title: E. litoralis ΔnepR-ecfG dark replicate 5

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
FastQ files from Illumina HiSeq were processed using CLC genomics workbench (Qiagen), RNA-seq data analysis pipeline. Reads were mapped to the Erythrobacter litoralis DSM 8509 genome (GenBank accession CP017057)
The RPKM values for each gene presented in the .txt files were generated by mapping reads to the E. litoralis DSM 8509 genome in CLC genomics workbench 11.0 using the default RNA-seq workflow.
Genome_build: ASM171916v1
Supplementary_files_format_and_content: RPKMs

organism: Erythrobacter litoralis

source_name: whole bacterial cells

growth_protocol: Erythrobacter litoralis DSM 8509 wild-type and mutant cultures were grown in shaken 13 mm tubes in 0.5x marine broth (Difco 2216) overnight. Cultures were diluted to OD660=0.001 in 3 x 2 ml of fresh 0.5x marine broth (in a 13 mm culture tube) and shaken at a 45 degree incline in the presence or absence of light for 24 hours at 30 degrees C. Final OD660 of cultures was between 0.15 and 0.25. Cells were rapidly pelleted and resuspended in Trizol for RNA purification and subsequent RNA-seq library preparation. Prior to all cultivation, media was autoclaved and filtered (0.22 micron) to remove precipitate.

extract_protocol:
Cell pellets were resuspended in 1 ml of TRIzol and stored at -80˚ C.  The sample was then heated for 10 min at 65°C and 200 µl of chloroform was added, mixed and incubated at room temperature for 5 min. Samples were centrifuged at 15,000 × g for 15 min at 4°C. The clear aqueous phase was transferred to a new tube and 0.7 volume of cold 100% isopropanol was added. Samples were then saved at -80°C overnight. The overnight precipitation was centrifuged at 15,000 × for 30 min at 4°C and the resulting nucleic acid pellet was washed twice with cold 70% ethanol. The pellet was centrifuged again at 15,000 × for 30 min at 4°C, ethanol was removed and the pellet was allowed to dry.  The nucleic acid pellet was resuspended with nuclease-free water. The samples were treated with with Turbo DNase (Invitrogen) and clean-up was performed with RNeasy Mini Kit (Qiagen).
TruSeq stranded total RNA kit, with ribo-zero ribosomal RNA reduction was used to prepare RNA-seq library, per manufacturer (Illumina) protocol

treatment_protocol: All strains were grown in shaken tubes either in the presence of fluorescent white light or in darkness inside foil-covered tubes

tag: genotype

value: {delta}nepR-ecfG

tag: stress

value: dark


title: APT032

status: Public on Feb 14 2019

type: genomic

city: Memphis

first: Tong

last: Lin

state: TN

address: 262 Danny Thomas Place

department: Biostatistics

country: USA

institute: St. Jude Children's Research Hospital

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized according to Illumina's standard protocol

scan_protocol: Arrays were imaged using BeadArray reader

data_processing: R library minfi

label: Cy5, Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Tumor resection

label_protocol: Standard Illumina protocol

extract_protocol: DNA isolation using DNA QIAamp FFPE Tissue Kit

tag: source

value: Primary Tumor

tag: disease state

value: Wilms tumor


title: APT031


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_26.3_Subject_T10

type: RNA

city: Montreal

first: Laura

last: Kervezee

state: Quebec

address: 6875 LaSalle Boulevard

department: Douglas Mental Health University Institute

country: Canada

institute: McGill University

description: PBMC sample taken at 26.3 h after habitual wake time during night-oriented schedule in Subject T10 in the BrightLight group

hyb_protocol: After fragmentation and labeling, 2.8 µg DNA target was hybridized on Clariom™S HT, Human (ThermoFisher Scientific-Affymetrix).

scan_protocol: Arrays were scanned on a Affymetrix GeneTitan instrument (ThermoFisher Scientific-Affymetrix) according to the manufacturer’s protocol.

data_processing: Affymetrix CEL files were normalized by RMA preprocessing methodology using the Oligo package (v1.38.0) in R (v3.4.1).

label: Biotin

molecule: total RNA

label_protocol: Sense-strand cDNA was synthesized from 10 ng of total RNA, and fragmentation and labeling were performed to produce ds-cDNA with the GeneChip® Pico Reagent Kit according to manufacturer’s instructions (ThermoFisher Scientific-Affymetrix).

growth_protocol: An indwelling catheter was inserted in a forearm vein at least 4 hours prior to the start of each 24-hour measurement period.

extract_protocol: Extraction of RNA was performed by addition of chloroform in order to separate organic and aqueous components. Isopropanol and subsequent ethanol washes were used to precipitate and purify the RNA. RNA was dissolved in RNase-free H2O (Qiagen, Toronto, ON, Canada). Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by centrifugation for 30 minutes at 1600rpm on a density gradient (Histopaque-1077, Sigma Aldrich, Oakville, ON, Canada). PBMCs were washed 3 times in phosphate-buffered saline (PBS), lysed in TRIzol (Life Technologies, Burlington, ON, Canada) and stored at -80°C until further processing.

tag: subject

tag: experimentalgroup

value: BrightLight

tag: condition

value: NightOrientedSchedule

tag: relclocktime


title: APT026


title: APT027


title: APT030


title: E. litoralis ΔnepR-ecfG dark replicate 4

type: SRA

library_source: transcriptomic

tag: strain


title: CD_fasted_1

city: Ann Arbor

first: Monica

last: Dus

state: MI

address: 1150 N. University Ave.

department: Department of Molecular, Cellular and Developmental Biology

institute: The University of Michigan

data_processing:
Reads were aligned using STAR  (version: 020201). --quantMode GeneCounts
Convert .sam files to .bam files using samtools (version 1.4).
Determine differential RNA abundance using DeSeq2 (version 1.18.0). dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ condition)
Genome_build: BDGP6
Supplementary_files_format_and_content: HTSeq counts, text format, gene ID, union, intersection_strict, intersection_nonempty

organism: Drosophila melanogaster

source_name: central brains

growth_protocol: Male w1118CS flies were collected 2 days after eclosure and housed in vials of 25 until 7 days old

extract_protocol:
Four biological replicates for each experimental condition were used for sequencing, and each replicate consisted of ten brains. For dissections, flies were briefly anesthetized on ice and brains were rapidly dissected in cold PBS before being transferred and frozen to an Eppendorf tube on dry ice. All dissections and RNA extractions were performed on the same day. Fly brains were manually homogenized in 700uL TRIzol + 4uL RiboLock using a plastic pestle and vortexing. RNA was extracted to the aqueous phase by adding 200uL chloroform with vigorous shaking, followed by centrifugation at 10,000 x g for 10 minutes at 4C. A second extraction was performed by adding equal parts chloroform to the aqueous phase, followed by centrifugation at 10,000 x g for 10 minutes at 4C. RNA was precipitated by adding equal parts 100% isopropanol, followed by a 15 minute incubation at room temperature and finally centrifugation at 10,000 x g for 15 minutes at 4C to pellet RNA. Supernatant was removed and the pellet was washed three times in 75% ethanol followed by centrifugation at 7500 x g for 5 minutes after each wash. The pellet was air-dried, and RNA was eluted in 15uL of RNase-free water.
Samples were ribo-depleted, DNase treated, and libraries were prepared using the Nugen Ovation Model Organisms kit (0350) by the University of Michigan sequencing core facility. Library concentrations were determined by qPCR.

treatment_protocol: "Starved” and “refed” groups were wet-starved with a kimwipe soaked in 2mL of water at 5PM the day before dissections. At lights on (9AM), “refed” flies were flipped to vials containing 400mM D-glucose and allowed to freely feed for 2 hours. “Starved” flies were flipped to new vials with wet kimwipes at the same time and remained starved during dissections of the “refed” group, for a total starvation time of 20 hours. “Sated” flies were wet-starved for one hour before dissections to synchronize their feeding state.

tag: tissue

value: central brains

value: fasted

tag: Sex

value: male


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_18.4_Subject_T10

description: PBMC sample taken at 18.4 h after habitual wake time during night-oriented schedule in Subject T10 in the BrightLight group


title: E. litoralis ΔnepR-ecfG dark replicate 3


title: APT024


title: APT045


title: Blood_HC_09

city: Davis

first: Charles

middle: E

last: Mordaunt

state: CA

address: 3318 Tupper Hall, One Shields Ave

department: Medical Microbiology and Immunology

institute: University of California, Davis

library_source: genomic

data_processing:
Filter using Illumina flag
Separate and trim reads based on adapter contamination
Align to hg38 using BSSeeker2
Combine aligned reads, both trimmed and no adapter contamination
Convert sam files to percent methylation bed files
Genome_build: hg38
Supplementary_files_format_and_content: Percent Methylation Bed file containing single base methylation information with ranged color coding

source_name: whole blood

extract_protocol:
DNA was isolated using the QIAamp DNA Mini Kit (Qiagen).
Diluted DNA was bisulfite converted using the EZ DNA Methylation Lightning kit (Zymo) according to the manufacturer’s instructions. WGBS libraries were prepared using the TruSeq DNA Methylation kit (Illumina) with indexed PCR primers and a 14-cycle PCR program.

tag: circumstances

value: blood draw

tag: diagnosis

value: Healthy control

value: Female

tag: age

tag: bmi


title: CD_sated_3

value: sated


title: APT028


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_16.3_Subject_T10

description: PBMC sample taken at 16.3 h after habitual wake time during day-oriented schedule in Subject T10 in the BrightLight group

value: DayOrientedSchedule


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_8.3_Subject_T10

description: PBMC sample taken at 8.3 h after habitual wake time during day-oriented schedule in Subject T10 in the BrightLight group


title: APT022


title: CD_fasted_2


title: APT029


title: Blood_HC_07


title: E. litoralis ΔnepR-ecfG dark replicate 1


title: APT021


title: CD_sated_1


title: APT025


title: Blood_HC_06


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_4.2_Subject_T10

description: PBMC sample taken at 4.2 h after habitual wake time during day-oriented schedule in Subject T10 in the BrightLight group


title: Blood_HC_10


title: APT020


title: HcpR mutant + nitrite - replicate 4

city: Richmond

first: Janina

middle: P

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

description: 02N vs 07N, 07 vs 07N

data_processing:
Base calls were done using CLC Genomic Workbench
Reads were aligned to the genome of Porphyromonas gingivalis W83 using Genomic Workbench
Reads per gene were determined using Genomic Workbench
Statistical analysis was done using Genomic Workbench
Supplementary_files_format_and_content: RPKMs, fold-change, etc.

organism: Porphyromonas gingivalis

source_name: bacterial cell

growth_protocol: Samples of wildtype and V2807 hcpR mutant P. gingivalis were grown in an overnight culture of BHI media. The overnight cultures served to inoculate cultures of mycoplasma media starting at an OD660 of approximately 0.15. Cultures were grown to mid-log phase and then exposed to 200 μM nitrite for 1 hour before being centrifuged and stored at -20 °C.

extract_protocol:
RNA isolation was carried out using the RNeasy mini-kit (Qiagen) following manufacturers protocol. Residual DNA was removed using the DNA-free DNase kit (Ambion) following manufacturers protocol.
For RNA-seq library generation, the Ovation complete Prokaryotic RNA-Seq DR multiplex kit (Nugen) was used. The library was generated following the manufacturers protocol and fragment sizes from sonication during library generation was confirmed using a bioanalyzer (Agilent Technologies). Libraries were sequenced by VCU nucleic acid sequencing core using Miseq Illumina sequencing.

treatment_protocol: 200 μM nitrite for 1 hour

tag: growth phase

value: logarithmic phase of growth

value: HcpR mutant

tag: treatment

value: nitrite


title: Blood_HC_05

value: Male


title: E. litoralis ΔnepR-ecfG light replicate 4

tag: genotype

value: {delta}nepR-ecfG

value: light


title: CD_refed_2

value: refed


title: APT023

value: Primary Tumor

value: Wilms tumor


title: APT075


title: E. litoralis ΔnepR-ecfG light replicate 5

tag: stress


title: E. litoralis ΔnepR-ecfG light replicate 3


title: Blood_HC_03


title: CD_refed_3

value: central brains


title: Blood_HC_04


title: HcpR mutant + nitrite - replicate 1

description: 02N vs 07N, 07 vs 07N


title: Chimp_00818_c5, NPC, Chimp (bulk RNA-seq)

city: La Jolla

first: Fred

middle: H

last: Gage

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

description:
Chimp_00818_c5
Marchetto_Gage_count.txt
Marchetto_Gage_tpm.txt

data_processing:
bulk RNA: trim raw FASTQ files, SolexaQA++
bulk RNA: alignment to hg19, STAR
bulk RNA: alignment to panTro4, STAR
bulk RNA: alignment to gorgor3, STAR
bulk RNA: alignment to rhemac2, STAR
bulk RNA: join all alignments for each sample and sort by read id
bulk RNA: select reads mapped uniquely to each genome (3mm same species, 5 mm different species)
bulk RNA: Count reads in genes corresponding to the hg19 transcriptome reference, HT-Seq
bulk RNA: Transform counts to TPM
single-cell RNA: cellranger v2.0.0
Genome_build: hg19 (grch37), pantro4 (CSAC 2.1.4), gorgor3 (gorGor3.1), and rhemac2(MGSC Merged 1.0)
Supplementary_files_format_and_content: tab-delimited text files report TPMs and counts.

molecule: polyA RNA

organism: Pan troglodytes

source_name: NPC

growth_protocol: Established iPSC colonies were kept in feeder-free conditions indefinitely and passed using mechanical dissociation. To obtain NPCs from iPSCs, embryoid bodies (EBs) were formed by mechanical dissociation of iPSC clusters and plated into low-adherence dishes in DMEM/F12 plus N2 and B27 (Invitrogen) medium in the presence of Noggin (R&D) for forebrain induction for approximately 7 days. Then, floating EBs were plated onto poly-ornithine/laminin (Sigma)-coated dishes in DMEM/F12 plus N2 and B27 (Invitrogen) with the addition of Noggin. Rosettes were collected after 7 days. Rosettes were then dissociated with accutase (Chemicon) and plated again onto coated dishes in DMEM/F12 plus N2 and B27 and 10 ng/ml of FGF2 (R&D). Homogeneous populations of NPCs were obtained after 1-2 passages with accutase under the same conditions.

extract_protocol:
Total cellular RNA was extracted from ~5x10e6 cells using the RNeasy Protect Mini kit or RNeasy Plus kit (Qiagen, Valencia, CA), according to the manufacturer's instructions.
RNA-seq: PolyA+ RNA was fragmented and prepared into sequencing libraries using the Illumina TruSeq RNA sample preparation kit. scRNA: library was prepared according to the 10X protocol

treatment_protocol: No additional treatment was performed

tag: sample id

tag: gender

value: F

tag: cell type

value: iPS-derived neural progenitor cells (NPCs)


title: APT071

tag: source

tag: disease state


title: APT074


title: E. litoralis ΔnepR-ecfG light replicate 2


title: E. litoralis ΔnepR-ecfG dark replicate 2

value: dark


title: HcpR mutant - replicate 3

description: 02 vs 07, 07 vs 07N

value: control


title: APT067


title: E. litoralis ΔnepR-ecfG light replicate 1


title: HcpR mutant + nitrite - replicate 3

description: 02N vs 07N, 07 vs 07N


title: Liver_WD_Hep_10

source_name: liver

value: liver transplant

value: Wilson disease - hepatic


title: APT066


title: HcpR mutant - replicate 2

description: 02 vs 07, 07 vs 07N


title: Liver_WD_Hep_09

value: Female


title: CD_refed_1

tag: condition

value: male


title: HcpR mutant + nitrite - replicate 2

description: 02N vs 07N, 07 vs 07N

value: logarithmic phase of growth

tag: strain

value: HcpR mutant


title: HcpR mutant - replicate 1

description: 02 vs 07, 07 vs 07N


title: Chimp_00818_c8, NPC, Chimp (bulk RNA-seq)

description:
Chimp_00818_c8
Marchetto_Gage_count.txt
Marchetto_Gage_tpm.txt


title: HcpR mutant - replicate 4

description: 02 vs 07, 07 vs 07N


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_0.8_Subject_T10

description: PBMC sample taken at 0.8 h after habitual wake time during day-oriented schedule in Subject T10 in the BrightLight group

tag: subject

tag: experimentalgroup

value: BrightLight

value: DayOrientedSchedule

tag: relclocktime


title: Liver_WD_Hep_08

tag: circumstances

tag: diagnosis

tag: Sex

value: Male


title: Wild type + nitrite - replicate 4

description: 02N vs 07N, 02 vs 02N

tag: growth phase

value: Wild type

value: nitrite


title: Blood_HC_02

value: blood draw

value: Healthy control

tag: age

tag: bmi


title: Blood_HC_01


title: E. litoralis ΔgsrK∆gsrP dark replicate 5

tag: genotype

value: {delta}gsrK{delta}gsrP

tag: stress


title: E. litoralis ΔgsrK∆gsrP dark replicate 3


title: E. litoralis ΔgsrK∆gsrP dark replicate 2


title: Liver_WD_Hep_07


title: C6orf141 overexpression 1

city: Kaohsiung

first: Sung-Chou

last: Li

state: Kaohsiung

address: No.386, Dazhong 1st Rd

department: Department of Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

description: RNA expression value derived from Expression Console software; gene-level analysis

hyb_protocol: Samples were hybridized with Clariom D array human microarray chip (Thermo Fisher) and scanned with the GeneChip Scanner 3000 7G in Genomics and Proteomics Core lab., Kaohsiung Chang Gung memorial Hospital, Taiwan.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Thermo Fisher)

data_processing: The raw data of Clariom D Human chips were first subject to quality control examination as suggested by Thermo Fisher manuals. And, the chips passing the quality control criteria were then analyzed with Partek.

label: biotin

source_name: SAS_C6orf141 overexpression

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT PLUS Kit (Thermo Fisher) and then fragmented and labeled with the WT Terminal Labeling Kit (Thermo Fisher).

growth_protocol: SAS cells were maintained in Dulbecco modified Eagle medium supplemented with 10% fetal bovine serum and penicillin–streptomycin.

extract_protocol: We used mirVanaTM miRNA Isolation Kit (Ambion, CA, USA) to extract RNA following the manufacturer’s protocols. The concentration of RNA was measured with NanoDrop 2000 spectrophotometer (Thermo scientific, MA, USA). All RNA samples passed the criterion of RIN≥ 7 assessed with Agilent 2100 Bioanalyzer (Agilent, CA, USA).

treatment_protocol: The full length of C6orf141 was cloned into the pLVX-IRES-Neo vector. Stable SAS cells with C6orf141 expression were generated by transfecting oral SAS cells with pLVX-C6orf141 for 48 h followed by G418 (1200 μg/mL) selection for 14 days

tag: cell line

value: SAS cell

value: tongue squamous carcinoma


title: scrambled control 2

tag: cell type


title: E. litoralis ΔgsrK∆gsrP light replicate 5

value: light


title: Blood_HC_08


title: E. litoralis ΔgsrK∆gsrP dark replicate 1

value: dark


title: Wild type + nitrite - replicate 3

description: 02N vs 07N, 02 vs 02N

tag: treatment


title: Liver_WD_Hep_06

value: liver transplant

value: Wilson disease - hepatic


title: C6orf141 overexpression 2


title: Wild type + nitrite - replicate 2

description: 02N vs 07N, 02 vs 02N


title: Liver_WD_Hep_05

value: percutaneous biopsy

value: Female


title: NEW005

hyb_protocol: Five micrograms of cDNA was hybridized for 16h at 45C on a Clariom S Human GeneChip array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

source_name: Pooled Fetal Kidney RNA Replicate 3

label_protocol: Sense target cDNA was prepared from 100ng of total RNA using the Affymetrix GeneChip WT Plus (Applied Biosystems P/N 902281). cDNA was fragmented and biotin-labeled using the GeneChip(tm) WT Terminal Labeling Kit (Applied Biosystems P/N 900670).

extract_protocol: Qiagen RNeasy Midi kit. Integrity, size and quantification of total RNA was assessed using a 2100 BioAnalyzer (Agilent, Santa Clara, CA).

tag: tissue

value: Pooled Fetal Kidney

tag: disease state

value: normal


title: E. litoralis ΔgsrK∆gsrP light replicate 4

tag: strain


title: Wild type + nitrite - replicate 1

description: 02N vs 07N, 02 vs 02N

value: logarithmic phase of growth


title: NEW002

source_name: Normal Kidney RNA

value: Normal Kidney


title: scrambled control 1


title: NEW001


title: E. litoralis ΔgsrK∆gsrP light replicate 3


title: Liver_WD_Hep_04


title: E. litoralis ΔgsrK∆gsrP light replicate 2


title: Wild type - replicate 1

description: 02 vs 07, 02 vs 02N

value: Wild type

value: control


title: E. litoralis ΔlovKR dark replicate 5

value: {delta}lovKR


title: Wild type - replicate 4

description: 02 vs 07, 02 vs 02N


title: NEW004

source_name: Pooled Fetal Kidney RNA Replicate 2


title: NEW003

source_name: Pooled Fetal Kidney RNA Replicate 1


title: Liver_WD_Hep_03

value: Male


title: HMCR11

city: Buffalo

first: Moises

middle: A

last: Bernal

state: NY

address: 109 Cooke Hall

department: Biological Sciences

institute: SUNY Buffalo

data_processing:
Removal of low-quality reads and PCR duplicates was done with fastq_quality_filter and fastx_clipper, part of the FastX Tool Kit
Adaptor trimming for the TagSeq reads was done with the script rnaseq_clipper.pl (https://github.com/z0on/tag-based_RNAseq).
Mapping to reference transcriptome done with Bowtie2
Scripts used to extract the number of reads that mapped to a particular transcript are available at https://github.com/z0on/tag-based_RNAseq
Differentially Expressed Genes (DEGs) were identified with DESeq2
Genome_build: Trinity-forblast-hmacro.fasta
Supplementary_files_format_and_content: SAM files resulting from assembly to reference transcriptome using Bowtie2

organism: Haemulon macrostomum

growth_protocol: Wild samples

extract_protocol:
RNAqueous Kit (Life Technologies)
The preparation of normalized cDNA libraries for transcriptome sequencing followed the protocol of Meyer et al., (2009), with modifications for Illumina sequencing. First-strand cDNA synthesis was prepared with 500ng of RNA.

value: liver


title: E. litoralis ΔgsrK∆gsrP dark replicate 4

value: {delta}gsrK{delta}gsrP


title: Wild type - replicate 3

description: 02 vs 07, 02 vs 02N


title: Wild type - replicate 2

description: 02 vs 07, 02 vs 02N


title: Liver_NAFLD_04

value: Non-alcoholic fatty liver disease


title: Liver_WD_Hep_02


title: CD_sated_2

value: central brains

tag: condition

value: sated

value: male


title: Liver_NAFLD_05


title: ANK016

source_name: Normal Kidney Specimen


title: HMCR10


title: Liver_WD_Hep_01

value: Wilson disease - hepatic


title: E. litoralis ΔgsrK∆gsrP light replicate 1

value: light


title: E. litoralis ΔlovKR dark replicate 3

value: dark


title: E. litoralis ΔlovKR dark replicate 4


title: Liver_NAFLD_03

value: percutaneous biopsy

value: Female


title: E. litoralis ΔlovKR dark replicate 1


title: HMCR9


title: E. litoralis ΔlovKR dark replicate 2


title: XKT076

source_name: Xenograft

value: Xenograft

value: Wilms tumor


title: Liver_NAFLD_01


title: E. litoralis ΔlovKR light replicate 5


title: HMCR8


title: HMCR7


title: E. litoralis ΔlovKR light replicate 4


title: XKT069


title: HMCR6


title: RED002


title: RED001


title: XKT060


title: Liver_HC_06

value: bariatric surgery

value: Healthy control


title: XKT058


title: HMCR4


title: Liver_HC_03


title: XKT052


title: Liver_HC_05


title: E. litoralis ΔlovKR light replicate 3

value: {delta}lovKR


title: HMCR5


title: Liver_HC_04


title: HMCR2


title: HMCR1


title: E. litoralis ΔphyR dark replicate 3

value: {delta}phyR


title: E. litoralis ΔphyR dark replicate 2


title: HFL18

organism: Haemulon flavolineatum

value: liver


title: E. litoralis ΔlovKR light replicate 2


title: cdc50-3

city: Durham

first: Hannah

middle: Elizabeth

last: Brown

state: NC

address: 303 Research Dr

department: Molecular Genetics and Microbiology

institute: Duke University

description:
HB9
S9-cdc50-3
Processed data files:
H99_v_cdc50_counts.csv
H99_v_cdc50_results.csv

data_processing:
Base-calling and demultiplexing were done using bcl2fastq.
STAR/DeSeq2
Reads were aligned to the C. neoformans genome using STAR alignment software with default parameters.
Differential expression analysis was performed in R with DESeq2 following an RNA-Seq Bioconductor workflow (Love, M. I., Anders, S., Kim, V. & Huber, W. RNA-Seq workflow: gene-level exploratory analysis and differential expression. F1000Res 4, 1070, doi:10.12688/f1000research.7035.1 (2015)).
Genome_build: The C. neoformans H99 reference genome used for this analysis was obtained from NCBI (assembly CNA3, accessed 07/2017).
Supplementary_files_format_and_content: H99_v_rim101_counts.csv: Comma-separated file with read counts for each strain/biological replicate.
Supplementary_files_format_and_content: H99_v_cdc50_counts.csv: Comma-separated file with read counts for each strain/biological replicate.

organism: Cryptococcus neoformans H99

source_name: fungal cells

growth_protocol: Three biological replicates of WT and rim101∆ and cdc50∆ mutant cells were incubated in YPD medium to mid-log phase and transferred to CO2-indepdendent medium for 1.5 hrs at 37˚C.

extract_protocol:
Cells were flash frozen, lyophilized, and lysed by vortexing with glass beads. RNA was extracted using the Qiagen RNeasy Plant Mini Kit with optional on-column DNase digestion.
Libraries were prepared by the Duke Sequencing and Genomic Technologies Shared Resource using the Kapa Stranded mRNA-Seq library prep kit (Catalog # KK8421). A single 6 bp index strategy was used, followed by pooling all 9 libraries.

tag: genotype/variation


title: HFL17


title: XKT033


title: cdc50-2

description:
HB8
S8-cdc50-2
Processed data files:
H99_v_cdc50_counts.csv
H99_v_cdc50_results.csv


title: Liver_NAFLD_02

value: Male


title: HMCR3


title: Liver_HC_02


title: XKT025


title: XKT051


title: E. litoralis ΔphyR dark replicate 4


title: E. litoralis ΔlovKR light replicate 1


title: Liver_HC_01


title: E. litoralis ΔphyR dark replicate 1


title: XKT021


title: XKT050


title: cdc50-1

description:
HB7
S7-cdc50-1
Processed data files:
H99_v_cdc50_counts.csv
H99_v_cdc50_results.csv


title: E. litoralis ΔphyR light replicate 4


title: E. litoralis ΔphyR light replicate 5


title: XKT024


title: XKT023


title: E. litoralis ΔphyR light replicate 2


title: WT-2

description:
HB2
S2-H99-2
Processed data files:
H99_v_rim101_counts.csv
H99_v_rim101_results.csv
H99_v_cdc50_counts.csv
H99_v_cdc50_results.csv

value: WT


title: HFL16


title: HFL15


title: Wild type E. litoralis dark replicate 5

value: Wild type


title: E. litoralis ΔphyR light replicate 1


title: HFL13


title: E. litoralis ΔphyR light replicate 3


title: rim101-1

description:
HB4
S4-rim101-1
Processed data files:
H99_v_rim101_counts.csv
H99_v_rim101_results.csv


title: rim101-2

description:
HB5
S5-rim101-2
Processed data files:
H99_v_rim101_counts.csv
H99_v_rim101_results.csv


title: HFL14


title: HFL12


title: Wild type E. litoralis dark replicate 4


title: rim101-3

description:
HB6
S6-rim101-3
Processed data files:
H99_v_rim101_counts.csv
H99_v_rim101_results.csv


title: WT-3

description:
HB3
S3-H99-3
Processed data files:
H99_v_rim101_counts.csv
H99_v_rim101_results.csv
H99_v_cdc50_counts.csv
H99_v_cdc50_results.csv


title: Wild type E. litoralis dark replicate 3


title: XKT074


title: APT058

source_name: Primary Tumor

value: Primary Tumor


title: HFL11


title: APT053


title: WT-1

description:
HB1
S1-H99-1
Processed data files:
H99_v_rim101_counts.csv
H99_v_rim101_results.csv
H99_v_cdc50_counts.csv
H99_v_cdc50_results.csv


title: Bonobo_NPC_10X (scRNA-seq)

description:
Bonobo
Marchetto_Gage_sc_count.txt.gz

organism: Pan paniscus

tag: sample id

tag: gender

value: M

value: iPS-derived neural progenitor cells (NPCs)


title: HFL9


title: XKT071


title: Wild type E. litoralis dark replicate 2


title: APT051


title: HCAR8

organism: Haemulon carbonarium


title: HFL8


title: HFL10


title: Wild type E. litoralis dark replicate 1


title: HFL7


title: APT052


title: Wild type E. litoralis light replicate 5

value: light


title: HCAR7


title: HFL6


title: APT050


title: HCAR6


title: HCAR5


title: APT033


title: Wild type E. litoralis light replicate 4


title: HFL5


title: APT036


title: HCAR4


title: APT024


title: HFL4


title: Wild type E. litoralis light replicate 3


title: HFL3


title: HCAR3


title: Wild type E. litoralis light replicate 2


title: Wild type E. litoralis light replicate 1


title: HFL2


title: APT023


title: HCAR1


title: HCAR2


title: Fetal myoblasts RNA-Seq rep2

status: Public on Feb 13 2019

city: Minneapolis

first: Tania

last: Incitti

state: Minnesota

address: 2231 6th Street SE

institute: University of Minnesota

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Trimmomatics v0.33), then mapped to mm10 whole genome using HISAT 2 v2.0.2.
Read assignments were performed by SUBREAD featureCounts v1.4.6.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include SUBREAD assigned raw reads for each sample.

organism: Mus musculus

source_name: E14.5 mouse fetus

growth_protocol: iPax3/iPax7 myogenic progenitors were generated thorugh sorting of Vcam1+Flk1- cells from EBs, plated and expanded upon Dox and bFGF administration for 3 passages, then collected with PBS-based dissociation buffer and submitted for downstream analyses.

extract_protocol:
Cultured Cells and freshly sorted tissue-derived cells were lysated with buffer RA1+TCEP of kit RNA XS (Machirey-Nagel) and RNA was extracted according to manufacturer's instructions.
Libraries were prepared using Illumina standard protocols (RNA-Seq); Chromium Single Cell 3’ Reagent kit 10X Genomics (single-cell RNA-Seq)

value: My5Cre Rosa26YFP

value: mouse myogenic progenitors


title: Neonatal satellite cells RNA-Seq rep1

source_name: P3 mouse hindlimb muscles

value: postnatal day 3


title: Fetal myoblasts RNA-Seq rep3


title: APT074


title: Fetal myoblasts RNA-Seq rep1


title: APT025


title: iPax7 RNA-Seq rep3

source_name: PSC-derived myogenic progenitors

value: ES-derived myogenic progenitors


title: APT021

value: Wilms tumor


title: Embryonic myoblasts RNA-Seq rep3

source_name: E10.5 mouse embryo


title: Embryonic myoblasts RNA-Seq rep1


title: APT071


title: Neonatal satellite cells RNA-Seq rep2


title: iPax3 RNA-Seq rep3


title: iPax3 RNA-Seq rep1


title: iPax3 RNA-Seq rep2


title: Neonatal satellite cells RNA-Seq rep3


title: iPax7 RNA-Seq rep2


title: Placenta 10, hypoxia

city: Los Angeles

first: David

last: Casero

address: 610 Charles Young Drive East

department: Pathology and Laboratory Medicine

institute: UCLA

description:
PH10
PlacentalHypoxia.genesfpkm.txt

data_processing:
Data quality check was done on an Illumina SAV. Demultiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program.
The STAR ultrafast universal RNA-seq aligner (v2.5.2b) was used to generate the genome index and perform single-end alignments. Reads were aligned to a genome index that includes both the genome sequence (GRCm38 primary assembly) and the exon/intron structure of known gene models (Gencode M12 genome annotation). Alignment files were used to generate strand-specific, gene-level count summaries with STAR's built-in gene counter. Differential expression analysis was performed with DESeq2.
Counts were normalized per-sample in units of RPKMs after correcting for gene mappable length and sample total counts.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab delimited, per-sample, gene expression estimates in units of RPKMs

source_name: whole placenta_hypoxia

growth_protocol: Whole placental tissues were obtained from LG-RA and LG-H groups (n=7-8/group) and snap-frozen. Tissue from single placentas was homogenized

extract_protocol:
RNA was extracted using the Zymo Direct-Zol RNA MiniPrep Plus (cat# R2070, Irvine, CA) as per the manufacturer’s instructions. Total RNA was quantified and 260/280 ratios determined using Nanodrop (all samples with a 260/280>1.97). 1μg of total RNA was used as starting material for each sample.
RNA sequencing and library preparation was performed by the UCLA Technology Center for Genomics and Bioinformatics using the KAPA Stranded mRNA-seq kit (Roche Sequencing, cat#KK8421, Pleasanton, CA, USA), according to the manufacturer’s instructions. The work flow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on the HiSeq3000 System for a single-read 50 run (Illumina).

treatment_protocol: Pregnant females were transferred to individual cages and reared on the same chow diet ad libitum until gestational day 14.5, at which point they were randomly assigned to two groups: 1) late gestation-room air (LG-RA) pregnant mice which were house in standard conditions, and 2) late gestation-hypoxia (LG-H) pregnant mice were exposed to hypoxia for 4 days (days 14.5 to 18.5 of gestation). Hypoxia exposure consisted of 10.5% fractional inspired oxygen concentrations continuously, which was maintained using a commercially available environmental system (Biospherix Proox model 360).

value: placenta

value: Female

tag: mother mouse age

value: 10 weeks

tag: embryo sex

tag: embryo gestational age

value: 18.5 days


title: Placenta 9, hypoxia

description:
PH9
PlacentalHypoxia.genesfpkm.txt

tag: Sex


title: Placenta 20, hypoxia

description:
PH20
PlacentalHypoxia.genesfpkm.txt


title: Placenta 11, hypoxia

description:
PH11
PlacentalHypoxia.genesfpkm.txt


title: Placenta 18, hypoxia

description:
PH18
PlacentalHypoxia.genesfpkm.txt


title: Placenta 8, hypoxia

description:
PH8
PlacentalHypoxia.genesfpkm.txt


title: Embryonic myoblasts RNA-Seq rep2

tag: age


title: iPax7 RNA-Seq rep1


title: Placenta 6, control

description:
PC6
PlacentalHypoxia.genesfpkm.txt

source_name: whole placenta_control


title: Placenta 5, control

description:
PC5
PlacentalHypoxia.genesfpkm.txt


title: Placenta 4, control

description:
PC4
PlacentalHypoxia.genesfpkm.txt


title: Placenta 3, control

description:
PC3
PlacentalHypoxia.genesfpkm.txt


title: Placenta 2, control

description:
PC2
PlacentalHypoxia.genesfpkm.txt


title: Placenta 1, control

description:
PC1
PlacentalHypoxia.genesfpkm.txt


title: Th17 + Vehicle 1

city: NASHVILLE

first: Aguirre

last: de Cubas

address: 2220 Pierce Ave

department: Hematology and Oncology

institute: Vanderbilt University Medical Center

data_processing:
Sequencing reads were aligned against the Mouse GENCODE genome, Version M14 (January 2017 freeze, GRCm38, Ensembl 89) using the Spliced Transcripts Alignment to a Reference (STAR) software (PMID: 26187010 and 23104886).
Reads were preprocessed and index using SAMtools (PMID: 19505943).
Mapped reads were assigned to gene features and quantified using featureCounts (PMID: 24227677).
Raw counts where read into R, and normalized using DESeq2 (PMID: 25516281) with the variance stabilizing normalization function.
Genome_build: Mouse GENCODE genome, Version M14 (January 2017 freeze, GRCm38, Ensembl 89)
Supplementary_files_format_and_content: Raw Counts

source_name: Th17 cells

growth_protocol: Primary mouse CD4+ T cells differentiated over 5 days with subset-specific cytokines and growth cytokine IL-2

extract_protocol:
CD4+ T cells isolated after treatment and total RNA extracted
At least 100ng of DNase-treated total RNA was used to generate polyA-enriched mRNA libraries using NEBNext polyA mRNA sample kits with indexed adaptors (New England Biolabs). Library quality was assessed using the 2100 Bioanalyzer (Agilent) and libraries were quantitated using KAPA Library Quantification Kits (Roche).
Pooled libraries were subjected to 75 bp paired-end sequencing according to the manufacturer’s protocol (Illumina HiSeq3000). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.

treatment_protocol: Cells were treated with glutaminase1 inhibitor or vehicle

tag: agent

value: Vehicle

value: Th17 cells


title: Th1 + Vehicle 1

source_name: Th1 cells

value: Th1 cells


title: Placenta 25, hypoxia

description:
PH25
PlacentalHypoxia.genesfpkm.txt

value: Male


title: Th17 + Vehicle 3


title: Th1 + CB839 1


title: Th17 + CB839 3


title: Placenta 7, control

description:
PC7
PlacentalHypoxia.genesfpkm.txt


title: KS9-S9

first: Karilyn

last: Sant

address: 1355 Bogue St., Life Science B440

department: Pharmacology & Toxicology

data_processing:
Illumina BaseSpace Sequence Hub platform
annotated and assessed using the Illumina RNA-Seq Alignment (v1.1.1) and Cufflinks Assembly & DE (v2.1.0) apps
Data provided as FRKM
Genome_build: Danio rerio UCSC danRer7 (RefSeq gene annotation)
Supplementary_files_format_and_content: Processed data files are given as .csv. Log2 FPKM values are presented, as well as q-values.

organism: Danio rerio

source_name: Pooled, whole zebrafish embryos

growth_protocol: Embryos were maintained in 100 mm petri dishes at 37 degrees Celsius throughout the study.

extract_protocol:
Samples collected at 4 dpf into FastPrep homogenization tubes containing TRIzol Reagent (Invitrogen, Carlsbad, CA) and 0.1 mm RNase-free glass beads (Next Advance Inc., Troy, NY). All contents were vortexed for 15 s and homogenized in a FastPrep-24 5G benchtop homogenizer equipped with the QuickPrep adapter (MP Biomedicals, Santa Ana, CA). The supernatant was transferred to a sterile tube, and total RNA was purified using the Direct-zol RNA MicroPrep kit with in-column DNase-I treatment following manufacturer instructions (Zymo Research, Irvine, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols. PolyA capture, paired ends. Total RNA (input of 1 microgram) was used to isolate poly(A) mRNA and prepare stranded libraries using the NEBNext Ultra-II Directional RNA Library Prep Kit for Illumina following manufacturer instructions (New England Biolabs, Ipswich, MA).

treatment_protocol: Embryos were manually dechorionated at 24 hpf. Exposures were renewed every 24 hours.

value: AB

tag: developmental stage

value: 96 hpf

tag: # embryos pooled per sample

tag: exposure

value: PFBS (32 uM)


title: Th1 + Vehicle 3

tag: cell type


title: Th17 + CB839 2


title: Th1 + Vehicle 2


title: KS7-S7


title: Th1 + CB839 3


title: Th17 + CB839 1


title: Placenta 12, hypoxia

description:
PH12
PlacentalHypoxia.genesfpkm.txt

tag: tissue


title: Th17 + Vehicle 2


title: KS4-S4

value: PFBS (16 uM)


title: NP_HuR knockdown 4

city: Philadelphia

first: Makarand

last: Risbud

state: PA

address: 1015 Walnut St.

department: Orthopaedic Surgery

institute: Thomas Jefferson University

description:
ShHuR 4
13657X16_S4_shHuR_Hx_normalized

data_processing:
HiSeq 50 Cycle Single-Read Sequencing version 4Sequencing libraries (25 pM) were chemically denatured and applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot.  Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (GD-401-4001).  Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50 cycle single-read sequence run was performed using HiSeq SBS Kit v4 sequencing reagents.
Genome_build: Rn5 Ensembl annotations (Build 75)
Supplementary_files_format_and_content: File containing Gene identifiers, log2FC, adusted p value, and normalized reads

organism: Rattus norvegicus

source_name: Rat nucleus pulposus_HuR knockdown

growth_protocol: Primary rat nucleus pulposus (NP) cells were dissected from Wistar rat spines, expanded from explant tissues, and maintained in DMEM containing 10% FBS and antibiotics

extract_protocol:
Total mRNA was extracted using Qiagen RNeasy mini columns and treated with DNAse1
Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero GoldTotal RNA samples (100-500 ng) were hybridized with Ribo-Zero Gold to substantially deplete cytoplasmic and mitochondrial rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold (RS-122-2301 and RS-122-2302).  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 10 nM and equal volumes were pooled in preparation for Illumina sequence analysis.

treatment_protocol: Rat NP cells were transduced with lentivirally-delivered control (MISSION PLKO.1 non-target ShRNA, ShCTR) or HuR-specific (ShHuR) shRNA. 24 h before collection of total mRNA, cells were cultured under 1% O2 conditions.

tag: strain background

value: Wistar

value: primary rat nucleus pulposus (NP) cells

value: shHuR-transduced

tag: culture condition

value: hypoxia (1% O2)


title: KS1-S1

tag: strain

value: Control (0.01% DMSO)


title: KS2-S2


title: NP_HuR knockdown 3

description:
ShHuR 3
13657X12_S3_shHuR_Hx_normalized

tag: genotype/variation


title: KS3-S3


title: NP_HuR knockdown 2

description:
ShHuR 2
13657X8_S2_shHuR_Hx_normalized


title: Th1 + CB839 2


title: NP_HuR knockdown 1

description:
ShHuR 1
13657X4_S1_shHuR_Hx_normalized


title: NP_control 3

description:
ShCTR 3
13657X11_S3_shCtr_Hx_normalized

source_name: Rat nucleus pulposus_control

value: PLKO.1 control-transduced


title: NP_control 1

description:
ShCTR 1
13657X3_S1_shCtr_Hx_normalized


title: NP_control 2

description:
ShCTR 2
13657X7_S2_shCtr_Hx_normalized


title: PARPi-6

city: Boston

first: Jean

last: Zhao

state: MA

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: Ion AmpliSeq Custom Panel seqiencing

data_processing:
Data were analyzed by Torrent Suite and ampliSeqRNA analysis plugin (Thermo Fisher) to generate read counts
Genome_build: WG00278_Reference (mm10)
Supplementary_files_format_and_content: One excel file, raw counts of sequencing reads for all samples

source_name: Ovarian tumor

growth_protocol: Brca1-deficient ovarian tumor (Trp53-/-; Brca1-/-; c-Myc) is generated by implantation of genetically engineered OSE cells. The primary ovarian tumors were digested and orthotopically transplanted to FVB/NJ mice for treatment.

extract_protocol:
About 50 to 100 mg of tumor samples were homogenized in 1 ml of TRIZOL reagent supplied with 200l of stainless steel beads and 0.2 ml of chloroform was added to the samples. Samples were vortexed vigorously for 15 seconds and then incubated at room temperature for 2 to 3 minutes. After centrifugation at 12,000 x g for 15 minutes at 4°C, upper aqueous phase of the samples was carefully removed to a new tube and the total RNA was purified by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction.
cDNA libraries were constructed using the Ion AmpliSeq Kit for proton sequencer(Thermo Fisher) with Ion AmpliSeq Custom Panel that was designed by the manufacturer (Thermo Fisher) using Ion AmpliSeq Designer for targeted amplification of 4,604 mouse genes
Ion AmpliSeq Custom Panel

treatment_protocol: Olaparib (50mg/kg/day)

value: FVB/NJ

value: Ovarian tumor

tag: treatment

value: Olaparib


title: PARPi-5

description: Ion AmpliSeq Custom Panel seqiencing


title: PARPi-2

description: Ion AmpliSeq Custom Panel seqiencing


title: PARPi-4

description: Ion AmpliSeq Custom Panel seqiencing


title: Control-6

description: Ion AmpliSeq Custom Panel seqiencing

value: Vehicle


title: PARPi-1

description: Ion AmpliSeq Custom Panel seqiencing


title: Control-4

description: Ion AmpliSeq Custom Panel seqiencing


title: Control-5

description: Ion AmpliSeq Custom Panel seqiencing


title: Control-1

description: Ion AmpliSeq Custom Panel seqiencing


title: Control-2

description: Ion AmpliSeq Custom Panel seqiencing


title: PARPi-3

description: Ion AmpliSeq Custom Panel seqiencing


title: KS8-S8


title: NP_control 4

description:
ShCTR 4
13657X15_S4_shCtr_Hx_normalized


title: Control-3

description: Ion AmpliSeq Custom Panel seqiencing


title: Mouse BMDM_Fibrin and IgG2b_biological replicate 1

city: San Francisco

first: Katerina

last: Akassoglou

address: 1650 Owens St

institute: Gladstone Institutes

description: Gene expression data from fibrin-stimulated BMDMs treated with IgG2b

hyb_protocol: GeneChip Expression Analysis Technical Manual 702232 Rev. 3

data_processing: Affymetrix AGCC 3.2.2

label_protocol: FL-Ovation cDNA Biotin Module (4200)

growth_protocol: Bone marrow cells were isolated from tibia and femur of 10-week-old mice and cultured in complete RPMI-1640 supplemented with MCSF. On day 6, adherent BMDMs were harvested from plates for experiments.

extract_protocol: RNA extraction from BMDMs was performed using RNeasy kit according to the manufacturer's instructions (Qiagen, Valencia, CA).  Genomic DNA was removed during the RNeasy cleanup using Rnase-Free Dnase set (Qiagen, Valencia, CA).

treatment_protocol: BMDMs were stimulated for 6 hr with fibrin treated with 5B8 or IgG2b.

value: BMDMs


title: Mouse BMDM_Fibrin and 5B8_biological replicate 2

description: Gene expression data from fibrin-stimulated BMDMs treated with 5B8


title: Control lens epithelial cells

city: Kahoku-gun

first: Yasuo

last: Yoshitomi

state: Ishikawa

address: 1-1 Daigaku, Uchinada-machi

department: Biochemistry

country: Japan

institute: Kanazawa Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were processed with Affymetrix Expression Console Software and the normalized intensity data were exported

source_name: lens epithelium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using Ambion WT Expression Kit.

extract_protocol: Lens tissue were separated from eyes and after carefully removed other tissues, lens epithelium were isolated. Lens epithelial cells were then extracted by TRI-Reagent and total RNA was purified using Rneasy Mini kits (QIAGEN, CA). RNA quality was assessed according to 28S/18S ratios of rRNA bands on electrophoresis gels under denaturing conditions.

treatment_protocol: Under the anathesia, mouse eyes were covered with aluminum foil and exposed to UVB radiation for negative control.

value: lens elithelial cells

value: non-irradiated


title: Mouse BMDM_Fibrin and IgG2b_biological replicate 2

source_name: fibrin-stimulated BMDMs treated with IgG2b


title: Mouse BMDM_Fibrin_biological replicate 3

description: Gene expression data from fibrin-stimulated BMDMs

source_name: fibrin-stimulated BMDMs


title: UVB-irradiated lens epithelial cells

treatment_protocol: Under the anathesia, mouse eyes were exposed to UVB radiation at the dose of 30 mJ/cm2

value: UVB-irradiated


title: UVB-irradiated lens epithelial cells 2


title: Mouse BMDM_Fibrin and 5B8_biological replicate 1

source_name: fibrin-stimulated BMDMs treated with 5B8


title: Mouse BMDM_Fibrin and IgG2b_biological replicate 3


title: Mouse BMDM_Fibrin_biological replicate 1


title: Mouse BMDM_Control_biological replicate 2

description: Gene expression data from unstimulated BMDMs

source_name: unstimulated BMDMs


title: Mouse BMDM_Fibrin_biological replicate 2


title: Mouse BMDM_Fibrin and 5B8_biological replicate 3


title: 5B8-treated 5XFAD biological replicate 3

description: Gene expression data from cortex of 5B8-treated 5XFAD mouse

source_name: cortex

extract_protocol: Qiagen Rneasy Lipid Tissue Mini Kit. Genomic DNA was eliminated with on-column DNAse digestion using Qiagen RNase-Free DNase Set.

treatment_protocol: Mice were injected i.p. every other day with 800 ug of 5B8 antibody or control IgG antibody for 2 months beginning at 3 months of age

value: brain

value: C57Bl6/SJL mix

value: 5B8 antibody

value: male


title: IgG-treated 5XFAD biological replicate 3

description: Gene expression data from cortex of IgG-treated 5XFAD mouse

value: IgG antibody

value: female


title: IgG-treated 5XFAD biological replicate 2


title: 5B8-treated 5XFAD biological replicate 1


title: 5B8-treated 5XFAD biological replicate 2


title: mutant_P1_3

city: kyoto

first: yoshiya

last: kawaguchi

address: 53, shogoin kawaharachou, sakyo

institute: kyoto university

hyb_protocol: Fragmented and labelled cDNA was hybridized to GeneChip Mouse Gene 1.0 ST (Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 TG.

data_processing: Mouse Gene 1.0 ST arrays were normalized using RMA16 implemented in the GeneSpring 14.9

source_name: pancreas

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix) were used according to Affymetrix protocol.

growth_protocol: To obtain Pdx1-conditional knock-out mice, Pdx1loxP mice and Elastase-Cre mice were interbred.

extract_protocol: The extraction of total RNA was performed by using RNeasy micro kit according to the manufacturer's instructions.

treatment_protocol: Pancreata were dissected from postneonatal day 1 and immediately submerged in RNAlater (Ambion, Inc., Austin, TX).

value: post neonatal day 1

value: Pancreas

value: Elastase-Cre mediated Pdx1 knock out


title: control_P1_2

value: not recombinated


title: Control lens epithelial cells 2


title: mutant_P1_2


title: Mouse BMDM_Control_biological replicate 1


title: IgG-treated 5XFAD biological replicate 1


title: control_P1_1


title: Mouse BMDM_Control_biological replicate 3


title: mutant_P1_1


title: KS5-S5

city: East Lansing

institute: Michigan State University

value: AB

value: 96 hpf

value: PFBS (16 uM)


title: D7_360min_1_TGFBneg: Day7 360min after-SDF1 donor1 TGFBneg

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

hyb_protocol: Standard Illumina protocol

scan_protocol: Arrays were scanned on a BeadArray reader

data_processing: Data were quantile normalised using Lumi for R.

source_name: Peripheral blood

growth_protocol:
b-cell isolation: Mononuclear cells were isolated by Lymphoprep (Axis Shield) density gradient centrifugation. Total B-cells were isolated by negative selection with the Memory B-cell Isolation Kit (Miltenyi).
culture conditions general: Cells were grown in 24 well plates in Iscove Modified Dulbecco Medium (IMDM) supplemented with Glutamax and 10% heat-inactivated fetal bovine serum (HIFBS, Invitrogen). This was supplementetd from Day 3 onwards with Hybridomax hybridoma growth supplement (11 µl/ml), Lipid Mixture 1, chemically defined and MEM Amino Acids solution (both at 1x).
culture conditions (day 0--3): B cells were cultured at 2.5 X 10^5/ml with IL-2 (20 U/ml), IL-21 (50 ng/ml), F(ab’)2 goat anti-human IgM & IgG (10 µg/ml) on γ-irradiated CD40L expressing L cells (6.25 X 104/well).
culture conditions (day 3--6): At day-3 cells were detached from the CD40L L-cell layer and reseeded at 1 X 10^5/ml in media supplemented with IL-2 (20 U/ml) and IL-21 (50 ng/ml).

extract_protocol: RNA was extracted with Trizol and amplified using Illumina® TotalPrepTM-96 RNA Amplification Kit

value: Peripheral blood

value: B cells

tag: culture-conditions

value: On day 6 cells were seeded at 1 X 10^6/ml in phenol red free media supplemented with 0.5% HIFBS, IL-6 (10 ng/ml) and IL-21 (10 ng/ml) for 20 hours. Sdf-1 (1ng/ml) was added and cells analysed at indicated times.

tag: gender

value: Male


title: D7_360min_2_TGFBpos: Day7 360min after-SDF1 donor2 TGFBpos

value: On day 6 cells were seeded at 1 X 10^6/ml in phenol red free media supplemented with 0.5% HIFBS, IL-6 (10 ng/ml), IL-21 (10 ng/ml) and TGFB3 (2.5ng/ml) for 20 hours. Sdf-1 (1ng/ml) was added and cells analysed at indicated times.

value: Female


title: D7_120min_3_TGFBpos: Day7 120min after-SDF1 donor3 TGFBpos


title: D7_360min_3_TGFBneg: Day7 360min after-SDF1 donor3 TGFBneg


title: D7_120min_2_TGFBpos: Day7 120min after-SDF1 donor2 TGFBpos


title: D7_0min_2_TGFBpos: Day7 0min after-SDF1 donor2 TGFBpos


title: D7_0min_3_TGFBpos: Day7 0min after-SDF1 donor3 TGFBpos


title: D7_120min_3_TGFBneg: Day7 120min after-SDF1 donor3 TGFBneg


title: D7_0min_3_TGFBneg: Day7 0min after-SDF1 donor3 TGFBneg


title: D7_0min_1_TGFBneg: Day7 0min after-SDF1 donor1 TGFBneg


title: D7_120min_1_TGFBpos: Day7 120min after-SDF1 donor1 TGFBpos


title: D7_0min_1_TGFBpos: Day7 0min after-SDF1 donor1 TGFBpos


title: D7_360min_1_TGFBpos: Day7 360min after-SDF1 donor1 TGFBpos


title: D13_4_C3: Day13 donor4 condition3

value: Condition 3:At day 6 cells were reseeded at 1 X 10^6/ml in media supplemented with IL-6 (10 ng/ml), IL-21 (50 ng/ml) and TGFB3 (2.5ng/ml) . Cells were re-fed at 3.5 day intervals and analysed at indicated times.


title: D7_360min_3_TGFBpos: Day7 360min after-SDF1 donor3 TGFBpos


title: D7_30min_3_TGFBpos: Day7 30min after-SDF1 donor3 TGFBpos


title: D7_120min_2_TGFBneg: Day7 120min after-SDF1 donor2 TGFBneg


title: D7_120min_1_TGFBneg: Day7 120min after-SDF1 donor1 TGFBneg


title: D7_30min_1_TGFBpos: Day7 30min after-SDF1 donor1 TGFBpos


title: D7_30min_2_TGFBneg: Day7 30min after-SDF1 donor2 TGFBneg


title: D13_3_C3: Day13 donor3 condition3


title: D13_2_C3: Day13 donor2 condition3


title: D7_30min_1_TGFBneg: Day7 30min after-SDF1 donor1 TGFBneg


title: KS6-S6


title: D7_360min_2_TGFBneg: Day7 360min after-SDF1 donor2 TGFBneg


title: D7_30min_2_TGFBpos: Day7 30min after-SDF1 donor2 TGFBpos


title: D13_1_C3: Day13 donor1 condition3


title: D7_30min_3_TGFBneg: Day7 30min after-SDF1 donor3 TGFBneg


title: D7_0min_2_TGFBneg: Day7 0min after-SDF1 donor2 TGFBneg


title: D20_4_C3: Day20 donor4 condition3


title: D6+12h_2_C3: Day6+12h donor2 condition3


title: D7_2_C3: Day7 donor2 condition3


title: D10_4_C3: Day10 donor4 condition3


title: D7_3_C3: Day7 donor3 condition3


title: D10_2_C3: Day10 donor2 condition3


title: D6+6h_1_C3: Day6+6h donor1 condition3


title: D6+3h_4_C3: Day6+3h donor4 condition3


title: D10_3_C3: Day10 donor3 condition3


title: D6+6h_2_C3: Day6+6h donor2 condition3


title: D8_4_C3: Day8 donor4 condition3


title: D8_1_C3: Day8 donor1 condition3


title: D7_1_C3: Day7 donor1 condition3


title: D8_3_C3: Day8 donor3 condition3


title: D6+12h_3_C3: Day6+12h donor3 condition3


title: D6+12h_1_C3: Day6+12h donor1 condition3


title: D20_3_C2: Day20 donor3 condition2

value: Condition 2:At day 6 cells were reseeded at 1 X 10^6/ml in media supplemented with IL-6 (10 ng/ml), IL-21 (50 ng/ml), IFN-α (100 U/ml) and TGFB3 (2.5ng/ml) . Cells were re-fed at 3.5 day intervals and analysed at indicated times.


title: D6+6h_4_C3: Day6+6h donor4 condition3


title: D20_4_C2: Day20 donor4 condition2


title: D6+1h_4_C3: Day6+1h donor4 condition3


title: D6+3h_2_C3: Day6+3h donor2 condition3


title: D6+1h_1_C3: Day6+1h donor1 condition3


title: D6+6h_3_C3: Day6+6h donor3 condition3


title: D6+3h_3_C3: Day6+3h donor3 condition3


title: D6+1h_2_C3: Day6+1h donor2 condition3


title: D6+1h_3_C3: Day6+1h donor3 condition3


title: D6+12h_4_C3: Day6+12h donor4 condition3


title: D7_4_C3: Day7 donor4 condition3


title: D6+3h_1_C3: Day6+3h donor1 condition3


title: D7_2_C2: Day7 donor2 condition2


title: D10_1_C2: Day10 donor1 condition2


title: D20_1_C2: Day20 donor1 condition2


title: D13_1_C2: Day13 donor1 condition2


title: D8_1_C2: Day8 donor1 condition2


title: D10_3_C2: Day10 donor3 condition2


title: D7_3_C2: Day7 donor3 condition2


title: D8_3_C2: Day8 donor3 condition2


title: D6+6h_4_C2: Day6+6h donor4 condition2


title: D7_4_C2: Day7 donor4 condition2


title: D13_4_C2: Day13 donor4 condition2


title: D6+3h_3_C2: Day6+3h donor3 condition2


title: D10_2_C2: Day10 donor2 condition2


title: D20_2_C2: Day20 donor2 condition2


title: D6+12h_1_C2: Day6+12h donor1 condition2


title: D13_2_C2: Day13 donor2 condition2


title: D6+12h_2_C2: Day6+12h donor2 condition2


title: D10_4_C2: Day10 donor4 condition2


title: D6+12h_4_C2: Day6+12h donor4 condition2


title: D8_2_C2: Day8 donor2 condition2


title: D6+3h_4_C2: Day6+3h donor4 condition2


title: D6+6h_2_C2: Day6+6h donor2 condition2


title: D6+12h_3_C2: Day6+12h donor3 condition2


title: D8_4_C2: Day8 donor4 condition2


title: D7_1_C2: Day7 donor1 condition2


title: D6+6h_3_C2: Day6+6h donor3 condition2


title: D13_3_C2: Day13 donor3 condition2


title: D8_2_C3: Day8 donor2 condition3


title: D6+6h_1_C2: Day6+6h donor1 condition2


title: D6+1h_3_C2: Day6+1h donor3 condition2


title: D6+3h_2_C2: Day6+3h donor2 condition2


title: D6+1h_2_C2: Day6+1h donor2 condition2


title: D20_1_C1: Day20 donor1 condition1

value: Condition 1:At day 6 cells were reseeded at 1 X 10^6/ml in media supplemented with IL-6 (10 ng/ml), IL-21 (50 ng/ml) and IFN-α (100 U/ml). Cells were re-fed at 3.5 day intervals and analysed at indicated times.


title: D6+3h_1_C2: Day6+3h donor1 condition2


title: D10_1_C3: Day10 donor1 condition3


title: D20_3_C1: Day20 donor3 condition1


title: D6+1h_1_C2: Day6+1h donor1 condition2


title: D13_3_C1: Day13 donor3 condition1


title: D8_4_C1: Day8 donor4 condition1


title: D20_2_C1: Day20 donor2 condition1


title: D13_1_C1: Day13 donor1 condition1


title: D10_3_C1: Day10 donor3 condition1


title: D20_4_C1: Day20 donor4 condition1


title: D8_3_C1: Day8 donor3 condition1


title: D7_3_C1: Day7 donor3 condition1


title: D8_1_C1: Day8 donor1 condition1


title: D7_4_C1: Day7 donor4 condition1


title: D10_1_C1: Day10 donor1 condition1


title: D10_4_C1: Day10 donor4 condition1


title: D7_2_C1: Day7 donor2 condition1


title: D6+12h_4_C1: Day6+12h donor4 condition1


title: D13_4_C1: Day13 donor4 condition1


title: D10_2_C1: Day10 donor2 condition1


title: D13_2_C1: Day13 donor2 condition1


title: D6+3h_4_C1: Day6+3h donor4 condition1


title: D8_2_C1: Day8 donor2 condition1


title: D6+3h_2_C1: Day6+3h donor2 condition1


title: D6+12h_2_C1: Day6+12h donor2 condition1


title: D6+12h_1_C1: Day6+12h donor1 condition1


title: D6+6h_3_C1: Day6+6h donor3 condition1


title: D7_1_C1: Day7 donor1 condition1


title: D6+6h_1_C1: Day6+6h donor1 condition1


title: D6+3h_1_C1: Day6+3h donor1 condition1


title: D6+6h_2_C1: Day6+6h donor2 condition1


title: D6+12h_3_C1: Day6+12h donor3 condition1


title: D6+3h_3_C1: Day6+3h donor3 condition1


title: D6+6h_4_C1: Day6+6h donor4 condition1


title: sgOlfr2_e2_CD8rep1_ATACseq

city: New York

first: Craig

last: Thompson

address: 411 East 67th Street RRL 469

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Fastq files were aligned to the mm9 genome with Bowtie2 on default settings.
The resulting Bam files were filtered for duplicates, mitrochondria, MAPQ<30, ENCODE blacklisted, and imperfectly aligned reads.
Peaks were called
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files were generated with bamCoverage tool on default settings.

source_name: CD8+CD4- T cells

growth_protocol: Naïve CD8+ T cells were isolated from spleen and lymph nodes of C57BL/6J mice by cell sorting (CD8+CD4-CD62L+CD44-CD25-) and cultured in T cell media (RPMI, 10% FBS, 4mM glutamine, 50uM BME, 20mM HEPES, 100U/mL human IL-2) for 7 days

extract_protocol:
T cells were sorted based on CD8 and CD4 expression after 5 additional days of culture.
Libraries were prepared as described in methods.

treatment_protocol: Immediately after sorting, T cells were electroporated with indicated sgRNAs and then activated in T cell media containing anti-CD3 and anti-CD28 (see methods for more details).

value: CD4+ T cells


title: sgDnmt3a_e19_rep2_ATACseq

source_name: CD8+CD4+ T cells

value: CD8+ T cells


title: shChaf1a.3118_CD8_ATACseq

extract_protocol:
T cells were sorted based on CD8 and CD4 expression after 5 additional days of culture following transduction with shRNA retroviruses.
Libraries were prepared as described in methods.

treatment_protocol: After 24hours of activation in T cell media containing anti-CD3 and anti-CD28, shRNA retroviral particles were added to cells for spin-infection.


title: sgOlfr2_e2_CD4rep2_ATACseq

source_name: CD4+CD8- T cells


title: D6+1h_4_C1: Day6+1h donor4 condition1


title: D6+1h_3_C1: Day6+1h donor3 condition1


title: D6+1h_2_C1: Day6+1h donor2 condition1


title: sgOlfr2_e2_CD4rep1_ATACseq


title: D6_3.1: Day6 donor3 biological replicate

value: At day-3 cells were detached from the CD40L L-cell layer and reseeded at 1 X 10^5/ml in media supplemented with IL-2 (20 U/ml) and IL-21 (50 ng/ml).


title: D6_2.1: Day6 donor2 biological replicate


title: D6_1.1: Day6 donor1 biological replicate


title: D6_4.1: Day6 donor4 biological replicate


title: sgDnmt3a_e19_rep1_ATACseq


title: D6_3: Day6 donor3


title: D6_4: Day6 donor4


title: D6+1h_4_C2: Day6+1h donor4 condition2


title: D6_2: Day6 donor2


title: shRenilla.713_CD4rep2_ATACseq


title: D6_1: Day6 donor1


title: shRenilla.713_CD4rep1_ATACseq


title: D3_4: Day3 donor4

value: B cells were cultured at 2.5 X 10^5/ml with IL-2 (20 U/ml), IL-21 (50 ng/ml), F(ab’)2 goat anti-human IgM & IgG (10 µg/ml) on γ-irradiated CD40L expressing L cells (6.25 X 104/well).


title: D3_1: Day3 donor1


title: shChaf1a.3118_CD8CD4_ATACseq


title: D3_3: Day3 donor3


title: D3_2: Day3 donor2


title: shDnmt1.4462_CD8CD4_ATACseq


title: shChaf1a.576_CD8CD4_ATACseq


title: shChaf1a.576_CD8_ATACseq


title: sgOlfr2_e2_CD8rep2_ATACseq


title: shDnmt1.4462_CD8_ATACseq


title: P218_P9

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

data_processing:
Individual Fastq files were aligned to the mouse Genome (Gencode M11 / GRCm38) using the STAR aligner version 2.5.2b with parameters STAR --runThreadN <cpu> --genomeDir <index> --genomeLoad LoadAndKeep --limitBAMsortRAM 20000000000 --readFilesIn <fastq> --readFilesCommand zcat --outFileNamePrefix <sampleID> --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate
Gene counts were obtained from BAM files using featureCounts v1.6.2 with parameters -a <Gencode_vM11.gtf> -G <GRCm38.primary_assembly.genome.fa> -o counts.txt -F GTF -R -g gene_id -t exon -T 10 –largestOverlap <bamfiles>
single cell RNAseq analysis and clustering was performed using RaceId/StemId2 (Grün, D., L. Kester, and A. van Oudenaarden. 2014. “Validation of noise models for single-cell transcriptomics.” Nat. Methods 11 (6): 637–40.). Cells with less than 500 detected genes, less than 5000 aligned reads or more than 700 000 aligned reads were discarded. Only genes with a count of 5 in at least a single cell were used for analysis.
Genome_build: Gencode M11 / GRCm38
Supplementary_files_format_and_content: comma separated (csv) file with gene counts per sample

extract_protocol:
After transcardial perfusion with PBS, brains were roughly minced and homogenized with a potter in HBSS containing 15 mM HEPES buffer and 0.54 % Glucose. Whole-brain homogenate was separated by 70/37/30 % layered Percoll gradient centrifugation at 800 g for 30 min at 4 °C (no brake). The CNS macrophages containing interphase was then collected and washed once with PBS containing 2% FCS and 10mM EDTA before staining. Cells were stained with primary antibodies directed against CD11b (M1/70, BioLegend), CD45 (30-F11, BD Biosciences), Ly6C (AL-21, BD Biosciences) and Ly6G (1A8, BD Biosciences) for 20 min, and CD206 (C068C2, BioLegend) for 45 min at 4 °C. After washing, cells were analyd using a MoFlo Astrios (Beckman Coulter). microglia were FACS-sorted from six different CNS regions of healthy and diseased brains (see gating strategy shown in supplementary Fig.2) into a 384-well plate containing a lysis buffer.
Single cell RNAseq libraries were generated following the published SmartSeq2 protocol (Picelli et al. Nature Metods 2013)

value: cerebellum


title: shDnmt1.1137_CD8CD4_ATACseq


title: shRenilla.713_CD8rep2_ATACseq


title: shRenilla.713_CD8rep1_ATACseq


title: P218_P3


title: P218_P23


title: P218_P8


title: P218_P7


title: P218_P20


title: P218_P4


title: P218_P18


title: P218_P5


title: P218_P24

source_name: blank

value: blank


title: P218_P16


title: D6+1h_1_C1: Day6+1h donor1 condition1


title: P218_P6


title: P218_P15


title: P218_P11


title: P218_P22


title: P218_P17


title: P218_P1


title: P218_P10


title: P218_P13


title: shDnmt1.1137_CD8_ATACseq


title: P218_P2


title: P218_P12


title: P218_O9


title: P218_P19


title: P218_P21


title: P218_O8


title: P218_O4


title: P218_O6


title: P218_O7


title: P218_O5


title: P218_O3


title: P218_O24


title: P218_O22


title: P218_O23


title: P218_O20


title: P218_O2


title: P218_O18


title: P218_O17


title: P218_P14


title: P218_O15


title: P218_O14


title: P218_O21


title: P218_O11


title: P218_O12


title: P218_O13


title: P218_O19


title: P218_N6


title: P218_N7


title: P218_O1


title: P218_O10


title: P218_N8


title: P218_N5


title: P218_N4


title: P218_N3


title: P218_N9


title: P218_O16


title: P218_N20


title: P218_N21


title: P218_N22


title: P218_N24


title: P218_N23


title: P218_N2


title: P218_N13


title: P218_N16


title: P218_N14


title: P218_N10


title: P218_N11


title: P218_N18


title: P218_N15


title: P218_M24


title: P218_M5


title: P218_N1


title: P218_M6


title: P218_M22


title: P218_M16


title: P218_M23


title: P218_M19


title: P218_N12


title: P218_M15


title: P218_M9


title: P218_M18


title: P218_M7


title: P218_M21


title: P218_N19


title: P218_M14


title: P218_M20


title: P218_M17


title: P218_M12


title: P218_M11


title: P218_N17


title: P218_M10


title: P218_M1


title: P218_M8


title: P218_L9


title: P218_M2


title: P218_M3


title: P218_M13


title: P218_L8


title: P218_L6


title: P218_L7


title: P218_L4


title: P218_L24


title: P218_L3


title: P218_L21


title: P218_L22


title: P218_L23


title: P218_L2


title: P218_L19


title: P218_L16


title: P218_L15


title: P218_L17


title: P218_L14


title: P218_L10


title: P218_L12


title: P218_L11


title: P218_L13


title: P218_L5


title: P218_K8


title: P218_K7


title: P218_K6


title: P218_K24


title: P218_K5


title: P218_L18


title: P218_K4


title: P218_K23


title: P218_K21


title: P218_K20


title: P218_K17


title: P218_K16


title: P218_K22


title: P218_K2


title: P218_K18


title: P218_K14


title: P218_K15


title: P218_K13


title: P218_K9


title: P218_L1


title: P218_K11


title: P218_K10


title: P218_K12


title: P218_K1


title: P218_J8


title: P218_K3


title: P218_J6


title: P218_J5


title: P218_K19


title: P218_J4


title: P218_L20


title: P218_J24


title: P218_J3


title: P218_J23


title: P218_J22


title: P218_J20


title: P218_J16


title: P218_J18


title: P218_J19


title: P218_J14


title: P218_J13


title: P218_J11


title: P218_J9


title: P218_J7


title: P218_J17


title: P218_J10


title: P218_J12


title: P218_J1


title: P218_I7


title: P218_I9


title: P218_I8


title: P218_I6


title: P218_I5


title: P218_I24


title: P218_I4


title: P218_I3


title: P218_J2


title: P218_J21


title: P218_I23


title: P218_J15


title: P218_I22


title: P218_I20


title: P218_I18


title: P218_I2


title: P218_I21


title: P218_I16


title: P218_I17


title: P218_M4


title: P218_I19


title: P218_I15


title: P218_I1


title: P218_H9


title: P218_I12


title: P218_I11


title: P218_H7


title: P218_I13


title: P218_H5


title: P218_H4


title: P218_H23


title: P218_H21


title: P218_H24


title: P218_H20


title: P218_H22


title: P218_H18


title: P218_H17


title: P218_H16


title: P218_H14


title: P218_I14


title: P218_H11


title: P218_H13


title: P218_I10


title: P218_H1


title: P218_H6


title: P218_H15


title: P218_H10


title: P218_H19


title: P218_G7


title: P218_H8


title: P218_G9


title: P218_G6


title: P218_H3


title: P218_G5


title: P218_H2


title: P218_G4


title: P218_G24


title: P218_G3


title: P218_G21


title: P218_G23


title: P218_G8


title: P218_G20


title: P218_G22


title: P218_G2


title: P218_H12


title: P218_G19


title: P218_G18


title: P218_G14


title: P218_G13


title: P218_G15


title: P218_G16


title: P218_G10


title: P218_G12


title: P218_G11


title: P218_F5


title: P218_F9


title: P218_F6


title: P218_F4


title: P218_F7


title: P218_F3


title: P218_F8


title: P218_F2


title: P218_F19


title: P218_F24


title: P218_F16


title: P218_F23


title: P218_F22


title: P218_F21


title: P218_F17


title: P218_F18


title: P218_G17


title: P218_G1


title: P218_F12


title: P218_F11


title: P218_F10


title: P218_E8


title: P218_E9


title: P218_E4


title: P218_E6


title: P218_F20


title: P218_E3


title: P218_E7


title: P218_F1


title: P218_E24


title: P218_E21


title: P218_E5


title: P218_E23


title: P218_E22


title: P218_F14


title: P218_E19


title: P218_E14


title: P218_E2


title: P218_E18


title: P218_E13


title: P218_F13


title: P218_E15


title: P218_E17


title: P218_E16


title: P218_E10


title: P218_E12


title: P218_E11


title: P218_D7


title: P218_D8


title: P218_D6


title: P218_D5


title: P218_D4


title: P218_D3


title: P218_D23


title: P218_D21


title: P218_D22


title: P218_E20


title: P218_D2


title: P218_D20


title: P218_D24


title: P218_D18


title: P218_D19


title: P218_E1


title: P218_D14


title: P218_D15


title: P218_D9


title: P218_D16


title: P218_D12


title: P218_D1


title: P218_D13


title: P218_D10


title: P218_D11


title: P218_C8


title: P218_C9


title: P218_C7


title: P218_C5


title: P218_C6


title: P218_C23


title: P218_C24


title: P218_C3


title: P218_C22


title: P218_C18


title: P218_C2


title: P218_C20


title: P218_C19


title: P218_C21


title: P218_C17


title: P218_C15


title: P218_F15


title: P218_C11


title: P218_C12


title: P218_C10


title: P218_C1


title: P218_C13


title: P218_B8


title: P218_C14


title: P218_C4


title: P218_B9


title: P218_D17


title: P218_B7


title: P218_C16


title: P218_B6


title: P218_B5


title: P218_B22


title: P218_B3


title: P218_B24


title: P218_B23


title: P218_B20


title: P218_B21


title: P218_B2


title: P218_B15


title: P218_B17


title: P218_B18


title: P218_B19


title: P218_B14


title: P218_B16


title: P218_B10


title: P218_B12


title: P218_A9


title: P218_A7


title: P218_A8


title: P218_A6


title: P218_B1


title: P218_A3


title: P218_A5


title: P218_B4


title: P218_A23


title: P218_B13


title: P218_A22


title: P218_A20


title: P218_B11


title: P218_A21


title: P218_A2


title: P218_A19


title: P218_A16


title: P218_A18


title: P218_A24


title: P218_A4


title: P218_A15


title: P218_A13


title: P218_A10


title: P218_A12


title: P218_A1


title: P218_A14


title: P217_P7

value: hippocampus


title: P217_P4


title: P217_P6


title: P217_P8


title: P217_P24


title: P217_P5


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