title: nasal_prox1_180

description: Nasal Prox1+ cells


title: GC0713172_S172

status: Public on Jul 12 2022

type: SRA

city: Bethesda

first: Keji

last: Zhao

state: MD

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

country: USA

institute: national Institute of Health

description:
genomic DNA and RNA
scPCOR-seq

library_source: genomic

data_processing:
Library strategy: scPCOR-seq
Basecalls performed
Pairs of reads were considered to be valid if read2 contain the exact linker sequences “AGAACCATGTCGTCAGTGT”.  The valid pairs of read will be further separated into either RNA part or chromatin occupancy part. If the linker sequences “GAGCG” for not-so-random primers or the linker sequences “CCTGCAGG” for oligodT were found in the location within 7-11th and 7- 14th base of read1, the pair of reads were belonged to RNA. The remaining valid pairs were belonged to chromatin occupancy. Using the information of the cell barcodes located at 5’ of read 2, both pairs of reads belonging to RNA and chromatin occupancy were separated into 96 sets of FASTQ files, respectively. The 96 pairs are shown in barcode_96.txt.  Reads were mapped to the human reference genome hg19 using Bowtie2 Duplicates using different trimming parameters. Finally, the mapping results were combined, and Duplicated reads were removed based on mapping position and UMI for the reads belonging to chromatin occupancy.
The top 30 barcodes are selected from each well based on read count, so 30 nuclei are sorted for each well with doublets removed, where the number removed was calculated based on the collision rate like in (Science. 2015 May 22; 348(6237): 910–914). These are denoted as single cells because of the low likelihood of two cells in the same well having the same barcode. We required that qualifying cells have more than 1000 reads. With these requirements, 2347 cells were obtained . For each cell, we calculated the RNA and PolII reads that were located within the gene body and stored the results in a matrix, which can be found from the file “RNA_count.txt.gz” and “POlII count.txt.gz”
Genome_build: hg19
Supplementary_files_format_and_content: barcode_96.txt: one column  refers to a DNA barcode starting from the 3' .
Supplementary_files_format_and_content: RNA_count.txt.gz: This file contains read count data for single cells in text format.  First column) Transcript ID, Second column) Chromosome, Third column) Start, Fourth column) End, Fifth column) Strand, Sixth column) RNA length, Seventh column) copies of transcript annotation in the genome, Eighth column) annotation information, other columns) readcount. The rows refer to genes. Reading the matrix results in a 65572 x 2355 matrix.
Supplementary_files_format_and_content: PolII_count.txt.gz: This file contains normalized read count data for single cells in text format. The rows refer to genes while the column refer to single cells. Reading the matrix results in a 68987 x 2348 matrix.

molecule: other

organism: Homo sapiens

source_name: 293T and H1 cells

extract_protocol:
The fixed cells were thawed on ice. To prepare PA-MNase and antibody complex, 1 μl antibody and 3 μl PA-MNase were pre-incubated on ice in 4 μl antibody binding buffer (10 mM Tris-Cl (pH 7.5), 1 mM EDTA, 150 mM sodium chloride, 0.1% Triton X-100) for 30 min. Meanwhile, H1 fixed cells (1 million) and HEK 293T fixed cells (1 million) were resuspended in 100 μl antibody binding buffer. Then, cell suspension was added to the PA-MNase and antibody complex, incubated on ice for 1 hour. Cells were washed three times with high salt buffer (10 mM Tris-Cl (pH 7.5), 1 mM EDTA, 400 mM sodium chloride and 1% (v/v) Triton X-100), followed by washing once with rinsing buffer (10 mM Tris pH7.5, 10 mM sodium chloride and 0.1% (v/v) Triton X-100). Then the cells were resuspended in 40 μl reaction solution buffer (10 mM Tris-Cl (pH 7.4), 10 mM sodium chloride, 0.1% (v/v) Triton X-100, 2 mM CaCl2), incubated at 37°C for 3min in water bath. The reaction was stopped by adding 4.4 μl 100mM EGTA. After washing twice with rinsing buffer, the cells were end-repaired by T4 Polynucleotide Kinase (PNK) in 150 μl reaction buffer (1 x PNK buffer, 1mM ATP, 150 unites PNK) at 37°C for 30min, followed by washing twice with rinsing buffer to stop the reaction.The cells were resuspended in 25 μl reverse transcription buffer (5 μl 10 x Maxima H Minus reverse transcription buffer, 1.25 μl 10% NP40, 16.75 μl H2O, 1 μl 100 μm not-so-random primer, 1 μl 10ng/μl Oligo dT22 primer (NNNNNNGAGCGTTTTTTTTTTTTTTTTTTTTTTVN)). After incubated at 65°C for 1min, the reaction was immediately put on ice, while the enzyme mix is prepared (8.75 μl H2O, 5 μl 10 x Maxima H Minus reverse transcription buffer, 8 μl 10 mM dNTPs, 2 μl Maxima H Minus reverse transcriptase, 0.625 μl SUPERase• In™ RNase Inhibitor, 0.625 μl RNaseOUT™ Recombinant Ribonuclease Inhibitor) and added into the reaction. The reverse transcription is performed as described in [15] (50 °C × 10 min; 3 cycles for the following: 8°C × 12s, 15°C × 45s, 20°C × 45s, 30°C × 30s, 42°C × 2min, 50°C × 5 min; 50 °C × 10 min and hold at 4 °C). The cells were washed twice with rinsing buffer, resuspended in 50 μl reaction buffer (5 μl 10 × Exo I buffer, 1 μl Exo I, 44 μl H2O) and incubated at 37°C for 20min. This is to remove the excess primers left after reverse transcription. After digestion, the cells were washed twice with rinsing buffer to stop the reaction.
96 barcode-P7 adaptors (10 μM) stored in a 96 well plate were thawed at 4 °C, then 1 μl of each was added to the corresponding well in a new 96 well plate with multichannel pipette. Downstream library construction was performed as described previously. Briefly, the cells were suspended with nuclei suspension buffer and mixed with enzyme dilution buffer, followed by aliquoted into 10 μl in 96 wells, mixing with the added barcode-P7 adaptors. The plate was sealed completely and incubated at 37°C for 60min. After incubation, the cells were pooled together in a solution trough containing 500 μl stop buffer, resuspended with 800 μl 1× PBS and send to flow cytometry core. 30 cells were sorted in each well of a new 96 well plate which contain 13 μl buffer mixture per well (3 μl reverse-crosslink buffer, 10 μl PBS containing 0.1% NP40). The plate was sealed completely and incubated at 65°C for 6 hours and 80°C for 10 min. After reverse crosslink, indexed PCR1 was performed by adding 13 μl 2x Phusion® High-Fidelity PCR Master Mix with HF Buffer (New England BioLabs) and 1 μl 2 μM index primer with the following condition: 98 °C 3 min, 12 cycles of 65 °C 30s, 72 °C 30s, followed by 72 °C 5 min. Then the libraries were pooled together, digested with Exo I and purified by MinElute® Reaction Cleanup Kit (Qiagen). Downstream A-tailing and P5 adaptor ligation were performed as described previously. PCR2 amplification with i5 index primer and P7-cs2 primer was set in the following condition:  98 °C 3 min, 57 °C 3 min, 72 °C 1 min, 7 cycles of 98 °C 10s, 65 °C 15s, 72 °C 30s, followed by 72 °C 5 min. The PCR products were run on the 2% E-Gel® EX Agarose Gel (Invitrogen). The fragments between 250–600 base pair (bp) were isolated and purified by the MinElute Gel Extraction Kit (Qiagen). The concentration of the library was measured by Qubit dsDNA HS kit (Thermo Fisher Scientific). The paired-end sequencing was performed on Illumina Hiseq 2500

tag: cell lines

value: 293T and H1 cells


title: ESCA_KZ-5

city: Beijing

first: Zhi

middle: John

last: Lu

address: Shuangqing Road

department: School of Life Sciences

country: China

institute: Tsinghua University

description:
cell-free RNA
RNA-seq of homo sapiens: Esophagus Cancer patient's plasma; Provided by Peking University First Affiliated Hospital; Constructed by SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian; Purpose: To explore novel plasma extracellular RNA biomarkers for cancer diagnosis

library_source: transcriptomic

data_processing:
Adaptors and low-quality sequences in the raw sequencing data were trimmed using cutadapt version 2.3. Remeined reads were mapped to ERCC's spike-in sequences, NCBI's UniVec sequences and human rRNA sequences sequentially. GC oligos introduced in reverse transcription were trimmed off, after which reads shorter than 30 nt were discarded.
STAR (version 2.5.3a_modified) was used to map clean reads to the hg38 genome index built with the GENCODE v27 annotation
Duplicates in the aligned reads were removed using Picard Tools MarkDuplicates (version 2.20.0)
The count matrix was constructed using featureCounts11 v1.6.2 with the GENCODE v27 annotation, transcripts with uncertain coding potential annotation extracted from mitranscriptome, circular RNA annotation from circBase, Promoter, enhancer and repeat regions frm UCSC Genome Browser. Reads mapped to mitochondrial RNAs were excluded.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

source_name: plasma

extract_protocol:
cfRNAs were extracted from 1 mL of plasma using the Plasma/Serum Circulating RNA and Exosomal Purification kit (Norgen)
SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian

tag: age

tag: gender

value: male

tag: disease

value: Esophagus Cancer patient


title: GC0713175_S175

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_172

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

description: Nasal Prox1+ cells

library_source: transcriptomic single cell

data_processing:
Demultiplexed fastq files were aligned to mm10 mouse reference genome by STAR aligner.
Raw read count matrix were made by featureCounts from Subread package
Raw read count matrix were read by Seurat (v3.1.1). Then, low quality cells (expressing less than 1000 genes), potential dead cells (>10% mitochondrial gene percentage) and contaminating Prox1- cells were removed for EC datasets. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for nasal Prox1+ cells from Prox1-GFP mouse

organism: Mus musculus

source_name: Nasal Prox1+ cells

growth_protocol: Smart-Seq3 single-cell RNA libraries

extract_protocol:
FACS sorted nasal Prox1+ cells were processed by Smart-Seq3 protocol
Libraries were generated following Smart-Seq3 protocol (Hagemann-Jensen M et al.,Single-cell RNA counting at allele and isoform resolution using Smartseq3. Nat Biotechnol 2020)

tag: cell type

value: Nasal Prox1+ cells

tag: strain

value: FVB


title: nasal_prox1_174

description: Nasal Prox1+ cells


title: ESCA_PKU-2412110


title: ESCA_KZ-20


title: GC0713178_S178

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_171

description: Nasal Prox1+ cells


title: nasal_prox1_176

description: Nasal Prox1+ cells


title: ESCA_KZ-7


title: nasal_prox1_169

description: Nasal Prox1+ cells


title: nasal_prox1_170

description: Nasal Prox1+ cells


title: GC0713169_S169

description:
genomic DNA and RNA
scPCOR-seq


title: ESCA_KZ-17


title: GC0713168_S168

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713171_S171

description:
genomic DNA and RNA
scPCOR-seq


title: ESCA_KZ-15


title: nasal_prox1_165

description: Nasal Prox1+ cells


title: ESCA_KZ-10


title: GC0713167_S167

description:
genomic DNA and RNA
scPCOR-seq


title: ESCA_569799


title: ESCA_KZ-19


title: GC0713173_S173

description:
genomic DNA and RNA
scPCOR-seq


title: ESCA_569608


title: nasal_prox1_168

description: Nasal Prox1+ cells


title: nasal_prox1_167

description: Nasal Prox1+ cells


title: GC0713164_S164

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_166

description: Nasal Prox1+ cells


title: nasal_prox1_173

description: Nasal Prox1+ cells


title: barcoded retroviral library

city: Shanghai

first: Zhiwen

last: You

address: 320 Yueyang Road

department: Institute of Neuroscience

institute: Chinese Academy of Sciences

description: Plasmid library

library_source: other

data_processing:
scRNA-seq data were aligned with the human reference genome, GRCh38-3.0.0, and demultiplexed using the default parameters of Cellranger software (10x Genomics, v3.0.2 or v4.0.0). Obtained filtered count matrix was used for downstream analysis.The filtered count matrix was analyzed and processed using Seurat (v3.1.4) and Scanpy (v3.0.46), including data filtering, normalization, highly variable genes selection, scaling, dimension reduction, and clustering.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: synthetic construct

source_name: barcoded retroviral library

extract_protocol:
For scRNA-seq, the neuro-spheres were digested by TrypLE Enzyme at 37℃ for 10 minutes and dissociated into single cells. After 35-µm cell sieve filtering, the digested cells were sorted by FACS to collected EGFP-positive cells, which were then concentrated by centrifuge at 400 g for 5 minutes. All the sorted EGFP-positive cells were used to construct single cell library using Chromium Single Cell 3' Reagent Kits (v2 and v3) following the manufacturer’s guidelines (10X Genomics).
scRNA-seq library was performed according to the manufacter’s instructions (single cell 3’ v2 and v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains 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 apropiated sized 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. For barcoded viral library, we designed primer pairs with illumina adaptors to amplify the random barcode sequences from the retroviral barcode library plasmid pool (Forward, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTATTCGGAGGACGACCCTATTTG; Reverse, CAAGCAGAAGACGGCATACGAGATAGGATTCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGATCACTCTCGGCATGGACG) with the following PCR program: 1, 98 °C, 3 min; 2, 98 °C, 10 s; 3, 60 °C, 10 s; 4, 72 °C, 25 s; 5, repeat steps 2–4 15 times; 6, 72 °C, 3 min; 7, 4 °C, hold. The PCR products were purified by 0.85× left-sided size selection using Ampure XP bead (Beckman Coulter, catalogue number A63880) and then sequenced on Illumina HiSeq PE150. For cell lineage barcode recovered from single cell transcriptome, following the reverse transcription of mRNA and first strand cDNA amplification, 50 ng of the unfragmented cDNA libraries were used as templates to specifically amplify cell barcodes and virus barcodes with primers pairs: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC and CAAGCAGAAGACGGCATACGAGATAGGATTCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGCATGGACGAGCTGTACAAATAA, using the following program: 1, 98 °C, 3 min; 2, 98 °C, 10 s; 3, 60 °C, 15 s; 4, 72 °C, 1 min; 5, repeat steps 2–4 20 times; 6, 72 °C, 3 min; 7, 4 °C, hold. The PCR products were then purified by 0.8-0.6× dual-sided size selection using Ampure XP bead and sequenced using Illumina HiSeq PE150.

value: barcoded retroviral library


title: GC0713166_S166

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713163_S163

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713170_S170

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_164

description: Nasal Prox1+ cells


title: GC0713162_S162

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_162

description: Nasal Prox1+ cells


title: nasal_prox1_163

description: Nasal Prox1+ cells


title: nasal_prox1_157

description: Nasal Prox1+ cells


title: nasal_prox1_161

description: Nasal Prox1+ cells


title: nasal_prox1_158

description: Nasal Prox1+ cells


title: EPZ, 5-4

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description: counts_raw.txt column: 8

data_processing:
Trimmed using Trim_Galore (v 0.5.0)
Aligned using STAR (v 2.6.0)
UMI collapsed using Lexogen’s supplied collapse_UMI_bam binary
Assembly: hg19
Supplementary files format and content: tab-delimited text of raw counts

growth_protocol: MDA-MB-231 cells were orthotopically injected into the right inguinal mammary fat pad of anesthetized mice at a concentration of 2 x10^6 cells resuspended in 50 μl of Matrigel (n = 10 mice per group)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
QuantSeq

treatment_protocol: When tumors reached 100 mm3 mice were treated 5 days/weeks by intraperitoneal (i.p.) injection with 4% DMSO-30% PEG 300-5% Tween 80 (control), P38i, SB202190 (1mg/kg/day), EZH2i, EPZ-6428 (10mg/kg/day) or a combination of SB202190 and EPZ-6438

tag: cell line

value: triple-negative breast cancer (TNBC) cell

tag: treatment

value: EPZ


title: nasal_prox1_154

description: Nasal Prox1+ cells


title: nasal_prox1_160

description: Nasal Prox1+ cells


title: nasal_prox1_159

description: Nasal Prox1+ cells


title: nasal_prox1_156

description: Nasal Prox1+ cells


title: nasal_prox1_152

description: Nasal Prox1+ cells


title: GC0713165_S165

description:
genomic DNA and RNA
scPCOR-seq


title: EPZ, 6-1

description: counts_raw.txt column: 9


title: EPZ, 5-3

description: counts_raw.txt column: 7


title: nasal_prox1_155

description: Nasal Prox1+ cells


title: P38-, 4-2

description: counts_raw.txt column: 5


title: GC0713160_S160

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_153

description: Nasal Prox1+ cells


title: P38-, 3-4

description: counts_raw.txt column: 5


title: nasal_prox1_149

description: Nasal Prox1+ cells


title: nasal_prox1_151

description: Nasal Prox1+ cells


title: GC0713159_S159

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713161_S161

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_147

description: Nasal Prox1+ cells


title: nasal_prox1_150

description: Nasal Prox1+ cells


title: GC0713157_S157

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_148

description: Nasal Prox1+ cells


title: P38, 3-3

description: counts_raw.txt column: 4


title: nasal_prox1_144

description: Nasal Prox1+ cells


title: control, 2-1

description: counts_raw.txt column: 3


title: nasal_prox1_145

description: Nasal Prox1+ cells


title: nasal_prox1_146

description: Nasal Prox1+ cells


title: GC0713156_S156

description:
genomic DNA and RNA
scPCOR-seq


title: control, 1-3

description: counts_raw.txt column: 2


title: GC0713158_S158

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_143

description: Nasal Prox1+ cells


title: GC0713155_S155

description:
genomic DNA and RNA
scPCOR-seq


title: control, 1-1

description: counts_raw.txt column: 1


title: nasal_prox1_141

description: Nasal Prox1+ cells


title: nasal_prox1_140

description: Nasal Prox1+ cells


title: COMBO, 9-2

description: counts_raw.txt column: 12

value: Combo (EPZ + P38i)


title: GC0713154_S154

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_137

description: Nasal Prox1+ cells


title: nasal_prox1_139

description: Nasal Prox1+ cells


title: nasal_prox1_142

description: Nasal Prox1+ cells


title: GC0713153_S153

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_136

description: Nasal Prox1+ cells


title: nasal_prox1_134

description: Nasal Prox1+ cells


title: nasal_prox1_135

description: Nasal Prox1+ cells


title: COMBO, 8-1

description: counts_raw.txt column: 10


title: nasal_prox1_133

description: Nasal Prox1+ cells


title: COMBO, 9-1

description: counts_raw.txt column: 11


title: GC0713152_S152

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713151_S151

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_131

description: Nasal Prox1+ cells


title: nasal_prox1_138

description: Nasal Prox1+ cells


title: GC0713149_S149

description:
genomic DNA and RNA
scPCOR-seq


title: MINA_KO_ChIPSeq

city: Stony Brook

first: Fei

last: Chen

state: New York

address: Lauterbur Drive Stony Brook, NY 11794

institute: Stony Brook Cancer Center

data_processing:
The 75-nt sequence reads were generated using Illumina NextSeq 500 platform.
The reads were mapped to the genome hg19 using the BWA algorithm with default settings.
The 75-nt reads were extended in silico (using Active Motif software) at their 3 ́- ends to a length of 200 bp fragments. The densities of fragments along the genome were determinated by dividing the genome into 32-nt bins and then counting the number of fragments in each bin. This signal maps were stored in bigWig files.
The peaks are called using SICER algorithm (version 1.1).
Normalized method is Drosophila spike-in adjustment
Assembly: hg19
Supplementary files format and content: bigWig files include fragment densities.

molecule: genomic DNA

source_name: Breast ( Breast Cancer)

growth_protocol: Cells were grown in DMEM/F-12 GlutaMAX™ medium (Gibco #10565018) supplemented with 10% FBS, , 1% Pen/strep Penicillin-Streptomycin (10,000 U/mL), and 2ug/ml Blasticidin.

extract_protocol:
Ten million WT and KO MDA-MB 231 cells were fixed and subjected to immunoprecipitation using ChIP-grade antibodies against H3K4me3 (Active Motif Cat# 39159), H3K9me3 (Active Motif Cat# 39161), H3K36me3 (Active Motif cat # 61101)  H4K20me3 (Abcam cat #ab9053) and MINA (Active Motif cat#61713).  ChIP and input/control DNA were prepared for sequencing using Illumina NextSeq 500.
Libraries were generated using Next Gen DNA library kit (active motif #53216)

treatment_protocol: Mdig KO cells and WT were generated by CRISPR-Cas9. KO cells do not express mdig/mina53 (Invitrogen # 397300), whereas  WT cells have normal mdig protein expression.

tag: tissue

value: Breast ( Breast Cancer)

value: MDA-MB 231 KO

tag: genotype

value: Triple negative breast cancer

tag: chip antibody

value: MINA/RIOX2  Active Motif Cat # 61713


title: nasal_prox1_128

description: Nasal Prox1+ cells


title: nasal_prox1_129

description: Nasal Prox1+ cells


title: nasal_prox1_127

description: Nasal Prox1+ cells


title: Input DNA_Seq

value: MDA-MB 231


title: nasal_prox1_126

description: Nasal Prox1+ cells


title: H4K20me3_KO_ChIPSeq

value: H4K20me3 Abcam Cat # ab9053


title: MINA_WT_ChIPSeq

value: MDA-MB 231 WT


title: nasal_prox1_125

description: Nasal Prox1+ cells


title: H4K20me3_WT_ChIPSeq


title: nasal_prox1_123

description: Nasal Prox1+ cells


title: GC0713148_S148

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713150_S150

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_130

description: Nasal Prox1+ cells


title: nasal_prox1_132

description: Nasal Prox1+ cells


title: GC0713147_S147

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_122

description: Nasal Prox1+ cells


title: H3K36me3_WT_ChIPSeq

value: H3K36me3 Active Motif Cat # 61101


title: nasal_prox1_121

description: Nasal Prox1+ cells


title: nasal_prox1_119

description: Nasal Prox1+ cells


title: nasal_prox1_118

description: Nasal Prox1+ cells


title: GC0713144_S144

description:
genomic DNA and RNA
scPCOR-seq

value: 293T and H1 cells


title: H3K36me3_KO_ChIPSeq


title: GC0713145_S145

description:
genomic DNA and RNA
scPCOR-seq


title: H3K9me3_KO_ChIPSeq

value: H3K9me3 Active Motif Cat # 39161


title: nasal_prox1_117

description: Nasal Prox1+ cells


title: GC0713146_S146

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_120

description: Nasal Prox1+ cells


title: H3K9me3_WT_ChIPSeq


title: nasal_prox1_124

description: Nasal Prox1+ cells


title: nasal_prox1_114

description: Nasal Prox1+ cells


title: nasal_prox1_115

description: Nasal Prox1+ cells


title: nasal_prox1_112

description: Nasal Prox1+ cells


title: H3K4me3_KO_ChIPSeq

value: H3K4me3 Active Motif Cat # 39159


title: GC0713141_S141

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713142_S142

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_113

description: Nasal Prox1+ cells

value: Nasal Prox1+ cells


title: H3K4me3_WT_ChIPSeq


title: nasal_prox1_111

description: Nasal Prox1+ cells

value: FVB


title: nasal_prox1_110

description: Nasal Prox1+ cells


title: MDA231_H182_2uM_3

city: Los Angeles

first: Peibin

last: Yue

state: CA

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

description: Total RNA

data_processing:
Sample libraries are multiplexed and sequenced on a NextSeq 500 platform (Illumina) using 75bp single-end sequencing. On average, about 20 million reads were generated from each sample. Raw reads obtained from RNA-Seq were aligned to the transcriptome using STAR (version 2.5.0) (Dobin A et al., 2013) / RSEM (version 1.2.25) (Li B and Dewey CN, 2011) with default parameters, using human GRCh38 transcriptome reference downloaded from http://www.gencodegenes.org, containing all protein coding genes and long non-coding RNA genes based on human GENCODE version 23 annotation.
Supplementary_files_format_and_content: Gene expression matrix (TPM)

source_name: Breast cancer cell line MDA-MB-231

extract_protocol:
Total RNA was prepared using Qiagen RNeasy Mini kit according to the manufacturer’s instructions.
Library construction was performed using the Illumina TruSeq Stranded mRNA library preparation kit. Briefly, total RNA samples were assessed for concentration using a Qubit fluorometer and quality using the 2100 Bioanalyzer. Up to one µg of total RNA per sample was used for poly-A mRNA selection. cDNA was synthesized from enriched and fragmented RNA using reverse transcriptase and random primers. The cDNA was further converted into double-stranded DNA (dsDNA), and the resulting dsDNA was enriched with PCR for library preparation. The PCR-amplified library was purified using Agencourt AMPure XP beads. The concentration of the amplified library was measured with a Qubit fluorometer and an aliquot of the library was resolved on a Bioanalyzer.

value: Breast cancer cell line

value: H182 at 2 uM for 2 hours


title: nasal_prox1_109

description: Nasal Prox1+ cells


title: nasal_prox1_108

description: Nasal Prox1+ cells


title: MDA231_H182_2uM_2

description: Total RNA


title: nasal_prox1_107

description: Nasal Prox1+ cells


title: GC0713143_S143

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713140_S140

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713138_S138

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713139_S139

description:
genomic DNA and RNA
scPCOR-seq


title: MDA231_Cont_3

description: Total RNA

value: DMSO


title: nasal_prox1_104

description: Nasal Prox1+ cells


title: nasal_prox1_116

description: Nasal Prox1+ cells


title: nasal_prox1_102

description: Nasal Prox1+ cells


title: nasal_prox1_106

description: Nasal Prox1+ cells


title: MDA231_Cont_2

description: Total RNA


title: nasal_prox1_103

description: Nasal Prox1+ cells


title: MDA231_H182_2uM_1

description: Total RNA


title: nasal_prox1_105

description: Nasal Prox1+ cells


title: GC0713136_S136

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_100

description: Nasal Prox1+ cells


title: nasal_prox1_101

description: Nasal Prox1+ cells


title: MDA231_Cont_1

description: Total RNA


title: nasal_prox1_98

description: Nasal Prox1+ cells


title: nasal_prox1_99

description: Nasal Prox1+ cells


title: GC0713134_S134

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713135_S135

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_95

description: Nasal Prox1+ cells


title: nasal_prox1_96

description: Nasal Prox1+ cells


title: nasal_prox1_97

description: Nasal Prox1+ cells


title: nasal_prox1_93

description: Nasal Prox1+ cells


title: GC0713132_S132

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713133_S133

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_94

description: Nasal Prox1+ cells


title: GC0713131_S131

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_91

description: Nasal Prox1+ cells


title: nasal_prox1_90

description: Nasal Prox1+ cells


title: GC0713137_S137

description:
genomic DNA and RNA
scPCOR-seq


title: RNA-seq_RELA4-R1

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

data_processing:
Raw RRBS FASTQ files were mapped to NCBI Human Reference Genome Build GRCh37 (hg19) using BSMAP RRBS mode (Xi and Li, 2009). DNA methylation ratio and differential methylated cytosine (DMCs/DMRs) were analyzed by using MOABS (Sun et al., 2014). CpG sites with five or more reads covered were used for downstream analysis. Bisulfite conversion rates were estimated on the basis of lambda phage genome spike-ins. The bedGraph files including single base pair DNA methylation ratios were transformed to bigwig file format which can be visualized using the UCSC genome browser. DNA methylation heatmaps were plotted using R package https://www.rdocumentation.org/packages/heatmap3/versions/1.1.6/topics/heatmap3 heatmap3 by taking the shared CpGs among all the samples as input. DNA methylation phylogenetics analysis was performed by using R package ape
To compare multiple groups’ DMCs, we merge all the DMCs in all two-group comparisons (union DMC sets). The UpSetR (Conway et al., 2017) package was used to visualize the union of DMC sets among multiple two-group comparisons. To analyze dynamic changes of DMCs among tumor recurrent, we first separate DMCs to three categories (Hyper; Hypo; NoChange) based on adjacent two recurrent stages. Then, by considering four adjacent recurrent stages (P vs. cerebellum; R1 vs. cerebellum; R2 vs. cerebellum and R3 vs. cerebellum), we filtered out those DMCs with hyper/hypo and hypo/hyper switch between any two adjacent stages due to the small numbers. We finally separated DMCs into seven categories: consistent Hyper; consistent Hypo; Gain Hyper; Gain Hypo; Loss Hyper; Loss Hypo and switch (between hyper/hypo and NoChange). R alluvial package (https://www.rdocumentation.org/packages/alluvial/versions/0.1-2/topics/alluvial) was used to visualize the dynamic changes of DMCs along tumor recurrence. Colored density scatterplot of DNA methylation ratios was performed by using R package smoothScatter (https://www.rdocumentation.org/packages/graphics/versions/3.6.1/topics/smoothScatter). GREAT (McLean et al., 2010) was used to predict DMRs’ functions.
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to do quality checks for raw fastq files. Raw FASTQ files were aligned to NCBI Human Reference Genome Build GRCh37 (hg19) using HISAT2 (Kim et al., 2019) with default settings. The uniquely mapped reads were used for downstream analysis. HTSeq (Anders et al., 2015) was used to count the reads count mapped in exon regions for each gene. Read counts matrix (row as genes; column as samples) were inputted to DESeq2 (Love et al., 2014) to identify differentially expressed genes (DEGs). We consider genes with FDR<=0.05 and fold change >= 2 folds as DEGs. Principal component analysis of DEGs was performed using R package DESeq2. DEGs’ function enrichment was using GSEA (Subramanian et al., 2005).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: GEO.merge.normalized2.txt: normalized counts for RNA-seq samples

source_name: brain

extract_protocol:
Freshly resected ependymoma tumor specimens from 10 patients undergoing serial surgical resections of primary and recurrent tumors (total 33, 3.67±1.76) over a period of 13 years (5.8 ±3.8) at Texas Children’s Hospital were obtained for this study.
Genomic DNA was extracted with Allprep DNA/RNA mini kit (Qiagen).  and concentrations measured using the Qubit® dsDNA BR Assay Kit (Thermo Fisher Scientific), followed by DNA quality assessment with the Fragment AnalyzerTM and either the DNF-487 Standard Sensitivity or the DNF-488 High sensitivity genomic DNA Analysis Kit (Advanced Analytical). RRBS libraries were prepared using the Premium Reduced Representation Bisulfite Sequencing (RRBS) Kit (Diagenode Cat# C02030033), according to the manufacturer's protocol. 100ng of genomic DNA were used to start library preparation for each sample. Following library preparation, samples were pooled together either by 8 (mouse contamination up to 10%), 7 (mouse contamination up to 25%), 5 (mouse contamination up to 40%) or 4 (mouse contamination up to 55%). In total, 16 pools were prepared. PCR clean-up after the final library amplification was performed using a 1.5x beads:sample ratio of Agencourt® AMPure® XP (Beckman Coulter). RRBS library pools quality control was performed by measuring DNA concentration of the pools using the Qubit® dsDNA HS Assay Kit (Thermo Fisher Scientific), and the profile of the pools was checked using the High Sensitivity DNA chip for 2100 Bioanalyzer (Agilent). Each RRBS library pool was deep sequenced on one lane HiSeq3000 (Illumina) using 50 bp single-read sequencing (SR50).
RNAseq libraries for transcriptome analysis were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) and Agilent Automation NGS system per manufacturers’ instructions. Sample prep began with 1 µg of total RNA from each sample. Poly-A RNA was purified from the sample with oligo dT magnetic beads, and the poly(A) RNA was fragmented with divalent cations. Fragmented poly-A RNA was converted into cDNA through reverse transcription and were repaired using T4 DNA polymerase, Klenow polymerase, and T4 polynucleotide kinase. 3’ A-tailing with exo-minus Klenow polymerase was followed by ligation of Illumina paired-end oligo adapters to the cDNA fragment. Ligated DNA was PCR amplified for 15 cycles and purified using AMPure XP beads. After purification of the PCR products with AMPure XP beads, the quality and quantity of the resulting

value: brain

tag: diagnosis

value: pediatric Ependymoma


title: RNA-seq_RELA3-P


title: RNA-seq_RELA2-R2


title: RNA-seq_RELA2-R1


title: RNA-seq_RELA3-R1


title: nasal_prox1_87

description: Nasal Prox1+ cells


title: nasal_prox1_89

description: Nasal Prox1+ cells


title: nasal_prox1_88

description: Nasal Prox1+ cells


title: GC0713130_S130

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713128_S128

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713127_S127

description:
genomic DNA and RNA
scPCOR-seq


title: RNA-seq_RELA5-P


title: nasal_prox1_85

description: Nasal Prox1+ cells


title: nasal_prox1_86

description: Nasal Prox1+ cells


title: RNA-seq_RELA2-P


title: nasal_prox1_92

description: Nasal Prox1+ cells


title: RNA-seq_RELA1-R4


title: nasal_prox1_82

description: Nasal Prox1+ cells


title: GC0713125_S125

description:
genomic DNA and RNA
scPCOR-seq


title: RNA-seq_RELA1-R7


title: nasal_prox1_83

description: Nasal Prox1+ cells


title: GC0713129_S129

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713126_S126

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_79

description: Nasal Prox1+ cells


title: nasal_prox1_80

description: Nasal Prox1+ cells


title: GC0713124_S124

description:
genomic DNA and RNA
scPCOR-seq


title: RNA-seq_RELA1-R3


title: RNA-seq_RELA1-R2


title: nasal_prox1_76

description: Nasal Prox1+ cells


title: nasal_prox1_78

description: Nasal Prox1+ cells


title: RNA-seq_PFA5-R2


title: nasal_prox1_84

description: Nasal Prox1+ cells


title: nasal_prox1_74

description: Nasal Prox1+ cells


title: nasal_prox1_73

description: Nasal Prox1+ cells


title: nasal_prox1_77

description: Nasal Prox1+ cells


title: GC0713122_S122

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_72

description: Nasal Prox1+ cells


title: RNA-seq_PFA5-R1


title: nasal_prox1_81

description: Nasal Prox1+ cells


title: nasal_prox1_71

description: Nasal Prox1+ cells


title: GC0713121_S121

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713120_S120

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_70

description: Nasal Prox1+ cells


title: RNA-seq_PFA4-P


title: nasal_prox1_68

description: Nasal Prox1+ cells


title: GC0713123_S123

description:
genomic DNA and RNA
scPCOR-seq


title: RNA-seq_PFA3-P


title: GC0713118_S118

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_69

description: Nasal Prox1+ cells


title: GC0713119_S119

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_75

description: Nasal Prox1+ cells


title: nasal_prox1_64

description: Nasal Prox1+ cells


title: nasal_prox1_67

description: Nasal Prox1+ cells


title: nasal_prox1_62

description: Nasal Prox1+ cells


title: nasal_prox1_61

description: Nasal Prox1+ cells


title: nasal_prox1_66

description: Nasal Prox1+ cells


title: nasal_prox1_63

description: Nasal Prox1+ cells


title: GC0713116_S116

description:
genomic DNA and RNA
scPCOR-seq


title: RNA-seq_PFA4-R1


title: GC0713115_S115

description:
genomic DNA and RNA
scPCOR-seq


title: RNA-seq_Cerebrum-a0417-nc


title: nasal_prox1_59

description: Nasal Prox1+ cells


title: RNA-seq_PFA1-R3


title: GC0713114_S114

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713117_S117

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_57

description: Nasal Prox1+ cells


title: RNA-seq_PFA2-R1


title: nasal_prox1_58

description: Nasal Prox1+ cells


title: RNA-seq_PFA1-R1


title: nasal_prox1_55

description: Nasal Prox1+ cells


title: nasal_prox1_56

description: Nasal Prox1+ cells


title: nasal_prox1_54

description: Nasal Prox1+ cells


title: RNA-seq_PFA2-R2


title: GC0713113_S113

description:
genomic DNA and RNA
scPCOR-seq


title: RNA-seq_Cerebrum-1215dipg-nc


title: GC0713111_S111

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_53

description: Nasal Prox1+ cells


title: nasal_prox1_52

description: Nasal Prox1+ cells


title: nasal_prox1_60

description: Nasal Prox1+ cells


title: RNA-seq_Cerebellum-h0712dipg-icb


title: nasal_prox1_65

description: Nasal Prox1+ cells


title: GC0713112_S112

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_49

description: Nasal Prox1+ cells


title: nasal_prox1_51

description: Nasal Prox1+ cells


title: WER653

city: Raleigh

first: Terri

middle: A

last: Long

state: NC

department: Plant & Microbial Biology

institute: North Carolina State University

data_processing:
sequenced using an Illumina HiSeq 2500 sequencing machine .
125bp single end reads
Adapters and low quality reads were filtered out using fastQC and fastq-mcf.
Assembly: Clean reads were mapped against the TAIR 10 reference genome using the tophat2
Supplementary files format and content: RPKM were acquired using RSubread, followed by edgeR to identify differentially expressed genes (DEGs), using a maximum false discovery rate (FDR) of 0.05 and minimum log fold change threshold of 0.75.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana roots

growth_protocol: Plants grown vertically on top of mesh placed on MS

extract_protocol:
Roots were seperated by a razor, flash frozen with liqiud nitrigen, and RNA was harvested using RNAeasy Plant RNA Purification Kit (Qiagen).
RNA libraries were prepared for sequencing by performing cDNA synthesis and amplification using the NEBNext® Poly(A) mRNA Magnetic Isolation Module followed by the NEBNext® Ultra™ II Directional RNA Library Prep and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1)

treatment_protocol:
4d +Fe then transferred for 3d - Fe
Iron-sufficient (+Fe) media is standard Murashige and Skoog media with 0.05% MES, 1% sucrose, 1% agar, and 0.1 mM FeEDTA. Iron deficient (−Fe) media is as mention above minus the 0.1mM FeEDTA, with the addition of 300 μM ferrozine, an iron chelator

value: Roots

value: Minus Iron

value: 7 day old

tag: gfp localization

value: EP


title: nasal_prox1_47

description: Nasal Prox1+ cells


title: WER651


title: nasal_prox1_46

description: Nasal Prox1+ cells


title: GC0713109_S109

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713107_S107

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_43

description: Nasal Prox1+ cells


title: WER131

value: EP-C


title: WER133


title: GC0713108_S108

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_50

description: Nasal Prox1+ cells


title: nasal_prox1_41

description: Nasal Prox1+ cells


title: nasal_prox1_48

description: Nasal Prox1+ cells


title: nasal_prox1_45

description: Nasal Prox1+ cells


title: nasal_prox1_42

description: Nasal Prox1+ cells


title: GC0713106_S106

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_38

description: Nasal Prox1+ cells


title: GC0713104_S104

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_40

description: Nasal Prox1+ cells


title: nasal_prox1_44

description: Nasal Prox1+ cells


title: PEP453

value: C-EN-V


title: GC0713110_S110

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713105_S105

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_39

description: Nasal Prox1+ cells


title: WER652


title: WER132


title: PEP452


title: SHR236

value: V-EN


title: GC0713103_S103

description:
genomic DNA and RNA
scPCOR-seq

value: 293T and H1 cells


title: nasal_prox1_36

description: Nasal Prox1+ cells


title: nasal_prox1_34

description: Nasal Prox1+ cells


title: nasal_prox1_35

description: Nasal Prox1+ cells


title: PEP451


title: GC0713101_S101

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_32

description: Nasal Prox1+ cells


title: nasal_prox1_33

description: Nasal Prox1+ cells


title: nasal_prox1_31

description: Nasal Prox1+ cells


title: nasal_prox1_37

description: Nasal Prox1+ cells


title: GC0713100_S100

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713099_S99

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_28

description: Nasal Prox1+ cells


title: nasal_prox1_30

description: Nasal Prox1+ cells


title: nasal_prox1_26

description: Nasal Prox1+ cells


title: SHR234


title: PPL2

value: PPL

value: V-EN-C-EP


title: nasal_prox1_25

description: Nasal Prox1+ cells

value: Nasal Prox1+ cells


title: nasal_prox1_27

description: Nasal Prox1+ cells

value: FVB


title: GC0713102_S102

description:
genomic DNA and RNA
scPCOR-seq


title: PPL3


title: GC0713098_S98

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_24

description: Nasal Prox1+ cells


title: PPL1


title: nasal_prox1_23

description: Nasal Prox1+ cells


title: nasal_prox1_21

description: Nasal Prox1+ cells


title: GC0713097_S97

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_19

description: Nasal Prox1+ cells


title: PYE2

value: PYE


title: nasal_prox1_20

description: Nasal Prox1+ cells


title: SHR235


title: GC0713096_S96

description:
genomic DNA and RNA
scPCOR-seq


title: PYE1


title: nasal_prox1_22

description: Nasal Prox1+ cells


title: GC0713095_S95

description:
genomic DNA and RNA
scPCOR-seq


title: PYE3


title: WTminus3

value: WT


title: nasal_prox1_29

description: Nasal Prox1+ cells


title: nasal_prox1_18

description: Nasal Prox1+ cells


title: nasal_prox1_16

description: Nasal Prox1+ cells


title: GC0713094_S94

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713093_S93

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_17

description: Nasal Prox1+ cells


title: nasal_prox1_14

description: Nasal Prox1+ cells


title: GC0713092_S92

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_15

description: Nasal Prox1+ cells


title: nasal_prox1_9

description: Nasal Prox1+ cells


title: WTminus1


title: nasal_prox1_13

description: Nasal Prox1+ cells


title: WTminus2


title: nasal_prox1_8

description: Nasal Prox1+ cells


title: GC0713091_S91

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713089_S89

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_12

description: Nasal Prox1+ cells


title: nasal_prox1_11

description: Nasal Prox1+ cells


title: GC0713090_S90

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_10

description: Nasal Prox1+ cells


title: WT3

treatment_protocol:
4d +Fe then transferred for 3d + Fe
Iron-sufficient (+Fe) media is standard Murashige and Skoog media with 0.05% MES, 1% sucrose, 1% agar, and 0.1 mM FeEDTA. Iron deficient (−Fe) media is as mention above minus the 0.1mM FeEDTA, with the addition of 300 μM ferrozine, an iron chelator

value: Plus Iron


title: nasal_prox1_5

description: Nasal Prox1+ cells


title: WT2


title: GC0713086_S86

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_7

description: Nasal Prox1+ cells


title: GC0713088_S88

description:
genomic DNA and RNA
scPCOR-seq


title: EC-095

city: University

first: Zhiqiang

last: Pan

state: MS

address: 1558 University Ave

institute: USDA-ARS-NPURU

description: Treated with 0.1percent EtOH ctrl for 24 h

data_processing:
Raw RNA-Seq data sequenced with Illumina HiSeq were imported into CLC Genomics Workbench version 7.0 as fastq files.
The raw reads underwent different types of trimming in the following sequential order: quality trimming, ambiguity trimming, adapter trimming, and length trimming.
The trimmed reads were them mapped against the Arabidopsis thaliana (Col-0 TAIR 10) reference sequence using CLC Genomics Workbench
The data was filtered using JMP Genomics version 7.0, and the filtered data was normalized using the TMM method.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

source_name: Roots

growth_protocol: Sterile square Petri dishes (100x15 mm) were prepared with 0.44% macro-and micronutrients and 1% sucrose in 0.8% agar. Twenty-four seeds were sown per plate, which were sealed with tape and placed in a growth chamber at 22 ºC and 16/8 h light/ dark photoperiod under light intensity of 120 µmol/m2sec.

extract_protocol:
Total RNAs were isolated from flash frozen Arabidopsis tissues using an RNeasy plant mini kit (Qiagen) according to the manufacturer’s instructions.
Library construction, quantification and qualification were performed by Global Biologics (Columbia, MO) using 1 ug  RNA and the IlluminaTruSeq RNA Library Preparation Kits.

treatment_protocol: Plants were grown on agar plates for 14 days in a growth chamber and then treated at 7 h after the beginning of the photoperiod by adding 8 mL per plate of the IC50 concentration (21 µM) of t-chalcone. After treatment, plants were incubated for 0, 1, 3, 6, 12 and 24 h.

tag: agent

value: 0.1percent EtOH ctrl

tag: time point


title: nasal_prox1_3

description: Nasal Prox1+ cells


title: GC0713087_S87

description:
genomic DNA and RNA
scPCOR-seq


title: nasal_prox1_4

description: Nasal Prox1+ cells


title: nasal_prox1_1

description: Nasal Prox1+ cells


title: nasal_prox1_6

description: Nasal Prox1+ cells


title: nasal_prox1_2

description: Nasal Prox1+ cells


title: GC0713085_S85

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713083_S83

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713084_S84

description:
genomic DNA and RNA
scPCOR-seq


title: WT in vitro Th17

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

data_processing:
Low quality reads and adaptor sequences were removed by Trim Galore v0.4.4 with parameters ‘-q 10 –length 30 –stringency 50.
Paired-end reads were mapped to the mm10 reference genome using Bowtie2 with –x2000.
Reads that aligned to the mitochondrial genome were filtered and PCR duplicates were removed with picard MarkDuplicates.
The uniquely mapped reads were used to call peak with MACS2 using a fdr value cutoff 0.01
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file

source_name: in vitro Th17

growth_protocol: Rorc_fl/fl (WT) or ERT2_cre Rorc_fl/fl (RorcERT2) naïve CD4+ T cells were activated with plate-bound anti-CD3 and anti-CD28 and cultured with TGF-β, IL-6, IL-1β and IL-23 for 3 days, and then treated with 4-OHT for another 96 hours.

extract_protocol: ATAC-seq DNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina and TruePrep Index Kit V2 for Illumina.

treatment_protocol: The cells were re-stimulated with plate-bound anti-CD3 for 4 hours before  genome extraction.


title: RorcERT2 in vitro Th17

value: ERT2cre Rorc_fl/fl


title: EC-093

description: Treated with Citral for 24 h

source_name: Shoots

value: Citral


title: 10X_whole_ct

description: Contorl nasal cells

data_processing:
Cell Ranger (v3.0.0) was used to process single cell 3' RNA-seq ouput. First, cell ranger mkfastq demultiplexed illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to mm10 mouse reference genome.
Aligned reads were then read by Seurat (v3.1.1) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 1000 genes), potential dead cells (>10% mitochondrial gene percentage) and contaminating CD31- cells were removed for EC datasets. Also, genes that are only expressed in less than 3 cells were discarded.
Expression matrices were made after quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for nasal ECs and whole cells from Ctrl mouse and AR model mouse

source_name: nasal cells

extract_protocol:
FACS sorted nasal cells or endothelial cells were processed on the 10X chromium system following the manufacturer's protocols
Using 10x single cell RNA sequencing 3' NEXT GEM v3.1 reagent Kit (10X genomics), cDNA libraries were constructed

value: nasal cells

tag: mouse model

value: Control

value: Adult


title: 10X_whole_ar

description: AR model nasal cells

growth_protocol: 10x single cell RNA sequencing 3' NEXT GEM v3.1

value: allergic rhinitis (AR)


title: GC0713082_S82

description:
genomic DNA and RNA
scPCOR-seq


title: EC-087


title: 10X_ec_ct

description: Control nasal EC

source_name: nasal endothelial cells (EC)s

value: nasal endothelial cells (EC)s


title: WT1

value: Roots

value: 7 day old


title: EC-096


title: GC0713081_S81

description:
genomic DNA and RNA
scPCOR-seq

value: 293T and H1 cells


title: EC-094


title: hop1∆/hop1∆ 0h cal WCE replicate 2

first: Shiv

last: Grewal

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

description: Calibrated ChIP was performed with a spike-in S. mikatae strain, The processed files show the calibrated chromatin immunoprecipitation/whole cell extract in reads per million (RPM). All strains have parS insert at the URA3 location between HindIII and SmaI restriction site and the Hop1 gene as shown in the title of the strain.

data_processing:
single ended fastq format sequences derived from ChIP-seq data were quality-trimmed using fastp (CHEN et al. 2018).
Trimmed fastqs from both IP and input were aligned separately to the SK1 target genome (YUE et al. 2017) modified to reflect the genotype of strains used and to the Saccharomyces mikatae IFO 1815 (KELLIS et al. 2003) spike-in control genome using minimap2 (LI 2018)
Reads that mapped uniquely to either genome were used to calculate the occupancy ratio (OR) i. e. ((ipSK1 / inSK1) / (ipSMIK / inSMIK))
Calibrated depths for reads mapping uniquely to the SK1 genome were determined by multiplying  read depths, normalized to reads per million mapped reads (RPM), by the OR computed in equation 1
Data processing was performed on the NIH HPC Biowulf cluster (http://hpc.nih.gov).
Assembly: SK1 target genome (YUE et al. 2017) modified have the parS insert at URA3 , deleted HIS4 and ARG4 genes and Hop1-ParB insert at HOP1 and Saccharomyces mikatae IFO 1815 (KELLIS et al. 2003) for spike-in genome
Supplementary files format and content: bigWig, calibrated ChIP/WCE in reads per million

organism: Saccharomyces cerevisiae

source_name: meiotic samples

growth_protocol: Strains were grown in liquid pre-sporulation medium and transferred to liquid sporulation medium as described (GOYON AND LICHTEN 1993)

extract_protocol:
Cells were fixed with 1% formaldehyde for 30 minutes. After quenching and cell lysis, chromatin was sonicated using Biorupter 300 (Diagnode).
ChIP-seq libraries were made using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, #E7645) and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs, New England Biolabs, #E6440). Sequencing was performed with an Illumina NextSeq 550 with the NextSeq 500/550 High Output Kit v2.5 (75 Cycles).

tag: time

value: meiotic samples

value: none (input)


title: hop1∆/hop1∆ 4h cal WCE replicate 2


title: EC-085


title: hop1∆/hop1∆ 4h cal WCE replicate 1


title: hop1∆/hop1∆ 3h cal WCE replicate 2


title: hop1∆/hop1∆ 3h cal WCE replicate 1


title: EC-084

description: Treated with Citral for 12 h


title: GC0713079_S79

description:
genomic DNA and RNA
scPCOR-seq

tag: cell lines


title: 10X_ec_ar

description: AR model nasal EC

tag: age


title: GC0713080_S80

description:
genomic DNA and RNA
scPCOR-seq


title: EC-092

description: Treated with Citral for 24 h


title: EC-083

description: Treated with Citral for 12 h


title: GC0713078_S78

description:
genomic DNA and RNA
scPCOR-seq


title: EC-078

description: Treated with 0.1percent EtOH ctrl for 12 h


title: GC0713077_S77

description:
genomic DNA and RNA
scPCOR-seq


title: HOP1-ParB HOP1/HOP1 0h cal WCE replicate 2

value: HOP1-ParB HOP1/HOP1


title: HOP1-ParB HOP1/HOP1 4h cal WCE replicate 2


title: HOP1-ParB HOP1/HOP1 3h cal WCE replicate 2


title: HOP1-ParB HOP1/HOP1 3h cal WCE replicate 1


title: hop1∆/hop1∆ 0h cal WCE replicate 1


title: HOP1-ParB HOP1/HOP1 4h cal WCE replicate 1


title: HOP1-ParB HOP1/HOP1 0h cal WCE replicate 1


title: HOP1/HOP1 4h cal WCE replicate 2


title: GC0713076_S76

description:
genomic DNA and RNA
scPCOR-seq


title: EC-077


title: HOP1/HOP1 3h cal WCE replicate 2


title: GC0713075_S75

description:
genomic DNA and RNA
scPCOR-seq


title: EC-075

description: Treated with Citral for 12 h


title: HOP1/HOP1 0h cal WCE replicate 2


title: EC-073

description: Treated with Citral for 12 h


title: EC-074

description: Treated with Citral for 12 h


title: EC-069


title: GC0713074_S74

description:
genomic DNA and RNA
scPCOR-seq


title: HOP1/HOP1 4h cal WCE replicate 1


title: HOP1/HOP1 0h cal WCE replicate 1


title: GC0713073_S73

description:
genomic DNA and RNA
scPCOR-seq


title: HOP1/HOP1 3h cal WCE replicate 1


title: hop1∆/hop1∆ 3h cal CHIP replicate 2

value: anti Hop1 antibody


title: GC0713072_S72

description:
genomic DNA and RNA
scPCOR-seq


title: hop1∆/hop1∆ 4h cal CHIP replicate 2


title: hop1∆/hop1∆ 0h cal CHIP replicate 2


title: hop1∆/hop1∆ 3h cal CHIP replicate 1


title: hop1∆/hop1∆ 4h cal CHIP replicate 1


title: GC0713071_S71

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713070_S70

description:
genomic DNA and RNA
scPCOR-seq


title: hop1∆/hop1∆ 0h cal CHIP replicate 1


title: HOP1-ParB HOP1/HOP1 4h cal CHIP replicate 2


title: EC-068


title: EC-067


title: EC-064

description: Treated with Citral for 6 h

value: 6 h


title: GC0713069_S69

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713068_S68

description:
genomic DNA and RNA
scPCOR-seq


title: EC-060

description: Treated with 0.1percent EtOH ctrl for 6 h


title: HOP1-ParB HOP1/HOP1 3h cal CHIP replicate 2


title: HOP1-ParB HOP1/HOP1 4h cal CHIP replicate 1


title: EC-059


title: GC0713066_S66

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713065_S65

description:
genomic DNA and RNA
scPCOR-seq


title: HOP1-ParB HOP1/HOP1 0h cal CHIP replicate 2


title: EC-066

description: Treated with Citral for 6 h


title: EC-065

description: Treated with Citral for 6 h


title: GC0713064_S64

description:
genomic DNA and RNA
scPCOR-seq


title: HOP1-ParB HOP1/HOP1 3h cal CHIP replicate 1


title: EC-058


title: HOP1-ParB HOP1/HOP1 0h cal CHIP replicate 1


title: GC0713067_S67

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713063_S63

description:
genomic DNA and RNA
scPCOR-seq


title: EC-057

description: Treated with Citral for 6 h


title: GC0713061_S61

description:
genomic DNA and RNA
scPCOR-seq


title: HOP1/HOP1 4h cal CHIP replicate 2


title: GC0713062_S62

description:
genomic DNA and RNA
scPCOR-seq


title: HOP1/HOP1 3h cal CHIP replicate 2


title: EC-056

description: Treated with Citral for 6 h


title: EC-055

description: Treated with Citral for 6 h


title: EC-051


title: EC-050


title: HOP1/HOP1 0h cal CHIP replicate 2


title: GC0713060_S60

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713059_S59

description:
genomic DNA and RNA
scPCOR-seq


title: Kidney_low salt_control_replicate_4 [Kidney_lsc_246]

type: RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: Standard Illumina protocol hybridizing 0.75 μg biotin-labeled cRNA at 58°C for 16 hours to Illumina's Rat RefExpression Bead Chips (Illumina, San Diego, CA). The arrays were washed, blocked, and biotin-labeled cRNA detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.8 μm using the Illumina BeadArray scanner.

data_processing: Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores is supplied.

organism: Rattus norvegicus

source_name: Kidney_low salt_control

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791). In short, 0.5 μg total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

growth_protocol: The experimental design of the study was approved by the Animal Care and Use Committee of the Intramural Research Program, National Institute on Aging, National Institutes of Health, and all procedures were performed in accordance with institutional guidelines. Six‐week‐old, male, Dahl salt‐sensitive (Dahl‐S, SS/JrHsd; Charles River Laboratories), body weight (BW) 218±6 g), were placed on a low salt (LS) diet (n=14; 0.1% NaCl; CAT#TD94268; Harlan Laboratories, Inc) or an HS diet (n=14; 8% NaCl; CAT#TD92012; Harlan Laboratories, Inc) and water ad libitum for 8 weeks.

extract_protocol: Total RNA was purified from the 50–60 ug  tissue per sample using the Qiagen RNeasy Mini Kit and following the manufacturers recommendations.  Total RNA was purified from the 50–60 ug  tissue sample using the Qiagen RNeasy Mini Kit (Qiagen Inc) kit following the manufacturers protocol.

treatment_protocol: Seven animals from each dietary salt group were treated once with mouse isotype IgG1 (50 μg IgG/kg BW; CAT#MAB002, clone 11711, R&D Systems, Inc) used as control (LS control [LSC] and HS control [HSC]), or with an anti‐marinobufagenin mAb (clone 3E9) intraperitoneally (50 μg IgG/kg BW) (groups LSAB and HSAB) at week 7 (15 weeks of age) on HS or LS diets. Antibodies were diluted in sterile 0.9% NaCl to the final concentration 50 μg IgG/mL.

value: SS/JrHsd

value: control antibody

value: Kidney

tag: Sex

value: Male

value: 16 week old


title: HOP1/HOP1 3h cal CHIP replicate 1


title: EC-049

value: 0.1percent EtOH ctrl


title: Kidney_low salt_control_replicate_6 [Kidney_lsc_257]


title: EC-048

description: Treated with Citral for 3 h

value: Citral

value: 3 h


title: GC0713057_S57

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713058_S58

description:
genomic DNA and RNA
scPCOR-seq


title: RRBS_RELA5-R1_PDOX_passage3

treatment_protocol: Patient derived orthotopic xenograft (PDOX) model were established by direct implantation of patient tumor tissues into matching locations in the brains of NOD/SCID mice (NOD.129S7(B6) -Rag1tm1Mom/J, Stock No: 003729,  https://www.jax.org/strain/003729.

value: brain

value: pediatric Ependymoma


title: EC-047

description: Treated with Citral for 3 h


title: Kidney_low salt_ab_replicate_5 [Kidney_lsab_258]

source_name: Kidney_low salt_ab

value: anti‐marinobufagenin antibody


title: HOP1/HOP1 0h cal CHIP replicate 1


title: Kidney_low salt_ab_replicate_6 [Kidney_lsab_259]


title: GC0713056_S56

description:
genomic DNA and RNA
scPCOR-seq

value: 293T and H1 cells


title: Kidney_low salt_control_replicate_3 [Kidney_lsc_242]


title: EC-046

description: Treated with Citral for 3 h


title: Kidney_low salt_control_replicate_1 [Kidney_lsc_240]


title: RRBS_RELA5-R1_PDOX_passage1


title: Kidney_low salt_control_replicate_2 [Kidney_lsc_241]


title: RRBS_RELA5-R1_monolayer_cells

source_name: cultured monolayer cells

value: cultured monolayer cells


title: GC0713055_S55

description:
genomic DNA and RNA
scPCOR-seq

source_name: 293T and H1 cells


title: EC-042

description: Treated with 0.1percent EtOH ctrl for 3 h


title: EC-041


title: GC0713054_S54

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713053_S53

description:
genomic DNA and RNA
scPCOR-seq


title: Kidney_low salt_ab_replicate_4 [Kidney_lsab_255]


title: Kidney_low salt_ab_replicate_2 [Kidney_lsab_231]


title: EC-040


title: Kidney_low salt_ab_replicate_1 [Kidney_lsab_230]


title: RRBS_RELA5-R1


title: Kidney_low salt_control_replicate_5 [Kidney_lsc_256]


title: Kidney_high salt_control_replicate_6 [Kidney_hsc_244]

source_name: Kidney_high salt_control


title: EC-038

description: Treated with Citral for 3 h


title: Kidney_low salt_ab_replicate_3 [Kidney_lsab_243]


title: RRBS_RELA4-R4


title: HOP1/HOP1 4h cal CHIP replicate 1

value: meiotic samples


title: GC0713051_S51

description:
genomic DNA and RNA
scPCOR-seq


title: RRBS_RELA4-R3


title: RRBS_RELA5-P


title: Kidney_high salt_control_replicate_4 [Kidney_hsc_238]


title: Kidney_high salt_control_replicate_3 [Kidney_hsc_237]


title: Kidney_high salt_control_replicate_5 [Kidney_hsc_239]


title: EC-037

description: Treated with Citral for 3 h


title: RRBS_RELA4-R1_PDOX_passage1

source_name: Patient derived orthotopic xenograft (PDOX)


title: EC-033


title: GC0713052_S52

description:
genomic DNA and RNA
scPCOR-seq


title: EC-039

description: Treated with Citral for 3 h


title: GC0713050_S50

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713048_S48

description:
genomic DNA and RNA
scPCOR-seq


title: EC-032


title: RRBS_RELA4-R1


title: RRBS_RELA4-P


title: EC-031


title: GC0713047_S47

description:
genomic DNA and RNA
scPCOR-seq


title: RRBS_RELA3-R1


title: GC0713045_S45

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713046_S46

description:
genomic DNA and RNA
scPCOR-seq


title: EC-030

description: Treated with Citral for 1 h

value: 1 h


title: RRBS_RELA2-R2


title: GC0713044_S44

description:
genomic DNA and RNA
scPCOR-seq


title: Kidney_high salt_ab_replicate_6 [Kidney_hsab_253]

source_name: Kidney_high salt_ab


title: Kidney_high salt_ab_replicate_5 [Kidney_hsab_251]


title: RRBS_RELA2-R1


title: Kidney_high salt_ab_replicate_4 [Kidney_hsab_249]


title: GC0713049_S49

description:
genomic DNA and RNA
scPCOR-seq


title: EC-023

description: Treated with 0.1percent EtOH ctrl for 1 h


title: EC-024


title: RRBS_RELA3-P


title: Kidney_high salt_control_replicate_2 [Kidney_hsc_235]


title: Kidney_high salt_control_replicate_1 [Kidney_hsc_234]


title: Kidney_high salt_ab_replicate_3 [Kidney_hsab_248]


title: RRBS_RELA2-P


title: GC0713041_S41

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713042_S42

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713043_S43

description:
genomic DNA and RNA
scPCOR-seq


title: EC-022


title: EC-029

description: Treated with Citral for 1 h


title: RRBS_RELA1-R7


title: Kidney_high salt_ab_replicate_1 [Kidney_hsab_232]


title: Kidney_high salt_ab_replicate_2 [Kidney_hsab_233]


title: EC-028

description: Treated with Citral for 1 h


title: GC0713039_S39

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713040_S40

description:
genomic DNA and RNA
scPCOR-seq


title: EC-021

description: Treated with Citral for 1 h


title: RRBS_RELA1-R5


title: EC-020

description: Treated with Citral for 1 h


title: Heart_Lateral ventricle_low salt_control_replicate_3 [LV_lsc_242]

value: Heart


title: Heart_Lateral ventricle_low salt_control_replicate_5 [LV_lsc_256]


title: Heart_Lateral ventricle_low salt_control_replicate_2 [LV_lsc_241]


title: RRBS_RELA1-R7_PDOX_passage1


title: Heart_Lateral ventricle_low salt_control_replicate_1 [LV_lsc_240]


title: RRBS_RELA1-R4


title: Heart_Lateral ventricle_low salt_control_replicate_4 [LV_lsc_246]


title: RRBS_RELA1-R3


title: GC0713038_S38

description:
genomic DNA and RNA
scPCOR-seq


title: EC-019

description: Treated with Citral for 1 h


title: EC-015


title: GC0713036_S36

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713037_S37

description:
genomic DNA and RNA
scPCOR-seq


title: EC-014


title: GC0713035_S35

description:
genomic DNA and RNA
scPCOR-seq


title: RRBS_RELA1-R2


title: RRBS_PFA5-R2


title: EC-013


title: GC0713034_S34

description:
genomic DNA and RNA
scPCOR-seq


title: RRBS_PFA5-R1


title: EC-012

description: Treated with 0.1percent EtOH at 0 h

value: 0.1percent EtOH

value: 0 h


title: GC0713033_S33

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713032_S32

description:
genomic DNA and RNA
scPCOR-seq


title: RRBS_PFA4-R1_PDOX_passage5


title: EC-011

description: Treated with 0.1percent EtOH at 0 h


title: EC-010

description: Treated with 0.1percent EtOH at 0 h


title: RRBS_PFA4-R1_neurosphere_cells

source_name: cultured neurosphere cells

value: cultured neurosphere cells


title: RRBS_PFA4-R1_PDOX_passage3


title: Heart_Lateral ventricle_low salt_ab_replicate_3 [LV_lsab_243]

source_name: Heart_Lateral ventricle_low salt_ab

value: SS/JrHsd


title: GC0713031_S31

description:
genomic DNA and RNA
scPCOR-seq


title: Heart_Lateral ventricle_low salt_ab_replicate_5 [LV_lsab_258]

value: Male


title: RRBS_PFA4-R1_monolayer_cells


title: EC-009

description: Treated without EtOH at 0 h


title: GC0713030_S30

description:
genomic DNA and RNA
scPCOR-seq


title: EC-008

description: Treated without EtOH at 0 h


title: GC0713029_S29

description:
genomic DNA and RNA
scPCOR-seq


title: RRBS_PFA4-R1

source_name: brain


title: Heart_Lateral ventricle_low salt_ab_replicate_6 [LV_lsab_259]

value: 16 week old


title: GC0713028_S28

description:
genomic DNA and RNA
scPCOR-seq


title: Heart_Lateral ventricle_low salt_ab_replicate_2 [LV_lsab_231]


title: Heart_Lateral ventricle_low salt_ab_replicate_4 [LV_lsab_255]


title: Heart_Lateral ventricle_high salt_control_replicate_4 [LV_hsc_238]

value: control antibody


title: Heart_Lateral ventricle_high salt_control_replicate_3 [LV_hsc_237]


title: Heart_Lateral ventricle_low salt_control_replicate_6 [LV_lsc_257]


title: Heart_Lateral ventricle_high salt_control_replicate_6 [LV_hsc_244]


title: Heart_Lateral ventricle_high salt_control_replicate_5 [LV_hsc_239]


title: EC-006

description: Treated with 0.1percent EtOH at 0 h


title: Heart_Lateral ventricle_low salt_ab_replicate_1 [LV_lsab_230]


title: GC0713027_S27

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713026_S26

description:
genomic DNA and RNA
scPCOR-seq


title: RRBS_PFA4-P_neurosphere_cells


title: Heart_Lateral ventricle_high salt_control_replicate_2 [LV_hsc_235]


title: EC-004

description: Treated with 0.1percent EtOH at 0 h


title: EC-005

description: Treated with 0.1percent EtOH at 0 h


title: RRBS_PFA3-R1


title: RRBS_PFA4-P


title: RRBS_PFA3-P


title: EC-003

description: Treated without EtOH at 0 h


title: GC0713025_S25

description:
genomic DNA and RNA
scPCOR-seq


title: RRBS_PFA4-P_PDOX_passage1


title: GC0713024_S24

description:
genomic DNA and RNA
scPCOR-seq


title: EC-007

description: Treated without EtOH at 0 h


title: Heart_Lateral ventricle_high salt_ab_replicate_6 [LV_hsab_253]

source_name: Heart_Lateral ventricle_high salt_ab


title: GC0713023_S23

description:
genomic DNA and RNA
scPCOR-seq


title: EC-002

description: Treated without EtOH at 0 h


title: LJ_9_WT_211_1m_M

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Image analysis and base calling were done with Illumina CASAVA-1.8.2. on HiSeq 2500 system.
sequenced reads were quality-tested using FASTQC
The reads were mapped to the mm10 genome using STAR v2.5.3a.
gene expression was quantified with HOMER v 4.10.4 using the fragments per kilobase per million mapped reads (FPKM) normalization across exons of the top isoform.
Heatmaps were constructed to show z-score normalized relative log2(FPKM+5) expression across conditions for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: normalized expression table in tab-separated format

molecule: polyA RNA

extract_protocol:
Total RNA was isolated from thymuses of 1 month-old mice (3 males and 3 females of WT and Axl -/-Mertk-/- mice) using the NucleoSpin RNA kit (Macherey-Nagel). The quality of the isolated total RNA was assessed using Agilent TapeStation 4200
RNA-Seq libraries were prepared with 500 ng total RNA using the TruSeq stranded mRNA Sample Preparation Kit according to the manufacturer’s protocol (Illumina). RNA-seq libraries were multiplexed, normalized and pooled for sequencing. The libraries were sequenced on the HiSeq 2500 system (Illumina) at single read 50bp.

tag: genetic background

value: WT

value: 1 month


title: RRBS_PFA2-R2_PDOX_passage3

value: brain


title: GC0713022_S22

description:
genomic DNA and RNA
scPCOR-seq


title: LJ_6_AMDKO_219_1m_F

value: AMDKO

value: Female


title: GC0713021_S21

description:
genomic DNA and RNA
scPCOR-seq

value: 293T and H1 cells


title: GC0713020_S20

description:
genomic DNA and RNA
scPCOR-seq


title: KO-2

data_processing:
Low quality reads and adaptor sequences were removed by Trim Galore v0.4.4
The clean reads were aligned to mm10 by bowtie2 with default parameter and uniquely mapping reads were summarized by featureCounts
FPKM (Fragments Per Kilobase of exon model per Million mapped reads) were calculated using edgeR TMM normalization
Differentially expressed genes  were calculated using Deseq2 by fdr cutoff 0.05
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including gene count and FPKM values for each sample

source_name: OVA+ CD8 TILs

growth_protocol: 1×106 E.G7 cells resuspended in 100 μL PBS was injected subcutaneously into the right flank of 6~10-week-old mice.

extract_protocol:
The total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions
RNA-seq library was constructed for deep sequencing by BGI Genomics.

treatment_protocol: OVA-specific CD8+ TILs from E.G7-bearing WT and Cd8CreSmad4fl/fl mice were sorted into lysis buffer using BD FACS Aria Cell Sorter.

value: Cd8-cre Smad4-fl/fl


title: Heart_Lateral ventricle_high salt_ab_replicate_4 [LV_hsab_249]

value: anti‐marinobufagenin antibody


title: LJ_5_AMDKO_202_1m_M


title: Heart_Lateral ventricle_high salt_control_replicate_1 [LV_hsc_234]


title: KO-1


title: RRBS_PFA2-R1

value: pediatric Ependymoma


title: RRBS_PFA1-R4


title: GC0713019_S19

description:
genomic DNA and RNA
scPCOR-seq


title: Heart_Lateral ventricle_high salt_ab_replicate_5 [LV_hsab_251]

value: Heart


title: Heart_Lateral ventricle_high salt_ab_replicate_2 [LV_hsab_233]


title: Heart_Lateral ventricle_high salt_ab_replicate_3 [LV_hsab_248]


title: LJ_2_WT_213_1m_F


title: WT-2


title: GC0713018_S18

description:
genomic DNA and RNA
scPCOR-seq


title: RRBS_PFA1-R3_PDOX_passage1


title: LJ_25_WT_210_1m_M_b


title: Heart_Lateral ventricle_high salt_ab_replicate_1 [LV_hsab_232]


title: RRBS_PFA2-R2


title: RRBS_PFA1-R3


title: EC-001

description: Treated without EtOH at 0 h


title: RRBS_PFA2-R2_PDOX_passage1


title: CD8 T cells Smad4

data_processing:
Low quality reads and adaptor sequences were removed by Trim Galore v0.4.4
Clean reads were mapped to the mm10 reference genome using Bowtie2
PCR duplicates were removed using picard MarkDuplicates
The uniquely mapped reads were used to call peak with MACS2 using a p value cutoff 0.01
ChIPseeker was used for peak annotation and homer was used for motif analysis

source_name: in vitro activated CD8

growth_protocol: naïve CD8+ T cells were activated in vitro by anti-CD3/CD28 for more than 48 hrs and harvested

extract_protocol:
The ChIP assay was performed using ChIP-IT Express Chromatin Immunoprecipitation Kits (Active Motif) according to manufacturer’s instructions with slight modifications.
ChIP-seq DNA library was constructed for deep sequencing by BGI Genomics.

value: wild-type B6 mice

tag: antibody

value: anti-SMAD4(Abcam, ab40759)


title: WT-1


title: RRBS_PFA1-R1


title: LJ_21_AMDKO_264_1m_M


title: LJ_17_WT_212_1m_M


title: RRBS_PFA1-R2


title: RRBS_cerebrum


title: LJ_18_WT_215_1m_F


title: HD NLCs 1

type: genomic

city: Columbus

first: Jonathan

middle: P

last: Butchar

state: OH

address: 400 W. 12th Avenue

department: Internal Medicine

institute: The Ohio State University

description: genomic DNA from healthy-donor NLCs derived in culture

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC/850k chip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Raw 850K data were normalized by a beta-mixture quantile normalization method using the RnBeads version 2.0 software. Probes present on sex chromosomes, non-cg, and those affected by proximity to known SNP were removed to generate a final probe set of 804,572 probes.

label: cy3 and Cy5

source_name: healthy-donor NLCs

label_protocol: Standard Illumina Protocol

growth_protocol: Monocytes were freshly isolated using MACS; NLCs were derived from 14-day PBMC cultures

extract_protocol: genomic DNA was extracted and purified using the Gentra Puregene cell kit (Qiagen, Germantown, MD)

tag: disease state

value: healthy donor

tag: cell type

value: NLCs derived from 21 days culture with CLL cells


title: RRBS_cerebellum


title: HD Monocytes 3

description: genomic DNA from healthy-donor monocytes

source_name: healthy-donor monocytes

value: monocytes isolated from peripheral blood by MACS


title: LJ_14_AMDKO_220_1m_F


title: HD NLCs 2


title: GC0713014_S14

description:
genomic DNA and RNA
scPCOR-seq

data_processing:
Library strategy: scPCOR-seq
Basecalls performed
Pairs of reads were considered to be valid if read2 contain the exact linker sequences “AGAACCATGTCGTCAGTGT”.  The valid pairs of read will be further separated into either RNA part or chromatin occupancy part. If the linker sequences “GAGCG” for not-so-random primers or the linker sequences “CCTGCAGG” for oligodT were found in the location within 7-11th and 7- 14th base of read1, the pair of reads were belonged to RNA. The remaining valid pairs were belonged to chromatin occupancy. Using the information of the cell barcodes located at 5’ of read 2, both pairs of reads belonging to RNA and chromatin occupancy were separated into 96 sets of FASTQ files, respectively. The 96 pairs are shown in barcode_96.txt.  Reads were mapped to the human reference genome hg19 using Bowtie2 Duplicates using different trimming parameters. Finally, the mapping results were combined, and Duplicated reads were removed based on mapping position and UMI for the reads belonging to chromatin occupancy.
The top 30 barcodes are selected from each well based on read count, so 30 nuclei are sorted for each well with doublets removed, where the number removed was calculated based on the collision rate like in (Science. 2015 May 22; 348(6237): 910–914). These are denoted as single cells because of the low likelihood of two cells in the same well having the same barcode. We required that qualifying cells have more than 1000 reads. With these requirements, 2347 cells were obtained . For each cell, we calculated the RNA and PolII reads that were located within the gene body and stored the results in a matrix, which can be found from the file “RNA_count.txt.gz” and “POlII count.txt.gz”
Genome_build: hg19
Supplementary_files_format_and_content: barcode_96.txt: one column  refers to a DNA barcode starting from the 3' .
Supplementary_files_format_and_content: RNA_count.txt.gz: This file contains read count data for single cells in text format.  First column) Transcript ID, Second column) Chromosome, Third column) Start, Fourth column) End, Fifth column) Strand, Sixth column) RNA length, Seventh column) copies of transcript annotation in the genome, Eighth column) annotation information, other columns) readcount. The rows refer to genes. Reading the matrix results in a 65572 x 2355 matrix.
Supplementary_files_format_and_content: PolII_count.txt.gz: This file contains normalized read count data for single cells in text format. The rows refer to genes while the column refer to single cells. Reading the matrix results in a 68987 x 2348 matrix.

extract_protocol:
The fixed cells were thawed on ice. To prepare PA-MNase and antibody complex, 1 μl antibody and 3 μl PA-MNase were pre-incubated on ice in 4 μl antibody binding buffer (10 mM Tris-Cl (pH 7.5), 1 mM EDTA, 150 mM sodium chloride, 0.1% Triton X-100) for 30 min. Meanwhile, H1 fixed cells (1 million) and HEK 293T fixed cells (1 million) were resuspended in 100 μl antibody binding buffer. Then, cell suspension was added to the PA-MNase and antibody complex, incubated on ice for 1 hour. Cells were washed three times with high salt buffer (10 mM Tris-Cl (pH 7.5), 1 mM EDTA, 400 mM sodium chloride and 1% (v/v) Triton X-100), followed by washing once with rinsing buffer (10 mM Tris pH7.5, 10 mM sodium chloride and 0.1% (v/v) Triton X-100). Then the cells were resuspended in 40 μl reaction solution buffer (10 mM Tris-Cl (pH 7.4), 10 mM sodium chloride, 0.1% (v/v) Triton X-100, 2 mM CaCl2), incubated at 37°C for 3min in water bath. The reaction was stopped by adding 4.4 μl 100mM EGTA. After washing twice with rinsing buffer, the cells were end-repaired by T4 Polynucleotide Kinase (PNK) in 150 μl reaction buffer (1 x PNK buffer, 1mM ATP, 150 unites PNK) at 37°C for 30min, followed by washing twice with rinsing buffer to stop the reaction.The cells were resuspended in 25 μl reverse transcription buffer (5 μl 10 x Maxima H Minus reverse transcription buffer, 1.25 μl 10% NP40, 16.75 μl H2O, 1 μl 100 μm not-so-random primer, 1 μl 10ng/μl Oligo dT22 primer (NNNNNNGAGCGTTTTTTTTTTTTTTTTTTTTTTVN)). After incubated at 65°C for 1min, the reaction was immediately put on ice, while the enzyme mix is prepared (8.75 μl H2O, 5 μl 10 x Maxima H Minus reverse transcription buffer, 8 μl 10 mM dNTPs, 2 μl Maxima H Minus reverse transcriptase, 0.625 μl SUPERase• In™ RNase Inhibitor, 0.625 μl RNaseOUT™ Recombinant Ribonuclease Inhibitor) and added into the reaction. The reverse transcription is performed as described in [15] (50 °C × 10 min; 3 cycles for the following: 8°C × 12s, 15°C × 45s, 20°C × 45s, 30°C × 30s, 42°C × 2min, 50°C × 5 min; 50 °C × 10 min and hold at 4 °C). The cells were washed twice with rinsing buffer, resuspended in 50 μl reaction buffer (5 μl 10 × Exo I buffer, 1 μl Exo I, 44 μl H2O) and incubated at 37°C for 20min. This is to remove the excess primers left after reverse transcription. After digestion, the cells were washed twice with rinsing buffer to stop the reaction.
96 barcode-P7 adaptors (10 μM) stored in a 96 well plate were thawed at 4 °C, then 1 μl of each was added to the corresponding well in a new 96 well plate with multichannel pipette. Downstream library construction was performed as described previously. Briefly, the cells were suspended with nuclei suspension buffer and mixed with enzyme dilution buffer, followed by aliquoted into 10 μl in 96 wells, mixing with the added barcode-P7 adaptors. The plate was sealed completely and incubated at 37°C for 60min. After incubation, the cells were pooled together in a solution trough containing 500 μl stop buffer, resuspended with 800 μl 1× PBS and send to flow cytometry core. 30 cells were sorted in each well of a new 96 well plate which contain 13 μl buffer mixture per well (3 μl reverse-crosslink buffer, 10 μl PBS containing 0.1% NP40). The plate was sealed completely and incubated at 65°C for 6 hours and 80°C for 10 min. After reverse crosslink, indexed PCR1 was performed by adding 13 μl 2x Phusion® High-Fidelity PCR Master Mix with HF Buffer (New England BioLabs) and 1 μl 2 μM index primer with the following condition: 98 °C 3 min, 12 cycles of 65 °C 30s, 72 °C 30s, followed by 72 °C 5 min. Then the libraries were pooled together, digested with Exo I and purified by MinElute® Reaction Cleanup Kit (Qiagen). Downstream A-tailing and P5 adaptor ligation were performed as described previously. PCR2 amplification with i5 index primer and P7-cs2 primer was set in the following condition:  98 °C 3 min, 57 °C 3 min, 72 °C 1 min, 7 cycles of 98 °C 10s, 65 °C 15s, 72 °C 30s, followed by 72 °C 5 min. The PCR products were run on the 2% E-Gel® EX Agarose Gel (Invitrogen). The fragments between 250–600 base pair (bp) were isolated and purified by the MinElute Gel Extraction Kit (Qiagen). The concentration of the library was measured by Qubit dsDNA HS kit (Thermo Fisher Scientific). The paired-end sequencing was performed on Illumina Hiseq 2500


title: LJ_10_WT_214_1m_F


title: GC0713015_S15

description:
genomic DNA and RNA
scPCOR-seq


title: LJ_13_AMDKO_203_1m_M

value: Male


title: HD Monocytes 2


title: HD Monocytes 1


title: GC0713013_S13

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713010_S10

description:
genomic DNA and RNA
scPCOR-seq


title: CLL NLCs 3

description: genomic DNA from CLL-patient NLCs derived in culture

source_name: patient NLCs

value: chronic lymphocytic leukemia

value: NLCs derived from 14 days culture in PBMC


title: GC0713011_S11

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713016_S16

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713017_S17

description:
genomic DNA and RNA
scPCOR-seq


title: CD8 T cells Input


title: LJ_22_AMDKO_231_1m_F

value: 1 month


title: GC0713009_S9

description:
genomic DNA and RNA
scPCOR-seq


title: CLL NLCs 2


title: CLL NLCs 1


title: GC0713012_S12

description:
genomic DNA and RNA
scPCOR-seq


title: CLL Monocytes 3

description: genomic DNA from CLL-patient monocytes

source_name: patient monocytes


title: GC0713008_S8

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713007_S7

description:
genomic DNA and RNA
scPCOR-seq


title: CLL Monocytes 2

description: genomic DNA from CLL-patient monocytes


title: PAM-1 SE 4C-seq

city: Sha Tin

first: Yile

last: Huang

state: Hong Kong

address: Room 503, Li Ka Shing Health and Science Buiding, Prince of Wales Hospital, Sha Tin

department: Chemical Pathology

institute: The Chinese University of HongKong

data_processing:
Library strategy: 4C-seq
The raw data were first preprocessed by initial quality assessment, adaptors trimming, and low-quality filtering. Only reads containing the bait sequence are remained.
The remaining reads were aligned to the mouse reference genome (mm9) by Bowtie2
The interaction regions are identified by software fourSig
Genome_build: mm9
Supplementary_files_format_and_content: bw

source_name: C2C12 myoblast

growth_protocol: Mouse C2C12 myoblast cell (CRL-1772) was obtained from American Type Culture Collection (ATCC) and cultured in DMEM medium with 10% fetal bovine serum, 1% penicillin/ streptomycin at 37°C in 5% CO2.

extract_protocol:
Paraformaldehyde fixed cells were digested with TatI restriction enzyme digestion, incubated overnight at 37ºC and circularized using T4 DNA ligase. Gradient range of annealing temperature (55-65ºC) were used to determine the optimum annealing temperature for inverse PCR.
NEBNext Ultra II DNA Library Preparation kit for Illumina (NEB)

value: C2C12 myoblast

tag: strain


title: PAM-1 ChIRP-seq input

data_processing:
Library strategy: ChIRP-seq
The raw data were first preprocessed by initial quality assessment, adaptors trimming, and low-quality filtering
The remaining reads were aligned to the mouse reference genome (mm9) by Bowtie2
The binding sites were identified by software MACS2
Genome_build: mm9

source_name: ASC

growth_protocol: Hindlimb skeletal muscles from Tg:Pax7-nGFP mice were dissected and minced, followed by digestion with Collagenase II (LS004177, Worthington, 1000 units/mL) for 90 min at 37°C in water bath shaker. Digested muscles were then washed in washing medium (Ham’s F-10 medium (N6635, Sigma) containing 10% heat inactivated horse serum (Gibco, 26050088) with 1% penicillin/ streptomycin, followed by incubating in digestion medium with Collagenase II (100 units/mL) and Dispase (1.1 unit/mL, Gibco, 17105-041) for additional 30 min. Suspensions were then passed through 20G syringe needle to release myofiber-associated SCs. Mononuclear cells were filtered with a 40mm cell strainer, followed by cell sorting using BD FACSAria Fusion Cell Sorter (BD Biosciences). BD FACSDiva (BD Biosciences, version 8.0.1) software was used to manage machine startup, data acquisition and analysis of flow cytometry data. Culture dish were coated with poly-D-lysine (Sigma, P0899) and Matrigel (BD Bioscience, 356234). FACS isolated SCs were seeded in coated culture dish and cultured in Ham’s F10 medium with 10% heat inactivated horse serum, 5ng/mL FGF-Basic (AA 10-155) (Gibco, PHG0026).

extract_protocol:
10 million cells were collected per ChIRP experiment for separated odd and even probe pools. Cell pellets were cross-linked with 1% Glutaraldehyde in 40mL PBS on rotator for 10 minutes at room temperature, followed by quenching the cross-linking reaction with 2mL 1.25M Glycine for 5 minutes and resuspend in 1mL chilled PBS. Cell pellets were collected at 2000RCF for 5 minutes at 4 °C, followed by removing PBS, snap frozen with liquid nitrogen and stored at -80°C. Cell pellets were lysed and sonicated using Covaris S220 sonicator, then aliquoted into two 1mL samples. Before ChIRP experiment, DNA were extracted for quality control with size ranging from 100-500bp. For ChIRP experiment, 10mL of lysate were saved for DNA input. 1mL of sonicated lysate was mixed with 2mL of hybridization buffer (750mM NaCl, 50mM Tris-HCl pH7, 1mM EDTA, 1% SDS, 15% Formamide, 1x protease inhibitor and 1x RNase inhibitor). 100pmol of odd and even ChIRP probes were added separately to the hybridization mixture and incubate at 37°C for 4 hours with rotation. After the hybridization was completed, 100uL of streptavidin magnetic C1 beads (Life Technologies, 65001) were washed thrice with hybridization buffer and added to each ChIRP reaction for extra 30 minutes incubation at 37°C with rotation. After the hybridization completed, 1mL of wash buffer (2X SSC, 0.5% SDS and 1x protase inhibitor) was used to wash the beads for 5 times using magnetic stand. Input control and PAM-1 bound DNA was eluted, followed by library construction.
NEBNext Ultra II DNA Library Preparation kit for Illumina (NEB)

value: ASC


title: GC0713006_S6

description:
genomic DNA and RNA
scPCOR-seq


title: Ddx5 ChIP-seq

data_processing:
The raw data were first preprocessed by initial quality assessment, adaptors trimming, and low-quality filtering
The remaining reads were aligned to the mouse reference genome (mm9) by Bowtie2
Peak regions were called by software MACS2
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

extract_protocol:
C2C12 cells were crosslinked with 1% formaldehyde at room temperature for 10 minutes, followed by quenching with 0.125M glycine for 10 minutes. Chromatin was fragmented using S220 sonicator (Covaris), followed by incubation with 5ug of antibodies and 50uL Dynabeads Protein G magnetic beads (Life Technologies) at 4°C on rotator for overnight. Anti Ddx5 (ab21696, Abcam) was used in ChIP assay. Beads were washed with 1mL RIPA buffer for 5 times, followed by decrosslink at 65°C for 16 hours and DNA extraction with phenol/chloroform. Immunoprecipitated DNA was resuspended in 50uL of water.
NEBNext Ultra II DNA Library Preparation kit for Illumina (NEB). The library was sequenced on Illumina HiSeq1500 instrument.

value: Ddx5 (ab21696, Abcam)


title: Sprague Dawley_SON Creb3l1 shRNA_rep5R

city: Bristol

first: Michael

middle: Paul

last: Greenwood

address: Whitson Street

department: Bristol Medical School / Translational Health Sciences

country: United Kingdom

institute: University of Bristol

data_processing:
RNA-seq reads were processed using RTA and CASAVA from Illumina’s suite of sequencing software.
All raw reads were merged per library, and pre-processed for quality assessment, adaptor removal, quality trimming and size selection using the FastQC toolkit to generate quality plots for all read libraries.
We adopted a phred30 quality cutoff (99.9% base call accuracy).
Paired end (2 x 75 bp) raw input data is initially aligned with STAR to the sixth iteration of the Rattus norvegicus reference genome (Rn6).
FeatureCounts is used to generate read counts for each gene present in the Rn6 genome annotation.
DEseq2 (v1.28.1) package in R was used to call differentially expressed genes.
Assembly: Rn6
Supplementary files format and content: FeatureCount output - ALL_Final_only_counts.gene.txt
Supplementary files format and content: Deseq2 differential gene expression analysis - SON_Creb3l1_RNAseq_processed_data.xls

source_name: Brain

growth_protocol: Male Sprague Dawley rats weighing 250-274 grams were purchased from commercial supplier Envigo. Rats were housed under a 12:12 light/dark cycle at a temperature of 21-22°C and a relative humidity of 40-50% with food and water ad libitum.

extract_protocol:
A 1 mm punch was used for tissue collection from frozen cryostat cut sections. QIAzol Lysis Reagent (Qiagen) followed by Direct-zol RNA miniprep extraction kit (Zymo research). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were constructed using TruSeq® Stranded mRNA library preparation kit (20020594, Illumina)

treatment_protocol: Animal were able to serve as their own controls with control virus (non-tergeting shRNA) sterotaxically injected into one SON and experimental virus (Creb3l1 knockdown) into the other.

tag: tissue

value: Brain

tag: brain region

value: Supraoptic nucleus

value: Sprague-Dawley

value: 3 weeks

tag: treatment

value: Knockdown

tag: shRNA construct

value: AAV Creb3l1 shRNA


title: GC0713005_S5

first: Keji

last: Zhao

description:
genomic DNA and RNA
scPCOR-seq

source_name: 293T and H1 cells

value: 293T and H1 cells


title: CLL Monocytes 1

description: genomic DNA from CLL-patient monocytes


title: Sprague Dawley_SON Creb3l1 shRNA_rep3R


title: Sprague Dawley_SON Creb3l1 shRNA_rep4R


title: PAM-1 ChIRP-seq even


title: PAM-1 ChIRP-seq odd


title: GC0713003_S3

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713002_S2

description:
genomic DNA and RNA
scPCOR-seq


title: Sprague Dawley_SON Creb3l1 shRNA_rep2R


title: eNOS HET White matter 3

city: Charlestown

first: Mahesh Chandra

last: Kodali

state: MA

department: Neurology

institute: Massachusetts General Hospital / Harvard Medical School

data_processing:
Libraries are loaded onto Novaseq6000 sequencing platform according to activity and expected data volume. A paired-end 150 bp sequencing strategy was used and all samples were sequenced to 20M PE Reads.
Transcript abundance from RNA-seq reads was quantified using Salmon, and gene-level counts were obtained using tximport, against the C57BL/6J mouse genome annotation Genome Reference Consortium Mouse Build 39  (GRCm39), obtained from the National Center for Biotechnology Information. Subsequently, raw counts were processed with DESeq2 to determine differentially expressed genes.
Assembly: Genome Reference Consortium Mouse Build 39 (GRCm39)

source_name: Brain - White Matter

extract_protocol:
RNA was extracted from mouse cerebral vessels after trizol homogenization, and then using QIAGEN miRNeasy micro Kit. Samples were later DNAse treated and cleaned up using RNEasy minelute clean up kit, finally eluted in RNAse free water from Qiagen.
Isolated RNA sample quality was assessed by High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA). Library construction is performed based on manufacturer’s recommendation for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio USA Inc., California, USA) followed by Nextera® XT DNA Library Prep Kit (Illumina, California, USA). Final library quantity was measured by KAPA SYBR® FAST qPCR and library quality evaluated by TapeStation D1000 ScreenTape (Agilent Technologies, CA, USA). Final library size was about 430bp with an insert size of about 200bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® HiSeq (Illumina, California, USA) with a read length configuration of 150 PE for 20M PE reads per sample (10M in each direction).

value: Brain - White Matter

tag: genotype

value: eNOS+/-


title: GC0713001_S1

institute: national Institute of Health

description:
genomic DNA and RNA
scPCOR-seq


title: GC0713004_S4

description:
genomic DNA and RNA
scPCOR-seq


title: eNOS HET White matter 2


title: Sprague Dawley_SON Creb3l1 shRNA_rep1R


title: TS3-4

city: Kawasaki

first: Takao

last: Inoue

state: Kanagawa

address: 3-25-26, Tonomachi

department: Division of Molecular Target and Gene Therapy Products

country: Japan

institute: National Institute of Health Sciences

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 Array using the GeneChip Hybridization Oven. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The scanned data were processed for signal values using Microarray Suite 5.0 software  .

label: biotin

source_name: The NMuLi cells transfected with TS3 at 10 nM using Lipofectamine 2000 for 24hr.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: The NMuLi cells were maintained at 37 °C and 5% CO2 in Dulbecco’s Modified Eagle's Medium supplemented with 10% heat-inactivated fetal bovine serum and antibiotics.

extract_protocol: Total RNA was isolated using a Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: The NMuLi cells transfected with the gapmer ASOs using Lipofectamine 2000 (Invitrogen, Gaithersburg, MD, USA) according to the manufacturer’s protocol. The cells treated with transfection reagent in the absence of ASO were used as a control.

tag: cell line

value: NMuLi

value: Liver


title: PAM-1 KO rep2 H3K27ac ChIP-seq

data_processing:
The raw data were first preprocessed by initial quality assessment, adaptors trimming, and low-quality filtering
The remaining reads were aligned to the mouse reference genome (mm9) by Bowtie2
Peak regions were called by software MACS2
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

extract_protocol:
C2C12 cells were crosslinked with 1% formaldehyde at room temperature for 10 minutes, followed by quenching with 0.125M glycine for 10 minutes. Chromatin was fragmented using S220 sonicator (Covaris), followed by incubation with 5ug of antibodies and 50uL Dynabeads Protein G magnetic beads (Life Technologies) at 4°C on rotator for overnight. Anti Ddx5 (ab21696, Abcam) was used in ChIP assay. Beads were washed with 1mL RIPA buffer for 5 times, followed by decrosslink at 65°C for 16 hours and DNA extraction with phenol/chloroform. Immunoprecipitated DNA was resuspended in 50uL of water.
NEBNext Ultra II DNA Library Preparation kit for Illumina (NEB)

treatment_protocol: To delete PAM-1 exon1, target-specific guide RNAs (gRNAs) were designed using CRISPR design tool (http://crispr.mit.edu), followed by cloning into BbsI digested px330 plasmid (Addgene, 42230). To perform genomic deletion, a pair of gRNAs containing plasmids were co-transfected into C2C12 cells with screening plasmid pSIREN-RetroQ (Clontech) using Lipotectamine 2000. Cells were selected with 2.5ug of puromycin for 3 days at 48 hours post-trasnsfection. Cells were diluted to 1 cell per well in 96 well plate. Individual colonies were PCR validated.

value: H3K27ac (ab4729, Abcam)


title: TS3-C1-7-1

source_name: The NMuLi cells transfected with TS3-C1-7 at 10 nM using Lipofectamine 2000 for 24hr.


title: TS3-C1-7-2

value: transfected with TS3-C1-7 at 10 nM using Lipofectamine 2000 for 24hr.


title: TS3-C1-7-3


title: TS3-3

value: transfected with TS3 at 10 nM using Lipofectamine 2000 for 24hr.


title: eNOS HET White matter 1

value: Male


title: TS3-1


title: Sprague Dawley_SON non-targeting shRNA_rep5L

value: control

value: AAV control shRNA


title: Control H3K27ac ChIP-seq

value: C2C12 myoblast