title: spinal_cord, B6_EAE_late, animal21-46_6_sliceD.7

city: Mainz

first: Tobias

last: Brummer

state: Rheinland-Pfalz

institute: Universitätsmedizin Mainz

data_processing:
spaceranger (version 1.3.1) count
spaceranger (version 1.3.1) aggr --normalize=none
Seurat 4.1.1: NormalizeData(...) -> FindVariableFeatures(...) -> ScaleData(...) -> RunPCA(npcs=10, ...)
Loupe Browser 6; Seurat 4.1.1: AddMetaData(...)
Assembly: mm10
Supplementary files format and content: HDF5 format, UMI count gene expression matrix of all spots ("raw")
Supplementary files format and content: HDF5 format, UMI count gene expression matrix of spots under tissue ("filtered")
Supplementary files format and content: HDF5 format, Seurat object with UMI count & log-normalized gene expression matrix of spots under tissue, variable features, PCA, metadata (libraryID of the samples, batch, animal, disease state)

source_name: Spinal cord

extract_protocol:
Visium Gene Expression Reagent Kit (10x Genomics)
spatial transciptomics RNA-Seq

value: Spinal cord

value: MOG EAE

value: EAE late


title: Adjacent normal LOCC_04

status: Public on Nov 22 2023

type: SRA

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

country: USA

institute: Saint John's Cancer Institute

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_04_N

library_source: transcriptomic

data_processing:
FASTQ ﬁles using Illumina BaseSpace BCL to FASTQ software version 2.2.0 and Illumina Local Run Manager Software version 2.0.0.
FASTQ ﬁles were analyzed with HTG EdgeSeq Parser software version v5.1.724.4793 to generate raw counts for a total of 1,410 genes.
Assembly: GRCh38.p13
Supplementary files format and content: HTG-EdgeSeq raw data counts and annotation data file as xlsx format

molecule: total RNA

organism: Homo sapiens

source_name: Colon cancer

extract_protocol:
Thirteen EOCC tumors, 13 LOCC tumors, and the respective 26 paired-adjacent normal colon tissues were processed. Normal tissues were defined as normal epithelial areas at least 2 cm away from the tumor margin. Using 5 µm unstained FFPE sections, the tumor areas were marked by referring to the H&E staining of the consecutive slide, with the accordance of a certificated pathologist. The estimated tissue areas were measured using Image J software. Then, the optimal amounts of tissue for each HTG EdgeSeq PIP assay were scraped and placed into microfuge tubes. The calculated volume of Lysis Buffer for the each collected sample was added, and the samples were then overlaid with 500 µl of HTG denaturation oil. After centrifugation, the samples were incubated at 95°C for 15-20 minutes to denature protein structures and remove paraffin wax from the FFPE tissue sections. Samples were cooled down for 10 minutes at room temperature (RT), and HTG-provided Proteinase K was pipetted into the aqueous (lysis, non-oil) phase of the samples at a volume 1/20th of the total lysis buﬀer. Finally, the samples were incubated at 50°C for three hours, with the aqueous phase being mixed by pipetting every 30 minutes. Subsequently, 25 µL of the sample lysate was loaded onto the HTG EdgeSeq instrument for probe-capture for 20 hours.
Probe-captured FFPE samples for EdgeSeq PIP assay were ampliﬁed and indexed via polymerase chain reaction (PCR) using the master mix (OneTaq HotStart 2X MasterMix in GC Buﬀer (New England Biolabs Inc., Ipswich, MA, USA), and indexing primers. The PCR reaction conditions were as follows: (1) 95°C for 4 min, (2) 95°C for 15 s, (3) 56°C for 45 s, (4) 68°C for 45 s, (5) repeating steps 2-4 for a total of 19 cycles, (6) 68°C for 10 min, and (7) holding at 4°C. Following PCR, library cleanup was performed with a mixture of Clean Up buﬀer (39% of 5M NaCl, 31.25% of 40% PEG 8000, 29.75% of molecular-grade water) and AMPure XP beads, by combining it with the PCR-ampliﬁed sample at 5:2 ratio, respectively. After 5 minutes of incubation, the samples were placed on the magnetic stand, then washed twice with 80% ethanol, followed by a 5-minute air drying period. The elution was performed using 40 µL of Trizma Hydrochloride, formulated at 10 mM Tris-HCl, pH 8.0.
Targeted mRNA Sequencing using HTG-EdgeSeq PIP assay

tag: tissue

value: Colon cancer

tag: tissue type

value: LOCC

tag: tissue site

value: Adjacent normal

tag: age of_patients


title: HAoSMC, EGF, Ao01

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

country: Germany

institute: Martin Luther University - Halle-Wittenberg

description:
Counts_HAoSMC.csv
a663

data_processing:
Read alignment (HISAT2 2.1.0)
Read counting (featureCounts - 2.0.0)
Annotation with biomaRt and Ensembl 101
Assembly: hg38
Supplementary files format and content: .csv file including annotation raw counts (output of featureCounts) for each sample

source_name: Human aortic smooth muscle

growth_protocol: HAoSMC and HCASMC were obtained from PromoCell (C-12533) and ATCC (PCS-100-021), respectively. were cultivated with “Smooth Muscle Cell Growth Medium 2” (low-serum cell culture media from PromoCell, Germany) supplemented with “Growth Medium 2 SupplementMix” (PromoCell, Germany) (Final supplementation concentrations after addition to the medium: 5% FCS, 0.5 ng/L EGF, 2 ng/mL FBF, 5 µg/mL Insulin)

extract_protocol:
Total RNA was isolated with BluZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies).
polyA enrichment (performed by Novogene Europe)

treatment_protocol: Cells were synchronized for 24h in media without supplementation (“Smooth Muscle Cell Growth Medium 2") and then incubated for 48h -/+ 10µg/L EGF.

value: Human aortic smooth muscle

tag: cell type

value: HAoSMC

tag: gender

value: female

tag: donor

tag: replicate

tag: treatment

value: EGF


title: Adjacent normal LOCC_10

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_10_N


title: SMC2_noc_with_auxin_rep2_hp1g

city: Shenzhen

first: Haoyue

last: Zhang

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

country: China

institute: Shenzhen Bay Lab

library_source: genomic

data_processing:
For ChIP experiments against histone modification marks H3K27ac, H3K36me3, H3K27me3 and H3K9me3, spike-in samples were included to control for global change of histone marks during mitosis, especially for those with large-scale broad range peaks (such as H3K9me3). ChIP-seq reads were first aligned to human genome assembly hg19 with default parameters. Unmapped reads were then aligned to mouse genome assembly mm9. Human and mouse alignments were then both filtered for low-quality reads (MAPC <30), PCR duplicates and reads that aligned to mitochondria random contigs and ENCODE blacklisted regions were removed. The final read counts aligned to human hg19 genome was determined by SAMtools (v1.9) and scaling factor was calculated as: 10e6/hg19_counts. Valid reads that aligned to mouse genome was then normalized using the above scaling factor through Deeptools (v3.1.3).
Assembly: mm9
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: G1E-ER4 cells

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
FACS purified cells were re-suspended in 1ml pre-cooled Cell Lysis Buffer supplemented with 1:500 protease inhibitor and 1:100 PMSF for 20min on ice. To control for global change of histone modification that cannot be detected by ChIP-seq, HEK293T cells were used as spike-in controls and added into FACS purified mitotic and asynchronous cells so that both samples contain comparable level of human genome (~10%). Nuclei were then re-suspended in 1ml Nuclear Lysis Buffer (50mM Tris pH 8, 10mM EDTA, 1% SDS, fresh supplemented with PI and PMSF) for 20min on ice. Chromatin was then fragmented to 200-300bp by sonication (Qsonica Q800R3, 80% amplitude, 20s ON, 40s OFF) for 17min. Samples were centrifuged at 15000g for 10min at 4℃ to remove cell debris. Chromatin in the supernatant was collected and diluted with 4 volumes of IP dilution buffer (20mM Tris pH 8.0, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS) and then supplemented with protease inhibitor, PMSF and 50ul of A/G agarose beads (Santa Cruz Cat#sc-2003). Preclear of chromatin was performed at 4℃ for 8h with rotation. Precleared chromatin was then incubated with 35μl A/G agarose beads (A:G = 1:1) pre-bound with ChIP antibody at 4℃ overnight. Beads were washed once with IP wash buffer I (20mM Tris pH 8, 2mM EDTA, 50mMNaCl, 1% Triton X-100, 0.1% SDS), twice with high salt buffer (20mMTris pH 8, 2mM EDTA, 500mMNaCl, 1% Triton X-100, 0.01% SDS), once with IP wash buffer II (10mMTris pH 8, 1mM EDTA, 0.25 M LiCl, 1% NP-40/Igepal, 1% sodium deoxycholate) and twice with TE buffer (10mM Tris pH 8, 1mM EDTA pH 8). All washing steps were performed on ice. Beads were moved to room temperature and DNA was eluted in 200μl fresh Elution Buffer (100mM NaHCO3, 1%SDS). ChIP and input chromatin were reverse crosslinked at 65℃ overnight in the prescence of proteinase K.  IP and input samples were supplemented with 10ul of 3M sodium acetate (pH 5.2), and DNA was purified with QIAquick PCR purification kit (QIAGEN Cat#28106).
ChIP-seq libraries were constructed using the AHTS Universal DNA Library Prep Kit for MGI (Vazyme, Cat#NDM607-02) according to the manufacture’s protocol.For cut and tag library: we performed CUT&TAG on asynchronously growing G1E-ER4 cells using lamin B1 antibody (ab16048) according to the manufacture’s protocol (Vazyme Hyperactive® Universal CUT&Tag Assay Kit for Illumina).

tag: cell line

value: G1E-ER4 cells

value: erythroid


title: spinal_cord, B6_EAE_early, animal21-46_10_sliceB.7

department: Neurology

tag: strain

tag: disease state

value: EAE early


title: SMC2_noc_with_auxin_rep2_input


title: SMC2_noc_with_auxin_rep2_k4me1


title: Adjacent normal LOCC_03

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_03_N


title: spinal_cord, B6_healthy, animal11.2_sliceA.7

value: control

value: healthy control


title: spinal_cord, B6_EAE_late, animal21-46_6_sliceD.6


title: HCPEpiC-Ctr-2

city: Guangdong

first: Di

last: Can

address: Guangzhou

institute: Sun Yat-Sen university

description: RNA-seq

data_processing:
1. sn-seq: Raw BCL files obtained from the 10x GENOMICS Single-nucleus RNA-seq platform were convert to FASTQ files. The resulting FASTQ files were demultiplexed and mapped to the mm10 transcriptome using the Cell Ranger package (10x GENOMICS). For quality control, nuclei were excluded from further analysis if they were outliers in terms of number of the genes, UMIs, and the percentage of mitochondrial genes using the R (v4.1.0) software package Seurat (v4.0.6) (http://satijalab.org/seurat). After filtering, a total of 20,198 nuclei (10,444 from normal, 9,754 from EO771-VM) remained for downstream analysis. 2. ST: Raw ST sequencing data were processed using the open source ST Pipeline v1.7.2 with the genome reference mm10 transcriptome. The ST pipeline was executed with two-pass mode enabled for alignment and discarding reads in which the UMI had at least 6 low quality bases. The count matrices (spots by genes) were filtered to keep only protein-coding, long non-coding, and antisense genes, and Ensembl IDs were replaced by gene names. The matrix of counts underwent another filtering step, where only spots inside the tissue were kept using the file generated in the previous step (image alignment).  3. RNA-seq: Raw sequencing reads were quality-filtered and adapter removal was performed by fastp (v.0.18.0). Paired-end clean reads were mapped to the human reference genome Ensembl_release106 using HISAT2 (v.2.4). Gene level quantification and normalization was using RSEM (v.1.3.3) software. Fragment per kilobase of transcript per million mapped reads (FPKM) was used as an index of gene quantification.
Assembly: mm10;human reference genome Ensembl_release106
Supplementary files format and content: 1.sn-seq: Tab-separated values files and matrix files. 2. ST: Tab-delimited text files containing genes by barcode counts matrices. Tissue_positions_list.csv includes cell barcode for X,Y coordinates. 3.RNA-seq: tab-delimited text files include RPKM values for each Sample

source_name: cell line

extract_protocol:
1. sn-seq: The lateral ventricles including the choroid plexus and an about 2 mm thin layer of tissue surrounding the ventricles were carefully micro-dissected and homogenized using scissors. The resulting homogenates were filtered through a 40 µm cell strainer and centrifuged at 500 g for 5 min to pellet nuclei. To purify nuclei, the pellet was resuspended and centrifuged at 25,000 rpm at 4 ℃ for 2 hr using an ultra-centrifuge equipped with swinging bucket rotor. The supernatant was carefully removed via aspiration. 1 ml of stain buffer was added to resuspend the nuclear pellet. The nuclei were pelleted at 500 g for 10 min at 4 ℃. Stain buffer with mouse anti-NeuN conjugated to Alexa-Fluor-488 was added. The samples were incubated for 30 min at 4 ℃ and then centrifuged for 5 min at 500 g to pellet nuclei. The pallets were resuspended in stain buffer that contained 0.1 µg/ml DAPI. Single nucleus sorting was carried out on FACSAria III. Nuclei were gated on their morphology and DAPI signal. Nuclei negative for NeuN were sorted. 2. ST: EO771-VM bearing mouse brains were embedded in Tissue-Tek O.C.T. Compound and frozen in isopentane on liquid nitrogen. The embedded mouse brains were cryosectioned coronally to a thickness of 10 mm (at -0.6 mm from the bregma) slice on a cryostat. Sections were placed respectively on Visium Spatial Tissue Optimization Slide and Visium Spatial slide within the capture area. 3. RNA-seq: The different mRNA profiles of HCPEpiC cells treated with or without 500 ng/mL recombinant human tryptase  were compared by RNA-seq. Total RNA was extractedusing the TRIzol  reagent according to the manufacturer’s instructions. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies).
1. sn-seq:Single nucleus was loaded on a 10x GENOMICS GemCode Single-nucleus instrument that generated single-nucleus Gel Bead-In-EMlusion (GEMs). Reverse transcription and libraries preparation were performed using the Chromium Next GEM Single nucleus 3’ Reagent Kits v3.1 (10x GENOMICS, CG000204) according to the manufacturer’s protocol. Libraries were sequenced on an lllumina NovaSeq 6000 system.  2.ST: After permeabilization, tissues were degraded and removed from the slides. Reverse transcription mix containing SuperScript III reverse transcriptase  was added to each section and incubated overnight at 42 ℃ to generated cDNA with spatial barcode information. The spatially barcoded, full-length cDNA was amplified via PCR to generate sufficient mass for library construction. The libraries were sequenced on the lllumina NovaSeq 6000 system using paired-end sequencing. 28 bases were sequenced on read 1 to determine the spatial barcode and UMIs, and 120 bases were sequenced on read 2 to cover the genetic region. 3. RNA-seq: Libraries of RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina. RNA-seq was performed using the Novaseq6000  with paired-end reads.

value: cell line

tag: age

value: choriod plexus epithelial cells


title: Adjacent normal LOCC_01

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_01_N


title: JC4_asyn_LB1_rep1_no_spiking


title: Adjacent normal LOCC_02

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_02_N


title: SMC2_noc_with_auxin_rep2_hp1b


title: spinal_cord, B6_EAE_late, animal21-46_4_sliceB.6

value: Spinal cord


title: SMC2_noc_with_auxin_rep2_hp1a


title: HCPEpiC-Ctr-1

description: RNA-seq


title: SMC2_noc_with_auxin_rep2_k27ac


title: HCPEpiC-Tryptase-1

description: RNA-seq

value: cells were treated with tryptase


title: Adjacent normal EOCC_15

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_15_N

value: EOCC


title: spinal_cord, B6_EAE_late, animal21-46_6_sliceC.7

value: MOG EAE

value: EAE late


title: Adjacent normal EOCC_14

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_14_N

value: Colon cancer

value: Adjacent normal


title: 20063X12 7d_Con

city: Salt Lake City

first: Micah

middle: J

last: Drummond

state: Utah

address: 520 Wakara Way

department: Physical Therapy and Athletic Training

institute: The University of Utah

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
20063R_counts.txt
20063X12

data_processing:
The human GRCh38 genome and gene annotation files were downloaded from Ensembl release 104
A reference database was created using STAR version 2.7.9a with splice junctions optimized for 150 base pair reads
Optical duplicates were removed using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.34.0
Assembly: GRCh38
Supplementary files format and content: FeatureCount output files combined into a single tab-delimited raw count matrix

source_name: Vastus Lateralis Muscle

extract_protocol:
Total RNA was isolated by homogenizing myotubes in Qiazol Lysis Reagent (Qiagen, cat# 79306). The RNA was separated and precipitated using chloroform and isopropanol. Extracted RNA was washed with ethanol then suspended in nuclease-free water.
Libraries were prepared with Illumina Stranded Total RNA Library Prep NEB Ultra II directional and RNA was sequenced using Illumina NovaSeq S4 Reagent Kit v1.5 150x150 bp Sequencing

treatment_protocol: Individuals were given placebo or metformin at 500 mg for the first four days. On days five through 9, participants took one capsule with breakfast and 2 with dinner (1.5 g total). From days ten to fourteen, and throughout bed rest participants took two capsules with breakfast and 2 with dinner (2g total). After bed rest, participants stopped treatments, i.e. no treatment was taken throughout the seven day recovery period.

tag: time

value: 7d recovery

value: Placebo

value: Vastus Lateralis Muscle

tag: Sex

value: F


title: HCPEpiC-Ctr-3

description: RNA-seq


title: SMC2_noc_with_auxin_rep1_polii

value: G1E-ER4 cells

value: erythroid


title: SMC2_noc_with_auxin_rep2_Rad21


title: Adjacent normal EOCC_12

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_12_N


title: SMC2_noc_with_auxin_rep1_k4me1


title: 20063X10 POSTbc_Con

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
20063R_counts.txt
20063X10

value: Post 5d bed rest


title: 20063X9 Day1_Con

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
20063R_counts.txt
20063X9

value: After 2 weeks of treatment


title: spinal_cord, B6_EAE_early, animal21-46_10_sliceD.5

value: EAE early


title: Adjacent normal EOCC_11

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_11_N


title: Adjacent normal EOCC_13

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_13_N


title: spinal_cord, B6_EAE_early, animal21-46_10_sliceC.5


title: spinal_cord, B6_EAE_early, animal21-46_5_sliceB.5


title: SMC2_noc_with_auxin_rep1_k36me3


title: 20063X7 PREbc_Con

description:
Pre intervention, fasted thigh muscle biopsy sample
20063R_counts.txt
20063X7

value: Pre bed rest


title: spinal_cord, B6_EAE_late, animal21-46_4_sliceA.6

value: Spinal cord


title: spinal_cord, B6_healthy, animal11.2_sliceD.4

value: control

value: healthy control


title: 20063X8 PREac_Con

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
20063R_counts.txt
20063X8

value: Pre bed rest Post clamp


title: spinal_cord, B6_EAE_early, animal21-46_5_sliceA.5

value: MOG EAE


title: Adjacent normal EOCC_09

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_09_N

value: Colon cancer

value: EOCC


title: SMC2_noc_with_auxin_rep1_hp1g


title: 20063X11 POSTac_Con

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
20063R_counts.txt
20063X11

value: Post 5d bed rest Post clamp


title: 20063X3 Day1_Con

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
20063R_counts.txt
20063X3

value: Placebo

value: M


title: spinal_cord, B6_EAE_early, animal20-05_21_sliceD.3


title: Adjacent normal EOCC_07

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_07_N

value: Adjacent normal


title: Adjacent normal EOCC_04

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_04_N


title: spinal_cord, B6_healthy, animal11.2_sliceC.4


title: Adjacent normal EOCC_08

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_08_N


title: Adjacent normal EOCC_06

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_06_N


title: 20063X5 POSTac_Con

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
20063R_counts.txt
20063X5

value: Vastus Lateralis Muscle


title: SMC2_noc_with_auxin_rep1_Rad21

value: G1E-ER4 cells

value: erythroid


title: 20063X6 7d_Con

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
20063R_counts.txt
20063X6

value: 7d recovery


title: SMC2_noc_with_auxin_rep1_k27ac


title: SMC2_noc_with_auxin_rep1_hp1b


title: 20063X2 PREac_Con

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
20063R_counts.txt
20063X2


title: spinal_cord, B6_EAE_early, animal20-05_21_sliceC.3

value: EAE early


title: SMC2_asyn_rep3_hp1b


title: spinal_cord, B6_EAE_early, animal20-05_21_sliceB.3


title: spinal_cord, B6_healthy, animal11.2_sliceA.4


title: 20063X4 POSTbc_Con

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
20063R_counts.txt
20063X4

value: Post 5d bed rest


title: 20063X1 PREbc_Con

description:
Pre intervention, fasted thigh muscle biopsy sample
20063R_counts.txt
20063X1

value: Pre bed rest


title: SMC2_noc_with_auxin_rep1_hp1a


title: SMC2_noc_with_auxin_rep1_k27me3


title: spinal_cord, B6_healthy, animal11.1_sliceD.2

value: Spinal cord

value: control


title: SMC2_asyn_rep2_k4me1


title: Adjacent normal EOCC_02

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_02_N


title: spinal_cord, B6_EAE_early, animal20-05_21_sliceA.3


title: SMC2_asyn_rep2_polii


title: Adjacent normal EOCC_01

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_01_N


title: Adjacent normal EOCC_03

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_03_N


title: Colon cancer LOCC_17

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_17_T

value: LOCC


title: 19565X98 Day1_Met

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X98

value: After 2 weeks of treatment

value: Metformin

value: F


title: Colon cancer LOCC_16

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_16_T

value: Colon cancer


title: 19565X100 POSTac_Met

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X100

value: Post 5d bed rest Post clamp


title: SMC2_asyn_rep2_k27ac


title: SMC2_asyn_rep2_k36me3


title: 19565X99 POSTbc_Met

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X99


title: spinal_cord, B6_EAE_late, animal20-01_11_sliceD.1

value: MOG EAE

value: EAE late


title: 19565X97 PREac_Met

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X97

value: Pre bed rest Post clamp

value: Vastus Lateralis Muscle


title: Colon cancer LOCC_12

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_12_T


title: Colon cancer LOCC_15

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_15_T


title: spinal_cord, B6_healthy, animal11.1_sliceA.2

value: healthy control


title: spinal_cord, B6_healthy, animal11.1_sliceB.2


title: SMC2_asyn_rep2_k27me3

value: G1E-ER4 cells

value: erythroid


title: spinal_cord, B6_healthy, animal11.1_sliceC.2


title: SMC2_asyn_rep2_hp1g


title: spinal_cord, B6_EAE_late, animal20-01_11_sliceC.1


title: Colon cancer LOCC_13

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_13_T


title: 19565X101 7d_Met

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X101

value: 7d recovery


title: 19565X96 PREbc_Met

description:
Pre intervention, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X96

value: Pre bed rest


title: SMC2_asyn_rep2_input


title: SMC2_asyn_rep2_hp1b


title: spinal_cord, B6_EAE_late, animal20-01_11_sliceB.1

value: Spinal cord


title: Colon cancer LOCC_09

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_09_T


title: Colon cancer LOCC_08

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_08_T


title: SMC2_asyn_rep2_hp1a


title: 19565X94 POSTac_Met

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X94


title: spinal_cord, B6_EAE_late, animal20-01_11_sliceA.1


title: SMC2_asyn_rep1_polii


title: Colon cancer LOCC_05

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_05_T


title: 19565X92 Day1_Met

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X92


title: SMC2_asyn_rep1_k4me1


title: 19565X93 POSTbc_Met

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X93

value: Post 5d bed rest


title: SMC2_asyn_rep1_k36me3


title: Peri-weaning

city: Basel

first: Jonas

middle: Alexander

last: Kretz

address: Schanzenstrasse 44

department: BSSE

country: Switzerland

institute: ETH

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The resulting Bcl files were demultiplexed with Space Ranger 1.2.0 (10x Genomics) using the mkfastq command.
Manually aligned to the fiducial frames with Loupe Browser 5.1.0 (10x Genomics) to generate a .json file.
Space Ranger 1.2.0 count pipeline was used for read alignment with mouse reference mm10-2020-A (GENCODE vM23/Ensembl 98)
Read counts per spot per gene were analysed using Seurat (v 4.0.0)
Assembly: mm10-2020-A
Supplementary files format and content: Sparse feature barcode count matrix (mtx.gz format), feature ID and name in the first and second column, features correspond to row indices of matrix.mtx.gz (.tsv.gz format), cell barcodes corresponding to column indices of matrix.mtx.gz (.tsv.gz format), full-resolution image (.png.gz format), scalefactors of pixel posiitons (.json.gz format), table with rows corresponding to spots (.csv.gz format) as well as a matrix with filtered gene counts for every gene in every barcoded tissue spot, with spatial coordinates (.h5 format).

molecule: polyA RNA

source_name: Brain

extract_protocol: RNA quality of all samples was assessed through RIN measurement, and only brains with a RIN > 8 were processed for sequencing. 10µm thick olfactory bulb sections were cut on a cryostat and placed on pre-chilled Visium Tissue Optimization Slides or Visium Spatial Gene Expression Slides. Tissue sections were then fixed for 30 minutes in methanol at -20°C and processed for a short immunofluorescence staining (CG000312 Rev C, 10x Genomics), using NeuN (ms) and DAPI. Tissue permeabilization time was set to 9 minutes, as evaluated by the maximal yield of fluorescent cDNA according to Visium Spatial Tissue Optimization User Guide (CG000238 Rev D, 10x Genomics). The mRNA extraction and library preparation were performed according to 10x Genomics protocols (CG000239 Rev D, 10x Genomics).

value: Brain cells

value: Brain

value: hGFAP::GFP mice

value: 4 months

tag: group

value: Peri-weaning


title: Colon cancer LOCC_10

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_10_T

value: Colon cancer

value: LOCC


title: 19565X91 PREac_Met

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X91

value: Metformin

value: F


title: Virgin 2

description: 10x Genomics

value: Virgin


title: Perinatal care

description: 10x Genomics

value: Perinatal care


title: Colon cancer LOCC_03

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_03_T


title: 19565X89 7d_Met

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X89

value: Vastus Lateralis Muscle

value: M


title: 19565X90 PREbc_Met

description:
Pre intervention, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X90


title: ST3

description: 10x Genomics

source_name: brain section

value: brain section

value: 9-12 weeks

value: mice injected EO771-VM cells


title: Colon cancer LOCC_04

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_04_T


title: ST2

description: 10x Genomics


title: Colon cancer LOCC_01

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_01_T


title: Colon cancer EOCC_15

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_15_T

value: EOCC


title: Virgin 1

description: 10x Genomics

value: Brain cells


title: SMC2_asyn_rep1_k27ac

value: G1E-ER4 cells

value: erythroid


title: SMC2_asyn_rep1_hp1g


title: SMC2_asyn_rep1_hp1b


title: 19565X88 POSTac_Met

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X88

value: Post 5d bed rest Post clamp


title: 19565X87 POSTbc_Met

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X87

value: Post 5d bed rest


title: SMC2_asyn_rep1_hp1a


title: ST1

description: 10x Genomics


title: Colon cancer EOCC_13

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_13_T

value: Colon cancer


title: Colon cancer EOCC_14

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_14_T


title: Colon cancer LOCC_02

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_02_T

value: LOCC


title: Colon cancer EOCC_12

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_12_T


title: SMC2_asyn_rep1_k27me3


title: 19565X84 PREbc_Met

description:
Pre intervention, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X84

value: Pre bed rest

value: Metformin


title: SMC2_asyn_rep1_Rad21


title: 19565X95 7d_Met

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X95

value: 7d recovery

value: F


title: Colon cancer EOCC_09

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_09_T


title: 19565X83 7d_Met

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X83

value: Vastus Lateralis Muscle


title: 19565X82 POSTac_Met

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X82


title: Colon cancer EOCC_08

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_08_T


title: 19565X80 Day1_Met

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X80

value: After 2 weeks of treatment


title: SMC2_noc_4h_with_auxin_dmso_rep2

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.

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:SMC2-mAID-mCherry cells were first arrested to prometaphase with nocodazole (200ng/ml) for 12 hours or 15 hours (for 8h release condition). Toward the end of mitotic arrest, cells were treated with auxin (1mM) for 0h (SMC2+), 0.5 hours, 1 hour, 4 hours or 8 hours respectively.


title: SMC2_noc_4h_with_auxin_JQ1_rep2


title: SMC2_noc_4h_with_auxin_JQ1_rep1


title: Colon cancer EOCC_11

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_11_T


title: 19565X79 PREac_Met

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X79

value: Pre bed rest Post clamp


title: Colon cancer EOCC_07

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_07_T


title: SMC2_noc_4h_with_auxin_dmso_rep1


title: Colon cancer EOCC_06

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_06_T


title: 3308_wt_ND

city: Rehovot

first: Avital

last: Sarusi Portuguez

state: Select a State/Province/Region

address: 234 Herzl Street, POB 26

department: G-INCPM

country: Israel

institute: Weizmann Institute of Science

data_processing:
cellranger-6.0.1 was run for bcl2fastq, Read filter and count
Genome_build: GRCm38
Supplementary_files_format_and_content: matrix files include mRNA molecule count values for each Sample

source_name: 10x run of mouse CD45+ cells of small intestines

extract_protocol:
Small intestines were harvested and cleaned of fat residue and Peyer’s patches. To obtain lamina propria cells (LPC), the small intestine was cut longitudinally and scraped in PBS 1X to clean the mucus and feces. The clean tissue was fragmented into pieces in 20ml HBSS 2% FCS. The pieces were filtered through a 100μm mesh and were incubated in 10ml HBSS 2mM EDTA in a shaker at 37°C for 20 min. The pieces were rinsed with HBSS through a 100μm mesh and incubated in 10ml HBSS 2mM EDTA in a shaker at 37°C for 20 min. The pieces were rinsed with HBSS, filtered through a 100μm mesh and incubated in 15 ml IMDM +10% FCS containing 1mg/ml collagenase VIII (Sigma) in a shaker at 37°C for 15 min in order to disaggregate the tissue. Single cell suspensions were then washed and filtered filtered (100 and 40μm cell strainer). Staining was performed using Live/Dead discrimination by using DAPI or ZombieDyeNIR according to the manufacturer´s instructions. After washing (~400g, 5min, 4°C), cells were stained with anti-CD45 antibody (Alexa Fluor® 700 anti-mouse CD45 Antibody, cat.no.103128, concentration 1:200) for 20min at 4°C and washed again. Samples for flow cytometry were fixed using eBioscience IC fixation (cat.no.00-8222-49) according to the manufacturer´s instruction. For sorting, a FACS Aria II and a FACSAria FUSION were used. After the isolation the cells were washed once with cold PBS + 0.1% KnockOut™ Serum Replacement (cat.no.10828010, TermoFisher Scientific) and subjected to single-cell RNA sequencing analysis using the Chromium System (10x Genomics, California, USA).
10x genomics according to the manufacturer protocol
single cell RNA-seq 3'

treatment_protocol: Mice were fed with normal diet (ND) or with choline-deficient high-fat diet (CD-HFD) for 6 months prior the intestinal immune cells sorting.

value: CD45+ cells from small intestine

value: ND (no diet)


title: SMC2_noc_4h_with_auxin_a485_rep2


title: 19565X86 Day1_Met

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X86

value: M


title: Colon cancer EOCC_04

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_04_T

value: EOCC


title: 19565X85 PREac_Met

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X85


title: Colon cancer EOCC_03

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_03_T


title: 19565X78 PREbc_Met

description:
Pre intervention, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X78


title: SMC2_asyn_M_sort_4h_auxin_rep1

value: G1E-ER4 cells


title: 19565X81 POSTbc_Met

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X81


title: 3307_wt_CDHFD

value: CD-HFD (choline-deficient high fat diet)


title: 19565X77 7d_Met

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X77


title: 19565X76 POSTac_Met

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X76

value: Post 5d bed rest Post clamp


title: SMC2_asyn_M_sort_4h_auxin_rep2

value: erythroid


title: Colon cancer EOCC_02

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_02_T

value: Colon cancer


title: SMC2_asyn_M_sort_no_auxin_rep2


title: G24_MHD

city: Barcelona

first: Laia

last: Ribas

address: Passeig Maritim 37-49

country: Spain

institute: Institut de Ciencies del Mar

data_processing:
raw reads were quality trimmed by the Trim Galore! software (v. 0.4.5) with the following parameters  --nextera, --quality 20, and --phred64
adapters, the number and quality of the reads were checked using the FastQC software (v. 0.11.6)
the alignments of the pair-end reads were performed using the function “bismark”: --bowtie2, --non-directional, and --score_min 0 + (−0.6 x read length). Bismark software (v. 16.0)
methylation calling  bismark_methylation_extractor”: --bedGraph
Supplementary_files_format_and_content: tab-delimited files (sample_name.txt) contain the coverage and the frequency of Cs (methylated cytosines) and of Ts (unmethylated cytosines) per CpG (chromosome, base, strand) covered
Genome_build: GRCz11 Danio rerio https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.5/

organism: Danio rerio

source_name: male high density

growth_protocol: Zebrafish were raised following:  Westerfield, M. (2000). The zebrafish book. A guide for the laboratory use of zebrafish (Danio rerio). 4th ed., Univ. of Oregon Press, Eugene.

extract_protocol:
Phenol-Chlorofrom DNA extraction
library preparation following protocol as in Anastasiadi et al 2018
Gonads were extracted, flash frozen in nitrogen liquid. DNA was extracted  following  the Phenol-Chlorofrom DNA extraction. Bisulfite conversion was carried out using D5020, Zymo Research from 1000 ng of genomic DNA in each sample. Illumina Hiseq 2500 was used for sequencing the library.
Library was constructed following the Illumina’s protocol: “16S metagenomic library preparation” using Nextera XT Index Kit V2 set A, FC-131–2001 kit.

treatment_protocol: zebrafish larva were reared at high density during sex differentiation. Methylation Bisulfite sequencing was performed as described in Anastasiadi el al., 2018

value: AB

tag: FISH origin

value: laboratory (reared in aquarium facilities)

value: 90 days old

value: gonads

value: male

tag: stress

value: high density


title: G22_FHD

source_name: female high density

tag: tissue

value: female


title: G25_MHD


title: G23_MHD


title: 19565X74 Day1_Met

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X74

value: After 2 weeks of treatment

value: Metformin

value: Vastus Lateralis Muscle


title: 19565X75 POSTbc_Met

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X75

value: Post 5d bed rest

value: M


title: SMC2_noc_4h_with_auxin_a485_rep1

value: G1E-ER4 cells


title: G21_MHD


title: SMC2_asyn_M_sort_no_auxin_rep1


title: ncaph2_asyn_rep2


title: ncaph2_8h_auxin_rep2


title: ncaph2_asyn_rep1


title: 19565X73 PREac_Met

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X73

value: Pre bed rest Post clamp


title: CRC_Y03_O03 013 Vim+FAP_i

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

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

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: LOCC

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: G20_MHD

value: AB

value: laboratory (reared in aquarium facilities)

tag: gender


title: CRC_Y03_O03 014 PanCK+

tag: age of_patients

value: PanCK+


title: CRC_Y03_O03 014 Vim+FAP_i


title: G26_FHD

tag: strain

value: 90 days old

value: gonads


title: 19565X72 PREbc_Met

description:
Pre intervention, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X72

value: Pre bed rest

tag: treatment

tag: age


title: Colon cancer EOCC_01

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
EOCC_01_T

value: Colon cancer

tag: tissue type

value: EOCC

tag: tissue site


title: 19565X70 POSTac_Met

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X70

tag: time

value: Post 5d bed rest Post clamp

value: Metformin

value: Vastus Lateralis Muscle

tag: Sex


title: ncaph2_4h_auxin_rep2

tag: cell line

value: G1E-ER4 cells

tag: cell type

value: erythroid


title: ncaph2_8h_auxin_rep1


title: 19565X71 7d_Met

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X71

value: 7d recovery

tag: tissue

value: M


title: CRC_Y03_O03 013 PanCK+

value: colon cancer

tag: type of_tissue

value: LOCC

tag: annotation geomx_dsp

tag: segment tag


title: G16_FHD

value: AB

tag: FISH origin

value: female

tag: stress

value: high density


title: G18_FHD

value: laboratory (reared in aquarium facilities)

value: 90 days old

tag: gender


title: CRC_Y03_O03 012 Vim+FAP_i

tag: age of_patients

tag: scan id

tag: roi id

tag: cell type specific morphological marker

value: Vim+FAPi

tag: histological region

value: TC


title: CRC_Y03_O03 011 Vim+FAP+

value: Vim+FAP+

value: TIM


title: G15_MHD

tag: strain

tag: age

value: gonads

value: male


title: 19565X69 POSTbc_Met

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X69

tag: time

value: Post 5d bed rest

tag: treatment

value: Metformin

value: Vastus Lateralis Muscle

tag: Sex


title: ncaph2_4h_auxin_rep1

tag: cell line

value: G1E-ER4 cells

tag: cell type

value: erythroid


title: CRC_Y03_O03 012 PanCK+

tag: tissue

value: colon cancer

tag: type of_tissue

value: LOCC

tag: annotation geomx_dsp

value: PanCK+


title: ncaph2_30min_auxin_rep2


title: CRC_Y03_O03 011 PanCK+

tag: segment tag


title: G14_FHD

value: AB

tag: FISH origin

tag: gender

value: female

tag: stress

value: high density


title: CRC_Y03_O03 010 Vim+FAP+

tag: age of_patients

tag: scan id

tag: roi id


title: 19565X66 PREbc_Met

description:
Pre intervention, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X66

value: Pre bed rest

value: M


title: G13_MHD

tag: strain

value: laboratory (reared in aquarium facilities)

value: 90 days old


title: 19565X68 Day1_Met

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X68

value: After 2 weeks of treatment

tag: age


title: G12_FHD

value: gonads


title: G11_FHD


title: CRC_Y03_O03 010 PanCK+

tag: cell type specific morphological marker

tag: histological region

value: TIM


title: 19565X65 7d_Met

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X65

tag: time

value: 7d recovery

tag: treatment

value: Metformin

tag: Sex

value: F


title: ncaph2_1h_auxin_rep2

tag: cell line

value: G1E-ER4 cells

tag: cell type

value: erythroid


title: ncaph2_30min_auxin_rep1


title: CRC_Y03_O03 009 Vim+FAP+

tag: tissue

value: colon cancer

tag: type of_tissue

value: EOCC

tag: annotation geomx_dsp

value: Vim+FAP+


title: ncaph2_1h_auxin_rep1


title: CRC_Y03_O03 009 PanCK+

tag: segment tag

value: PanCK+


title: G10_MHD

value: AB

tag: FISH origin

tag: gender

value: male

tag: stress

value: high density


title: 19565X64 POSTac_Met

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X64

value: Post 5d bed rest Post clamp

value: Vastus Lateralis Muscle


title: G8_MHD

value: laboratory (reared in aquarium facilities)

value: 90 days old


title: 19565X63 POSTbc_Met

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X63

value: Post 5d bed rest


title: CRC_Y03_O03 008 Vim+FAP_i

tag: age of_patients

tag: scan id

tag: roi id

value: Vim+FAPi

value: AN


title: ncaph2_0h_auxin_rep1


title: 19565X62 Day1_Met

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X62

value: After 2 weeks of treatment

value: Metformin

tag: age

value: F


title: 19565X67 PREac_Met

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X67

value: Pre bed rest Post clamp

value: M


title: ncaph_asyn_rep2

value: G1E-ER4 cells

value: erythroid


title: G6_FHD

tag: strain

value: AB

value: gonads

value: female


title: CRC_Y03_O03 008 PanCK+

value: colon cancer

value: EOCC

tag: cell type specific morphological marker

value: PanCK+

tag: histological region


title: 19565X61 PREac_Met

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X61

tag: time

tag: treatment

value: Vastus Lateralis Muscle

tag: Sex


title: 19565X60 PREbc_Met

description:
Pre intervention, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X60

value: Pre bed rest

tag: tissue


title: ncaph_asyn_rep1

tag: cell line

tag: cell type


title: G5_MHD

value: laboratory (reared in aquarium facilities)

value: 90 days old

value: male

value: high density


title: CRC_Y03_O03 007 Vim+FAP_i

tag: type of_tissue

tag: annotation geomx_dsp

tag: segment tag

value: Vim+FAPi

value: AN


title: ncaph_8h_auxin_rep2


title: CRC_Y03_O03 007 PanCK+


title: G2_FHD

tag: FISH origin

tag: gender

tag: stress


title: G3_FHD


title: 19565X59 7d_Met

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X59

value: 7d recovery

value: Metformin

value: F


title: ncaph_8h_auxin_rep1

value: G1E-ER4 cells

value: erythroid


title: 19565X58 POSTac_Met

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X58

value: Post 5d bed rest Post clamp


title: ncaph_4h_auxin_rep2


title: 19565X57 POSTbc_Met

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X57

value: Post 5d bed rest


title: G26_MLD

source_name: male control

value: AB

value: gonads

value: control


title: ncaph2_0h_auxin_rep2


title: CRC_Y03_O03 006 Vim+FAP_i

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

value: colon cancer

value: EOCC

tag: age of_patients

tag: scan id

tag: roi id

value: TC


title: ncaph_4h_auxin_rep1


title: CRC_Y03_O03 006 PanCK+

tag: cell type specific morphological marker

value: PanCK+


title: CRC_Y03_O03 005 Vim+FAP_i

tag: histological region


title: G21_MLD

tag: strain

value: laboratory (reared in aquarium facilities)

tag: age

value: 90 days old

value: male


title: 19565X56 Day1_Met

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X56

tag: time

value: After 2 weeks of treatment

tag: treatment

value: Vastus Lateralis Muscle

tag: Sex


title: G24_MLD

tag: tissue


title: CRC_Y03_O03 005 PanCK+

tag: type of_tissue


title: G20_MLD


title: 19565X55 PREac_Met

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X55

value: Pre bed rest Post clamp

value: Metformin

value: F


title: CRC_Y03_O03 004 Vim+FAP_i

tag: annotation geomx_dsp

value: Vim+FAPi


title: CRC_Y03_O03 004 PanCK+

tag: segment tag


title: G19_FLD

source_name: female control

tag: FISH origin

value: female


title: ncaph_30min_auxin_rep1

tag: cell line

value: G1E-ER4 cells

tag: cell type

value: erythroid


title: 19565X54 PREbc_Met

description:
Pre intervention, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X54

value: Pre bed rest


title: ncaph_1h_auxin_rep2


title: 19565X53 7d_Met

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X53

value: 7d recovery

value: M


title: ncaph_30min_auxin_rep2


title: G18_MLD

value: AB

value: gonads

tag: gender

tag: stress

value: control


title: 19565X52 POSTac_Met

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X52

value: Post 5d bed rest Post clamp


title: ncaph_1h_auxin_rep1


title: G17_FLD

value: laboratory (reared in aquarium facilities)

value: 90 days old


title: CRC_Y03_O03 002 Vim+FAP+

value: colon cancer

value: EOCC

tag: age of_patients

tag: scan id

tag: roi id

value: Vim+FAP+

value: TIM


title: ncaph_0h_auxin_rep1


title: ncaph_0h_auxin_rep2


title: CRC_Y03_O03 003 PanCK+

value: LOCC

tag: cell type specific morphological marker

value: PanCK+

tag: histological region


title: G15_FLD

tag: strain

tag: age

value: female


title: 19565X50 Day1_Met

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X50

tag: time

value: After 2 weeks of treatment

tag: treatment

value: Metformin

value: Vastus Lateralis Muscle

tag: Sex


title: G14_FLD

tag: tissue


title: CRC_Y03_O03 002 PanCK+

tag: type of_tissue

tag: annotation geomx_dsp

tag: segment tag


title: CRC_Y03_O03 001 Vim+FAP+


title: G12_FLD

tag: FISH origin


title: hp1a_b_g_noc_6h_with_a_with_d_clone21

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


title: CRC_Y03_O03 001 PanCK+

tag: age of_patients


title: hp1a_b_g_noc_6h_no_a_no_d_clone21


title: 19565X48 PREbc_Met

description:
Pre intervention, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X48

value: Pre bed rest

value: M


title: hp1a_b_g_noc_6h_with_a_with_d_clone20


title: G11_MLD

value: AB

value: gonads

tag: gender

value: male

tag: stress

value: control


title: CRC_Y03_O03 003 Vim+FAP+

value: colon cancer

tag: scan id

tag: roi id

tag: cell type specific morphological marker


title: G10_MLD

tag: strain

value: laboratory (reared in aquarium facilities)

tag: age

value: 90 days old


title: G9_MLD


title: 19565X45 POSTbc_Met

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X45

tag: time

value: Post 5d bed rest

tag: treatment


title: 19565X47 7d_Met

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X47

value: 7d recovery

tag: tissue

tag: Sex


title: CRC_Y01_O01 017 Vim+FAP+

tag: type of_tissue

value: EOCC

tag: annotation geomx_dsp

value: Vim+FAP+

tag: histological region

value: TIM


title: 19565X51 POSTbc_Met

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X51

value: Metformin

value: Vastus Lateralis Muscle


title: 19565X43 PREac_Met

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X43

value: Pre bed rest Post clamp


title: hp1a_b_g_noc_6h_no_a_no_d_clone20

tag: cell line

value: G1E-ER4 cells

value: erythroid


title: hp1a_b_g_noc_1h_no_a_no_d_clone21

tag: cell type


title: 19565X46 POSTac_Met

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X46

value: Post 5d bed rest Post clamp

value: M


title: hp1a_b_g_noc_1h_with_a_with_d_clone21


title: G5_FLD

value: AB

tag: FISH origin

value: gonads

value: female


title: CRC_Y01_O01 015 PanCK+

value: colon cancer

value: LOCC

tag: age of_patients

tag: segment tag

value: PanCK+

value: AN


title: 19565X49 PREac_Met

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X49


title: G7_FLD

value: laboratory (reared in aquarium facilities)

value: 90 days old

tag: gender

tag: stress

value: control


title: hp1a_b_g_noc_1h_with_a_with_d_clone20


title: 19565X44 Day1_Met

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X44

value: After 2 weeks of treatment

value: Metformin


title: CRC_Y01_O01 015 Vim+FAP_i

tag: scan id

tag: roi id

tag: cell type specific morphological marker

value: Vim+FAPi


title: CRC_Y01_O01 014 Vim+FAP_i

value: TC


title: G4_MLD

tag: strain

tag: age

value: male


title: hp1a_b_g_noc_1h_no_a_no_d_clone20

value: G1E-ER4 cells

value: erythroid


title: SMC2_Noc_auxin_8h_rep4

description: hic

tag: genotype

tag: treatment

value: nocodazole 12h + auxin 8h


title: CRC_Y01_O01 017 PanCK+

tag: tissue

tag: type of_tissue

value: EOCC

value: TIM


title: CRC_Y01_O01 013 Vim+FAP_i

value: colon cancer

tag: annotation geomx_dsp

tag: histological region


title: 19565X41 7d_Con

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X41

tag: time

value: 7d recovery

value: Placebo

value: Vastus Lateralis Muscle

tag: Sex

value: M


title: 19565X40 POSTbc_Con

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X40

value: Post 5d bed rest


title: G3_MLD

value: AB

tag: FISH origin

value: laboratory (reared in aquarium facilities)

value: 90 days old

value: gonads

value: control


title: SMC2_Noc_auxin_8h_rep3

description: hic

tag: cell line

tag: cell type


title: G2_FLD

tag: gender

value: female

tag: stress


title: G6_FLD


title: 19565X39 Day1_Con

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X39

value: After 2 weeks of treatment


title: CRC_Y01_O01 013 PanCK+

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

value: LOCC

tag: age of_patients

tag: segment tag

tag: scan id

tag: roi id

value: PanCK+

value: TC


title: SMC2_Noc_auxin_8h_rep1

description: hic

value: G1E-ER4 cells

value: erythroid

tag: genotype

value: nocodazole 12h + auxin 8h


title: G1_FLD

tag: strain

tag: age


title: 19565X42 PREbc_Met

description:
Pre intervention, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X42

value: Pre bed rest

tag: treatment

value: Metformin

tag: tissue


title: SMC2_Noc_auxin_30min_rep4

description: hic

value: nocodazole 12h + auxin 30min


title: CRC_Y01_O01 012 Vim+FAP_i

value: colon cancer

tag: type of_tissue

tag: annotation geomx_dsp

tag: cell type specific morphological marker

value: Vim+FAPi

tag: histological region


title: 19565X37 PREbc_Con

description:
Pre intervention, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X37

tag: time

value: Placebo

value: Vastus Lateralis Muscle

tag: Sex

value: M


title: CRC_Y01_O01 012 PanCK+


title: B cells,ATAC, KO2

city: Beijing

first: Ligong

last: Chen

address: Shuangqing Road No.30

institute: tsinghua university

data_processing:
Clean fastq files were mapped to the GRCm38/mm10 using Bowtie2 with default parameters.
peaks were called using MACS2 (parameters:  -g mm --nomodel --shift -100 --extsize 200 -q 0.005)
Assembly: mm10
Supplementary files format and content: BIGWIG files containing dense and continuous genomic information

source_name: spleen

growth_protocol: The cells were cultured in RPMI-1640 medium supplemented with 10% FBS, 50 μM β-mercaptoethanol, GlutaMax and nonessential amino acids.

extract_protocol:
Nuclei isolated from 50,000 B cells were used for ATAC-seq. B cells were harvested at 500 g 4°C for 5 min, and then cell pellets were re-suspended in 100 μL of lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40) and then nuclei were centrifuged at 500 g 4°C for 15 min. The nuclei pellets were re-suspended in the transposition reaction mix containing Tn5 transposase (Vazyme Biotech, Nanjing, China).
The library was sequenced on an Illumina HiSeq X Ten sequencer

treatment_protocol: B cells were stimulated for 3 days using 10 μg/mL LPS and 50 ng/mL IL-4 to induce B cells CSR in vitro.

value: spleen

tag: cell line

value: primary

tag: cell type

value: B cell

value: LPS and IL4 for 3 days

value: 3 days


title: SMC2_Noc_auxin_30min_rep3

description: hic


title: CRC_Y01_O01 011 Vim+FAP+

value: LOCC

tag: age of_patients

value: Vim+FAP+

value: TIM


title: B cells,ATAC, KO1


title: CRC_Y01_O01 014 PanCK+

tag: segment tag

value: PanCK+

value: TC


title: B cells,ATAC, WT2


title: SMC2_Noc_auxin_8h_rep2

description: hic

value: G1E-ER4 cells

value: erythroid

value: nocodazole 12h + auxin 8h


title: SMC2_noc_12h_k36me3_rep2_10_percent_293T


title: 19565X35 POSTac_Con

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X35

value: Post 5d bed rest Post clamp

value: F


title: CRC_Y01_O01 010 Vim+FAP+

value: colon cancer

tag: scan id


title: B cells,ATAC, WT1


title: B cells,H3K27Ac_CHIP,KO-3

data_processing:
Clean fastq files were mapped to the GRCm38/mm10 using Bowtie2 with default parameters.
peaks were called using MACS2 (parameters: -f BAM -g mm --nomodel --shift 0 --extsize 228 --keep-dup all -q 0.001)
Assembly: mm10
Supplementary files format and content: BIGWIG files containing dense and continuous genomic information

extract_protocol:
2×107 cells were fixed with 1% methanol-free formaldehyde for 10 min at room temperature. Fixation was halted by introduction of glycine for 5 min at room temperature. A ChIP assay was performed using the SimpleChIP enzymatic ChIP kit (Cell Signaling Technology).
The library was sequenced on an Illumina HiSeq X Ten sequencer

tag: chip antibody


title: 19565X34 POSTbc_Con

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X34

value: Post 5d bed rest

value: Placebo

value: Vastus Lateralis Muscle


title: 19565X33 Day1_Con

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X33

value: After 2 weeks of treatment


title: CRC_Y01_O01 010 PanCK+

tag: roi id


title: B cells,H3K27Ac_CHIP,KO-2

value: spleen

value: primary

value: B cell


title: SMC2_noc_12h_k27me3_rep3_10_percent_293T


title: 19565X38 PREac_Con

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X38

value: Pre bed rest Post clamp

value: M


title: CRC_Y01_O01 009 Vim+FAP+

value: LOCC

value: Vim+FAP+

value: TIM


title: 19565X32 PREac_Con

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X32


title: SMC2_noc_12h_k27me3_rep2_10_percent_293T

value: G1E-ER4 cells

value: erythroid


title: SMC2_noc_12h_k36me3_rep1_10_percent_293T


title: B cells,H3K27Ac_CHIP,KO-1


title: 19565X36 7d_Con

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X36

value: 7d recovery


title: B cells,H3K27Ac_CHIP,Con-3


title: SMC2_noc_12h_k27me3_rep1_10_percent_293T


title: 19565X31 PREbc_Con

description:
Pre intervention, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X31

value: Pre bed rest

value: F


title: 19565X30 7d_Con

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X30


title: SMC2_noc_12h_k36me3_rep3_10_percent_293T


title: CRC_Y01_O01 011 PanCK+

value: colon cancer

value: PanCK+


title: SMC2_noc_12h_k27ac_rep3_10_percent_293T


title: CRC_Y01_O01 008 PanCK+

value: EOCC

value: TC


title: SMC2_noc_12h_k27ac_rep2_10_percent_293T


title: CRC_Y01_O01 007 Vim+FAP_i

value: Vim+FAPi


title: 19565X29 POSTac_Con

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X29

value: Post 5d bed rest Post clamp

value: Placebo

value: Vastus Lateralis Muscle


title: CRC_Y01_O01 007 PanCK+


title: SMC2_noc_12h_k9me3_rep3_10_percent_293T


title: B cells,H3K27Ac_CHIP,Con-1

value: spleen

value: primary

value: B cell


title: CRC_Y01_O01 006 Vim+FAP_i


title: 19565X28 POSTbc_Con

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X28

value: Post 5d bed rest


title: 19565X27 Day1_Con

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X27

value: After 2 weeks of treatment


title: SMC2_noc_12h_k27ac_rep1_10_percent_293T

value: G1E-ER4 cells

value: erythroid


title: 19565X26 PREac_Con

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X26

value: Pre bed rest Post clamp


title: MA9, Shp-1 Δ/Δ + chemo, scRNA-seq

city: Guangzhou

first: Guo

last: Qiu

state: Guangdong

address: Guangzhou Avenue

institute: Nanfang Hospital, Southern Medical University

description: 10X Genomics

data_processing:
The scRNA-Seq data were demultiplexed and aligned to the mouse genome, version mm10, and UMI-collapsed using the CellRanger toolkit (version 3.0.2, 10X Genomics).
Cells that expressed fewer than 300 genes were excluded, as were genes expressed in fewer than three cells per sample.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
We isolated single cells from the bone marrow of leukemic mice, which were generated by transfecting MLL-AF9 or Hoxa9-Meis1 fusion gene into mouse embryonic stem cells. We used 2% EDTA-PBS to flush out the bone marrow cells and lysed the red blood cells. We counted and assessed the cell viability by flow cytometry and adjusted the cell concentration to 1000 cells/ul.
scRNA-seq libraries were constructed using a Chromium Single Cell 30 v2 Reagent Kit, according to the manufacturer’s protocol.

value: bone marrow

value: MLL-AF9 AML model

tag: genotype

value: MLL-AF9 Shp-1 delta/delta + chemo

value: Arac+Dox


title: MA9, Shp-1 Δ/Δ, scRNA-seq

description: 10X Genomics

value: MLL-AF9 Shp-1 delta/delta

value: PBS


title: CRC_Y01_O01 006 PanCK+

value: colon cancer

value: EOCC

value: PanCK+

value: TC


title: CRC_Y01_O01 009 PanCK+

value: LOCC

value: TIM


title: 19565X25 PREbc_Con

description:
Pre intervention, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X25

value: Pre bed rest

value: Placebo

tag: age

value: Vastus Lateralis Muscle

value: F


title: CRC_Y01_O01 008 Vim+FAP_i

value: Vim+FAPi


title: SMC2_noc_12h_k9me3_rep1_10_percent_293T

value: G1E-ER4 cells

value: erythroid


title: B cells,H3K27Ac_CHIP,Con-2

value: spleen

value: primary

value: B cell


title: CRC_Y01_O01 005 Vim+FAP_i

value: AN


title: MA9, Shp-1 f/f, scRNA-seq

description: 10X Genomics

value: bone marrow

value: MLL-AF9 AML model

value: MLL-AF9 Shp-1 f/f

tag: treatment

value: PBS


title: CRC_Y01_O01 005 PanCK+

tag: tissue

value: colon cancer

value: EOCC

value: PanCK+


title: SMC2_noc_12h_input_rep1_10_percent_293T


title: 19_pseudo_3_S19_R1_001

city: Albany

first: Prashanth

last: Rangan

state: NY

address: 1400 Washington

department: Biological Sciences

institute: RNA Institute

data_processing:
Sequenced reads were aligned to the D. melanogaster genome (UCSC dm6) using HISAT2 (version 2.1.0)
Raw counts were generated using featureCounts (version 1.4.6.p5)
Differential gene expression was assayed by DEseq2 (version 1.24.0), using a false discovery rate of (FDR) of 0.05, and genes with 2-fold or higher Fold Change were considered significant.
Assembly: UCSC dm6
Supplementary files format and content: RNA-seq from pseudouridine pulldown libraries
Library strategy: Pseudouridine pulldown

organism: Drosophila melanogaster

source_name: Ovaries

growth_protocol: Ovaries dissected in 1x PBS.

extract_protocol:
RNA from input and pulldown was isolated using TRIzol (Invitrogen, 15596026) or phenol-chloroform treatment, treated with DNase (TURBO DNA-free Kit, Life Technologies, AM1907).  mRNA-enriched libraries were obtained by treating total RNA with poly(A)tail selection beads and then following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08).
Following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08), except RNA was fragmented for 13 minutes

tag: rna population

value: RNA from pseudouridine pulldown

value: WT

tag: antibody

value: mouse anti-pseudouridine (1:1000, MBL Life Sciences


title: 19565X24 7d_Con

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X24

value: 7d recovery

value: Placebo

value: Vastus Lateralis Muscle

value: F


title: 19565X23 POSTac_Con

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X23

value: Post 5d bed rest Post clamp


title: 17_In_3_S17_R1_001

value: Input for pulldown

value: none (input)


title: 19565X22 POSTbc_Con

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X22

value: Post 5d bed rest


title: CRC_Y01_O01 004 Vim+FAP+

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

tag: type of_tissue

tag: annotation geomx_dsp

tag: cell type specific morphological marker

value: Vim+FAP+

value: TIM


title: SMC2_asyn_k36me3_rep2_10_percent_293T

value: G1E-ER4 cells

value: erythroid


title: MA9, Shp-1 f/f + chemo, scRNA-seq

description: 10X Genomics

value: bone marrow

value: MLL-AF9 AML model

value: MLL-AF9 Shp-1 f/f + chemo

value: Arac+Dox


title: SMC2_asyn_k36me3_rep3_10_percent_293T


title: SMC2_noc_12h_k9me3_rep2_10_percent_293T


title: CRC_Y01_O01 004 PanCK+

value: colon cancer

value: EOCC

value: PanCK+

tag: histological region


title: SMC2_asyn_k36me3_rep1_10_percent_293T

tag: cell line


title: 13_pseudo_1_S13_R1_001

value: RNA from pseudouridine pulldown

value: WT

value: mouse anti-pseudouridine (1:1000, MBL Life Sciences


title: CRC_Y01_O01 003 Vim+FAP_i

value: LOCC

value: Vim+FAPi

value: AN


title: 19565X20 PREac_Con

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X20

tag: time

value: Pre bed rest Post clamp

value: Placebo

value: Vastus Lateralis Muscle

tag: Sex

value: F


title: 19565X21 Day1_Con

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X21

value: After 2 weeks of treatment


title: 11_In_1_S11_R1_001

value: Input for pulldown

value: none (input)


title: SMC2_asyn_k27me3_rep3_10_percent_293T

value: G1E-ER4 cells

tag: cell type

value: erythroid


title: HSBAM1P_S8_R1_001

data_processing:
Sequenced reads were aligned to the D. melanogaster genome (UCSC dm6) using HISAT2 (version 2.1.0)
Raw counts were generated using featureCounts (version 1.4.6.p5)
Differential gene expression was assayed by EdgeR on the RIVET Bioinformatics website (https://ruggleslab.shinyapps.io/RIVET/). Targets were defined as p-value (FDR) of 0.05 or less, and genes with 2-fold or higher Fold Change were considered significant.
Assembly: UCSC dm6
Supplementary files format and content: Polysome-seq libraries
Library strategy: Polysome-seq

extract_protocol: The ovaries were immediately flash frozen on liquid nitrogen. Samples were homogenized by motorized pestle in lysis buffer and 20% of lysate was used as input for mRNA isolation and library preparation (as described above). Samples were loaded onto 10-45% CHX supplemented sucrose gradients in 9/16 x 3.5 PA tubes (Beckman Coulter, #331372) and spun at 35,000 x g in an SW41 rotor for 3 hours at 4°C. Gradients were fractionated with a Density Gradient Fractionation System (#621140007). RNA was isolated using TRIzol (Invitrogen, 15596026) or phenol-chloroform treatment, treated with DNase (TURBO DNA-free Kit, Life Technologies, AM1907).  mRNA-enriched libraries were obtained by treating total RNA with poly(A)tail selection beads and then following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08).

value: Polysome fraction

tag: condition

value: Cyst Control

value: ovaries


title: CRC_Y01_O01 003 PanCK+

value: colon cancer

tag: age of_patients

tag: segment tag

tag: scan id

value: PanCK+


title: CRC_Y01_O01 002 Vim+FAP+

value: EOCC

tag: roi id

value: Vim+FAP+

value: TIM


title: 19565X19 PREbc_Con

description:
Pre intervention, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X19

value: Pre bed rest

tag: treatment

tag: age


title: SMC2_asyn_k27me3_rep2_10_percent_293T


title: SMC2_asyn_k27me3_rep1_10_percent_293T


title: 19565X18 7d_Con

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X18

value: 7d recovery

value: Placebo

tag: tissue


title: 19565X17 POSTac_Con

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X17

value: Post 5d bed rest Post clamp

value: Vastus Lateralis Muscle

value: F


title: CRC_Y01_O01 002 PanCK+


title: 20_HBAM2T_S17_R1_001

tag: rna population

value: Input


title: 21_HBAM2P_S18_R1_001


title: CRC_Y01_O01 001 Vim+FAP_i

tag: type of_tissue

value: Vim+FAPi

value: AN


title: SMC2_asyn_k27ac_rep2_10_percent_293T

value: G1E-ER4 cells

value: erythroid


title: 12_Nop60_2P_S11_R1_001

value: Polysome fraction

value: Nop60B RNAi

value: ovaries


title: 19565X16 POSTbc_Con

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X16

value: Post 5d bed rest


title: SMC2_asyn_k27ac_rep1_10_percent_293T


title: CRC_Y01_O01 001 PanCK+

value: colon cancer

value: EOCC

tag: annotation geomx_dsp

value: PanCK+


title: 11_Nop60_1P_S10_R1_001


title: CRC_Y05_O05 015 Vim+FAP+

tag: cell type specific morphological marker

value: Vim+FAP+

value: TIM


title: SMC2_asyn_k9me3_rep3_10_percent_293T


title: 08_YWT_P2_S8_R1_001

value: Young control


title: 19565X13 PREbc_Con

description:
Pre intervention, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X13

value: Pre bed rest

value: Placebo

value: Vastus Lateralis Muscle


title: 19565X14 PREac_Con

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X14

value: Pre bed rest Post clamp

value: F


title: 07_YWT_P1_S7_R1_001


title: CRC_Y05_O05 015 PanCK+

tag: histological region


title: HSBAM1T_S7_R1_001

value: Input

value: Cyst Control


title: CRC_Y05_O05 014 Vim+FAP_i

value: LOCC

value: Vim+FAPi

value: AN


title: SMC2_asyn_k9me3_rep2_10_percent_293T

tag: cell line

value: G1E-ER4 cells

value: erythroid


title: CRC_Y05_O05 014 PanCK+

value: colon cancer


title: 19565X12 7d_Con

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X12

tag: time

value: 7d recovery

value: M


title: SMC2_asyn_k9me3_rep1_10_percent_293T


title: 19565X11 POSTac_Con

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X11

value: Post 5d bed rest Post clamp

tag: Sex


title: 06_Nop60_2_In_S6_R1_001

value: Nop60B RNAi

value: ovaries


title: SMC2_asyn_k27ac_rep3_10_percent_293T

tag: cell type


title: SMC2_asyn_input_rep1_10_percent_293T


title: 05_Nop60_1_In_S5_R1_001

tag: condition


title: CRC_Y05_O05 013 Vim+FAP_i

tag: age of_patients


title: 19565X10 POSTbc_Con

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X10

value: Post 5d bed rest

value: Placebo


title: 02_YWT2_In_S2_R1_001

value: Young control


title: 19565X15 Day1_Con

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X15

value: After 2 weeks of treatment

value: Vastus Lateralis Muscle

value: F


title: 19565X9 Day1_Con

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X9


title: HP1a_b_tir2_6h_with_a_with_d_rep2

description: hic

tag: genotype

value: noc 8h release 6h + 5-Ph-IAA 8h + dtag13 8h


title: CRC_Y05_O05 012 Vim+FAP_i

value: LOCC

tag: segment tag

tag: scan id

value: Vim+FAPi

value: TC


title: 01_YWT1_In_S1_R1_001

value: Input


title: 19565X8 PREac_Con

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X8

value: Pre bed rest Post clamp

tag: treatment


title: CRC_Y05_O05 012 PanCK+

value: colon cancer

tag: roi id

value: PanCK+


title: oe_pankla_npb_rep2

city: Boston

first: Marcos

last: Simoes-Costa

state: Massachusetts

address: 300 Longwood Ave

department: Pathology

institute: Boston Children's Hospital

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.
To begin the spike-in normalization process, adapter trimmed PanKla CUT&RUN fastq files, corresponding to each sample/replicate, were aligned to the E. coli genome (GCA_001606525, assembly ASM160652v1) 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 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). The BAM files for both galGal6 and E. coli genome alignments were then converted to BED files with the bedtools bamtobed function. A new column containing the fragment length (of each position) was added to each BED file and the columns containing chromosome name (1st), start position (2nd column), end position (3rd column), and fragment length (last column) were extracted to generate new BED files (for both galGal6 and E. coli genome alignments corresponding to each sample/replicate). The C-shell script for spike-in calibration of CUT&RUN data, previously published by Skene et al. (https://doi.org/10.1038/nprot.2018.015) was then used to obtain normalized bedgraph files for each sample/replicate with the scale argument, min_len argument, and max_len argument set to 10000, 1, and 1000 respectively. The normalized bedgraph files were converted to BigWig format using the bedGraphToBigWig function and the average signal between replicates for each sample was calculated using the wiggletools mean function. Tornado and profile plots were generated using the python package DeepTools (https://doi.org/10.1093/nar/gku365). The computeMatrix function was used in reference-point mode with the following arguments “-bs 50, --skipZeros, --missingDataAsZero, --referencePoint center”.
To begin TMM normalization of the PanKla CUT&RUN data from the GOF experiment, a representative aggregate peakset was generated by first concatenating the called peaks (bed files) from all samples/replicates and then merging the peaks using the bedtools merge function. The featureCounts function was then used to generate a peak count matrix (using the aggregate peakset as a reference) for all BAM files (without duplicate reads). The peak count matrix was then imported into R and TMM normalization factors were calculated for each sample using the calcNormFactors() function of the edgeR package with the method = “TMM” argument specified. Size factors were calculated using the formula Size Factor=TMM Factor*Library Size/1000000. The Library Size variable is defined as the total number of reads of a sample in the peak count matrix and differs between samples. The reciprocal of the size factors (1/Size Factor) was then obtained. The bamCoverage function was then used to generate TMM and library size normalized bigwig files with the following arguments specified -bs 50 --scaleFactor {1/Size Factor}. The TMM normalized bigwig files for each sample were then averaged using the wiggle tools mean function and profile plots were generated using the python package DeepTools as previously described.
Assembly: Ensembl galGal6
Supplementary files format and content: BAM file, BedGraph file, BigWig file
Library strategy: CUT&RUN

organism: Gallus gallus

source_name: Ex ovo cultured embryos (HH6 stage)

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:
Embryos were collected in Ringer’s solution when they reached HH6 and were dissected to enrich for neural plate border cells as previously described (http://www.genome.org/cgi/doi/10.1101/gr.249680.119). CUT&RUN for PanKla (n=2 embryos/sample) were performed on control and experimental samples as described previously.
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.

treatment_protocol: Whole embryos were electroporated at HH4 with either 2.5 ug/ul of pCI-H2B-RFP (control condition) or a mixture containing 1.25 ugl/ul pCI-H2B-SOX9 and 1.25 ug/ul TEA1-VPR over-expression constructs. Control embryos and experimental embryos (SOX9/TEA1-VPR) were cultured in albumen containing.

value: Ex ovo cultured embryos (HH6 stage)

value: HH4 embryos electroporated with mixture containing 1.25 ugl/ul pCI_H2B_SOX9 and 1.25 ug/ul TEA1-VPR over-expression constructs

value: Embryos were cultured ex ovo in thin albumen

value: PTM Biolabs - PTM-1401 (polyclonal)


title: HP1a_b_tir2_6h_with_a_no_d_rep2

description: hic

value: G1E-ER4 cells

value: erythroid

value: noc 8h release 6h + 5-Ph-IAA 8h


title: CRC_Y05_O05 011 Vim+FAP_i

tag: tissue


title: 19565X6 7d_Con

description:
After 7 days of recovery and no treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X6

value: 7d recovery

value: Placebo

tag: age

value: Vastus Lateralis Muscle

value: M


title: HP1a_b_tir2_6h_with_a_no_d_rep1

description: hic


title: CRC_Y05_O05 011 PanCK+

tag: type of_tissue

value: LOCC


title: oe_pankla_npb_rep1

description: CUT&RUN


title: HP1a_b_tir2_6h_no_a_with_d_rep2

description: hic

value: noc 8h release 6h + dTag13 8h


title: 19565X5 POSTac_Con

description:
Post 5d bed rest, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X5

value: Post 5d bed rest Post clamp


title: rfp_control_pankla_npb_rep2

description: CUT&RUN

value: HH4 embryos electroporated with 2.5 ug/ul of pCI-H2B-RFP (control condition) and collected at HH6


title: 19565X3 Day1_Con

description:
After 2 weeks of treatment, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X3

value: After 2 weeks of treatment


title: 19565X4 POSTbc_Con

description:
Post 5d bed rest, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X4

value: Post 5d bed rest


title: CRC_Y05_O05 013 PanCK+

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

value: colon cancer

tag: annotation geomx_dsp

value: PanCK+

value: AN


title: HP1a_b_tir2_6h_no_a_with_d_rep1

description: hic


title: HP1a_b_tir2_6h_no_a_no_d_rep2

description: hic

value: noc 8h release 6h


title: gne140_atac_explant_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.
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

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: 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: Primary Neural Crest Cells

tag: Stage

value: HH9 stage

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

tag: transposase

value: Tn5 enzyme (Illumina 20034210)


title: rfp_control_pankla_npb_rep1

description: CUT&RUN

tag: cell line

value: Ex ovo cultured embryos (HH6 stage)

value: Embryos were cultured ex ovo in thin albumen

value: PTM Biolabs - PTM-1401 (polyclonal)


title: CRC_Y05_O05 010 Vim+FAP_i

value: LOCC

tag: cell type specific morphological marker

value: Vim+FAPi

tag: histological region

value: TC


title: CRC_Y05_O05 010 PanCK+


title: HP1a_b_tir2_6h_no_a_no_d_rep1

description: hic

value: G1E-ER4 cells

tag: cell type

value: erythroid


title: CRC_Y05_O05 009 Vim+FAP+

value: Vim+FAP+

value: TIM


title: 19565X1 PREbc_Con

description:
Pre intervention, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X1

tag: time

value: Pre bed rest

value: Placebo

value: Vastus Lateralis Muscle

tag: Sex

value: M


title: CRC_Y05_O05 009 PanCK+

value: colon cancer

tag: age of_patients

value: PanCK+


title: 19565X7 PREbc_Con

description:
Pre intervention, fasted thigh muscle biopsy sample
19565R_counts.txt
19565X7


title: 19565X2 PREac_Con

description:
Pre intervention, post hyperinsulinemic euglycemic clamp thigh muscle biopsy sample
19565R_counts.txt
19565X2

value: Pre bed rest Post clamp


title: HP1a_b_tir2_1h_with_a_with_d_rep2

description: hic

tag: genotype

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


title: HP1a_b_tir2_6h_with_a_with_d_rep1

description: hic

value: noc 8h release 6h + 5-Ph-IAA 8h + dtag13 8h


title: dmso_atac_explant_rep2

description: ATAC-seq

value: Primary Neural Crest Cells

value: HH9 stage

value: Neural crest cells explants cultured on fibronectin-coated tissue culture plates treated with vehicle (DMSO)

value: Tn5 enzyme (Illumina 20034210)


title: CRC_Y05_O05 008 Vim+FAP+

value: LOCC

tag: segment tag

tag: scan id


title: dmso_atac_explant_rep1

description: ATAC-seq

tag: treatment