title: H3.1WT H3K36me3 rep1

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie version 2.0.0-beta6 with parameters -D 15 -R 2 -N 0 -L 32 -i S,1,0.75 -M 10000
Reads aligned to mitochondrial genome and unassigned sequences were removed. Reads overlap the blacklist regions generated by ENCODE project were also removed.
Then the ChIP-seq were transformed into read coverage files normalized to 1x sequencing depth at 10 bp resolution and minus input file using deepTools package(http://deeptools.github.io).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig ChIP minus Input file. Signal value represent the ChIP-seq normalized read coverage minus the input normalized read coverage.

extract_protocol:
Chromatin of cross-linked mESCs with H3.1WT overexpressing were sonicated into near 500bp length, the chromatin solution were captured by 2ug of rabbit polyclonal anti-H3K36me3 antibody (Abclonal, Cat.#A2366, lot# 40648)
The ChIP DNAs were measured with the Qubit 2.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific). The libraries were prepared using NEBNext Ultra™ DNA Library Prep Kit for Illumina (NEB, #E7370) according to the manual instruction.

tag: chip antibody


title: H3.1WT input rep2

status: Public on Aug 01 2019

type: SRA

city: shanghai

first: Jin

last: Sun

department: life science and technology

country: China

institute: Tongji University

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: mES

growth_protocol: Mouse embryonic stem cells (mESCs, J1 strain) seeded on inactivated mouse embryonic fibroblast cells (MEF) feeder were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco#11995) supplemented with 10% fetal bovine serum (FBS, Gibco#16000-044), 1×non-essential amino acids (NEAA, Gibco#11140), 1×GlutaMAX-I (Gibco#35050-061), 7μM β-mercaptoethanol (Ameresco, Biotechnology grade, Cat#M8210), 10ng/ml mouse leukemia inhibitory factor (Millipore, Chemicon, Cat#LIF2050) and 1% antibiotic (Pen Strep, Gibco#15140-122). All mES cells were sub-passaged every 3-4 days by digesting the cell clone into single cell suspension using 0.25% Trypsin-EDTA (Gibco#25200072), and the resulted cells were divided on 3-5 fresh feeder-plates.

tag: cell type

value: embryonic stem cell

tag: strain


title: Single Sert+ neuron 82

city: Stanford

first: Alina

last: Isakova

state: CA

address: 318 Campus drive

department: Bioengineering

country: USA

institute: Stanford University

description:
C15_SER25
Adult_DR_GEO_counts_cpm.txt

library_source: transcriptomic

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: tissue

value: Sert+ neurons

tag: age

value: 40–45 days

tag: brain region

value: Principal DR

tag: genotype

value: Sert-tdTomato-Cre cross with Ai14


title: Single Sert+ neuron 92

description:
C21_SER25
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 81

description:
C14_SER40
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 80

description:
C13_SER39
Adult_DR_GEO_counts_cpm.txt


title: shNC rep1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimed for adaptor and low-quality sequence and then mapped to mm10 whole genome using tophat v2.0.13 with default parameters
Differences in expression were determined using Cuffdiff v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

extract_protocol:
A total amount of 2μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manual instructions and index codes were added to attribute sequences to each sample. RNA-seq libraries were prepared with TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer instruction, and were sequenced on an Illumina HiSeq X-10).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: total RNA were extracted using Trizol reagent and used for mRNA capture.


title: H3.1WT input rep1


title: Single Sert+ neuron 79

description:
C13_SER25
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 78

description:
C12_SER40
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 77

description:
C11_SER39
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21Degron_polIIhet_chipseq_Rad21_auxinAmanitintreated_auxinWash

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

data_processing:
base calling: illumina CASAVA 1.8.2
Promter Capture HiC-Seq: alignment: bowtie 2.3.4.3 with default parameter to hg19
Promter Capture HiC-Seq: alignment and filter: HiCUP v0.5.9
Promter Capture HiC-Seq: Normalization: randomly selecting enough reads in order to obtain 73 million read pairs in cis and >10 b apart from each bait
Promter Capture HiC-Seq: Interaction call: with default parameter by using CHiCAGO 1.10.1
BSseq:triming: remove first 8nt with cutadapt program
BSseq:alignment: aliged to mm9 with default parameter using Bismark
BSseq:filter: low quality sequences and PCR duplicates are removed by BSseeker2
BSseq:bedgraph generation: bismark_methylation_extractor in Bismark pacakge
Genome_build: mm9, hg19
Supplementary_files_format_and_content: Promter Capture HiC-Seq: .txt file generated by CHiCAGO for significant interaction calls
Supplementary_files_format_and_content: BSseq:bedgraph to show the methylation %

organism: Homo sapiens

source_name: HCT-116 cell line

extract_protocol:
Promoter Capture  HiC-Seq:  we used the same protocol at Montefiori et al., (Elife, 2018 Jul 10; 7)                                                                                BS-seq: Genomic DNA was isolated from 3×106 cells using Qiagen DNeasy blood and tissue kit (Cat #: 69506). The bisulfite conversion was performed using the EZ DNA Methylation-Gold™ Kit (Cat #: D5005) from Zymo Research. Whole-genome bisulfite sequencing libraries were prepared from 50 ng converted DNA using Illumina TruSeq® DNA Methylation Kit (Cat #: EGMK91324), which was performed following the manufacturer’s protocol.
Promoter Capture HiC-seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 100 cycles of sequencing data were acquired on the HiSeq 3000 (Illumina).                                                                                BS-seq: standard RNA-Seq   library   preparation   was performed following  the genomic DNA protocol with 20% PhiX. 50 cycles of sequencing data were acquired on HiSeq 3000 (Illumina)

value: colon carcinoma cell line

value: Abcam, ab992


title: hct116_Rad21Degron_polIIhet_chipseq_PolII_untreated

value: Abcam, ab817


title: hct116_Rad21Degron_polIIhet_chipseq_Rad21_auxinAmanitintreated


title: hct116_Rad21Degron_polIIhet_chipseq_Rad21_amanitintreated


title: H3.1WT H3K36me3 rep2


title: hct116_Rad21Degron_polIIhet_chipseq_Med26_amanitintreated

value: Cell signalling technologies, 13641S


title: hct116_Rad21Degron_polIIhet_chipseq_PolII_amanitintreated


title: Single Sert+ neuron 74

description:
C1_SER39
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 75

description:
C10_SER40
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21DegronPolIIhet_PCHiC_untreated_br2

description: Promoter Capture HiC


title: hct116_Rad21DegronPolIIhet_PCHiC_untreated_br1

description: Promoter Capture HiC


title: Single Sert+ neuron 73

description:
C1_SER25
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 71

description:
B9_SER25
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 72

description:
B9_SER39
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21DegronPolIIhet_PCHiC_auxin_br2

description: Promoter Capture HiC


title: Single Sert+ neuron 70

description:
B8_SER40
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 76

description:
C11_SER25
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 69

description:
B7_SER39
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21DegronPolIIhet_PCHiC_auxinamanitin_br5

description: Promoter Capture HiC


title: Single Sert+ neuron 68

description:
B7_SER25
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21DegronPolIIhet_PCHiC_auxinamanitin_br4

description: Promoter Capture HiC


title: hct116_Rad21DegronPolIIhet_PCHiC_auxin_br1

description: Promoter Capture HiC


title: Single Sert+ neuron 66

description:
B5_SER39
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21Degron_polIIhet_chipseq_Med26_untreated


title: Single Sert+ neuron 65

description:
B5_SER25
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21DegronPolIIhet_PCHiC_amanitin_br3

description: Promoter Capture HiC


title: Single Sert+ neuron 64

description:
B4_SER40
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21DegronPolIIhet_HiC_auxinamanitin_br4

description:
processed data file:
hct116_Rad21DegronPolIIhet_HiC_auxinamanitin_inter30.hic


title: hct116_Rad21DegronPolIIhet_HiC_auxinamanitin_br5


title: Single Sert+ neuron 67

description:
B6_SER40
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21DegronPolIIhet_PCHiC_amanitin_br4

description: Promoter Capture HiC


title: Single Sert+ neuron 63

description:
B3_SER39
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21DegronPolIIhet_HiC_auxinamanitin_br2_tr2

description:
processed data file:
hct116_Rad21DegronPolIIhet_HiC_auxinamanitin_br2_inter30.hic
hct116_Rad21DegronPolIIhet_HiC_auxinamanitin_inter30.hic


title: Single Sert+ neuron 60

description:
B23_SER39
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 59

description:
B23_SER25
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 61

description:
B24_SER40
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21DegronPolIIhet_HiC_auxinamanitin_br1_tr1

description:
processed data file:
hct116_Rad21DegronPolIIhet_HiC_auxinamanitin_br1_inter30.hic
hct116_Rad21DegronPolIIhet_HiC_auxinamanitin_inter30.hic


title: hct116_Rad21DegronPolIIhet_HiC_amanitin_br4

description:
processed data file:
hct116_Rad21DegronPolIIhet_HiC_amanitin_inter30.hic


title: hct116_Rad21DegronPolIIhet_HiC_auxinamanitin_br1_tr2


title: hct116_Rad21DegronPolIIhet_HiC_auxinamanitin_br2_tr1


title: Single Sert+ neuron 58

description:
B22_SER40
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21DegronPolIIhet_HiC_amanitin_br3


title: Single Sert+ neuron 57

description:
B21_SER39
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 56

description:
B21_SER25
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21DegronPolIIhet_HiC_amanitin_br1_tr2

description:
processed data file:
hct116_Rad21DegronPolIIhet_HiC_amanitin_br1_inter30.hic
hct116_Rad21DegronPolIIhet_HiC_amanitin_inter30.hic


title: hct116_Rad21DegronPolIIhet_HiC_amanitin_br2_tr1

description:
processed data file:
hct116_Rad21DegronPolIIhet_HiC_amanitin_br2_inter30.hic
phct116_Rad21DegronPolIIhet_HiC_amanitin_inter30.hic


title: Single Sert+ neuron 55

description:
B20_SER40
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 54

description:
B2_SER40
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 53

description:
B19_SER39
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 51

description:
B18_SER40
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 62

description:
B3_SER25
Adult_DR_GEO_counts_cpm.txt


title: hct116-Rad21Degron_chipseq_Med26_untreated


title: hct116-Rad21Degron_chipseq_Rad21_auxintreated


title: hct116-Rad21Degron_chipseq_Rad21_untreated


title: Single Sert+ neuron 50

description:
B17_SER39
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 49

description:
B17_SER25
Adult_DR_GEO_counts_cpm.txt


title: ch12_wt_Hic_APR60h_tr7

description:
processed data file: ch12_wt_Hic_APR60h_tr7_inter.hic
processed data file: ch12_wt_Hic_APR60h_tr7_inter_30.hic
processed data file: ch12_wt_Hic_APR60h_inter.hic
processed data file: ch12_wt_Hic_APR60h_inter_30.hic

data_processing:
Base calling: Illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
ATAC-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ATAC-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ATAC-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
HiC-Seq: alignment: bwa-sw with default parameter (map each read separately)
HiC-Seq: filter: remove duplicates and near duplicates, removes reads that map to the same fragment and low quality reads (MAPQ <30)
HiC-Seq: generate contact matrix: juicer running with default parameter
4C-Seq: filtering: each read pair was tested for the presence of a perfect match to the respective bait primer as well as the bait spacer between the end of the primer and the restriction sites used in the corresponding experiment.
4C-Seq: mapping: bowtie-1.1.1/bowtie -X 500 -p 3 -v2 -k2 -m1 --phred64-quals -sam
4C-Seq: frequency: assign to NlaIII/CSP6i fragment (human) or DpnII/CSP6i fragment (mouse)to calculate fraction of restriction fragments for which 4C reads were found
CRISPR screen: Build artificial genome with primer and sgRNA constructs and make index with bowtie
CRISPR screen: alignment: bowtie -S -m 1 -p 4 -a --best --strata -n 2 -l 80
CRISPR screen: filtering and sort: samtools view -S -b -F4 | samtools sort -@ 2
CRISPR screen: samtools idxstats on aligned file
CRISPR screen: calculate frequency of each sgRNAs in each pool
CRISPR screen: samtools idxstats on aligned file
Genome_build: mm9 (MGSCv37), hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm).
Supplementary_files_format_and_content: ATAC-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm).
Supplementary_files_format_and_content: HiC-Seq: .hic format including contact matrix, normalization information generated by juicer.sh.
Supplementary_files_format_and_content: 4C-Seq: bed file showing read frequency in 100K window normalized by the number of fragments in each window.
Supplementary_files_format_and_content: mRNA-Seq:.wig files tag density divided by library size in millions to obtain normalized read density (rpkm).
Supplementary_files_format_and_content: CRISPRscreen: summarized text file on each codition, replicates, gene, sgRNAs.

source_name: CH12 B cell line

growth_protocol: Cas9 expressing cells: Primary CD4+ cells expressing Cas9 were isolated from a Cas9 expressing mouse (Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh) (Platt et al., Cell, 2014). Spleen was triturated in DMEM, supernatant was filtered and immediately processed according to the MACS mouse CD4+ T Cell Isolation Kit (Miltenyi Biotec, Cologne, Germany), following the manufacturer’s protocol. Isolated cells were seeded in a six-well plate that was previously coated with aCD3 and aCD28 at a final concentration of 10 ug/mL in 1.6 mL of PBS. The plate was incubated at 37°C for a minimum of 30 min. The PBS was then removed and the cells added to the plate. Cas9 expression in E14 ES cells was obtained through infection with lentiCas9-blast virus (Addgene plasmid #52962). After Blasticidin selection (7.5 ug/mL), clones expressing Cas9 were isolated and expanded to be used for the multiCRISPR screen for essential Mediator subunits. Cas9 expression was assessed by Western blot analysis and cutting efficiency after transfection with sgRNA plasmids.

extract_protocol:
Extraction protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with MNase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at 37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or MNase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. MNase-Seq: 4x10^7 resting and activated B cells were digested with 24 different concentrations of MNaseI. After an initial RT-qPCR analysis and curve-fitting, the MNaseI concentrations for the most representative nucleosomal fraction was determined. The lowest three nucleosomal fractions (which corresponded to MNaseI concentrations of 0U, 0U, and 0.0026U) were pooled together and used as input control. Nucleosomal fractions 16-18 (which corresponded to enzyme concentrations of 0.068U, 0.045U, and 0.03U) were also pooled for further processing. Input samples were sonicated to obtain similar fragment sizes as the MNaseI-digested samples. DNA was then concentrated and each sample was spiked with 0.055mg of l DNA (also sonicated to match the sample size as was input DNA).
HiC-Seq: We used the same protocol for in situ HiC libraries as Rao et al., (Cell, 2014 Dec; 159:1-16).
4C-seq: The 4C assay was performed as previously described van de Werken et al. (2012) with minor modifications. Ten million of CH12 B cell line were crosslinked in 2% formaldehyde at 37°C for 10 min. The reaction was quenched by the addition of glycine (final concentration of 0.125 M). Cells were then washed with cold PBS and lysed (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% NP-40, 1× complete protease inhibitors [Roche]) at 4°C for 1 hr. Nuclei were incubated at 65°C for 30 min, 37°C for 30 min in 500 μl of restriction buffer (New England BioLabs DpnII buffer) containing 0.3% SDS. To sequester SDS, Triton X-100 was then added to a final concentration of 1.8%. DNA digestion was performed with 400 U of DpnII (New England Biolabs) at 37°C overnight. After heat inactivation (65°C for 30 min), the reaction was diluted to a final volume of 7 ml with ligation buffer containing 100 U T4 DNA Ligase (Roche) and incubated at 16°C overnight. Samples were then treated with 500 μg Proteinase K (Ambion) and incubated overnight at 65°C to reverse formaldehyde crosslinking. DNA was then purified by phenol extraction and ethanol precipitation. For circularization, the ligation junctions were digested with Csp6I (Fermentas) at 37°C overnight. After enzyme inactivation and phenol extraction, the DNA was religated in a 7 ml volume (1,000 U T4 DNA Ligase, Roche). Three micrograms of 4C library DNA was amplified with Expand Long template PCR System (Roche). Thermal cycle conditions were DNA denaturing for 2 min at 94°C, followed by 30 cycles of 15 s at 94°C, 1 min at 58°C, 3 min at 68°C, and a final step of 7 min at 68°C. Bait was amplified with inverse PCR primers as follows: 3RR with DpnII: _4C 5′- GCTTATCTGTAAAGAATGGGTC-3′, 3RR_Csp6i 5′-GGCCTTAGAAGGCTCTGTAC-3′. 4C-amplified DNA was microsequenced with the Illumina platform.
mRNA-seq: Total RNA from 10^6 of WT or ZF9-11 CH12 cells was isolated by Trizol extraction. mRNA was then isolated. ERCC-spike-in was added on some samples for quantitative comparison between two conditions.
ATACseq: One hundred thousand cultured cells were harvested for each point. Cell lysis and Transposition reaction were immediately performed according to Greenleaf’s group protocol (Corces et al., Nat Meth 2017; Buenrostro et al., Nat Meth 2013). Transposed DNA was immediately purified and stored at -20C before library preparation according to the above protocol.
CRISPRscreen: Cells were harvested at an early reference time-point (second day after infection) and two late time-points (14 and 21 days after infection). DNA was extracted using DNeasy Blood and tissue kit according to the manufacturer’s instructions (#69506, Qiagen).
Library construction protocol:
ChIP-Seq  Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on the HiSeq 2500 or 3000 (Illumina).
HiC-seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 100 cycles of sequencing data were acquired on the HiSeq 2500 (Illumina).
4C-seq: DNA was prepared for paired-end Illumina sequencing. 50 cycles of sequencing data were acquired on the HiSeq 2500 (Illumina).
mRNA-seq: Standard RNA-Seq library preparation was performed following Illumina's RNA-Seq protocol v2. 50 cycles of sequencing data were acquired on HiSeq 2000, 2500 or 3000 (Illumina).
ATAC-seq: DNA was prepared for single-end Illumina sequencing. 50 cycles of sequencing data were acquired on the HiSeq 2000 (Illumina).
CRISPRscreen: DNA was prepared for single-end Illumina sequencing using staggered GeCKO readout primers (Shalem et al. 2013). 80 cycles of sequencing data were acquired on the MiSeq (Illumina).

treatment_protocol: CRISPR infection: The viral libraries which contain sgRNAs were used to infect Cas9 expressing E14 ES cells and primary CD4+ T cells isolated from the Rosa26-Cas9 expressing mice. Two hundred thousand cells were seeded in a six-well plate the day before infection. Concentrated viruses were added to the media in presence of Polybrene (6 ug/mL). The amount of virus was adjusted according to the viral titer to obtain a MOI of 0.3. Cells were transduced by spinfection at 1,350g for 90 min and 28-32°C. Infected cells were selected 24h after infection, using Puromycin at a final concentration of 1 ug/ml for ES cells and 2 ug/mL for CD4+ T cells.

tag: cell line

value: lymphoma cell line

tag: genotype/variation

value: WT

tag: treatment


title: PilocyticAstrocytoma_13_tumor

type: RNA

city: Ribeirão Preto

first: Carlos

middle: Alberto

last: Scrideli

state: São Paulo

address: Avenida Bandeirantes 3900

department: Pediatrics

country: Brazil

institute: Ribeirao Preto Medicine School - University of Sao Paulo

hyb_protocol: The labeled RNA was purified (MicroBioSpin 6, Bio-Rad, 732-6221), hybridized (overnight for 20 hours at 55°C and 20 rpm) and washed (Agilent, 5188-5327) before scanning.

scan_protocol: Microarray slides were scanned at 535 nm with 5 μm/pixel resolution using a DNA Microarray Scanner with SureScan High-Resolution Technology (Agilent Technologies) and the fluorescent intensities were determined by the Feature Extraction Software Version 11.5 (Agilent Technologies), to obtain Processed Signals (resulting from all intra-array pre-processing, including background corrections)  corresponding to the transcript levels.

data_processing:
The spot images were processed with Feature Extraction Software v10.7.3.1 (Agilent Technologies). Each miRNA microarray was analyzed with respect to signal intensity, background signal, as well as internal control blade and spike in controls. A box-plot was  generated in order to determine the distribution of signals  from each spot on each microarray as well as sample integrity and quality.
An empirical Bayesian approach was used to determine differential expression and the false discovery rate (FDR) was used to control the false-positive rate. Normalization was performed by the 75% quartile method.

source_name: Pilocytic astrocytoma, tumor, patient13

label_protocol: The microRNA library was constructed using 100 ng of total RNA and investigated with the Agilent  Human microRNA Microarray Kit (v3)” (G4470C, Agilent Technologies, Santa Clara, CA, USA) to determine the expression profile of microRNAs according to manufacturer’s instructions. This array contains 866 human and 89 human viral microRNA sequences. Each miRNA species is printed 20 times with replicate probes on the array.

extract_protocol: Fresh surgical tissues were immediately snap-frozen in liquid nitrogen, stored at −80 °C and microdissected prior to RNA extraction and only specimen with at least 80% of tumor cells were included in the study. Total cellular RNA was extracted using TRIzol LS Reagent (Invitrogen, Carlsbad, CA, USA) according to the  anufacturer’s instructions. The RNA was reverse transcribed to single-stranded cDNA using the High Capacity Kit (Applied Biosystems, Foster  City, CA, USA).

value: Tumor

tag: gender

value: Female

tag: age at diagnosis

tag: chemotherapy

value: No

tag: neurofibromatosis type 1 (nf1)

tag: follow up (month)

tag: kiaaa159-braf fusion

value: Positive

tag: relapse

tag: vital status

value: Alive


title: ChIP-Seq_PC3_KDM2B

city: Houston

first: Filippo

last: Giancotti

state: Texas

address: 1881 East Road

department: Cancer Biology

institute: UT MD Anderson Cancer Center

data_processing:
Reads were trimmed by trimmomatic prior to alignment, as recommended by the ChIP kit manufacturer.
The trimmed reads were then aligned to the hg19 reference genome using bowtie2.
Only uniquely aligned reads were kept for downstream 45 analysis, with duplicate reads removed by the same tools software v1.9.
To visualize ChIP-seq signal at individual genomic regions, we generated bedGraph file by using HOMER software v4.10.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

source_name: Human prostatic adenocarcinoma

growth_protocol: PC3 cells were obtained from ATCC and cultured according to the manufacturers' instructions.

extract_protocol:
Cell nuclei from approximately 20 million formaldehyde crosslinked (1%; 10 minutes at room temperature) were isolated and chromatin was fragmented using sonicator (bioruptor). Lysate were cleared and protein-DNA complexes were isolated using target antibodies and protein-G coated magnetic beads. Chromatin IP was conducted following the standard protocol from ActiveMotif ChIP-IT High Sensitivity® (HS) Kit.
Libraries were prepared according to standard Illumina HiSeq 3000 protocol/Illumina HiSeq 4000. Samples were sequenced at Integrated Genomics Operation Core at UT MD Anderson Cancer Center.

value: prostate; derived from metastatic site:bone

tag: disease

value: grade IV, adenocarcinoma

value: 62 years adult

tag: chip antibody

value: millipore, 09-864


title: Single Sert+ neuron 47

description:
B15_SER39
Adult_DR_GEO_counts_cpm.txt

tag: strain

tag: tissue

value: Sert+ neurons

value: 40–45 days

value: Principal DR


title: Single Sert+ neuron 48

description:
B16_SER40
Adult_DR_GEO_counts_cpm.txt

tag: age

tag: brain region

value: Sert-tdTomato-Cre cross with Ai14


title: ChIP-Seq_PC3_PHC2

tag: cell line

value: active motif, 39661


title: Single Sert+ neuron 46

description:
B15_SER25
Adult_DR_GEO_counts_cpm.txt

tag: genotype


title: ChIP-Seq_PC3_PCGF1

value: santa cruz, Sc-515371


title: ChIP-Seq_PC3_Input

value: none (input)


title: ChIP-Seq_PC3_RNF2


title: Single Sert+ neuron 44

description:
B13_SER39
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21DegronPolIIhet_HiC_amanitin_br2_tr2

description:
processed data file:
hct116_Rad21DegronPolIIhet_HiC_amanitin_br2_inter30.hic
hct116_Rad21DegronPolIIhet_HiC_amanitin_inter30.hic

tag: cell type

value: colon carcinoma cell line


title: Single Sert+ neuron 45

description:
B14_SER40
Adult_DR_GEO_counts_cpm.txt


title: ChIP-Seq_PC3_BMI1

value: active motif, 39993


title: Single Sert+ neuron 43

description:
B13_SER25
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21DegronPolIIhet_HiC_amanitin_br1_tr1


title: Single Sert+ neuron 42

description:
B12_SER40
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 41

description:
B11_SER39
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21Degron_chipseq_PolII_untreated_tr2

tag: genotype/variation

value: Abcam, ab817


title: hct116_Rad21Degron_chipseq_PolII_untreated_tr1


title: Single Sert+ neuron 52

description:
B19_SER25
Adult_DR_GEO_counts_cpm.txt


title: hct116-Rad21Degron_chipseq_Med26_auxintreated

value: Cell signalling technologies, 13641S


title: hct116_Rad21Degron_chipseq_PolII_auxintreated_tr2

tag: treatment

value: auxin


title: Single Sert+ neuron 40

description:
B11_SER25
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 39

description:
B10_SER40
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 37

description:
B1_SER25
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21Degron_chipseq_input_untreated


title: hct116_Rad21Degron_chipseq_input_auxintreated


title: Single Sert+ neuron 38

description:
B1_SER39
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 36

description:
A9_SER39
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 31

description:
A6_SER40
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 33

description:
A7_SER39
Adult_DR_GEO_counts_cpm.txt


title: hct116_Rad21Degron_chipseq_PolII_auxintreated_tr1


title: Single Sert+ neuron 34

description:
A8_SER40
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 28

description:
A4_SER40
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 32

description:
A7_SER25
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 30

description:
A5_SER39
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 27

description:
A3_SER39
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 26

description:
A3_SER25
Adult_DR_GEO_counts_cpm.txt


title: root meristem stele in the shr -2 expressing pCRE1::SHRΔNLELDV:nlsGFP, biological replicate 1

city: Seoul

first: Ji-Young

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

description: expression profile of the stele from the 6 day old seedling root

hyb_protocol: Samples were submitted to Cornell Genomics Facility for hybridization to Affymetrix ATH1 microarrays.

data_processing: Microarray data from Tiling 1.0R array CDF that contains gene-specific single-copy exonic probe sets were normalized using RMA algorithm. References: Irizarry, R.A. et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostat 4, 249-264 (2003). Naouar, N. et al. Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant J. 57, 184-194 (2009).

label: biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis roots of 6 day old seedlings

label_protocol: Probe preparation were carried out according to the manufacturer’s instructions (GeneChip Whole Transcript Double-Stranded Target Assay Manual from Affymetrix Inc.), and then biotinylated double stranded DNA probes were hybridized to the Arabidopsis Tiling 1.0R arrays (Affymetrix Inc.).

growth_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on standard media. Standard media prepared in square plates include 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar, which were adjusted to pH 5.7 with KOH. Nylon mesh was placed on top of the solidified media and seeds were evenly placed on the mesh. Seedlings were germinated and grown on upright position in the lighted growth chamber with the cycle of 16 hr in the light and 8 hr in the dark.

extract_protocol: Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen). RNA integrity was determined on a Bioanalyzer (Agilent BioAnalyzer 2100).

treatment_protocol: The protoplast preparation and FACS facilitated cell sorting were done as described in Birnbaum et al. (2004)

value: root

tag: development

value: 6 day old seedling

value: shr-2 mutant expressing pCRE1::SHRΔNLELDV:nlsGFP


title: root meristem stele in the shr-2, biological replicate 1

scan_protocol: Samples were submitted to Cornell Genomics Facility for hybridization to Affymetrix ATH1 microarrays.

value: shr-2 mutant


title: root meristem stele in the Col-0, biological replicate 3

value: Col-0 wild type


title: root meristem stele in the Col-0, biological replicate 2


title: root meristem stele in the Col-0, biological replicate 1


title: Single Sert+ neuron 35

description:
A9_SER25
Adult_DR_GEO_counts_cpm.txt

value: Sert+ neurons


title: Single Sert+ neuron 23

description:
A23_SER25
Adult_DR_GEO_counts_cpm.txt

value: 40–45 days


title: Single Sert+ neuron 24

description:
A23_SER39
Adult_DR_GEO_counts_cpm.txt

value: Principal DR


title: Single Sert+ neuron 22

description:
A22_SER40
Adult_DR_GEO_counts_cpm.txt

value: Sert-tdTomato-Cre cross with Ai14


title: Single Sert+ neuron 25

description:
A24_SER40
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 29

description:
A5_SER25
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 21

description:
A21_SER39
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 19

description:
A20_SER40
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 20

description:
A21_SER25
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 18

description:
A2_SER40
Adult_DR_GEO_counts_cpm.txt


title: Sinorhizobium meliloti RFF231 pMB865, biological rep3

first: Melanie

middle: J

last: Barnett

address: 371 Jane Stanford Way

department: Biology

hyb_protocol: Four micrograms of biotinylated cDNA was hybridized to each chip at 48 degrees celsius for 16 hours as described by Barnett et al. 2004. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: Chips were scanned at the Stanford PAN facility using an Affymetrix Scanner 3000 7G

data_processing: The data were analyzed using Partek Genomics Suite 6.6 software, with the following settings: RMA for background correction; quantile normalization; log base 2 transformation; median polish summarization

organism: Sinorhizobium meliloti

source_name: rpoH1rpoH2 deletion strain RFF231 pMB865 (strain carrying S. meliloti rpoH1 on pSRKGm)

label_protocol: cDNA was fragmented and biotinylated as described by Barnett et al. 2004.

growth_protocol: Starter cultures were diluted to ~0.1 OD-600 in 20 ml M9 sucrose medium with 50 ug ml-1 Gm and 500 ug ml-1 Sm, in 250 ml baffled flasks, and allowed to grow to mid-exponential phase (~0.5 to ~0.7 OD-600), with replicates from a single experiment grown to within ~0.1 OD-600 units of each other, and shaking (250 rpm) at 30°C.  At mid-exponential phase, IPTG was added to a final concentration of 0.5 mM and the cells were grown for one hour before harvest.

extract_protocol: Total RNA was extracted using a Qiagen RNeasy kit with modifications as described by Barnett et al. 2004 Proc Natl Acad Sci USA volume 101 pages 16636 to 16641.

treatment_protocol: Stop solution (5% buffer equilibrated phenol in ethanol) was added to bacterial cultures, at one tenth the culture volume, before centrifugation at 4 degrees celsius. Bacterial cell pellets were frozen in liquid nitrogen and stored at -80 degrees celsius until RNA extraction.

value: rpoH1rpoH2 deletion

value: RFF231 pMB865


title: Sinorhizobium meliloti MB1102 pMB877, biological rep3

source_name: visNR deletion strain MB1102 pMB877 (strain carrying codon-optimized Ca. L. asiaticus visNR on pSRKGm)

value: visNR deletion


title: Sinorhizobium meliloti MB1102 pMB877, biological rep2


title: Sinorhizobium meliloti RFF231 pMB861, biological rep3

source_name: rpoH1rpoH2 deletion strain RFF231 pMB861 (strain carrying codon optimized Ca. L. asiaticus rpoH on pSRKGm)

value: RFF231 pMB861


title: Sinorhizobium meliloti MB1102 pMB877, biological rep1


title: Single Sert+ neuron 17

description:
A19_SER39
Adult_DR_GEO_counts_cpm.txt


title: Sinorhizobium meliloti MB1102 pSRKGm, biological rep3

source_name: visNR deletion strain MB1102 pSRKGm (control strain, carrying empty vector)

value: MB1102 pSRKGm


title: Sinorhizobium meliloti MB1102 pSRKGm, biological rep1


title: Single Sert+ neuron 16

description:
A19_SER25
Adult_DR_GEO_counts_cpm.txt


title: root meristem stele in the shr -2 expressing pCRE1::SHRΔNLELDV:nlsGFP, biological replicate 2


title: root meristem stele in the shr-2, biological replicate 2


title: Sinorhizobium meliloti RFF231 pMB861, biological rep2


title: Sinorhizobium meliloti RFF231 pMB865, biological rep1


title: Single Sert+ neuron 15

description:
A18_SER40
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 14

description:
A17_SER39
Adult_DR_GEO_counts_cpm.txt


title: Sinorhizobium meliloti RFF231 pMB861, biological rep1


title: Sinorhizobium meliloti RFF231 pSRKGm, biological rep3

source_name: rpoH1rpoH2 deletion strain RFF231 pSRKGm (control strain, carrying empty vector)

value: RFF231 pSRKGm


title: Sinorhizobium meliloti RFF231 pMB865, biological rep2


title: Sinorhizobium meliloti MB1142 pMB875, biological rep3

source_name: phrR1phrR2 deletion strain MB1142 pMB875 (strain carrying codon-optimized Ca. L. asiaticus phrR on pSRKGm)

value: phrR1phrR2 deletion


title: Single Sert+ neuron 11

description:
A15_SER39
Adult_DR_GEO_counts_cpm.txt


title: Sinorhizobium meliloti RFF231 pSRKGm, biological rep2


title: Sinorhizobium meliloti RFF231 pSRKGm, biological rep1


title: Single Sert+ neuron 10

description:
A15_SER25
Adult_DR_GEO_counts_cpm.txt


title: Sinorhizobium meliloti MB1142 pSRKGm, biological rep3

source_name: phrR1phrR2 deletion strain MB1142 pSRKGm (control strain, carrying empty vector)

value: MB1142 pSRKGm


title: Sinorhizobium meliloti MB1142 pMB875, biological rep2


title: Sinorhizobium meliloti MB1142 pMB875, biological rep1


title: Sinorhizobium meliloti MB1142 pSRKGm, biological rep2


title: Single Sert+ neuron 7

description:
A13_SER25
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 8

description:
A13_SER39
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 13

description:
A17_SER25
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 9

description:
A14_SER40
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 12

description:
A16_SER40
Adult_DR_GEO_counts_cpm.txt


title: Sinorhizobium meliloti MB1142 pSRKGm, biological rep1


title: Single Sert+ neuron 6

description:
A12_SER40
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 3

description:
A10_SER40
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 4

description:
A11_SER25
Adult_DR_GEO_counts_cpm.txt


title: Sinorhizobium meliloti MB1105 pMB874, biological rep1

source_name: lsrB deletion strain MB1105 pMB874 (strain carrying codon-optimized Ca. L. asiaticus lsrB on pSRKGm)

value: lsrB deletion


title: Sinorhizobium meliloti MB1105 pSRKGm, biological rep1

source_name: lsrB deletion strain MB1105 pSRKGm (control strain, carrying empty vector)

value: MB1105 pSRKGm


title: Single Sert+ neuron 1

description:
A1_SER25
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 5

description:
A11_SER39
Adult_DR_GEO_counts_cpm.txt


title: Sinorhizobium meliloti MB1105 pSRKGm, biological rep3


title: Sinorhizobium meliloti MB1105 pSRKGm, biological rep2


title: Sinorhizobium meliloti MB1101 pMB878, biological rep1

source_name: ldtR deletion strain MB1101 pMB878 (strain carrying codon-optimized Ca. L. asiaticus ldtR on pSRKGm)

value: ldtR deletion


title: Sinorhizobium meliloti MB1101 pMB878, biological rep2


title: Sinorhizobium meliloti MB1105 pMB874, biological rep3


title: Mbnl1high1

city: Basel

first: Panagiotis

last: Papasaikas

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
Basecalling was performed using RTA v. 2.4.11.
Reads were aligned using STAR version 2.5.0 with parameters --outFilterMultimapNmax 10 --alignSJoverhangMin 6 --alignSJDBoverhangMin 3 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 50 --twopassMode Basic
Gene counts were obtained from the STAR using --quantMode and gencode vM4 annotation
Genome_build: mm10
Supplementary_files_format_and_content: Gene level raw counts (STAR quantmode output)

source_name: mouse embryonic stem cell

growth_protocol: Mouse embryonic stem cells (129xC57BL/6 Rosa26Cre-ERT2/BirA-V5 [cMB063 (Ostapcuk et al., 2018)]) were cultured on gelatin-coated dishes in mES medium (DMEM [Gibco; 11995065]) supplemented with 15% fetal bovine serum [Gibco], 1 x non-essential amino acids [Gibco], 1mM sodium pyruvate [Gibco], 2mM L-glutamine [Gibco], 0.1 mM ß-mercaptoethanol [Sigma], 50 µg/ml penicillin, 80 µg/ml streptomycin, 1x MycoZap™ Prophylactic [Lonza; VZA-2032], 1x ESGRO® LIF [MerckMillipore; ESG1107]) at 37 °C in 5% CO2.

extract_protocol:
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
TruSeq Illumina Total RNA-seq (stranded - high input); NextSeq 500 platform (75 nt paired-end reads)

treatment_protocol: mES (129xC57BL/6) Rosa26Cre-ERT2/BirA-V5 stable transfection MBNL1::T2A::Puromycin

value: mESC

tag: background strain


title: mutMbnl2

treatment_protocol: mES (129xC57BL/6) Rosa26Cre-ERT2/BirA-V5 Mbnl13’UTR(mut)/3'UTR(mut)


title: mutMbnl1


title: Sinorhizobium meliloti MB1101 pMB878, biological rep3


title: Sinorhizobium meliloti MB1101 pSRKGm, biological rep3

source_name: ldtR deletion strain MB1101 pSRKGm (control strain, carrying empty vector)

value: MB1101 pSRKGm


title: K2

treatment_protocol: mES (129xC57BL/6) Rosa26Cre-ERT2/BirA-V5 TRIM71-/-

value: Rosa26Cre-ERT2/BirA-V5 TRIM71-/-


title: Single Sert+ neuron 2

description:
A1_SER39
Adult_DR_GEO_counts_cpm.txt

source_name: Sert+ neurons

value: Sert+ neurons

value: 40–45 days


title: K1


title: W2


title: Sinorhizobium meliloti MB1101 pSRKGm, biological rep1


title: Sinorhizobium meliloti MB1105 pMB874, biological rep2


title: W1


title: Sinorhizobium meliloti CL150 pMB913, biological rep1

source_name: wild type strain CL150 pMB913 (strain carrying S. meliloti ctrA on pSRKGm)

value: wild type


title: Mbnl1high2

value: Rosa26Cre-ERT2/BirA-V5 stable transfection MBNL1::T2A::Puromycin


title: Sinorhizobium meliloti CL150 pMB913, biological rep2


title: Sinorhizobium meliloti CL150 pMB913, biological rep3


title: LE1Sed

city: Dallas

first: Eric

middle: N

last: Olson

state: TX

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

data_processing:
Raw reads were mapped using Bowtie2 to obtain about 50 million uniquely mapped single end reads per library.
Peak calling was performed by MACS/MACS2.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Sample bigwig files

growth_protocol: Six-week old wild type mice were randomly assigned to housing in individual cages with or without a running wheel for a total of 8 weeks.

extract_protocol:
ChIP assays were performed on powdered tibialis anterior muscle using ChIP-IT High Sensitivity (53040, Active motif, USA) according to the manufacturer’s instructions.
ChIP-seq libraries were constructed using the Kapa Hyper Prep Kit (KK8500, Roche).

tag: group

value: Sedentary

value: tibialis anterior

value: WT

tag: antibody


title: LE2Ex

value: Exercise


title: G1297 NanogKRAB 4d HA

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

data_processing:
The sequencing quality was checked using fastqc.
Low quality sequencing reads were trimmed and sequencing adaptor sequences were removed using cutadapt (-e 0.05 -O 4 -q 20 -m 31).
The trimmed reads were mapped to mm10 using bowtie2 (--very-sensitive).
Reads which had low mapq (<30), mapped to blacklisted regions or were duplicates were removed using samtools and picard.
bigWig files were generated using deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: G1297 cell line

growth_protocol: G1297; DMEM + 10% FBS, PS/ MEFs; DMEM + 10%FBS, PS, NEAA, L-Glu, 2-ME/ iPSCs;  Knockout DMEM + 15%FBS, PS, NEAA, L-Glu, 2-ME, LIF

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies; anti-HA mouse monoclonal antibody, Nacalai cat# 06340-54; anti-H3K27ac mouse monoclonal antibody, Wako MABI0309.
Libraries were prepared according to the manual of Illumina's Trueseq ChIP sample prep kit set A (Part# IP-202-1012).

treatment_protocol: "Dox ON" samples were treated with Doxycycline (0.2µg/ml) containing medium for indicated time.


title: G1297_Input


title: Sinorhizobium meliloti MB1101 pSRKGm, biological rep2


title: Sinorhizobium meliloti CL150 pMB876, biological rep2

source_name: wild type strain CL150 pMB876 (strain carrying codon optimized Ca. L. asiaticus ctrA on pSRKGm)


title: G1297 NanogKRAB 48h HA

value: anti-HA mouse monoclonal antibody, Nacalai cat# 06340-54


title: Sinorhizobium meliloti CL150 pMB876, biological rep1


title: G1297 Ebf1KRAB 48h HA


title: G1297 Ebf1KRAB 4d HA


title: Sinorhizobium meliloti CL150 pSRKGm, biological rep3

source_name: wild type strain CL150 pSRKGm (control strain, carrying empty vector)

value: CL150 pSRKGm


title: iTreg, KO3

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

source_name: spleen, Lymph nodes

extract_protocol:
natural Tregs were sorted according to CD4+GFP+, and RNA was harvested using QIAGEN Rneasy Mini Kit. For induced iTreg, CD4 T cells were isolated and polarized with IL2/TGFbeta for 5 days to induce FoxP3 induction. Day 5, GFP positive cells were isolated and RNA were harvested using QIAGEN RNeasy mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen, Lymph nodes

tag: genetype

value: Hrd1 flox/flox, FoxP3-cre+-GFP

value: 8 weeks


title: iTreg, KO2


title: Sinorhizobium meliloti CL150 pSRKGm, biological rep2


title: Sinorhizobium meliloti CL150 pSRKGm, biological rep1


title: iTreg, KO1


title: iTreg, WT3

value: Hrd1 +/flox, FoxP3-cre+-GFP


title: Sinorhizobium meliloti CL150 pMB876, biological rep3


title: ND, MTG sample 95--34

type: genomic

city: Tempe

first: Danielle

middle: Lisa

last: Brokaw

state: AZ

address: Biodesign Institute Building C, 1001 S McAllister Ave

department: Center for Neurodegeneration, Biodesign

institute: Arizona State University

description:
control MTG sample
MTG 95--34

hyb_protocol: Samples were randomly assigned to one of nine Illumina 450K plates and hybridized according to protocol.

scan_protocol: iScan System according to user protocol

data_processing:
Data was analyzed in R (version 3.4.2) using minfi (1.23.4) and SVA (3.26.0). Poorly performing probes (detection p-value < 0.05) and sex chromosome probes were removed from the analysis. NOOB and functional normalization were performed using the minfi package according author guidelines. Confounding variables were detected using SVA and, alongside batch/plate effects, were accounted for using the ComBat algorithm.
Normalized Average betas included as supplementary files (processedSamples*.txt) on the Series record.
Methylated and unmethylated signal intensities included as supplementary files (signalIntensities*.txt) on the Series record.

label: Cy5 and Cy3

source_name: MTG sample 95--34

label_protocol: Standard Illumina Protocol

extract_protocol: Tissue was incubated in lysis buffer (100 mM Tris HCL pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl, 100 ug/mL Proteinase K) overnight at 55°C.  and disassembled using a pestle. Disassociated tissue was treated with 4 uL of Rnase A for 30 minutes at RT and then treated with ethanol overnight at -20°C. 1 ug of extracted DNA per sample was treated with bisulfite and used in the assay.

tag: plate

tag: bead chip

tag: well position

value: brain

value: MTG

tag: gender

value: M

tag: diagnosis

value: ND


title: iTreg, WT2

tag: strain

tag: tissue

tag: age


title: ND, MTG sample 95--21

description:
control MTG sample
MTG 95--21

source_name: MTG sample 95--21

tag: brain region


title: iTreg, WT1


title: ND, MTG sample 01--36

description:
control MTG sample
MTG 01--36

source_name: MTG sample 01--36

value: F


title: ND, MTG sample 04--21

description:
control MTG sample
MTG 04--21

source_name: MTG sample 04--21


title: nTreg, KO3


title: ND, MTG sample 00--34

description:
control MTG sample
MTG 00--34

source_name: MTG sample 00--34


title: nTreg, KO2


title: nTreg, KO1


title: Aohan-bodyside-rep1

city: Qingdao

first: Hegang

last: Li

state: Shandong

address: 149 Xiazhuang Road, Licang District

department: Animal Reproduction and Breeding

institute: Qingdao Institute of Animal Science and Veterinary Medicine

description: Gene expression at 12 month body side skin

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2505B, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: Agilent Feature Extraction software (version 10.5.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.0 software package (Agilent Technologies). After Quantile normalization of the raw data, genes that at least 1 out of 6 samples have flags in Present (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.0).

organism: Ovis aries

source_name: skin(Aohan fine wool sheep),12 month body side

label_protocol: 1 μg of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: These six sheep were reared normally in pens.

extract_protocol: All samples were immediately put into collection tubes and stored in liquid nitrogen for RNA extraction. TRIzol (Invitrogen) was used for total RNA extractions according to the manufacturer’s protocol. RNA quantity and quality were measured by NanoDrop ND-1000. Its OD260/OD280 ratio was confirmed to be higher than 1.8. RNA integrity was assessed by standard denaturing agarose gel electrophoresis. The RNA samples were sent to Kangchen Biotechnology Limited Company (Shanghai, China) for hybridization to the Agilent Sheep Gene Expression Microarray (Santa Clara, CA, USA).

treatment_protocol: All animals were treated in accordance with the animal protocols deﬁned by national and local animal welfare bodies, and all animal work was approved by the Shandong Province Biological Studies Animal Care and Use Committee.One ram and two ewes of 12-month-old Aohan fine wool sheep and small tail Han sheep were used in the microarray study. These animals were half sibs (sharing the same father) for each breed. In August 2010, full-thickness skin from body side were sampled from each animal under local anaesthesia for microarray and proteomic experiments. The area of each sample was about 1 cm2.

tag: breed

value: Aohan fine wool sheep

value: skin


title: small-bodyside-rep3

source_name: skin(small tail Han sheep),12 month body side

value: small tail Han sheep


title: Aohan-bodyside-rep3


title: Aohan-bodyside-rep2


title: small-bodyside-rep2


title: ND, MTG sample 01--31

description:
control MTG sample
MTG 01--31

source_name: MTG sample 01--31


title: nTreg, WT1


title: ND, MTG sample 08--35

description:
control MTG sample
MTG 08--35

source_name: MTG sample 08--35


title: ND, MTG sample 04--08

description:
control MTG sample
MTG 04--08

source_name: MTG sample 04--08


title: ND, MTG sample 07--70

description:
control MTG sample
MTG 07--70

source_name: MTG sample 07--70


title: RNA.Control.Dorsal.Untreated.R2

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

data_processing:
Alignment: data were aligned to mouse assembly mm10 using STAR v2.5.2a with parameters --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000
Quantitation: tags were counted over exons to give gene-level tag counts with HTSeq v0.6.1p1 with parameters -f sam -r pos -s reverse -t exon -i gene_id
Genome_build: mm10
Supplementary_files_format_and_content: Tag counts per gene per HTSeq are provided as a text table

source_name: dorsal hippocampus

growth_protocol: Male mice were aged to 8 weeks

extract_protocol:
Cells were lyzed using QIAzol (Qiagen) and RNA was extracted using the RNeasy Mini Kit (Qiagen).
RNAseq libraries were prepared using the NEBNext Ultra II Directional RNA library prep kit (NEB).

treatment_protocol: EtOH injection: ethanol was administered via intraperitoneal injection and dosed at 2 g/kg (20% solution in saline, filtered through a Stericup GV filter). ACSS2 shRNA: adult mice (8+ weeks of age) were anaesthetized with isoflurane gas (1–5% to maintain surgical plane) and placed in a sterile field within a stereotaxic device. Artificial tears were applied to eyes to ensure sufficient lubrication. Animals received an injection of bupivacaine (2.5 mg kg−1) for local anaesthesia before the skin was disinfected with betadine solution and the skull exposed with a short incision using sterile surgical equipment. A small hole (about 0.5 mm) was drilled in the skull over the target area using a stereotax and a stereotactic drill. A micro-syringe filled with viral vector was inserted into the dorsal hippocampus and slowly removed following injection (AP, − 2.0 mm; DV, − 1.4 mm; ML, ± 1.5 mm from bregma). ACSS2 knockdown vector, AAV2/9; U6.shACSS2.CMV.EGFP. All animals received a single dose of subcutaneous meloxicam (5 mg kg) as analgesia at induction and one dose per day for two days postoperatively as needed.

tag: knockdown

value: Control


title: ND, MTG sample 06--21

description:
control MTG sample
MTG 06--21

source_name: MTG sample 06--21


title: RNA.Control.Dorsal.Untreated.R1

tag: treatment


title: RNA.ACSS2_KD.Dorsal.Untreated.R2


title: ND, MTG sample 96--28

description:
control MTG sample
MTG 96--28

source_name: MTG sample 96--28


title: ND, MTG sample 99--27

description:
control MTG sample
MTG 99--27

source_name: MTG sample 99--27


title: RNA.Control.Ventral.EtOH.R4

source_name: ventral hippocampus

value: EtOH


title: small-bodyside-rep1


title: RNA.ACSS2_KD.Dorsal.Untreated.R1


title: RNA.Control.Ventral.EtOH.R3


title: RNA.Control.Ventral.EtOH.R2


title: ND, MTG sample 97--03

description:
control MTG sample
MTG 97--03

source_name: MTG sample 97--03


title: nTreg, WT3

source_name: spleen, Lymph nodes


title: ND, MTG sample 98--19

description:
control MTG sample
MTG 98--19

source_name: MTG sample 98--19


title: ND, MTG sample 00--49

description:
control MTG sample
MTG 00--49

source_name: MTG sample 00--49


title: RNA.Control.Ventral.EtOH.R1


title: ND, MTG sample 96--08

description:
control MTG sample
MTG 96--08

source_name: MTG sample 96--08


title: RNA.Control.Dorsal.EtOH.R2


title: RNA.Control.Dorsal.EtOH.R3


title: nTreg, WT2


title: ND, MTG sample 95--36

description:
control MTG sample
MTG 95--36

source_name: MTG sample 95--36


title: RNA.ACSS2_KD.Ventral.EtOH.R4


title: RNA.Control.Dorsal.EtOH.R1


title: RNA.ACSS2_KD.Ventral.EtOH.R3


title: ND, MTG sample 02--38

description:
control MTG sample
MTG 02--38

source_name: MTG sample 02--38


title: ND, MTG sample 93--07

description:
control MTG sample
MTG 93--07

source_name: MTG sample 93--07


title: ND, MTG sample 01--37

description:
control MTG sample
MTG 01--37

source_name: MTG sample 01--37


title: RNA.ACSS2_KD.Ventral.EtOH.R2


title: ND, MTG sample 01--14

description:
control MTG sample
MTG 01--14

source_name: MTG sample 01--14


title: RNA.ACSS2_KD.Ventral.EtOH.R1


title: ND, MTG sample 03--15

description:
control MTG sample
MTG 03--15

source_name: MTG sample 03--15


title: RNA.ACSS2_KD.Dorsal.EtOH.R5


title: RNA.ACSS2_KD.Total.EtOH.R1

source_name: hippocampus


title: ND, MTG sample 99--54

description:
control MTG sample
MTG 99--54

source_name: MTG sample 99--54


title: RNA.ACSS2_KD.Dorsal.EtOH.R4

source_name: dorsal hippocampus


title: ND, MTG sample 04--11

description:
control MTG sample
MTG 04--11

source_name: MTG sample 04--11


title: ND, MTG sample 97--53

description:
control MTG sample
MTG 97--53

source_name: MTG sample 97--53


title: ND, MTG sample 07--30

description:
control MTG sample
MTG 07--30

source_name: MTG sample 07--30


title: RNA.ACSS2_KD.Dorsal.EtOH.R3


title: RNA.ACSS2_KD.Dorsal.EtOH.R2


title: ND, MTG sample 06--43

description:
control MTG sample
MTG 06--43

source_name: MTG sample 06--43


title: RNA.ACSS2_KD.Dorsal.EtOH.R1


title: ND, MTG sample 07--72

description:
control MTG sample
MTG 07--72

source_name: MTG sample 07--72


title: ND, MTG sample 08--47

description:
control MTG sample
MTG 08--47

source_name: MTG sample 08--47


title: Input.ACSS2_KD.EtOH.R3

data_processing:
Alignment: chIP-seq tags generated with the NextSeq 500 platform were demultiplexed with the bcl2fastq utility and aligned to the mouse reference genome (assembly  GRCm38/mm10) using STAR v2.5.2a with parameters --outFilterMultimapNmax 20 --outFilterMismatchNmax 999
Tracks: aligned tags were pooled across replicates and tracks were generated using BEDtools genomeCoverageBed -bg, then the resulting bedGraphs were adjusted for library size by multiplying tag counts by the RPM coefficient and subtracting a similarly adjusted input track. BedGraphs were then converted to bigWig using the UCSC Genome Browser tool bedGraphToBigWig.
Peaks: aligned tags were pooled across replicates and peaks were called using MACS2 callpeak (with matched input as a control) and peaks were filtered with a q-value of 0.001 or lower to correct for the multiple hypothesis testing problem
Genome_build: mm10
Supplementary_files_format_and_content: BigWigs are track files and BED files are peak files

extract_protocol:
ChIP-seq was performed as previously described (Nativio et al, Nat Neuroscience 2018) with modifications for mouse brain preparation. Briefly, ~20 mg dorsal hippocampus from each mouse was minced on ice and crosslinked with 1% formaldehyde for 10 min and quenched with 125 mM glycine for 5 min. Nuclei were prepared by dounce homogenization of crosslinked tissue in nuclei isolation buffer (50 mM Tris-HCl at pH 7.5, 25 mM KCl, 5 mM MgCl2, 0.25 M sucrose) with freshly added protease inhibitors and sodium butyrate. Nuclei were lysed in nuclei lysis buffer (10 mM Tris-HCl at pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine) with freshly added protease inhibitors and sodium butyrate and chromatin was sheared using a Covaris S220 sonicator to ~250 bp size. Equal aliquots of sonicated chromatin were used per immunoprecipitation reaction with 5 ul H3K9ac antibody (Active Motif, cat # 39137; lot # 09811002 ) or 4 ul H3K27ac antibody (Abcam, cat #4729; lot # GR323132-1 (Piazza et al, Nat Commun 2018)) preconjugated to Protein G Dynabeads (Life Technologies). 10% of the chromatin was saved as Input. ChIP reactions were incubated overnight at 4°C with rotation and washed three times in wash buffer. Immunoprecipitated DNA was eluted from the beads, reversed crosslinked and purified together with Input DNA.
10 ng DNA (either ChIP or Input) was used to construct sequencing libraries using the NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, NEB). Libraries were multiplexed using NEBNext Multiplex Oligos for Illumina (dual index primers) and single-ended sequenced (75 bp) on the NextSeq 500 platform (Illumina) in accordance with the manufacturer’s protocol.

value: hippocampus

tag: chip antibody

value: input

tag: genotype

value: ACSS2 KD


title: Input.ACSS2_KD.EtOH.R2


title: Input.ACSS2_KD.EtOH.R1


title: ND, MTG sample 06--05

description:
control MTG sample
MTG 06--05

source_name: MTG sample 06--05


title: ND, MTG sample 06--61

description:
control MTG sample
MTG 06--61

source_name: MTG sample 06--61


title: ND, MTG sample 06--66

description:
control MTG sample
MTG 06--66

source_name: MTG sample 06--66


title: Input.ACSS2_KD.Untreated.R3


title: ND, MTG sample 06--57

description:
control MTG sample
MTG 06--57

source_name: MTG sample 06--57


title: Input.ACSS2_KD.Untreated.R1


title: Input.Control.EtOH.R3


title: ND, MTG sample 96--35

description:
control MTG sample
MTG 96--35

source_name: MTG sample 96--35


title: Input.Control.EtOH.R2


title: ND, MTG sample 98--23

description:
control MTG sample
MTG 98--23

source_name: MTG sample 98--23


title: ND, MTG sample 08--23

description:
control MTG sample
MTG 08--23

source_name: MTG sample 08--23


title: ND, MTG sample 93--20

description:
control MTG sample
MTG 93--20

source_name: MTG sample 93--20


title: Input.Control.EtOH.R1

source_name: hippocampus


title: ND, MTG sample 07--73

description:
control MTG sample
MTG 07--73

source_name: MTG sample 07--73


title: ND, MTG sample 99--47

description:
control MTG sample
MTG 99--47

source_name: MTG sample 99--47


title: ND, MTG sample 96--03

description:
control MTG sample
MTG 96--03

source_name: MTG sample 96--03


title: Input.Control.Untreated.R1


title: ND, MTG sample 95--30

description:
control MTG sample
MTG 95--30

source_name: MTG sample 95--30


title: ND, MTG sample 97--02

description:
control MTG sample
MTG 97--02

source_name: MTG sample 97--02


title: H3K27ac.ACSS2_KD.EtOH.R3

description:
07232018_H3K27ac.KD.EtOH.bw
H3K27ac-Input.KD.EtOH_peaks.FDR_0.001.bed


title: ND, MTG sample 99--44

description:
control MTG sample
MTG 99--44

source_name: MTG sample 99--44


title: ND, MTG sample 03--63

description:
control MTG sample
MTG 03--63

source_name: MTG sample 03--63


title: H3K27ac.ACSS2_KD.EtOH.R2


title: Sinorhizobium meliloti MB1102 pSRKGm, biological rep2

source_name: visNR deletion strain MB1102 pSRKGm (control strain, carrying empty vector)

tag: genotype/variation

value: visNR deletion

value: MB1102 pSRKGm


title: ND, MTG sample 00--38

description:
control MTG sample
MTG 00--38

source_name: MTG sample 00--38


title: Input.ACSS2_KD.Untreated.R2


title: H3K27ac.ACSS2_KD.Untreated.R2

description:
07232018_H3K27ac.KD.Untreated.bw
H3K27ac-Input.KD.Untreated_peaks.FDR_0.001.bed


title: ND, MTG sample 96--39

description:
control MTG sample
MTG 96--39

source_name: MTG sample 96--39


title: H3K27ac.ACSS2_KD.Untreated.R3


title: H3K27ac.ACSS2_KD.Untreated.R1


title: H3K27ac.Control.EtOH.R3

description:
07232018_H3K27ac.WT.EtOH.bw
H3K27ac-Input.WT.EtOH_peaks.FDR_0.001.bed


title: ND, MTG sample 07--58

description:
control MTG sample
MTG 07--58

source_name: MTG sample 07--58


title: ND, MTG sample 00--53

description:
control MTG sample
MTG 00--53

source_name: MTG sample 00--53


title: ND, MTG sample 05--61

description:
control MTG sample
MTG 05--61

source_name: MTG sample 05--61


title: Input.Control.Untreated.R3


title: ND, MTG sample 06--32

description:
control MTG sample
MTG 06--32

source_name: MTG sample 06--32


title: H3K27ac.Control.EtOH.R2


title: ND, MTG sample 05--36

description:
control MTG sample
MTG 05--36

source_name: MTG sample 05--36


title: ND, MTG sample 05--12

description:
control MTG sample
MTG 05--12

source_name: MTG sample 05--12


title: ND, MTG sample 06--68

description:
control MTG sample
MTG 06--68

source_name: MTG sample 06--68


title: H3K27ac.Control.Untreated.R2

description:
07232018_H3K27ac.WT.Untreated.bw
H3K27ac-Input.WT.Untreated_peaks.FDR_0.001.bed

source_name: hippocampus


title: H3K27ac.Control.EtOH.R1


title: H3K27ac.Control.Untreated.R3


title: H3K27ac.ACSS2_KD.EtOH.R1


title: H3K27ac.Control.Untreated.R1


title: ND, MTG sample 95--38

description:
control MTG sample
MTG 95--38

source_name: MTG sample 95--38


title: ND, MTG sample 95--02

description:
control MTG sample
MTG 95--02

source_name: MTG sample 95--02


title: H3K9ac.ACSS2_KD.EtOH.R2

description:
07232018_H3K9ac.KD.EtOH.bw
H3K9ac-Input.KD.EtOH_peaks.FDR_0.001.bed

value: H3K9ac (Active Motif, cat # 39137; lot # 09811002)


title: ND, MTG sample 02--36

description:
control MTG sample
MTG 02--36

source_name: MTG sample 02--36


title: H3K9ac.ACSS2_KD.EtOH.R3


title: ND, MTG sample 99--59

description:
control MTG sample
MTG 99--59

source_name: MTG sample 99--59


title: ND, MTG sample 96--22

description:
control MTG sample
MTG 96--22

source_name: MTG sample 96--22


title: Single Sert+ neuron 1536

description:
P9_SER64
Adult_DR_GEO_counts_cpm.txt

source_name: Sert+ neurons

value: Sert+ neurons

value: 40–45 days

value: All DR

value: Sert-tdTomato-Cre cross with Ai14


title: Single Sert+ neuron 1535

description:
P9_SER60
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 02--12

description:
control MTG sample
MTG 02--12

source_name: MTG sample 02--12

value: brain

value: MTG

value: M

value: ND


title: ND, MTG sample 02--27

description:
control MTG sample
MTG 02--27

source_name: MTG sample 02--27


title: ND, MTG sample 01--46

description:
control MTG sample
MTG 01--46

source_name: MTG sample 01--46

value: F


title: Single Sert+ neuron 1534

description:
P9_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1531

description:
P8_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1533

description:
P8_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1532

description:
P8_SER63
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 03--17

description:
control MTG sample
MTG 03--17

source_name: MTG sample 03--17


title: ND, MTG sample 08--64

description:
control MTG sample
MTG 08--64

source_name: MTG sample 08--64


title: ND, MTG sample 07--11

description:
control MTG sample
MTG 07--11

source_name: MTG sample 07--11


title: Single Sert+ neuron 1529

description:
P7_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1530

description:
P7_SER64
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 05--21

description:
control MTG sample
MTG 05--21

source_name: MTG sample 05--21


title: ND, MTG sample 04--64

description:
control MTG sample
MTG 04--64

source_name: MTG sample 04--64


title: Single Sert+ neuron 1528

description:
P7_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1527

description:
P6_SER67
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 05--18

description:
control MTG sample
MTG 05--18

source_name: MTG sample 05--18


title: ND, MTG sample 06--03

description:
control MTG sample
MTG 06--03

source_name: MTG sample 06--03


title: H3K9ac.ACSS2_KD.EtOH.R1

source_name: hippocampus


title: Single Sert+ neuron 1526

description:
P6_SER63
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 96--30

description:
control MTG sample
MTG 96--30

source_name: MTG sample 96--30


title: ND, MTG sample 94--17

description:
control MTG sample
MTG 94--17

source_name: MTG sample 94--17


title: ND, MTG sample 96--38

description:
control MTG sample
MTG 96--38

source_name: MTG sample 96--38


title: Single Sert+ neuron 1523

description:
P5_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1525

description:
P6_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1522

description:
P5_SER56
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 03--41

description:
control MTG sample
MTG 03--41

source_name: MTG sample 03--41


title: ND, MTG sample 92--32

description:
control MTG sample
MTG 92--32

source_name: MTG sample 92--32


title: Single Sert+ neuron 1520

description:
P4_SER63
Adult_DR_GEO_counts_cpm.txt

source_name: Sert+ neurons


title: ND, MTG sample 97--46

description:
control MTG sample
MTG 97--46

source_name: MTG sample 97--46


title: Single Sert+ neuron 1521

description:
P4_SER67
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 07--26

description:
control MTG sample
MTG 07--26

source_name: MTG sample 07--26


title: ND, MTG sample 08--81

description:
control MTG sample
MTG 08--81

source_name: MTG sample 08--81


title: Single Sert+ neuron 1518

description:
P3_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1517

description:
P3_SER60
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 95--03

description:
control MTG sample
MTG 95--03

source_name: MTG sample 95--03


title: Single Sert+ neuron 1516

description:
P3_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1519

description:
P4_SER57
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 03--11

description:
control MTG sample
MTG 03--11

source_name: MTG sample 03--11


title: Single Sert+ neuron 1524

description:
P5_SER64
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 01--51

description:
control MTG sample
MTG 01--51

source_name: MTG sample 01--51


title: Single Sert+ neuron 1514

description:
P24_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1515

description:
P24_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1513

description:
P24_SER57
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 03--50

description:
control MTG sample
MTG 03--50

source_name: MTG sample 03--50


title: Single Sert+ neuron 1512

description:
P23_SER64
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 02--01

description:
control MTG sample
MTG 02--01

source_name: MTG sample 02--01


title: ND, MTG sample 03--28

description:
control MTG sample
MTG 03--28

source_name: MTG sample 03--28


title: Single Sert+ neuron 1510

description:
P23_SER56
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 01--44

description:
control MTG sample
MTG 01--44

source_name: MTG sample 01--44


title: Single Sert+ neuron 1509

description:
P22_SER67
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 08--55

description:
control MTG sample
MTG 08--55

source_name: MTG sample 08--55


title: ND, MTG sample 07--28

description:
control MTG sample
MTG 07--28

source_name: MTG sample 07--28


title: Single Sert+ neuron 1511

description:
P23_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1507

description:
P22_SER57
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 06--13

description:
control MTG sample
MTG 06--13

source_name: MTG sample 06--13


title: ND, MTG sample 06--15

description:
control MTG sample
MTG 06--15

source_name: MTG sample 06--15


title: Single Sert+ neuron 1505

description:
P21_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1504

description:
P21_SER56
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 06--25

description:
control MTG sample
MTG 06--25

source_name: MTG sample 06--25


title: Single Sert+ neuron 1503

description:
P20_SER67
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 06--33

description:
control MTG sample
MTG 06--33

source_name: MTG sample 06--33


title: ND, MTG sample 05--14

description:
control MTG sample
MTG 05--14

source_name: MTG sample 05--14


title: Single Sert+ neuron 1501

description:
P20_SER57
Adult_DR_GEO_counts_cpm.txt

source_name: Sert+ neurons


title: Single Sert+ neuron 1500

description:
P2_SER67
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 96--44

description:
control MTG sample
MTG 96--44

source_name: MTG sample 96--44


title: Single Sert+ neuron 1502

description:
P20_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1499

description:
P2_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1498

description:
P2_SER57
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 98--22

description:
control MTG sample
MTG 98--22

source_name: MTG sample 98--22


title: Single Sert+ neuron 1496

description:
P19_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1497

description:
P19_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1508

description:
P22_SER63
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 99--04

description:
control MTG sample
MTG 99--04

source_name: MTG sample 99--04


title: ND, MTG sample 92--14

description:
control MTG sample
MTG 92--14

source_name: MTG sample 92--14


title: Single Sert+ neuron 1495

description:
P19_SER56
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 06--02

description:
control MTG sample
MTG 06--02

source_name: MTG sample 06--02


title: ND, MTG sample 03--58

description:
control MTG sample
MTG 03--58

source_name: MTG sample 03--58


title: ND, MTG sample 99--25

description:
control MTG sample
MTG 99--25

source_name: MTG sample 99--25


title: ND, MTG sample 99--02

description:
control MTG sample
MTG 99--02

source_name: MTG sample 99--02


title: Input.Control.Untreated.R2

source_name: hippocampus

value: Control


title: Single Sert+ neuron 1506

description:
P21_SER64
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 97--17

description:
control MTG sample
MTG 97--17

source_name: MTG sample 97--17


title: Single Sert+ neuron 1493

description:
P18_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1494

description:
P18_SER67
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 95--39

description:
control MTG sample
MTG 95--39

source_name: MTG sample 95--39


title: Single Sert+ neuron 1492

description:
P18_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1491

description:
P17_SER64
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 99--58

description:
control MTG sample
MTG 99--58

source_name: MTG sample 99--58


title: Single Sert+ neuron 1490

description:
P17_SER60
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 99--31

description:
control MTG sample
MTG 99--31

source_name: MTG sample 99--31


title: Single Sert+ neuron 1489

description:
P17_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1488

description:
P16_SER67
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 99--50

description:
control MTG sample
MTG 99--50

source_name: MTG sample 99--50


title: Single Sert+ neuron 1487

description:
P16_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1486

description:
P16_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1485

description:
P15_SER64
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 00--03

description:
control MTG sample
MTG 00--03

source_name: MTG sample 00--03


title: ND, MTG sample 04--26

description:
control MTG sample
MTG 04--26

source_name: MTG sample 04--26


title: Single Sert+ neuron 1484

description:
P15_SER60
Adult_DR_GEO_counts_cpm.txt

source_name: Sert+ neurons


title: ND, MTG sample 02--04

description:
control MTG sample
MTG 02--04

source_name: MTG sample 02--04


title: ND, MTG sample 04--19

description:
control MTG sample
MTG 04--19

source_name: MTG sample 04--19


title: ND, MTG sample 00--15

description:
control MTG sample
MTG 00--15

source_name: MTG sample 00--15


title: ND, MTG sample 98--33

description:
control MTG sample
MTG 98--33

source_name: MTG sample 98--33


title: Single Sert+ neuron 1481

description:
P14_SER63
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 03--39

description:
control MTG sample
MTG 03--39

source_name: MTG sample 03--39


title: ND, MTG sample 08--04

description:
control MTG sample
MTG 08--04

source_name: MTG sample 08--04


title: Single Sert+ neuron 1482

description:
P14_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1480

description:
P14_SER57
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 07--10

description:
control MTG sample
MTG 07--10

source_name: MTG sample 07--10


title: ND, MTG sample 05--28

description:
control MTG sample
MTG 05--28

source_name: MTG sample 05--28


title: ND, MTG sample 99--66

description:
control MTG sample
MTG 99--66

source_name: MTG sample 99--66


title: Single Sert+ neuron 1478

description:
P13_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1477

description:
P13_SER56
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 07--37

description:
control MTG sample
MTG 07--37

source_name: MTG sample 07--37


title: ND, MTG sample 06--08

description:
control MTG sample
MTG 06--08

source_name: MTG sample 06--08


title: ND, MTG sample 06--53

description:
control MTG sample
MTG 06--53

source_name: MTG sample 06--53


title: Single Sert+ neuron 1474

description:
P12_SER57
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 04--38

description:
control MTG sample
MTG 04--38

source_name: MTG sample 04--38


title: Single Sert+ neuron 1483

description:
P15_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1473

description:
P11_SER64
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 92--10

description:
control MTG sample
MTG 92--10

source_name: MTG sample 92--10


title: ND, MTG sample 99--22

description:
control MTG sample
MTG 99--22

source_name: MTG sample 99--22


title: Single Sert+ neuron 1475

description:
P12_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1472

description:
P11_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1471

description:
P11_SER56
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 03--26

description:
control MTG sample
MTG 03--26

source_name: MTG sample 03--26


title: ND, MTG sample 02--33

description:
control MTG sample
MTG 02--33

source_name: MTG sample 02--33


title: Single Sert+ neuron 1469

description:
P10_SER63
Adult_DR_GEO_counts_cpm.txt

source_name: Sert+ neurons


title: Single Sert+ neuron 1470

description:
P10_SER67
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 95--27

description:
control MTG sample
MTG 95--27

source_name: MTG sample 95--27


title: ND, MTG sample 96--32

description:
control MTG sample
MTG 96--32

source_name: MTG sample 96--32


title: Single Sert+ neuron 1479

description:
P13_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1468

description:
P10_SER57
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 01--23

description:
control MTG sample
MTG 01--23

source_name: MTG sample 01--23


title: Single Sert+ neuron 1466

description:
P1_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1467

description:
P1_SER64
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 07--52

description:
control MTG sample
MTG 07--52

source_name: MTG sample 07--52


title: ND, MTG sample 03--10

description:
control MTG sample
MTG 03--10

source_name: MTG sample 03--10


title: Single Sert+ neuron 1465

description:
P1_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1476

description:
P12_SER67
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 06--19

description:
control MTG sample
MTG 06--19

source_name: MTG sample 06--19


title: ND, MTG sample 05--20

description:
control MTG sample
MTG 05--20

source_name: MTG sample 05--20


title: ND, MTG sample 04--31

description:
control MTG sample
MTG 04--31

source_name: MTG sample 04--31


title: Single Sert+ neuron 1463

description:
O9_SER60
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 07--04

description:
control MTG sample
MTG 07--04

source_name: MTG sample 07--04


title: Single Sert+ neuron 1462

description:
O9_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1461

description:
O8_SER67
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 04--30

description:
control MTG sample
MTG 04--30

source_name: MTG sample 04--30


title: Single Sert+ neuron 1460

description:
O8_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1459

description:
O8_SER57
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 94--35

description:
control MTG sample
MTG 94--35

source_name: MTG sample 94--35


title: Single Sert+ neuron 1458

description:
O7_SER64
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 06--35

description:
control MTG sample
MTG 06--35

source_name: MTG sample 06--35


title: Single Sert+ neuron 1457

description:
O7_SER60
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 98--32

description:
control MTG sample
MTG 98--32

source_name: MTG sample 98--32


title: ND, MTG sample 07--63

description:
control MTG sample
MTG 07--63

source_name: MTG sample 07--63


title: Single Sert+ neuron 1456

description:
O7_SER56
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 99--29

description:
control MTG sample
MTG 99--29

source_name: MTG sample 99--29


title: Single Sert+ neuron 1454

description:
O6_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1455

description:
O6_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1464

description:
O9_SER64
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 96--45

description:
control MTG sample
MTG 96--45

source_name: MTG sample 96--45


title: ND, MTG sample 08--85

description:
control MTG sample
MTG 08--85

source_name: MTG sample 08--85


title: ND, MTG sample 95--40

description:
control MTG sample
MTG 95--40

source_name: MTG sample 95--40


title: ND, MTG sample 92--06

description:
control MTG sample
MTG 92--06

source_name: MTG sample 92--06


title: ND, MTG sample 03--66

description:
control MTG sample
MTG 03--66

source_name: MTG sample 03--66


title: Single Sert+ neuron 1450

description:
O5_SER56
Adult_DR_GEO_counts_cpm.txt

source_name: Sert+ neurons


title: Single Sert+ neuron 1453

description:
O6_SER57
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 02--08

description:
control MTG sample
MTG 02--08

source_name: MTG sample 02--08


title: Single Sert+ neuron 1452

description:
O5_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1449

description:
O4_SER67
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 02--24

description:
control MTG sample
MTG 02--24

source_name: MTG sample 02--24


title: ND, MTG sample 96--13

description:
control MTG sample
MTG 96--13

source_name: MTG sample 96--13


title: Single Sert+ neuron 1448

description:
O4_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1447

description:
O4_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1446

description:
O3_SER64
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 07--46

description:
control MTG sample
MTG 07--46

source_name: MTG sample 07--46


title: ND, MTG sample 08--52

description:
control MTG sample
MTG 08--52

source_name: MTG sample 08--52


title: Single Sert+ neuron 1445

description:
O3_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1444

description:
O3_SER56
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 06--63

description:
control MTG sample
MTG 06--63

source_name: MTG sample 06--63


title: ND, MTG sample 08--44

description:
control MTG sample
MTG 08--44

source_name: MTG sample 08--44


title: Single Sert+ neuron 1443

description:
O24_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1442

description:
O24_SER63
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 06--27

description:
control MTG sample
MTG 06--27

source_name: MTG sample 06--27


title: Single Sert+ neuron 1451

description:
O5_SER60
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 06--49

description:
control MTG sample
MTG 06--49

source_name: MTG sample 06--49


title: Single Sert+ neuron 1441

description:
O24_SER57
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 04--52

description:
control MTG sample
MTG 04--52

source_name: MTG sample 04--52


title: Single Sert+ neuron 1440

description:
O23_SER64
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 94--25

description:
control MTG sample
MTG 94--25

source_name: MTG sample 94--25


title: Single Sert+ neuron 1439

description:
O23_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1438

description:
O23_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1436

description:
O22_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1437

description:
O22_SER67
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 97--45

description:
control MTG sample
MTG 97--45

source_name: MTG sample 97--45


title: ND, MTG sample 08--40

description:
control MTG sample
MTG 08--40

source_name: MTG sample 08--40


title: ND, MTG sample 97--19

description:
control MTG sample
MTG 97--19

source_name: MTG sample 97--19


title: ND, MTG sample 04--05

description:
control MTG sample
MTG 04--05

source_name: MTG sample 04--05


title: ND, MTG sample 05--10

description:
control MTG sample
MTG 05--10

source_name: MTG sample 05--10


title: Single Sert+ neuron 1435

description:
O22_SER57
Adult_DR_GEO_counts_cpm.txt

source_name: Sert+ neurons


title: ND, MTG sample 08--83

description:
control MTG sample
MTG 08--83

source_name: MTG sample 08--83


title: Single Sert+ neuron 1434

description:
O21_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1433

description:
O21_SER60
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 92--05

description:
control MTG sample
MTG 92--05

source_name: MTG sample 92--05


title: Single Sert+ neuron 1432

description:
O21_SER56
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 96--06

description:
control MTG sample
MTG 96--06

source_name: MTG sample 96--06


title: ND, MTG sample 95--26

description:
control MTG sample
MTG 95--26

source_name: MTG sample 95--26


title: Single Sert+ neuron 1429

description:
O20_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1430

description:
O20_SER63
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 02--06

description:
control MTG sample
MTG 02--06

source_name: MTG sample 02--06


title: ND, MTG sample 99--46

description:
control MTG sample
MTG 99--46

source_name: MTG sample 99--46


title: Single Sert+ neuron 1428

description:
O2_SER67
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 03--47

description:
control MTG sample
MTG 03--47

source_name: MTG sample 03--47


title: ND, MTG sample 05--16

description:
control MTG sample
MTG 05--16

source_name: MTG sample 05--16


title: Single Sert+ neuron 1426

description:
O2_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1427

description:
O2_SER63
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 04--62

description:
control MTG sample
MTG 04--62

source_name: MTG sample 04--62


title: ND, MTG sample 96--16

description:
control MTG sample
MTG 96--16

source_name: MTG sample 96--16


title: Single Sert+ neuron 1423

description:
O19_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1422

description:
O18_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1425

description:
O19_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1421

description:
O18_SER63
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 08--90

description:
control MTG sample
MTG 08--90

source_name: MTG sample 08--90


title: Single Sert+ neuron 1420

description:
O18_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1419

description:
O17_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1431

description:
O20_SER67
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 98--27

description:
control MTG sample
MTG 98--27

source_name: MTG sample 98--27


title: ND, MTG sample 97--10

description:
control MTG sample
MTG 97--10

source_name: MTG sample 97--10


title: ND, MTG sample 97--09

description:
control MTG sample
MTG 97--09

source_name: MTG sample 97--09


title: Single Sert+ neuron 1418

description:
O17_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1417

description:
O17_SER56
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 08--72

description:
control MTG sample
MTG 08--72

source_name: MTG sample 08--72


title: ND, MTG sample 08--77

description:
control MTG sample
MTG 08--77

source_name: MTG sample 08--77


title: Single Sert+ neuron 1416

description:
O16_SER67
Adult_DR_GEO_counts_cpm.txt

source_name: Sert+ neurons


title: AD, MTG sample 04--33

description:
Alzheimer's MTG sample
MTG 04--33

source_name: MTG sample 04--33

value: AD


title: Single Sert+ neuron 1415

description:
O16_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1424

description:
O19_SER60
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 07--18

description:
control MTG sample
MTG 07--18

source_name: MTG sample 07--18


title: ND, MTG sample 08--88

description:
control MTG sample
MTG 08--88

source_name: MTG sample 08--88


title: Single Sert+ neuron 1414

description:
O16_SER57
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 92--16

description:
Alzheimer's MTG sample
MTG 92--16

source_name: MTG sample 92--16


title: AD, MTG sample 97--08

description:
Alzheimer's MTG sample
MTG 97--08

source_name: MTG sample 97--08


title: Single Sert+ neuron 1412

description:
O15_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1413

description:
O15_SER64
Adult_DR_GEO_counts_cpm.txt


title: ND, MTG sample 97--37

description:
control MTG sample
MTG 97--37

source_name: MTG sample 97--37


title: ND, MTG sample 94--30

description:
control MTG sample
MTG 94--30

source_name: MTG sample 94--30


title: AD, MTG sample 96--04

description:
Alzheimer's MTG sample
MTG 96--04

source_name: MTG sample 96--04


title: ND, MTG sample 97--14

description:
control MTG sample
MTG 97--14

source_name: MTG sample 97--14


title: Single Sert+ neuron 1409

description:
O14_SER63
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 03--53

description:
Alzheimer's MTG sample
MTG 03--53

source_name: MTG sample 03--53


title: Single Sert+ neuron 1410

description:
O14_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1408

description:
O14_SER57
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 00--13

description:
Alzheimer's MTG sample
MTG 00--13

source_name: MTG sample 00--13


title: Single Sert+ neuron 1407

description:
O13_SER64
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 05--37

description:
Alzheimer's MTG sample
MTG 05--37

source_name: MTG sample 05--37


title: Single Sert+ neuron 1406

description:
O13_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1405

description:
O13_SER56
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 07--64

description:
Alzheimer's MTG sample
MTG 07--64

source_name: MTG sample 07--64


title: AD, MTG sample 03--19

description:
Alzheimer's MTG sample
MTG 03--19

source_name: MTG sample 03--19


title: Single Sert+ neuron 1404

description:
O12_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1400

description:
O11_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1411

description:
O15_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1403

description:
O12_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1398

description:
O10_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1399

description:
O11_SER56
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 96--21

description:
Alzheimer's MTG sample
MTG 96--21

source_name: MTG sample 96--21


title: AD, MTG sample 98--10

description:
Alzheimer's MTG sample
MTG 98--10

source_name: MTG sample 98--10


title: AD, MTG sample 98--12

description:
Alzheimer's MTG sample
MTG 98--12

source_name: MTG sample 98--12


title: AD, MTG sample 97--01

description:
Alzheimer's MTG sample
MTG 97--01

source_name: MTG sample 97--01


title: AD, MTG sample 05--27

description:
Alzheimer's MTG sample
MTG 05--27

source_name: MTG sample 05--27


title: AD, MTG sample 06--28

description:
Alzheimer's MTG sample
MTG 06--28

source_name: MTG sample 06--28


title: AD, MTG sample 05--01

description:
Alzheimer's MTG sample
MTG 05--01

source_name: MTG sample 05--01


title: AD, MTG sample 04--36

description:
Alzheimer's MTG sample
MTG 04--36

source_name: MTG sample 04--36


title: Single Sert+ neuron 1396

description:
O10_SER57
Adult_DR_GEO_counts_cpm.txt

source_name: Sert+ neurons


title: AD, MTG sample 00--54

description:
Alzheimer's MTG sample
MTG 00--54

source_name: MTG sample 00--54


title: Single Sert+ neuron 1402

description:
O12_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1395

description:
O1_SER64
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 04--22

description:
Alzheimer's MTG sample
MTG 04--22

source_name: MTG sample 04--22


title: AD, MTG sample 04--55

description:
Alzheimer's MTG sample
MTG 04--55

source_name: MTG sample 04--55


title: Single Sert+ neuron 1393

description:
O1_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1401

description:
O11_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1392

description:
N9_SER64
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 06--67

description:
Alzheimer's MTG sample
MTG 06--67

source_name: MTG sample 06--67


title: AD, MTG sample 06--56

description:
Alzheimer's MTG sample
MTG 06--56

source_name: MTG sample 06--56


title: AD, MTG sample 05--52

description:
Alzheimer's MTG sample
MTG 05--52

source_name: MTG sample 05--52


title: Single Sert+ neuron 1391

description:
N9_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1390

description:
N9_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1389

description:
N8_SER67
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 98--36

description:
Alzheimer's MTG sample
MTG 98--36

source_name: MTG sample 98--36


title: AD, MTG sample 00--56

description:
Alzheimer's MTG sample
MTG 00--56

source_name: MTG sample 00--56


title: AD, MTG sample 05--39

description:
Alzheimer's MTG sample
MTG 05--39

source_name: MTG sample 05--39


title: AD, MTG sample 00--04

description:
Alzheimer's MTG sample
MTG 00--04

source_name: MTG sample 00--04


title: Single Sert+ neuron 1386

description:
N7_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1394

description:
O1_SER60
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 03--32

description:
Alzheimer's MTG sample
MTG 03--32

source_name: MTG sample 03--32


title: AD, MTG sample 00--28

description:
Alzheimer's MTG sample
MTG 00--28

source_name: MTG sample 00--28


title: Single Sert+ neuron 1384

description:
N7_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1385

description:
N7_SER60
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 08--07

description:
Alzheimer's MTG sample
MTG 08--07

source_name: MTG sample 08--07


title: AD, MTG sample 01--32

description:
Alzheimer's MTG sample
MTG 01--32

source_name: MTG sample 01--32


title: Single Sert+ neuron 1388

description:
N8_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1381

description:
N6_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1383

description:
N6_SER67
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 01--16

description:
Alzheimer's MTG sample
MTG 01--16

source_name: MTG sample 01--16


title: Single Sert+ neuron 1379

description:
N5_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1380

description:
N5_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1382

description:
N6_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1377

description:
N4_SER67
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 08--06

description:
Alzheimer's MTG sample
MTG 08--06

source_name: MTG sample 08--06


title: AD, MTG sample 08--15

description:
Alzheimer's MTG sample
MTG 08--15

source_name: MTG sample 08--15


title: AD, MTG sample 08--20

description:
Alzheimer's MTG sample
MTG 08--20

source_name: MTG sample 08--20


title: AD, MTG sample 94--28

description:
Alzheimer's MTG sample
MTG 94--28

source_name: MTG sample 94--28