title: low-dose 3dpi,  replicate 3

city: Leipzig

first: Vincent

middle: D

last: Friedrich

address: Härtelstraße 16-18

department: Institute for Medical Informatics, Statistics, and Epidemiology

country: Germany

institute: University of Leipzig

data_processing:
Phodopus roborovskii raw sequencing files were processed using Cellranger mkfastq (10x Genomics). Fastq files were aligned to the Roborovski hamster genome assembly PHOROB, filtered and counted using cell ranger count (10x Genomics). R (Version 4.2.2) was used to create a feature-barcode Matrix and the Seurat-object applying the R-package SeuratV5 4.9.9.9044.
Assembly: GCA_943737965.1 (PHOROB)
Supplementary files format and content: R object including feature-barcode Matrix

organism: Phodopus roborovskii

source_name: whole blood

extract_protocol:
500 μL whole blood per animal was lysed in red blood cell lysis buffer (ChemCruz), washed and centrifuged according to the manufacturer’s instructions. Each resulting RBC-free pellet was resuspended in low-BSA buffer (1× PBS, 0.04% BSA) and filtered with 40 μm FloMi filters (Merck).
Isolated cells were processed for single-cell RNA sequencing according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1; 10x Genomics, Pleasanton, CA, USA).

value: whole blood

value: low-dose 3dpi


title: Ophiomastix wendtii specimen 3, tissue sample 4, whole arm segment, read pair 1

status: Public on Dec 13 2024

type: SRA

city: Kannapolis

first: Robert

last: Reid

state: NC

address: 150 Research Campus Drive, Suite 3333

department: Bioinformatics and Genomics

country: USA

institute: UNC Charlotte

library_source: transcriptomic

data_processing:
The quality of the raw sequencing data was assessed with FastQC v0.11.9, focusing on identifying and correcting common issues, such as low-quality bases and leftover adapter sequences.
De novo transcriptome assembly was performed with Trinity v2.14.0.
We quantified transcript and gene abundance across three different sample types: the whole arm segments, the inner arm core, and the stomach (control). The count tables were generated by the RSEM v1.3.3 and Bowtie v2.5.1 in OmicsBox and used as input for a comprehensive differential expression analysis with edgeR v3.18.
Assembly: No reference genome exists for Ophiomastix wendtii. Assembled contigs are available in TSA (https://www.ncbi.nlm.nih.gov/nuccore/GKWM00000000)
Supplementary files format and content: counts_genes.txt

molecule: polyA RNA

organism: Ophiomastix wendtii

source_name: Whole arm segments

growth_protocol: Adult individuals of O. wendtii were collected at the Keys Marine Laboratory (Lay- ton, FL) and transported in the natural seawater chilled in a box with water ice to the University of North Carolina at Charlotte. Once in the laboratory, the animals were allowed to acclimate gradually to the ambient room temperature overnight. The next day, the brittle stars were transferred to a tank with artificial aerated seawa- ter (“InstantOcean”), whose salinity was adjusted to the natural seawater from the animal habitat (40 ppt). The animals were allowed to acclimate for five days.

extract_protocol:
Tissue samples for RNA isolation (13–95 mg) were homogenized in 500 μL of ice-cold TRI Reagent (Millipore Sigma, cat. no. T9424) using sterile closed-system disposable microtissue homogenizers (Kimble, cat. no. K7496250030). The homogenized samples were briefly vortexed, and an additional 500 μL of the TRI Reagent was added to each sample. The samples were frozen at -80◦C for one week before RNA extraction. Upon retrieval from storage, the samples were thawed on ice, the insoluble material was precipitated by brief centrifugation, and the clear supernatant was transferred into fresh tubes. After a 5-minute incubation at room temperature, 100 μL of 1-bromo-2-chloropropane (BCP) was added to each tube. The samples were then emulsified by vigorous shaking and allowed to sit at room temperature for 10 minutes. The organic and aqueous phases were separated by centrifugation at 16,000×g for 45 min at 4◦C, and the aqueous phase was carefully aspirated and transferred into a fresh tube. The RNA was precipitated by adding 500 μL of isopropanol to each sample, incubating at -20◦C for 1 hour, and centrifugation. The pellet was washed twice with ice-cold 70% ethanol and dissolved in 50 μL of RNase-free water. The quantity of total RNA was determined with a NanoDrop Spectrophotometer.
The RNA-Seq libraries were prepared using the Illumina Stranded mRNA Prep kit (Illumina, USA), following Illumina Stranded mRNA Prep Reference Guide (25). The fragmentation was enzyme-based. We conducted quality control on the final libraries to assess RNA concentration with a Qubit dsDNA BR (broad range) assay kit and quality by Tapestation 4200 analysis using the High Sensitivity D1000 Screentape (Agilent, USA). We prepared 16 Illumina paired-end read sequencing libraries to account for both the biological and technical replicates.
Sequencing was performed on an Illumina NextSeq 2000 (Illumina, USA)

treatment_protocol: The animals were anesthetized in 0.1% solution of 1-phenoxy-2-propanol (Millipore Sigma, cat. no. 484423) in seawater until they stopped responding to touch. Tissue samples for both RNA-Seq and microscopic analysis were harvested from three individuals, including one male and two females.

tag: tissue

value: Whole arm segments


title: RNAseq, HMX3 KMT2A-MLLT3 AML, HMX3 KD, rep1

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

data_processing:
The GRCh38 reference genome was indexed using STAR aligner (version 2.7.9a) with Ensembl gene annotation
Paired-end reads were trimmed and quality was assessed using Trim Galore (v0.6.6) (https://github.com/FelixKrueger/TrimGalore).
The resulting trimmed reads were mapped against the indexed reference genome in two-pass mode with the same parameters as the GDC mRNA Analysis Pipeline version Dr15plus (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/#rna-seq-alignment-workflow).
Gene expression levels were determined using FeatureCounts (v2.0.3) with protein coding gene annotation from Ensembl GRCh38 (version 95)
Assembly: GRCh38
Supplementary files format and content: tab-delimited value file include raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: primary

growth_protocol: Mononuclear cells from KMT2A::MLLT3-positive patients (>90% blasts) were cultured for 3 days on an MSC feeder layer in StemSpan SFEM (Stemcell Technologies, cat# 9655) supplemented with 100 ng/mL rh-TPO (Peprotech, cat# AF-300-18), 150 ng/mL rh-SCF (Immunotools, cat#, 11343327), 10 ng/mL rh-Flt3L (Immunotools, cat#, 11343305), 10 ng/mL rh-IL3 (Immunotools, cat#, 11340035), 10 ng/mL rh-GM-CSF (Immunotools, cat#, 11343125), 1.35 µM UM729 (Stemcell Technologies, cat# 72332), and 750 nM Stem regenin-1 (Bio-connect, cat# c7710-1s)) before transduction

extract_protocol:
RNA was isolated using the Nucleospin RNA plus kit (Macherey-Nagel).
Library generation was performed using KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems, Potters Bar, UK), with an RNA fragmentation of approximately 300 bp fragments

value: primary

tag: cell type

value: blasts

tag: treatment

value: shRNA HMX3 KD (1)


title: Con_2, N2A

city: Nantong

first: Baoying

last: Hu

state: JIANGSU

address: No.9 Seyuan road

country: China

institute: Nantong University

data_processing:
The sequencing data was filtered with SOAPnuke by removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Assembly: The clean reads were mapped to the reference genome using HISAT2
Supplementary files format and content: Ericscript (v0.5.5) and rMATS (V3.2.5) were used to detect fusion genes and differential splicing genes (DSGs), respectively

organism: Rattus norvegicus

growth_protocol: H9C2 cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS) in a humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
RNA was harvested using the Trizol reagent (Life Technologies). 200ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the BGI mRNA-Seq Library Kit following the manufacture's protocols.

treatment_protocol: The H/R injury cell model group was established by culturing H9C2 cells in 1% oxygen, 5% CO2, and 94% nitrogen in a tri-gas incubator for 12 h and then reoxygenated in 5% CO2 normal oxygen conditions for 6 h.  While H9C2 cells without H/R treatment were the control group.

tag: cell line

value: cardiomyocytes

value: Control


title: low-dose 3dpi,  replicate 2

library_source: transcriptomic single cell


title: RNAseq, MOLM13, HMX3 KD 2355, rep 1

growth_protocol: Cells were cultured at 37 °C and 5% CO2, and were cultured in RPMI Medium 1640 (1X) (DMEM, Gibco, cat# 21875-034) supplemented with 10% heat inactivated Fetal Calf Serum (FCS) (Biowest, cat# S1810-500). Cells were passed according to the manufacturer’s instructions.

value: HMX3 shRNA


title: Con_1, N1A


title: RNAseq, HMX3 KMT2A-MLLT3 AML, non-targeting control

value: non-transduced control


title: Ophiomastix wendtii specimen 1, tissue sample 3, inner arm core, read pair 1

source_name: Inner arm core

value: Inner arm core


title: low-dose 3dpi,  replicate 1


title: Ophiomastix wendtii specimen 2, tissue sample 3, whole arm segment, read pair 1


title: RNAseq, HMX3 KMT2A-MLLT3 AML, wild-type

value: untreated


title: Ophiomastix wendtii specimen 1, tissue sample 5, whole arm segment, read pair 1


title: low-dose 2dpi,  replicate 3

value: low-dose 2dpi


title: RNAseq, CD34 HSPC,  HMX3 overexpression T2A GFP 2397, rep 3

source_name: healthy donor

growth_protocol: G-CSF mobilized CD34+ cells from a healthy donors were isolated with CliniMACS CD34 Microbeads (Miltenyi Biotec, cat# 130-100-453). After 4 days of culturing in StemSpan AOF medium (Stemcell Technologies, cat# 100-0130) supplemented with 100 ng/mL rh-SCF (Immunotools, cat# 11343325), 100 ng/mL Rh-Flt3L (Immunotools, cat# 11343307), 100 ng/mL rh-IL3 (Immunotools, cat# 11340035), 100 ng/mL rh-IL6 (Immunotools, cat# 11340066), 100 ng/mL rh-TPO (Peprotech, cat# AF-300-18), and 1 µM Stem Regenin-1 (Stemcell Technologies, cat# 72342)

value: healthy donor

value: HSPC

value: HMX3 overexpression T2A GFP


title: Mouse, retina, 24mo, Rep1

city: Camperdown

first: Katharina

last: Bell

state: NSW

address: Medical Foundation Building, Levels 4-6, 92-94 Parramatta Rd

country: Australia

institute: The University of Sydney

description:
Library name: Sample 7
Set 1

data_processing:
CellRanger (10x Genomics) v6.0.2 counts was used to align the FASTQ files to the reference transcriptome and generate processed output files (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/6.0/using/tutorial_ct). Filtered feature-barcode matrices available in sample wise supplementary information.
Assembly: Mouse mm10
Supplementary files format and content: Tab separated value files and matrix files

organism: Mus musculus

source_name: Retina

extract_protocol:
2 non-injured retinae were collected from C57BL/6J mice per condition. Retinal tissue was digested using the papain dissociation system (Worthington) following the manufacturer’s protocol. Cells were passed through a 30 µm filter (Miltenyi) to obtain a single-cell suspension. Following this different magnetic activated cell sorting methods (MACS®) enrichment/depletion methods were used on the cell pool collected. ACSA-2 and Thy1.2 enrichment (Set 1): Cell pool was enriched for RGCs and macroglia using Thy1.2 and ACSA-2 (astrocyte cell surface antigen-2) antibodies respectively. Two retinas from 2 mice per age group were pooled for this method - 3-month (young), 12-month (middle-aged) and 24-month-old (old).         CD73 depletion (Set 2): The cell pool was depleted of rod photoreceptors using the CD73 antibody. Retinae from four 12-mo mice were prepared this way (2 retinas per pooled for each replicate).                                                                                Thy1.2 enrichment and CD73 depletion (Set 3 and 4): Cell pool was split into two halves and each half was subjected to either Thy1.2 enrichment or CD73 depletion. Following this, the two portions were combined again. Two retinas from 2 mice per age group were used for this method - 3-mo (Set 3) and 12-mo (Set 4).
Libraries were constructed according to manufacturer's protocol (10x Genomics Chromium Next GEM Single Cell 3' Kit v3.1 )

value: Retina

tag: age

tag: strain

value: C57BL/6J (NNT mutation positive)


title: Mouse retina, 12mo, Rep 4

description:
Library name: Sample 6
Set 4


title: Mouse retina, 12mo, Rep 3

description:
Library name: Sample 5
Set 2_2


title: low-dose 2dpi,  replicate 1

value: whole blood


title: Ophiomastix wendtii specimen 1, tissue sample 3, whole arm segment, read pair 1

value: Whole arm segments


title: RNAseq, CD34 HSPC, HMX3 overexpression T2A GFP 2397, rep 2


title: WT DNs rep2

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

institute: University of Melbourne

description:
10B lane, 300 cycle kit
24_22N3C3LT3_ATTCCT_L008

data_processing:
Bulk sequencing reads were aligned to the GRCm39 reference genome and transcriptome (version 105) using the STAR aligner (version 2.7.8a) and counted using featureCounts (version 2.0.0)
Assembly: GRCm39 v 105
Supplementary files format and content: tab seperated gene counts

source_name: Spleen

extract_protocol:
RNA extraction from sorted P14 T cells was performed following the manufacturer’s protocol using the RNAeasy Plus Mini Kit (Qiagen)
Libraries were generated following the manufacturer's protocol using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, USA).

value: Spleen

value: CD8 T cells

tag: genotype


title: RNAseq, CD34 HSPC, HMX3 overexpression T2A GFP 2397, rep 1


title: Mouse retina, 12mo, Rep 2

description:
Library name: Sample 4
Set 2_1


title: WT CD62L+ rep2

description:
10B lane, 300 cycle kit
23_22N3C3LT3_ACTGAT_L008


title: high-dose 3dpi,  replicate 3

value: high-dose 3dpi


title: Mouse retina, 12mo, Rep 1

description:
Library name: Sample 3
Set 1


title: high-dose 3dpi,  replicate 2


title: ID3-KO DNs rep2

description:
10B lane, 300 cycle kit
22_22N3C3LT3_GAGTGG_L008


title: high-dose 3dpi,  replicate 1


title: RNAseq, CD34 HSPC, empty vector GFP overexpression control 843, rep 2

value: empty vector GFP overexpression


title: ID3-KO CD62L+ rep2

description:
10B lane, 300 cycle kit
21_22N3C3LT3_CGTACG_L008


title: Mouse retina, 3mo, Rep 2

description:
Library name: Sample 2
Set 3


title: RNAseq, CD34 HSPC, empty vector GFP overexpression control 843, rep 1


title: MLE-12 cell, CSE, replicate #3

city: Zhengzhou

first: Jiazhen

last: Wang

address: 156 Jinshui East Road

institute: Henan University of Chinese Medicine

data_processing:
Quality control of the raw fastq files was performed with FastQC (v0.12.1). Data cleaning and adapter trimming were performed with fastp (v0.20.1).
Pseudoalignment of the reads was performed with kallisto (v0.46.2). Gene level quantification and differential gene expression analysis was performed with an R package Deseq2 (v1.40.2).
Heatmap plot was made with R package pheatmap (v1.0.12). Network analysis were performed with Cytoscape (v3.10.1). Gene set enrichment analysis was performed with GSEA software (4.3).
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file includes raw count and TPM (transcripts per million) values for each sample.

growth_protocol: MLE-12 were cultured in DME/F12 (Hyclone), supplemented with 2% FBS, 1% ITS and 1% penicillin/streptomycin.

extract_protocol:
Total RNA from lung tissue was purified using TRIzol (Life Technologies) according to the manufacturer’s instructions.
Library preparation was performed with TruePrep RNA Library Prep Kit for Illumina (Vazyme, #TR502-01) according to the manufacturer's instruction.

treatment_protocol: MLE-12 cells were routinely subcultured. Upon achieving a cell density of 30%, a 5% solution of Cigarette Smoke Extract (OD:2.0) was added to the medium, namely CSE group, while the PBS group received an equivalent volume of PBS. Samples were harvested 24 hours following the treatment.

value: murine lung epithelial cell

value: WT

value: CSE


title: high-dose 2dpi,  replicate 2

value: high-dose 2dpi


title: high-dose 2dpi,  replicate 3


title: Mouse retina, 3mo, Rep 1

description:
Library name: Sample 1
Set 1


title: WT CD62L+ rep1

description:
10B lane, 300 cycle kit
19_22N3C3LT3_GTGGCC_L008


title: low-dose 2dpi,  replicate 2


title: WT DNs rep1

description:
10B lane, 300 cycle kit
20_22N3C3LT3_GTTTCG_L008


title: SNU398-D1D3-DpnII

city: Boston

first: Mahmoud

middle: Adel

last: Bassal

state: Massachusetts

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

library_source: genomic

data_processing:
Library strategy: 4C-Seq
For WGBS analysis, the leading 3 bases and adaptor sequences were trimmed from paired-end reads by TrimGalore. The resulting FASTQ files were analyzed by BISMARK.  PCR duplicates were removed by SAMtools rmdup. Then bismark_methylation_extractor continued the extraction of the DNA methylation status on every cytosine sites.
For 4C-Seq analysis, raw fq files were aligned to a masked hg19 reference. Bam files were converted to read coverage files by bedtools genomecov. Read coverage was normalized according to the sequencing depth. Processed alignment files were analyzed using r3CSeq. Chromosome 9 was selected as the viewpoint, and Csp6I, DpnII were used as the restriction enzyme to digest the genome. Smoothed bam coverage maps were generate using bamCoverage from the deeptools suite and plotted using the Bioconductor package Sushi to get the viewpoint coverage depth maps.  BigInteract files for UCSC and bedpe files were manually generated with the “score” values being calculated as -log( interaction_q-value_from_r3CSeq + 1*10-10 ).
Genome_build: hg19
Supplementary_files_format_and_content: bed, bw files

molecule: genomic DNA

growth_protocol: SNU-398 (wild type and DAC and CRISPR-DiR treated) cells were cultured in Roswell Park Memorial Institute 1640 medium (RPMI) (Life Technologies, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS) (Invitrogen) and 2 mM L-Glutamine (Invitrogen). Maintained at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
1). WGBS: gDNA was harvested by lysing the cells in 50mM Tris-HCl pH8, 100mM NaCl, 25mM EDTA and 1%SDS buffer with 1mg/mL of proteinase K and incubate at 65C overnight.   2). 4C-Seq: Cell were fixed with 1% formaldehyde and the chromatin fraction were isolated. Chromatin were digested by restriction enzyme Csp6I or DpnII, followed by ligation and second digestion with NlaIII and second ligation. The library was constructed by inverse PCR and nested PCR. And 200 to 600 bp DNA were sequenced.
1). WGBS library were prepared by BGI using standard Illumina WGBS protocol.   2). Libraries were prepared using KAPA HiFi HotStart ReadyMix (KK2602) with primers containing i5 and i7 barcodes. Constructed libraries were PAGE purified and only libraries with 250 to 600bp were used for sequencing. NextSeq 500/550 Mid Output kit V2.5 (150 Cycles) (20024904, Illumina) was used for single end Nextseq sequencing.

treatment_protocol: 1). For WGBS, 2.5uM Decitabine was added to fresh medium everyday for 3 days.   2). For 4C-Seq, cells were stably introduced with CRISPR-DiR non-targeting (DN2) or Targeting (D1+D3).

value: HCC cell line

value: CRISPR-DiR targeting (D1+D3) Viewpoint 2 (DpnII)

tag: culturing days

value: 13 days


title: SNU398-D1D3-Csp6I

value: CRISPR-DiR targeting (D1+D3) Viewpoint 1 (Csp6I)


title: ID3-KO DNs rep1

description:
10B lane, 300 cycle kit
18_22N3C3LT3_GTGAAA_L008


title: SNU398-GN2-DpnII

value: CRISPR-DiR non-targeting (GN2) Viewpoint 2 (DpnII)


title: ID3-KO CD62L+ rep1

description:
10B lane, 300 cycle kit
17_22N3C3LT3_GTCCGC_L008


title: MLE-12 cell, CSE, replicate #2


title: control, replicate 3

value: control


title: MLE-12 cell, PBS, replicate #3

value: PBS


title: SNU398-GN2-Csp6I

value: CRISPR-DiR non-targeting (GN2) Viewpoint 1 (Csp6I)


title: high-dose 2dpi,  replicate 1

value: whole blood


title: MLE-12 cell, PBS, replicate #2


title: SNU398-WT-DpnII

value: Wild type


title: control, replicate 1


title: RNAseq, CD34 HSPC, empty vector GFP overexpression control 843, rep 3

value: healthy donor

value: HSPC


title: control, replicate 2


title: Femur bone marrow

city: Okayama

first: Ikue

last: Tosa

state: Okayama

address: Shikata-cho2-5-1, Kita-ku

country: Japan

institute: Okayama University

description:
Library name: Femur bone marrow
10x Genomics

data_processing:
The sequencing data was first pre-processed using the 10X Genomics software Cell Ranger.
Assembly: GRCm39
Supplementary files format and content: Tab-sepalated values files and matrix files

source_name: Femur bone marrow

extract_protocol:
For hematopoietic and CAR cells analyses, the cells were collected, respectively from C57BL6J and Cxcl12-GFP mice. For CAR cell isolation, hematopoietic cells and endothelial cells were depleted using the autoMACS Pro Separator (Miltenyi Biotec). FCM analyses were carried out using the FACS Diva 8.0.1 software (BD Biosciences). Dead cells and debris were excluded by FSC, SSC and DAPI staining. Cell sorting was performed on FACSAria III Cell Sorter (BD Biosciences).
Hematopoietic and CAR cells were combined and then processed with Chromium Next GEM Single Cell 3ʹ GEM kit v.3.1 (10X Genomics) according to the manufacturer’s instruction.

value: Femur bone marrow

value: Hematopoietic cells and CAR cells

value: WT and Cxcl12-GFP


title: MLE-12 cell, PBS, replicate #1

value: murine lung epithelial cell

value: WT


title: islets from FXR knockout mice,male No.2,3months

status: Public on Dec 12 2024

city: Shenzhen

first: Lianqi

last: Shao

state: Guangdong

address: 3688 Nanhai Avenue, Nanshan District

department: School of basic medicine

institute: Shenzhen University

data_processing:
Illumina HiSeqTM 2000
Assembly: HISAT(hierarchical indexing for spliced alignment of transcripts)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: islets

extract_protocol:
The total RNA of each group of islets was extracted separately and the RNA purity was detected to meet the requirements
After the total RNA extracted from the sample was treated with DNase I, the eukaryotic mRNA was enriched with magnetic beads with Oligo (dT).The interrupting reagent was added to break the mRNA into short fragments, and a strand of cDNA was synthesized with six-base random hexamers using the interrupted mRNA as a template, and the second strand of cDNA was synthesized by adding buffer, dNTPs and DNA polymerase I.After kit purification and recovery, sticky end repair, adding base "A" to the 3 'end and connecting the sequencing connector, the obtained fragment was amplified and enriched by PCR after size selection.

value: islets

tag: Sex

value: male

value: FXR knockout

value: isolated from pancreas


title: SNU398-WT-Csp6I

value: HCC cell line

value: 13 days


title: islets from FXR knockout mice,female,3months

value: female


title: islets from wild type mice,male No.2,3months


title: islets from wild type mice,female,3months


title: islets from FXR knockout mice,male No.1,3months


title: MLE-12 cell, CSE, replicate #1

value: CSE


title: 799 eWAT-Obese-Myriocin

type: RNA

city: Iowa City

first: Bhagirath

last: Chaurasia

address: 431 Newton Road

institute: University of Iowa

description: SAMPLE 10

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Using Partek Genomic Suite, we extracted background-corrected, summarized expression levels (AVG Signal), number of beads used (Avg NBEADS) and detection scores (Detection Pval). Data were normalized with the global average. Subsequently, the data were averaged and log2 fold chage were determined using the Microsoft Excel.
Illumina Probe IDs were not available. All raw and procesed data in supplementary text file uses Illumina Search_Key as ID.

label: Biotin

source_name: eWAT

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: 30-50 mg tissue was homogenized using bullet blender and the lysate was used for the RNA extraction using the RNAeasy kit (Qiagen) as per the manufacturer instructions

treatment_protocol: Animals were fed either a normal chow or high fat diet for 12-weeks and subsequently, treated with either a vehicle or myriocin on alternate days for subsequent 8 weeks while being maintained the respective diet.

value: eWAT

tag: diet

value: High fat Diet


title: 798 eWAT-Obese-Myriocin

description: SAMPLE 9


title: 805 eWAT-Obese-Myriocin

description: SAMPLE 12


title: Input_rep2

city: Milan

first: Chiara

last: Lanzuolo

address: Via Francesco Sforza 35

country: Italy

institute: CNR and Istituto Nazionale Genetica Molecolare

data_processing:
ChIP-seq reads were aligned to the mm9 mouse reference genome using bwa aln (version 0.7.12) with options -n 2 -k 2 and save in sam format with bwa samse.
The sam files were converted to bam and coordinate sorted with samtools (version 1.3.1).
wig files were generated using the "writewig" function of spp package and represent the smoothed read density.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary_files_format_and_content: wiggle files with smoothed signal generated using spp R package

source_name: muscle stem cells

extract_protocol:
DNA was isolated through standard phenol/chloroform extraction, followed by precipitation and resuspension in 31 μL of 10 mM Tris-HCl pH 8.0.
Libraries were created using Biomek FX automatic liquid handler (Beckman Coulter). Libraries with distinct adapter indexes were multiplexed and, after cluster generation on FlowCell, were sequenced for 50 bases in the single read mode on a HiSeq 2000 sequencer.

treatment_protocol: cell extraction protocol: Satellite cells were isolated from hind-limb muscle and fixed before sorting using FACS

value: muscle stem cells

tag: chip antibody


title: islets from wild type mice,male No.1,3months


title: 793 eWAT-Obese-Vehicle

description: SAMPLE 5

value: Normal Chow Diet


title: 782 eWAT-Lean-Vehicle

description: SAMPLE 4


title: 795 eWAT-Obese-Vehicle

description: SAMPLE 7


title: H3K27me3_rep1

description: Example of succesfull  H3K27me3 ChIP-seq

data_processing:
ChIP-seq reads were aligned to the mm9 mouse reference genome using bwa aln (version 0.7.12) with options -n 2 -k 2 and save in sam format with bwa samse.
The sam files were converted to bam and coordinate sorted with samtools (version 1.3.1)
wig files were generated using the "writewig" function of spp package and represent the smoothed read density.!Sample_data_processing = Genome_build: mm9

value: H3K27me3 antibody (Millipore 07-449)


title: 780 eWAT-Lean-Vehicle

description: SAMPLE 2


title: 800 eWAT-Obese-Myriocin

description: SAMPLE 11


title: BMP-2 induced ectopic bone

description:
Library name: BMP-2 induced ectopic bone
10x Genomics

source_name: BMP-2 induced ectopic bone

value: BMP-2 induced ectopic bone

value: Hematopoietic cells and CAR cells


title: 781 eWAT-Lean-Vehicle

description: SAMPLE 3


title: 779 eWAT-Lean-Vehicle

description: SAMPLE 1


title: larvae sima Mutant2

city: Bloomington

first: Jason

middle: M

last: Tennessen

state: Indiana

address: 1001 E 3rd St

institute: Indiana University

description:
Library name: Mutant2
Sima_larvae_FPKMs.csv

data_processing:
Aligned to BDGP6.46 genome assembly from Ensembl and clipped using star/2.7.11a
Read assignment and count matrix creation was completed using featureCounts from the Bioconductor Rsubread library and the BDGP6.46.113 annotation from Ensembl
Normalization was completed using DESeq2
Assembly: BDGP6.46
Supplementary files format and content: csv file containing FPKMs for larval samples and csv file containing FPKMs for embryo samples

organism: Drosophila melanogaster

source_name: whole larvae

extract_protocol:
RNA was extracted using a Qiagen Rneasy kit. 2ug total RNA was used for library construction.
Illumina TruSeq Stranded mRNA HT sample prep

value: whole larvae

value: Sima 1/20


title: larvae sima Mutant3

description:
Library name: Mutant3
Sima_larvae_FPKMs.csv


title: larvae heterozygous Control3

description:
Library name: Control3
Sima_larvae_FPKMs.csv

value: Sima 1/+


title: lib1_DNA_biol rep2

city: Seattle

first: Lukas

last: Oesinghaus

state: WA

address: 3946 W Stevens Wy NE

institute: University of Washington

description: Library name: lib1_DNA_r2

library_source: other

data_processing:
The UMI was extracted and added to the read name using custom python scripts.
Libraries were aligned to the reference sequences using BWA-MEM.
Alignments were filtered using a custom python script.
UMIs were deduplicated using UMI-tools with unique matching.
Alignments for each reference were counted using a custom python script. Fold-change values were calculated from the count data of the two replicates using PyDESeq2.
Assembly: Not applicable.
Supplementary files format and content: CSV files contain count data and the DESeq2 output for each cell line.
Supplementary files format and content: CSV files contain count data normalized stability data for each cell line.

molecule: other

organism: synthetic construct

source_name: plasmid

growth_protocol: HEK293T, HeLa, MCF7, A549, HUH7, and HaCaT cells were cultured in DMEM supplemented with 10% FBS and 100 U/ml Penicillin/Streptomycin (ThermoFisher 15140122). SKNSH and JEG3 cells were cultured in EMEM supplemented with 10% FBS and 100 U/ml Penicillin-Streptomycin. K562 and PC3 cells were cultured in RPMI supplemented with 10% FBS and 100 U/ml Penicillin-Streptomycin. Tera1 cells were cultured in McCoy's 5A medium supplemented with 15% FBS and 100 U/ml Penicillin-Streptomycin.

extract_protocol:
We detached cells with TrypLE, added media, then spun down for 5 min at 210 g. We resuspended the cells in 1 ml of cold PBS and placed them on ice. We took 25 µl of each sample, added 175 µl of PBS, and measured the GFP fluorescence on the Attune NxT flow cytometer to determine cell numbers and transfection efficiencies. We used the Monarch Total RNA Miniprep Kit (NEB, T2010S) to purify total RNA. We eluted in 100 µl of nuclease-free water and determined concentrations using a NanoDrop 2000c (Thermo Fisher). mRNA was purified using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L). We eluted in 18 µl of nuclease-free water.
mRNA was reverse transcribed and amplified using custom primers.

treatment_protocol: Transient transfection with plasmid libraries using Lipofectamine 3000.

value: plasmid


title: lib1_DNA_biol rep1

description: Library name: lib1_DNA_r1


title: H3K27me3_rep2_bad

description: Example of un-successfull  H3K27me3 ChIP-seq


title: larvae heterozygous Control1

description:
Library name: Control1
Sima_larvae_FPKMs.csv


title: embryos 16-20HPE mutant 3

description:
Library name: 16-20 mutant 3
Sima_embryo_FPKMs.csv

source_name: embryo

value: embryo


title: 796 eWAT-Obese-Vehicle

description: SAMPLE 8


title: embryos 16-20HPE mutant 1

description:
Library name: 16-20 mutant 1
Sima_embryo_FPKMs.csv


title: embryos 16-20HPE mutant 2

description:
Library name: 16-20 mutant 2
Sima_embryo_FPKMs.csv


title: embryos 12-16HPE mutant 3

description:
Library name: 12-16 mutant 3
Sima_embryo_FPKMs.csv


title: 794 eWAT-Obese-Vehicle

description: SAMPLE 6


title: embryos 8-12HPE mutant 2

description:
Library name: 8-12 mutant 2
Sima_embryo_FPKMs.csv


title: embryos 8-12HPE mutant 3

description:
Library name: 8-12 mutant 3
Sima_embryo_FPKMs.csv


title: embryos 16-20HPE control 3

description:
Library name: 16-20 control 3
Sima_embryo_FPKMs.csv


title: embryos 16-20HPE control 2

description:
Library name: 16-20 control 2
Sima_embryo_FPKMs.csv


title: embryos 8-12HPE mutant 1

description:
Library name: 8-12 mutant 1
Sima_embryo_FPKMs.csv


title: embryos 12-16HPE mutant 2

description:
Library name: 12-16 mutant 2
Sima_embryo_FPKMs.csv


title: embryos 12-16HPE control 3

description:
Library name: 12-16 control 3
Sima_embryo_FPKMs.csv


title: embryos 12-16HPE mutant 1

description:
Library name: 12-16 mutant 1
Sima_embryo_FPKMs.csv


title: embryos 16-20HPE control 1

description:
Library name: 16-20 control 1
Sima_embryo_FPKMs.csv


title: embryos 8-12HPE control 3

description:
Library name: 8-12 control 3
Sima_embryo_FPKMs.csv


title: embryos 12-16HPE control 2

description:
Library name: 12-16 control 2
Sima_embryo_FPKMs.csv


title: embryos 8-12HPE control 2

description:
Library name: 8-12 control 2
Sima_embryo_FPKMs.csv


title: embryos 12-16HPE control 1

description:
Library name: 12-16 control 1
Sima_embryo_FPKMs.csv


title: larvae sima Mutant1

description:
Library name: Mutant1
Sima_larvae_FPKMs.csv


title: larvae heterozygous Control2

description:
Library name: Control2
Sima_larvae_FPKMs.csv


title: embryos 8-12HPE control 1

description:
Library name: 8-12 control 1
Sima_embryo_FPKMs.csv


title: lib2_Tera1_biol rep2

description: Library name: lib2_Tera1_r2


title: lib2_Tera1_biol rep1

description: Library name: lib2_Tera1_r1


title: lib2_SKNSH_biol rep2

description: Library name: lib2_SKNSH_r2

source_name: SKNSH

value: SKNSH


title: lib2_SKNSH_biol rep1

description: Library name: lib2_SKNSH_r1


title: lib2_PC3_biol rep1

description: Library name: lib2_PC3_r1


title: lib2_PC3_biol rep2

description: Library name: lib2_PC3_r2


title: lib2_MCF7_biol rep1

description: Library name: lib2_MCF7_r1


title: lib2_JEG3_biol rep2

description: Library name: lib2_JEG3_r2


title: lib2_JEG3_biol rep1

description: Library name: lib2_JEG3_r1


title: lib2_HeLa_biol rep2

description: Library name: lib2_HeLa_r2

source_name: HeLa

value: HeLa


title: lib2_HeLa_biol rep1

description: Library name: lib2_HeLa_r1


title: lib2_HaCaT_biol rep2

description: Library name: lib2_HaCaT_r2

source_name: HaCaT

value: HaCaT


title: lib2_MCF7_biol rep2

description: Library name: lib2_MCF7_r2


title: lib2_HaCaT_biol rep1

description: Library name: lib2_HaCaT_r1


title: Uterus at GD6 (control group 1)

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

description: Gene expression data from CTR

hyb_protocol: 3.75 μg of single strand cDNAs were hybridized on a GeneChip Mouse Gene 2.0 ST Array (Affymetrix) at 45°C for 16 h in a GeneChip Hybridization Oven 645 (Affymetrix). After hybridization, GeneChips were stained and washed using a GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Arrays were immediately scanned, and images were analyzed and rigorously quality controlled for hybridization artefacts.

data_processing: The resulting CEL files were processed using the oligo package available performed in R/Bioconductor (Gentleman et al., 2004). Data were then normalized and background corrected using the SCAN.UPC method with the Brainarray custom CDF file for directly mapping Affymetrix probe to Entrez gene identifiers (mogene20stmmentrezg.db_21.0.0) (Dai et al., 2005).

label: biotin

source_name: Uterus

label_protocol: cRNA targets were synthesized from 250 ng of total RNA using the Ambion WT Expression kit (Thermo Fisher). The GeneChip WT Terminal Labeling and Controls kit (Affymetrix) was used to label and fragment the cRNA.

growth_protocol: 9-11 weeks old female mice (Control Smad4 fx/fx and Mutant Amhr2-cre; Smad4 fx/fx) were mated with wild-type male mice and uteri were collected at gestational day 6.

extract_protocol: According to the manufacturer's instructions, total RNA were isolated from oviduct or uterus using te PicoPure RNA isolation kit (Arcturus) or the RNeasy Plus Mini kit (Qiagen), respectively

treatment_protocol: To dissect the whole oviduct, the mesovarium was removed and the ovarian ligament was cut. The mesosalpinx was carefully removed and the oviduct (from the infundibulum to the rostral uterotubal junction) was retrieved. For the uterus, after removing the mesometrium, only the implantation sites were collected by excluding the inter-implantation sites.

tag: gender

value: Female

value: Uterus

tag: developmental stage

value: control


title: lib2_HUH7_biol rep1

description: Library name: lib2_HUH7_r1


title: Uterus at GD6 (mutant group 1)

description: Gene expression data from CTR

value: mutant


title: Oviduct at GD6 (mutant group 3)

description: Gene expression data from CTR

source_name: Oviduct

value: Oviduct


title: Uterus at GD6 (control group 3)

description: Gene expression data from CTR


title: Oviduct at GD6 (mutant group 2)

description: Gene expression data from CTR


title: Oviduct at GD6 (control group 2)

description: Gene expression data from CTR


title: lib2_HEK293T_biol rep2

description: Library name: lib2_HEK293T_r2


title: Oviduct at GD6 (control group 3)

description: Gene expression data from CTR


title: Uterus at GD6 (mutant group 2)

description: Gene expression data from CTR


title: Oviduct at GD6 (control group 1)

description: Gene expression data from CTR


title: Uterus at GD6 (control group 2)

description: Gene expression data from CTR


title: Uterus at GD6 (mutant group 3)

description: Gene expression data from CTR


title: lib2_HEK293T_biol rep1

description: Library name: lib2_HEK293T_r1


title: Oviduct at GD6 (mutant group 1)

description: Gene expression data from CTR


title: lib2_A549_biol rep2

description: Library name: lib2_A549_r2


title: lib2_A549_biol rep1

description: Library name: lib2_A549_r1


title: lib2_HUH7_biol rep2

description: Library name: lib2_HUH7_r2


title: PDX16-V3

city: Portland

first: Pengtao

last: Dang

address: 2720 S Moody Ave

institute: Oregon Health & Science University

description:
Library name: Sample 12
Merged_counts_ILMN1297.txt
PDX16-V3_S3_L001

data_processing:
Data is mapping to genome UCSC mm10 or GRCH38 using STAR software
Assembly: UCSC mm10; GRCH38
Supplementary files format and content: txt; counts

source_name: MPNST Tumor Tissue

growth_protocol: Growth protocol - In vitro studies: Cells were cultured in serum-free medium supplemented with B27 and N2, plus EGF and FGF (10 ng/ml each) in 5% oxygen at 37C. Every culture was passaged for no longer than 4 weeks. In vivo studies: were performed with NP and NI mutant GEMMs and PDX models. For GEMM experiments, NI and NP mutant MPNST cells (5000 cells) were injected into nu/nu mice. For PDX experiments, tumor chunks of equal size were implanted adjacent to the sciatic nerve of nude mice. Mice were divided into 4 groups once tumors reached a volume of 250-500 mm3.

extract_protocol:
Extract protocol - Primary tumors were dissected and minced into small tissue blocks, and then were dissociated by using a gentleMACS Octo Dissociator (Miltenyi Biotec) and 1g/ml collagenase (Sigma-Aldrich, Cat# C8051), following the preset protocol. The dissociated cells were washed in PBS 3 times and treated with blood cell lysate buffer (Sigma-Aldrich, Cat# R7757).
RNA was extracted from mice with NP mutant MPNST tumors treated with SHP2i for 5 or 20-28 days (n=3 animals each). RNA was extracted from a 20-30 mg portion of  flash-frozen NP mutant MPNST tumor tissue using the Qiagen RNeasy Plus kit following the manufacturer’s protocol. Tissue homogenization/disruption was by mortar and pestle and Buffer RLT Plus supplemented with beta-mercaptoethanol followed by passing homogenized samples over Qiagen QIAshredder columns. Qiagen RNase-Free DNase Set was used for on-column DNA digestion. Total RNA was submitted to the IU Center for Medical Genomics (CMG) for library preparation and sequencing. Total RNA was first evaluated for its quantity and quality using an Agilent Bioanalyzer 2100. A RIN number of above 8 was achieved for all samples. One hundred nanograms of total RNA was used. cDNA library preparation included mRNA purification/enrichment, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification, following the KAPA mRNA Hyper Prep Kit Technical Data Sheet, KR1352 – v4.17 (Roche Corporate). Each resulting indexed library was quantified, its quality was accessed by Qubit and Agilent Bioanalyzer, and multiple libraries were pooled at equal molarity. Pooled libraries were then denatured and neutralized before loading onto a NovaSeq 6000 sequencer at 300pM final concentration for 100bp paired-end sequencing (Illumina, Inc.). Approximately 30-40M reads per library were generated. was used to measure the quality of sequencing. More than 90% of the sequencing reads reached a Phred quality score Q30 of (99.9% base call accuracy)

treatment_protocol: Treatment protocol - Vehicle and drugs were administered by oral gavage at the following doses and schedules. SHP099 and Trametinib combination studies: SHP099 50 mg/kg daily, trametinib 0.25 mg/kg daily, or the combination (SHP099 50 mg/kg every other day and trametinib 0.25 mg/kg daily). SHP099 and HQ combination studies: Hydroxychloroquine (50 mg/kg daily), SHP099 (50mg/kg daily), or the combination of SHP099 (50 mg/kg daily) plus HQ (50 mg/kg daily).

value: MPNST Tumor Tissue

value: WT

value: Vehicle Control

tag: batch

value: Control


title: PDX16-S3

description:
Library name: Sample 14
Merged_counts_ILMN1297.txt
PDX16-S3_S9_L001

value: SHP099 treated


title: PDX16-V1

description:
Library name: Sample 13
Merged_counts_ILMN1297.txt
PDX16-V1_S1_L001


title: PDX16-S1

description:
Library name: Sample 15
Merged_counts_ILMN1297.txt
PDX16-S1_S7_L001


title: PDX16-S4

description:
Library name: Sample 11
Merged_counts_ILMN1297.txt
PDX16-S4_S10_L001


title: PDX16-V2

description:
Library name: Sample 10
Merged_counts_ILMN1297.txt
PDX16-V2_S2_L001


title: p1492s4_Prol_SRSF7_control_Papantonis

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str. 40

department: Institute of Pathology

institute: University Medical Center Göttingen

description: Library name: GTCGGAGCTTATAACC_p1492s4_Prol_SRSF7_control_Papantonis

data_processing:
Sequencing data were processed as follows: Sequence images were transformed into BCL files using Illumina's BaseCaller software. The BCL files were subsequently demultiplexed into FASTQ files using bcl2fastq v2.20. Sequencing quality was evaluated with FastQC (Andrews, S. (2014). FastQC: A Quality Control tool for High Throughput Sequence Data).
The Cogent NGS Analysis Pipeline (CogentAP) from Takara Bio (v2.0.1) was applied to further process the FASTQ files, including demultiplexing and generating gene expression matrices. Reads were aligned to the human genome (GRCh38) using the Ensembl reference genome (https://www.ensembl.org/Homo_sapiens/Info/Index).
Assembly: hg38
Supplementary files format and content: Expression matrix
Library strategy: APEX-seq

source_name: Lung Tissue

extract_protocol:
Total RNA was isolated with the DirectZol RNA mini-prep kit (ZymoReaserch, R2052). The extracted RNA was afterwards used in Streptavidin pull-downs for enrichment of biotinylated RNA content. Briefly, 40 µl of Dynabeads_MyOne_Streptavidin C1 magnetic beads (Thermo Fisher, 65002) were prepared per 100 µg of RNA according to manufacturer’s instructions. The beads were incubated with the extracted RNA in 1M NaCl, 5 mM  Tris-HCl pH 7.5, 0.5 mM EDTA and 25 Units/ml RiboLock RNase Inhibitor for 15 min at room temperature under gentle rotation. Finally, the enriched RNA was eluted form the beads with Trizol, purified with the RNA Clean & Concentrator-5 (ZymoResearch, R1014) according to manufacturer’s instructions and quantified with the Qubit™ RNA High Sensitivity (HS) Assay Kit (Thermo Fisher, Q3285).
Library preparation was performed using the SMART-Seq Total RNA Pico Input with UMIs kit (ZapR Mammalian; TAKARA Bio; Cat. N° 634354). This kit is specifically designed to efficiently prepare Illumina sequencing libraries from minimal input amounts (250 pg–10 ng) of total RNA, including RNA of high quality, partially degraded, or low quality. The resulting libraries retain strand information and incorporate indexes and adapters during the reverse-transcription and PCR amplification steps. Unique molecular identifiers (UMIs) are introduced during the reverse-transcription step to reduce potential PCR bias and provide additional precision for transcript quantification.

treatment_protocol: Cells were incubated at 37oC, under 5% CO2 in medium containing 500 µM Biotinyl-Tyramid (Merck, SML2135). Activation of labelling was achieved by adding 1 mM H2O2 (Merck, H1009) to each plate, gently agitating for exactly 1 min. Immediately after quenching the reaction (Quench Buffer: Trolox 10 mM, Sodium ascorbate 20 mM and Sodium azide 20 mM in PBS containing RiboLock RNase Inhibitor (ThermoFisher, EO0382), the cells were lysed in Trizol Reagent (ThermoFisher, 15596018). The non-labelled control samples were processed the same way, without adding H2O2.

value: Lung Tissue

value: Human Embryonic Fibroblast

value: untreated (control)


title: p1492s6_ICM_SRSF7_control_Papantonis

description: Library name: GCGCAAGCCGGCGTGA_p1492s6_ICM_SRSF7_control_Papantonis

value: ICM 6 days


title: p1492s3_Prol_SRSF7_H2O2_Papantonis

description: Library name: CGGCGTGAACAGGCGC_p1492s3_Prol_SRSF7_H2O2_Papantonis


title: RLI1_depl, R42L, replicate 1 [RIBO-seq]

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

data_processing:
Reads, excluding the rRNA seqeunces, were mapped to the genome (Ensembl R64-1-1 release101) using STAR-v2.7.2b with ENCODE option.
RSEM-v1.2.31 was used to calculate read counts and normalize.
Assembly: R64-1-1
Supplementary files format and content: tab separated RSEM results
Library strategy: RIBO-Seq

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: fmt1 S. cerevisiae expressing EcFMT or EcFMTR42L were grown at 30°C in SC-media until A600 of ~0.5

extract_protocol:
~50 A260 unit of cell lysates were supplemented with RNase I and incubated 1 hr at room temperature with gentle rotation. Resulting samples were layered onto 10%-50% sucrose gradient and centrifuged at 39,000 rpm at 4 °C for 2.5 hr using SW-41 Ti rotor. Resulting sucrose gradients were monitor and digested 80S fractions were collected, followed by centrifugal filtration. Sequentially, samples were mixed with release buffer and incubated on ice for 10 min, followed by centrifugation and transferred the flowthrough into a new sterile tube. The flowthroughs were adjusted to 1% SDS, followed by the addition of 1 volume of Acid-Phenol:Chloroform (pH4.5), vortex, incubation at 65°C for 5 min, and incubation on ice for 1 min. Resulting samples were centrifuged at 12,000xg at 4°C for 5 min, and resulting aqueous top was transferred to new sterile 1.5 ml tubes. RNA from the resulting samples were ethanol precipitated by adding NaOAc (pH 5.5) containing 1/100 volume Glycoblue, followed by 2.5 volumes of 100% ethanol and incubation at -20°C overnight.
Harvested RNA fragments were dephosphorylated, following adaptor ligation using 3’-adaptor. The Ligated RNAs were reverse transcribed using RT-primer, circularized and PCR-amplified for 12. Following PCR products are purified and subjected to 150bp-double end sequencing using the Illumina Nextseq 1000 system.

treatment_protocol: Cells were rapidly vacuum filtered and snap frozen in liquid nitrogen. Frozen cells were resuspended in the ribosome lysis buffer, followed by mechanical disruption using bead beater.

value: yeast cells


title: RLI1_depl, R42L, replicate 2 [RIBO-seq]


title: p1492s1_Prol_NLS_H2O2_Papantonis

description: Library name: TTATAACCTCGATATC_p1492s1_Prol_NLS_H2O2_Papantonis


title: p1492s5_ICM_SRSF7_H2O2_Papantonis

description: Library name: CGTTAGAAGACCTGAA_p1492s5_ICM_SRSF7_H2O2_Papantonis


title: p1492s2_Prol_NLS_control_Papantonis

description: Library name: GACCTGAACTCACCAA_p1492s2_Prol_NLS_control_Papantonis


title: 624Mel_siMITF+IFNg_2

city: Reykjavík

first: Berglind

middle: Ósk

last: Einarsdóttir

address: Sturlugata 8

country: Iceland

institute: University of Iceland

description: Library name: Sample8

data_processing:
FASTQ files were cleaned using Trimmomatic version 0.39 using default parameters
Quantified gene expression from generated FASTQ files using Kallisto version 0.46.137  and the Ensembl Homo sapiens GRCh38 reference transcriptome
DESeq2 version 1.26.0 was uesed to determine statistically significant differentially expressed genes (DEGs) across experimental conditions (Benjamini–Hochberg correction α = 0.1; adjusted P < 0.05)
Filtered out those DEGs that, when compared across conditions were expressed at very low levels (max expression < 2 TPM) or showed relatively small fold-change (FC) differences (abs log2 FC < 1). This filter resulted in a set of 1,129 response genes that we used as input for downstream non-additive response analysis
Assembly: Ensembl Homo sapiens GRCh38 reference transcriptome
Supplementary files format and content: TSV files including TPMs per sample at the gene level

source_name: skin

growth_protocol: 624Mel melanoma cells were grown in RPMI1640 supplemented with 10% heat-inactivated featal bovine serum (FBS) and 1% Penicillin/Streptomycin in a humidified atmosphere with 5% CO2 and 37°C

extract_protocol:
Total RNA was extracted using a Quick-RNA Miniprep Kit acquired from Zymo Research. The standard protocol of the kit was followed with an additional washing step using 400 μL RNA wash buffer prior to the elution step.
For cDNA library preparation, each RNA sample was diluted to 20 ng/μL in 50 μL final volumes. The cDNA libraries were then made using the TruSeq RNA v2 Sample Prep Kit (Illumina) and SuperScript IV Reverse Transcriptase (Invitrogen). The cDNA libraries were quantified using LabChip GX and diluted to 3 nM prior to sequencing. The sequencing was performed on a NovaSeq6000 sequencer, and the results were exported as FASTQ files using bclfastq2 v2.20.

treatment_protocol: Cells were subjected to reverse siRNA transfection with wither siMITF or siCTRL. 24 hours post transfection the cells were treated with interferon gamma (final concentration = 5 ng/mL). The cells were then harvested after 24 hours of interferon treatment.

value: skin

value: melanoma

value: MITF knockdown

value: interferon gamma


title: 624Mel_siMITF_2

description: Library name: Sample7


title: 624Mel_siMITF+IFNg_1

description: Library name: Sample4


title: PDX16-V4

description:
Library name: Sample 16
Merged_counts_ILMN1297.txt
PDX16-V4_S4_L001


title: 624Mel_siMITF+IFNg_3

description: Library name: Sample12


title: 624Mel_siCTRL+IFNg_3

description: Library name: Sample10

value: siCTRL


title: 624Mel_siMITF_1

description: Library name: Sample3


title: 624Mel_siCTRL+IFNg_2

description: Library name: Sample6


title: RLI1_depl, EcFMT, replicate 2 [RIBO-seq]

value: EcFMT


title: PDX16-S2

description:
Library name: Sample 17
Merged_counts_ILMN1297.txt
PDX16-S2_S8_L001


title: 624Mel_siCTRL_3

description: Library name: Sample9


title: RLI1_depl, EcFMT, replicate 1 [RIBO-seq]


title: 624Mel_siCTRL+IFNg_1

description: Library name: Sample2


title: 624Mel_siCTRL_2

description: Library name: Sample5


title: 624Mel_siMITF_3

description: Library name: Sample11


title: NIP1_depl, R42L, replicate 2 [RIBO-seq]


title: NIP1_depl, R42L, replicate 1 [RIBO-seq]


title: Perturb-seq of DE with gRNA library, gene expression readout

city: New York

first: Hyein

middle: Sophia

last: Cho

state: NY

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: DE perturb-seq_cDNA
perturb-seq

data_processing:
Alignment and quantification using CellRanger
Assignment of cell barcode based on gRNA count readout
Assembly: hg38
Supplementary files format and content: Gene quantification sparse matrix (.mtx)

growth_protocol: Human ESCs were maintained in Essential 8 medium on tissue culture-treated polystyrene plates coated with 5 μg/mL vitronectin

extract_protocol: The cells were loaded onto a 10x chromium controller v5.0 and processed with 10x Genomics Chromium Single Cell 3′ Reagent Kit v.3 following the manufacturer’s instructions (CG000204 Rev D)

treatment_protocol: 1 μg/mL puromycin from Day 1 to Day 3 to select infected cells, and 2 μg/mL doxycycline from Day 0 to Day 6 to induce dCas9-KRAB

value: DE


title: Perturb-seq of DE with gRNA library, guide RNA readout

description:
Library name: DE perturb-seq_gRNA
perturb-seq


title: NIP1_depl, EcFMT, replicate 1 [RIBO-seq]


title: Perturb-seq of ESC with gRNA library, gene expression readout

description:
Library name: ESC perturb-seq_cDNA
perturb-seq

value: ESC


title: NE 72h WT replicate 3

description:
Library name: RNAseq_NE72h_rep3
NE_72h_R3

data_processing:
Alignment using STAR STAR_2.5.1b
Quantification using RSEM v1.2.23
Assembly: hg38
Supplementary files format and content: Gene quantification text file

extract_protocol:
Total RNA was isolated from cell pellets using Quick-RNA Miniprep kits (ZYMO Research, R1055) per the manufacturer’s instructions, including the digestion and removal of DNA.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 100-500 ng of total RNA with RIN values of 9.4-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit; RS-122-2102). Samples were amplified by 8 cycles of PCR, barcoded, and run on a NovaSeq 6000 platform in a PE100 run, using the NovaSeq 6000 S2 Reagent Kit (200 Cycles) (Illumina).

value: WT


title: Perturb-seq of ESC with gRNA library, guide RNA readout

description:
Library name: ESC perturb-seq_gRNA
perturb-seq


title: hrc1D, R42L, replicate 2 [RIBO-seq]


title: hrc1D, EcFMT, replicate 1 [RIBO-seq]


title: hrc1D, EcFMT, replicate 2 [RIBO-seq]


title: ESC e2het26 replicate 3

description:
Library name: RNAseq_e2het26_rep3
26-4-Aligned.sortedByCoord.out.bam


title: hrc1D, R42L, replicate 1 [RIBO-seq]


title: ESC e2het26 replicate 2

description:
Library name: RNAseq_e2het26_rep2
26-2-Aligned.sortedByCoord.out.bam


title: F2_1

city: Tianjin

first: Mei

last: Zhou

address: Heping district，qixiangtai road 22

institute: Tianjin Medicial University

data_processing:
Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit) detects the concentration of total RNA
BGISEQ-500 was used to build gene library
Data were filtered by the software SOAPnuke (version 1.5.2)
Genome_build: mm9

source_name: aortic tissue

extract_protocol:
Total RNA extraction using TRIzol reagent (Thermo Fisher, Carlsbad, CA, USA) according to the manufacturer’s instructions. The poly A-containing mRNA molecules were enriched and purified using poly T oligo-attached magnetic beads. After purification, the mRNA fragments were fragmented into small pieces using divalent cations at elevated temperatures. cDNA synthesis using DNA Polymerase I and RNase H was performed following the purification of poly A-containing mRNA molecules. The products were then purified and amplified using PCR. The cDNA library was constructed using Qubit and pooled together to form a single strand DNA circle (ssDNA circle).
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

value: 32 weeks

value: untreated


title: 624Mel_siCTRL_1

description: Library name: Sample1


title: arf1D, EcFMT, replicate 1 [RIBO-seq]


title: F1_1


title: arf1D, R42L, replicate 2 [RIBO-seq]


title: NIP1_depl, EcFMT, replicate 2 [RIBO-seq]


title: ESC e2het26 replicate 1

description:
Library name: RNAseq_e2het26_rep1
26-1-Aligned.sortedByCoord.out.bam


title: Plasma negative_6

city: Viborg

first: Maibritt

last: Mardahl

address: Blichers Alle 20

department: Department of Animal and Veterinary Research

country: Denmark

institute: Aarhus University

data_processing:
The data submitted are processed data files. The associated articles generated these fasta files as briefly described below.
1) umi_extract
2) cutadapt with arguments: -j 8 --minimum-length=18 —maximum-length=30 -a AACTGTAGGCACCATCAAT
3) bowtie with arguments: -v 2 -a --norc --best --strata --threads 16 AND reference was to S. vulgaris miRNA precursor complement identified for this study and build to a bowtie index using bowtie_build before alignment.
4) samtools view -h -F 4 filename.sam > filename.bam”
5) samtools sort filename.bam
6) samtools index filename.bam
7) umicollapse with parameters: bam -k 1
8) samtools fastq with parameter: -0
9) fastx_collapser
10) Rename each entry with gsed -i "s/>/>$name\_/g; s/-/_x/g" filename.fasta”
Assembly: Bowtie build of svulgarisPrecursormiRNAComplement.fa
Supplementary files format and content: Fasta of processed raw fasta files with the data processing steps given.

organism: Equus caballus

source_name: Plasma

extract_protocol:
miRNeasy Serum/Plasma Kit and miRNeasy mini kit (Qiagen, MD, USA).
QIAseq miRNA Library Kit

treatment_protocol: Live L4 and L5 S. vulgaris larvae were collected from the cranial mestenteric artery of naturally infected foals. A subset of the live larvae (still separated into L4s, L5Ms and L5Fs) were transferred in groups of 2-5 larvae, to T25 culture cell flasks (Thermo Fisher Scientific, Waltham, MA, USA), containing 37˚C Roswell Park Memorial Institute 1640 medium (RPMI 1640 medium) with Antibiotic-Antimycotic Solution, containing 10.000 U/mL penicillin, 10 mg/mL streptomycin and 25 µg/ml Amphotericin B (Sigma-Aldrich, Merck-group, St. Louis, MO, USA). Four ml of RPMI medium were added per flask, regardless of the number of larvae. The larvae were then incubated at 37˚C, and after 30 min., the media was discarded, replaced, and the larvae incubated for another 30 min. This step was performed three times to promote clear-out of the larvae’s intestinal tracts. After the initial three consecutive 30 min. incubation cycles, both the T25 flask and media were replaced, and the larvae were incubated for six hours at 37˚C. Hereafter, the media were collected, and the larvae were incubated with new media for another 6 hours.

value: Plasma

tag: infection status

value: Uninfected


title: Plasma negative_3


title: ESC WT replicate 3

description:
Library name: RNAseq_WT_rep3
WT-4-Aligned.sortedByCoord.out.bam


title: ESC WT replicate 2

description:
Library name: RNAseq_WT_rep2
WT-2-Aligned.sortedByCoord.out.bam


title: arf1D, R42L, replicate 1 [RIBO-seq]


title: Plasma negative_2


title: Plasma negative_1


title: W3_1

value: wild type


title: Plasma positive_5

value: Infected


title: ESC WT replicate 1

description:
Library name: RNAseq_WT_rep1
WT-1-Aligned.sortedByCoord.out.bam


title: Plasma positive_6


title: NE 72h WT replicate 1

description:
Library name: RNAseq_NE72h_rep1
NE_72h_R1


title: HOS cells treated with ruxolitinb and infected with SFV4

city: Uppsala

first: Miika

last: Martikainen

address: Dag Hammarskjölds Väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala Universitet

description: Library name: Ruxolitinib_SFV4

data_processing:
Readcounts were mapped to the library sequences using MAGeCK/0.5.9.4
Assembly: GRCh38
Supplementary files format and content: tab-delimited .txt file with mapped readcounts
Supplementary files format and content: Library strategy: CRISPR screen, knock-out

source_name: HOS

extract_protocol:
QIAamp DNA Blood Mini (Qiagen) according to manufacturer's instructions
PCR one amplicon with adaptor-containing primers

value: HOS


title: F3_1


title: W2_1


title: Plasma negative_5


title: W1_1


title: Plasma negative_4


title: HOS cells infected with SFV4

description: Library name: SFV4


title: Plasma positive_4


title: HOS cells

description: Library name: Uninfected


title: FFGRD_4

city: TUCSON

first: Ravi

last: Goyal

state: Arizona

address: 1501 N. Campbell Ave

institute: University of Arizona

data_processing:
data quality was validated for RNAseq analysis using FastQC Version 0.11.9.
aligned with the sequencing data using Salmon
Integrated differential expression and pathway analysis were conducted with iDep.96 web-based applications
DESEQ2
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: allgenes.txt

organism: Ovis aries

source_name: Perirenal Differentiated Preadipocytes

extract_protocol:
adipose tissue was thawed in Trizol and homogenized using 3 pulses, 4-6 seconds each. Then, 0.2 mL of chloroform was added per 1 mL of Trizol (0.1 mL per sample). Samples were centrifuged for 15 minutes at 14,000 x g (4 ˚C) and the mixture separated into a lower red phenol-chloroform, interphase, and a colorless upper aqueous solution. The aqueous phase containing RNA was transferred to a new tube very carefully to ensure proteins and other cell components did not contaminate the RNA. Then, 250 µl of isopropanol was added to the aqueous phase (0.5 ml/ ml of Trizol) and incubated for 10 minutes. The sample was centrifuged for 10 minutes at 14,000 x g (4˚C) and the RNA precipitate formed a white gel-like pellet at the bottom of the tube. The supernatant was discarded and the sample was vortexed briefly before centrifugation for 5 minutes at 8000 x g (4˚C). The supernatant was discarded and the RNA pellet was air-dried for 10 minutes. Pellets were resuspended in 50 µl of RNase-free water. The RNA was further purified by Zymo Purelink RNA columns.
library was constructed from samples using a Swift RNA Library Kit – (Catalog # R1024) and Swift Dual Combinatorial Indexing Kit – (Catalog # X8096)

value: female

tag: group

value: growth restricted female

value: Perirenal Differentiated Preadipocytes

value: Differentiated to Mature Adipocytes


title: FFGRD_3


title: Plasma positive_2


title: UCLA TBIE #1, [UCLA_TBIE_s3045]

city: Kuopio

first: Mette

last: Heiskanen

address: Neulaniementie 2, P.O.B. 1627

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

data_processing:
Fastq files were uploaded to QIAGEN GeneGlobe Data Analysis Center (DAC), a freely available web resource to analyze data from QIAGEN’s QIASeq NGS library kits (https://geneglobe.qiagen.com/in/analyze/). Primary quantification of read counts was performed in DAC.
The processing steps included (i) trimming of the 3'-adapter and low-quality bases with cutadapt, (ii) identification of insert sequences and unique molecular indices (UMIs) (reads with < 16 bp inser sequences or < 10 bp UMI sequences were discarded), (iii) alignment of the processed reads to rat reference genome RGSC Rnor_6.0 with a sequential alignment strategy using bowtie (perfect match to miRBase nature, miRBase hairpin, non-coding RNA, mRNA and other RNA, and ultimately a second mapping to miRBase nature with toleration of up to 2 mismatches).
Annotation of miRNAs in the DAC portal was performed with miRBase v. 21.
Assembly: Rnor_6.0, miRBase v21
Supplementary files format and content: compiled matrix table with raw counts for every miRNA in every sample

source_name: plasma

extract_protocol:
Whole blood was collected under isoflurane anesthesia from the lateral tail vein into K2 EDTA tubes. Plasma was separated by centrifugation at 1300 g for 10 min at 4 °C. RNA was extracted from 200 μl plasma using miRNeasy serum/plasma kit with elution volume of 14 μl.
Small RNA library preparation was conducted with QIASeq miRNA library kit. Small RNA-seq. Single-end sequencing of 75-bp reads was performed at 12M depth by Illumina NextSeq 550.

value: plasma

value: Sprague-Dawley

value: adult

value: male

tag: time

value: traumatic brain injury

tag: outcome

value: epilepsy


title: UCLA TBIE #2, [UCLA_TBIE_s3022]

tag: tissue


title: arf1D, EcFMT, replicate 2 [RIBO-seq]

value: yeast cells

tag: treatment

value: EcFMT


title: HOS cells treated with ruxolitinib

description: Library name: Ruxolitinib

tag: cell line


title: FFGRD_2

tag: cell type


title: UCLA TBIN #3, [UCLA_TBIN_s3030]

tag: strain

tag: age

value: no epilepsy


title: UCLA TBIE #3, [UCLA_TBIE_s3027]


title: Plasma positive_1

value: Plasma


title: UCLA TBIN #2, [UCLA_TBIN_s3028]


title: Plasma positive_3


title: FFGRD_1


title: UCLA TBIN #1, [UCLA_TBIN_s3026]


title: FFGR_4

source_name: Perirenal Preadipocytes

value: Perirenal Preadipocytes

value: Control


title: UCLA sham #3, [UCLA_sham_s3004]

value: sham


title: 3D_EDV

city: Kizugawa

first: Sawa

last: Yamashiro

address: 6-5-4 Kunimidai

institute: Rohto Pharmaceutical Co., Ltd.

description: Library name: Sample 3

data_processing:
alignment of the raw fastq-data with the programm cellranger 7.1.0 to the reference genome
filtering of the data with cellranger
filtering of data with seurat
combination of samples with seurat
Assembly: hg38
Supplementary files format and content: counts

source_name: Skin equivalent

growth_protocol: The THS model was generated via the following procedure. A total of 24 × 105 NHDFs and 30 × 10^5 HUVECs were resuspended in 2.4 ml of 1.25 mg ml-1 bovine dermis-derived native collagen solution that was mixed with 1× DMEM, 15 mM HEPES, 10 mM NaHCO3, and 5 mg ml-1 fibrinogen from bovine plasma type I-S (Merck KGaA, Darmstadt, Germany); then, the cells were plated in a high-density translucent-membrane cell culture insert (0.4-µm pore size) in 6-well plates. After solidification, the dermal equivalents were held in place by a Snapwell culture insert (Corning). NHEKs were seeded at a density of 1.1 × 10^6 cells/well on fixed dermal equivalents, and they were cultured in growth medium under submersion conditions for 4 d in a humidified atmosphere at 37 °C with 5% CO2 and 12.5% O2. After maintenance in a submersion culture, the HSEs were exposed to the air-liquid interface in a humidified atmosphere at 37 °C with 5% CO2. The growth medium for culturing HSEs consisted of DMEM supplemented with 10% FBS, 1% penicillin/streptomycin, 5 µg ml-1 insulin, 500 mM ascorbic acid, 10 ng ml-1 bFGF (PeproTech, NJ, USA), 1 µM hydrocortisone, and 5 nM VEGF 165 Human Recombinant and was replaced with fresh medium every 48 to -72 h.

extract_protocol:
NHEKs, NHDFs, and HUVECs cultured to a subconfluent state were harvested through trypsinization according to the product protocol. Briefly, the cells were washed with HEPES-buffered solution to remove the medium and treated with 0.025% trypsin/EDTA solution for 3–7 min, followed by the addition of a trypsin-neutralizing solution and centrifugation to obtain a cell pellet. Constituent HSE cells were harvested through enzymatic digestion. On day 14 of air-liquid interface culture, the epidermis and dermis of the HSE were mechanically separated using forceps. The epidermal layer was enzymatically dissociated with 0.025% trypsin/EDTA solution, while the dermal layer was incubated in 10% FBS-supplemented DMEM containing 5000 U/ml collagenase type 1 in a 37 °C water bath. The resulting cell suspension was filtered through a 70-µm cell strainer to remove debris and centrifuged to obtain a cell pellet.
Single-cell RNA sequencing was conducted using the Chromium Next GEM Single Cell 3ʹ Kit v3.1, Chromium Next GEM Chip G Single Cell Kit, and Dual Index Kit TT Set A according to the manufacturer's protocol. Cell viability and count were assessed using a Countess 3 Automated Cell Counter following trypan blue staining and visual inspection. The cell suspension was processed on a chromium controller for gel bead-in-emulsion (GEM) generation, where polyadenylated mRNA was reverse transcribed to cDNA and uniquely barcoded. The cDNA was subjected to amplification, quality assessment via electrophoresis, and library preparation involving fragmentation, end-repair, A-tailing, adaptor ligation, and PCR amplification.

value: Skin equivalent

value: mixed culture

value: skin


title: UCLA sham #1, [UCLA_sham_s3001]


title: 2D

description: Library name: Sample 1


title: UCLA sham #2, [UCLA_sham_s3003]


title: FFGR_3

value: female

value: growth restricted female


title: 3D_ED

description: Library name: Sample 2


title: Monash TBIE #1, [Mon_TBIE_s2081]

value: plasma

value: Sprague-Dawley


title: Monash TBIE #2, [Mon_TBIE_s2204]

value: adult

value: male


title: Monash TBIN #3, [Mon_TBIN_s2295]

value: traumatic brain injury


title: FFGR_2


title: BEAS-2B 3, DEP treated ACP5 KO, 48hr

first: Aaron

last: Yu

address: Gwanak-ro 1

institute: Seoul national university

data_processing:
Differentially expressed genes were subjected to gene enrichment analysis with the R package clusterProfiler
GSEA v3.0
Trimmed DEGs were used for pathway analysis using QIAGEN's Ingenuity® Pathway Analysis
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each example

growth_protocol: BEAS2B cells were incubated with IMDM containing 10% FBS, 1X Antibiotic-Antimycotic

extract_protocol:
Total RNA was extracted and purified from DEP treated BEAS2B cells studied in vitro using the TRIzol reagent. 1.2ug of total RNA was used to construct sequencing library
Libraries were generated using the Illumina TruSeq strand mRNA sample preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer's protocol.

treatment_protocol: To evaluate the effect of DEP, 50 μg/mL of DEP were added to BEAS2B cells for 48hr

value: lung epithelial cell

value: 50 μg/mL of DEP for 48hr


title: FFGR_1


title: Monash TBIN #2, [Mon_TBIN_s2193]

value: no epilepsy


title: BEAS-2B 1, DEP treated ACP5 KO, 48hr


title: FCD_4

value: control female

value: Perirenal Differentiated Preadipocytes

value: Differentiated to Mature Adipocytes


title: FCD_3


title: Monash sham #2, [Mon_sham_s2206]

value: sham


title: BEAS-2B 2, DEP treated ACP5 KO, 48hr


title: Monash sham #3, [Mon_sham_s2289]


title: FCD_2


title: UEF TBIE #4, [UEF_TBIE_s1144]

value: epilepsy


title: UEF TBIE #2, [UEF_TBIE_s1029]


title: BEAS-2B 3, ACP5 KO, 48hr

value: negative control


title: UEF TBIE #3, [UEF_TBIE_s1140]


title: BEAS-2B 1, ACP5 KO, 48hr


title: UEF TBIN #4, [UEF_TBIN_s1145]


title: FCD_1


title: UEF TBIE #1, [UEF_TBIE_s1031]


title: Monash TBIN #1, [Mon_TBIN_s2286]


title: UEF TBIN #2, [UEF_TBIN_s1105]


title: FC_4

value: Perirenal Preadipocytes

value: Control


title: Monash sham #1, [Mon_sham_s2281]


title: BEAS-2B 2, ACP5 KO, 48hr


title: UEF sham #3, [UEF_sham_s1146]


title: UEF TBIN #3, [UEF_TBIN_s1138]


title: FC_2

value: female


title: IPF66_TGFb_2

city: Chicago

first: Kun Woo

last: Shin

state: IL

address: 5841 S Maryland Ave

department: Medicine

institute: The University of Chicago

data_processing:
RNA-seq reads were pseudoaligned using Kallisto v.0.46.1
The Kallisto index was made with default parameters and the GENCODE (Release 45 (GRCh38.14) and was run in quant mode with default parameters
Assembly: hg38
Supplementary files format and content: est_counts      tpm

source_name: Lung

growth_protocol: Primary normal human lung fibroblasts (HLFs) were grown in DMEM containing 0.1% bovine serum albumin, 5.5mM glucose, 2 mM glutamine, and 1mM pyruvate for 24 hours. Primary normal, control male, and IPF patient's HLFs were gorwn in HPLM containing 0.1% bovine serum albumin for 24 hours.

extract_protocol:
Total RNA was isolated from fibroblasts using, GenElute™ Mammalian Total RNA Miniprep Kit
Oligo-dT mRNA directional

treatment_protocol: HLFs were treated with TGF-beta (Peprotech) or left untreated.

value: Lung

value: Primary Fibroblast

value: Fibroblast

value: HPLM + TGFb

tag: clone

value: IPF

value: Male


title: IPF66_TGFb_3

tag: Sex


title: IPF66_UT_3

value: HPLM


title: UEF sham #1, [UEF_sham_s1017]

value: plasma

value: Sprague-Dawley

value: adult

value: male


title: UEF TBIN #1, [UEF_TBIN_s1038]

value: traumatic brain injury

value: no epilepsy


title: FC_1

value: control female


title: UEF sham #2, [UEF_sham_s1143]

value: sham


title: UEF sham #4, [UEF_sham_s1155]


title: MFGRD_4

value: growth restricted male

value: Perirenal Differentiated Preadipocytes

value: Differentiated to Mature Adipocytes


title: IPF66_TGFb_1

value: Lung

value: Primary Fibroblast


title: IPF66_UT_1

value: Fibroblast


title: scav-4(unk49), Microbacterium sp. JUb74 fed, L4

city: HK

first: Chaogu

last: Zheng

address: The University of Hong Kong, Pokfulam Road

department: School of Biological Science

country: Hong Kong

institute: University of Hong Kong

description: Library name: CGZ337 JUb74

data_processing:
The trimmed sequencing reads were mapped to C. elegans reference genome (WB235) using STAR (2.7.10) with the option --quantMode geneCounts. The counts were then normalized and the differentially expressed genes were then identified using the standard pipeline of DESeq2 in R.
Assembly: WBcel235
Supplementary files format and content: tab-delimited text files contain the read count generated by STAR

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: The animals were bleached to obtain eggs, which were hatched in M9 overnight. The next day, L1s were seeded onto NGM plates with OP50 or JUb74 bacteria and grown until L4 stage before being harvested.

extract_protocol:
The L4 animals were washed with water and the worm pellet was extracted using TRIzol reagent (Invitrogen).
The library was constructed by BGI using the standard DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing service (P_Stranded Library & PE100 Seq).

value: Whole worm

tag: genotype

value: Microbacterium sp. JUb74 fed


title: scav-4(unk59), E. coli OP50 fed, L4

description: Library name: CGZ413 OP50

value: E. coli OP50 fed


title: scav-4(unk59), Microbacterium sp. JUb74 fed, L4

description: Library name: CGZ413 JUb74


title: MFGRD_3


title: WT, Microbacterium sp. JUb74 fed, L4

description: Library name: N2 JUb74

value: WT


title: IPF35_TGFb_3

value: HPLM + TGFb

value: IPF

value: Male


title: WT, E. coli OP50 fed, L4

description: Library name: N2 OP50


title: MFGRD_2

value: male


title: FC_3

value: female

value: Perirenal Preadipocytes

value: Control


title: IPF66_UT_2

value: HPLM


title: MFGR_4

value: growth restricted male


title: MFGRD_1

value: Perirenal Differentiated Preadipocytes

value: Differentiated to Mature Adipocytes


title: SW837 cells, siKRAS, replicate3

city: Porto

first: Flávia

middle: Oliveira

last: Martins

address: Rua Alfredo Allen, 208

country: Portugal

description: Library name: SW837_siKRAS3_S47

data_processing:
The quality of reads was evaluated using FASTQC
Adapters were trimmed and reads of poor quality or aligning to rRNA sequences were filtered using Trimmomatic
he cleaned reads were aligned to the human genome (hg38) using STAR
Counts for each condition were estimated from mapped reads using RSEM
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample

source_name: colorectal cancer

growth_protocol: SW480 cells were maintained in RPMI supplmeneted with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin (PS) in humidified atmosphere with 5% CO2 at 37ºC, and SW837 cells were maintained in DMEM supplmeneted with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin (PS) in humidified atmosphere with 5% CO2 at 37ºC

extract_protocol:
RNA was harvested using TRIzol Reagent
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads in Illumina platform

treatment_protocol: Prior to 3D cultures, CRC cell lines were seeded in 2D conditions in six-well plates, cultured for approximately 16 hours and then transfected using Lipofectamine RNAiMAX (Invitrogen, Thermo Fisher Scientific, USA) in reduced-serum Opti-MEM medium (Gibco, Thermo Fisher Scientific, USA) according to the manufacturer’s guidelines. Gene silencing was performed using ON-TARGETplus SMARTpool small interfering RNA specific for KRAS (siKRAS; L-005069-00-0010) from Dharmacon (USA) at a final concentration of 10 nM. A non-targeting (siControl) siRNA (D-001810-01-50; ON-TARGETplus Non-targeting siRNA #1) was used as negative control at the same concentration as the siRNA targeting KRAS. Twenty-four hours post-transfection, cells were harvested with 0.05% Trypsin-EDTA (Gibco, Thermo Fisher Scientific, USA) for 5 min at 37ºC, resuspended in completed medium, and seeded in 3D CoSeedis

value: colorectal cancer

value: siKRAS

value: total RNA

value: single


title: IPF35_UT_3

value: Lung

value: Primary Fibroblast

value: Fibroblast


title: scav-4(unk49), E. coli OP50 fed, L4

description: Library name: CGZ337 OP50

value: Whole worm

value: E. coli OP50 fed


title: SW837 cells, siControl, replicate3

description: Library name: SW837_siCTRL3_S44

value: siControl


title: SW837 cells, siKRAS, replicate1

description: Library name: SW837_siKRAS1_S45


title: SW837 cells, siKRAS, replicate2

description: Library name: SW837_siKRAS2_S46


title: SW837 cells, siControl, replicate1

description: Library name: SW837_siCTRL1_S42


title: IPF35_TGFb_2

value: HPLM + TGFb

value: IPF

value: Male


title: SW837 cells, siControl, replicate2

description: Library name: SW837_siCTRL2_S43


title: IPF35_UT_2

value: HPLM


title: MFGR_3

value: male

value: growth restricted male

value: Perirenal Preadipocytes

value: Control


title: SW480 cells, siKRAS, replicate3

description: Library name: SW480_siKRAS3_S41

value: colorectal cancer

value: siKRAS


title: IPF35_TGFb_1


title: MFGR_2


title: SW480 cells, siControl, replicate3

description: Library name: SW480_siCTRL3_S38

value: total RNA

value: single


title: SW480 cells, siKRAS, replicate1

description: Library name: SW480_siKRAS1_S39


title: IPF35_UT_1

value: Lung

value: Primary Fibroblast


title: SW480 cells, siKRAS, replicate2

description: Library name: SW480_siKRAS2_S40


title: SW480 cells, siControl, replicate2

description: Library name: SW480_siCTRL2_S37


title: MFGR_1


title: IPF24_TGFb_3

value: Fibroblast


title: TGFb_Torin1_4

data_processing:
RNA-seq reads were pseudoaligned using Salmon v.1.10.1
The Salmon index was made with default parameters and the GENCODE (Release 45 (GRCh38.14) and was run in quant mode with default parameters
Assembly: hg38
Supplementary files format and content: sf

growth_protocol: primary normal human lung fibroblasts (HLFs) were grown in DMEM containing 0.1% bovine serum albumin, 5.5mM glucose, 2 mM glutamine, and 1mM pyruvate for 24 hours

treatment_protocol: For inhibition of ATF4, HLFs were transfected with ON-TARGETplus siRNA (Dharmacon). Cells were plated on 10cm dishes for 24 hours and then replated for experiments as growth protocol. For inhibition of mTOR, HLFs were treated with TORIN1 (R&D Systems) 30 minutes prior to treatment of TGF-beta or left untreated. HLFs were treated with TGF-beta (Peprotech) or left untreated.

value: wt

value: TGF-beta + Torin4


title: MCD_4

value: control male

value: Perirenal Differentiated Preadipocytes

value: Differentiated to Mature Adipocytes


title: SW480 cells, siControl, replicate1

description: Library name: SW480_siCTRL1_S36

value: siControl


title: IPF24_TGFb_2

value: HPLM + TGFb

value: IPF

value: Male


title: TGFb_Torin1_3

value: TGF-beta + Torin3


title: MCD_3

value: male


title: TGFb_Torin1_2

value: TGF-beta + Torin2


title: MCD_1


title: IPF24_UT_3

value: HPLM


title: MC_3

value: Perirenal Preadipocytes

value: Control


title: Torin1_3

value: Lung

value: Primary Fibroblast


title: Torin1_2

value: Fibroblast

value: wt


title: Torin1_1


title: Torin1_4


title: IPF24_UT_2


title: MC_4

value: control male


title: TGFb_2

value: TGF-beta


title: MCD_2

value: Perirenal Differentiated Preadipocytes

value: Differentiated to Mature Adipocytes


title: IPF24_TGFb_1

value: HPLM + TGFb


title: IPF24_UT_1

value: IPF


title: MC_2


title: Male71_TGFb_3

value: Male


title: TGFb_4


title: TGFb_3


title: TGFb_1


title: UT_4


title: Male71_TGFb_2


title: UT_3


title: UT_2


title: UT_1


title: Male71_TGFb_1


title: TGFb_Torin1_1

value: TGF-beta + Torin1


title: Shp-21-Day-6

description:
Library name: Sample 31
Merged_counts_ILMN1656.txt
24_Shp-21-Day-6_S62_L002

data_processing:
Data is mapping to genome UCSC mm10 or GRCH38 using STAR software
Assembly: UCSC mm10; GRCH38
Supplementary files format and content: txt; counts

value: MPNST Tumor Tissue

value: WT

value: SHP099 treated

value: 21 days


title: siATF4_TGFb_3

value: ATF4KD + TGFb


title: MC_1

value: male

value: Perirenal Preadipocytes

value: Control


title: siATF4_TGFb_2

value: Lung

value: Primary Fibroblast

value: Fibroblast

value: wt


title: Male71_UT_3

value: HPLM


title: Shp-21-Day-2

description:
Library name: Sample 29
Merged_counts_ILMN1656.txt
20_Shp-21-Day-2_S58_L002


title: siATF4_TGFb_1


title: siATF4_UT_3


title: Male71_UT_2


title: siATF4_UT_2


title: VEH-5-Day-1

description:
Library name: Sample 28
Merged_counts_ILMN1656.txt
15_VEH-5-Day-1_S53_L002

value: Vehicle Control

value: 5 days


title: Male53_TGFb_3

value: HPLM + TGFb

value: Male


title: siControl_TGFb_2

value: Control KD + TGFb


title: siControl_TGFb_1


title: Shp-5-Day-2

description:
Library name: Sample 30
Merged_counts_ILMN1656.txt
2_Shp-5-Day-2_S42_L002

value: MPNST Tumor Tissue

value: WT


title: siControl_TGFb_3


title: Shp-5-Day-4

description:
Library name: Sample 27
Merged_counts_ILMN1656.txt
4_Shp-5-Day-4_S44_L002

value: SHP099 treated


title: Male53_TGFb_2


title: siControl_UT_3

value: Control KD


title: siATF4_UT_1


title: siControl_UT_1


title: Male53_TGFb_1


title: Shp-21-Day-3

description:
Library name: Sample 25
Merged_counts_ILMN1656.txt
21_Shp-21-Day-3_S59_L002

value: 21 days


title: Male53_UT_3


title: in situ Hi-C on CyT49 differentiated to definitive endoderm with MboI - 4DNEXVGPPF1H

city: Boston

last: DCIC

state: MA

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

description:
lab: Bing Ren, UCSD
award: 1U54DK107977-01
4DN accession: 4DNEXVGPPF1H
pcr_cycles: 11
submitted_by: Bin Li
ligation_time: 240
biotin_removed: Yes
digestion_time: 920
tagging_method: biotin-14-dATP
experiment_type: in situ Hi-C
ligation_volume: 0.95
digestion_enzyme: MboI
crosslinking_time: 10
biosample_quantity: 2000000 cells
crosslinking_method: 1% Formaldehyde
fragment_size_range: 150-500
fragmentation_method: sonication
ligation_temperature: 20
average_fragment_size: 300
digestion_temperature: 37
crosslinking_temperature: 20
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXVGPPF1H/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/10c31789-03db-45e5-9e45-b761a72812b5/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIQA17XX1.bam, 4DNFI9OAHK5E.bam, 4DNFIGPYHYZ2.bam, 4DNFIPYJ6JX4.bam, 4DNFISZX8LAZ.bam, 4DNFIDK1LXL4.bam, 4DNFI1FPC9QS.bam, 4DNFISCG5MEV.bam, 4DNFI68DEZKJ.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFI4LG5248.pairs.gz

source_name: biosource_summary: CyT49 differentiated to definitive endoderm

growth_protocol:
url: https://www.ncbi.nlm.nih.gov/pubmed/18288110
description: Kroon et al. 2008 describes differentiation of human embryonic stem cells to pancreatic endoderm

extract_protocol:
description: The Official 4DN Standard in situ Hi-C protocol adapted from Rao et al. 2014 PMID: 25497547 - with accepted deviations approved by SC 02/21/2017
download: https://data.4dnucleome.org/protocols/fdc20e37-f22e-42dc-8026-0a132739bad1/@@download/attachment/4DN_in_situ_Hi-C_protocol_20170729.pdf

value: definitive endoderm

value: male

value: in vitro differentiated cells

tag: url

value: embryonic


title: Shp-21-Day-5

description:
Library name: Sample 26
Merged_counts_ILMN1656.txt
23_Shp-21-Day-5_S61_L002

extract_protocol:
Extract protocol - Primary tumors were dissected and minced into small tissue blocks, and then were dissociated by using a gentleMACS Octo Dissociator (Miltenyi Biotec) and 1g/ml collagenase (Sigma-Aldrich, Cat# C8051), following the preset protocol. The dissociated cells were washed in PBS 3 times and treated with blood cell lysate buffer (Sigma-Aldrich, Cat# R7757).
RNA was extracted from mice with NP mutant MPNST tumors treated with SHP2i for 5 or 20-28 days (n=3 animals each). RNA was extracted from a 20-30 mg portion of  flash-frozen NP mutant MPNST tumor tissue using the Qiagen RNeasy Plus kit following the manufacturer’s protocol. Tissue homogenization/disruption was by mortar and pestle and Buffer RLT Plus supplemented with beta-mercaptoethanol followed by passing homogenized samples over Qiagen QIAshredder columns. Qiagen RNase-Free DNase Set was used for on-column DNA digestion. Total RNA was submitted to the IU Center for Medical Genomics (CMG) for library preparation and sequencing. Total RNA was first evaluated for its quantity and quality using an Agilent Bioanalyzer 2100. A RIN number of above 8 was achieved for all samples. One hundred nanograms of total RNA was used. cDNA library preparation included mRNA purification/enrichment, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification, following the KAPA mRNA Hyper Prep Kit Technical Data Sheet, KR1352 – v4.17 (Roche Corporate). Each resulting indexed library was quantified, its quality was accessed by Qubit and Agilent Bioanalyzer, and multiple libraries were pooled at equal molarity. Pooled libraries were then denatured and neutralized before loading onto a NovaSeq 6000 sequencer at 300pM final concentration for 100bp paired-end sequencing (Illumina, Inc.). Approximately 30-40M reads per library were generated. was used to measure the quality of sequencing. More than 90% of the sequencing reads reached a Phred quality score Q30 of (99.9% base call accuracy)


title: Male53_UT_2

value: Lung

value: Primary Fibroblast

value: Fibroblast

value: Control


title: in situ Hi-C on CyT49 with MboI - 4DNEXFRAFIWZ

description:
lab: Bing Ren, UCSD
award: 1U54DK107977-01
4DN accession: 4DNEXFRAFIWZ
pcr_cycles: 11
submitted_by: Bin Li
ligation_time: 240
biotin_removed: Yes
digestion_time: 920
tagging_method: biotin-14-dATP
experiment_type: in situ Hi-C
ligation_volume: 0.95
digestion_enzyme: MboI
crosslinking_time: 10
biosample_quantity: 2000000 cells
crosslinking_method: 1% Formaldehyde
fragment_size_range: 150-500
fragmentation_method: sonication
ligation_temperature: 20
average_fragment_size: 300
digestion_temperature: 37
crosslinking_temperature: 20
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXFRAFIWZ/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/4aa56dd0-afaf-4944-8f59-1af4d7e0d0b4/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI8H6H4CR.bam, 4DNFIVTZNUUX.bam, 4DNFIARJZO5D.bam, 4DNFIJBB3PCN.bam, 4DNFI9YIG73F.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFIKGQSUNZ.pairs.gz

source_name: biosource_summary: CyT49

value: stem cell

value: stem cells


title: in situ Hi-C on CyT49 differentiated to definitive endoderm with MboI - 4DNEXLV2KQRB

description:
lab: Bing Ren, UCSD
award: 1U54DK107977-01
4DN accession: 4DNEXLV2KQRB
pcr_cycles: 11
submitted_by: Bin Li
ligation_time: 240
biotin_removed: Yes
digestion_time: 920
tagging_method: biotin-14-dATP
experiment_type: in situ Hi-C
ligation_volume: 0.95
digestion_enzyme: MboI
crosslinking_time: 10
biosample_quantity: 2000000 cells
crosslinking_method: 1% Formaldehyde
fragment_size_range: 150-500
fragmentation_method: sonication
ligation_temperature: 20
average_fragment_size: 300
digestion_temperature: 37
crosslinking_temperature: 20
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXLV2KQRB/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/9cd8f805-2747-4a63-a8df-bc0afa83cca4/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIFNNHM1L.bam, 4DNFIRX7JVEB.bam, 4DNFIOFC1OH5.bam, 4DNFIJI2VXGN.bam, 4DNFII26ENWX.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFIKZHGYEO.pairs.gz


title: Male71_UT_1

value: HPLM

value: Male


title: Shp-5-Day-1

description:
Library name: Sample 24
Merged_counts_ILMN1656.txt
1_Shp-5-Day-1_S41_L002

value: MPNST Tumor Tissue

value: 5 days


title: in situ Hi-C on CyT49 with MboI - 4DNEX94DX4XP

description:
lab: Bing Ren, UCSD
award: 1U54DK107977-01
4DN accession: 4DNEX94DX4XP
pcr_cycles: 11
submitted_by: Bin Li
ligation_time: 240
biotin_removed: Yes
digestion_time: 920
tagging_method: biotin-14-dATP
experiment_type: in situ Hi-C
ligation_volume: 0.95
digestion_enzyme: MboI
crosslinking_time: 10
biosample_quantity: 2000000 cells
crosslinking_method: 1% Formaldehyde
fragment_size_range: 150-500
fragmentation_method: sonication
ligation_temperature: 20
average_fragment_size: 300
digestion_temperature: 37
crosslinking_temperature: 20
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEX94DX4XP/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/9f507bad-0b75-447e-8e75-04e93e6bce71/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI3J24YBH.bam, 4DNFIODA78ZP.bam, 4DNFIK9SZD33.bam, 4DNFI1T8E4KU.bam, 4DNFIYSQSPA2.bam, 4DNFIXB3NTLU.bam, 4DNFIDYXY4QW.bam, 4DNFI2U1JM5V.bam, 4DNFIMCZEPR5.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFI9VR75SS.pairs.gz


title: Shp-5-Day-3

description:
Library name: Sample 22
Merged_counts_ILMN1656.txt
3_Shp-5-Day-3_S43_L002

value: WT

value: SHP099 treated


title: Male24_TGFb_3

value: HPLM + TGFb


title: VEH-5-Day-2

description:
Library name: Sample 23
Merged_counts_ILMN1656.txt
16_VEH-5-Day-2_S54_L002

value: Vehicle Control


title: siControl_UT_2

value: wt

value: Control KD


title: Male53_UT_1


title: ovary_OA_rep3

city: Norwich

first: David

middle: C.

last: Prince

address: Norwich Research Park

country: United Kingdom

institute: University of East Anglia

description: NEL0067581_exp1a_ovary_all_expressed_genes.csv

data_processing:
Sequencing reads were pseudoaligned to the Bombus terrestris transcriptome using Kallisto v0.46.1 with parameters --single -l 200 -s 20
Estimated transcript counts were summarised per gene for brain, fat body and ovary samples in R v4.1.3 using the tximport package v1.22.0 with parameter type="kallisto". For egg samples, the parameter countsFromAbundance = "scaledTPM" was used.
Differential expression analysis was conducted on brain, fat body and ovary samples in R v4.1.3 using the DESeq2 package v1.34.0, with technical replicates (sequencing the same library on different lanes of the sequencing machine) collapsed using the collapseReplicates() function.
Assembly: Bombus_terrestris.Bter_1.0.cdna.all.fa
Supplementary files format and content: CSV file with scaled TPM counts from tximport for all genes expressed in eggs
Supplementary files format and content: CSV file with normalized abundance measurements from DESeq2 for all genes expressed in brain
Supplementary files format and content: CSV file with normalized abundance measurements from DESeq2 for all genes expressed in fat body
Supplementary files format and content: CSV file with normalized abundance measurements from DESeq2 for all genes expressed in ovary

organism: Bombus terrestris

source_name: ovary

extract_protocol:
B. terrestris workers were quickly dissected on ice to minimize RNA degradation, with the brains and ovary being stored in RNAlater (Sigma-Aldrich) and the fat body being stored in AllProtect (Qiagen). Tissue from seven individuals were pooled together to make a sample. Samples were ground in liquid nitrogen using a 2 ml pestle (Eppendorf) and the powder resuspended in Tri-Reagent (Ambion). The RNA was then extracted using a Direct-zolTM RNA extraction kit (Zymo Research), including an on-column DNase treatment. The eluted RNA was further treated with TurboTM DNase (Ambion). The same protocol was used for preparation of RNA from eggs.
Standard mRNA-seq was conducted for the brain, fat body and ovary samples by Edinburgh Genomics (The University of Edinburgh, Edinburgh, UK) on an Illumina HiSeq 2500 sequences using Illumina TruSeq adapters. The two egg mRNA-seq libraries were constructed and sequenced by Baseclear (Leiden, The Netherlands) using an Illumina HiSeq 2500 sequences with Illumina TruSeq adapters.

treatment_protocol: Bombus terrestris audax colonies were reared in wooden boxes (300 x 200 x 170 mm) in constant darkness at 28oC and 60% humidity, and were supplied with sugar solution and pollen ad libitum.

value: ovary

tag: phenotype

value: active ovaries


title: VEH-5-Day-4

last: Dang

address: 2720 S Moody Ave

description:
Library name: Sample 21
Merged_counts_ILMN1656.txt
18_VEH-5-Day-4_S56_L002

source_name: MPNST Tumor Tissue


title: Male24_TGFb_1

value: Lung

value: Primary Fibroblast


title: egg_rep2

source_name: egg

value: egg


title: in situ Hi-C on CyT49 differentiated to pancreatic endoderm with MboI - 4DNEXON87MIM

description:
lab: Bing Ren, UCSD
award: 1U54DK107977-01
4DN accession: 4DNEXON87MIM
pcr_cycles: 11
submitted_by: Bin Li
ligation_time: 240
biotin_removed: Yes
digestion_time: 920
tagging_method: biotin-14-dATP
experiment_type: in situ Hi-C
ligation_volume: 0.95
digestion_enzyme: MboI
crosslinking_time: 10
biosample_quantity: 2000000 cells
crosslinking_method: 1% Formaldehyde
fragment_size_range: 150-500
fragmentation_method: sonication
ligation_temperature: 20
average_fragment_size: 300
digestion_temperature: 37
crosslinking_temperature: 20
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXON87MIM/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/af3a5ccb-ed67-4d49-b305-9943605f1e20/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI8YWYODK.bam, 4DNFI5GJ2MWB.bam, 4DNFI1Z3DZIV.bam, 4DNFIL1C5AYT.bam, 4DNFI98BYYN2.bam, 4DNFIWM1YSXF.bam, 4DNFI3YTCD8P.bam, 4DNFIC592UTJ.bam, 4DNFIOQ4MSIV.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFIELSHHII.pairs.gz

source_name: biosource_summary: CyT49 differentiated to pancreatic endoderm

value: pancreatic endoderm

value: male

value: in vitro differentiated cells

value: embryonic


title: egg_rep1


title: Male24_TGFb_2

value: Fibroblast

value: Control

value: Male


title: in situ Hi-C on CyT49 differentiated to endoderm of foregut with MboI - 4DNEX3JHGDNA

description:
lab: Bing Ren, UCSD
award: 1U54DK107977-01
4DN accession: 4DNEX3JHGDNA
pcr_cycles: 11
submitted_by: Bin Li
ligation_time: 240
biotin_removed: Yes
digestion_time: 920
tagging_method: biotin-14-dATP
experiment_type: in situ Hi-C
ligation_volume: 0.95
digestion_enzyme: MboI
crosslinking_time: 10
biosample_quantity: 2000000 cells
crosslinking_method: 1% Formaldehyde
fragment_size_range: 150-500
fragmentation_method: sonication
ligation_temperature: 20
average_fragment_size: 300
digestion_temperature: 37
crosslinking_temperature: 20
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEX3JHGDNA/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/084a2a71-c014-47f2-8339-e0de133f4819/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI2YVAEVW.bam, 4DNFICZGF6PJ.bam, 4DNFI5A9593L.bam, 4DNFIK46HCP1.bam, 4DNFICCNB3J6.bam, 4DNFIT6VXTHS.bam, 4DNFIZYZ1X3D.bam, 4DNFIM254J46.bam, 4DNFIRHY7T6O.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFIZ1BMAHE.pairs.gz

source_name: biosource_summary: CyT49 differentiated to endoderm of foregut

value: endoderm of foregut