title: Brn1p localization in Wild Type strain arrested in nocodazole

first: lorenzo

last: costantino

address: 16 Barker Hall # 3202

department: MCB

institute: university of california, berkeley

data_processing:
The sequencing files were aligned to the SacCer3 yeast genome using Bowtie2 tool
Genome_build: SacCer3
Supplementary_files_format_and_content: bigwig

growth_protocol: cells were grown to early-log phase (OD600 0.1-0.2) at the temperature indicated (23°C or 30°C) overnight and arrested in G1 using the pheromone alpha factor at a concentration of 10-8M (Sigma-Aldrich T6901-5MG).  Cells were released from G1 by washing with YPD containing auxin (if indicated) and 0.15mg/mL pronase E (Sigma Aldrich) three times, and once with YPD. After the last wash Cells were resuspended in YPD medium containing 15 µg/mL nocodazole (Sigma Aldrich) and auxin if indicated. Cultures were then once again incubated at 23°C/30°C for 3h. For the time course cells were released from alpha-factor into fresh media and collected every 15min with no other drugs.

extract_protocol:
60OD of mid-M cells were collected, fixed for one hour with 1% formaldehyde, quenched with 5mM glycine and processed for ChIP as previously described (Robison and Koshland 2017, with the following modifications). Frozen cell pellets were disrupted 3 times using a FastPrep-24 5G instrument (40 seconds, 6.0m/sec each) (MP Bio, Santa Ana, CA).  Chromatin was sheared 10 x 30s ON/30s OFF with a Bioruptor Pico (Diagenode, Denville, NJ). For ChIP-qPCR, 1/20 of sheared and cleared lysate was reserved as input. Chromatin extracts were incubated with 4uL of the following antibodies monoclonal mouse anti-MYC (Roche), or polyclonal rabbit anti-Mcd1p (Covance Biosciences, Princeton, NJ) overnight at 4C. Antibody-bound lysates were incubated with 120uL Protein A dynabeads (Invitrogen, Cat#: 10001D) for 1h.
Following ChIP, the library was prepared using the Accel-NGS 1S Plus DNA Library Kit (Swift Bioscience) following the manufacturer protocol. Libraries were sequenced using Illumina Hiseq 4000. The sequencing files were aligned to the SacCer3 yeast genome using Bowtie2 tool.

treatment_protocol: If indicated, auxin was added to a final concentration of 500µM to deplete AID-tagged proteins after a 2:30h arrest.

tag: chip antibody


title: Patient_ASSESS_50

status: Public on Nov 04 2020

type: RNA

city: Strasbourg

first: Jacques-Eric

last: Gottenberg

address: 15 Renee Descartes Street

country: France

institute: Institut de Biologie Moleculaire et Cellulaire

hyb_protocol: After purification according to Affymetrix’s protocol, 5.5 µg of Sens Target DNA were fragmented and biotin-labelled. After control of fragmentation using Bioanalyzer 2100, cDNA was then hybridized to GeneChip® Clariom S Human (Affymetrix) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips were washed on the GeneChip Fluidics Station 450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G. The scanned images were then analyzed with Expression Console software (Affymetrix) to obtain raw data (.cel files) and Quality Control metrics

data_processing: Data were loaded  and normalised using the oligo R package. Briefly Cel files were loaded using the read.celfiles function and normalised with the rma function with default parameter. Absence of possible outliers was checked using hist function. Correspondance between probes and genes was obtained through the clariomshumanhttranscriptcluster.db package.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

label_protocol: After validation of the RNA quality with Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit), 75 ng of total RNA was reverse transcribed using the GeneChip® WT Plus Reagent Kit (Affymetrix) without globin mRNA reduction. Briefly, the resulting double-stranded cDNA was used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Affymetrix)

extract_protocol: whole bood

tag: tissue

value: Whole blood

tag: Sex

value: female

tag: antissa status

value: Negative

tag: antissb status

tag: disease state

value: Sjögren’s syndrome


title: Patient_ASSESS_49


title: 36540350_RNA

type: SRA

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: patient 24 tumor tissue RNA_seq

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
The reads were mapped to hg19 whole genome using STAR v2.5.1.
Read counts were calculated using a STAR standard protocol.
Heat map was constructed using Mev (v. 4.9.0). Statistical analyses were performed using R (v. 3.3.0) and PYTHON (v. 2.7.6).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each sample

source_name: colorectal tumor tissue

extract_protocol:
Total RNA was isolated from the colorectal tumor tissues using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit (Illumina).
The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.

tag: patient number

value: patient 24

value: colorectal tumor


title: Mcd1p localization in WPL1-AID strain arrested in nocodazole with Auxin

city: Berkeley

state: CA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Saccharomyces cerevisiae

tag: strain

value: Rabbit polyclonal Anti-Mcd1p V. Guacci (via Covance)


title: Patient_ASSESS_48


title: Patient_ASSESS_53

value: Positive


title: 36467330_RNA

description: patient 23 tumor tissue RNA_seq

value: patient 23


title: Patient_ASSESS_47


title: 36091795_RNA

description: patient 22 tumor tissue RNA_seq

value: patient 22


title: Mcd1p localization in PDS5-AID strain arrested in nocodazole with Auxin


title: Patient_ASSESS_51


title: BISCD56P_rep2

city: Boston

first: Sarah

middle: J.

last: Hill

state: MA

address: 450 Brookline Avenue

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
The RNA sequencing reads were aligned to the human GRCh38 reference genome using STAR (v2.6.1)
Genes were quantified using RSEM (v1.3.3)
Genome_build: hg38
Supplementary_files_format_and_content: gene expression matrix output from RSEM V1.3.3

source_name: Organoid co-culture generated from ovarian tumor

growth_protocol: Organoid co-cultures were grown in DMEM/10% FBS/pen/strep with IL2.

extract_protocol:
For bulk RNA sequencing, NK or CD8 T cells were sorted from the treated co-cultures and RNA was extracted using a Qiagen RNEasy mini kit.
Libraries were prepared according to Illumina's instructions. For additional methods and details, please see Wan and Hill, Cancer Research 2020, in press

treatment_protocol: Co-cultures were treated with the listed agent for 96 hours prior to harvest.

tag: cell type

value: NK cell

tag: treatment

value: Bispecific anti-PD-1/PD-L1

tag: tumor type

value: High grade seorus ovarian cancer


title: Mcd1p localization in Wild Type arrested in nocodazole replicate 2


title: IGGGZMBN_rep1

value: CD8 T cell

value: Isotype control


title: Patient_ASSESS_46


title: Mcd1p localization in Wild Type arrested in nocodazole


title: BISCD56P_rep1


title: PEMCD56P_rep2


title: IGGGZMBN_rep2


title: PEMCD56P_rep1


title: Patient_ASSESS_45


title: Patient_ASSESS_43


title: Patient_ASSESS_44


title: 36434594_RNA

description: patient 19 tumor tissue RNA_seq

value: patient 19


title: Mcd1p localization in Wild Type 60min release from alpha-factor arrest at 30°C replicate 2


title: 36421404_RNA

description: patient 18 tumor tissue RNA_seq

value: patient 18


title: 36360198_RNA

description: patient 17 tumor tissue RNA_seq

value: patient 17


title: Patient_ASSESS_41

value: Whole blood

value: female


title: Mcd1p localization in Wild Type 75min release from alpha-factor arrest at 30°C replicate 2


title: Mcd1p localization in Wild Type 45min release from alpha-factor arrest at 30°C replicate 2


title: 27126851_RNA

description: patient 16 tumor tissue RNA_seq

value: patient 16


title: IGGCD56P_rep2


title: Mcd1p localization in Wild Type 30min release from alpha-factor arrest at 30°C replicate 2


title: 36457782_RNA

description: patient 20 tumor tissue RNA_seq

value: patient 20


title: Patient_ASSESS_42

value: Negative

value: Sjögren’s syndrome


title: 36452453_RNA

description: patient 15 tumor tissue RNA_seq

value: patient 15

value: colorectal tumor


title: 36525445_RNA

description: patient 21 tumor tissue RNA_seq

value: patient 21


title: IGGCD56P_rep1

value: NK cell


title: Mcd1p localization in Wild Type 15min release from alpha-factor arrest at 30°C replicate 2

value: Rabbit polyclonal Anti-Mcd1p V. Guacci (via Covance)


title: Patient_ASSESS_39

value: Positive


title: 36389904_RNA

description: patient 14 tumor tissue RNA_seq

value: patient 14


title: Mcd1p localization in Wild Type 90min release from alpha-factor arrest at 30°C replicate 2


title: 2019OMB

source_name: Ovarian tumor

growth_protocol: Tumors were snap frozen on dry ice

extract_protocol:
For bulk RNA sequencing, RNA was extracted using a Qiagen RNEasy mini kit after pulverization of the tissue.
Libraries were prepared according to Illumina's instructions. For additional methods and details, please see Wan and Hill, Cancer Research 2020, in press

value: Mixture of cells from fresh frozen tumor

value: Untreated patient

value: High grade seorus ovarian cancer


title: PDL1CD56_rep2


title: PDL1CD56_rep1


title: Mcd1p localization in Wild Type 90min release from alpha-factor arrest at 30°C


title: Patient_ASSESS_37


title: 2019OMA


title: 36419449_RNA

description: patient 13 tumor tissue RNA_seq

value: patient 13


title: Patient_ASSESS_36

value: Whole blood


title: 2019LOVB


title: 36348617_RNA

description: patient 12 tumor tissue RNA_seq

value: patient 12


title: 2019LOVA


title: Mcd1p localization in Wild Type 45min release from alpha-factor arrest at 30°C


title: 20-35-B


title: 36229398_RNA

description: patient 10 tumor tissue RNA_seq

value: patient 10


title: Mcd1p localization in Wild Type 30min release from alpha-factor arrest at 30°C


title: Mcd1p localization in Wild Type 75min release from alpha-factor arrest at 30°C


title: Patient_ASSESS_35

value: female


title: Mcd1p localization in Wild Type 60min release from alpha-factor arrest at 30°C


title: 20-35-A


title: 20-30-B


title: Mcd1p localization in Wild Type 15min release from alpha-factor arrest at 30°C


title: Patient_ASSESS_40

value: Negative


title: Patient_ASSESS_38

value: Sjögren’s syndrome


title: 10970579_RNA

description: patient 8 tumor tissue RNA_seq

value: patient 8


title: Patient_ASSESS_33


title: Patient_ASSESS_34


title: 36212864_RNA

description: patient 7 tumor tissue RNA_seq

value: patient 7

value: colorectal tumor


title: Mcd1p localization in Wild Type 120min release from alpha-factor arrest at 23°C


title: 36382369_RNA

description: patient 11 tumor tissue RNA_seq

value: patient 11


title: Mcd1p localization in Wild Type 105min release from alpha-factor arrest at 23°C

value: Rabbit polyclonal Anti-Mcd1p V. Guacci (via Covance)


title: 20-29-B


title: Patient_ASSESS_30

value: Positive


title: 36163506_RNA

description: patient 6 tumor tissue RNA_seq

value: patient 6


title: 14101724_RNA

description: patient 5 tumor tissue RNA_seq

value: patient 5


title: Patient_ASSESS_29


title: Mcd1p localization in Wild Type 90min release from alpha-factor arrest at 23°C


title: 36260041_RNA

description: patient 9 tumor tissue RNA_seq

value: patient 9


title: Patient_ASSESS_31


title: Mcd1p localization in Wild Type 75min release from alpha-factor arrest at 23°C


title: 36219719_RNA

description: patient 4 tumor tissue RNA_seq

value: patient 4


title: 20-20-B

value: Mixture of cells from fresh frozen tumor

value: Patient post-neoadjuvant chemotherapy

value: High grade seorus ovarian cancer


title: Patient_ASSESS_32

value: Whole blood


title: 20-20-A


title: Patient_ASSESS_28

value: female


title: Mcd1p localization in Wild Type 45min release from alpha-factor arrest at 23°C


title: 35862280_RNA

description: patient 3 tumor tissue RNA_seq

value: patient 3


title: 36178894_RNA

description: patient 2 tumor tissue RNA_seq

value: patient 2


title: 20-30-A

value: Untreated patient


title: 27056495_RNA

description: patient 1 tumor tissue RNA_seq

value: patient 1


title: Mcd1p localization in Wild Type 30min release from alpha-factor arrest at 23°C


title: Patient_ASSESS_27

value: Negative

value: Sjögren’s syndrome


title: 20-11-A


title: 19-109-B


title: Mcd1p localization in Wild Type 15min release from alpha-factor arrest at 23°C

value: Rabbit polyclonal Anti-Mcd1p V. Guacci (via Covance)


title: 20-29-A


title: Mcd1p localization in Wild Type 60min release from alpha-factor arrest at 23°C


title: 19-109-A


title: M17_25

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

country: China

institute: ablife

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:TGGAATTCTCGGGTGCCAAGG;end2:GATCGTCGGACTGTAGAACTCTGAAC) trimmed with fastx_clipper
discovering novel miRNAs using miRDeep2,then predicting miRNA target gene using miRanda
mapped using bowtie -v 1
detecting different expression miRNA (TPM value) using Fisher exact test
Genome_build: Maize(B73)
Supplementary_files_format_and_content: tab-delimited text files include gene TPM values for each Sample

organism: Zea mays

source_name: endosperm

growth_protocol: Maize inbred line Mo17 was grown in the field in the summer of 2013 in Chengdu, China. Ears were self-pollinated on the same day.

extract_protocol:
Total RNA was extracted by using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions, and RQ1 DNase (Promega, Madison, WI, USA) was used to remove contaminating genomic DNA. The quality and quantity of the purified RNA was monitored at the ratios of A260/A280 and A260/230 on SmartSpec Plus Spectrophotometer (BioRad, Philadelphia, PA, USA). RNA integrity was further verified by 1.5% agarose gel electrophoresis.
Three μg of total RNA was used for small RNA cDNA library preparation with Balancer NGS Library Preparation Kit for small/microRNA (GnomeGen, San Diego, CA, USA) based on manufacturer’s instruction. Briefly, RNAs were ligated to 3’ and 5’ adaptor sequentially, reverse transcribed to cDNA and PCR amplified. Whole library was applied to 10% native PAGE gel electrophoresis and bands corresponding to miRNA insertion were cut and eluted.  After ethanol precipitation and washing, the purified small RNA libraries were quantified with Qubit Fluorometer (Invitrogen, Carlsbad, CA, USA), used for cluster generation and applied to Illumina GAIIx (Illumina, San Diego, CA, USA) 73 nt single-end sequencing or Illumina NextSeq 500 76 nt pair-end sequencing according to the manufacturer’s instructions. The small RNA libraries sequencing was perfomed in ABLife, Inc. (Wuhan, China).The smallRNA libraries sequencing was perfomed in ABLife, Inc. (Wuhan, China).

treatment_protocol: Samples (seed, endosperm and leaf) were collected by manual dissection at midday and frozen immediately in liquid nitrogen, and stored at -80℃ before processing.

tag: time period

value: 25 days after pollination

tag: line

value: endosperm


title: M17_leaf

source_name: ear leaf

value: 13 days after pollination

value: ear leaf


title: M17_20

value: 20 days after pollination


title: 3D7-GFPAP214-HP1glmS-ON-36-44-input

city: Nijmegen

first: Roel

last: Cooijmans

address: Geert Grooteplein Zuid 30

department: Molecular biology

country: Netherlands

institute: RIMLS

data_processing:
merging all fastq files beloing to one sample. zcat {file1} {file2} (file n)
read quality assement. Software name: fastqc. Version: v0.11.8. parameters: -o ${output_directory} --noextract ${fastq_file}
read aliging. Software name: bwa aln. Version: 0.7.17-r1188. parameters: ${fastq_file} > ${sai_file}
read mapping. Software name: bwa samse. Version: 0.7.17-r1188. parameters: ${refrence_genome} ${sai_file} ${fastq_file} > ${sam_file}
filter on mapping quility. Software name: Samtools view. Version: 1.9. parameters: -h -q ${mapping quility (15)} ${bam_file}
exstract uniqly mapped reads. Software name: grep. Version: . parameters: -w "XT:A:U"
removing apicoplast and mitochondria read. Software name: grep . Version: . parameters: -w -v PFC10_API_IRAB and M76611
determining libary size. Software name: Samtools view . Version: 1.9 . parameters: -c ${bam file}
calculating libary size per milion reads. Software name: bc . Version: . parameters: 1000000/${libary_size}
produce bed graph file. Software name: Bedtools genomeCoverageBed . Version: v2.27.1. parameters: -ibam ${bam_file} -bga -scale ${libary_size_perM}
produce a perposition bed graph file. Software name: Bedtools genomeCoverageBed . Version: v2.27.1. parameters: -ibam ${bam_file} -d -scale ${libary_size_perM}
caluclate the enrichment over input (ratio tracks bed graph). Software name: calc_ratio_track (bespoke python code, made avaleble on request). Version: . parameters: -t -p -n ${ChIP_perposition_bed graph_file} -d ${input_perposition_bed graph_file} -o ${ratio track}
calculating enrichment at coding genes. Software name: calc_average_enrichment_per_gene (bespoke bash code, made avaleble on request). Version: . parameters: -a ${anotation.bed} -b ${enrichment_file/ratio file.bed} -i ${optional second intupt fiel like -b} -o ${output_name}
Genome_build: Plasmodb-26-Pfalciparum3D7_Genome
Supplementary_files_format_and_content: fasta= fasta format, Bed= bed format, Bedgraph= bedgraph format. Merged_gene_values= output of  calc_average_enrichment_per_gene code. It is a tab deliminated file contain: col 1= gene name, col2= average enrichment at this gene of the -b provided file, col3= average enrichment at this gene of the -i provided file.

organism: Plasmodium falciparum 3D7

source_name: Bloodstage parasites 36-44 hours post infection

growth_protocol: P. falciparum 3D7 parasites were cultured in RPMI Medium 1640 [+] L-Glutamine  with 25 mM HEPES, 100 mM hypoxanthine, 24 mM sodium bicarbonate and 0.5% Albumax II. 2 mM choline chlorid. Parasites were Synchronisation repeated sorbitol treatments of ring stage parasites. Parasite cultures were kept at 37 ºC under a gaseous mixture of 4% CO2, 3% O2 and 93% N2

extract_protocol:
Synchronised parasites were harvested at peak PfAP2-HC expression at 36-44 hpi at 4-5% parasitemia. Parasites were crosslinked with 1% formaldehyde for 10 min at 37 °C before quenching with 0.125 M glycine. The RBC membrane was lysed with 0.15% saponin and cytoplasmic lysis buffer (CLB: 20 mM Hepes, 10 mM KCl, 1 mM EDTA, 1 mM EGTA, 0.65% NP-40, 1 mM DTT, 1x protease inhibitor (Roche) was added to the parasite pellet to isolate nuclei. These were then snap-frozen in liquid nitrogen in CLB supplemented with 50% glycerol and stored at - 80 °C. Chromatin isolation, shearing and immunoprecipitation was performed according to previously published protocols (Filarsky et al. 2018). To prepare chromatin, frozen nuclei were thawed, pelleted and resuspended in 150 µl sonication buffer (50 mM Tris pH 8, 1% SDS, 10 mM EDTA, 1x protease inhibitor (Roche)), and were sonicated for 20 cycles of 30 sec ON/30 sec OFF (setting high, BioruptorTM Next Gen, Diagenode) to shear DNA to fragments of 100-600 bps. Fragment size was confirmed by de-crosslinking a 15 µl aliquot and visualising the purified DNA on a 2% agarose gel. ChIPs were performed by combining sonicated chromatin (500 ng DNA content) with either 1 µg mouse mAb α-GFP (Roche Diagnostics #11814460001) or 1 µg rabbit α-PfHP1 (Brancucci et al. 2014a). Reactions contained incubation buffer (5% Triton-X-100, 750 mM NaCl, 5 mM EDTA, 2.5 mM EGTA, 100 mM Hepes pH 7.4), 0.2% bovine serum albumin, 1x protease inhibitor (Roche) and 10 μl protA and 10 μl protG Dynabeads (Life Technologies, #10008D and #10009D, respectively). ChIP reactions were incubated overnight at 4 °C with rotation. Beads were washed for 5 min at 4 °C, with rotation, with 400 µl wash buffers as follows: 2x wash buffer 1 (0.1% SDS, 0.1% DOC, 1% Triton-X100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM Hepes pH 7.4), 1x wash buffer 2 (0.1% SDS, 0.1% DOC, 1% Triton-X100, 500 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM Hepes pH 7.4), 1x wash buffer 3 (250 mM LiCl, 0.5% DOC, 0.5% NP-40, 1 mM EDTA, 0.5 mM EGTA, 20 mM Hepes pH 7.4), 2x wash buffer 4 (1 mM EDTA, 0.5 mM EGTA, 20 mM Hepes pH 7.4). Immunoprecipitated chromatin was eluted from the beads by shaking at room temperature for 20 min in 200 µl elution buffer (1% SDS, 0.1 M NaHCO3) and de-crosslinked at 45 °C overnight in 1% SDS, 0.1 M NaHCO3 and 1 M NaCl. Simultaneously, 30 µl of sonicated input chromatin was de-crosslinked under the same conditions. DNA was purified with QIAquick MinElute PCR columns (Qiagen). Twenty separate α-GFP ChIPs or four separate α-PfHP1 ChIPs were combined, with the exception of 3D7/GFP-PfAP2-HC/PfHP1-mScarlet-glmS α-PfHP1 ChIPs for which eight separate reactions were combined.
The obtained ChIPed DNA fragments were used to generate Illumina sequencing libraries according to Filarsky et al. (2018). In brief, 1 ng of α-PfHP1 ChIP, α-GFP ChIP, or input DNA were end-repaired with T4 DNA polymerase (NEB, M0203L), Klenow DNA polymerase (NEB, M0210L), and T4 Polynucleotide Kinase (NEB, M0201L). The 3’ends of end-repaired DNA was extended with an A-overhang with 3’ to 5’ exonuclease-deficient Klenow DNA polymerase (NEB, M0212L). The resulting fragments were ligated to Nextflex 6bp adaptors (Bio Scientific, #514122) with the use of T4 DNA ligase (Promega, M1804). The libraries were amplified using an AT-rich optimized KAPA protocol using KAPA HiFi HotStart ready mix (KAPA Biosystems, KM2602), NextFlex primer mix (Bio Scientific, #514122) with the following PCR program: 98°C for 2 min; four cycles of 98°C for 20 sec, 62°C for 3 min; 62°C for 5 min. The fragments originating from mono-nucleosomes + 125 bp NextFlex adapter were selected using 2% E-Gel Size Select agarose gels (Invitrogen, #G6610-02) and amplified by PCR for nine cycles using the above conditions. Libraries were purified and adapter dimers removed with Agencourt AMPure XP beads purification using a 1:1 library:beads ratio (Beckman Coulter, #A63880). ChIP-seq libraries were sequenced on the Illumina NextSeq 500 system with a 20% phiX spike-in (Illumina, FC-110-3001) to generate 75 bp single-end reads (NextSeq 500/550 High Output v2 kit).

treatment_protocol: see sample information

tag: cell line

tag: compound added to culture medium

value: GlcN


title: Patient_ASSESS_25

value: Positive


title: 3D7-AP214-v3-Pf-3D7-input


title: Patient_ASSESS_24


title: 3D7-GFPAP214-HP1glmS-ON-36-44-HP1-ChIP

tag: chip target


title: 19-107-A

value: Mixture of cells from fresh frozen tumor

value: High grade seorus ovarian cancer


title: M17_13


title: M17_15

value: 15 days after pollination


title: 19-107-B


title: 3D7-GFPAP214-HP1glmS-ON-36-44-GFP-ChIP

value: GFP


title: 19-101-B


title: M17_11

value: 11 days after pollination


title: Patient_ASSESS_26

value: Whole blood

value: female


title: Patient_ASSESS_21

value: Negative


title: Patient_ASSESS_22

value: Sjögren’s syndrome


title: Patient_ASSESS_20


title: 19-101-A

value: Untreated patient


title: 3D7-DDGFPAP214-ON-G13-HP1-ChIP


title: Patient_ASSESS_19


title: 33920065_RNA

description: patient 32 tumor tissue RNA_seq

value: patient 32

value: colorectal tumor


title: Patient_ASSESS_23


title: 3D7-DDGFPAP214-OFF-G13-HP1-ChIP


title: 19-100-B


title: Patient_ASSESS_18


title: 3D7-AP214-KO-input


title: 19-100-A


title: ATAC-seq_KHYG1_299_rep2

data_processing:
The ATAC sequencing reads were aligned to human GRCh38 genome using bwa mem (v0.7.15)
We called ATAC-seq peaks using MACS2 (v2.2.7.1)
Genome_build: hg38
Supplementary_files_format_and_content: Narrow peak file from MACS2 and bigwig file

source_name: NK cells

growth_protocol: KHYG1 cells were grown in DMEM/10% FBS/pen/strep with IL2.

extract_protocol:
For ATAC-seq, samples were harvested as described previously in Buenrostro et al., Curr Protoc Mol Biol 2015;109:21 9 1- 9 9.
Libraries were prepared according to Illumina's instructions. For additional methods and details, please see Wan and Hill, Cancer Research 2020, in press

treatment_protocol: NK cells were treated with the listed agent for 96 hours prior to harvest.

value: KHYG1 NK cell line

value: BAY 299

value: NK cell leukemia


title: ATAC-seq_KHYG1_299_rep1


title: M17_7

value: 7 days after pollination

value: endosperm


title: M17_9

value: 9 days after pollination


title: M17_5

source_name: seed

value: 5 days after pollination

value: whole seed


title: GFPAP214-v2-ChIP-input


title: 3D7-AP214-KO-HP1-ChIP


title: 3D7-GFPAP214-GFP-ChIP

value: GFP


title: Patient_ASSESS_17

value: Positive


title: M17_3

value: 3 days after pollination


title: M17_10

value: 10 days after pollination


title: ATAC-seq_KHYG1_DMSO_rep1

value: DMSO


title: GFPAP214-v2-ChIP-aHP1


title: Patient_ASSESS_14

value: Whole blood

value: female

value: Negative

value: Sjögren’s syndrome


title: ATAC-seq_KHYG1_DMSO_rep2

value: KHYG1 NK cell line


title: Patient_ASSESS_15


title: mRNA-BisSeq of HAP1 NSUN2/6-dKO cells

city: Shenzhen

first: Guipeng

last: Li

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

description: HAP1 NSUN2/6-dKO

data_processing:
RNA-m5C pipeline
Genome_build: hg38
Supplementary_files_format_and_content: txt, m5C sites

molecule: polyA RNA

source_name: HAP1 cells

extract_protocol:
Total RNA was extracted by TRIzol® Reagent (Ambion). mRNA was enriched using VAHTS mRNA Capture Beads (Vazyme, #N401). 200 ng mRNA was converted by EZ RNA methylation kit (Zymo Research) according to the manufacturer’s protocol with minor modification. More specifically, mRNA was incubated at 70 °C for 10 min, and 60 °C for 1 h. Converted RNA was then reverse transcribed into cDNA using HiScript II Q Select RT SuperMix (Vazyme, #R233-01).
VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme)
mRNA bisulfite sequencing

tag: genotype

value: HAP1 NSUN2/6-dKO


title: GFPAP214stop-ChIP-input


title: Young_POD14_replicate1

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

data_processing:
All sequence reads were extracted in FASTQ format using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
Adapters were trimmed using Trimmomatic 0.36 and 0.33
Mapping to the reference genome(mm9) was performed by tophat 2.1.1 and 2.0.14
Calculation of gene expression value and normalization were performed by RPKMforgenes.
Genome_build: The sequence reads were mapped to mm9 reference genes.
Supplementary_files_format_and_content: The processed data file contains Genename, Transcript, RPKM, and Rawcount columns (from left to right), and the expression level was represented by RPKM.

organism: Mus musculus

source_name: cells in pancreatic islets

growth_protocol: Mice were housed in a 14h light-10h dark cycle with free access to water and standard chow.

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (QIAGEN).
Sequencing libraries were generated using SMARTer® Ultra Low Input RNA Kit for Sequencing - v3 accoding to the manifacturer's instruction.

treatment_protocol: Mice in PPTx group received 50% partial pancreatectomy 2 days before islet isolation. Mice in control group received no treatment.

tag: age

tag: operation

value: PPTx

value: pancreatic islets


title: Young_POD7_replicate2


title: Young_POD14_replicate2


title: mRNA-BisSeq of HAP1 NSUN6-KO cells

description: HAP1 NSUN6-KO

value: HAP1 NSUN6-KO


title: GFPAP214stop-ChIP-aHP1

source_name: Bloodstage parasites 36-44 hpi


title: Patient_ASSESS_13

tag: tissue

tag: Sex

value: male


title: Young_POD7_replicate1


title: mRNA-BisSeq of HAP1 NSUN2-KO cells

description: HAP1 NSUN2-KO

value: HAP1 NSUN2-KO


title: Young_POD2_replicate4

description: Sample_W0054_SMB512_DMRNA_170219_2_1.RPKMforgenes.tsv


title: mRNA-BisSeq of HAP1 cells rep5

description: HAP1 WT rep5

value: HAP1 WT


title: GFPAP214stop-ChIP-aGFP

value: GFP


title: Patient_ASSESS_11

tag: antissa status

value: Positive

tag: antissb status


title: Patient_ASSESS_16

tag: disease state


title: Patient_ASSESS_10


title: Patient_ASSESS_12


title: GFPAP214-HPmSglmSON-ChIP-input

value: GlcN


title: Young_POD2_replicate3


title: mRNA-BisSeq of HAP1 cells rep4

description: HAP1 WT rep4


title: GFPAP214-HPmSglmSON-ChIP-aHP1


title: mRNA-BisSeq of HAP1 cells rep3

description: HAP1 WT rep3


title: Young_POD2_replicate2


title: GFPAP214-HPmSglmSON-ChIP-aGFP-v2


title: Young_POD2_replicate1


title: Patient_ASSESS_7


title: scRNA_Spleen_S4

city: Gosselies

first: Stanislas

last: Goriely

address: Rue Adrienne Bolland 8

country: Belgium

institute: Université Libre de Bruxelles

description: Single-cell RNA-seq in mouse splenocytes

data_processing:
Reads were demultiplexed into fastq files using CellRanger's mkfastq function
Fastq files were aligned to the mouse genome mm10 using CellRanger’s count function
Cells were filtered using R scripts
Data between samples was normalized with sctransform
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz: Barcode labels for counts matrix in tab-separated format
Supplementary_files_format_and_content: features.tsv.gz: Feature labels for counts matrix in tab-separated format
Supplementary_files_format_and_content: matrix.mtx.gz: Counts matrix in MatrixMarket format

source_name: Spleen

extract_protocol:
10X Chromium Single Cell 3' v3 Chemistry
According to manufacturer’s protocol

value: splenocytes


title: scRNA_Spleen_S46


title: Young_Cont_replicate4

value: control


title: mRNA-BisSeq of HAP1 cells rep1

description: HAP1 WT rep1


title: Patient_ASSESS_5

value: Whole blood


title: Patient_ASSESS_6

value: female


title: CIGAR-seq of HAP1 cells

data_processing:
m5C level
Genome_build: hg38
Supplementary_files_format_and_content: txt, m5C level for each gRNA

extract_protocol:
2x108 HAP1 cells were infected with CIGAR-seq viral particles (MOI = 0.3) and treated with 1 µg/ml of Puromycin for 24 h post infection. Puromycin resistant cells were cultured for additional seven days, and then 2x108 HAP1 cells were collected for RNA extraction. 100 ng of bisulfite-treated mRNA (see above) was quantified using Agilent RNA 6000 Pico Kit (Agilent, #NC1711873) and reverse transcribed into cDNA using HiScript II Q Select RT SuperMix (Vazyme, #R233-01). Finally, using the cDNA, CIGAR-seq NGS library was amplified with forward primer 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-GGGTTGGTTTAGGAGATATTTGAGGG-3’ and reverse primer 5’- CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-AACAATCCTAATACTCAAAAAAAAAAACACCA-3’
Finally, using the cDNA, CIGAR-seq NGS library was amplified with forward primer 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-GGGTTGGTTTAGGAGATATTTGAGGG-3’ and reverse primer 5’- CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-AACAATCCTAATACTCAAAAAAAAAAACACCA-3’
targeted RNA-seq


title: Patient_ASSESS_9


title: Patient_ASSESS_8

value: Negative


title: Young_Cont_replicate2


title: RNA Polymerase II ChIP-Seq CPSF73-AID plus auxin rep 2

city: Exeter

first: Steven

last: West

state: Devon

address: Stocker Rd

department: Living Systems Institute

country: United Kingdom

institute: University of Exeter

description:
single nucleotide bigwig coverage files were generated for total reads
cpsf73_IAA_ChIP_rep2

data_processing:
RNA-seq: Adapters were removed from nuclear RNA-seq reads using Trim Galore! v0.4.4 (wrapper tool for Cutadapt v1.15).
RNA-seq: Alignment of nuclear RNA-Seq reads with Hisat2 v2.1.0 to ensembl GRCh38.
RNA-seq: Properly mapped single-end reads were extracted and indexed using samtools v1.4.1.
RNA-seq: Replicates were merged using bamtools v2.4.0.
RNA-seq: For stranded coverage analysis, sense and antisense reads were seperated from merged BAMs using samtools v1.4.1
RNA-seq: Bigwig files of nuclear RNA-seq reads were generated from BAM files using the bamCoverage of Deeptools v3.0.2
Genome_build: GRCh38
Supplementary_files_format_and_content: RNA-seq: Bigwig files of nuclear RNA-seq reads represent normalised read coverage (RPKM) at a single nucleotide resolution across the genome.
EPAP RNA-seq: Adapters were removed from nuclear RNA-seq reads using Trim Galore! V.0.6.5 (wrapper tool for Cutadapt v2.9).
EPAP RNA-seq: Poly(A) and poly(T) reads were manually selected and removed from adapter trimmed RNA-Seq reads using Trim Galore! V.0.6.5 (wrapper tool for Cutadapt v.2.9).
EPAP RNA-seq: Alignment of nuclear RNA-Seq reads with Hisat2 v2.1.0 to ensembl GRCh38.
EPAP RNA-seq: Properly mapped single-end reads were extracted and indexed using samtools v1.10
EPAP RNA-seq: For stranded coverage analysis, sense and antisense reads were seperated from merged BAMs using samtools v1.10
EPAP RNA-seq: Bigwig files of nuclear RNA-seq reads were generated from BAM files using the bamCoverage of Deeptools v3.4.2
Supplementary_files_format_and_content: EPAP RNA-seq: Bigwig files of nuclear RNA-seq reads represent normalised read coverage (RPKM) at a single nucleotide nucleotide across the genome.
ONT: Basecalling of raw Fast5 reads using guppy v2.3.7
ONT: Isolation and orientation of full-length reads using pychopper v2.0.2
ONT: Adapters removed from long-reads using porechop v0.2.4
ONT: Alignment of long ONT reads using minimap2 v2.16-r934-dirty; -a -k 15 -w 5 --splice -g 2000 -G 200k -A 1 -B 2 -O 2,32 -E 1,0 -C 9 -z 200 -u f --junc-bonus=9 --splice-flank=yes --no-long-join --secondary=no
ONT: Properly mapped ONT reads were extracted and indexed using samtools v1.10
ONT: Replicates were merged using bamtools v2.4.0.
ONT: For stranded coverage analysis, sense and antisense reads were seperated from merged BAMs using samtools v1.10
ONT: BigWig files of mapped ONT reads were generated from BAM files using the bamCoverage of Deeptools v3.4.2 with the 'BPM' option (equivalent to TPM for RNA-seq data).
Supplementary_files_format_and_content: ONT: Bigwig files of nuclear long-read ONT sequence represent normalised read coverage (TPM) of separate strands at a single nucleotide resolution across the genome.
mNET-Seq: Adapters were removed from nuclear RNA-seq reads using Trim Galore! v0.4.4 (wrapper tool for Cutadapt v.1.15).
mNET-Seq: Alignment with Hisat2 v2.1.0 to ensembl GRCh38. mNET-seq files used the paired-end parmameter '--fr' to select concordatly mapped pairs.
mNET-Seq: mNET-seq profiles were generated with the 3' most nucleotide of fragments (reverse complement of the 5' most nucleotide of the second read displayed with the strandedness of the first read) for concordantly mapped reads with the samflag pairs 99/147 and 83/163.
Supplementary_files_format_and_content: mNET-Seq: Final BAM files represent the mapped 3’ most read fragments at a single nucleotide resolution
ChIP-Seq: Adapters were removed from nuclear RNA-seq reads using Trim Galore! V.0.6.5 (wrapper tool for Cutadapt v2.9).
ChIP-Seq: Alignment of ChIP-Seq reads with Hisat2 v2.1.0 to ensembl GRCh38.
ChIP-Seq: Properly paired mapped paired-end reads were extracted and indexed using samtools v1.10
ChIP-Seq: Replicates were merged using bamtools v2.4.0.
ChIP-Seq: Bigwig files of ChIP-Seq reads were generated from BAM files using the bamCoverage of Deeptools v3.4.2
Supplementary_files_format_and_content: ChIP-Seq: Bigwig files of ChIP-Seq reads represent normalised read coverage (RPKM) at a single nucleotide nucleotide across the genome.

source_name: RNA polymerase II ChIP-Seq CPSF73-AID Doxycycline inducible (TIR1) plus auxin

growth_protocol: HCT116 cell lines were maintianed in DMEM with 10% fetal bovine serum, pen/strep at 37 °C and 5% CO2.

extract_protocol:
RNA Pol II associated DNA for ChIP-Seq analysis was extracted using the Simple ChIP enzymatic chromatin IP kit (Cell Signalling Technologies #9003) Antibody (5ug Pol II 8WG16) was coupled to sheep anti-mouse dynabeads (Life Technologies) instead of the beads included in the kit.
Sequencing libraries were generated with the NEBNext® Ultra™ II DNA Library Prep Kit (NEB #E7645).

treatment_protocol: First treated with dox (1ug/ml) for 18h then auxin was added to cell media at a final concentration of 500 µM  3 h  prior to collection.

tag: genotype/variation

value: Auxin untreated total RNA PolII-associated DNA

tag: molecule subtype

value: Polymerase bound DNA


title: Patient_ASSESS_3

value: Sjögren’s syndrome


title: scRNA_Native-tracheas_S52

description: Single-cell RNA-seq in mouse mesenchymal progenitors originating from native trachea

source_name: Native trachea

tag: cell type

value: mesenchymal progenitors


title: Young_Cont_replicate1

value: pancreatic islets


title: RNA Polymerase II ChIP-Seq CPSF73-AID plus auxin rep 1

description:
single nucleotide bigwig coverage files were generated for total reads
cpsf73_IAA_ChIP_rep1

tag: treatment


title: Patient_ASSESS_4


title: scRNA_Native-tracheas_S38


title: mRNA-BisSeq of HAP1 cells rep2

description: HAP1 WT rep2


title: TubRNAi-rep3-16h

city: London

first: James

last: Budzak

address: Exhibition Road

institute: Imperial College London

data_processing:
Illumina RTA2 base calling
Reads were trimmed for quality and adapter removal with Trim Galore v0.4.4 [-q 28 --illumina --stringency 3 --length 50 --max_n 10 --trim-n --paired –trim1]
Trimmed reads were aligned to an in silico hybrid genome consisting of the T. brucei TREU927/4 assembly supplemented with T. brucei Lister 427 BES and MES sequences using bowtie2 v2.3.4 [--no-mixed --no-discordant -I 50 -X 500]
Total transcript abundance was assessed using HTSeq v0.5.4 considering only fragments mapping with MAPQ ≥ 2
Genome_build: An in silico hybrid genome consisting of the T. brucei TREU927/4 genome was usedwere supplemented with BES and MES sequences of T. brucei 427  for figure 5 and supplementary figure S5 and S6.         To compare transcriptomic changes due to TbSAP RNAi to those in the metacyclic transcriptome, databases were remapped to the long-read assembly of the T. brucei 427 genome (v46 based on the work of (Muller, L.S.M., Cosentino, R.O., Forstner, K.U., Guizetti, J., Wedel, C., Kaplan, N., Janzen, C.J., Arampatzi, P., Vogel, J., Steinbiss, S. et al. (2018) Genome organization and DNA accessibility control antigenic variation in trypanosomes. Nature, 563, 121-125.)) for figures 6A, 7B and S9.
Supplementary_files_format_and_content: HTseq count files with RPKM values for each sample.

organism: Trypanosoma brucei

source_name: BNII VO2+ pSMOx2 α-Tub RNAi

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy Mini kit with genomic DNA depleted using Turbo DNase (Ambion) according to manufacturer’s instructions
Each RNA sample will be quantified using Qubit and run on a Tapestation to assess sample integrity. mRNA will be isolated from total RNA using oligo dT beads. After fragmentation the sample will be converted to double stranded DNA and ligated to Illumina adapters. The second strand cDNA is then degraded by the UNG enzyme providing directional information to the library. Indexing of each sample will be performed by PCR.0. Carried out at Imperial College London BRC genomics facility.

value: Bloodstream form

value: 16h + tetracycline


title: Patient_ASSESS_1


title: scRNA_Native-tracheas_S24


title: RNA Polymerase II ChIP-Seq CPSF73-AID minus auxin rep 2

description:
single nucleotide bigwig coverage files were generated for total reads
cpsf73_noIAA_ChIP_rep2

source_name: RNA polymerase II ChIP-Seq CPSF73-AID Doxycycline inducible (TIR1) minus auxin

treatment_protocol: Control: Treated for 18h with dox (1ug/ml) then 3 h with ethanol (absolute 1ul per ml media).

value: Control:auxin untreated total RNA PolII-associated DNA


title: Old_POD14_replicate2

value: PPTx


title: Old_POD14_replicate1


title: RNA Polymerase II ChIP-Seq CPSF73-AID minus auxin rep 1

description:
single nucleotide bigwig coverage files were generated for total reads
cpsf73_noIAA_chIP_rep1


title: Young_Cont_replicate3


title: TubRNAi-rep1-16h


title: scRNA_Native-tracheas_S10


title: TubRNAi-rep3-0h

value: 0h + tetracycline


title: Old_POD7_replicate2


title: SAM68_overexpression_3

city: guangzhou

first: jizhong

last: wang

address: 63 Duobao Road

institute: Guangzhou Medical University

description:
A3SS.MATS.JC.txt
A5SS.MATS.JC.txt
MXE.MATS.JC.txt
RI.MATS.JC.txt
SE.MATS.JC.txt

data_processing:
Basecalls performed using CASAVA version 1.4
Raw fastq files were processed using fastp 0.20.0 with default parameters
RNA-seq reads were mapped to GRCh38 human reference genome using hisat2 2.1.0
Alternative Splicing was analysised using rmats 4.0.2. Human genecode v29 annotation gtf was used for finding splicing events, no novo splicing events are included.
Genome_build: GRCh38: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
Supplementary_files_format_and_content: rmats output format: http://rnaseq-mats.sourceforge.net/user_guide.htm

extract_protocol:
The RNAs from NCl-H1975 cells over-exprssing SAM68 or control were isolated using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: NCl-H1975 cells were seeded in 6-well plates the day before transfection and infected with PCDNA3.1-SAM68 plasmid (2ug per well) or a PCDNA3.1 plasmid (Control) using lipofectamine 2000 (Invitrogen) for 48h.

value: lung

tag: disease

value: Adenocarcinoma

tag: transfection

value: PCDNA3.1-SAM68 plasmid


title: Old_POD7_replicate1


title: scRNA_Spleen_S18

value: splenocytes


title: scRNA_Spleen_S32


title: SAM68_overexpression_2

tag: cell line


title: scRNA_Tracheal-allograft_S51

description: Single-cell RNA-seq in mouse mesenchymal progenitors originating from tracheal allograft

source_name: Tracheal allograft


title: TubRNAi-rep2-0h


title: Old_POD2_replicate4


title: TubRNAi-rep1-0h


title: Old_POD2_replicate3


title: control 3

value: PCDNA3.1 plasmid (Control)


title: scRNA_Tracheal-allograft_S37


title: SAM68_overexpression_1


title: TubRNAi-rep2-16h


title: scRNA_Tracheal-allograft_S23


title: SAP-72h-3

value: 72h + tetracycline


title: control 2


title: scRNA_Tracheal-allograft_S9


title: SAP-72h-2


title: Old_POD2_replicate2


title: Old_POD2_replicate1


title: control 1


title: Old_Cont_replicate4

value: control


title: Endothelial cells - Ccm3 ko 2

city: Uppsala

first: Elisabetta

last: Dejana

address: Dag Hammarskjolds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description: brain endothelial cells CD45-/CD31+ were collected and processed for scRNA-seq with 10x Chromium.

data_processing:
Cell Ranger (10× Genomics, 2.1.0 version) was used for sample demultiplexing, barcode processing, reads alignment to mouse reference genome (mm10) and single-cell 3′ gene counting
The R package Seurat (v.3.1) was used to perform integrated analysis of the pre-processed data from the Cell Ranger pipeline, such as filtering, normalization and clustering.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: freshly isolated brain endothelial cells

extract_protocol:
The brains of Ccm3 ko and Ccm3 wt mice were disgregated following the manufacturer instructions for Adult Brain Dissociation kits (Miltenyi Biotech, 130-107-677). Endothelial cells were enriched by depletion of CD45-positive cells using CD45 MicroBeads (Miltenyi Biotech, #130-052-301) and selection of CD31-positive cells using CD31 MicroBeads (Miltenyi Biotech, #130-097-418). Then, the collected brain endothelial single cells were processed for scRNA-seq.
RNA libraries were prepared for sequencing using standard 10× Genomics Chromium system and Illumina protocol.

treatment_protocol: Ccm3 flox/flox (either CRE+ or CRE-) mice were treated with tamoxifen (100ug) at postnatal day 1 to induce Cre activity and genetic modifications.

value: brain

tag: deveolpmental stage

value: Postnatal day 8

value: mice were tamoxifen treated at postnatal day 1

value: Ccm3 fl/fl CRE+ (Ccm3 ko)


title: SAP-72h-1


title: SAP-0h-3


title: Endothelial cells - Ccm3 ko 1

value: tamoxifen treated at postnatal day 1


title: Endothelial cells - Ccm3 wt 2

value: Ccm3 fl/fl CRE- (Ccm3 wt)


title: SAP-0h-2

value: Bloodstream form


title: SAP-0h-1


title: Old_Cont_replicate3

value: pancreatic islets


title: Endothelial cells - Ccm3 wt 1


title: Old_Cont_replicate2


title: Old_Cont_replicate1


title: Paeruginosa_PA2952_1_5

city: Vancouver

first: Shannon

last: Coleman

state: BC

address: 2259 Lower Mall

country: Canada

institute: University of British Columbia

data_processing:
Illumina software used for basecalling.
Sequence reads were mapped to the Pseudomonas aeruginosa genome using STAR v2.6.
Count data was generated from STAR produced BAM files using HTSeq v0.61p1.
Genome_build: PAO1 (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=208964)
processed_file_content: *.count: Tab-delimited text files include counts.

organism: Pseudomonas aeruginosa PAO1

source_name: bacterial culture

growth_protocol: Bacteria were grown on swarm plates.

extract_protocol:
Swarm fronts were harvested and suspended in RNA-Protect Bacteria Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Wildtype overexpressing PA2952.1

tag: condition

value: Swarming


title: MES-GFP-BLA-3

value: Untreated


title: Paeruginosa_PA2952_1_3


title: MES-GFP-BLA-2


title: Young_POD2_rep3

data_processing:
All sequence reads were extracted in FASTQ format using BCL2FASTQ Conversion Software 2.20.0.422.
Mapping to the reference genome (UCSC mm10), and calcutating the gene expression values were perfomed by  SureCell RNA Single-Cell 1.2.0
Genome_build: UCSC mm10
Supplementary_files_format_and_content: filtered.csv files contain genewise UMI counts for all cells in a csv format.

extract_protocol:
Single cells were directory lyzed in droplets generated by ddSEQ Single-Cell Isolator.
Sequencing libraries were generated using Chromium Single Cell 3’ Reagent Kits v2 accoding to the manifacturer's instruction.

value: PPTx


title: Paeruginosa_PA2952_1_2


title: MES-GFP-BLA-1


title: Young_POD2_rep2


title: DevSeed_N22_EGF_HeatAndDrought_Rep3

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

country: Germany

institute: MPI of Molecular Plant Physiology

description: R

data_processing:
RNA-seq reads were filtered for minimum length of 80bp and Illumina adapter were trimmed
Mapping reads against N22 transcriptome using kallisto v0.45 (sequenced with PacBio IsoSeq, raw data available under BioProject Number PRJNA640670)
Imported kallisto output with DESeq2 command DESeqDataSetFromTximport
Extracted and saved estimated counts for all samples
Genome_build: de novo reconstructed N22 transcriptome
Supplementary_files_format_and_content: Tab-delimited file for each sample including all genes/transcripts, length, effective length, estimated counts and counts per million (TPM)
Supplementary_files_format_and_content: Matrix table with estimated gene counts for every gene and every sample

organism: Oryza sativa

source_name: Developing seed

growth_protocol: Rice plants were grown in the field during the dry season at the International Rice Research Institute in the Philippines.

extract_protocol:
Developing seeds collected from field-grown plants were immediately frozen in liquid nitrogen after harvest and total mRNA was extracted using the Ribospin Seed/Fruit and Riboclear plus! kit from GeneAll Biotechnology.
RNA libraries were prepared with NEBNext Ultra Directional RNA Library Prep Kit for Illumina.

treatment_protocol: Control plants were fully flooded while under stress condition plants were exposed to combined heat and drought stress during the early grain-filling stage, with drought imposed using a rainout shelter.

value: Developing seed

tag: subgroup

value: aus

value: heat and drought

tag: cultivar


title: 20-11-B

source_name: Ovarian tumor

value: Mixture of cells from fresh frozen tumor

value: Untreated patient

tag: tumor type

value: High grade seorus ovarian cancer


title: Paeruginosa_PA2952_1_1


title: Young_POD2_rep1

tag: age

tag: operation


title: DevSeed_N22_EGF_Control_Rep3

description: O

tag: tissue

value: control


title: DevSeed_N22_EGF_HeatAndDrought_Rep1

description: P


title: Young_Cont_rep3


title: Paeruginosa_PAO1_EmptyVector 3

value: Wildtype with empty vector


title: Young_Cont_rep4


title: Paeruginosa_PAO1_EmptyVector 5


title: Paeruginosa_PAO1_EmptyVector 4


title: Paeruginosa_PAO1_EmptyVector 2


title: Young_Cont_rep1


title: Young_Cont_rep2


title: DevSeed_N22_EGF_Control_Rep1

description: M


title: Paeruginosa_PA2952_1_4


title: Paeruginosa_PAO1_EmptyVector 1


title: Young_POD2_rep4


title: DevSeed_N22_EGF_Control_Rep2

description: N


title: DevSeed_N22_EGF_HeatAndDrought_Rep2

description: Q


title: ILEUM CUS_Probiotic_3

status: Public on Nov 03 2020

city: New York

first: Susan

last: Westfall

state: NY

address: 1468 Madison Ave, 20-02

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Direct hybridization with Epifluorescent tagged probes

scan_protocol: standard Nanostring protocol

data_processing: data was analyzed with the commercially available nCounter software from Nanostring

source_name: fresh brain tissue

label_protocol: standard Nanostring protocol

growth_protocol: animals were kept in a vivarium with ad libitum access to polyphenol-free food and water

extract_protocol: RNA was extracted using Qiagne RNeasy kit following company directions.

treatment_protocol: all fresh tissue specimans were extracted, immediately placed on dry ice and stored at -80C until RNA extraction.

tag: Sex

value: male

value: ileum

tag: stress

value: yes

value: Probiotic


title: ILEUM CUS_BDPP_2

value: BDPP


title: ILEUM CUS_Synbiotic_2

value: Synbiotic


title: ILEUM CUS_BDPP_3


title: ILEUM CUS_Probiotic_2


title: ILEUM CUS_Probiotic_1


title: ILEUM CUS_BDPP_1


title: ILEUM CUS_Synbiotic_1


title: ILEUM CUS_Control_3


title: ILEUM CUS_Control_1


title: ILEUM CUS_Synbiotic_3


title: ILEUM noCUS_Control_3

value: no


title: LIVER CUS_Synbiotic_3

value: liver


title: ILEUM noCUS_Control_1


title: ILEUM CUS_Control_2


title: LIVER CUS_Synbiotic_1


title: LIVER CUS_Synbiotic_2


title: LIVER CUS_Probiotic_3


title: LIVER CUS_BDPP_3


title: LIVER CUS_Control_3


title: LIVER CUS_Probiotic_1


title: LIVER CUS_Control_1


title: LIVER CUS_BDPP_2


title: LIVER CUS_BDPP_1


title: LIVER CUS_Control_2


title: ILEUM noCUS_Control_2


title: LIVER noCUS_Control_3


title: LIVER noCUS_Control_2


title: LIVER CUS_Probiotic_2


title: HIPP CUS_Synbiotic_1

value: hippocampus


title: HIPP CUS_BDPP_1


title: LIVER noCUS_Control_1


title: HIPP CUS_Synbiotic_2


title: HIPP CUS_Control_3


title: HIPP CUS_Probiotic_1


title: HIPP CUS_BDPP_3


title: HIPP CUS_Synbiotic_3


title: HIPP noCUS_Control_3


title: HIPP CUS_Control_1


title: PFC CUS_Synbiotic_1

value: prefrontal cortex


title: HIPP noCUS_Control_2


title: PFC CUS_Synbiotic_3


title: HIPP noCUS_Control_1


title: PFC CUS_Synbiotic_2


title: PFC CUS_Probiotic_2


title: PFC CUS_Probiotic_3


title: PFC CUS_BDPP_2


title: PFC CUS_Probiotic_1


title: PFC CUS_BDPP_3


title: HIPP CUS_Control_2


title: PFC CUS_Control_2


title: PFC noCUS_Control_3


title: HIPP CUS_Probiotic_2


title: HIPP CUS_Probiotic_3


title: HIPP CUS_BDPP_2


title: PFC CUS_Control_3


title: PFC CUS_BDPP_1


title: PFC CUS_Control_1


title: Ascl1_d4_plate1_P18

city: Zürich

first: Baptiste

middle: N

last: Jaeger

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zürich

description: dentate gyrus dissection

data_processing:
Single-end 126nt-long reads were adaptor removed and trimmed using cutadapt v1.16 and sickle v1.33 with default parameters. Reads were mapped against the mouse GRCm38.90 primary assembly 126 with the Ensembl GRCm38.90 GTF annotation using STAR v2.6.0c
cells / genes filtered with scater v.1.12.2 and Seurat v3.0.2. Cells with 1000-6000 genes detected, less than 8% of mitochondrial reads and more than 50000 total reads were kept for downstream analysis.
Data normalized with Seurat v3.0.2 pipeline (log normalization)
Analysis(UMAP,DEG) performed with Seurat v3.0.2
RNA velocity was run with velocyto.R v0.6 using default parameters
Slingshot and pseudotime were computed using slingshot v1.3.2 and fastICA v1.2-2 Packages
Prediction was computed using caret caret_6.0-84 package
Data analysis was carried out in R v3.6.1
Supplementary_files_format_and_content: metadata and matrix with counts for all cells in txt file

source_name: dentate gyrus tdTomato+ single cells

extract_protocol:
single-cell
illumina nextera
Smart-seq2

tag: mouse strain

value: Ascl1_CreERT2 x CAG_tdTomato

tag: age of the mice at time of injection

value: 7-8 week old

tag: time of dissection

value: 12 weeks after last tamoxifen injection

tag: cells

value: Hoechst- tdTomato+ single cells


title: PFC noCUS_Control_2

tag: treatment


title: Ascl1_d4_plate1_P20

description: dentate gyrus dissection


title: Ascl1_d4_plate1_P19

description: dentate gyrus dissection


title: Ascl1_d4_plate1_P17

description: dentate gyrus dissection


title: PFC noCUS_Control_1


title: Ascl1_d4_plate1_P15

description: dentate gyrus dissection


title: Ascl1_d4_plate1_P16

description: dentate gyrus dissection


title: Ascl1_d4_plate1_P12

description: dentate gyrus dissection


title: Ascl1_d4_plate1_P10

description: dentate gyrus dissection


title: Ascl1_d4_plate1_P07

description: dentate gyrus dissection


title: Ascl1_d4_plate1_P11

description: dentate gyrus dissection


title: Ascl1_d4_plate1_P06

description: dentate gyrus dissection


title: Ascl1_d4_plate1_P03

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O23

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O19

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O18

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O22

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O17

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O15

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O14

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O10

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O11

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O13

description: dentate gyrus dissection


title: Patient_ASSESS_2

city: Strasbourg

data_processing: Data were loaded  and normalised using the oligo R package. Briefly Cel files were loaded using the read.celfiles function and normalised with the rma function with default parameter. Absence of possible outliers was checked using hist function. Correspondance between probes and genes was obtained through the clariomshumanhttranscriptcluster.db package.

source_name: Whole blood

extract_protocol: whole bood

value: Whole blood

value: female

tag: antissa status

value: Negative

tag: antissb status

tag: disease state

value: Sjögren’s syndrome


title: Ascl1_d4_plate1_P14

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O12

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O09

description: dentate gyrus dissection


title: Ascl1_d4_plate1_P05

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O03

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O05

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O02

description: dentate gyrus dissection


title: Ascl1_d4_plate1_N22

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O16

description: dentate gyrus dissection


title: Ascl1_d4_plate1_N12

description: dentate gyrus dissection


title: Ascl1_d4_plate1_N14

description: dentate gyrus dissection


title: Ascl1_d4_plate1_N13

description: dentate gyrus dissection


title: Ascl1_d4_plate1_N17

description: dentate gyrus dissection


title: Ascl1_d4_plate1_N18

description: dentate gyrus dissection


title: Ascl1_d4_plate1_N10

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O04

description: dentate gyrus dissection


title: Ascl1_d4_plate1_N16

description: dentate gyrus dissection


title: Ascl1_d4_plate1_N15

description: dentate gyrus dissection


title: Ascl1_d4_plate1_N06

description: dentate gyrus dissection


title: Ascl1_d4_plate1_N04

description: dentate gyrus dissection


title: Ascl1_d4_plate1_N03

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M23

description: dentate gyrus dissection


title: Ascl1_d4_plate1_N01

description: dentate gyrus dissection


title: Ascl1_d4_plate1_N02

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O06

description: dentate gyrus dissection


title: Ascl1_d4_plate1_O07

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M21

description: dentate gyrus dissection


title: Ascl1_d4_plate1_N21

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M20

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M19

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M17

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M18

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M16

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M13

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M15

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M14

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M12

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M09

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M11

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M05

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M06

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M01

description: dentate gyrus dissection


title: Ascl1_d4_plate1_L18

description: dentate gyrus dissection


title: Ascl1_d4_plate1_L19

description: dentate gyrus dissection


title: Ascl1_d4_plate1_N05

description: dentate gyrus dissection


title: Ascl1_d4_plate1_L16

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M10

description: dentate gyrus dissection


title: Ascl1_d4_plate1_L15

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M07

description: dentate gyrus dissection


title: Ascl1_d4_plate1_L14

description: dentate gyrus dissection


title: Ascl1_d4_plate1_N07

description: dentate gyrus dissection


title: Ascl1_d4_plate1_L17

description: dentate gyrus dissection


title: Ascl1_d4_plate1_L06

description: dentate gyrus dissection


title: Ascl1_d4_plate1_L10

description: dentate gyrus dissection


title: Ascl1_d4_plate1_L04

description: dentate gyrus dissection


title: Ascl1_d4_plate1_L07

description: dentate gyrus dissection


title: Ascl1_d4_plate1_L02

description: dentate gyrus dissection


title: Ascl1_d4_plate1_L05

description: dentate gyrus dissection


title: Ascl1_d4_plate1_L12

description: dentate gyrus dissection


title: Ascl1_d4_plate1_K22

description: dentate gyrus dissection


title: Ascl1_d4_plate1_L01

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M04

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M03

description: dentate gyrus dissection


title: Ascl1_d4_plate1_M02

description: dentate gyrus dissection


title: Ascl1_d4_plate1_K18

description: dentate gyrus dissection


title: Ascl1_d4_plate1_K12

description: dentate gyrus dissection


title: Ascl1_d4_plate1_K14

description: dentate gyrus dissection


title: Ascl1_d4_plate1_K11

description: dentate gyrus dissection


title: Ascl1_d4_plate1_K07

description: dentate gyrus dissection


title: Ascl1_d4_plate1_K06

description: dentate gyrus dissection


title: Ascl1_d4_plate1_K16

description: dentate gyrus dissection


title: Ascl1_d4_plate1_K13

description: dentate gyrus dissection


title: Ascl1_d4_plate1_K15

description: dentate gyrus dissection


title: Ascl1_d4_plate1_L11

description: dentate gyrus dissection


title: Ascl1_d4_plate1_J18

description: dentate gyrus dissection


title: Ascl1_d4_plate1_J22

description: dentate gyrus dissection


title: Ascl1_d4_plate1_J19

description: dentate gyrus dissection


title: Ascl1_d4_plate1_K10

description: dentate gyrus dissection


title: Ascl1_d4_plate1_K02

description: dentate gyrus dissection


title: Ascl1_d4_plate1_K05

description: dentate gyrus dissection


title: Ascl1_d4_plate1_J14

description: dentate gyrus dissection


title: Ascl1_d4_plate1_J15

description: dentate gyrus dissection


title: Ascl1_d4_plate1_J17

description: dentate gyrus dissection


title: Ascl1_d4_plate1_K01

description: dentate gyrus dissection


title: Ascl1_d4_plate1_J12

description: dentate gyrus dissection


title: Ascl1_d4_plate1_J11

description: dentate gyrus dissection


title: Ascl1_d4_plate1_J13

description: dentate gyrus dissection


title: Ascl1_d4_plate1_J09

description: dentate gyrus dissection


title: Ascl1_d4_plate1_J07

description: dentate gyrus dissection


title: Ascl1_d4_plate1_J16

description: dentate gyrus dissection


title: Ascl1_d4_plate1_J02

description: dentate gyrus dissection


title: Ascl1_d4_plate1_J06

description: dentate gyrus dissection


title: Ascl1_d4_plate1_J05

description: dentate gyrus dissection


title: Ascl1_d4_plate1_K04

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I24

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I20

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I19

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I22

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I17

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I16

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I12

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I11

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I18

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I07

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I10

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I15

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I01

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I02

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I05

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I03

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H24

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I06

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I04

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H20

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H22

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H19

description: dentate gyrus dissection


title: Ascl1_d4_plate1_I09

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H23

description: dentate gyrus dissection


title: Ascl1_d4_plate1_J01

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H13

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H12

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H18

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H09

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H11

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H04

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H02

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H10

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H01

description: dentate gyrus dissection


title: Ascl1_d4_plate1_G20

description: dentate gyrus dissection


title: Ascl1_d4_plate1_G19

description: dentate gyrus dissection


title: Ascl1_d4_plate1_G16

description: dentate gyrus dissection


title: Ascl1_d4_plate1_G14

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H06

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H07

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H05

description: dentate gyrus dissection


title: Ascl1_d4_plate1_G22

description: dentate gyrus dissection


title: Ascl1_d4_plate1_H21

description: dentate gyrus dissection


title: Ascl1_d4_plate1_F17

description: dentate gyrus dissection


title: Ascl1_d4_plate1_F22

description: dentate gyrus dissection


title: Ascl1_d4_plate1_G04

description: dentate gyrus dissection


title: Ascl1_d4_plate1_F16

description: dentate gyrus dissection


title: Ascl1_d4_plate1_G02

description: dentate gyrus dissection


title: Ascl1_d4_plate1_G11

description: dentate gyrus dissection


title: Ascl1_d4_plate1_G12

description: dentate gyrus dissection


title: Ascl1_d4_plate1_G18

description: dentate gyrus dissection


title: Ascl1_d4_plate1_F12

description: dentate gyrus dissection


title: Ascl1_d4_plate1_G10

description: dentate gyrus dissection


title: Ascl1_d4_plate1_G09

description: dentate gyrus dissection


title: Ascl1_d4_plate1_G07

description: dentate gyrus dissection


title: Ascl1_d4_plate1_G06

description: dentate gyrus dissection


title: Ascl1_d4_plate1_F14

description: dentate gyrus dissection


title: Ascl1_d4_plate1_F10

description: dentate gyrus dissection


title: Ascl1_d4_plate1_F06

description: dentate gyrus dissection


title: Ascl1_d4_plate1_G05

description: dentate gyrus dissection


title: Ascl1_d4_plate1_E23

description: dentate gyrus dissection


title: Ascl1_d4_plate1_F04

description: dentate gyrus dissection


title: Ascl1_d4_plate1_F03

description: dentate gyrus dissection


title: Ascl1_d4_plate1_F19

description: dentate gyrus dissection


title: Ascl1_d4_plate1_F11

description: dentate gyrus dissection


title: Ascl1_d4_plate1_G17

description: dentate gyrus dissection


title: Ascl1_d4_plate1_F01

description: dentate gyrus dissection


title: Ascl1_d4_plate1_E20

description: dentate gyrus dissection


title: Ascl1_d4_plate1_F07

description: dentate gyrus dissection


title: Ascl1_d4_plate1_E19

description: dentate gyrus dissection


title: Ascl1_d4_plate1_F09

description: dentate gyrus dissection


title: Ascl1_d4_plate1_E18

description: dentate gyrus dissection


title: Ascl1_d4_plate1_E17

description: dentate gyrus dissection


title: Ascl1_d4_plate1_E11

description: dentate gyrus dissection


title: Ascl1_d4_plate1_E09

description: dentate gyrus dissection


title: Ascl1_d4_plate1_E10

description: dentate gyrus dissection


title: Ascl1_d4_plate1_E15

description: dentate gyrus dissection


title: Ascl1_d4_plate1_E03

description: dentate gyrus dissection


title: Ascl1_d4_plate1_E01

description: dentate gyrus dissection


title: Ascl1_d4_plate1_E14

description: dentate gyrus dissection


title: Ascl1_d4_plate1_E16

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D21

description: dentate gyrus dissection


title: Ascl1_d4_plate1_E07

description: dentate gyrus dissection


title: Ascl1_d4_plate1_E04

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D20

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D19

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D17

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D16

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D18

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D14

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D15

description: dentate gyrus dissection


title: Ascl1_d4_plate1_E02

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D12

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D11

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D06

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D05

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D04

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D23

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D03

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D09

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D02

description: dentate gyrus dissection


title: Ascl1_d4_plate1_D01

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C22

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C19

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C17

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C23

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C21

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C20

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C14

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C12

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C13

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C10

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C09

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C18

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C07

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C03

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C15

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C05

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C02

description: dentate gyrus dissection


title: Ascl1_d4_plate1_B17

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C01

description: dentate gyrus dissection


title: Ascl1_d4_plate1_B22

description: dentate gyrus dissection


title: Ascl1_d4_plate1_B18

description: dentate gyrus dissection


title: Ascl1_d4_plate1_B14

description: dentate gyrus dissection


title: Ascl1_d4_plate1_B16

description: dentate gyrus dissection


title: Ascl1_d4_plate1_B12

description: dentate gyrus dissection


title: Ascl1_d4_plate1_B15

description: dentate gyrus dissection


title: Ascl1_d4_plate1_B11

description: dentate gyrus dissection


title: Ascl1_d4_plate1_B10

description: dentate gyrus dissection


title: Ascl1_d4_plate1_C04

description: dentate gyrus dissection


title: Ascl1_d4_plate1_B09

description: dentate gyrus dissection


title: Ascl1_d4_plate1_B05

description: dentate gyrus dissection


title: Ascl1_d4_plate1_B06

description: dentate gyrus dissection


title: Ascl1_d4_plate1_B04

description: dentate gyrus dissection


title: Ascl1_d4_plate1_B23

description: dentate gyrus dissection


title: Ascl1_d4_plate1_B03

description: dentate gyrus dissection


title: Ascl1_d4_plate1_A17

description: dentate gyrus dissection


title: Ascl1_d4_plate1_B19

description: dentate gyrus dissection


title: Ascl1_d4_plate1_A19

description: dentate gyrus dissection


title: Ascl1_d4_plate1_A12

description: dentate gyrus dissection


title: Ascl1_d4_plate1_A11

description: dentate gyrus dissection


title: Ascl1_d4_plate1_A10

description: dentate gyrus dissection


title: Ascl1_d4_plate1_A09

description: dentate gyrus dissection


title: Ascl1_d4_plate1_A05

description: dentate gyrus dissection


title: Ascl1_d4_plate1_A03

description: dentate gyrus dissection


title: Ascl1_d4_plate1_A06

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_O05

description: dentate gyrus dissection


title: Ascl1_d4_plate1_A02

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_N11

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_M08

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_M05

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_M06

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_M04

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_M03

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_L24

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_L23

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_L17

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_L19

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_M02

description: dentate gyrus dissection


title: Ascl1_d4_plate1_A16

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_L21

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_L16

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_L12

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_L13

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_K23

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_L09

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_L14

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_L02

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_L03

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_K22

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_K17

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_O03

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_K19

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_M07

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_K20

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_K15

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_L11

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_K12

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_K14

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_K11

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_K03

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_K01

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_J23

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_J22

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_K10

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_J24

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_J20

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_J21

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_K21

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_J19

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_K18

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_J17

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_J18

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_J15

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_J11

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_J12

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_J09

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_J10

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_I23

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_I22

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_I19

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_J01

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_K13

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_I21

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_I17

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_I18

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_J16

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_I15

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_I14

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_I16

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_I12

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_I11

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_J13

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_I10

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_H23

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_I01

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_H22

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_H19

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_H12

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_H15

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_H09

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_H06

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_H05

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_H07

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_H03

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_G22

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_H04

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_H02

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_J03

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_G23

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_G17

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_G18

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_G14

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_G16

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_G13

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_I13

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_I09

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_G10

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_H18

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_G12

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_G11

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_G03

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_G09

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_G01

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_G21

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_F19

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_G19

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_F20

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_F17

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_F22

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_F16

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_F13

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_F14

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_F12

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_F11

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_F10

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_F08

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_F02

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_E22

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_E21

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_E17

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_E23

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_F21

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_E19

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_E15

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_E18

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_F18

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_F15

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_E13

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_E14

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_E10

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_E11

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_E12

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_E09

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_F09

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_E01

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_D22

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_E02

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_D19

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_D20

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_G20

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_D21

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_E16

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_D17

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_D15

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_D13

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_D12

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_E08

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_D11

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_D09

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_C23

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_D10

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_C21

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_C17

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_C20

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_C16

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_C12

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_C11

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_C06

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_C13

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_C02

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_B23

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_C14

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_B21

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_C19

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_D16

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_B17

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_B14

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_B18

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_B09

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_B06

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_B12

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_C22

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_A24

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_C18

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_A20

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_A12

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_A15

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_A07

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_A09

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_A01

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_B22

description: dentate gyrus dissection


title: Ascl1_12wk_P15

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_A22

description: dentate gyrus dissection


title: Ascl1_12wk_P13

description: dentate gyrus dissection


title: Ascl1_12wk_O21

description: dentate gyrus dissection


title: Ascl1_12wk_2_20190514BJ_A18

description: dentate gyrus dissection


title: Ascl1_12wk_M17

description: dentate gyrus dissection


title: Ascl1_12wk_M18

description: dentate gyrus dissection


title: Ascl1_12wk_O02

description: dentate gyrus dissection


title: Ascl1_12wk_M07

description: dentate gyrus dissection


title: Ascl1_12wk_M13

description: dentate gyrus dissection


title: Ascl1_12wk_L22

description: dentate gyrus dissection


title: Ascl1_12wk_L18

description: dentate gyrus dissection


title: Ascl1_12wk_K22

description: dentate gyrus dissection


title: Ascl1_12wk_J15

description: dentate gyrus dissection


title: Ascl1_12wk_I23

description: dentate gyrus dissection


title: Ascl1_12wk_I22

description: dentate gyrus dissection


title: Ascl1_12wk_I16

description: dentate gyrus dissection


title: Ascl1_12wk_K07

description: dentate gyrus dissection


title: Ascl1_12wk_J20

description: dentate gyrus dissection


title: Ascl1_12wk_I03

description: dentate gyrus dissection


title: Ascl1_12wk_I15

description: dentate gyrus dissection


title: Ascl1_12wk_I11

description: dentate gyrus dissection


title: Ascl1_12wk_I01

description: dentate gyrus dissection


title: Ascl1_12wk_H21

description: dentate gyrus dissection


title: Ascl1_12wk_H03

description: dentate gyrus dissection


title: Ascl1_12wk_H23

description: dentate gyrus dissection


title: Ascl1_12wk_H01

description: dentate gyrus dissection


title: Ascl1_12wk_P21

description: dentate gyrus dissection


title: Ascl1_12wk_G10

description: dentate gyrus dissection


title: Ascl1_12wk_G11

description: dentate gyrus dissection


title: Ascl1_12wk_G14

description: dentate gyrus dissection


title: Ascl1_12wk_K19

description: dentate gyrus dissection


title: Ascl1_12wk_F17

description: dentate gyrus dissection


title: Ascl1_12wk_F20

description: dentate gyrus dissection


title: Ascl1_12wk_E22

description: dentate gyrus dissection


title: Ascl1_12wk_D02

description: dentate gyrus dissection


title: Ascl1_12wk_F18

description: dentate gyrus dissection


title: Ascl1_12wk_E07

description: dentate gyrus dissection


title: Ascl1_12wk_F10

description: dentate gyrus dissection


title: Ascl1_12wk_C18

description: dentate gyrus dissection


title: Ascl1_12wk_D04

description: dentate gyrus dissection


title: Ascl1_12wk_C11

description: dentate gyrus dissection


title: Ascl1_12wk_C09

description: dentate gyrus dissection


title: Ascl1_12wk_D01

description: dentate gyrus dissection


title: Ascl1_12wk_C07

description: dentate gyrus dissection


title: Ascl1_12wk_C10

description: dentate gyrus dissection


title: Ascl1_12wk_B01

description: dentate gyrus dissection


title: Ascl1_12wk_B02

description: dentate gyrus dissection


title: Ascl1_12wk_B22

description: dentate gyrus dissection


title: Ascl1_12wk_B17

description: dentate gyrus dissection


title: Ascl1_12wk_A23

description: dentate gyrus dissection


title: Ascl1_12wk_B08

description: dentate gyrus dissection


title: Ascl1_12wk_A22

description: dentate gyrus dissection


title: Ascl1_12wk_G02

description: dentate gyrus dissection


title: Ascl1_12wk_E17

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_J22

description: dentate gyrus dissection

value: Gli1_CreERT2 x CAG_tdTomato


title: Ascl1_12wk_E14

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_J23

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_J24

description: dentate gyrus dissection


title: Ascl1_12wk_C20

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_J20

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_J19

description: dentate gyrus dissection


title: Ascl1_12wk_C05

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_J18

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_J21

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_J12

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_J15

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_J17

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_J11

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_J10

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_J13

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_J14

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_J09

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_J07

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_J08

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I21

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I24

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I17

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I20

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I18

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I23

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I14

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I15

description: dentate gyrus dissection


title: Ascl1_12wk_A18

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I13

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I12

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I10

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I11

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I07

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I06

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I02

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I05

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I01

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H19

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H22

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H20

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H15

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H21

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H24

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H12

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H11

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H18

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_I04

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H14

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H10

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H04

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H06

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H03

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H02

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G24

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H01

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G23

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G21

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G20

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G22

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G19

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G18

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H16

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G17

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G16

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G15

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H08

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G12

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G14

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G13

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G11

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_H07

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G06

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G04

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G01

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G02

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F24

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F23

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G05

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F21

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F19

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F22

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F17

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F18

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F15

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F16

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F13

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F14

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F12

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F08

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F10

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F07

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F05

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_G09

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F04

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F03

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F02

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E24

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E20

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E19

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E17

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E18

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E16

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E15

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E21

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E12

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F06

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E11

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_F11

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E09

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E07

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E05

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E04

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E03

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E02

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E01

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D23

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D24

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D22

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D21

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D20

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D19

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D18

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D17

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D08

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D11

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D09

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E14

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D07

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D06

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D05

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D16

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_E10

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D03

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D04

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D14

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D02

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_D01

description: dentate gyrus dissection


title: Gli1_12wk_20180822BJ_C22

description: dentate gyrus dissection