title: Donor 3; Sivelestat 100 µg/ml

city: Boston

first: Jonathan

last: Dreyfuss

address: 1 Joslin Pl

institute: Joslin Diabetes Center

data_processing:
The single-cell RNA-seq data was based on the 10X Genomics platform. Raw sequencing data were demultiplexed, aligned to the human genome (Gencode GRCh38.p12) and UMI-collapsed by using CellRanger (v2.2.0)
Genome_build: Gencode GRCh38.p12
Supplementary_files_format_and_content: CSV file of counts with genes as rows and cells-per-sample as columns

source_name: Human islets

extract_protocol:
scRNA-seq was performed using the 3' Chromium Single-Cell Library kit according to manufacturer's instructions
Libraries were constructed using Illumina chemistry: The Single Cell 3’ Protocol produces Illumina-ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1, while Read 2 is used to sequence the cDNA fragment. Sample index sequences are incorporated as the i7 index read. Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired-end sequencing.

treatment_protocol: Human islets were starved in Final Wash media for 3 hours. After, IEQs were treated with DMSO, telaprevir (1 and 100 µg/ml), tebipenem (1 and 100 µg/ml), sivelestat (100 µg/ml), 5-IT (1 µM), Ovalbumin (1 µg/ml) and SerpinB1 (1 µg/ml) for 24 hours. At the end of the incubation, islets were collected and dispersed with Accutase treatment for 30 min at 37°C. After dispersion, cell pellets were washed in PBS and dead cells were sorted out using Miltenyi columns according to the manufacturer's instructions. Finally, cells were counted and resuspended in PBS-0.01% BSA at 1000 cells/µl. 10,000 cells were used as imput for scRNA-Seq procedures.

tag: diabetes status

value: Non diabetic

tag: unos id/rrid

tag: date of treatments


title: RIP_4A2_input_rep1

status: Public on Feb 13 2024

type: SRA

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

country: Japan

institute: RIKEN

library_source: transcriptomic

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: hg38
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

molecule: total RNA

organism: Homo sapiens

source_name: HEK293 T-REx

growth_protocol: DMEM + GlutaMAX-I with 10% FBS at 5% CO2, 37°C

extract_protocol:
Cells were directly lysed in lysis buffer on culture dishes.
For ribosome profiling (Ribo), RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification. For RNA-Seq (RNA), RNA extraction and TruSeq Stranded mRNA Library Prep Kit (Illumina). For RNA pulldown-Seq (RIP), pulldown by streptavidin beads, elution by biotin, RNA extraction, and TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: PP242 treatment was performed for 30 min at 37°C. siRNAs transfection was performed using the TransIT-X2 Dynamic Delivery System for 72 h.

tag: cell line

value: HEK293 T-REx

tag: genotype


title: Donor 3; Telaprevir 100 µg/ml

middle: M

state: MA

department: Bioinformatics & Biostatistics Core

country: USA

growth_protocol: Human islets were obtained by Prodo Lab or IIDP. Upon receipt, human islets were cultured in Miami Media at 37 C 5% CO2. After overnight incubation, 150/200 size-matched IEQs per condition were hand-picked for the following procedure


title: Donor 3; Telaprevir 1 µg/ml


title: DC_28

city: NEW DELHI

first: Anita

last: Chopra

state: DELHI

address: Dr BRA-IRCH AIIMS

department: Laboratory Oncology

country: India

institute: All India Institute of Medical Science

data_processing:
Quality check by FastQC
Trimming of adaptors by Trimmomatic 0.33
Alignment through TopHat2 2.1.1
Assemblies of samples and DEG analysis through Cufflinks package.
GSEA through DAVID data base
Assembly: hg38
Supplementary files format and content: Normalized FPKM values in a text matrix

source_name: Blood

extract_protocol:
RNA was isolated from patient samples by the TRIzol method.
Illumina Truseq total RNA sample preparation kit

tag: tissue

value: Blood

tag: cell type

value: PBMC

tag: disease state


title: DC_27


title: Experiment 3: HA-Tnrc6a_Ago2KO_IP_1

city: Basel

first: Helge

last: Grosshans

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedriche Miescher Institute for Biomedical Research (FMI)

description: Experiment 3

data_processing:
Base calling and quality scoring is performed using RTA software (v3.4.4), demultiplexing with  bcl2fastq2 v2.20.
Alignment was performed as follows: Samples were aligned against the GRCm38 mouse genome assembly from GENCODE (Frankish et al., 2021), primary assembly from release M24).(Rosenbloom et al., 2015) Alignments were performed using STAR version 2.7.3a with settings --outFilterType BySJout --outFilterMultimapNmax 20 --outMultimapperOrder Random --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMmultNmax 1(Gaidatzis et al., 2015). These settings follow ENCODE guidelines and report a single randomly selected alignment for reads that map to the genome no more than 20 times(Langmead et al., 2009) Gene annotations were also obtained from GENCODE release M24, transforming the gtf file into a Bioconductor TxDb object using the makeTxDbFromGFF function from the GenomicFeatures package (version 1.44.0, (Lawrence et al., 2013). Gene-level read counts were obtained by summing the counts from the union of all exons per gene, using the qCount function from the QuasR package (version 1.32.0, (Gaidatzis et al., 2015)) with the created TxDb and parameters orientation = “opposite”.
Assembly: mm10
Supplementary files format and content: csv: First column contains ENSEMBL transcript ID, second column contains ENSEMBL gene ID,  third column contains ENTREZ gene ID, fourth column contains gene symbol (Ensembl identifiers), fifth column contains gene nams (EMSENBL), sixth column contains summed width of exons per gene (quasr package),  columns named 'raw.count' contain raw counts of reads overlapping each gene for each sample, columns named 'rpkm' contain rpkm read counts overlapping each gene for each sample.

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: Mouse embryonic stem cells (mES [129S6/SvEvTac], yGlob [GFP_5xT71BS], stable transfection FLAG-Cas9::T2A::Blasticidin) were cultured on gelatin-coated dishes in mES medium (DMEM [Gibco; 11995065]) supplemented with 15% fetal bovine serum [Gibco], 1 x non-essential amino acids [Gibco], 1mM sodium pyruvate [Gibco], 2mM L-glutamine [Gibco], 0.1 mM ß-mercaptoethanol [Sigma], 50 µg/ml penicillin, 80 µg/ml streptomycin, 1x MycoZap™ Prophylactic [Lonza; VZA-2032], 1x ESGRO® LIF [MerckMillipore; ESG1107]) at 37 °C in 5% CO2.

extract_protocol:
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
TruSeq Illumina Total RNA-seq (stranded - high input)

value: GFP_5xT71BS, HA-AVI-Tnrc6a,Ago2-/-

tag: group

value: IP

value: embryonic stem cells


title: Donor 3; DMSO


title: Experiment 3: HA-Tnrc6a_IP_3

description: Experiment 3

value: GFP_5xT71BS, HA-AVI-Tnrc6a


title: DC_26


title: Donor19, Oleic Acid, 3h

city: Leiden

first: Thomas

middle: B

last: Kuipers

address: Einthovenweg 20

country: Netherlands

institute: LUMC

description:
Passed QC
D19-OA-3h

data_processing:
FastQC v0.11.9 was used for checking raw read QC
Adapter clipping was performed using Cutadapt v2.10
RNAseq reads were aligned to human reference genome GRCh38 using Ensembl v99 & star v2.7.5a
Gene quantification was then performed using htseq-count v0.12.4
Assembly: GRCh38
Supplementary files format and content: TSV, gene raw count

source_name: Buffy Coat

growth_protocol: CD4+ T cells were isolated from a buffy coat using magnetic beads and rested for 24h in DMEM supplemented with 5% fetal calf serum (FCS), pen/strep, glutamax, and IL-2 in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Zymo Quick-DNA/RNA Microprep Plus Kit (Zymo). 1μg of total RNA was used for the construction of sequencing libraries.
RNA-Seq libraries were prepared from 200ng RNA using the Illumina Truseq stranded mRNA library prep (Illumina, 20020595) after depletion of ribosomal RNA with Ribo Zero Gold (Illumina, 20037135)

treatment_protocol: After 24h resting, the cells were exposed to either 30μg/mL oleic acid diluted in ethanol and dissolved in DMEM supplmented with 2% fatty acid free (FAF) bovine serum albumin (BSA), pen/strep, and glutamax or to the control, ethanol dissolved in DMEM supplmented with 2% FAF BSA, pen/strep, and glutamax for either 30min, 3 hours, 24 hours, 48 hours, or 72 hours.

value: Buffy Coat

value: CD4+ T cell

tag: treatment

value: Oleic Acid

tag: donor

value: Donor 19

tag: time

tag: batch

value: batch 2


title: RNA_naive_rep2

value: Naive


title: PPSR ICB Untreated Cell Line 1

city: Notre Dame

first: Xin

last: Lu

state: IN

address: 109 Galvin Life Science Center

department: Biological Sciences

institute: University of Notre Dame

data_processing:
PolyA selection for mRNA species (eukaryotic)
STAR Transcripts were generated

source_name: PPS-ICBR

extract_protocol:
Zymo Research Miniprep was used to extract the RNA of the cels
Samples were sent to GeneWiz

value: PPS-ICBR

value: Immunotherapy and Castration Resistant Prostate Cancer Cell Line

value: PTEN/P53/SMAD4 Knock Out

value: No Treatent


title: Experiment 3: HA-Tnrc6a_IP_2

description: Experiment 3


title: DC_25


title: Donor19, Oleic Acid, 30m

description:
Passed QC
D19-OA-30m


title: Donor 2; Sivelestat 100 µg/ml

value: Non diabetic


title: Donor19, Ethanol, 72h

description:
Passed QC
D19-EtOH-72h

value: Ethanol


title: DC_23

value: Blood

value: PBMC


title: Experiment 3: HA-Tnrc6a_IP_1

description: Experiment 3

value: IP


title: Donor 2; Telaprevir 100 µg/ml


title: DC_24


title: Donor19, Oleic Acid, 24h

description:
Passed QC
D19-OA-24h


title: Donor 2; Telaprevir 1 µg/ml


title: DC_22


title: Donor19, Ethanol, 24h

description:
Passed QC
D19-EtOH-24h


title: Experiment 3: untagged control_IP_3

description: Experiment 3

value: GFP_5xT71BS (mES [129S6/SvEvTac], yGlob [GFP_5xT71BS], stable transfection FLAG-Cas9::T2A::Blasticidin)

value: embryonic stem cells


title: DC_21


title: Donor19, Ethanol, 48h

description:
Passed QC
D19-EtOH-48h

value: Buffy Coat


title: Donor19, Ethanol, 30m

description:
Passed QC
D19-EtOH-30m

value: CD4+ T cell


title: DC_20


title: Donor 2; DMSO


title: DC_19


title: Donor 1; Telaprevir 100 µg/ml


title: Donor17, Oleic Acid, 72h

description:
Passed QC
D17-OA-72h

value: Oleic Acid

value: Donor 17


title: Experiment 3: HA-Tnrc6a_Upf1KO_input_3

description: Experiment 3

value: GFP_5xT71BS, HA-AVI-Tnrc6a, Upf1-/-

value: input


title: Donor 1; Telaprevir 1 µg/ml


title: Donor17, Oleic Acid, 48h

description:
Passed QC
D17-OA-48h

value: batch 2


title: DC_18


title: DC_17


title: Donor17, Oleic Acid, 24h

description:
Passed QC
D17-OA-24h


title: Experiment 3: HA-Tnrc6a_Upf1KO_input_1

description: Experiment 3


title: Donor 1; DMSO


title: Experiment 3: untagged control_IP_2

description: Experiment 3


title: Donor19, Ethanol, 3h

description:
Passed QC
D19-EtOH-3h

value: Donor 19


title: RIP_4A1_siLARP1_pulldown

description: RIP-Seq SBP pulldown

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Genome_build: hg38
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

value: HEK293 T-REx

value: LARP1 siRNA


title: Experiment 3: HA-Tnrc6a_Ago2KO_input_3

description: Experiment 3

value: GFP_5xT71BS, HA-AVI-Tnrc6a, Ago2-/-


title: Experiment 3: untagged control_IP_1

description: Experiment 3


title: DC_16


title: RIP_4A1_siLARP1_input_replicate2

description: RIP-Seq input


title: Donor 1; Sivelestat 100 µg/ml

value: Non diabetic


title: Experiment 3: HA-Tnrc6a_Ago2KO_input_2

description: Experiment 3


title: Donor17, Ethanol, 72h

description:
Passed QC
D17-EtOH-72h

value: Ethanol


title: Donor17, Oleic Acid, 3h

description:
Passed QC
D17-OA-3h


title: RIP_4A1_siLARP1_input_replicate1

description: RIP-Seq input


title: Experiment 3: HA-Tnrc6a_Upf1KO_input_2

description: Experiment 3


title: DC_14

value: Blood

value: PBMC


title: Experiment 3: HA-Tnrc6a_input_3

description: Experiment 3

value: GFP_5xT71BS, HA-AVI-Tnrc6a


title: RIP_4A1_siControl_pulldown_replicate2

description: RIP-Seq SBP pulldown

value: Control siRNA


title: DI_13


title: Experiment 3: HA-Tnrc6a_input_2

description: Experiment 3

value: embryonic stem cells


title: Donor17, Ethanol, 24h

description:
Passed QC
D17-EtOH-24h

value: Buffy Coat

value: CD4+ T cell


title: RIP_4A1_siControl_pulldown_replicate1

description: RIP-Seq SBP pulldown


title: DI_12


title: Donor17, Ethanol, 48h

description:
Passed QC
D17-EtOH-48h

value: Donor 17


title: Experiment 3: HA-Tnrc6a_input_1

description: Experiment 3


title: Experiment 3: untagged control_input_3

description: Experiment 3

value: GFP_5xT71BS (mES [129S6/SvEvTac], yGlob [GFP_5xT71BS], stable transfection FLAG-Cas9::T2A::Blasticidin)


title: RIP_4A1_siControl_input_replicate1

description: RIP-Seq input


title: DI_11


title: Donor17, Ethanol, 30m

description:
Passed QC
D17-EtOH-30m


title: DI_9


title: RIP_4A1_pulldown_replicate2

description: RIP-Seq SBP pulldown


title: Experiment 3: HA-Tnrc6a_Ago2KO_input_1

description: Experiment 3

value: input


title: DC_15


title: DI_10


title: Donor16, Oleic Acid, 72h

description:
Passed QC
D16-OA-72h

value: Oleic Acid

value: Donor 16

value: batch 2


title: Donor16, Oleic Acid, 48h

description:
Passed QC
D16-OA-48h


title: DI_8


title: Experiment 3: untagged control_input_1

description: Experiment 3


title: Donor17, Oleic Acid, 30m

description:
Passed QC
D17-OA-30m


title: RIP_4A1_input_replicate2

description: RIP-Seq input

value: HEK293 T-REx


title: Experiment 3: untagged control_input_2

description: Experiment 3


title: Donor16, Oleic Acid, 24h

description:
Passed QC
D16-OA-24h


title: Peripheral Blood Mononuclear Cells, PI-ME/CFS, Baseline MECFS_321

city: Bethesda

first: Avindra

last: Nath

state: Maryland

address: 10 Center Drive

institute: NIH/NINDS

data_processing:
Illuminasoftware bcl2fastq v.2.17
RNA sequences were subjected to quality control  through FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Adapters were removed using Trimmomatic: https://github.com/timflutre/trimmomatic
Alignment to the human genome (GRCh38) using STAR
Gene expression levels were quantified using FeaturesCounts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene expression levels for each sample

extract_protocol:
RNA was extracted from PBMC’s of participants using miRNeasy Micro Kit (QIAGEN).
Dual index libraries were constructed with at least one unique index per each patient library using the TruSeq Stranded Total RNA HT Kit (Illumina).

tag: Sex

value: Female


title: DI_7


title: DI_6


title: Donor16, Oleic Acid, 3h

description:
Passed QC
D16-OA-3h


title: Donor17, Ethanol, 3h

description:
Passed QC
D17-EtOH-3h


title: Ribo_4A1KO_PP242_1uM

description: Ribosome profiling

data_processing:
Library strategy: Ribo-seq
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Genome_build: hg38
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

value: EIF4A1 KO

value: PP242 1 microM


title: Donor16, Oleic Acid, 30m

description:
Passed QC
D16-OA-30m


title: Peripheral Blood Mononuclear Cells, HV, Baseline MECFS_116

value: Blood


title: RIP_4A1_input_replicate1

description: RIP-Seq input


title: RIP_4A1_siControl_input_replicate2

description: RIP-Seq input


title: DI_5

value: PBMC


title: RIP_4A1_pulldown_replicate1

description: RIP-Seq SBP pulldown


title: DI_4


title: Peripheral Blood Mononuclear Cells, HV, Baseline MECFS_111

value: Male


title: Donor16, Ethanol, 72h

description:
Passed QC
D16-EtOH-72h

value: Ethanol


title: Peripheral Blood Mononuclear Cells, HV, Baseline MECFS_109


title: Ribo_4A1KO_DMSO_replicate2

description: Ribosome profiling

value: DMSO


title: Donor16, Ethanol, 48h

description:
Passed QC
D16-EtOH-48h

value: Buffy Coat


title: Peripheral Blood Mononuclear Cells, PI-ME/CFS, Baseline MECFS_308


title: DI_2


title: Peripheral Blood Mononuclear Cells, HV, Baseline MECFS_106


title: Ribo_4A1KO_PP242_10uM

description: Ribosome profiling

value: PP242 10 microM


title: Peripheral Blood Mononuclear Cells, HV, Baseline MECFS_108


title: DI_3


title: Ribo_4A1KO_DMSO_replicate1

description: Ribosome profiling


title: Donor16, Ethanol, 24h

description:
Passed QC
D16-EtOH-24h

value: CD4+ T cell


title: Donor16, Ethanol, 3h

description:
Passed QC
D16-EtOH-3h


title: Ribo_naive_PP242_10uM

description: Ribosome profiling

value: Naive


title: Peripheral Blood Mononuclear Cells, HV, Baseline MECFS_104


title: Ribo_naive_PP242_1uM

description: Ribosome profiling


title: Donor16, Ethanol, 30m

description:
Passed QC
D16-EtOH-30m


title: DI_1


title: Ribo_naive_DMSO_replicate2

description: Ribosome profiling


title: Cardiac mac from TAC HSC rep3

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

institute: Chiba University

description: Cardiac macrophage

data_processing:
Reads were aligned to the mm10 mouse genome using STAR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bedGraph files were generated using Homer.

source_name: Cardiac mac from TAC HSC rep3

growth_protocol: CD45.2 mice underwent TAC operations, and CD45.1 mice underwent the sham operations. Four weeks after the operation, HSCs were isolated. The mixture of 100 HSCs from control CD45.1 mice and post-TAC CD45.2 mice was transplanted into irradiated CD45.1/CD45.2 mice with 100,000 of CD34+ Lin- Sca1+ cKit+ cells isolated from CD45.1/CD45.2 mice. Two months after HSC transplantation, blood monocytes and cardiac tissue macrophages were isolated.

extract_protocol:
The biventricles excised from mice were mechanically minced. The tissue from 1 heart was then incubated in 1 ml of DMEM containing 450 U/ml of collagenase I (Sigma-Aldrich), 60 U/ml of hyaluronidase (Sigma-Aldrich), and 60 U/ml of DNase-I (Sigma-Aldrich) for 45 min at 37 °C. The cells in the suspension were vortexed for 20 sec, filtered through a 40 μm cell strainer, and washed by 12 ml cold HBSS supplemented with 2% FBS and 0.2% BSA. The cells were then washed with PBS, and resuspended in FACS buffer. Cd45+Cd11b+Cd64+Ly6c-Ly6g- cells were separated as cardiac macrophages by FACS Aria III. Peripheral blood was collected by retro-orbital bleeding into tubes coated with K3-EDTA (Greiner). Cd45+Cd11b+Ly6c+Ly6g- cells were separated as circulating monocytes by FACS Aria III. Sorted cells were lysed in Buffer RLT plus (QIAGEN), and RNA was purified using RNeasy micro Kit (QIAGEN).
Poly-A mRNA was extracted from total RNA by using an Oligo-dT beads of NEBNext Poly(A) RNA Magnetic Isolation Module (NEB), after which RNA-seq libraries were prepared using a NEBNext Ultra II RNA Library Preo Kit for Illumina (NEB) according to the manufacturer’s protocol.

tag: strain

value: Cardiac resident macrophages

value: Transverse aortic constriction operation


title: Ribo_naive_DMSO_replicate1

description: Ribosome profiling


title: Donor15, Oleic Acid, 72h

description:
Passed QC
D15-OA-72h

value: Oleic Acid

value: Donor 15


title: Donor15, Oleic Acid, 48h

description:
Passed QC
D15-OA-48h

value: batch 2


title: Peripheral Blood Mononuclear Cells, HV, Baseline MECFS_103

value: Female


title: Cardiac mac from TAC HSC rep2

description: Cardiac macrophage

source_name: Cardiac mac from TAC HSC rep2


title: NCH644_diff_3

type: RNA

city: Lille

first: Mohamed

last: Elati

address: Bd du Professeur Jules Leclercq

country: France

institute: University of Lille

hyb_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and

scan_protocol: scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm. Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2.

data_processing: CEL files were further processed with Affymetrix Expression Console software version 1.4.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

label: biotin

source_name: NCH644 cell line differentitated state

label_protocol: Following fragmentation and end-labeling, 3 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Human Gene 2.0 ST arrays (Affymetrix) interrogating over 40 0000 RefSeq transcripts and ~ 11000 LncRNAs represented by approximately 27 probes spread across the full length of the transcript.

extract_protocol: Biotinylated single strand cDNA targets were prepared, starting from 200 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations.

value: glioblastoma


title: MMP-9-IN-1,ear skin,mouse No. 4

city: Kaifeng

first: ruizhen

last: wang

address: Jinming Avenue, Kaifeng City, Henan Province

country: China

institute: Henan University

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows: 1) Remove the reads containing the adaptor(adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
The filtered "Clean Reads" are saved in FASTQ format. SOAPnuke(Version v1.5.2)  Official Websitehttps://github.com/BGI-flexlab/SOAPnuke
Hierarchical Indexing for Spliced Alignment of Transcripts (HISTAT) is software for mapping RNA-seq reads.HISAT will use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these
Species: Mus_musculus；Source: NCBI；Reference Genome Version: GCF_000001635.27_GRCm39

source_name: ear

growth_protocol: Healthy C57BL/6 mice (6-8 weeks) were selected and bred in Specific pathogen-free (SPF) animal chambers in separate cages. The room temperature was maintained at 20-27℃ and the normal day and night alternated, during which the normal diet was guaranteed.

extract_protocol:
After the completion of the experiment, the left ear tissue samples of mice were collected for RNA extraction and sent to Wuhan Huada BGI Sequencing Company for sequencing.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSeq platform (BGI-Wuhan, China).

treatment_protocol: All mice were intraperitoneally smeared with 25 μL of 0.3 % DNFB on the first day. On the sixth day, 10 μL 0.25 % DNFB was applied to the left ear of the experimental group and 10 mg / Kg MMP-9-IN-1 was injected intraperitoneally. The left ear of the control group was coated with 10 μL 0.25 % DNFB and injected intraperitoneally with an equal volume of solvent ( 10 % DMSO + 40 % PEG300 + 50 % PBS ). After 4 days of continuous operation, the ears were collected for RNA-Seq.

value: ear


title: MMP-9-IN-1,ear skin,mouse No. 3


title: Cardiac mac from control HSC rep2

description: Cardiac macrophage

source_name: Cardiac mac from control HSC rep2

value: Sham operation


title: Donor15, Ethanol, 48h

description:
Passed QC
D15-EtOH-48h


title: MMP-9-IN-1,ear skin,mouse No. 2


title: Donor15, Oleic Acid, 24h

description:
Passed QC
D15-OA-24h


title: NCH421_stem_3

source_name: NCH421k cell line stem like state


title: Vehicle,ear skin,mouse No. 3


title: Vehicle,ear skin,mouse No. 2


title: NCH421_diff_3

source_name: NCH421k cell line differentitated state


title: Donor15, Ethanol, 3h

description:
Passed QC
D15-EtOH-3h


title: Blood monocyte from control HSC rep3

description: Monocyte

source_name: Blood monocyte from control HSC rep3

value: Monocytes in peripheral blood


title: MMP-9-IN-1,ear skin,mouse No. 1


title: Donor15, Ethanol, 72h

description:
Passed QC
D15-EtOH-72h


title: NCH644_diff_2


title: Donor15, Oleic Acid, 30m

description:
Passed QC
D15-OA-30m


title: post-TAC HSC rep3 [ATAC-seq]

description: TAC HSC ATAC-seq

library_source: genomic

molecule: genomic DNA

source_name: Hematopoietic stem cell

extract_protocol:
Sorted 5,000 CD45.2+Lin-Sca1+cKit+CD34-Flt3-CD150+ were washed with 400 μl of resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2), and lysed in 50 μl of resuspension buffer supplemented with 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin for 3 min on ice. Nuclei were washed with 1 ml of resuspension buffer supplemented with 0.1% Tween-20, and then 50 μl of transposition mix (16.5 μl PBS, 5 μl water, 25 μl 2× TD Buffer, 2.5 μl Tn5 enzyme (Illumina), 0.5 μl 1% digitonin, and 0.5 μl 10% Tween-20) was added to the cell pellet. The samples were incubated for 30 min at 37 °C. Reactions were cleaned up with MinElute Reaction Cleanup Kit (QIAGEN) and eluted by 12 μl of EB buffer.
Fragmented DNA were amplified by NEBNext Ultra II Q5 with ATAC primers for five cycles. Additional PCR cycles were evaluated by real-time PCR. Final product was cleaned with Ampure XP Beads (Beckman Coulter).

value: Hematopoietic stem cells


title: WT_YPD_excess_R2

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

country: Canada

institute: Universite de Montreal

data_processing:
Sequencing reads were filtered with fastp version 0.23.2
Filtered reads were mapped to the reference genome sequence of strain SC5314 with STAR version 2.7.9a
The number of reads mapping on each of the genes was calculated by featurecount version 2.0.1
Differential gene expression was calculated with DESeq2 version 1.26.0.
Assembly: reference genome sequence of strain SC5314
Supplementary files format and content: raw_counts_Mn.txt

organism: Candida albicans

source_name: Yeast cells

growth_protocol: Overnight cultures of SC5314 strain were diluted to an OD600 of 0.1 in 60 ml of fresh SC-Mn medium and grown at 30°C under agitation (200 rpm) to early logarithmic phase (OD600=0.4).

extract_protocol:
Total RNA was extracted using an RNAeasy purification kit (Qiagen) and glass bead lysis in a Biospec Mini 24 bead-beater
The NEBNext UltraTM II RNA Library Prep Kit for Illumina was used to construct the RNA-seq library following the manufacturer’s instruction.

treatment_protocol: Cultures were then either left untreated or exposed to 1 mM MnCl2 and incubated at 30°C for 5 and 90 min. For RNA-seq profiling of Mn excess, overnight cultures of WT cells were diluted to an OD600 of 0.1 in fresh 100 ml YPD and incubated with shaking at 30°C to an OD600 of 0.8 and split into 50-ml cultures. MnCl2 was added to the experimental culture to a final concentration of 7.5 mM, while an equal volume of sterile water was added to the control culture and incubated for 30 min. Cells were harvested by centrifugation and were quick-frozen and stored at -80°C.

value: Yeast cells

value: WT

value: 30 min in YPD MnCl2-free medium


title: Donor15, Ethanol, 30m

description:
Passed QC
D15-EtOH-30m

value: Buffy Coat

value: Ethanol


title: Cardiac mac from control HSC rep1

description: Cardiac macrophage

source_name: Cardiac mac from control HSC rep1


title: Vehicle,ear skin,mouse No. 4


title: NCH421_stem_2


title: Cardiac mac from TAC HSC rep1

description: Cardiac macrophage

source_name: Cardiac mac from TAC HSC rep1


title: post-TAC HSC rep2 [ATAC-seq]

description: TAC HSC ATAC-seq


title: NCH644_stem_2

source_name: NCH644 cell line stem like state


title: NCH421_diff_2


title: NCH644_stem_3


title: WT_Mn_excess_R2

value: 30 min with 7.5 mM MnCl2


title: Blood monocyte from control HSC rep2

description: Monocyte

source_name: Blood monocyte from control HSC rep2


title: Donor14, Oleic Acid, 24h

description:
Passed QC
D14-OA-24h

value: CD4+ T cell

value: Donor 14

value: batch 1


title: Donor15, Oleic Acid, 3h

description:
Passed QC
D15-OA-3h

value: Oleic Acid

value: Donor 15


title: Cardiac mac from control HSC rep3

description: Cardiac macrophage

source_name: Cardiac mac from control HSC rep3

value: Cardiac resident macrophages


title: Control HSC rep3 [ATAC-seq]

description: Control HSC ATAC-seq


title: SD and BD HTO library lane 2

description:
10X Genomics Chromium
AXL2

library_source: other

data_processing:
Barcode processing, alignment, filtering, and UMI counting were performed using the Cell Ranger analysis pipeline (v. 6.1) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Sample demultiplexing was performed using the CITE-seq-Count pipeline (v. 1.4) (https://hoohm.github.io/CITE-seq-Count/).
Cells with larger than 500 UMI counts in the demultiplexing step were used for downstream analysis in R (v. 4.1).
Assembly: The mouse transcriptome reference (refdata-gex-mm10-2020-A.tar.gz) provided by Cell Ranger is used.
Supplementary files format and content: Cell barcodes and feature names are in the format of .tsv. The count matrix is of the format of .mtx.

molecule: protein

source_name: Tumor

extract_protocol:
10x genomics Single Cell RNA Sequencing  The following protocol was followed to prepare samples for 10x genomics single cell RNA sequencing:  1, Single cell preparation   1, prepare the dissociation medium based on mouse Tumor Dissociation Kit (130-096-730, Miltenyi Biotec) in 15ml tube   2, Cut 0.04-1g tumor in 10cm dish and add appropriate dissociation medium followed by mincing the tumor with razor into tissue slurry.   3, Transferring the tissue slurry with cutted 1ml tip into 15ml tube with dissociation medium and rotating in 37 degree for 1h  4, After rotating, entrifuge the sample at 400g, 4oC for 5min    5, Vacuum the supernatant away and add 10ml cold PBS and filtering through 40 or 70uM strainer on the top of 50ml tube  6, transferring the cell suspension to 15ml tube and centrifuge at 400g, 4oC for 5min.   7, Aspirate supernatant from cell pellet. Resuspend cell pellet in 3.5 mL 70% Percoll by pipetting up and down. Bring total volume to 4 217 mL with 70% Percoll.   8. Carefully layer a total of 4 mL of 37% Percoll on top of the 70% layer without allowing intermixing of the two Percoll densities. This can be achieved by using a p1000 micropipette and slowly dripping the 37% Percoll onto the sidewall of the conical tube while the conical tube is held at a slight (~45 degree) angle.   9. Carefully layer a total of 4 mL of 30% Percoll on top of the 37% layer without allowing intermixing of the two Percoll densities. This can be achieved as described above. The final layered solution should consist of three distinct layers.   10. Centrifuge sample in a swinging bucket centrifuge for 25 minutes at 800g at room temperature with the acceleration at the lowest setting and no break. Following centrifugation, there will be a buffy leukocyte layer at the interface of the red 37% and clear 70% Percoll layers and a thick myelin layer at the top of the sample.  11. Using a vacuum aspirator connected to a p1000 micropipette tip, remove layers above buffy leukocyte layer at the interface of the 37% and 70% Percoll layers. Perform this step slowly, keeping the micropipette tip at the surface of the liquid (as opposed to submerged) to ensure the myelin layer is thoroughly removed and minimizing disturbance of the buffy leukocyte layer. Once within 1-2 mL of the buffy leukocyte layer, use a p1000 micropipette with a wide-bore tip to gently remove the remaining Percoll above the buffy leukocyte layer.   12. Using a p1000 micropipette with a fresh tip, extract the buffy leukocyte layer and place it in a new 15 mL conical tube. No more than 2 mL of Percoll on the top or bottom of the buffy leukocyte layer should be extracted.   13. Bring the volume of extracted cells up to 15 mL with cold 1x PBS and centrifuge for 7 minutes at 400g at 4C with the acceleration and brake set to medium settings.   14. Aspirate supernatant from cell pellet, leaving as minimal of a volume of residual liquid as possible without disturbing the cell pellet. Resuspend cell in 1ml staining buffer.  A small aliquot of cells may be taken out to verify the preparation largely consists of debris-free single cells and to obtain a cell count and/or examine viability.     CRITICAL: Centrifuge used for Percoll gradient centrifugation in step 10 must be set according to the indicated speed and temperature settings. A very low acceleration and no break will prevent early and late disturbances of the Percoll gradient, which could significantly reduce cell yield. Also, centrifugation must occur at room temperature as the density of Percoll would be changed at lower or higher temperatures, compromising cell yield.  CRITICAL: Once the Percoll gradient is fully layered in step 9, the sample should be  centrifuged within 10 min as the 70%layer containing cells can begin to partition, slightly  compromising cell yield. Prepared gradients should be maintained at room temperature  before centrifugation.  CRITICAL: Minimize the amount of Percoll taken up when extracting the buffy leukocyte  layer in step 12. Extracting excessive amounts of Percoll will make it impossible to pellet  the cells, which is necessary to optimally remove Percoll.  2, Cell Blocking, Staining, and Washing  1, Pellet 0.5 million cell and Resuspend cell pellet in 50 uL pre-prepared Fc Receptor block. Incubate on ice for 20 min.  2. Prepare CITE-seq antibody cocktail as shown below. Add 50 uL antibody cocktail to sample, pipetting up and down to mix with the sample. Incubate on ice for 25 min.     3. Add at least 5mL CITE-seq staining buffer to sample and centrifuge for 5 min at 350–400g at 4oC with the acceleration and brake set to medium settings.  4. Aspirate supernatant from the cell pellet. Resuspend in at least 5 mL CITE-seq Wash Buffer A and centrifuge for 5min at 400g at 4oC with the acceleration and brake set to medium settings.  5. Aspirate supernatant from the cell pellet. Resuspend in at least 5 mL CITE-seq Wash Buffer B and centrifuge for 5min at 400g at 4oC with the acceleration and brake set to medium settings.  6. Aspirate supernatant from the cell pellet. If multiple samples were prepared and hashed, combine individual samples in one tube. Resuspend individual sample or pooled samples in 500 mL CITE-seq Wash Buffer C and aliquot 40 uL of the sample to perform a cell count. Add at least 4.5 mL CITE-seq Wash Buffer C and centrifuge sample for 5 min at 400g at 4oC with the acceleration and brake set to medium settings. While cells are pelleting, count the aliquoted cells.  7. Resuspend cells in CITE-seq staining buffer at a concentration of 1,600 cells/mL for 10X superloading.
scRNAseq using the 10X Genomics Chromium platform

treatment_protocol: A 1,3 Butanediol Supplemented Diet (BD) was made by means of using a mixture of 80mL of 1,3- butanediol (Sigma-Aldrich 309443) and 120mL of water mixed with 198g of standard chow (Teklad 2918) and 2g of Saccharine (Sigma-Aldrich 109185). Mice on a BD diet were given fresh food every other day.

value: Tumor

value: PPS-ICBR

tag: phenotype

value: ICB resistant prostate cancer cells

value: Standard diet (SD); 1,3 butanediol diet (BD)


title: Control HSC rep2 [ATAC-seq]

description: Control HSC ATAC-seq

value: Hematopoietic stem cells

value: Sham operation


title: Donor15, Ethanol, 24h

description:
Passed QC
D15-EtOH-24h

source_name: Buffy Coat

value: batch 2


title: Vehicle,ear skin,mouse No. 1

value: ear


title: Blood monocyte from control HSC rep1

description: Monocyte

source_name: Blood monocyte from control HSC rep1

value: Monocytes in peripheral blood


title: Donor14, Oleic Acid, 72h

description:
Passed QC
D14-OA-72h

value: Buffy Coat


title: WT_Mn_90min_R1

value: Yeast cells

value: WT

value: 90 min in SC+MN


title: Control HSC rep1 [ATAC-seq]

description: Control HSC ATAC-seq


title: Donor14, Oleic Acid, 48h

description:
Passed QC
D14-OA-48h

value: CD4+ T cell

value: Donor 14

value: batch 1


title: WT_YPD_excess_R1

value: 30 min in YPD MnCl2-free medium


title: ICB and BD & ICB HTO library lane 2

description:
10X Genomics Chromium
BXL2

value: Tumor

value: 0.2 mg PD-1 and CTLA-4 biweekly (ICB); 1,3 butanediol diet + 0.2 mg PD-1 and CTLA-4 biweekly (BD ICB)


title: post-TAC HSC rep1 [ATAC-seq]

description: TAC HSC ATAC-seq

value: Transverse aortic constriction operation


title: post-TAC HSC rep3 [RNA-seq]

extract_protocol:
Bone marrow cells were harvested from tibias, femurs, pelvis, and vertebrae by crushing with a mortar and pestle in MACS buffer (PBS supplemented with 0.5% bovine serum albumin and 2 mM EDTA). The cells were passed through a 25G needle several times and filtered with a 70 μm cell strainer. After washed and filtered with a 40 μm cell strainer, the samples were incubated with Mouse CD117 Microbeads (Miltenyi) and separated by autoMACS (Miltenyi). Isolated cells in positive selection were mixed with antibodies for flow cytometry. CD45+ Lin- Sca1+cKit+CD34-Flt3-CD150+CD48- cells were sorted as HSCs. Sorted cells were lysed in Buffer RLT plus (QIAGEN) and RNA was harvested using RNeasy micro Kit (QIAGEN).
Poly-A mRNA was extracted from total RNA by using an Oligo-dT beads of NEBNext Poly(A) RNA Magnetic Isolation Module (NEB), after which RNA-seq libraries were prepared using a NEBNext Ultra II RNA Library Preo Kit for Illumina (NEB) according to the manufacturer’s protocol.


title: WT_YNB_90min_R2

value: 90 min in SC-MN


title: Donor14, Ethanol, 48h

description:
Passed QC
D14-EtOH-48h

value: Ethanol


title: ICB and BD & ICB HTO library lane 1

description:
10X Genomics Chromium
BXL2

value: PPS-ICBR

value: ICB resistant prostate cancer cells


title: WT_Mn_excess_R1

value: 30 min with 7.5 mM MnCl2


title: NCH421_diff_1

value: glioblastoma


title: NCH644_diff_1


title: Donor14, Oleic Acid, 3h

description:
Passed QC
D14-OA-3h

value: Buffy Coat

value: Oleic Acid


title: NCH421_stem_1


title: NCH644_stem_1


title: WT_Mn_90min_R2

value: Yeast cells

value: WT


title: WT_Mn_5min_R2

value: 5 min in SC+MN


title: Donor14, Oleic Acid, 30m

description:
Passed QC
D14-OA-30m

value: CD4+ T cell

value: Donor 14


title: WT_Mn_5min_R1


title: Control HSC rep3 [RNA-seq]

value: Hematopoietic stem cells

value: Sham operation


title: Donor14, Ethanol, 30m

description:
Passed QC
D14-EtOH-30m

value: batch 1


title: Donor14, Ethanol, 72h

description:
Passed QC
D14-EtOH-72h


title: SD and BD HTO library lane 1

description:
10X Genomics Chromium
AXL2

value: Tumor

value: Standard diet (SD); 1,3 butanediol diet (BD)


title: ICB and BD & ICB library

description:
10X Genomics Chromium
BXL2

library_source: transcriptomic single cell

value: 0.2 mg PD-1 and CTLA-4 biweekly (ICB); 1,3 butanediol diet + 0.2 mg PD-1 and CTLA-4 biweekly (BD ICB)


title: post-TAC HSC rep2 [RNA-seq]

value: Transverse aortic constriction operation


title: WT_YNB_5min_R1

value: 5 min in SC-MN


title: PPS-ICBR Vorinostat 2

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed using Applied Biosystems Transcriptome Analysis Console. RMA.

organism: Mus

source_name: Cultured PPS-ICBR cells

label_protocol: Standard Affymetrix protocol

growth_protocol: DMEM + 10% FBS + P/S

extract_protocol: Zymo research Quick-RNA Miniprep & Invitrogen Superscript III Reverse Transcriptase kits

treatment_protocol: 5 µM Vorinostat in DMSO or 5 µL DMSO in 10 mL medium

value: Prostate cancer cells

value: Vorinostat

value: PPS-ICBR


title: SD and BD library

description:
10X Genomics Chromium
AXL2

value: ICB resistant prostate cancer cells


title: WT_YNB_90min_R1

value: Yeast cells

value: 90 min in SC-MN


title: PPS-ICBR Vorinostat 1


title: Donor14, Ethanol, 24h

description:
Passed QC
D14-EtOH-24h

value: Buffy Coat

value: Ethanol


title: PPS-ICBR DMSO 2

value: DMSO


title: Mttp Flox Con 3

status: Public on Feb 12 2024

city: Saint Louis

first: Nicholas

last: Davidson

state: Missouri

address: 425 South Euclid Ave, Box 8124

department: Internal Medicine

institute: Washington University in St Louis School of Medicine

data_processing:
RNA-seq reads were aligned using STAR version 2.0.4b.
Gene counts were derived by Subread:featureCount version 1.4.5.
Transcript counts were produced by Sailfish version 0.6.3
Assembly: Aligned to m_musculus reference build Ensembl_R76
Supplementary files format and content: Gene counts, CPM, and RPKM values in tab-delimited text format.

source_name: liver

extract_protocol:
Total RNA was isolated using Trizol and treated with DNAse1.   For each genotype, 3 pools were prepared, each containing RNA from 3 mice.
10µg RNA per pool was Oligo(dT) selected and used to construct cDNA libraries.

treatment_protocol: Male mice were treated with diethylnitrosamine (DEN,25mg/kg, IP) at 14d of age and fed standard chow diet.  Liver was collected at 6 months

value: liver

value: M

value: Mttp f/f

value: Diethylnitrosamine


title: Fabp1 Mttp DKO 2

value: Fabp1 Mttp DKO


title: Fabp1 Mttp DKO 1


title: Donor14, Ethanol, 3h

description:
Passed QC
D14-EtOH-3h

value: CD4+ T cell

value: Donor 14

value: batch 1


title: post-TAC HSC rep1 [RNA-seq]

value: Hematopoietic stem cells

value: Transverse aortic constriction operation


title: Control HSC rep1 [RNA-seq]

value: Sham operation


title: WT_YNB_5min_R2

value: WT

value: 5 min in SC-MN


title: Control HSC rep2 [RNA-seq]


title: Donor13, Oleic Acid, 72h

description:
Passed QC
D13-OA-72h

value: Oleic Acid

value: Donor 13


title: 231_cont

city: 福岡市

first: Yuya

last: Yoshida

state: 福岡県

address: 東区馬出3-1-1 九州大学薬学部棟本館3F 薬剤学教室, 薬物動態学分野

institute: Kyushu-university

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

extract_protocol:
The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set  according protocols

tag: genter

value: female

tag: tissue  source

value: breast cancer

value: control


title: MCF7_cont

address: 東区馬出3-1-1 九州大学薬学部棟本館3F 薬剤学教室, 薬物動態学分野


title: 231_MCS

address: 東区馬出3-1-1 九州大学薬学部棟本館3F 薬剤学教室, 薬物動態学分野

value: microcurrent-stimulation


title: N2a_siEXOSC3_RNA_rep3

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

data_processing:
RNA-seq reads were aligned to mouse genome (mm9) by Tophat version 2.1.0 with default parameter.
Aligned reads in bam file were sorted by genomic coordinate by SAMtools
Gene differential expression (DE) analysis was conducted by Cuffdiff version 2.2.1. Significant DE genes were defined by FDR<0.05.
Assembly: mm9
Supplementary files format and content: genes.fpkm

source_name: N2a cell

growth_protocol: Neuro2A (N2A) (ATCC) was maintained in a humidified incubator with 5% CO2 at 37°C in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 100 units/mL penicillin G and 100 mg/mL streptomycin antibiotics (1%).

extract_protocol:
Total RNA was isolated from N2A cells using the TRIzol reagent (Invitrogen) according to the manufacturer’s protocol.
For the rRNA-depleted RNA-seq library, sample quality was assessed by Bioanalyzer 2100 Eukaryote Total RNA Pico (Agilent Technologies, CA, USA) and samples were quantified by Qubit RNA HS assay (ThermoFisher #Q32852). Ribosomal RNA depletion was performed with Ribo-zero rRNA Removal Kit (Illumina Inc., San Diego, CA) followed by NEBNext® UltraTM II Nondirectional RNA Library Prep Kit for Illumina® per manufacturer’s recommendation.

treatment_protocol: Individual siRNAs were ransfected into cultured cells using Lipofectamine® 2000 (Invitrogen) and Opti-MEM® (ThermoFisher) according to the manufacturer’s protocol in antibiotic-free media.

value: N2a cell

value: mouse neuroblastoma cell

value: EXOSC3 knockdown

value: Untreated


title: Fabp1 Mttp DKO 3

value: liver

value: M

value: Fabp1 Mttp DKO

value: Diethylnitrosamine


title: N2a_siEXOSC3_RNA_rep1


title: N2a_siDDX1_RNA_rep3

value: DDX1 knockdown


title: N2a_siDDX1_RNA_rep2


title: Mttp LKO 2

value: Mttp LKO


title: Mttp LKO 1


title: N2a_siDDX1_RNA_rep1


title: Mttp Flox Con 2

value: Mttp f/f


title: PPS-ICBR DMSO 1

value: Prostate cancer cells

value: DMSO

value: PPS-ICBR


title: Mttp Flox Con 1


title: N2a_siScramble_RNA_rep2

value: WT


title: N2a_siEXOSC3_DRIP_rep3

data_processing:
DRIP-seq reads were aligned to mouse genome sequence (mm9) by Bowtie2 version 2.4.4 with default parameter.
Aligned reads in bam file were sorted by genomic coordinate by SAMtools.
Peaks for each library were identified by MACS2 version 2.2.6 with input bam file.
DRIP-seq peaks identified from Scramble and siEXOSC3/siDDX1 were merged and reads were re-counted in the merged peak regions. Differential analysis was conducted by DESeq2 based on the reads count matrix in the merged peak regions and significantly changed regions were defined by FDR<0.05.
The differential regions were annotated to genes by annotatePeaks.pl from HOMER version 4.11
Assembly: mm9
Supplementary files format and content: peak files
Library strategy: DRIP-seq

extract_protocol:
Genomic DNA was extracted from ~4 million N2A cells and fragmented with restriction enzymes (BsrGI, EcoRI, HindIII, SspI, XbaI, 30 U/each, NEB). Fragmented nucleic acids were recovered by phenol-chloroform extraction. Fragmented gDNA (4 μg) was digested with 20 U of RNase H (NEB #M0297S) for 6 hr to serve as a negative control. Fragmented gDNA or RNase H-digested DNA (4 μg) were immunoprecipitated with 8 μg of S9.6 antibody (Millipore #MABE1095) overnight at 4°C in DRIP binding buffer (10 mM sodium phosphate, 140 mM sodium chloride, 0.05% (v/v) Triton-X-100, pH 7.0). DNA-antibody complex was then incubated with 40 μL of Protein G beads (Invitrogen #10003D) for 2 hr at 4°C, and beads were washed three times with DRIP binding buffer. Antibody-captured DNA-RNA hybrids were then eluted in (50 mM Tris, 10 mM EDTA, 0.5% (v/v) SDS, pH 8.0) and subjected to phenol-chloroform extraction. The immunoprecipitated DNA-RNA hybrids were quantified by Qubit (ThermoFisher Scientific #Q32854).
DNA-RNA hybrids (10 ng) were treated with 5 U of RNase H for 1 h and then were sonicated into small fragments (~100-500 bp) using a Covaris Focused-Ultrasonicator Me220. Fragmented DNA was blunted, 5′ phosphorylated and 3’ A-tailed by NEBNext Ultra II End Prep Enzyme Mix following the manufacturer’s instruction (New England Biolabs #E7645L). An adaptor was ligated, and USER enzyme was used for U excision to yield adaptor-ligated double-strand DNA. The DNA was then PCR-amplified using barcoded PCR primers (New England Biolabs #E7335L, #E7500L). After AMPure XP bead purification (Beckman Coulter #A63881) and Qubit quantification, the libraries were sent to Admera Health for quality analysis and sequencing with Illumina with a read length configuration of 150 PE.

tag: drip antibody

value: S9.6 (Sigma, MABE1095)


title: N2a_siScramble_RNA_rep1


title: MCF7_MCS

address: 東区馬出3-1-1 九州大学薬学部棟本館3F 薬剤学教室, 薬物動態学分野

value: female

value: breast cancer

value: microcurrent-stimulation


title: N2a_siEXOSC3_RNA_rep2

value: N2a cell

value: mouse neuroblastoma cell

value: EXOSC3 knockdown


title: KrasD12 MLF- 493 B

city: Houston

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol

data_processing:
Analysis was performed using dChip software
Gene expression analysis was conducted using Transcriptome Analysis Console Software (TAC) using comparing method (SKY vs WT).

label_protocol: Standard Affymetrix Protocol

growth_protocol: After tissue digestion samples were centrifuged at 252 g suspended in complete DMEM medium (20% FBS,1% PS) and seeded in 6-well dish. Usually fibroblasts outgrowth was observed between 7 to 14 days in culture. Immunofluorescence analysis validated the purity of the myofibroblast culture.

extract_protocol: Mouse lung tissues were minced thoroughly using sterile blades and digested with Collagenase type 1 (300 U/mg) in DMEM medium alone. After tissue digestion samples were centrifuged at 252 g suspended in complete DMEM medium and seeded in 6-well dish. Cells were homogenized in TRIzol reagent and total RNA was extracted according to the manufacturer’s protocol. After treatment with DNAse reverse transcription was performed using High-capacity cDNA Reverse transcription Kit and RNase inhibitor according to the manufacturer’s protocol.

treatment_protocol: No treatment was applied to the cell lines used for this analysis

value: Lung fibroblast

tag: genotype/variation


title: N2a_siDDX1_DRIP_rep3

tag: cell line

value: Untreated


title: N2a_siDDX1_DRIP_rep2

tag: genotype


title: N2a_siDDX1_DRIP_rep1


title: N2a_siScramble_DRIP_rep2


title: N2a_siScramble_RNA_rep3


title: N2a_siEXOSC3_RH_DRIP

value: gDNA treated with RNaseH


title: WT MLF- 494 B

tag: tissue


title: N2a_siEXOSC3_DRIP_rep1

tag: cell type


title: N2a_Input


title: KrasD12 MLF- 493 A


title: GLR glia, replicate 4 [NS42]

city: New York

first: Nikolaos

last: Stefanakis

state: NY

address: 1230 York Avenue

department: Laboratory of Developmental Genetics

institute: The Rockefeller University

data_processing:
Fastq files were generated with CASAVA v1.8.2 (illumina), and examined using the FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) application for sequence quality. The alignment results were evaluated through RNA-SeQC v1.17 to make sure all samples had a consistent alignment rate and no obvious 5′ or 3′ bias. Aligned reads were summarized through featureCounts with gene models from Ensemble (Caenorhabditis_elegans. WBcel235.77.gtf). at gene level unstranded: specifically, the uniquely mapped reads (NH “tag” in bam file) that overlapped with an exon (feature) by at least 1 bp on either strand were counted and then the counts of all exons annotated to an Ensemble gene (meta features) were summed into a single number.
Assembly: WBcel235
Supplementary files format and content: tab delimited text

organism: Caenorhabditis elegans

source_name: GLR glia

extract_protocol:
For isolation of the GLR glia, synchronized L1 larvae expressing nuclear localized YFP in the GLR glia cells (OS11715) were grown on thirty 10cm plates seeded with HB101 E. coli bacteria. After 48 hours at 20oC, L4 larvae animals were washed off plates and subsequently washed ten times with M9 to remove excess bacteria. Each wash consisted of a brief (10 second, 1300 rpm) centrifugation, such that most animals were pelleted, but bacteria stayed in suspension. Animals were then dissociated using SDS-DTT (0.25% SDS; 200 mM DTT; 20 mM HEPES, pH 8.0; 3% sucrose) and Pronase E (15 mg/ml). We used 2:1 ratio of SDS-DTT to a volume of packed animals pellet, followed by 4 min incubation on ice. After washes, 4:1 ratio of Pronase E was added to the packed animals pellet and animals were incubated rotating at 20 °C for 5 min, followed by 12 min of gentle homogenization (7 mL dounce homogenizer, pestle clearance 0.02−0.056 mm, Kimble Chase). After washes with ice-cold egg buffer (1.18 M NaCl; 480 mM KCl; 20 mM CaCl2; 20 mM MgCl2; 250 mM HEPES, pH 7.3) to remove Pronase E, cells were filtered through a 5μM filter to remove undigested animal fragments, and immediately sorted by FACS.
mRNA amplification and cDNA preparation were performed using the SMARTer mRNA amplification kit (Takara #634940) according to manufacturer's instructions.

value: GLR glia


title: control, replicate 3 [NS38]

source_name: control (all cells apart from GLR glia)

value: control (all cells apart from GLR glia)


title: GLR glia, replicate 2 [NS40]


title: N2a_siDDX1_RH_DRIP

value: DDX1 knockdown


title: N2a_siEXOSC3_DRIP_rep2


title: control, replicate 2 [NS36]


title: N2a_siScramble_DRIP_rep1


title: wild-type (Ovation), quiescence, day 7, steady state RNA, 5781, replicate 1

city: Seattle

first: Alison

middle: C

last: Greenlaw

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutch Cancer Center

description: R1 and R3 are, respectively, forward and reverse reads; R2 are UMI indices.

data_processing:
Paired-end reads underwent quality assessment with FastQC and MultiQC. Unique Molecular Identifier (UMI) sequences were appended to the reads using UMI-tools, and adapter and quality trimming were performed with Atria. For nascent transcriptome assembly, reads were additionally subjected to k-mer adjustment using Rcorrector. For more details, see Greenlaw et al.
Using the aligner STAR, processed reads were aligned to a concatenated multi-organism reference genome consisting of the S. cerevisiae, K. lactis, and 20S narnavirus genomes. Non-k-mer-adjusted bams (*.UTPD.bam) were indexed and filtered (with Samtools) to retain only primary alignments, and technical duplicates were removed using UMI-tools. k-mer-adjusted bams (*.UTKPSSc.bam) were indexed and filtered to retain both primary and secondary alignments; alignments associated with the K. lactis and 20S narnavirus genomes were then filtered out. For more details, see Greenlaw et al.
Gene Transfer Format (gtf) and Gene Feature Format (gff3) files were obtained or derived from publicly available sources using custom scripts. Additionally, some files were generated via nascent transcriptome assembly and annotation using Trinity, GffRead, and custom scripts. To perform feature-level quantification, we used htseq-count with the gtf and gff3 files in conjunction with processed non-k-mer-adjusted bams. For more details, see Greenlaw et al.
To generate normalized coverage tracks (*.bw), we used processed non-k-mer-adjusted bams as input to the utility bamCoverage (deepTools) in one of two ways: (a) For the bins per million (BPM) normalization method, mapped reads were normalized by their library size while excluding all rRNA and tRNA regions. The bin size for this method was set to 1 base pair. (b) For the K. lactis scaled coverage (SC) method, library size estimates were first calculated using K. lactis spike-in counts. The bam files were then processed by supplying the reciprocals of the estimates as arguments (--scaleFactor) to bamCoverage. Again, the bin size was set to 1 base pair. For more details, see Greenlaw et al.
Assembly: sacCer3 R64-1-1
Supplementary files format and content: bams for individual replicates (non-k-mer-adjusted and k-mer-adjusted) and merged replicates (k-mer-adjusted)
Supplementary files format and content: bw files for individual and merged replicates, derived from non-k-mer-adjusted bams, and normalized using either the BPM calculation or the K. lactis spike-in-scaled coverage calculation
Supplementary files format and content: gtf and gff3 files obtained or derived from publicly available sources, or generated via custom transcriptome assembly and annotation
Supplementary files format and content: tab-delimited text files containing sample-specific raw counts for features in the various gtf and gff3 files

organism: Saccharomyces cerevisiae

growth_protocol: Quiescent cells were grown for 7 days to saturation in YEP with 2% glucose and then purified using a gradient method.

extract_protocol:
To generate 4tU-seq libraries, we employed the Ovation® SoLo® RNA-Seq library preparation kit and custom yeast rRNA depletion (AnyDeplete®).
RNA was extracted using yeast RiboPure™ RNA Purification Kit from Invitrogen™
4tU-seq


title: wild-type (Ovation), quiescence, day 7, steady state RNA, 5782, replicate 2


title: N2a_siScramble_RH_DRIP


title: control, replicate 4 [NS41]


title: N2a_siScramble_DRIP_rep3


title: GLR glia, replicate 1 [NS35]


title: wild-type (Ovation), quiescence, day 7, nascent RNA, 5782, replicate 2


title: wild-type (Ovation), quiescence, day 7, nascent RNA, 5781, replicate 1


title: wild-type (Ovation), G1, day 1, steady state RNA, 5781, replicate 1

growth_protocol: G1 arrest was induced by adding α factor at a concentration of 5 μg/ml to early log phase yeast. The arrest was evaluated via microscope, and a second dose of α factor was added at 90 minutes if necessary.


title: WT MLF- 494 A


title: wild-type (Ovation), G1, day 1, nascent RNA, 5781, replicate 1


title: Mttp LKO 3

value: liver

value: M

value: Mttp LKO

value: Diethylnitrosamine


title: wild-type, diauxic shift +48 hrs, day 4, steady state RNA, 5782, replicate 2

growth_protocol: For diauxic shift (DS) experiments, we measured glucose exhaustion using glucose strips (Precision Laboratories). Time points after the diauxic shift were precisely taken. Cells were then spun out of the media and snap-frozen immediately.

extract_protocol:
To prepare RNA-seq libraries, we employed the Universal Plus™ Total RNA-Seq library preparation kit and custom yeast rRNA depletion (AnyDeplete®).
RNA was extracted using yeast RiboPure™ RNA Purification Kit from Invitrogen™
4tU-seq

value: WT


title: wild-type (Ovation), G1, day 1, steady state RNA, 5782, replicate 2


title: wild-type, diauxic shift +48 hrs, day 4, steady state RNA, 5781, replicate 1


title: wild-type, diauxic shift +2 hrs, day 2, steady state RNA, 5782, replicate 2


title: control, replicate 1 [NS33]


title: wild-type, diauxic shift +2 hrs, day 2, steady state RNA, 5781, replicate 1


title: rrp6∆, diauxic shift +48 hrs, day 4, steady state RNA, 7079, replicate 1


title: wild-type, diauxic shift –2 hrs, day 2, steady state RNA, 5782, replicate 2

growth_protocol: For diauxic shift (DS) experiments, we measured glucose exhaustion using glucose strips (Precision Laboratories). Optical density (OD) was measured in the hours leading up to the diauxic shift to estimate the DS-2 hours timepoint. This timepoint occurs atendent OD (between 4-5 OD depending on the strain).


title: wild-type, diauxic shift –2 hrs, day 2, steady state RNA, 5781, replicate 1


title: rrp6∆, diauxic shift +24 hrs, day 3, steady state RNA, 7079, replicate 1


title: GLR glia, replicate 2 [NS37]


title: wild-type, diauxic shift +24 hrs, day 3, steady state RNA, 5781, replicate 1


title: rrp6∆, diauxic shift +2 hrs, day 2, steady state RNA, 7078, replicate 2


title: rrp6∆, diauxic shift +48 hrs, day 4, steady state RNA, 7078, replicate 2


title: rrp6∆, diauxic shift –2 hrs, day 2, steady state RNA, 7078, replicate 2


title: wild-type (Ovation), G1, day 1, nascent RNA, 5782, replicate 2


title: Neutrophilic Dermatosis 31

city: Lausanne

first: JEREMY

last: DI DOMIZIO

state: Vaud

address: Av Boveresses 155, 1066 Epalinges

institute: CHUV

description: internal positive and negative controls were used

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: Data were normalized and log2 transformed using nSolver® 4.0 (Nanostring Technologies). Basically, housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library

label: NanoString indexing

source_name: skin biopsy

label_protocol: NanoString indexing

extract_protocol: mRNA expression of 600 targets was analysed with the nCounter Human Immunology V2 panel including 20 customized probes (Nanostring Technologies, Seattle, WA, USA) on the nCounter® platform (Nanostring Technologies) using 100 ng of RNA per skin sample.

treatment_protocol: samples were snap-frozen without any treatment

value: skin biopsy

tag: condition

value: Neutrophilic Dermatosis


title: wild-type, diauxic shift +24 hrs, day 3, steady state RNA, 5782, replicate 2


title: Neutrophilic Dermatosis 16


title: Neutrophilic Dermatosis 122


title: rrp6∆, diauxic shift +2 hrs, day 2, steady state RNA, 7079, replicate 1


title: Neutrophilic Dermatosis 41


title: Neutrophilic Dermatosis 42


title: Neutrophilic Dermatosis 90


title: Lichen Planus 88

value: Lichen Planus


title: Lichen Planus 29


title: Lichen Planus 93


title: Neutrophilic Dermatosis 189


title: rrp6∆, diauxic shift +24 hrs, day 3, steady state RNA, 7078, replicate 2


title: Lichen Planus 109


title: Lichen Planus 105


title: rrp6∆, diauxic shift –2 hrs, day 2, steady state RNA, 7079, replicate 1


title: Lichen Planus 124


title: Lichen Planus 82


title: Lichen Planus 22


title: Lichen Planus 101


title: Lichen Planus 32


title: Cutaneous Lupus Erythematosus 251

value: Cutaneous


title: Cutaneous Lupus Erythematosus 34


title: Cutaneous Lupus Erythematosus 32


title: Neutrophilic Dermatosis 34


title: Neutrophilic Dermatosis 18


title: Cutaneous Lupus Erythematosus 66


title: Cutaneous Lupus Erythematosus 64


title: Lichen Planus 201


title: Cutaneous Lupus Erythematosus 65


title: Cutaneous Lupus Erythematosus 190


title: Lichen Planus 87


title: Cutaneous Lupus Erythematosus 30


title: Atopic Dermatitis 11

value: Atopic Dermatitis


title: Cutaneous Lupus Erythematosus 59


title: Cutaneous Lupus Erythematosus 6


title: Atopic Dermatitis 225


title: Atopic Dermatitis 228


title: Atopic Dermatitis 19


title: Atopic Dermatitis 7


title: Atopic Dermatitis 21


title: Atopic Dermatitis 102


title: Atopic Dermatitis 15


title: Atopic Dermatitis 18


title: Atopic Dermatitis 43


title: Atopic Dermatitis 12


title: Atopic Dermatitis 30


title: Atopic Dermatitis 5


title: Atopic Dermatitis 226


title: Atopic Dermatitis 135


title: Cutaneous Lupus Erythematosus 162


title: Atopic Dermatitis 4


title: PalmoPlantar Psoriasis 73

value: PalmoPlantar Psoriasis


title: PalmoPlantar Psoriasis 141


title: PalmoPlantar Psoriasis 116


title: Psoriasis Vulgaris 204

value: Psoriasis


title: Cutaneous Lupus Erythematosus 112


title: Psoriasis Vulgaris 138


title: Psoriasis Vulgaris 202


title: Psoriasis Vulgaris 98


title: Psoriasis Vulgaris 199


title: Psoriasis Vulgaris 132


title: Psoriasis Vulgaris 68


title: Psoriasis Vulgaris 46


title: Psoriasis Vulgaris 213


title: Psoriasis Vulgaris 86


title: Psoriasis Vulgaris 6


title: Atopic Dermatitis 2


title: Psoriasis Vulgaris 137


title: Psoriasis Vulgaris 83


title: Psoriasis Vulgaris 209


title: Generalized Pustular Psoriasis 57

value: Generalized Pustular Psoriasis


title: Generalized Pustular Psoriasis 134


title: Psoriasis Vulgaris 136


title: Generalized Pustular Psoriasis 96


title: Generalized Pustular Psoriasis 220


title: PalmoPlantar Pustular Psoriasis 62

value: PalmoPlantar Pustular Psoriasis


title: PalmoPlantar Pustular Psoriasis 68


title: PalmoPlantar Pustular Psoriasis 127


title: PalmoPlantar Pustular Psoriasis 74


title: Psoriasis Vulgaris 1


title: PalmoPlantar Pustular Psoriasis 97


title: PalmoPlantar Pustular Psoriasis 106


title: Generalized Pustular Psoriasis 131


title: Healthy Donor 155

value: Healthy Donor


title: PalmoPlantar Pustular Psoriasis 107


title: PalmoPlantar Pustular Psoriasis 24


title: PalmoPlantar Pustular Psoriasis 87


title: Healthy Donor 42


title: PalmoPlantar Pustular Psoriasis 27


title: Healthy Donor 45


title: Healthy Donor 19


title: Healthy Donor 154


title: Healthy Donor 153


title: Healthy Donor 152


title: Generalized Pustular Psoriasis 109


title: Generalized Pustular Psoriasis 84


title: Healthy Donor 18


title: 1 hiPSCs-ENCSCs D0

city: Guangzhou

first: Weiqiang

last: Li

address: Zhongshan Road 2

institute: Sun Yat-sen university

description: enteric neural crest stem cells, which were differentiated from hiPSCs by chemically defined protocol.

data_processing:
Trimmomatic v0.39
FastQC v0.11.9 software was used to perform quality control on raw data and clean data respectively.
Q20, Q30 and GC content were calculated through in-house python scripts.
Assembly: ENSEMBL release_75
Supplementary files format and content: Microsoft Excel spreadsheet file include RPKM value of each gene for each sample.
Supplementary files format and content: Tab-delimited text file include RPKM values for samples.

source_name: HEF-iPSCs

extract_protocol:
RNA extraction from cells was used TRIzol™ (Invitrogen™ 15596026) and Direct-zol™ RNA Miniprep(zymo R2050)
Sequencing libraries were generated using the SEQUMED ® MustSeq ® 3'mRNA DEG kit（Sequmed，China）

value: HEF-iPSCs

value: differentiated enteric neural crest cells

value: neural crest differentiation


title: 2 ENCSCs-ENs D14-NaB

description: enteric neurons, which expressed several enteric neural markers by chemically defined protocol for 14 days.

value: differentiated enteric neurons

value: neuronal differentiation


title: 3 ENCSCs-ENs D28-NaB

description: enteric neurons, which expressed several enteric neural markers and possessed typical electrophysiological characteristics of mature neurons by chemically defined protocol for 28 days.


title: Colon IBD

first: Mohammad

last: Arifuzzaman

address: 413 E 69th Street, 7th Floor

department: Department of Medicine

institute: Weill Cornell Medicine

description: generated from colon biopsies from a pan-colitic IBD patient

data_processing:
Raw scRNAseq data was obtained from Celsius Therapeutics and the reads were processed by 10X’s Cell Ranger version 3.1.0 using the GRCg38-95 reference genome, resulting in filtered matrix, barcode, and feature files for each of two samples.
Assembly: GRCg38-95
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon

extract_protocol:
Single cells suspensions generated from colon biopsies from a non-IBD healthy control and a pan-colitic IBD patient were used for scRNA-seq. Tissue samples were thawed into warm media with fetal bovine serum (FBS) and preservation media was removed by washing. Samples were treated with EDTA pre-digestion with rotation for to remove dead/damaged epithelial cells. Samples were then dissociated enzymatically into a single-cell suspension with rotation. Cells were washed, strained and counted for viability using AO/PI and 10,000 cells were loaded onto 10X channels
The GEX 3’ V3 protocol was followed throughout sequencing. Libraries were sequenced on an Illumina NovaSeq instrument.

value: Colon

tag: group

value: IBD


title: Colon NonIBD

description: generated from colon biopsies from a non-IBD healthy control

value: NonIBD


title: PalmoPlantar Pustular Psoriasis 110

value: skin biopsy


title: sepsis_preserve_7

city: Hirakata

first: Natsuki

last: Anada

state: Osaka

address: 5-1 Shinmachi2

department: Anesthesiology

institute: Kansai Medical University

data_processing:
Using trimmomatic (ver. 0.36), the Illumina adapter sequences were trimmed from raw reads and sequence reads including low quality bases were excluded from raw reads.
Mapping of reads to reference sequences was performed using BWA (ver. 0.7.17).
Raw read counts were created using samtools (ver. 1.6). Using the information of GeneID, read counts for each transcript were summarized into those for each gene.
Normalization of Gene Expression: Normalization of Gene Expression was performed with the following procedure.
(1) Total count normalization was performed, based on the following calculation.
(Total Read Count of the Sample) × Total Read Count of the Reference Sample
(2) A Trimmed Mean of M-values (TMM) normalization was performed using the edgeR (ver. 3.16.5) package.
Differential expression analysis was performed using the edgeR (ver. 3.16.5) package.
Gene annotations were added to the results, using our in-house script.
assembly: hg38
Supplementary files format and content: Tab-delimited text file include mapped raw read counts, mapped read counts normalized with total count, mapped read counts normalized with TMM-normalization, for each sample.

source_name: Platelet

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Libraries were prepared using the NovaSeq 6000 S4 Reagent Kit according to the manufacturer’s instructions.

value: Platelet

tag: disease state

value: sepsis without thrombocytopenia


title: sepsis_preserve_10


title: sepsis_preserve_3


title: sepsis_preserve_6


title: sepsis_preserve_5


title: sepsis_preserve_9


title: sepsis_preserve_8


title: sepsis_preserve_4


title: sepsis_decrease_8

value: sepsis with thrombocytopenia


title: sepsis_decrease_7


title: sepsis_decrease_5


title: sepsis_decrease_4


title: sepsis_decrease_3


title: sepsis_decrease_9


title: sepsis_preserve_1


title: sepsis_decrease_6


title: control_20

value: control


title: sepsis_decrease_2


title: control_19


title: sepsis_preserve_11


title: control_17


title: control_18


title: control_16


title: control_13


title: control_14


title: control_12


title: sepsis_preserve_2


title: control_9


title: control_11


title: control_10


title: control_7


title: control_8


title: control_4


title: control_5


title: control_6


title: control_2


title: control_3


title: 147positive-2

city: Nanjing

first: Qi

last: Yuan

address: school of pharmacy

institute: China Pharmaceutical University

data_processing:
The integrity and concentration of RNA were analyzed using Agilent RNA 6000 Nano Kit and Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).
Transcriptome sequencing was performed using an Illumina Nova 6000 platform (Illumina Inc., San Diego, CA, USA).
Raw sequenced reads in FASTQ format were filtered to achieve high-quality reads and then mapped to the human genome (GRCh38.100.chr) using HISAT2.
Differentially expressed genes (DEGs) were analyzed using the R package DESeq2 with cutoff of fold change > 1.5 or < 0.67 and p value < 0.05.
Assembly: GRCh38.100.chr
Supplementary files format and content: fpkm.xls file includes FPKM values for each Sample
Supplementary files format and content: total_count.xls file includs count values for each sample

growth_protocol: HEK293T cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% fetal bovine serum, 100 U/mL penicillin and 1 μg/mL streptomycin at 37 ℃ in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated using TRIzolTM reagent (Thermo Scientific, cat.no.15596026)
RNA-seq was performed by Annoroad Gene Technology (Beijing, China)

treatment_protocol: HEK293T cells were co-transfected with KlaRS1/tRNA pair and ALDOA-147TAG plasmids with and without Klac (5 mM, 48 h).

value: Human embryonic kidney cell

value: model

tag: treatment

value: Klac


title: 147positive-4


title: sepsis_decrease_1


title: 147positive-3


title: 147positive-1


title: 147negative-4

value: Control

value: solvent


title: control_1


title: 147negative-2


title: control_15


title: UHRF1-AID/DNMT1-AID_RNAseq_Day4_Rep2

city: Paris

first: Pierre-Antoine

last: Defossez

address: 35 rue Hélène Brion

institute: Epigenetics and Cell Fate Unit

data_processing:
RNA-Seq reads were processed using STAR.https://github.com/alexdobin/STAR.
read counts from featureCounts.
Genome_build: hg38
Assembly: hg38
Supplementary files format and content: Processed data files were obtained with above data processing steps. Supplementary files format and content: read counts

molecule: polyA RNA

growth_protocol: HCT116 cells were maintained in McCoy’s 5A medium with L-glutamine supplemented with 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol:
Total RNA was isolated using the RNAeasy Plus Mini Kit (Qiagen) according to the manufacturer's protocol.
The library preparation for RNA-seq was performed by Novogene company. mRNA-seq libraries were prepared by NEB Next® Ultra™ RNA Library Prep Kit.

treatment_protocol: To facilitate the auxin treatment, HCT116 cells were cultured in a medium supplemented with 2 μg/mL doxycycline and 20 μM auxinole for a duration of one day. Subsequently, the cells were maintained in a medium containing 2 μg/mL doxycycline and 500 μM auxin. During the course of the auxin treatment, the medium was refreshed every two days to ensure a consistent concentration of doxycycline and auxin throughout the experimental period.

value: Colorectal cancer cell

value: Auxin treatment for 4 days


title: 147negative-1


title: UHRF1-AID/DNMT1-AID_RNAseq_Day4_Rep3


title: DNMT1-AID_RNAseq_Day4_Rep3


title: UHRF1-AID/DNMT1-AID_RNAseq_Day4_Rep1


title: UHRF1-AID_RNAseq_Day4_Rep3


title: UHRF1-AID_RNAseq_Day4_Rep2


title: UHRF1-AID_RNAseq_Day4_Rep1


title: DNMT1-AID_RNAseq_Day4_Rep2


title: DNMT1-AID_RNAseq_Day4_Rep1


title: WT_RNAseq_Day4_Rep3


title: WT_RNAseq_Day4_Rep2


title: UHRF1-AID/DNMT1-AID_RNAseq_Day0_Rep2

value: Before auxin treatment


title: UHRF1-AID/DNMT1-AID_RNAseq_Day0_Rep1


title: UHRF1-AID/DNMT1-AID_RNAseq_Day0_Rep3


title: DNMT1-AID_RNAseq_Day0_Rep3


title: DNMT1-AID_RNAseq_Day0_Rep2


title: WT_RNAseq_Day4_Rep1


title: 147negative-3


title: UHRF1-AID_RNAseq_Day0_Rep3


title: DNMT1-AID_RNAseq_Day0_Rep1


title: UHRF1-AID_RNAseq_Day0_Rep1


title: WT_RNAseq_Day0_Rep1


title: WT_RNAseq_Day0_Rep3


title: UHRF1-AID_RNAseq_Day0_Rep2


title: Ctrl_2_549

city: Wuhan

first: Tinglin

last: Yang

state: Hubei

address: Jiefang Avenue 1277, Wuhan, Hubei Province, P. R. China

department: Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Control

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: cell line

growth_protocol: MDA-MB-231 and BT-549 cells were maintained in DMEM medium with 10%FBS in a 5% CO2 incubator under humidified 37°C conditions.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ER- breast cancer cell lines MDA-MB-231 and BT-549 were treated with the conditioned medium generated from TAM-treated ER+ cell line MCF7 for 72h. MDA-MB-231 and BT-549 cells treated with the conditioned medium from DMSO-treated MCF7 was used as control groups. RNA sequencing was conducted to analyze the diffrentially expressed genes.

value: cell line

value: breast cancer cells

value: WT

value: cultured with conditioned medium from DMSO-treated MCF7 cells


title: WT_RNAseq_Day0_Rep2

value: Colon


title: Ctrl_1_231

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Control


title: Ctrl_1_549

description: Control


title: Ctrl_2_231

description: Control


title: CM_2_549

description: cultured with conditioned medium from TAM-treated MCF7 cells


title: CM_1_549

value: cultured with conditioned medium from TAM-treated MCF7 cells


title: CM_1_231


title: CM_2_231


title: Ishikawa cells, MPA treatment

city: Jinan

first: Yao

last: Liu

state: Shandong

address: Wenhuaxi Road 107#

institute: Qilu Hospital of Shandong University

data_processing:
Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq/Novaseq instrument  according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out  using a 2x150 paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq  Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Assembly: Human_GeCKOv2_Library _B
Supplementary files format and content: Processed data .txt files contain read count and statistical data

source_name: Ishikawa cell line

extract_protocol: The library construction method employed a two-step PCR approach. Firstly, based on the sample type, different reaction numbers were determined. Universal primers were designed upstream and downstream of the sgRNA region, and a high-fidelity enzyme was utilized to construct the reaction system. The first step of PCR was conducted to obtain the target fragment, with the cycle number typically controlled at 18-22 cycles. The second step of PCR added index and adapter sequences to the target fragment, with the cycle number typically controlled at 8-12 cycles. Following the first and second steps of PCR, gel extraction was performed to obtain a single desired band. After library purification, the library concentration was quantified using qubit 3.0 (Invitrogen, Carlsbad, CA, USA), and the fragment size of the library was assessed using the 2200 system (Agilent Technologies, Palo Alto, CA, USA), followed by Nano QC (Illumina, San Diego, CA, USA).  The DNA libraries labeled with different indices were pooled, and sequencing was conducted according to the 2x150bp paired-end sequencing (PE) instructions of the Illumina instrument (Illumina, San Diego, CA, USA).

value: Ishikawa cell line

value: Human endometrial cancer cells

value: medroxyprogesterone for 10 days


title: Ishikawa cells, Baseline

value: no treatment for 0 day


title: Ishikawa cells, Control

value: DMSO for 10 days


title: HMLE HORMAD1_CT83 rep3

data_processing:
FASTQ reads were trimmed using Trimmomatic (Bolger et al., 2014) (v0.39) and parameters: ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36.
Read pairs that survived trimming were aligned to the human reference genome (build hg38) using STAR (Dobin et al., 2013) (v2.7.5c) and default single-pass parameters.
PCR duplicate read alignments were flagged using Picard-tools (2019) MarkDuplicates (v2.23.4).
Uniquely aligned, non-PCR-duplicate reads were kept for downstream analysis using Samtools (Li et al., 2009) view (v1.10) and parameters: -q 255 -F 1540.
Gene expression values were calculated over the hg19 NCBI RefSeq Genes annotation using VisRseq (Younesy et al., 2015) (v0.9.12)
Assembly: hg19
Supplementary files format and content: tab-delimited tsv file include raw counts for each sample

source_name: Mammary gland

growth_protocol: HMLE cell lines were maaintained in DMEM:F12 medium supplemented with

extract_protocol:
RNA was harvest using RNA easy Mini kit plus (quiagen). A total amount of 1 μg total RNA per sample was used as input material for the RNA sample preparations.
RNA samples were spiked with ERCC RNA Spike-In Mix (Thermo Fisher Scientific). Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) following the manufacturer’s recommendations.

treatment_protocol: Puroselection

value: Mammary gland

value: HMLE

value: Mammary epithelial cells


title: HMLE HORMAD1_CT83 rep2


title: HMLE HORMAD1_CT83 rep1


title: HMLE HORMAD1  rep3


title: HMLE HORMAD1  rep2


title: HMLE CT83  rep3


title: HMLE HORMAD1  rep1


title: HMLE Control rep3

value: Control


title: HMLE CT83  rep2


title: HMLE Control rep2


title: P26_fs970

city: Boston

first: Cristina

last: Guarducci

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
Reads were aligned to hg19 using STAR
For peak calling STAR was used.
Assembly: hg19
Supplementary files format and content: bw files were generated using STAR using the VIPER pipeline

growth_protocol: MCF7 cells with a doxycycline-inducible Y537S  mutation in ER (DOX-Y537S) were grown in DMEM supplemented with 10% fetal bovine serum (FBS) and 10 µg/ml penicillin-streptomycin-glutamine (PSG) (Full media: FM) + 500 µg/ml of G418. MCF7 DOX-Y537S were treated with 1µg/ml doxycycline in FM for 3 days to induce the expression of the mutation and subsequently maintained in phenol-red-free DMEM supplemented with 10% Charcoal Stripped FBS and PSG (Hormone deprived: HD) + G418 + doxycycline. MCF7 DOX-Y537S with the C312S CDK7 mutation were maintened in  HD + G418 + doxycycline + 1mg/mL puromycin. MCF7 cells with a stable TALEN knock-in Y537S ESR1 mutation were grown in HD. Palbociclib sensitive (PalboS) and Palbociclib resistant (PalboR) cells (T47D and MCF7) were grown in FM without or with Palbociclib 1µM, respectively. PDXs were were dipped in 50% matrigel and implanted into the cleared fourth mammary fat pads of ovariectomized NOD-SCID-IL2Rgc–/– mice, without Estradiol (E2) supplements for the ER-mutant PDX1526 model and supplemented with 0.18 mg (60 days release) E2 pellets for the ER-WT PDX1415 model.

extract_protocol:
Total RNA isolation was performed using the RNeasy Mini Kit (Qiagen). DNA was degraded on columns with DNase I (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II non-directional RNA Library Prep kit following manufacturer's protocols.

treatment_protocol:
Cell lines were treated with DMSO or SY-1365 50nM or 150nM for: short time (4 or 6 hrs) or long time (12 or 24 hrs).
PDXs were treated with Vehicle, SY-1365 (30mg/kg/twice a week IV), Fulvestrant (5mg/mouse/week SQ ) or their combination (SY-1365+Fulvestrant) for 28 days.

value: Breast carcinoma PDX

tag: culturimg media

value: ovarectomy

value: Fulvetrsant  5mg/mouse/week + SY-1365 30mg/mouse/week

tag: time

value: 28 days


title: P26_s981

value: SY-1365 30mg/mouse/week


title: P26_s974


title: P26_fs967


title: P26_f984

value: Fulvestrant 5mg/mouse/week


title: P26_c968

value: 10% ethanol and castor oil + 20% captisol pH 4-6 with 1M HCl


title: HMLE Control rep1


title: P26_c987


title: WT_fs756

value: ER-WT

value: ovarectomy + E2


title: WT_fs747


title: WT_sy739


title: WT_sy762


title: WT_c761


title: WT_f760


title: WT_c738


title: WT_f757


title: WT_c734


title: HMLE CT83  rep1


title: T47D_P-R_CTR_2

value: Breast carcinoma cell line

value: ER-WT, PalboR

value: FM + Palbociclib

value: DMSO


title: T47D_P-R_SY12_3


title: T47D_P-S_SY12_3

value: ER-WT, PalboS

value: FM


title: T47D_P-R_CTR_1


title: T47D_P-S_SY12_1


title: MCF7_P-R_SY12_3


title: T47D_P-S_CTR_1


title: T47D_P-S_CTR_3


title: P26_f977


title: MCF7_P-R_SY12_2


title: MCF7_P-S_SY12_2


title: MCF7_P-S_CTR_3


title: MCF7_P-R_CTR_3


title: MCF7_P-R_CTR_2


title: MCF7_P-S_CTR_1


title: MCYS_talen37_WM_SY_50nM_6h_2

value: HD


title: MCYS_talen37_WM_SY_50nM_24h_2


title: WT_c752


title: MCYS_talen37_WM_1


title: MCYS_p-ind_WM+Dox_SY_50nM_24h_2

value: HD + G418 + doxycycline


title: MCYS_talen37_WM_SY_50nM_6h_1


title: T47D_P-R_SY12_2


title: MCYS_p-ind_WM+Dox_SY_50nM_6h_2


title: MCYS_p-ind_WM+Dox_SY_50nM_6h_1


title: MCYS_talen37_WM_2


title: MCYS_p-ind_WM+Dox_SY_50nM_24h_1


title: MCYS_p-ind_WM+Dox_1


title: MCYS_p-ind_WM+Dox_2


title: MCF7_FM_SY_50nM_24h_2


title: MCF7_P-S_SY12_1


title: MCF7_FM_1


title: MCF7_FM_SY_50nM_6h_2


title: MCF7_FM_SY_50nM_24h_1


title: MCF7_FM_2


title: MCF7_FM_SY_50nM_6h_1


title: MCYS_talen37_WM_SY_50nM_24h_1


title: MCF7_Y537S_CS_4h_sy50_3

value: ER-Mutant_Y537S and CDK7-Mutant_C312S

value: HD + G418 + doxycycline + puromycin


title: MCF7_Y537S_CS_4h_sy150_1


title: MCF7_Y537S_CS_4h_sy150_3


title: MCF7_Y537S_CS_4h_sy150_2


title: MCF7_Y537S_CS_veh_3


title: MCF7_Y537S_CS_4h_sy50_1


title: MCF7_Y537S_CS_veh_2


title: MCF7_Y537S_CS_veh_1


title: MCF7_Y537S_CS_4h_sy50_2


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, dTAG-13-1µM, Menin, rep3

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

description: Figure 3D-E, Supplemental Figure 3O-P

data_processing:
To obtain quality reads, raw reads were processed and trimmed with Trim_galore (v0.4.4) from cutadapt (DOI: 10.14806ej.17.1.200) and FASTQC analysis. A default quality score cutoff of Q20 is used.  Quality trimmed reads were then mapped to "hg38+rDNA” (DOI: 10.1101/2022.11.10.514243) genome build by bwa (v0.7.12-r1039) and converted to a bam file by samtools (v1.2).
Duplicate reads were marked with biobambam2 (v2.0.87, DOI: 10.1186/175109473-9-13). Uniquely mapped and properly paired reads were then extracted with samtools (v1.2, "-F 1804 -q 1") and sorted by read name using biobambam2 (v2.0.87)
bedtools(v2.17.0, PMID: 20110278) were used to convert bam file to bedpe file as fragments. Fragments with size shorter than 2000bp were extracted and center 80bp of each fragment were used to generate bigwig track files by UCSC tools (v4) and visualized using IGV (v2.16.0).
Narrow peaks were called with MACS2 (v2.1.1.20160309, parameters "-q 0.05") and broad peaks were called by SICER (v1.1, parameters "hg38 1 200 fragmentsize 0.86 600 0.00001").
To perform statistical test between experimental groups (DMSO/dTAG), fragments for each reference peak were counted with intersect command from pybedtools (v0.9.1). Next, the number of raw reads mapping per peak were converted to FPKM unit (Fragments Per Kilo base per Million mapped reads), and TMM (trimmed mean of M-values) from edgeR package. Next, we used limma-voom approach to assess the significance of differential peak binding.  Significant peaks were defined by log2FC < -1 or > 1 and FDR < 0.05.
Assembly: hg38+ custom rDNA build from  DOI:  https://doi.org/10.1101/2022.11.10.514243
Supplementary files format and content: bw
Library strategy: CUT&RUN

source_name: Human cord-blood CD34+ cells

growth_protocol: Cells were growin in SFEM II supplemented with pen-strep, I-glutamine, and recombinant human SCF, FLT-3, TPO and IL-6 (all 50ng/mL PeproTech), UM729 (#72332, STEMCELL Technologies) and SR-1 (1µmol/L, #72344, STEMCELL Technologies)

extract_protocol:
CUT&RUN was performed following the kit from EpiCypher (cat# 14-1048)
CUT&RUN DNA libraries were made following NEBNext Ultra II DNA Library Prep Kit for Illumina (cat# E7103), PCR amplification was done for 12 cycles

tag: expression vector

value: dTAG-13, 1µM

value: Human cord-blood CD34+ cells

tag: chip antibody

value: MEN1 (Bethyl Laboratories, A300-105A)


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, dTAG-13-1µM, KMT2A, rep2

description: Figure 3D-E, Supplemental Figure 3O-P

value: KMT2A (Bethyl Laboratories, A300-086A)


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, dTAG-13-1µM, HA, rep3

description: Figure 3D-E, Supplemental Figure 3O-P

value: HA (Cell Signaling Technologies, 3724)


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, dTAG-13-1µM, Menin, rep2

description: Figure 3D-E, Supplemental Figure 3O-P


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, dTAG-13-1µM, HA, rep2

description: Figure 3D-E, Supplemental Figure 3O-P


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, dTAG-13-1µM, KMT2A, rep3

description: Figure 3D-E, Supplemental Figure 3O-P


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, DMSO, Menin, rep2

description: Figure 3D-E, Supplemental Figure 3O-P


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, DMSO, Menin, rep3

description: Figure 3D-E, Supplemental Figure 3O-P


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, DMSO, HA, rep3

description: Figure 3D-E, Supplemental Figure 3O-P


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, DMSO, KMT2A, rep3

description: Figure 3D-E, Supplemental Figure 3O-P


title: UBTF-TD patient-derivied xenograft, Menin

description: Figure 2A

source_name: Human UBTF-TD Patient Derived Xenograft sample


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, dTAG-13-1µM, Menin, rep1

description: Figure 3D-E, Supplemental Figure 3O-P


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, DMSO, HA, rep1

description: Figure 3D-E, Supplemental Figure 3O-P


title: UBTF-TD patient-derivied xenograft, UBTF

description: Figure 2A

value: Human UBTF-TD Patient Derived Xenograft sample

value: UBTF (Santa Cruz, sc-13125)


title: cord-blood CD34+ cells, UBTF, rep 2

description: Figure 2A

value: normal hematopoeitic cells, rep #2


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, IgG

description: Figure 3D-E, Supplemental Figure 3O-P

value: IgG (EpiCypher, 13-0042)


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, dTAG-13-1µM, KMT2A, rep1

description: Figure 3D-E, Supplemental Figure 3O-P


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, DMSO, HA, rep2

description: Figure 3D-E, Supplemental Figure 3O-P


title: cord-blood CD34+ cells, UBTF, rep 3

description: Figure 2A

value: normal hematopoeitic cells, rep #3


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, DMSO, Menin, rep1

description: Figure 3D-E, Supplemental Figure 3O-P

value: DMSO


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, DMSO, KMT2A, rep1

description: Figure 3D-E, Supplemental Figure 3O-P


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, dTAG-13-1µM, HA, rep1

description: Figure 3D-E, Supplemental Figure 3O-P


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD, HA, Day 45

description: Supplemental Figure 2A

value: MPC-nHA-UBTF-TD

value: 45 days in culture


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD, HA, Day 32

description: Supplemental Figure 2A

value: 32 days in culture


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD, UBTF

description: Figure 2B, Supplemental Figure 2D


title: cord-blood CD34+ cells, UBTF, rep 1

description: Figure 2A

value: normal hematopoeitic cells, rep #1


title: cord-blood CD34+ cells, IgG

description: Figure 2A

value: normal hematopoeitic cells


title: UBTF-TD patient-derivied xenograft, KMT2A

description: Figure 2A


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD, HA, Day10

description: Supplemental Figure 2A

value: 10 days in culture


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD, rep 3, HA

description: Figure 2B, Supplemental Figure 2D


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD, menin

description: Figure 2B


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD, H3K27ac

description: Figure 2B

value: H3K27ac (Cell Signaling Technologies,  8173)


title: KMT2A-rearranged patient-derivied xenograft, UBTF

description: Figure 2A

source_name: Human KMT2Ar Patient Derived Xenograft sample


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD, H3K4me3

description: Figure 2B

value: Human cord-blood CD34+ cells

value: H3K4me3 (EpiCypher, 13-0041)


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD, rep 2, HA

description: Figure 2B, Supplemental Figure 2D


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD, rep1 HA

description: Figure 2B, Supplemental Figure 2D


title: cord-blood CD34+ cells, MPC-nHA-UBTF-WT, HA, Day10

description: Supplemental Figure 2A

value: MPC-nHA-UBTF-WT


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD, KMT2A

description: Figure 2B

value: KMT2A (Bethyl Laboratories, A300-086A)


title: RNA-seq of bone marrow cells from UBTF-TD PDX model treated with SNDX, R20

description:
RNASeq_SNDX-Veh_log2CPM.txt
SJAML015373_R20- HMP_18_PDX_FMZVC_S14_bm_SNDX

data_processing:
RNA-Seq reads were mapped to GRCh38/hg38 human genome assembly using STAR v2.7.9a
Gene expression count matrix was generated using RSEM (v1.3.0)
The count data were transformed to log2-counts per million (log2CPM) using Voom method available from R package Limma (v3.50.3). Limma was also used to perform differential expression analysis between DMSO and dTAG-13 treated samples.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file for log2-counts per million (log2CPM) , one gene per row and one sample per column.

source_name: human blasts from UBTF-TD PDX Model

extract_protocol:
RNA was harvested using Quikc-RNA Miniprep Kit (Zymo Research R1055)). RNA was then quantified using the Quant-iT RiboGreen RNA assay (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation.
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020599). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) or by low pass sequencing with a MiSeq nano kit (Illumina).
Paired end 100 cycle sequencing was performed on a NovaSeq 6000 (Illumina).

value: human blasts from UBTF-TD PDX Model

value: UBTF-TD PDX model treated with SNDX


title: RNA-seq of bone marrow cells from UBTF-TD PDX model treated with Veh, R16

description:
RNASeq_SNDX-Veh_log2CPM.txt
SJAML015373_R16- HMP_18_PDX_FMZVC_S03_bm_Veh

value: UBTF-TD PDX model treated with Veh


title: RNA-seq of bone marrow cells from UBTF-TD PDX model treated with SNDX, R19

description:
RNASeq_SNDX-Veh_log2CPM.txt
SJAML015373_R19- HMP_18_PDX_FMZVC_S13_bm_SNDX


title: RNA-seq of bone marrow cells from UBTF-TD PDX model treated with SNDX, R18

description:
RNASeq_SNDX-Veh_log2CPM.txt
SJAML015373_R18- HMP_18_PDX_FMZVC_S12_bm_SNDX


title: RNA-seq of bone marrow cells from UBTF-TD PDX model treated with Veh, R15

description:
RNASeq_SNDX-Veh_log2CPM.txt
SJAML015373_R15- HMP_18_PDX_FMZVC_S02_bm_Veh


title: RNA-seq in FKBP12 tagged UBTF-TD54 cbCD34+ cells treated with dTAG-13, C5

description:
RNASeq_DTAG-DMSO_log2CPM.txt
SJNORM077216_C5_F_DTAG

source_name: cord-blood CD34+ Cells expressing FKPB12-F36V::UBTF-TD

value: cbCD34+ cells treated with dTAG-13


title: RNA-seq in FKBP12 tagged UBTF-TD54 cbCD34+ cells treated with dTAG-13, C6

description:
RNASeq_DTAG-DMSO_log2CPM.txt
SJNORM077216_C6_F_DTAG

value: cord-blood CD34+ Cells expressing FKPB12-F36V::UBTF-TD


title: RNA-seq in FKBP12 tagged UBTF-TD54 cbCD34+ cells treated with dTAG-13, C4

description:
RNASeq_DTAG-DMSO_log2CPM.txt
SJNORM077216_C4_F_DTAG


title: RNA-seq in FKBP12 tagged UBTF-TD54 cbCD34+ cells treated with DMSO, C3

description:
RNASeq_DTAG-DMSO_log2CPM.txt
SJNORM077216_C3_F_DMSO

value: cbCD34+ cells treated with DMSO


title: RNA-seq in FKBP12 tagged UBTF-TD54 cbCD34+ cells treated with DMSO, C2

description:
RNASeq_DTAG-DMSO_log2CPM.txt
SJNORM077216_C2_F_DMSO