title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell84

description:
SMART-seq2
D4Cas9R1-P1-G12


title: Plate3-472-Liver

status: Public on Sep 15 2022

type: SRA

city: Durham

first: Scott

last: Auerbach

state: North Carolina

address: 111 TW Alexander Drive

country: USA

institute: Division of the National Toxicology Program at NIEHS

description: Plate 3_LIVER_F09

library_source: transcriptomic

data_processing: Data were processed using the Tempo-SeqR software package

molecule: total RNA

organism: Rattus norvegicus

source_name: Liver

growth_protocol: Male and female SD rats were placed on NTP-2000 diet and housed up to 5 animals per cage. After a 10-14 day quarantine, 8-10 week old animals were randomly assigned to treatment and control groups.

extract_protocol: All animals were euthanized the day after the last dose of chemical was administered and the liver and kidney were removed during necropsy. Two samples from each the left liver lobe and right kidney were collected within five minutes of termination for toxicogenomic evaluation. Tissue samples were cut into approximately 5 cubic mm pieces, aliquoted into screw-cap tubes, flash frozen in liquid nitrogen, and stored at -80 degreees C. RNA was extracted from one of the two collected samples and the extraction batch information recorded in the metadata along with the quantity and quality of each RNA sample. The RNA samples and metadata file were sent to BioSpyder for evaluation using the whole transcriptome TempOSeq platform with a minimum of 10 million reads/sample.

treatment_protocol: Each of six chemicals was given at nine doses (5 mL/kg dosing volume) to the treatment groups. A vehicle control group was also included for each treatment group. Rats received the test formulations via gavage for five consecutive days.

tag: strain

value: Sprague Dawley (SD)

tag: Sex

value: Male

tag: tissue

value: Liver

tag: chemical

tag: concentration

tag: unit

value: mg/kg

tag: vehicle

value: corn oil

tag: duration

value: day

tag: platfrom

value: TempO-Seq


title: Genomic DNA from Cervical cancer sample 1856 A T

type: genomic

city: London

first: Andy

last: Feber

address: 72 Huntley St

country: United Kingdom

institute: University College London

description: Cervical cancer sample

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: Cy5 and Cy83

molecule: genomic DNA

organism: Homo sapiens

source_name: Tumour

label_protocol: standard Illumina protocol

extract_protocol: none provided by the submitter

tag: gender

value: Female

tag: sample type

value: Cervical Cancer

tag: disease state

value: Tumour


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell83

city: Boston

first: Joana

middle: Graca

last: Marques

state: MA

address: 360 Longwood Avenue

institute: Dana-Farber Cancer Institute

description:
SMART-seq2
D4Cas9R1-P1-G11

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were aligned by bowtie, and gene counts were quantified using RSEM as transcript-per-million, or TPM.
Expression levels were calculated as Ei,j = log2(TPMi,j/10 + 1) for gene i in sample j. TPM values were divided by 10 for better approximation of the estimated complexity of single-cell libraries.
We filtered out low quality cells with less than 2,500 detected genes or an average housekeeping expression level below 2.5 and removed low expressed genes with TPM greater than 16 in less than 5 cells.
We defined relative expression as centered expression levels, Eri,j = Ei,j − average[Ei,1...n] for the remaining cells and genes.
Assembly: hg19
Supplementary files format and content: TPM values for each gene in each cell and in every condition. Control AAVS1 (CTRL) and SMARCA4 knockout (SM4KO) TPM data are gathered in one csv file per replicate.

growth_protocol: BT869 cells were grown as neurospheres in tumor stem media base supplemented with B27 minus vitamin A (Thermo Fisher Scientific), human growth factors (EGF, FGF, PDGF-AA, PDGF-BB [Shenandoah Biotechnology]) and heparin (Stemcell Technologies) in ultra-low attachment flasks  in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Live cells were FACS sorted into 96-well plates containing TCL lysis buffer (Qiagen) and plates were frozen prior to processing for Smart-seq2
SMART-seq2

tag: cell line

tag: cell type

tag: genotype

value: Cas9 only control knockout

tag: treatment

value: nucleofection

tag: time

value: 4 days


title: Plate3-465-Liver

description: Plate 3_LIVER_E08

tag: strain


title: DND-41_PIK-75_rep2

city: Singapore

first: Rui

last: Yokomori

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore, National University of Singapore

description: Replicate 2

data_processing:
RNA-seq reads were mapped to transcript sequences of curated RefSeq (NM and NR transcripts) and ERCC spike-in controls using salmon (version 1.1.0) with the options “--gcBias --seqBias –validateMappings”.
The index file for the transcript sequences was created with default settings.
Transcript-level read counts were converted to gene-level read counts using tximport (version 1.14.2).
The genes that did not have more than 5 read counts in at least two samples were removed.
RUVSeq (version 1.20.0) was applied to estimate a factor (k=1) of unwanted variation between samples.
Differentially expressed genes were estimated using DESeq2 (version 1.26.0).
The estimated unwanted factor was included in the design formula of DESeq2 for spike-in normalization.
Supplementary_files_format_and_content: txt file for differentially expressed genes

source_name: DND-41 cells

growth_protocol: Jurkat and DND-41 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol:
ERCC RNA spike-in controls (1:10) were added at 1 uL per 1 million cells. Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).
Strand-specific library construction and 100-bp paired-end sequencing with a sequencing depth of 20 M reads on the DNBSEQ platform were performed at BGI Genomics.

treatment_protocol: The cells were treated with DMSO or PIK-75 for 4 hours, after which total RNA were harvested.

value: T-ALL

tag: agent

value: PIK-75 treatment


title: DND-41_PIK-75_rep1

description: Replicate 1


title: Genomic DNA from Cervical cancer sample 1268 B T

description: Cervical cancer sample

label: Cy5 and Cy81


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell82

description:
SMART-seq2
D4Cas9R1-P1-G10


title: Genomic DNA from Cervical cancer sample 1543 C T

description: Cervical cancer sample

label: Cy5 and Cy82


title: Plate3-462-Liver

description: Plate 3_LIVER_A08

tag: Sex

tag: tissue


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell81

description:
SMART-seq2
D4Cas9R1-P1-G09


title: Plate3-463-Liver

description: Plate 3_LIVER_B11

tag: chemical

tag: concentration


title: DND-41_DMSO_rep2

description: Replicate 2

value: DMSO treatment (control)


title: DND-41_DMSO_rep1

description: Replicate 1


title: Genomic DNA from Cervical cancer sample 967 C T

description: Cervical cancer sample

label: Cy5 and Cy80


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell80

description:
SMART-seq2
D4Cas9R1-P1-G08


title: Plate3-461-Liver

description: Plate 3_LIVER_G02

tag: unit

tag: vehicle


title: Genomic DNA from Cervical cancer sample 868 A T

description: Cervical cancer sample

label: Cy5 and Cy79


title: Jurkat_PIK-75_rep2

description: Replicate 2

source_name: Jurkat cells


title: Genomic DNA from Normal Sample 557 B N SQ

description: Normal Sample

label: Cy5 and Cy78

source_name: Normal

value: Histological Normal Cervix

value: Normal


title: Jurkat_PIK-75_rep1

description: Replicate 1


title: Plate3-459-Liver

description: Plate 3_LIVER_F12

value: Sprague Dawley (SD)

tag: duration

tag: platfrom


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell78

description:
SMART-seq2
D4Cas9R1-P1-G06


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell79

description:
SMART-seq2
D4Cas9R1-P1-G07


title: Plate3-464-Liver

description: Plate 3_LIVER_B05

value: Male

value: Liver


title: Genomic DNA from Cervical cancer sample 557 A T

description: Cervical cancer sample

label: Cy5 and Cy77

tag: gender

tag: sample type


title: Plate3-458-Liver

description: Plate 3_LIVER_H02

value: mg/kg

value: corn oil


title: Jurkat_DMSO_rep2

description: Replicate 2

tag: cell line


title: Genomic DNA from Cervical cancer sample 252 A T

description: Cervical cancer sample

label: Cy5 and Cy76

tag: disease state


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell77

description:
SMART-seq2
D4Cas9R1-P1-G05

tag: cell type

tag: genotype


title: Plate3-457-Liver

description: Plate 3_LIVER_A02

value: day

value: TempO-Seq


title: Jurkat_DMSO_rep1

description: Replicate 1


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell76

description:
SMART-seq2
D4Cas9R1-P1-G04

tag: treatment

tag: time


title: Genomic DNA from Cervical cancer sample 1518 A T

description: Cervical cancer sample

label: Cy5 and Cy75

value: Female

value: Cervical Cancer


title: Genomic DNA from Cervical cancer sample 1215 A T

description: Cervical cancer sample

label: Cy5 and Cy74

value: Tumour


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell75

description:
SMART-seq2
D4Cas9R1-P1-G03

value: Cas9 only control knockout

value: nucleofection


title: LiverC_Goat [WGBS]

city: Beijing

first: Siqian

last: Chen

address: 2rd, Yuanmingyuan West Road

department: College of Animal Science and Technology

country: China

institute: China Agricultural University

library_source: genomic

data_processing:
FastQC v 0.11.2 and Trim Galore v 0.4.0 was used to assess the quality of the sequence data and filter low-quality reads (q < 30), respectively. The cleaned data were then mapped to the sscrofa11.1 genomes using bowtie2 under the Bismark software (0.14.5) with default parameters
Duplicated reads were removed using deduplicate_bismark
symmetric-cpgs was employed to obtain methyl CpG site information using methpipe software
Assembly: ARS-UCD1.2, Oar_rambouillet_v1.0, ARS1
Supplementary files format and content: CpG report files

organism: Capra hircus

source_name: liver

extract_protocol:
DNA was extracted according to the TIANamp Genomic DNA Kit protocol
DNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: developmental stage

value: adult


title: Plate3-456-Liver

description: Plate 3_LIVER_D12

tag: strain

tag: Sex


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell74

description:
SMART-seq2
D4Cas9R1-P1-G02

value: 4 days


title: Plate3-454-Liver

description: Plate 3_LIVER_F03

tag: tissue

tag: chemical


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell73

description:
SMART-seq2
D4Cas9R1-P1-G01


title: LiverA_Goat [WGBS]


title: Plate3-460-Liver

description: Plate 3_LIVER_A07

tag: concentration

tag: unit


title: Genomic DNA from Cervical cancer sample 945 B1 T

description: Cervical cancer sample

label: Cy5 and Cy73


title: Plate3-452-Liver

description: Plate 3_LIVER_E06

tag: vehicle

tag: duration


title: Genomic DNA from Cervical cancer sample 852 A T

description: Cervical cancer sample

label: Cy5 and Cy72

tag: gender


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell72

description:
SMART-seq2
D4Cas9R1-P1-F12


title: LiverC_Goat

data_processing:
The adapter sequences and low-quality bases were filtered using Trimmomatic v0.39
The trimmed reads were mapped to the Ensembl 103 version of reference genomes with annotated genes using STAR aligner v 2.7.6 with the following options: “--outFilterMismatchNmax 3 –outFilterType BySJout –quantMode GeneCounts –outFilterMismatchNoverLmax 0.04 –outSAMtype SAM SortedByCoordinate”.
Gene expression levels were quantified as counts using featureCounts
Assembly: ARS-UCD1.2, Oar_rambouillet_v1.0, ARS1
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

extract_protocol:
Total RNA were extracted using TRIzol method from frozen liver samples
mRNA were enriched using magnetic beads with Oligo(dT) and sheared. The cDNA was synthesized using random hexamers, end-repaired, and ligated to A base and sequencing adapters.

tag: development stage


title: Genomic DNA from Normal Sample 513 A N SQ

description: Normal Sample

label: Cy5 and Cy71

tag: sample type

value: Histological Normal Cervix


title: LiverB_Goat


title: Plate3-451-Liver

description: Plate 3_LIVER_B12

tag: platfrom


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell71

description:
SMART-seq2
D4Cas9R1-P1-F11

tag: cell line

tag: cell type


title: Plate3-450-Liver

description: Plate 3_LIVER_C03


title: LiverA_Goat


title: Plate3-449-Liver

description: Plate 3_LIVER_E04


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell69

description:
SMART-seq2
D4Cas9R1-P1-F09

tag: genotype

tag: treatment


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell70

description:
SMART-seq2
D4Cas9R1-P1-F10

tag: time


title: Genomic DNA from Normal Sample 237 A N SQ

description: Normal Sample

label: Cy5 and Cy69

tag: disease state

value: Normal


title: rat_7-week-old-2VO_rep3 [V4]

first: Kaiyue

last: Zhao

address: 1 Tiantan Xili, Dongcheng District, Beijing

department: Institute of medicinal biotechnology

institute: Peking union medical college

description: gene expression

data_processing:
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by Trimmomatic (version 0.36) according to several steps: 1) Removing adaptor sequence if reads contains; 2) Removing low quality bases from reads 3’ to 5’ (Q < 20); 3) Removing low quality bases from reads 5’ to 3’ (Q < 20); 4) Using a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp); 5) Removing reads with reads length less than 35 nt and its pairing reads. And the remaining clean data was used for further analysis.
Cutadapt V1.14 was used to remove adaptors (cutoff value Q lower than 20). The clean reads were obtained by using Trimmomatic V0.36 after removing low-quality bases at both ends. Reads were compared with the reference genome via miRBase database.
DESeq2 (version 1.12.4) was used to determine differentially expressed genes (DEGs) between two samples. Genes were considered as significant differentially expressed if q-value <0.001 and |FoldChange| >2.
Assembly: the rats reference genome (http://asia.ensembl.org/ index.html)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: cerebral cortex

growth_protocol: All the animals were housed under a 12-h light-dark cycle (lights on 8 a.m.) at 25°C and 60 ± 10% humidity and given ad libitum access to food and water.

extract_protocol:
Total RNA was extracted using the Total RNA Extractor (Trizol) kit (B511311, Sangon, China) according to the manufacturer’s protocol
A total amount of 2 g RNA per sample was used as input material for the RNA sample preparations. Next, miRNA sequencing libraries were constructed using TruSeq Small RNA Sample Prep Kits (RS-200-0024, Illumina, USA) following manufacturers recommendations. The library quality was assessed on the Agilent Bioanalyzer 2100 system. mRNA sequencing libraries were constructed from six total RNA samples using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (NR601-02, Vazyme, China)

treatment_protocol: Rats were anesthetized with 2% sodium pentobarbital administered intraperitoneally (30mg/kg). The surgery gently separated the bilateral common carotid arteries permanently ligated with 5-0 silk thread. Rats in the sham group underwent the same procedure with the exception of arterial ligation. Each group contained three rats. The cerebral cortex was collected after the Morris water maze test and quickly preserved in liquid nitrogen.

tag: strain

value: Sprague-Dawley

value: bilateral common carotid artery occlusion


title: LiverB_Goat [WGBS]

tag: tissue

tag: developmental stage


title: Genomic DNA from Cervical cancer sample 513 A T

description: Cervical cancer sample

label: Cy5 and Cy70


title: Genomic DNA from Cervical cancer sample 237 B T

description: Cervical cancer sample

label: Cy5 and Cy68


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell68

description:
SMART-seq2
D4Cas9R1-P1-F08


title: rat_7-week-old-2VO_rep1 [V1]

description: gene expression


title: Genomic DNA from Cervical cancer sample 1512 A T

description: Cervical cancer sample

label: Cy5 and Cy67


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell67

description:
SMART-seq2
D4Cas9R1-P1-F07


title: Plate3-444-Liver

description: Plate 3_LIVER_H12

value: Sprague Dawley (SD)

tag: Sex

value: Liver

tag: chemical

tag: concentration


title: rat_7-week-old-2VO_rep2 [V2]

description: gene expression


title: Genomic DNA from Cervical cancer sample 1204 A T

description: Cervical cancer sample

label: Cy5 and Cy66


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell66

description:
SMART-seq2
D4Cas9R1-P1-F06


title: Plate3-442-Liver

description: Plate 3_LIVER_A06

tag: unit

value: mg/kg

tag: vehicle

value: corn oil

tag: duration


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell65

description:
SMART-seq2
D4Cas9R1-P1-F05


title: Genomic DNA from Cervical cancer sample 841 A T

description: Cervical cancer sample

label: Cy5 and Cy64

tag: gender

tag: sample type


title: Genomic DNA from Normal Sample 841 A N SQ

description: Normal Sample

label: Cy5 and Cy65


title: rat_7-week-old-Sham-operated_rep2 [C2]

description: gene expression

value: sham surgery


title: rat_7-week-old-Sham-operated_rep3 [C3]

description: gene expression


title: Plate3-440-Liver

description: Plate 3_LIVER_H09

value: Male

value: day

tag: platfrom

value: TempO-Seq


title: rat_7-week-old-Sham-operated_rep1 [C1]

description: gene expression


title: Plate3-439-Liver

description: Plate 3_LIVER_E10


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell64

description:
SMART-seq2
D4Cas9R1-P1-F04

tag: cell line

tag: cell type

value: Cas9 only control knockout


title: Plate3-448-Liver

description: Plate 3_LIVER_D07

value: Female


title: Genomic DNA from Cervical cancer sample 457 A T

description: Cervical cancer sample

label: Cy5 and Cy62

value: Cervical Cancer

value: Tumour


title: SVF treated, replicate 3

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the Rattus norvegicus reference genome assembly (rn6) using Star version 2.6.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using Ensembl annotations
Genome_build: Rn6
Supplementary_files_format_and_content: htseq-count derived matrix table with raw gene counts for every gene and every sample.

molecule: polyA RNA

source_name: coronary arterioles

growth_protocol: Coronary microvessels were freshly isolated from branches off the left anterior descending artery in the apical region.

extract_protocol:
RNA was isolated from ≥ 5 microvessels from pooled within the group using RNAeasy Micro plus kit (Qiagen).
Libraries were prepared using the Universal Plus mRNA-Seq with NuQuant (NuGEN(TECAN) Cat# 0520-24).

treatment_protocol: No treatment for young and old control replicates. Adipose-derived stromal vascular fraction cells were administered to 23 month old female Fisher 344 rats via single tail vein injection of 10^7 cells. Coronary microvessels were fershly haarvested 4 weeks later.

value: female

tag: age

value: 24 months

tag: treatment

value: single intravenous injection of 10^7 adipose-derived stromal vascular fraction cells


title: SVF treated, replicate 2


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell61

description:
SMART-seq2
D4Cas9R1-P1-F01

tag: genotype

value: nucleofection

tag: time

value: 4 days


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell62

description:
SMART-seq2
D4Cas9R1-P1-F02


title: Plate3-437-Liver

description: Plate 3_LIVER_F08

tag: strain

value: Sprague Dawley (SD)

tag: tissue


title: SVF treated, replicate 4

tag: Sex


title: Genomic DNA from Cervical cancer sample 941 B1 T

description: Cervical cancer sample

label: Cy5 and Cy63

tag: disease state


title: Genomic DNA from Cervical cancer sample 224 A T

description: Cervical cancer sample

label: Cy5 and Cy60


title: Plate3-436-Liver

description: Plate 3_LIVER_E09

value: Liver

tag: chemical

tag: concentration


title: Plate3-438-Liver

description: Plate 3_LIVER_A10

tag: unit

value: mg/kg

tag: vehicle


title: Genomic DNA from Normal Sample 224 A N SQ

description: Normal Sample

label: Cy5 and Cy61

tag: gender

value: Histological Normal Cervix

value: Normal


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell60

description:
SMART-seq2
D4Cas9R1-P1-E12


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell63

description:
SMART-seq2
D4Cas9R1-P1-F03


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell59

description:
SMART-seq2
D4Cas9R1-P1-E11


title: SVF treated, replicate 1


title: Old control, replicate 4


title: Plate3-435-Liver

description: Plate 3_LIVER_C10

value: Male

value: corn oil

tag: duration


title: Plate3-441-Liver

description: Plate 3_LIVER_B09

value: day

tag: platfrom

value: TempO-Seq


title: Genomic DNA from Cervical cancer sample 1185 A T

description: Cervical cancer sample

label: Cy5 and Cy58

value: Female

tag: sample type


title: Plate3-434-Liver

description: Plate 3_LIVER_B10


title: Plate3-432-Liver

description: Plate 3_LIVER_E07


title: Old control, replicate 3


title: Genomic DNA from Normal Sample 927 B N SQ

description: Normal Sample

label: Cy5 and Cy57


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell57

description:
SMART-seq2
D4Cas9R1-P1-E09

tag: cell line

tag: cell type

value: Cas9 only control knockout


title: Old control, replicate 2

tag: age

tag: treatment


title: Genomic DNA from Normal Sample 1498 A N SQ

description: Normal Sample

label: Cy5 and Cy59


title: Plate3-431-Liver

description: Plate 3_LIVER_B08


title: Genomic DNA from Normal Sample 831 A N SQ

description: Normal Sample

label: Cy5 and Cy55


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell55

description:
SMART-seq2
D4Cas9R1-P1-E07

tag: genotype

tag: time


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell56

description:
SMART-seq2
D4Cas9R1-P1-E08


title: Young control, replicate 4

tag: strain

value: 3 months


title: Genomic DNA from Cervical cancer sample 831 A T

description: Cervical cancer sample

label: Cy5 and Cy54

value: Cervical Cancer

value: Tumour


title: Plate2-430-Liver

description: Plate 2_LIVER_C05

tag: Sex

tag: tissue

value: 6:1 FTOH

value: water/tween


title: Old control, replicate 1

value: female

value: 24 months


title: Genomic DNA from Cervical cancer sample 927 A T

description: Cervical cancer sample

label: Cy5 and Cy56

tag: disease state


title: Young control, replicate 3


title: Plate2-427-Liver

description: Plate 2_LIVER_F09

value: Sprague Dawley (SD)

value: Liver

tag: chemical

tag: concentration


title: Young control, replicate 2


title: Plate2-428-Liver

description: Plate 2_LIVER_D05

tag: unit

value: mg/kg

tag: vehicle


title: Genomic DNA from Cervical cancer sample 434 A T

description: Cervical cancer sample

label: Cy5 and Cy53

tag: gender


title: Plate2-426-Liver

description: Plate 2_LIVER_A04

tag: duration

tag: platfrom


title: Young control, replicate 1


title: Genomic DNA from Cervical cancer sample 210 A T

description: Cervical cancer sample

label: Cy5 and Cy52

tag: sample type


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell52

description:
SMART-seq2
D4Cas9R1-P1-E04

tag: cell line

tag: cell type

value: nucleofection

value: 4 days


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell53

description:
SMART-seq2
D4Cas9R1-P1-E05

tag: treatment


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell58

description:
SMART-seq2
D4Cas9R1-P1-E10

tag: genotype


title: Plate2-421-Liver

description: Plate 2_LIVER_B03

value: Male


title: Genomic DNA from Normal Sample 1174 A N SQ

description: Normal Sample

label: Cy5 and Cy50

value: Histological Normal Cervix

value: Normal


title: Plate2-420-Liver

description: Plate 2_LIVER_G03

value: Female

value: day

value: TempO-Seq


title: neoCM_2

city: Chapel Hill

first: LI

last: QIAN

address: 111 Mason Farm Road, MBRB

department: Department of pathology

institute: UNC

data_processing:
Data quality was checked with FastQC and MultiQC.
Reads matching adapter sequences or with a mean quality score less than 20 were trimmed with Bbduk. Pseudoalignment was performed with Salmon using the mm10 cDNA transcriptome as reference.
Differential gene expression analysis was performed with DESeq2. Genes with an adjusted p value less than 0.1 and an absolute fold change greater than 1.5 compared to the relevant control.
Genome_build: mm10 reference
Supplementary_files_format_and_content: 1 csv files containg tpm of  neonatal cardiomyocyte in replicates

organism: Mus musculus

source_name: Cardiomyocytes

growth_protocol: Mice were raised and maintained under standard laboratory conditions.

extract_protocol:
RNA was extracted with TRIzol (Thermo Fisher) according to the manufacturer’s protocol.
Library preparation was performed with the Roche KAPA Stranded mRNA-Seq kit. Paired-end sequencing was performed on the HiSeq2000 platform.

treatment_protocol: Cardiomyocytes were isolated using Pierce™ Primary Cardiomyocyte Isolation Kit

value: Cardiomyocytes

value: heart

tag: age

value: 1-3 days

value: wild type


title: Genomic DNA from Cervical cancer sample 1484 B T

description: Cervical cancer sample

label: Cy5 and Cy51

value: Cervical Cancer

value: Tumour


title: neoCM_1

tag: strain


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell50

description:
SMART-seq2
D4Cas9R1-P1-E02

value: Cas9 only control knockout

tag: time


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell54

description:
SMART-seq2
D4Cas9R1-P1-E06


title: Genomic DNA from Cervical cancer sample 1174 A T

description: Cervical cancer sample

label: Cy5 and Cy49


title: Genomic DNA from Normal Sample 924 A2 N SQ

description: Normal Sample

label: Cy5 and Cy48


title: Plate2-418-Liver

description: Plate 2_LIVER_B08

value: Sprague Dawley (SD)

tag: Sex

tag: tissue

value: Liver

value: 6:1 FTOH

value: water/tween


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell48

description:
SMART-seq2
D4Cas9R1-P1-D12

value: nucleofection

value: 4 days


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell49

description:
SMART-seq2
D4Cas9R1-P1-E01


title: pbmc, after chemotherapy, scRNAseq

city: Guangzhou

first: Yunshan

last: Ning

state: Guangdong

address: No.1023-1063, Shatai South Road, Baiyun District

department: School of Laboratory Medicine and Biotechnology

institute: Southern Medical University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pbmc

extract_protocol:
Within 6 hours after isolation, solid specimens were enzymatically dissociated into single cells. Briefly, the tissue was minced with a scalpel and enzymatically digested using 2 mg/mL Collagenase I (Worthington Biochemical) and 2 mg/mL Collagenase IV (Worthington Biochemical) for 30 minutes in a shaker (250 rpm) at 37°C. The digestion was terminated with DMEM + 5% fetal bovine serum (Thermo Fisher Scientific). The cell suspensions were sequentially filtered through 100 μm and then 70 μm cell strainers. Red blood cells were lysed by incubating the cell suspensions in RBC Lysis Solution (Sigma- Aldrich) for 3–10 minutes at 4°C. After centrifugation and resuspension, the concentrations of the single-cell suspensions were adjusted to 7–12×105 cells/ml with 5% fetal bovine serum DMEM. Ascites was centrifuged for 10 min at 4°C, and the remaining pellet was resuspended in PBS, filtered, subjected to RBC lysis, and resuspended as described for the tumor samples. Peripheric blood was collected into heparin tubes (Becton, Dickinson and Co.) and processed within 2 hours of collection. PBMCs were isolated by density gradient centrifugation using Ficoll-Paque Plus medium and washed with Ca/Mg-free PBS. The isolated cells derived from above samples were used for further single cell sequencing.
The suspensions of live cells in sterile-filtered PBS (Corning) with 0.04% BSA (Sigma Aldrich) were used as input for the 10× Chromium controller system (10× Genomics Inc.). Using 10× GemCode Technology, the cells were barcoded to separately index each cell’s transcriptome by partitioning oil and gel beads to generate the Gel Bead-in-EMulsions (GEMs). Barcoded Single Cell 50 Gel Beads, RT Master Mix with cells and Partitioning Oil were combined on a microfluidic chip, and GEMs were generated. The GEM RT reactions were activated in a thermocycler (53°C for 45 min, 85°C for 5 min, 4°C hold overnight). Post RT incubation, the GEMs were disrupted and the first-strand cDNA was recovered. cDNA amplification was performed by PCR to generate sufficient material. According to the manufacturer’s instructions, scRNA-seq libraries of tumor tissue and ascites were generated using Chromium™ Single Cell 3’ Library (v3 chemistry) reagents. For PBMC samples, scRNA-seq libraries were processed using the Chromium™ single cell 5’ library & gel bead kit and coupled TCR/BCR libraries were obtained using the Chromium™ single cell V(D)J enrichment kit (10× Genomics). Libraries of scRNA-seq were sequenced on the Illumina Novaseq 6000.

value: pbmc

tag: diagnosis

value: high-grade serous ovarian carcinoma

tag: tumor stage(figo)

value: III C

value: 53 year old


title: pbmc, after chemotherapy, scTCRseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scTCR-seq


title: Genomic DNA from Cervical cancer sample 825 A T

description: Cervical cancer sample

label: Cy5 and Cy46

value: Female

tag: disease state


title: Genomic DNA from Cervical cancer sample 924 A T

description: Cervical cancer sample

label: Cy5 and Cy47


title: Plate2-413-Liver

description: Plate 2_LIVER_H06

value: Male

tag: chemical

tag: concentration

tag: unit

value: mg/kg

tag: vehicle

value: day

value: TempO-Seq


title: pbmc, during second debulking surgery before chemotherapy, scBCRseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scBCR-seq


title: Plate2-416-Liver

description: Plate 2_LIVER_C03

tag: duration

tag: platfrom


title: Plate2-417-Liver

description: Plate 2_LIVER_G12


title: pbmc, after chemotherapy, scBCRseq

description: 10x Genomics


title: Genomic DNA from Cervical cancer sample 399 A T

description: Cervical cancer sample

label: Cy5 and Cy45

tag: gender

tag: sample type

value: Cervical Cancer

value: Tumour


title: pbmc, during second debulking surgery before chemotherapy, scTCRseq

description: 10x Genomics


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell45

description:
SMART-seq2
D4Cas9R1-P1-D09

tag: cell line

tag: cell type

tag: genotype

value: Cas9 only control knockout

tag: treatment


title: Genomic DNA from Cervical cancer sample 208 B T

description: Cervical cancer sample

label: Cy5 and Cy44


title: Plate2-412-Liver

description: Plate 2_LIVER_F04

tag: strain

value: Sprague Dawley (SD)

tag: Sex

value: Liver


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell51

description:
SMART-seq2
D4Cas9R1-P1-E03

tag: time


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell44

description:
SMART-seq2
D4Cas9R1-P1-D08


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell46

description:
SMART-seq2
D4Cas9R1-P1-D10


title: Plate2-411-Liver

description: Plate 2_LIVER_A12

tag: tissue

value: 6:1 FTOH

value: water/tween


title: ascites, during second debulking surgery before chemotherapy, scRNAseq

description: 10x Genomics

source_name: ascites

value: ascites

tag: diagnosis

tag: tumor stage(figo)

tag: age


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell43

description:
SMART-seq2
D4Cas9R1-P1-D07

value: nucleofection

value: 4 days


title: Plate2-419-Liver

description: Plate 2_LIVER_C11

tag: chemical

tag: concentration

tag: unit


title: Genomic DNA from Cervical cancer sample 1763 A T

description: Cervical cancer sample

label: Cy5 and Cy43

tag: disease state


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell47

description:
SMART-seq2
D4Cas9R1-P1-D11


title: Genomic DNA from Cervical cancer sample 1469 B2 T

description: Cervical cancer sample

label: Cy5 and Cy42

tag: gender


title: Plate2-409-Liver

description: Plate 2_LIVER_H11

tag: vehicle

tag: duration

tag: platfrom


title: tumor, during second debulking surgery before chemotherapy, scRNAseq

description: 10x Genomics

source_name: tumor

value: tumor

value: high-grade serous ovarian carcinoma

value: III C


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell42

description:
SMART-seq2
D4Cas9R1-P1-D06

tag: cell line

tag: cell type

tag: genotype


title: Genomic DNA from Cervical cancer sample 1168 B T

description: Cervical cancer sample

label: Cy5 and Cy41

value: Female

tag: sample type


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell41

description:
SMART-seq2
D4Cas9R1-P1-D05

tag: treatment

tag: time


title: Genomic DNA from Cervical cancer sample 744 A T

description: Cervical cancer sample

label: Cy5 and Cy40


title: Plate2-408-Liver

description: Plate 2_LIVER_D03

tag: strain

tag: Sex

tag: tissue

value: mg/kg


title: Plate2-406-Liver

description: Plate 2_LIVER_A02

tag: chemical

value: day


title: Plate2-407-Liver

description: Plate 2_LIVER_A03

tag: concentration

value: TempO-Seq


title: Genomic DNA from Cervical cancer sample 913 A T

description: Cervical cancer sample

label: Cy5 and Cy38

value: Cervical Cancer


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell39

description:
SMART-seq2
D4Cas9R1-P1-D03


title: pbmc, during second debulking surgery before chemotherapy, scRNAseq

description: 10x Genomics

value: pbmc

tag: diagnosis

tag: tumor stage(figo)

tag: age

value: 53 year old


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell38

description:
SMART-seq2
D4Cas9R1-P1-D02

value: Cas9 only control knockout


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell40

description:
SMART-seq2
D4Cas9R1-P1-D04


title: Plate2-405-Liver

description: Plate 2_LIVER_G08

value: Sprague Dawley (SD)

value: Male

value: Liver

tag: unit

tag: vehicle


title: Genomic DNA from Normal Sample 913 A N SQ

description: Normal Sample

label: Cy5 and Cy39

tag: gender

value: Histological Normal Cervix

tag: disease state

value: Normal


title: Genomic DNA from Cervical cancer sample 395 B T

description: Cervical cancer sample

label: Cy5 and Cy37

value: Tumour


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell37

description:
SMART-seq2
D4Cas9R1-P1-D01

tag: cell line

tag: cell type

value: nucleofection

value: 4 days


title: 293T_MBD6_KO

city: Chicago

first: Lu

last: Wang

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

institute: Northwestern University

description: MBD6 depleted cells

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9 for single-end or bwa version 0.7.12 for paired-end.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9 or Star version 2.5.2.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: hg19
Supplementary files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: Cells were maintained with either DMEM (Gibco, Gaithersburg, MD) or ATCC-formulated RPMI-1640 medium  containing 10% FBS (Sigma)

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: no treatment

value: kidney cell

tag: passages

value: Low passages (6-10)

tag: chip antibody

value: anti-MBD6 (home made)

tag: genotype

value: MBD6 depleted cells


title: 293T_MBD5_KO

description: MBD5 depleted cells

value: anti-MBD5 (home made)

value: MBD5 depleted cells


title: Plate2-404-Liver

description: Plate 2_LIVER_A08

tag: strain

value: 6:1 FTOH

value: mg/kg

value: water/tween

tag: duration

value: day

tag: platfrom

value: TempO-Seq


title: 293T_MBD6_WT

description: normal cells

value: normal cells


title: Genomic DNA from Normal Sample 1778 A N SQ

description: Normal Sample

label: Cy5 and Cy115

value: Female

tag: sample type

value: Histological Normal Cervix


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell36

description:
SMART-seq2
D4Cas9R1-P1-C12

value: Cas9 only control knockout

tag: treatment

tag: time


title: Genomic DNA from Cervical cancer sample 175 A T

description: Cervical cancer sample

label: Cy5 and Cy36

value: Cervical Cancer

value: Tumour


title: 293T_ASXLWT_MBD6

description: normal cells

value: small cell lung cancer

value: ASXLWT

tag: antibody


title: 293T_ASXLKO_MBD5

description: ASXLs depleted cells

value: Low passages (6-10)

value: ASXLKO


title: 293T_ASXLKO_MBD6

description: ASXLs depleted cells

value: anti-MBD6 (home made)


title: Plate2-410-Liver

description: Plate 2_LIVER_B05

value: Sprague Dawley (SD)

tag: Sex

tag: tissue

value: Liver

tag: chemical

tag: concentration


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell35

description:
SMART-seq2
D4Cas9R1-P1-C11

value: nucleofection

value: 4 days


title: Plate2-402-Liver

description: Plate 2_LIVER_E07

value: Male

value: 6:1 FTOH

tag: unit

value: mg/kg

tag: vehicle

value: water/tween

value: day


title: 293T_ASXLKO_BAP1

description: ASXLs depleted cells

tag: cell type

tag: cell line

value: anti-BAP1 (home made)


title: Genomic DNA from Cervical cancer sample 1027 A T

description: Cervical cancer sample

label: Cy5 and Cy34

tag: gender

value: Female

value: Cervical Cancer

tag: disease state


title: Genomic DNA from Normal Sample 903 A N SQ

description: Normal Sample

label: Cy5 and Cy33

value: Histological Normal Cervix

value: Normal


title: Plate2-400-Liver

description: Plate 2_LIVER_F03

tag: strain

value: TempO-Seq


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell34

description:
SMART-seq2
D4Cas9R1-P1-C10

tag: genotype

value: Cas9 only control knockout


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell33

description:
SMART-seq2
D4Cas9R1-P1-C09


title: 293T_ASXLWT_BAP1

description: normal cells

value: small cell lung cancer

tag: passages

value: Low passages (6-10)

value: ASXLWT

tag: chip antibody


title: 293T_Input

description: normal cells

value: WT


title: Plate2-398-Liver

description: Plate 2_LIVER_F07

value: Sprague Dawley (SD)

value: Liver

tag: duration

tag: platfrom


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell32

description:
SMART-seq2
D4Cas9R1-P1-C08

tag: treatment

value: nucleofection

tag: time

value: 4 days


title: Genomic DNA from Cervical cancer sample 903 B T

description: Cervical cancer sample

label: Cy5 and Cy32

tag: sample type

value: Tumour


title: Plate2-397-Liver

description: Plate 2_LIVER_F12

tag: Sex

tag: tissue

tag: chemical

value: 6:1 FTOH

value: mg/kg

value: water/tween

value: day


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell31

description:
SMART-seq2
D4Cas9R1-P1-C07


title: Genomic DNA from Cervical cancer sample 381 A T

description: Cervical cancer sample

label: Cy5 and Cy30

value: Female

value: Cervical Cancer


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell30

description:
SMART-seq2
D4Cas9R1-P1-C06


title: Plate2-394-Liver

description: Plate 2_LIVER_A11

value: Male

tag: concentration

tag: unit

tag: vehicle

value: TempO-Seq


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell29

description:
SMART-seq2
D4Cas9R1-P1-C05

tag: cell line

tag: cell type

value: Cas9 only control knockout


title: Genomic DNA from Cervical cancer sample 694 A T

description: Cervical cancer sample

label: Cy5 and Cy31

tag: gender

tag: disease state


title: Genomic DNA from Cervical cancer sample 1425 A T

description: Cervical cancer sample

label: Cy5 and Cy35


title: Plate2-403-Liver

description: Plate 2_LIVER_G10

tag: strain


title: 293T_ASXLWT_MBD5

description: normal cells

value: small cell lung cancer

tag: passages

value: Low passages (6-10)

tag: genotype

tag: antibody

tag: chip antibody

value: anti-MBD5 (home made)


title: Genomic DNA from Cervical cancer sample 121 A T

description: Cervical cancer sample

label: Cy5 and Cy28


title: Plate2-396-Liver

description: Plate 2_LIVER_C09

value: Sprague Dawley (SD)

tag: duration

tag: platfrom


title: Genomic DNA from Normal Sample 121 B1 N SQ

description: Normal Sample

label: Cy5 and Cy29

tag: sample type

value: Histological Normal Cervix

value: Normal


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell27

description:
SMART-seq2
D4Cas9R1-P1-C03

tag: treatment

value: nucleofection

tag: time

value: 4 days


title: Plate2-392-Liver

description: Plate 2_LIVER_E02

tag: Sex

tag: tissue

value: Liver

tag: chemical

value: 6:1 FTOH

tag: concentration


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell28

description:
SMART-seq2
D4Cas9R1-P1-C04

tag: cell line

tag: cell type


title: Plate2-393-Liver

description: Plate 2_LIVER_H09

tag: unit

value: mg/kg

tag: vehicle

value: water/tween


title: Plate2-391-Liver

description: Plate 2_LIVER_E11

tag: strain

value: day


title: Genomic DNA from Cervical cancer sample 1013 A T

description: Cervical cancer sample

label: Cy5 and Cy27

tag: gender

value: Female

value: Cervical Cancer

tag: disease state

value: Tumour


title: Genomic DNA from Normal Sample 901 B N Adeno.

description: Normal Sample

label: Cy5 and Cy26


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell26

description:
SMART-seq2
D4Cas9R1-P1-C02

tag: genotype

value: Cas9 only control knockout


title: Genomic DNA from Normal Sample 665 A N SQ

description: Normal Sample

label: Cy5 and Cy24


title: Plate2-388-Liver

description: Plate 2_LIVER_G11

tag: duration

value: TempO-Seq


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell24

description:
SMART-seq2
D4Cas9R1-P1-B12


title: Plate2-389-Liver

description: Plate 2_LIVER_C07

tag: platfrom


title: Plate2-386-Liver

description: Plate 2_LIVER_F08


title: Plate2-387-Liver

description: Plate 2_LIVER_D07


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell22

description:
SMART-seq2
D4Cas9R1-P1-B10


title: Plate2-385-Liver

description: Plate 2_LIVER_D09

value: Male


title: Genomic DNA from Normal Sample 98 A N SQ

description: Normal Sample

label: Cy5 and Cy21

tag: sample type


title: Genomic DNA from Cervical cancer sample 98 A T

description: Cervical cancer sample

label: Cy5 and Cy20


title: Plate2-384-Liver

description: Plate 2_LIVER_E06


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell21

description:
SMART-seq2
D4Cas9R1-P1-B09

tag: treatment


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell19

description:
SMART-seq2
D4Cas9R1-P1-B07

tag: time


title: Genomic DNA from Cervical cancer sample 1358 A T

description: Cervical cancer sample

label: Cy5 and Cy19


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell20

description:
SMART-seq2
D4Cas9R1-P1-B08


title: Plate2-381-Liver

description: Plate 2_LIVER_H07

tag: Sex


title: Plate2-382-Liver

description: Plate 2_LIVER_G04

tag: tissue


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell18

description:
SMART-seq2
D4Cas9R1-P1-B06


title: Plate2-380-Liver

description: Plate 2_LIVER_A07

tag: chemical


title: Genomic DNA from Cervical cancer sample 894 B T

description: Cervical cancer sample

label: Cy5 and Cy17


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell17

description:
SMART-seq2
D4Cas9R1-P1-B05


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell16

description:
SMART-seq2
D4Cas9R1-P1-B04


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell23

description:
SMART-seq2
D4Cas9R1-P1-B11


title: Plate2-379-Liver

description: Plate 2_LIVER_G01

tag: concentration


title: Genomic DNA from Cervical cancer sample 639 C T

description: Cervical cancer sample

label: Cy5 and Cy16


title: Genomic DNA from Cervical cancer sample 665 A T

description: Cervical cancer sample

label: Cy5 and Cy23


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell25

description:
SMART-seq2
D4Cas9R1-P1-C01

tag: cell line


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell15

description:
SMART-seq2
D4Cas9R1-P1-B03

tag: cell type


title: Genomic DNA from Cervical cancer sample 347 A T

description: Cervical cancer sample

label: Cy5 and Cy14


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell14

description:
SMART-seq2
D4Cas9R1-P1-B02


title: Plate2-376-Liver

description: Plate 2_LIVER_F11

tag: unit


title: Genomic DNA from Cervical cancer sample 901 A T

description: Cervical cancer sample

label: Cy5 and Cy25


title: Genomic DNA from Normal Sample 77 A N SQ

description: Normal Sample

label: Cy5 and Cy13


title: Genomic DNA from Cervical cancer sample 1010 A T

description: Cervical cancer sample

label: Cy5 and Cy18


title: Genomic DNA from Cervical cancer sample 77 A T

description: Cervical cancer sample

label: Cy5 and Cy12


title: Plate2-375-Liver

description: Plate 2_LIVER_G05

tag: vehicle


title: Plate2-374-Liver

description: Plate 2_LIVER_D12

tag: strain


title: Genomic DNA from Cervical cancer sample 1572 A T

description: Cervical cancer sample

label: Cy5 and Cy11

tag: gender


title: Plate2-373-Liver

description: Plate 2_LIVER_B04


title: Plate2-372-Liver

description: Plate 2_LIVER_E05


title: Genomic DNA from Cervical cancer sample 1331 A T

description: Cervical cancer sample

label: Cy5 and Cy10

tag: disease state


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell10

description:
SMART-seq2
D4Cas9R1-P1-A10

tag: genotype


title: Genomic DNA from Cervical cancer sample 1005 A T

description: Cervical cancer sample

label: Cy5 and Cy9


title: Plate2-378-Liver

description: Plate 2_LIVER_G06

tag: duration


title: Genomic DNA from Normal Sample 347 B N SQ

description: Normal Sample

label: Cy5 and Cy15


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell9

description:
SMART-seq2
D4Cas9R1-P1-A09


title: Genomic DNA from Cervical cancer sample 892 B T

description: Cervical cancer sample

label: Cy5 and Cy7


title: Genomic DNA from Normal Sample 892 A N SQ

description: Normal Sample

label: Cy5 and Cy8


title: Plate2-367-Liver

description: Plate 2_LIVER_F06

tag: platfrom


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell8

description:
SMART-seq2
D4Cas9R1-P1-A08


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell7

description:
SMART-seq2
D4Cas9R1-P1-A07


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell6

description:
SMART-seq2
D4Cas9R1-P1-A06


title: Plate2-368-Liver

description: Plate 2_LIVER_B06


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell5

description:
SMART-seq2
D4Cas9R1-P1-A05


title: Plate2-366-Liver

description: Plate 2_LIVER_B09


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell12

description:
SMART-seq2
D4Cas9R1-P1-A12


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell13

description:
SMART-seq2
D4Cas9R1-P1-B01


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell11

description:
SMART-seq2
D4Cas9R1-P1-A11


title: Genomic DNA from Cervical cancer sample 335 B T

description: Cervical cancer sample

label: Cy5 and Cy5

tag: sample type


title: Genomic DNA from Cervical cancer sample 13 A T

description: Cervical cancer sample

label: Cy5 and Cy4


title: Plate2-364-Liver

description: Plate 2_LIVER_G09


title: ciOG [scRNA-Seq]

city: Cheonansi

first: Ji-Young

last: Yoon

state: Chungnam

address: Dandaero 119

department: Nanbiomedical science

country: South Korea

institute: Dankook University

description: 10x Genomics

data_processing:
Samples were sequenced paired-end 100bp by Illumina NovaSeq 6000 platform and preliminary sequencing results were converted to FASTQ files with Cell Ranger
The 10x Genomics standard seq protocol by trimming the barcode and unique molecular identifier (UMI) end to 28 bp, and the mRNA end to 91 bp.
the FASTQ files were aligned to the human reference genome (GRCh38).
Quality control of the processed expression matrix were performed by evaluating detected transcripts, detected counts, cell doublets, mito-ratio
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Dermal fibroblasts

growth_protocol: HDFs were cultured in growth medium (DMEM-HG, 10% FBS, 1% Penicillin-Streptomycin, 1% MEM non-essential amino acids solution, 2 mM Glutamax, and 0.1 mM 2- mercaptoethanol) and the medium was changed every 2-3 days.and hOBs (human osteoblasts; C-127220, PromoCell) were cultured  in an osteoblast growth medium (C-27001) supplemented with growth medium SupplementMix (C-39615).

extract_protocol: Library construction was performed using the 10X Chromium Single Cell 3’ Reagent Kits v3.1.

treatment_protocol: ciOG : HDFs were seeded at -1 day in 24 well plates at a density of 60,000 cells/well and cultured in GM. The medium was replaced at 0, 2, and 4 days into an osteogenic medium containing low concentration of FBS (DMEM-HG, 2% FBS, 1% P/S, 50 mg/ml ascorbic acid, 10 mM b-glycerophosphate, and 10 nM dexamethasone) with three chemicals (R, F, P) for 7 days.

value: Dermal fibroblasts

value: WT

tag: treatment

value: 3 chemicals (Repsox, Forskolin, Phenamil) treatment at 0, 2, 4 days in the osteogenic medium under low concentration of FBS (2%) for 7 days in fibroblast seeded in tissue culture plate


title: Plate2-365-Liver

description: Plate 2_LIVER_H02

value: Sprague Dawley (SD)


title: Plate2-371-Liver

description: Plate 2_LIVER_D11


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell4

description:
SMART-seq2
D4Cas9R1-P1-A04

value: nucleofection

tag: time


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell3

description:
SMART-seq2
D4Cas9R1-P1-A03

value: 4 days


title: 293T_MBD6KO_Rep2

description: cells with MBD6 knockout by a pair of CRISPR-Cas9

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9 for single-end or bwa version 0.7.12 for paired-end.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9 or Star version 2.5.2.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

value: kidney cell

tag: passages

value: Low passages (6-10)

value: MBD6 knockout cells


title: Plate2-363-Liver

description: Plate 2_LIVER_E10

tag: Sex

tag: tissue

value: Liver

value: 6:1 FTOH

value: mg/kg

value: water/tween


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell2

description:
SMART-seq2
D4Cas9R1-P1-A02


title: LacZ control Replicate 2

data_processing:
Salmon
Sequence reads were QCed with FastQC and no trimming was performed for these libraries.
FastQ reads were then pesudo-align to the mm10 transcriptome using salmon with default parameters.
Read count extraction and normalization were performed Deseq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes read counts for each Sample

source_name: Cardiac Fibroblast

growth_protocol: Reprogrammed cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 20% M199 and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIZOL following manufacturer's protocol.
RNA libraries for RNA-seq were prepared using KAPA stranded mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cardiac fibroblast was infected with retrovirus encoding Ascl1 and Mef2c.

value: Cardiac Fibroblast

value: control


title: Plate2-369-Liver

description: Plate 2_LIVER_H12

value: Female

tag: chemical

tag: concentration

value: day

value: TempO-Seq


title: Plate2-362-Liver

description: Plate 2_LIVER_A10

value: Male


title: 293T_MBD6KO_Rep1

tag: cell type

tag: cell line


title: LacZ control Replicate 1

value: WT


title: Genomic DNA from Cervical cancer sample 586 B T

description: Cervical cancer sample

label: Cy5 and Cy6

value: Cervical Cancer

value: Tumour


title: 293T_MBD5KO_Rep2

description: cells with MBD5 knockout by a pair of CRISPR-Cas9

value: MBD5 knockout cells


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell1

description:
SMART-seq2
D4Cas9R1-P1-A01

value: Cas9 only control knockout

value: nucleofection

value: 4 days


title: Plate2-361-Liver

description: Plate 2_LIVER_H03

value: Sprague Dawley (SD)

value: Liver

tag: unit

tag: vehicle


title: A+M reprogramming D50 Replicate 2

value: Cardiac reprogramming


title: 293T_MBD5KO_Rep1

value: kidney cell

value: Low passages (6-10)


title: Plate2-360-Liver

description: Plate 2_LIVER_H01

tag: strain

value: 6:1 FTOH

value: mg/kg

value: water/tween


title: 293T_WT_Rep2

description: normal cells

value: normal cells


title: A+M reprogramming D25 Replicate 2

value: Cardiac Fibroblast


title: Plate2-358-Liver

description: Plate 2_LIVER_B12

value: Female

value: day

value: TempO-Seq


title: 293T_WT_Rep1

description: normal cells


title: A+M reprogramming D25 Replicate 1

value: WT


title: H1963_sgBAP1_2_Rep2

description: cells transduced with BAP1 specific sgRNA #2 Replication 2

value: small cell lung cancer


title: ChIPseq_BT869_H3K27me3

data_processing:
Reads were aligned using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads were used.
Human reads were normalized to Drosophila reads and extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome.  The resulting histograms (genomic “signal maps”) were stored in bigWig files and genome tracks were visualized by loading such files into IGV.
H3K27ac and BRG1 peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7. H3K27me3-enriched regions were identified using the SICER algorithm at a cutoff of FDR 1E-10 and a max gap parameter of 600 bp.
Peaks that were on the ENCODE blacklist of known false ChIPseq peaks were removed.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Assembly: hg38 and dm3
Supplementary files format and content: bigwig
Supplementary files format and content: excel file with the locations of BRG1 peaks

growth_protocol: BT869 cells were grown as neurospheres in tumor stem media base supplemented with B27 minus vitamin A (Thermo Fisher Scientific), human growth factors (EGF, FGF, PDGF-AA, PDGF-BB [Shenandoah Biotechnology]) and heparin (Stemcell Technologies) in ultra-low attachment flasks, humidified atmosphere, 5% CO2, and at 37C.

extract_protocol:
Cell pellets were frozen at -80C, and sent to Active Motif Services (Carlsbad, CA) to be processed for ChIPseq. Cells were fixed with 1% formaldehyde for 15 min and chromatin was sheared sheared to an average length of 300-500 bp.
Illumina sequencing libraries were prepared from the ChIP and input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

value: wildtype

value: spiked-in with 200 ng of Drosophila chromatin

tag: chip antibody

value: H3K27me3, Active Motif, #39155


title: ChIPseq_BT869_SMARCA4ko_H3K27me3

tag: genotype

value: SMARCA4 knockout

value: 4 days


title: ChIPseq_BT869_H3K27ac

value: H3K27ac, Active Motif, #39133


title: ChIPseqBT869_SMARCA4ko_H3K27ac


title: Plate2-355-Liver

description: Plate 2_LIVER_E04

data_processing: Data were processed using the Tempo-SeqR software package

value: Sprague Dawley (SD)

value: Male

value: Liver

tag: duration


title: ChIPseq_BT869_BRG1

value: BRG1, Abcam, ab110641


title: Plate2-354-Liver

description: Plate 2_LIVER_H08

value: 6:1 FTOH

value: mg/kg

value: water/tween

tag: platfrom


title: ChIPseq_BT869_SMARCA4ko_Input


title: H1963_sgBAP1_2_Rep1

description: cells transduced with BAP1 specific sgRNA #2 Replication 1

value: Low passages (6-10)

value: normal cells


title: ChIPseq_BT869_Input


title: Plate2-357-Liver

description: Plate 2_LIVER_D10

value: Female

value: day

value: TempO-Seq


title: H1963_sgBAP1_1_Rep2

description: cells transduced with BAP1 specific sgRNA #1 Replication 2

value: small cell lung cancer


title: H1963_sgASXL3_2_Rep2

description: cells transduced with ASXL3 specific sgRNA #2 Replication 2

value: ASXL2 depleted cells


title: A+M reprogramming D50 Replicate 1

value: Cardiac Fibroblast

value: WT

value: Cardiac reprogramming


title: Plate2-353-Liver

description: Plate 2_LIVER_H10

value: Sprague Dawley (SD)


title: H1963_sgASXL3_2_Rep1

description: cells transduced with ASXL3 specific sgRNA #2 Replication 1


title: Plate2-351-Liver

description: Plate 2_LIVER_C08

value: Male


title: Plate2-352-Liver

description: Plate 2_LIVER_H04

value: Liver


title: Plate2-349-Liver

description: Plate 2_LIVER_D06


title: ATACseq_BT869_JQdS4_48h

data_processing:
Raw fastq reads were trimmed of adapters and aligned using Bowtie2 version 2.4.2. PCR duplicates were removed.
Chromatin accessibility peaks were called using MACS2 using custom parameters for ATAC-seq (–nomodel –nolambda –call-summits).
A signal track in .bdg form was emitted from the peak calling function that was subsequently converted into a .bigwig for visualization with the —SPMR flag.
To establish a uniform feature set, we used all 1 bp summits from the MACS2 peak calls per population and expanded these to uniform 500 bp.
Summits overlapping the same window were iteratively centered at the summit with the strongest signal (measured by -log10 FDR) until all summits were accounted. A peak x sample fragment counts matrix was completed using the getCounts function in chromVAR.
Assembly: hg19
Supplementary files format and content: bigwig in hg38
Supplementary files format and content: ATAC_500bp.counts.tsv - count matrix for all samples

extract_protocol:
40,000-50,000 live cells were sorted by FACS and lysed in 0.1% NP40 (Sigma/Roche 11332473001), 0.1% Tween-20 (Sigma/Roche 11332465001), and 0.01% digitonin (Promega, G9441), followed by tagmentation with 100 nM Tn5 transposase (Illumina, 15027865) for 30 min at 37 °C.
Tagmented DNA was purified using the MinElute PCR Cleanup kit (Qiagen) and PCR amplified using NEBNext-Fidelity 2X PCR Master Mix (NEB M0541S) and primers containing Illumina adapter sequences. Final library was purified by MinElute PCR Cleanup kit (Qiagen). Libraries were prepared and sequenced in two technical replicates on a Nextseq 500 sequencer (Illumina) using Nextseq High Output Cartridge kits by paired-end reads.

value: wildtype

value: 1uM BRG1/BRM degrader JQdS4


title: ATACseq_BT869_DMSO_48h

value: DMSO


title: ATACseq_BT869_AU15330_24h_biolrep2

value: 1uM BRG1/BRM degrader AU15330


title: H1963_sgASXL3_1_Rep2

description: cells transduced with ASXL3 specific sgRNA #1 Replication 2

value: Low passages (6-10)


title: Plate2-348-Liver

description: Plate 2_LIVER_F02

value: 6:1 FTOH

value: mg/kg

value: water/tween


title: ATACseq_BT869_AU15330_24h_biolrep1


title: H1963_sgASXL3_1_Rep1

description: cells transduced with ASXL3 specific sgRNA #1 Replication 1


title: Plate2-356-Liver

description: Plate 2_LIVER_A05

value: Female

value: day

value: TempO-Seq


title: ATACseq_BT869_JQdS4_24h_biolrep2


title: H1963_sgNONT_Rep6

description: cells transduced with non-targeting shRNA Replication 6

value: small cell lung cancer

value: normal cells


title: Plate2-347-Liver

description: Plate 2_LIVER_E12


title: H1963_sgNONT_Rep5

description: cells transduced with non-targeting shRNA Replication 5


title: H1963_sgBAP1_1_Rep1

description: cells transduced with BAP1 specific sgRNA #1 Replication 1

value: BAP1 depleted cells


title: Plate2-346-Liver

description: Plate 2_LIVER_C02

value: Sprague Dawley (SD)


title: H1963_sgASXL2_2_Rep2

description: cells transduced with ASXL2 specific sgRNA #2 Replication 2

value: ASXL2 depleted cells


title: Plate2-345-Liver

description: Plate 2_LIVER_B10

value: Male

value: Liver


title: ATACseq_BT869_JQdS4_24h_biolrep1

value: wildtype

value: 1uM BRG1/BRM degrader JQdS4


title: Plate2-344-Liver

description: Plate 2_LIVER_D04


title: ATACseq_BT869_Compound14_24h_biolrep1

value: 1uM BRG1/BRM inhibitor Compound 14


title: H1963_sgASXL2_1_Rep2

description: cells transduced with ASXL2 specific sgRNA #1 Replication 2

value: Low passages (6-10)


title: ATACseq_BT869_Compound14_24h_biolrep2


title: H1963_sgASXL2_2_Rep1

description: cells transduced with ASXL2 specific sgRNA #2 Replication 1


title: ATACseq_BT869_Compound11_24h_biolrep2

value: 1uM BRG1/BRM inhibitor Compound 11


title: Plate2-343-Liver

description: Plate 2_LIVER_D02

value: 6:1 FTOH

value: mg/kg


title: H1963_sgASXL2_1_Rep1

description: cells transduced with ASXL2 specific sgRNA #1 Replication 1


title: Plate2-342-Liver

description: Plate 2_LIVER_C10

value: water/tween


title: Genomic DNA from Cervical cancer sample 376 A T

description: Cervical cancer sample

data_processing: standard Illumina protocol

label: Cy5 and Cy22

tag: gender

value: Female

tag: sample type

value: Cervical Cancer

tag: disease state

value: Tumour


title: ATACseq_BT869_Compound11_24h_biolrep1

tag: treatment

tag: time


title: ATACseq_BT869_DMSO_24h_biolrep2

value: DMSO


title: ATACseq_BT869_DMSO_24h_biolrep1


title: Plate2-340-Liver

description: Plate 2_LIVER_E08

tag: Sex

tag: tissue

value: day

value: TempO-Seq


title: Plate2-338-Liver

description: Plate 2_LIVER_A09

value: Sprague Dawley (SD)

tag: chemical

tag: concentration


title: Plate2-341-Liver

description: Plate 2_LIVER_H05

value: Male


title: H1963_sgASXL1_1_Rep1

description: cells transduced with ASXL1 specific sgRNA #1 Replication 1

tag: cell type

value: small cell lung cancer

tag: passages

tag: cell line

value: ASXL1 depleted cells


title: H1963_sgASXL1_2_Rep1

description: cells transduced with ASXL1 specific sgRNA #2 Replication 1


title: H1963_sgNONT_Rep4

description: cells transduced with non-targeting shRNA Replication 4

value: normal cells


title: ATACseq_BT869_SMARCA4ko_d4

value: SMARCA4 knockout

value: nucleofection

value: 4 days


title: ATACseq_BT869_AAVS1ko_d4

value: AAVS1 control knockout


title: H1963_sgASXL1_1_Rep2

description: cells transduced with ASXL1 specific sgRNA #1 Replication 2

value: Low passages (6-10)


title: H1963_sgNONT_Rep3

description: cells transduced with non-targeting shRNA Replication 3


title: Plate2-333-Liver

description: Plate 2_LIVER_B07

tag: strain

value: Liver

value: 6:1 FTOH

tag: unit

value: mg/kg

tag: vehicle

value: water/tween


title: Plate2-337-Liver

description: Plate 2_LIVER_D08

value: Female

tag: duration


title: ciOG (M7p) in PCL NF

description: d

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

growth_protocol: HDFs were cultured in growth medium (DMEM-HG, 10% FBS, 1% Penicillin-Streptomycin, 1% MEM non-essential amino acids solution, 2 mM Glutamax, and 0.1 mM 2- mercaptoethanol) and the medium was changed every 2-3 days.

extract_protocol:
Total RNA was isolated from cells of four groups [ciOG_NF, ciOG_film, ciOG(M7p)_NF, and ciOG(M7P)_film] using RibospinTM according to manufacturer's instruction.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: ciOG in PCL film or NF : HDFs were seeded at -1 day in PCL nanofiber or PCL film at a density of 60,000 cells/well and cultured in GM. The medium was replaced at 0, 2, and 4 days into an osteogenic medium containing low concentration of FBS (DMEM-HG, 2% FBS, 1% P/S, 50 mg/ml ascorbic acid, 10 mM b-glycerophosphate, and 10 nM dexamethasone) with three chemicals (R, F, P). ciOG(M7p) in PCL film or NF : The ciOG in PCL film or NFwere then matured to osteoblasts for 7 days in osteogenic medium with 10% FBS in the presence of phenamil.

value: Dermal fibroblasts

tag: genotype

value: WT

value: ciOG(M7p) of PCL NF (2) followed by treatment phenamil under osteogenic medium per 3 days further 7 days from 7th days


title: ATACseq_BT869_untreated_d4

value: untreated control

value: 5 days


title: ciOG (M7p) in PCL film

description: c

value: ciOG(M7p) of PCL film (1) followed by treatment phenamil under osteogenic medium per 3 days further 7 days from 7th days


title: Plate2-336-Liver

description: Plate 2_LIVER_F10

value: Sprague Dawley (SD)

value: day

tag: platfrom

value: TempO-Seq


title: H2171_RNA

description: normal cells

value: small cell lung cancer

value: normal cells


title: ciOG in PCL NF

value: 3 chemicals (Repsox, Forskolin, Phenamil) treatment at 0, 2, 4 days in the osteogenic medium under low concentration of FBS (2%) for 7 days in fibroblasts seeded onto PCL nf


title: Plate2-332-Liver

description: Plate 2_LIVER_C12

value: Liver


title: H526_RNA

description: normal cells

value: Low passages (6-10)


title: H1963_sgASXL1_2_Rep2

description: cells transduced with ASXL1 specific sgRNA #2 Replication 2

value: ASXL1 depleted cells


title: Plate2-330-Liver

description: Plate 2_LIVER_A06

value: Male

value: 6:1 FTOH

value: mg/kg

value: water/tween


title: Plate2-331-Liver

description: Plate 2_LIVER_G07

value: Female


title: ciOG in PCL film

value: Dermal fibroblasts

value: WT

value: 3 chemicals (Repsox, Forskolin, Phenamil) treatment at 0, 2, 4 days in the osteogenic medium under low concentration of FBS (2%) for 7 days in fibroblasts seeded onto PCL film


title: H510_RNA

description: normal cells


title: H1963_sgMBD6_2_Rep2

description: cells transduced with MBD6 specific sgRNA #2 Replication 2

value: MBD6 depleted cells


title: Plate2-329-Liver

description: Plate 2_LIVER_C06

value: Sprague Dawley (SD)

value: day


title: H1963_sgMBD6_2_Rep1

description: cells transduced with MBD6 specific sgRNA #2 Replication 1

value: small cell lung cancer


title: Subcutaneously vaccinated mice

city: Madison

first: Colin

last: Dewey

address: 425 Henry Mall, 5420 Genetics/Biotechnology Center

institute: University of Wisconsin-Madison

data_processing:
Cell Ranger v3.1.0 was used to perform demultiplexing, alignment, filtering, barcode counting, and UMI counting
Assembly: GRCm38 with the curated 10x genomics reference for mouse (mm10-3.0.0)
Supplementary files format and content: Filtered feature-barcode matrices in HDF5 format for each sample

source_name: tetramer-positive CD4+ T cells

growth_protocol: C57BL/6 mice from Jackson Laboratory were bred at our facility and cared for per guidelines from the University of Wisconsin Animal Care Committee

extract_protocol:
Lungs were harvested from challenged animals (10 SC mice and 14 IN mice) and dissociated in Miltenyi MACS tubes (Miltenyi Inc., Germany) and digested with collagenase (1 mg/mL) and DNase (1 µg/mL) for 25 min at 37 °C. Digested lungs were resuspended in 5 mL of 40% percoll, and 3 mL of 66% percoll was underlaid (GE healthcare 17–0891–01). Samples were spun for 20 min at 2000 rpm at room temperature. Lymphocytes were then harvested from the buffy coat layer and resuspended in complete RPMI (10% FBS, 1% penicillin and streptomycin). Lymphocytes from each treatment group were pooled, resulting in two cell samples (SC and IN).  The cells were spun down (1500 rpm/5 minutes at room temperature) and stained with LIVE/DEAD™ Fixable Near-IR Dead Cell Stain Kit (Invitrogen) and Fc Block (BD) for 10 min at room temperature. Then the cells were stained with Bl-Eng2 tetramer (MHC class II tetramer-PE, NIH) for 1 hour at room temperature, and 30 minutes at 4°C with the following surface antibodies: CD8 PerCP-Cy5.5 (clone 53–6.7, Biolegend, cat#100734), CD44 BV650 (clone IM7, Biolegend, cat#103049), CD11b APC (clone M1/70, Biolegend, cat#101212), CD11c APC (clone N418, Biolegend, cat#117310), NK1.1 APC (clone PK136, Biolegend, cat#108710), B220 APC (clone RA3–62B, Biolegend, cat#103212), CD4 BUV737 (clone RM4–5, BD, cat#565246), and CD90.2 BV421 (clone 30-H12, Biolegend, cat105341). All panels included a dump channel to decrease background in CD4+ T cells (Dump: CD11b, CD11c, NK1.1, and B220).  The cells were fixed in 2% paraformaldehyde and sorted using the cell sorting flow cytometer FACSAria (BD). Following fluorescent labeling, cells from 10-15 animals from each vaccine (SC or IN) group were combined into one tube each for cell sorting.  Tetramer+ cells were sorted into microcentrifuge tubes containing RPMI media on a FACs Aria using a 130 micron nozzle. The sorted cells (Live, Dump-CD90.2+CD4+CD44+Tetramer+) were collected directly into 1.5 ml microtubes
Sorted tetramer+ cells were counted on a Countless II cell counter with 0.4% trypan blue and concentrated to 300-400 cells/ml (total volume of 43.3 ml) and reverse transcribed. The libraries were generated with the 3' kit version 3.1 chemistry (10x Genomics).

treatment_protocol: Mice were vaccinated intranasally (IN) or subcutaneously (SC) with 10 μg of Bl-Eng2 in glucan chitin particles (CGP) a total of three times, two weeks apart. Two weeks after the final vaccination, mice were challenged intratracheally with 2x10^4 Blastomyces dermatitidis (Bd, ATCC strain 26199) and analyzed at day 3 post-infection.

tag: sample id

tag: age

value: 7-8 weeks

tag: age id

value: CD4-positive, alpha-beta memory T cell

tag: cell type id

value: lung

tag: tissue id

tag: vaccination route of administration

value: subcutaneous route

tag: vaccination route of administration id

tag: infection pathogen

value: Blastomyces dermatitidis ATCC 26199

tag: infection pathogen id


title: H2AZ_knockout

city: Cold Spring Harbor

first: Olaf

last: Klingbeil

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
Sequence reads were mapped into reference human genome hg19 by using Bowtie2.
Peakcaling was done by using MACS2 FDR cutt off 5% with narrow peak option.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: glioblastoma

growth_protocol: A382 cells were cultured in DMEM with 10% FBS and penicillin/streptomycin

extract_protocol:
Cells were lysed and tagmented using transposase. Tagmented chromatin was purified using MinElute kits.
Purified tagmented chromatin was amplified using KAPA HiFi HotStart Readymix. Amplified library was purified with MinElute kits, and quantified with Bioanalyzer using high sensitivity DNA chips (Agilent).

treatment_protocol: A382 cells were infected with sgNeg, sgBRD8#2, or sgH2AZ#2

value: A382 cells expressing Cas9

tag: treatment

value: Cas9-expressing A382 cells were infected with sgH2AZ#2 lentivirus


title: H1963_sgMBD6_1_Rep2

description: cells transduced with MBD6 specific sgRNA #1 Replication 2

tag: cell type

tag: passages

value: Low passages (6-10)

tag: cell line


title: H2AZ_control

value: Cas9-expressing A382 cells were infected with sgNeg lentivirus


title: Intranasally vaccinated mice

tag: strain

tag: tissue

value: intranasal route


title: Plate2-328-Liver

description: Plate 2_LIVER_B11

extract_protocol: All animals were euthanized the day after the last dose of chemical was administered and the liver and kidney were removed during necropsy. Two samples from each the left liver lobe and right kidney were collected within five minutes of termination for toxicogenomic evaluation. Tissue samples were cut into approximately 5 cubic mm pieces, aliquoted into screw-cap tubes, flash frozen in liquid nitrogen, and stored at -80 degreees C. RNA was extracted from one of the two collected samples and the extraction batch information recorded in the metadata along with the quantity and quality of each RNA sample. The RNA samples and metadata file were sent to BioSpyder for evaluation using the whole transcriptome TempOSeq platform with a minimum of 10 million reads/sample.

tag: Sex

value: Male

value: Liver

tag: chemical

value: 6:1 FTOH

tag: concentration

tag: unit

value: mg/kg

tag: vehicle

value: water/tween

tag: duration

value: TempO-Seq


title: BRD8_knockout

value: Cas9-expressing A382 cells were infected with sgBRD8#2 lentivirus


title: H1963_sgMBD6_1_Rep1

description: cells transduced with MBD6 specific sgRNA #1 Replication 1

value: small cell lung cancer

tag: genotype

value: MBD6 depleted cells


title: Plate2-326-Liver

description: Plate 2_LIVER_E03

value: Sprague Dawley (SD)

value: day

tag: platfrom


title: Plate2-325-Liver

description: Plate 2_LIVER_E09


title: Plate2-324-Liver

description: Plate 2_LIVER_G02


title: H1963_sgMBD5_2_Rep2

description: cells transduced with MBD5 specific sgRNA #2 Replication 2

value: MBD5 depleted cells


title: MGT_Mef2c_rep2_input

description: MGT_M_R2_CHIP_ACCTTGGC-GGCCTCAT_S43_ME_peaks.narrowPeak

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Reads were aligned to the mm10 reference genome using Bowtie2.
MACS2 were used for peak calling with following parameter -extsize 200 --nolambda -g mm -p 1e-5
Genome_build: mm10 reference
Supplementary_files_format_and_content: 20 txt files containg  Ascl1, Mef2c, and H3K27ac Peaks of A, M, and AM  infected fibroblast in replicates

source_name: Mouse Embryonic Fibroblast

extract_protocol:
Chromatin were harvested using truChIP® Chromatin Shearing Kit (Covaris, PN 520154) following the manufacturer’s protocol. Briefly, five million cells were cross-linked with Fixing Buffer A at room temperature for 10 minutes. Quenching Buffer E was added to the fixed cells and the cells were incubated at room temperature for an additional 5 minutes. The cells were washed twice with ice-cold PBS. To extract the nuclei, Lysis Buffer B containing 1x protease inhibitors were added to the cells. Incubate the cell on ice for 10 minutes on a rocker at 4 degree. Intact nuclei were collected by centrifugation at 1,700 x g for 5 minutes at 4 degree. The nuclei were washed once with Wash Buffer C and then Shearing Buffer D3.   The pelleted nuclei were resuspended in 1ml Shearing Buffer D3 and transfer to  milliTUBE (Covaris, PN 520135). The chromatin shearing were performed with E220 Focused-ultrasonicator (Covaris) with 60sec on and 30sec off, 14 cycles. The chromatin solution was clarified by centrifugation at 20,000 g at 4C for 45 minutes and then pre-cleared with Dynabeads protein A (Life Technologies) for 2 hours at 4C. The pre-cleared chromatin sample was incubated with 50 mL of Dynabeads protein A loaded with 5 mg antibody (anti-H3K27ac, ab4729; anti-Mef2c, ab211493; anti-Ascl1, ab74065) overnight at 4C. The beads were washed three times with 0.1% SDS lysis buffer, once with 0.1% SDS lysis buffer/0.35 M NaCl, once with 10 mM Tris-Cl (pH 8)/1 mM EDTA/0.5% NP40/ 0.25% LiCl/0.5% NaDOC, and once with TE buffer (pH8.0). The immunoprecipitated material was eluted from the beads by heating for 45 minutes at 68C in 50 mM Tris-Cl (pH 7.5), 10 mM EDTA, 1% SDS. To reverse the crosslinks, samples were incubated with 1.5 mg/ml Pronase at 42C for 2 hr followed by 67C for 6 hr. The samples were then extracted with MinElute PCR purification Kit (QIAGEN) and eluted in TE buffer.
ChIP DNA were then sent to UNC Chapel Hill’s High-Throughput Sequencing Facility libraries for ChIP-seq library preparation with Thruplex DNA Seq Library Prep kit (Takara).

treatment_protocol: MEF were infected with viruses encoding the  reprogramming factors with polybrene(4ug/ml)

value: Mouse Embryonic Fibroblast

tag: antibody

value: No antibody

value: Infected with MGT virus


title: Plate2-323-Liver

description: Plate 2_LIVER_C04

source_name: Liver


title: RNA-Hela-TLN68_Rep 6

city: Orsay

first: Olivier

last: Namy

address: Rue Gregor Mendel, bat 400

country: France

institute: CNRS, Université Paris-Sud

description: Cells are treated during 48h with TLN68

data_processing:
RiboDoc package
Sequenced reads were trimmed for adaptor sequence
Reads are mapped using bowtie2 and Hisat2 on Hg38
Differential expression is obtained using DESeq2 package
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Hela cell line

growth_protocol: HeLa cells were plated on day 0 (D0) at a density of 1 million cells per plate in 10 mL MEM supplemented with 10% fetal bovine serum, 1% Gln, non-essential amino acids and a mixture of antibiotics and antimycotics (Gibco).

extract_protocol:
the extraction is performed by adding 2x complete EDTA-free protease inhibitor (Roche) and 1 U per microliter murine RNase inhibitor (Biolabs ref: MO314S).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Small RNA preparation kits

treatment_protocol: Cells are treated during 48h with either DMSO, G418 (712µM) or TLN468 (80 µM), before the extraction of RNA.

value: Cell line


title: RNA-Hela-TLN68_Rep 4

description: Cells are treated during 48h with TLN68


title: H1963_sgMBD5_1_Rep2

description: cells transduced with MBD5 specific sgRNA #1 Replication 2

value: Low passages (6-10)


title: BRD8_control

value: A382 cells expressing Cas9

value: Cas9-expressing A382 cells were infected with sgNeg lentivirus


title: Plate2-322-Liver

description: Plate 2_LIVER_F05

value: Male

value: Liver

value: 6:1 FTOH


title: H1963_sgMBD5_1_Rep1

description: cells transduced with MBD5 specific sgRNA #1 Replication 1


title: RNA-Hela-G418_Rep 3

description: Cells are treated during 48h with G418


title: RNA-Hela-TLN68_Rep 5

description: Cells are treated during 48h with TLN68


title: Plate2-321-Liver

description: Plate 2_LIVER_B02

value: mg/kg

value: water/tween

value: TempO-Seq


title: MGT_Mef2c_rep1

description: MGT_M_R1_CHIP_GTTCCAAT-AATTCTGC_S41_ME_peaks.narrowPeak

value: anti-Mef2c, ab211493


title: MA_Mef2c_rep2_input

description: MA_M_R2_CHIP_GCGCAAGC-TCACGCCG_S39_ME_peaks.narrowPeak

value: Infected with Ascl1, Mef2c  virus


title: MGT_Mef2c_rep2


title: H1963_sgNONT_Rep2

description: cells transduced with non-targeting shRNA Replication 2

value: small cell lung cancer

value: normal cells


title: MA_Mef2c_rep1_input

description: MA_M_R1_CHIP_ATATGGAT-CTGTATTA_S37_ME_peaks.narrowPeak

value: Mouse Embryonic Fibroblast


title: RNA-Hela-G418_Rep 2

description: Cells are treated during 48h with G418


title: MA_Mef2c_rep2


title: H1963_sgNONT_Rep1

description: cells transduced with non-targeting shRNA Replication 1


title: 293T_H3K27me3

description: normal cells

value: kidney cell

tag: chip antibody


title: Plate12-315-Kidney

description: Plate 12_KIDNEY_A04

source_name: Kidney

value: Sprague Dawley (SD)

value: Kidney

value: 10:2 FTOH

value: day


title: RNA-Hela-DMSO_Rep 3

description: Cells are treated during 48h with DMSO

value: Cell line

value: DMSO


title: MA_Mef2c_rep1


title: MGT_Mef2c_rep1_input

value: No antibody

value: Infected with MGT virus


title: H1963_sgMBD5_2_Rep1

description: cells transduced with MBD5 specific sgRNA #2 Replication 1

value: Low passages (6-10)

value: MBD5 depleted cells


title: Mef2c_Mef2c_rep2_input

description: M_M_R2_CHIP_GGAGCGTC-GTCCGTGC_S27_ME_peaks.narrowPeak

value: Infected with Mef2c virus


title: Plate12-314-Kidney

description: Plate 12_KIDNEY_F02

value: Male

value: mg/kg

value: water/tween

value: TempO-Seq


title: 293T_H3K4me3

description: normal cells

value: anti-H3K4me3 (CST #9751)

value: normal cells


title: 293T_H3K4me1

description: normal cells

value: kidney cell

value: anti-H3K4me1 (CST #5326)


title: Plate12-312-Kidney

description: Plate 12_KIDNEY_D04

value: Sprague Dawley (SD)

value: Kidney

value: 10:2 FTOH


title: RNA-Hela-DMSO_Rep 2

description: Cells are treated during 48h with DMSO

value: Cell line

value: DMSO


title: RNA-Hela-DMSO_Rep 1

description: Cells are treated during 48h with DMSO


title: Mef2c_Mef2c_rep1_input

description: M_M_R1_CHIP_AAGATACT-ACTTACAT_S25_ME_peaks.narrowPeak

value: Mouse Embryonic Fibroblast

value: No antibody


title: 293T_H3K27Ac

description: normal cells

value: Low passages (6-10)

value: anti-H3K27Ac (CST #8173)


title: Plate12-307-Kidney

description: Plate 12_KIDNEY_B02

value: Female

value: day


title: Mef2c_Mef2c_rep2

value: anti-Mef2c, ab211493

value: Infected with Mef2c virus


title: 293T_MBD6

description: normal cells

value: anti-MBD6 (home made)


title: Plate12-306-Kidney

description: Plate 12_KIDNEY_F03

value: mg/kg

value: water/tween

value: TempO-Seq


title: Mef2c_Mef2c_rep1


title: Plate12-317-Kidney

description: Plate 12_KIDNEY_B04

value: Sprague Dawley (SD)


title: mRNA 20_hifa si DMOG

city: GDANSK

first: Rafal

middle: A

last: Bartoszewski

address: Hallera 107

country: Poland

institute: Medical University of Gdansk

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
Raw sequence FASTQ files were uploaded to Qiagen's GeneGlobe Data Analysis Center and followed their analysis pipeline.
Differential expression was also analyzed with GeneGlobe using the DESeq2 option for normalization
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited Excel file containing each sample (columns) with UMI values for each microRNA

source_name: HUVEC

growth_protocol: Primary human umbilical vein endothelial cells (HUVEC) that were pooled from ten individual donors were purchased from Cellworks (Caltag Medsystems Ltd, UK) and cultured in EGM-2 Bulletkit Medium (Lonza). All experiments were conducted between passage 2 and 6 at a confluence of 70-80%.

extract_protocol: Total RNA (containing both mRNA and miRNA) was isolated using miRNeasy kit (Qiagen). RNA concentrations were calculated based on the absorbance at 260 nm. RNA samples were stored at -70°C until use.

treatment_protocol: Hypoxia was induced in a CO2/O2 incubator/chamber specific for hypoxia research (Invivo2 Baker Ruskin). Briefly, cells were cultured in 35 mm or 60 mm dishes (for RNA isolation and protein isolation, respectively) at 0.9% O2 for the time periods specified (PO2 was 10-12 mm Hg). Control cells were maintained in normoxia in a CO2/O2 incubator (Binder). The hypoxia mimetics – Dimethyloxalylglycine; N-(Methoxyoxoacetyl)-glycine (DMOG, Sigma, D3695) and CoCl2 (Sigma, 60818) were used at final concentrations of 200 µM and 1 mM for 16 h. siRNA transfections. siRNA for HIF1A (Ambion assay id s6539) and EPAS1 (Ambion assay id s4698) were purchased from Ambion. HUVECs were transfected using the Lipofectamine RNAiMax (Invitrogen, 13778030) according to manufacturer's protocol. The siRNAs were used at a final concentrations of 40 nM. The transfected cells were cultured for 2 days prior to further analysis. Ambion siRNA Negative Control 1 (Ambion assay id MC22484) was used as a control. After 24 h, the transfected cells were put into a hypoxia chamber or treated with CoCl2 or DMOG, whereas the control cells remained in an incubator in normoxic conditions.The RIP assay kit for miRNA (#RN1005, MBL) was used following the manufacturer’s protocol. HUVECs (80% confluence) from four 100 mm culture dishes were collected for each condition 17, 18. Cell lysis was conducted in hypoxia or normoxia using a cell scraper and ice-cold PBS and mi-Lysis Buffer(+) was added to the cell pellet. Lysates were snap-frozen and stored at -70°C until use. For immunoprecipitation, 15 µg of anti-EIF2C2/AGO2 (#RN003M, MBL) or mouse IgG2a (isotype control; # M076-3, MBL) and agarose beads (Pierce Protein A/G Agarose, #20421, Thermo Scientific) were used. RNA was isolated using a miRNeasy Mini Kit (Qiagen, Hilden, Germany). 700 µl of QIAzol Lysis Reagent was added to the washed beads and the obtained RNA was eluted in 30 µl of nuclease-free water and used in the next generation RNA sequencing experiments

tag: sample type

value: 10 donors derived endothelial cells

value: Treated for 16h with 1mM DMOG

tag: genotype/variation

value: with HIF1A knockdown


title: RNA-Hela-G418_Rep 1

description: Cells are treated during 48h with G418

value: Cell line

tag: treatment


title: Plate12-305-Kidney

description: Plate 12_KIDNEY_A03

value: Male

value: Kidney

value: 10:2 FTOH


title: mRNA 20_DMOG ctrl si

value: control sample


title: LacZ_Mef2c_rep2_input

description: LACZ_M_R2_CHIP_GCAATGCA-GGAACGTT_S19_ME_peaks.narrowPeak

tag: cell type

value: Mouse Embryonic Fibroblast

value: No antibody

value: Infected with LACZ virus


title: 293T_MBD5

description: normal cells

value: kidney cell

tag: passages

value: Low passages (6-10)

tag: cell line

value: anti-MBD5 (home made)

value: normal cells


title: 293T_BAP1

description: normal cells

value: anti-BAP1 (home made)


title: mRNA 20_hif2 si CoCl2

value: Treated for 16h with 200 µM CoCl2

value: with EPAS1 knockdown


title: mRNA 20_hif1a Si CoCl2

value: 10 donors derived endothelial cells


title: LacZ_Mef2c_rep1_input

description: LACZ_M_R1_CHIP_ATGGCATG-AAGGTACC_S17_ME_peaks.narrowPeak


title: Plate12-292-Kidney

description: Plate 12_KIDNEY_H03

tag: strain

value: Sprague Dawley (SD)

tag: tissue

value: mg/kg

value: water/tween

value: day

value: TempO-Seq


title: Plate12-291-Kidney

description: Plate 12_KIDNEY_C03

tag: Sex

value: Male

value: Kidney

tag: chemical

value: 10:2 FTOH


title: LacZ_Mef2c_rep2

value: Mouse Embryonic Fibroblast

value: anti-Mef2c, ab211493

value: Infected with LACZ virus


title: H510_Input

description: normal cells

value: small cell lung cancer

value: Low passages (6-10)


title: Plate12-289-Kidney

description: Plate 12_KIDNEY_C04

value: Female

tag: concentration

tag: unit


title: mRNA 20_CoCL2 ctrl si)

value: Treated for 16h with 200 µM CoCl2

value: control sample


title: LacZ_Mef2c_rep1


title: mRNA 20_hif si hypoxia 8h

value: 10 donors derived endothelial cells

value: Exposed to hypoxia (1 % Oxygen) for 8 hours

value: with EPAS1 knockdown


title: H510_MBD6

description: normal cells

value: anti-MBD6 (home made)

value: normal cells


title: H510_BAP1

description: normal cells

value: anti-BAP1 (home made)


title: Plate12-283-Kidney

description: Plate 12_KIDNEY_D03

value: Sprague Dawley (SD)

value: Male

value: mg/kg

tag: vehicle

value: water/tween

tag: duration

value: day

value: TempO-Seq


title: mRNA 20_hif2a si DMOG

value: Treated for 16h with 1mM DMOG


title: H1963_Input_sgMBD6_2

description: cells transduced with MBD6 specific sgRNA #2

value: small cell lung cancer

value: Low passages (6-10)

tag: genotype

value: MBD6 depleted cells


title: mRNA 20_hif1a si hypoxia 8h

value: with HIF1A knockdown


title: LacZ_Ascl1_rep1_input

description: LACZ_A_R1_CHIP_TGCGAGAC-CATTGTTG_S13_ME_peaks.narrowPeak

value: Mouse Embryonic Fibroblast

tag: antibody

value: No antibody

value: Infected with LACZ virus


title: Plate12-293-Kidney

description: Plate 12_KIDNEY_G03

value: Kidney

value: 10:2 FTOH

tag: platfrom


title: H1963_Input_sgMBD6_1

description: cells transduced with MBD6 specific sgRNA #1


title: LacZ_Ascl1_rep2

description: LACZ_A_R2_CHIP_CATAGAGT-TGCCACCA_S15_ME_peaks.narrowPeak

value: anti-Ascl1, ab74065


title: mRNA R_8h hypoxia

tag: sample type

value: 10 donors derived endothelial cells

value: Exposed to hypoxia (1 % Oxygen) for 8 hours

value: RISC complexes


title: H1963_Input_sgNONT

description: cells transduced with non-targeting shRNA

value: normal cells


title: Plate12-281-Kidney

description: Plate 12_KIDNEY_E03

value: Sprague Dawley (SD)

value: Male

value: mg/kg

value: water/tween

value: day


title: mRNA R_normoxia control

value: Normoxia exposed

tag: genotype/variation


title: Plate12-273-Kidney

description: Plate 12_KIDNEY_A02

value: TempO-Seq


title: Plate12-264-Kidney

description: Plate 12_KIDNEY_H02


title: mRNA R_2h hypoxia

tag: treatment

value: Exposed to hypoxia (1 % Oxygen) for 2 hours


title: Plate12-257-Kidney

description: Plate 12_KIDNEY_C02

value: Female


title: LacZ_Ascl1_rep1

tag: cell type

value: Mouse Embryonic Fibroblast

value: Infected with LACZ virus


title: H1963_ASXL3_sgMBD6_2

value: small cell lung cancer

tag: passages

value: Low passages (6-10)

tag: chip antibody

value: anti-ASXL3 (home made)

value: MBD6 depleted cells


title: MA_Ascl1_rep2_input

description: MA_A_R2_CHIP_TGGCCGGT-TAGAGCGC_S35_ME_peaks.narrowPeak

value: No antibody

value: Infected with Ascl1, Mef2c  virus


title: H1963_ASXL3_sgMBD6_1

tag: cell line


title: mRNA R_negative Igg

value: 10 donors derived endothelial cells

value: Nonspecific antibody used for immunoprecypitation of RISC

value: RISC complexes


title: LacZ_Ascl1_rep2_input


title: Plate12-238-Kidney

description: Plate 12_KIDNEY_B03

tag: strain

value: Sprague Dawley (SD)

tag: tissue

value: Kidney

value: 10:2 FTOH

value: mg/kg

value: water/tween


title: H1963_BAP1_sgMBD6_2

value: anti-BAP1 (home made)


title: H1963_ASXL3_sgNONT

value: normal cells


title: MA_Ascl1_rep1

description: MA_A_R1_CHIP_CAATTAAC-CGAGATAT_S33_ME_peaks.narrowPeak

value: Mouse Embryonic Fibroblast

value: anti-Ascl1, ab74065


title: MA_Ascl1_rep2


title: Plate12-237-Kidney

description: Plate 12_KIDNEY_E02

tag: Sex

value: Female

tag: chemical

value: day

value: TempO-Seq


title: MA_Ascl1_rep1_input

value: No antibody


title: mRNA 4_Hypoxia 2h

value: Exposed to hypoxia (1 % Oxygen) for 2 hours


title: Ascl1_Ascl1_rep2_input

description: A_A_R2_CHIP_GACGTCTT-GGTTCACC_S7_ME_peaks.narrowPeak

value: Infected with Ascl1 virus


title: Plate11-320-Liver

description: Plate 11_LIVER_G02

value: Liver

tag: concentration

tag: unit


title: Plate12-214-Kidney

description: Plate 12_KIDNEY_G02

value: Male

tag: vehicle

tag: duration


title: H1963_BAP1_sgNONT

value: small cell lung cancer

value: Low passages (6-10)

tag: genotype


title: Ascl1_Ascl1_rep1_input

description: A_A_R1_CHIP_AGTACTCC-AACCTGTT_S5_ME_peaks.narrowPeak

tag: antibody


title: mRNA 3_Hypoxia 16hr

tag: sample type

value: 10 donors derived endothelial cells

value: Exposed to hypoxia (1 % Oxygen) for 16 hours


title: Ascl1_Ascl1_rep2


title: mRNA 4_Normoxia (Control Group)

value: Normoxia exposed


title: H1963_BAP1_sgMBD6_1

value: anti-BAP1 (home made)

value: MBD6 depleted cells


title: Plate11-317-Liver

description: Plate 11_LIVER_C04

value: Sprague Dawley (SD)

value: 10:2 FTOH

value: mg/kg

value: water/tween

tag: platfrom


title: H1963_MBD6

description: normal cells

value: anti-MBD6 (home made)

value: normal cells


title: H1963_ASXL2

description: normal cells

value: anti-ASXL2 (home made)


title: Plate12-255-Kidney

description: Plate 12_KIDNEY_D02

value: Kidney

value: day

value: TempO-Seq


title: mRNA 3_Hypoxia 8h

tag: treatment

value: Exposed to hypoxia (1 % Oxygen) for 8 hours


title: Plate11-314-Liver

description: Plate 11_LIVER_E03

value: Male

value: Liver


title: Ascl1_Ascl1_rep1

tag: cell type

value: Mouse Embryonic Fibroblast

value: anti-Ascl1, ab74065

value: Infected with Ascl1 virus


title: H1963_ASXL1

description: normal cells

value: small cell lung cancer

tag: passages

value: Low passages (6-10)

value: anti-ASXL1 (home made)


title: mRNA 3_Hypoxia 2h

value: 10 donors derived endothelial cells

value: Exposed to hypoxia (1 % Oxygen) for 2 hours


title: mRNA R_16h hypoxia

value: Exposed to hypoxia (1 % Oxygen) for 16 hours

tag: genotype/variation

value: RISC complexes


title: mRNA 4_Hypoxia 8h


title: Plate11-313-Liver

description: Plate 11_LIVER_D04

value: Sprague Dawley (SD)

value: 10:2 FTOH

value: mg/kg

value: water/tween


title: H1963_BAP1

description: normal cells

tag: cell line

tag: chip antibody

value: anti-BAP1 (home made)

value: normal cells


title: mRNA 1_Hypoxia 16h


title: Plate11-303-Liver

description: Plate 11_LIVER_C02

tag: strain

value: Male

tag: tissue

value: Liver

value: day

value: TempO-Seq


title: LacZ_H3K27ac_rep2

description: LACZ_27_R2_CHIP_CGGACAAC-TCCGGATT_S11_ME_peaks.narrowPeak

value: Mouse Embryonic Fibroblast

value: Anti-Histone H3K27 antibody - ChIP Grade (ab4729)

value: Infected with LACZ virus


title: LacZ_H3K27ac_rep1_input

description: LACZ_27_R1_CHIP_TAAGTGGT-CTTAAGCC_S9_ME_peaks.narrowPeak

value: No antibody


title: Plate11-301-Liver

description: Plate 11_LIVER_F02

tag: Sex

tag: chemical


title: LacZ H3K27ac rep1


title: Plate11-296-Liver

description: Plate 11_LIVER_F03

value: Female

tag: concentration

tag: unit


title: Atac HD-MSNs_GM02173_#1

city: Saint Louis

first: Youngmi

last: Oh

state: MO

address: 660 S. Euclid Avenue

department: Development department

institute: Washington University in St. Louis

data_processing:
At least 45 million omni-ATAC reads per sample were processed by Atac-seq Integrative Analysis Pipeline (AIAP, https://github.com/Zhang-lab/ATAC-seq_QC_analysis).
AIAP trims adapters using Cutadapt
AIAP aligns fragments using BWA-MEM to the hg38 human reference genome
AIAP removes low quality reads using methylQA
AIAP normalizes count signal by 10 million input single end reads
AIAP call peaks by macs2 with q-value less than 0.01
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files of biological replicates for ATAC-seq experiments

growth_protocol: Direct neuronal reprogramming of human fibroblasts to neurons was performed as previously described (Abernathy et al., 2017; Richner et al., 2015).

extract_protocol:
Omni-ATAC-seq preparation was performed as outlined in Corces et al. (Corces et al., 2017)
Omni-ATAC-seq preparation was performed as outlined in Corces et al. (Corces et al., 2017)

value: Coriell GM02173

tag: overexpression 1

tag: overexpression 2

value: CTIP2, DLX1, DLX2, MYT1L


title: Plate11-293-Liver

description: Plate 11_LIVER_D02

value: Sprague Dawley (SD)

tag: vehicle

tag: duration


title: Atac HD-MSNs_GM02173_#2


title: MA_H3K27ac_rep2_input

description: MA_27_R2_CHIP_CGTTAGAA-TTCAGGTC_S31_ME_peaks.narrowPeak

tag: antibody

value: Infected with Ascl1, Mef2c  virus


title: Atac HD-MSNs_GM04198_126

value: Coriell GM04198


title: Plate11-285-Liver

description: Plate 11_LIVER_H02

value: 10:2 FTOH

value: mg/kg

value: water/tween

tag: platfrom


title: Atac HD-MSNs_GM04198_125


title: MA_H3K27ac_rep1_input

description: MA_27_R1_CHIP_TACCGAGG-CCTGAACT_S29_ME_peaks.narrowPeak

tag: cell type

tag: treatment


title: RNA 20_hif2a si DMOG

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
STAR version 2.7.3a was used to align the raw sequences to the human genome using parameters: --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Cufflinks version 2.2.1 was used to estimate transcript abundances using parameters: --library-type fr-firststrand -G -L
Cuffmerge merged the samples together and Cuffdiff (using default parameters) was used for differential expression
Genome_build: Gencode GRCh38 p13 Release 32
Supplementary_files_format_and_content: tab-delimited Excel files with sample (columns) and their respective FPKM values for each gene (rows)

tag: sample type

value: 10 donors derived endothelial cells

value: Treated for 16h with 1mM DMOG

tag: genotype/variation

value: with EPAS1 knockdown


title: LacZ_H3K27ac_rep2_input