title: KDR-siRNA_PBS_rep2

city: Salt Lake City

first: Mary Elizabeth

last: Hartnett

state: Utah

address: 65 Mario Capecchi Dr

department: Ophthalmology and Vision Sciences

institute: University of Utah

data_processing:
Fastq reeads were de-duplicated of optical duplicates only using BBMap Clumpify (version 38.34) with an optical distance of 12000.
Fastq reqds were trimmed using Cutadapt (version 1.16) with adapter sequences AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT,  a minimum matching adapter overlap of 6 bp (option -O 6), and a minimum output read length of 20 bp (option -m 20).
Fastq reads were aligned to the human genome using STAR (version 2.7.9a) with basic two pass mode using an index built using Ensembl GRCh38 annotation (release 104).
Gene counts were collected with Subread featureCounts (version 1.6.3) using Ensembl GRCh38 annotation (release 104), counting paired-end alignments (option -p), counting reverse-strand alignments (option -s 2), and recording only those overlapping genes with the greatest overlap (option --largestOverlap).
Assembly: GRCh38, Ensembl Release 104
Supplementary files format and content: Gene count table from featureCounts

source_name: retina

extract_protocol:
HRMECs were lysed in buffer RLT supplemented with β-mercaptoethanol (1:100, Sigma-Aldrich, St. Louis, MO, USA) and RNA was isolated from lysates using the Qiagen RNeasy Kit following the protocol provided by the manufacturer (Qiagen, Valencia, CA, USA).
Intact poly(A) RNA was purified from total RNA samples (10-500 ng) using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490Stranded RNA sequencing libraries were prepared as described using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L).  Purified libraries were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 5 nM in preparation for Illumina sequence analysis.

value: retina

tag: cell type

value: microvascular endothelial cells

value: KDR siRNA

value: PBS


title: KDR-siRNA_VEGF_rep3

status: Public on Dec 28 2022

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

tag: genotype

tag: treatment

value: VEGF


title: KDR-siRNA_VEGF_rep1


title: QZ3

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

data_processing:
Adapters were trimmed during demultiplexing by the core facility and trimmed reads were aligned to the genome using RNA-Seq Alignment version 1.1.1 (Illumina BaseSpace software application). The application uses STAR for alignment to the mouse genome (UCSC mm10) and Salmon was used to generate count tables.
Differential expression analysis of count tables was performed using the default settings of DESeq2 (Benjamini-Hochberg FDR correction).
Assembly: mm10
Supplementary files format and content: Microsoft Excel Worksheet (.xlsx), contains counts from DESeq2 used for differential expression analysis.

molecule: total RNA

organism: Mus musculus

source_name: Cerebellum

growth_protocol: Male and female YY1-floxed and GFAP-cre mice were purchased from the Jackson Laboratory (Bar Harbor, ME). Animals were kept on a 12 hour light-dark cycle. Food and water were provided ad libitum. Mice were group housed. After delivery, YY1-floxed and YY1-cKO mice were kept up to 12 weeks prior to euthanization by rapid decapitation.

extract_protocol:
The cortex, midbrain and cerebellum were dissected and rapidly frozen in liquid nitrogen and stored at -80 degrees. Total RNA was extracted from the entire tissue from each animal using TRIZol Reagent (Life Technologies) and RNA clean and concentrator-5 with DNase I (Zymo Research) according to manufacturer’s directions. mRNA was isolated from the total RNA using an NEBNext Poly(A) mRNA Magnetic Isolation Module as per instructions (New England Biolabs).
cDNA libraries were generated from the isolated mRNA using an NEBNext Ultra RNA library prep kit for Illumina (New England Biolabs) and 8 nucleotide i7 and i5 dual-index primers (NEBNext multiplex oligos for Illumina, Dual Index Primers) were incorporated into each sample.  The library construction was done according to NEB instructions, modified for use with a Beckman Biomek 4000 at the Florida State University Biological Sciences core lab.  The unique dual-index (barcode) primers were added to each library to multiplex the forty-two libraries. The multiplexed sample was quantified with qPCR (Kapa Biosystems) specific for Illumina sequencing primers and the average fragment size was determined with a Bioanalyzer high sensitivity DNA chip (Agilent Technologies). The pooled sample was sequenced, with paired-end, 50 base reads on an Illumina NovaSeq 6000 located in the Translational Science Laboratory at the College of Medicine, Florida State University.  The pooled data were demultiplexed into individual sample data.

tag: age

value: 12 weeks

tag: strain

tag: Sex

value: Male

value: astrocytic Yy1-cKO


title: KDR-siRNA_VEGF_rep2


title: KDR-siRNA_PBS_rep1


title: control-siRNA_VEGF_rep3

value: control siRNA


title: control-siRNA_VEGF_rep2


title: QZ2


title: control-siRNA_PBS_rep3


title: QY7

source_name: Midbrain

value: Female


title: QY4


title: HTyr treatment (bio rep 3)

city: Verona

first: Marzia

last: Rossato

state: Italy

address: Strada Le Grazie,15

department: Department of Biotechnology

country: Italy

institute: University of Verona

data_processing:
Raw reads  with  more  than  10%  of undetermined bases or more than 50 bases with a quality score <7 were discarded. Subsequently, reads were clipped from adapter sequences using Scythe software , and low-quality ends (Q score <20 on a 15-nt window) were trimmed with Sickle
Filtered reads were aligned to the Human reference genome GRCh38 using STAR aligner
Gene  expression  quantification  has  been  performed  using  RSEM  and  Ensembl  v104  annotation.
Supplementary files format and content: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: The human CRC-derived cell lines, HCT116 and LoVo, were acquired from the American Type Culture Collection (ATCC, Manassas, VA, USA) and cultured at 37°C under 5% CO2 in RPMI 1640 (Life Technologies, Carlsbad, CA, USA) supplemented with 10% v/v fetal bovine serum (Life Technologies, Carlsbad, CA, USA), 2 mM L-glutamine, 100 U mL−1 penicillin/streptomycin

extract_protocol:
Total RNA was extracted from cells in culture with Trizol (Invitrogen, Carlsbad, CA, USA), following the manufacturer’s instructions
RNA-seq librarieswere generated using the TruSeq stranded mRNA kit (Illumina) from 1000 ng of RNA samples, after poly(A) capture and according to manufacturer’s instructions.

treatment_protocol: In all experiments, HCT116 cells were treated with 0.0154 mg mL−1 HTyr or 0.0154 mg mL−1 OPWPs extracts for 72 h; LoVo cells were treated with 0.0231 mg mL−1 HTyr or 0.0231 mg mL−1 OPWPs extracts for 72 h

tag: cell line

value: colorectal cancer cells

value: WT

value: HTyr treatment


title: QY6


title: control-siRNA_PBS_rep1


title: control-siRNA_PBS_rep2


title: QY5


title: control-siRNA_VEGF_rep1


title: QY2


title: JGCT02

type: genomic

city: New York

first: Varshini

last: Vasudevaraja

state: NY

address: 240 E 38th street

department: Pathology

institute: NYU Langone Health

description: DNA methylation data from juvenile granulosa cell tumors

hyb_protocol: The DNA is bisulfite-converted using the EZ-96 DNA Methylation Kit from Zymo Research.  After bisulfite conversion, the DNA then undergoes restoration using the Illumina Infinium HD FFPE DNA Restore Kit. The DNA then undergoes a whole-genome overnight amplification.  The amplified DNA is then enzymatically fragmented using end-point fragmentation.  The DNA is then isolated and precipitated in isopropanol and re-suspended in Illumina RA1 buffer.  The re-suspended DNA is then denatured at 95⁰C, and the resulting single-stranded DNA is dispensed directly onto the Illumina Array for hybridization.  The DNA hybridizes with the array overnight in an oven at 48⁰C.  After hybridization, the BeadChips are then washed with Illumina PB1 buffer to remove any unhybridized and non-specifically hybridized DNA.

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: minfi- R package was used to analyze the data. Data was preprocessed and quantile normalized.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Genomic DNA from ovarian juvenile granulosa cell tumors

label_protocol: Standard Illumina Protocol

extract_protocol: Using a Promega Maxwell 16 instrument, DNA was extracted from formalin-fixed paraffin-embedded (FFPE) specimens with the Maxwell® 16 FFPE Plus LEV DNA Purification Kit

value: ovary

tag: gender


title: QY3


title: QY1


title: QX7


title: HTyr treatment (bio rep 1)


title: QX6

source_name: Cortex


title: QZ1


title: OPWPs from Sicily treatment  (bio rep 3) [T3]

value: OPWPs treatment


title: OPWPs from Sicily treatment  (bio rep 1) [T1]


title: QX5


title: QX4


title: OPWPs from Sicily treatment  (bio rep 2) [T2]


title: OPWPs from Tuscany treatment (bio rep 3) [S3]


title: OPWPs from Tuscany treatment (bio rep 2) [S2]


title: QX3


title: OPWPs from Tuscany treatment (bio rep 1) [S1]


title: QX2


title: HTyr treatment (bio rep 2)


title: PZ4


title: PZ5


title: OPWPs from Apulia treatment  (bio rep 1) [P1]


title: Control samples (bio rep 3)

value: Control samples


title: Control samples (bio rep 2)


title: OPWPs from Apulia treatment  (bio rep 2) [P2]


title: Control samples (bio rep 1)


title: OPWPs from Apulia treatment  (bio rep 3) [P3]


title: PZ1


title: PY7


title: PZ3


title: PZ7


title: HTM cells, LV-TIPARP, rep 3

city: Shanghai

first: Youjia

last: Zhang

address: 83 Fenyang Road

country: China

institute: Eye & ENT Hospital

data_processing:
CLC Genomics Workbenchv 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to NCBI_GRCh38.p13 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Human trabecular meshwork cells were transduced with lentivirus-GFP-TIPARP to upregulate the expression of TIPARP.

growth_protocol: Primary human trabecular meshwork cells, purchased from ScienCell (Carlsbad, CA), was cultured in Trabecular Meshwork Cell Medium (TMCM, Cat. #6591) at 37 °C under 5% CO2, according to the manufacturer's instructions. For HTM cell characterization, dexamethasone (500 nM) was added to the HTM cell medium for 5 days. The control group was cultured without dexamethasone. The expression of myocilin was measured using both Western blot analyses and immunocytochemistry.

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
Then the libraries were constructed using TruSeq Stranded mRNALTSample Prep Kit(Ilumina,San Diego, CA, USA) . 1 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: HTM cells were transduced with lentivirus-GFP-TIPARP to upregulate the expression of TIPARP. Lentivirus-GFP was used as a control. Lentivirus-GFP-TIPARP and lentivirus-GFP were produced by Hanheng (Shanghai, China). According to the manufacturer’s instructions, lentivirus-GFP-TIPARP and lentivirus-GFP were diluted in complete medium containing 8 µg/mL polybrene at a final multiplicity of infection (MOI) of 15.

value: HTM

value: human trabecular meshwork cell

value: TIPARP upregulated

value: lentivirus-GFP-TIPARP


title: HTM cells, LV-TIPARP, rep 2


title: PY6


title: PZ2


title: HTM cells, LV-TIPARP, rep 1


title: PY5


title: HTM cells, LV-GFP, rep 3

source_name: Human trabecular meshwork cells were transduced with lentivirus-GFP.

value: NC

value: lentivirus-GFP


title: PZ6

value: 12 weeks


title: PY4

value: Male


title: HTM cells, LV-GFP, rep 2


title: KDR-siRNA_PBS_rep3

value: retina

value: microvascular endothelial cells

value: KDR siRNA

value: PBS


title: PY2


title: PY3


title: 231_Synchronized RNA-seq_control

city: BEIJING

first: Haili

last: Qian

address: 17 South Panjiayuan Lane, Chaoyang District

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
After all the fastq files were quality controlled, BAM files and FPKM values of transcripts were analyzed with HISAT2 and StringTie, data were mapped with the GRCH38 genome, and the frequency of alternative splicing was calculated with rmats4.0.1.
Assembly: GRCH38 genome
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: MDA-MB-231 cell lines were cultured in DMEM plus 10% FBS. All cells were maintained in humidified incubators with 5% CO2.

extract_protocol:
MDA-MB-231 cells were collected with trypsin digestion and washed with PBS, and RNA was extracted using TRIzol.
After strand-specific library construction, Novaseq6000 was used for sequencing, and the raw data of each sample were more than 10 Gb.

treatment_protocol: Cells were plated into 6 cm dishes in complete media at 30% confluency and allowed to attach for 16 hours. For MDA-MB-231 cells, the first round of blockade was carried out by treatment with 2 mM thymidine for 22 hr, 3 washes with PBS, and then supplementation with fresh complete media for 8 hr; in the second round of blockade, the cells were treated with 2 mM thymidine for 18 hr, and successful blockade of the cell cycle in G1/S phase was confirmed.

value: Breast cancer cells

value: WT

value: Control

tag: time

value: without treatment


title: PY1


title: 231_Synchronized RNA-seq_double-thymidine_Nocodazole_ActinomycinD_time 5

value: When MDA-MB-231 cells were released from G1/S phase, 1 ug/ml nocodazole was added, and after 10 hr, they were supplemented with 5 ug/ml actinomycin D.

value: with Actinomycin D for 6h


title: 231_Synchronized RNA-seq_double-thymidine_Nocodazole_ActinomycinD_time 4

value: with Actinomycin D for 4.5h


title: PX6

value: Female


title: 231_Synchronized RNA-seq_double-thymidine_Nocodazole_ActinomycinD_time 3

value: with Actinomycin D for 3h


title: PX5


title: 231_Synchronized RNA-seq_double-thymidine_Nocodazole_ActinomycinD_time 2

value: with Actinomycin D for 1.5h


title: HTM cells, LV-GFP, rep 1

value: HTM

value: human trabecular meshwork cell

value: NC

value: lentivirus-GFP


title: PX4

value: 12 weeks

value: Male


title: 231_Synchronized RNA-seq_double-thymidine_Nocodazole_ActinomycinD_time 1

value: with Actinomycin D for 0h


title: PX7


title: PX3


title: 26-FU: Fundus_undifferentiated_rep3

type: RNA

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Infection Biology

description: non transformed human primary cells

hyb_protocol: Hybridization of 0.75 µg was performed according to the supplier's protocol (Agilent Technologies)

scan_protocol: Scanning was performed with 3 µm resolution using the G2565CA Agilent high-resolution laser microarray scanner

data_processing: Microarray images were processed using default settings of the Agilent Feature Extraction software (G2567AA, Version A.10.10.1) and the GE1_1105_Oct12 protocol. Extracted single-color raw data txt files were further analyzed in the R/Bioconductor environment and the package limma. Background correction was perfomred using normexp with offset 15 and the data were normalized by quantile normalization.

source_name: undifferentiated fundus mucosoids

label_protocol: RNA was labeled with the Agilent single-color Low Input Quick Amp Labeling Kit according to the manufacturer's protocol

growth_protocol: Human primary gastric epithelial cells were isolated and cultivated as described in Boccellato et al., 2018, Gut

extract_protocol: Total RNA was isolated folllowing the Trizol extraction method protocol

treatment_protocol: Differentiation was induced by removing Wnt and R-spondin from the cell culture medium for seven days

value: stomach

value: female


title: hGAT26 A 5aza: Antrum_undifferentiated_5aza_rep2

description: non transformed human primary cells

source_name: undifferentiated antrum mucosoids 5aza

treatment_protocol: Differentiation was induced by removing Wnt and R-spondin from the cell culture medium for seven days. 5-aza-2'-deoxycytidine treatment was performed for 10 days by adding 4 µM 5-aza-2'-deoxycytidine every 24h.

value: undifferentiated antrum mucosoids 5aza


title: 26-FD: Fundus_differentiated_rep3

description: non transformed human primary cells

source_name: differentiated fundus mucosoids


title: Mouse #17, 34BC-D

city: Hannover

first: Tobias

last: Maetzig

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

description: Galaxy27-(N2696_N2698_N2705_vs_N2704_N2697_N2699_DESeq2_result_overview)   Galaxy54-(N2996_N2698_N2705_vs._N2700_N2702_N2703_DESeq2_result_overview)

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina).
Reads of sequence read 2 (R2) fastq data were trimmed with the Linux command ‘awk’ to remove the first 8 nucleotides.
Raw data processing was conducted by use of nfcore/rnaseq (v 1.4.2). The pipeline uses Nextflow ( v20.01.0) workflow tool and includes read trimming (Trim Galore! v0.6.4), alignment (STAR v2.6.1d), and counting (featureCounts  v1.6.4).
Normalization and differential expression analysis was performed with DESeq2 (Galaxy Tool v2.11.40.2) with default settings except for “Output normalized counts table”, “Turn off outliers filtering”, and “Turn off independent filtering”, all of which were set to “True”.
Assembly: GRCm38.p6; release M25
Supplementary files format and content: Tab-delimited text files include normalized espression values as a matrix table for all or a part of the samples (DESeq2 output)

source_name: spleenocytes; leukemic

extract_protocol:
Sorting of cells directly into RLT-buffer and RNA extraction by RNeasy Micro Kit (Qiagen).
Library generation:   0.67ng  of total RNA were used for library preparation with the ‘SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian – 96 Rxns’ (#634487; Takara Bio USA, Inc.) according to conditions recommended in user manual #120720. Generated libraries were barcoded by dual indexing approach and were finally amplified with 13 cycles of pcr. Fragment length distribution of generated libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific).    Sequencing run:   Equal molar amounts of ten libraries were pooled for a common sequencing run. Accordingly, each analyzed library constitutes 10% of overall flowcell capacity. The library pool was denatured with NaOH and was finally diluted to 1.3pM. 1.3 ml of denatured pool was loaded on an Illumina NextSeq 550 sequencer using a High Output Flowcell for single reads (20024906; Illumina). Sequencing was performed with the following settings: Sequence reads 1 and 2 with 38 bases each; Index reads 1 and 2 with 8 bases each.

tag: replicates

value: stably expanded replicate

tag: cultivation

value: clonally-derived sample


title: 26-AU: Antrum_undifferentiated_rep3

description: non transformed human primary cells

source_name: undifferentiated antrum mucosoids


title: 26-CU: Corpus_undifferentiated_rep3

description: non transformed human primary cells

source_name: undifferentiated corpus mucosoids


title: Mouse #17, 33BC-D

description: Galaxy23-(N2700_N2702_N2703_vs_N2704_N2697_N2699_DESeq2_result_overview)   Galaxy27-(N2696_N2698_N2705_vs_N2704_N2697_N2699_DESeq2_result_overview)

value: de novo expanded replicate


title: hGAT23 A 5aza: Antrum_undifferentiated_5aza_rep1

description: non transformed human primary cells


title: hGAT26 A Mock: Antrum_undifferentiated_mock_rep2

description: non transformed human primary cells

source_name: undifferentiated antrum mucosoids mock

value: undifferentiated antrum mucosoids mock

value: mock


title: 24-FD: Fundus_differentiated_rep2

description: non transformed human primary cells

value: male


title: 231_Synchronized RNA-seq_double-thymidine_time 10

value: Breast cancer cells

value: WT

value: double-thymidine

value: 16h after G1/S phase release


title: hGAT23 A Mock: Antrum_undifferentiated_mock_rep1

description: non transformed human primary cells


title: 26-AD: Antrum_differentiated_rep3

description: non transformed human primary cells

source_name: differentiated antrum mucosoids


title: PX2


title: 231_Synchronized RNA-seq_double-thymidine_time 9

value: 13h after G1/S phase release


title: Mouse #15, 43BC-D

description: Galaxy23-(N2700_N2702_N2703_vs_N2704_N2697_N2699_DESeq2_result_overview)   Galaxy54-(N2996_N2698_N2705_vs._N2700_N2702_N2703_DESeq2_result_overview)

source_name: spleenocytes; pre-leukemic

value: preleukemic replicate


title: 23-FU: Fundus_undifferentiated_rep1

description: non transformed human primary cells


title: 26-CD: Corpus_differentiated_rep3

description: non transformed human primary cells

source_name: differentiated corpus mucosoids


title: Oncotice (oncoT)_HTO

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

description:
OncoT_barcodes.tsv.gz
OncoT_features.tsv.gz
OncoT_matrix.mtx.gz

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Sequence read quality was evaluated from FastQC.
Human Total-Seq C Hashtag antibodies [1, 2 and 3] (Biolegend) were used for individual multiplexing
Assembly: GRCh38-2020-A
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

molecule: protein

source_name: PBMC

extract_protocol:
After co-culture of PBMC with BCG, for 7 days in RPMI complete medium, high viability single-cell suspensions were obtained using the Dead Cell Remove Kit (Miltenyi Biotec), and cells were pooled and resuspended in PBS+0.04% BSA prior to sequencing
[library construction protocol: Low Input]  Library was generated according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads to generate partitioned cells (GEMs, Gel beads-in-Emulsion). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, incorporating an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate size fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
[chemistry]  SC5P-R2 with sample multiplexing

tag: individual

value: 3 healthy donors

value: PBMC

value: BCG sub-strain Oncotice

tag: hto

value: C0251_TotalSeqC Antibody Capture (donor 1), C0252_TotalSeqC Antibody Capture (donor 2), C0253_TotalSeqC Antibody Capture (donor 3)


title: Mouse #15, 38BC-D


title: 231_Synchronized RNA-seq_double-thymidine_time 7

value: 10h after G1/S phase release


title: 24-CD: Corpus_differentiated_rep2

description: non transformed human primary cells

value: stomach


title: Oncotice (oncoT)_GEX

library_source: transcriptomic single cell


title: 231_Synchronized RNA-seq_double-thymidine_time 6

value: 9h after G1/S phase release


title: 24-CU: Corpus_undifferentiated_rep2

description: non transformed human primary cells


title: 23-CD: Corpus_differentiated_rep1

description: non transformed human primary cells

value: female


title: 23-AU: Antrum_undifferentiated_rep1

description: non transformed human primary cells


title: 231_Synchronized RNA-seq_double-thymidine_time 5

value: 7h after G1/S phase release


title: 231_Synchronized RNA-seq_double-thymidine_time 4

value: 6h after G1/S phase release


title: Mouse #14, 43BC-D

value: de novo expanded replicate

value: clonally-derived sample


title: iBCG (IBCG)_GEX

description:
IBCG_barcodes.tsv.gz
IBCG_features.tsv.gz
IBCG_matrix.mtx.gz

value: BCG sub-strain iBCG


title: Mouse #13, 38BC-D


title: 24-FU: Fundus_undifferentiated_rep2

description: non transformed human primary cells

value: male


title: Mouse #13, 34BC-D

value: stably expanded replicate


title: 231_Synchronized RNA-seq_double-thymidine_time 3

value: Breast cancer cells

value: WT

value: double-thymidine

value: 4.5h after G1/S phase release


title: Mouse #14, 34BC-D


title: PX1

value: 12 weeks

value: Male


title: 24-AD: Antrum_differentiated_rep2

description: non transformed human primary cells


title: 23-FD: Fundus_differentiated_rep1

description: non transformed human primary cells


title: 231_Synchronized RNA-seq_double-thymidine_time 8

value: 11.5h after G1/S phase release


title: 24-AU: Antrum_undifferentiated_rep2

description: non transformed human primary cells

value: stomach


title: 23-CU: Corpus_undifferentiated_rep1

description: non transformed human primary cells


title: 23-AD: Antrum_differentiated_rep1

description: non transformed human primary cells


title: Mouse #15, 33BC-D

value: preleukemic replicate


title: iBCG (IBCG)_HTO

value: 3 healthy donors

value: PBMC

value: C0251_TotalSeqC Antibody Capture (donor 1), C0252_TotalSeqC Antibody Capture (donor 2), C0253_TotalSeqC Antibody Capture (donor 3)


title: T128-hm5-vac

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

data_processing:
Raw reads were trimmed for low quality reads and miscalled nucleotides using Trimmomatic v. 0.36.
Reads that passed the trimming step were aligned to rhesus macaque genome (Ensembl Mmul_8.0.1 release 88) using the STAR aligner (version 2.5.3a).
Aligned reads were counted using HTSeq (version 0.9.1).
Genome_build: Ensembl Mmul_8.0.1 release 88.
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample.

organism: Macaca mulatta

source_name: Whole Blood

extract_protocol:
RNA was extracted from PAXgene samples using the PAXgene Blood RNA kit (PreAnalytiX) according to the manufacturer’s instructions. GLOBINclear kit (Ambion, Austin, TX, USA) was used to remove globin transcript.
Libraries were loaded on Illumina Truseq Paired-End stranded mRNA Kits.

tag: animal id

tag: timepoint

value: old

tag: time of acquisition


title: 231_Synchronized RNA-seq_double-thymidine_time 2

tag: cell type

value: 3h after G1/S phase release


title: 231_Synchronized RNA-seq_double-thymidine_time 1

value: 0h after G1/S phase release


title: T128-h24-vac


title: ZYQ_post

city: Chongqing

first: Xiaoming

last: Bai

address: Zhongshan Road, Yuzhong district

institute: children's hospital of chongqing medical universty

description: 10x Genomics

data_processing:
The 10x Genomics Cell Ranger (7.0.1 version) pipeline was used to demultiplex raw files into FASTQ files, extract barcodes and UMI, filter, and map reads to the corresponding reference genome, and generate a matrix containing UMI counts.
A 10x Genomics Cell Ranger pipeline was used to identify clonotypes by alignment and annotation with the default settings.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
The protoplast suspension was loaded into Chromium microfluidic chips with 30 (v3) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (NovaSeq 6000) according to the manufacturer’s instructions (Illumina).
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger) using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat
In brief, for each gene and each cell barcode (filtered by CellRanger), unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells.

tag: tissue

value: Immune cell


title: T127-h24-vac


title: Jurkat Tat, PMA/Ion [KB1-PMA-1]

city: Vancouver

first: Ivan

last: Sadowski

state: British Columbia

address: 2350 Health Sciences Mall

country: Canada

institute: University of British Columbia

data_processing:
De-multiplexed read sequences were aligned to the reference sequence using STAR.
featureCounts was used to count the number of reads per annotated genome.
Counts were analyzed by DESeq2 analysis.
Assembly: hg38
Supplementary files format and content: Galaxy420-Normalized_counts_file_on_KB1_vs_KB1_P_I.txt: Tab-delimited text file includes featureCounts counts.
Supplementary files format and content: Galaxy418-DESeq2_KB1_vs_KB1_P_I.tab: Tab-delimited text file includes DESeq2 results file.

source_name: Jurkat Tat

growth_protocol: Jurkat Tat cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen) and used for the construction of sequencing libraries.
Qualifying samples were prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs).

treatment_protocol: T cell activation was elicited by incubating with 10 nM PMA and 1 μM Ionomycin for 4 hrs.

value: Jurkat Tat

value: T lymphocyte

tag: genotype

value: PMA/Ionomycin

tag: time point

value: 4 hrs


title: Jurkat Tat, PMA/Ion [KB1-PMA-3]

value: WT

tag: treatment


title: F2 -  Blue Light positive

city: Nagoya

first: Koichi

last: Inoue

state: Aichi

address: 1 Kawasumi Mizuho-cho, Mizuho-ku

department: Department of Integrative Anatomy

country: Japan

institute: Nagoya City University School of Medical Sciences

description: Gene expression data fromF2 cells transfected with hBACCS2 and irradiated with blue light

hyb_protocol: Following fragmentation, 2.3 ug of cDNA were hybridized for 16 hr at 45C on mouse Clariom S Assay. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with Microarray Data Analysis Tool Ver3.2 pvovided by Filgen Inc. (Nagoya, Japan).

label: biotin

source_name: F2 -  Blue Light positive

label_protocol: Biotinylated cDNA were prepared from 250 ng total RNA using GeneChip WT PLUS Reagent Kit according to the manufacturer's protocol

growth_protocol: Mouse vascular endothelial  F2 cells were transfected with either hBACCS2-expressing plasmid or mock plasmid.

extract_protocol: Column extraction (Nucleospin RNA plus, Takara) of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Those cells were irradiated with blue light (470 nm, ~0.4 mW/mm-2) for 2 min, followed by 18 min interval, for 4 hours.

tag: treatement

value: hBACCS2 transfection and blue light irradiation

tag: strain

value: heterologous BALB/c and C57BL/6 background

tag: properties

value: vascular endothelial cell propertes

tag: cell

value: a cell line oritented from UV irradiation-induced tomor


title: CYT_post

description: 10x Genomics


title: Jurkat Tat, PMA/Ion [KB1-PMA-2]

tag: cell line


title: F2 -  Blue Light negative

description: Gene expression data fromF2 cells transfected with hBACCS2

source_name: F2 -  Blue Light negative

value: hBACCS2 transfection


title: Jurkat Tat [KB1-3]

value: Untreated


title: T126-hm5-vac

tag: age


title: ZZY_post

description: 10x Genomics

value: PBMC


title: Jurkat Tat [KB1-1]


title: T125-hm5-vac


title: Jurkat Tat [KB1-2]


title: T125-h24-vac


title: CYT_pre

description: 10x Genomics


title: FXX_pre

description: 10x Genomics


title: T123-hm5-vac


title: ZZY_pre

description: 10x Genomics


title: T127-hm5-vac


title: T123-h24-vac


title: Jurkat Tat, TFII-I shRNA rep1

data_processing:
De-multiplexed read sequences were  aligned to the reference sequence using STAR
featureCounts was used to count the number of reads per annotated genome
Counts were analyzed by DESeq2 analysis
Assembly: hg38
Supplementary files format and content: tab-delimited text files include DESeq2 results file

growth_protocol: Jurkat Tat cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) and used for the construction of sequencing libraries.
Qualifying samples were  prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs).

treatment_protocol: T cell activation was elicited by incubating with 10 nM PMA and 1 μM Ionomycin for 4 hrs

value: TFII-I knockdown

value: PMA/Ionomycin activation

tag: time


title: Jurkat Tat, TFII-I shRNA rep3


title: Jurkat Tat, TFII-I shRNA rep2


title: Jurkat Tat, LKO rep3

value: shRNA control


title: 086_TRK_SX

city: Birmingham

first: Kaleen

middle: M

last: Lavin

state: Alabama

address: 908 20th Street South, Room 201-C

institute: University of Alabama at Birmingham

data_processing:
STAR (v2.6+) was used to align RNA to human genome (GCHr38)
Count data were generated using featureCounts
Assembly: GCHr38
Supplementary files format and content: tsv file containing read counts for all genes and samples

source_name: Skeletal Muscle

extract_protocol:
bead homogenization in Qiazol, Qiagen miRNeasy Kit
SMARTer Stranded Total RNA-Seq kit v2 Pico Input Mammalian  and SMARTer RNA Unique Dual Index Kit

value: Skeletal Muscle

tag: Sex

value: Female

tag: limb

value: Surgical (SX)


title: T121-hm5-vac

tag: animal id

value: old


title: FXX_post

description: 10x Genomics

value: Immune cell


title: Jurkat Tat, LKO rep2

value: Jurkat Tat

value: T lymphocyte

value: 4 hrs


title: T126-h24-vac

tag: timepoint


title: T121-h24-vac

tag: time of acquisition


title: 086_TRK_CTRL

value: Contralateral (non-surgical; CTRL)


title: Jurkat Tat, TRIM24 KO rep3

tag: cell type

value: TRIM24 knockout


title: T115-hm5-vac


title: Jurkat Tat, LKO rep1


title: Jurkat Tat, TRIM24 KO rep2


title: 074_TRK_SX

tag: tissue


title: T115-h24-vac


title: ZYQ_pre

description: 10x Genomics

tag: genotype

value: WT


title: T114-hm5-vac


title: Jurkat Tat, TRIM24 KO rep1


title: cKO, PD10, 4

city: College station

first: Qinglei

last: Li

address: 400 Bizzell St

institute: Texas A&M University

data_processing:
Trimmomatic was used to trim poor quality bases and remove low quality reads.
Quality check was performed using FastQC. Sample reads were aligned to the mouse genome (GRCm38_mouse) using HISAT2 and counted using FeatureCounts.
Finally, differential gene expression was analyzed using Edger.
Assembly: GRCm38_mouse
Supplementary files format and content: FeatureCounts

source_name: whole uterus

extract_protocol: TruSeq stranded mRNA library

value: whole uterus

value: Ezh2 f/f; Acre

value: Conditional knockout


title: 073_TRK_CTRL


title: cKO, PD10, 3


title: T114-h24-vac


title: 072_TRK_SX


title: cKO, PD10, 1


title: Jurkat Tat, WT rep1


title: 072_TRK_CTRL


title: Jurkat Tat, WT rep2


title: T112-hm5-vac


title: cKO, PD10, 2


title: R976-hm5-vac


title: 073_TRK_SX


title: R968-hm5-vac


title: 070_TRK_CTRL


title: 067_TRK_SX


title: Ctrl, PD10, 4

value: Ezh2 f/f

value: Ctrl


title: R976-h24-vac


title: Ctrl, PD10, 2


title: Ctrl, PD10, 1


title: 066_TRK_SX


title: R968-h24-vac


title: Ctrl, PD10, 3


title: R966-hm5-vac


title: 067_TRK_CTRL


title: Female Vehicle Mouse S35

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

institute: Goethe University Frankfurt

data_processing:
Sequence reads were processed using Qiagen's software CLC Genomics workbench (v21.0.5) with CLC's default settings for RNA-Seq analysis. Reads were aligned to GRCm38 genome. Expression value unit is TPM.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include feature counts for each sample and the feature ID. tab-delimited text file with normalized counts of valid genes including gene Ids and GO terms are included as Suppl. File

source_name: mouse brain cortex

growth_protocol: does not apply

extract_protocol:
Perilesional brain tissue was removed, flash frozen in liquid nitrogen. Total RNA was isolated using RNeasy plus micro kit (Qiagen). Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Nano chip on Agilent's bioanalyzer.
Barcoded mRNA seq libraries were prepared from 400 ng total RNA using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual with a final amplification of 12 cycles. Concentration was determined using Invitrogen’s Qubit HS assay and fragment size was analyzed on Agilent’s 2100 Bioanalyzer on a HS DNA chip.

treatment_protocol: PLX3397 versus vehicle from d1-d5 after TBI

value: post TBI cortex

tag: gender

value: female

value: Vehicle

tag: time after tbi

value: 30 days


title: 066_TRK_CTRL

value: Skeletal Muscle

value: Female


title: Jurkat Tat, WT rep3

value: Jurkat Tat

tag: treatment

value: PMA/Ionomycin activation


title: R966-h24-vac

value: old


title: 074_TRK_CTRL

value: Contralateral (non-surgical; CTRL)


title: R963-hm5-vac


title: 070_TRK_SX

value: Surgical (SX)


title: 064_TRK_SX


title: Female Vehicle Mouse S34

tag: strain


title: Female Vehicle Mouse S33


title: R963-h24-vac


title: Female Vehicle Mouse S32


title: R962-hm5-vac


title: 064_TRK_CTRL


title: T112-h24-vac


title: 059_TRK_SX


title: Female Vehicle Mouse S31


title: 048_TRK_CTRL


title: 059_TRK_CTRL


title: R962-h24-vac


title: Male Vehicle Mouse S19

value: male


title: R960-h24-vac


title: Male Vehicle Mouse S10


title: Male Vehicle Mouse S9


title: R960-hm5-vac


title: 041_TRK_CTRL


title: 041_TRK_SX


title: 037_TRK_SX


title: R958-hm5-vac


title: Male Vehicle Mouse S4


title: R958-h24-vac


title: Male Vehicle Mouse S3


title: R957-hm5-vac


title: Female PLX Mouse S30


title: Female PLX Mouse S29


title: 033_TRK_SX


title: R957-h24-vac


title: 037_TRK_CTRL


title: H35R-hm5-vac

value: young


title: 033_TRK_CTRL


title: H35R-h24-vac


title: 048_TRK_SX


title: Female PLX Mouse S23


title: Female PLX Mouse S27


title: H35H-hm5-vac


title: 030_TRK_SX


title: 030_TRK_CTRL


title: H35H-h24-vac


title: Male PLX  Mouse S18


title: 029_TRK_CTRL


title: H28Y-hm5-vac


title: H28Y-h24-vac


title: Male PLX  Mouse S12


title: 029_TRK_SX


title: H28V-hm5-vac


title: CTCF-WT_plus_R2

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

description: add IAA for 6hrs that CTCF were acute degraded

library_source: genomic

data_processing:
Paired-end 100-cycle sequencing was performed on NovaSeq6000 sequencer following the manufacturer’s instructions (Illumina)
Raw reads were first trimmed using TrimGalore (v0.6.3). Filtered reads are then aligned the Homo sapiens reference genome GRCm37.p13 using BWA (v0.7.17-r1198). Duplicated reads are then marked using the “bamsormadup” function from the biobambam2 tool (v2.0.87)
PCR duplicates and low mapping quality reads (MAPQ < 1) were removed using samtools (version 1.9, parameter ‘-q 1 -F 1024’).
The uniquely mapped reads were then used to estimate the average fragment length in each sample based on the cross-correlation profile calculated from SPP (v1.11) [PMID:19029915]. The smallest fragment size estimated by SPP was used to center and extend reads to generate bigwig files. The bigiwig signal in all samples is  scaled to 15 million reads (ie: scaling-factor=15e6/libSize). Macs2 (v 2.1.1) was used to call peaks using parameters “-g hs  --nomodel --extsize <SPP_fragmentSize>”. Two sets of peaks were generated: Strong peaks called with parameter ‘-q 0.05’ and weak peaks called with parameter ‘-q 0.5’. Peaks were considered reproducible if they were supported by a strong peak from each replicate or at least one strong peak and a weak peak
Assembly: hg19
Supplementary files format and content: bed, tsv, bw

source_name: cell line

growth_protocol: CTCFAID2 cells were maintained in RPMI-1640 medium (Lonza) containing 10% fetal bovine serum (Hyclone), 2 mM glutamine (Sigma), and 1% penicillin/streptomycin (Thermo Fisher Scientific).

extract_protocol: 20million cells were fixed for 5mins with 1% formaldehyde.  Covaris truChIP chromatin shearing kit was used to prepare chromatin.  Spike-in control was included (Active Motif). Chromatin was incubated overnight with 10ug CTCF antibody (Diagenode). 50ul Protein G dynabeads were added and incubated for 4hrs at 4oC.  For HA tagged samples, spike in was not included.  Sheared chromatin was incubated for 4hrs with  25ul Anti-HA magnetic beads (Pierce).  For all samples, after washing DNA was decrosslinked and eluted in TE+1%SDS, Proteinase K, 400uM NaCl.  DNA was purified by phenol cholorform isoamyl alcohol.

treatment_protocol: CTCFAID2 cells were treated with 10uM 5-Ph-IAA (Med Chem Express). For cells with HA tagged CTCFs, 1ug/ml doxycycline was added to induce expression.

value: SEM

tag: antibody

value: CTCF

value: IAA 6hrs


title: CTCF-WT_minus_R2

description: no IAA

value: no IAA


title: Male PLX  Mouse S11

value: post TBI cortex


title: 028_TRK_CTRL


title: Male PLX  Mouse S1


title: INPUT-delta_RBR_plus_R2


title: H28V-h24-vac


title: 025_TRK_SX


title: Female PLX Mouse S28

value: female


title: H28T-hm5-vac


title: 025_TRK_CTRL


title: H28T-h24-vac


title: CTCF-delta_Z10_plus_R2


title: Male PLX  Mouse S17


title: erythroblasts, Nm-3

city: Yangzhou

first: Lei

last: Yang

state: Jiangsu

address: 136 Jiangyang Road

institute: Yangzhou University Medical College

data_processing:
Illumina Casava software used for basecalling.
Remove adapter polluted reads. Remove low-quality reads. Remove reads which contain N higher than 5%.
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Reads Count for each gene in each sample was counted by HISAT v2.1.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: erythroblasts

extract_protocol:
Isolation of erythroblasts was performed according to the manufacturer’s recommendations (130-049-901, Miltenyi Biotec), and RNA was harvested using Trizol reagent. Illumina VAHTS Universal V6 RNA-seq Library Prep Kit (NR604-01/02) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: erythroblasts


title: CTCF-delta_RBR_plus_R2


title: INPUT-delta_Z10_plus_R2


title: 022_TRK_SX

value: Skeletal Muscle


title: CTCF-delta_Z1_plus_R2


title: erythroblasts, Nm-2


title: H24H-hm5-vac


title: 028_TRK_SX

value: Female


title: erythroblasts, Nm-1


title: INPUT-WT_plus_R2


title: INPUT-delta_Z1_plus_R2


title: H24H-h24-vac


title: INPUT-WT_minus_R2

description: no IAA


title: 022_TRK_CTRL


title: 021_TRK_SX


title: erythroblasts, N-3


title: erythroblasts, N-2


title: H24G-hm5-vac


title: CTCF-delta_RBR_plus_R1


title: 018_TRK_SX


title: H24D-hm5-vac


title: erythroblasts, m-3


title: erythroblasts, N-1


title: H24G-h24-vac


title: CTCF-delta_Z1_plus_R1


title: 018_TRK_CTRL


title: erythroblasts, m-1


title: H24D-h24-vac


title: Osteosarcoma, fresh isolated tissue, Day14, rep3

city: Taiyuan

first: Sen

address: 382 Wuyi Road

institute: Shanxi Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Ensembl/v101
Supplementary files format and content: FPKMs, counts

source_name: Osteosarcoma

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Osteosarcoma

value: transplanted tumor

value: WT

value: growth in vivo


title: erythroblasts, WT-3

value: wild type


title: CTCF-WT_minus_R1

description: no IAA


title: CTCF-WT_plus_R1


title: erythroblasts, WT-1


title: H22F-h24-vac


title: H22F-hm5-vac


title: Osteosarcoma, fresh isolated tissue, Day14, rep2


title: Osteosarcoma, fresh isolated tissue, Day14, rep1


title: H22E-hm5-vac


title: INPUT-delta_Z10_plus_R1


title: H22E-h24-vac


title: Osteosarcoma, isolated tissue, Day14, rep2

value: 3D cells, tissue

value: culture in vitro


title: Osteosarcoma, isolated tissue, Day14, rep3


title: CTCF-delta_Z10_plus_R1

value: SEM


title: INPUT-delta_RBR_plus_R1


title: 021_TRK_CTRL

value: Contralateral (non-surgical; CTRL)


title: H22D-hm5-vac

value: young


title: 21 days post trickle infection wild-type mouse sample 03

city: Calgary

first: Constance

last: Finney

state: Alberta

address: 2500 University Drive NW

institute: University of Calgary

hyb_protocol: Hybridization was performed according to manufacturer's instructions.

scan_protocol: nCounter Sprint profiler was used for scanning and image acquisition

data_processing: nanoString data were analyzed in R. Raw counts were normalized using NanoStringNorm (using the positive control, negative control, and Eif2b4, Polr1b, and Edc3 housekeeping probes)

source_name: 6-8 week old male C57BI/6 mouse host, 200 H. polygyrus larvae

label_protocol: Labeling was performed according to manufacturer's instructions.

extract_protocol: Total RNA was extracted using a phenol-chloroform extraction (Trizol) and stored at -80C.

treatment_protocol: Mice were infected with H. polygyrus larvae according to infection regime group. After 7 or 21 days, granulomas in the small intestine were isolated for RNA extraction.

value: 6-8 week old

value: male

tag: infection

value: 200 H. polygyrus larvae

tag: infection type

value: Trickle

value: 21 days post infection

value: worm-induced intestinal granuloma in mouse


title: 21 days post trickle infection wild-type mouse sample 04

tag: age


title: H22D-h24-vac


title: Osteosarcoma, isolated tissue, Day14, rep1

tag: cell line


title: INPUT-delta_Z1_plus_R1

value: IAA 6hrs


title: INPUT-WT_plus_R1


title: 21 days post trickle infection wild-type mouse sample 02

tag: Sex

tag: time


title: 21 days post trickle infection wild-type mouse sample 01


title: INPUT-WT_minus_R1

description: no IAA

value: no IAA


title: Osteosarcoma, 3D cell printed tissue,Day14, rep2

value: Osteosarcoma

value: cell 3D printing


title: H21Y-hm5-vac

tag: animal id


title: Line #4 Day 14 Gene edited_3

city: Rotterdam

first: Mike

last: Broeders

state: Zuid-Holland

address: Dr.Molewaterplein 40

department: Department of Pediatrics, Department of Clinical Genetics, Center for Lysosomal and Metabolic Diseases

country: Netherlands

institute: Erasmus MC

description: Line #4_GE_D14_3

data_processing:
Data were processed per sample using STAR (v2.3.0) picard (v1.90), and GATK (v2.8).
Transcript quantification was performed using featureCounts (v1.4.3) against all 57,820 gene features in GENCODE (version date; 2013-12-05)
Raw counts per gene were normalized using the edgeR (v3.8.6) trimmed mean of M-values method to counts per million values.
Assembly: GRCh38.p13
Supplementary files format and content: comma-delimited text file (CSV) include CPM values for each Sample

source_name: Line #4

growth_protocol: hiPSCs were cultured with Vitronectin XF (Stem Cell) as coating and mTeSR™ Plus (Stem Cell) as media. hiPSCs were differentiated into chondrogenic cells using a 14-day differentiation protocol that was modified from Oldershaw et al.

extract_protocol:
RNA was isolated using the RNAeasy miniprep kit with on-column DNase treatment (Qiagen) according to manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: isogenic pairs were generated using CRISPR/Cas9 gene editing by knock-in of either a healthy copy of ARSB or an emtpy vector

value: Line #4

value: hIPSC derived chondrogenic cells

value: ARSB r.691_898del

tag: group

value: Gene edited

value: Day 14


title: H21Y-h24-vac

tag: timepoint

tag: time of acquisition


title: H02V-hm5-vac


title: Osteosarcoma, 3D cell printed tissue,Day14, rep1

tag: tissue

tag: cell type

value: WT

value: culture in vitro


title: 7 days post trickle infection wild-type mouse sample 03

source_name: 6-8 week old female C57BI/6 mouse host, 200 H. polygyrus larvae

value: 6-8 week old

value: female

value: 7 days post infection


title: Line #4 Day 14 Gene edited_2

description: Line #4_GE_D14_2

tag: genotype


title: Line #4 Day 14 Gene edited_1

description: Line #4_GE_D14_1


title: H02V-h24-vac

value: young


title: Line #4 Day 14 Empty vector_3

description: Line #4_EV_D14_3

value: Empty vector


title: 7 days post trickle infection wild-type mouse sample 02

value: 200 H. polygyrus larvae

value: Trickle

value: worm-induced intestinal granuloma in mouse


title: 7 days post trickle infection wild-type mouse sample 01


title: 21 days post bolus infection wild-type mouse sample 09

value: male

value: Bolus

value: 21 days post infection


title: Osteosarcoma, 3D cell printed tissue,Day1, rep2

value: Osteosarcoma

value: cell 3D printing


title: Ketamine_2

city: Kayseri

first: Duygu

last: Yücel

address: Erciyes University Genome and Stem Cell Center Melikgazi

country: Turkey

institute: Erciyes University

data_processing:
FASTQ output files were aligned to the C. elegans reference genome (WBcel235) using Hisat2 v2.0.5. The mapped reads were assembled by StringTie (v1.3.3b)
FPKM of each gene was calculated using featureCounts v1.5.0-p3. Differential expression analysis was performed using the DESeq2R package (1.20.0).
Assembly: WBcel235
Supplementary files format and content: xls file for gene count
Supplementary files format and content: xls file for fpkm

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Animals were grown on OP50-seeded NGM plates  at 25 degrees (Celsius).

extract_protocol:
Total RNA was isolated using Trizol and Direct-zol RNA kit (Zymo Research)
mRNA libraries were constructed using the Illumina Tru-Seq Stranded mRNA Library Construction Kit

treatment_protocol: Synchronised L1 wild-type animals were grown on OP50-seeded NGM plates containing 2.5 mM ketamine and in M9 buffer as vehicle for control condition and grown to adult day 1 stage

value: Whole animal

value: Wild-type (N2)

value: Ketamine


title: Osteosarcoma, 3D cell printed tissue,Day1, rep3

value: WT

value: culture in vitro


title: 21 days post bolus infection wild-type mouse sample 08

value: 6-8 week old


title: Osteosarcoma, 3D cell printed tissue,Day1, rep1


title: Line #4 Day 14 Empty vector_2

description: Line #4_EV_D14_2

value: Line #4

value: hIPSC derived chondrogenic cells

value: ARSB r.691_898del

value: Day 14


title: Osteosarcoma, 3D cell printed tissue,Day14, rep3


title: Osteosarcoma, 3D cells, Day14, rep3

value: 3D cells


title: Line #4 Day 14 Empty vector_1

description: Line #4_EV_D14_1

value: Empty vector


title: 21 days post bolus infection wild-type mouse sample 07

value: male

value: 200 H. polygyrus larvae

value: worm-induced intestinal granuloma in mouse


title: Ketamine_1


title: 7 days post bolus infection wild-type mouse sample 06

value: female

value: Bolus

value: 7 days post infection


title: Line #3 Day 14 Gene edited_3

description: Line #3_GE_D14_3

source_name: Line #3

value: Line #3

value: ARSB c.937C>T

value: Gene edited


title: Control_1

value: Whole animal

value: Wild-type (N2)

value: M9 buffer


title: Line #3 Day 14 Gene edited_2

description: Line #3_GE_D14_2

value: hIPSC derived chondrogenic cells


title: Osteosarcoma, 3D cells, Day14, rep2

value: Osteosarcoma

value: WT

value: culture in vitro


title: Osteosarcoma, 3D cells, Day14, rep1

value: 3D cells


title: SV_rep3

city: Salt Lake City

first: Mary Elizabeth

last: Hartnett

address: 65 Mario Capecchi Dr

institute: University of Utah

data_processing:
Fastq reads were aligned to Hg38 genome using Novocraft novoalign (version 2.8) using a genome index that also includes all known splice indexes, allowing for up to 50 alignments to be reported. Sequencing adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT) were provided for masking during alignment. The transcriptome splice index was generated using USeq MakeTranscriptome (version 8.8.8) with 50 bp radius and Ensembl GRCh38 transcripts (release 84).  Alignments against transcript splices were converted to genomic coordinates using USeq SamTranscriptomeParser (version 8.8.8), allowing for one alignment per read.
Alignments were counted over gene models using USeq DefinedRegionsDifferentialSeq (version 8.8.8) and Ensembl GRCh38 annotation (release 84). Genes with a sum of counts below 10 or exceeding 50000 were excluded from further analysis.
Assembly: GRCh38, Ensembl Release 84
Supplementary files format and content: Gene count table from USeq DRDS

source_name: retina

extract_protocol:
HRMECs were lysed in buffer RLT supplemented with β-mercaptoethanol (1:100, Sigma-Aldrich, St. Louis, MO, USA) and RNA was isolated from lysates using the Qiagen RNeasy Kit following the protocol provided by the manufacturer (Qiagen, Valencia, CA, USA).
Library construction was performed using the Illumina TruSeq Stranded mRNA Library Preparation Kit (cat# RS-122-2101, RS-122-2102).  Briefly, total RNA (100 ng to 4 ug) was poly-A selected using poly-T  oligo-attached magnetic beads.  Poly-A RNA eluted from the magnetic beads was fragmented and primed with random hexamers in preparation for cDNA synthesis.  First strand reverse transcription was performed using Superscript II Reverse Transcriptase (Invitrogen cat#18064-014).  Second strand cDNA synthesis was performed using DNA polymerase I and Rnase H with dUTP  substituted for dTTP.  An A-base was added to the blunt ends by the polymerase.  Adapters containing a T-base overhang  were ligated to the A-tailed DNA fragments.  Ligated fragments were PCR-amplified (12-15 cycles) under conditions that enabled amplification of the first strand cDNA product only.  The PCR-amplified library was purified using Agencourt AMPure XP beads (Beckman Coulter Genomics cat#A63881).  The concentration of the amplified library was measured with a NanoDrop spectrophotometer and an aliquot of the library resolved on an Agilent 2200 Tape Station using a D1K (cat# 5067-5361 and 5067-5362) or a High Sensitivity D1K (cat# 5067-5363 and 5067-5364) assay to define the size distribution of the sequencing library.  Libraries were adjusted to a concentration of approximately 10 nM and quantitative PCR performed using the KapaBiosystems Kapa Library Quant Kit (cat# KK4824) to calculate the molarity of adapter ligated library molecules.  The concentration was further adjusted following qPCR to prepare the library for Illumina sequence analysis.

value: retina

value: microvascular endothelial cells

value: STAT3 siRNA

value: VEGF


title: 7 days post bolus infection wild-type mouse sample 05

value: 6-8 week old

value: female

value: 200 H. polygyrus larvae

value: Bolus

value: worm-induced intestinal granuloma in mouse


title: 7 days post bolus infection wild-type mouse sample 04

value: 7 days post infection


title: SV_rep2


title: Osteosarcoma, 2D cells, Day14, rep3

value: 2D cells


title: Line #3 Day 14 Gene edited_1

description: Line #3_GE_D14_1

value: Line #3

value: ARSB c.937C>T

value: Gene edited

value: Day 14


title: Control_2

value: Whole animal

value: Wild-type (N2)

value: M9 buffer


title: Osteosarcoma, 2D cells, Day14, rep1

value: Osteosarcoma

value: WT

value: culture in vitro


title: Line #3 Day 14 Empty vector_2

description: Line #3_EV_D14_2

value: hIPSC derived chondrogenic cells

value: Empty vector


title: S_rep3

value: retina

value: microvascular endothelial cells

value: STAT3 siRNA

value: PBS


title: Line #3 Day 14 Empty vector_1

description: Line #3_EV_D14_1


title: Skin_T_728_day_365

city: Vienna

first: Georg

last: Stary

address: Spitalgasse 23

department: Dermatology

country: Austria

institute: Medical University of Vienna

data_processing:
Single-end reads were trimmed for low quality bases and removal of low-quality reads using ReadTools
Trimmed reads were mapped to the Homo sapiens genome (GRCh38.92 assembly) using STAR (v2.5.3a) mapper
The reads mapped in multiple genomic locations were eliminated by using Samtools (v1.4)
Read counts for features (exons) were generated using the featureCounts function from the Subread package (v 1.22.1)
Assembly: hg38
Supplementary files format and content: Raw gene count matrix was generated using featureCounts function from the Subread package (v 1.22.1) with Ensembl Known Gene models (version GRCh38.92) as reference annotations

source_name: T cells

growth_protocol: freshly isolated cells from human tissue

extract_protocol:
cells were isolated from skin biopsies using collagenase IV + mesh filtering
Illumina
SMART-seq

value: Skin

value: Day 365 (after transplantation)


title: Naïve wild-type mouse sample 09

source_name: 6-8 week old male C57BI/6 mouse host, 0 H. polygyrus larvae

value: 6-8 week old

value: male

value: Uninfected

value: 21 days post infection

value: mouse intestinal tissue


title: S_rep2


title: Input_ChIPseq_HepG2

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

description:
PE150 by NovaSeq6000
A2_ChIPseq

data_processing:
Illumina RTA was used to create .bcl files, and bcl2fastq v2.20.0.422 software was used for base calling (for samples split between flowcells and later merged per run)
ChIP-seq reads were aligned to the GRCh38 genome assembly using BWA with the following configurations…
Aligned reads were then sorted by samtools (version 1.10) and duplicated reads were tagged and removed by Picard MarkDuplicates tool (version 2.21.1)
peaks were called using MACS2 (version 2.1.1) and --SPMR option was used to generate normalized pileup files for downstream analysis.
RNA-seq reads aligned to the GRCh38 genome assembly using STAR_2.6.0a, Aligned reads was normalized by edgeR bioconductor package and outputed as rpkm.txt file
Assembly: Genome Reference Consortium GRCh38
Supplementary files format and content: bigwig file were generating using MACS2 and bdgToBW, scores represent pileup signals
Supplementary files format and content: raw count table in txt format of every sample in RNAseq project

source_name: HepG2 cells

growth_protocol: dCas9-Krab-expressing HepG2 and U87 cells transduced with sgiNTC or sgiACTR5 and seleted in 2 ug/ml puromycine for 10 days.

extract_protocol: ACTR5-TST cautured genomic DNA was submitted for ChIP-seq at Novogene (PE150, NovaSeq6000).

treatment_protocol: sgiNTC and sgiACTR5 were cloned into ipUSEPR vector and transduced via lentiviral infection.

value: Hepatocellular carcinoma

tag: condition

value: expressing a pLNV-ACTR5-TST construct

tag: chip target

value: none (input)


title: Skin_T_727_day_365


title: S_rep1

tag: treatment


title: Line #2 Day 14 Gene edited_3

description: Line #2_GE_D14_3

source_name: Line #2

value: Line #2

value: ARSB c.995T>G

value: Gene edited

value: Day 14


title: Line #2 Day 14 Gene edited_2

description: Line #2_GE_D14_2

value: hIPSC derived chondrogenic cells


title: ACTR5_TST_ChIPseq_HepG2

description:
PE150 by NovaSeq6000
A1_ChIPseq

extract_protocol:
the Twin-Strep-Tag (TST) tagged ACTR5-TST was captured by MagStrep "type3" XT Beads (2-4090-002, IBA; 1:1000) at 4    for 30 minutes. The beads were washed three times in 1x Buffer W (2-1003-100, IBA) and the TST-captured proteins were eluted by 1x Buffer BXT (2-1042-025, IBA; containing biotin).
ACTR5-TST cautured genomic DNA was submitted for ChIP-seq at Novogene (PE150, NovaSeq6000).

value: ACTR5 captured by the TST-tag


title: Skin_T_723_day_365


title: Line #3 Day 14 Empty vector_3

description: Line #3_EV_D14_3

value: Line #3

value: ARSB c.937C>T

value: Empty vector


title: Osteosarcoma, 2D cells, Day14, rep2

value: Osteosarcoma

value: 2D cells

value: WT

value: culture in vitro


title: SV_rep1

value: retina

value: microvascular endothelial cells

value: STAT3 siRNA

value: VEGF


title: Skin_T_722_day_365

value: Skin

value: Day 365 (after transplantation)


title: RNAseq_U87_sgiNTC_2

description:
PE150 by NovaSeq6000
B2

source_name: U87 cells

extract_protocol:
Total RNA was extracted using the RNeasy kit (QIAGEN) for RNAseq.
Eukaryotic mRNA directional library prep were used for RNAseq.

value: Glioblastoma

value: sgiNTC


title: CV_rep2

value: control siRNA


title: RNAseq_U87_sgiNTC_1

description:
PE150 by NovaSeq6000
B1


title: Line #2 Day 14 Gene edited_1

description: Line #2_GE_D14_1

value: Line #2

value: hIPSC derived chondrogenic cells

value: ARSB c.995T>G

value: Gene edited

value: Day 14


title: Naïve wild-type mouse sample 10

tag: strain

value: 6-8 week old

value: male

value: Uninfected

value: 21 days post infection

value: mouse intestinal tissue


title: CV_rep3

value: retina

value: microvascular endothelial cells


title: Skin_T_721_day_365

value: Skin


title: Line #2 Day 14 Empty vector_3

description: Line #2_EV_D14_3

value: Empty vector


title: RNAseq_U87_sgiACTR5_3

description:
PE150 by NovaSeq6000
A1

value: Glioblastoma


title: RNAseq_U87_sgiACTR5_4

description:
PE150 by NovaSeq6000
A2


title: C_rep3

value: PBS


title: Skin_T_718_day_365

value: Day 365 (after transplantation)


title: Line #2 Day 14 Empty vector_2

description: Line #2_EV_D14_2

value: Line #2


title: CV_rep1

value: control siRNA

value: VEGF


title: Line #2 Day 14 Empty vector_1

description: Line #2_EV_D14_1

value: hIPSC derived chondrogenic cells

value: ARSB c.995T>G


title: RNAseq_HepG2_sgiNTC_2

description:
PE150 by NovaSeq6000
A8_FRRB202323982-1a_H3CVFDSXY_L3

value: Hepatocellular carcinoma

value: sgiNTC


title: C_rep2


title: Skin_T_713_day_365


title: Skin_T_719_day_365


title: RNAseq_HepG2_sgiNTC_1

description:
PE150 by NovaSeq6000
A7_FRRB202323981-1a_H33NTDSXY_L3


title: RNAseq_HepG2_sgiACTR5_4

description:
PE150 by NovaSeq6000
A6_FRRB202323980-1a_H33NTDSXY_L3


title: Skin_T_712_day_365


title: Line #1 Day 14 Gene edited_2

description: Line #1_GE_D14_2

source_name: Line #1

value: Line #1

value: Gene edited

value: Day 14


title: C_rep1

value: retina


title: Line #1 Day 14 Gene edited_3

description: Line #1_GE_D14_3


title: Skin_T_728_day_14

value: Day 14 (after transplantation)


title: Line #1 Day 14 Empty vector_3

description: Line #1_EV_D14_3


title: RNAseq_HepG2_sgiACTR5_3

description:
PE150 by NovaSeq6000
A5_FRRB202323979-1a_H33NTDSXY_L3


title: Skin_T_723_day_14

value: Skin


title: Line #1 Day 14 Gene edited_1

description: Line #1_GE_D14_1


title: Cx43_KO3

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

data_processing:
FastQC was used to observe read quality
cutadapt was used to trim data
Bowtie v1.3.1  to align reads to the reference genome
FeatureCounts  (v1.5.0-p3) was used to count reads mapping to genes
DESeq2 Bioconductor package (v1.26.0) to identify differentially expressed genes
Genome_build: Ensembl reference genome for homo sapiens, GRCh38
Supplementary_files_format_and_content: text file of counts for miRNAs

growth_protocol: Nontumorigenic HMT-3522 S1 (S1) human breast epithelial cells between passages 52 and 60, were routinely maintained as a monolayer on plastic (2D culture) in chemically defined serum-free H14 medium at 37 ˚C and 5% CO2 in a humidified incubator. H14 medium was changed every 2–3 days. For 2D cultures, cells were plated on plastic substrata at a density of 2.3 × 104 cells/cm2. The drip method of 3D culture was used to induce the formation of acini. Briefly, cells were plated on MatrigelTM (50 μl/cm2; BD Biosciences, 354234) at a density of 4.2 × 104 cells/cm2 in the presence of culture medium containing 5% MatrigelTM  was omitted from the culture medium after day 7 to allow completion of acinar differentiation (usually observed on day 8 or 9) .

extract_protocol:
Total RNA from cells in 3D culture was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s protocol. Purity and concentration of RNA samples were examined spectrophotometrically by absorbance measurements at 260, 280 and 230 nm using the NanoDrop ND-1000 (Thermo Fisher Scientific, Wilmington, DE, USA). OD260/OD280 ratios between 1.8 and 2.1 were deemed acceptable.
The Purdue Genomics Facility prepared libraries using the NEXTflex Illumina Small RNA Sequencing Kit v3 (Bioo, Austin, TX) with barcoding performed using UDI primers.  A total of 15 PCR cycles were performed. 2x50 bp reads were sequenced using the NovaSeq6000.

treatment_protocol: Cx43 was down-regulated in S1 cells via retroviral delivery of shRNA, as described by Bazzoun et al.

value: Cx43 Knock-down (short hairpin)


title: CTCF_Cut_and_Run_Control

city: Bangalore

first: Bharath

last: Saravanan

state: Karnataka

address: Bellary Road

department: Genetics and Development

country: India

institute: National centre for Biological Sciences

description: Cut and Run

data_processing:
Library strategy: CUT&RUN
Basecalls performed using standard illumina pipeline
We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to GRCh38 of Homo sapiens genomic sequence obtained from UCSC.
We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map paired-end reads to Ensembl masked R64-1-1 of Saccharomyces cerevisiae
We counted the properly paired reads from the D.melanogaster alignments.
We used the bedtools 2.21.0 genomecov command with a scaling factor of (10000/number of fragments mapped to D.melanogaster) to create a normalized human track file
Genome_build: GRCh38
Supplementary_files_format_and_content: bedgraph

source_name: HeLa

growth_protocol: HeLa cell grown as per ATCC protocol.

extract_protocol:
Cut and Run CTCF as described in https://doi.org/10.1101/784835
Library preparation from CUT&RUN DNA and subsequent sequencing on the Illumina HiSeq 2500 platform were car-ried out as described previously (Skene and Henikoff, 2017)

treatment_protocol: RNAseA treatment

tag: treatments

tag: antibody

value: CTCF (Cat # 07-729, Millipore Sigma)

value: HeLa


title: Cx43_KO2


title: Line #1 Day 14 Empty vector_2

description: Line #1_EV_D14_2

value: Empty vector


title: Line #1 Day 14 Empty vector_1

description: Line #1_EV_D14_1


title: Skin_T_722_day_14


title: Skin_T_721_day_14


title: Healthy control #2 Day 0 Healthy control

description: Healthy control #2_iPS

source_name: Healthy control #2

value: Healthy control #2

value: hIPSC

value: WT

value: Healthy control

value: Day 0


title: Control3

value: control


title: Skin_T_719_day_14


title: CTCF_Cut_and_Run_RNAseA

description: Cut and Run

value: RNAseA


title: Healthy control #1 Day 0 Healthy control

description: Healthy control #1_iPS

source_name: Healthy control #1

value: Healthy control #1


title: Skin_T_727_day_14


title: Control2


title: Skin_T_713_day_14


title: 8_F181B

city: NEWCASTLE

first: Megan

middle: Saphana Rose

last: Hasoon

address: Newcastle University

country: United Kingdom

institute: Newcastle University

data_processing:
Sequence reads were trimmed using Trimmomatic then aligned to the human refence genome using STAR
Counts were quantified using HTSEQ
Genome_build: hg38
Supplementary_files_format_and_content: csv file containing raw counts for each gene for all samples

source_name: Retinal Pigment Epithelium cells-derived extracellular vesicles

growth_protocol: RPE cells were grown in medium consisiting of Advanced RPMI 1640, 10% KnockOut serum replacement, 2% B27 supplement, 1% GlutaMAX and 1% Penicillin-Streptomycin (all ThermoFisher). Media was partially replaced 2-3  times a week. Cells were grown on Matrigel (Corning) coated 0.4µm PET hanging cell culture inserts (Merck).

extract_protocol:
Extracellular vesicles isolation: CCM was pre-clarified by centrifugation at 3000×g for 10 minutes and concentrated to 500 µl using Amicon 15 10 kDa or 30 kDa MWCO (Merck). The concentrate was applied onto the qEV original 70 nm size exclusion chromatography column (SEC, Izon) and EVs were eluted in Phosphate Buffered Saline (PBS, Sigma) in fractions 7, 8 and 9 as indicated by the manufacturer. The EV suspension was finally concentrated using the Amicon 15 3 kDa MWCO ultrafiltration units (Merck) to approximately 200 µl. EV RNA was isolated using the Ambion mirVana miRNA Isolation Kit (ThermoFisher) according to the manufacturer’s protocol. EV suspensions were not treated with proteinase K and RNase, as these involve incubations at higher than ambient temperatures and small vesicles permeability increases rapidly from 36.5°C (Blicher et al. 2009). SUPERase-In RNase Inhibitor (ThermoFisher) was added to the purified RNA samples at a final concentration of 1 u/µl. RNA was further precipitated with ethanol according to the following protocol: 0.1 volume of 3 M Sodium acetate RNA grade, Glycogen RNA grade (both ThermoScientific) to a final concentration of 1 µg/µl and 3 volumes of ice cold 100% ethanol molecular biology grade (Sigma) were added to the samples, thoroughly mixed and precipitated overnight at -80°C. Samples were centrifuged at 16,100 × g, 4°C for 30 minutes. The pellets were washed twice with 0.5 ml of ice cold 75% ethanol, spun at 4°C for 10 minutes each time. The traces of ethanol were removed by a brief centrifugation and the pellets air dried and re-suspended in nuclease free water (Promega).
The EVs sequencing libraries were prepared using the SMART-Seq Stranded Total RNA kit (Takara) following manufacturer’s instructions choosing the ultra-low input method with no sample fragmentation and sequenced on an Illumina NovaSeq 6000 at ~40 million 2 x 100 bp reads per sample.

treatment_protocol: Before cell conditioned media collection for extracellular vesicles isolation, RPE cells were maintained in exosome free medium (Advanced RPMI 1640, 1% exosome depleted Fetal Bovine Serum, 1% GlutaMAX and 1% Penicillin-Streptomycin (all ThermoFisher)). Media was changed every 48-72 hours.

tag: rna population

value: extracellular vesicle RNA

value: Patients

tag: region

value: B


title: Line #4 Day 0 Empty vector

description: Line #4_EV_iPS

tag: cell line

value: Line #4

value: ARSB r.691_898del


title: 6_F180B

value: Retinal Pigment Epithelium cells-derived extracellular vesicles


title: 7_F181A

value: A


title: Skin_T_710_day_14

value: Skin

tag: time

value: Day 14 (after transplantation)


title: Cx43_KO1

value: Cx43 Knock-down (short hairpin)


title: Line #3 Day 0 Gene edited

description: Line #3_GE_iPS

value: Line #3

value: hIPSC

value: ARSB c.937C>T

value: Gene edited


title: Line #3 Day 0 Empty vector

description: Line #3_EV_iPS

value: Empty vector

value: Day 0


title: 5_F180A


title: Line #2 Day 0 Gene edited

description: Line #2_GE_iPS

value: Line #2

value: ARSB c.995T>G


title: Skin_T_727_day_100

value: Day 100 (after transplantation)


title: HL60_cl15_Apicidin_Day6

city: Tokushima

first: Taigo

last: Horiguchi

address: 3-18-15, Kuramoto-cho

institute: Tokushima University

description:
8_37-6
Gene expression after 6 day differentiation induction with Apicidin in HL-60 clone 15 cells.

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE Unrestricted Microarrays (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel was set to Green and Green PMT was set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028282_D_F_20110531) to obtain background subtracted and spatially detrended processed signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HL-60 clone 15 cells, treated with Apicidin, Day 6

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using RNeasy mini kit (QIAGEN, Valencia, CA) following manufacturer's instruction.

tag: gender

value: female

value: Apicidin

tag: time point

value: Day 6


title: HL60_cl15_Apicidin_Day4

description:
7_37-4
Gene expression after 4 day differentiation induction with Apicidin in HL-60 clone 15 cells.

source_name: HL-60 clone 15 cells, treated with Apicidin, Day 4

value: Day 4


title: 4_AD3B

value: Retinal Pigment Epithelium cells-derived extracellular vesicles

value: extracellular vesicle RNA

tag: group

value: Control

value: B


title: Skin_T_718_day_14

value: Skin

value: Day 14 (after transplantation)


title: Skin_T_728_day_100


title: Line #4 Day 0 Gene edited

description: Line #4_GE_iPS

source_name: Line #4

value: Line #4

value: hIPSC

value: ARSB r.691_898del


title: HL60_cl15_Apicidin_Day0

description:
5_37-0
Gene expression after 0 day differentiation induction with Apicidin in HL-60 clone 15 cells.

source_name: HL-60 clone 15 cells, treated with Apicidin, Day 0

value: Day 0


title: Line #2 Day 0 Empty vector

description: Line #2_EV_iPS

value: Line #2

value: Empty vector


title: HL60_AK2 KO#47_ATRA_Day4

description:
4_47-4
Gene expression after 4 day differentiation induction with ATRA in HL-60 Ak2 hetero-knockout clone #47 cells.

source_name: HL-60 AK2 hetero-knockout clone #47 cells, treated with ATRA, Day 4

value: AK2 hetero-knockout

value: ATRA


title: HL60_cl15_Apicidin_Day2

description:
6_37-2
Gene expression after 2 day differentiation induction with Apicidin in HL-60 clone 15 cells.

source_name: HL-60 clone 15 cells, treated with Apicidin, Day 2

value: female

value: Apicidin

value: Day 2


title: Skin_T_717_day_14


title: HL60_AK2 KO#5_ATRA_Day4

description:
8_5-4
Gene expression after 4 day differentiation induction with ATRA in HL-60 Ak2 hetero-knockout clone #5 cells.

source_name: HL-60 AK2 hetero-knockout clone #5 cells, treated with ATRA, Day 4

value: Day 4


title: HL60_AK2 KO#47_ATRA_Day2

description:
3_47-2
Gene expression after 2 day differentiation induction with ATRA in HL-60 Ak2 hetero-knockout clone #47 cells.

source_name: HL-60 AK2 hetero-knockout clone #47 cells, treated with ATRA, Day 2


title: HL60_AK2 KO#47_ATRA_Day0

description:
1_47-0
Gene expression after 0 day differentiation induction with ATRA in HL-60 Ak2 hetero-knockout clone #47 cells.

source_name: HL-60 AK2 hetero-knockout clone #47 cells, treated with ATRA, Day 0


title: HL60_AK2 KO#47_ATRA_Day1

description:
2_47-1
Gene expression after 1 day differentiation induction with ATRA in HL-60 Ak2 hetero-knockout clone #47 cells.

source_name: HL-60 AK2 hetero-knockout clone #47 cells, treated with ATRA, Day 1

value: Day 1


title: 3_AD3A

value: Retinal Pigment Epithelium cells-derived extracellular vesicles

value: extracellular vesicle RNA

value: Control

value: A


title: Skin_T_723_day_100

source_name: T cells

value: Skin

value: Day 100 (after transplantation)


title: 2_F018B

value: B


title: Line #1 Day 0 Gene edited

description: Line #1_GE_iPS

value: Line #1

value: hIPSC

value: Gene edited

value: Day 0


title: Skin_T_722_day_100


title: 1_F018A


title: HL60_AK2 KO#5_ATRA_Day2

description:
7_5-2
Gene expression after 2 day differentiation induction with ATRA in HL-60 Ak2 hetero-knockout clone #5 cells.

source_name: HL-60 AK2 hetero-knockout clone #5 cells, treated with ATRA, Day 2

value: AK2 hetero-knockout

value: ATRA


title: Line #1 Day 0 Empty vector

description: Line #1_EV_iPS

source_name: Line #1

value: Empty vector


title: siLong2_2

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Read alignments were performed using STAR version 2.4.0f1. Read counts were tabulated for ENSEMBL genes build 75 using the featureCounts() function from the R package Rsubread (version 1.20.6) with options useMetaFeatures=TRUE, isPairedEnd=TRUE, nthreads=18, minMQS=30, requireBothEndsMapped=TRUE, checkFragLength=FALSE, countChimericFragments=FALSE, strandSpecific=2.
Genome_build: hg19
Supplementary_files_format_and_content: A single processed file contains one row for each gene in ENSEMBL genes build 75. There is one column for each sample in this record. Each data value is the raw, un-normalized counts value reported by featureCounts(). Each gene is denoted by the ENSEMBL gene ID in the first column.

source_name: HCT116 colon cancer cell line

growth_protocol: HCT116 cells were grown in McCoy's 5A (Modified) Medium (Thermo Fisher Scientific) with 10% FBS (Atlanta Biologicals) at 37°C and 5% CO2.

extract_protocol:
Total cellular RNA was prepared from each cell pellet using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s instructions.
RNA-seq libraries were prepared by Genome Quebec using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Custom siRNAs targeting all NFYA transcripts (siTotal; ACUAGAGGCAGAAGGGAAA; UGGUGAAGGUGGACGAUUU), NFYA transcripts with the longest 3’ UTR in RefSeq (siLong; AGUGAUCAUUGUAGGGUAA; GGUCAUUCCUUUAGCAUCA), or no known mammalian transcripts (siGENOME non-targeting siRNA #3; D-001210-03-05) were purchased from Dharmacon. For NFYA siRNAs, sequences were input into Dharmacon’s custom siRNA website as the sense strand, and then the website populated the anti-sense strand and added UU overhangs to the 3’ end of each strand. HCT116 cells were seeded at 25,000 cells per well of a 6-well plate, then transfected after 24 hours with siRNAs. Transfection for a single well of a 6-well plate was as follows: 250 µL of OptiMEM (Thermo Fisher Scientific) was mixed with 1.25 µL of 100 µM siRNA, and then mixed with 250 µL OptiMEM containing 5 µL Lipofectamine 2000 (Thermo Fisher Scientific). siRNA:Lipofectamine complexes were formed by incubation at room temperature for 20 minutes, and then all 500 µL of the siRNA:Lipofectamine mixture added to a well containing 1.5 mL of media, for a final siRNA concentration of 62.5 nM. 72 hours after siRNA transfection, cells were harvested (approximately 75% confluence) by PBS wash, scraping into PBS, pelleting at 500g for 2 minutes, and storage of cell pellet at -80°C.

tag: knockdown

value: siRNA #2 to long-isoform NFYA


title: Skin_T_719_day_100

tag: tissue


title: HL60_AK2 KO#5_ATRA_Day1

description:
6_5-1
Gene expression after 1 day differentiation induction with ATRA in HL-60 Ak2 hetero-knockout clone #5 cells.

source_name: HL-60 AK2 hetero-knockout clone #5 cells, treated with ATRA, Day 1

value: female


title: 18_F181B_R

tag: cell type

value: Patients


title: Skin_T_718_day_100


title: siLong2_1


title: siLong1_2

value: siRNA #1 to long-isoform NFYA


title: Skin_T_717_day_100


title: Skin_T_713_day_100


title: siLong1_1


title: Skin_T_721_day_100


title: 16_F180B_R

value: Retinal Pigment Epithelium cells-derived extracellular vesicles

value: extracellular vesicle RNA


title: 15_F180A_R

value: A


title: siTotal2_2

value: siRNA #2 to total NFYA


title: HL60_ATRA_Day4

description:
4_60-4
Gene expression after 4 day differentiation induction with ATRA in HL-60 cells.

source_name: HL-60 cells, treated with ATRA, Day 4

value: Day 4


title: 14_AD3B_R

source_name: Retinal Pigment Epithelium cells-derived extracellular vesicles

value: Control

value: B


title: Skin_T_712_day_100

value: Skin

value: Day 100 (after transplantation)


title: 13_AD3A_R


title: Skin_T_710_day_100


title: 17_F181A_R


title: siTotal2_1


title: Skin_T_728_day_0

value: Day 0 (day of transplantation)


title: HL60_ATRA_Day1

description:
2_60-1
Gene expression after 1 day differentiation induction with ATRA in HL-60 cells.

source_name: HL-60 cells, treated with ATRA, Day 1

value: Day 1


title: HL60_AK2 KO#5_ATRA_Day0

description:
5_5-0
Gene expression after 0 day differentiation induction with ATRA in HL-60 Ak2 hetero-knockout clone #5 cells.

source_name: HL-60 AK2 hetero-knockout clone #5 cells, treated with ATRA, Day 0

tag: genotype

value: AK2 hetero-knockout

value: ATRA

value: Day 0


title: siTotal1_1

value: siRNA #1 to total NFYA


title: Skin_T_723_day_0


title: HL60_ATRA_Day2

description:
3_60-2
Gene expression after 2 day differentiation induction with ATRA in HL-60 cells.

source_name: HL-60 cells, treated with ATRA, Day 2

value: female

value: Day 2


title: HL60_ATRA_Day0

description:
1_60-0
Gene expression after 0 day differentiation induction with ATRA in HL-60 cells.

source_name: HL-60 cells, treated with ATRA, Day 0


title: 11_F018A_R

value: Retinal Pigment Epithelium cells-derived extracellular vesicles


title: siControl_2

value: non-targeting siRNA


title: 103627-001-146

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

institute: University Medical Center Utrecht

data_processing:
The reads obtained were aligned to human genome (GRCh38 build 99) using STAR aligner (version 020201) and mapped reads were counted using HTSeq-count (version 0.9.0)
Genome_build: GRCh38 build 99
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: normal skin

extract_protocol:
Skin samples were derived from 4mm punch biopsies were embedded in Tissue-Tek® and directly snap-frozen in liquid nitrogen, until further processing. Sections were cut (20µm) and dissolved and lysed in RLT plus (+BME) buffer. Samples were vortexed and homogenized by pipets before RNA isolation. RNA isolation was performed using a Qiagen Universal Kit, according to manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: diagnosis

value: Ankylosing Spondylitis

tag: age

tag: Sex

value: Male


title: Skin_T_722_day_0


title: siControl_1


title: siTotal1_2


title: mock_2

value: mock transfected


title: 12_F018B_R

value: extracellular vesicle RNA

value: Control


title: 103627-001-145

source_name: non-lesion

value: Psoriasis

value: Skin

value: Female


title: 103627-001-144

source_name: lesion


title: Skin_T_721_day_0

value: Day 0 (day of transplantation)


title: Skin_T_719_day_0


title: 103627-001-143


title: 21N

city: Tokyo

first: Daisuke

last: Ohki

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Gastroenterology, Graduate School of Medicine

institute: The University of Tokyo

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

scan_protocol: Arrays were scanned using the Agilent Technologies G2600D SG12494263.

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

source_name: Human colorectal normal mucosa

label_protocol: Cyanine-3 (Cy3) labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit.

extract_protocol: Total RNA was extracted (miRNeasy Mini kit, Qiagen) from tissue samples, and its integrity was verified by Nanodrop 1000 spectrometer.

treatment_protocol: One biopsy sample was obtained from each tumor and surrounding normal mucosa.

value: normal tissue

value: M


title: 17N

value: F


title: 17T

source_name: Human SSAP mucosa

value: SSAP


title: 14N


title: 14T


title: 21T


title: mock_1


title: Skin_T_718_day_0


title: Skin_T_717_day_0


title: S49-bcl2-48hr-dex-4

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

data_processing:
RNA-SEQ reads (~60-120M per sample) were aligned to the UCSC mm10 reference genome using STAR
The quantification results from FeatureCounts were then analyzed with the Bioconductor package DESeq2, which fits a negative binomial distribution to estimate technical and biological variability.
Assembly: mm10
Supplementary files format and content: excel table; log2 transformed and normalized abundance measurements by DESeq2

source_name: S49.1 mouse lymphoma cells

growth_protocol: S49 (Neo) cells and S49 (Bcl2) cells were both cultured in RPMI-1640 medium containing 10% heat-inactivated fetal calf serum, 4.8 mM glutamine, 100 ug/ml streptomycin and 100 U/ml penicillin at 37oC, 7% CO2 atmosphere.

extract_protocol:
S49 (Neo) cells and S49 (Bcl2) cells were lysed and total RNA was extracted and purified using a QIAGEN RNeasy RNA isolation kit according to the manufacturer’s protocol.
RNA-seq libraries were generated with 1 mg of RNA as input using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) and poly(A)-enriched according to the TruSeq protocol.

treatment_protocol: S49 (Neo) cells and S49 (Bcl2) cells were treated with or without dexamethasone (Dex) (250nM) for 24 or 48 hours.

tag: cell transfection

value: stably expresses G418 (neomyocin) antibiotic resistance gene and Bcl-2 proto-oncogene

tag: timepoint

value: 48 hour

tag: treatment

value: Dexamethasone 250nM


title: 103627-001-141


title: S49-bcl2-48hr-control-4

value: vehicle


title: Skin_T_712_day_0

source_name: T cells


title: 103627-001-140

value: Ankylosing Spondylitis


title: S49-neo-48hr-dex-4

value: stably expresses G418 (neomyocin) antibiotic resistance gene


title: Skin_T_710_day_0


title: S49-neo-48hr-control-4


title: Skin_T_728_day_7

value: Baseline


title: 103627-001-139

value: Psoriatic Arthritis


title: S49-bcl2-24hr-dex-4

value: 24 hour


title: 103627-001-138


title: 13T


title: 13N


title: 12T


title: 10T


title: 10N


title: 103627-001-137

value: Male


title: 08T


title: Skin_T_727_day_7

value: Skin


title: S49-neo-24hr-dex-4


title: S49-bcl2-24hr-control-4


title: 103627-001-136


title: 12N


title: Skin_T_721_day_7


title: 103627-001-135

value: Psoriasis

value: Female


title: S49-bcl2-48hr-dex-3


title: Skin_T_722_day_7


title: S49-neo-24hr-control-4


title: Skin_T_719_day_7


title: S49-bcl2-48hr-control-3


title: S49-neo-48hr-dex-3


title: Skin_T_723_day_7


title: 08N

value: normal tissue


title: 103627-001-134


title: 103627-001-142


title: 103627-001-133


title: 103627-001-132


title: Skin_T_717_day_7


title: Skin_T_718_day_7


title: S49-neo-48hr-control-3


title: 103627-001-131


title: S49-bcl2-24hr-dex-3


title: 103627-001-130


title: Skin_T_713_day_7


title: GC, ATACseq, rep2

city: Austin

first: Keiko

middle: U

last: Torii

address: 2506 SPEEDWAY

institute: University of Texas at Austin

data_processing:
data processing step: basecalling:  Using bcl2fastq (Illumina) with parameters --no-lane-splitting --barcode-mismatches 0
data processing step: alignment:  Using bowtie2 with parameter preset (--sensitive)
data processing step: filtering:  Alignment quality score >1, centromeric regions removed
data processing step: peak-calling:  MACS2 with parameters: (--nomodel --shift -20 --extsize 150 --call-summits)
data processing step: cut counts per peak:  Using Bedtools function bedmap with parameters: --echo --sum
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: tab-delimited text file includes cutcount value for each THSs

organism: Arabidopsis thaliana

source_name: Nuclei of stomatal lineage cell

growth_protocol: 3 days old seedling under continous light

extract_protocol:
Biotinylated nuclei were isolated with strepratvidin beads.
Libraries were prepared according to Illumina's instructions accompanying the Nextera reagents  (Illumina; FC-121-1030). And libraries were sequenced on the Illumina HiSeq 4000 system following the manufacturer's protocols.

treatment_protocol: Tn5 Transposase Tagment DNA enzyme

value: Guard Cell

tag: pulldown reagent

value: streptavidin  beads (Invitrogen, Cat#11205D, Lot#00600299)


title: 03T

value: SSAP

value: F


title: Skin_T_710_day_7


title: 04T

value: M


title: S49-bcl2-24hr-control-3

value: stably expresses G418 (neomyocin) antibiotic resistance gene and Bcl-2 proto-oncogene


title: GC, ATACseq, rep1


title: S49-neo-24hr-dex-3

value: Dexamethasone 250nM


title: 04N


title: 103627-001-129


title: 01N


title: 103627-001-128


title: Skin_DR_727_day_365

source_name: Mononuclear phagocytes

value: Day 365 (after transplantation)


title: GMC, ATACseq, rep3

value: Guard Mother Cell


title: 01T


title: 103627-001-127


title: S49-neo-24hr-control-3

value: stably expresses G418 (neomyocin) antibiotic resistance gene

value: vehicle


title: Skin_DR_722_day_365


title: GMC, ATACseq, rep2


title: 103627-001-126


title: GC, ATACseq, rep3


title: S49-bcl2-48hr-dex-2

value: 48 hour


title: Skin_DR_721_day_365


title: S49-bcl2-48hr-control-2


title: Skin_DR_728_day_365


title: S49-neo-48hr-dex-2


title: MC, ATACseq, rep4

value: Mestemoid Cell


title: 103627-001-124

value: Psoriatic Arthritis

value: Skin

value: Male


title: MC, ATACseq, rep3


title: MC, ATACseq, rep2


title: 103627-001-123

value: Psoriasis

value: Female


title: Skin_DR_728_day_14

value: Day 14 (after transplantation)


title: S49-neo-48hr-control-2


title: 103627-001-121


title: Skin_DR_713_day_365


title: S49-bcl2-24hr-dex-2

value: 24 hour


title: 103627-001-125


title: S49-bcl2-24hr-control-2


title: GMC, ATACseq, rep1

value: streptavidin  beads (Invitrogen, Cat#11205D, Lot#00600299)


title: 103627-001-122


title: Skin_DR_727_day_14


title: MC, ATACseq, rep1


title: Skin_DR_722_day_14


title: 103627-001-120


title: S49-neo-24hr-dex-2


title: Skin_DR_723_day_14


title: Skin_DR_718_day_365


title: 103627-001-119


title: S49-neo-24hr-control-2


title: MMC, ATACseq, rep2

value: Mestemoid mother cell


title: Skin_DR_718_day_14


title: MMC, ATACseq, rep1


title: S49-bcl2-48hr-dex-1

value: stably expresses G418 (neomyocin) antibiotic resistance gene and Bcl-2 proto-oncogene


title: 103627-001-118


title: Protodermal, ATACseq, rep3

value: Protodermal Cell


title: Skin_DR_717_day_14


title: S49-bcl2-48hr-control-1


title: MMC, ATACseq, rep3


title: Skin_DR_713_day_14


title: Protodermal, ATACseq, rep2


title: Skin_DR_728_day_100

value: Day 100 (after transplantation)


title: 103627-001-116


title: 103627-001-115


title: 103627-001-114


title: S49-bcl2-24hr-control-1


title: S49-bcl2-24hr-dex-1

value: Dexamethasone 250nM


title: S49-neo-48hr-control-1

value: stably expresses G418 (neomyocin) antibiotic resistance gene


title: KO_24h_23

city: State College

first: Sougat

last: Misra

state: PA

address: 107 Shortlidge Road

department: Veterinary and Biomedical Sciences

institute: The Pennsylvania State University

data_processing:
The data was mapped to the reference genome using Hisat2.
Reads mapped to the genes were counted using featureCounts
Normalization of raw gene counts and differential expresssion analysis were performed using DESeq2 package in R
Assembly: Mus_musculus.GRCm38 genome build
Supplementary files format and content: Tab delimited file with gene-level raw read counts

source_name: Selenow knock-out BMDMs, 24 h

extract_protocol:
RNeasy Plus Mini Kit (Qiagen) with on column DNase treatment
100 base pair paired end reads were sequenced.

value: Bone marrow-originated

value: bone marrow-derived macrophages

value: Selenow knock-out

value: LPS (100 ng/ml)


title: Skin_DR_722_day_100

value: Skin


title: 103627-001-113

value: Psoriatic Arthritis

value: Male


title: KO_24h_22


title: Protodermal, ATACseq, rep1


title: S49-neo-24hr-dex-1


title: KO_8h_21

source_name: Selenow knock-out BMDMs, 8 h


title: 103627-001-112


title: S49-neo-48hr-dex-1

value: 48 hour


title: KO_8h_20


title: Skin_DR_721_day_100


title: S49-neo-24hr-control-1

value: vehicle


title: 103627-001-111

value: Female


title: KO_8h_19


title: Skin_DR_719_day_100


title: 103627-001-117

value: Psoriasis


title: 103627-001-110


title: KO_4h_18

source_name: Selenow knock-out BMDMs, 4 h


title: Skin_DR_727_day_100


title: Skin_DR_723_day_100


title: Skin_DR_718_day_100


title: 103627-001-109


title: KO_4h_17


title: Skin_DR_717_day_100


title: 103627-001-108


title: KO_4h_16


title: 103627-001-107

value: Ankylosing Spondylitis


title: Skin_DR_713_day_100