title: Glioma-005 aCTLA4 TILs TCR

city: La Jolla

first: Kathryn

last: Lande

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

data_processing:
The generated scRNA-seq data were aligned and quantified using the Cell Ranger Single-Cell toolkit (version 3.0.2) against the mm10 mouse reference genome. The preliminary filtered data generated from Cell Ranger were used for downstream analysis. The TCR sequence data from 10X Genomics was processed using Cell Ranger software (version 3.1) with the manufacturer-supplied mouse VDJ reference genome.
Assembly: mm10
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5
Supplementary files format and content: CellRanger output files: clonotypes.csv

extract_protocol:
Single cell suspension of glioma-005 cell line was stereotactically injected into the hippocampus of 8- to 12-week-old C57BL/6J mice. 7 days after tumor implantation, mice were randomly divided into groups and injected with antibodies αCTLA-4 (Syrian hamster clone 9H10), Isotype control antibodies rat IgG2a (clone LTF-2) and depletion antibody aCD4 (clone GK1.5) were administered intraperitoneally (i.p.) . All mice were perfused with ice-cold PBS after euthanasia to reduce the influence of peripheral blood derived cells. All the brains were collected in ice-cold PBS, and then mechanically and enzymatically dissociated using a papain-based neural tissue dissociation kit P (Miltenyi Biotec) supplemented with 0.1% type I collagenase (Thermo Fisher Scientific) in a C-tube (Miltenyi Biotec), and then dissociated with a gentleMACS Qcto Dissociator, followed by filtration with 70 µm cell strainers. Filtered cells were incubated with ACK lysis buffer (Invitrogen) to lyse red blood cells. For immune cell suspension, filtered cells were resuspended in 5 mL 37% Percoll, and slowly added beneath the 70% Percoll, and then centrifuged with brakes off. The immune cells were isolated from the interface of 37% and 70% Percoll and transferred into excessive RPMI 1640 medium containing 10% fetal bovine serum. scRNAseq and scTCRseq were performed in brain harvested T cells from 005 bearing mice treated with IgG or αCTLA-4 (35 days post implantation). CD3+ cells were sorted and immediately loaded onto a 10x Chromium Chip G using reagents from the Chromium Single-Cell 5’ Library and Gel Bead Kit v1.1 (10x Genomics) according to the manufacturer’s protocol. 5’ gene expression libraries were generated using 10X Genomics Chromium Single Cell 5’ Library Construction Kits according to manufacturer protocols. TCR enrichment libraries were prepared following mouse T cell Single Cell V(D)J Enrichment Kits (10x Genomics).
10x Chromium Single cell 5’ + VDJ Library

tag: library type

value: V(D)J


title: 4T1 cells - NSi_heavy_rep2

status: Public on Jun 01 2023

type: SRA

city: New York

first: Robert

middle: J

last: Schneider

state: NY

address: 550 First Ave, MSB 238

department: Microbiology

country: USA

institute: NYU School of Medicine

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Bowtie used to align the reads to the reference, and the aligned reads were counted per gene.
DGE and translational efficiency were calculated using RIVET (Ernlund etal, BMC Gen, 2018)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

molecule: total RNA

organism: Mus musculus

source_name: breast cancer cells

growth_protocol: Cells were passaged whenevr they reached 70% confluency.

extract_protocol:
Sucrose gradients were run; RNA was extracted using Trizol, heavy and light fractions were combined aacordinlgy and cleaned through Zymo clean and concentrate.
Illumina automated stranded RNA-seq library prep, polyA selection

treatment_protocol: Doxycycline (2ug/ml) induction for 6 days

tag: cell type

value: 4T1 TNBC breast cancer cells

tag: strain

value: BALB/c

tag: molecule

value: heavy polysome fraction polyA RNA


title: 4T1 cells - shDap5_heavy_rep1


title: hiPSCs, myogenic_diff, DMD, Day14, plate1

city: Nantes

first: Jean-Baptiste

last: Dupont

address: 22 boulevard Benoni Goullin

department: INSERM

country: France

institute: Nantes Université

description: sci-RNA-Seq

library_source: transcriptomic single cell

data_processing:
basecalling (bcl2fastq v 2.16.0.10)
demultiplexing based on the P5 barcode
adaptor trimming (trim_galore v 0.4.5)
alignment to the human genome (STAR v 2.5.2b)
demultiplexing based on RT barcodes
secondary analysis (monocle 2 and 3,as published by Qiu et al. 2017, Nature Methods, DOI: 10.1038/nmeth.4402; http://cole-trapnell-lab.github.io/monocle-release/)
Assembly: hg19
Supplementary files format and content: matrix of expression values aggregated in a csv (.csv) file
Supplementary files format and content: cell and feature (gene) informations providede as csv files

organism: Homo sapiens

source_name: hiPSCs

growth_protocol: Myogenic differentiation protocol as published by Chal et al. 2016, Nature Protocols, DOI: 10.1038/nprot.2016.110

extract_protocol:
Cells were detached with Trypsin-EDTA + collagenase IV and resuspended in DPBS prior to fixation and permeabilization with pre-chilled 100 % methanol
single-cell combinatorial indexing RNA-Seq (sci-RNA-Seq) as published by Cao et al. (2017) Science (DOI: 10.1126/science.aam8940)

tag: tissue

value: hiPSCs

tag: cell line

tag: condition

tag: genotype

value: DMD


title: hiPSCs, myogenic_diff, DMD, Day10, plate1

description: sci-RNA-Seq


title: 4T1 cells - shDap5_light_rep3

value: light polysome fraction polyA RNA


title: Glioma-005 aCTLA4 TILs RNA

state: CA

value: mRNA


title: hiPSCs, myogenic_diff, DMD, Day22, plate1

description: sci-RNA-Seq


title: hiPSCs, myogenic_diff, DMD, Day18, plate1

description: sci-RNA-Seq


title: hiPSCs, myogenic_diff, DMD, Day7, plate1

description: sci-RNA-Seq


title: hiPSCs, myogenic_diff, DMD, Day4, plate1

description: sci-RNA-Seq


title: 4T1 cells - NSi_heavy_rep1


title: Glioma-005 IgG TILs RNA


title: Glioma-005 IgG TILs TCR

library_source: genomic

molecule: genomic DNA


title: Normal Brain

description:
10x Genomics
DC3-Normalbrain

data_processing:
The generated scRNA-seq data were aligned and quantified using the Cell Ranger Single-Cell toolkit (version 3.0.2) against the mm10 mouse reference genome. The preliminary filtered data generated from Cell Ranger were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: Cellranger output files: Tab-separated values files and matrix files

source_name: Healthy Brain

extract_protocol:
Single cell suspension of glioma-005 cell line was stereotactically injected into the hippocampus of 8- to 12-week-old C57BL/6J mice. 7 days after tumor implantation, mice were randomly divided into groups and injected with antibodies αCTLA-4 (Syrian hamster clone 9H10), Isotype control antibodies rat IgG2a (clone LTF-2) and depletion antibody aCD4 (clone GK1.5) were administered intraperitoneally (i.p.) . All mice were perfused with ice-cold PBS after euthanasia to reduce the influence of peripheral blood derived cells. All the brains were collected in ice-cold PBS, and then mechanically and enzymatically dissociated using a papain-based neural tissue dissociation kit P (Miltenyi Biotec) supplemented with 0.1% type I collagenase (Thermo Fisher Scientific) in a C-tube (Miltenyi Biotec), and then dissociated with a gentleMACS Qcto Dissociator, followed by filtration with 70 µm cell strainers. Filtered cells were incubated with ACK lysis buffer (Invitrogen) to lyse red blood cells. For immune cell suspension, filtered cells were resuspended in 5 mL 37% Percoll, and slowly added beneath the 70% Percoll, and then centrifuged with brakes off. The immune cells were isolated from the interface of 37% and 70% Percoll and transferred into excessive RPMI 1640 medium containing 10% fetal bovine serum.Microglia (CD45intCX3CR1+), myeloid cells (CD45hiCD11b+), T cells (CD45hiCD3+) and all remaining immune cells (CD45hiCD11b-CD3-) were sorted from normal brain and 005 glioma-bearing brains treated with IgG, αCTLA-4, or αCTLA-4 combined with CD4 depletion. Cells from each treatment group were pooled at equal ratios and then subjected to scRNA-seq. Sorted cells were partitioned into an emulsion of nanoliter-sized droplets using a 10x Genomics Chromium Single Cell Controller and RNA sequencing libraries were constructed using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10X Genomics, Cat# PN-120237)
10x Chromium Single cell 3’

value: Healthy Brain


title: 4T1 cells - shDap5_light_rep2


title: hiPSCs, myogenic_diff, DMD, Day2, plate1

description: sci-RNA-Seq


title: 4T1 cells - shDap5_light_rep1


title: Glioma-005 IgG

description:
10x Genomics
DC3-IgG_S1


title: 4T1 cells - NSi_light_rep3


title: hiPSCs, myogenic_diff, DMD, Day1, plate1

description: sci-RNA-Seq


title: 4T1 cells - NSi_light_rep2


title: hiPSCs, myogenic_diff, DMD, Day0, plate1

description: sci-RNA-Seq


title: P1210R

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

data_processing:
Base calls were generated in real-time on the NovaSeq6000 instrument (RTA 3.1.5); (2) demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4); (3) sequence read and base quality are checked using the FASTX-toolkit (v0.0.13); (4) sequences are aligned to GRCh38 with reference transcriptome GENCODE release 29 using STAR (v2.6.1d) and RSEM (v1.3.1).
Briefly, 100bp paired-end reads were trimmed and aligned to the GENCODE reference transcriptome using STAR and reads were quantified using HT-Seq. Gene counts were generated for each sample and collated into a singular matrix for fixed-effects regression model in DESeq2.
Assembly: GrCh38, GENCODE release 29
Supplementary files format and content: "Pheno.csv" contains sample metadata, "counts.csv" contains raw counts, "SummaryStats.csv" contains the number and percentages of reads mapped for each sample

molecule: polyA RNA

source_name: Right Colon

growth_protocol: Normal 3D colon organoids included in the study were developed from biopsies of proximal or distal colon using a modification of the method described by Sato et al. After isolation, colon crypts were embedded in Matrigel, and cell lines were established in growth media that included: advanced DMEM/F-12, 100U/ml penicillin, 100μg/ml streptomycin, 10mM Hepes, 1x N2, 1x B27, 2mM GlutaMAX, 1mM N-acetyl-cysteine, 10mM gastrin, 50% L-WRN conditioned media, 500nM A83-01, 10uM SB202190, 10mM nicotinamide, 50ng/ml EGF, 10μM Y27632. Colon organoids were grown and passaged as needed in 48-well culture plates.

extract_protocol:
For RNA isolation, media was gently removed and 300μl RNA lysis Solution RA1 + 6μl TCEP (Machery-Nagel; Cat No: 740902.50) was added to each well. The lysate was collected in a 1.5ml Eppendorf tube. Each tube was vortexed vigorously and placed on ice. Further steps were carried out according to manufacturer’s protocol of the Machel-Nagel RNA XS kit. RNA was checked for quality using the Agilent 4200 Tapestation. Samples with RIN > =8.5 were considered for library preparation and sequencing using the Illumina NovoSeq
Total RNA is normalized to 7.5ng/ul in a total volume of 50ul on the Perkin Elmer Janus Workstation (Perkin Elmer, Janus II). Poly-A selection and cDNA synthesis are performed using the TruSeq Stranded mRNA kit as outlined by the manufacturer (Illumina, cat#RS-122-2103).  All steps are automated on the Perkin Elmer Sciclone NGSx Workstation to reduce batch to batch variability and to increase sample throughput.  Final RNASeq libraries are quantified using the Quant-it dsDNA High Sensitivity assay, and library insert size distribution is checked using a fragment analyzer (Advanced Analytical; kit ID DNF474).  Samples where adapter dimers constitute more than 4% of the electopherogram area are failed prior to sequencing.  Technical controls (K562,Thermo Fisher Scientific, cat# AM7832), are compared to expected results to ensure that batch to batch variability is minimized.  Successful libraries are normalized to 10nM for submission to sequencing.
Libraries were multiplexed and sequenced on Illumina Novaseq6000 to generate 100bp PE reads.

value: Right Colon

value: Colon Organoid

tag: Sex

value: Female

tag: phenotype

value: Healthy

tag: age

tag: smoking

value: Never

tag: sample type

value: RNA-sequencing


title: P1215R

value: Lynch

value: Former/Current


title: 4T1 cells - NSi_light_rep1


title: Glioma-005 anti_CTLA4+ CD4_depletion

description:
10x Genomics
DC3-CD4_S3


title: P1202R


title: hiPSCs, myogenic_diff, Healthy, Day28, plate2

description: sci-RNA-Seq

value: UC3-4 Healthy

value: WT


title: hiPSCs, myogenic_diff, Healthy, Day22, plate2

description: sci-RNA-Seq


title: P1183R


title: 4T1 cells - shDap5_input_rep3

value: 4T1 TNBC breast cancer cells

value: BALB/c

value: polyA RNA


title: Dnmt1_ko1

city: Beijng

first: Chuanrong

last: Zhao

address: 38 Xue yuan Road, Peking University Health Science Center

department: School of Basic Medical Sciences

country: China

institute: Peking University

data_processing:
Cluster was generated using cBot Cluster Generation System with TruSeq PE Cluster Kit v3-cBot-HS (Illumia).
After cluster generation, sequencing was performed on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the mus musculus genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: RNA-seq data.txt
Supplementary files format and content: tab-delimited text file of 2,750 genes differentially expressed (2750.txt)

source_name: Peritoneal macrophage

extract_protocol:
Total RNA from the Dnmt1KO and Dnmt1fl/fl peritoneal macrophages was extracted using the RNeasy kit with DNase treatment (Qiagen) and RNA integrity (RIN > 9) was checked by a Bioanalyzer 2100 system (Agilent Technologies).
cDNA libraries were constructed using the NEBNext UltraTM RNA Library Prep Kit according to the manufacturer’s instructions (Illumina).

value: Peritoneal macrophage

value: No

value: macrophage

value: myeloid-specific Dnmt1 knockout

tag: treatment

value: isolate


title: Dnmt1_ko2


title: P1143R

value: Right Colon

value: Colon Organoid


title: Dnmt1_f_f2

value: wt


title: hiPSCs, myogenic_diff, Healthy, Day18, plate2

description: sci-RNA-Seq

value: hiPSCs


title: P1229R

value: Female

value: Healthy

value: Never

value: RNA-sequencing


title: hiPSCs, myogenic_diff, Healthy, Day14, plate2

description: sci-RNA-Seq

value: UC3-4 Healthy

value: WT


title: 4T1 cells - shDap5_input_rep1

value: 4T1 TNBC breast cancer cells

value: BALB/c


title: 4T1 cells - shDap5_input_rep2

value: polyA RNA


title: P1135R

value: Lynch


title: 4T1 cells - NSi_input_rep3


title: P1122R


title: hiPSCs, myogenic_diff, Healthy, Day10, plate2

description: sci-RNA-Seq


title: Glioma-005 anti_CTLA4 sample1

description:
10x Genomics
DC3-CTLA4_S2


title: Dnmt1_f_f1

value: Peritoneal macrophage

value: No

value: macrophage


title: P1117R

value: Right Colon

value: Former/Current


title: 4T1 cells - NSi_input_rep2


title: hiPSCs, myogenic_diff, Healthy, Day7, plate2

description: sci-RNA-Seq


title: MWT00-2683: Gulo +/+ wildtype male mouse with no ascorbate supplementation

city: Québec

first: Antoine

last: BODEIN

state: QC

address: 2705 bd Laurier

country: Canada

institute: Université Laval

data_processing:
read trimmig with fastp (v0.20.0)
read alignement with Kallisto (v0.46.2)
Assembly: Ensembl Mus musculus release 104
Supplementary files format and content: tab-delimited text file with TPM

source_name: liver

extract_protocol:
Total RNA was extracted using the miRNeasy Mini kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions
NEBNext Ultra II directional RNA library prep kit for Illumina following the manufcturer's protocol

value: liver

value: liver cell type

value: Male

value: Wildtype

value: no vitC supplementation


title: MWT00-2682: Gulo +/+ wildtype male mouse with no ascorbate supplementation


title: hiPSCs, myogenic_diff, Healthy, Day4, plate2

description: sci-RNA-Seq

value: hiPSCs


title: MWT00-2677: Gulo +/+ wildtype male mouse with no ascorbate supplementation


title: Zak-KO-48h

city: Shang Hai

first: Yan

last: Wang

address: Yue yang Road 320

institute: Chinese Academy of Science

data_processing:
Transcriptomic reads from the RNA-Seq experiments were mapped to a reference genome (mm10) using Bowtie.
Gene expression levels were quantified using the RSEM software package.
Differentially expressed genes were subsequently analyzed using the DAVID bioinformatics platformand IPA.
Genome_build: mm10
Supplementary_files_format_and_content: gene expression FPKM

source_name: Zak-KO_CD4+ T cells

growth_protocol: The 6-8-week-old wild-type and T cells-conditional deficient mice were sacrificed, and primary T cells were isolated from the spleen and lymph nodes. Naive CD4+CD44loCD62Lhi T cells were purified by flow cytometry and clutured for 0, 6 or 48 hours in RPMI medium supplemented with anti-CD3 and anti-CD28.

extract_protocol:
RNA was harvested using Trizol reagent followed by RNeasy Mini kit (Qiagen) cleanup. Total RNA was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Stimulated with anti-CD3 and anti-CD28 for 0, 6 or 48 hours

tag: strain background

value: Zak-/-

value: spleen and lymph nodes

value: CD4+ T cells

value: Stimulated with α-CD3/28 for 48 h


title: hiPSCs, myogenic_diff, Healthy, Day2, plate2

description: sci-RNA-Seq

value: UC3-4 Healthy

value: WT


title: P1111R

value: Colon Organoid

value: Female

value: Lynch

value: Never

value: RNA-sequencing


title: MGLR40-2831: Gulo -/- female mouse treated with added back 0.40% vitC from 2 months ascorbate removal

value: liver

value: Gulo -/-

value: 0.40% vitC  supplementation


title: P1109R

value: Right Colon

value: Healthy


title: Zak-KO-0h

value: Stimulated with α-CD3/28 for 0 h


title: P1102R


title: hiPSCs, myogenic_diff, Healthy, Day1, plate2

description: sci-RNA-Seq

value: hiPSCs


title: MGLR40-2828: Gulo -/- male mouse treated with added back 0.40% vitC from 2 months ascorbate removal

value: liver cell type

value: Male


title: hiPSCs, myogenic_diff, Healthy, Day0, plate2

description: sci-RNA-Seq


title: P1082R

value: Former/Current


title: WT-48h

source_name: WT_CD4+ T cells

value: wild type

value: spleen and lymph nodes

value: CD4+ T cells

value: Stimulated with α-CD3/28 for 48 h


title: P1086R

value: Colon Organoid

value: Female

value: Lynch


title: hiPSCs, myogenic_diff, Healthy, Day28, plate1

description: sci-RNA-Seq

value: UC3-4 Healthy

value: WT


title: MGLR40-2829: Gulo -/- male mouse treated with added back 0.40% vitC from 2 months ascorbate removal

value: liver

value: Gulo -/-

value: 0.40% vitC  supplementation


title: hiPSCs, myogenic_diff, Healthy, Day18, plate1

description: sci-RNA-Seq


title: WT-6h

value: Stimulated with α-CD3/28 for 6 h


title: WT-0h

value: Stimulated with α-CD3/28 for 0 h


title: 4T1 cells - NSi_input_rep1

value: 4T1 TNBC breast cancer cells

value: BALB/c

value: polyA RNA


title: P1112R

value: Right Colon

value: Healthy

value: Never

value: RNA-sequencing


title: hiPSCs, myogenic_diff, Healthy, Day14, plate1

description: sci-RNA-Seq

value: hiPSCs


title: MGL40-2690: Gulo -/- male mouse treated with 0.40% vitC

value: liver cell type

value: Male


title: P1055R

value: Colon Organoid

value: Female


title: X11M_Old3-TCR

description: Stimulation with α-CD3/28 for 6 hours

data_processing:
Transcriptomic reads from the RNA-Seq experiments were mapped to a reference genome (GRCm38/mm10) using Bowtie.
Gene expression levels were quantified using the RSEM software package.
Differentially expressed genes were subsequently analyzed using the DAVID bioinformatics platformand IPA and GraphPad.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Processed data were xls format and all samples gene expression FPKM  were contained in the xls file.

source_name: CD4+ T cells

growth_protocol: The 6-8-week-old young and11-month-old aged wild-type mice were sacrificed, and primary T cells were isolated from the spleen and lymph nodes. CD4+ T cells were purified by flow cytometry and then clutured  for 6 hours in RPMI medium supplemented with anti-CD3 and anti-CD28.

extract_protocol:
RNA was harvested using RNeasy Mini kit (Qiagen) cleanup. Total RNA was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Stimulated for  6 hours with  anti-CD3 and anti-CD28

value: wild type

value: spleen and lymph nodes

value: CD4+ T cells


title: KP4 cells, Metformin+FK866-Replicate3

city: Montreal

first: Thulaj

last: Meharwade

address: 110 Pine Ave W,

department: Division of Systems Biology

institute: Montreal Clinical Research Institute

data_processing:
Galaxy version 22.05.rc1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt.
Trimmed sequence reads were mapped to Grch38/hg38 using RNA Star.
Read count extraction and normalization were performed using feature counts and DEseq2 respectively.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes normalized count values for each sample

growth_protocol: KP4 (Riken) were cultured in Dulbecco's modiﬁed Eagle's medium (DMEM) (Wisent, St-Bruno, QC) supplemented with 10 % of fetal bovine serum (FBS) (Wisent).

extract_protocol:
Cells were washed with PBS1X and collected in Trizol (#15596018, Invitrogen) and RNA extraction was performed using RNeasy® Mini Kit ( #74104, QIAGEN), according to the manufacturer’s instructions.
cDNA libraries for sequencing were prepared using the Kapa RNA HyperPrep Kit with RiboErase (Roche)  and UDI 96 indexes (Illumina). Sequencing was performed using NovaSeq 6000 flowcell S4 PE100.

treatment_protocol: KP4 cells were seeded in 6cm plates and treated with DMSO, Metformin 10 mM, FK866 5 nM or Metformin 10mM and FK866 5 nM for 24h.

value: Pancreatic ductal cell carcinoma

value: WT

tag: time


title: MGL40-2719: Gulo -/- male mouse treated with 0.40% vitC

value: liver

value: Gulo -/-

value: 0.40% vitC  supplementation


title: MGL05-2898: Gulo -/- male mouse treated with 0.05% vitC

value: 0.05% vitC  supplementation


title: X11M_Old2-TCR

description: Stimulation with α-CD3/28 for 6 hours


title: Zak-KO-6h

value: Zak-/-

value: Stimulated with α-CD3/28 for 6 h


title: hiPSCs, myogenic_diff, Healthy, Day10, plate1

description: sci-RNA-Seq

value: UC3-4 Healthy


title: MGL05-2897: Gulo -/- male mouse treated with 0.05% vitC


title: hiPSCs, myogenic_diff, Healthy, Day22, plate1

description: sci-RNA-Seq

value: hiPSCs


title: KP4 cells, Metformin+FK866-Replicate1


title: hiPSCs, myogenic_diff, Healthy, Day7, plate1

description: sci-RNA-Seq


title: MGL05-2890: Gulo -/- male mouse treated with 0.05% vitC

value: liver cell type


title: X1M_Young3-TCR

description: Stimulation with α-CD3/28 for 6 hours


title: X11M_Old1-TCR

description: Stimulation with α-CD3/28 for 6 hours


title: hiPSCs, myogenic_diff, Healthy, Day4, plate1

description: sci-RNA-Seq


title: KP4 cells, FK866-Replicate3


title: KP4 cells, FK866-Replicate2


title: X1M_Young2-TCR

description: Stimulation with α-CD3/28 for 6 hours


title: MGL01-2713: Gulo -/- male mouse treated with 0.01% vitC

value: Male

value: 0.01% vitC  supplementation


title: hiPSCs, myogenic_diff, Healthy, Day1, plate1

description: sci-RNA-Seq


title: KP4 cells, FK866-Replicate1


title: KP4 cells, Metformin-Replicate3

value: Metformin


title: MGL40-2691: Gulo -/- male mouse treated with 0.40% vitC


title: X1M_Young1-TCR

description: Stimulation with α-CD3/28 for 6 hours

value: wild type


title: MGL01-2711: Gulo -/- male mouse treated with 0.01% vitC


title: MGL00-2787: Gulo -/- male mouse without vitC intake

value: no vitC supplementation


title: hiPSCs, myogenic_diff, Healthy, Day0, plate1

description: sci-RNA-Seq


title: KP4 cells, Metformin+FK866-Replicate2


title: RH4-04

city: Sunnyvale

first: Xin

last: Zhou

state: CA - California

address: 3165 Porter Drive

department: Department of Genetics

institute: Stanford University

data_processing:
Sequencing reads were demultiplexed and mapped to the Homo sapiens genome assembly GRCh38 using software Cell Ranger V3.0 (10X Genomics). Mapped reads were aggregated into an expression matrix by Cell Ranger V3.0 (10X Genomics).
This matrix was loaded to R and a Seurat object was created using package “Seurat” V4.0.0. 40,029 cells were obtained for quality control. Doublets were removed by removing cells whose nFeature < 0.22*nCount – 170.
For samples using chemistry V2, cells with less than 13% mitochondrial genes and 2,100 unique genes with more than 1,100 reads were kept for downstream analysis. For samples using chemistry V3, cells with less than 20% of mitochondrial genes and 3,500 unique genes, with more than 2,100 reads were kept for downstream analysis. Cells expressing less than 50 housekeeping genes according to a relevant search [PMID: 27124452] were removed. 35,557 samples carrying 20,746 unique features were preserved for downstream analysis.
Clean data were transformed and aggregated using sct transform follow standard protocol. [PMID: 31870423] Briefly, the two batches (V2 chemistry and V3 chemistry) were integrated based on 3,000 selected features across all samples. Principal Components Analysis (PCA) was performed based on 2,000 most variable genes within the integrated dataset. Uniform Manifold Approximation and Projection (UMAP) based on 30 principal components was applied for visualizing cells in two dimensions. Clusters were called at resolution of 1.3 in Seurat using a shared nearest neighbor (SNN) modularity optimization-based clustering method. Representative gene markers of each cluster were calculated by building a logistic regression model for each unique gene in one cluster and then compare this with null model with a likelihood ratio test.
Assembly: Sequencing reads were demultiplexed and mapped to the Homo sapiens genome assembly GRCh38 using software Cell Ranger V3.0 (10X Genomics).
Supplementary files format and content: Matrix table with raw gene counts for every gene (Unique Molecular Identifier)

source_name: blood

extract_protocol:
PBMC were isolated by Ficoll-Paque (Histopaque™, Sigma Aldrich, St Louis, MO) from 15 mL of whole blood as previously described1. Enriched monocytes were isolated from peripheral blood mononuclear cells (PBMC) via two methods: Magnetic bead isolation and FACS sorting. Cells were diluted to 107 cells/mL for optimal viability and taken to the Stanford Genomic Core for scRNA seq processing as per the 10X Genomics specified protocol, briefly outlined below.
Cell Counting, GEM Generation and Barcoding: An aliquot of each cell suspension was stained with trypan blue. Concentration and viability were determined using the BioRad TC20 automated cell counter. Cells were counted for correct suspension volume for 5,000 cells total. Following addition of the 10X Master Mix™ (real time reagent mix, real time primer, Additive A and real time enzyme mix) to the Single Cell A Chip, cells were loaded into the same well. Single CellGel Bead suspension was added in a separate well on the chip, as well as the partitioning oil in a third separate well. The chip is covered with a gasket and loaded into the 10X Genomics Chromium™ Controller. Following the completion of the run, the GEMs are transferred into a PCR tube for amplification.
Library Preparation, and Sequencing: Single-cell libraries were prepared using the 10X Genomics Chromium 3’ Gene Expression Solution. The average fragment size of each completed library was determined using the Fragment Analyzer (Agilent). Final library concentration was determined using the Qubit High Sensitivity dsDNA Assay (Thermo Fisher). Libraries were normalized to a common concentration prior to being pooled and sequenced on the Illumina HiSeq-4000.

value: blood

value: PBMC

value: Control


title: KP4 cells, Metformin-Replicate2

value: Pancreatic ductal cell carcinoma

value: WT


title: RH4-02


title: KP4 cells, Metformin-Replicate1


title: C76

city: Nottingham

first: Akhil

last: Jain

address: University Park

country: United Kingdom

institute: University of Nottingham

data_processing:
The “Demultiplex QIAseq UPX 3’ reads” tool of the CLC Genomics Workbench 20.0.4 was used to demultiplex the raw sequencing reads according to the sample indices.
The “Quantify QIAseq UPX 3’ workflow” was used to process the demultiplexed sequencing reads with default settings.
The “Quantify QIAseq UPX 3’ workflow” was used to process the demultiplexed sequencing reads with default settings. In short, the reads are annotated with their UMI and are then trimmed for poly(A) and adapter sequences, minimum reads length (15 nucleotides), read quality, and ambiguous nucleotides (maximum of 2). They are then deduplicated using their UMI. Reads are grouped into UMI groups when they (1) start at the same position based on the end of the read to which the UMI is ligated (i.e., Read2 for paired data), (2) are from the same strand, and (3) have identical UMIs. Groups that contain only one read (singletons) are merged into non-singleton groups if the singleton’s UMI can be converted to a UMI of a non-singleton group by introducing an SNP (the biggest group is chosen). The reads were then mapped to the Human genome hg38 and annotated using the refseq GRCh38.p13 mRNA annotation.
The ‘Empirical analysis of DGE’ algorithm of the CLC Genomics Workbench 21.0.4 was used for differential expression analysis with default settings. It is an implementation of the ‘Exact Test’ for two-group comparisons developed by Robinson and Smyth, 2008 and incorporated in the EdgeR Bioconductor package Robinson et al., 2010.    For all unsupervised analysis, only genes were considered with at least 10 counts summed over all samples. A variance stabilizing transformation was performed on the raw count matrix using the function vst of the R package DESeq2 version 1.28.1. 500 genes with the highest variance were used for the principal component analysis. The variance was calculated agnostically to the pre-defined groups (blind=TRUE). 35 genes with the highest variance across samples were selected for hierarchical clustering.
Supplementary files format and content: tab-delimited text files include quantification and statistics in xlsx format

source_name: GCE 31

growth_protocol: GIN and GCE cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. While cerebellar astrocytes (HCEA. Cat. No. 1810, ScienCell)  were cultured in astrocyte medium (AM) containing 2% FBS, 1% astrocyte growth supplement, 1% Penicillin/Streptomycin from ScienCell.

extract_protocol:
RNA was isolated from 200000 cells using the RNeasy Micro (QIAGEN) according to manufacturer’s instructions with an elution volume of 14µl.
The library preparation was done using the QIAseq UPX 3’ Transcriptome Kit (QIAGEN).

treatment_protocol:
24 hours after seeding the cells, the cell culture medium was replaced with fresh medium containing bio-nanoantennae (25 g/mL) and incubated for 8 h. The cells were washed twice with PBS.
The cells were stimulated with alternating current electric fields (AC-EFs) with frequency of 3 MHz and a peak voltage amplitude of 0.65 V/cm for a period of 2 h or 12 h. Immediately after the ES (3 MHz, 0.65V/cm, 2 hours) cells were washed with PBS, trypsinised, and centrifuged to obtain a pellet. The cell pellets were snap frozen in liquid nitrogen for 5 min and stored at T = - 80C until shipment (in dry ice) to Qiagen genomics facility at Hilden, Germany.

value: GCE 31

value: Glioma Core Enhanced Cells isolated from Glioma Patient

value: NP2 EF+

value: immediately after treatment


title: hiPSCs, myogenic_diff, Healthy, Day2, plate1

description: sci-RNA-Seq

value: UC3-4 Healthy


title: MGL01-2712: Gulo -/- male mouse treated with 0.01% vitC

value: liver

value: Gulo -/-


title: C64


title: RH4-01


title: KP4 cells, DMSO-Replicate3

value: DMSO


title: MGL00-2783: Gulo -/- male mouse without vitC intake

value: liver cell type

value: Male


title: RH4-03


title: ST15-2


title: C52


title: FWT00-2643: Gulo +/+ wildtype femele mouse with no ascorbate supplementation

value: Female

value: Wildtype


title: ST11-2

value: blood


title: KP4 cells, DMSO-Replicate1


title: C28

value: NP1 EF+


title: FWT00-2641: Gulo +/+ wildtype femele mouse with no ascorbate supplementation

value: no vitC supplementation


title: RH-02

value: PBMC

value: IPAH


title: SUM159 JQ1 and Palboclib Resistant

city: Boston

first: Andrew

middle: Ryan

last: Field

state: MA

address: 25 Shattuck St

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description:
Precision Run-On Sequencing (PRO-seq)
Nascent RNA
TNBC
SUM159_JPAL

data_processing:
All custom scripts described herein are available on the AdelmanLab Github (https://github.com/AdelmanLab/NIH_scripts). Using a custom script (trim_and_filter_PE.pl), FASTQ read pairs were trimmed to 41bp per mate, and read pairs with a minimum average base quality score of 20 retained. Read pairs were further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases (--match-read-wildcards -m 20 -q 10). R1 reads, corresponding to RNA 3’ ends, were then aligned to the spiked in Drosophila genome index (dm3) using Bowtie 1.2.2 (-v 2 -p 6 --best --un), with those reads not mapping to the spike genome serving as input to the primary genome alignment step (using Bowtie 1.2.2 options -v 2 --best). Reads mapping to the hg38 reference genome (GRCh38) were then sorted, via samtools 1.3.1 (-n), and subsequently converted to bedGraph format using a custom script (bowtie2stdBedGraph.pl) that counts each read once at the exact 3’ end of the nascent RNA. Because R1 in PRO-seq reveals the position of the RNA 3’ end, the “+” and “-“ strands were swapped to generate bedGraphs representing 3’ end positions at single nucleotide resolution.
Assembly: mm10
Supplementary files format and content: Mapped PRO-seq data is provided in bigWig format either normalized by DESeq size factors (SUM149 and SUM159 drug resistant lines) or raw counts (all others).
Library strategy: PRO-seq

extract_protocol:
Aliquots of frozen (-80°C) permeabilized cells were thawed on ice and pipetted gently to fully resuspend. Aliquots were removed and permeabilized cells were counted using a Luna II, Logos Biosystems instrument. For each sample, 1 million permeabilized cells were used for nuclear run-on, with 50,000 permeabilized Drosophila S2 cells added to each sample for normalization.
Nuclear run on assays and library preparation were performed essentially as described (Reimer KA, Mimoso CA, Adelman K, Neugebauer KM. Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis. Mol Cell [Internet]. Elsevier Inc.; 2021;81:998-1012.e7. Available from: https://doi.org/10.1016/j.molcel.2020.12.018) with modifications noted: 2X nuclear run-on buffer consisted of (10 mM Tris (pH 8), 10 mM MgCl2, 1 mM DTT, 300mM KCl, 20uM/ea biotin-11-NTPs (Perkin Elmer), 0.8U/uL SuperaseIN (Thermo), 1% sarkosyl). Run-on reactions were performed at 37°C. Adenylated 3' adapter was prepared using the 5' DNA adenylation kit (NEB) and ligated using T4 RNA ligase 2, truncated KQ (NEB, per manufacturer’s instructions with 15% PEG-8000 final) and incubated at 16°C overnight. 180uL of betaine blocking buffer (1.42g of betaine brought to 10mL with binding buffer supplemented to 0.6 uM blocking oligo (TCCGACGATCCCACGTTCCCGTGG/3InvdT/)) was mixed with ligations and incubated 5 min at 65°C and 2 min on ice prior to addition of streptavidin beads. After T4 polynucleotide kinase (NEB) treatment, beads were washed once each with high salt, low salt, and blocking oligo wash (0.25X T4 RNA ligase buffer (NEB), 0.3uM blocking oligo) solutions and resuspended in 5' adapter mix (10 pmol 5' adapter, 30 pmol blocking oligo, water). 5' adapter ligation was per Reimer but with 15% PEG-8000 final. Eluted cDNA was amplified 5-cycles (NEBNext Ultra II Q5 master mix (NEB) with Illumina TruSeq PCR primers RP-1 and RPI-X) following the manufacturer's suggested cycling protocol for library construction. A portion of preCR was serially diluted and for test amplification to determine optimal amplification of final libraries. Pooled libraries were sequenced using the Illumina NovaSeq platform.

value: triple-negative breast cancer

value: JQ1 and Palboclib Resistant


title: FGLR40-2718: Gulo -/- female mouse treated with added back 0.40% vitC from 2 months ascorbate removal

value: 0.40% vitC  supplementation


title: RH-03


title: SUM159 JQ1 and Paclitaxel Resistant

description:
Precision Run-On Sequencing (PRO-seq)
Nascent RNA
TNBC
SUM159_JTAX

value: JQ1 and Paclitaxel Resistant


title: SUM159 JQ1 Resistant

description:
Precision Run-On Sequencing (PRO-seq)
Nascent RNA
TNBC
SUM159_JQ1

value: JQ1 Resistant


title: FGLR40-2717: Gulo -/- female mouse treated with added back 0.40% vitC from 2 months ascorbate removal

value: liver


title: RH-01


title: C4

value: GCE 31

value: Glioma Core Enhanced Cells isolated from Glioma Patient

value: WT

value: EF+

value: immediately after treatment


title: MGL00-2784: Gulo -/- male mouse without vitC intake

value: liver cell type

value: Male

value: Gulo -/-


title: KP4 cells, DMSO-Replicate2

value: Pancreatic ductal cell carcinoma

value: DMSO


title: C40

value: NP1 EF+


title: FWT00-2642: Gulo +/+ wildtype femele mouse with no ascorbate supplementation

value: Female

value: Wildtype

value: no vitC supplementation


title: FGLR40-2716: Gulo -/- female mouse treated with added back 0.40% vitC from 2 months ascorbate removal

value: 0.40% vitC  supplementation


title: C75


title: SUM159 Palbociclib Resistant

description:
Precision Run-On Sequencing (PRO-seq)
Nascent RNA
TNBC
SUM159_PAL

value: triple-negative breast cancer

value: Palbociclib Resistant


title: FGL40-2696: Gulo -/- female mouse treated with 0.40% vitC

value: liver


title: C87

value: GCE 31

value: Glioma Core Enhanced Cells isolated from Glioma Patient


title: C16

value: WT


title: SUM159 Paclitaxel Resistant

description:
Precision Run-On Sequencing (PRO-seq)
Nascent RNA
TNBC
SUM159_TAX

value: Paclitaxel Resistant


title: C63

value: EF-

value: immediately after treatment


title: ST14-2

value: blood

value: PBMC

value: IPAH


title: FGL40-2695: Gulo -/- female mouse treated with 0.40% vitC

value: liver cell type

value: Gulo -/-


title: ST12-1


title: SUM159

description:
Precision Run-On Sequencing (PRO-seq)
Nascent RNA
TNBC
SUM159


title: FGL40-2694: Gulo -/- female mouse treated with 0.40% vitC

value: Female


title: FGL05-2896: Gulo -/- female mouse treated with 0.05% vitC

value: 0.05% vitC  supplementation


title: SUM149 JQ1 Resistant

description:
Precision Run-On Sequencing (PRO-seq)
Nascent RNA
TNBC
SUM149_JQ1

value: JQ1 Resistant


title: SUM149 Doxorubicin Resistant

description:
Precision Run-On Sequencing (PRO-seq)
Nascent RNA
TNBC
SUM149_DOXO

value: triple-negative breast cancer

value: Doxorubicin Resistant


title: C39


title: Non-Targeting shRNA Monoclone Biol Rep 2

city: Dunedin

first: Anita

last: Dunbier

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

data_processing:
Reads were aligned to GRCh38/hg38 of the human genome using STAR ultrafast univerisal RNAseq alignment software.
Aligned sequence was imported into Rstudio (R v3.6) and feature counting was performed with the NCBI RefSeq annotation of the human genome (build hg38.2), using Rsubread.
Feature counts were normalised using the voom (Limma) analysis pipline in Rstudio.
Differential expression analysis was perfomed independently on siRNA and shRNA knockdown samples using Limma in Rstudio.
Assembly: GRCh38/hg38
Supplementary files format and content: Unnormalised read counts for NCBI RefSeq features

growth_protocol: MCF7 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from MCF7 cells using the Zymo Quick RNA Mini-Prep kit according to the manufacteurs instructions
RNA libraries for RNA-seq were prepared using the Illuminq TruSeq Stranded Total RNA Gold UDI kit following manufacturer's protocols.

treatment_protocol:
MCF7 cells were transfected with 25 pmol TRIB1 or Non-Targeting ON-TARGET SMARTpool siRNAs using Lipofectamine RNAiMAX according to the manufacteurs instructions. Cells were treated for 48 hours before total RNA was collected.
MCF7 monoclone cells stably transduced with an inducible TRIB1 or Non-Targeting shRNA vector were treated with 2ug/mL doxycycline to induce shRNA expression. Cells treated for 48 hours before total RNA was collected.

value: Breast cancer cell line

tag: genetic modification

value: Inducible Non-Targeting shRNA vector

value: 2ug/mL Doxycycline, 48hrs


title: C27

source_name: GIN 31

value: GIN 31

value: Glioma Invasive Marginal cells from Glioma Patient

value: WT

value: NP2 EF+


title: FGL05-2895: Gulo -/- female mouse treated with 0.05% vitC

value: liver


title: FGL05-2894: Gulo -/- female mouse treated with 0.05% vitC


title: TRIB1 shRNA Monoclone Biol Rep 3

value: Inducible TRIB1 shRNA vector


title: C15

value: immediately after treatment


title: SUM149

description:
Precision Run-On Sequencing (PRO-seq)
Nascent RNA
TNBC


title: SUM149 Paclitaxel Resistant

description:
Precision Run-On Sequencing (PRO-seq)
Nascent RNA
TNBC
SUM149_TAX

value: Paclitaxel Resistant


title: FGL01-2724: Gulo -/- female mouse treated with 0.01% vitC

value: liver cell type

value: Gulo -/-

value: 0.01% vitC  supplementation


title: C3


title: ST13

value: blood

value: PBMC

value: IPAH


title: Hs578T

value: triple-negative breast cancer


title: FGL01-2722: Gulo -/- female mouse treated with 0.01% vitC

value: Female


title: TRIB1 shRNA Monoclone Biol Rep 1

value: Breast cancer cell line

value: 2ug/mL Doxycycline, 48hrs


title: C74

value: GIN 31

value: Glioma Invasive Marginal cells from Glioma Patient

value: NP1 EF+


title: FGL01-2723: Gulo -/- female mouse treated with 0.01% vitC

value: liver


title: MDAMB157


title: C51

value: GCE 31

value: Glioma Core Enhanced Cells isolated from Glioma Patient

value: WT

value: EF-


title: MDAMB436


title: C62

value: immediately after treatment


title: Non-Targeting shRNA Monoclone Biol Rep 1

value: Inducible Non-Targeting shRNA vector


title: FGL00-2791: Gulo -/- female mouse without vitC intake

value: liver cell type

value: Gulo -/-

value: no vitC supplementation


title: C50

value: EF+


title: FGL00-2790: Gulo -/- female mouse without vitC intake

value: Female


title: Non-Targeting siRNA Biol Rep 2

value: Breast cancer cell line

value: 25pmol Non-Targeting SMARTpool, 48hrs


title: Non-Targeting siRNA Biol Rep 1


title: C38

value: GIN 31


title: TRIB1 shRNA Monoclone Biol Rep 2

value: Inducible TRIB1 shRNA vector

value: 2ug/mL Doxycycline, 48hrs


title: HCC1143

value: triple-negative breast cancer


title: TRIB1 siRNA Biol Rep 3

value: 25pmol TRIB1 siRNA SMARTpool, 48hrs


title: FGL00-2788: Gulo -/- female mouse without vitC intake

value: liver


title: EMG3


title: TRIB1 siRNA Biol Rep 2


title: C26

value: Glioma Invasive Marginal cells from Glioma Patient

value: WT


title: Non-Targeting shRNA Monoclone Biol Rep 3


title: Wild-type, day +8, RepF

city: Cambridge

first: David

middle: B

last: Savage

address: Addenbrooke's Hospital

department: Institute of Metabolic Science

institute: University of Cambridge

description:
WT_dp8_F
S1_Appendix.xlsx

data_processing:
Adapter sequences were removed from raw FASTQ files using cutadapt and aligned to Mus musculus reference genome (GRCm38) using STAR.
Binary alignment/map (BAM) files were sorted using samtools and counts were performed using featureCounts
Assembly: GRCm38
Supplementary files format and content: CSV with raw counts per sample

source_name: Mouse embryonic fibroblast

growth_protocol: Mouse embryonic fibroblasts (MEFs) null for Mfn1-/-, Mfn2-/-, Mfn1-/-2-/-, and Opa1-/-, and wild-type MEFs, originally derived by Chen et al.[14], were obtained for use in this study from American Type Culture Collection in February 2019 (see S1 Table for a list of reagents).  MEFs were cultured in Dulbecco’s Modified Eagle’s Medium supplemented with 10% (vol/vol) foetal bovine serum (FBS), 1% sodium pyruvate, 1% non-essential amino acids, 1% penicillin/streptomycin, 2mM L-glutamine, and 50mM 2-mercaptoethanol. All cells were grown at 37°C in 20% O2 and 5% CO2.   Cells were maintained and passaged whilst sub-confluent prior to adipogenic differentiation. To initiate differentiation, cells were grown to confluence (day -2) in 6- or 12-well plates and then, two days later, treated with 8μg/mL D-pantothenic acid, 8μg/mL biotin, 1μM rosiglitazone, 0.5mM 3-isobutyl-1-methylxanthine (IBMX), 1μM dexamethasone, and 1μM insulin. Treatment with D-pantothenic acid, biotin, rosiglitazone, and insulin was repeated on day +2, +4, and +6. Differentiation continued until day +8.

extract_protocol:
Cells were cultured and differentiated as described above, then briefly washed in PBS and lysed in RLT Buffer (Qiagen) with 1% 2-mercaptoethanol then passed through Qiashredder tubes (Qiagen). RNA was extracted using the RNeasy Isolation Kit (Qiagen) according to the manufacturers’ protocol.  RNA was quantified using Agilent 2100 Bioanalyzer (Agilent Technologies Inc) and only samples with RNA Integrity Number ≥8 were used for library preparation.
cDNA libraries were made using Illumina TruSeq RNA sample kits and sequencing was performed on Illumina NovaSeq 6000 with paired-end 150 bp reads (Novogene, Cambridge, UK). Raw reads all passed quality control for Qscore, error rate distribution, and AT/GC distribution.

treatment_protocol: Bulk RNA sequencing (RNAseq) was performed on wild-type (WT) and Mfn1-/- MEFs at four time points: day -2 (pre-adipocyte), day 0 (initiation of adipogenic differentiation), day +3 (early adipocyte), and day +8 (mature adipocyte). RNAseq was performed on Mfn2-/- MEFs at two time points: day -2 (pre-adipocyte) and day +8 (mature adipocyte). Three independent biological replicates of each sample were used for analysis.

value: Mouse embryonic fibroblast

value: Wild-type

value: Day +8 adipogenic differentiation


title: C86

value: NP1 EF+

value: immediately after treatment


title: HCC2185


title: C14

value: EF-


title: Non-Targeting siRNA Biol Rep 3


title: Wild-type, day +8, RepD

description:
WT_dp8_D
S1_Appendix.xlsx


title: Wild-type, day +8, RepE

description:
WT_dp8_E
S1_Appendix.xlsx


title: SUM229PE


title: C2


title: Noness, scRNA-seq

first: Peiyao

last: Wu

address: 9500 Gilman Dr

department: Chemistry

institute: University of California, San Diego

description: 10x Genomics

data_processing:
The barcode processing, gene counting, and aggregation were performed using the 10x Genomics Cellranger (v7.0.0)
low-quality single cells were filtered out if they did not satisfy (percent.mt < 5) & (nCount_RNA > 5000) & (nCount_RNA < 50000), using Seurat (v4.1.0)
Single cells were clustered to pseudobulk samples using FindNeighbors and FindClusters, with Seurat (v4.1.0)
Gene count file `gene_cnt.all_pseudobulk_samples.txt` was generated by summing up the raw gene counts for cells in the pseudobulk cluster
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: HDF5 files containing per-molecule information for all molecules that contain a valid barcode, a valid UMI, and were assigned with high confidence to a gene or Feature Barcode
Supplementary files format and content: Tab-separated values file of the raw gene counts for all the pseudobulk samples

growth_protocol: K562 cells that stably express Cas9-mCherry were infected with lentivirus expressing a hub-targeting pgRNA and EGFP. The cells were then cultured for 10 days and sorted for mCherry/GFP dual positivity.

extract_protocol:
according to the single-cell 3’ RNA v3 protocol from 10x Genomics Chromium. First, a gel bead-in-emulsion (GEM) was created by mixing the cell suspension with partitioning oil and gel beads on a flow chip. Then, each single cell was lysed in its own GEM, and the poly-A RNAs were captured and retrotranscribed to cDNA using a primer that contained the Ilumina R1 sequence, a Unique Molecular Identifier (UMI), and the 10x Barcode. Next, the barcoded cDNA was pooled and cleaned up, and then amplified.
according to the single-cell 3’ RNA v3 protocol from 10x Genomics Chromium. The cDNA was size-selected using SPRIselect reagent for subsequent library construction. During library construction, the Ilumina R2 primer sequence, sample index, and P5 and P7 sequences were added to the cDNA.

treatment_protocol: The sorted cells were washed in PBS-BSA (0.04% w/v) and resuspended in the same solution to proceed to Gel Bead-In-Emulsions (GEMs) generation and barcoding.

value: blood

value: Lymphoblast


title: SUM185


title: UACC3199


title: C85


title: Ess, scRNA-seq

description: 10x Genomics


title: C73

source_name: Cortical Astrocytes

value: Cortical Astrocytes

value: Healthy cells from human cerebellar

value: NP2 EF+


title: Tumor-720_MeRIP

city: Guangzhou

first: Youqin

last: Xu

address: No.1023 North Shatai Road

institute: Southern Medical University

data_processing:
Illumina Bcl2FastQ  software was used for basecalling.
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36), and the clean reads undergone rRNA deleting through RNAcentral to get effective reads.Genomic alignment (hg19 from UCSC genome browser) was using Tophat(version:2.0.13)to get uniquely mapping reads.
MACS2(version 2.1.0.20151222)/exomePeak was employed to perform m6A peak calling.Then using Hommer(version:4.8)  to annotate the m6A Peaks.The nucleotides in m6A Peaks region were used for detection of the consensus  m6A motif by DREME (version:4.11.1) and MEME(version:4.11.1). Motif central enrichment was performed by  CentriMo (version:4.11.1).Differential methylation was determined by MetDiff.
Assembly: hg19
Supplementary files format and content: a tabular file which contains information about called peaks

source_name: breast cancer tisssue

extract_protocol:
Total RNA was isolated from tissues using the Magzol Reagent (Magen, China)according to the manufacturer’s protocol.
The  library was constructed using NEBNext® Ultra RNA LibraryPrep Kit for Illumina (NEB, USA).Briefly, RNA were fragmented to approximately 200bp. Then, the RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle.

value: breast cancer tisssue

tag: disease state

value: breast duct cancer

tag: rip antibody


title: Wild-type, day +8, RepC

description:
WT_dp8_C
S1_Appendix.xlsx

tag: cell type


title: hMN-D42-2

first: Jiehui

last: Chen

address: 320 Longwood Ave

institute: Boston Children’s Hospital

description:
hMN-D42-2
count2.csv

data_processing:
For data analysis, reference genome and gene annotation files were downloaded from GENECODE (hg38). Fastq files were pre-processed by Fastp (v0.12.1) (Chen et al., 2018) with default parameters. Cleaned data were then aligned to the reference genome via Hisat2 (v2.1.0) (Kim et al., 2015). FeatureCounts (v1.5.3) (Liao et al., 2014) was used to count the reads mapped to each gene.
RNA-seq data in this paper were compared with nmps (Verrier et al., 2018) after removing batch effects by the R package “combat” (Johnson et al., 2007). Principal Components Analysis (PCA) (Jolliffe, 2002) was used to show the correlation of these samples.
The ‘Developmental Transcriptome Dataset’ of BRAINSPAN (https://www.brainspan.org/static/download.html) was also downloaded. We merged the brain samples of same stage and calculated Pearson correlation coefficients between the merged samples and RNA-seq data in this paper.  Pseudo-bulk RNA-seq of human spinal cord, GSE171892 (Rayon et al., 2021), was conducted through the R package “scuttle” (McCarthy et al., 2017). After that, samples at same stages were merged and pearson correlation coefficients were calculated between the pseudo-bulk RNA-seq and RNA-seq data in this paper.
The SCENIC (Aibar et al., 2017) was used to infer the gene regulatory network (regulon). Binary regulon-activity matrix for all samples was used in principal components analysis. GO enrichment analysis of related target genes was carried out by Metascape (https://metascape.org/) with default parameters (Zhou et al., 2019).
Assembly: hg38
Supplementary files format and content: csv files include counts for each Sample.

source_name: cell line

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen).
RNA libraries were prepared for sequencing according to the manufacturer’s protocol (NEBNext® UltraTM RNA Library Prep Kit for Illumina®).

value: cell line

value: hMNs

value: Neural differentiation


title: Wild-type, day +8, RepB

description:
WT_dp8_B
S1_Appendix.xlsx


title: hMN-D42-3

description:
hMN-D42-3
count2.csv

value: WT


title: hMN-D42-1

description:
hMN-D42-1
count2.csv


title: Tumor-720_input

value: none (input)


title: C49


title: hMN-D30-3

description:
hMN-D30-3
count2.csv


title: Wild-type, day +8, RepA

description:
WT_dp8_A
S1_Appendix.xlsx

value: Mouse embryonic fibroblast

value: Wild-type


title: Wild-type, day +3, RepC

description:
WT_dp3_C
S1_Appendix.xlsx

value: Day +3 adipogenic differentiation


title: C61

value: immediately after treatment


title: Tumor-706_input


title: hMN-D30-2

description:
hMN-D30-2
count2.csv


title: Wild-type, day +3, RepB

description:
WT_dp3_B
S1_Appendix.xlsx


title: TRIB1 siRNA Biol Rep 1

value: Breast cancer cell line

value: 25pmol TRIB1 siRNA SMARTpool, 48hrs


title: Wild-type, day +3, RepA

description:
WT_dp3_A
S1_Appendix.xlsx


title: C37

value: NP1 EF+


title: C25

value: Cortical Astrocytes


title: C13

value: Healthy cells from human cerebellar

value: EF+


title: hMN-D30-1

description:
hMN-D30-1
count2.csv


title: hMN-D24-3

description:
hMN-D24-3
count2.csv


title: Wild-type, day -2, RepF

description:
WT_dm2_F
S1_Appendix.xlsx

value: Day -2 adipogenic differentiation


title: C1


title: normal-720_input

source_name: breast tissue

value: breast tissue

value: adjacent normal


title: hMN-D24-2

description:
hMN-D24-2
count2.csv

value: cell line

value: hMNs


title: normal-706_MeRIP


title: C96

value: WT


title: Wild-type, day -2, RepD

description:
WT_dm2_D
S1_Appendix.xlsx


title: normal-706_input

value: none (input)


title: Wild-type, day -2, RepE

description:
WT_dm2_E
S1_Appendix.xlsx

value: Mouse embryonic fibroblast


title: Tumor-706_MeRIP

value: breast cancer tisssue

value: breast duct cancer


title: hMN-D24-1

description:
hMN-D24-1
count2.csv

value: Neural differentiation


title: Wild-type, day -2, RepC

description:
WT_dm2_C
S1_Appendix.xlsx

value: Wild-type


title: Wild-type, day -2, RepB

description:
WT_dm2_B
S1_Appendix.xlsx


title: C72

value: EF-

value: immediately after treatment


title: C84

value: Cortical Astrocytes


title: SiHa-1-IP 1

city: Shenzhen

first: sheng

last: zhong

address: The Xinhu Road 1333

institute: The Sourthern Medical University

data_processing:
Clustered libraries were loaded onto reagem cartridge and ftxwarded to sequencing nm on Illumina Hiseq 4000 system
The sequence data obtained by Illumina HiSeq sequencing and filtering will be used for the following analysis: Quality control with FastQC (v0.11.7);
high quality data with adapter sequences and low quality parts removed (ClHmmomatic V0.32) are compared to the reference genome (H1SAT2 v2.L0);
use exomePeak (v2.13.2) to determine the peaks of each sample and the differentially methylated peaks of each comparison, and annotate the obtained peaks
according to the annotation information of the Ensembl database; count the regions of each transcript Whether there are peaks in each sample;   finally perform a motif analysis on the obtained peaks
Assembly: hg19
Supplementary files format and content: tab-delimited text files include fold  enrichment for each Sample
Library strategy: MeRIP-seq

extract_protocol:
The purity and coDceniration of total RNA samples were detennined with NanoDrop ND-1000. Results were provided m Sample QC report.
RNA-scq libraries of m6A antibody enriched mRNAs and input mRNAs were prepared using KAPA Stranded mRNA-seq Kit (Illumina). And finally, the completed libraries were qualified by Agilent 2100 Bioanalyzer.

value: SiHa

value: cervical cancer cells


title: hMN-D18-2

description:
hMN-D18-2
count2.csv


title: C60

value: Healthy cells from human cerebellar


title: normal-720_MeRIP

value: breast tissue


title: Wild-type, day -2, RepA

description:
WT_dm2_A
S1_Appendix.xlsx

value: Day -2 adipogenic differentiation


title: SiHa-2-Input

data_processing:
Clustered libraries were loaded onto reagem cartridge and ftxwarded to sequencing nm on Illumina Hiseq 4000 system
The sequence data obtained by Illumina HiSeq sequencing and filtering will be used for the following analysis: Quality control with FastQC (v0.11.7);
high quality data with adapter sequences and low quality parts removed (ClHmmomatic V0.32) are compared to the reference genome (H1SAT2 v2.L0);
use exomePeak (v2.13.2) to determine the peaks of each sample and the differentially methylated peaks of each comparison, and annotate the obtained peaks
according to the annotation information of the Ensembl database; count the regions of each transcript Whether there are peaks in each sample;   finally perform a motif analysis on the obtained peaks
Assembly: hg19
Supplementary files format and content: tab-delimited text files include fold  enrichment for each Sample

value: cell line


title: hMN-D18-1

description:
hMN-D18-1
count2.csv

value: hMNs


title: SiHa-1-Input


title: hMN-D12-3

description:
hMN-D12-3
count2.csv

value: WT


title: H8-1-IP 2

value: Immortalized human cervical epithelial cells


title: Wild-type, day 0, RepB

description:
WT_dm0_B
S1_Appendix.xlsx

value: Mouse embryonic fibroblast

value: Day 0 adipogenic differentiation


title: Wild-type, day 0, RepC

description:
WT_dm0_C
S1_Appendix.xlsx


title: hMN-D12-2

description:
hMN-D12-2
count2.csv


title: Newly diagnosed multiple myeloma 3

city: Changsha

first: Liwen

state: Hunan

address: 138 Tongzipo road

department: Department of Hematology

institute: Third Xiangya Hospital, Central South University

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8
Sequencing quality are examined by FastQC and trimmed reads (pass Illumina quality filter, trimmed adaptor bases by cutadapt ) are aligned
The trimmed reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2
The abundance of miRNA are evaluated using their sequencing counts with miRDeep2
Assembly: miRBase mature.fa
Supplementary files format and content: Tab-delimited text files include raw counts for total sample

source_name: Bone marrow

extract_protocol:
Total RNA and Exosomal RNA were isolated using Trizol reagent. The RNA concentration and purity were confifirmed using absorbance measurements with a NanoDrop 2000 (Thermo Scientifific, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for miRNA-seq were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina

value: Bone marrow

value: multiple myeloma


title: Newly diagnosed multiple myeloma 4


title: hMN-D18-3

description:
hMN-D18-3
count2.csv

value: Neural differentiation


title: SiHa-1-IP 2


title: hMN-D12-1

description:
hMN-D12-1
count2.csv


title: Newly diagnosed multiple myeloma 1


title: Mfn2-/-, day +8, RepF

description:
m2_dp8_F
S1_Appendix.xlsx

value: Day +8 adipogenic differentiation


title: H8-1-IP 1


title: hMN-D6-3

description:
hMN-D6-3
count2.csv


title: H8-2-Input


title: Mfn2-/-, day +8, RepE

description:
m2_dp8_E
S1_Appendix.xlsx


title: Newly diagnosed multiple myeloma 2


title: H8-1-Input


title: hMN-D6-2

description:
hMN-D6-2
count2.csv


title: Healthy control 1

value: healthy


title: Mfn2-/-, day +8, RepD

description:
m2_dp8_D
S1_Appendix.xlsx


title: hMN-D6-1

description:
hMN-D6-1
count2.csv


title: Wild-type, day 0, RepA

description:
WT_dm0_A
S1_Appendix.xlsx

value: Wild-type


title: Mfn2-/-, day -2, RepF

description:
m2_dm2_F
S1_Appendix.xlsx


title: hSCNPC-P40-3

description:
hSCNPC-P40-3
count1.csv

value: hSCNPCs


title: 7F8-48h rep1

city: Shanghai

first: Zhan

last: Ding

address: FengLin 300

institute: CAS Center for Excellence in Molecular Plant Science

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapped to GRCh38 whole genome using STAR(v2.6.1a) with default parameters. Reference genome and gene model annotation files were downloaded from NCBI.
FeatureCounts (v1.6.3) was used to count the reads numbers mapped to each gene.
The abundance of each gene was calculated by stringtie (v2.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: *.gene_abund.txt: Tab-delimited text files include gene abundance values for each Sample.

source_name: A549 lung cancer cell line

extract_protocol:
Total RNAs from drug treated A549-CD63-nluc cells were isolated by TRIzol (TIANGEN) and treated with RNase-free DNase I (Invitrogen). For RT-PCR, cDNAs were reverse transcribed using RevertAid Reverse Transcriptase (Thermo) and amplified by Ex-Taq (TaKaRa). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line design

value: Overexpression of CD63-Nluc fusion protein

value: 4uM inhibitor 7F8 for 48h


title: 7F8-48h rep2


title: Mfn2-/-, day -2, RepE

description:
m2_dm2_E
S1_Appendix.xlsx


title: hSCNPC-P40-2

description:
hSCNPC-P40-2
count1.csv

tag: tissue


title: 7F8-4h rep2

tag: cell line

value: 4uM inhibitor 7F8 for 4h


title: Mfn2-/-, day -2, RepD

description:
m2_dm2_D
S1_Appendix.xlsx

value: Day -2 adipogenic differentiation


title: 7F8-4h rep1


title: Cartridge 4

city: Créteil

first: Mehdi

last: Khelfa

address: 5 Rue Gustave Eiffel

institute: Institut Mondor de Recherche Biomédicale

description: BD Rhapsody

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using SevenBridges (https://www.sevenbridges.com/) and SeqGeq software (https://www.bdbiosciences.com/en-fr/products/software/seqgeq-bioinformatics-software)
Supplementary files format and content: Comma-separated values files

source_name: Blood

extract_protocol:
Fresh whole blood was collected from patients and HDs. PBMCs were isolated by density gradient centrifugation. Leukocytes were labeled with Aqua LIVE/DEAD (Thermo Fisher Scientific) stain to remove non-viable cells, and with the following antibodies against: CD45RA-APC-H7, CD3-BV650 and CD4-R718 (BD Biosciences) antibodies. CD45RA-CD3+CD4+ TLs were isolated from PBMCs by flow cytometry sorting.
Targeted scRNA-seq analysis was performed with the BD Rhapsody Single-Cell Analysis System (BD Biosciences), according to the manufacturer’s instructions. Each sample was stained with 20 BD AbSeq antibodies (Supplemental Table 5). The BD Human Single-Cell Multiplexing Kit was used to multiplex up to seven subjects per Rhapsody cartridge. For library construction, the samples were pooled before cartridge loading. The BD Rhapsody Immune Response Targeted Panel for Humans was used to assess mRNA levels for 399 genes (#633750).

value: Blood

value: Leukocytes

value: CD4+ CD45RA-


title: Mfn1-/-, day +8, RepC

description:
m1_dp8_C
S1_Appendix.xlsx


title: Cartridge 3

description: BD Rhapsody


title: Cartridge 1

description: BD Rhapsody


title: Healthy control 2


title: Mfn1-/-, day +8, RepB

description:
m1_dp8_B
S1_Appendix.xlsx


title: 6D7-48h rep2

value: 4uM inhibitor 6D7 for 48h


title: 6D7-48h rep1


title: Cartridge 2

description: BD Rhapsody


title: hSCNPC-P40-1

description:
hSCNPC-P40-1
count1.csv

value: cell line

value: WT


title: hSCNPC-P30-2

description:
hSCNPC-P30-2
count1.csv


title: Mfn1-/-, day +8, RepA

description:
m1_dp8_A
S1_Appendix.xlsx

value: Mouse embryonic fibroblast


title: hSCNPC-P30-3

description:
hSCNPC-P30-3
count1.csv


title: Sheep 19011 Thymus

city: Winston Salem

first: Maria Graça

last: Almeida-Porada

state: NC

address: 391 Technology Way

institute: Wake Forest Institute for Regnerative Medicine

description:
homo sapiens PLCs engrafted in ovis aries thymus
Sheep 19011 thymus-specific transcripts

data_processing:
FASTQ files were uploaded to QIAGEN RNA-seq Analysis Portal (https://geneglobe.qiagen.com/us/analyze/) and aligned to Homo sapiens (GRCh38.noalt.103) with analysis workflow version: 1.0.
Assembly: GRCh38.noalt.103
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: IUTx End-of-Study #19011

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
total RNA was subjected to ribosomal RNA (rRNA) suppression using QIAseq FastSelect rRNA removal kits HMR and then reverse transcribed into cDNA using random hexamers and oligo-dt primers for 90 minutes at 42C.   During cDNA synthesis each sample receives a unique sample ID that allows for cDNA pooling and all subsequent library construction steps of pooled samples was done in a single tube to minimize batch affects. Following cDNA pooling, 2 rounds of bead selection / reaction clean-up was done with QIAseq beads.  The cDNA was then amplified with unique-dual sample indexes using the (331801) QIAseq UX 12 Index Kit IL UDI.    Completed libraries were then purified using 2 rounds of bead-based cleanup with QIAseq beads.  Final libraries were quality controlled using an Agilent Bioanalyzer and quantitated by real-time qPCR using the (333314) QIAseq Library Quant Assay Kit and sequenced using an illumina Next-Seq 500 using 75 base paired end sequencing using NextSeq 500/550 Mid Output Kit (150 Cycles)

tag: animal id

value: Sheep 19011

value: human PLCs were transplanted into fetal sheep

value: 3 years post-transplant


title: Sheep 19011 Ovary

description:
homo sapiens PLCs engrafted in ovis aries ovary
Sheep 19011 Ovary-specific transcripts


title: 6D7-4h rep1

value: 4uM inhibitor 6D7 for 4h


title: hSCNPC-P20-3

description:
hSCNPC-P20-3
count1.csv

tag: genotype

value: Neural differentiation


title: Mfn1-/-, day +3, RepC

description:
m1_dp3_C
S1_Appendix.xlsx

value: Day +3 adipogenic differentiation


title: 6D7-4h rep2

value: Overexpression of CD63-Nluc fusion protein


title: hSCNPC-P30-1

description:
hSCNPC-P30-1
count1.csv

value: hSCNPCs


title: Sheep 19011 Liver

description:
homo sapiens PLCs engrafted in ovis aries liver
Sheep 19011 Liver transcripts


title: Mfn1-/-, day +3, RepB

description:
m1_dp3_B
S1_Appendix.xlsx


title: Sheep 19007 Ovary

description:
homo sapiens PLCs engrafted in ovis aries ovary
Sheep 19007 Ovary-specific transcripts

source_name: IUTx End-of-Study #19007

value: Sheep 19007


title: hSCNPC-P20-2

description:
hSCNPC-P20-2
count1.csv


title: Mfn1-/-, day +3, RepA

description:
m1_dp3_A
S1_Appendix.xlsx


title: 5G6-48h rep1

value: 4uM inhibitor 5G6 for 48h


title: hSCNPC-P20-1

description:
hSCNPC-P20-1
count1.csv


title: Sheep 19007 Thymus

description:
homo sapiens PLCs engrafted in ovis aries thymus
Sheep 19007 thymus-specific transcripts


title: hSCNPC-P10-3

description:
hSCNPC-P10-3
count1.csv


title: Sheep 19007 Lung

description:
homo sapiens PLCs engrafted in ovis aries lung
Sheep 19007 Lung transcripts


title: 5G6-4h rep1

value: 4uM inhibitor 5G6 for 4h


title: Sheep 19007 Liver

description:
homo sapiens PLCs engrafted in ovis aries liver
Sheep 19007 Liver transcripts


title: 5G6-4h rep2


title: DMSO-48h rep2

value: 4uM DMSO for 48h


title: hSCNPC-P10-2

description:
hSCNPC-P10-2
count1.csv


title: Mfn1-/-, day -2, RepC

description:
m1_dm2_C
S1_Appendix.xlsx

value: Day -2 adipogenic differentiation


title: Mfn1-/-, day -2, RepA

description:
m1_dm2_A
S1_Appendix.xlsx


title: Sheep 19011 Lung

description:
homo sapiens PLCs engrafted in ovis aries lung
Sheep 19011 Lung transcripts


title: Mfn1-/-, day -2, RepB

description:
m1_dm2_B
S1_Appendix.xlsx


title: hSCNPC-P10-1

description:
hSCNPC-P10-1
count1.csv


title: Sheep 18009 Ovary

description:
homo sapiens PLCs engrafted in ovis aries ovary
Sheep 18009 Ovary-specific transcripts

source_name: IUTx End-of-Study #18009

value: Sheep 18009


title: Mfn1-/-, day 0, RepC

description:
m1_dm0_C
S1_Appendix.xlsx

value: Day 0 adipogenic differentiation


title: DMSO-48h rep1


title: Sheep 18009 Thymus

description:
homo sapiens PLCs engrafted in ovis aries thymus
Sheep 18009 thymus-specific transcripts


title: hSCNPC-P5-3

description:
hSCNPC-P5-3
count1.csv

value: cell line

value: WT


title: Mfn1-/-, day 0, RepB

description:
m1_dm0_B
S1_Appendix.xlsx

value: Mouse embryonic fibroblast


title: 5G6-48h rep2


title: DMSO-4h rep2

value: 4uM DMSO for 4h


title: hSCNPC-P5-2

description:
hSCNPC-P5-2
count1.csv


title: DMSO-4h rep1


title: Sheep 18009 Lung

description:
homo sapiens PLCs engrafted in ovis aries lung
Sheep 18009 Lung transcripts

value: human PLCs were transplanted into fetal sheep

value: 3 years post-transplant


title: Mfn1-/-, day 0, RepA

description:
m1_dm0_A
S1_Appendix.xlsx


title: Sheep 18009 Liver

description:
homo sapiens PLCs engrafted in ovis aries liver
Sheep 18009 Liver transcripts


title: hSCNPC-P5-1

description:
hSCNPC-P5-1
count1.csv

value: Neural differentiation


title: NeuDet-D6-3

description:
NeuDet-D6-3
count1.csv


title: janus miRNA Rep2

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to TAIR10 whole genome with miRNA annotation using bowtie bowtie -v 0 -S -a --best --strata
Reads counts for each miRNA with  htseq-count
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: 16 hour light; 8 hour dark;  at 22 oC

extract_protocol:
Flower inflorescences were collected and total RNA was extracted by Trizol. Illumina TruSeq Small RNA Sample Prep Kits was used with 1 ug of total RNA for the construction of sequencing libraries.
Illumina mRNA library protocol and small RNA library protocol
mRNA-seq and small RNA-seq

value: inflorescence

value: janus

tag: fraction

value: small RNA


title: Sheep 17021 Ovary

description:
homo sapiens PLCs engrafted in ovis aries ovary
Sheep 17021 Ovary-specific transcripts

source_name: IUTx End-of-Study #17021

value: Sheep 17021


title: F - Cre control  2

city: Blacksburg

first: Hehuang

last: Xie

state: VA

address: 1015 Life Science Cir

department: Department of Biomedical Sciences and Pathobiology

institute: Virginia Tech

description:
HP4047
sampletable.csv

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore-3.8.2 (parameter --paired --phred33 --fastqc --illumina -q 30 --length 30)
Trimmed sequence reads were mapped to GRCm38 using STAR 2.7.9  (parameters- default settings)
Read count is extracted using STAR-2.7.9 --quant mode
Assembly: GRCm38
Supplementary files format and content: comma-delimited text files from the second column of STAR-2.7.9 quant output
Supplementary files format and content: sample information of the read count table

source_name: hippocampus

extract_protocol:
RNA extraction was performed using Rneasy mini kit (Qiagen). 1.5 ug of total RNA was used for non-stranded RNA-seq.
non-stranded RNA-seq

value: hippocampus

tag: gender

value: Female

value: endocrine


title: janus miRAN Rep1


title: NeuDet-D6-2

description:
NeuDet-D6-2
count1.csv

value: hSCNPCs


title: F - Cre control  1

description:
HP4046
sampletable.csv


title: F - Cre control  3

description:
HP4048
sampletable.csv


title: Sheep 17021 Lung

description:
homo sapiens PLCs engrafted in ovis aries lung
Sheep 17021 Lung transcripts


title: NeuDet-D6-1

description:
NeuDet-D6-1
count1.csv


title: Sheep 17021 Liver

description:
homo sapiens PLCs engrafted in ovis aries liver
Sheep 17021 Liver transcripts


title: Col WT miRNA Rep2

value: WT Col


title: NeuDet-D5-3

description:
NeuDet-D5-3
count1.csv

value: differentiating hSCNPCs


title: Col WT  miRNA Rep1


title: M - Cre control  3

description:
HP4052
sampletable.csv

value: Male


title: Sheep 17020 Ovary

description:
homo sapiens PLCs engrafted in ovis aries ovary
Sheep 17020 Ovary-specific transcripts

source_name: IUTx End-of-Study #17020

value: Sheep 17020


title: NeuDet-D5-2

description:
NeuDet-D5-2
count1.csv

value: cell line

value: WT


title: M - Cre control  2

description:
HP4051
sampletable.csv


title: janus mRNA Rep1

value: mRNA


title: Sheep 17020 Thymus

description:
homo sapiens PLCs engrafted in ovis aries thymus
Sheep 17020 thymus-specific transcripts

value: human PLCs were transplanted into fetal sheep

value: 3 years post-transplant


title: M - Cre control  1

description:
HP4049
sampletable.csv


title: Col WT mRNA Rep2

value: inflorescence


title: NeuDet-D4-3

description:
NeuDet-D4-3
count1.csv

value: Neural differentiation


title: NeuDet-D5-1

description:
NeuDet-D5-1
count1.csv


title: Sheep 17020 Lung

description:
homo sapiens PLCs engrafted in ovis aries lung
Sheep 17020 Lung transcripts


title: F - complete wild type  3

description:
HP4056
sampletable.csv


title: F - complete wild type  2

description:
HP4055
sampletable.csv


title: Sheep 17020 Liver

description:
homo sapiens PLCs engrafted in ovis aries liver
Sheep 17020 Liver transcripts


title: NeuDet-D4-2

description:
NeuDet-D4-2
count1.csv


title: Sheep 17010 Ovary

description:
homo sapiens PLCs engrafted in ovis aries ovary
Sheep 17010 Ovary-specific transcripts

source_name: IUTx End-of-Study #17010

value: Sheep 17010


title: Col WT  mRNA Rep1


title: F - complete wild type  1

description:
HP4045
sampletable.csv


title: root, P, 3-4

first: baoxing

last: xie

address: Tianhe

institute: South China Agricultural University

description: Low phosphorus treatment of GmVP2 overexpression Arabidopsis

data_processing:
Remove the adaptor-polluted reads (Reads containing more than 5 adapter-polluted baseswere regarded as adaptor-polluted reads andwould be filtered out)
Remove the low-quality reads (Readswith the number of low quality bases(phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low -quality reads).
Remove readswith number of N bases accounting for more than 5 %.
Reads Count for each gene in each samplewas counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads )was then calculated to estimate the expression level of genes in each sample
Screening DEGs using NOISeq.
Assembly: Arabidopsis_thaliana.TAIR10.37
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample .

source_name: root

extract_protocol:
Ethanol precipitation protocol and CTAB-PBIOZOL reagent for the purification of total RNA from the plant tissue
BGI RNA-Seq kit

value: root

value: GmVP2 overexpression

value: Low phosphorus


title: Sheep 17010 Thymus

description:
homo sapiens PLCs engrafted in ovis aries thymus
Sheep 17010 thymus-specific transcripts


title: M - complete wild type  3

description:
HP4054
sampletable.csv

value: hippocampus

value: endocrine


title: NeuDet-D4-1

description:
NeuDet-D4-1
count1.csv


title: root, P, 3-2


title: NeuDet-D3-3

description:
NeuDet-D3-3
count1.csv


title: janus mRNA Rep2

value: janus


title: M - complete wild type  2

description:
HP4053
sampletable.csv


title: NeuDet-D3-2

description:
NeuDet-D3-2
count1.csv

value: differentiating hSCNPCs


title: root, P, 3-1


title: M - complete wild type  1

description:
HP4042
sampletable.csv

value: Male


title: root, 3-4

description: Normal phosphorus treatment of GmVP2 overexpression Arabidopsis

value: Normal phosphorus


title: Sheep 17010 Liver

description:
homo sapiens PLCs engrafted in ovis aries liver
Sheep 17010 Liver transcripts


title: F - Egr1cKO 3

description:
HP4946
sampletable.csv

value: Female


title: root, 3-3


title: NeuDet-D3-1

description:
NeuDet-D3-1
count1.csv

value: cell line

value: WT


title: root, 3-2


title: Sheep 1002 Lung

description:
homo sapiens PLCs engrafted in ovis aries lung
Sheep 1002 Lung transcripts

source_name: IUTx Newborn #1002 (HA animal)

value: Sheep 1002

value: human PLCs were transplanted into fetal sheep

value: Day 90 post-transplant


title: F - Egr1cKO 2

description:
HP4945
sampletable.csv


title: NeuDet-D2-2

description:
NeuDet-D2-2
count1.csv

value: Neural differentiation


title: root, P, WT-4

description: Low phosphorus treatment ofwild-type Arabidopsis

value: wild-type


title: NeuDet-D2-1

description:
NeuDet-D2-1
count1.csv


title: M - Egr1cKO 3

description:
HP4948
sampletable.csv


title: root, P, WT-3

value: root


title: NeuDet-D1-3

description:
NeuDet-D1-3
count1.csv


title: Sheep 18008 Thymus

description:
homo sapiens PLCs engrafted in ovis aries thymus
Sheep 18008 thymus-specific transcripts

source_name: IUTx Newborn #1808

value: Sheep 18008


title: root, P, WT-2

value: Low phosphorus


title: M - Egr1cKO 2

description:
HP4947
sampletable.csv

value: hippocampus


title: Sheep 1002 Thymus

description:
homo sapiens PLCs engrafted in ovis aries thymus
Sheep 1002 thymus-specific transcripts


title: Sheep 18008 Liver

description:
homo sapiens PLCs engrafted in ovis aries liver
Sheep 18008 Liver transcripts


title: NeuDet-D1-2

description:
NeuDet-D1-2
count1.csv


title: M - Egr1cKO 1

description:
HP4939
sampletable.csv

value: endocrine


title: NeuDet-D1-1

description:
NeuDet-D1-1
count1.csv


title: Sheep 18002 Thymus

description:
homo sapiens PLCs engrafted in ovis aries thymus
Sheep 18002 thymus-specific transcripts

source_name: IUTx Newborn #1802

value: Sheep 18002


title: F - Egr1cKO control  3

description:
HP4953
sampletable.csv


title: Sheep 17010 Lung

description:
homo sapiens PLCs engrafted in ovis aries lung
Sheep 17010 Lung transcripts

value: Sheep 17010

value: 3 years post-transplant


title: root, WT-3

description: Normal phosphorus treatment ofwild-type Arabidopsis

value: Normal phosphorus


title: hNMP-D4-3

description:
hNMP-D4-3
count1.csv

source_name: cell line

value: hNMPs


title: Sheep 1002 Liver

description:
homo sapiens PLCs engrafted in ovis aries liver
Sheep 1002 Liver transcripts


title: Sheep 18008 Lung

description:
homo sapiens PLCs engrafted in ovis aries lung
Sheep 18008 Lung transcripts


title: F - Egr1cKO 1

description:
HP4944
sampletable.csv

value: Female


title: root, WT-4


title: F - Egr1cKO control  2

description:
HP4952
sampletable.csv


title: Sheep 18002 Lung

description:
homo sapiens PLCs engrafted in ovis aries lung
Sheep 18002 Lung transcripts


title: root, WT-2


title: hNMP-D4-2

description:
hNMP-D4-2
count1.csv

value: cell line

value: WT


title: Sheep 18002 Liver

description:
homo sapiens PLCs engrafted in ovis aries liver
Sheep 18002 Liver transcripts

value: human PLCs were transplanted into fetal sheep


title: M - Egr1cKO control  2

description:
HP4950
sampletable.csv

value: Male


title: Sheep 18001 Liver

description:
homo sapiens PLCs engrafted in ovis aries liver
Sheep 18001 Liver transcripts

source_name: IUTx Newborn #1801

value: Sheep 18001

value: Day 90 post-transplant


title: F - Egr1cKO control  1

description:
HP4951
sampletable.csv


title: hNMP-D4-1

description:
hNMP-D4-1
count1.csv

value: Neural differentiation


title: M - Egr1cKO control  3

description:
HP4955
sampletable.csv


title: Sheep 18001 Thymus

description:
homo sapiens PLCs engrafted in ovis aries thymus
Sheep 18001 thymus-specific transcripts


title: hNMP-D3-3

description:
hNMP-D3-3
count1.csv

value: differentiating hNMPs


title: M - Egr1cKO control  1

description:
HP4935
sampletable.csv


title: hNMP-D3-1

description:
hNMP-D3-1
count1.csv


title: PLCs before in utero transplantation

description:
human PLCs
PLCs before in utero transplantation

source_name: homo sapiens PLCs, prior to in utero transplant

value: human PLCs

value: Day 0


title: P1: NEDAMSS patient1

type: RNA

city: Tochigi

first: Ken-ichi

last: INOUE

address: 880 Kitakobayashi, Mibu-machi, Shimotsuga-gun

country: Japan

institute: Dokkyo Medical University

description: feeder-free growth

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: iPS cells

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: RNA was prepared using Acid Guanidinium Thiocyanate Phenol chloroform extraction method (RNA iso plus, Takara Bio Inc., Shiga, Japan). RNA was quantified using a NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific, Inc., Waltham, MA, USA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: male

value: NEDAMSS

value: iPS cells

tag: differentiation status

value: undifferentiated


title: hNMP-D2-2

description:
hNMP-D2-2
count1.csv


title: Sheep 18001 Lung

description:
homo sapiens PLCs engrafted in ovis aries lung
Sheep 18001 Lung transcripts


title: P11: NEDAMSS patient1

description: feeder-free growth


title: hNMP-D3-2

description:
hNMP-D3-2
count1.csv


title: PMSCV-HA-TWIST1 ChIP

city: Jupiter

first: Christopher

middle: Lee

last: Haga

state: Florida

address: 130 Scripps Way, BldgA261A

department: Molecular Medicine

institute: UF Scripps Biomedical Research

data_processing:
Barcode adapter sequences were trimmed using the CutAdapt software package.
The BWA software package was used to map genomic DNA fragments to the hg19 human genome.
Uniquely aligned fragments were called into peaks using the MACS2 software package.
Assembly: hg19
Supplementary files format and content: bedgraph

source_name: bone marrow

extract_protocol:
Cell monolayers were fixed with 1% paraformaldehyde, quenched, lysed, and sonicated to produce 500bp chromatin fragments.
Libraries were prepared using the NEBNext Ultra II DNA library prep kit

treatment_protocol: Cells were transduced with either an empty vector PMSCV-Pig or HA-TWIST1 retrovirus

value: bone marrow

value: mesenchymal stem cell

value: PMSCV-HA-TWIST1 transduced


title: PMSCV-Pig Empty Vector ChIP

value: PMSCV-Pig transduced


title: WT replicate 2

city: Cincinnati

first: Soona

last: Shin

state: Cincinnati

address: 3333 Burnet Ave, OH

institute: Cincinnati Children's Hospital Medical Center

description: RNAseq

data_processing:
Sequence reads were trimmed using Trim Galore! v0.4.2 and cutadapt v1.9.1.
The trimmed reads were aligned to the reference mouse genome version mm10 using STAR v2.6.1e.
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8.
Read counting was done with the program featureCounts v1.6.2 from the Rsubread package.
Raw counts were normalized as  transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Hematopoietic

growth_protocol: MLL-AF9 leukemic cells were grown in RPM1-1640 supplemented with FBS, pen/strep, and cytokines (100ng/mL SCF, 50 ng/mL IL6, 20ng/mL IL3)

extract_protocol:
Cells were lysed in buffer RLT (Qiagen) and DNAse-treated RNA extracted using the Qiagen RNeasy Miniprep kit with on-column DNAse. Quality of RNA was confirmed by RIN using a fragment analyzer (Agilent)
poly-A stranded RNAseq libraries were generated from raw RNA
Libraries were pooled and sequenced on a NovaSeq with 100bp paired-end reads to a depth of approximately 120 million reads/sample

treatment_protocol: To induce Chaf1b deletion by CreERT2-mediated recombination of the floxed alleles, cells were treated with B-estradiol at 10e-7M for 48 hours

value: Hematopoietic

value: retroviral MLL-AF9

value: AML

value: WT

value: Vehicle


title: WT replicate 1

description: RNAseq


title: PMSCV-HA-TWIST1 Input


title: WT replicate 3

description: RNAseq


title: hNMP-D1-3

description:
hNMP-D1-3
count1.csv

value: cell line

value: Neural differentiation


title: hNMP-D2-3

description:
hNMP-D2-3
count1.csv

value: differentiating hNMPs


title: KO replicate 3

description: RNAseq

value: KO

value: B-estradiol


title: KO replicate 1

description: RNAseq


title: PolyAconst_Illumina_R3

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

institute: University of Oxford

data_processing: The data was processed using a custom pipeline 'pipeline_count' written using cgatcore and included within the TallyNNN repository (https://github.com/cribbslab/TallyNNN). Briefly, the polyA associated UMI sequence by searching for the polyA region and reverse complementing the read if it does not appear in the correct orientation. The 30bp UMI is then identified upstream of the SMART primer by pattern matching for GTACTCTGCGTTGATACCACTGCTT. We then corrected for errors or remove the read based the number of UMI errors and then the UMI is added to the read name. Next, the TSO associated UMI is identified using the SMART primer sequence AAGCAGTGGTATCAACGCAGAGTAAT. The 30bp UMI sequence is then corrected for errors or remove the read based the number of UMI errors and then the UMI is added to the read name. Both the TSO and polyA associated UMIs and primer sequences are removed from the read sequence.  For transcrip0t level analysis, the fastq file is then mapped against the transcriptome using minimap2 (v2.22) with the following settings: -ax map-ont -p 0.9 --end-bonus 10 -N 3. The resulting sam file was then sorted and indexed using samtools18. A custom script was then used to add the transcript name to the XT tag of the samfile for downstream counting by homotrimer deduplication, UMI-tools or mclUMI. For gene level analysis, the fastq data was mapped using minimap2 using the following setting: -ax splice -k 14 --sam-hit-only --secondary=no --junc-bed. The resulting sam file was then sorted and indexed followed by feature annotation using featurecounts (v2.0.1) using the following settings to generate an annotated bam file: featureCounts -a (gtf) -o (output) -R BAM. This bam file was then used for downstream counting by UMI-tools or mclUMI. The reference transcriptome and genomes used for the analysis were hg38_ensembl98 and mm10_ensembl88. Downstream differential expression was performed using Deseq2.

source_name: JJN3 and 5TGM1 cells

growth_protocol: JJN3, 5TGM1 and RM82  cells were cultured in RPMI with 10% FBS and 1% Pen/Strep in a 37oC incubator with 5% CO2.

extract_protocol:
RNA from cells was harvested using Trizol reagent. Libraries were constructed using NEBNext® Ultra RNA Library Prep Kit for Illumina®
RNA libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: RM82 cells were treated with either DMSO control or SGC-CLK1 inhibitor

value: JJN3 and 5TGM1 cells


title: hNMP-D1-2

description:
hNMP-D1-2
count1.csv


title: PolyAconst_Illumina_R2


title: S8: Sibling control of Patient2

description: feeder-free growth

value: female

value: control

value: iPS cells


title: B7: Reference iPS

description: feeder-free growth

value: undifferentiated


title: E1: NEDAMSS patient2

description: feeder-free growth

value: male

value: NEDAMSS


title: hNMP-D1-1

description:
hNMP-D1-1
count1.csv


title: E10: Maternal control of Patient1

description: feeder-free growth


title: N9 Fructose replicate_3

city: Madison

first: Daniel

last: Shippy

address: 1111 Highland Avenue

institute: UW-Madison

description: Each processed file has all the groups in one file.

data_processing:
Library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Paired-end clean reads were aligned to the reference genome using HiStat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include gene counts for each sample.
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample.

growth_protocol: N9 microglial cells were routinely cultured in RPMI 1640 media with FBS (5%) and penicillin/streptomycin (1%).

extract_protocol:
RNA was extracted from cells using Qiagen Rneasy Plus Mini Kit.
RNA libraries were prepared for sequencing using standard protocols by Novogene.

treatment_protocol: N9 microglial cells were cultured in control media (glucose-free dmem, dialyzed serum (5%), glucose (3 mM) and fructose (5 mM)), high glucose media (control media with 15 mM glucose), and high fructose media (control media with 15 mM fructose) for 18 hours and stimulated with LPS (1 µg/ml) for an additional 6 hours.

value: Microglia

value: High fructose media + LPS


title: E4: Sibling control of Patient1

description: feeder-free growth


title: KO replicate 2

description: RNAseq

value: Hematopoietic

value: retroviral MLL-AF9

value: AML


title: hESC-3

description:
hESC-3
count1.csv

value: cell line

value: embryonic stem cells

value: WT


title: PolyAconst_Illumina_R1


title: N9 Fructose replicate_2


title: hESC-2

description:
hESC-2
count1.csv

value: Neural differentiation


title: hESC-1

description:
hESC-1
count1.csv


title: PMSCV-Pig Empty Vector Input

value: bone marrow

value: mesenchymal stem cell

value: PMSCV-Pig transduced


title: N9 Fructose replicate_1


title: N9 Glucose replicate_3

value: High glucose media + LPS


title: hNMP-D2-1

description:
hNMP-D2-1
count1.csv

value: differentiating hNMPs


title: N9 Glucose replicate_2


title: SNU-449, TGFb + Galunisertib, rep2

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

institute: INSERM

description: SNU-449 cells cotreated with TGFb1 and Galunisertib - Replicate 2

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µ of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (G2565) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09_ssSurrogates and Grid: 028004_D_F_20110325). Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies).

label_protocol: Total RNA was amplified and labeled with Cy3 fluorescent dye using Agilent one color low-input QuickAmp labeling kit following according to the manufacturer's instructions. Starting from 150 ng total RNA, amplification yield was 3.14 ± 0.49 µg cRNA and specific activity was 24.13 ± 3.02 pmol Cy3 per µg cRNA.

growth_protocol: PRC/PRF/5 and SNU-449 HCC cell lines were purchased from ATCC (www.lgcstandards-atcc.org) and cultured as previously described (PMID: 34825776). ATCC performed cell line authentication by STR DNA profiling. Cells were treated for 16 hours with 1 ng/mL recombinant human TGF-β1 (R&D Systems, Minneapolis, MN) and/or 10 μM LY2157299 (Sigma-Aldrich, St. Louis, MO) after overnight serum starvation. All cell cultures were conducted at 37 ◦C in a 5% CO2 atmosphere. Independent culture experiments were carried out in triplicate.

extract_protocol: Total RNA was extracted and purified using the RNAeasy kit (Qiagen, Valencia, CA, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: All cell cultures were conducted at 37°C in a 5% CO2 atmosphere and then submitetd to RNA extration and gene expression profiling. Independent culture experiments were carried out in triplicate.


title: SNU-449, TGFb + Galunisertib, rep1

description: SNU-449 cells cotreated with TGFb1 and Galunisertib - Replicate 1


title: wild type, 1 h, replicate 1

city: Kyoto

first: Rifat

middle: Ara

last: Najnin

state: Kyoto

address: Yoshida Konoe, Sakyo-ku

department: Radiation Genetics

institute: Kyoto University

description: Nascent RNA

data_processing:
CAGE libraries were sequenced using single-end reads of 75 nt on a NextSeq 500 instrument (Illumina). Obtained reads (CAGE tags) were mapped to the human hg38 genome using BWA (version 0.5.9) (https://arxiv.org/abs/1303.3997). Unmapped reads were then mapped by HISAT2 (version 2.0.5). CAGE tag count data were clustered through the CAGEr toolbox using Paraclu algorithm  with default parameters. Clusters with count per million (CPM) <0.2 were discarded. Differentially expressed genes at each timepoint were detected using DESeq2 (version 1.20.0).
Assembly: hg38
Supplementary files format and content: BigWig
Library strategy: NET-CAGE

source_name: Breast

growth_protocol: MCF-7 cells were cultured in a serum-free medium for 24–26 h before treatment with estrogen.

extract_protocol:
RNA was extracted as described previously (Hirabayashi et al.,PMID: 31477927).Briefly, fresh cells were lysed in the presence of α-amanitin, and the nuclear insoluble fraction was isolated. Following DNase treatment, RNA was purified using the miRNeasy Mini kit (Qiagen) according to the manufacturer’s instructions.
NET-CAGE library preparation, sequencing, mapping, and gene expression analysis were performed by DNAFORM (Kanagawa, Japan). In brief, the cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5′ cap structures of RNAs were oxidized and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both cDNA ends, double-stranded cDNA libraries (CAGE libraries) were constructed.

treatment_protocol: To assess the effect of ATM loss on the E2 response, 10 µM of ATMi was added to the medium together with E2 or ethanol; DMSO was added 30 min prior to the E2 treatment as a control. Three replicates of cells cultured in three 15-cm dishes (approximately 10 million cells per dish) were treated simultaneously and pooled for analysis. Replicates were processed simultaneously throughout to avoid potential batch effects.

value: Breast

value: Breast cancer cell

value: Wild-type

value: Estrogen


title: wild type + DMSO + ethanol, 2 h, rep 1

description: Nascent RNA

value: DMSO,Ethanol


title: wild type, 0 h, replicate 1

description: Nascent RNA

value: No treatment


title: N9 Glucose replicate_1

value: Microglia


title: SNU-449, TGFb + Galunisertib, rep3

description: SNU-449 cells cotreated with TGFb1 and Galunisertib - Replicate 3


title: SNU-449, Galunisertib, rep2

description: SNU-449 cells treated with Galunisertib - Replicate 2

source_name: SNU-449 cells treated with Galunisertib

value: Galunisertib


title: E6: NEDAMSS patient2

description: feeder-free growth

value: male

value: NEDAMSS

value: iPS cells

value: undifferentiated


title: SNU-449, Galunisertib, rep3

description: SNU-449 cells treated with Galunisertib - Replicate 3


title: N9 LPS replicate_3

value: Control media + LPS


title: wild type + DMSO + E2, 2 h, rep 1

description: Nascent RNA

value: DMSO,Estrogen


title: wild type + ATMi + ethanol, 2 h, rep 1

description: Nascent RNA

value: ATMi,Ethanol (vehicle)