title: cca1 lhy_CL_6h_3

value: 32 h light

value: 6 h


title: Dia_NONCACMEL_1

status: Public on Feb 28 2022

type: SRA

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

country: USA

institute: St. Jude Children's Research Hospital

description: bearing a non-cachectic (NONCAC) melanoma without rFibcd1 treated replicate 1

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to mm10 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for all 59 samples

molecule: total RNA

organism: Mus musculus

source_name: diaphragm muscles (Dia) from 4-month-old female NCI Ath/nude mice

extract_protocol:
Tissues were homogenized in Trizol and RNA extracted by isopropanol precipitation from the aqueous phase. RNA sequencing was performed as previously described from UBR4 mKO tibialis anterior muscle at 6 and 24 months of age.
For sequencing, biological replicates were prepared with the TruSeq stranded mRNA library prep kit (Illumina) and sequenced on the Illumina HiSeq 2000 platform.

tag: strain

value: NCI Ath/nude

tag: tissue

value: diaphragm muscles

tag: age

value: 4 months

tag: Sex

value: female

tag: treatment


title: WT_control_12h_2

city: Berlin

first: Anne

last: Cortleven

address: Albrecht-Thaer-Weg 5

department: Institut fur Biologie

country: Germany

institute: FU Berlin

data_processing:
base-calling was done with BGISEQ500, version 1.1.2.29164
After removal of adaptors and low quality reads, the obtained clean reads (approximately 23 million) were stored as FASTQ format   SOAPnuke, version v1.5.2, parameters: -I15 -q 0.5 -n0.1
The clean reads were mapped to the reference genome (TAIR10) using HISAT, version v2.0.4, parameters: -p8 --phred64 --sensitive -I 1 -X10000
For gene expression analysis clean reads were mapped to reference using Bowtie2, v2.2.5, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k  200
Gene expression levels based on the FPKM method were quantified using RSEM v1.2.12, Parameters: default
Genome_build: TAIR10
Supplementary_files_format_and_content: txt file includes FPKM values for each Sample

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis plants were grown for 5 weeks on soil under short day (SD) conditions (8 h light/16 h dark) in a growth chamber with light intensities of 100 to 150 µmol m-2 s-1, using a combination of Philips Son-T Agros 400W and Philips Master HPI-T Plus, 400W/645 lamps, at 22°C and 60% relative humidity.

extract_protocol:
Total RNA was extracted from leaf material, flash-frozen in liquid nitrogen using the NucleoSpin® RNA plant kit (Machery and Nagel, Düren, Germany) as described in the user’s manual.
RNA libraries were prepared by the BGISEQ-500 RNA-Seq Library Preparation Protocol. In brief, mRNA was purified with oligo(dt) magnetic beads, mRNA was chemically fragmented and cDNA was generated using random hexamer-primed reverse transcription. End-repair and 3'adenylation was done and adapters were ligated to the adenylated cDNA. adapter-ligated was amplified via PCR and purified with Ampure XP Beads (Agencourt). The library was validated on the Agilent Technologies 2100 bioanalyzer and the double stranded PCR products were denaturated and circularized.

treatment_protocol: 5-weeks-old plants were exposed to a light period of 32 h (CL) or remained under control conditions (SD).

tag: genotype

value: WT

value: control (SD conditions)

tag: sampling time point

value: leaf


title: TA_CACMEL_5

description: bearing a cachectic (CAC) melanoma replicate 5

source_name: tibilias anterior (TA) muscles from 4-month-old female NCI Ath/nude mice

value: tibilias anterior muscles

value: bearing a cachectic (CAC) melanoma


title: Control 2

city: Grand Rapids

first: Bin

last: Chen

state: Michigan

address: 400 Monroe Ave NW

department: Department of Pediatrics and Human Development

institute: MICHIGAN STATE UNIVERSITY

description: Total RNA was isolated form Calu-3 cells

data_processing:
RNA-Seq reads were mapped on Hg38 transcriptome using the ENSEMBL GRCh38.p3 annotation with the STAR aligner
Normalized count was obtained from the STAR aligner
Genome_build: UCSC human reference genome (hg38)
Supplementary_files_format_and_content: CSV file includes human ensembl_gene_id and normalized counts (TPM) for each gene in individual samples

organism: Homo sapiens

growth_protocol: Equal number of Calu-3 cells were grown for 30 min.

extract_protocol:
The total RNA was extracted using KAPA RNA HyperPrep Kit as per manufacturer instructions. Quality and quantity of RNA were checked using a 2100 Bioanalyzer (Agilent Technologies, CA, USA) and the samples with an RNA integrity number ≥ 7 were sequenced.
Ribo-depleted RNA was used for Library preparation and paired end sequencing was performed using Illumina platform (Nextera sequencing) and sequencing chemistry according to the manufacturer’s instructions (Life Technologies, USA).

treatment_protocol:
Cells were grown for 24h without any infection or treatment
For control, no treatment was given to the cells, and they were grown for 24h. For infection, after 30 min of growth a MOI of 0.1 of SARS-CoV-2 was used to infect the cells followed by culture till 24h. For drug treatment groups, cells along with IMD-0354 were grown for 30 min followed by addition of MOI of 0.1 of SARS-CoV-2 and culture them for 24h.

tag: cell line

value: Mock

tag: time

tag: replicates


title: Duo.IBSC 25_S30

city: Rochester

first: Ting

last: Wei

state: MN

address: 507 3rd St SW

institute: Mayo Clinic

description: Duo.IBSC

data_processing:
Image data and base calling were processed using the Illumina Standard Pipeline.
Fastq data were analyzed by Mayo Analysis Pipeline for RNA Sequencing (MAPRSeq v3.1.3) with STAR (2.6.1) for reads alignment to the human genome reference GRCh38 (hg38) and RSeqQC for gene expression.
After read counts and library size filtration, normalized counts and RPKM for samples were calculated by edgeR (v4.0.1) and differentially expressed genes between groups were determined
Gene set enrichment analysis (GSEA, v4.0.1) was conducted using preranked module based on gene expression ranks
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts and RPKM (merged)

source_name: Duodenum

extract_protocol:
RNA extracted using Qiagen miRNeasy kit for total RNA (Cat# 217004)
Illumina NovaSeq 6000 S2 flow cell (paired-end libraries 2×50bp)

treatment_protocol: Biopsies were collected, immediately placed in Qiagen Allprotect Tissue Reagent (Cat# 76405) and flash frozen in LN2. Storage at -80°C.

value: Duodenum

value: IBS-C

tag: gender

value: F

tag: bmi


title: Jej.IBSC 27_S32

description: Jej.IBSC

source_name: Jejunum

value: Jejunum

value: M


title: Control 3


title: Jej.IBSC 24_S29

description: Jej.IBSC


title: Dia_NONCACMELwithRFIBCD1_10

description: bearing a non-cachectic (NONCAC) melanoma with rFibcd1 treated repliacte 10


title: Dia_NONCACMELwithRFIBCD1_8

description: bearing a non-cachectic (NONCAC) melanoma with rFibcd1 treated repliacte 8


title: Dia_NONCACMELwithRFIBCD1_9

description: bearing a non-cachectic (NONCAC) melanoma with rFibcd1 treated repliacte 9


title: Dia_NONCACMELwithRFIBCD1_7

description: bearing a non-cachectic (NONCAC) melanoma with rFibcd1 treated repliacte 7


title: Duo.HV 26_S31

description: Duo.HV

value: Healthy


title: WT_control_12h_1


title: Control 1


title: SARS-CoV-2-infected 1


title: cca1 lhy_CL_6h_2

value: cca1 lhy

value: 32 h light

value: 6 h


title: Duo.IBSD 23_S28

description: Duo.IBSD

value: IBS-D


title: Dia_NONCACMELwithRFIBCD1_5

description: bearing a non-cachectic (NONCAC) melanoma with rFibcd1 treated repliacte 5

value: NCI Ath/nude

value: diaphragm muscles

value: 4 months

value: female


title: ahk2 ahk3_CL_6h_3

value: ahk2 ahk3

value: leaf


title: Dia_NONCACMELwithRFIBCD1_6

description: bearing a non-cachectic (NONCAC) melanoma with rFibcd1 treated repliacte 6


title: cca1 lhy_CL_6h_1


title: Duo.IBSD 22_S27

description: Duo.IBSD


title: CGE-WT

city: Bethesda

first: Apratim

last: Mitra

state: MD

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

institute: NICHD

data_processing:
Basecalls were performed with Illumina RTA version 1.18.64
Read alignment and transcript counting was performed with the 10X cellranger version 3.0.0
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: h5 file

molecule: polyA RNA

source_name: Caudal ganglionic eminence

extract_protocol:
Embryonic LGE, MGE, CGE and cortical tissues were incubated in 1 mg/mL Pronase (Roche #10165921001) in ACSF for 20 minutes at RT. Pronase solution was removed and 2 ml of reconstitution solution (1% fetal bovine serum + DNAse (1:10,000, Roche #47167280001)) in oxygenated ACSF was added. Cells were triturated sequentially with fire-polished large, medium and small bore Pasteur pipettes to mechanically dissociate tissue. For scRNA-Seq, DRAQ5 (20 μM) and DAPI (1:10,000) was added to the single cell suspension, which was passed through a pre-wet 30 μm filter and then processed on an SH800 cell sorter to purify the sample. DRAQ5+/DAPI- live cells were collected in low-bind 1.5 mL tubes containing 100 μL ACSF. Cell solutions were centrifuged at 300 x G for 5 min at 4oC in a swinging bucket centrifuge and then counted on a hemocytometer. 15,000 cells (or highest amount recovered after sorting) was used for 10X Genomics scRNA-Seq experiments.
cDNA synthesis and library amplification was carried out following 10X Genomics ATAC User Guide (revision C), libraries were prepared following 10X Genomics and Illumina guidelines

value: WT

value: Brain

tag: tissue region

value: CGE


title: ahk2 ahk3_CL_6h_2


title: Duo.IBSC 21_S26

description: Duo.IBSC

value: Duodenum

value: IBS-C


title: MGE-WT

source_name: Medial ganglionic eminence

value: MGE


title: ahk2 ahk3_CL_6h_1


title: Dia_NONCACMELwithRFIBCD1_4

description: bearing a non-cachectic (NONCAC) melanoma with rFibcd1 treated repliacte 4


title: Dia_NONCACMELwithRFIBCD1_3

description: bearing a non-cachectic (NONCAC) melanoma with rFibcd1 treated repliacte 3


title: Duo.IBSC 20_S1

description: Duo.IBSC

value: F


title: Duo.IBSD 19_S25

description: Duo.IBSD

value: M


title: Jej.HV 18_S24

description: Jej.HV

value: Jejunum

value: Healthy


title: Dia_NONCACMELwithRFIBCD1_2

description: bearing a non-cachectic (NONCAC) melanoma with rFibcd1 treated repliacte 2


title: WT_CL_6h_3

value: 32 h light

value: 6 h


title: LGE-WT

source_name: Lateral ganglionic eminence

value: LGE


title: WT_CL_6h_2


title: MGE-Nes_3

value: Nestin-dVenus


title: Dia_NONCACMELwithRFIBCD1_1

description: bearing a non-cachectic (NONCAC) melanoma with rFibcd1 treated repliacte 1

value: NCI Ath/nude

value: diaphragm muscles

value: 4 months

value: female


title: WT_CL_6h_1

value: WT

value: leaf


title: Dia_CACMEL_10

description: bearing a cachectic (CAC) melanoma without rFibcd1 treated replicate 10


title: CGE-Nes_3

value: Brain

value: CGE


title: Duo.HV 17_S23

description: Duo.HV

value: Duodenum


title: LGE-Nes_3


title: Jej.IBSC 16_S22

description: Jej.IBSC

value: IBS-C

value: F


title: cca1 lhy_control_6h_3

value: cca1 lhy

value: control (SD conditions)


title: Dia_CACMEL_9

description: bearing a cachectic (CAC) melanoma without rFibcd1 treated replicate 9


title: CGE-Nes_2


title: Jej.IBSD 14_S20

description: Jej.IBSD

value: Jejunum

value: IBS-D

value: M


title: MGE-Nes_2

value: Nestin-dVenus

value: MGE


title: Dia_CACMEL_8

description: bearing a cachectic (CAC) melanoma without rFibcd1 treated replicate 8

value: NCI Ath/nude

value: diaphragm muscles


title: Dia_CACMEL_7

description: bearing a cachectic (CAC) melanoma without rFibcd1 treated replicate 7

value: 4 months

value: female


title: cca1 lhy_control_6h_2

value: 6 h

value: leaf


title: cca1 lhy_control_6h_1


title: LGE-Nes_2

value: Brain

value: LGE


title: Duo.IBSD 13_S19

description: Duo.IBSD

value: Duodenum


title: CGE-Nes_1

value: CGE


title: Duo.IBSC 12_S18

description: Duo.IBSC

value: IBS-C

value: F


title: ahk2 ahk3_control_6h_3

value: ahk2 ahk3

value: control (SD conditions)


title: ahk2 ahk3_control_6h_2


title: MGE-Nes_1


title: Dia_CACMEL_4

description: bearing a cachectic (CAC) melanoma without rFibcd1 treated replicate 4


title: ahk2 ahk3_control_6h_1


title: Jej.IBSD 11_S17

description: Jej.IBSD

value: Jejunum

value: IBS-D

value: M


title: Dia_CACMEL_5

description: bearing a cachectic (CAC) melanoma without rFibcd1 treated replicate 5

value: NCI Ath/nude


title: LGE-Nes_1

value: Nestin-dVenus


title: Dia_CACMEL_2

description: bearing a cachectic (CAC) melanoma without rFibcd1 treated replicate 2

value: diaphragm muscles

value: 4 months


title: Duo.IBSC 9_S15

description: Duo.IBSC


title: Duo.IBSD 10_S16

description: Duo.IBSD


title: Dia_CACMEL_3

description: bearing a cachectic (CAC) melanoma without rFibcd1 treated replicate 3

value: female


title: WT_control_6h_3

value: WT

value: 6 h

value: leaf


title: Jej.IBSD 15_S21

description: Jej.IBSD


title: Jej.HV 8_S14

description: Jej.HV

value: Healthy


title: WT_control_6h_1


title: WT_control_6h_2


title: Dia_CACMEL_1

description: bearing a cachectic (CAC) melanoma without rFibcd1 treated replicate 1


title: Jej.IBSC 7_S13

description: Jej.IBSC


title: S30_low_EX_RRBS

city: Amherst

last: Pilsner

state: Massachusetts

address: 686 N PLEASANT

department: Environmental Health Sciences

institute: University of Massachusetts Amherst

library_source: genomic

data_processing:
RRBS data was trimmed using TrimGalore, mapping and methylation calling were performed with Bowtie2 and Bismark respectively. Differential methylation analysis was performed with methylkit R package.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
RNA-seq data was trimmed with TrimGalore, mapping, SNP calling and differention expression analysed were performed tophat, samtools and edgeR respectively
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include beta and CPM values for each sample .
Supplementary_files_format_and_content: Matrix table with raw beta values and gene counts for every region/gene and every sample

molecule: genomic DNA

source_name: Extra-embryo

growth_protocol: Exposures were 2.5 and 25mg/kg/day for low and high groups respectively

extract_protocol: DNA and RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DNA(Sperm and embryo) isolation was performed using rapid extraction protocol involving homogenization with beeds in lyisis buffer mixture of guanidine thyiocyanate and TCEP; total RNA (embryo) was isolated  using the Roche High Pure RNA Isolation Kit

value: C57BL/6 * DBA/2J

value: Extra-embryo

value: Embryonic day 7.5

value: wild type

value: male

value: Low DEHP (2.5mg/kg/day)


title: S29_low_EX_RRBS


title: Dia_CACMELwithRFIBCD1_10

description: bearing a cachectic (CAC) melanoma with rFibcd1 treated replicate 10


title: S28_low_EX_RRBS


title: cca1 lhy_CL_4h_3

value: cca1 lhy

value: 32 h light

value: 4 h


title: Dia_CACMELwithRFIBCD1_9

description: bearing a cachectic (CAC) melanoma with rFibcd1 treated replicate 9

value: NCI Ath/nude


title: Dia_CACMEL_6

description: bearing a cachectic (CAC) melanoma without rFibcd1 treated replicate 6

value: diaphragm muscles


title: S27_high_EX_RRBS

value: High DEHP (25mg/kg/day)


title: cca1 lhy_CL_4h_2


title: Dia_CACMELwithRFIBCD1_8

description: bearing a cachectic (CAC) melanoma with rFibcd1 treated replicate 8

value: 4 months

value: female


title: S26_high_EX_RRBS


title: cca1 lhy_CL_4h_1


title: CTX-Nes

source_name: Cortex

value: Nestin-dVenus

value: Brain

value: CTX


title: ahk2 ahk3_CL_4h_3

value: ahk2 ahk3

value: leaf


title: Jej.IBSD 4_S10

description: Jej.IBSD

value: Jejunum

value: IBS-D

value: F


title: S25_high_EX_RRBS

value: C57BL/6 * DBA/2J

value: Extra-embryo

value: Embryonic day 7.5

value: wild type

value: male


title: Jej.HV 3_S9

description: Jej.HV

value: Healthy

value: M


title: Jej.HV 2_S8

description: Jej.HV


title: Dia_CACMELwithRFIBCD1_7

description: bearing a cachectic (CAC) melanoma with rFibcd1 treated replicate 7

value: NCI Ath/nude

value: diaphragm muscles

value: 4 months


title: ahk2 ahk3_CL_4h_1

value: 32 h light

value: 4 h


title: Dia_CACMELwithRFIBCD1_5

description: bearing a cachectic (CAC) melanoma with rFibcd1 treated replicate 5

value: female


title: ahk2 ahk3_CL_4h_2

value: ahk2 ahk3

value: leaf


title: S24_control_EX_RRBS

value: Unexposed


title: WT_CL_4h_3

value: WT


title: S23_control_EX_RRBS

value: C57BL/6 * DBA/2J


title: Dia_CACMELwithRFIBCD1_4

description: bearing a cachectic (CAC) melanoma with rFibcd1 treated replicate 4


title: S22_control_EX_RRBS

value: Extra-embryo


title: EoE like 13

city: Bern

first: Shida

last: Yousefi

state: Bern

address: Inselspital, INO-F

department: Pharmacology

country: Switzerland

institute: University of Bern

description:
N76
EoE_with_low_Eos.Control.DEResults.xlsx
p431_first6Groups.counts.txt

data_processing:
The quality of the RNA-seq data was assessed using fastq.gzc v. 0.11.5 and RSeQC v. 2.6.4. The reads were mapped to the reference genome using HiSat2 v. 2.1.0. FeatureCounts v. 1.6.0 was used to count the number of reads overlapping with each gene as specified in the genome annotation (Homo_sapiens.GRCh38.94).
FeatureCounts v. 1.6.0 was used to count the number of reads overlapping with each gene as specified in the genome annotation (Homo_sapiens.GRCh38.94).
The Bioconductor packages DESeq2 and TopGo were used to analyze differentially expressed genes and their corresponding gene ontology class. Data exploration and visualization of the RNA-seq results was performed using the interactive Shiny application.
Genome_build: Homo_sapiens.GRCh38.94
Supplementary_files_format_and_content: Excel file including RPKM values for each sample

source_name: EoE like

extract_protocol:
FFPE esophageal biopsy tissue blocks were shipped from each center to the Swiss EoE Clinic. Esophageal biopsies from patients with classical EoE (10 samples), EoE-like esophagitis (13 samples), non-specific esophagitis (10 samples), lymphocytic esophagitis (5 samples), and esophagus-healthy individuals (7 samples) were processed. Automated RNA Extraction from FFPE was performed using the Maxwell® RSC RNA FFPE Kit in Maxwell® RSC Instrument (Promega, Dübendorf, Switzerland).
RNA-seq libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio USA, Inc., CA, USA) and were sequenced in a NovaSeq S1 flow cell (2 x 50 bp) (Illumina, CA, USA) as previously described.
RNA sequencing was performed at the RNAseq core (Next Generation Sequencing (NGS) Platform) of the University of Bern.

tag: disease state

value: EoE like

value: esophagus


title: WT_CL_4h_2


title: Dia_CACMELwithRFIBCD1_3

description: bearing a cachectic (CAC) melanoma with rFibcd1 treated replicate 3


title: S21_low_EM_RRBS

source_name: Embryo

value: Embryo

value: Embryonic day 7.5

value: wild type

value: male

value: Low DEHP (2.5mg/kg/day)


title: EoE like 12

description:
N62
EoE_with_low_Eos.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: Jej.IBSD 5_S11

description: Jej.IBSD

value: Jejunum

value: IBS-D

value: M


title: WT_CL_4h_1

value: 32 h light

value: 4 h


title: Dia_CACMELwithRFIBCD1_2

description: bearing a cachectic (CAC) melanoma with rFibcd1 treated replicate 2

value: NCI Ath/nude

value: diaphragm muscles

value: 4 months

value: female


title: S20_low_EM_RRBS

value: C57BL/6 * DBA/2J


title: cca1 lhy_control_4h_3

value: cca1 lhy

value: control (SD conditions)

value: leaf


title: S19_low_EM_RRBS

value: Embryo

value: Embryonic day 7.5


title: Dia_CACMELwithRFIBCD1_6

description: bearing a cachectic (CAC) melanoma with rFibcd1 treated replicate 6


title: Control 7

description:
N137
GERD.Control.DEResults.xlsx
p431_first6Groups.counts.txt

source_name: Control

value: Control

value: esophagus


title: EoE like 11

description:
N17
EoE_with_low_Eos.Control.DEResults.xlsx
p431_first6Groups.counts.txt

value: EoE like


title: Jej.HV 1_S7

description: Jej.HV

value: Jejunum

value: Healthy

value: F


title: LLC_2

description:
LLC_2
LCC replicate 2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to mm10 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for all 17 samples

source_name: diaphragm muscles from 4-month-old male C57BL/6J mice

tag: sample group

value: LCC


title: S17_high_EM_RRBS

value: wild type

value: male

value: High DEHP (25mg/kg/day)


title: ahk2 ahk3_control_4h_3

value: ahk2 ahk3

value: 4 h


title: Control 6

description:
N134
GERD.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: S16_high_EM_RRBS

value: C57BL/6 * DBA/2J


title: Control 5

description:
N132
GERD.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: GERD 6

description:
N124
GERD.Control.DEResults.xlsx
p431_first6Groups.counts.txt

source_name: GERD

value: GERD


title: ahk2 ahk3_control_4h_2

value: control (SD conditions)

value: leaf


title: cca1 lhy_control_4h_1

value: cca1 lhy


title: LLCandFIBCD1_4

description:
LLCandFIBCD1_4
LCC with rFibcd1 treated repliacte 4

value: diaphragm muscles

value: 4 months

value: LCC with rFibcd1 treated


title: GERD 5

description:
N122
GERD.Control.DEResults.xlsx
p431_first6Groups.counts.txt

value: esophagus


title: LLCandFIBCD1_3

description:
LLCandFIBCD1_3
LCC with rFibcd1 treated repliacte 3


title: S14_control_EM_RRBS

value: Embryo

value: Embryonic day 7.5

value: Unexposed


title: ahk2 ahk3_control_4h_1


title: GERD 4

description:
N118
GERD.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: S15_control_EM_RRBS

value: wild type


title: LLCandFIBCD1_2

description:
LLCandFIBCD1_2
LCC with rFibcd1 treated repliacte 2


title: S13_control_EM_RRBS

value: male


title: Dia_CACMELwithRFIBCD1_1

description: bearing a cachectic (CAC) melanoma with rFibcd1 treated replicate 1

value: NCI Ath/nude

value: female


title: EoE 10

description:
N100
Conventional.Control.DEResults.xlsx
p431_first6Groups.counts.txt

source_name: conventional EoE

value: conventional EoE


title: S18_high_EM_RRBS

value: C57BL/6 * DBA/2J

value: High DEHP (25mg/kg/day)


title: cca1 lhy_control_4h_2

value: control (SD conditions)

value: 4 h


title: LLC_3

description:
LLC_3
LCC replicate 3

value: LCC


title: WT_control_4h_2

value: WT

value: leaf


title: S12_low_SP_RRBS

source_name: Sperm

value: Sperm

value: 14 weeks

value: Low DEHP (2.5mg/kg/day)


title: LLCandFIBCD1_1

description:
LLCandFIBCD1_1
LCC with rFibcd1 treated repliacte 1

value: diaphragm muscles

value: 4 months

value: LCC with rFibcd1 treated


title: EoE 9

description:
N98
Conventional.Control.DEResults.xlsx
p431_first6Groups.counts.txt

value: esophagus


title: LLC_1

description:
LLC_1
LCC replicate 1


title: WT_control_4h_1


title: CONTROL_4

description:
CONTROL_4
control replicate 4

value: control


title: S10_low_SP_RRBS

value: wild type

value: male


title: cca1 lhy_CL_0h_3

value: cca1 lhy

value: 32 h light

value: 0 h


title: EoE 7

description:
N106
Conventional.Control.DEResults.xlsx
p431_first6Groups.counts.txt

value: conventional EoE


title: CONTROL_3

description:
CONTROL_3
control replicate 3


title: EoE 8

description:
N110
Conventional.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: EoE 6

description:
N105
Conventional.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: S9_low_SP_RRBS


title: WT_control_4h_3

value: control (SD conditions)

value: 4 h


title: S8_high_SP_RRBS

value: High DEHP (25mg/kg/day)


title: lymphocytic 5

description:
N202
Lymphocytic.Control.DEResults.xlsx
p431_first6Groups.counts.txt

source_name: lymphocytic

value: lymphocytic


title: cca1 lhy_CL_0h_1

value: leaf


title: ahk2 ahk3_CL_0h_3

value: ahk2 ahk3


title: CONTROL_2

description:
CONTROL_2
control replicate 2

value: diaphragm muscles


title: CONTROL_1

description:
CONTROL_1
control replicate 1

value: 4 months


title: lymphocytic 4

description:
N187
Lymphocytic.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: CONTROLandFIBCD1_5

description:
CONTROLandFIBCD1_5
control with rFibcd1 treated replicate 5

value: control with rFibcd1 treated


title: S6_high_SP_RRBS

value: Sperm

value: 14 weeks


title: ahk2 ahk3_CL_0h_2


title: Non specific 10

description:
N47
Non-specific.Control.DEResults.xlsx
p431_first6Groups.counts.txt

source_name: nonspecific

value: nonspecific

value: esophagus


title: ahk2 ahk3_CL_0h_1


title: S5_high_SP_RRBS

value: wild type

value: male


title: Non specific 9

description:
N42
Non-specific.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: S11_low_SP_RRBS

value: Low DEHP (2.5mg/kg/day)


title: CONTROLandFIBCD1_4

description:
CONTROLandFIBCD1_4
control with rFibcd1 treated replicate 4


title: CONTROLandFIBCD1_3

description:
CONTROLandFIBCD1_3
control with rFibcd1 treated replicate 3


title: cca1 lhy_CL_0h_2

value: cca1 lhy

value: 32 h light

value: 0 h


title: CONTROL_5

description:
CONTROL_5
control replicate 5

value: control


title: WT_CL_0h_3

value: WT


title: S4_control_SP_RRBS

value: Unexposed


title: WT_CL_0h_2

value: leaf


title: S3_control_SP_RRBS


title: Non specific 8

description:
N41
Non-specific.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: CONTROLandFIBCD1_1

description:
CONTROLandFIBCD1_1
control with rFibcd1 treated replicate 1

value: diaphragm muscles


title: cca1 lhy_control_0h_3

value: control (SD conditions)


title: S7_high_SP_RRBS

value: High DEHP (25mg/kg/day)


title: Non specific 7

description:
N37
Non-specific.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: S2_control_SP_RRBS

value: Sperm


title: S1_control_SP_RRBS

value: 14 weeks


title: WT5

city: Jinan

first: Sisi

last: Luan

state: Shandong

address: 544 Jingsi Road

department: Endocrinology

country: China

institute: Shandong Provincial Hospital Affiliated to Shandong University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia). After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Hippocampus

extract_protocol:
The hippocampal tissues were removed, flash frozen with liquid nitrogen, and RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hippocampus


title: cca1 lhy_control_0h_2


title: WT4


title: EoE like 9

description:
N44
EoE_with_low_Eos.Control.DEResults.xlsx
p431_first6Groups.counts.txt

value: EoE like

value: esophagus


title: cca1 lhy_control_0h_1


title: H3K27me3_ChIP_NPC_WT_rep2

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
fastq: Illumina's HiSeq Control Software
Each fastq file was mapped to mouse genom (mm10) with BWA -aln (Li and Durbin, 2009) and PCR duplicates were removed using Picard MarkDuplicate. The bigWig files were created using deepTools (Ramírez et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: The processed files (bigWig) were created using deepTools (Ramírez et al., 2016).

source_name: neural precursor cells

growth_protocol: Cells were grown in DMEM supplemented with 100 U/mL penicillin, 100 mg/mL streptomycin, 15% KnockOut Serum Replacement (ThermoFisher, 10828028), Glutamax (Gibco, 35050), 0.1 mM non-essential amino acid, 0.1mM beta-mercaptoethanol, and 500 U/ml LIF at 37°C and 5% CO2

extract_protocol:
ChIP and input library preparation were carried out as described in ENCODE experiments (“Ren Lab ENCODE Chromatin Immunoprecipitation Protocol” in https://www.encodeproject.org/documents/)
ChIP-seq library sequencing procedures were carried out as previously described according to Illumina HiSeq4000 or HiSeq2500 protocols (Illumina, San Diego, CA).

tag: cell type

value: E14 mouse neural precursor cell

tag: chip antibody

value: H3K27me3 (Active Motif, 61017)


title: WT3

tag: strain

value: wild type


title: EoE like 8

description:
N32
EoE_with_low_Eos.Control.DEResults.xlsx
p431_first6Groups.counts.txt

tag: tissue


title: WT2


title: ahk2 ahk3_control_0h_3

value: ahk2 ahk3


title: CONTROLandFIBCD1_2

description:
CONTROLandFIBCD1_2
control with rFibcd1 treated replicate 2

tag: age

value: 4 months

value: control with rFibcd1 treated


title: EoE like 7

description:
N29
EoE_with_low_Eos.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: H3K27me3_ChIP_ESC_Mll34dCD_rep2

source_name: embryonic stem cells

value: E14 mouse embryonic stem cell


title: WT1


title: ahk2 ahk3_control_0h_2

value: 0 h


title: WT_CL_0h_1

value: WT

value: 32 h light

value: leaf


title: Control 4

description:
N136
GERD.Control.DEResults.xlsx
p431_first6Groups.counts.txt

value: Control


title: H3K27me3_ChIP_ESC_Mll34dCD_rep1


title: KO5

value: Tshr-/-


title: H3K27me3_ChIP_ESC_WT_rep2


title: Non specific 6

description:
N30
Non-specific.Control.DEResults.xlsx
p431_first6Groups.counts.txt

value: nonspecific


title: EoE like 6

description:
N45
EoE_with_low_Eos.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: H3K27me3_ChIP_ESC_WT_rep1


title: KO4

value: hippocampus


title: WT_control_0h_3

value: control (SD conditions)


title: EoE like 10

description:
N192
EoE_with_low_Eos.Control.DEResults.xlsx
p431_first6Groups.counts.txt

value: EoE like

value: esophagus


title: WT_control_0h_2


title: Control 3

description:
N133
GERD.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: Control 2

description:
N131
GERD.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: H3K4me3_ChIP_NPC_Mll34dCD_rep2

value: E14 mouse neural precursor cell

value: H3K4me3 (Millipore, 04-745)


title: H3K27me3_ChIP_NPC_WT_rep1

value: H3K27me3 (Active Motif, 61017)


title: WT_control_0h_1


title: KO2


title: H3K4me3_ChIP_NPC_Mll34dCD_rep1


title: Control 1

description:
N130
GERD.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: GERD 3

description:
N119
GERD.Control.DEResults.xlsx
p431_first6Groups.counts.txt

value: GERD


title: KO1


title: ahk2 ahk3_control_0h_1

value: ahk2 ahk3


title: EoE 5

description:
N104
Conventional.Control.DEResults.xlsx
p431_first6Groups.counts.txt

value: conventional EoE


title: GERD 1

description:
N117
GERD.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: GERD 2

description:
N120
GERD.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: EoE 4

description:
N102
Conventional.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: KO3


title: EoE 3

description:
N101
Conventional.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: DSRCT-PDX1-AR-ASO#1204

type: protein

city: Houston

first: Joseph

middle: A.

last: Ludwig

state: Texas

department: Sarcoma Medical Oncology

institute: UT-MD-Anderson Cancer Center

scan_protocol: Slides were scanned on a flatbed scanner to produce 16-bit tiff images. Spots from tiff images were identified and their densities were quantified by MicroVigene. Relative protein levels for each sample were determined by interpolation of each dilution curve from the standard curve (supercurve) of the slide (antibody). Supercurve is constructed from a script in R written by the informatics department. These values are given as log2 values.

data_processing: Expression data was normalized for possible unequal protein loading, taking into account the signal intensity for each sample for all antibodies tested. Log2 values were media-centered by protein to account for variability in signal intensity by time and were calculated using the formula log2 signal – log2 median. Principal component analysis was used to check for a batch effect and feature-by-feature two-sample t-tests were used to assess differences between treatment and control groups. We also used feature-by-feature one-way analysis of variance (ANOVA) followed by the Tukey test to perform pair comparisons for all groups. Beta-uniform mixture models were used to fit the resulting p value distributions to adjust for multiple comparisons. The cutoff p values and number of significant proteins were computed for several different false discovery rates (FDRs). Biostatistical analyses comparing two groups were performed using an unpaired t-test with Gaussian distribution followed by the Welch correction. To distinguish between treatment groups, we used one-way ANOVA with the Geisser-Greenhouse correction. Differences with p values <0.05 were considered significant. Within clustered image maps (CIM), unsupervised double hierarchical clustering used the Pearson correlation distance and Ward’s linkage method as the clustering algorithm to link entities (proteins or genes) and samples.

label: 377 Primary Antibodies

molecule: protein

label_protocol: Using a 2470 Arrayer (Aushon BioSystems, tumor or cell lysates were serially diluted 2-fold for 5 dilutions (From undiluted to 1:16 dilutio) and arrayed on nitrocellulose-coated FAST slides in an 11X11 format. Samples were probed with antibodies using the Dako CSA tyramide-amplification approach and visualized by DAB colorimetric reaction.

growth_protocol: Male NOD (SCID)-IL-2Rgnull mice (The Jackson Laboratory; Farmington, CT) were subcutaneously injected with JN-DSRCT cells (5X106 cells/animal) or received PDX explants (2 mm) to generate xenografts. All mice were maintained under barrier conditions and treated using protocols approved by The University of Texas MD Anderson Cancer Center’s Institutional Animal Care and Use Committee.

extract_protocol: Protein extraction from tumor was performed by homogenizing an approximate 10 mg of frozen tissue in 500 ul of the lysis buffer containing protease and phosphatase inhibitors using an electric tissue homogenizer (Pro Scientific). Total lysed proteins were quantified using BCA protein assay kit and stored for further analyses for RPPA.

treatment_protocol: Once their tumors reached a volume of 150 mm3, 5 mice per group received AR ASOs (50 mg/kg subcutaneously daily, 5 times per week), or control ASOs (50 mg/kg subcutaneously daily, 5 times per week), or a placebo control (sterile vehicle buffer). Tumor volumes were measured using digital calipers at study initiation and 2–5 times per week after that for up to 85 days, or until their tumors reached 1500 mm3, whichever came first.

value: DSRCT-PDX1 Tumor

value: AR-ASO


title: DSRCT-PDX1-AR-ASO#1197

hyb_protocol: Samples were probed with antibodies using the Dako CSA tyramide-amplification approach and visualized by DAB colorimetric reaction.


title: DSRCT-PDX1-AR-ASO#1196


title: DSRCT-PDX1-AR-ASO#1193


title: EoE 1

description:
N99
Conventional.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: lymphocytic 3

description:
N51
Lymphocytic.Control.DEResults.xlsx
p431_first6Groups.counts.txt

value: lymphocytic


title: lymphocytic 2

description:
N36
Lymphocytic.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: DSRCT-PDX1-Placebo#1188

value: Placebo


title: lymphocytic 1

description:
N13
Lymphocytic.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: DSRCT-PDX1-Placebo#1184


title: DSRCT-PDX1-Control-ASO#1213

value: Control-ASO


title: DSRCT-PDX1-Control-ASO#1208


title: Non specific 5

description:
N28
Non-specific.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: DSRCT-PDX1-Control-ASO#1207


title: DSRCT-PDX1-Placebo#1192


title: JN-DSRCT-Xenograft-AR-ASO_PD#1381

value: JN-DSRCT-Xenograft Tumor


title: Non specific 3

description:
N12
Non-specific.Control.DEResults.xlsx
p431_first6Groups.counts.txt

value: nonspecific


title: Non specific 2

description:
N10
Non-specific.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: JN-DSRCT-Xenograft-AR-ASO_PD#1378


title: Non specific 1

description:
N8
Non-specific.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: DSRCT-PDX1-Control-ASO#1200


title: Non specific 4

description:
N14
Non-specific.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: EoE 2

description:
N103
Conventional.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: DSRCT-PDX1-Placebo#1214


title: EoE like 5

description:
N191
EoE_with_low_Eos.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: DSRCT-PDX1-Control-ASO#1187


title: JN-DSRCT-Xenograft-AR-ASO_PD#1361


title: EoE like 4

description:
N57
EoE_with_low_Eos.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: JN-DSRCT-Xenograft-AR-ASO_PD#1351


title: EoE like 3

description:
N27
EoE_with_low_Eos.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: EoE like 2

description:
N152
EoE_with_low_Eos.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: JN-DSRCT-Xenograft-AR-ASO_PD#1336


title: JN-DSRCT-Xenograft-AR-ASO#1079

source_name: JN-DSRCT-Xenograft-AR-ASO


title: EoE like 1

description:
N1
EoE_with_low_Eos.Control.DEResults.xlsx
p431_first6Groups.counts.txt


title: JN-DSRCT-Xenograft-AR-ASO#1078


title: JN-DSRCT-Xenograft-AR-ASO#1056


title: JN-DSRCT-Xenograft-AR-ASO#1019


title: JN-DSRCT-Xenograft-Placebo#1064

source_name: JN-DSRCT-Xenograft-Placebo


title: JN-DSRCT-Xenograft-Placebo#1055


title: HBR227-B

city: Dresden

first: Anastasios

last: Koutsoumparis

address: Tatzberg 47-49

institute: TU Dresden

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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.
Genome_build: WBcel235
Supplementary_files_format_and_content: Excel file with raw counts per strain

organism: Caenorhabditis elegans

source_name: L1 arrested (48 hours)

growth_protocol: Worms were grown on NEP plates from which eggs were harvested by hypclorite treatment. The eggs were then suspended in M9 buffer. After 48 hours the L1 arrested larvae were collected.

extract_protocol:
C elegans was disrupted by bead beating and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: Whole C. elegans tissue

tag: replicate

value: B


title: HBR227-A

value: A


title: HBR227-D

value: D


title: N2-D

value: Wild-type


title: JN-DSRCT-Xenograft-Placebo#1040


title: N2-C

value: C


title: N2-A


title: N2-B


title: HBR227-C


title: JN-DSRCT-Xenograft-Placebo#1037


title: JN-DSRCT-Xenograft-Control ASO#1071

source_name: JN-DSRCT-Xenograft-Control ASO

value: Control ASO


title: JN-DSRCT-Xenograft-Control ASO#1069


title: JN-DSRCT-Xenograft-Control ASO#1063


title: JN-DSRCT-Xenograft-Control ASO#1070


title: JN-DSRCT-Xenograft-Control ASO#1068


title: JN-DSRCT-Xenograft-Placebo#1038


title: HBR2340_D

description: L1 arrested (48 hours)

source_name: Whole C. elegans tissue


title: HBR2340_C

description: L1 arrested (48 hours)


title: PHX2193_D

description: L1 arrested (48 hours)


title: PHX2193_C

description: L1 arrested (48 hours)


title: PHX2193_A

description: L1 arrested (48 hours)


title: PHX2193_B

description: L1 arrested (48 hours)


title: HBR2340_B

description: L1 arrested (48 hours)


title: osteoblast-like cells, irradiated, rep1

type: RNA

city: Tokyo

first: Sayaka

last: Katagiri

country: Japan

institute: Tokyo Medical and Dental University

description:
Gene expression after 6hr in 3.3 J/cm2-irradiated osteoblast-like cells
L1

hyb_protocol: cRNAs were analyzed by hybridization onto an Agilent SurePrint G3 Unrestricted Gene Expression 8 × 60 K Microarray (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Fluorescence signals from the hybridized microarrays were detected using the Agilent Microarray Scanner System (Agilent Technologies) according to the manufacturer’s instructions.

data_processing:
Raw microarray data were extracted using Feature Extraction Software (ver. 11.0.1.1; Agilent Technologies).
Microarray data were quantile normalized and log2-transformed (Shippy et al., 2006) using R (ver. 3.6.0).

organism: Rattus norvegicus

source_name: osteoblast-like cells, irradiated, 3.3 J/cm2, 60 s

label_protocol: The Agilent Low Input Quick Amp Labeling kit (Agilent Technologies, Santa Clara, California, USA) was used to generate cRNA with a sample input of 200 ng total RNA for single-color microarray (Cy3) analysis according to the manufacturer’s instructions.

growth_protocol: Cultured in 35-mm diches in a humidified atmosphere of 95% air and 5% CO2 at 37°C. The medium was changed every 3 days.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, California, USA) with NucleoSpin RNA (TaKaRa Bio, Shiga, Japan). cDNA was synthesized using a PrimeScript RT Master Mix (TaKaRa Bio) according to the manufacturer’s instructions.

treatment_protocol: The growth medium was alpha minimal essential medium (α-MEM; Wako, Osaka, Japan), supplemented with 10% fetal bovine serum (FBS; Gibco, Carlsbad, California, USA) and 1% antibiotic-antimycotic mixture (Invitrogen, Carlsbad, California, USA). Osteoinduction medium was the growth medium containing 50 μg/mL ascorbic acid (Wako, Osaka, Japan), 10 mM β-glycerophosphate (Sigma-Aldrich), and 10 nM dexamethasone (Sigma-Aldrich).

value: calvaria

value: osteoblast-like cells

tag: treatment

value: irradiated

value: 3-5-day old


title: osteoblast-like cells, non-irradiated, rep2

description:
Gene expression after 6hr in 0 J/cm2-irradiated osteoblast-like cells
C2

source_name: osteoblast-like cells, non-irradiated

value: non-irradiated


title: osteoblast-like cells, irradiated, rep3

description:
Gene expression after 6hr in 3.3 J/cm2-irradiated osteoblast-like cells
L3


title: DYNAMIC 3d #2

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

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

country: Italy

institute: università di padova

description: Gene expression data from human cells used to recellularized mouse dECM in dynamic condition

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

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using RMA

label: biotin

source_name: Human myogenic cells and fibroblasts used to recellularized diaphragm dECM

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol starting  from 100ng of Total RNA using the Affymetrix Whole Trascriptome Plus Kit

growth_protocol: 3D diaphragmatic constructs were maintened in proliferating medium (1 g/L D-glucose, 20% FBS, 10-6 M dexamethasone, 10 ng/mL bFGF, 10 mg/mL insulin and 1% pen/strep) from day 0 to day 4, than differentiation medium (aMEM, 2% HS, 10 mg/mL insulin and 1% pen/strep) was used until day 7. From day 8 to day 14 constructs were maintaned in proliferating medium.

extract_protocol: RNA was extracted using Trizol

treatment_protocol: STATIC: cells were cultured inside dECM without mechanical stimulation; DYNAMIC: cells were cultured insiede dECM with mechanical stimulation from day 3 to day 14

value: 3D diaphragm-like construct cultivated for 3 days and mechanically stimulated

tag: tissue source

value: Skeletal muscle


title: osteoblast-like cells, irradiated, rep2

description:
Gene expression after 6hr in 3.3 J/cm2-irradiated osteoblast-like cells
L2


title: DYNAMIC 3d #3


title: DYNAMIC 14d #1

value: 3D diaphragm-like construct cultivated for 14 days and mechanically stimulated


title: osteoblast-like cells, non-irradiated, rep3

description:
Gene expression after 6hr in 0 J/cm2-irradiated osteoblast-like cells
C3


title: IB3b 2

city: Parma

first: Mariolina

last: Gulli

address: Parco Area delle Scienze 11a

department: Life Sciences

institute: University of Parma

description: test heterozygote

data_processing: Amplification signal was checked on each sample by SDS® software 2.3. Ct value was determined using auto-baseline and a threshold value of 0.2. The relative quantification analysis was performed with Expression Suite v1.1 software (Applied Biosystems, Foster City, USA). The small non-coding U6 RNA and RNU 48 were selected as endogenous genes, and RNA extracted from 16HBE14o- cell line was used as calibrator sample. Ct values >34 were considered as undetermined. Contamination was excluded by the analysis of a negative control. MiRNAs showing fold-changes (FC) ≥ +2 or FC ≤ -2 with a p value ≤ 0.05 were considered as differentially expressed.

label: FAM

source_name: immortalised  epithelial cell

label_protocol: A total of 100 ng of RNA from cell lines were reverse transcribed using the TaqMan® MicroRNA Reverse Transcription Kit in combination with the Megaplex™ RT Primers Pool A and Pool B, which together permit the analysis of 754 human microRNAs of greatest interest to the research community (functionally defined and/or broadly/highly expressed),  three endogenous controls and one negative control. The thermal profile consisted of 40 cycles at 16°C for 2 minutes, 42°C for 1 minute and 50°C for 1 second followed by one step at 85°C for 5 minutes. The pre-amplification of the miRNA cDNA target (2,5 μl) was performed using TaqMan® PreAmp Master Mix Kit and Megaplex™ PreAmp Primers Pool A and Pool B (Applied Biosystems). The thermal profile consisted of denaturation at 95°C for 10 minutes, one step at 55°C for 2 minutes followed by 2 minutes at 72°C, and 12 cycles at 95°C for 15 sec and 60°C for 4 minutes. According to manufacturer’s instructions, the preamplified cDNA product was mixed with the TaqMan® Universal PCR Master Mix, No AmpErase UNG, and loaded onto the TaqMan® MicroRNA Array A and B for PCR amplification. The following real-time PCR protocol was employed: 50°C for 2 minutes, 94.5°C for 10 minutes and 40 cycles at 97°C for 30 seconds and 59.7°C for 1 minute. All reactions (reverse transcription, preamplification and real-time PCR) were performed on a 7900HT Fast Real-Time PCR System (Applied Biosystems).

extract_protocol: Total RNA, including small RNAs, was extracted from cell lysates using mirVana isolation kit (Ambion, Austin, USA) according to the manufacturer’s protocol.

value: brochial epitelium

tag: pathology

value: heterozygote F508del/W1282X (derived from CF bronchial epithelium)


title: DYNAMIC 3d #1


title: N2_D

description: L1 arrested (48 hours)

tag: genotype


title: IB3b1

description: test heterozygote


title: DYNAMIC 14d #2


title: osteoblast-like cells, non-irradiated, rep4

description:
Gene expression after 6hr in 0 J/cm2-irradiated osteoblast-like cells
C4


title: CFBE41o- 2

description: test homozygous

value: homozygous for the F508del mutation, (derived from a bronchial isolate of a CF patient homozygous for the F508del CFTR mutation),


title: STATIC 14d #3

description: Gene expression data from human cells used to recellularized mouse dECM in static condition

value: 3D diaphragm-like construct cultivated for 14 days


title: osteoblast-like cells, non-irradiated, rep1

description:
Gene expression after 6hr in 0 J/cm2-irradiated osteoblast-like cells
C1


title: N2_C

description: L1 arrested (48 hours)


title: osteoblast-like cells, irradiated, rep4

description:
Gene expression after 6hr in 3.3 J/cm2-irradiated osteoblast-like cells
L4


title: HBR2340_A

description: L1 arrested (48 hours)

value: A


title: N2_A

description: L1 arrested (48 hours)


title: DYNAMIC 14d #3


title: MA6-He45-BRU4: Pooled Male FHM High Brain RepE

status: Public on Feb 27 2022

city: Saskatoon

first: Markus

last: Hecker

state: SK

address: 44 Campus Drive

country: Canada

institute: University of Saskatchewan

data_processing:
https://galaxy.ecotoxxplorer.ca/
Trim Galore! -- trimmed to a minimum phred score of 20 and a minimum sequence length of 35 bases per paired read
Kallisto quant -- alignment
Count data was normalized by use of the trimmed mean of M values approach (Robinson and Oshlack, 2010)
Genome_build: Fathead minnow reference transcriptome NCBI Acc# GCA_016745375.1
Supplementary_files_format_and_content: csv -- Differential expression results using DESeq2

organism: Pimephales promelas

source_name: Brain tissue

growth_protocol: Adult fathead minnows were exposed to graded aqueous fluoxetine concentrations (2.42, 10.7, 56.7 µg/L)  in 20L tanks for 96 hours. Two males and three females were in each tank. Tanks were in a flow-through design maintained at 25°C and a 16:8h light:dark cycle

extract_protocol:
Total RNA was extracted from tissue samples of individual fish using the RNeasy Plus Universal Mini Kit (Qiagen, Hilden, Germany) in a QiaCube instrument (Qiagen).  Pooled samples with an RNA Integrity Number (RIN) ≥ 9 were used for mRNA sequencing
Steps for generating libraries from total RNA included the following: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs, Ipswich, MA, USA); cDNA synthesis was done using NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs).  Subsequent steps of library preparation were done using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs).  Adapters and PCR primers were purchased from New England BioLabs.  Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems, Wilmington, MA, USA).  Determination of average fragment size was done with a LabChip GX (PerkinElmer, Waltham, MA, USA) instrument.   Once libraries were normalized and pooled, they denatured in 0.02N NaOH and neutralized using HT1 buffer.  The pool was loaded at 225pM on an Illumina NovaSeq (Illumina, San Diego, CA, USA) S4 lane using Xp protocol.  The run was performed for 2x100 cycles (paired-end mode).  A phiX library was used as a control and mixed with libraries at 1% level.  Base calling was performed with RTA v3.4.4. Program bcl2fastq2 v2.20 was applied to demultiplex samples and generate fastq reads.

treatment_protocol: Fathead minnows were exposed for 96 hours

tag: Sex

value: Male

value: Brain

value: 56.7µg FLX/L

value: E

tag: exposure time

value: 96 hours


title: MA6-Hd45-BRU4: Pooled Male FHM High Brain RepD

value: D


title: 16HBE14o- 1

description: control

value: derived from normal bronchus


title: 16HBE14o- 2

description: control


title: MA6-Hc45-BRU4: Pooled Male FHM High Brain RepC

value: C


title: N2_B

description: L1 arrested (48 hours)

value: B

value: Wild-type


title: STATIC 14d #1

value: Skeletal muscle


title: STATIC 14d #2


title: STATIC 3d #3

value: 3D diaphragm-like construct cultivated for 3 days


title: STATIC 3d #2


title: MA6-Md45-BRU4: Pooled Male FHM Medium Brain RepD

value: 10.7µg FLX/L


title: MA6-Hb45-BRU4: Pooled Male FHM High Brain RepB


title: STATIC 3d #1


title: MA6-Ma45-BRU4: Pooled Male FHM Medium Brain RepA


title: MA6-Ha45-BRU4: Pooled Male FHM High Brain RepA


title: MA6-Me45-BRU4: Pooled Male FHM Medium Brain RepE


title: MA6-Mc45-BRU4: Pooled Male FHM Medium Brain RepC


title: MA6-Cb45-BRU4: Pooled Male FHM Control Brain RepB

value: Negative control


title: MA6-Cd45-BRU4: Pooled Male FHM Control Brain RepD


title: MA6-Hd45-LU4: Pooled Male FHM High Liver RepD

source_name: Liver tissue

value: Liver


title: MA6-Me45-LU4: Pooled Male FHM Medium Liver RepE


title: MA6-Ce4-BRU4: Pooled Male FHM Control Brain RepE


title: MA6-Mb45-BRU4: Pooled Male FHM Medium Brain RepB


title: MA6-Md45-LU4: Pooled Male FHM Medium Liver RepD


title: MA6-Cc45-BRU4: Pooled Male FHM Control Brain RepC


title: MA6-Ca45-BRU4: Pooled Male FHM Control Brain RepA


title: MA6-He45-LU4: Pooled Male FHM High Liver RepE


title: MA6-Hc45-LU4: Pooled Male FHM High Liver RepC


title: MA6-Ha45-LU4: Pooled Male FHM High Liver RepA


title: MA6-Hb45-LU4: Pooled Male FHM High Liver RepB


title: MA6-Ce4-LU4: Pooled Male FHM Control Liver RepE


title: MA6-Cb45-LU4: Pooled Male FHM Control Liver RepB


title: MA6-Ca45-LU4: Pooled Male FHM Control Liver RepA


title: MA6-Ma45-LU4: Pooled Male FHM Medium Liver RepA


title: MA6-Mc45-LU4: Pooled Male FHM Medium Liver RepC


title: MA6-Mb45-LU4: Pooled Male FHM Medium Liver RepB


title: MA6-Cd45-LU4: Pooled Male FHM Control Liver RepD


title: MA6-Cc45-LU4: Pooled Male FHM Control Liver RepC


title: ZF 10hpf rep1

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

data_processing:
Basecalls performed using illumina bcl2fastq 2.17.
Adapters were trimmed with cutadapt. Adapter-trimmed reads were quality trimmed with Trimmomatic.
Clean reads were firstly mapped to the genome and then transcriptome with hisat2-2.10
Pileup was performed using samtools API pysam.
Customized scripts were used to call m5C sites from samples
Genome_build: Zv9.78
Supplementary_files_format_and_content: CSV files recording the coverage, m5C level, P-value for m5C sites

organism: Danio rerio

source_name: embryo

growth_protocol: Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.

extract_protocol:
For the embryonic stages, ~200 embryos were collected and for the larval stage ~150 larvae were collected.  Total RNA was isolated with TRIzol reagent and Direct-zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).
100ng-1μg of polyadenylated RNA was converted using the EZ RNA methylation kit (Zymo Research) with modified high-stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150~200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). The fragmented RNA was then used for library construction, following the manufacturer’s protocol (NEBNext Ultra II Directional RNA Library Prep Kit, NEB).

value: embryo

tag: developmental stage

value: 10 hpf

value: wild type AB fish


title: ZF 8hpf rep1

value: 8 hpf


title: ZF 8hpf rep2


title: XL stage0 rep1

data_processing:
Basecalls performed using illumina bcl2fastq 2.17.
Adapters were trimmed with cutadapt. Adapter-trimmed reads were quality trimmed with Trimmomatic.
Clean reads were firstly mapped to the genome and then transcriptome with hisat2-2.10
Pileup was performed using samtools API pysam.
Customized scripts were used to call m5C sites from samples
Genome_build: Xenbase XL 9.2
Supplementary_files_format_and_content: CSV files recording the coverage, m5C level, P-value for m5C sites

organism: Xenopus laevis

source_name: early embryo

extract_protocol:
~200 embryos were used for RNA isolation.  Total RNA was isolated with TRIzol reagent and Direct-zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).
100ng-1μg of polyadenylated RNA was converted using the EZ RNA methylation kit (Zymo Research) with modified high-stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150~200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). The fragmented RNA was then used for library construction, following the manufacturer’s protocol (NEBNext Ultra II Directional RNA Library Prep Kit, NEB).

value: stage 0


title: XT stage25 rep2

value: stage 25


title: ZF 48hpf rep1

value: 48 hpf


title: ZF 24hpf rep2

value: 24 hpf


title: ZF 16hpf rep2

value: 16 hpf


title: XL stage0 rep2


title: ZF 16hpf rep1


title: ZF 24hpf rep1


title: ZF 48hpf rep2


title: ZF 6hpf rep2

value: 6 hpf


title: XT stage25 rep1


title: ZF 10hpf rep2


title: ZF 2hpf rep1

value: 2 hpf


title: ZF 2hpf rep2


title: ZF 4hpf rep1

value: 4 hpf


title: ZF 0hpf rep1

value: 0 hpf


title: ZF 6hpf rep1


title: ZF 4hpf rep2


title: NSUN2 KO 2-3hr

data_processing:
Basecalls performed using illumina bcl2fastq 2.17.
Adapters were trimmed with cutadapt-1.13 (-e 0.1 -q 25 –trim-n -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAG).
Clean reads were mapped to genome and transcriptome with tophat2. Only unique alignments were used.
FPKM values were calculated with cufflinks.
Genome_build: BDGP5.78
Supplementary_files_format_and_content: Tabular files recording the FPKM values

organism: Drosophila melanogaster

extract_protocol:
NSUN2-/- female virgins or w1118 virgins were crossed with w1118 males for two days in advance. For each time period, 70-100 embryos were collected to ensure RNA yield and that samples were representative. Total RNA was isolated with TRIzol reagent and Direct-zol RNA MiniPrep kit. For each sample, 1ug total RNA was used for library construction. 1.2μl of 1:50 diluted SIRVs E1 RNA spike-in mix (Spike-in RNA Variant Control Mixes, Lexogen) was added to 1ug total RNA to allow for normalization between the samples. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).
NEBNext Ultra II Directional RNA Library Prep Kit was used in library construction.

value: early embryo

value: NSUN2 Knockout


title: NSUN2 KO 0-0.5hr


title: D7

city: PULLMAN

first: Michael

middle: A

last: Crowley

state: WA

address: 100 Dairy Rd

department: VMP

institute: Washington State University

data_processing:
Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Following rRNA removal, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X).
First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. After adenylation of 3’ ends of cDNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB，USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. Lastly, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using HiSeq PE Cluster Kit cBot-HS (Illumina). After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated. Raw data of fastq format was firstly processed through in-house perl scripts. In this step, clean reads were obtained by removing reads containing adapter, reads containing ploy-N, and low-quality reads. Alignment of clean reads to reference genome was performed with used Bowtie2-2.2.3. HTSeq v0.6.1 was used to count the read numbers mapped to each gene. Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis between the strains was performed using the DEGSeq R package (1.20.0). P values were adjusted using the Benjamini & Hochberg method.
Genome_build: https://www.patricbrc.org/view/Genome/224326.49#view_tab=sequences
Supplementary_files_format_and_content: read count, D7vsWT.Differential_analysis_results.xls

organism: Borreliella burgdorferi

source_name: Culture

growth_protocol: Triplicate cultures of wild type and D7 (SR0726 deletion mutant) were grown in BSK-II under standard conditions until mid-log phase, sub-cultured (1:100) to room temperature BSK-II, grown back to mid-log phase, subcultured (1:100) to 35°C, grown to late-phase, and pelleted.

extract_protocol:
Modified hot phenol method
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Temperature-shift to induce SR0726 transcription

tag: culture density


title: Wild type


title: ZF 0hpf rep2


title: WIII8 3-4hr

value: wild type


title: NSUN2 KO 4-5hr


title: WIII8 2-3hr


title: NSUN2 KO 0-0.5hr rep1

description:
processed data file:
Ovary_KO.csv

data_processing:
Basecalls performed using illumina bcl2fastq 2.17.
Adapters were trimmed with cutadapt. Adapter-trimmed reads were quality trimmed with Trimmomatic.
Clean reads were firstly mapped to the genome and then transcriptome with hisat2-2.10
Pileup was performed using samtools API pysam.
Customized scripts were used to call m5C sites from samples
Genome_build: BDGP5.78
Supplementary_files_format_and_content: CSV files recording the coverage, m5C level, P-value for m5C sites

extract_protocol:
500-1,000 embryos, ~50 larvae, ~50 pupa, ~50 ovaries, and ~50 adult flies were used for RNA isolation in each stage.  Total RNA was isolated with TRIzol reagent and Direct-zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).
100ng-1μg of polyadenylated RNA was converted using the EZ RNA methylation kit (Zymo Research) with modified high-stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150~200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). The fragmented RNA was then used for library construction, following the manufacturer’s protocol (NEBNext Ultra II Directional RNA Library Prep Kit, NEB).

value: NSUN2 KO


title: NSUN2 KO Ovary rep2

description:
processed data file:
em0-0.5_KO.csv

source_name: ovary

value: Adult, female


title: NSUN2 KO Ovary rep1

description:
processed data file:
em0-0.5_KO.csv


title: WT Ovary rep2

description:
processed data file:
Ovary.csv

value: Wild type


title: NSUN2 KO 0-0.5hr rep2

description:
processed data file:
Ovary_KO.csv


title: WT Pupa rep2

description:
processed data file:
Pupa.csv

source_name: pupa

value: Pupa


title: WIII8 1-2hr


title: WIII8 0-0.5hr


title: WT L3 rep2

description:
processed data file:
L3.csv

source_name: larva

value: L3 larva


title: WT L3 rep1

description:
processed data file:
L3.csv


title: WT Pupa rep1

description:
processed data file:
Pupa.csv


title: WT Ovary rep1

description:
processed data file:
Ovary.csv


title: WT L1 rep1

description:
processed data file:
L1.csv

value: L1 larva


title: WT 6-8hr rep1

description:
processed data file:
em_6-8.csv

value: 6-8hr embryo


title: WT 6-8hr rep2

description:
processed data file:
em_6-8.csv


title: WT 4-6hr rep1

description:
processed data file:
em_4-6.csv

value: 4-6hr embryo


title: WT 3-4hr rep2

description:
processed data file:
em_3-4.csv

value: 3-4hr embryo


title: WT 22-24hr rep2

description:
processed data file:
em_22_24.csv

value: 22-24hr embryo


title: WT 3-4hr rep1

description:
processed data file:
em_3-4.csv


title: WT 22-24hr rep1

description:
processed data file:
em_22_24.csv


title: WT 10-12hr rep1

description:
processed data file:
em_10_12.csv

value: 10-12hr embryo


title: WT 8-10hr rep1

description:
processed data file:
em_8-10.csv

value: 8-10hr embryo


title: WT 10-12hr rep2

description:
processed data file:
em_10_12.csv


title: WIII8 4-5hr


title: WT 8-10hr rep2

description:
processed data file:
em_8-10.csv


title: WT 4-6hr rep2

description:
processed data file:
em_4-6.csv


title: WT 2-3hr rep2

description:
processed data file:
em_2-3.csv

value: 2-3hr embryo


title: WT L1 rep2

description:
processed data file:
L1.csv


title: WT 2-3hr rep1

description:
processed data file:
em_2-3.csv


title: WT 1-2hr rep2

description:
processed data file:
em_1-2.csv

value: 1-2hr embryo


title: WT 0.5-1hr rep2

description:
processed data file:
em_0.5-1.csv

value: 0.5-1hr embryo


title: WT 0.5-1hr rep1

description:
processed data file:
em_0.5-1.csv


title: WT 0-0.5hr rep2

description:
processed data file:
em_0-0.5.csv

value: 0-0.5hr embryo


title: NPM1c+ DNMT3AR882H FLT3-ITD AML blasts for H3K27me3 ChIP

first: Xiaotian

state: TX

address: 6431 Fannin St

department: Biochemistry and Molecular Biology

institute: The University of Texas Health Science Center at Houston

description: AML-5583 H3K27me3

data_processing:
ChIP-seq raw reads were mapped to the hg19 human reference genome or mm9 reference genome using Bowtie2 (version 2.3.4) . Quality control for the alignment BAM files was performed by samtools, allowing only uniquely mapped reads to be retained and then PCR duplicates were removed by Picard (http://broadinstitute.github.io/picard/) using the MarkDuplicates tool with the parameters “VALIDATION_STRINGENCY = LENIENT REMOVE_DUPLICATES = true” for downstream analyses. Significant NPM1 and CRM1 peaks calling were performed by MACS2  callpeak command with default parameters except with “-q 0.05 --nolambda --broad --broad-cutoff 0.05”. The peaks were then filtered by the length of >=500bp and the hg19 ENCODE blacklist (https://www.encodeproject.org/files/ENCFF001TDO/). Statistically significant differential elements were identified using MAnorm [4], which normalizes read density levels and produces P values using MA plot methods. Regions with an absolute M value of >1 and a P value of <0.01 were considered as gained or lost regions. Bigwig files were build from bam files using deeptools with options “-binSize 50 and --normalizeUsing RPGC”. Identified peaks were annotated by intersection with the genome using BEDTools. The Integrative Genomics Viewer (IGV)  was used to visualize the genome browser track.
Genome_build: hg19; mm9
Supplementary_files_format_and_content: bigwig

source_name: NPM1c+ DNMT3AR882H FLT3-ITD AML blasts

growth_protocol: All human leukemia cell lines are maintained in RPMI-1640 medium with 10% FBS and 1% Pen/Strep, mouse progenitor cell lines are maintained in RPMI-1640 medium with 1% CHO-SCF condidtion medium and 1uM betaestrodial

extract_protocol:
Briefly, one million cells were fixed with 1% formaldehyde and sonicated with Covaris E220 or Bioruptor Plus. Sonicated chromatin was then incubated with antibody against H3K27me3(Cell Signaling, #9733), H3K27ac (Diagenode, #C15410196) overnight. Protein A/G beads (ThermoFisher) were added to the sonicated chromatin for 2 hours. After washes with low-salt, high-salt and LiCl wash buffer. Following washes, beads were de-crosslinked with Proteinase K (Zymo Research) at 55 °C overnight. Pull-downed DNA was extracted by DNA clean and concentration kit (Zymo Research).
Accel-NGS® 1S Plus  DNA Library Swiftbio Science (IDT XGEN DNA ssDNA low input since 2022 )

treatment_protocol: OCI-AML3 NPM1c degron2 cell line treated with DMSO or 500nM dTag-13 was added to culture medium for 24hrs.

tag: tissue and cell origin

value: Genetic enginnered cell line allow for dTag-13 mediated degradation of NPM1c


title: OCI-AML3 NPM1c degron2 cell line treated with DMSO for ENL ChIP

source_name: OCI-AML3 NPM1c degron2 cell line


title: OCI-AML3 NPM1c degron2 cell line treated with dTag-13-6hr for ENL ChIP


title: OCI-AML3 NPM1c degron2 cell line treated with dTag-13 and wash-off for 10 day for H3K27me3 ChIP

description: NPM1c-degron2-dTag-10day-wash-off-H3K27me3


title: NPM1c+ IDH1R132H AML blasts for H3K27me3 ChIP

description: AML-5577 H3K27me3

source_name: NPM1c+ IDH1R132H AML blasts


title: NPM1c+ IDH1R132H AML blasts for H3K27ac ChIP

description: AML-5577 H3K27ac


title: OCI-AML3 NPM1c degron2 cell line treated with dTag-13 and wash-off for 10 day for H3K27ac ChIP

description: NPM1c-degron2-dTag-10day-wash-off-H3K27ac


title: OCI-AML3 NPM1c degron2 cell line treated with dTag-13-24hr and wash-off for 4 days for H3K27ac ChIP

description: NPM1c-degron2-dTag-4day-wash-off-H3K27ac


title: OCI-AML3 NPM1c degron2 cell line treated with dTag-13 and SAHA-24hr for H3K27ac ChIP


title: OCI-AML3 NPM1c degron2 cell line treated with dTag-13-24hr for H3K27ac ChIP


title: OCI-AML3 NPM1c degron2 cell line treated with dTag-13-24hr for HDAC1 ChIP


title: OCI-AML3 NPM1c degron2 cell line treated with DMSO for H3K27ac ChIP


title: OCI-AML3 NPM1c degron2 cell line treated with DMSO for HDAC1 ChIP


title: WT 1-2hr rep1

description:
processed data file:
em_1-2.csv


title: MOLM13 cells treated with DMSO for Cut&Run of XPO1

data_processing:
Library strategy: CUT&RUN
CUT&RUN raw reads were mapped to the hg19 human reference genome using Bowtie2 (version 2.3.4) . Quality control for the alignment BAM files was performed by samtools, allowing only uniquely mapped reads to be retained and then PCR duplicates were removed by Picard (http://broadinstitute.github.io/picard/) using the MarkDuplicates tool with the parameters “VALIDATION_STRINGENCY = LENIENT REMOVE_DUPLICATES = true” for downstream analyses. Significant NPM1 and CRM1 peaks calling were performed by MACS2 callpeak command with default parameters except with “-q 0.05 --nolambda --broad --broad-cutoff 0.05”. The peaks were then filtered by the length of >=500bp and the hg19 ENCODE blacklist (https://www.encodeproject.org/files/ENCFF001TDO/). Statistically significant differential elements were identified using MAnorm [4], which normalizes read density levels and produces P values using MA plot methods. Regions with an absolute M value of >1 and a P value of <0.01 were considered as gained or lost regions. Bigwig files were build from bam files using deeptools with options “-binSize 50 and --normalizeUsing RPGC”. Identified peaks were annotated by intersection with the genome using BEDTools. The Integrative Genomics Viewer (IGV) was used to visualize the genome browser track.
CUT&RUN raw reads from NPM1-WT were mapped to the CHMT13 human reference genome using Bowtie2 (version 2.3.4) . Quality control for the alignment BAM files was performed by samtools, allowing only uniquely mapped reads to be retained and then PCR duplicates were removed by Picard (http://broadinstitute.github.io/picard/) using the MarkDuplicates tool with the parameters “VALIDATION_STRINGENCY = LENIENT REMOVE_DUPLICATES = true” for downstream analyses. Bigwig files were build from bam files using deeptools with options “-binSize 50 and --normalizeUsing RPGC”. Identified peaks were annotated by intersection with the genome using BEDTools. The Integrative Genomics Viewer (IGV) was used to visualize the genome browser track.
Genome_build: hg19; CHMT13; mm9
Supplementary_files_format_and_content: bigwig

source_name: MOLM13 leukemia cell line

extract_protocol:
Cut & Run and RNase Cut & Run were performed with nuclear extraction. Basically, 0.5 to 2 X106 cells were harvested and extracted for the nucleus using nuclear extraction buffer (20mM HEPES pH 7.9, 0.5mM Spermidine, 10mM KCl, 0.1% Triton-X, 20% Glycerol with Protease inhibitor) on ice for 5-10min. After washing with Wash Buffer 2 (20mM HEPES pH 7.5, 0.5mM Spermidine, 0.1% BSA, 150mM NaCl with Protease inhibitor), nuclei were incubated together with activated Concanavalin A Beads (Bang Labs) for 10 minutes at room temperature. Nuclei were then washed incubated with antibodies at 4℃ with 35 rpm rotation for 2 hours (H3K4me3, H3K27me3, Menin, XPO1), 4 hours (NPM1c, NPM1-WT), or overnight (RNA Pol II). pA/G-MNase (Epicypher) or pA-MNase (Gift from Dr. Steve Henikoff ) were then incubated with the nuclei-bead mixture in Wash Buffer 2 at 4℃ with 35 rpm rotation for 1hour. After washing with Wash buffer 2 for two times, CaCl2 was added to nuclei to activate the MNase to release chromatin. Stop buffer (340mM NaCl, 20mM EDTA pH 8.0, 4mM EGTA, 50μg/mL RNase A, 50μg/mL Glycogen) was added to stop the MNase and digestion of chromatin was performed with 5uL proteinase K at 55℃ overnight. DNA was extracted using Phenol:Chloroform:Isoamyl Alcohol (Sigma) extraction and MaXtract High Density tube (Qiagen). The aqueous phase was taken, and DNA was precipitated with 1/10 volume of 3M Sodium Acetate, pH 5.2, and 2.5 volume of 100% Ethanol at -20°C overnight. DNA was precipitated by 30min centrifugation at 4℃ and washed with 70% cold ethanol. Libraries were made using Swift Bioscience Acce-NGS 2G plus kit according to the manufacturer’s manual. The library was sequenced 150bp paired-end on HiSeq2000 by Fulgent Genomics.
Accel-NGS® 1S Plus  DNA Library Swiftbio Science (IDT XGEN DNA ssDNA low input since 2022 )

value: human AML cell line

tag: drug treatment

value: DMSO


title: Kasumi-1 cell line for for Cut&Run of XPO1

source_name: human Kasumi-1 leukemia cell line


title: MOLM13 cell treated with 25nM Eltanexor for for Cut&Run of XPO1

value: 25nM Selinexor 24hr


title: CD34+ Normal hematopietic stem cell for for Cut&Run of XPO1

source_name: CD34+ Normal hematopoietic stem and progenitor cell

value: human normal hematopietic stem and progenitor cells


title: WT 0-0.5hr rep1

description:
processed data file:
em_0-0.5.csv

value: 0-0.5hr  embryo

value: Wild type


title: NPM1c+ DNMT3AR882H FLT3-ITD AML blasts for Cut&Run of XPO1

value: primiary human AML blast


title: NPM1c+ IDH1R132H AML blasts for Cut&Run of NPM1c


title: CFBE41o- 1

description: test homozygous

value: brochial epitelium

value: homozygous for the F508del mutation, (derived from a bronchial isolate of a CF patient homozygous for the F508del CFTR mutation),


title: NPM1c+ DNMT3AR882H FLT3-ITD AML blasts for Cut&Run of NPM1c


title: NPM1c+ WT1mut TET2mut AML blast for Cut&Run of NPM1c

source_name: NPM1c+ WT1mut TET2mut AML blast


title: NPM1c+ IDH1R132H AML blasts for Cut&Run of XPO1


title: OCI-AML3 NPM1c degron2 cell line treated with DMSO for Cut&Run of IgG


title: NPM1c+ DNMT3AR882H FLT3-ITD AML blasts for H3K27ac ChIP

description: AML-5583 H3K27ac


title: OCI-AML3 NPM1c degron2 cell line treated with dTag13 for 24hrs for Cut&Run of IgG

value: 500nM dTag-13 24hr


title: OCI-AML3 NPM1c degron2 cell line treated with dTag-13 and SAHA-24hr and wash-off for 4 days for H3K27ac ChIP

description: NPM1c-degron2-dTag+SAHA-4day-wash-off-H3K27ac


title: OCI-AML3 NPM1c degron2 cell line treated with dTag-13-24hr and wash-off for 4 days for H3K27me3 ChIP

description: NPM1c-degron2-dTag-4day-wash-off-H3K27me3


title: OCI-AML3 cell line treated with DMSO for Cut&Run of NPM1c

source_name: OCI-AML3 cell line

value: NPM1c Acute Myeloid Leukemia cell line


title: OCI-AML3 cell line treated with DMSO for Cut&Run of NPM1c with RNase treatment


title: OCI-AML3 NPM1c degron2 cell line treated with 500nM dTag-13 for 3hr for Cut&Run of Menin

value: 500nM dTag-13 3hr


title: OCI-AML3 NPM1c degron2 cell line treated with 500nM dTag-13 for 6hr for Cut&Run of Menin

value: 500nM dTag-13 6hr


title: OCI-AML3 NPM1c degron2 cell line treated with DMSO for Cut&Run of Menin

description:
used as control for NPM1c-degron2-dTag_1hr-Pol2_short-time, NPM1c-degron2-dTag_3hr_Pol2_short-time
NPM1c-degron2-DMSO_Menin_short-time


title: OCI-AML3 NPM1c degron2 cell line treated with 500nM dTag-13 for 1 day and 4 day wash-off for Cut&Run of XPO1

description: NPM1c-degron2-neg-dTag-4day-wash-off-XPO1

value: 500nM dTag-13 24hr and Wash-off 4day


title: OCI-AML3 NPM1c degron2 cell line treated with 500nM dTag-13 for 3hr for Cut&Run of RNA Polmerase 2


title: OCI-AML3 NPM1c degron2 cell line treated with 500nM dTag-13 for 3hr for Cut&Run of NPM1c


title: OCI-AML3 NPM1c degron2 cell line treated with 500nM dTag-13 for 6hr for Cut&Run of NPM1c

description: NPM1c-degron2-dTag_6hr_NPM1c-short-term-dtag


title: OCI-AML3 NPM1c degron2 cell line treated with DMSO for Cut&Run of NPM1c

description:
used as control for NPM1c-degron2-dTag-3hr-NPM1c, NPM1c-degron2-dTag_6hr_NPM1c-short-term-dtag
NPM1c-degron2-DMSO_NPM1c_short-time-dTag


title: OCI-AML3 NPM1c degron2 cell line treated with 25nM Selinexor for 24hr for Cut&Run of XPO1


title: OCI-AML3 NPM1c degron2 cell line treated with 25nM Selinexor for 24hr for Cut&Run of NPM1c


title: OCI-AML3 NPM1c degron2 cell line treated with 500nM dTag-13 for 1hr for Cut&Run of RNA Polmerase 2

value: 500nM dTag-13 1hr


title: Mouse granulocytic and monocytic progenitors for H3K27ac ChIP

value: Wild type mouse hematopoietic progenitors immortalized by HOXB8 overexpression

value: wild-type


title: OCI-AML3 NPM1c degron2 cell line treated with dTag-13-24hr for Cut&Run of XPO1

value: Genetic enginnered cell line allow for dTag-13 mediated degradation of NPM1c


title: OCI-AML3 NPM1c degron2 cell line treated with dTag-13-24hr for Cut&Run of NPM1c


title: Mouse hematopoietic progentor cell line immortalized with HOXB8-ER for H3K27me3 ChIP

value: Engineered mouse hematopoietic progenitor line with NPM1c knock-in

value: NPM1c knock-in


title: OCI-AML3 NPM1c degron2 cell line treated with DMSO for Cut&Run of of NPM1c, used as control for NPM1c-degron2-dTag_NPM1c

value: DMSO


title: Mouse hematopoietic progentor cell line immortalized with HOXB8-ER for H3K27ac ChIP

source_name: Engineered mouse hematopoietic progenitor line


title: scRNA_mESC_K562

city: Stanford

first: Amy

address: 279 Campus Drive West

institute: Stanford University

description: single cell RNA-seq

data_processing:
For ADT and HTO processing, raw sequencing data were converted to fastq format using bcl2fastq (Illumina). ADTs and HTOs were then assigned to individual cells and antibodies based on cell and antibody barcode sequences. Counts for each antibody were tabulated by counting UMIs. In the barnyard experiment, cells with fewer than 200 ADT+HTO UMIs were excluded from analysis. In the CD4 T cell experiment, cells with fewer than 75 HTO UMIs or 100 ADT UMIs were excluded.
For the mouse-human mixture, raw ATAC-seq and RNA-seq data were converted to fastq format, and aligned to a chimeric hg38 and mm10 reference genome using cellranger-ARC v1.0.1 from 10x Genomics. First, we filtered droplets for high-quality cells, based on >7,500 RNA UMIs, >10,000 unique ATAC fragments, and TSS enrichment > 10. TSS enrichment was calculated using the combined set of mouse + human TSS coordinates and the default parameters of ArchR’s TSS enrichment.
For CD4 T cell scATAC-seq data, raw sequencing data were converted to fastq format and aligned to the hg38 reference genome using cellranger-ARC v.1.0.1 from 10X Genomics. Fragment files were then loaded into ArchR (v1.0.2) using the createArrowFiles function.
For CD4 T cell scRNA-seq data, raw sequencing data were converted to fastq format and aligned to the reference genome using cellranger-ARC v.1.0.1 from 10X Genomics. For each lane, the gene expression matrix from the filtered_feature_bc_matrix was used to create a Seurat object using Seurat v3.2.1. The two lanes of CD4 memory T cell data were then merged into one Seurat object and filtered for cells used in the scATAC-seq analysis.

organism:
Homo sapiens
Mus musculus

source_name: ESCs, K562 mixture

growth_protocol: Mouse V6.5 ESCs were cultured on gelatin-coated plates in Knockout DMEM (Thermo Fisher #10829018) supplemented with 7.5% ES-qualified serum (Applied Stem Cell #ASM-5017), 7.5% Knockout Serum replacement (Thermo Fisher #10828-028), 2mM L-glutamine (Gibco #35050061), 10mM HEPES (Gibco #15630080), 100 units/mL penicillin/streptomycin (Gibco #151401222), 0.1mM non-essential amino acids (Gibco #11140050), 0.1mM beta-mercaptoethanol (Gibco #21985023), and LIF. The human chronic myeloid leukemia cell line, K562, was purchased from ATCC and cultured in RPMI 1640 medium (Gibco #11875119) containing 15% FBS and 100 units/mL penicillin/streptomycin. HEK 293T cells were cultured in DMEM with GlutaMAX (Gibco #10566024) containing 10% FBS and 100 units/mL penicillin/streptomycin.

extract_protocol:
Single nuclei were stained and loaded onto a 10x Genomics Chromium controller for generation of NEAT-seq libraries
Antibody-stained cells in 1X Nuclei buffer were processed using the 10X Genomics Multiome kit as indicated in the standard protocol (Rev A) to generate ATAC-seq and RNA-seq libraries. During the pre-amplification step, Truseq read 2 (CAGACGTGTGCTCTTCCGATC) and Nextera read 2 (GGCTCGGAGATGTGTATAAGAGACAG) primers were spiked in at 0.2uM final concentration to amplify ADT and HTO oligos. To generate ADT and HTO libraries, 35ul of pre-amplification product from step 4.3p was amplified with indexing primers using 2X NEB Next High-Fidelity PCR Master Mix (M0541). A double-sided SPRI bead clean up was performed using 0.6X SPRI beads (retaining supernatant) and then adding additional SPRI beads to a final concentration of 1.2X, washing with 80% ethanol, and eluting ADT or HTO libraries from beads using EB buffer.

tag: neat-seq antibodies

value: GATA1, OCT4, SOX2, NPC


title: OCI-AML3 NPM1c degron2 cell line treated with DMSO for Cut&Run of H3K27me3


title: scATAC_mESC_K562

description: single cell ATAC-seq


title: OCI-AML3 NPM1c degron2 cell line treated with 500nM dTag-13 for 1 day and 4 day wash-off for Cut&Run of NPM1c

description: NPM1c-degron2-neg-dTag-4day-wash-off-NPM1c


title: Mouse hematopoietic progentor cell line with NPM1c knock-in for H3K27ac ChIP


title: NPM1-Cterm Cut&Run in OCI-AML3 cell line


title: OCI-AML3 NPM1c degron2 cell line treated with DMSO for Cut&Run of RNA Polmerase 2

description:
used as control for NPM1c-degron2-dTag_1hr-Pol2_short-time, NPM1c-degron2-dTag_3hr_Pol2_short-time
NPM1c-degron2-DMSO_pol2_short-time


title: Mouse hematopoietic progentor cell line with NPM1c knock-in for H3K27me3 ChIP


title: Mouse granulocytic and monocytic progenitors for H3K27me3 ChIP

source_name: Wild type mouse hematopoietic progenitors


title: OCI-AML3 NPM1c degron2 cell line treated with dTag-13-24hr for Cut&Run of H3K27me3


title: NPM1-Cterm Cut&Run in MV4:11 cell line

source_name: MV4;11 leukemia cell line

value: MLL-AF4 Acute Myeloid Leukemia Cell line


title: Mouse hematopoietic progentor cell line immortalized with HOXB8-ER for Cut&Run of XPO1

value: Engineered mouse progenitor line


title: NPM1-Cterm Cut&Run in MOLM13 Cell line

value: MLL-AF9 Acute Myeloid Leukemia cell line


title: RNA-Seq - HOXB8 imortailized cells rep2

data_processing:
RNA-seq raw reads were mapped to the human genome (hg19)  or mouse genome mm9 using STAR-2.6.1 with default parameters. Transcript levels were calculated as TPM and count using RSEM . Those genes having a count greater than 5 in at least 50% of the samples were kept for further examination. The DESeq2 R package was used to perform differential gene expression analysis between groups . Significantly differentially expressed genes were defined as those with a log2fold change (LFC) value of > 1 and a false discovery rate (FDR) of < 0.05.
Genome_build: hg19 mm9
Supplementary_files_format_and_content: RSEM transcript count

source_name: Mouse hematopoietic progentor cell line  immortalized by HOXB8

extract_protocol:
RNA was extracted with Qiagen RNeasy micro
NEBNext Ultra II RNA-seq library kit was used to construct to library of mouse hematopietic progenitors. Swiftbio's rapid RNA-seq kit was used to construct the library for human AML cells.

treatment_protocol: For dTag-13 treatment, OCI-AML3-NPM1c-degron cells were treated with DMSO or 500nM dTag-13 for 24 hrs. For Selinexor treatment, OCI-AML3 cells were treated with 25nM Selinexor for 24 hrs.

tag: genome type


title: Mouse hematopoietic progentor cell line with NPM1c knock-in for Cut&Run of XPO1


title: RNA-Seq - HOXB8 imortailized cells with NPM1c knock-in clone4

source_name: Mouse hematopoietic progentor cell line immortalized by HOXB8  with NPM1c knock-in


title: RNA-Seq - HOXB8 imortailized cells with NPM1c knock-in clone12

source_name: Mouse hematopoietic progentor cell line  immortalized by HOXB8 with NPM1c knock-in


title: Mouse hematopoietic progentor cell line with NPM1c knock-in for Cut&Run of NPM1c


title: BJ2020-12049-5

city: Qingdao

first: Yong

last: Zhao

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes
map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Genome_build: susScr11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

organism: Sus scrofa

source_name: Cecum cell

extract_protocol: Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V3 (10x Genomics Inc., Pleasanton, CA, USA) following the manufacture’s introduction.

value: 21 day

value: cecum

value: male


title: OCI-AML3 NPM1c degron2 cell line treated with DMSO for Cut&Run of XPO1


title: RNA-Seq - OCI-AML3 NPM1c degron2 cell line treated with 500nM dTag-13 rep1

value: 500nM dTag-13 treatment for 24hr


title: Oocyte_mutant rep2

city: Wuhan

first: Li-quan

last: Zhou

state: Hubei

address: 13 Hangkong road

department: Tongji Medical College

institute: Huazhong University of Science and Technology

data_processing:
Raw reads were processed with Cutadapt v1.16. Trimmed reads were mapped to mouse genome using STAR with default settings.
RSEM was used to calculate FPKM values.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: oocyte

extract_protocol:
Oocytes were collected in tubes with lysis component, then amplification was carried out by the Smart-Seq2 method; RNA of mouse ESCs was harvested using Trizol reagent, and Illumina TruSeq RNA Sample Prep Kit was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: oocyte

value: Mutant


title: BJ2020-12049-4

value: 14 day


title: RNA-Seq - OCI-AML3 NPM1c degron2 cell line treated with 500nM dTag-13 rep2


title: RNA-Seq - OCI-AML3 NPM1c treated with 25nM Selinexor rep2

value: 25nM Selinexor (KPT-330) for 24hr


title: BJ2020-12049-3

value: 7 day


title: RNA-Seq - OCI-AML3 NPM1c treated with 25nM Selinexor rep1


title: Oocyte_control rep2

tag: strain

value: Control


title: BJ2020-12049-2

value: 1 day

tag: tissue


title: Oocyte_control rep1


title: BJ2020-12049-1

tag: age

value: 0 day


title: RNA-Seq - HOXB8 imortailized cells rep1

source_name: Mouse hematopoietic progentor cell line immortalized by HOXB8

value: wild-type


title: RNA-Seq - OCI-AML3 NPM1c degron2 cell line treated with DMSO rep1

source_name: OCI-AML3 NPM1c degron2 cell line

value: DMSO control for dTag-13 for 24hr


title: RNA-Seq - OCI-AML3 cell line treated with DMSO rep2

value: DMSO control for Selinexor for 24hr


title: HuCCT1-2

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

data_processing:
The sequence reads were aligned to the human reference genome assembly (Ensemble GRCh38) and UMI counts of genes were calculated with the celseq2 pipeline (https://github.com/yanailab/celseq2).
The fastq files were demultiplexed with the bc_demultiplex program in the celseq2 pipeline package. UMIs of each sequence are indicated in the header of the fastq files.
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma-delimited text files include raw count values of all samples

source_name: Human bile duct carcinomas

growth_protocol: In monolayer culture, iLCCs were cultured in DMEM/F12 and Fibrolife mixture medium with 4% FBS, 1 µg/ml insulin, 10-7 M dexamethasone, 10 mM nicotinamide, 2mM L-glutamine, 50 µM 2-mercaptoethanol, and penicillin/streptomycin, containing 1 µM A83-01, and 5 µM Y27632. HepG2 cells, HuH7 cells, and Huh6 cells were cultured in DMEM containing 10% FBS, 2mM L-glutamine, and penicillin/streptomycin. HuCCT1 cells were cultured in RPMI1640 medium containing 10% FBS.

extract_protocol:
RNA was extracted using the Isogen II (Nippongene)
Detailed protocol is described in "CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq (PMID: 27121950)".

treatment_protocol: We purchased HUVECs on the market. To generate iLCCs, HUVECs were electroporated with episomal plasmids expressing the genes encoding transcription factors indicated above.

value: bile duct, ascites meta

value: Human bile duct carcinomas

tag: transfection

value: non-treated

tag: Stage

value: in vitro monolayer culture condition


title: Huh7

source_name: Human hepatocarcinomas

value: liver

value: Human hepatocarcinomas


title: RNA-Seq - HOXB8 imortailized cells with NPM1c knock-in clone18

source_name: Mouse hematopoietic progentor cell line with  immortalized by HOXB8 NPM1c knock-in

value: NPM1c knock-in


title: Oocyte_mutant rep1

value: oocyte

value: Mutant


title: RNA-Seq - OCI-AML3 cell line treated with DMSO rep1


title: OCI-AML3 NPM1c degron2 cell line treated with 500nM dTag-13 rep1

description:
BrUTP labeled RNA
Bru-seq-dTag-1

data_processing:
Library strategy: BRU-Seq
Bru-seq raw reads were mapped to the hg19 human reference genome using Bowtie2 (version 2.3.4) . Quality control for the alignment BAM files was performed by samtools, allowing only uniquely mapped reads to be retained and then PCR duplicates were removed by Picard (http://broadinstitute.github.io/picard/) using the MarkDuplicates tool with the parameters “VALIDATION_STRINGENCY = LENIENT REMOVE_DUPLICATES = true” for downstream analyses.
Bigwig files were build from bam files using deeptools  with options “-binSize 50 and --normalizeUsing RPGC”.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
After the indicated treatment time, BrU was added to the culture medium to label the nascent transcripted RNA for 30 mins. Cells were lysed in Trizol buffer and RNA was extracted.
Library construction protocol is described in Paulsen. et al. [PMID: 23345452]

treatment_protocol: 500nM dTag-13 was used to treat cells for 12hrs, 25nM Selinexor was used to treat cells for 12hrs

value: dTag-13 treated replicate 1


title: TFEB_4OHT_3

city: Tampa

first: Mario

last: Fernandez

address: 12902 Magnolia Dr.

department: Tumor Biology

institute: Moffitt Cancer Center

description:
B-cell lymphoma transduced with a bicistronic vector expressing TFEB-ERT2 and puromycin and treated with 250 nM 4-OHT replicate 3
BBF139-T-4OHT-3

data_processing:
Sequencing reads were subjected to adaptor trimming, series of quality assessment before being aligned with STAR-2.5.3 against mouse reference genome mm10.
Quantification of read counts aligned to the region associated with each gene was performed using HTSeq v0.6.1 based on National Center for Biotechnology information (NCBI) RefSeq gene model.
Read counts of all samples were normalized using the median-of-ratios method implemented in R/Bioconductor package DESeq2 v1.6.3.
Differential expression analysis between the two groups was performed by serial dispersion estimation and statistical model fitting procedures implemented in DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Text file of normalized gene abundance

source_name: Lymph Node

growth_protocol: Eµ-Myc;Eµ-rtTA transgenic B-Cell Lymphoma maintained in 1:1 mix of IMDM/DMEM containing 4 mM L-Glutamine, 1 mM Sodium Pyruvate, 1% Penicillin/Streptomycin,  27.5 μM β-mercaptoethanol, 10% fetal bovine serum, and 10 ng/mL IL-7 and split every 3-4 days

extract_protocol:
Cells were washed with 1x PBS twice and cell pellets were lysed and total RNA extracted using the MACHEREY-NAGEL NucleoSpin RNA Mini Kit for RNA purification (REF 740955.50)
Nugen_Ovation_Mouse RNASeq Kit protocol

treatment_protocol: Lymphomas were treated with vehicle or 250 nM 4-OHT for 4 days

tag: cell line

value: Eu-Myc;Eu-rtTA transgenic B-Cell Lymphoma

tag: gene insert

tag: treatment


title: TFEB_4OHT_2

description:
B-cell lymphoma transduced with a bicistronic vector expressing TFEB-ERT2 and puromycin and treated with 250 nM 4-OHT replicate 2
BBF139-T-4OHT-2


title: HuCCT1-1


title: ATAC-Seq OCI-AML3 NPM1c degron2 cell line treated with DMSO rep1

data_processing:
ATAC-seq raw reads were mapped to the hg19 human reference genome using Bowtie2 (version 2.3.4) . Quality control for the alignment BAM files was performed by samtools, allowing only uniquely mapped reads to be retained and then PCR duplicates were removed by Picard (http://broadinstitute.github.io/picard/) using the MarkDuplicates tool with the parameters “VALIDATION_STRINGENCY = LENIENT REMOVE_DUPLICATES = true” for downstream analyses.
Bigwig files were build from bam files using deeptools  with options “-binSize 50 and --normalizeUsing RPGC”.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
50,000 cells were harvested and permeabilized in 50 μL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). The transposition reaction was carried out at 37°C for 30 min with agitation in 50 μL volume containing 25 μL of 2× TD buffer and 2.5 μL of Nextera Tn5 transposase. DNA was purified with Qiagen MinElute PCR purification kit. Library amplification was done with KAPA HiFi HotStart ReadyMix PCR kit, and the resulting libraries were purified with Qiagen MinElute PCR Purification Kit. Libraries were sequenced in the Illumina HiSeq 4000 platform to generate paired-end reads of 2 × 150 bp.
Library construction protocol is described in Himadewi. et al. [PMID: 34585664]

treatment_protocol: 500nM dTag-13 was used to treat cells for 24hrs.

value: DMSO treated OCI-AML3 NPM1c-degron2 cells