title: R1 Day150

city: Taipei

first: Pinghsing

last: Tsai

state: Taiwan

address: Rm. 825, 7F., No.322, Sec. 2, Shipai Rd., Beitou D

country: Taiwan

institute: Taipei Veterans General Hospital

description:
XLRS patient-derived iPSC cells with CRISPR/Cas9-mediated RS1 gene correction and undergo 3D retinal differentiation for 150 days
D150_R1

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

growth_protocol: hiPSCs were cultured on Geltrex (Gibco)-coated dish with mTeSR1 medium (STEMCELL Technologies) according to the manufacturer’s protocol. Cells were passaged every 5-7 days at about 80% confluence. For differentiation into retinal organoids, we adapted previously described method with slight modifications (Meyer et al., 2011; Meyer et al., 2009; Ohlemacher et al., 2015; Phillips et al., 2012; Wahlin et al., 2017; Zhong et al., 2014). In brief, hiPSCs were detached by treatment with Vercene (Gibco), dissociated into single cells and cultured in low attachment dish with ROCK inhibitor Y27632 (10 μM, Cayman Chemical Company) and 3:1 mixture of mTeSR1 and neural induction medium (NIM) containing DMEM/F12 (1:1, Life Technologies), 1% N2 supplement, 1 × NEAAs and 2 μg/ml heparin (Sigma) at day 0 to induce embryonic body (EB) formation. EBs were gradually transitioned into NIM by replacing the medium with a 1:1 ratio of mTeSR1/NIM on day 3, 1:3 on day 5. On day 7, EBs were seeded to six-well plate containing NIM with 10% FBS at approximate density of 30-40 EBs/well. On day 16, the medium was changed from NIM to retinal differentiation medium (RDM) containing DMEM/F12 (3:1), 2% B27 supplement without vitamin A (Life Technologies), 1 × NEAAs, and penicillin/streptomycin. Around day 18-25, the loosely adherent central portions of the neural clusters were lifted by pipetting with a P1000 pipettor. The collected aggregates were cultured in suspension with RDM, which allowed them to form three-dimensional optic cups structures. Between days 30 and 40, the aggregates of optic cups with “golden circle” morphology were manually separated from the poor quality cell aggregates. For long-term suspension culture, the medium was supplemented with 10% fetal bovine serum (Gibco), 100 mM Taurine (Sigma) and 2 mM GlutaMAX (Invitrogen) beginning on day 35. From days 60-90, the culture medium was supplemented with 1 μM retinoic acid (Sigma) to induce photoreceptor maturation. The medium was supplemented with N2 instead of B27 after day 90. The cell medium was changed every 2-3 days until the desired stage was reached.

extract_protocol:
iPSCs and retinal cups were washed and collected, and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: individual

value: XLRS patient

value: iPSC

value: differentiated retinal organoid

tag: time

value: post differentiation day 150


title: R2 Day150

status: Public on Sep 03 2022

type: SRA

description:
XLRS patient-derived iPSC cells with CRISPR/Cas9-mediated RS1 gene correction and undergo 3D retinal differentiation for 151 days
D150_R2

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: tissue

tag: genotype


title: female, hepatopancreas, rep2

city: Hangzhou

first: Jindong

last: Ren

address: No.198, Shiqiao Road

country: China

institute: Zhejiang Academy of Agricultural Sciences

data_processing:
The libraries were sequenced on an Illumina Hiseq 4000 platform (Illumina, San Diego, CA, USA) and 150 bp paired-end reads were generated.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to M. rosenbergii transcriptome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.10.1)  with an adjusted P-value <0.05 found by DESeq were assigned  as differentially expressed.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: No reference
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Macrobrachium rosenbergii

source_name: Hepatopancreas

extract_protocol:
Each shrimp was put on ice 1 min for anesthetizing, firstly. After anesthetizing, samples of ovaries (Ov), testicles (Tt) and hepatopancreas (Hp) were collected separately and dissected. Each fresh sample was washed in phosphate-buffered saline (PBS; Gibco, Fisher Scientific, Waltham, MA, USA) and immediately frozen in liquid nitrogen. Total RNA was extracted from each sample using an RNeasy Plus Micro Kit (QIGEN Group, Germany)
Total RNA was used to generate sequencing libraries with varied index label using a NEBNextUltra™ Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA) according to the manufacturer’s instructions

value: Hepatopancreas

tag: strain

tag: Sex

value: female

tag: developmental stage

value: adult

tag: weight gain


title: Alzheimer's Disease CSF021

type: RNA

city: Portland

first: Julie

middle: A

last: Saugstad

state: Oregon

address: 3181 SW Sam Jackson Park Road

department: Anesthesiology & Perioperative Medicine

country: USA

institute: Oregon Health & Science University

description:
EXR-JSAUG1UH2021-BS
total cell-free biofluid RNA

data_processing:
miRNAs with low (<~20%) detection rates in samples or less than that number of adequately quantified Ct values were excluded in order to restrict focus to targets with adequate biomarker potential; 617 miRNAs were excluded for these reasons.
miRNAs with raw Ct values at a threshold of 36 and higher were marked as censored, and viewed as miRNA below the lower limit of detection.
Ct values were normalized by subtracting the mean of the 4 same-plate U6 snRNA reference values for the sample for each plate, and recentered by subsequently adding the globally maximum (across all samples) U6 value; miRNAs whose raw Ct value appear as 36 in the non-normalized data matrix should be considered censored measurements in the normalized data matrix, regardless of the normalized value.

label: FAM

source_name: Cerebrospinal fluid

label_protocol: As per Life Technologies Human miRNA Megaplex Pool (A + B) protocol. Concentrated RNA samples were reverse transcribed using a custom MiRNA RT pool (4459652, Thermo Fisher Scientific) and TaqMan® MicroRNA Reverse Transcription Kit (4366596, TFS), then pre-amplified using a custom MiRNA PreAmp pool (4459660, TFS) and TaqMan® PreAmp Master Mix w/QRC (4391128, TFS). The pre-amplification products were diluted 1:4 in RNase/DNase-free water, then 18 µL of diluted samples were mixed with TaqMan® Universal PCR Master Mix II, no UNG (4440040, TFS) and RNase/DNase-free water to a final volume of 450 µL, loaded onto a custom TaqMan® Array Card (4449140, TFS) and amplified on a QuantStudio™ 12K Flex Real-Time PCR instrument (4471089, TFS).

extract_protocol: Total RNA was isolated from 0.5 ml CSF using the mirVana PARIS kit (Life Technologies/Ambion) without enrichment for small RNAs. Isolated RNAs from each sample were concentrated using Zymo RNA Clean & Concentrator-5 (Zymo Research, Irvine CA) spin columns. RNA concentrations were measured using Quant-iT RiboGreen RNA Assay Kit (Life Technologies/Invitrogen). RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA 6000 Pico chips (Agilent Technologies).

tag: diagnosis

value: Healthy Control

value: Female

tag: age

value: Cerebrospinal fluid

tag: anatomical location

value: Structure of nervous tissue

tag: sample collection method

value: Lumbar puncture

tag: starting amount

tag: holding temperature


title: Alzheimer's Disease CSF020

description:
EXR-JSAUG1UH2020-BS
total cell-free biofluid RNA

value: Alzheimer's Disease


title: Pt-1 Day120

description:
XLRS patient-derived iPSC cells undergo 3D retinal differentiation for 120 days
D120_Pt-1

source_name: XLRS patient-derived iPSCs

value: post differentiation day 120


title: Pt-1 Day150

description:
XLRS patient-derived iPSC cells undergo 3D retinal differentiation for 150 days
D150_Pt-1


title: Pt-1 Day90

description:
XLRS patient-derived iPSC cells undergo 3D retinal differentiation for 90 days
D90_Pt-1

value: post differentiation day 90


title: Pt-1 Day0

description:
XLRS patient-derived iPSC cells
D0_Pt-1

value: Non-differentiated


title: Ctrl-1 Day150

description:
healthy donor-derived iPSC cells undergo 3D retinal differentiation for 150 days
D150_Ctrl

source_name: control donor-derived iPSCs

value: Control donor

value: wild type


title: Ctrl-1 Day50

description:
healthy donor-derived iPSC cells undergo 3D retinal differentiation for 50 days
D50_Ctrl

value: iPSC

value: post differentiation day 50


title: Ctrl-1 Day90

description:
healthy donor-derived iPSC cells undergo 3D retinal differentiation for 90 days
D90_Ctrl

value: differentiated retinal organoid


title: Ctrl-1 Day120

description:
healthy donor-derived iPSC cells undergo 3D retinal differentiation for 120 days
D120_Ctrl


title: Alzheimer's Disease CSF018

description:
EXR-JSAUG1UH2018-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF017

description:
EXR-JSAUG1UH2017-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF016

description:
EXR-JSAUG1UH2016-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF015

description:
EXR-JSAUG1UH2015-BS
total cell-free biofluid RNA


title: E12.5-rep2

city: Shenzhen

first: Peng

last: Han

state: Guangdong

address: 1088 Xueyuan Avenue, Nanshan District

department: Department of biology

institute: Southern University of Science and Technology

description: mouse dorsal spinal cord

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using R package oligo and gene level expression were summarized from the corrected intensities and then quantile normalized.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.core.ps

label: biotin

organism: Mus musculus

source_name: dorsal spinal cord commissural neurons at E12.5

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mouse embryonic dorsal spinal cord dissected at E10.5, E11.5 and E12.5

extract_protocol: GFP+ cells were collected by fluorescence-activated cell sorting (FACS) and RNA were extracted using Trizol reagent.

treatment_protocol: not applicable

tag: development stage

value: dorsal spinal cord


title: Ctrl-1 Day0

description:
healthy donor-derived iPSC cells
D0_Ctrl


title: hypoAkkW7-4_scRNA-seq

city: Los Angeles

first: Xia

last: Yang

state: California

address: 610 Charles E. Young Drive East

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

description: DropSeq

library_source: transcriptomic single cell

data_processing:
DropSeqPipe version 1.13 (https://github.com/Hoohm/dropSeqPipe) was used to preprocess the sequencing data and generate digital gene expression matrix files.
Gene expression matrix from each sample was loaded into the Seurat R package version 4.0.3
Quality control was conducted based on number of genes (200-4000), unique molecular identifiers (UMIs; 500-5000) and percent of mitochondrial genes (<10%) to filter out cells that did not meet these thresholds (Figure S1). Potential doublets were removed using DoubletDecon version 1.1.6 with default parameters
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hypothalamus

extract_protocol:
Freshly dissected hypothalami were dissociated with papain (Worthington, Lakewood, NJ, USA) for single cell isolation (Brewer and Torricelli, 2007).  Cells were suspended in 0.01% BSA-PBS at a final concentration of 100 cells/μl for as previously described (Arneson et al., 2018).
Single cells were barcoded using single-cell transcriptomes attached to microparticles (STAMPs) followed by generating cDNA library with the Drop-seq protocol by Macosko et al 2015 (Macosko et al., 2015).

value: Hypothalamus

value: DBA/2J (DBA)


title: Pt-1 Day50

description:
XLRS patient-derived iPSC cells undergo 3D retinal differentiation for 50 days
D50_Pt-1

value: XLRS patient


title: hippocampus Htr6 knockout [Sample_H_KO]

city: Ashburn

first: Shu-Hsien

last: Sheu

state: VA

address: 19700 Helix Drive

institute: Janelia Research Campus/Howard Hughes Medical Institute

library_source: genomic

data_processing:
Fastqs were generated for each sample using cellranger-atac (v1.2.0) mkfastq command.
Feature counts and metadata were generated for each sample using cellranger-atac (v1.2.0) count command using the cellranger-atac-mm10 reference included with the software.
Seurat (v4.0.4) and Signac (v1.3.0) R v4.1.1 packages were used to import the 10x feature counts and metadata for the cell barcodes discovered by the cellranger-atac count algorithm.
All code necessary to reproduce the figures and supplemental file are available by request.
Genome_build: refdata-cellranger-atac-mm10-1.2.0
Supplementary_files_format_and_content: Excel file containing DA peaks and gene activity markers for original clusters, merged clusters, and CA1 cells, plus CA1 KO vs. WT bed files for GREAT analysis.

molecule: genomic DNA

source_name: hippocampus

extract_protocol:
Whole hippocampus was dissected and flash frozen.
Nuclei were isolated from frozen hippocampus according to 10X Genomics demonstrated protocol (CG000212) for flash frozen tissue.  Isolated nuclei were subjected to 10X Chromium Single Cell ATAC-seq library preparation protocol (CG000209).

tag: genotype/variation

value: Htr6 knockout

value: adult

value: hippocampus

tag: tissue prep

value: flash frozen

tag: 10x genomics barcode


title: Alzheimer's Disease CSF014

description:
EXR-JSAUG1UH2014-BS
total cell-free biofluid RNA

value: Healthy Control

value: Female

value: Cerebrospinal fluid

value: Structure of nervous tissue

value: Lumbar puncture


title: hypoAkkW7-1_scRNA-seq

description: DropSeq


title: Alzheimer's Disease CSF019

description:
EXR-JSAUG1UH2019-BS
total cell-free biofluid RNA

value: Alzheimer's Disease


title: E11.5-rep2

description: mouse dorsal spinal cord

source_name: dorsal spinal cord commissural neurons at E11.5


title: hippocampus wild-type [Sample_H_WT]

value: wild type


title: Alzheimer's Disease CSF012

description:
EXR-JSAUG1UH2012-BS
total cell-free biofluid RNA


title: E11.5-rep1

description: mouse dorsal spinal cord


title: hypoAkkF10-4_scRNA-seq

description: DropSeq


title: hypoAkkF10-3_scRNA-seq

description: DropSeq


title: Alzheimer's Disease CSF011

description:
EXR-JSAUG1UH2011-BS
total cell-free biofluid RNA


title: E10.5-rep2

description: mouse dorsal spinal cord

source_name: dorsal spinal cord commissural neurons at E10.5


title: E12.5-rep1

description: mouse dorsal spinal cord


title: Alzheimer's Disease CSF009

description:
EXR-JSAUG1UH2009-BS
total cell-free biofluid RNA


title: hypoAkkF10-2_scRNA-seq

description: DropSeq


title: hypoABW4-3_scRNA-seq

description: DropSeq


title: Alzheimer's Disease CSF008

description:
EXR-JSAUG1UH2008-BS
total cell-free biofluid RNA

value: Male


title: hypoAkkW7-2_scRNA-seq

description: DropSeq


title: E10.5-rep1

description: mouse dorsal spinal cord


title: hypoABW4-2_scRNA-seq

description: DropSeq


title: Alzheimer's Disease CSF013

description:
EXR-JSAUG1UH2013-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF007

description:
EXR-JSAUG1UH2007-BS
total cell-free biofluid RNA


title: hypoABF5-3_scRNA-seq

description: DropSeq


title: hypoABF5-2_scRNA-seq

description: DropSeq


title: hypoABW3-1_scRNA-seq

description: DropSeq


title: Alzheimer's Disease CSF010

description:
EXR-JSAUG1UH2010-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF006

description:
EXR-JSAUG1UH2006-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF005

description:
EXR-JSAUG1UH2005-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF004

description:
EXR-JSAUG1UH2004-BS
total cell-free biofluid RNA


title: hypoABF5-1_scRNA-seq

description: DropSeq


title: Alzheimer's Disease CSF003

description:
EXR-JSAUG1UH2003-BS
total cell-free biofluid RNA


title: PR8/MRSA_GKO, scRNAseq

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: matrix files in h5 format

source_name: Bronchoalveolar

extract_protocol:
BALF were collected by making an incision in the trachea and lavaging the lung twice with 0.8 ml PBS, pH 7.4. Cells were washed and re-suspended in PBS and stained with a Viability Dye.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, immune cells 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.

tag: cell type

value: Immune cells

value: Bronchoalveolar

value: 6-10 weeks old


title: PR8/MRSA_WT, replicate 2, scRNAseq

description: 10x Genomics

tag: tissue


title: DLD-1 cell line with episomally-transfected Snail doxycycline-inducible

city: Cambridge

first: Fatima

last: Junaid

address: Puddicombe Way

country: United Kingdom

institute: Cancer Research UK - CI

hyb_protocol: Manufacturer's protocols were followed for the RT2 Profiler PCR Array Human Epithelial to Mesenchymal Transition (QIAGEN) kit.

scan_protocol: Plates were run on a QuantStudio 6 Flex Real-Time PCR System (Thermo Fisher Scientific) with the following programme: 95oC 10 minutes then 40 cycles of 95oC 15 seconds and 60oC 60 seconds, where fluorescence data was collected at the final step of each cycle.

data_processing:
Data was analysed using the Ct method normalised to the kit-specific panel of housekeeping genes in the PCR Array Data Analysis Software (QIAGEN).
gene expression normalised to DLD-1 cell line without Snail overexpression

label: SYBR Green

source_name: colorectal cancer cell line

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (Gibco) containing 4.5g/L D-Glucose and L-Glutamine and supplemented with 10% tetracycline-free foetal bovine serum (Clontech) and 1% penicillin and streptomycin (Gibco). Cells were passaged when confluent with 0.05% trypsin (Gibco) and incubated in a Heracell 150 incubator, 20% oxygen and 5% carbon dioxide at 37oC.

extract_protocol: RNA was extracted from cell pellets with an RNeasy Plus Mini Kit (QIAGEN) and complementary DNA synthesised with an RT2 First Strand Kit (QIAGEN), all following standard protocols.

treatment_protocol: Cells were incubated with 100ng/ml doxycycline for 5 (Snail-hi) -14 (Snail-lo) days.

value: male

tag: type

value: adenocarcinoma

tag: Stage

value: Duke's C

tag: cell line


title: PR8/MRSA_IFNgRKO, scRNAseq

description: 10x Genomics

tag: strain


title: SNU-449 control R2

city: LJubljana

first: Tadeja

last: Rezen

address: Vrazov trg 2

department: Faculty of Medicine

country: Slovenia

institute: University of Ljubljana

hyb_protocol: Hybridisation, washing and stainnig was done according to manufacturer protocol on Fluidics Station 450 and Hybridization Oven 640.

scan_protocol: Microarrays were scaned using GCS 3000 7G.

data_processing: The data was analysed in Transcriptome Analysis Console (TAC).

source_name: SNU-449 cell line

label_protocol: Transcriptome analysis of HCC model cell lines was performed using Clariom S Array, human in triplicates from each cell line according to manufacturer`s protocol.

growth_protocol: The Huh-7 cell line (300156, CLS, Eppelheim, Germany) and SNU-499 cell line (CRL-2234, ATCC, Manassas, VA, USA) were cultured in Dulbecco’s Modified Eagle’s Media (DMEM) high glucose, supplemented with 10% FBS and 1% penicillin/streptomycin. Cells were cultured in a humidified chamber at a constant 37 °C and 5% CO2.

extract_protocol: Total RNA was isolated by TRI reagent using the protocol provided by the manufacturer. Each replicate was isolated from a separate well.

treatment_protocol: For transient overexpression (OE)  in the Huh-7 cell line, we prepared a mini-gene plasmid system for circRNA overexpression (pRR) by using a modified pcDNA3.1(+) ZKSCAN1 MCS Exon Vector and cDNA generated from the RNA of the Huh-7 cell line. For control, we used an empty vector. We used GenJet In Vitro DNA Transfection Reagent and followed the manufacturer`s protocol. For the generation of stable knockdown (KD) in the SNU-449 cell line, we prepared a lentiviral system using the transfer plasmid system pLKO.1 – TRC cloning vector for the cloning of the shRNA sequence targeting the circRNA backsplice junction. For control, we used scramble shRNA plasmid derived from pLKO.1 plasmid.

tag: genotype

value: Stable transduction with lentiviral system, scramble shRNA.

value: SNU-449 cell line


title: Alzheimer's Disease CSF001

description:
EXR-JSAUG1UH2001-BS
total cell-free biofluid RNA

tag: diagnosis

tag: Sex


title: SNU-449 control R3


title: SNU-449 KD R2

value: Stable transduction with lentiviral system, knockdown of hsa_circ_0062682 expression.


title: SNU-449 KD R1


title: SNU-449 KD R3


title: PR8/MRSA_WT, replicate 1, scRNAseq

description: 10x Genomics

tag: age


title: Huh-7 OE R3

source_name: Huh-7 cell line

value: Transient transfection with vector for overexpression of hsa_circ_0062682.

value: Huh-7 cell line


title: Huh-7 OE R2


title: Huh-7 OE R1


title: St41_reads

status: Public on Sep 02 2022

city: New York

first: Maria

middle: ANTONIETTA

last: Tosches

address: 1212 Amsterdam Ave

institute: Columbia University

data_processing:
Reads were assigned to the combined P.waltl transcriptome using Alevin (Salmon v1.6.0). Library type was set to automatic and keepCBFraction was set to 1. All other parameters were set as default.
Count matrices were obtained after alignment with Alevin (Salmon v1.6.0) and knee plots were generated for each library. Low UMI counts were filtered out and a single Seurat object containing all libraries was created using Seurat 4.0.2.
Assembly: p.waltl_transcriptome. FASTA and t2g files are available on the SuperSeries record.
Supplementary files format and content: .rds of gene count

organism: Pleurodeles waltl

source_name: Telencephalon

growth_protocol: Animal grown in lab specified developmental stage

extract_protocol:
For brain dissociation, animals were deeply anesthetized by submersion in 0.2% MS-222. The brain was perfused transcardially with ice-cold oxygenated Amphibian Ringer’s solution (96 mM NaCl; 20 mM NaHCO3; 2 mM KCl; 10 mM HEPES; 11 mM glucose; 2 mM CaCl2; 0.5 mM MgCl2), and the animal decapitated. The whole brain or telencephalon was dissected out, and embedded in 4% LM Agarose in Ringer. The brain was then sliced coronally on a vibratome into 500 um sections, and cut into 500 um cubes in cold carbogenated Ringer. The tissue pieces were transferred to a 5 mL tube in 2.5 mL Dissociation Buffer (20 U/mL Papain, 200 U/mL DNase, 5 ug/mL Liberase, 1 uM TTX), and incubated at RT for 30 minutes on a rotator. Following enzymatic dissociation, the tissue was mechanically dissociated by trituration with fire polished, silanized glass pipettes of decreasing tip diameter on ice. The supernatant was passed through a 100 um cell strainer, with fresh carbogenated Hibernate A-Ca media added between each subsequent pipette until a uniform suspension was obtained. Hibernate A-Ca was added up to a total volume of 20 mL, and the solution was passed through a 70 um cell strainer. To the bottom of the tube, 5 mL of 4% BSA in Hibernate A-Ca - phenol red was added. To filter out cell debris, the cell suspension was centrifuged through the density gradient at 300xg (4°C) for 5 min. The supernatant was removed, and the pellet resuspended in 50-100 uL Hibernate A-Ca - Mg. The cell concentration was determined by counting on a Fuchs- Rosenthal chamber with trypan blue, and diluted to 1000 cells/uL in Hibernate A- Ca - Mg
The cells were loaded into a 10x Chromium Chip G with a targeted cell recovery of 5000-8000 cells for GEM Generation and cell barcoding. Single cell RNA-seq libraries were prepared with 10x Chromium Next GEM Single Cell 3' Reagent Kit v3.0 or v3.1 (Dual Index)

treatment_protocol: No treatment

tag: animals

value: 16 larvae

tag: brain region

value: Telencephalon (CMO305,306,307) Midbrain (CMO308)


title: St41_mpx


title: St46_T1_reads

data_processing:
Reads were assigned to the combined P.waltl transcriptome using Alevin (Salmon v1.6.0). Library type was set to automatic and keepCBFraction was set to 1. All other parameters were set as default.
Count matrices were obtained after alignment with Alevin (Salmon v1.6.0) and knee plots were generated for each library. Low UMI counts were filtered out and a single Seurat object containing all libraries was created using Seurat 4.0.2.
Assembly: p.waltl_transcriptome
Supplementary files format and content: .rds of gene count

source_name: Telencephalon + midbrain

extract_protocol:
For brain dissociation, animals were deeply anesthetized by submersion in 0.2% MS-222. The brain was perfused transcardially with ice-cold oxygenated Amphibian Ringer’s solution (96 mM NaCl; 20 mM NaHCO3; 2 mM KCl; 10 mM HEPES; 11 mM glucose; 2 mM CaCl2; 0.5 mM MgCl2), and the animal decapitated. The whole brain or telencephalon was dissected out, and embedded in 4% LM Agarose in Ringer. The brain was then sliced coronally on a vibratome into 500 um sections, and cut into 500 um cubes in cold carbogenated Ringer. The tissue pieces were transferred to a 5 mL tube in 2.5 mL Dissociation Buffer (20 U/mL Papain, 200 U/mL DNase, 5 ug/mL Liberase, 1 uM TTX), and incubated at RT for 30 minutes on a rotator. Following enzymatic dissociation, the tissue was mechanically dissociated by trituration with fire polished, silanized glass pipettes of decreasing tip diameter on ice. The supernatant was passed through a 100 um cell strainer, with fresh carbogenated Hibernate A-Ca media added between each subsequent pipette until a uniform suspension was obtained. Hibernate A-Ca was added up to a total volume of 20 mL, and the solution was passed through a 70 um cell strainer. To the bottom of the tube, 5 mL of 4% BSA in Hibernate A-Ca - phenol red was added. To filter out cell debris, the cell suspension was centrifuged through the density gradient at 300xg (4°C) for 5 min. The supernatant was removed, and the pellet resuspended in 50-100 uL Hibernate A-Ca - Mg. The cell concentration was determined by counting on a Fuchs- Rosenthal chamber with trypan blue, and diluted to 1000 cells/uL in Hibernate A- Ca - Mg
The cells were loaded into a 10x Chromium Chip G with a targeted cell recovery of 5000-8000 cells for GEM Generation and cell barcoding. Single cell RNA-seq libraries were prepared with 10x Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.0 or v3.1 (Dual Index)

value: 10 larvae

value: Telencephalon (CMO305,306) Midbrain (CMO307,308)


title: Alzheimer's Disease CSF002

description:
EXR-JSAUG1UH2002-BS
total cell-free biofluid RNA

value: Alzheimer's Disease

value: Cerebrospinal fluid

tag: anatomical location

value: Structure of nervous tissue

tag: sample collection method

value: Lumbar puncture

tag: starting amount

tag: holding temperature


title: St_46_M2_mpx


title: St46_M1_mpx


title: st50_D2_2

data_processing:
Reads were assigned to the combined P.waltl transcriptome using Alevin (Salmon v1.6.0). Library type was set to automatic and keepCBFraction was set to 1. All other parameters were set as default.
Count matrices were obtained after alignment with Alevin (Salmon v1.6.0) and knee plots were generated for each library. Low UMI counts were filtered out and a single Seurat object containing all libraries was created using Seurat 4.0.2.
Assembly: p.waltl_transcriptome. FASTA  and t2g files are available on the SuperSeries record.
Supplementary files format and content: .rds of gene count

value: Telencephalon


title: st50_D2_1


title: DLD-1 cell line with single-extra copy of Snail that is doxycycline-inducible

label_protocol: Manufacturer's protocols were followed for the RT2 Profiler PCR Array Human Epithelial to Mesenchymal Transition (QIAGEN) kit.

value: male


title: Huh-7 control R2

value: Transient transfection with empty vector.


title: D1_1


title: D1_2


title: St36_mpx

extract_protocol:
For brain dissociation, animals were deeply anesthetized by submersion in 0.2% MS-222. The brain was perfused transcardially with ice-cold oxygenated Amphibian Ringer’s solution (96 mM NaCl; 20 mM NaHCO3; 2 mM KCl; 10 mM HEPES; 11 mM glucose; 2 mM CaCl2; 0.5 mM MgCl2), and the animal decapitated. The whole brain or telencephalon was dissected out, and embedded in 4% LM Agarose in Ringer. The brain was then sliced coronally on a vibratome into 500 um sections, and cut into 500 um cubes in cold carbogenated Ringer. The tissue pieces were transferred to a 5 mL tube in 2.5 mL Dissociation Buffer (20 U/mL Papain, 200 U/mL DNase, 5 ug/mL Liberase, 1 uM TTX), and incubated at RT for 30 minutes on a rotator. Following enzymatic dissociation, the tissue was mechanically dissociated by trituration with fire polished, silanized glass pipettes of decreasing tip diameter on ice. The supernatant was passed through a 100 um cell strainer, with fresh carbogenated Hibernate A-Ca media added between each subsequent pipette until a uniform suspension was obtained. Hibernate A-Ca was added up to a total volume of 20 mL, and the solution was passed through a 70 um cell strainer. To the bottom of the tube, 5 mL of 4% BSA in Hibernate A-Ca - phenol red was added. To filter out cell debris, the cell suspension was centrifuged through the density gradient at 300xg (4°C) for 5 min. The supernatant was removed, and the pellet resuspended in 50-100 uL Hibernate A-Ca - Mg. The cell concentration was determined by counting on a Fuchs- Rosenthal chamber with trypan blue, and diluted to 1000 cells/uL in Hibernate A- Ca - Mg. Cells were multiplexed using the Chromium Next GEM Single Cell 3' v3.1: Cell Multiplexing kit
The cells were loaded into a 10x Chromium Chip G with a targeted cell recovery of 5000-8000 cells for GEM Generation and cell barcoding. Single cell RNA-seq libraries were prepared with 10x Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.0 or v3.1 (Dual Index)

value: 35 larvae


title: SNU-449 control R1

value: Stable transduction with lentiviral system, scramble shRNA.


title: St36_reads_T2


title: Huh-7 control R1


title: St36_reads


title: E4_4

data_processing:
Reads were assigned to the combined P.waltl transcriptome using Alevin (Salmon v1.6.0). Library type was set to automatic and keepCBFraction was set to 1. All other parameters were set as default.
Count matrices were obtained after alignment with Alevin (Salmon v1.6.0) and knee plots were generated for each library. Low UMI counts were filtered out and a single Seurat object containing all libraries was created using Seurat 4.0.2.
Assembly: p.waltl_transcriptome. FASTA  and t2g files are available on the SuperSeries record.
Supplementary files format and content: .rds of count_matrix

growth_protocol: Animal grown in lab to adulthood

tag: animal


title: E4_2


title: E4_3


title: St36_mpx_M2


title: E6_2

data_processing:
Reads were assigned to the combined P.waltl transcriptome using Alevin (Salmon v1.6.0). Library type was set to automatic and keepCBFraction was set to 1. All other parameters were set as default.
Count matrices were obtained after alignment with Alevin (Salmon v1.6.0) and knee plots were generated for each library. Low UMI counts were filtered out and a single Seurat object containing all libraries was created using Seurat 4.0.2.
Genome_build: p.waltl transcriptome
Supplementary_files_format_and_content: rds file of gene count matrix


title: E6_3


title: E6_4


title: Huh-7 control R3


title: St46_T2_reads

source_name: telencephalon + midbrain


title: E4_1


title: E2_3

data_processing:
Reads were assigned to the combined P.waltl transcriptome using Alevin (Salmon v1.6.0). Library type was set to automatic and keepCBFraction was set to 1. All other parameters were set as default.
Count matrices were obtained after alignment with Alevin (Salmon v1.6.0) and knee plots were generated for each library. Low UMI counts were filtered out and a single Seurat object containing all libraries was created using Seurat 4.0.2.
Genome_build: p.waltl_transcriptome
Supplementary_files_format_and_content: .rds file of count matrix for animal A2

value: Whole brain


title: E2_2


title: E1_4

data_processing:
Reads were assigned to the combined P.waltl transcriptome using Alevin (Salmon v1.6.0). Library type was set to automatic and keepCBFraction was set to 1. All other parameters were set as default.
Count matrices were obtained after alignment with Alevin (Salmon v1.6.0) and knee plots were generated for each library. Low UMI counts were filtered out and a single Seurat object containing all libraries was created using Seurat 4.0.2.
Genome_build: P.waltl_transcriptome
Supplementary_files_format_and_content: rds file of gene count matrix(all libraries combined into one file)

value: whole brain


title: E1_3


title: E2_1


title: E1_1


title: E5_5

data_processing:
Reads were assigned to the combined P.waltl transcriptome using Alevin (Salmon v1.6.0). Library type was set to automatic and keepCBFraction was set to 1. All other parameters were set as default.
Count matrices were obtained after alignment with Alevin (Salmon v1.6.0) and knee plots were generated for each library. Low UMI counts were filtered out and a single Seurat object containing all libraries was created using Seurat 4.0.2.
Genome_build: merged_pleurodeles transcriptome
Supplementary_files_format_and_content: gene count matrix in rds format


title: E5_6


title: E5_2


title: E5_3


title: E6_5


title: E5_1


title: E6_6


title: E6_1


title: E2_4


title: No Template Control 1

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

country: Australia

institute: University of Queensland

data_processing:
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_COVID19_v1.0.pkc)
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: Values represented in the collapsed target counts tab are the geometric mean of the probes for a given target--in the case that multiple probes were used-- and excludes any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments and features.

organism: blank sample

source_name: blank sample

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.
OTHER: GeoMx Seq

value: blank sample

tag: tma


title: E1_2


title: No Template Control 2

tag: tissue


title: E5_4


title: Adult_96_1728_S128

city: Sacramento

first: Thomas

middle: H

last: Ambrosi

address: 2700 Stockton Blvd

institute: UC Davis

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_96_1728_S128

data_processing:
demultiplexing using bcl2fastq2 2.18 (Illumina)
raw reads were further processed using skewer11 for 3′ quality-trimming, 3′ adaptor-trimming, and removal of degenerate reads (Jiang et al., 2014).
trimmed reads were then mapped to the human genome h38 using STAR 2.4 (Dobin et al., 2013)
counts for gene and transcript reads were calculated using RSEM 1.2.21 (Li and Dewey, 2011)
Assembly: GRCh38.p12.gencode.v29
Supplementary files format and content: tab-delimited text file with raw gene counts for every gene and every sample

source_name: Skeletal Tissue

growth_protocol: freshly purified cells without prior in vitro culture

extract_protocol:
Bone tissue with mechanically and enzymatically digested, stained with antibodies, and purified via FACS.
SmartSeq2 pipeline (Picelli et al.)

treatment_protocol: no treatment

value: vertebrae

tag: status

value: Body L4-5

value: 40 years


title: Adult_81_1698_S98

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_81_1698_S98


title: Adult_93_1722_S122

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_93_1722_S122


title: Adult_95_1726_S126

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_95_1726_S126


title: Adult_92_1720_S120

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_92_1720_S120


title: Adult_82_1700_S100

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_82_1700_S100


title: Adult_84_1704_S104

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_84_1704_S104


title: Adult_85_1706_S106

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_85_1706_S106


title: Adult_88_1712_S112

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_88_1712_S112


title: Adult_83_1702_S102

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_83_1702_S102


title: Adult_87_1710_S110

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_87_1710_S110


title: Adult_89_1714_S114

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_89_1714_S114


title: Adult_94_1724_S124

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_94_1724_S124


title: Adult_91_1718_S118

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_91_1718_S118


title: Adult_90_1716_S116

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_90_1716_S116


title: Adult_80_1696_S96

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_80_1696_S96


title: Adult_86_1708_S108

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_86_1708_S108


title: Adult_78_1692_S92

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_78_1692_S92


title: Adult_79_1694_S94

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_79_1694_S94


title: Adult_76_1688_S88

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_76_1688_S88


title: Adult_74_1684_S84

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_74_1684_S84


title: Adult_75_1686_S86

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_75_1686_S86


title: Adult_73_1682_S82

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_73_1682_S82


title: Adult_72_1680_S80

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_72_1680_S80


title: Adult_71_1678_S78

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_71_1678_S78


title: Adult_69_1674_S74

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_69_1674_S74


title: Adult_70_1676_S76

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_70_1676_S76


title: Adult_68_1672_S72

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_68_1672_S72


title: Adult_67_1670_S70

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_67_1670_S70


title: Adult_66_1668_S68

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_66_1668_S68


title: Adult_62_1660_S60

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_62_1660_S60


title: Adult_59_1654_S54

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_59_1654_S54


title: Adult_56_1648_S48

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_56_1648_S48


title: Adult_65_1666_S66

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_65_1666_S66


title: Adult_55_1646_S46

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_55_1646_S46


title: Adult_77_1690_S90

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_77_1690_S90


title: Adult_54_1644_S44

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_54_1644_S44


title: Adult_63_1662_S62

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_63_1662_S62


title: Adult_52_1640_S40

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_52_1640_S40


title: Adult_60_1656_S56

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_60_1656_S56


title: Adult_57_1650_S50

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_57_1650_S50


title: Adult_61_1658_S58

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_61_1658_S58


title: Adult_64_1664_S64

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_64_1664_S64


title: Adult_49_1634_S34

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_49_1634_S34


title: Adult_53_1642_S42

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_53_1642_S42


title: Adult_47_1630_S30

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_47_1630_S30


title: Adult_58_1652_S52

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_58_1652_S52


title: Adult_48_1632_S32

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_48_1632_S32


title: Adult_44_1624_S24

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_44_1624_S24


title: Adult_45_1626_S26

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_45_1626_S26


title: Adult_43_1622_S22

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_43_1622_S22


title: Adult_46_1628_S28

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_46_1628_S28


title: Adult_42_1620_S20

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_42_1620_S20


title: Adult_41_1618_S18

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_41_1618_S18


title: Adult_40_1616_S16

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_40_1616_S16


title: Adult_39_1614_S14

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_39_1614_S14


title: Adult_51_1638_S38

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_51_1638_S38


title: Adult_50_1636_S36

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_50_1636_S36


title: Adult_35_1606_S6

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_35_1606_S6


title: Adult_38_1612_S12

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_38_1612_S12


title: Adult_31_1598_S398

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_31_1598_S398


title: Adult_36_1608_S8

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_36_1608_S8


title: Adult_34_1604_S4

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_34_1604_S4


title: Adult_33_1602_S2

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_33_1602_S2


title: Adult_37_1610_S10

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_37_1610_S10


title: Adult_27_1590_S390

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_27_1590_S390


title: Adult_30_1596_S396

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_30_1596_S396


title: Adult_24_1584_S384

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_24_1584_S384


title: Adult_32_1600_S400

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_32_1600_S400


title: Adult_26_1588_S388

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_26_1588_S388


title: Adult_23_1582_S382

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_23_1582_S382


title: Adult_22_1580_S380

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_22_1580_S380


title: Adult_29_1594_S394

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_29_1594_S394


title: Adult_28_1592_S392

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_28_1592_S392


title: Adult_25_1586_S386

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_25_1586_S386


title: Adult_20_1576_S376

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_20_1576_S376


title: Adult_16_1568_S368

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_16_1568_S368


title: Adult_18_1572_S372

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_18_1572_S372


title: Adult_19_1574_S374

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_19_1574_S374


title: Adult_17_1570_S370

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_17_1570_S370


title: Adult_15_1566_S366

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_15_1566_S366


title: Adult_14_1564_S364

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_14_1564_S364


title: Adult_12_1560_S360

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_12_1560_S360


title: Adult_10_1556_S356

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_10_1556_S356


title: Adult_13_1562_S362

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_13_1562_S362


title: Adult_11_1558_S358

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_11_1558_S358


title: Adult_9_1554_S354

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_9_1554_S354


title: Adult_8_1552_S352

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_8_1552_S352


title: Adult_21_1578_S378

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_21_1578_S378


title: Adult_6_1548_S348

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_6_1548_S348


title: Adult_7_1550_S350

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_7_1550_S350


title: Adult_4_1544_S344

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_4_1544_S344


title: Adult_5_1546_S346

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_5_1546_S346


title: Adult_3_1542_S342

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_3_1542_S342


title: Adult_2_1540_S340

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_2_1540_S340


title: DIPG17_BRG1KO_H3K27Ac_rep1

first: Zhiguo

last: Zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the human (hg19) reference genome using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. RNA-Seq reads were mapped using STAR.
Coverage for each base pair of the human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
Sparse Enrichment Analysis for CUT&RUN (SEACR version 1.3) was used for peak calling (Meers et al., 2019).
Read count on gene body or promoters were calculated by FeatureCount. Differential genes and log fold change were calculated by edgeR
Assembly: hg19
Supplementary files format and content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores represent the normalization reads density.
Library strategy: CUT&RUN

source_name: patient-derived cell culture

growth_protocol: The patient-derived cell lines (DIPG6, DIPG17, DIPG4 and DIPG36) were kind gift from Dr. Michelle Monje (Standford University School of Medicine). DIPG6, DIPG17, DIPG4 and DIPG36 are all cultured in neuro stem medium (Knockout/F12 medium supplemented with 10% neuro stem supplement, 20 µg/ml EGF, 20 µg/ml FGF-b, 1% penicillin/strepmycin and 1% L-glutamine). GBM22, GBM43 and GBM28 were nice gift from Mayo Clinic by Dr. Jann Sakaria and cultured in 10% FBS DMEM medium supplemented with L-Glutamine and penicillin/streptomycin. SF8628, KNS42, SF9427 cell lines were cultured in DMEM supplemented with 10% FBS, penicillin/streptomycin and L-Glutamine as previously described (Fang et al., 2018). 293T cells were purchased from ATCC. All the cells were cultured in 37 °C, 5% CO2 and 95% humidity and were tested negative for mycoplasma.

extract_protocol:
CUT&RUN was performed as previously described (Skene and Henikoff, 2017) with minor modifications. Total RNA samples were purified the same as for RT-PCR.
RNA-seq libraries were prepared and deep sequencing was performed by Columbia University Genome Center. CUT&RUN libraries were prepared using ACCEL-NGSTM 1S plus DNA library kit and library PCR was performed using standard Illumina Nextera Dual Indexing primers. Samples were pooled and sequenced using paired-end sequencing on Illumina NextSeq 500 platforms at Columbia University Genome Center.

tag: experiments

tag: cell type

value: Diffuse intrinsic pontine glioma (DIPG) cells

value: BRG1 KO

tag: chip antibody

tag: spike-in

value: Mus musculus


title: DIPG17_WT_H3K4me3_rep1

tag: genotype

value: WT


title: DIPG17_BRG1KO_H3K4me3_rep2


title: DIPG17_WT2_H3K27Ac_rep2


title: DIPG17_BRG1KO_H3K4me3_rep1


title: DIPG17_BRG1KO_ATAC_rep2

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the human (hg19) reference genome using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. RNA-Seq reads were mapped using STAR.
Coverage for each base pair of the human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
Sparse Enrichment Analysis for CUT&RUN (SEACR version 1.3) was used for peak calling (Meers et al., 2019).
Read count on gene body or promoters were calculated by FeatureCount. Differential genes and log fold change were calculated by edgeR
Assembly: hg19
Supplementary files format and content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores represent the normalization reads density.


title: DIPG17_WT_H3K27me3_rep1


title: DIPG17_BRG1KO_ATAC_rep1


title: DIPG17_H33K27MKO_H3K27me3_rep2

value: H33K27M KO


title: DIPG17_H33K27MKO_H3K27me3_rep1


title: DIPG17_WT_ATAC_rep1


title: D35_HIO from spheroid_21

city: Charleston

first: Jorge

last: Munera

state: SC

address: 173 Ashley Avenue

institute: Medical University of South Carolina

description:
Clump and Spheroid _Normalized_counts
Sph_37D HIO_U

data_processing:
For HIO and HIO+RA, the sequecing data was analyzed by BGI. For clump and spheroid data, Fastq files were imported into the Partek Flow system
BGI used HISAT2 and Bowtie2 to map the data to human genome. Partek Flow used STAR to do the data alignment.
BGI used RSEM to quantify the aligned data. Partek Flow used Partek E/M for the data quantification
Both BGI and Partek Flow used DEseq2 to obtain differentially expressed gene data.
Assembly: hg38
Supplementary files format and content: Excel file of normalized data

source_name: D35_HIO from spheroid

extract_protocol: RNA libraries were prepared by BGI and sequencing was performed on BGI DNBseq platform using single end or paired end.

treatment_protocol: HIO were cultured in basic gut medium with EGF only, HIO+RA were cultured in EGF with 2uM RA until D35.

tag: group

value: D35_HIO from spheroid

value: human intestinal organoids (HIO)


title: DIPG17_WT_H3K27me3_rep2


title: D35_HIO from spheroid_11

description:
Clump and Spheroid _Normalized_counts
Sph_36D HIO_K


title: Adult_1_1538_S338

description: SSCz_DiscL4to5_hSSC_na_AdultSpine_Adult_1_1538_S338

tag: age

tag: Sex

value: male


title: D35_HIO from clump_36

description:
Clump and Spheroid _Normalized_counts
Clu_HIO_JJ

source_name: D35_HIO from clump

value: D35_HIO from clump


title: h967_4

city: Shanghai

first: Yulong

last: Tang

address: Songhu Road 2005

institute: Fudan University

data_processing:
FastQC and FASTX_Toolkit were used for quality control of the sequencing data
Kallisto1 (v0.44.0) was used to quantify mRNA and lncRNA expression levels with default settings
Tximport2 (version 1.16.1) package was used to integrate “abundance.h5” files (generated by kallisto) to a matrix of gene counts.
processed data can be followed by DESeq2 or other DE-analysis tools
Assembly: hg38
Supplementary files format and content: comma-delimited csv files include counts values for each Sample, including mRNA and lncRNA respectively

source_name: Hair follicle (vertex)

extract_protocol:
A total of 2-3 mg of RNA per patient was used as input material for RNA library preparation.
Sequencing libraries of mRNA and lincRNA were generated using TreSeq RNA Kits Prep Kit (Illumina) according to the manufacturer’s recommendations.

value: Hair follicle (vertex)

tag: disease state

value: androgenetic alopecia

tag: cell line

value: Primary hair follicle cells

value: Hair follicle cells

tag: treatment


title: PRB-0432

first: Shengmei

last: Zhou

state: CA

address: 4650 Sunset Blvd.

department: Pathology and Laboratory Medicine

institute: Children's Hospital Los Angeles

data_processing:
RNAseq data were analyzed using Partek Flow
Raw sequencing reads were first trimmed for base quality using the Quality Score method
Trimmed reads were aligned to human genome GRCh38 using STAR 2.6.1d with Gencode 32 as guidance.
Aligned reads were then quantified to Gencode 32 using Partek E/M.
Raw reads were normalized using Upper Quartile normalization with an offset of 1.
Genome_build: GRCh38

source_name: liver

extract_protocol:
For frozen samples, RNA was extracted with Qiagen RNeasy Mini RNA Extraction Kit (Qiagen, Hilden, Germany). For FFPE samples, RNA was extracted with the Beckman Coulter FormaPure RNA Extraction Kit (Beckman Coulter, Brea, CA)
Libraries were prepared using the KAPA RNA Hyper Prep Kit (KAPA Biosystems, Wilmington, MA) with an initial input quantity of 100 ng purified RNA. Hybridization was performed using the Twist Biosciences Human Core Exome and the Human RefSeq Panel probes and the Fast Hybridization and Wash Kit (Twist Biosciences, San Francisco, CA).

value: M

value: Control


title: DIPG17_BRG1KO_H3K27Ac_rep2


title: D35_HIO from clump_17

description:
Clump and Spheroid _Normalized_counts
Clu_HIO_Q


title: PRB-0436


title: DIPG17_WT1_H3K27Ac_rep1


title: DIPG17_WT_H3K4me3_rep2


title: D35_HIO from clump_6

description:
Clump and Spheroid _Normalized_counts
Clu_HIO_F


title: h902_4


title: h898_4


title: PRB-0434


title: D7_Spheroid_47

description:
Clump and Spheroid _Normalized_counts
Sph_Sph_UU


title: h893_4


title: h878_4


title: D7_Spheroid_45

description:
Clump and Spheroid _Normalized_counts
Sph_Sph_SS


title: D7_Clumps_48

description:
Clump and Spheroid _Normalized_counts
Clu_Clu_VV


title: PRB-0433

value: Tumor


title: D7_Clumps_46

description:
Clump and Spheroid _Normalized_counts
Clu_Clu_TT


title: h872_4


title: PRB-0374


title: PRB-0377


title: HIO+RA_23

description:
HIO and HIO + RA  GeneExpression TPM.xls
23_TPM

source_name: D35 HIO+RA

value: D35 HIO+RA


title: D7_Clumps_44

description:
Clump and Spheroid _Normalized_counts
Clu_Clu_RR


title: D7_Clumps_4

description:
Clump and Spheroid _Normalized_counts
Clu_Clu_D


title: D7_Clumps_28

description:
Clump and Spheroid _Normalized_counts
Clu_Clu_BB


title: h1018_4 [S4]


title: PRB-0378


title: HIO+RA_19

description:
HIO and HIO + RA  GeneExpression TPM.xls
19_TPM


title: h936_4 [S3]


title: HIO+RA_15

description:
HIO and HIO + RA  GeneExpression TPM.xls
15_TPM


title: DIPG17_BRG1KO_RNAseq_rep2

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the human (hg19) reference genome using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. RNA-Seq reads were mapped using STAR.
Coverage for each base pair of the human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
Sparse Enrichment Analysis for CUT&RUN (SEACR version 1.3) was used for peak calling (Meers et al., 2019).
Read count on gene body or promoters were calculated by FeatureCount. Differential genes and log fold change were calculated by edgeR
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores represent the normalization reads density.

value: Diffuse intrinsic pontine glioma (DIPG) cells


title: HIO_21

description:
HIO and HIO + RA  GeneExpression TPM.xls
21_TPM

source_name: D35 HIO

value: D35 HIO


title: h948_4 [S2]


title: HIO+RA_11

description:
HIO and HIO + RA  GeneExpression TPM.xls
11_TPM


title: HIO_17

description:
HIO and HIO + RA  GeneExpression TPM.xls
17_TPM


title: h942_4 [S1]


title: HIO_13

description:
HIO and HIO + RA  GeneExpression TPM.xls
13_TPM


title: DIPG17_WT_ATAC_rep2


title: DIPG17_WT_RNAseq


title: DIPG17_BRG1KO_RNAseq_rep1

value: BRG1 KO


title: D7_Spheroid_43

description:
Clump and Spheroid _Normalized_counts
Sph_Sph_QQ


title: h902_1

source_name: Hair follicle (occipital)

value: Hair follicle (occipital)

value: WT


title: DIPG6_BRG1KO_RNAseq_rep2


title: fast5 Pol2RELexo_rep1

city: new york

first: clemence

last: claussin

state: New York

address: 1275 York Avenue

department: molecular biology

institute: Memorial sloan kettering cancer center

description:
Biological replicates for Pol2RELexo mutants
DNA replicons
MinION nanopore

data_processing:
Base calling was performed using Guppy (Oxford Nanopore)
Reads were mapped to the genome using Minimap2
BrdU containing reads were call using DNAscent V2, reads were split into 250bp interval to assign as BrdU positive or negative reads, BrdU score was then calculated, and only reads with a BrdU > or = 0.5 were selected
position and orientation of the reads primers were defined using LAST ( kielbasa et al, 2011)
Assembly: Custom genome was constructed from Nanopre reads using Canu.

organism: Saccharomyces cerevisiae

source_name: MATa

growth_protocol: yeast were grown at 30C in rich media

extract_protocol:
DNA was extracted as in Replicon-seq protocol after calcium induction of MNase
Library was constructed using SQK-SKL109 or SQK-SKL110 kit (Oxford Nanopore)
Nanopore MinION FLO-MIN106 flow cells R9

treatment_protocol: Cells are arrested in G1 with alpha factor; 400ug/mL of BrdU was added 30min before release from G1 , cells were released into pre-warmed media containing 400ug/mL BrdU.

value: MATa

value: MATa pol2-exo-REL::Kan MCM4-N-ter-MNase LEU2::BrdU-Inc URA3::GPD-TK7

value: G1 arrested with alpha factor and released with BrdU at 25C


title: HIO_9

description:
HIO and HIO + RA  GeneExpression TPM.xls
9_TPM

value: human intestinal organoids (HIO)


title: fast5 Pol2REL_rep2

description:
Biological replicates for Pol2REL mutants
DNA replicons
MinION nanopore

value: MATa pol2-REL::Kan MCM4-N-ter-MNase LEU2::BrdU-Inc URA3::GPD-TK7


title: fast5 Pol2REL_rep1


title: h898_1

value: androgenetic alopecia

value: male


title: fq Pol2REL_rep2


title: fq Pol2RELexo_rep1


title: fq Pol2REL_rep1


title: DIPG17_H33K27MKO_H3K27Ac_rep2

data_processing:
Library strategy: CUT&RUN
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the human (hg19) reference genome using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. RNA-Seq reads were mapped using STAR.
Coverage for each base pair of the human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
Sparse Enrichment Analysis for CUT&RUN (SEACR version 1.3) was used for peak calling (Meers et al., 2019).
Read count on gene body or promoters were calculated by FeatureCount. Differential genes and log fold change were calculated by edgeR
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores represent the normalization reads density.

value: H33K27M KO

value: Mus musculus


title: h893_1

value: Primary hair follicle cells

value: Hair follicle cells


title: DIPG6_WT_RNAseq


title: fq Pol2RELexo_rep2


title: h878_1


title: h872_1


title: DIPG17_H33K27MKO_H3K27Ac_rep1


title: h1018_1 [C4]


title: DIPG17_WT_H3K27Ac_rep2


title: h936_1 [C3]


title: fast5 Pol2RELexo_rep2


title: DIPG17_WT_H3K27Ac_rep1


title: DIPG17_H33K27MKO_SOX10_rep2


title: DIPG6_BRG1KO_RNAseq_rep1


title: h948_1 [C2]


title: h942_1 [C1]


title: DIPG17_H33K27MKO_SOX10_rep1


title: SA10: Ro2D_rep1 RNA-seq

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

description: Human derived cell line

data_processing:
Illumina software used for basecalling.
The R1 sequenced reads were trimmed for adaptor sequence,  then mapped to mm10 and hg38 whole genome using BMX-seq pipeline
Reads mapped uniquely were counted to Gencode annotations for mm10(vM10) and hg38 (v24)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from the gene count matrix and median length of the transcripts of a gene annotation.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each gene (row) each Sample (column)

source_name: Homo sapiens

growth_protocol: Brain metastases derived from an intracardiac injection of human tumor cells into mice

extract_protocol:
Total RNA was extracted using Rneasy Lipid Tissue Qiagen Kit with on-column Dnase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 25mg/kg osimertinib via oral gavage

tag: setting

value: growing in culture

value: osimertimib

tag: treatment time

value: 24 hours


title: SA12: Ro2D_rep3 RNA-seq

description: Human derived cell line


title: SA35: RoL_rep4 RNA-seq

description: Human derived cell line

organism:
Homo sapiens
Mus musculus

source_name: Homo sapiens+athymic nu/nu mice (Charles River, strain code 088)

value: growiing in mouse brain

value: at resistance


title: SA34: RoL_rep3 RNA-seq

description: Human derived cell line


title: SA33: RoL_rep2 RNA-seq

description: Human derived cell line


title: SA11: Ro2D_rep2 RNA-seq

description: Human derived cell line


title: DIPG17_H33K27MKO_BRG1_rep1

value: Diffuse intrinsic pontine glioma (DIPG) cells


title: DIPG17_WT_SOX10_rep1

value: WT


title: DIPG17_WT_SOX10_rep2


title: DIPG17_H33K27MKO_BRG1_rep2


title: SA9: Rv2D_rep3 RNA-seq

description: Human derived cell line

value: vehicle


title: SA32: RoL_rep1 RNA-seq

description: Human derived cell line


title: SA31: CoL_rep4 RNA-seq

description: Human derived cell line

value: time-matched to R2 at resistance


title: DIPG17_WT_BRG1_rep2


title: exosomes from parental SNU-668 cells 3

city: shanghai

first: Ming

middle: zhe

last: Ma

email: mmz666@163.com, mmz666@shca.org.cn

address: Dongan Road 270

department: Department of gastric surgery

institute: Fudan university shanghai cancer center

description: lncRNA expression in exosomes from parental SNU-668 cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to8x60K Human lncRNA Expression Microarray (Arraystar v4.01) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: parental SNU-668 cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: SNU-668 Erastin-resistant cells and parental cells  were routinely generated by re-plating d 4 in DMEM supplemented with 10% FBS.

extract_protocol: RNA extraction was performed using a SeraMir Exosome RNA Purification kit.

treatment_protocol: SNU-668 Erastin-resistant cells and parental cells  were were cultured for 48–72 h in advanced RPMI-1640 medium (Gibco) without supplements. Culture medium was collected and centrifuged at 3,000 r.p.m. for 10 min at 4 °C, followed by a centrifugation step of 10,000 × g for 30 min at 4 °C to remove cellular debris. Next, the supernatant was filtered using a 0.22-μm filter. EVs were isolated using Exosome Precipitation Solution (ExoQuick-TC, System Biosciences) or ultracentrifuged at 100,000 × g for 90 min.

value: exosome

value: parental SNU-668 cells


title: exosomes from SNU-668 Erastin-resistant cells 2

description: lncRNA expression in exosomes from SNU-668 Erastin-resistant cells

source_name: SNU-668 Erastin-resistant cells

value: SNU-668 Erastin-resistant cells


title: SA8: Rv2D_rep2 RNA-seq

description: Human derived cell line


title: exosomes from parental SNU-668 cells 2


title: exosomes from SNU-668 Erastin-resistant cells 3


title: exosomes from SNU-668 Erastin-resistant cells 1


title: SA28: CoL_rep1 RNA-seq

description: Human derived cell line

value: osimertinib


title: exosomes from parental SNU-668 cells 1


title: DIPG17_WT_BRG1_rep1


title: DIPG17_sgSOX10_BRG1_rep2

value: SOX10 KO


title: SA26: RoE_rep3 RNA-seq

description: Human derived cell line

value: 3 days


title: SA25: RoE_rep2 RNA-seq

description: Human derived cell line


title: SA5: Co2D_rep2 RNA-seq

description: Human derived cell line


title: SA30: CoL_rep3 RNA-seq

description: Human derived cell line


title: SA29: CoL_rep2 RNA-seq

description: Human derived cell line


title: SA23: RvE_rep4 RNA-seq

description: Human derived cell line


title: SA7: Rv2D_rep1 RNA-seq

description: Human derived cell line


title: SA27: RoE_rep4 RNA-seq

description: Human derived cell line


title: SA24: RoE_rep1 RNA-seq

description: Human derived cell line


title: SA6: Co2D_rep3 RNA-seq

description: Human derived cell line


title: SA22: RvE_rep3 RNA-seq

description: Human derived cell line


title: DIPG17_sgSOX10_BRG1_rep1


title: SA4: Co2D_rep1 RNA-seq

description: Human derived cell line


title: h967_1

value: Hair follicle (occipital)

value: androgenetic alopecia

value: male

value: Primary hair follicle cells


title: SA21: RvE_rep2 RNA-seq

description: Human derived cell line


title: DIPG17_sgNeg_BRG1_rep1


title: SA20: RvE_rep1 RNA-seq

description: Human derived cell line


title: SA3: Cv2D_rep3 RNA-seq

description: Human derived cell line

value: growing in culture

value: 24 hours


title: SA19: CoE_rep3 RNA-seq

description: Human derived cell line

value: growiing in mouse brain


title: DIPG17_SOX10_rep2

value: Diffuse intrinsic pontine glioma (DIPG) cells


title: SA2: Cv2D_rep2 RNA-seq

description: Human derived cell line


title: SA16: CvE_rep4 RNA-seq

description: Human derived cell line


title: DIPG6_SOX10_rep2

value: WT


title: SA17: CoE_rep1 RNA-seq

description: Human derived cell line


title: SA1: Cv2D_rep1 RNA-seq

description: Human derived cell line

value: vehicle


title: DIPG17_SOX10_rep1


title: SA14: CvE_rep2 RNA-seq

description: Human derived cell line


title: UKE1 cells, MCL+ruxolitinib (Combo) treated, rep3

city: Tianjin

first: Huijun

last: Huang

address: 288 Nanjing Road

department: Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Sequence reads were aligned to the reference genome using Hisat2 v.2.0.5. The reference assembly used is hg38.
FeatureCounts v.1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of the two groups was conducted using the DESeq2 R package (1.16.1)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared for sequencing using standard Illumina protocols

value: hematopoietic cells

value: TNF-a stimulated and then MCL+ruxolitinib treated

tag: timepoint

value: 3 h after treatment


title: SA13: CvE_rep1 RNA-seq

description: Human derived cell line


title: UKE1 cells, MCL+ruxolitinib (Combo) treated, rep2


title: icb98_biol rep2

city: London

first: Michalis

last: Barkoulas

address: SAF Building, South Kensington

institute: Imperial College London

data_processing:
Reads were aligned to C. elegans genome WS235
Reads were counted using Kallisto
Transcript abundance was quantified using the Sleuth and Wald test
Assembly: WormBase Release WS235
Supplementary files format and content: H5 files having raw TPM counts for all genes

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Wild-type and pals-25(icb98gf) worm strains were prepared by bleaching gravid adults to isolate embyros which were grown until L4 stage

extract_protocol:
TRIzol (Life Technologies)
By BGI

treatment_protocol: Nematode Growth Media agar plates supplemented with E. coli OP50 at 20°C

value: Whole animal

tag: Stage


title: icb98_biol rep3

tag: tissue


title: DIPG6_SOX10_rep1


title: UKE1 cells, MCL+ruxolitinib (Combo) treated, rep1


title: DIPG17_BRG1_rep2


title: SA18: CoE_rep2 RNA-seq

description: Human derived cell line

value: osimertinib


title: SA15: CvE_rep3 RNA-seq

description: Human derived cell line


title: icb98_biol rep1


title: UKE1 cells, ruxolitinib treated, rep3

value: TNF-a stimulated and then ruxolitinib treated


title: DIPG6_BRG1_rep2


title: (N2)icbIs4_biol rep3


title: PRB-0378

type: genomic

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium MethylationEPIC BeadChip array (EPIC850) using standard Illumina protocol

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

data_processing: Methylation data were analyzed using Partek® Genomics Suite® software (PGS), v7.18 (Partek Inc. Missouri, USA).

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: For frozen samples, DNA was extracted using Gentra Puregene Tissue Kit (Qiagen Inc., Valencia, CA) , for FFPE samples, DNA was isolated using the QIAamp DNA FFPE Tissue Kit (QIAGEN)

value: M

value: HCN-NOS tumor


title: UKE1 cells, ruxolitinib treated, rep1


title: (N2)icbIs4_biol rep2


title: UKE1 cells, MCL treated, rep2

value: TNF-a stimulated and then MCL treated


title: PRB-0434

value: non-tumor control


title: DIPG6_BRG1_rep1


title: UKE1 cells, MCL treated, rep1


title: UKE1 cells, TNF-α stimulated, rep3

value: TNF-a stimulated


title: UKE1 cells, ruxolitinib treated, rep2


title: DIPG17_H3K4me3


title: (N2)icbIs4_biol rep1


title: DIPG6_H3K4me3


title: UKE1 cells, TNF-α stimulated, rep1


title: UKE1 cells, untreated, rep3

value: Untreated


title: HN00143595_input

city: Singapore

first: Pierce

middle: Kah Hoe

last: Chow

address: 11 Hospital Cres

country: Singapore

institute: National Cancer Center Singapore

data_processing:
The reads in ChIP-seq data were first trimmed of the adapter and index sequences using BBDuk from BBTools (Bushnell, 2014). Read alignment and index generation were done using Bowtie2 (Langmead & Salzberg, 2012) and Samtools (Li, et al., 2009). Duplicated reads and unmapped reads were removed using Sambamba (Tarasov, et al., 2015). DeepTools bamCoverage (Ramírez, et al., 2014) was used to generate bigwig files for visualization
Assembly: hg38
Supplementary files format and content: bigwig

source_name: tumour

extract_protocol:
50 mg of snap frozen liver tissue was excised and pulverized into fine powder in liquid nitrogen. The samples were washed twice in cold 1X PBS with protease inhibitor, cross-linked with formaldehyde (1%) for 10 min at room temperature, quenched with glycine (125mM) for 5 min, and rinsed twice with cold 1X PBS. Lysis was performed for 30 minutes in cold lysis buffer (50mM HEPES-KOH, pH 7.5, 150mM NaCl, 1mM EDTA, 1% Triton X, 0.1% Sodium deoxycholate, 0.1% SDS, Takara 1X protease inhibitors) to release nuclei. Pellets were centrifugated at 2,500G for 10 min at 4ºC to collect the nuclei pellet. Nuclei was sonicated in nuclei lysis buffer (50mM HEPES-KOH, pH 7.5, 150mM NaCl, 1mM EDTA, 1% Triton X, 0.1% Sodium deoxycholate, 1% SDS, Takara, 1x protease inhibitor) using the Bioruptor sonicator to obtain chromatin fragments between 200 to 500 bp. The fragmented chromatin was immunoprecipitated overnight with 5 µg of H3K27ac antibody (catalogue #: ab4729, Abcam) and 50 µl of protein G beads (Invitrogen). Elution of DNA was done in 200 µl of elution buffer (50mM Tris-HCI, pH7.5 and 10mM EDTA), followed by decrosslinking which was performed at 65ºC overnight.
Library preparation was performed using eluted ChIP DNA with NEB ultra II library preparation kit, according to manufacturer’s protocol. 10-12 PCR cycles were performed using indexed primers and libraries size between 300 to 500 bp were selected. The libraries were sequenced at Macrogen using 2 x 150 bp read lengths.

value: HCC

value: tumour

tag: library


title: HN00143168_193_input


title: DIPG17_BRG1_rep1

tag: experiments

value: Diffuse intrinsic pontine glioma (DIPG) cells


title: UKE1 cells, MCL treated, rep3

tag: cell type

value: WT


title: UKE1 cells, TNF-α stimulated, rep2


title: UKE1 cells, untreated, rep2


title: PRB-0374


title: UKE1 cells, untreated, rep1


title: HN00141162_B006_input

tag: chip antibody


title: PRB-0432


title: Normal_21

source_name: Myocardium

value: Myocardium

tag: tma


title: Normal_24


title: DIPG6_H33K27M

tag: genotype


title: DIPG17_H33K27M


title: XE_scRNA seq

city: Dallas

first: Philipp

middle: E

last: Scherer

state: TX

address: 5323 Harry Hines Boulevard

department: Touchstone Diabetes Center, Internal Medicine

institute: UT Southwestern Medical Center

description: tdTomato-EGFP+ cells

data_processing:
Data was analyzed using Cell Ranger (v3.1.0) to perform demultiplexing, aligning reads, filtering, clustering, and gene expression analyses, using default parameters.
mm10 + EGFP
The processed data files contain the unfiltered barcodes, matrix, and genes.

source_name: Primary cells

extract_protocol:
Cells were isolated from breast tumor as previously decscribed (Sharon, et al. J Vis Exp 2013).
Library prepared followed by 10X Genomics standard protocol.
Single-cell RNA-Seq

value: Met-1 xenograft tumor

tag: strain

value: inAd-Chaser-mTmG mice


title: Normal_22

data_processing:
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_COVID19_v1.0.pkc)
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: Values represented in the collapsed target counts tab are the geometric mean of the probes for a given target--in the case that multiple probes were used-- and excludes any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments and features.


title: PRB-0433

city: Los Angeles

tag: age

tag: group


title: PRB-0377

tag: Sex


title: Py_scRNA seq

description: tdTomato-EGFP+ cells

value: PyMT breast tumor


title: Normal_20


title: PRB-0436


title: PRB-0429


title: HN00141162_Hep_255_input

tag: disease state


title: Normal_19


title: Normal_16


title: Timepoint 4, P5, run 2

city: Maastricht

first: Tobias

last: Messmer

address: Watermolen 28

department: Cell Biology

country: Netherlands

institute: Mosa Meat

description: 10x Genomics

data_processing:
Raw base call files of the separate runs were demultiplexed using the cellranger mkfastq function (CellRanger 6.0.1). Reads were aligned to Bos Taurus genome (build ARS-UCD1.2) with Ensembl annotations (release 101), using CellRanger count function.
Default filtering parameters of CellRanger were applied to obtain a gene expression matrix. Genotypes were then deconvoluted and assigned to individual cells using demuxlet, based on VCF files generated via genotyping of each donor animal.
Quality control was performed within each timepoint, where cells were removed when outside of 3 median absolute deviations of the median for expressed genes, total counts and percentage mitochondrial genes. The cells of all timepoints were then pooled for downstream analysis (combined_counts.tsv).
Assembly: ARS-UCD1.2
Supplementary files format and content: Tab-separated values files and matrix files

organism: Bos taurus

source_name: SCs, FAPs, Unsorted

growth_protocol:
Tissue culture vessels were coated with fibronectin for unsorted cells, ECs, and SMMCs, with laminin-521 (0.5 µg cm-2, LN521-05, Biolamina) for SCs, or with collagen I (0.6 µg cm-2, bovine skin collagen, Sigma-Aldrich) for FAPs for 1 h prior to plating. Unsorted cells, SCs and FAPs were cultured in SFGM (except where otherwise noted), and passaged every 3-4 days upon reaching confluency. ECs and SMMCs were cultured in BioAMF-3 (01-196-1A, Sartorius).
isolation protocol: Cells were isolated from semitendinosus muscles of 10 Belgian Blue cattle by collagenase digestion (CLSAFA, Worthington; 1 h; 37 °C), filtration with 100 µm cell strainers, red blood lysis using a Ammonium-Chloride-Potassium (ACK) lysis buffer, and final filtration with 40 µm cell strainers. Cells from each donor animal were plated as separate cultures in serum-free growth medium (SFGM) on fibronectin-coated (4 µg cm-2 bovine fibronectin; F1141, Sigma-Aldrich) tissue culture vessels, or (where denoted) in growth medium (GM) containing 20% foetal bovine serum (heat-inactivated FBS; 10500-064, Gibco)

extract_protocol:
Five timepoints throughout long-term in vitro culture were selected for single-cell RNA sequencing (scRNA-seq), for each of which cells from all genotypes (donor animals) were pooled in equal ratios and washed with 1% BSA in PBS prior to injection. Timepoints 1 to 5 corresponded to unsorted cells directly after isolation (‘Muscle’) and after 72 h (‘passage 0’), and to cultured cells (unsorted cells, SCs and FAPs) at passages 2, 5, and 8 respectively.
25000 cells were injected for each timepoint into Chromium Single Cell Controller, emulsified with bar-coded gel beads and libraries were constructed following the protocol of the Chromium NextGEM Single Cell 3’ Kit V3.1 (10x Genomics).
Quality control of the DNA library was performed on Qiaxcel (QIAgen) and quantified by qPCR  using the KAPA SYBR Fast qPCR Master Mix (Illumina). Paired- end single cell 3' gene expression libraries were sequenced on a Novaseq 6000 System (Illumina) using a NovaSeq S1 flow-cell to a depth of at least 3.5 x 108 reads/timepoint.

tag: origin

value: Cell culture

value: SCs, FAPs, Unsorted

tag: passage


title: HN00131675_276T_input


title: HN00131675_319_input


title: Normal_15


title: Timepoint 5, P8, run 1

description: 10x Genomics


title: Timepoint 4, P5, run 1

description: 10x Genomics


title: Normal_14


title: HN00131675_T_input


title: Normal_23


title: HN00131675_276N_input

source_name: adjacent normal

value: adjacent normal


title: Normal_13


title: Normal_18


title: Normal_12


title: HN00131675_N_input


title: Normal_9


title: Normal_17


title: Normal_11


title: HN00131675_194_input


title: Normal_10


title: Timepoint 2, P0, run 2

description: 10x Genomics


title: Timepoint 3, P2, run 2

description: 10x Genomics


title: HN00125215_T3_input


title: HN00125215_T2_input


title: Normal_7


title: Timepoint 3, P2, run 1

description: 10x Genomics


title: Timepoint 2, P0, run 1

description: 10x Genomics


title: Normal_6


title: HN00125215_T1_input


title: DIPG17_sgNeg_BRG1_rep2

source_name: patient-derived cell culture

tag: cell line


title: Normal_5


title: Timepoint 1, Muscle, run 1

description: 10x Genomics

source_name: Unsorted

tag: timepoint

value: Muscle

value: Unsorted


title: Normal_3


title: HN00124129_T_input


title: Normal_4


title: Normal_2


title: Normal_1


title: HN00124129_N_input


title: Normal_8


title: HN00123744_T_input


title: pH1N1_24


title: Control_23


title: Control_21


title: HN00123744_N_input


title: Adult_adb1-2

city: Worcester

first: Summer

last: Thyme

state: MA

address: 364 Plantation St

institute: UMass Chan Medical School

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.0 to 3.1.0, depending on the sample (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Raw BCL files from Illumina nextseq were demultiplexed into paired end, gzip-compressed FASTQ files using cellranger mkgastq.
Both FASTQs were then provided as input to cell ranger count which partitioned reads into cell of origin based on a 16 bp barcode on the left read.
Reads were aligned to a zebrafish reference transcriptome (ENSEMBL Zv10, release 86 reference transcriptome) and transcript counts quantified for each annotated gene.
10bp UMI on the left read was used to collapse PCR duplicates.
Assembly: GRCz10 (release-86)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: telencephalon

extract_protocol:
Forebrains were dissected from wild-type fish in Neurobasal supplemented with 1X B27 and promptly dissociated with the Papain Dissociation Kit. The cells were dissociated by gentle trituration 20 times and spun at 300xg for 5 minutes, resuspended in papain inhibitor in EBSS, spun at 300xg for 5 minutes. The resulting pellet was then washed in Neurobasal supplemented with B27 before final resuspension in 50 µL PBS + 200 µg/mL BSA. To avoid cell loss during each wash, the supernatant was saved and spun a second time to recover the remaining cells. The cells were then mixed with the final suspension to increase cell count. Viability and cell number were assessed by trypan blue staining on 10ul of the sample.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: telencephalon

tag: developmental stage

value: Adult

value: wild type


title: Control_22

tag: tissue


title: Adult_adb2-1

description: 10x Genomics


title: SARS_CoV2_19


title: pH1N1_18


title: Adult_adb1-1

description: 10x Genomics


title: HN00120212_input

tag: library


title: 15dpf_b4

description: 10x Genomics


title: HN00148421_input


title: Control_20


title: 15dpf_b3

description: 10x Genomics


title: 15dpf_b2

description: 10x Genomics


title: SARS_CoV2_15


title: SARS_CoV2_13


title: SARS_CoV2_14


title: HN00148717_HN00148718_input


title: Adult_adb2-2

description: 10x Genomics


title: pH1N1_17


title: 15dpf_b1

description: 10x Genomics


title: HN00148890_HN00148891_HN00148892_HN00148893_input


title: SARS_CoV2_10


title: SARS_CoV2_11


title: 6dpf_b8

description: 10x Genomics


title: HN00146504_input


title: HEP277_T3 H3K27ac ChIPseq

value: H3K27ac (catalogue #:ab4729, Abcam


title: SARS_CoV2_9


title: pH1N1_16


title: 6dpf_b7

description: 10x Genomics


title: pooled (20) whole embryos 1.77 mg/kg HBCD RepE

city: Sasaktoon

first: Susari

last: Malala Irugal Bandaralage

state: Saskatchewan

address: 44 Campus Drive

department: Toxicology

country: Canada

institute: University of Saskatchewan

description:
ME8-WT7-MEP
ME8_transcript1.txt
deseq_list_DESeq_DE_MvS.csv

data_processing:
https://galaxy.ecotoxxplorer.ca/
Raw files were trimmed to a minimum phred score of 20 and a minimum sequence length of 35 bases per paired read using Trim Galore!
Trimmed fastq files were pseudoaligned to the reference fathead minnow transcriptome (NCBI Acc# GCA_016745375.1) using Kallisto quant
Only features with at least 20 counts per million in at least 5 samples were kept for differential expression analyses. Significance of differentially expressed genes were assessed using DESeq2 in R, with a cut-off FDR (Benjamini-Hochberg) < 0.05
Assembly: Fathead minnow (Pimephales promelas) reference transcriptome NCBI Acc# GCA_016745375.1 from Martinson, J., Bencic, D.C., Toth, G.P., Kostich, M.S., Flick, R.W., See, M.J., Lattier, D., Biales, A.D., Huang, W., n.d. De novo assembly and annotation of a highly contiguous reference genome of the fathead minnow (Pimephales promelas) reveals an AT-rich repetitive genome with compact gene structure. https://doi.org/10.1101/2021.02.24.432777
Supplementary files format and content: csv - differential expression results using DESeq2
Supplementary files format and content: tabular - raw counts of all samples

organism: Pimephales promelas

source_name: whole embryo bodies

growth_protocol: Fathead minnow embryos (20 embryos per replicate) were maternally exposed to graded concentrations (measured concentrations: solvent control, 0.576, 1.77, 5.89 mg/kg ) of HBCD  and reared in glass petri dishes in clean water, maintained at (23 oC, 16:8 light:dark cycle)

extract_protocol:
Total RNA was extracted from pools of 20 larvae using QIAGEN RNeasy plus universal mini kit following the manufacturer's protocol
Libraries were generated from 250 ng of total RNA. mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps were done using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.

treatment_protocol: Embryos were exposed via maternal transfer and reared in cllean water for  7-days post-fertilization in a flow-through  system.

value: whole embryo bodies

value: 7-days post-fertilization

tag: treatment

value: hexabromoclyclododecane (HBCD)

tag: treatment (measured concentration)

value: 1.77 mg/kg HBCD


title: HEP277_T2 H3K27ac ChIPseq

value: HCC

tag: chip antibody

value: tumour


title: SARS_CoV2_8

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.
OTHER: GeoMx Seq

value: Myocardium

tag: tma


title: HEP277_T1 H3K27ac ChIPseq


title: pooled (20) whole embryos 1.77 mg/kg HBCD RepD

description:
ME8-WT7-MDP
ME8_transcript1.txt
deseq_list_DESeq_DE_MvS.csv


title: SARS_CoV2_12


title: pooled (20) whole embryos 1.77 mg/kg HBCD RepC

description:
ME8-WT7-MCP
ME8_transcript1.txt
deseq_list_DESeq_DE_MvS.csv


title: 6dpf_b6

description: 10x Genomics

tag: genotype


title: pooled (20) whole embryos 1.77 mg/kg HBCD RepB

description:
ME8-WT7-MBP
ME8_transcript1.txt
deseq_list_DESeq_DE_MvS.csv


title: 6dpf_b5

description: 10x Genomics


title: HEP229_T3 H3K27ac ChIPseq


title: SARS_CoV2_6


title: 6dpf_b3

description: 10x Genomics


title: pooled (20) whole embryos 1.77 mg/kg HBCD RepA

description:
ME8-WT7-MAP
ME8_transcript1.txt
deseq_list_DESeq_DE_MvS.csv


title: SARS_CoV2_5


title: HEP229_T2 H3K27ac ChIPseq


title: SARS_CoV2_4


title: 6dpf_b4

description: 10x Genomics


title: HEP229_T1 H3K27ac ChIPseq


title: pooled (20) whole embryos 0.576 mg/kg HBCD RepE

description:
ME8-WT7-LEP
ME8_transcript1.txt
deseq_list_DESeq_DE_LvS.csv

value: 0.576 mg/kg HBCD


title: 6dpf_b2

description: 10x Genomics


title: SARS_CoV2_3


title: SARS_CoV2_7


title: pooled (20) whole embryos 0.576 mg/kg HBCD RepD

description:
ME8-WT7-LDP
ME8_transcript1.txt
deseq_list_DESeq_DE_LvS.csv


title: HEP193_T3 H3K27ac ChIPseq


title: SARS_CoV2_2


title: HEP193_T1 H3K27ac ChIPseq


title: SARS_CoV2_1


title: pooled (20) whole embryos 0.576 mg/kg HBCD RepC

description:
ME8-WT7-LCP
ME8_transcript1.txt
deseq_list_DESeq_DE_LvS.csv


title: pooled (20) whole embryos 0.576 mg/kg HBCD RepB

description:
ME8-WT7-LBP
ME8_transcript1.txt
deseq_list_DESeq_DE_LvS.csv


title: 6dpf_b1

description: 10x Genomics


title: HEP193_T2 H3K27ac ChIPseq


title: Serbp1 2nd

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

data_processing:
Illumina bcl2fastq software used for basecalling.
First, the raw reads containing more than 2 N bases were discarded
FASTX Toolkit (version 0.0.13) was used to trim the adaptors and low-quality bases from sequencing reads. Short reads less than 16 nt were also removed.
The R Bioconductor package edgeR (Robinson, McCarthy et al. 2010) was used to identify DEGs. The cutoff criteria for identifying DEGs were set as false discovery rate < 0.05 and fold change > 2 or < 0.5.
TopHat2 was used to align the clean reads to the GRCh38 genome (Kim, Pertea et al. 2013), allowing up to 4 mismatches. Uniquely mapped reads were used for gene read number counting and fragments per kilobase of transcript per million fragments mapped (FPKM) calculation (Trapnell, Williams et al. 2010).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: HeLa cells

growth_protocol: The pIRES-hrGFP-1a vector was digested for 2~3 h at 37°C by XhoI (NEB) and EcoRI.  Then, the enzyme-digested vector was run on a 1.0% agarose gel and purified with a Qiagen column kit.

extract_protocol:
HeLa cells were ground into fine powder to extract RNA. Total RNA was extracted with TRIzol (Ambion). RNA was purified with two phenol-chloroform treatments, and then the DNA was digested with RQ1 DNase (Promega, Madison, WI, USA). SmartSpec Plus (Bio-Rad, USA) was used to redetermine the quality and quantity of purified RNA by measuring the absorbance at 260 nm/280 nm (A260/A280). The integrity of RNA was verified by 1.5% agarose gel electrophoresis.
One microgram of the total RNA from each sample was used for RNA-seq library preparation with the VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). The polyadenylated mRNAs were converted into double-stranded cDNA after purification and fragmentation. The DNAs were ligated to VAHTS RNA Adapters (Vazyme) after end repair and A tailing. Heat-labile UDG was used to digest the purified ligation products corresponding to 200-500 bp, after which the fragments were amplified and purified. Single-stranded cDNA was quantified, stored at -80°C and sequenced.  The libraries were prepared following the manufacturer’s instructions. The Illumina HiSeq X Ten system was used for 150 nt paired-end sequencing, and high-throughput sequencing was performed. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to the Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

treatment_protocol: Total RNA was isolated from HeLa cells with TRIzol.   The oligo dT primer was used to reverse transcribe purified RNA to cDNA.   PCR amplification was used to synthesize the insert fragment.   The digested vector and the PCR insert were placed into a PCR microtube for ligation with a ClonExpress® II One Step Cloning Kit (Vazyme).   Then, the plasmids were transformed into an Escherichia coli strain.   The cells were plated onto LB agar plates containing 1 µL/ml ampicillin and incubated overnight at 37°C.   Universal primers (complementary to the backbone vector) were used to screen the colonies by colony PCR (28 cycles).   Sanger sequencing was used to verify the insert sequence.   The primer pairs used for Hot Fusion were designed with CE Design V1.04.   Each of the primers contains a gene-specific sequence and a 17–30 bp sequence of the pIRES-hrGFP-1a vector.

value: SERBP1 overexpression in HeLa  cell


title: pooled (20) whole embryos 0.576 mg/kg HBCD RepA

description:
ME8-WT7-LAP
ME8_transcript1.txt
deseq_list_DESeq_DE_LvS.csv


title: pooled (20) whole embryos solvent control RepE

description:
ME8-WT7-SEP
ME8_transcript1.txt

value: ethanol (EtOH)

value: solvent control


title: HEP255_T3 H3K27ac ChIPseq


title: HEP255_T2 H3K27ac ChIPseq


title: B006_T2 H3K27ac ChIPseq


title: Ctrl 1st

value: SERBP1 (control plasmid)