title: plX_HALO_YY1_DBD_ampDAPseq

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters and amplified 11 cycles, next it was incubated with in-vitro translated AquYY1 DNA binding domain fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.


title: MDA-MB-453

status: Public on Aug 02 2019

type: genomic

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmus MC

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
Data was processed using default settings in Genotyping Console Software (Affymetrix). Copy number values for individual SNPs were extracted, smoothed and segmented into copy number states according to the default settings in Genotyping Console
log2ratio copy number

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Breast cancer cell line

label_protocol: Standard Affymetrix protocol

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted using the DNeasy kit of Qiagen

tag: cell line


title: single-cells_#10_Twin2.2

type: SRA

city: Planegg-Martinsried

first: Eduardo

last: Beltrán

state: Bayern

address: Großhaderner Str. 9

department: Institute of Clinical Neuroimmunology

country: Germany

institute: University Hospital, LMU Munich

library_source: transcriptomic

data_processing:
Short sequencing reads were aligned to the UCSC hg38 transcriptome using HISAT2
featureCounts to count mapped reads
Data were log-transformed [log(TPM + 1)] for all downstream analyses
unbiased graph-based clustering of single cell data, and identification of markers for each cluster, were performed with Seurat
Genome_build: UCSC hg38
Supplementary_files_format_and_content: first tab-delimited text file include TPM values of all single-cells in all samples; first tab-delimited text file include single-cell information (metadata)

molecule: total RNA

source_name: CSF sample

tag: tissue

value: CSF

tag: cell types

value: ALL cells types in the CSF sample

tag: diagnosis

value: subclinical neuro-inflammation

tag: Sex

value: female

tag: age


title: WT_HFD_2

city: Philadelphia

first: Ellen

last: Pure

state: PA

address: 380 S University Ave

country: USA

institute: University of Pennsylvania

data_processing:
fastq files were aligned to version 79 of mouse reference genome GRCm38 using Kallisto (Bray, Pimentel, Melsted, & Pachter, 2016) .
.tsv files resulting from imported to R using Tximport
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
GSEA analysis was carried out  in R using the GSVA package
Genome_build: version 79 of mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes log2 transcripts per million (TPM) values for each sample

organism: Mus musculus

source_name: WT_HFD, total subcutaneous mammary adipose

extract_protocol:
Inguinal fat pads were flash frozen and then homogenized in QIAzol reagent using an OMNI tissue homogenizer. RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

treatment_protocol: Female FVB mice were fed on ingredient matched low- or high-fat diet from 12 weeks of age to 30 weeks of age

tag: strain

value: FVB

tag: genotype

value: wild-type

tag: diet

value: High fat diet (60% kcal from fat)

value: total subcutaneous mammary adipose


title: MPE600


title: single-cells_#9_Twin2.1

value: clinically definite MS


title: plX_HALO_SP41_ampDAPseq

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

library_source: genomic

data_processing:
Library strategy: ampDAP-seq
CASAVA v1.8.2
For Bisulfite-seq and TAB-seq, adapters were trimmed using fastp as default, then aligned to the reference genome using Bowtie2 and BSseeker2 with the option --bt2--end-to-end. PCR duplicates were removed using Sambamba v.0.6.6 before methylation quantification with BSseeker2. For DAP-seq and ampDAP-seq, reads where trimmed with fastp and mapped to the genome using bowtie with the parameters "-m 1 -v 1", then peaks where called using macs2 using pIX Halo empty bam as background and parameters "-q 0.05 --down-sample -g 166679601".
Genome_build: Amphimedon queenslandica genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/amphimedon_queenslandica/dna/Amphimedon_queenslandica.Aqu1.dna.toplevel.fa.gz, Sycon ciliatum genome assembly was downloaded from http://www.compagen.org/datasets/SCIL_WGA_130802.zip, Nematostella vectensis genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/nematostella_vectensis/dna/Nematostella_vectensis.ASM20922v1.dna.toplevel.fa.gz, Mnemiopsis leidyi genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/mnemiopsis_leidyi/dna/Mnemiopsis_leidyi.MneLei_Aug2011.dna.toplevel.fa.gz
Supplementary_files_format_and_content: Bisulfite-seq files (CGmap files) are the direct output from BSseeker2 (https://github.com/BSSeeker/BSseeker2), they contain chromosome position, (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C / (#_of_C + #_of_T). (7) #_of_C (methylated C, the count of reads showing C here) (8) = #_of_C + #_of_T (all Cytosines, the sum of reads showing C or T in that position). Macs2 xls files are described in https://github.com/taoliu/MACS/blob/master/README.rst.

organism: Amphimedon queenslandica

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters and amplified 11 cycles, next it was incubated with in-vitro translated AquSP41 fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.

tag: developmental stage

tag: individuals

value: individuals from Heron Island

tag: experimental variable


title: Null_LFD_3

source_name: Null_LFD, total subcutaneous mammary adipose

value: FAP-/-

value: Low fat diet (10% kcal from fat)


title: plX_HALO_NRF_DBD_ampDAPseq

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters and amplified 11 cycles, next it was incubated with in-vitro translated AquNRF DNA binding domain fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.


title: single-cells_#8_Twin1.2


title: WT_HFD_1


title: MDA-MB-415


title: OCUB-M

value: OCUB-M


title: plX_HALO_NRF_ampDAPseq

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters and amplified 11 cycles, next it was incubated with in-vitro translated AquNRF fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.


title: MEF_old_rep2

type: RNA

city: Taipei

first: Chih-Yun

last: Yu

address: Room 403, No. 81, Chang-Xing St.

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

description:
C57BL/6, mouse, embryonic fibroblast, P6.
replicate 2
8491191070_H

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: P6 MEF

label_protocol: Cy3 cRNA were prepared with the Cy3® labeling kit for Illumina arrays

growth_protocol: MEF cultured with 5% CO2 and ambient oxygen (20%) in Dulbecco’s modified Eagle’s medium (DMEM, Carlsbad, CA, USA) supplemented with 10% FBS, 100 U/ml penicillin and 100 µg/ml streptomycin.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: For the DNMT3L-treated samples: Mouse DNMT3L or control eGFP was cloned into a constitutive pCAG vector with neomycin resistance. Plasmid DNA was purified and transfected into MEFs using Lipofectamine 2000 (Thermo Fisher, CA, USA) according to the manufacturer’s instructions.

value: Mouse embryonic fibroblast (MEF)


title: MEF_DNMT3L-treated_(E)_rep2

description:
C57BL/6, mouse, embryonic fibroblast, P33 post-DNMT3L-treacfected (transient DNMT3L-transfected at P5), cultured in ES cell cultured medium.
Treated ES replicate 2
8491191070_G

source_name: DNMT3L-treated MEF_ES cell medium


title: single-cells_#7_Twin1.1


title: Null_LFD_2


title: plX_HALO_empty_DAPseq

data_processing:
Library strategy: DAP-seq
CASAVA v1.8.2
For Bisulfite-seq and TAB-seq, adapters were trimmed using fastp as default, then aligned to the reference genome using Bowtie2 and BSseeker2 with the option --bt2--end-to-end. PCR duplicates were removed using Sambamba v.0.6.6 before methylation quantification with BSseeker2. For DAP-seq and ampDAP-seq, reads where trimmed with fastp and mapped to the genome using bowtie with the parameters "-m 1 -v 1", then peaks where called using macs2 using pIX Halo empty bam as background and parameters "-q 0.05 --down-sample -g 166679601".
Genome_build: Amphimedon queenslandica genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/amphimedon_queenslandica/dna/Amphimedon_queenslandica.Aqu1.dna.toplevel.fa.gz, Sycon ciliatum genome assembly was downloaded from http://www.compagen.org/datasets/SCIL_WGA_130802.zip, Nematostella vectensis genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/nematostella_vectensis/dna/Nematostella_vectensis.ASM20922v1.dna.toplevel.fa.gz, Mnemiopsis leidyi genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/mnemiopsis_leidyi/dna/Mnemiopsis_leidyi.MneLei_Aug2011.dna.toplevel.fa.gz
Supplementary_files_format_and_content: Bisulfite-seq files (CGmap files) are the direct output from BSseeker2 (https://github.com/BSSeeker/BSseeker2), they contain chromosome position, (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C / (#_of_C + #_of_T). (7) #_of_C (methylated C, the count of reads showing C here) (8) = #_of_C + #_of_T (all Cytosines, the sum of reads showing C or T in that position). Macs2 xls files are described in https://github.com/taoliu/MACS/blob/master/README.rst.

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters, incubated with in-vitro translated HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.


title: single-cells_#6_SCNI4


title: MDA-MB-175VII


title: Null_LFD_1


title: MDA-MB-330


title: single-cells_#11_Twin3.1


title: plX_HALO_SP41_DBD_DAPseq

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters, incubated with in-vitro translated AquSP DNA binding domain fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.


title: MEF_DNMT3L-treated_(E)_rep1

description:
C57BL/6, mouse, embryonic fibroblast, P29 post-DNMT3L-treacfected (transient DNMT3L-transfected at P5), cultured in ES cell cultured medium.
Treated ES replicate 1
8491191070_F


title: WT_LFD_2

source_name: WT_LFD, total subcutaneous mammary adipose


title: single-cells_#5_SCNI3


title: single-cells_#4_SCNI2


title: MEF_DNMT3L-treated_rep2

description:
C57BL/6, mouse, embryonic fibroblast, P23 post-DNMT3L-treacfected (transient DNMT3L-transfected at P5), cultured in standard MEF culture medium.
Treated replicate 2
8491191070_E

source_name: DNMT3L-treated MEF


title: MDA-MB-436


title: MEF_DNMT3L-treated_rep1

description:
C57BL/6, mouse, embryonic fibroblast, P22 post-DNMT3L-treacfected (transient DNMT3L-transfected at P5), cultured in standard MEF culture medium.
Treated replicate 1
8491191070_D


title: plX_HALO_GLI_DBD_DAPseq

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters, incubated with in-vitro translated AquGLI DNA binding domain fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.


title: single-cells_#3_SCNI1

value: male


title: PI270443-innoculated rep2

city: Raleigh

first: Ramsey

last: Lewis

state: NC

address: 101 Derieux PI

department: Crop and Soil Sciences Department

institute: North Carolina State University

data_processing:
Reads were mapped against tomato Heinz 1706 genome assembly SL3.0 using hisat2 version 2.1.0
Reads mapped to gene assembly were manipulated using samtools  for sorting/indexing
Raw count of reads mapped to annotated gene model (ITAG3.2 version) were extracted using bedtools version 2.25.0
Genome_build: Heinz 1706 genome assembly SL3.0
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

organism: Solanum lycopersicum

source_name: Leaf

growth_protocol: Tomato lines were sown in 4P soil mixture (Fafard®, Florida, USA) in 24-cell trays for a greenhouse experiment. Six plants per genotype were planted in two replications in a completely randomized design. Plants were fertilized using a mixture of fertilizer containing a ratio of 20:20:20 of nitrogen, phosphorus, and potassium, respectively. Standard greenhouse treatments for insects and fungal diseases management were used, but copper was not applied to control the bacterial diseases. Humidity near the plants was maintained using humidifiers  from 24 hours before inoculation to 48 hours after inoculation and by covering the seedlings with clear plastic.

extract_protocol:
Leaf samples were collected and frozen and ground in liquid nitrogen, and RNA was purified using Plant Rneasy mini kit of Qiagen.
100 ng total RNA samples was used for RNA-seq library construction using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA)  followed the protocol for normal insertion size option.

treatment_protocol: Plants were artificially inoculated with Isolate 9 of Xanthomonas perforans, which was found to be extremely virulent. The strain was maintained in pure culture and stored at -80°C. The isolate was grown in Yeast Dextrose Chalk (YDC) agar medium (Lelliott and Stead, 1987) plates for 24-48 hours at 28°C and were overlaid with sterile distilled water and bacteria were dislodged from the plates and the resulting bacterial suspensions were pooled in a sterile glass container. The suspension was standardized by determining its optical density at 600 nm using an Spectrophotometer, and diluted as needed to obtain an OD600 of 0.3 (approximately 2-5×108 CFU/mL). Diluted cells were immediately used for inoculations. The seedlings were sprayed with the bacterial suspension till foliar runoff using a hand sprayer around sunset. Sterile water was used for mock inoculation. Leaf tissue samples after inoculation were collected in liquid nitrogen and stored at -80°C until further processed.

value: Leaf

tag: time

value: 48 hours after innoculation with bacterial spot suspended in water

tag: susceptiblity status

value: Resistance line


title: MDA-MB-231


title: MDA-MB-435s


title: plX_HALO_SP41_DAPseq

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters, incubated with in-vitro translated AquSP fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.


title: single-cells_#2_NIC2

value: CSF

value: ALL cells types in the CSF sample

value: non-inflammatory control


title: MDA-MB-157


title: MDA-MB-361


title: MEF_young_rep2

description:
C57BL/6, mouse, embryonic fibroblast, P5.
Old replicate 1
8491191070_C

source_name: P3 MEF


title: plX_HALO_YY1_DBD_DAPseq

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters, incubated with in-vitro translated AquYY1 DNA binding domain fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.


title: single-cells_#1_NIC1

value: female


title: MEF_old_rep1

description:
C57BL/6, mouse, embryonic fibroblast, P3.
Young replicate 2
8491191070_B

source_name: P5 MEF


title: PI270443-control rep2

value: 48 hours after innoculation with water only


title: plX_HALO_YY1_ampDAPseq

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters and amplified 11 cycles, next it was incubated with in-vitro translated AquYY1 fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.


title: hmC_Nvectensis_gastrula

data_processing:
Library strategy: TAB-seq
CASAVA v1.8.2
For Bisulfite-seq and TAB-seq, adapters were trimmed using fastp as default, then aligned to the reference genome using Bowtie2 and BSseeker2 with the option --bt2--end-to-end. PCR duplicates were removed using Sambamba v.0.6.6 before methylation quantification with BSseeker2. For DAP-seq and ampDAP-seq, reads where trimmed with fastp and mapped to the genome using bowtie with the parameters "-m 1 -v 1", then peaks where called using macs2 using pIX Halo empty bam as background and parameters "-q 0.05 --down-sample -g 166679601".
Genome_build: Amphimedon queenslandica genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/amphimedon_queenslandica/dna/Amphimedon_queenslandica.Aqu1.dna.toplevel.fa.gz, Sycon ciliatum genome assembly was downloaded from http://www.compagen.org/datasets/SCIL_WGA_130802.zip, Nematostella vectensis genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/nematostella_vectensis/dna/Nematostella_vectensis.ASM20922v1.dna.toplevel.fa.gz, Mnemiopsis leidyi genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/mnemiopsis_leidyi/dna/Mnemiopsis_leidyi.MneLei_Aug2011.dna.toplevel.fa.gz
Supplementary_files_format_and_content: Bisulfite-seq files (CGmap files) are the direct output from BSseeker2 (https://github.com/BSSeeker/BSseeker2), they contain chromosome position, (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C / (#_of_C + #_of_T). (7) #_of_C (methylated C, the count of reads showing C here) (8) = #_of_C + #_of_T (all Cytosines, the sum of reads showing C or T in that position). Macs2 xls files are described in https://github.com/taoliu/MACS/blob/master/README.rst.

organism: Nematostella vectensis

source_name: 24 hours post fertilization

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, and subjected to 7 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).

value: 24 hours post fertilization

value: Vienna strain


title: plX_HALO_YY1_DAPseq

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters, incubated with in-vitro translated AquYY1 fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.


title: PI270443-control rep1


title: GH6

city: York

first: Gideon

last: Hughes

address: University of York, Wentworth Way

department: Biology

institute: University of York

data_processing:
A quality check was carried out using FastQC to make sure there were enough high quality reads.
The adaptor sequences were trimmed with cutadapt 1.16
Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome.
Sleuth 0.30.0 was used to test for differential expression.
Genome_build: GRCZ11
Supplementary_files_format_and_content: tab-delimited text file including RPKM values for each transcript, hypertext markup language document including read counts per sample

organism: Danio rerio

source_name: Brain

extract_protocol:
Brains were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator-5 kit (Cat No. R1013) was used to clean up the total RNA.
RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® Poly(A) mRNA Magnetic Isolation Module following manufacturers instructions.

value: LWT

value: Brain

value: 12 weeks post fertilisation


title: GH5


title: NCCELBR1-innoculated rep2

value: NC CELBR1

value: Medium resistance line


title: MCF-7


title: WT_LFD_1

value: FVB

value: wild-type

value: Low fat diet (10% kcal from fat)

value: total subcutaneous mammary adipose


title: mC_Nvectensis_gastrula

data_processing:
CASAVA v1.8.2
For Bisulfite-seq and TAB-seq, adapters were trimmed using fastp as default, then aligned to the reference genome using Bowtie2 and BSseeker2 with the option --bt2--end-to-end. PCR duplicates were removed using Sambamba v.0.6.6 before methylation quantification with BSseeker2. For DAP-seq and ampDAP-seq, reads where trimmed with fastp and mapped to the genome using bowtie with the parameters "-m 1 -v 1", then peaks where called using macs2 using pIX Halo empty bam as background and parameters "-q 0.05 --down-sample -g 166679601".
Genome_build: Amphimedon queenslandica genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/amphimedon_queenslandica/dna/Amphimedon_queenslandica.Aqu1.dna.toplevel.fa.gz, Sycon ciliatum genome assembly was downloaded from http://www.compagen.org/datasets/SCIL_WGA_130802.zip, Nematostella vectensis genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/nematostella_vectensis/dna/Nematostella_vectensis.ASM20922v1.dna.toplevel.fa.gz, Mnemiopsis leidyi genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/mnemiopsis_leidyi/dna/Mnemiopsis_leidyi.MneLei_Aug2011.dna.toplevel.fa.gz
Supplementary_files_format_and_content: Bisulfite-seq files (CGmap files) are the direct output from BSseeker2 (https://github.com/BSSeeker/BSseeker2), they contain chromosome position, (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C / (#_of_C + #_of_T). (7) #_of_C (methylated C, the count of reads showing C here) (8) = #_of_C + #_of_T (all Cytosines, the sum of reads showing C or T in that position). Macs2 xls files are described in https://github.com/taoliu/MACS/blob/master/README.rst.

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, bisulfite converted and subjected to 6 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).


title: GH4


title: plX_HALO_NRF_DAPseq

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters, incubated with in-vitro translated AquNRF fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.

value: individuals from Heron Island


title: Hs578T

extract_protocol: Genomic DNA was extracted using the DNeasy kit of Qiagen


title: NCCELBR1-innoculated rep1

value: Leaf

value: 48 hours after innoculation with bacterial spot suspended in water


title: MDA-MB-134VI


title: EVSA-T

value: EVSA-T


title: GH3

value: wild type


title: NCCELBR1-control rep2

value: 48 hours after innoculation with water only


title: hmC_Aqueenslandica_precompetent_larva

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, ß-glucosyltransferase treated, Tet1 oxidated, ligated to methylated Illumina TruSeq adapters, bisulfite treated and subjected to 7 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).


title: GH2


title: hmC_Aqueenslandica_juvenile

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, and subjected to 5 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).


title: NCCELBR1-control rep1


title: CAMA-1


title: MEF_young_rep1

description:
C57BL/6, mouse, embryonic fibroblast, P3.
Young replicate 1
8491191070_A

value: Mouse embryonic fibroblast (MEF)


title: GH1


title: BT549


title: mC_Aqueenslandica_juvenile

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, bisulfite converted and subjected to 7 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).


title: mC_Aqueenslandica_adult

source_name: adult

value: adult


title: mC_Mleidyi_14hpf

organism: Mnemiopsis leidyi

source_name: embryos 14 hours post fertilization

extract_protocol:
DNAzol
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, bisulfite converted and subjected to 7 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).

value: embryos 14 hours post fertilization

value: kept at Sars, Bergen


title: mC_Aqueenslandica_competent_larva


title: mC_Nvectensis_planula

source_name: 72 hours post fertilization

value: 72 hours post fertilization

value: Vienna strain


title: NC714-innoculated rep2

value: Susceptible line


title: NC714-control rep2


title: mC_Mleidyi_4.5hpf

source_name: embryos 4.5 hours post fertilization

value: embryos 4.5 hours post fertilization


title: mC_Aqueenslandica_precompetent_larva


title: Sam_0062_lowantibiotic

first: Sam

last: Willcocks

address: Keppel St

institute: LSHTM

data_processing:
Raw sequencing data from three independent repeats in FASTQ format were analysed for the presence of the terminal ten base pair nucleotides of the transposon sequence with no mismatches, and then the transposon sequence was trimmed using a custom PERL script. Reads were curated for quality control and trimmed to 36 base pairs using Trimmomatic software. Bowtie software was used to map reads against the reference genome (European Molecular Biology Laboratory accession number: BX936398) with no mismatches allowed to establish the transposon insertion sites; non-unique mapping reads were discarded.    The TraDIS toolkit  determines gene essentiality based on the empirically observed bimodal distribution of insertion sites over genes when normalized for gene length using a method adapted from Langridge et al and Barquist et al.  Briefly, a loess curve is fit to the distribution of insertion indices and used to fit a gamma distribution curve from which log-odds ratios are generated to determine the threshold for gene essentiality. Pseudogenes, and genes that were not conserved among multiple strains as identified by BLAST were excluded as false positives.
Genome_build: BX936398

organism: Yersinia pseudotuberculosis IP 32953

source_name: LSHTM

growth_protocol: 28 oC in BAB media

extract_protocol:
Genomic DNA was extracted using ArchivePure DNA Extraction Kit, 5Prime
Y. pseudotuberculosis strain IP32953 was previously used to generate a transposon library of approximately 40,000 unique insertion mutants using the Ez-Tn5 Kan2 transposome complex (Epicentre, UK) as described and validated in Willcocks et al (Willcocks SJ, Stabler RA, Atkins HS, Oyston PF, Wren BW. High-throughput analysis of Yersinia pseudotuberculosis gene essentiality in optimised in vitro conditions, and implications for the speciation of Yersinia pestis. BMC Microbiol. 2018;18(1):46.).
Library preparation for Illumina MiSeq sequencing was performed as described in Willcocks et al (Willcocks SJ, Stabler RA, Atkins HS, Oyston PF, Wren BW. High-throughput analysis of Yersinia pseudotuberculosis gene essentiality in optimised in vitro conditions, and implications for the speciation of Yersinia pestis. BMC Microbiol. 2018;18(1):46.)

treatment_protocol: Ez-Tn5 Kan2 transposome library +/- ciprofloxacin


title: NC714-control rep1


title: mC_Mleidyi_8.5hpf

source_name: embryos 8.5 hours post fertilization

value: embryos 8.5 hours post fertilization


title: BT20

source_name: Breast cancer cell line


title: NC714-innoculated rep1


title: mC_Mleidyi_3hpf

source_name: embryos 3 hours post fertilization

value: embryos 3 hours post fertilization


title: mC_Sciliatum_syconoid

organism: Sycon ciliatum

source_name: adult syconoids

extract_protocol:
Qiagen AllPrep Kit
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, bisulfite converted and subjected to 6 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).

value: adult syconoids

value: collected in Bergern fjords


title: Sam11_high antibiotic


title: DU4475


title: BT483


title: CuO NPs 250

status: Public on Aug 01 2019

city: Brisbane

first: Zhaoyu

last: Chen

address: Research Road | St. Lucia campus |

department: Advanced Water Management Centre

country: Australia

institute: The University of Queensland

data_processing:
NGS QC Toolkit (v2.3.3) was used to check the quality and trim the raw sequence reads.
The clean reads were aligned to the reference genome (NC_002937) of D. vulgaris by SeqAlto (version 0.5)
Cufflinks (version 2.2.1) was applied to test the differential expression and regulation between controls and treated cultures.
The abundance of gene expression was indicated as reads per kilobase of a gene per million mapped reads (RPKM)
The log2 fold-change (LFC) of RPKM value was used to express the differences in fold-change values between controls and NPs-treated samples (0, 1, 50, 250 mg CuO NPs/L).
Genome_build: NC_002937
Supplementary_files_format_and_content: xlsx files are generated from the gff files of Cufflinks, including the abundance of gene expression as indicated by RPKM and the log2 fold-change (LFC) of RPKM value between controls and NPs-treated samples (1, 50, 250 mg CuO NPs/L)

organism: Nitratidesulfovibrio vulgaris

source_name: Desulfovibrio vulgaris Hildenborough

growth_protocol: D. vulgaris was grown on a defined lactate sulfate medium (LS4D medium).

extract_protocol:
Total RNA was extracted using the QIAGEN miRNeasy Mini Kit (Catalog number 217004). An extra bead-beating step was included to ensure the complete lysis of cells. Additional DNase treatment was performed with the total RNA using a commercially available kit (QIAGEN RNase-Free DNase Set) to exclude the possible contained DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When suspended bacteria grew to OD600 value around 0.2, they were amended with different levels of CuO NPs at concentrations of 1, 50, and 250 mg/L for further 24 h incubation.


title: plX_HALO_EGR_DBD_DAPseq

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters, incubated with in-vitro translated AquEGR DNA binding domain fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.

value: individuals from Heron Island


title: CuO NPs 1


title: CuO NPs 50


title: Control


title: W03_miRNA

city: Beijing

first: Xiao

state: Beijing

address: Haidian Xiangshan Beigou No.1

country: China

institute: Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

description: processed data file: Readcount_TPM_miRNA.xlsx

data_processing:
For miRNA library preparation, a total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The library preparations were sequenced on an Illumina Hiseq 2500 platform and 50bp single-end reads were generated. A total of three small libraries were constructed using ovaries of honey bee workers. The small RNA tags were mapped to reference sequence (Amel_4.5) by Bowtie. The characteristics of hairpin structure of miRNA precursor can be used to predict new miRNA. The available software miREvo60 and mirdeep261 were integrated to predict new miRNA. Predicting the target gene of miRNA was performed by miRanda.
A total amout of 3 μg total RNA per sample was used as input material for the mRNA and lncRNA library. Sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. The libraries were sequenced on an Illumina Hiseq 4000 platform and 150bp paired-end reads were generated. A total of three libraries were constructed using ovaries of honey bee workers. Index of reference genome (Amel_4.5) was built using Bowtie V2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (FPKM, expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
For circRNA library preparation, a total amount of 5 μg RNA per sample was used as input material for RNA sample preparation. Firstly, ribosomal RNAs were depleted by using Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA) to get rRNA-depleted RNAs. rRNA-depleted RNAs were further treated with RNase R (Epicentre, USA) and then were subjected to Trizol extraction. Subsequently, sequencing libraries were generated using the rRNA-depleted and RNase R digested RNAs by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. The library preparations were sequenced on an Illumina Hiseq 4000 platform and 150bp paired-end reads were generated. A total of three small libraries were constructed using ovaries of honey bee workers. Reference genome was Amel_4.5. For circRNA identification, unmapped reads were kept and 20-mers from 5’ and 3’ end of these reads were extracted and aligned independently to reference sequences by Bowtie. Anchor sequences were extended by find_circ such that the complete read aligned and the breakpoints were flanked by GU/AG splice sites. Then the back-spliced reads with at least two supporting reads were annotated as circRNAs.
Genome_build: Amel_4.5
Supplementary_files_format_and_content: counts, count RPM

organism: Apis mellifera

extract_protocol:
Trizol reagent (Invitrogen, Carlsbad, CA, USA) was used to extract total RNA, according to the manufacturer’s instructions. mRNA and lncRNA sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. CircRNA sequencing libraries were generated using the rRNA-depleted and RNase R digested RNAs by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. miRNA sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: social caste

value: honey bee workers

value: ovaries

tag: molecule subtype

value: miRNA


title: W02_miRNA


title: W01_miRNA


title: mC_Aqueenslandica_cleavage


title: HCC1937


title: mC_Mleidyi_juvenile

source_name: small (1cm) adult

value: small (1cm) adult


title: BT474


title: Liver-LXR_WT_FB1-rep4

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 35980 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 33417 rows each corresponding to a unique ProbeName.

source_name: Liver

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: WT and LXRalpha beta KO female mice (sv129/C57) 8 week old were used.

extract_protocol: Standard RNA extraction with TriZol was used.

treatment_protocol: Mice were treated with either water (control) or 10 mg/kg body weight / day of Fumonisin B1 (FB1) for one month.

tag: treatment

value: female


title: Liver-LXR_WT_Control-rep6

value: Control


title: Liver-LXR_KO_FB1-rep3


title: Liver-LXR_KO_Control-rep4


title: Liver-LXR_KO_FB1-rep1


title: Liver-LXR_WT_FB1-rep1


title: Liver-LXR_KO_Control-rep1


title: Liver-LXR_KO_FB1-rep6


title: Liver-LXR_WT_Control-rep4


title: Liver-LXR_KO_FB1-rep4


title: Liver-LXR_WT_FB1-rep2


title: Liver-LXR_KO_Control-rep6


title: Liver-LXR_WT_Control-rep1


title: Liver-LXR_WT_Control-rep3


title: Liver-LXR_WT_FB1-rep6


title: Liver-LXR_KO_FB1-rep2


title: Liver-LXR_KO_Control-rep2


title: Liver-LXR_KO_FB1-rep5


title: Liver-LXR_KO_Control-rep5


title: Liver-LXR_WT_Control-rep5


title: Liver-LXR_WT_FB1-rep5


title: Arabidopsis QC marker_wox5-1 mutant genetic background_forth biological replicate

first: Adam

last: Fisher

state: North Carolina

address: 112 Derieux Place

data_processing:
cDNA libraries were sequenced using an Illumina HiSeq 2500 sequencing machine
Adapters and low quality reads were filtered out using ea-utils software. Reads longer than 30bp with a quality score was greater than 30 were kept.
FPKM values acquired using Cufflinks
Differential gene expression analysis performed by PoissonSeq

organism: Arabidopsis thaliana

source_name: WOX5:GFP sorted cells

growth_protocol: Growth Media: Standard media for 5 days

extract_protocol: cDNA synthesis and amplification was performed using the SMARTer Ultra Low Input RNA Kit for sequencing v3. Fragmentation was done using Covaris ultrasonicator. Libraries were prepared using the Low Input Library Prep Kit.

treatment_protocol: Seedling roots were protoplasted 5 days after germination

tag: ecotype

value: wox5-1 mutant


title: Arabidopsis QC marker_wox5-1 mutant genetic background_second biological replicate


title: Liver-LXR_KO_Control-rep3


title: plX_HALO_NRF_DBD_DAPseq

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters, incubated with in-vitro translated AquNRF DNA binding domain fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.


title: Arabidopsis QC marker_wox5-1 mutant genetic background_first biological replicate


title: Arabidopsis QC marker_WT genetic background_third biological replicate

value: wild type


title: Arabidopsis CEI marker_wox5-1 mutant genetic background_third biological replicate

source_name: CYCD6::GUS-GFP sorted cells


title: Arabidopsis QC marker_WT genetic background_first biological replicate


title: Arabidopsis QC marker_WT genetic background_second biological replicate


title: Liver-LXR_WT_FB1-rep3


title: Arabidopsis CEI marker_WT genetic background_third biological replicate


title: Arabidopsis CEI marker_WT genetic background_first biological replicate


title: ros1-14_H2AZ_ChIP_rep2

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

data_processing:
ChIP-Seq: Reads were mapped to TAIR10 by Bowtie2 with parameter "-k 2 --very-sensitive --no-unal --no-mixed --no-discordant", duplicated reads were removed using samtools rmdup.
processed data files format and content: For ChIP-Seq:  The bedGraph files were generated using genomeCoverageBed from bedtools with parameter  -bg -pc
Genome_build: TAIR10

source_name: seedlings

growth_protocol: Seedlings were grown on 1/2 MS medium with 1% Glucose and 0.8% agar

extract_protocol: Five grams of seedlings were cross-linked with 1% formaldehyde in PBS buffer and ground in liquid nitrogen. Sonicated chromatin was incubated overnight with anti-H2A.Z3, anti-H3K18ac (ab1191, Abcam), anti-H3K23ac (07-355, Millipore), anti-MYC (05-724, Millipore), anti-FLAG (F1804, Sigma). Immunoprecipitated DNA was treated with RNase A (Qiagen) and purified with the QIAquick purification kit (Qiagen). For individual locus detection, ChIP products were diluted with 80 μL of TE buffer and inputs were diluted with TE buffer at the ratio of 1:100

tag: tissue

value: seedlings


title: Arabidopsis CEI marker_WT genetic background_second biological replicate


title: Liver-LXR_WT_Control-rep2


title: mC_Nvectensis_blastula

source_name: 9 hours post fertilization

value: 9 hours post fertilization

value: Vienna strain


title: ros1-14_H2AZ_ChIP_rep1


title: ros1-14_H2AZ_Input_for_H2AZ


title: PI270443-innoculated rep1

source_name: Leaf

extract_protocol:
Leaf samples were collected and frozen and ground in liquid nitrogen, and RNA was purified using Plant Rneasy mini kit of Qiagen.
100 ng total RNA samples was used for RNA-seq library construction using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA)  followed the protocol for normal insertion size option.

value: Leaf

value: 48 hours after innoculation with bacterial spot suspended in water

value: Resistance line


title: pie1-6_H2AZ_ChIP_rep2


title: idm1-9_H2AZ_ChIP_rep2


title: idm1-9_H2AZ_ChIP_rep1


title: Arabidopsis QC marker_wox5-1 mutant genetic background_third biological replicate


title: pie1-6_H2AZ_Input_for_H2AZ


title: idm1-9_H2AZ_Input_for_H2AZ


title: pie1-6_H2AZ_ChIP_rep1


title: arp6-4_H2AZ_ChIP_rep1


title: arp6-4_H2AZ_Input_for_H2AZ


title: 35S:SUC2_H2AZ_Input_for_H2AZ

value: wild-type


title: Arabidopsis CEI marker_wox5-1 mutant genetic background_second biological replicate


title: Arabidopsis CEI marker_wox5-1 mutant genetic background_first biological replicate


title: 35S:SUC2_H2AZ_ChIP_rep1


title: atmbd9-4npx1-4_H3K23Ac_ChIP_rep2


title: atmbd9-4npx1-4_Input_for_H3KAc


title: atmbd9-4npx1-4_H3K23Ac_ChIP_rep1


title: atmbd9-4npx1-4_H3K18Ac_ChIP_rep2


title: idm1-9_Input_for_H3KAc


title: idm1-9_H3K23Ac_ChIP_rep2


title: idm1-9_H3K23Ac_ChIP_rep1


title: arp6-4_Input_for_H3KAc


title: arp6-4_H3K23Ac_ChIP_rep1


title: idm1-9_H3K18Ac_ChIP_rep1


title: idm1-9_H3K18Ac_ChIP_rep2


title: arp6-4_H3K18Ac_ChIP_rep2


title: arp6-4_H3K23Ac_ChIP_rep2


title: arp6-4_H3K18Ac_ChIP_rep1


title: 35S:SUC2_Input_for_H3KAc


title: 35S:SUC2_H3K23Ac_ChIP_rep1


title: 35S:SUC2_H3K18Ac_ChIP_rep2


title: arp6-4_H2AZ_ChIP_rep2


title: 35S:SUC2_H3K23Ac_ChIP_rep2


title: 35S:SUC2_H3K18Ac_ChIP_rep1


title: mC_Mleidyi_30hpf

source_name: embryos 30 hours post fertilization

value: embryos 30 hours post fertilization

value: kept at Sars, Bergen


title: 35S:SUC2_H2AZ_ChIP_rep2


title: atmbd9-4npx1-4_BS_rep2

description: treated with bisulfite

data_processing:
MethylC-Seq： For data analysis, data were trimmed using trimmomatic with  parameter "LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:50". Clean reads were mapped to Arabidopsis thaliana TAIR 10 genome using BSMAP with parameter "-m 0 -x 1000  -w 2", and python script of BSMAP was used to remove potential PCR duplicates and extract methylation ratios.
processed data files format and content: For MethylC-Seq: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ).
Genome_build: TAIR10

extract_protocol: Genomic DNA was extracted from 14-day-old seedlings using the DNeasy Plant Maxi Kit (Qiagen, 68163) and sent to the Genomics Core Facilities of the PSC (Shanghai Center for Plant Stress Biology, Shanghai, China) for bisulfite treatment. Libraries were prepared for sequencing according to the manufacturer’s (Illumina) instructions and sequenced on an Illumina Hiseq 2500 platform.


title: atmbd9-4npx1-4_BS_rep1

description: treated with bisulfite


title: pie1-6_BS_rep2

description: treated with bisulfite


title: ros1-14_BS_rep2

description: treated with bisulfite


title: ros1-14_BS_rep1

description: treated with bisulfite


title: atmbd9-4npx1-4_H3K18Ac_ChIP_rep1


title: Single passage_Sam10


title: pie1-6_BS_rep1

description: treated with bisulfite


title: idm1-9_BS_rep2

description: treated with bisulfite


title: idm1-9_BS_rep1

description: treated with bisulfite


title: arp6-4_BS_rep2

description: treated with bisulfite


title: arp6-4_BS_rep1

description: treated with bisulfite


title: h2a.z-2_BS_rep2

description: treated with bisulfite


title: h2a.z-2_BS_rep1

description: treated with bisulfite


title: 35S:SUC2_BS_rep2

description: treated with bisulfite


title: 35S:SUC2_BS_rep6

description: treated with bisulfite


title: 35S:SUC2_BS_rep5

description: treated with bisulfite


title: 35S:SUC2_BS_rep4

description: treated with bisulfite


title: 35S:SUC2_BS_rep1

description: treated with bisulfite


title: 35S:SUC2_BS_rep3

description: treated with bisulfite


title: THP1-GABA-input

city: Fukuoka

first: Yoshikane

last: Kikushige

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

data_processing:
The raw sequence reads were aligned to the mouse and human reference genomes (hg19) using bowtie2 (version 2.2.6), and the uniquely mapped reads were retained.
The bigWig files were generated using signal intensities which were calculated as the RPKM of the ChIP sample with the RPKM of the input subtracted using agplus.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain signal data for visualization via tools such as the Integrative Genomics Viewer.

source_name: Immortal cell line

growth_protocol:
RMPI-1640 medium supplemented with heat-inactivated 10% FBS
In vitro experiments, THP-1 cells, primary CD34+ ALL cells and CD34+ AML cells were cultured in RMPI-1640 medium supplemented with heat-inactivated 10% FBS with or without gabapentin. In vivo experiments, NSG mice reconstituted with human ALL cells were fed with control diet or BCAA-free diet.

extract_protocol:
Fixed cells were lysed and histone-DNA complexes were isolated with antibodies.
Libraries were prepared on the Illumina Next-Seq 500 platform.

treatment_protocol:
9-16 hours of culture with gabapentin (40mM)
In vitro experiments, THP-1 cells, primary CD34+ ALL cells and CD34+ AML cells were treated with or without gabapentin (40mM). In vivo experiments, NSG mice reconstituted with human ALL cells were fed with control diet or BCAA-free diet. After dietary restriction of BCAA, human ALL cells were harvested from the recipient mice.

tag: cell line

tag: antibody target

tag: primary antibody


title: AML-GABA-H3K27me3

source_name: primary cell

value: mouse monoclonal anti-H3K27me3 (MABI0323, MAB Institute)


title: ALL-2nd-free-input

growth_protocol:
NA
In vitro experiments, THP-1 cells, primary CD34+ ALL cells and CD34+ AML cells were cultured in RMPI-1640 medium supplemented with heat-inactivated 10% FBS with or without gabapentin. In vivo experiments, NSG mice reconstituted with human ALL cells were fed with control diet or BCAA-free diet.

treatment_protocol:
NSG mice reconstituted with human ALL cells were fed with BCAA-freel diet, and reconstituted human CD34+ ALL cells were purified (BCAA-restriction)
In vitro experiments, THP-1 cells, primary CD34+ ALL cells and CD34+ AML cells were treated with or without gabapentin (40mM). In vivo experiments, NSG mice reconstituted with human ALL cells were fed with control diet or BCAA-free diet. After dietary restriction of BCAA, human ALL cells were harvested from the recipient mice.


title: ALL-non-input

treatment_protocol:
9-16 hours of culture without gabapentin (control)
In vitro experiments, THP-1 cells, primary CD34+ ALL cells and CD34+ AML cells were treated with or without gabapentin (40mM). In vivo experiments, NSG mice reconstituted with human ALL cells were fed with control diet or BCAA-free diet. After dietary restriction of BCAA, human ALL cells were harvested from the recipient mice.


title: ALL-2nd-non-input

treatment_protocol:
NSG mice reconstituted with human ALL cells were fed with control diet, and reconstituted human CD34+ ALL cells were purified (control;non-restriction)
In vitro experiments, THP-1 cells, primary CD34+ ALL cells and CD34+ AML cells were treated with or without gabapentin (40mM). In vivo experiments, NSG mice reconstituted with human ALL cells were fed with control diet or BCAA-free diet. After dietary restriction of BCAA, human ALL cells were harvested from the recipient mice.


title: ALL-GABA-H3K27me3


title: ALL-GABA-input


title: ALL-2nd-free-H3K27me3


title: AML-non-input


title: AML-non-H3K27me3


title: AML-GABA-input


title: THP1-non-H3K27me3


title: THP1-non-input


title: ALL-2nd-non-H3K27me3


title: ACLD_7day_n2

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

description: Cultured ITGA8+/PDGFRA-/SIX2-GFP+ population from induced iPS cells for 7 days

data_processing:
Basecalls performed using bcl2fastq v2.17.
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.32 tool.
The sequence reads were aligned to the human reference genome (hg19) using TopHat 2.1.1 (bowtie2-2.2.3) with the option '-g 1 --no-discordant'.
NuDup ver.2.3 (NuGEN Technologies, San Carlos, CA) analyzing the redundancy of 8 bp molecular barcodes was used to remove PCR duplicate reads.
The read counts allocated for each gene and transcript (RefSeq version 2015.10.5) were quantified by Transcripts Per Kilobase Million (TPM) method using StrandNGS 3.1 software (Agilent Technologies, Santa Clara, CA).
Genome_build: hg19
Supplementary_files_format_and_content: An excel format file (XLSX) includes TPM quantification values and gene annotations of all samples.

source_name: Cultured iPS-derived human NPC in Activin condition media for 7days

growth_protocol: SIX2-GFP iPSC lines were generated, and nephron progenitor cells were induced from human iPS cells by the established protocol (Taguchi. et al., Cell Stem Cell. 2017). ITGA8+/PDGFRA-/SIX2-GFP+ cells were isolated from iPS-derived nephron progenitors by FACS. ITGA8+/PDGFRA-/SIX2-GFP+ cells were maintained ActivinA- or BMP7- based conditioned medium for 7days.

extract_protocol:
Each cultured cells were sorted by a FACS Aria II (Becton Dickinson). Total RNA was extracted using "Rneasy Plus Micro Kit" purchased from QIAGEN following manufacture's protocol.
Total RNA obtained from each sample was subjected to a sequencing library construction using Ovation Solo RNA-Seq System (NuGEN Technologies, San Carlos, CA) according to the manufacture's protocol.

value: human iPS cells

tag: clone

tag: genome edit

value: GFP insertion at exon1 of SIX2 loci

tag: cell type

value: Cultured iPS-derived human NPC


title: ITGA8+/SIX2GFP-_n2

description: ITGA8+/PDGFRA-/SIX2-GFP- population from induced iPS cells

source_name: iPS-derived human NPC

value: iPS-derived human NPC


title: BCLD_7day_n1

source_name: Cultured iPS-derived human NPC in BMP7 condition media for 7days


title: BCLD_7day_n2


title: ITGA8+/SIX2GFP-_n1


title: ACLD_7day_n1


title: ALL-non-H3K27me3


title: ITGA8+/SIX2GFP+_n1

description: ITGA8+/PDGFRA-/SIX2-GFP+ population from induced iPS cells


title: XL22 U2AF65 rep2

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Adapters were trimmed using Flexbar (v2.5).
Libraries were demultiplexed using bctools (https://github.com/dmaticzka/bctools, v0.2.0) and Flexbar (v2.5).
Possible readthroughs into the barcoded regions were removed by clipping 13 nt from the 3'-ends of first mate reads.
Reads were mapped to reference genome hg19 using bowtie2 (v2.2.6) with parameters --very-sensitive --end-to-end --no-mixed --no-discordant --maxins 500.
Alignments of uniquely mapped reads were extracted and used to determine crosslinking events as previously described (Ilik, I. A. et al. Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila. Mol. Cell 51, 156–173 (2013)) with bctools (https://github.com/dmaticzka/bctools, v0.2.0).
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing coordinates of crosslinking event alignments with id of a representative read in name column and number of merged PCR-duplicates in score column. bigWig profiles of crosslinking event alignments for each strand.

extract_protocol:
Cells are crosslinked with 0.15mJ/cm2 UV-C irradiation, lysed with 1xNLB and homogenized by waterbath-sonication. Target protein of interest is pulled-down with paramagnetic beads pre-coupled to antibodies against the protein of interest.
After a brief RNAseI-digestion, RNA 3'-ends are healed with T4 PNK. Custom-made, barcoded adapters are ligated using T4 RNA Ligase 1 or T4 RNA Ligase 2KQ (if pre-adenylated adapters are used) for 1 hr at 25˚C. Custom FLASH adapters contained two barcodes and random nucleotides adjacent to the 3'-adapters according to the pattern NNBBNTTTTTTNN (N: random tag nucleotide, T: tag nucleotide, B: RY-space tag nucleotide). Random tags are used to merge PCR-duplicates, regular tags are used to specify the pulldown condition, and semi-random RY-space tags are used to distinguish the biological replicates (RR: replicate A, YY: replicate B, R: purine, Y: pyrimidine). Excess adapters are washed away, negative controls (IgG) are mixed with experimental controls and RNA is isolated with Proteinase K treatment and column purification. Isolated RNA is reverse-transcribed and RNaseH-treated. cDNA is column-purified and circularized with CircLigase for 2-16hrs. Circularized cDNA is directly PCR amplified, quantified with Qubit / Bioanalyzer and sequenced on Illumina NextSeq 500 in paired-end mode.

tag: purification (ab or affinity)

tag: 3' tag

value: TGGAAC


title: XL22 U2AF65 rep1

value: TGTGAG


title: XL21 U2AF65 rep1

value: CAAGTG


title: THP1-GABA-H3K27me3


title: XL21 GFP rep2


title: XL21 U2AF65 rep2

value: TTAGCC


title: XL21 GFP rep1

value: GTGGAA


title: XL18 U2AF65 rep2

value: Ab:U2AF65 cat:U4758 (Sigma) lot:02M4831


title: XL18 U2AF65 rep1


title: XL18 IgG rep2

value: Ab:mouse IgG cat:sc-2025 (Santa Cruz) lot:D1416


title: ITGA8+/SIX2GFP+_n2


title: XL18 IgG rep1


title: XL17 U2AF65 rep1


title: XL17 U2AF65 rep2


title: XF7 QKI-A repB

value: CAAGTG, RY-space tag:YY


title: XF7 QKI-B repB

value: TTAGCC, RY-space tag:YY


title: XF8 QKI-A repB


title: XF8 QKI-A repA

value: CAAGTG, RY-space tag:RR


title: XF8 QKI-B repB


title: XL17 IgG rep2


title: XF8 control repB

value: GTGGAA, RY-space tag:YY


title: XL17 IgG rep1


title: XF7 QKI-A repA


title: XF8 QKI-B repA

value: TTAGCC, RY-space tag:RR


title: XF8 control repA

value: GTGGAA, RY-space tag:RR


title: XF6 QKI-B repA


title: XF7 QKI-B repA


title: XF7 control repA


title: XF7 control repB


title: XF6 QKI-A repA


title: XF6 QKI-A repB


title: XF5 QKI-B repB


title: XF6 control repB


title: XF5 QKI-B repA


title: XF6 control repA


title: XF5 QKI-A repA


title: XF5 control repB


title: XF6 QKI-B repB


title: XF4 QKI-B repB


title: XF4 control repB


title: XF4 QKI-B repA


title: XF4 QKI-A repB


title: XF3 QKI-B repB


title: XF3 control repB


title: XF4 control repA


title: XF3 QKI-A repB


title: XF3 QKI-A repA


title: XF2 QKI-B repB


title: XF5 QKI-A repB


title: XF2 QKI-B repA


title: XF2 QKI-A repA


title: XF3 QKI-B repA


title: XF2 QKI-A repB


title: XF2 control repB


title: XF1 QKI-B repA


title: XF1 QKI-B repB


title: XF1 QKI-A repB


title: XF5 control repA


title: XF1 control repA


title: SR9 SRSF4 rep2


title: SR9 SRSF4 rep1


title: SR8 SRSF3 rep2

value: GGTTAC


title: SR8 SRSF3 rep1


title: XF4 QKI-A repA


title: XF3 control repA


title: SR7 SRSF2-P95H rep2


title: XF2 control repA


title: SR7 GFP rep2


title: SR7 SRSF2-P95H rep1


title: SR5 SRSF2 rep1


title: SR5 SRSF2 rep2


title: SR1 SRSF1 rep1


title: SR1 GFP rep2


title: SR5 GFP rep2


title: SR5 GFP rep1


title: XF1 QKI-A repA


title: SR1 GFP rep1


title: SR1 SRSF1 rep2


title: SR13 SRSF9 rep2


title: SR12 SRSF7 rep2


title: SR12 GFP rep1


title: XF1 control repB


title: SR14 SRSF11 rep1


title: SR12 GFP rep2


title: SR11 SRSF6 rep1


title: SR10 SRSF5 rep2


title: SR7 GFP rep1


title: SR10 SRSF5 rep1


title: Taf1_26_father

city: Kensington

first: Sara

last: Ballouz

state: NSW

address: High St

institute: UNSW

data_processing:
Base calling:
Artifacts filter: fastx_artifacts_filter  -v -Q 33, (fastX toolbox)
Quality filter: fastq_quality_filter -v -Q 33 -q 30 -p 50 , (fastX toolbox),
Combine paired reads: fastQCombinePairedEnd.py (https://github.com/enormandeau/Scripts/blob/master/fastqCombinePairedEnd.py)
Alignment: STAR 2.4.2a, GENCODE v22 and GENCODEv24, parameters: --outFilterType BySJout   --outFilterMultimapNmax 20   --outFilterMismatchNmax 999   --outFilterMismatchNoverReadLmax 0.04  --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJoverhangMin 8   --alignSJDBoverhangMin 1   --sjdbScore 1 --outSAMtype None --quantMode GeneCounts --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0.66
Quantification: RSEM v1.2.29, GENCODE v22, parameters: rsem-calculate-expression --bam --no-bam-output --seed 12345  -p 8 --paired-end --forward-prob 0 [Aligned.toTranscriptome.out.bam] [RSEMGenome] Quant
Genome_build: GRCh38, GENCODE v22, v24
Supplementary_files_format_and_content: tab-delimited files, rows contain ensemblIDs for gene level counts, TPM, FPKM

source_name: TAF1_Unaffected_Father_Whole blood

extract_protocol:
RNA was precipitated with ammonium acetate, washed and resuspended in 14 µl TE (10 mM Tris-HCl pH 8, 1 mM EDTA).
For each sample 1.1 µg RNA were hybridized with the provided streptavidin beads and purified. 1 µl of a 1:100 dilution of ERCC RNA Spike-In control (Thermo Fisher) was added to 1 µg RNA and libraries generated according to the TruSeq Stranded mRNA Library Kit-v2 (Illumina).
Quality control of the generated libraries was performed on a Bioanalyzer High Sensitivity DNA chip (Agilent) and the concentration was measured using Qubit dsDNA HS Assay (Life Technologies). To eliminate primer dimers in the libraries, additional purifications were performed using the Agencourt AMPure XP system (Beckman Coulter). The libraries were pooled to 2-10 nM total concentration and sequenced on a NextSeq, PE100, mid output. Libraries were generated independently for each family and family-pools sequenced on separate lanes.

treatment_protocol: Globin mRNA was depleted from the samples using the GLOBINclear Kit (Life Technologies).

tag: subject group

value: TAF1 syndrome cohort

tag: disease status

value: Unaffected

tag: family status

value: Father

value: Whole blood


title: SR11 SRSF6 rep2


title: Taf1_24_prb

source_name: TAF1_Affected_Proband_Whole blood

value: Affected

value: Proband


title: SR13 SRSF9 rep1

value: TGGAAC


title: SR12 SRSF7 rep1

value: CAAGTG


title: Taf1_25_mother

source_name: TAF1_Unaffected_Mother_Whole blood

value: Mother


title: SR14 SRSF11 rep2


title: Taf1_20_sib

source_name: TAF1_Unaffected_Sibling_Whole blood

value: Sibling


title: Taf1_22_father


title: Taf1_21_prb


title: Taf1_23_mother


title: Taf1_18_father


title: Taf1_19_mother

source_name: TAF1_Carrier_Mother_Whole blood

value: Carrier


title: Taf1_15_father


title: Taf1_16_mother


title: Taf1_14_prb


title: Taf1_11_prb


title: Taf1_13_father


title: Taf1_12_mother


title: Single Sert+ neuron 1282

city: Stanford

first: Alina

last: Isakova

state: CA

address: 318 Campus drive

department: Bioengineering

institute: Stanford University

description:
M2_SER57
Adult_DR_GEO_counts_cpm.txt

data_processing:
Sequences from the NextSeq were de-multiplexed using bcl2fastq version 2.19.0.316. Reads were aligned to the mm10 genome using STAR version 2.6.1a (Dobin et al., 2013). Gene counts were produced using HTseq version 0.11.2 (Anders et al., 2015) with default parameters, except ‘stranded’ was set to ‘false’, and ‘mode’ was set to ‘intersection-nonempty’. Genes located on Y chromosome were removed from the count table to exclude sex bias.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include CPM values for all Samples passing quality threshhold

molecule: polyA RNA

source_name: Sert+ neurons

extract_protocol:
Lysis plates were prepared by dispensing 4 μl lysis buffer as described in (Tabula Muris et al., 2018). After dissociation, single tdTomato+ cells were sorted in 96-well plates using SH800S (Sony). Immediately after sorting, plates were sealed with a pre-labelled aluminum seal, centrifuged, and flash frozen on dry ice. cDNA synthesis and library preparation were performed using the Smart-seq2 protocol (Picelli et al., 2014). Wells of each library plate were pooled using a Mosquito liquid handler (TTP Labtech). Pooling was followed by two purifications using 0.7x AMPure beads (Fisher, A63881). Library quality was assessed using capillary electrophoresis on a Fragment Analyzer (AATI), and libraries were quantified by qPCR (Kapa Biosystems, KK4923) on a CFX96 Touch Real-Time PCR Detection System (Bio-Rad). Libraries were sequenced on the NextSeq 500 Sequencing System (Illumina) using 2 × 75-bp paired-end reads and 2 × 8-bp index reads.
Smrt-seq2

tag: strain

value: Sert+ neurons

tag: age

value: 40–45 days

tag: brain region

value: All DR

tag: genotype

value: Sert-tdTomato-Cre cross with Ai14


title: Single Sert+ neuron 1281

description:
M19_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1283

description:
M2_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1284

description:
M2_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1285

description:
M20_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1288

description:
M21_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1286

description:
M20_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1289

description:
M21_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1280

description:
M19_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1273

description:
M17_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1277

description:
M18_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1276

description:
M18_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1279

description:
M19_SER56
Adult_DR_GEO_counts_cpm.txt


title: Taf1_17_prb


title: Single Sert+ neuron 1278

description:
M18_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1274

description:
M17_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1275

description:
M17_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1271

description:
M16_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1270

description:
M16_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1269

description:
M15_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1268

description:
M15_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1267

description:
M15_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1266

description:
M14_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1287

description:
M20_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1264

description:
M14_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1265

description:
M14_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1261

description:
M13_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1262

description:
M13_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1272

description:
M16_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1259

description:
M12_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1258

description:
M12_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1253

description:
M10_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1249

description:
M1_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1251

description:
M1_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1256

description:
M11_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1252

description:
M10_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1254

description:
M10_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1263

description:
M13_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1257

description:
M11_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1243

description:
L8_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1244

description:
L8_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1241

description:
L7_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1246

description:
L9_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1247

description:
L9_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1248

description:
L9_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1237

description:
L6_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1236

description:
L5_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1242

description:
L7_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1239

description:
L6_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1233

description:
L4_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1250

description:
M1_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1235

description:
L5_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1240

description:
L7_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1255

description:
M11_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1232

description:
L4_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1230

description:
L3_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1231

description:
L4_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1238

description:
L6_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1260

description:
M12_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1227

description:
L24_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1226

description:
L24_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1234

description:
L5_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1221

description:
L22_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1216

description:
L21_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1219

description:
L22_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1224

description:
L23_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1217

description:
L21_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1222

description:
L23_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1225

description:
L24_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1223

description:
L23_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1213

description:
L20_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1215

description:
L20_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1220

description:
L22_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1211

description:
L2_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1209

description:
L19_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1212

description:
L2_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1214

description:
L20_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1210

description:
L2_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1206

description:
L18_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1207

description:
L19_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1228

description:
L3_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1205

description:
L18_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1204

description:
L18_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1203

description:
L17_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1218

description:
L21_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1229

description:
L3_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1200

description:
L16_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1201

description:
L17_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1245

description:
L8_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1208

description:
L19_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1199

description:
L16_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1202

description:
L17_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1197

description:
L15_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1196

description:
L15_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1198

description:
L16_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1194

description:
L14_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1195

description:
L15_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1193

description:
L14_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1192

description:
L14_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1188

description:
L12_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1187

description:
L12_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1191

description:
L13_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1189

description:
L13_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1186

description:
L12_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1185

description:
L11_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1184

description:
L11_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1183

description:
L11_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1181

description:
L10_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1180

description:
L10_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1182

description:
L10_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1176

description:
K9_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1178

description:
L1_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1177

description:
L1_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1174

description:
K9_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1179

description:
L1_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1175

description:
K9_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1173

description:
K8_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1190

description:
L13_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1172

description:
K8_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1168

description:
K7_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1169

description:
K7_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1171

description:
K8_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1167

description:
K6_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1166

description:
K6_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1164

description:
K5_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1162

description:
K5_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1165

description:
K6_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1170

description:
K7_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1158

description:
K3_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1159

description:
K4_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1160

description:
K4_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1157

description:
K3_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1153

description:
K24_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1154

description:
K24_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1152

description:
K23_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1151

description:
K23_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1148

description:
K22_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1150

description:
K23_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1146

description:
K21_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1147

description:
K22_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1144

description:
K21_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1163

description:
K5_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1142

description:
K20_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1141

description:
K20_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1139

description:
K2_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1138

description:
K2_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1161

description:
K4_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1137

description:
K19_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1155

description:
K24_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1136

description:
K19_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1130

description:
K17_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1132

description:
K18_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1131

description:
K17_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1133

description:
K18_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1129

description:
K17_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1128

description:
K16_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1145

description:
K21_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1126

description:
K16_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1127

description:
K16_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1125

description:
K15_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1156

description:
K3_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1123

description:
K15_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1134

description:
K18_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1124

description:
K15_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1149

description:
K22_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1122

description:
K14_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1120

description:
K14_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1140

description:
K2_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1118

description:
K13_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1135

description:
K19_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1113

description:
K11_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1114

description:
K12_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1116

description:
K12_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1117

description:
K13_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1110

description:
K10_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1112

description:
K11_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1115

description:
K12_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1108

description:
K10_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1109

description:
K10_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1106

description:
K1_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1107

description:
K1_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1103

description:
J9_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1111

description:
K11_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1119

description:
K13_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1101

description:
J8_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1105

description:
K1_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1102

description:
J9_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1100

description:
J8_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1121

description:
K14_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1098

description:
J7_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1097

description:
J7_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1099

description:
J8_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1094

description:
J6_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1093

description:
J6_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1092

description:
J5_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1091

description:
J5_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1090

description:
J5_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1088

description:
J4_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1087

description:
J4_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1086

description:
J3_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1089

description:
J4_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1085

description:
J3_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1082

description:
J24_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1083

description:
J24_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1080

description:
J23_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1081

description:
J24_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1079

description:
J23_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1076

description:
J22_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1077

description:
J22_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1095

description:
J6_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1074

description:
J21_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1096

description:
J7_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1075

description:
J22_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1073

description:
J21_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1078

description:
J23_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1066

description:
J2_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1072

description:
J21_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1071

description:
J20_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1065

description:
J19_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1069

description:
J20_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1068

description:
J2_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1063

description:
J19_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1070

description:
J20_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1060

description:
J18_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1084

description:
J3_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1067

description:
J2_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1059

description:
J17_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1064

description:
J19_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1061

description:
J18_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1057

description:
J17_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1058

description:
J17_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1056

description:
J16_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1054

description:
J16_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1053

description:
J15_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1052

description:
J15_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1051

description:
J15_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1049

description:
J14_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1050

description:
J14_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1048

description:
J14_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1047

description:
J13_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1046

description:
J13_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1035

description:
J1_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1039

description:
J11_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1042

description:
J12_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1045

description:
J13_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1044

description:
J12_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1040

description:
J11_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1034

description:
J1_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1043

description:
J12_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1031

description:
I9_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1143

description:
K20_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1062

description:
J18_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1036

description:
J10_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1038

description:
J10_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1055

description:
J16_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1037

description:
J10_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1041

description:
J11_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1025

description:
I7_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1029

description:
I8_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1020

description:
I5_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1021

description:
I6_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1022

description:
I6_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1028

description:
I8_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1027

description:
I8_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1026

description:
I7_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1024

description:
I7_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1030

description:
I9_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1033

description:
J1_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1032

description:
I9_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1017

description:
I4_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1018

description:
I5_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1013

description:
I3_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1015

description:
I4_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1012

description:
I3_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1023

description:
I6_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1016

description:
I4_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1009

description:
I24_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1019

description:
I5_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1010

description:
I24_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1011

description:
I24_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1007

description:
I23_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1008

description:
I23_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1004

description:
I22_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1006

description:
I23_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1005

description:
I22_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1003

description:
I22_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1002

description:
I21_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 999

description:
I20_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 998

description:
I20_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 997

description:
I20_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 996

description:
I2_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1000

description:
I21_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 993

description:
I19_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1014

description:
I3_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 995

description:
I2_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 994

description:
I2_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 992

description:
I19_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 991

description:
I19_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 988

description:
I18_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 986

description:
I17_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 982

description:
I16_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 989

description:
I18_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 990

description:
I18_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 983

description:
I16_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 981

description:
I15_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 979

description:
I15_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 987

description:
I17_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 984

description:
I16_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 978

description:
I14_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 976

description:
I14_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 980

description:
I15_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 977

description:
I14_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1001

description:
I21_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 973

description:
I13_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 972

description:
I12_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 969

description:
I11_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 975

description:
I13_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 970

description:
I12_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 967

description:
I11_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 968

description:
I11_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 974

description:
I13_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 985

description:
I17_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 965

description:
I10_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 963

description:
I1_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 964

description:
I10_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 966

description:
I10_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 962

description:
I1_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 961

description:
I1_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 955

description:
H7_SER51
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 959

description:
H9_SER50
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 957

description:
H8_SER52
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 958

description:
H8_SER55
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 952

description:
H6_SER52
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 953

description:
H6_SER55
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 951

description:
H6_SER48
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 950

description:
H5_SER51
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 960

description:
H9_SER51
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 948

description:
H4_SER55
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 949

description:
H5_SER50
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 971

description:
I12_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 946

description:
H4_SER48
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 945

description:
H3_SER51
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 944

description:
H3_SER50
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 942

description:
H24_SER52
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 943

description:
H24_SER55
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 941

description:
H24_SER48
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 939

description:
H23_SER50
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 956

description:
H8_SER48
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 940

description:
H23_SER51
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 937

description:
H22_SER52
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 938

description:
H22_SER55
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 936

description:
H22_SER48
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 954

description:
H7_SER50
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 933

description:
H20_SER55
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 935

description:
H21_SER51
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 931

description:
H20_SER48
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 930

description:
H2_SER55
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 932

description:
H20_SER52
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 929

description:
H2_SER52
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 928

description:
H2_SER48
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 934

description:
H21_SER50
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 927

description:
H19_SER51
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1104

description:
J9_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 926

description:
H19_SER50
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 924

description:
H18_SER52
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 947

description:
H4_SER52
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 923

description:
H18_SER48
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 922

description:
H17_SER51
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 921

description:
H17_SER50
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 925

description:
H18_SER55
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 918

description:
H16_SER48
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 916

description:
H15_SER50
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 919

description:
H16_SER52
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 917

description:
H15_SER51
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 914

description:
H14_SER52
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 915

description:
H14_SER55
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 913

description:
H14_SER48
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 908

description:
H12_SER48
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 907

description:
H11_SER51
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 906

description:
H11_SER50
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 896

description:
G8_SER48
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 898

description:
G8_SER55
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 904

description:
H10_SER52
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 903

description:
H10_SER48
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 905

description:
H10_SER55
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 900

description:
G9_SER51
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 910

description:
H12_SER55
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 895

description:
G7_SER51
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 911

description:
H13_SER50
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 920

description:
H16_SER55
Adult_DR_GEO_counts_cpm.txt