & Concentrator kit (ZYMO).
Libraries were prepared according to the Illumina instruction. DNA samples were firstly end-repaired by NEBNext End Repair Enzyme Mix. Then we added adapters by T4 ligase buffer.

tag: cell type

value: Proximal tubular epithelial cells


title: RNAseq rep2

description: mRNA


title: HIF1α _ChIPSeq_rep2

tag: chip antibody

value: HIF1alpha (Novus, NB100-134)


title: HIF1α _ChIPSeq_rep1


title: PR1643_566-L1-3

tag: gender


title: PR1643_558-L1-1

tag: breed


title: PR1643_558-L1-3

tag: animal id


title: PR1643_558-L1-2

tag: sample flourecent label


title: PR1643_550-L1-6

tag: sample san (sino-atrial node) projecting/san non-projecting


title: PR1643_550-L1-1


title: PR1643_542-L1-4


title: PR1643_550-L1-3


title: PR1643_550-L1-4


title: RNA-seq_Pulmonary artery endothelial cells - ST_RepA

city: Stanford

first: Jan-Renier

last: Moonen

state: CA

address: 269 Campus Drive, CCSR 1220

department: Pediatrics

institute: Stanford University

data_processing:
Basecalls were performed using Bcl2fastq.
Reads were aligned to the human genome using STAR v.2.5.4b. Aligned transcripts were quantitated by RSEM v. 1.3.1 (http://deweylab.biostat.wisc.edu/rsem/).
Genome_build: hg19
Supplementary_files_format_and_content: Gene count matrix files

source_name: Pulmonary artery endothelial cells

growth_protocol: PAEC were grown in commercial EC media containing 5% FBS (Sciencell) in a 5% CO2 air atmosphere and used at passages 3–7.

extract_protocol:
RNA was extracted using RNeasy Plus Mini Kit (Qiagen)
Libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina)

treatment_protocol: PAEC were exposed to 15 dyn/cm2 of LSS, or static culture conditions, for 24h.

value: Pulmonary artery endothelial cells

value: static control


title: RNA-seq_Pulmonary artery endothelial cells - LSS_RepB

value: 15 dyne/cm2 of LSS


title: RNA-seq_Pulmonary artery endothelial cells - ST_RepB


title: PR1643_550-L1-8

value: female


title: Pulmonary artery endothelial cells - LSS_siKLF_RepB

treatment_protocol: PAEC were transfected with siRNA targeting KLF2 and KLF4 (siKLF), or non targeting controls (siC). followed by 24 h of exposure to 15 dyne/cm2 of LSS.

value: siKLF


title: PR1643_542-L1-3

value: Yucatan mini pig

value: Cresyl violet


title: Pulmonary artery endothelial cells - LSS_siC_RepB_for_siKLF

value: siC


title: Pulmonary artery endothelial cells - LSS_siC_RepC_for_siKLF


title: PR1643_530-L1-5


title: PR1643_530-L1-3


title: PR1643_530-L1-4


title: PR1643_542-L1-1


title: PR1643_542-L1-2


title: PR1643_530-L1-2


title: PR1643_506-L1-3


title: PR1643_506-L1-4


title: Pulmonary artery endothelial cells - LSS_siC_RepA_for_siKLF


title: Pulmonary artery endothelial cells - LSS_siC_RepC

extract_protocol:
RNA was extracted using RNeasy Plus Mini Kit (Qiagen)
Libraries were prepared using QuantSeq 3' mRNA-Seq Library Prep Kit FWD (Lexogen).

treatment_protocol: PAEC were transfected with siRNA targeting DUSP5 (siDUSP5), or non targeting controls (siC). followed by 24 h of exposure to 15 dyne/cm2 of LSS.


title: Pulmonary artery endothelial cells - LSS_siC_RepB


title: Pulmonary artery endothelial cells - LSS_siKLF_RepA


title: RNA-seq_Pulmonary artery endothelial cells - LSS_RepA


title: PR1534_92-L1-7

value: male


title: Pulmonary artery endothelial cells - LSS_siDUSP5_RepA


title: Pulmonary artery endothelial cells - LSS_siC_RepA


title: Pulmonary artery endothelial cells - LSS_siDUSP5_RepB


title: PR1534_80-L1-6


title: Pulmonary artery endothelial cells - Input DNA_Control_RepB_forKLFandhistone

data_processing:
Basecalls were performed using Bcl2fastq.
FASTQ files were processed using the Kundaje Lab ChIP-seq processing pipeline (https://github.com/kundajelab/chipseq_pipeline).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig coverage files from merged replicates.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min, quenched with 2 M glycine, washed with PBS and pellets were snap-frozen and stored at -80°C.
Libraries were prepared using standard protocols from the Genomics of Gene Regulation (GGR) project, NHGRI, as performed in the Snyder Lab. Briefly, purified ChIP-DNA samples were end repaired using End-It DNA End Repair Kit (Lucigen) and A-tailed using Klenow Fragment and dATP (New England Biolabs). Illumina TruSeq adapters (Illumina) were ligated using LigaFast (Promega) and size-selected by gel extraction before PCR amplification.

value: ad.GFP transduced


title: Pulmonary artery endothelial cells - Input DNA_Control_RepA_forKLFandhistone


title: Pulmonary artery endothelial cells - Control_KLF4_RepB

value: KLF4 (sc20691, Santa Cruz Biotechnology)


title: Pulmonary artery endothelial cells - Input DNA_caMEK5_RepA_forKLFandhistone

value: ad.caMEK5 transduced


title: Pulmonary artery endothelial cells - Input DNA_caMEK5_RepB_forKLFandhistone


title: PR1643_506-L1-2

value: Non-SAN projecting


title: PR1534_80-L1-5

value: Fast Blue and Cresyl violet


title: PR1534_92-L1-5


title: PR1534_80-L1-8

value: SAN projecting


title: PR1534_72-L1-8


title: PR1534_80-L1-3


title: PR1534_72-L1-6


title: PR1534_92-L1-8


title: PR1534_80-L1-4


title: PR1534_80-L1-7


title: Pulmonary artery endothelial cells - caMEK5_KLF4_RepB


title: Pulmonary artery endothelial cells - Control_KLF4_RepA


title: Pulmonary artery endothelial cells - caMEK5_KLF4_RepA


title: PR1534_72-L1-7


title: PR1534_92-L1-6


title: Pulmonary artery endothelial cells - caMEK5_H3K27ac_RepA

value: H3K27ac (#8173, Cell signaling Technology)


title: Pulmonary artery endothelial cells - Input DNA_Control_RepA

extract_protocol:
Cells were cross-linked with 2 mM of DSG (Pierce) for 45 min at RT, washed with PBS followed by cross-linking using 1% formaldehyde for 10 min, quenched with 2 M glycine, washed with PBS after which pellets were snap-frozen and stored at -80°C.
Libraries were prepared using standard protocols from the Genomics of Gene Regulation (GGR) project, NHGRI, as performed in the Snyder Lab. Briefly, purified ChIP-DNA samples were end repaired using End-It DNA End Repair Kit (Lucigen) and A-tailed using Klenow Fragment and dATP (New England Biolabs). Illumina TruSeq adapters (Illumina) were ligated using LigaFast (#M8221, Promega) and size-selected by gel extraction before PCR amplification.

treatment_protocol: PAEC were transduced with adenoviral vectors encoding a constitutively active mutant of MEK5, or GFP as control.


title: PR1534_62-L1-6


title: Pulmonary artery endothelial cells - caMEK5_H3K4me1_RepA

value: H3K4me1 (#5326, Cell Signalling Technology)


title: Pulmonary artery endothelial cells - Control_H3K4me1_RepA

value: Pulmonary artery endothelial cells


title: PR1534_62-L1-4


title: Pulmonary artery endothelial cells - LSS_siKLF_RepC


title: Pulmonary artery endothelial cells - Control_H3K27ac_RepA


title: Pulmonary artery endothelial cells - Input DNA_caMEK5_RepA


title: PR1534_239-L1-8


title: PR1534_239-L1-7


title: PR1534_62-L1-3


title: PR1534_239-L1-6


title: Pulmonary artery endothelial cells - caMEK5_H3K27ac_RepB


title: PR1534_239-L1-5


title: Pulmonary artery endothelial cells - control BRG1_RepA

value: BRG1 (A303-877A, Bethyl Laboratories)


title: Pulmonary artery endothelial cells - Control_H3K4me1_RepB


title: PR1534_62-L1-1


title: PR1534_62-L1-2


title: Pulmonary artery endothelial cells - Control_H3K27ac_RepB


title: PR1534_239-L1-2


title: PR1534_61-L1-7


title: PR1534_20-L1-1


title: Pulmonary artery endothelial cells - caMEK5_H3K4me1_RepB


title: Pulmonary artery endothelial cells - Input DNA_Control_RepB


title: Pulmonary artery endothelial cells - Input DNA_caMEK5_RepB


title: PR1534_53-L1-7


title: PR1534_53-L1-1


title: PR1534_53-L1-3


title: Pulmonary artery endothelial cells - control BRG1_RepB


title: ATAC-seq_Pulmonary artery endothelial cells - caMEK5_RepB

data_processing:
Basecalls were performed using Bcl2fastq.
FASTQ files were processed using the Kundaje Lab ATAC-seq processing pipeline (https://github.com/kundajelab/atac_dnase_pipelines).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig coverage files from merged replicates.
Supplementary_files_format_and_content: bed file containing the union peaks

extract_protocol:
Cells were trypsinized, washed with ice-cold PBS, and lysed to isolate the nuclei.
Isolated nuclei were incubated at 37°C for 30 min in the presence of 5 ul of TDE1 (Nextera Tn5 transposase, Illumina), followed by PCR amplification and gel purification as previously described (Buenrostro et al. Nat Methods 2013)

treatment_protocol: PAEC were transduced with adenoviral vectors encoding caMEK5, or GFP as control.


title: ATAC-seq_Pulmonary artery endothelial cells - caMEK5_RepC


title: Pulmonary artery endothelial cells - caMEK5 BRG1_RepB


title: PR1534_239-L1-4


title: Pulmonary artery endothelial cells - caMEK5 BRG1_RepA


title: PR1534_53-L1-8


title: ATAC-seq_Pulmonary artery endothelial cells - Control_RepC


title: ATAC-seq_Pulmonary artery endothelial cells - Control_RepB


title: PR1534_239-L1-3


title: ATAC-seq_Pulmonary artery endothelial cells - Control_RepA


title: ATAC-seq_Pulmonary artery endothelial cells - ST_RepA

value: static control


title: PR1534_239-L1-1


title: PR1534_20-L1-2


title: ATAC-seq_Pulmonary artery endothelial cells - LSS_siC_RepB

treatment_protocol: PAEC were transfected with siRNA targeting KLF2 and KLF4 (siKLF), or non targeting controls (siC), followed by 24 h of exposure to 15 dyne/cm2 of LSS.

value: non-targeting siControl


title: ATAC-seq_Pulmonary artery endothelial cells - caMEK5_RepA


title: PR1534_209-L1-4


title: PR1534_209-L1-2


title: PR1534_209-L1-9


title: PR1534_209-L1-6


title: ATAC-seq_Pulmonary artery endothelial cells - ST_RepC


title: PR1534_209-L1-1


title: ATAC-seq_Pulmonary artery endothelial cells - ST_RepB


title: PR1534_188-L1-7


title: ATAC-seq_Pulmonary artery endothelial cells - LSS_RepC

value: 15 dyne/cm2 of LSS


title: ATAC-seq_Pulmonary artery endothelial cells - LSS_siC_RepA


title: PR1534_209-L1-5

value: Yucatan mini pig


title: PR1534_209-L1-3

value: Cresyl violet


title: PR1534_209-L1-7


title: ATAC-seq_Pulmonary artery endothelial cells - LSS_RepB


title: ATAC-seq_Pulmonary artery endothelial cells - LSS_siKLF_RepB

value: siRNA targeting KLF2/4


title: ATAC-seq_Pulmonary artery endothelial cells - LSS_RepA


title: ATAC-seq_Pulmonary artery endothelial cells - LSS_siKLF_RepC


title: ATAC-seq_Pulmonary artery endothelial cells - LSS_siKLF_RepA


title: ATAC-seq_Pulmonary artery endothelial cells - LSS_siC_RepC


title: cytoEV rep2

city: Rochester

first: Naureen

last: Javeed

state: MN

address: 200 First St SW

institute: Mayo Clinic

data_processing:
Illumina's RTA version 2.7.7. for basecalling
Fragment reads were aligned using TopHat version 2.0.6 (Trapnell et al., 2012), assembled using StringTie version 2.1.3 (Pertea et al., 2015), and counted using StringTie’s script (PrepDE.py) via Python version 3.6, all with default settings. The count matrix was then imported into R version 3.6.1 and differentially expressed genes were identified using edgeR version 3.1.1 (Robinson et al., 2010) using a cutoff of p<0.05 and a fold change greater than 1.5.
Genome_build: mm10
Supplementary_files_format_and_content: normalized CPM

source_name: Islet

growth_protocol: Isolated C57BL/6 islets were cultured in standard 11 mM glucose RPMI media and allowed to recover overnight. Islet treatments were conducted in this media as well.

extract_protocol:
Islets were picked and mRNA was isolated using the Rneasy Plus Minikit (Qiagen). RNA libraries were prepared using 200 ng of total RNA.
RNA libraries were prepared for sequencing according to the manufacturer's instructions for the TruSeq Stranded mRNA Sample Prep Kit (Illumina)

treatment_protocol: 2 replicates were untreated (UT) islets and 2 replicates received cytoEV treatments every day for 48 h prior to RNA extraction for RNA-Seq analysis.

value: Pancreatic islets

value: cytoEV-treated

tag: genotype

value: wild type


title: cytoEV rep1


title: UT rep2

value: untreated


title: UT rep1


title: E13 MGE RNA-Seq Rep 2

data_processing: For differential expression analysis, reads were pseudoaligned to the mouse transcriptomes, Gencode GRCm38 release M16, using kallisto (v0.43.1) with default settings. Gene-level differential expression analysis was performed with Sleuth (0.30.0) using the transformation function = function(x) log2(x + 0.5) convert b value output from Sleuth into log2 fold-change.

source_name: Embryonic Mouse Telencephalon

extract_protocol: Total RNA was extracted using TRIzol (Thermo # 15596018) and purified using Direct-Zol RNA kit (Zymo). Total RNA was subjected to rRNA depletion using ribo-depletion kit (NEB#E6310). Libraries for sequencing were prepared using NEB’s Next Ultra II direction library kit (NEB#E7760) following manufacturer’s protocol.

value: Embryonic Mouse Telencephalon

tag: developmental stage

value: Embryonic Day 13


title: E13 LGE RNA-Seq Rep 2


title: E13 V1 RNA-Seq Rep 2


title: E13 MGE RNA-Seq Rep 1


title: E13 PFC RNA-Seq Rep 2


title: E13 PFC RNA-Seq Rep 1


title: E13 LGE RNA-Seq Rep 1


title: PR1534_142-L1-5

value: male

value: Non-SAN projecting


title: PR1534_160-L1-1

value: Fast Blue and Cresyl violet

value: SAN projecting


title: PR1534_180-L1-6


title: PR1534_170-L1-6


title: PR1534_160-L1-3


title: PR1534_180-L1-8


title: PR1534_188-L1-2


title: PR1534_188-L1-3


title: PR1534_170-L1-7


title: PR1534_180-L1-7


title: PR1534_160-L1-4


title: PR1534_160-L1-5


title: PR1534_170-L1-3


title: PR1534_142-L1-3


title: PR1534_170-L1-2


title: E13 V1 RNA-Seq Rep 1


title: PR1534_122-L1-3


title: PR1534_170-L1-5


title: E13 Liver IgG GO-CaRT Rep 2

source_name: Embryonic Mouse Liver

value: Embryonic Mouse Liver

value: (C57BL/6 x BALB/cBy)F1


title: E13 Lung IgG GO-CaRT Rep 2

source_name: Embryonic Mouse Lung

value: Embryonic Mouse Lung


title: PR1534_112-L1-5


title: PR1534_122-L1-1


title: PR1534_142-L1-4


title: E13 Lung IgG GO-CaRT Rep 1


title: PR1534_122-L1-2


title: PR1534_112-L1-2


title: E13 NesGFP MGE LaminB GO-CaRT Rep 2

description:
Nes_Subpallium_LmnB_Rep2.bw
Nes_Subpallium_LmnB_Rep2_peaks_clean.bed


title: E13 NesGFP PFC IgG GO-CaRT Rep 2


title: E13 NesGFP PFC LaminB GO-CaRT Rep 2

description:
Nes_Pallium_LmnB_Rep2.bw
Nes_Pallium_LmnB_Rep2_peaks_clean.bed


title: E13 Liver IgG GO-CaRT Rep 1


title: E13 NesGFP LGE LaminB GO-CaRT Rep 2


title: E13 NesGFP MGE IgG GO-CaRT Rep 2


title: E13 NesGFP LGE IgG GO-CaRT Rep 2


title: E13 NesGFP V1 LaminB GO-CaRT Rep 2


title: E13 NesGFP LGE IgG GO-CaRT Rep 1


title: E13 NesGFP MGE IgG GO-CaRT Rep 1


title: E13 NesGFP LGE LaminB GO-CaRT Rep 1

description:
Nes_Subpallium_LmnB.bw
Nes_Subpallium_LmnB_peaks_clean.bed


title: E13 NesGFP V1 IgG GO-CaRT Rep 2


title: E13 NesGFP PFC IgG GO-CaRT Rep 1


title: E13 NesGFP PFC LaminB GO-CaRT Rep 1

description:
Nes_Pallium_LmnB.bw
Nes_Pallium_LmnB_peaks_clean.bed


title: E13 NesGFP V1 IgG GO-CaRT Rep 1


title: PR1534_10-L1-2

description:
Single Neuron excised from Right Atrial Ganglionic Plexus (RAGP) of the heart
Neuron Identified using Cresyl violet flourescent signal and Sinoatrial Node connected neurons identified by Fast Blue flourescent signal collected using Laser Capture microdissection
BioMark-qRTPCR


title: PR1534_10-L1-3


title: PR1534_10-L1-4


title: PR1534_112-L1-1


title: PR1534_10-L1-5


title: E13 NesGFP V1 LaminB GO-CaRT Rep 1


title: E13 NesGFP MGE LaminB GO-CaRT Rep 1


title: SM006

city: New York

first: Job

last: de Jong

address: 1051 Riverside Drive

department: Psychiatry

institute: Columbia University

description:
single cell RNA sequencing
exprMatrix.tsv.gz

data_processing:
Libraries were sequenced using Illumina HiSeq2000 at the Columbia Genome Center. Multiplex samples with unique barcodes were mixed in each lane, which yields targeted number of single-end 100 bp reads for each sample, as a fraction of 180 million reads for the whole lane. RTA software (Illumina) was used for base calling, and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. The reads were mapped to a reference human genome (hg19) using Tophat2.0 (version 2.0.4) with four mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
single cell RNAseq data were processed by 10X genomic cellranger 4.0.0 with counts and aggr functions; data analysis was conducted using scanpy, liger, singleR and MAST software
Genome_build: hg19; hg38 for single cell RNAseeq
Supplementary_files_format_and_content: for single cell RNAseq the processed data including:meta.tsv; exprMatrix.tsv.gz
Supplementary_files_format_and_content: scRNAseq expression matrix
Supplementary_files_format_and_content: scRNAseq meta annotation

source_name: patient derived iPSC

growth_protocol: hiPSCs were dissociated with 0.5 mM EDTA in PBS and triturated to generate a single cell suspension. A total of 10,000 cells were then plated into each well of an ultra-low-attachment 96-well plate (Nunc) to form embryoid bodies (EBs) in medium containing mTesR1, 1 µg/ml heparin and Penicillin-Streptomycin antibiotics. EBs were exposed to medium containing the ROCK inhibitor Y27632 (50 µM) for the first 24h, followed by 5 days without interference in 96-well plates. On day 5, the medium was switched to medium containing DMEM/F12 (1:1) (Gibco; 11330), N-2 supplement (Gibco; 17502-048), MEM-NEAA (Invitrogen), Glutamax (Invitrogen 35050-061), Penicillin-Streptomycin and 0.1 mM ®-Mercaptoethanol, Dorsomorphin (2 µM), SB431542 (10 µM) and IWR1e (3 µM). On day 25, 0.2% Chemically Defined Lipid Concentrate was added to this medium until day 39. On day 40, EBs were transferred to ultra-low attachment 24 well plates with 1 ml of medium per organoid/well. Between day 40 and 80, 1 ml of medium containing DMEM/F12 (1:1) (N-2 supplement MEM-NEAA, Glutamax, Penicillin-Streptomycin and 0.1 mM ®-Mercaptoethanol, 10% fetal bovine serum (FBS) and 1% Matrigel (Corning) was replaced weekly. After day 80 medium was replaced once per week. Matrigel was added bi-weekly to prevent excess Matrigel deposition on the outer shell of the organoid.

extract_protocol:
3 organoids per samples and dissociated using the papain dissociation protocol (Worthington Biochemicals)
The 10x Genomics Chromium Single Cell 3' Solution
The resulting pooled, 3'-end libraries are typically sequenced on a NovaSeq 6000
Ten forebrain organoids per line (i.e., 3 control-derived lines, 3 patient-derived lines) were collected at 8 weeks in vitro. Total RNA was isolated from hiPSC-derived cortical neurons using miRNeasy kit (Qiagen, USA) according to instructions of the manufacturer.A poly-A pull-down step was performed to enrich mRNAs from total RNA samples (200 ng to 1 µg per sample, RIN > 8 required)
library preparation was done using Illumina TruSeq RNA prep kit
Libraries were sequenced using Illumina HiSeq2000 at the Columbia Genome Center. Multiplex samples with unique barcodes were mixed in each lane, which yields targeted number of single-end 100 bp reads for each sample, as a fraction of 180 million reads for the whole lane. RTA software (Illumina) was used for base calling, and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. The reads were mapped to a reference human genome (hg19) using Tophat2.0 (version 2.0.4) with four mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).

treatment_protocol: growth and treatment described in growth protocol

value: mutant

tag: batch


title: Club cells from 4 Atgl KO/cTg  mice [A0C-3111-3114]

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

description: Gene expression data from club cells withouth ATGL

hyb_protocol: Affymetrix Mouse Gene 2.0 ST Array (Cat No. 902118); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip® fluidics station 450: protocol FS450_0002 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software AGCC 4.0.0)

data_processing: Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files.

label: Biotin

source_name: Knock-out cells

label_protocol: 50ng for NuGen Ovation Pico WTA System V2, M01224v2 (NuGEN Technologies Inc; San Carlos, CA; Cat No. 3302-24)

growth_protocol: All animals were kept on a regular light-dark cycle (14 h light-10 h dark) at 22±1 °C in a specific pathogen-free environment, and were fed a standard laboratory chow diet ad libitum.

extract_protocol: 200 μL of chloroform was put on the 1 mL of trizol containing the club cells and centrifuged. Further steps  for isolation were followed according to the kit protocol. Kit used: miRNeasy Micro Kit (Qiagen, Hilden, Germany; Cat No 217084) including DNAse treatment on the column with RNase-Free DNase Set (Qiagen, Hilden, Germany; Cat No 79254)

treatment_protocol: No specific treatments were involved. For isolation of the cells, animals were first deeply anesthesised and sacrificed. Club cells were  isolated from the extracted lung according to the standard protocol. Isolated cells were then used for RNA extraction.

tag: genotype/variation

value: Atgl KO/cTg

tag: age

value: 43-45 weeks

tag: tissue/cell type

value: Club cells from Lung


title: SM005

tag: cell line


title: Club cells from 4 Atgl KO/cTg  mice [A0C-3149-3152]

value: 38-43 weeks


title: SB-9: PMN-Cre+/+

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

hyb_protocol: Fifteen micrograms of fragmented cRNA were hybridized for 16 hrs at 45°C under constant rotation. After hybridization, chips were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol EukGE-WS2v5_450). Staining was made with streptavidin-conjugated phycoerythrin (SAPE, Molecular Probes), followed by amplification with a biotinylated anti17 streptavidin antibody (Vector Laboratories), and followed by a second round of SAPE.

scan_protocol: The arrays were scanned using the Affymetrix GCS 3000 7G and the Gene-Chip Operating Software (Affymetrix, Santa Clara, CA), to produce the intensity files. Microarray hybridization was carried out at the Microarrays Facility of the Research Center of Laval University CRCHUL.

data_processing: Background subtraction and normalization of probe set intensities were performed using the method of Robust Multiarray Analysis (Irizarry et al, 2003), as impelemented by TAC 4.0 software..

source_name: Control Flox+/+ Leucocytes that have migrated into the mouse air pouches injected with LPS

label_protocol: Total RNA (100 ng per sample) was labeled using the GeneChip® WT Plus Reagent Kit protocol and hybridized to the arrays as described by the manufacturer (Affymetrix, Thermofisher).

extract_protocol: Total RNA was isolated from PMNs. Total RNA extraction was performed with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol, and potential genomic DNA contamination was eliminated with the RNase-free DNase set (Qiagen). Total RNA was eluted in RNAse-free water and its concentration was quantified with a NanoDrop 1000 microvolume spectrophotometer (Thermo Scientific). Ribonucleic acid quality was assessed with the Eukaryote Total RNA Pico Series II kit (Agilent) on a 2100 Bioanalyzer by the transcriptomic core facility of the CHUQ. The minimal accepted number for RNA integrity was 7.

treatment_protocol: Leucocytes that have migrated into the mouse air pouches injected with LPS were collected from the Arf6 cKO and the control groups (homozygous Cre+/+ and flox+/+Cre-/- mice, respectively). For each mouse genotype, three independent groups of 5 mice were used. Air pouch PMNs were pooled and purified by negative selection as described above. The cell suspensions were 98% Ly6G positive as estimated by flow cytometry

value: Leucocytes

value: control flox-/-Cre+/+


title: 3T3 MEFs H3K27me3 IgG GO-CaRT Soluble Rep 2

source_name: NIH/3T3 cells

tag: tissue

value: NIH/3T3 cells


title: SB-5: PMN-Arf6 cKO

value: Arf6 cKO (flox+/+Cre+/+)


title: Club cells from 4 wt/cTg  mice [A2C-3153-3156]

description: Gene expression data from club cells with ATGL

source_name: Control

value: wt/cTg

value: 41-48 weeks


title: Club cells from 4 Atgl KO/cTg  mice [A0C-3107-3110]

value: 44-46 weeks


title: SB-6: PMN-Arf6 cKO

source_name: Control Cre+/+ Leucocytes that have migrated into the mouse air pouches injected with LPS


title: Club cells from 3 wt/cTg  mice [A2C-3104-3106]

value: 44-45 weeks


title: Club cells from 4 wt/cTg mice [A2C-3205-3208]

value: 42-44 weeks


title: Club cells from 3 wt/cTg mice [A2C-3266-3268]

value: 42 weeks


title: SB-7: PMN-Cre+/+


title: SM004


title: 3T3 MEFs IgG GO-CaRT Total Rep 2


title: 3T3 MEFs H3K9me2 GO-CaRT Rep 2


title: 3T3 MEFs LaminB IgG GO-CaRT Soluble Rep 2


title: 3T3 MEFs LaminB GO-CaRT Soluble Rep 2


title: 3T3 MEFs H3K27me3 GO-CaRT Soluble Rep 2


title: SM002

value: wildtype


title: SM001


title: 3T3 MEFs H3K9me2 IgG GO-CaRT Total Rep 2


title: 3T3 MEFs IgG GO-CaRT Soluble Rep 1


title: 3T3 MEFs IgG GO-CaRT Total Rep 1


title: SB-4: PMN-Arf6 cKO


title: NC

city: Nanjing

first: Yuhui

last: Zang

address: 163 Xianlin Road

institute: Nanjing University

data_processing:
Basecalls performed using CASAVA version 1.4
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data
RNA-seq reads were aligned to the hg18 genome assembly using HISAT2 v2.0.5
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg18
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

molecule: polyA RNA

source_name: HepG2 cells

growth_protocol: Hepatoma cell line HepG2 was maintained in DMEM(Invitrogen) containing 10% fetal calf serum, penicillin (100 units/ml) and streptomycin (100 μg/ml). All cells were incubated at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted from HepG2 subline cells with TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To generate the HepG2 cells that stably express Sox9, HepG2 cells were infected with the recombinant lentivirus expressing Sox9 (Lv-Sox9) or the control virus (Lv-NC) respectively. After lentivirus infection, the stable cell lines were selected using 0.5 mg/ml of puromycin. The stable lines were maintained in DMEM supplemented with 10% FBS and 0.25 mg/ml of puromycin. The stable expression of Sox9 was confirmed by qRT-PCR

value: hepatoma cell

tag: treatment

value: control


title: OB21d

city: Jiujiang

first: Xiaoyuan

last: Xu

address: 17 Lufeng Road

institute: Jiujiang University

data_processing:
cDNA libraries for single‐end sequencing were processed for the Proton Sequencing process following the commercially available protocols after constructing using Ion Total RNA‐Seq Kit v2.0 (Life Technologies Inc., Gaithersburg, MD) according to the manufacturer's instructions.
The aligned single‐end reads Tophat (version tophat‐2.0.11) were put into Cufflinks (Version 2.1.1) to quantify gene expression into units known as fragments per kilobase of exon per million fragments mapped (FPKM) with quality checked with FastQC and low expression removed.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human mesenchymal stem cells

growth_protocol: Expanded to passage 6, the human mesenchymal stem cells (hMSCs) were with 80-90% and 70% confluence separately for adipogenesis and osteoblastogenesis. Adipogenesis was stimulated with adipogenic cocktails with 0.01 mg/mL insulin, 0.5 mM 3-isobutyl-1-methyl-xanthine, and 1.0 μM dexamethasone (Sigma, St. Louis, Mo, USA) in Gibco MEMα (Minimum Essential Medium Alpha) every three days, and osteoblastogenesis was inspired with the medium supplemented with ascorbic acid, FBS, dexamethasone, L-glutamine, β-glycerophosphate, penicillin, and streptomycin (St. Louis, MO, USA).

extract_protocol:
TRIzol reagent (Invitrogen, Carlsbad, CA, USA) was used to isolate the total RNA from the freshly harvested adipo-osteobalstogenic cells.
The cDNA library for Proton Sequencing was constructed using a Ion Total RNA-Seq kit v2.0 (Life Technologies Inc., Gaithersburg, MD) according to the manufacturer’s instructions.

treatment_protocol: Three replicates were induced at 0, 7, 14, 21, and 28 d separately for adipogenesis and osteoblastogenesis.

tag: stem cells

value: human marrow mesenchymal stem cells (hMSCs)

value: osteoblastogenesis

tag: time point

value: 21 day


title: OB14d

value: 14 day


title: OB28d

value: 28 day


title: AD21d

value: adipogenesis


title: OB0d

description: HMSC

value: 0 day


title: OB7d

value: 7 day


title: AD28d


title: AD0d


title: AD14d


title: AD7d


title: SVZ-cNSCs IgG GO-CaRT

growth_protocol: Following microdissection of the V-SVZ, cells were dissociated and cultured in proliferative medium (DMEM/F12 with Glutamax, 5% Fetal Bovine Serum, N2 supplement, 35 µg/mL bovine pituitary extract, 20 ng/mL EGF, 20 ng/mL FGF, antibiotic/antimycotic) for 3-4 passages. To allow for differentiation, cultures were switched to differentiation medium (DMEM/F12 with Glutamax, 2% Fetal Bovine Serum, N2 supplement, 35 µg/mL bovine pituitary extract, antibiotic/antimycotic) and cultured for 7 days.

value: Derived from postnatal day 7

tag: strain


title: SB-1: PMN-Arf6flox

source_name: Arf6-KO Leucocytes that have migrated into the mouse air pouches injected with LPS

tag: cell type

value: Leucocytes

value: control flox+/+Cre-/-


title: Sox9

value: SOX9 stable expression


title: spleen_KO_2

city: beijing

first: Minghang

last: Yu

address: No.10 Xitoutiao, You An Men

institute: Capital Medical University

data_processing:
The library was sequenced in a paired-end 150-bp cycle using Illumina HiSeqTM 2500
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie Hista2
The expression level of protein-coding genes was calculated using FPKM  method(Roberts, A., Trapnell, C., Donaghey, J. et al. Genome Biol 12, R22,2011), which is the number of Fragments from a protein-coding gene Per kilobase length Per Million Fragments.
Genome_build: mm9

source_name: Spleen

extract_protocol:
NK cells((CD3-CD19-NKp46+NK1.1+) ) were purified from the spleen of mice using FACS sorting (BD FACSAria III, San Jose, USA).RNA was harvested using Trizol reagent.
RNA-seq libraries were prepared using the NEB Next RNA library prep kit for Illumina using TruSeq indexes according to the manufacturer’s protocol

value: spleen

value: Ezh2fl/fl; Ncr1iCre


title: Heart Endothelial 24 mo rep3

city: Portland OR

first: Anthony

middle: Paul

last: Barnes

state: OR

address: HRC 545B, 3181 SW Sam Jackson Park Rd

institute: OHSU

data_processing:
Sample demulitiplexing was done using Bcl2Fastq (Illumina)
single analysis used Cellranger (10x Genomics)
Seurat 2.3.4 and R version 3.4.2
Genome_build: mouse mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every cell for every sample

source_name: Heart Endothelial 24 mo

growth_protocol: Acute cells were harvested for this study

extract_protocol:
sequencing libraries of captured single cells were generated using the V2 barcoding chemistry of 10X Genomic library kit in accordance with manufacturers protocol
single cell sequencing, 50,000 reads per cell

treatment_protocol: Organs were dissected, minced and digested in media containing Collagenase II and DNAase I. Endothelial cells were enriched using anti-CD31 magnetic beads with Magnetic Assisted Cell Sorting (MACS) (AutoMACS, Miltinyi Biotec). For increased purity, the post- MACS sorted cells were subjected to fluorescent-activated cell sorting using a positive sort for anti-CD31, and negative sort against anti-GP38 and anti-CD45. Purified ECs were loaded onto the 10X Chromium platform for single cell sequencing.

value: 24 months

value: wild type

value: Heart

value: Endothelial cell


title: spleen_WT_3


title: spleen_WT_2


title: spleen_KO_1


title: Heart Endothelial 3 mo rep3

source_name: Heart Endothelial 3 mo

value: 3 months


title: Heart Endothelial 24 mo rep2


title: spleen_WT_1