title: KO3_atria

value: atria


title: AU_iTBS_PCTX3

status: Public on May 30 2023

type: RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

molecule: total RNA

organism: Rattus norvegicus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: Male Long–Evans rats (Charles River Laboratories) were individually housed and maintained under specific pathogen-free conditions on a 12-h light/dark cycle at the National Institute on Aging/National Institute on Drug Abuse (NIA/NIDA) animal facilities in the Biomedical Research Center (Baltimore, MD). Standard rat chow and water were available ad libitum throughout the experiments.Baseline cognitive status of the animals was obtained  for individiual rats in a 'place' version of the Morris water maze task as previously described24. Training continued over 8 consecutive days, three training trials per day. Every other day, the third trial was a probe in which the platform was inaccessible for 30 seconds. A learning index score was calculated for each animal from their average proximity to the escape platform during training; lower scores indicate better task performance. Aged rats that performed on par with young animals were denoted aged unimpaired (AU), while rats that scored greater than the young were classified as aged impaired (AI)25. To control for non-mnemonic deficits, rats were tested in a single session of a hippocampus-independent cued water maze protocol the following day. No animals that performed outside the normal range on this version of the task were included in the present experiments.

extract_protocol: RNA was extracted using Qiagen RNeasy Mini kits (#74104). Brain tissues were homogenized using a Precellys 24 Tissue homogenizer (Bertin Instruments, Rockville, MD) at 5500-6000rpm for 30 seconds, using 1 mL cold RLT buffer and glass beads. Homogenates were centrifuged at 12,000 rpm for 4 mins at 4°C to pellet any unhomogenized  tissue and beads, and RNA  isolated according to the manufacturer's instructions. RNA concentration and quality was assayed on an RNA6000 Bioanalyzer chip (Agilent).

treatment_protocol: Prior to rTMS administration,  aged (26-27 months, 714-1150 g) and young male rats (6-7 months, 502-788 g) were lightly anesthetized with isoflurane to reduce restraint stress and head movement during the stimulation procedure. The rats then received an intra-muscular injection of Dexmedetomidine (aged: 0.03 mg kg-1 body weight; young: 0.035 mg kg-1 body weight, the minimum required to prevent movement throughout the stimulation period). Antisedan (aged: 0.03 mg kg-1 body weight; young: 0.035 mg kg-1 body weight) was given after stimulation to reverse the sedation.  Physiological parameters (heart rate, arterial blood oxygen saturation, body temperature) were monitored during anesthesia (Starr Life Sciences MouseOx Plus, Starr Life Sciences Corp. Oakmont, PA, USA) to ensure light and consistent anesthetic depth throughout stimulation. Rats were positioned on a heating pad and body temperature was maintained within 2˚C of the initial measurement.  Rats received either iTBS or sham stimulation: the coil was centered 8 mm above the rat’s skull, oriented with the handle to the left of the rat to produce a mediolaterally oriented electric field, aimed towards maximally stimulating the axons of the corpus callosum. The rat’s head was elevated with a small plastic conical ramp to ensure the skull was roughly parallel with the coil base and to minimize head movement and off-target body stimulation. Stimulator output intensity was adjusted to just below the level that elicited muscle twitching in the neck and head [aged: 15.0 ± 0.9% (11-17%); young: 15.3 ± 1.4% (12-19%) of maximal stimulator output], consistent with earlier preclinical studies in rats. rTMS was applied using a Magstim Rapid¬¬¬2 stimulator with a 70-mm figure-eight coil (The Magstim Company, Whitland, Dyfed, UK). 1 Hz stimulation was applied in 5 blocks of 600 pulses lasting 10 minutes repeated at 15-minute intervals for a total of 3000 pulses in 70 minutes. iTBS was administered in 5 blocks repeated every fifteen minutes with each block consisting of 20 trains of 3 50-Hz pulse bursts repeated at 5 Hz for 2 seconds with a 10-second inter-train interval as described elsewhere30. Each iTBS block consisted of 600 pulses in 192 seconds for a total of 3000 pulses delivered in 63.2 minutes. Sham stimulation was performed with the coil 20 cm away from the rats’ heads. Forty-eight hours later animals were deeply anesthetized with 5% isoflurane and sacrificed, and the neocortex and dorsal hippocampus under the center of the TMS coil during stimulation were freshly microdissected and immediately frozen for storage at -80˚ C.

tag: tissue

value: Brain

tag: tissue region

value: Parietal cortex

tag: strain

value: Long-Evans

tag: age

value: Aged

value: 26-27 months

tag: Sex

value: Male

tag: cognitive status

value: unimpaired

tag: tms

value: AU

tag: post-treatment (hrs)


title: 4T2_DD_Liver

type: SRA

city: Irvine

first: Muntaha

middle: Fatima

last: Samad

state: CA

address: Campus Dr

department: CS

institute: UC Irvine

library_source: transcriptomic

data_processing:
Trimming performed using trimmomatic
alignment to reference assembly mm10 using Tuxedo Tophat
Read counting for each gene to FPKM values performed using Tuxedo cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: FPKM value for each gene

organism: Mus musculus

source_name: Liver

extract_protocol:
TRIZOL RNA extraction
Truseq mRNA stranded kit

tag: timepoint

tag: light condition

value: DD

tag: diet

value: Tryptophan depleted


title: WT_untreat_Abl_RCbait_Rep2

city: Boston

first: Frederick

last: Alt

state: MA

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital / Harvard Medical School

description: aligned to mm9

library_source: genomic

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203)
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
The junctions from Chr12 were extracted and counted for normalization. All 3C-libraires were normalized to the smallest libraries from the same batch of experiments.
Assembly: mm9 or AJ851868/mm9
Supplementary files format and content: bedgraph files were generated for displaying (Jane et al., 2018, PMC6026039)
Library strategy: 3C-HTGTS-Seq

molecule: genomic DNA

source_name: v-Abl pro B cells

growth_protocol:
v-Abl pro-B cells were cultured at 37 °C and 5% CO2 in RPMI supplemented with 15% (vol/vol) FCS, 50 U/mL penicillin/streptomycin (ThermoFisher), 2 mM L-glutamine (ThermoFisher), 1× MEM-NEAA (ThermoFisher), 1 mM sodium pyruvate (ThermoFisher), 50 μM 2-mercap- toethanol (Sigma), and 20 mM Hepes (pH 7.4)
Bone marrow pro-B cells were cultured with Opti-MEM; 10% (v/v) FBS plus 10 ng/mL IL-7 and 2 ng/mL SCF for 4-5 days

extract_protocol:
About 10 million cells were crosslinked with 2% formaldehyde for 10 minutes at room temperature and quenched with glycine at a final concentration of 125 mM. Then, the crosslinked cells were lysed in the 3C lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, protease inhibitors) and nuclei were digested with NlaIII enzyme (NEB, R0125) at 37 ℃ overnight.  They were then brought to 16℃, 100U of T4 ligase added  (Promega, M1801) and they incubated again overnight at 16℃.  The ligated products were de-crosslinked with Proteinase K (Roche, #03115852001) at 56 ℃ overnight and the 3C templates were purified by phenol/chloroform.
Libraries were prepared using 3C samples by HTGTS (Jane et al., 2018, PMC6026039).

treatment_protocol:
G1-arrested Abl cells were treated with STI-571 (3µM) for 96h. 150 μM IAA with 2 µg/mL Dox treatment was added to some of the samples.
Bone marrow pro-B cells were purified via anti-B220 MicroBeads (Miltenyi, #130-049-501)

tag: cell type

value: v-Abl pro B cells

tag: genotype

value: RAG1-/-, Emu-Bcl2, WAPL degron, single Igh

tag: purification

value: 3 uM STI-571 treated for 4 days

tag: treatment


title: 4T1_DD_Liver


title: WT3_atria

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Sequencing data were demultiplexed using bcl2fastq2 v.2.2 and aligned to mouse reference genome (mm10).
Alignment and quantification with STAR v.2.5.1 using the default parameters
Normalization using DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: normalized txt files

extract_protocol:
The samples were frozen in liquid nitrogen (-80° C) and extracted using a RNeasy Micro kit (Qiagen).
The cDNA library was generated according to the SMART-Seq2 protocol.

value: wild-type

tag: pupid

tag: prepdate

tag: litter


title: AU_iTBS_PCTX2

tag: tissue

tag: tissue region


title: CBE1inv_Abl_Vh81xbait_C2_Rep6

description: aligned to AJ851868/mm9

tag: strain

value: RAG2-/-, CBE1inv/inv


title: AU_iTBS_PCTX1

tag: age

tag: Sex


title: AU_Sham_PCTX3

tag: cognitive status

tag: tms


title: WT2_atria


title: AU_Sham_PCTX4

tag: post-treatment (hrs)


title: AU_Sham_PCTX2


title: KO2_atria

value: MyHC-Creld1 KO


title: WT2_vent

value: ventricles


title: WT1_vent


title: CBE1inv_Abl_Vh81xbait_C2_Rep5

description: aligned to AJ851868/mm9


title: 4T3_DD_Liver

tag: timepoint

tag: light condition


title: 0T2_DD_Liver

tag: diet


title: CBE2mut_Abl_Vh81xbait_C2_Rep5

description: aligned to AJ851868/mm9

tag: cell type

tag: genotype


title: 0T1_DD_Liver


title: KO1_atria

value: atria


title: WT1_atria


title: 20C3_DD_Liver

value: Control


title: AU_Sham_PCTX1

value: Brain

value: Parietal cortex

value: Long-Evans


title: Y_iTBS_PCTX3

value: Young

value: 6-7 months

value: Male

value: Y


title: AU_iTBS_PCTX4

value: Aged

value: 26-27 months

value: unimpaired

value: AU


title: 0T3_DD_Liver

value: DD

value: Tryptophan depleted


title: Y_iTBS_PCTX4


title: CBE12mut_Abl_Vh81xbait_C2_Rep5

description: aligned to AJ851868/mm9

value: v-Abl pro B cells

tag: treatment


title: CBE12mut_Abl_Vh81xbait_C2_Rep6

description: aligned to AJ851868/mm9


title: 16C3_DD_Liver


title: WT_Abl_Vh81xbait_C2_Rep5

description: aligned to AJ851868/mm9


title: WT_Abl_Vh81xbait_C2_Rep6

description: aligned to AJ851868/mm9


title: KO2_E13

value: whole heart

value: MyHC-Creld1 KO

tag: pupid


title: CBE2inv_Abl_RCbait_C2_Rep6

description: aligned to AJ851868/mm9

value: RAG2-/-, CBE2inv/inv


title: Y_iTBS_PCTX2

value: Brain


title: Y_Sham_PCTX3

value: Parietal cortex


title: WT2_E13

value: wild-type

tag: prepdate


title: CBE2inv_Abl_RCbait_C2_Rep5

description: aligned to AJ851868/mm9


title: CBE1mut_Abl_Vh81xbait_C2_Rep6

description: aligned to AJ851868/mm9


title: KO1_E13

tag: litter


title: KO4_E13

tag: tissue


title: CBE1mut_Abl_Vh81xbait_C2_Rep5

description: aligned to AJ851868/mm9


title: CBE2mut_Abl_Vh81xbait_C2_Rep6

description: aligned to AJ851868/mm9


title: WT4_E13


title: WT3_E13


title: KO3_E13


title: 20C1_DD_Liver

value: Control


title: 16C1_DD_Liver


title: 16C2_DD_Liver


title: 12C3_DD_Liver


title: 20C2_DD_Liver


title: WT1_E13


title: 12C1_DD_Liver


title: CBE1inv_Abl_RCbait_C2_Rep5

description: aligned to AJ851868/mm9

value: RAG2-/-, CBE1inv/inv


title: 12C2_DD_Liver


title: Y_Sham_PCTX1

tag: tissue region

value: Long-Evans

value: Young

value: 6-7 months

value: Male


title: AI_iTBS_HIPP2

value: Hippocampus

tag: strain

value: Aged

value: 26-27 months

value: impaired

value: AI


title: 8C3_DD_Liver

value: DD


title: AI_iTBS_HIPP3

tag: age


title: CBE1inv_Abl_RCbait_C2_Rep6

description: aligned to AJ851868/mm9

value: v-Abl pro B cells


title: CBE2mut_Abl_RCbait_C2_Rep6

description: aligned to AJ851868/mm9


title: Y_iTBS_PCTX1

tag: Sex

value: unimpaired

value: Y


title: Y_Sham_PCTX2

value: Brain

value: Parietal cortex

tag: cognitive status


title: 8C2_DD_Liver

value: Control


title: CBE2mut_Abl_RCbait_C2_Rep5

description: aligned to AJ851868/mm9


title: Y_Sham_PCTX4

tag: tms


title: 8C1_DD_Liver


title: 4C3_DD_Liver


title: surface_d9_wt3

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

description: IECs from middle/distal colon regions (pooled from 2-4 mice per sample) were isolated with DTT, followed by EDTA, and then sorted into three populations (All were CD45-LD-EpCAM1+): CEACAM1Hi Surface, CEACAM1Int/lo SSCHi Large Crypt, and CEACAM1- FSClo SSClo Small Crypt cells

data_processing:
The raw reads were trimmed of the adaptors and aberrant reads were removed by TrimGalore (version 0.4.5). The quality controlled reads were mapped onto the mouse genome build GRCm38 using STAR (version2.5.3) (Dobin et al.2013). BAM files were sorted using SAMtools (version 0.1.18) (Li et al., 2009), and reads were counted for each gene using HTSeq (version 0.7.2) (Anders et al., 2015)
Differential expression analysis was performed using DESeq2 (version 1.18.1) (Love et al., 2014) using R (version 3.4.3).
Genome_build: GRCm38-mm10
Supplementary_files_format_and_content: tab-delimited text files include htseq count values for each sample

source_name: EpCAM1+ CEACAM1hi CD45- L/D dye- FSChi SSChi

growth_protocol: All mouse strains were bred and maintained at UAB in accordance with IACUC guidelines.

extract_protocol:
IECs were directly sorted into Qiazol LS and RNA was isolated the SAME DAY with chloroform extract followed by Qiagen miRNAeasy kit
Nugen Universal Plus mRNA-seq

treatment_protocol: Citrobacter rodentium i.g. 2 x 10^9

value: Surface IEC

tag: time

value: IL22 fl/fl CD4-Cre -


title: surface_naive_wt2

value: Naïve


title: surface_d9_wt1


title: surface_d9_wt2


title: CBE1mut_Abl_RCbait_C2_Rep6

description: aligned to AJ851868/mm9


title: CBE1mut_Abl_RCbait_C2_Rep5

description: aligned to AJ851868/mm9


title: AI_Sham_HIPP4

value: Long-Evans

tag: post-treatment (hrs)


title: AI_iTBS_HIPP1

value: Male


title: 4C2_DD_Liver

tag: timepoint

tag: light condition


title: surface_d9_wt4


title: Smcrypt_naive_wt1

source_name: EpCAM1+ CEACAMlo CD45- L/D dye- FSClo SSClo

value: Small Crypt IEC


title: CBE12mut_Abl_RCbait_C2_Rep6

description: aligned to AJ851868/mm9

tag: cell type


title: CBE12mut_Abl_RCbait_C2_Rep5

description: aligned to AJ851868/mm9

tag: genotype


title: WT_Abl_RCbait_C2_Rep6

description: aligned to AJ851868/mm9

tag: treatment


title: Smcrypt_d9_wt3


title: AI_Sham_HIPP2

value: Hippocampus

value: Aged


title: AU_iTBS_HIPP5

value: 26-27 months

value: AU


title: 0C2_DD_Liver

value: DD

tag: diet


title: 0C3_DD_Liver


title: Smcrypt_d9_wt4


title: Smcrypt_d9_wt2


title: WT_Abl_RCbait_C2_Rep5

description: aligned to AJ851868/mm9

value: v-Abl pro B cells


title: AI_Sham_HIPP1

value: impaired

value: AI


title: AI_Sham_HIPP3

value: Brain


title: AU_iTBS_HIPP4

value: unimpaired


title: AU_iTBS_HIPP3


title: AU_iTBS_HIPP1


title: 0C1_DD_Liver

value: Control


title: Smcrypt_d9_wt1


title: 20T3_LD_Liver

value: LD

value: Tryptophan depleted


title: Lgcrypt_naive_wt2

source_name: EpCAM1+ CEACAM1int CD45- L/D dye- FSChi SSCint

value: Large Crypt IEC

value: Naïve

value: IL22 fl/fl CD4-Cre -


title: CBE12mut_BM_RCbait_Rep1

description: aligned to AJ851868/mm9

source_name: Primary BM pro-B cells

value: Primary BM pro-B cells

tag: purification

value: Purified via anti-B220 MicroBeads (Miltenyi, #130-049-501)

value: Opti-MEM; 10% (v/v) FBS plus 10 ng/mL IL-7 and 2 ng/mL SCF for 4-5 days


title: 20T2_LD_Liver


title: Lgcrypt_naive_wt1


title: 16T2_LD_Liver


title: 4C1_DD_Liver


title: WT_BM_RCbait_Rep1

description: aligned to AJ851868/mm9


title: WT_BM_RCbait_Rep2

description: aligned to AJ851868/mm9


title: Lgcrypt_d9_wt3


title: 16T1_LD_Liver


title: Lgcrypt_d9_wt2


title: 12T3_LD_Liver


title: 3CBEdel_DoxIAA_Abl_Rep3

description: aligned to mm9

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203)
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Assembly: mm9 or AJ851868/mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)
Library strategy: HTGTS-VDJ-Seq

growth_protocol: v-Abl pro-B cells were cultured at 37 °C and 5% CO2 in RPMI supplemented with 15% (vol/vol) FCS, 50 U/mL penicillin/streptomycin (ThermoFisher), 2 mM L-glutamine (ThermoFisher), 1× MEM-NEAA (ThermoFisher), 1 mM sodium pyruvate (ThermoFisher), 50 μM 2-mercap- toethanol (Sigma), and 20 mM Hepes (pH 7.4)

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina Miseq or Nextseq sequencing

treatment_protocol: G1-arrested cells were treated with STI-571 (3µM) for 96h. 150 μM IAA with 2 µg/mL Dox treatment was added to some of the samples.

value: RAG1-/-, Emu-Bcl2, WAPL degron, single Igh, 3IghCBEs deletion

value: RAG1/2 retrovirus infected, 3 uM STI 1 day, then 150 μM IAA, 3 uM STI-571 with 2 µg/mL Dox treated for 3 days


title: Lgcrypt_d9_wt1


title: 3CBEdel_DoxIAA_Abl_Rep2

description: aligned to mm9


title: surface_naive_cKO2

value: Surface IEC

value: IL22 fl/fl CD4-Cre +


title: 12T2_LD_Liver


title: 3CBEdel_DoxIAA_Abl_Rep1

description: aligned to mm9

value: v-Abl pro B cells


title: surface_naive_cKO1


title: AU_Sham_HIPP4

value: Hippocampus

value: Long-Evans

value: Aged

value: 26-27 months

value: Male

value: AU


title: 12T1_LD_Liver

value: LD

value: Tryptophan depleted


title: 3CBEdel_untreat_Abl_Rep3

description: aligned to mm9

value: RAG1/2 retrovirus infected, 3 uM STI-571 treated for 4 days


title: surface_d9_cKO4


title: 20T1_LD_Liver


title: 8T3_LD_Liver


title: AU_iTBS_HIPP2

value: Brain

value: unimpaired


title: WT_BM_RCbait_Rep3

description: aligned to AJ851868/mm9

value: Primary BM pro-B cells

value: Purified via anti-B220 MicroBeads (Miltenyi, #130-049-501)

value: Opti-MEM; 10% (v/v) FBS plus 10 ng/mL IL-7 and 2 ng/mL SCF for 4-5 days


title: Lgcrypt_d9_wt4

value: Large Crypt IEC

value: IL22 fl/fl CD4-Cre -


title: AU_Sham_HIPP2


title: 16T3_LD_Liver


title: 3CBEdel_untreat_Abl_Rep2

description: aligned to mm9

value: v-Abl pro B cells

value: RAG1-/-, Emu-Bcl2, WAPL degron, single Igh, 3IghCBEs deletion


title: Y_iTBS_HIPP4

value: Hippocampus

value: Long-Evans

value: Young

value: 6-7 months

value: Y


title: surface_d9_cKO3

value: Surface IEC

value: IL22 fl/fl CD4-Cre +


title: 8T2_LD_Liver

value: LD

value: Tryptophan depleted


title: AU_Sham_HIPP1

value: Brain

value: Aged

value: 26-27 months

value: Male

value: unimpaired

value: AU


title: WT_DoxIAA_Abl_Rep3

description: aligned to mm9

value: v-Abl pro B cells

value: RAG1-/-, Emu-Bcl2, WAPL degron, single Igh

value: RAG1/2 retrovirus infected, 3 uM STI 1 day, then 150 μM IAA, 3 uM STI-571 with 2 µg/mL Dox treated for 3 days


title: Y_iTBS_HIPP3

value: Hippocampus

value: Long-Evans


title: Y_iTBS_HIPP1

value: Young

value: 6-7 months


title: Y_Sham_HIPP4

value: Y


title: CBE12mut_BM_RCbait_Rep2

description: aligned to AJ851868/mm9

value: Primary BM pro-B cells

value: Purified via anti-B220 MicroBeads (Miltenyi, #130-049-501)

value: Opti-MEM; 10% (v/v) FBS plus 10 ng/mL IL-7 and 2 ng/mL SCF for 4-5 days


title: Y_iTBS_HIPP2

value: Brain


title: AU_Sham_HIPP3

value: Aged


title: Y_Sham_HIPP3


title: 4T2_LD_Liver

value: LD

value: Tryptophan depleted


title: Smcrypt_d9_cKO4

value: Small Crypt IEC

value: IL22 fl/fl CD4-Cre +


title: AI_iTBS_4

treatment_protocol: Four young (5-6 months), four age-unimpaired (AU, 24-25 months)), and four age-impaired (AI, 24-25 months) male Long-Evans rats were sacrificed. Under RNase-free conditions, brains were removed, and the hippocampi were isolated and placed in cold, artificial cerebrospinal fluid (aCSF; 120 mM NaCl, 2.5 mM KCl, 1 mM NaH¬2PO4, 26 mM NaHCO¬3, 1.3 mM MgSO4, 10 mM D-Glucose, 3.3 mM CaCl2) saturated with 100% O2.  Each hippocampus was then quickly cut into approximately 7 to 9, 1mm-thick slabs using a McIlwain tissue chopper (Pt#: MTC/2E; The Mickle Laboratory Engineering Co.), yielding approximately 15-18 hippocampal slices for each brain. Serial slices were distributed equally into 3 separate dishes (1 Hz, iTBS, sham) and incubated in fresh aCSF for 1 hour at 32˚C before administering rTMS. Hippocampal slices from young, AU, and AI rats were arranged 1 cm under the center of the coil and received either 1 Hz, iTBS, or sham stimulation, with the stimulation intensity set to 15% of the machine’s maximum output. Sham stimulation was applied to hippocampal slices arranged 20 cm from the coil. Hippocampal slices from one given animal were equally distributed across conditions (1 Hz, iTBS, and sham) and rested in aCSF for two hours before RNA collection.

value: hippocampal slice

tag: age (group)

value: AI

tag: age (months)

value: 25-26 months

value: Male

value: iTBS


title: 3CBEdel_untreat_Abl_Rep1

description: aligned to mm9

value: v-Abl pro B cells

value: RAG1-/-, Emu-Bcl2, WAPL degron, single Igh, 3IghCBEs deletion

value: RAG1/2 retrovirus infected, 3 uM STI-571 treated for 4 days


title: CBE12mut_BM_RCbait_Rep3

description: aligned to AJ851868/mm9

value: Primary BM pro-B cells


title: Y_Sham_HIPP1

tag: tissue

tag: tissue region

value: Hippocampus

value: Long-Evans

value: Young

value: 6-7 months

value: unimpaired

value: Y


title: surface_d9_cKO1

tag: strain

value: Surface IEC


title: 4T3_LD_Liver

value: LD

value: Tryptophan depleted


title: WT_DoxIAA_Abl_Rep2

description: aligned to mm9

value: RAG1-/-, Emu-Bcl2, WAPL degron, single Igh

value: RAG1/2 retrovirus infected, 3 uM STI 1 day, then 150 μM IAA, 3 uM STI-571 with 2 µg/mL Dox treated for 3 days


title: 8T1_LD_Liver


title: WT_untreat_Abl_Rep2

description: aligned to mm9


title: Smcrypt_naive_cKO1

value: Small Crypt IEC

value: Naïve

value: IL22 fl/fl CD4-Cre +


title: Smcrypt_d9_cKO2


title: surface_d9_cKO2


title: WT_untreat_Abl_Rep3

description: aligned to mm9

value: v-Abl pro B cells


title: WT_DoxIAA_Abl_Rep1

description: aligned to mm9


title: Smcrypt_d9_cKO1


title: 0T3_LD_Liver


title: Smcrypt_d9_cKO3


title: WT_BM_Rep3

description: aligned to AJ851868/mm9

data_processing:
Reads were aligned using bowtie2 with --non-deterministic flag
wig files were generated using USCS utilities bedGraphToBigWig
Assembly: AJ851868/mm9
Supplementary files format and content: bigwig files were generated for displaying
Library strategy: GRO-Seq

growth_protocol: Bone marrow pro-B cells were cultured with Opti-MEM; 10% (v/v) FBS plus 10 ng/mL IL-7 and 2 ng/mL SCF for 4-5 days

extract_protocol:
Briefly, 10 million cells were collected and permeabilized with the buffer (10 mM Tris-HCl pH 7.4, 300 mM sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40 substitute, 0.5 mM DTT, protease inhibitors and Rnase inhibitor). The permeabilized cells were resuspended in 100 ml of storage buffer (10 mM Tris-HCl pH 8.0, 25% (V/V) glycerol, 5 mM MgCl2, 0.1 mM EDTA and 5 mM DTT) for nuclear run-on with 2X run-on mix (5 mM Tris-HCl PH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 0.5 mM BrUTP, RNase inhibitor, 1% sarkosyl) at 37o for 5 min. RNA was extracted by Trizol and followed by hybrolyzation with NaOH at a final concentration of 0.2 N on ice for 18 min. After quenching with ice-cold Tris-HCl PH6.8 at a final concentration of 0.55 M and exchanging buffer via Bio-Rad P30 columns, the RNA was incubated with Br-dU antibody-conjugated beads (Santa Cruz biotechnology, sc-32323-ac) for 1 hr. The enriched run-on samples were incubated with RppH (NEB, M0356S) and hydroxyl repair with T4 PNK (NEB, M0201S), followed by ligating the 5’ and 3’ RNA adaptor. RT-PCR was performed from the adaptor-ligated RNA to obtain cDNA
Half of the cDNA was subjected to making GRO-seq libraries by two rounds of PCR with barcode primers.  200-500 bp products from the first round of PCR were subjected to the second round of PCR with the number of PCR cycles determined by test PCR amplification. The second round of PCR products were size-selected by SPRIselect beads (Beckman Coulter, B23318).

treatment_protocol: Purified via anti-B220 MicroBeads (Miltenyi, #130-049-501)

value: WT

tag: fraction

value: Run-on RNA


title: 0T2_LD_Liver


title: 4T1_LD_Liver


title: WT_BM_Rep2

description: aligned to AJ851868/mm9

value: Primary BM pro-B cells

value: Purified via anti-B220 MicroBeads (Miltenyi, #130-049-501)

value: Opti-MEM; 10% (v/v) FBS plus 10 ng/mL IL-7 and 2 ng/mL SCF for 4-5 days


title: 0T1_LD_Liver


title: WT_untreat_Abl_Rep1

description: aligned to mm9

value: RAG1/2 retrovirus infected, 3 uM STI-571 treated for 4 days


title: 20C2_LD_Liver

value: Control


title: 20C1_LD_Liver


title: AI_iTBS_3

value: Brain

value: hippocampal slice

value: AI

value: 25-26 months

tag: Sex

value: Male

value: iTBS


title: AI_CTR_3

tag: tms

value: SHAM


title: NTC 2

city: London

first: Matthew

middle: Peter

last: Caley

state: london

address: Centre for Cutaneous Research, BLizard Building, Newark Street

country: United Kingdom

institute: QMUL

data_processing:
TopHat
Cufflinks
HISAT2
HTSeq
DESeq2
Assembly: HG19
Supplementary files format and content: Fragemtns per KB measured for each sample

organism: Homo sapiens

source_name: Skin

extract_protocol:
Phenol:Chloroform
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skin

value: primary keratinocyte

value: Non-Targetting siRNA COntrol


title: Y_Sham_HIPP2

value: Hippocampus

value: Long-Evans

tag: age

value: Young

value: 6-7 months

tag: cognitive status

value: unimpaired

value: Y


title: AI_CTR_4

tag: post-treatment (hrs)


title: AI_1Hz_4


title: Lgcrypt_naive_cKO2

value: Large Crypt IEC

tag: time

value: Naïve

value: IL22 fl/fl CD4-Cre +


title: 20C3_LD_Liver

tag: timepoint

tag: light condition

value: LD

value: Control


title: 16C1_LD_Liver


title: siSTS 3

tag: cell type

tag: treatment

value: siRNA against STS


title: 12C3_LD_Liver

tag: diet


title: AI_1Hz_3

value: Brain

value: hippocampal slice

tag: age (group)

value: AI

value: 25-26 months

value: Male


title: Lgcrypt_naive_cKO1

tag: genotype


title: WT_BM_Rep1

description: aligned to AJ851868/mm9

value: Primary BM pro-B cells

value: WT

tag: purification

value: Purified via anti-B220 MicroBeads (Miltenyi, #130-049-501)

value: Opti-MEM; 10% (v/v) FBS plus 10 ng/mL IL-7 and 2 ng/mL SCF for 4-5 days

value: Run-on RNA


title: NTC 3

tag: tissue

value: Skin

value: primary keratinocyte

value: Non-Targetting siRNA COntrol


title: siSTS 2


title: Lgcrypt_d9_cKO4

tag: strain

value: Large Crypt IEC

value: IL22 fl/fl CD4-Cre +


title: siSTS 1


title: Lgcrypt_d9_cKO3


title: 12C1_LD_Liver

value: LD

value: Control


title: 16C3_LD_Liver


title: AI_CTR_2

value: Brain

tag: tissue region

tag: age (months)

value: SHAM


title: 16C2_LD_Liver


title: MDA-MB-468_S4_50_2_RNAseq

city: Cleveland

first: Ruth

last: Keri

state: OH

address: 9500 Euclid Avenue

department: Cancer Biology

institute: Cleveland Clinic Lerner Research Institute

description: RNA isolated 48h post treatment

data_processing:
fastq files were aligned to version hg19 for both the RNA-Seq and the ChIP-Seq.
For RNA-Seq, Differential expression was determined using the DESeq2 R package, where differentially expressed genes were deemed significantly changed if the Benjamini-Hochberg adjusted p-value was <0.05.
For ChIP-Seq, quality filter with FastQ. Reads were aligned to hg19 using Bowtie2. Data was sorted, indexed and filtered with Samtools-1.3.1. Peaks were called with MACS2. Rank ordering of super-enhancers (ROSE) was used to rank enhancers in hg19 with a stitch size of 12.5 kb. MACS2 was then used to make bedgraphs that were converted to wig files.
Genome_build: hg19

source_name: epithelial breast cancer cell line; derived from metasatic pleural effusion

growth_protocol: MDA-MB-231 and MDA-MB-468 cells were cultured in RPMI-1640 supplmented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol: RNA was isolated using a trizol extraction and precipitation protocal. Illumina platform was ised with Pair-end reads and mapped to hg19.

treatment_protocol: Cells were treated with either vehicle or THZ1 for 48hrs for the RNA-Seq. Cells were not treated for the ChIP-Seq

value: epithelial breast cancer cell line

tag: cell line

value: 75nM THZ1


title: 8C3_LD_Liver


title: NTC 1


title: AI_iTBS_2_TR

description: AI1672-1Hz-TMS7_6 repeat

value: hippocampal slice

value: AI

value: 25-26 months

tag: Sex

value: Male

tag: tms

value: iTBS


title: PROseq_WN.rep2

city: Ithaca

first: Hojoong

last: Kwak

state: NY

address: 516 Campus Rd Biotechnology Bldg

department: Molecular Biology and Genetics

institute: Cornell University

description: Replicate 2

data_processing:
DNA-seq data is aligned to hg38 genome using bwa aligner.
Aligned reads are binned in 1 kb tiles and sum of fragment counts in 1 kb intervals are processed to bedgraph format
PRO-seq data is first trimmed off the 8 base unique molecular identifier and 3’ adaptor using cutadapt.
Trimmed sequences are aligned to hg38 genome using STAR aligner.
Read alignments are separated by the opposite strand they were aligned to.
Sum of readcounts per each genomic base coordinates at the 5’ end of aligned sequences are processed to strand specific bedgraph data (.pl.bedgraph are reads aligned to the sense strand of hg38, and mn.bedgraph are reads aligned to the antisense strand of hg38).
Assembly: Hg38
Supplementary files format and content: bedgraph, sum of read counts in genomic coordinates
Library strategy: PRO-seq

source_name: HeLa

extract_protocol:
Approximately 4 million cells were collected from 10 cm culture dishes by rinsing the plates with cold PBS twice and applying 1.5 mL of buffer A (100 mM Tris-HCl pH 7.4, 100 mM NaCl, 30 mM MgCl2, 0.2% Triton, 0.5 mM DTT, 100 mM sucrose) to the plates. The cells were then scraped off and transferred directly to dounce homogenizers, where they were homogenized by applying 40 strokes, 1 second up and 1 second down using the tight pestle (pestle B). After adding 1.5 mL of buffer B (100 mM Tris-HCl pH 7.4, 100 mM NaCl, 30 mM MgCl2, 0.1% Triton, 0.5 mM DTT, 250 mM sucrose) and mixing, the A/B buffer cell pool was layered onto the top of 8 mL of 1 M sucrose cushion in a 15 mL falcon tube, with minimal mixing of the cell suspension with the sucrose cushion. The samples were then centrifuged at 1000 x g for 5 min at 4°C to pellet nuclei, and supernatants were discarded. The nuclei were resuspended in 250 µL of MNase buffer (50 mM Tris-HCl, 5 mM CaCl2 pH 7.9 @ 25°C) supplemented with 100 µg/mL BSA and the resuspended nuclei were re-pooled. A 50 µL mix was taken out and saved as a whole nuclei (WN) fraction. The remaining 200 µL sample was sonicated for 20 total seconds, with 1 second on and 1 second off at 50% power, resulting in 10 seconds of total sonication. A 10 µL mix was taken out and saved as sonicated untreated nuclei for quality control analysis. To the 200 µL sonicated nuclei, 4 µL of the 1.25 U/µL MNase enzyme dilution in 1x MNase buffer was added. The samples were incubated for 5 minutes at 37°C. The samples were immediately placed on ice and 12.5 µL of 100 mM EGTA was added at a final concentration of 6.25 mM to terminate MNase activity. A 10 µL of the mix was saved for the quality control of sonicated treated nuclei. ~200 µL of light MNase-treated fraction was spun at 3000 x g for 3 minutes. Then, 50 µL of the supernatant from the light MNase-treated fraction should be taken out and saved for quality control. All remaining supernatants were removed. The pellet was resuspended in 50 µL of buffer D (50 mM Tris-Cl pH 8.0, 25% (v/v) glycerol, 5 mM MgAc2, 0.1 mM EDTA, 5 mM DTT) for nuclear condensate (NC) fraction. 50 µL of WN fraction from the previous step was also spun at 3000 x g for 3 minutes and resuspended in 50 µL of buffer D. 5 µL of the NC and WN fractions were saved for quality control analysis. Finally, the WN and NC fractions were rapidly frozen in liquid nitrogen and stored at -80°C.
For DNA-seq, Genomic DNA from the whole nuclei or nuclear condensate fractions were extracted using genomic DNA extraction kit (New England Biolabs). DNA-seq library was prepared from 50 ng of extracted genomic DNA using Illumina Nextera DNA Library Prep kit. DNA-seq experiments were performed in biological replicates. PRO-seq was performed on whole nuclei or nuclear condensate fractions in the storage buffer (Buffer D) as described previously (Kwat et al, 2013), with the following modifications. Briefly, isolated fractions were incubated in the nuclear run-on reaction condition (5 mM Tris-HCl pH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5% Sarkosyl, 0.4 units / μl of RNase inhibitor) with biotin-NTPs and rNTPs supplied (18.75 μM rATP, 18.75 μM rGTP, 1.875 μM biotin-11-CTP, 1.875 μM biotin-11-UTP for uPRO; 18.75 μM rATP, 18.75 μM rGTP, 18.75 μM rUTP, 0.75 μM CTP, 7.5 μM biotin-11-CTP for pChRO) for 5 min at 37°C. Run-On RNA was extracted using TRIzol, and fragmented under 0.2 N NaOH for 15 min on ice. Fragmented RNA was neutralized, and buffer exchanged by passing through P-30 columns (Biorad). 3′ RNA adaptor (/5Phos/NNNNNNNNGAUCGUCGGACUGUAGAACUCUGAAC/3InvdT/) is ligated at 5 μM concentration for 1 hours at room temperature using T4 RNA ligase (NEB), followed by 2 consecutive streptavidin bead bindings and extractions. Extracted RNA is converted to cDNA using template switch reverse transcription with 1 μM RP1-short RT primer (GTTCAGAGTTCTACAGTCCGA), 3.75 μM RTP-Template Switch Oligo (GCCTTGGCACCCGAGAATTCCArGrGrG), 1x Template Switch Enzyme and Buffer (NEB) at 42°C for 30 min. After a SPRI bead clean-up, the cDNA is PCR amplified up to 20 cycles using primers compatible with Illumina Small RNA sequencing.

value: HeLa

tag: compartment

value: whole nuclear

value: Whole nuclei isolation

tag: fraction

value: Nascent RNA


title: AI_iTBS_2

tag: post-treatment (hrs)


title: PROseq_WN.rep1

description: Replicate 1


title: PROseq_WN.rep4

description: Replicate 4


title: 8C2_LD_Liver

tag: timepoint

tag: light condition


title: MDA-MB-468_S4_50_1_RNAseq

description: RNA isolated 48h post treatment

tag: treatment


title: AI_1Hz_2


title: PROseq_WN.rep3

description: Replicate 3


title: 12C2_LD_Liver

tag: diet


title: PROseq_WN.HEK

description: Wild type

value: Wild type


title: Lgcrypt_d9_cKO2

value: Large Crypt IEC

tag: time

value: IL22 fl/fl CD4-Cre +


title: AI_1Hz_1

tag: age (group)


title: AI_iTBS_1_TR

description: AI1667-iTBS-TMS4_11 repeat


title: Lgcrypt_d9_cKO1

tag: genotype


title: MDA-MB-468_S4_50_3_RNAseq

description: RNA isolated 48h post treatment

tag: tissue


title: 8C1_LD_Liver

value: LD

value: Control


title: 4C2_LD_Liver


title: 4C1_LD_Liver


title: AU_iTBS_4

value: Brain

value: AU


title: MDA-MB-231_S2_75_3_RNAseq

description: RNA isolated 48h post treatment

value: epithelial breast cancer cell line

value: 75nM THZ1


title: MDA-MB-468_S4V3_RNAseq

description: RNA isolated 48h post treatment

value: Veh


title: PROseq_WN.FUS

description: FUS overexpression

value: FUS overexpression


title: MDA-MB-231_S2_75_2_RNAseq

description: RNA isolated 48h post treatment


title: AI_CTR_1

value: hippocampal slice

value: AI

value: 25-26 months

value: Male

value: SHAM


title: MDA-MB-231_S2_75_1_RNAseq

description: RNA isolated 48h post treatment


title: PROseq_NC.rep4

description: Replicate 4

value: HeLa

value: nuclear condensate

value: Nuclear Condensate fraction

value: Nascent RNA


title: PROseq_NC.HEK

description: Wild type

value: Wild type


title: 4C3_LD_Liver

value: LD

value: Control


title: MDA-MB-468_S4V2_RNAseq

description: RNA isolated 48h post treatment


title: 0C1_LD_Liver


title: PROseq_NC.FUS

description: FUS overexpression

data_processing:
DNA-seq data is aligned to hg38 genome using bwa aligner.
Aligned reads are binned in 1 kb tiles and sum of fragment counts in 1 kb intervals are processed to bedgraph format
PRO-seq data is first trimmed off the 8 base unique molecular identifier and 3’ adaptor using cutadapt.
Trimmed sequences are aligned to hg38 genome using STAR aligner.
Read alignments are separated by the opposite strand they were aligned to.
Sum of readcounts per each genomic base coordinates at the 5’ end of aligned sequences are processed to strand specific bedgraph data (.pl.bedgraph are reads aligned to the sense strand of hg38, and mn.bedgraph are reads aligned to the antisense strand of hg38).
Assembly: Hg38
Supplementary files format and content: bedgraph, sum of read counts in genomic coordinates
Library strategy: DNA-seq


title: 20T3_DD_SCN

source_name: Suprachiasmatic nucleus

value: Suprachiasmatic nucleus

value: DD

value: Tryptophan depleted


title: MDA-MB-231_S2V_2_RNAseq

description: RNA isolated 48h post treatment

value: epithelial breast cancer cell line

value: Veh


title: AU_CTR_4_TR

description: AU1674-CTR-TMS12_1 repeat

value: Brain

value: hippocampal slice

value: AU


title: PROseq_NC.rep3

description: Replicate 3


title: PROseq_NC.rep2

description: Replicate 2


title: AI_iTBS_1

value: AI

value: 25-26 months

value: Male

value: iTBS


title: MDA-MB-468_S4V1_RNAseq

description: RNA isolated 48h post treatment


title: AU_CTR_4

value: SHAM


title: DNAseq_WN.rep2

description: Replicate 2

value: HeLa

value: whole nuclear

value: Whole nuclei isolation

value: DNA


title: AU_1Hz_4


title: PROseq_NC.rep1

description: Replicate 1

value: nuclear condensate

value: Nuclear Condensate fraction

value: Nascent RNA


title: 0C4_LD_Liver

value: LD

value: Control


title: AU_iTBS_3

value: Brain


title: AU_CTR_3

value: hippocampal slice


title: AU_CTR_2

value: AU


title: AU_1Hz_2


title: 0C2_LD_Liver


title: MDA-MB-231_S2V_3_RNAseq

description: RNA isolated 48h post treatment

value: epithelial breast cancer cell line

value: Veh


title: AU_1Hz_3

value: 25-26 months

value: Male


title: DNAseq_WN.rep3

description: Replicate 3


title: 20T2_DD_SCN

value: Suprachiasmatic nucleus

value: DD

value: Tryptophan depleted


title: AU_1Hz_1


title: AU_iTBS_1

value: iTBS


title: 16T3_DD_SCN


title: AU_iTBS_2


title: 20T1_DD_SCN


title: DNAseq_WN.rep1

description: Replicate 1

value: HeLa

value: whole nuclear

value: Whole nuclei isolation

value: DNA


title: DNAseq_NC.rep2

description: Replicate 2

value: nuclear condensate

value: Nuclear Condensate fraction


title: DNAseq_NC.rep3

description: Replicate 3


title: MDA-MB-231_S2V_1_RNAseq

description: RNA isolated 48h post treatment


title: CBE2inv_Abl_Vh81xbait_C2_Rep4

description: aligned to AJ851868/mm9

tag: strain

tag: cell type

value: v-Abl pro B cells

value: RAG2-/-, CBE2inv/inv


title: mNSC-sh902-30_08_18

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB

data_processing:
RNA-seq data quality was monitored via FASTQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapters and overrepresented sequences have been removed using cutadapt software (https://cutadapt.readthedocs.io/ en/stable/).
Further reads preprocessing was performed by Trimmomatic (version 0.36) with the parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50.
Mapping of RNA-seq reads was done using STAR_2.5.0a (Dobin et al., 2013) with default parameters for RNA-seq data; the mouse ENSEMBL gene annotation model GRCm38 (Ensembl release 93).
RSEM software (Li and Dewey, 2011)  were used to quantify the gene-level expression.
Genome_build: GRCm38 (Ensembl release 93)
Supplementary_files_format_and_content: txt format; raw counts for three experimental conditions with 3 replicates each.

source_name: Neural stem cells

growth_protocol: Primary mouse embryonic neural stem cells (mNSC) were cultured in laminin (5 µg/mL, overnight, 37°C) precoated dishes. mNSC were maintained in NeuroCult Proliferation mNSC media (05702, Stem Cell Technologies) supplemented with fibroblast growth factor (FGF) (F0291, Sigma) and epidermal growth factor (EGF) (E4127, Sigma) at 10 and 20 ng/mL, respectively.

extract_protocol:
Tree days after treatment, cells were harvested and total RNA were extracted with RNeasy® Micro Kit (Qiagen).
The mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, a ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: mNSC were treated either with non-targeting or Phf2 targeting shRNA.

value: brain subventricular zone (SVZ)

value: Primary mouse neural stem cells


title: mNSC-sh900


title: 12T3_DD_SCN


title: mNSC-sh902-03_09_18


title: mNSC-sh900-03_09_18


title: 16T2_DD_SCN


title: mNSC-sh900-30_08_18


title: DNAseq_NC.rep1

description: Replicate 1


title: mNSC-sh902


title: 12T2_DD_SCN


title: CBE2inv_Abl_Vh81xbait_C1_Rep3

description: aligned to AJ851868/mm9


title: CBE2inv_Abl_Vh81xbait_C1_Rep1

description: aligned to AJ851868/mm9


title: 8T3_DD_SCN


title: 16T1_DD_SCN


title: CBE1inv_Abl_Vh81xbait_C2_Rep4

description: aligned to AJ851868/mm9

value: RAG2-/-, CBE1inv/inv


title: CBE2inv_Abl_Vh81xbait_C1_Rep2

description: aligned to AJ851868/mm9


title: 12T1_DD_SCN


title: mNSC-shNT


title: mNSC-shNT-30_08_18


title: CBE1inv_Abl_Vh81xbait_C1_Rep3

description: aligned to AJ851868/mm9


title: mNSC-shNT-03_09_18


title: 8T2_DD_SCN


title: 8T1_DD_SCN


title: CBE1inv_Abl_Vh81xbait_C1_Rep2

description: aligned to AJ851868/mm9


title: 4T3_DD_SCN


title: Y_CTR_4_TR

description: Y484-CTR-TMS2_1 repeat

value: Brain

tag: tissue region

value: hippocampal slice

value: Y

tag: age (months)

value: 5-6  months

value: SHAM


title: Y_iTBS_4

tag: Sex

value: Male

value: iTBS


title: AU_CTR_1

value: AU

value: 25-26 months

tag: tms


title: Y_iTBS_3


title: 4T2_DD_SCN

value: Suprachiasmatic nucleus

value: DD

value: Tryptophan depleted


title: CBE1inv_Abl_Vh81xbait_C1_Rep1

description: aligned to AJ851868/mm9

value: v-Abl pro B cells


title: 4T1_DD_SCN


title: Y_CTR_4


title: Y_1Hz_4


title: 0T3_DD_SCN


title: 0T2_DD_SCN


title: CBE2mut_Abl_Vh81xbait_C1_Rep2

description: aligned to AJ851868/mm9


title: 917_5 SHOCKplusMom (PN12 Pups)

city: Philadelphia

first: Gordon

middle: Alfred

last: Barr

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Anesthesiology

institute: CHOP

description: Gene expression data from the amydala of PN12 pups in the three conditions

hyb_protocol: They were hybridized to Affymetrix rat 2.0 gene arrays as specified by Affymetrix (Santa Clara, CA) and NuGEN (Pico System; San Carlos, CA).

scan_protocol: Affymetrix protocol

data_processing:
Expression:  Expression values were preprocessed, background-corrected, and normalized by RMA using BRAINARRAY [University of Michigan; CDF: Rat 1.0_Rn_ENTREZG] resulting in approximately 19,000 distinct genes
Significant effects:  Rank Products, which simulates probabilities based on pairwise comparison differences, was used to assess differential expression in each experimental condition compared to the other.
GO:  All genes were input with the fold change or pfp values (percentage of false positive predictions) calculated by the Rank Products analysis into ErmineJ using the gene score resampling method
Networks:  To define networks of related probes we input probes with fold change that exceeded ±1.25, using the direct connection option. We included up- and downregulated genes together

label: biotin

source_name: Amygdala

label_protocol: Affymetrix protocol

extract_protocol:
Dissection storage: The infant brains were rapidly frozen (-45oC - total time from decapitation to frozen ~ 2min), amygdala dissected, stored in a (-80oC) freezer
RNA processing: Total RNA (Qiagen RNeasy Micro Kit). mRNA was amplified linearly

treatment_protocol: Immediately following the acute tests of shock with and without the dam, pups were euthanized, as were Controls at the same time

value: SHOCKplusMOM

value: Amygdala

value: Female

tag: age

value: PN12 Pups


title: Y_CTR_3

value: Brain


title: Y_1Hz_3

value: hippocampal slice


title: Y_iTBS_2

value: Y


title: CBE2mut_Abl_Vh81xbait_C1_Rep1

description: aligned to AJ851868/mm9


title: Y_1Hz_2

value: 5-6  months


title: Y_iTBS_1


title: CBE2mut_Abl_Vh81xbait_C2_Rep4

description: aligned to AJ851868/mm9


title: 0T1_DD_SCN


title: CBE2mut_Abl_Vh81xbait_C1_Rep3

description: aligned to AJ851868/mm9


title: CBE1mut_Abl_Vh81xbait_C2_Rep4

description: aligned to AJ851868/mm9


title: Y_CTR_2

value: SHAM


title: 917_3 NAÏVE (PN12 Pups)

value: NAIVE

value: Male


title: Y_CTR_1


title: 915_7 SHOCKplusMom (PN12 Pups)


title: 917_2 SHOCK_NoMOM (PN12 Pups)

value: SHOCKnoMOM


title: Y_1Hz_1


title: 20C3_DD_SCN

value: Control


title: 915_3 NAÏVE (PN12 Pups)


title: CBE1mut_Abl_Vh81xbait_C1_Rep3

description: aligned to AJ851868/mm9


title: 20C2_DD_SCN

value: Suprachiasmatic nucleus


title: iTBS_8H_REP1

growth_protocol: Primary cultures of hippocampal neurons were prepared using hippocampi collected from E18 Sprague Dawley rats as previously described26. Dissociated cells were counted and plated (106 cells/dish) in polyethyleneimine (Sigma-Aldrich) pre-coated coverslips on 35 mm dishes (zero days in vitro). Neurons were maintained in Neurobasal medium (GIBCO) supplemented with B27 (GIBCO), 2 mM glutamine, 100 U/mL penicillin, 100 µg/mL streptomycin, and 0.25 µg/mL amphotericin B. T

treatment_protocol: The cultures were placed in an incubator with extra insulation to prevent CO2 loss and decrease in temperature. The plates were placed centered directly on the inverted coil and received either 1 Hz, iTBS, or sham stimulation. Stimulation intensity was set at 15% of the machine’s maximum output (stimulation intensity for in vitro and ex vivo experiments was chosen as the average intensity for all groups in the in vivo experiment, detailed below). Neuronal cultures received either 1 Hz, iTBS, or sham stimulation. For the sham treatment, the plate was placed in the incubator with the coil approximately 20 cm away. Following stimulation, the plates were returned to the home incubator without the coil.  RNA was isolated at 0, 2, 8 24, and 48 hours after the end of stimulation.

value: Sprague-Dawley

value: iTBS


title: 20C1_DD_SCN

value: DD


title: 892_7  SHOCK_NoMOM (PN12 Pups)


title: CBE1mut_Abl_Vh81xbait_C1_Rep1

description: aligned to AJ851868/mm9

value: v-Abl pro B cells


title: 915_11 SHOCK_NOMom (PN12 Pups)

value: Amygdala


title: iTBS_8H_REP3


title: 16C3_DD_SCN


title: 12C3_DD_SCN


title: 892_9 NAÏVE (PN12 Pups)


title: iTBS_8H_REP2


title: iTBS_48H_REP4


title: CBE12mut_Abl_Vh81xbait_C2_Rep4

description: aligned to AJ851868/mm9


title: 16C2_DD_SCN


title: 891_6 SHOCK_NoMOM (PN12 Pups)

value: Female


title: 891_8 NAÏVE (PN12 Pups)

value: PN12 Pups


title: CBE12mut_Abl_Vh81xbait_C1_Rep3

description: aligned to AJ851868/mm9


title: 12C1_DD_SCN


title: 892_11 SHOCKplusMOM (PN12 Pups)

value: SHOCKplusMOM


title: iTBS_48H_REP2

value: Brain


title: iTBS_48H_REP3


title: CBE12mut_Abl_Vh81xbait_C1_Rep1

description: aligned to AJ851868/mm9


title: CBE1mut_Abl_Vh81xbait_C1_Rep2

description: aligned to AJ851868/mm9


title: 16C1_DD_SCN


title: CBE12mut_Abl_Vh81xbait_C1_Rep2

description: aligned to AJ851868/mm9


title: iTBS_2H_REP4


title: WT_Abl_Vh81xbait_C1_Rep1

description: aligned to AJ851868/mm9


title: 12C2_DD_SCN


title: 891_12 SHOCKplusMOM (PN12 Pups)


title: 4C3_DD_SCN


title: 890_8 NAÏVE (PN12 Pups)


title: 889_7 SHOCK_NoMOM (PN12 Pups)


title: 889_11 SHOCKplusMom (PN12 Pups)


title: iTBS_48H_REP1


title: iTBS_2H_REP3


title: V63_8_SHOCKplusMOM (PN7 Pups)

description: Gene expression data from the amydala of PN7 pups in the three conditions

value: PN7 Pups


title: iTBS_24H_REP1


title: iTBS_2H_REP1


title: 890_6 SHOCK_NoMOM (PN12 Pups)


title: CBE2inv_Abl_RCbait_C1_Rep3

description: aligned to AJ851868/mm9

value: RAG2-/-, CBE2inv/inv


title: iTBS_24H_REP2


title: WT_Abl_Vh81xbait_C1_Rep3

description: aligned to AJ851868/mm9


title: WT_Abl_Vh81xbait_C1_Rep2

description: aligned to AJ851868/mm9


title: 890_12 SHOCKpllusMOM (PN12 Pups)


title: iTBS_2H_REP2


title: 8C2_DD_SCN


title: 0C3_DD_SCN


title: 8C3_DD_SCN


title: WT_Abl_Vh81xbait_C2_Rep4

description: aligned to AJ851868/mm9


title: 889_9 NAÏVE (PN12 Pups)


title: 8C1_DD_SCN


title: V63_6_SHOCKnoMOM (PN7 Pups)


title: 0C2_DD_SCN


title: iTBS_0H_REP2


title: CBE2inv_Abl_RCbait_C2_Rep4

description: aligned to AJ851868/mm9


title: 4C2_DD_SCN


title: 4C1_DD_SCN


title: CBE2inv_Abl_RCbait_C1_Rep2

description: aligned to AJ851868/mm9


title: CBE2inv_Abl_RCbait_C1_Rep1

description: aligned to AJ851868/mm9


title: CBE1inv_Abl_RCbait_C2_Rep4

description: aligned to AJ851868/mm9

value: RAG2-/-, CBE1inv/inv


title: CBE1inv_Abl_RCbait_C1_Rep2

description: aligned to AJ851868/mm9


title: CBE1inv_Abl_RCbait_C1_Rep3

description: aligned to AJ851868/mm9


title: 20T3_LD_SCN

value: LD

value: Tryptophan depleted


title: CBE1inv_Abl_RCbait_C1_Rep1

description: aligned to AJ851868/mm9


title: 0C1_DD_SCN


title: iTBS_24H_REP3


title: V63_2_SHOCKplusMOM (PN7 Pups)


title: V63_4_NAIVE (PN7 Pups)

value: NAIVE


title: CBE2mut_Abl_RCbait_C2_Rep4

description: aligned to AJ851868/mm9


title: V63_5_SHOCKnoMOM (PN7 Pups)

value: SHOCKnoMOM


title: V63_7_SHOCKplusMOM (PN7 Pups)


title: V63_12_SHOCKnoMOM (PN7 Pups)


title: 16T3_LD_SCN

value: Suprachiasmatic nucleus


title: CBE2mut_Abl_RCbait_C1_Rep3

description: aligned to AJ851868/mm9


title: V63_13_SHOCKplusMOM (PN7 Pups)


title: CBE2mut_Abl_RCbait_C1_Rep1

description: aligned to AJ851868/mm9


title: V63_11_SHOCKnoMOM (PN7 Pups)


title: iTBS_0H_REP1

value: Sprague-Dawley


title: iTBS_0H_REP4

value: iTBS


title: iTBS_0H_REP3


title: 20T1_LD_SCN


title: 20T2_LD_SCN


title: CBE2mut_Abl_RCbait_C1_Rep2

description: aligned to AJ851868/mm9


title: 1Hz_8H_REP2


title: 1Hz_8H_REP4


title: 1Hz_48H_REP4


title: V63_10_NAIVE (PN7 Pups)


title: 1Hz_8H_REP3


title: V63_1_SHOCKplusMOM (PN7 Pups)


title: V62_6_SHOCKnoMOM (PN7 Pups)


title: 16T2_LD_SCN


title: 12T2_LD_SCN


title: 1Hz_48H_REP3


title: V62_5_SHOCKnoMOM (PN7 Pups)


title: 1Hz_8H_REP1


title: V62_3_NAIVE (PN7 Pups)


title: 12T1_LD_SCN


title: 16T1_LD_SCN


title: CBE1mut_Abl_RCbait_C1_Rep1

description: aligned to AJ851868/mm9


title: CBE1mut_Abl_RCbait_C2_Rep4

description: aligned to AJ851868/mm9


title: 12T3_LD_SCN


title: CBE12mut_Abl_RCbait_C2_Rep4

description: aligned to AJ851868/mm9


title: CBE1mut_Abl_RCbait_C1_Rep3

description: aligned to AJ851868/mm9


title: CBE1mut_Abl_RCbait_C1_Rep2

description: aligned to AJ851868/mm9


title: CBE12mut_Abl_RCbait_C1_Rep3

description: aligned to AJ851868/mm9


title: CBE12mut_Abl_RCbait_C1_Rep2

description: aligned to AJ851868/mm9


title: CBE12mut_Abl_RCbait_C1_Rep1

description: aligned to AJ851868/mm9


title: 8T3_LD_SCN


title: 8T2_LD_SCN


title: 8T1_LD_SCN


title: 1Hz_48H_REP1


title: 4T3_LD_SCN


title: V62_2_SHOCKplusMOM (PN7 Pups)


title: V62_1_SHOCKplusMOM (PN7 Pups)


title: 4T2_LD_SCN


title: 1Hz_48H_REP2


title: 319_1_NAIVE (PN7 Pups)


title: 316_7_SHOCKnoMOM (PN7 Pups)


title: 1Hz_24H_REP3


title: WT_Abl_RCbait_C1_Rep2

description: aligned to AJ851868/mm9


title: 1Hz_2H_REP1


title: 1Hz_2H_REP2


title: 1Hz_2H_REP3


title: 1Hz_0H_REP3


title: 319_3_NAIVE (PN7 Pups)


title: 1Hz_0H_REP2


title: WT_Abl_RCbait_C2_Rep4

description: aligned to AJ851868/mm9


title: 4T1_LD_SCN


title: 0T2_LD_SCN


title: 1Hz_24H_REP2


title: 1Hz_24H_REP1


title: 0T3_LD_SCN


title: WT_Abl_RCbait_C1_Rep3

description: aligned to AJ851868/mm9


title: 316_5_NAIVE (PN7 Pups)


title: 1Hz_0H_REP1


title: SHAM_8H_REP3

value: Sham


title: ∆essRS replicate 3

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:
CLC Genomic Workbench 21.0.4
Paired-end sequences were mapped to NC_009504 and NC_009505 using CLC Genomic Workbench (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
RPKM, TPM, CPM, and total counts of each replicate was calculated using the gene expression tool in CLC Genomic Workbench
Assembly: NC_009504 and NC_009505
Supplementary files format and content: excel file, contains RPKM, TPM, CPM, and total counts of each replicate

organism: Brucella ovis

source_name: cells

growth_protocol: Cells were started at OD600 = 0.05 in 12 ml Brucella broth and incubated on rotor at 37˚C with 5% CO2 for 7h.

extract_protocol:
Cells were incubated on rotor at 37˚C in 5% CO2 for 7h. 9 ml of each culture were spun down and the pellets were resuspended in 1 ml TRIzol. Samples were stored at -80˚C until RNA extraction. To extract the RNA, samples were thawed and incubated at 65˚C for 10 minutes. 200 µl of chloroform was added to each sample and mixed by vortexing for 15 seconds. Samples were then incubated at room temperature for 5 minutes. Samples were spun at 17,000 x g for 15 minutes at 4˚C and the aqueous layer was collected. Sample was mixed with 500 µl isopropanol and stored at -20˚C for 2h. After thawing, samples were spun down at 13, 300 x g for 30 minutes at 4˚C. Supernatants were discarded and 1 ml of ice cold 70% ethanol was added. Samples were spun down at 13,300 x g at 4˚C for 5 minutes. Supernatants were discarded and pellets were let completely dry. 100 µl RNAse-free H2O was added to each sample and incubated at 60˚C for 10 minutes. RNA samples were cleaned up using RNeasy Mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using Illumina Stranded RNA library preparation with RiboZero Plus rRNA depletion.

value: cells

value: BOV_1472 deletion mutant


title: ∆essRS replicate 2


title: 20C3_LD_SCN

value: Control


title: WT_Abl_RCbait_C1_Rep1

description: aligned to AJ851868/mm9

value: v-Abl pro B cells


title: CBE2mut_BM_Rep3

description: aligned to AJ851868/mm9

value: Primary BM pro-B cells

value: Bone marrow-derived pro-B cells were purified from 129SVE mice by sorting  (B220+IgM-CD43+)


title: ∆essRS replicate 1


title: CBE2mut_BM_Rep2

description: aligned to AJ851868/mm9


title: 20C2_LD_SCN


title: ∆cenR replicate 3

value: BOV_1929 deletion mutant


title: CBE2mut_BM_Rep1

description: aligned to AJ851868/mm9


title: 316_3_NAIVE (PN7 Pups)

value: Amygdala

value: PN7 Pups


title: 20C1_LD_SCN

value: LD


title: ∆cenR replicate 2


title: CBE2inv_BM_Rep3

description: aligned to AJ851868/mm9


title: 16C3_LD_SCN


title: CBE2inv_BM_Rep2

description: aligned to AJ851868/mm9


title: 16C2_LD_SCN


title: 316_6_SHOCKnoMOM (PN7 Pups)


title: ∆cenR replicate 1


title: CBE2inv_BM_Rep1

description: aligned to AJ851868/mm9


title: 316_3_NAIVE_10115 (PN7 Pups)


title: 16C1_LD_SCN


title: 316_2_SHOCKplusMOM (PN7 Pups)

value: SHOCKplusMOM


title: WT replicate 3

value: WT


title: SHAM_48H_REP3

value: Brain


title: 0T1_LD_SCN

value: Suprachiasmatic nucleus

value: Tryptophan depleted


title: SHAM_8H_REP2

value: Sprague-Dawley


title: CBE1inv_BM_Rep3

description: aligned to AJ851868/mm9


title: 12C2_LD_SCN


title: SHAM_8H_REP1

value: Sham


title: 12C3_LD_SCN


title: SHAM_48H_REP2


title: SHAM_48H_REP1


title: WT replicate 2

value: cells


title: WT replicate 1


title: 8C2_LD_SCN


title: BOV_1472(D64E)_output_1

data_processing:
ChIP-seq analysis was done on Galaxy
Output and input sequences were first mapped to the reference genome (Brucella ovis ATCC 25840, Genbank accessions NC_009504 and NC_009505) using bowtie2
Genrich was performed using the output file and its corresponding input file with parameters set as maximum q-value = 0.05, and minimum AUC (area under the curve) = 20. PCR duplicates were removed. bamCoverage was used to create bigwig files for each replicate.
Assembly: NC_009504 and NC_009505
Supplementary files format and content: bigWig for output files

source_name: bacterial

growth_protocol: Cells were grown on TSA blood plates supplemented with 30 µg/ml oxytetracycline

extract_protocol:
Cells were crosslinked with formaldehyde for 10 minutes and quenched with glycine. After sonication, lysates were applied to pre-washed anti-FLAG magnetic beads and incuated for 3h. After washed, beads were washed and DNA-protein complex were eluted. After reverse crosslinking and proteinase K treatment at 65˚C overnight, ChIP DNA was cleaned up using Zymo ChIP DNA clean & concentrator kit.
ChIP-seq libaray was prepared using Illumina DNA prep kit and IDT 10bp UDI indices

value: bacterial

tag: chip antibody

value: anti-FLAG


title: 12C1_LD_SCN

value: Control


title: 8C3_LD_SCN


title: BOV_1472(D64E)_input_2


title: SHAM_2H_REP4

tag: post-treatment (hrs)


title: CBE1mut_BM_Rep3

description: aligned to AJ851868/mm9

value: Primary BM pro-B cells


title: CBE1mut_BM_Rep1

description: aligned to AJ851868/mm9

value: Bone marrow-derived pro-B cells were purified from 129SVE mice by sorting  (B220+IgM-CD43+)


title: CBE1inv_BM_Rep2

description: aligned to AJ851868/mm9


title: SHAM_2H_REP3


title: CBE1mut_BM_Rep2

description: aligned to AJ851868/mm9


title: SHAM_2H_REP1


title: SHAM_2H_REP2


title: 4C3_LD_SCN

tag: timepoint


title: CBE1inv_BM_Rep1

description: aligned to AJ851868/mm9


title: 8C1_LD_SCN

tag: light condition


title: CBE12mut_BM_Rep3

description: aligned to AJ851868/mm9

tag: treatment


title: SHAM_24H_REP1


title: BOV_1929(D55E)_output_3


title: 4C1_LD_SCN

tag: diet


title: CBE12mut_BM_Rep2

description: aligned to AJ851868/mm9


title: WT_BM_Rep3

description: aligned to AJ851868/mm9


title: BOV_1472(D64E)_input_1


title: CBE12mut_BM_Rep1

description: aligned to AJ851868/mm9


title: BOV_1929(D55E)_input_3


title: BOV_1929(D55E)_input_2


title: 0C1_LD_SCN


title: WT_BM_Rep2

description: aligned to AJ851868/mm9


title: 4C2_LD_SCN


title: SHAM_24H_REP2


title: BOV_1929(D55E)_input_1


title: BOV_1929(D55E)_output_1


title: SHAM_24H_REP3


title: WT_BM_Rep1

description: aligned to AJ851868/mm9


title: BOV_1929(D55E)_output_2


title: SAI5, day 56, scRNAseq

status: Public on May 29 2023

city: Toronto

first: Biren

last: Dave

state: Ontario

address: 686 Bay Street

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v2.0.0 pipeline
Assembly: GRCh38.p13
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Cryopreserved cell suspensions were prepared in growth medium supplemented with 10% DMSO
Cells were thawed and nuclei were isolated according to protocol CG000365, Revision C by 10X Genomics (Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing)
GEMs were generated and barcoded using the Chromium Next GEM Chip J. ATAC and gene expression libraries were then constructed according to protocol CG000338, Revision E by 10X Genomics (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression)

tag: cell line

value: hindbrain neuroepithelial stem cell

value: cerebellar granule neuron differentiation

tag: time

value: Day 56


title: SAI5, day 14, scRNAseq

description: 10x Genomics

tag: genotype

value: Day 14


title: SAI5, day 7, scRNAseq

description: 10x Genomics

value: Day 7


title: SAI5, hbNES cells, day 56

description: fpkm.csv

data_processing:
Reads were mapped to GRCh38.p13 reference transcriptome using Salmon (v1.1.0)
Downstream analysis was performed in R (v4.1.2) using the tximport package.
Assembly: GRCh38.p13
Supplementary files format and content: one comma delimited files containing FPKM expression values for all samples

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 250 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II Directional poly(A) mRNA library prep kit following manufacturer's protocols.

value: WT


title: 0C4_LD_SCN

tag: tissue

value: LD


title: SAI5, hbNES cells, day 28

description: fpkm.csv

value: Day 28


title: SAI5, hbNES cells, day 21

description: fpkm.csv

value: Day 21


title: SAI5, hbNES cells, day 14

description: fpkm.csv


title: SAI5 hbNES cells, day 4

description: fpkm.csv

value: Day 4


title: 0C2_LD_SCN

value: Suprachiasmatic nucleus


title: SAI5, hbNES cells, day 7

description: fpkm.csv


title: SHAM_0H_REP4

data_processing: Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

value: Brain

tag: strain

value: Sprague-Dawley

value: Sham


title: SHAM_0H_REP2


title: SAI5, hbNES cells, day 0

description: fpkm.csv

tag: cell type

value: Day 0


title: SAI3, hbNES cells, day 28

description: fpkm.csv


title: SAI3, hbNES cells, day 56

description: fpkm.csv


title: SAI3, hbNES cells, day 14

description: fpkm.csv


title: SAI3, hbNES cells, day 21

description: fpkm.csv


title: SAI3 hbNES cells, day 4

description: fpkm.csv


title: SAI3, hbNES cells, day 0

description: fpkm.csv


title: SHAM_0H_REP3


title: SAI2, hbNES cells, day 56

description: fpkm.csv


title: SAI2, hbNES cells, day 28

description: fpkm.csv


title: SAI2, hbNES cells, day 7

description: fpkm.csv


title: CTR_0H_REP3


title: SAI2, hbNES cells, day 0

description: fpkm.csv


title: SHAM_0H_REP1


title: SAI1, hbNES cells, day 56

description: fpkm.csv


title: SAI2, hbNES cells, day 4

description: fpkm.csv


title: SAI2, hbNES cells, day 14

description: fpkm.csv


title: SAI1, hbNES cells, day 28

description: fpkm.csv


title: SAI1, hbNES cells, day 7

description: fpkm.csv


title: SAI1, hbNES cells, day 21

description: fpkm.csv


title: SAI1, hbNES cells, day 4

description: fpkm.csv


title: SAI5, day 0, scRNAseq

description: 10x Genomics


title: SAI1, hbNES cells, day 0

description: fpkm.csv


title: SAI5, day 56, scATACseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v2.0.0 pipeline
Assembly: GRCh38.p13
Supplementary files format and content: Tab-separated ATAC fragments file


title: CTR_0H_REP4


title: SAI5, day 14, scATACseq

description: 10x Genomics


title: CTR_0H_REP2


title: SAI5, day 7, scATACseq

description: 10x Genomics


title: SAI5, day 0, scATACseq

description: 10x Genomics


title: dsrct PDX combo (PDX_4C)

city: Milano

first: Stefano

last: Percio

address: VIa Amadeo 42

country: Italy

institute: Istituto Nazionale dei Tumori

data_processing:
Sequence reads were checked for quality using fastQC
Sequence reads mapping to GrCh38/hg38 and count extration were performed using STAR with default parameters
Assembly: hg38
Supplementary files format and content: pdx_dsrct_treated_processed_GEOsubmission.xlsx

source_name: dsrct PDX

growth_protocol: From 6 to 8 week-old female SCID mice were implanted into the right flank with the PDX.  When tumor burden reached about 150-200 mm3 (after around 60 days from small fragment implant), SCID mice were randomized to receive different drugs.

extract_protocol:
Total RNA extracted from untreated PDXs and PDX exposed to one round of treatment with irinotecan or trabectedin as single agent or in combination was processed with an RNeasy mini kit (Qiagen) in accordance with the manufacture's protocol.
RNA was processed according to standard NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® protocol and mRNA was selected with oligo-dT beads. All the RNA libraries were generated starting from 800ng total RNA. Libraries were quantified and quality checked on an Agilent 4200 TapeStation system (High Sensitivity D5000), and then sequenced on an Illumina NovaSeq platform with paired-end reads 150bp long, with a depth of 27 million cluster/sample.

tag: disease state

value: Desmoplastic small round cell tumor (DSRCT)

value: dsrct PDX

value: irinotecan + trabectidin


title: dsrct PDX Tr (PDX_3C)

value: trabectidin


title: dsrct PDX ctrl (PDX_1C)

value: control


title: dsrct PDX combo (PDX_4B)


title: dsrct PDX Iri (PDX_2C)

value: irinotecan


title: dsrct PDX Iri (PDX_2B)


title: dsrct PDX combo (PDX_4A)


title: dsrct PDX Tr (PDX_3A)


title: dsrct PDX ctrl (PDX_1B)


title: dsrct PDX Iri (PDX_2A)


title: dsrct PDX ctrl (PDX_1A)


title: Doxazosin 10µM

city: New Haven, US & Trento, Italy

first: Toma

last: Tebaldi

state: CT

address: 300 George Street

department: CIBIO & Department of Internal Medicine, Yale Cancer Center

institute: Yale University & University of Trento

description: iCell8 cx Takara

data_processing:
The sample/cell demultiplexing was made using the Illumina Basespace BCL2Fastq Software followed by a preliminary quality control check of the raw sequencing reads. Adapter sequences were removed using fastp (v.0.23.3) and alignment was performed with STAR (v.2.7.8a) using the human assembly GRCh38.p13 as reference genome. Feature counting was done using featureCounts from the Rsubread R package (v.1.22.2) with the GTF annotation file GRCh37.75. Further processing was performed using the R package Seurat (v.4.3.0). Quality controls included the exclusion of the cells with UMIs < 400, features < 400 and mitoRatio > 0.4.
Assembly: GRCh38.p13
Supplementary files format and content: Matrix of gene counts of each cell in txt format

source_name: Human neuroblastoma tumour mass of left adrenal gland

growth_protocol: CHP134 were maintained in DMEM medium supplemented with 10% v/v fetal bovine serum (FBS), 1% v/v L-glutamine, 100U/ml penicillin, and 100 U/ml streptomycin and maintained at 37°C in 5% CO2 at constant humidity.

extract_protocol:
All on-chip liquid handling was performed using the SMARTerTM ICELL8® Single-Cell System, and full-length cDNA synthesis, Illumina P5/P7 index addition, and tagmentation were performed on-chip. Following round 1 PCR, the amplicons were pooled by centrifugation of the chip and purified using Ampure beads. These steps were followed by round 2 PCR amplification off-chip.
Library was prepared according to the manufacter’s instructions (SMARTerTM ICELL8® Single-Cell Full-Lenght Analysis, Takara). The four single-cell suspensions (CHP134 cells and three treatments) were fluorescently labeled with live/dead stain using READYPROBES VIABILITY BLU/RED1 kit (Invitrogen) and diluted (in 1 ml) to have 1.4 cells in 50 nl. Each cell type suspension was dispensed using the SMARTer ICELL8® Single-Cell System from a 384-well source plate into individually addressable wells in a 5,184 nano-well, 250 nl volume ICELL8 chip (SMARTerTM ICELL8® 250 v Chip). Wells containing individual live cells were identified by imaging using the CellSelect software to generate a well-selection map (filter file:1287 cells), which was used to enable individual addressing of the selected wells for the addition of library preparation reagents. This procedure certifies that only single live cells will be used in the protocol.
Library was prepared according to the manufacter’s instructions (SMARTerTM ICELL8® Single-Cell Full-Lenght Analysis, Takara). The four single-cell suspensions (CHP134 cells and three treatments) were fluorescently labeled with live/dead stain using READYPROBES VIABILITY BLU/RED1 kit (Invitrogen) and diluted (in 1 ml) to have 1.4 cells in 50 nl. Each cell type suspension was dispensed using the SMARTer ICELL8® Single-Cell System from a 384-well source plate into individually addressable wells in a 5,184 nano-well, 250 nl volume ICELL8 chip (SMARTerTM ICELL8® 250 v Chip). Wells containing individual live cells were identified by imaging using the CellSelect software to generate a well-selection map (filter file:1287 cells), which was used to enable individual addressing of the selected wells for the addition of library preparation reagents. This procedure certifies that only single live cells will be used in the protocol. All on-chip liquid handling was performed using the SMARTerTM ICELL8® Single-Cell System, and full-length cDNA synthesis, Illumina P5/P7 index addition, and tagmentation were performed on-chip. Following round 1 PCR, the amplicons were pooled by centrifugation of the chip and purified using Ampure beads. These steps were followed by round 2 PCR amplification off-chip.

treatment_protocol: CHP134 cells were seeded in 6-well plates and treated the day after with DMSO (0.04%) 13cRA(5μM), doxazosin (10μM) and a combination of the two. After 24h of treatment, the cells were collected and seeded at a density of 2240 cells/well. Before processing, cells were washed in 1x PBS and cell concentration and viability were determined using a Denovix CELL DROP

value: CHP134 cells

value: Doxazosin 10µM


title: 13cRA 5µM

description: iCell8 cx Takara

value: Human neuroblastoma tumour mass of left adrenal gland

value: 13cRA 5µM


title: DMSO 0.04%

description: iCell8 cx Takara


title: 2724_PD_PUT

city: New York

first: Caryn

middle: R

last: Hale

state: New York

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
Illumina's bcl2fastq2 Conversion Software v2.19 was used for basecalling.
Salmon quantifications were derived using Salmon (version 0.8.2) from raw FastQ against the hg38 transcriptome sequences retrieved in the Bioconductor TxDb.Hsapiens.UCSC.hg38.knownGene
Gene expression values (log2-cpm) were generated by edgeR (version 3.36.0) using the cpm function with log = TRUE and prior.count = 3
Assembly: hg38 - (From Bioconductor package - BSgenome.Hsapiens.UCSC.hg38)
Supplementary files format and content: Salmon transcript quantifications against the hg38 transcriptome sequences.

source_name: Post-mortem brain tissue

extract_protocol:
RNA was extracted from powdered, frozen brain tissue using standard TRIzol (Invitrogen) extraction method. RNA samples were treated with RQ1 RNase-free DNase (Promega), purified by TRIzol LS (Ambion) and checked on Agilent Bioanalyzer
Polyadenylated mRNA was collected by Dynabeads mRNA Purification Kit (Ambion). The libraries were prepared by TruSeq RNA Sample Preparation Kit v2 (Illumina) following manufacturer’s instructions. High-throughput sequencing was performed on NovaSeq (Illumina) to obtain 150 nucleotide paired-end reads.
polyA selection, TruSeq library prep (stranded)

tag: disease

value: PD

tag: region

value: PUT

tag: age at disease onset

tag: age at death

tag: disease duration

tag: post mortem index (pmi)

tag: gender (m

value: male, f:female):F

tag: ethnicity (w

value: white, b:black, nw:non-white):H

tag: patient

tag: rna integrity number (rin)

tag: dementia

value: UK

tag: dyskinesia

tag: cholinesterase inhibitors


title: 13cRA 5µM+Doxazosin 10µM

description: iCell8 cx Takara

tag: cell line

tag: tissue

tag: treatment

value: 13cRA 5µM+Doxazosin 10µM


title: 2723_PD_CAU

value: CAU


title: 2721_PD_CAU

value: male, f:female):M

value: white, b:black, nw:non-white):NW


title: 2720_CTRL_PUT

value: Control

value: CTRL


title: SAI1, hbNES cells, day 14

description: fpkm.csv

tag: cell type

value: hindbrain neuroepithelial stem cell

tag: genotype

value: WT

value: cerebellar granule neuron differentiation

tag: time

value: Day 14


title: 2718_CTRL_PUT

tag: disease

tag: region

tag: age at disease onset


title: CTR_0H_REP1

extract_protocol: RNA was extracted using Qiagen RNeasy Mini kits (#74104). Brain tissues were homogenized using a Precellys 24 Tissue homogenizer (Bertin Instruments, Rockville, MD) at 5500-6000rpm for 30 seconds, using 1 mL cold RLT buffer and glass beads. Homogenates were centrifuged at 12,000 rpm for 4 mins at 4°C to pellet any unhomogenized  tissue and beads, and RNA  isolated according to the manufacturer's instructions. RNA concentration and quality was assayed on an RNA6000 Bioanalyzer chip (Agilent).

value: Brain

tag: strain

value: Sprague-Dawley

tag: age

tag: tms

tag: post-treatment (hrs)


title: 2717_CTRL_CAU

tag: age at death

tag: disease duration

tag: post mortem index (pmi)

tag: gender (m

tag: ethnicity (w

tag: patient

tag: rna integrity number (rin)


title: 2716_PD_PUT

value: PD

value: white, b:black, nw:non-white):W

tag: dementia

tag: dyskinesia

tag: cholinesterase inhibitors

value: No


title: BOV_1472(D64E)_output_2

tag: cell type

value: bacterial

tag: chip antibody

value: anti-FLAG


title: SAI2, hbNES cells, day 21

description: fpkm.csv

tag: cell line

tag: genotype

tag: treatment

tag: time

value: Day 21


title: 2715_PD_CAU

tag: disease

tag: region

value: CAU

tag: age at disease onset

value: UK


title: dsrct PDX Tr (PDX_3B)

tag: disease state

value: Desmoplastic small round cell tumor (DSRCT)

tag: tissue

value: dsrct PDX

value: trabectidin


title: 2713_PD_CAU

tag: age at death

tag: disease duration

tag: post mortem index (pmi)

tag: gender (m

value: male, f:female):M

tag: ethnicity (w


title: 2712_CTRL_PUT

value: Control

value: PUT

value: CTRL

value: white, b:black, nw:non-white):H

tag: patient

tag: rna integrity number (rin)

tag: dementia

tag: dyskinesia

tag: cholinesterase inhibitors


title: 2722_PD_PUT

value: white, b:black, nw:non-white):NW


title: 2709_CTRL_CAU


title: 2707_CTRL_CAU

value: white, b:black, nw:non-white):B


title: 2706_CTRL_PUT

value: white, b:black, nw:non-white):W


title: 2710_CTRL_PUT


title: 2708_CTRL_PUT


title: 2705_CTRL_CAU


title: 2682_PD_PUT

value: PD

value: Yes

value: No


title: 2684_CTRL_PUT

value: male, f:female):F


title: 2683_CTRL_CAU

value: CAU


title: 2681_PD_CAU

value: UK


title: 2719_CTRL_CAU


title: 2703_PD_CAU


title: 2650_PD_PUT


title: 2649_PD_CAU


title: SAI3, hbNES cells, day 7

description: fpkm.csv

tag: cell line

tag: cell type

value: hindbrain neuroepithelial stem cell

tag: genotype

value: WT

tag: treatment

value: cerebellar granule neuron differentiation

value: Day 7


title: 2704_PD_PUT

tag: disease

tag: region

tag: age at disease onset

value: male, f:female):M


title: 2648_PD_PUT

value: PUT

tag: age at death


title: 2644_CTRL_PUT

value: Control

value: CTRL

tag: disease duration


title: 2647_PD_CAU

tag: post mortem index (pmi)


title: 2711_CTRL_CAU

tag: gender (m

value: white, b:black, nw:non-white):H


title: 2645_PD_CAU

tag: ethnicity (w


title: 2714_PD_PUT

tag: patient


title: 2640_CTRL_PUT

tag: rna integrity number (rin)


title: 2641_CTRL_CAU

tag: dementia


title: 2643_CTRL_CAU

tag: dyskinesia


title: 2638_CTRL_PUT

tag: cholinesterase inhibitors


title: 2639_CTRL_CAU


title: 2628_PD_PUT


title: 2636_CTRL_PUT


title: 2623_CTRL_CAU


title: 2625_PD_CAU


title: 2621_CTRL_CAU


title: 2622_CTRL_PUT


title: 2634_PD_PUT


title: 2633_PD_CAU


title: 2627_PD_CAU


title: 2635_CTRL_CAU


title: 2626_PD_PUT


title: 2620_CTRL_PUT


title: 2637_CTRL_CAU


title: 2624_CTRL_PUT


title: 2646_PD_PUT


title: 2616_CTRL_PUT


title: 2619_CTRL_CAU


title: 2618_CTRL_PUT


title: 2642_CTRL_PUT


title: 2602_CTRL_PUT


title: 2615_CTRL_CAU


title: 2601_CTRL_CAU


title: 2600_CTRL_PUT


title: 2598_CTRL_PUT


title: 2597_CTRL_CAU


title: 2599_CTRL_CAU


title: 2596_CTRL_PUT


title: 2595_CTRL_CAU


title: 2592_CTRL_PUT


title: 2588_CTRL_PUT


title: 2591_CTRL_CAU


title: 2617_CTRL_CAU


title: 2586_PD_PUT


title: 2584_PD_PUT


title: 2587_CTRL_CAU


title: 2581_PD_CAU


title: 2580_PD_PUT


title: 2803_PD_CAU

value: white, b:black, nw:non-white):B


title: 2805_CTRL_CAU


title: 2802_PD_PUT


title: 2582_PD_PUT

value: white, b:black, nw:non-white):W


title: 2579_PD_CAU

value: PD


title: 2793_PD_PUT


title: 2804_CTRL_PUT


title: 2583_PD_CAU

value: Yes


title: 2792_PD_CAU

value: No


title: 2788_PD_CAU


title: 2789_PD_PUT


title: 2790_PD_CAU

value: male, f:female):F


title: 2594_PD_PUT


title: 2791_PD_PUT


title: 2784_PD_CAU

value: CAU


title: 2786_PD_CAU


title: 2785_PD_PUT


title: 2585_PD_CAU

value: UK


title: 2787_PD_PUT


title: 2781_PD_PUT


title: 2782_PD_CAU


title: 2780_PD_CAU


title: 2593_PD_CAU


title: 2777_PD_PUT


title: 2779_PD_PUT


title: 2776_PD_CAU


title: 2778_PD_CAU


title: 2756_CTRL_CAU


title: 2759_CTRL_PUT


title: 2774_PD_CAU


title: 2755_CTRL_PUT


title: 2757_CTRL_PUT


title: 2749_CTRL_PUT


title: 2748_CTRL_CAU


title: 2751_CTRL_PUT


title: 2754_CTRL_CAU


title: 2753_CTRL_PUT


title: 2734_CTRL_PUT


title: 2783_PD_PUT


title: 2752_CTRL_CAU


title: 2732_CTRL_PUT


title: 2733_CTRL_CAU


title: 2730_CTRL_PUT


title: spinal cord-syringomyelia 4w-6w, replicate 2 [scRNA-seq]

city: Beijing

first: Xianming

last: Wu

state: Chaoyang District

address: Unit 2, No.1 West Beichen Road

country: China

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

description: DNBelab C4

data_processing:
DNBC4tools used tor analysis
Assembly: Rnor_6.0(Ensembl release 89)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Spinal cord

extract_protocol:
The purity of RNA was determined by NanoPhotometer (IMPLEN, CA, USA). RNA integrity and concentration was assessed using the RNA Nano6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Qualified RNA was subjected to construct double stranded PCR library using MGI Easy RNA library preparation kit. Sequencing was performed on DNBSEQ-T7 and 150bp double ended sequencing reads was obtained.
The volume of single-cell suspension that was required to generate single-cell GEMs (gel beads in the emulsion) per sample was loaded onto the Chromium Controller (DNBSEQ-T7). Libraries were prepared using the DNBelab C series single-cell RNA library preparation kit according to the manufacturer’s specifications. Final library quantification and quality control were performed using a Qubit 3.0 and LabChip GX Touch, followed by sequencing on DNBSEQ-T7.

tag: time point/treatment

value: 4w-6w after extradural compression

tag: tissue

value: Spinal cord

tag: strain

value: Sprague-Dawley

tag: age


title: spinal cord-syringomyelia 4w-6w, replicate 3 [scRNA-seq]

description: DNBelab C4


title: spinal cord-syringomyelia 4w-6w, replicate 1 [scRNA-seq]

description: DNBelab C4


title: 2775_PD_PUT

tag: disease


title: 2758_CTRL_CAU

tag: region


title: 2728_PD_PUT

tag: age at disease onset


title: 2727_PD_CAU

tag: age at death


title: 2750_CTRL_CAU

tag: disease duration


title: 2726_PD_PUT

tag: post mortem index (pmi)


title: spinal cord-syringomyelia 6w, replicate 2 [scRNA-seq]

description: DNBelab C4

value: 6w after extradural compression


title: spinal cord-syringomyelia 4w [scRNA-seq]

description: DNBelab C4

value: 4w after extradural compression


title: spinal cord-syringomyelia 6w, replicate 1 [scRNA-seq]

description: DNBelab C4


title: spinal cord-syringomyelia 2w [scRNA-seq]

description: DNBelab C4

value: 2w after extradural compression


title: 2731_CTRL_CAU

value: Control

tag: gender (m

value: male, f:female):M


title: 2686_PD_PUT

value: PUT

tag: ethnicity (w


title: 2688_PD_PUT

value: white, b:black, nw:non-white):B

tag: patient


title: 2680_PD_PUT

value: white, b:black, nw:non-white):W

tag: rna integrity number (rin)


title: 2690_PD_PUT

value: PD

tag: dementia


title: 2729_CTRL_CAU

value: CTRL

tag: dyskinesia


title: spinal cord-syringomyelia 4w-6w, biol rep 1 [4w-6w1]

data_processing:
Sequence reads were trimmed by trim_galore
Trimmed sequence reads were mapped to Ensembl.Rnor_v6.0.89 by HISAT2
Read count extraction and normalization were performed using featureCounts
DESeq2 were used to do differential gene expression analysis based on the negative binomial distribution
FPKM table  was created by our R script based on read counts results and genome annotation
Assembly: Rattus_norvegicus.Ensembl.Rnor_v6.0.89

extract_protocol:
The spinal cord tissue centered on the syringomyelia segments were collected at different time points after operation. The fresh tissue for bulk RNA-seq was homogenized in 1mL TRIzol (Invitrogen) for further purification and RNA-seq.
The tissue for single-cell RNA-seq was dissociated using PDS Kit, Papain Vial with a concentration of 25 U/ml in EBSS. The tissue was digested at a constant temperature of 37°C for one hour, and gently triturated with fire-polished Pasteur pipettes once every 10 minutes. The single-cell suspension was filtered through a 40 μm cell strainer and then centrifuged at 400 r/min for 5 min at 4 ℃. The pellet was washed with DMEM basic containing 0.1% bovine serum albumin (BSA). Cell viabilities were assessed by trypan blue staining. The cells were diluted to a final concentration of 1 × 106/mL in PBS with 0.1% BSA.

tag: strain background

tag: genotype


title: spinal cord-syringomyelia 4w-6w, biol rep 2 [4w-6w2]

source_name: spinal cord tissue centered on the syringomyelia segments

tag: tissue


title: 2687_PD_CAU

value: No

value: Yes

tag: cholinesterase inhibitors


title: 2685_PD_CAU

value: CAU

value: male, f:female):F


title: 2689_PD_CAU

value: UK


title: spinal cord-syringomyelia 6w, replicate 3 [scRNA-seq]

description: DNBelab C4

tag: time point/treatment

value: Spinal cord

tag: strain

tag: age


title: 2725_PD_CAU

tag: disease

tag: region

tag: age at disease onset


title: spinal cord-syringomyelia 4w, biol rep 3 [4w3]

value: Sprague-Dawley

value: spinal cord tissue centered on the syringomyelia segments


title: spinal cord-syringomyelia 6w, biol rep 1 [6w1]


title: spinal cord-syringomyelia 6w, biol rep 2 [6w2]


title: spinal cord-syringomyelia 4w-6w, biol rep 3 [4w-6w3]


title: 2678_CTRL_PUT

tag: age at death

tag: disease duration

tag: post mortem index (pmi)


title: 2679_PD_CAU

tag: gender (m

tag: ethnicity (w

tag: patient


title: spinal cord-syringomyelia 4w, biol rep 2 [4w2]


title: 2677_CTRL_CAU

tag: rna integrity number (rin)

tag: dementia

tag: dyskinesia


title: spinal cord-syringomyelia 4w, biol rep 1 [4w1]

tag: strain background

tag: tissue

tag: genotype


title: 2676_CTRL_PUT

tag: cholinesterase inhibitors


title: spinal cord-syringomyelia 2w, biol rep 3 [2w3]

tag: age


title: spinal cord-control [scRNA-seq]

description: DNBelab C4

tag: time point/treatment

value: sham control

tag: strain


title: spinal cord-syringomyelia 6w, biol rep 3 [6w3]


title: 2675_CTRL_CAU

tag: disease

tag: region

tag: age at disease onset


title: spinal cord-syringomyelia 2w, biol rep 2 [2w2]


title: spinal cord-syringomyelia 2w, biol rep 1 [2w1]


title: spinal cord-Control, biol rep 2 [Sham2]


title: 2673_CTRL_CAU

tag: age at death

tag: disease duration

tag: post mortem index (pmi)


title: 2672_CTRL_PUT

tag: gender (m

tag: ethnicity (w

tag: patient


title: spinal cord-Control, biol rep 3 [Sham3]


title: spinal cord-Control, biol rep 1 [Sham1]


title: 2667_CTRL_CAU

tag: rna integrity number (rin)

tag: dementia

tag: dyskinesia


title: 2670_CTRL_PUT


title: 2671_CTRL_CAU


title: 2654_PD_PUT


title: 2668_CTRL_PUT


title: 2669_CTRL_CAU


title: 2589_CTRL_CAU


title: Cultured normal human epidermal keratinocytes at 38 degrees C (mRNA)

first: Jun-Ichi

last: Sakabe

address: Blk4 Lv3, Outram Rd

department: Plastic Reconstructive and Aesthetic Surgery

institute: Singapore General Hospital (SGH)

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and pairedend clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other nonsplice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Assembly: Homo Sapiens(GRCh38)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Epidermis

growth_protocol:
cells are cultured at 38 degrees C
Cells were cultured with 3T3J2 feeder cells in cFAD medium at each temperature (32, 35, 36, 37 and 38 degrees C)

extract_protocol:
Followed a protocol of miRNAeasy mini kit (QIAGEN)
RNA libraries were prepared for sequencing by using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technology, CA, USA) in Novogen Experimental Department

treatment_protocol: 100 nM Rapamycin was added into medium which are inchubated at 37 degrees C from day0 to end of cell culture

tag: tissue

value: epidermis

tag: cell type

value: keratinocytes

tag: cell line

tag: treatment

value: 38 degrees C


title: Cultured normal human epidermal keratinocytes with 100 nM Rapamycin at 37 degrees C (mRNA)

growth_protocol:
cells are cultured at 37 degrees C
Cells were cultured with 3T3J2 feeder cells in cFAD medium at each temperature (32, 35, 36, 37 and 38 degrees C)

value: 37 degrees C , rapamycin


title: 2674_CTRL_PUT

value: Control

value: PUT

value: male, f:female):M

tag: cholinesterase inhibitors


title: Cultured normal human epidermal keratinocytes at 37 degrees C (mRNA)

value: 37 degrees C


title: Cultured normal human epidermal keratinocytes at 32 degrees C (mRNA)

growth_protocol:
cells are cultured at 32 degrees C
Cells were cultured with 3T3J2 feeder cells in cFAD medium at each temperature (32, 35, 36, 37 and 38 degrees C)

value: 32 degrees C


title: Cultured normal human epidermal keratinocytes at 35 degrees C (mRNA)

growth_protocol:
cells are cultured at 35 degrees C
Cells were cultured with 3T3J2 feeder cells in cFAD medium at each temperature (32, 35, 36, 37 and 38 degrees C)

value: 35 degrees C


title: 2653_PD_CAU

tag: disease

value: PD

value: CAU

value: white, b:black, nw:non-white):W

value: Yes

value: No


title: 2590_CTRL_PUT

tag: region

value: CTRL


title: NLRP3def_con_c

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

hyb_protocol: Equal amounts of Cy3-labelled samples were hybridized onto Whole Human Genome 4 × 44 K one-color oligonucleotide arrays (G4112F, Agilent Technologies) for 17 h in a Tecan  HS 4800TM Pro hybridization Station.

scan_protocol: The arrays were scanned on an Agilent G2565BA microarray scanner and further processed using Agilent Feature Extraction Software (version 10.7.3.1). For each feature (or spot) on the array, the feature extraction output file contains the Cy3 fluorescence signal, together with feature quality and gene information.

data_processing: Fluorescence signals were log2-transformed, quantile normalized, and filtered with regard to reliability of the feature. Reliable features were defined as features: (1) of which the intensity was higher than the feature noise level, (2) of which the intensity was below the feature saturation level, (3) that were not a population outlier, (4) that were uniform spots, and (5) that were not a control feature.

source_name: THP-1 monocytes

label_protocol: Labelled RNA was prepared and hybridized for each of the eight test conditions. This was performed for three biological replicates, resulting in 24 samples. Fluorescently labelled samples were obtained using the Quick Amp Labelling kit (Agilent). Briefly, 1 µg of total RNA was reverse transcribed into complementary DNA (cDNA) using a T7-promotor primer and MMLV reverse transcrip_x0002_tase. The cDNA was transcribed into complementary RNA (cRNA), during which, it was fluorescently labelled by incorporation of Cy3-CTP. After purification using the RNeasy mini kit (Qiagen), cRNA yield and specific activity were determined using a NanoDrop spectrophotometer.

growth_protocol: THP-1 cells (ATCC TIB-202), THP1-defASC cells, and THP1-defNLRP3 cells (Invivo_x0002_Gen, Toulouse, France) were used in this study. The cells were cultured in CCM (RPMI 1640 (Gibco) supplemented with foetal calf serum (10% v/v, Greiner-Bio), penicillin (100 U/mL), and streptomycin (100 µg/mL) (Gibco)). Additionally, the ASC- and NLRP3-deficient THP-1 cells were cultured in CCM supplemented with HygroGold (200 µg/mL, InvivoGen) to maintain the siRNA responsible for suppression of ASC or NLRP3. All cell lines were sub-cultured twice per week, seeded to a cell density of 2 × 10^5 cells/mL, and not allowed to grow to a density greater than 1 × 10^6 cells/mL. Cells were not cultured beyond twenty passages to prevent genetic divergence. The wildtype, ASC-deficient, and NLRP3-deficient THP-1 cells were differentiated into macrophage-like cells by culturing for 3 h in the presence of 100 ng/mL phorbol 12-myristate 13-acetate (PMA) (Sigma) in 96-well format at a cell density of 5 × 10^5 cells/mL, 100 µL/well. After this incubation, the cells were adherent. The medium was replaced with fresh culture medium without PMA and the plates were incubated for 24 h at standard conditions (humidified incubator at 37°C, 5% CO2). After this incubation period, the cells were exposed to a two-fold dilution series of gold nanoparticles (GNPs), at 0.05 nM for 48 h at standard conditions.

extract_protocol: For each exposure condition, the cell lysates of two replicate wells were pooled to obtain sufficient RNA. Total RNA was isolated using the miniRNeasy RNA isolation kit, according to the specifications of Qiagen. The RNA concentration was determined using a NanoDrop Spectrophotometer. RNA integrity was analysed using the Agilent 2100 Bioanalyzer. Samples showing an RNA Integrity Number value above 7 were qualified for microarray analysis. RNA was stored in RNase-free water (Qiagen) at −80°C until further use.

treatment_protocol: After centrifugation of the plates and taking off the supernatants, 120 µL consisting of 5 parts RNAprotect Cell Reagent (Qiagen) and 1 part PBS (Gibco) was added to each well. The cell lysates were frozen at −80°C until further use.

tag: genotype

value: NLRP3 deficient

tag: particle

tag: date

value: THP-1 monocytes


title: NLRP3def_GNP6_c

value: GNP6 (rods)


title: WT_con_c

value: wild type


title: ASCdef_GNP6_c

value: ASC deficient