title: SEC-seq Replicate for VEGF-A on Normoxic MSC-loaded Nanovials, VEGF-A barcode

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

institute: University of California, Los Angeles

description:
SECseq.normalizedData_MSC.Norm.Nanovials.Replicate.txt.gz
SECseq.metadata_MSC.Norm.Nanovials.Replicate.txt.gz
SECseq_Normoxic_MSCs_Nanovials_Rep_VEGFA.Barcode

data_processing:
library strategy: Single cell VEGF-A antibody barcode library
Data was demultiplexed and output as FASTQ in Basespace using library indexes
FASTQs were mapped to their respective genomes using the Cellranger utility to construct a gene by cell matrix for each sample
Oligo barcodes (SEC-seq or nanovial hashing tags) were also mapped to cells using Cellranger multiconfig setup.
Gene by cell matrixes were processed and filtered in R using Seurat and basic utilities
For the mixed species experiment, the data was mapped to a joined human-mouse contig genome using Cellranger. Cells were assigned to each species based on the ratio of human to mouse reads
Assembly: GRCh38 (human), GRCm38 (mouse)
Supplementary files format and content: Data was filtered and normalized in Seurat. Nanovial barcodes and VEGFA barcodes are provided in metadata as raw unnormalized reads, while the cell-gene matrix is log transformed and normalized to cell depth.
Supplementary files format and content: For the purpose of filtering based on Nanovial barcodes, cell were removed from processed data which did not satisfy either barcode to barcode ratio cutoffs ("Mixed") or which had insufficient barcode impying separation from the nanovial

source_name: adipose

growth_protocol: Immortalized human adipose-derived MSCs (ATCC SCRC-4000) were cultured in MSC Basal Medium supplemented with Low Serum MSC Growth Kit for adipose MSCs.

extract_protocol:
Nanovials were loaded directly into the cell mix at a concentration of 500 nanovials per ul for use in the 10x Chromium workflow.
Libraries were constructed as described in the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index) with Feature Barcoding technology for Cell Surface Protein and Cell Multiplexing)
scRNAseq libraries were constructed as typically described in the guide above.
SEC-seq libraries proceeded via normal workflow, with inclusion of construction of a library to detect the oligo-barcoded antibody using the Feature Barcode library workflow in the Single Cell User guide above

treatment_protocol: MSCs were cultured and loaded onto gelatin coated nanovials for 2 hours before straining excess cells. Cells were bound and allowed to secrete for a 12 hour incubation. Nanovials are then collected and incubated with anti human VEGF-A antibody for 30 minutes. Nanovials containing single cells were isolated by FACS using calcein stain. Cell-loaded nanovials were then diluted and added directly to the single cell RNA-seq workflow.

tag: tissue

value: adipose

value: ATCC SCRC-4000

value: Mesenchymal Stromal Cell


title: HP1a_b_tir2_1h_with_a_with_d_rep1

status: Public on Nov 22 2023

type: SRA

city: Shenzhen

first: Haoyue

last: Zhang

address: Gaoke Innovation Center, Guangqiao Road, Guangming District, Shenzhen

country: China

institute: Shenzhen Bay Lab

description: hic

library_source: genomic

data_processing:
In-situ Hi-C data from each individual clone or biological replicates were aligned to mouse reference genome mm9 using bowite2 (global parameters: --very-sensitive -L 30 --score-min L, -0.6,-0.2 --end-to-end –reorder; local parameters: --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder). Reads were paired up and PCR duplicates were removed through the Hi-C Pro software (v3.0.0) to generate a valid interaction pair file. The output pair files were then converted to “.hic” files using the hicpro2juicebox utility. HiC files were also converted to “.cool” files using the Hicexplorer (v3.7). For replicate or clone-merged samples, similar steps were taken on reads merged from each clone or biological replicates.
Assembly: mm9
Supplementary files format and content: cool and hic files of each individual biological replicate of hic data are provided.

molecule: genomic DNA

organism: Mus musculus

source_name: G1E-ER4 cells

growth_protocol: G1E-ER4 is a subline of the GATA1-null proerythroblast cell line G1E (Weiss et al, Mol. Cell. Biol. 17, 1642–51 (1997).). Cells were cultered in IMDM medium, supplemented with 15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha at 37 degrees with 5% CO2 (as described in Weiss et al., 1997).

extract_protocol:
FACS purified cells (0.1 million) were lysed in 1ml cold Cell Lysis Buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40/Igepal) for 10min on ice. Nuclei were pelleted at 4℃ and washed once with cold 1.4 × NEB buffer 3.1 (NEB Cat#B7203S). Nuclei were then re-suspended in 25ul of 1.4 × NEB buffer 3.1 and treated with 0.1% SDS for 10min at 65℃. Nuclei were then treated with 1% Triton X-100 to quench SDS for 1h at 37℃. Chromatin was digested with 25U DpnII restriction enzyme (NEB, Cat#R0543M) at 37℃ overnight with shaking (950rpm on a thermal mixer). After overnight digestion, an additional stroke of 25U DpnII was added into the system to further digest the genome for 4 hours at 37℃. After the 2nd stroke of digestion, nuclei were incubated at 65℃ for 20min to inactivate DpnII. Digested chromatin fragments were then cooled down to room temperature and blunted with dCTP, dGTP, dTTP (Diamond Cat#B110049, B110050, B110051) and Biotin-14-dATP (active motif, Catalog No: 14138) using 6.6U DNA Polymerase I, Large (Klenow) fragment (NEB, Cat#M0210). Chromatin was then ligated in-situ with 2000U T4 DNA ligase (NEB, Cat#M0202M) for 4 hours at 16℃ followed by further incubation for 2 hours at room temperature. Chromatin was then reverse-crosslinked overnight at 65℃ in the presence of 1% SDS and proteinase K (G-clone Cat#EZ0970). After reverse-crosslinking, DNase-free RNase A (Vazyme Cat#DE111-01) was added to the system for 30min at 37℃ to remove RNA. DNA was then extracted by phenol-chloroform extraction, precipitated, and dissolved in 130ul of nuclease free water.
DNA was sonicated to 200-300bp fragments with a QSonica Q800R3 sonicator (40% amplitude, 15s ON and 15s OFF, 13min sonication) and purified with VAHTS DNA Clean Beads (Vazyme Cat#N411). Biotin-labeled DNA fragments was enriched by incubation with 100μl Dynabeads MyOne Streptavidin C1 beads (Thermal Fisher Scientific, Cat#65002) at room temperature for 15min. Streptavidin C1 beads were then washed twice with 1 × B&W buffer (5mM Tris-HCl, pH 7.5; 0.5mM EDTA; 1M NaCl). Beads were re-suspended in 30ul of 1 × NEB Buffer2 (NEB Cat#7002S) containing 9U of T4 DNA polymerase (NEB, Cat#M0203S) and 40uM dATG/dGTP and incubated at 20℃ for 4 hours to remove unligated fragments. Beads were then washed twice with 1 × B&W buffer and subject to library construction. DNA end repair, dA-tailing and adaptor ligation were constructed on beads, using the AHTS Universal DNA Library Prep Kit for Illumina or MGI (Vazyme, Cat# ND627-01, NDM607-02) based on the manufacture’s protocol. To eluted DNA from streptavidin beads, the library mixture was treated with 0.1% SDS and incubated at 98℃ for 10min. Released DNA was collected from the supernatant and purified with VAHTS DNA Clean Beads. Finally, the library was amplified for 9 cycles on a thermal cycler, using the VAHTS® HiFi Amplification Mix. PCR products were then purified with VAHTS DNA Clean Beads and sequenced on an Illumina NextSeq500 or MGI DNBSEQ-T7 sequencing platform.

treatment_protocol: G1E-ER4:HP1a-AID-mCherry/HP1b-FKBPF36V-GFP cells were arrested to prometaphase through nocodazole treatment for 8h. During the last 4 hours of nocodazole treatment, cells were treated with one of the following combinations of drugs: (i) 5-Ph-IAA(-)/dTag13(-); (ii) 5-Ph-IAA(+)/dTag13(-); (iii) 5-Ph-IAA(-)/dTag13(+) and (iv) 5-Ph-IAA(+)/dTag13(+). Cells were then allowed to be released from nocodazole and proceed toward the next cell cycle. After 1h and 6h of nocodazole release, early-G1 and late-G1 cells under different HP1 protein configurations were collected. Note, that drug treatment was maintained during the course of nocodazole release.

tag: cell line

value: G1E-ER4 cells

tag: cell type

value: erythroid

tag: genotype

tag: treatment

value: noc 8h release 1h + 5-Ph-IAA 8h + dtag13 8h


title: control_mo_atac_nf_rep2

city: Boston

first: Marcos

last: Simoes-Costa

state: Massachusetts

address: 300 Longwood Ave

department: Pathology

country: USA

institute: Boston Children's Hospital

description: ATAC-seq

data_processing:
For ATAC-seq data analysis, paired-end sequencing reads were trimmed using Cutadapt (v2.10) using the following arguments “cutadapt -a CTGTCTCTTATACACATCT -A AGATGTGTATAAGAGACAG --minimum-length=25”.
Bowtie2 (v2.4.2) was used to align trimmed reads to the reference chicken galGal6 assembly using the following arguments “--no-unal --no-mixed --no-discordant -X 2000”. Duplicate reads were then marked by the Picard MarkDuplicates tool and SAMtools was used to filter BAM files to discard unmapped reads, reads which were not the primary alignment, reads failing platform/vendor quality checks, and PCR/optical duplicates (-F 1804 -f 2).
MACS2 was used to call peaks genome-wide with a q value cutoff equal to 0.05 with the following arguments “-f BAMPE -g 1218492533 -q 0.05 call-summits --nomodel --shift 37 --extsize 73”. Consensus peaksets between biological replicates were determined by intersecting the peaksets of each replicate by using the BEDTools intersect function and only keeping peaks present in both replicates.
Differential accessibility analysis between GTBlue -Control MO and Sox9 MO ATAC-seq samples was performed using the R package DiffBind (version 2.14.0). Peak files corresponding to each sample/replicate were first filtered to include only peaks that map to chromosomes (not contigs). Reads from each sample/replicate were counted at a consensus peakset containing peaks that were present in at least 2 out of the 4 samples. This was done by specifying minOverlap=2 in the dba.count() function. Binding affinity matrix scores were reported after performing a TMM normalization using full library size. The consensus peakset was filtered to remove peaks with low read counts (filter=50 with filterFun applied to the scores of each interval). The comparison between samples was set up with the dba.contrast() function accounting for the fact that the samples were unpaired (i.e., Control MO and Sox9 MO transfected NFS came from different embryos). Differential accessibility statistical analysis was performed using the DBA_EDGER method. Assignment of differential peaks to their closest gene was done using the R package ChIPseeker.
Assembly: Ensembl galGal6
Supplementary files format and content: bw file

organism: Gallus gallus

source_name: Primary Neural Crest Cells

growth_protocol: Prior to embryo dissection, tissue cultureware were coated with 25 ug/ml fibronectin (Sigma, F1141) and incubated for 45 min in a 37°C humidified incubator maintained at 5%CO2 atmosphere. After incubation, the fibronectin solution was removed from the cultureware and DMEM (Sigma, D6046) supplemented with 10% FBS (Thermo Fisher Scientific, 10-437-028) was added. NCC explants were obtained by thinly micro-dissecting dorsal neural folds from HH9 (6-7 somite) embryos in Ringer’s solution as previously described (http://www.genome.org/cgi/doi/10.1101/gr.249680.119). Each dissected neural fold was then aspirated in a minimal amount of Ringer’s solution (2.5 ul) and placed in a well of the fibronectin-coated tissue cultureware containing media. The explants were incubated for at least 12 hours under normoxic conditions in a humidified 37°C incubator maintained at 5% CO2 atmosphere. The duration of incubation was determined by the appropriate conditions pertaining to specific experiments.

extract_protocol:
NFs were dissected from HH9 embryos as described in the CUT&RUN protocol (n=2 embryos, n=4 NFs) and dissociated in Accumax (Innovative Cell Technologies, AM105) for 30 min at room temperature to achieve a single cell suspension.
ATAC-seq was performed as previously described (https://doi.org/10.1038/nmeth.4396). Briefly, dissociated cells were collected by centrifugation at 500 rcf for 5 min in a swinging bucket centrifuge and washed in resuspension buffer containing 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2. After washing, the cells were resuspended in lysis buffer composed of the resuspension buffer with 0.1% NP-40 (Sigma, I8896), 0.1% Tween-20 (Sigma, P1379), and 0.01% Digitonin (Millipore, 300410). The samples were incubated on ice for 3 min, at which point the lysis buffer was washed out with resuspension buffer containing only 0.1% Tween-20. Upon centrifugation at 500 rcf for 5 min, the supernatant was aspirated, and nuclei were resuspended in 50 ul of transposition mixture containing 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 10% Dimethyl Formamide (Sigma, D4551), 1X PBS, 0.1% Tween-20, 0.01% Digitonin, and 5 ul Tn5 transposase (Illumina, 20034210). Transposition was performed for 1 hour at 37°C in a thermal mixer. The pre-amplification DNA was purified using the Qiagen Minelute Reaction Cleanup Kit (Qiagen, 28204). Library amplification PCR was performed using the Q5® High-Fidelity 2X Master Mix (NEB, M0492S). Library size selection and cleanup was carried out using Ampure XP beads (Beckman Coulter, A63881). Prepared libraries were run on an Agilent 4200 Tapestation with D5000 Reagents and D500 ScreenTape for quality control and final libraires were pooled to equimolar concentrations using the NEB Library Quantification Kit.

treatment_protocol: Sox9 knock-down was achieved using a translation-blocking MO targeted to the mRNA of the gene (https://doi.org/10.1073/pnas.0906596107). Whole embryos were injected with either the Sox9 MO or the GTBlue-Control MO at a final concentration of 1 mM in Tris-HCl pH 8.0 supplemented with 1 ug/ul carrier DNA. Embryos were cultured until HH9 (6-7 somites) as described previously and transferred to Ringer’s where the dorsal neural folds of Sox9 MO or GTBlue-Control MO transfected embryos were micro-dissected (n=2 embryos, n=4 NFs per biological replicate) and subjected to the ATAC-seq protocol (described above).

value: Primary Neural Crest Cells

tag: Stage

value: HH9 stage

value: Embryos electroporated with GTBlue-Control morpholino (1mM) at HH4 and allowed to develop ex ovo iuntil HH9

tag: transposase

value: Tn5 enzyme (Illumina 20034210)


title: control_mo_atac_nf_rep1

description: ATAC-seq


title: CRC_Y05_O05 006 Vim+FAP_i

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

description:
RNA (amplified oligo nucleotide probes)
112AOIs_n1222_5LOQ_Filtered_all_linear_normalized_counts.xlsx
Annotation_112AOIs.xlsx
Probe_QC_112_AOIs.xlsx

library_source: transcriptomic

data_processing:
GeoMx_NGS_Pipeline_ 2.0.0
Counts from barcodes corresponding to RNA probes were normalized with internal positive and negative controls and then normalized to ROI area.
The FastQ files generated by the Illumina sequencing were converted into digital count conversion (dcc) files, then loaded into the GeoMx DSP analysis suite as raw counts. The GeoMx DSP software captures the number of SYTO13 positive nuclei in each segment as well as the surface area of each segment, which were exported for data calibrations. From the software, the counts for oligonucleotides per segment were also exported into a package for quality control and data normalization protocols. Biological probe quality control was performed using default settings. A total of 112 AOIs were all carefully reviewed for segments with sequencing saturation of less than 45%, nuclei of fewer than 160, negative probe counts of less than 8, or a surface area of less than 12,000 squared microns. All 112 AOIs were included for further analysis following the NanoString user’s manual recommendations. Background correction and scaling were performed using geometric means and normalization was performed using Q3 averages of housekeeping genes. Genes with expression levels at or lower than the limit of quantification (LOQ) in at least 5% of segments were filtered out. A total of 1,223 genes passed quality control and were analyzed. Eight patients with four sporadic EOCC and four sporadic LOCC were processed. Per patient, a total of six ROIs with tumor invasive margin (TIM, three ROIs) and tumor center (TC, three ROIs), were selected, respectively.
Assembly: GRCh38.p13
Supplementary files format and content: Nanostring GeoMx normalized data, annotation, and probe data files as xlsx format
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: colon cancer

extract_protocol:
FFPE tissue sections of 5 µm thickness was prepared according to vendor's protocol with slight modifications. Sections baked at 60°C for 30 min, and incubated sequentially 3x 5 min in xylene, then 2x 5 min each in 100% EtOH, 95% EtOH, and H2O. Antigen retrieved by placing in EDTA at 100°C 20 min, followed by PBS 5 min. Slides then placed in staining jar of 1mg/mL Proteinase K at 37°C 15 min. This was followed by washing in 10% NBF 10 min, 2x washes in NBP stop buffer, and 1x PBS. RNA probe mix was added to tissue slides with a hybridization coverslip at 37°C overnight. Then, slides were washed 2x with SSC buffer and formamide at 37°C, then 2x with SSC buffer. Slides stained for morphology markers SYTO13, PanCK+, VIM, and FAP. Slides were loaded onto NanoString GeoMx DSP for imaging/barcode acquisition, following the manufacturer's protocol. Manual selection of 600-650 µm ROIs and AOIs were performed based on pathology defined areas and morphological markers.
Libraries constructed using NanoString NGS readout protocol. Dried aspirates in the collection plate were resuspended with 10 μL of nuclease-free water for 10 min, and 4 μL were transferred to a polymerase chain reaction (PCR) plate. Two μL of 5X PCR Master Mix (NanoString Technologies, Inc., Seattle, WA) and 4 μL of 17 a unique primer mix (NanoString) assigned by their position on the collection plate were added to each well. Contents were mixed by pipetting and the sealed PCR plate was transferred to a thermal cycler for an amplification for 18 cycles. PCR products were pooled in equal amounts. Pooled library was purified twice with a 1.2X magnetic beads-to-sample ratio with KAPA Pure Beads (Roche, Basel, Switzerland), each followed by two 80% ethanol washes, then eluted with Elution Buffer (Nanostring). The quality and quantity of the purified pooled library were assessed with High Sensitivity D1000 ScreenTape System (Agilent, Santa Clara, CA) and Qubit dsDNA High Sensitivity assay (Invitrogen, Waltham, MA), respectively. The library was denatured following Illumina’s recommendations and sequenced on NextSeq 550 (Illumina, San Diego, CA) with 27 paired-end cycles, achieving the minimum read depth (30 reads per μm2) or higher determined by the selected AOI’s sizes.

value: colon cancer

tag: type of_tissue

value: EOCC

tag: age of_patients

tag: annotation geomx_dsp

tag: segment tag

tag: scan id

tag: roi id

tag: cell type specific morphological marker

value: Vim+FAPi

tag: histological region

value: TC


title: HP1a_b_tir2_1h_with_a_no_d_rep1

description: hic

value: noc 8h release 1h + 5-Ph-IAA 8h


title: SEC-seq for VEGF-A on Hypoxic MSC-loaded Nanovials, VEGF-A barcode

description:
SECseq.normalizedData_MSC.Norm.and.Hypo.Pooled.Nanovials.txt.gz
SECseq.metadata_MSC.Norm.and.Hypo.Pooled.Nanovials.txt.gz
SECseq_Hypoxic_MSCs_Nanovials_VEGFA.Barcode

value: 500 µM deferoxamine


title: sox9_mo_atac_nf_rep2

description: ATAC-seq

value: Embryos electroporated with SOX9 morpholino (1mM) at HH4 and allowed to develop ex ovo iuntil HH9


title: gne140_atac_explant_rep1

description: ATAC-seq

data_processing:
For ATAC-seq data analysis, paired-end sequencing reads were trimmed using Cutadapt (v2.10) using the following arguments “cutadapt -a CTGTCTCTTATACACATCT -A AGATGTGTATAAGAGACAG --minimum-length=25”.
Bowtie2 (v2.4.2) was used to align trimmed reads to the reference chicken galGal6 assembly using the following arguments “--no-unal --no-mixed --no-discordant -X 2000”. Duplicate reads were then marked by the Picard MarkDuplicates tool and SAMtools was used to filter BAM files to discard unmapped reads, reads which were not the primary alignment, reads failing platform/vendor quality checks, and PCR/optical duplicates (-F 1804 -f 2).
MACS2 was used to call peaks genome-wide with a q value cutoff equal to 0.05 with the following arguments “-f BAMPE -g 1218492533 -q 0.05 call-summits --nomodel --shift 37 --extsize 73”. Consensus peaksets between biological replicates were determined by intersecting the peaksets of each replicate by using the BEDTools intersect function and only keeping peaks present in both replicates.
The R package DiffBind (version 2.14.0) was used to perform the differential accessibility analysis between DMSO and (R)-GNE-140 ATAC-seq samples. The consensus control peakset between DMSO replicates (generated using BEDTools as described in the “ATAC-seq Data Analysis” section) was first filtered to include only peaks that map to chromosomes (not contigs). This consensus peakset was then used to count reads from each sample/replicate. Binding affinity matrix scores were reported after performing a TMM normalization using full library size. The consensus peakset was filtered to remove peaks with low read counts (filter=50 with filterFun applied to the scores of each interval). The comparison between samples was set up to account for the fact that the DMSO and (R)-GNE-140 samples from each set of biological replicates were paired (i.e., tissue came from the same set of embryos for each condition). This was done by specifying the block=DBA_REPLICATE argument when setting up contrasts using the dba.contrast() function. Differential accessibility statistical analysis was performed using the DBA_EDGER method. Assignment of differential peaks to their closest gene was done using the R package ChIPseeker.
Assembly: Ensembl galGal6
Supplementary files format and content: bw file

treatment_protocol: NFs were dissected from six HH9 embryos and cultured as described above in paired fashion in media containing DMSO or 40 uM (R)-GNE-140 (Selleck Chemicals, S6675) (n=6 neural folds per control/treatment). This experiment was performed with two biological replicates. Explants were cultured for 12 hours using previously described settings, at which point they were collected from the plate by incubation with Accumax (Innovative Cell Technologies, AM105) for 10 minutes at 37°C. The single cells from each condition/sample were subjected to the ATAC-seq protocol (described above).

value: Neural crest cells explants cultured on fibronectin-coated tissue culture plates treated with 40 uM R-GNE-140


title: CRC_Y05_O05 006 PanCK+

value: PanCK+


title: SEC-seq for VEGF-A on Normoxic MSC-loaded Nanovials, VEGF-A barcode

description:
SECseq.normalizedData_MSC.Norm.and.Hypo.Pooled.Nanovials.txt.gz
SECseq.metadata_MSC.Norm.and.Hypo.Pooled.Nanovials.txt.gz
SECseq_Normoxic_MSCs_Nanovials_VEGFA.Barcode

value: adipose

value: ATCC SCRC-4000

value: Mesenchymal Stromal Cell


title: SEC-seq for VEGF-A on Hypoxic MSC-loaded Nanovials, mRNA

description:
SECseq.normalizedData_MSC.Norm.and.Hypo.Pooled.Nanovials.txt.gz
SECseq.metadata_MSC.Norm.and.Hypo.Pooled.Nanovials.txt.gz
SECseq_Hypoxic_MSCs_Nanovials_scGEX

library_source: transcriptomic single cell

data_processing:
Data was demultiplexed and output as FASTQ in Basespace using library indexes
FASTQs were mapped to their respective genomes using the Cellranger utility to construct a gene by cell matrix for each sample
Oligo barcodes (SEC-seq or nanovial hashing tags) were also mapped to cells using Cellranger multiconfig setup.
Gene by cell matrixes were processed and filtered in R using Seurat and basic utilities
For the mixed species experiment, the data was mapped to a joined human-mouse contig genome using Cellranger. Cells were assigned to each species based on the ratio of human to mouse reads
Assembly: GRCh38 (human), GRCm38 (mouse)
Supplementary files format and content: Data was filtered and normalized in Seurat. Nanovial barcodes and VEGFA barcodes are provided in metadata as raw unnormalized reads, while the cell-gene matrix is log transformed and normalized to cell depth.
Supplementary files format and content: For the purpose of filtering based on Nanovial barcodes, cell were removed from processed data which did not satisfy either barcode to barcode ratio cutoffs ("Mixed") or which had insufficient barcode impying separation from the nanovial


title: HP1a_b_tir2_1h_no_a_no_d_rep2

description: hic

value: G1E-ER4 cells

value: erythroid

value: noc 8h release 1h


title: CRC_Y05_O05 005 Vim+FAP_i


title: sox9_mo_atac_nf_rep1

description: ATAC-seq

value: Primary Neural Crest Cells

value: HH9 stage


title: atac_nf_rep2

description: ATAC-seq

data_processing:
For ATAC-seq data analysis, paired-end sequencing reads were trimmed using Cutadapt (v2.10) using the following arguments “cutadapt -a CTGTCTCTTATACACATCT -A AGATGTGTATAAGAGACAG --minimum-length=25”.
Bowtie2 (v2.4.2) was used to align trimmed reads to the reference chicken galGal6 assembly using the following arguments “--no-unal --no-mixed --no-discordant -X 2000”. Duplicate reads were then marked by the Picard MarkDuplicates tool and SAMtools was used to filter BAM files to discard unmapped reads, reads which were not the primary alignment, reads failing platform/vendor quality checks, and PCR/optical duplicates (-F 1804 -f 2).
MACS2 was used to call peaks genome-wide with a q value cutoff equal to 0.05 with the following arguments “-f BAMPE -g 1218492533 -q 0.05 call-summits --nomodel --shift 37 --extsize 73”. Consensus peaksets between biological replicates were determined by intersecting the peaksets of each replicate by using the BEDTools intersect function and only keeping peaks present in both replicates.
Similar to CUT&RUN data processing, featureCounts was used to generate peak count matrices for specific BAM files (when applicable) using the following arguments “--fracOverlap 0.5 --minOverlap 5 -p” and the edgeR package was used to first obtain TMM-normalized effective library sizes that were then used to normalize raw peak counts with the cpm() function. Peaks were annotated based on their closest gene using the R package ChIPSeeker and tornado and profile plots were generated using the DeepTools package. The bamCoverage function of DeepTools was used to generate RPGC-normalized BigWig files, for visualization of normalized read pile-up in a genome browser (IGV v2.13.0), using the following arguments “--outFileFormat bigwig --binSize 5 --numberOfProcessors 10 --normalizeUsing RPGC --effectiveGenomeSize 1218492533 --extendReads”.
Assembly: Ensembl galGal6
Supplementary files format and content: bw file

growth_protocol: Fertilized White Leghorn eggs were purchased from the University of Connecticut (Department of Animal Sciences). The eggs were incubated at 37°C until the embryos reached HH9 (6-7 somites) stage of development.

extract_protocol:
NFs were dissected from HH9 embryos as described in the CUT&RUN protocol (n=4 embryos, n=8 NFs) and dissociated in Accumax (Innovative Cell Technologies, AM105) for 30 min at room temperature to achieve a single cell suspension.
ATAC-seq was performed as previously described (https://doi.org/10.1038/nmeth.4396). Briefly, dissociated cells were collected by centrifugation at 500 rcf for 5 min in a swinging bucket centrifuge and washed in resuspension buffer containing 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2. After washing, the cells were resuspended in lysis buffer composed of the resuspension buffer with 0.1% NP-40 (Sigma, I8896), 0.1% Tween-20 (Sigma, P1379), and 0.01% Digitonin (Millipore, 300410). The samples were incubated on ice for 3 min, at which point the lysis buffer was washed out with resuspension buffer containing only 0.1% Tween-20. Upon centrifugation at 500 rcf for 5 min, the supernatant was aspirated, and nuclei were resuspended in 50 ul of transposition mixture containing 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 10% Dimethyl Formamide (Sigma, D4551), 1X PBS, 0.1% Tween-20, 0.01% Digitonin, and 5 ul Tn5 transposase (Illumina, 20034210). Transposition was performed for 1 hour at 37°C in a thermal mixer. The pre-amplification DNA was purified using the Qiagen Minelute Reaction Cleanup Kit (Qiagen, 28204). Library amplification PCR was performed using the Q5® High-Fidelity 2X Master Mix (NEB, M0492S). Library size selection and cleanup was carried out using Ampure XP beads (Beckman Coulter, A63881). Prepared libraries were run on an Agilent 4200 Tapestation with D5000 Reagents and D500 ScreenTape for quality control and final libraires were pooled to equimolar concentrations using the NEB Library Quantification Kit.

treatment_protocol: The collected embryos were wild-type.

value: wild-type

value: embryos developed in ovo until HH9

value: Tn5 enzyme (Illumina 20034210)


title: HP1a_b_tir2_1h_no_a_with_d_rep2

description: hic

value: noc 8h release 1h + dTag13 8h


title: CRC_Y05_O05 005 PanCK+

value: colon cancer

value: EOCC

value: TC


title: Normoxic and Hypoxic MSC-loaded Nanovials pooled scRNAseq, Nanovial barcode

description:
scGEX.normalizedData_MSC.Norm.Hypo.Pooled.Nanovials.txt.gz
scGEX.metadata_MSC.Norm.Hypo.Pooled.Nanovials.txt.gz
Normoxic_Hypoxic_MSCs_Pooled_Nanovials_Nano.Barcode

data_processing:
library strategy: Single cell nanovial barcode library
Data was demultiplexed and output as FASTQ in Basespace using library indexes
FASTQs were mapped to their respective genomes using the Cellranger utility to construct a gene by cell matrix for each sample
Oligo barcodes (SEC-seq or nanovial hashing tags) were also mapped to cells using Cellranger multiconfig setup.
Gene by cell matrixes were processed and filtered in R using Seurat and basic utilities
For the mixed species experiment, the data was mapped to a joined human-mouse contig genome using Cellranger. Cells were assigned to each species based on the ratio of human to mouse reads
Assembly: GRCh38 (human), GRCm38 (mouse)
Supplementary files format and content: Data was filtered and normalized in Seurat. Nanovial barcodes and VEGFA barcodes are provided in metadata as raw unnormalized reads, while the cell-gene matrix is log transformed and normalized to cell depth.
Supplementary files format and content: For the purpose of filtering based on Nanovial barcodes, cell were removed from processed data which did not satisfy either barcode to barcode ratio cutoffs ("Mixed") or which had insufficient barcode impying separation from the nanovial

value: 500 µM deferoxamine for the hypoxic MSCs


title: HP1a_b_tir2_1h_with_a_no_d_rep2

description: hic

value: noc 8h release 1h + 5-Ph-IAA 8h


title: CRC_Y05_O05 008 PanCK+

value: LOCC

value: PanCK+

value: TIM


title: SEC-seq Replicate for VEGF-A on Normoxic MSC-loaded Nanovials, mRNA

description:
SECseq.normalizedData_MSC.Norm.Nanovials.Replicate.txt.gz
SECseq.metadata_MSC.Norm.Nanovials.Replicate.txt.gz
SECseq_Normoxic_MSCs_Nanovials_Rep_scGEX

value: adipose

value: ATCC SCRC-4000

value: Mesenchymal Stromal Cell


title: CRC_Y05_O05 004 Vim+FAP_i

value: Vim+FAPi


title: atac_nf_rep1

description: ATAC-seq

value: Primary Neural Crest Cells

value: HH9 stage


title: SEC-seq for VEGF-A on Normoxic MSC-loaded Nanovials, mRNA

description:
SECseq.normalizedData_MSC.Norm.and.Hypo.Pooled.Nanovials.txt.gz
SECseq.metadata_MSC.Norm.and.Hypo.Pooled.Nanovials.txt.gz
SECseq_Normoxic_MSCs_Nanovials_scGEX


title: Normoxic and Hypoxic MSC-loaded Nanovials pooled scRNAseq, mRNA

description:
scGEX.normalizedData_MSC.Norm.Hypo.Pooled.Nanovials.txt.gz
scGEX.metadata_MSC.Norm.Hypo.Pooled.Nanovials.txt.gz
Normoxic_Hypoxic_MSCs_Pooled_Nanovials_scGEX


title: HP1a_b_tir2_1h_no_a_no_d_rep1

description: hic

value: G1E-ER4 cells

value: erythroid

value: noc 8h release 1h


title: CRC_Y05_O05 004 PanCK+

value: colon cancer


title: MSC-loaded Nanovials scRNAseq, Nanovial barcode

description:
scGEX.normalizedData_MSC.Suspended.Sorted.and.Nanovial.txt.gz
scGEX.metadata_MSC.Suspended.Sorted.and.Nanovial.txt.gz
MSC_Nanovials_Nano.Barcode


title: CRC_Y05_O05 003 PanCK+

value: EOCC


title: CRC_Y05_O05 003 Vim+FAP+

value: Vim+FAP+


title: h3k18la_nf_rep1

description: CUT&RUN

data_processing:
Processing the CUT&RUN data involved trimming Illumina adapter sequences from the paired-end reads using Cutadapt (v2.10) (https://doi.org/10.14806/ej.17.1.200) and selecting reads that were at least 25-bp long using the following arguments -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25 -j 0.
The reads were then aligned to the reference chicken galGal6 assembly using Bowtie2 (v2.4.2) (https://doi.org/10.1038/nmeth.1923) with the following arguments “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 1000”. Duplicate reads were then marked by the Picard MarkDuplicates tool (https://github.com/broadinstitute/picard) and BAM files were filtered with SAMtools to discard unmapped reads, reads which were not the primary alignment, reads failing platform/vendor quality checks, and PCR/optical duplicates (-F 1804 -f 2).
MACS2 (https://doi.org/10.1186/gb-2008-9-9-r137) was used to call peaks with a q value cutoff equal to 0.05 with the following arguments “-f BAMPE -g 1218492533 -q 0.05 call-summits”. Consensus peaksets between biological replicates for each assayed histone mark or factor were determined by intersecting the peaksets of each replicate by using the BEDTools (https://doi.org/10.1093/bioinformatics/btq033) intersect function and only keeping peaks that were called in both replicates.
The subread package function featureCounts (https://doi.org/10.1093/bioinformatics/btt656) was used to generate peak count matrices for specific BAM files using the following arguments “--fracOverlap 0.5 --minOverlap 5 -p”. Before analyzing peak matrices, the R package edgeR was employed to first obtain TMM-normalized effective library sizes that were then used to normalize raw peak counts with the cpm() function. Peaks were annotated based on their closest gene using the R package ChIPSeeker (https://doi.org/10.1002/cpz1.585). Tornado and profile plots were generated using the python package DeepTools (https://doi.org/10.1093/nar/gku365). Motif enrichment was performed using HOMER. Reads per genomic content (RPGC) normalized BigWig files, for visualization of normalized read pile-up in a genome browser (IGV v2.13.0) (https://doi.org/10.1038/nbt.1754), were generated with the bamCoverage function of DeeTools using the following arguments “--outFileFormat bigwig --binSize 5 --numberOfProcessors 16 --normalizeUsing RPGC --effectiveGenomeSize 1218492533 --extendReads”.
Assembly: Ensembl galGal6
Supplementary files format and content: bw file
Library strategy: CUT&RUN

extract_protocol:
Neural crest cells were obtained by micro-dissecting dorsal neural folds (NFs) from HH9 embryos (n=5 embryos, n=10 NFs) and pre-somitic mesoderm (PSM) tissue was obtained by dissecting the posterior region of HH9 embryos (n=5 embryos, n=10 PSM strips). A cell suspension was achieved by dissociating embryonic tissue with Accumax (Innovative Cell Technologies, AM105) for 30 min at room temperature under mild agitation and gentle pipetting halfway through the incubation time. The cells were then subjected to the low-salt CUT&RUN protocol (as described in dx.doi.org/10.17504/protocols.io.zcpf2vn and the Methods section of the present study).
DNA libraries for CUT&RUN experiments were performed using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645) following the manufacturer’s protocol. Quality control of prepared libraries was performed using an Agilent 4200 Tapestation with D5000 Reagents (Agilent Part# 5067-5589) and D500 ScreenTape (Agilent Part# 5067-5588). Libraires were pooled to equimolar concentrations using the NEB Library Quantification Kit (NEB E730S) and sequenced with paired-end 37-bp reads on an Illumina NextSeq 500 instrument.

value: wild-type

value: embryos developed in ovo until HH9

tag: antibody

value: PTM Biolabs - PTM-1406 (polyclonal)


title: h3k18la_nf_rep2

description: CUT&RUN


title: CRC_Y05_O05 002 Vim+FAP+

value: LOCC


title: MSC-loaded Nanovials scRNAseq, mRNA

description:
scGEX.normalizedData_MSC.Suspended.Sorted.and.Nanovial.txt.gz
scGEX.metadata_MSC.Suspended.Sorted.and.Nanovial.txt.gz
MSC_Nanovials_scGEX


title: sox9_nf_rep1

description: CUT&RUN

value: Millipore Sigma - AB5535


title: Suspended MSCs (sorted) scRNAseq

description:
scGEX.normalizedData_MSC.Suspended.Sorted.and.Nanovial.txt.gz
scGEX.metadata_MSC.Suspended.Sorted.and.Nanovial.txt.gz
MSC_Suspended_Sorted_scGEX

value: adipose


title: sox9_nf_rep2

description: CUT&RUN


title: CRC_Y05_O05 002 PanCK+

value: PanCK+

value: TIM


title: Suspended MSCs scRNAseq

description:
scGEX.normalizedData_MSC.Suspended.Sorted.and.Nanovial.txt.gz
scGEX.metadata_MSC.Suspended.Sorted.and.Nanovial.txt.gz
MSC_Suspended_scGEX

value: ATCC SCRC-4000

value: Mesenchymal Stromal Cell


title: CRC_Y05_O05 001 Vim+FAP+


title: h3k27ac_psm_rep2

description: CUT&RUN

value: Primary Neural Crest Cells

value: HH9 stage

value: Abcam - ab177178


title: h3k27ac_psm_rep1

description: CUT&RUN


title: pankla_psm_rep2

description: CUT&RUN

value: PTM Biolabs - PTM-1401 (polyclonal)


title: CRC_Y05_O05 001 PanCK+

value: colon cancer


title: Line 1208-2, hCO, scRNA-seq

city: Stanford

first: Xiao

last: Yang

address: 318 Campus Drive

institute: Stanford University

description: 10x Genomics

data_processing:
Mapping to the human reference genome (Human (GRCh38) 2020-A provided by 10x Genomics) and generation of count matrices (including introns) were performed using 10x Genomics Cloud Analysis using Cell Ranger software (version 7.0.0).
Samples were aggregated including normalization for mapped reads using the aggregate function in 10x Genomics Cloud Analysis.
Assembly: GRCh38 2020-A
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

extract_protocol:
Dissociation of hCOs into single cells for scRNA-seq was performed as previously described (Birey et al., 2022) with minor optimizations. 3–4 hCOs at day 100 were pooled from KiriE-integrated condition or control condition from each hiPS cell line. hCOs were transferred to a 6-well plate (Corning, 3506) and incubated for 45–60 min at 37°C with 3 ml enzymatic dissociation solution. The enzymatic solution consisted of 30 U/ml papain (Worthington Biochemical, LS003127), 1x EBSS (Sigma-Aldrich, E7150), 0.46% D(+)-glucose, 0.5 mM EDTA, 26 mM NaHCO3, 10 μM Y-27632, 125 U/ml Deoxyribonuclease I (Worthington Biochemical, LS002007), and 6.1 mM L-cysteine (Sigma-Aldrich, C7880). Upon the completion of papain incubation, samples were collected in a 15 ml Falcon tube and centrifuged at 1,200 rpm for 1 min. After removing the supernatant, the samples were washed with 1 ml inhibitor solution with 2% trypsin inhibitor (Worthington Biochemical, LS00308) and resuspended in 1 ml of the same solution for trituration. Upon the completion of trituration, 1 ml inhibitor solution with 4% trypsin inhibitor was slowly added beneath the cell suspension to create a gradient layer. The gradient solution was centrifuged at 1,200 rpm for 5 min. Cell pellets were resuspended in 0.2% BSA/PBS and passed through a 40 μm cell strainer (Corning, 352340). The inhibitor solution differs from the enzyme solution in that it does not contain papain nor EDTA. All centrifugation steps were performed at RT.
Libraries were generated with the Chromium Next GEM Single Cell 3’ Library Kit v3.1 (10x Genomics, PN-1000157) using the Dual Index Kit TT Set A (10x Genomics, PN-1000215).

value: without KiriE integration

value: day 100 of in vitro differentiation


title: pankla_psm_rep1

description: CUT&RUN

value: wild-type


title: Line 0524-1, hCO, scRNA-seq

description: 10x Genomics


title: Line 1208-2, KiriE/hCO, scRNA-seq

description: 10x Genomics

value: with KiriE integration


title: CRC_Y02_O02 012 Vim+FAP_i

value: Vim+FAPi

value: TC


title: CRC_Y02_O02 012 PanCK+

value: LOCC


title: CRC_Y02_O02 011 Vim+FAP_i


title: Line 0524-1, KiriE/hCO, scRNA-seq

description: 10x Genomics


title: pankla_nf_rep1

description: CUT&RUN

value: embryos developed in ovo until HH9


title: HP1a_b_tir2_1h_no_a_with_d_rep1

description: hic

value: G1E-ER4 cells

value: erythroid

value: noc 8h release 1h + dTag13 8h


title: HH9 Neural Fold scATAC-seq

description: scATAC-seq library

library_source: genomic single cell

data_processing:
Demultiplexing, cellranger-atac 2.0.0 mkfastq
Alignment and cell calling, cellranger-atac 2.0.0 count
Assembly: Ensembl galGal6
Supplementary files format and content: .txt file displaying cell barcodes with UMAP embeddings, biological replicate, and cluster assignment

source_name: Chicken embryo dorsal midline dissection

growth_protocol: Fertilized White Leghorn eggs were purchased from the University of Connecticut (Department of Animal Sciences). The eggs were incubated at 37°C until the embryos reached HH9 stage of development.

extract_protocol:
Dorsal neural folds were manually dissected from HH9 embryos . After tissue collection, cells were dissociated in Accumax (Innovative Cell Technologies, AM105) for 20 min at RT under mild agitation and nuclei preparation was perfomed according to the 10X Genomics suggested protocol. Cells were lysed in cold lysis buffer containing 10mM Tis-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 1% BSA, 0.01% Tween 20, 0.01% % Nonidet P40 Substitute, and 0.001% digitonin for 5 minutes on ice. Following cell lysis, cells were washed in 10mM Tis-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 1% BSA, and 0.1% Tween 20 and resuspended in 1x Nuclei Buffer (10x Genomics, 2000153/2000207) at a concentration of 3,500 nuclei per uL.
scATAC-seq libraries were generated via the Chromium Single Cell ATAC pipeline (10x Genomics, PN-1000175).


title: DAOY_Nd

type: RNA

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

description: Gene expression data from DAOY cells

hyb_protocol: 5.5ug of sscDNA were fragmentated and 5.2 uf were hybridized for 16 hr at 45°C on GeneChip Human Clariom S Array (GPL23159 Platform). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using TAC software using RMA and Repated Measure for cell line type was applied

label: biotin

source_name: DAOY cells

label_protocol: Biotinylated cRNA were prepared according to the standardThermoFisher protocol starting  from 100ng of Total RNA using the ThermoFisher WTA Kit

growth_protocol: DAOY cells were cultured in MEM-ALPHA supplemented with 10% fetal bovine serum (FBS), 1% glutamine and 1% Penicillin-Streptomycin. HD-MB03 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% glutamine and 1% Penicillin-Streptomycin. Primary HuTuP33 cells were cultured DMEM/F12 supplemented with 2% B27, 40ng/ml basic Fibroblast Growth Factor and 40ng/ml Epidermal Growth Factor and maintained in an atmosphere of 2% oxygen, 5% carbon dioxide and balanced nitrogen in a H35 hypoxic cabinet.

extract_protocol: RNA was extracted using QIAzol and miRNeasy Micro Kit from Qiagen.

treatment_protocol: Untreated cells (sensitive) or treated with chemotherapy cycles (VECC) until acquisition of drug resistance (resistant).

value: MB cell line

tag: response to chemotherapy

value: Sensitive

value: DAOY


title: CRC_Y02_O02 011 PanCK+

tag: tissue

value: PanCK+


title: K562_2mark_H3K4me3

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

institute: Peking University

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 20 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Assembly: hg19
Supplementary files format and content: The processed files were aggregate bigwig files.

extract_protocol:
Following uCoTarget protocol.
After PCR enrichment, products were purified and selected by AMPure XP beads for 200-1000 bp.

treatment_protocol: Cells were collocted by centrifugation at 300g for 3 minutes

tag: cell line

tag: cell statement

value: Fixed by Formaldehyde

tag: chip antibody


title: Kasumi_2mark_H3K4me3

source_name: Kasumi

value: Kasumi


title: CRC_Y02_O02 010 Vim+FAP_i

value: colon cancer


title: HuTuP33_#d

description: Gene expression data from HuTuP33 cells after acquisition of chemotherapy resistance

tag: cell type

value: primary MB cells

value: Resistant


title: Kasumi_2mark_H3K27me3


title: DAOY_#d

description: Gene expression data from DAOY cells after acquisition of chemotherapy resistance


title: CRC_Y02_O02 010 PanCK+


title: HuTuP33_#c

source_name: HuTuP33 cells after acquisition of chemotherapy resistance


title: D-09-b

city: Shanghai

first: Libin

last: Song

address: 270 Dongan Road

institute: Fudan University Shanghai Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using HISAT2 with default parameters.
StringTie was used to quantify gene expression levels
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

extract_protocol:
Total RNA was collected using TRIzol Reagent (Invitrogen); then, rRNAs were removed by using the RiboMinus Eukaryote Kit (QIAGEN, Valencia, CA, USA). We next prepared the RNA-seq libraries using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Beverly, MA, USA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease

value: Pancreatic cancer

tag: treatment

value: activating blood and removing stasis


title: D-08-b


title: DAOY_#c

source_name: DAOY cells after acquisition of chemotherapy resistance


title: HuTuP33_#b


title: DAOY_#a


title: K562_2mark_H3K27me3


title: pankla_nf_rep2

description: CUT&RUN

value: Primary Neural Crest Cells

tag: Stage

value: HH9 stage

tag: genotype

value: wild-type

value: PTM Biolabs - PTM-1401 (polyclonal)


title: DAOY_#b


title: HuTuP33_Nd

description: Gene expression data from HuTuP33 cells

source_name: HuTuP33 cells


title: D-06-C


title: Astrocytes rep4

city: Seoul

first: Haeryung

last: Lee

state: Seoul

address: Chungpa-dong, Yongsan-Gu, Yongsan-Gu

country: South Korea

institute: Sookmyung Women's University

data_processing:
At first, reads for each sample were mapped to the reference genome by Tophat(v2.0.13).
The aligned results were added to Cuffdiff(v2.2.0) to report differentially expressed genes.
For library normalization and dispersion estimation, geometric and pooled (“blind” when each condition has single replicates, or “pooled” when multiple replicates are available) methods were applied.
Assembly: Human hg19
Supplementary files format and content: Processed data files include FPKM values for each sample.

growth_protocol: Human fibroblast was maintained in fibroblast growth medium (PromoCell, C-23120) and human induced pluripotent stem cells were maintained in mTeST1 medium (Stem Cell Technologies) on Matrigel-coated plates in humidified atmosphere with 5% CO2. at 37C

extract_protocol:
mRNA was purified and fragmented from total RNA (1ug) using poly-T oligo-attached magnetic beads using two rounds of purification.
mRNA sequencing libraries were prepared according to the manufacturer’s instructions (Illumina Truseq stranded mRNA library prep kit).

value: induced pluripotent stem cells

value: WT

value: differentiation of astrocytes


title: D-04-C


title: CRC_Y02_O02 009 Vim+FAP+

tag: type of_tissue

value: LOCC

tag: age of_patients

tag: annotation geomx_dsp

value: Vim+FAP+

value: TIM


title: CRC_Y02_O02 009 PanCK+

tag: segment tag

tag: scan id

tag: roi id

value: PanCK+


title: HuTuP33_Nc

description: Gene expression data from HuTuP33 cells

value: Sensitive


title: HuTuP33_#a


title: HuTuP33_Nb

description: Gene expression data from HuTuP33 cells


title: CRC_Y02_O02 008 Vim+FAP+

value: colon cancer

tag: cell type specific morphological marker

tag: histological region


title: CRC_Y02_O02 007 Vim+FAP+

tag: tissue


title: Astrocytes rep3

tag: cell line


title: CRC_Y02_O02 008 PanCK+


title: D-01-b


title: C-10-b

value: eliminating heat by nourishing yin


title: Pericytes rep4

value: differentiation of pericytes


title: Astrocytes rep1


title: Astrocytes rep2


title: HuTuP33_Na

description: Gene expression data from HuTuP33 cells

value: primary MB cells

tag: response to chemotherapy


title: HD-MB03_#d

description: Gene expression data from HD-MB03 cells after acquisition of chemotherapy resistance

value: MB cell line

value: Resistant


title: Pericytes rep3


title: C-07-b

value: Pancreatic cancer


title: C-05-C


title: CRC_Y02_O02 007 PanCK+


title: CRC_Y02_O02 006 Vim+FAP_i

value: EOCC

value: Vim+FAPi

value: TC


title: C-04-b


title: C-01-b


title: Pericytes rep1

value: induced pluripotent stem cells

value: WT


title: CRC_Y02_O02 006 PanCK+


title: Pericytes rep2


title: HD-MB03_#a

source_name: HD-MB03 cells after acquisition of chemotherapy resistance


title: HD-MB03_#c


title: HD-MB03_Nd

description: Gene expression data from HD-MB03 cells

source_name: HD-MB03 cells


title: HD-MB03_Nc

description: Gene expression data from HD-MB03 cells


title: B-08-b

value: strengthening spleen and regulating qi-flowing


title: Endothelial cells rep4

value: differentiation of endothelial cells


title: B-07-C


title: HD-MB03_#b


title: CRC_Y02_O02 005 Vim+FAP_i


title: HD-MB03_Nb

description: Gene expression data from HD-MB03 cells


title: HD-MB03_Na

description: Gene expression data from HD-MB03 cells


title: B-06-b


title: Endothelial cells rep3


title: Endothelial cells rep2


title: B-05-b


title: CRC_Y02_O02 004 PanCK+


title: CRC_Y02_O02 005 PanCK+


title: DAOY_Na

description: Gene expression data from DAOY cells

value: DAOY


title: Endothelial cells rep1


title: CRC_Y02_O02 003 Vim+FAP+

value: Vim+FAP+

value: TIM


title: Posterior part, stage 53, rep1

city: Málaga

first: Juan

last: Pascual-Anaya

address: Campus de Teatinos, s/n

department: Departament of Animal Biology

country: Spain

institute: University of Málaga

data_processing:
Adaptor removal of raw paired-end reads were performed by using NGmerge (Gaspar, 2018) (version 0.3) with the following parameters: -a -e 30. The filtered reads were aligned to the reference genomes by using bowtie2 (version 2.4.2) (Langmead and Salzberg, 2012) with the following parameters: -k 4 -X 2000 --sensitive.
Picard (version 2.23.8) was used to remove duplicate reads from properly paired aligned reads, which had been filtered by using SAMtools (Li et al., 2009) (version 1.10). First, to deplete ATAC-seq reads derived from the transposition events that happened on both sides of a nucleosome, we removed the properly paired reads whose mate is more than 120 bp for identification of accessible chromatin reginos (ACRs).
Then, the start position of every aligned ATAC-seq read was corrected to account for the 9-bp insert between the adaptors, which was introduced by Tn5 transposase (Buenrostro et al., 2013), and the single 5’-most base of each read was retained to obtain single-base resolution. For each sample, the data for the two replicates were pooled into a single dataset.
For the pooled data and those for each replicate data, peak calling was performed by using MACS (Zhang et al., 2008) (version 2.2.7.1) with the following parameters: callpeak --nomodel --keepdup 1 --llocal 10000 --extsize 74 --shift -37 -p 0.07. Finally, on the basis of replicate information, we obtained the high confidence ACRs by using the IDR framework (Li et al., 2011) (idr 2.0.4 with the following parameter: -i 0.1).
Only for visualization, bigwig files from filtered bam files were produced by using bedtools bamCoverage (Quinlan and Hall, 2010) with the following parameters: -binSize 10 --normalizeUsing RPGC.
Assembly: Eburgeri_4.0
Supplementary files format and content: Processed data files contain bed files (ACRs) and bigwig files (for genome browser visualizations).

organism: Eptatretus burgeri

source_name: Posterior half of whole embryos

growth_protocol: Hagfish embryos were obtained from adult hagfish individuals captured in the Japan Sea off Shimane prefecture during August of a given year. Eggs were laid in a cage deposited in the natural environment in the sea in October of the same year. Deposited eggs were then incubated in laboratory aquariums with artificial sea water at 16°C under controlled conditions, until developing embryos were apparent around February or March of the following year.

extract_protocol:
Hagfish embryos, at stages Dean 45 and 53, were divided into two parts, anterior and posterior halves, at the level of the somite pair 27. Nuclei were extracted separately from each part of embryos using 2 mL glass bouncers in ice-cold PBS and lysed in cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% Igepal). Each pool was further divided into two to obtain data from technical replicates.
Transposition reaction was done on ~50,000 nuclei per sample and per replicate (total of 200,000 cells per embryo), with Tn5 enzyme (Illumina Nextera DNA Library Prep Kit), during 5 min at 37℃. DNA was purified using a QIAGEN MinElute kit following manufacturer instructions. Number of PCR cycles per sample were first determined as previously described (Buenrostro et al., 2013) using 1 uL of the Tn5’ed chromatin, and then a final PCR reaction with the rest of the chromatin was performed for each sample, with the following number of cycles: 7 for the embryo at stage 45, and 8 cycles for the embryo at stage 53. PCRs were performed with the NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs), using different sets of primers to multiplex the libraries. The resulting multiplexed libraries were checked in an Agilent 2100 BioAnalyzer using High Sensitivity DNA chips.

value: Posterior half of whole embryos

tag: developmental stage

value: Stage 53


title: Posterior part, stage 53, rep2


title: DAOY_Nc

description: Gene expression data from DAOY cells

tag: cell type

value: Sensitive


title: A-09-C

tag: disease

value: clearing Heat and removing Dampness


title: Anterior part, stage 53, rep2

source_name: Anterior half of whole embryos

value: Anterior half of whole embryos


title: A-primary-R3_rep3

city: Milwaukee

first: Heather

last: Himburg

state: Wisconsin

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

data_processing:
Data was trimmed and quality assessed with FastQC and RSeQC
Reads were aligned to the mouse reference Gencode v32 (based on Ensembl v98) using the STAR aligner and MAPR-Seq workflow v3.0
Differential gene expression was processed through EdgeR utilizing pairwise statistics with the cutoffs set at an FDR <0.05 and log 2 fold change ≥1 or ≤-1.
Assembly: Gencode v32 (GRCh38.p13)
Supplementary files format and content: excel tables with gene counts (GeneCount.xlsx) and differential analysis results (DEAnalyses_pairwise.xlsx)

source_name: Oral squamous cell carcinoma

extract_protocol:
Samples were transferred to RNAlater ice prior to extraction in Qiagen Rneasy mini kit
RNA libraries were prepared according to manufacturer’s protocols utilizing Illumina’s TruSeq stranded mRNA library kit

treatment_protocol: Resected tumor samples were cryopreserved in liquid nitrogen

tag: primary/recurrent

value: primary

tag: patient


title: CRC_Y02_O02 003 PanCK+

value: colon cancer

value: PanCK+


title: DAOY_Nb

description: Gene expression data from DAOY cells

value: MB cell line


title: Anterior part, stage 53, rep1


title: A-07-C

value: Pancreatic cancer

tag: treatment


title: CRC_Y02_O02 004 Vim+FAP_i

tag: type of_tissue

value: EOCC

value: Vim+FAPi

value: TC


title: CRC_Y02_O02 002 PanCK+

tag: age of_patients


title: Posterior part, stage 45, rep2

value: Stage 45


title: A-03-b


title: B-02-b

value: strengthening spleen and regulating qi-flowing


title: A-02-C


title: A-primary-R2_rep2


title: C-recurrent3_rep3

value: recurrent


title: Posterior part, stage 45, rep1


title: A-01-b


title: CRC_Y02_O02 001 Vim+FAP+

tag: annotation geomx_dsp

value: Vim+FAP+

value: TIM


title: CRC_Y02_O02 001 PanCK+

tag: segment tag


title: A-primary-R1_rep1


title: Anterior part, stage 45, rep1


title: Anterior part, stage 45, rep2


title: Inguinal adipose tissue, wound skin, c57BL/6 mouse, sample6

status: Public on Nov 21 2023

city: Guangzhou

first: Juzi

last: Liu

state: --- Select One ---

address: North Guangzhou Avenue 1838, Nanfang Hospital

institute: Southern Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Clean reads were separately aligned to the reference genome using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software.
The expression of each gene was calculated using the transcripts per million reads (TPM) method.
Differential expression analysis was performed using the DESeq2 v1.24.0.
Assembly: GRCm38
Supplementary files format and content: TXT files include TPM values for each Sample

source_name: Inguinal adipose tissue

extract_protocol:
The total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA). RNA quality was evaluated using a 2100 Bioanalyser (Agilent Technologies) and quantified using an ND-2000 (NanoDrop Technologies). Only high-quality RNA samples (OD 260 nm/280 nm = 1.8–2.2, OD 260 nm/230 nm ≥ 2.0, RIN ≥ 8.0, 28S:18S ≥1.0, > 1 μg) were used to construct the sequencing library.
RNA samples from each mouse were used to generate RNA-seq libraries with a TruSeq TM RNA sample Prep kit (Illumina, San Diego, CA, USA). Libraries were size-selected for cDNA target fragments of 300 bp on 2% low-range ultra agarose gels, followed by PCR amplification using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantification using TBS380, the paired-end RNA-seq sequencing libraries were sequenced using an Illumina NovaSeq 6000 sequencer (2 × 150 bp read length). The raw paired-end reads were trimmed and quality controlled using fastp (https://github.com/OpenGene/fastp) with default parameters.

value: Inguinal adipose tissue

tag: strain

tag: group

value: wound skin

tag: genotype

value: wildtype


title: Inguinal adipose tissue, wound skin, prdm16-KO mouse, sample3


title: Inguinal adipose tissue, wound skin, c57BL/6 mouse, sample2


title: Inguinal adipose tissue, normal skin, c57BL/6 mouse, sample3

value: normal skin


title: Inguinal adipose tissue, wound skin, c57BL/6 mouse, sample5


title: Inguinal adipose tissue, wound skin, prdm16-KO mouse, sample1


title: Inguinal adipose tissue, wound skin, c57BL/6 mouse, sample3


title: CRC_Y02_O02 002 Vim+FAP+

tag: scan id

tag: roi id

tag: cell type specific morphological marker

tag: histological region


title: C-recurrent2_rep2


title: Mouse_2997-3_heart_AAV_GFP

city: Iowa City

first: Ethan

middle: J.

last: Anderson

state: Iowa

address: 180 South Grand Ave, CPB 548

department: Pharmaceutical Sciences and Experimental Therapeutics

institute: University of Iowa - College of Pharmacy

data_processing:
Reads were aligned using Kallisto version 0.43.1, to Ensemble transcriptome release 98 (119215 transcript targets), run using default settings, with specific input parameters of 100 bootstraps and 16 threads.
Differential gene expression was quantified using Sleuth version 0.30.0, aggregating abundance on Ensemble genes, with a two-step Likelihood Ratio Test and Wald Test
Gene ontology analyses were performed by inputting the indicated gene sets into the using ToppFun web-server tool, ToppGene Suiteand using default settings. Results were exported and up to the top 50 enriched terms in each “Category” were tabulated in Supplement Tables
Assembly: ftp://ftp.ensembl.org/pub/release-98/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz
Supplementary files format and content: TSV; Sleuth differential expression table, aggregated on ensembl Gene ID, with Wald test, likelihood ratio test, and "scaled reads per base" sample matrix per gene.

source_name: heart

extract_protocol:
Total RNA was isolated from TRIzol according to the manufacturer’s instructions (Thermo Fisher) and dissolved in nuclease-free water and quantified on a Nanodrop Spectrophotometer. RNA was DNase-treated using a DNA-free kit (Thermo Fisher). RNA quality assessment and sequencing were performed by the Iowa Institute of Human Genetics, Genomics Division, at the University of Iowa. RNA quality and concentrations were determined with the Agilent 2100 Bioanalyzer, and DropSense or Little Lunatic (Unchained Labs, Pleasanton, CA) reads. The RNA integrity number (RIN) values for samples were >7.5.
Illumina TruSeq® Stranded mRNA Library Prep kits (Illumina) were used to prepare sequencing libraries from mRNA, followed by reverse transcription to cDNA, fragment purification and ligation to indexed (barcoded) adaptors. Indexed libraries were pooled for multiplex sequencing and run on an SP flow cell on the Illumina NovaSeq 6000 sequencer for 100 cycles with 50-base paired-end reads.

treatment_protocol: 3-5 week old C57BL6J mice were injected via jugular vein with AAV virus to deliver miR-29a or GFP. After 3 weeks, mice were euthanized and hearts were dissected and snap frozen in liquid nitrogen.

tag: tissue

value: heart

tag: virus serotype


title: Mouse_2997-2_heart_AAV_miR-29a


title: Inguinal adipose tissue, normal skin, c57BL/6 mouse, sample2


title: C-recurrent1_rep1


title: Mouse_2997-1_heart_AAV_GFP


title: Inguinal adipose tissue, wound skin, prdm16-KO mouse, sample2


title: Mouse_2996-3_heart_AAV_GFP


title: Mouse_2996-1_heart_AAV_miR-29a


title: Mouse_2996-4_heart_AAV_miR-29a


title: Inguinal adipose tissue, normal skin, c57BL/6 mouse, sample1


title: Inguinal adipose tissue, wound skin, c57BL/6 mouse, sample4


title: NB, scRNAseq

city: Xiamen

first: Lingjuan

address: Xiangan South Street

institute: Xiamen University

data_processing:
The raw sequencing data was demultiplexed and aligned to the reference genome mm10-1.2.0 using Cell Ranger v3.0.2 pipiline(10x Genomics).
The generated raw gene expression matrix was converted into Seurat objects using the R package Seurat v2.0.
To remove doublets and poor-quality cells, we utilized the following procedures to control for cell quality: >200 genes/cell, <5000 genes/cell; >25,000 unique molecular identifiers(UMIs)； and <8% mitochondrial gene expression.
Low quality cells and outliers were discarded, and only ～22,826 viable cells were used for downstream analysis. These included ~5,237 cells – NB(10days mice); ~4,804 cells – Adult-M(2months mice); ~6,561cells-SD-10M(10month mice) ; ~6,224cells-SD-1d5Y (18month mice)
Unsupervised clustering and gene expression were visualized with the Seurat 2.0 on R studio, and assignment of cell clusters was based on expression of validated marker genes.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: lung

extract_protocol:
Using collagenase D and DNase1, the lung biopsies were minced and digested to isolate individual lung cells, following the protocol described. Dead cells were excluded using the DeadCell Removal kit (Miltenyi Biotic,130-090-101), as per the manufacturer's instructions. Subsequently, live cells were enumerated with a hemocytometer, resuspended in 2% BSA at a density of 3,000 cells/uL, and processed with the 10x Genomics GemCode Single-cell instrument to create single-cell Gel Bead-In-EMlusions (GEMs).
Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v 2. cDNA libraries were sequenced on an Illumina Novaseq6000 platform (Illumina).

value: lung

tag: age

value: 10days old

tag: Sex

value: Male

value: Wild type


title: Adult-M, scRNAseq

value: 2Months old


title: SD-1d5Y, scRNAseq

value: 18Months old


title: SD-10M, scRNAseq

value: 10Months old


title: Inguinal adipose tissue, wound skin, c57BL/6 mouse, sample1


title: zona incerta, left, fasted, 1434

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
Basecalling was performed using Illumina's bcl2fastq (v2.20.0).
Sequenced reads were then mapped to the GRCm39 build of the Mus musculus genome using STAR (v2.7.3a) with an overhang length of 50.
The files for the reads, specified in the format of fastq, were processed individually.
The read files were provided as input to STAR, using a "zcat" command to read the compressed files.
Quantification mode was set to GeneCounts in the STAR alignment to obtain count data for each gene.
Following the alignment process, raw counts for each sample were combined using R (v4.1.3) and the tidyverse (v2.0.0) package to create a count matrix.
Assembly: The metadata for sample 142.3_SCL_chow and sample 145.4_SCL_fast were corrected to account for the fact that they were erroneously swapped during handling and sequencing.
Supplementary files format and content: GRCm39
Supplementary files format and content: csv file of raw read counts for each sample

source_name: zona incerta

extract_protocol:
RNA extraction was performed using the RNeasy Micro Kit
RNA libraries for RNA-seq were prepared using NEBNext Kits with rRNA depletion and Multiplex Oligos for Illumina

treatment_protocol: In the 24 hour study sample processing was randomized in blocks of 24

value: zona incerta

tag: hemisphere

value: left

tag: diet

value: fasted

tag: diet kcal

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment

tag: food weight_end_experiment

tag: kcal intake

tag: kcal per_hour

tag: notes

tag: qc

value: fail STAR

tag: flowcell

value: SP


title: zona incerta, left, fasted, 1454

tag: tissue

tag: hemisphere

tag: diet

tag: diet kcal

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

value: Sup. Colliculus for 145.4 is in tube 142.3


title: inferior colliculus, left, fasted, 1453

source_name: inferior colliculus

value: inferior colliculus

tag: time of_euthanasia

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: bodyweight before_euthanasia

tag: bodyweight change


title: inferior colliculus, left, fasted, 1444

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment

tag: food weight_end_experiment

tag: kcal intake

tag: kcal per_hour

tag: notes


title: superior colliculus, left, fasted, 1435

source_name: superior colliculus

tag: tissue

value: superior colliculus

tag: hemisphere

tag: diet

tag: diet kcal

tag: animal id

value: Uncertain hypothalamus

tag: qc

tag: flowcell


title: superior colliculus, left, fasted, 1433

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

value: Slightly apathetic


title: hippocampus, left, fasted, 1444

source_name: hippocampus

value: hippocampus

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: superior colliculus, left, fasted, 1424

tag: tissue

tag: hemisphere

tag: diet

tag: diet kcal

tag: animal id

tag: kcal per_hour

tag: notes


title: Mouse_2996-5_heart_AAV_GFP

value: heart

tag: virus serotype

tag: genotype

tag: treatment


title: hypothalamus, both, fasted, 1455

source_name: hypothalamus

value: hypothalamus

value: both

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: bodyweight before_euthanasia

tag: qc

tag: flowcell


title: hippocampus, left, fasted, 1424

tag: tissue

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight change

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: Mouse_2996-2_heart_AAV_miR-29a

tag: virus serotype

tag: genotype

tag: treatment


title: hypothalamus, both, fasted, 1435

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: kcal per_hour

tag: notes


title: zona incerta, left, chow, 1432

tag: tissue

tag: hemisphere

tag: diet

value: chow

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: qc

tag: flowcell


title: hypothalamus, both, fasted, 1445

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: food weight_start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: inferior colliculus, left, chow, 1452

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: kcal per_hour

tag: notes


title: zona incerta, left, chow, 1423

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

value: Sup. Colliculus for 142.3 is in tube 145.4


title: zona incerta, left, chow, 1442

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: food weight_start_experiment

tag: qc

tag: flowcell


title: inferior colliculus, left, chow, 1442

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: superior colliculus, left, chow, 1422

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: kcal per_hour

tag: notes


title: hippocampus, left, chow, 1452

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: hippocampus, left, chow, 1441

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: qc

tag: flowcell


title: zona incerta, left, fasted, 1455

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: food weight_end_experiment

tag: kcal intake

value: ok


title: hippocampus, left, chow, 1431

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: kcal per_hour

tag: notes


title: hypothalamus, both, chow, 1451

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment

value: Inf. Colliculus suboptimal


title: zona incerta, left, fasted, 1453

value: zona incerta

tag: hemisphere

value: left

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: qc

tag: flowcell


title: zona incerta, left, fasted, 1445

value: fasted

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: food weight_end_experiment

tag: kcal intake


title: zona incerta, left, fasted, 1444

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: kcal per_hour

tag: notes


title: hypothalamus, both, chow, 1422

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment

value: fail STAR

value: SP


title: zona incerta, left, fasted, 1435

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: qc

tag: flowcell


title: superior colliculus, left, fasted, 1434

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: zona incerta, left, fasted, 1433

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: kcal per_hour

tag: notes


title: zona incerta, left, fasted, 1424

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: inferior colliculus, left, fasted, 1455

tag: tissue

value: inferior colliculus

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: qc

tag: flowcell


title: inferior colliculus, left, fasted, 1454

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: food weight_end_experiment

tag: kcal intake

value: Sup. Colliculus for 145.4 is in tube 142.3


title: inferior colliculus, left, fasted, 1433

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: kcal per_hour

tag: notes


title: inferior colliculus, left, fasted, 1434

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: inferior colliculus, left, fasted, 1435

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

value: Uncertain hypothalamus

tag: qc

tag: flowcell


title: inferior colliculus, left, fasted, 1425

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: food weight_end_experiment

tag: kcal intake


title: inferior colliculus, left, fasted, 1445

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: kcal per_hour

tag: notes


title: inferior colliculus, left, fasted, 1424

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: superior colliculus, left, fasted, 1454

value: superior colliculus

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: qc

tag: flowcell


title: superior colliculus, left, fasted, 1453

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: superior colliculus, left, fasted, 1425

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: kcal per_hour

tag: notes


title: superior colliculus, left, fasted, 1455

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment

value: fail PCA


title: superior colliculus, left, fasted, 1445

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: qc

tag: flowcell


title: hippocampus, left, fasted, 1455

value: hippocampus

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: food weight_end_experiment

tag: kcal intake


title: zona incerta, left, fasted, 1425

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: kcal per_hour

tag: notes


title: hippocampus, left, fasted, 1445

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: hippocampus, left, fasted, 1454

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: qc

tag: flowcell


title: hippocampus, left, fasted, 1434

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: food weight_end_experiment

tag: kcal intake


title: hippocampus, left, fasted, 1453

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: kcal per_hour

tag: notes


title: hippocampus, left, fasted, 1435

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: hypothalamus, both, fasted, 1444

value: hypothalamus

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: qc

tag: flowcell


title: hippocampus, left, fasted, 1425

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: hypothalamus, both, fasted, 1434

tag: hemisphere

value: both

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: kcal per_hour

tag: notes


title: hypothalamus, both, fasted, 1453

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: hypothalamus, both, fasted, 1454

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: qc

tag: flowcell


title: hippocampus, left, fasted, 1433

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: food weight_end_experiment

tag: kcal intake

value: Slightly apathetic


title: hypothalamus, both, fasted, 1425

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: kcal per_hour

tag: notes


title: hypothalamus, both, fasted, 1433

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: superior colliculus, left, fasted, 1444

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: qc

tag: flowcell


title: zona incerta, left, chow, 1431

value: chow

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: food weight_end_experiment

tag: kcal intake


title: zona incerta, left, chow, 1451

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: kcal per_hour

tag: notes

value: ok


title: zona incerta, left, chow, 1441

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: zona incerta, left, chow, 1452

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: qc

tag: flowcell


title: zona incerta, left, chow, 1422

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: inferior colliculus, left, chow, 1423

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: kcal per_hour

tag: notes

value: Sup. Colliculus for 142.3 is in tube 145.4


title: inferior colliculus, left, chow, 1431

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: inferior colliculus, left, chow, 1432

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: qc

tag: flowcell


title: inferior colliculus, left, chow, 1422

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: food weight_end_experiment

tag: kcal intake


title: inferior colliculus, left, chow, 1451

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: kcal per_hour

tag: notes

value: Inf. Colliculus suboptimal


title: superior colliculus, left, chow, 1443

tag: tissue

value: left

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: inferior colliculus, left, chow, 1441

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: qc

tag: flowcell


title: superior colliculus, left, chow, 1423

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: food weight_end_experiment

tag: kcal intake


title: superior colliculus, left, chow, 1452

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: kcal per_hour

tag: notes


title: hypothalamus, both, fasted, 1424

tag: hemisphere

tag: diet

value: fasted

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: superior colliculus, left, chow, 1432

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: qc

tag: flowcell


title: superior colliculus, left, chow, 1442

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: hippocampus, left, chow, 1423

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: kcal per_hour

tag: notes


title: hippocampus, left, chow, 1422

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: hypothalamus, both, chow, 1443

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: qc

tag: flowcell


title: hippocampus, left, chow, 1451

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: food weight_end_experiment

tag: kcal intake


title: superior colliculus, left, chow, 1441

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: kcal per_hour

tag: notes


title: hippocampus, left, chow, 1443

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: hippocampus, left, chow, 1442

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: qc

tag: flowcell


title: inferior colliculus, left, chow, 1443

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: food weight_end_experiment

tag: kcal intake


title: zona incerta, left, chow, 1443

tag: tissue

value: zona incerta

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: kcal per_hour

tag: notes


title: superior colliculus, left, chow, 1431

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: hypothalamus, both, chow, 1442

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: qc

tag: flowcell


title: hippocampus, left, chow, 1432

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: hypothalamus, both, chow, 1441

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: kcal per_hour

tag: notes

value: fail STAR


title: hypothalamus, both, chow, 1423

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: hypothalamus, both, chow, 1431

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: qc

tag: flowcell


title: prefrontal cortex, right, HFD, 18

source_name: prefrontal cortex

value: prefrontal cortex

tag: hemisphere

value: right

tag: diet

value: HFD

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: food weight_end_experiment

tag: kcal intake

value: OBS. Lost weight.


title: superior colliculus, left, chow, 1451

value: superior colliculus

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: kcal per_hour

tag: notes


title: prefrontal cortex, right, HFD, 17

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: prefrontal cortex, right, HFD, 16

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: qc

tag: flowcell


title: prefrontal cortex, left, HFD, 14

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: food weight_end_experiment

tag: kcal intake


title: inferior colliculus, right, HFD, 18

tag: tissue

value: inferior colliculus

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: kcal per_hour

tag: notes


title: inferior colliculus, right, HFD, 16

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment

value: fail PCA


title: inferior colliculus, right, HFD, 17

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: qc

tag: flowcell


title: prefrontal cortex, left, HFD, 13

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: inferior colliculus, left, HFD, 14

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: kcal per_hour

tag: notes


title: inferior colliculus, left, HFD, 13

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: superior colliculus, right, HFD, 17

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: qc

tag: flowcell


title: hypothalamus, both, chow, 1452

value: hypothalamus

tag: hemisphere

value: both

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: food weight_end_experiment

tag: kcal intake


title: inferior colliculus, left, HFD, 15

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: kcal per_hour

tag: notes


title: superior colliculus, right, HFD, 16

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: superior colliculus, left, HFD, 15

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: qc

tag: flowcell


title: superior colliculus, left, HFD, 13

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: food weight_end_experiment

tag: kcal intake


title: superior colliculus, left, HFD, 14

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: kcal per_hour

tag: notes


title: hypothalamus, both, chow, 1432

tag: hemisphere

tag: diet

value: chow

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: hippocampus, right, HFD, 17

value: hippocampus

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: qc

value: ok

tag: flowcell


title: hippocampus, right, HFD, 16

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: hippocampus, right, HFD, 18

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: kcal per_hour

tag: notes


title: hippocampus, left, HFD, 14

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: hypothalamus, both, HFD, 18

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: qc

tag: flowcell


title: hippocampus, left, HFD, 13

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: food weight_end_experiment

tag: kcal intake


title: hypothalamus, both, HFD, 17

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: kcal per_hour

tag: notes


title: hypothalamus, both, HFD, 16

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: hypothalamus, both, HFD, 15

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: qc

tag: flowcell


title: hypothalamus, both, HFD, 14

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: food weight_end_experiment

tag: kcal intake


title: prefrontal cortex, left, HFD, 15

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: kcal per_hour

tag: notes


title: prefrontal cortex, left, fasted, 9

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: prefrontal cortex, right, fasted, 11

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: qc

tag: flowcell


title: prefrontal cortex, right, fasted, 12

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: hypothalamus, both, HFD, 13

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: kcal per_hour

tag: notes


title: superior colliculus, right, HFD, 18

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: prefrontal cortex, left, fasted, 8

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: qc

tag: flowcell


title: prefrontal cortex, right, fasted, 10

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: food weight_end_experiment

tag: kcal intake


title: prefrontal cortex, left, fasted, 7

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: kcal per_hour

tag: notes


title: superior colliculus, left, fasted, 9

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: inferior colliculus, left, fasted, 7

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: qc

tag: flowcell


title: superior colliculus, right, fasted, 10

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: food weight_end_experiment

tag: kcal intake


title: superior colliculus, right, fasted, 12

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: kcal per_hour

tag: notes


title: inferior colliculus, right, fasted, 11

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: superior colliculus, right, fasted, 11

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: qc

tag: flowcell


title: superior colliculus, left, fasted, 8

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: hippocampus, left, HFD, 15

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: kcal per_hour

tag: notes


title: hippocampus, right, fasted, 11

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: inferior colliculus, left, fasted, 9

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: qc

tag: flowcell


title: inferior colliculus, left, fasted, 8

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: food weight_end_experiment

tag: kcal intake


title: hippocampus, left, fasted, 9

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: kcal per_hour

tag: notes


title: superior colliculus, left, fasted, 7

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: hippocampus, right, fasted, 12

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: qc

tag: flowcell


title: hippocampus, right, fasted, 10

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: food weight_end_experiment

tag: kcal intake


title: hypothalamus, both, fasted, 10

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: kcal per_hour

tag: notes


title: hippocampus, left, fasted, 8

tag: hemisphere

tag: diet

tag: diet kcal

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: hypothalamus, both, fasted, 12

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight change_percent

tag: qc

tag: flowcell