title: Organoid8M_R71_C68


title: Organoid8M_R71_C36

status: Public on Apr 25 2019

type: SRA

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

country: USA

institute: Baylor Colleage of Medicine

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling. Individual FASTQ files obtained were demultiplexed using the well-specific barcode identifiers for downstream data processing and analysis.
FASTQ sequences were mapped to human genome hg19 (GRCh37) downloaded from UCSC genome browser website and aligned using TopHat2
Transcript structure and abundance were estimated using HTseq and Cufflelink
Read count profile were analyzed for the differential expression analysis using DESeq2 (version 1.10.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample ...

molecule: total RNA

organism: Homo sapiens

growth_protocol: Retinal cell differentiation from H1 hESCs was performed. Briefly, cysts and adherent cultures were generated as described previously, with the starting day of cell differentiation designated as day 0. On day 15, adherent cultures were partially lifted at edges via one-minute dispase treatment (1 mg/ml in DMEM/F12), rinsed with DMEM/F12 medium, and then grown in a B27 medium (DMEM/F12 (3:1), 2% B27, NEAA). In a few hours, the adherent cultures were spontaneously detached as floating aggregates. In about one week, retinal organoids with a bright ring under an inverted microscope spontaneously formed, and were grown in a serum medium (DMEM/F12 (3:1), 8% fetal calf serum (Gibco), 2% B27, NEAA, 100 mM Taurine (Sigma), and 2mM GlutaMAX) on an orbital shaker. The medium was changed every three days unless stated otherwise.Retinal organoids and adherent cultures were fixed in 4% PFA for 15-30 minutes at room temperature and then processed for cryosectioning at 8 month.

extract_protocol:
Using ICELL8 multisample nanodispenser (Wafergen Biosystems), 50nl (3E4/ml) of the live cell or nuclear suspension was precisely dispensed into an ICELL8 nanowell microchip containing 5184 wells (150nl capacity) as described previously (Goldstein et al., 2017). Assuming a Poisson distribution frequency for the number of cells per well, about 30% of the nanowells were expected to contain a single nucleus under optimal conditions. Automated scanning fluorescent microscopy (using Olympus BX43 fluorescent microscope with a robotic stage) of the microchip was used to select ~1400 wells containing a single live cell or a single nucleus (CellSelect software, Wafergen Biosystems).  The candidate wells were manually evaluated for debris or clumps as an additional QC.
The chip was subjected to freeze-thaw in order to lyse the cells and 50 nl of reverse transcription and amplification solution (following ICELL8 protocol) was dispensed using the multisample nanodispenser to candidate wells. SCRB-seq was then performed on the candidate wells using pre-printed primer that adds a well-specific barcode to the (A)n mRNA tail of the cellular transcript. The cDNA libraries were pooled, concentrated (Zymo Clean and Concentrator kit, Zymogen) and purified (using 0.6x AMPure XP beads). 3’ transcriptome enriched library was made by Nextera XT Kit and 3’-specific P5 primer, and sequenced on Illumina Hiseq2500.

tag: tissue

value: retinal organoid

tag: culture time

value: 8 month


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title: Organoid8M_R18_C49


title: Organoid8M_R18_C32


title: Organoid8M_R18_C33


title: Organoid8M_R18_C28


title: Organoid8M_R18_C26


title: Organoid8M_R18_C24


title: Organoid8M_R18_C10


title: Organoid8M_R17_C7


title: Organoid8M_R18_C21


title: Organoid8M_R17_C67


title: Organoid8M_R18_C14


title: Organoid8M_R18_C22


title: Organoid8M_R18_C56


title: Organoid8M_R18_C45


title: Organoid8M_R17_C65


title: Organoid8M_R17_C35


title: Organoid8M_R17_C63


title: Organoid8M_R17_C60


title: Organoid8M_R17_C59


title: Organoid8M_R17_C44


title: Organoid8M_R17_C61


title: Organoid8M_R17_C64


title: Organoid8M_R18_C30


title: Organoid8M_R17_C27


title: Organoid8M_R17_C40


title: Organoid8M_R17_C24


title: Organoid8M_R17_C20


title: Organoid8M_R17_C39


title: Organoid8M_R18_C39


title: Organoid8M_R17_C16


title: Organoid8M_R17_C1


title: Organoid8M_R17_C10


title: Organoid8M_R18_C15


title: Organoid8M_R16_C6


title: Organoid8M_R16_C65


title: Organoid8M_R16_C62


title: Organoid8M_R16_C60


title: Organoid8M_R16_C53


title: Organoid8M_R16_C4


title: Organoid8M_R16_C42


title: Organoid8M_R16_C31


title: Organoid8M_R16_C40


title: Organoid8M_R16_C30


title: Organoid8M_R16_C15


title: Organoid8M_R16_C24


title: Organoid8M_R16_C16


title: Organoid8M_R16_C10


title: Organoid8M_R16_C13


title: Organoid8M_R15_C69


title: Organoid8M_R15_C67


title: Organoid8M_R15_C63


title: Organoid8M_R15_C61


title: Organoid8M_R15_C55


title: Organoid8M_R15_C38


title: Organoid8M_R15_C56


title: Organoid8M_R15_C36


title: Organoid8M_R15_C37


title: Organoid8M_R15_C50


title: Organoid8M_R15_C33


title: Organoid8M_R16_C9


title: Organoid8M_R15_C31


title: Organoid8M_R15_C27


title: Organoid8M_R15_C24


title: Organoid8M_R15_C12


title: Organoid8M_R15_C18


title: Organoid8M_R15_C13


title: Organoid8M_R15_C10


title: Organoid8M_R14_C9


title: Organoid8M_R14_C7


title: Organoid8M_R15_C8


title: Organoid8M_R14_C71


title: Organoid8M_R14_C64


title: Organoid8M_R14_C70


title: Organoid8M_R14_C66


title: Organoid8M_R14_C3


title: Organoid8M_R14_C40


title: Organoid8M_R14_C62


title: Organoid8M_R14_C38


title: Organoid8M_R14_C39


title: Organoid8M_R14_C29


title: Organoid8M_R14_C28


title: Organoid8M_R14_C35


title: Organoid8M_R14_C31


title: Organoid8M_R14_C45


title: Organoid8M_R15_C39


title: Organoid8M_R14_C37


title: Organoid8M_R14_C16


title: Organoid8M_R14_C13


title: Organoid8M_R15_C26


title: Organoid8M_R13_C7


title: Organoid8M_R13_C66


title: Organoid8M_R13_C70


title: Organoid8M_R13_C5


title: Organoid8M_R13_C32


title: Organoid8M_R13_C65


title: Organoid8M_R13_C11


title: Organoid8M_R13_C12


title: Organoid8M_R13_C15


title: Organoid8M_R13_C23


title: Organoid8M_R12_C9


title: Organoid8M_R12_C5


title: Organoid8M_R12_C57


title: Organoid8M_R14_C23


title: Organoid8M_R14_C20


title: Organoid8M_R12_C48


title: Organoid8M_R12_C42


title: Organoid8M_R12_C39


title: Organoid8M_R12_C30


title: Organoid8M_R12_C2


title: Organoid8M_R12_C27


title: Organoid8M_R12_C22


title: Organoid8M_R12_C17


title: Organoid8M_R12_C21


title: Organoid8M_R12_C0


title: Organoid8M_R11_C69


title: Organoid8M_R11_C6


title: Organoid8M_R11_C8


title: Organoid8M_R11_C64


title: Organoid8M_R11_C63


title: Organoid8M_R11_C57


title: Organoid8M_R11_C47


title: Organoid8M_R11_C50


title: Organoid8M_R11_C40


title: Organoid8M_R11_C35


title: Organoid8M_R11_C39


title: Organoid8M_R11_C33


title: Organoid8M_R11_C19


title: Organoid8M_R11_C38


title: Organoid8M_R11_C31


title: Organoid8M_R11_C15


title: Organoid8M_R10_C69


title: Organoid8M_R10_C57


title: Organoid8M_R10_C51


title: Organoid8M_R10_C38


title: Organoid8M_R12_C23


title: Organoid8M_R11_C0


title: Organoid8M_R10_C3


title: Organoid8M_R10_C22


title: Organoid8M_R10_C16


title: Organoid8M_R10_C27


title: Organoid8M_R11_C56


title: Organoid8M_R10_C13


title: Organoid8M_R0_C67


title: Organoid8M_R0_C9


title: Organoid8M_R10_C20


title: Organoid8M_R10_C12


title: Organoid8M_R0_C40


title: Organoid8M_R0_C41


title: Organoid8M_R0_C38


title: Organoid8M_R0_C37


title: Organoid8M_R0_C51


title: Organoid8M_R0_C21


title: Organoid8M_R0_C29


title: Organoid8M_R0_C30


title: Organoid8M_R10_C54


title: Organoid8M_R0_C12


title: 1 month cortical organoids

city: La Jolla

first: Jing

last: Gu

state: CA

address: 9500 Gilman Dr. MC0767

department: CMM

institute: UC San Diego

library_source: genomic

data_processing:
base-calling: cellranger mkfastq (version 2.1.1)
alignment, cell barcode processing, umi processing, feature-barcode matrix generation: cellranger count (version 2.1.1)
Supplementary files including lists of barcodes, genes, and feature-barcode matrix were generated by Cell Ranger v2.1.1.
Genome_build: hg38
Supplementary_files_format_and_content: barcodes.csv.gz, features.tsv.gz, and matrix.mtx.gz

molecule: genomic DNA

source_name: Cortical organoids

growth_protocol: Free-floating iPSC aggregates were kept under aggitation for 1, 3, 6 and 10 months and the media was replaced in order to promote neuronal induction (Dual SMAD inhibition), proliferation (FGF2 and EGF), differentiation (growth factors such as BDNF, GDNF) and maturation.

extract_protocol:
Dissociated cells were first placed on ice, diluted in 2-5 ml of cell media and then treated with flavopiridol (5 µM, Sigma-Aldrich, F3055-5MG) to arrest transcriptional activity. Cells were then stained with the DNA-dyes DAPI (300 nM, Invitrogen, D1306) and DRAQ5 (2.5 µM, Thermo-Fischer, 62251) and incubated on ice for 10 minutes prior to sorting.
Single cell RNA-seq libraries were generated using the Chromium™ Single Cell 3’ v2 Library kit (10x Genomics) from 12,000 input cells. Reverse transcription and other amplification steps were carried out on a T100 thermal cycler (Bio-Rad). After reverse transcription, GEMs (Gel beads in emulsion) were lysed and cDNA was cleaned up with MyOne Silane Beads (Thermo Fisher Scientific). Next, single stranded cDNA was PCR-amplified for 12 cycles and purified using SPRIselect Reagent Kit (Beckman Coulter). Next, cDNA was enzymatically fragmented followed by double size selection with SPRIselect Reagent Kit (B23317, Beckman Coulter). Subsequently, adapters were ligated and libraries were constructed by PCR. Another round of double size selection was performed using SPRIselect Reagent Kit to generate final libraries with a size of 200-700bp. Libraries were sequenced on a HiSeq4000 (Illumina; Read1 26 cycles; Index 1 8 cycles; Read 2 98 cycles)
Chromium™ Single Cell 3’ v2 Library kit (10x Genomics)

treatment_protocol: Cortical organoids were dissociated using ACCUMAX  and mechanical dissociation for 30min. Dissociated cells were placed on ice, diluted with cell media including flavopiridol (5 µM, Sigma-Aldrich, F3055-5MG) to arrest transcriptional activity. Cells were stained with DAPI (300 nM, Invitrogen, D1306) and DRAQ5 (2.5 µM, Thermo-Fischer, 62251) and incubated on ice for 10 minutes. Viable cells were sorted using a SH800 sorter (Sony) into cell media. Sorted cells were pelleted (3 min, 100 x g, 4°C), resuspended in 40 µl of fresh cell media and counted.

tag: cell line

value: WT - iPSC

tag: passage

tag: age of organoid

value: 1 month

tag: reprogramming strategy

value: Retroviral


title: 6 month cortical organoids

value: 6 month


title: 10 month cortical organoids

value: 10 month


title: PA_NO2CLA_3

city: Ann Arbor

first: Haocheng

last: Lu

state: Michigan

address: 2800 plymouth road

department: Internal Medicine

institute: University of Michigan

data_processing:
The quality control of the sequencing reads from each sample was assessed with FastQC  v0.11.7
The reference was indexed with Salmon v0.10.0 and  gene expression quantification was performed with Salmon in its non-alignment-based mode
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM and read numbers for each Sample

molecule: polyA RNA

source_name: coronary artery endothelial cells

growth_protocol: HCAECs that isolated from the male and non-smoking donor were purchased from Lonza (# CC-2585) and cultured in the EGMTM-2MV microvascular endothelial cell growth medium-2 containing 5% fetal bovine serum (Lonza, # CC-3202) at a 37°C/5% CO2-humidified incubator. HCAECs for the treatments and analysis in this study were used at passages 3-5.

extract_protocol:
Total RNA from HCAECs was extracted with RNeasy Mini Kit (Qiagen) and treated with on-column RNase-free DNase I following the manufacturer’s protocol (Qiagen). Total RNA samples were assessed for quality with the BioAnalyzer (Agilent)
RNA library preparation and sequencing were performed by the DNA sequencing core of University of Michigan. Briefly, the RNA library was prepared with TruSeq RNA Library Prep Kit v2 (Illumine, WI) and sequenced on a Hiseq 4000 platform (Illumine, WI) to generate non-stranded single end 51bp reads according to the manufacturer’s protocols

treatment_protocol: For RNA-seq experiment, HCAECs at 90% confluence were treated with DMSO, CLA (10µM) or NO2-CLA (10µM) for 1 hour, followed by adding with either ethanol (Control) or PA (200 µM) (Cayman Chemical) for the subsequent 6 hours. There are 6 groups for RNA seq: DMSO + control (ethanol), CLA (10µM) + control, NO2-CLA (10µM) + control, DMSO + PA, CLA (10µM) + PA, NO2-CLA (10µM) + PA. Each group has 4 biological replicates.

tag: cell type

value: coronary artery endothelial cells

tag: group

value: Palmitic acid

tag: treatment


title: PA_NO2CLA_4


title: PA_NO2CLA_1


title: PA_CLA_4

value: CLA


title: PA_NO2CLA_2


title: Organoid8M_R0_C39


title: Control_NO2CLA_4

value: Control (Ethanol)


title: PA_DMSO_2

value: DMSO


title: PA_CLA_2


title: PA_CLA_1


title: PA_DMSO_3


title: PA_CLA_3


title: PA_DMSO_4


title: Control_NO2CLA_2


title: Control_NO2CLA_3


title: Organoid8M_R0_C10


title: Control_CLA_1


title: Control_CLA_4


title: Control_CLA_2


title: 3 month cortical organoids

value: 3 month


title: Control_NO2CLA_1


title: Control_CLA_3


title: Control_DMSO_4


title: Control_DMSO_2


title: Control_DMSO_3


title: PA_DMSO_1


title: Control_DMSO_1


title: CGC42_H3K27me3_ChIP_input

city: Geneva

first: Florian

last: Steiner

address: 30, Quai Ernest-Ansermet

department: Department of Molecular and Cellular Biology

country: Switzerland

institute: University of Geneva

data_processing:
The paired-end reads (length=50 bp) were mapped with the novoalign (default parameters) software to the C. elegans reference genome (producing SAM format files).
Reads were transformed into bins of the desired size (JSON format) with a custom UNIX script.
JSON files were transformed into bedgraphs annotating maximum amount of reads present in each bin with a custom R script.
All files were normalized to the same number of reads. For each ChIP experiment, IP files were normalized either via subtraction of or division by the input file with the corresponding bin size. Operation was performed using a custom R script.
ChiP experiment biological replicates that passed the quality control were merged on the level of aligned reads (SAM files), and the downstream pipeline was performed again using the merged file to obtain the final normalized bedgraph for each experiment.
Genome_build: WBcel215
Supplementary_files_format_and_content: Processed data are bedgraphs containing normalized ChIP results. Normalization was performed by input subtraction (to avoid low number of read biases; marked in the file name by _delta), by division of input (marked in the file name by _ratio), or by dividision of input  followed by  log2 transformation (marked in the file name by _logratio). Bin sizes used in the analysis were 100bp (marked in the file name by _100bp), 1 kb (marked in the file name by _1kb) or 10 kb (marked in the file name by 10kb). The appropriate bin size was selected for each analysis.

organism: Caenorhabditis elegans

source_name: Adult total nuclei (enriched for germ cell nuclei)

growth_protocol: Nematodes were cultured using standard procedures at 20°C and harvested as young adults to perform the experiment.

extract_protocol:
Native ChIP was performed as described previously (Steiner and Henikoff, 2014f) with minor modifications. Briefly, synchronized worm populations were grown on 15-cm plates seeded with NA22 bacteria. Worms were harvested as young adults, washed in M9 and resuspended in buffer A supplemented with 0.5% NP-40 and 0.1% Tx-100. Total nuclei, which are enriched for germ cell nuclei based on morphologic analysis, were obtained by light grinding of the worms under liquid nitrogen followed by douncing, low speed spin and washing of the nuclei. Chromatin was digested to mononucleosomes using MNase (NEB, #M0247S) at 37°C using 5 µl of enzyme per 150 µl of nuclei in 1000 µl of the buffer. Each sample was divided in 6 parts that were incubated for 3, 5, 8, 10, 12 and 15 minutes, respectively, and then pooled together in order to obtain nucleosomal ladders. Following the digestion, chromatin was extracted, solubilized and pre-cleared with empty beads. ChIP was performed overnight at 4°C from the soluble chromatin fraction using antibodies against H3K27me2/me3 (Active Motif #39535), OLLAS (Novus Biologicals #NBP1-06713B), H3.3K27M mutant (Milipore #C946H91) or H3K36me3 (Abcam #ab9050). ChIP was followed by 1 h incubation of antibody-bound chromatin with magnetic beads at 4°C (50 µl 1:1 mixture of Dynabeads Protein A and Dynabeads Protein G, Invitrogen). DNA from both input and IP samples was then extracted using phenol/chloroform.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads using 100 ng of input DNA. Libraries were sequenced using the TruSeq SBS HS v3 chemistry on an Illumina HiSeq 2500 sequencer.
NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads

tag: strain

tag: genotype

tag: chip antibody

tag: developmental stage

value: adult


title: FAS104_H3K27me3_ChIP_input

description:
FAS104_H3K27me3_100bp_delta.bed
FAS104_H3K27me3_1kb_logratio.bed

value: his-72(uge68[K27M A87S A88V I89A G90M]) III


title: FAS93_H3K27me3_ChIP_IP

value: H3K27me3me3 (Active Motif #39535)


title: FAS104_H3K27me3_ChIP_IP


title: CGC42_H3K27me3_ChIP_IP


title: FAS100_H3K27me3_ChIP_IP

description:
FAS100_H3K27me3_100bp_delta.bed
FAS100_H3K27me3_1kb_logratio.bed

value: his-72(uge67[A87S A88V I89A G90M]) III


title: FAS100_H3K27me3_ChIP_input


title: FAS58_H3K36me3_ChIP_IP

description:
FAS58_H3K36me3_100bp_delta.bed
FAS58_H3K36me3_10kb_logratio.bed

value: his-72(uge40[K27M]) III

value: H3K36me3 (Abcam #ab9050)


title: FAS58_H3K36me3_ChIP_input


title: N2_H3K36me3_ChIP_IP

description:
N2_H3K36me3_100bp_delta.bed
N2_H3K36me3_10kb_logratio.bed

value: wildtype


title: N2_H3K36me3_ChIP_input


title: C2

city: Minhang district of Shanghai

first: yani

last: Kang

address: Dongchuan Road 800

country: China

institute: Shanghai Jiaotong University

description:
miRNA
processed data file: miRNA.xlsx
processed data file: novel_miRNA.xlsx

data_processing:
After sequencing, adapters and low-quality sequences were removed from obtained raw reads and clean data was counted by Fastqc program. 15-30nt fragments were reserved for subsequent analysis and mapped to the reference genome using Bowtie2 program.
Genome_build: Not provided
Supplementary_files_format_and_content: miRNA.xlsx: Excel file includes abundance measurements.
Supplementary_files_format_and_content: novel_miRNA.xlsx: Excel file includes abundance measurements.

source_name: Colorectal Cancer

extract_protocol:
After collected, samples were put in liquid nitrogen quickly, and preserved in low temperature environment. TRIzol (Invitrogen, Waltham, Massachusetts, USA) was used to isolate total RNA from tissue samples following a manufacturer’s protocol. Total RNA quantity was determined with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA) and quality was assessed by running an 1% agarose gel electrophoresis, stained with 4S Red Plus Nucleic Acid Stain (Sango, Shanghai, China).
miRNA-seq libraries were prepared using the TruSeq® Small RNA Library Preparation kit from Illumina® and sequenced using a 50 bp single-end reads Illumina NextSeq 500 Sequencer (Illumina Inc., San Diego, CA, USA).

tag: disease state

value: Colorectal cancer

value: Rectum  - cancer tissue

tag: tumor stage

tag: histopathological type

value: Adenocarcinoma


title: N2

source_name: Normal

value: Rectum - normal tissue


title: FAS119_H3.3K27M_OLLAS_ChIP_IP

description:
FAS119_H3.3K27M::OLLAS_100bp_delta.bed
FAS119_H3.3K27M::OLLAS_1kb_delta.bed
FAS119_H3.3K27M::OLLAS_1kb_logratio.bed

value: his-72(uge79[OLLAS::his-72 K27M]) III

value: OLLAS (Novus Biologicals #NBP1-06713B)


title: N1


title: FAS107_H3.3_OLLAS_ChIP_input

description:
FAS107_H3.3::OLLAS_100bp_delta.bed
FAS107_H3.3::OLLAS_1kb_logratio.bed

value: his-72(uge69[OLLAS::his-72]) III


title: FAS107_H3.3_OLLAS_ChIP_IP


title: FAS119_H3.3K27M_OLLAS_ChIP_input


title: HepG2/metR

city: Daejeon

first: Yi-deun

last: Jung

address: 125 Gahac-ro, Yusung-Gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Mapping : STAR-2.5.1b : PMID 23104886
Quality Check : FastQC-0.11.5 : Unpublished : Available online at http://www.bioinformatics.babraham.ac.uk/projects/fastqc
cufflinks-2.2.1 : PMID 23222703
Genome_build: hg19 from UCSC
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: hepatocellular carcinoma cell

growth_protocol: Human hepatocellular carcinoma HepG2 and HepG2/metR cells were cultured in Dulbecco’s modified Eagle’s medium (Welgene, LM001-65) supplemented with 10% fetal bovine serum (Gibco, 16000-044), 100 units/ml penicillin, and 100 µg/ml streptomycin (Gibco, 15140-122) in a humidified atmosphere containing 5% CO2 at 37 °C.

extract_protocol:
RNA was extracted using Trizol reagent (Invitrogen, 15596-018).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HepG2/metR cells were incubated at 37°C in 5% CO2 and grown to 50-60 % confluence, added oxamate (40mM for 24 h) to cell culture medium.

value: liver

value: exposure to metformin for more than 5 months


title: treated IL-8 RSkMC -rep3

type: RNA

city: Warszawa

first: Alicja

last: Majewska

address: Nowoursynowska 159

department: Department of Physiology Sciences

country: Poland

institute: Warsaw University of Life Sciences-SGGW Faculty of Veterinary Medicine

hyb_protocol: Each Cyanine-3-labeled RNA samples were hybridized onto microarray for 20h at 55°C in hybridization rotating oven (Agilent Technologies).

scan_protocol: Acquisition and analysis of hybridization intensities were performed using Agilent DNA Microarray Scanner G2505C. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: The scanned images were analyzed with Feature Extraction Software (version 10.10.1.1) using default parameters (protocol miRNA_1010_Sep10 and Grid: 046066_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Rat primary skeletal muscle cells (RSkMC)

label_protocol: One hundred ng of total RNA with miRNA Spike-In (microRNA Spike-In Kit, Agilent Technologies) added were taken for labeling reaction. miRNA was labeled with Cyanine 3-pCp using the Complete Labeling and Hyb Kit (Agilent Technologies) according to the manufacturer’s procedure. The labeled RNA samples were purified on Micro Bio-Spin 6 columns to remove DMSO and unbound Cyanine 3-pCp.

growth_protocol: Cell cultures were maintained free of contamination at the exponential growth phase in 10% FBS/DMEM (Fetal Bovine Serum/Dulbecco’s modified Eagle’s medium, Gibco MA, USA) supplemented with an antibiotic-antimycotic mixture (Life Technologies) in controlled humidified air with 5% CO2, at 37°C. The growth medium was changed every other day. When the cells reached ~80% confluence, myogenic differentiation was induced after switching to a medium containing 2% HS (Horse serum, Gibco MA, USA). Cells were subjected to 11 days of differentiation in the presense of IL-8 (recombinant, expressed in E.coli and suitable for cell culture, final concentration – 1 ng/ml, Sigma-Aldrich, St. Louis, MO, USA) and were used for the study.

extract_protocol: Total RNA, which also included miRNA, was isolated using miRNeasy Mini Kit (Qiagen) according to the manufacturer’s procedure. RNA quality was determined using Agilent 2100 Bioanalyzer (USA) and RNA 6000 Nano Kit (Agilent, Germany). All RNA samples taken for microarray analysis were of high quality (RIN was  between 9.5 and 10.0).

tag: agent

value: RSkMC are isolated from the limbal skeletal muscle of neonates and cryopreserved at second passage were purchased from European Collection of Animal Cell Culture (ECACC).

tag: time point

value: cell cultures on 11th day after induction of differentiation


title: HepG2/metR+oxamate

tag: tissue

value: oxamate 40mM treatment 24h in HepG2/metR cells


title: FAS93_H3K27me3_ChIP_input

value: adult


title: treated IL-8 RSkMC -rep2


title: control RSkMC -rep3


title: control RSkMC -rep1


title: control RSkMC -rep2


title: HepG2/wild

tag: cell line


title: treated IL-8 RSkMC -rep1


title: NR3ZT18

city: College Station

first: Jerome

last: Menet

state: Texas

address: Texas A&M University Biology Department 3258 TAMU College Station, TX 77843

department: Biology

institute: Texas A&M University

description:
RAW_Table.txt
TPM_Table.txt

data_processing:
Libraries were sequenced on an Illumina NextSeq. Base calling and demultiplexing were performed with the accompanying software
Sequenced reads were trimmed to remove the first 12nt, trailing and embedded polyA sequences, poor quality bases at the 3' end, and removed if under 36nt
Trimmed reads were aligned to mm10 transcriptome using STAR v2.4.2a with options "--outSAMstrandField intronMotif --quantMode GeneCounts --outFilterIntronMotifs RemoveNoncanonical"
Read counts were quantified to raw values with the R package GenomicRanges and normalized to 1 million transcripts per library (TPM)
Genes with under 1 TPM in 36 or more of the 72 libraries were removed from final consideration
Genome_build: mm10, GRCm38.p5
Supplementary_files_format_and_content: Tab-delimited text files with RAW (unnormalized or filtered) or TPM values for each gene and sample

organism: Mus musculus

source_name: Fed under night-restricted feeding paradigm; sacrificed at ZT18

growth_protocol: Male C57BL/6J mice from Charles River Laboratories (starting age 43-49 days) were housed in a 12 hour light:12 hour dark facility with ad libitum access to water and variable access to food

extract_protocol:
Total RNA was extracted using TRIzol reagent and purified with an acid phenol-chloroform extraction
3' mRNA libraries were prepared following manufacturer instructions for Lexogen's QuantSeq 3' mRNA-Seq Kit. 2μg input total RNA was used

value: Wild-type

tag: Sex

value: male

value: Liver


title: NR3ZT22

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under night-restricted feeding paradigm; sacrificed at ZT22


title: NR3ZT14

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under night-restricted feeding paradigm; sacrificed at ZT14


title: FAS58_H3K27me3_ChIP_input

description:
FAS58_H3K27me3_100bp_delta.bed
FAS58_H3K27me3_1kb_ratio.bed
FAS58_H3K27me3_1kb_logratio.bed
FAS58_H3K27me3_10kb_logratio.bed

value: his-72(uge40[K27M]) III


title: N2_H3K27me3_ChIP_input

description:
N2_H3K27me3_100bp_delta.bed
N2_H3K27me3_1kb_ratio.bed
N2_H3K27me3_1kb_logratio.bed
N2_H3K27me3_10kb_logratio.bed

value: wildtype


title: FAS58_H3K27me3_ChIP_IP

value: H3K27me3me3 (Active Motif #39535)


title: C1

value: Colorectal cancer

value: Rectum  - cancer tissue

value: Adenocarcinoma


title: N2_H3K27me3_ChIP_IP_rep1


title: FAS43 isolated gonads replicate 2

data_processing:
The reads (length=50 bp) were mapped with the TopHat v2.0.13 (default parameters) software to the C. elegans reference genome.
Read counts representing the total number of reads aligning to each genomic feature were produced from aligned reads by the Python software htseq-count (-- mode=union, with HTSeq v.0.6.1) with the reference .gtf file.
The normalization and differential expression analysis between N2 and FAS43 samples was performed with the R/Bioconductor package edgeR v.3.10.5, for the genes annotated in the reference genome. Briefly, very lowly expressed genes were filtered out, and the data were normalized according to the library size.
Differentially expressed genes were estimated using a GLM approach (General Linear Model), negative binomial distribution and a quasi-likelihood F-test.
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include raw counts and normalized abundance measurements (by edgeR)

source_name: Adult gonads

growth_protocol: Nematodes were cultured using standard procedures at 25°C.

extract_protocol:
RNA was isolated from N2 and FAS43 mixed-stage embryos and L1 larvae grown at 20°C using Trizol, in duplicates for all samples.
The TruSeq mRNA stranded kit from Illumina was used for the library preparation with 1000 ng of total RNA as input. Reads of 50 bases were generated using the TruSeq SBS HS v3 chemistry on an Illumina HiSeq 2500 sequencer.


title: NR3ZT06

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under night-restricted feeding paradigm; sacrificed at ZT06


title: NR2ZT22

description:
RAW_Table.txt
TPM_Table.txt


title: N2 isolated gonads replicate 2


title: NR3ZT02

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under night-restricted feeding paradigm; sacrificed at ZT02


title: N2 isolated gonads replicate 1


title: NR2ZT18

description:
RAW_Table.txt
TPM_Table.txt


title: Rice, wildtype control for miR390 TALEN mutant, rep 2

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
Sequencing data quality was assessed using FastQC. Reads were processed by removing the adaptor sequences using Trimmomatic and mapped to the Rice MSU genome version 7 using Bowtie. sRNA expression was performed using miRbase v22 annotated small RNAs and Bowtie alignment software.
Sequenced reads were trimmed to remove adapters and converted to flat file format using the pre-processing script described in Mathioni et al. (DOI: 10.1002/cppb.20043)med to remove adapters and converted to flat file format using the pre-processing script described in Mathioni et al. (DOI: 10.1002/cppb.20043)
Genome_build: Rice MSU genome version 7
Supplementary_files_format_and_content: tag count format

organism: Oryza sativa

source_name: callus

growth_protocol: plants grown in greenhouse condition

extract_protocol:
Total RNAs were prepared using a Trizol reagent-based method. The plant materials were homogenized and reconstituted in Trizol solution. The solution in turn was extracted by chloroform. Isopropanol was used to precipitate the total RNA. The whole process was performed under RNase free environment. DEPC-treated water was used to dissolve RNA. The total RNA underwent miRNA isolation using Qiagen miRNA purification kit according to the manufacturer’s manual. Small RNA libraries were made using 5 µg total RNA with NEBNext Small RNA library Prep Set, as described, and sequenced on the Illumina HiSeq 2500 platform.
Small RNA libraries were made using 5 µg total RNA with NEBNext Small RNA library Prep Set, as described, and sequenced on the Illumina HiSeq 2500 platform.

value: callus

value: wild type

tag: environment

value: incubator

tag: library

value: SMRTbell sequencing


title: NR2ZT10

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under night-restricted feeding paradigm; sacrificed at ZT10


title: Rice, wildtype control for miR390 TALEN mutant, rep 1


title: NR2ZT06

description:
RAW_Table.txt
TPM_Table.txt


title: Rice mir390 TALEN mutant, rep 1

value: TALEN-induced mutation on miR-390


title: Rice miR8 adult (osa-MIR408)

source_name: leaf

value: leaf

value: TALEN-induced mutation on miR-408

value: greenhouse


title: Rice miR7b adult (osa-MIR398b)

value: TALEN-induced mutation on miR-398b


title: NR3ZT10

description:
RAW_Table.txt
TPM_Table.txt

value: Wild-type

value: male


title: Rice miR2 adult (osa-MIR159b)

value: TALEN-induced mutation on miR-159b


title: NR1ZT14

description:
RAW_Table.txt
TPM_Table.txt

value: Liver


title: Rice WT Kitaake adult


title: NR1ZT10

description:
RAW_Table.txt
TPM_Table.txt


title: Organoid8M_R0_C47

value: retinal organoid

tag: culture time

value: 8 month


title: Rice mir390 TALEN mutant, rep 2


title: FAS43 isolated gonads replicate 1

value: his-72(uge40[K27M]) III


title: NR1ZT02

description:
RAW_Table.txt
TPM_Table.txt


title: NR1ZT06

description:
RAW_Table.txt
TPM_Table.txt


title: PCGF135fl_TAM_PCGF1_rep2

city: Oxford

first: Nadezda

middle: A

last: Fursova

address: South Parks Rd

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
Paired-end reads were aligned to the genome sequence of concatenated mouse and spike-in genomes (mm10+dm6 for native cChIP-seq and mm10+hg19 for cross-linked cChIP-seq) using Bowtie 2 with the “--no-mixed” and “--no-discordant” options specified. Reads that were mapped more than once were discarded, followed by removal of PCR duplicates with SAMTools for native cChIP-seq or Sambamba for cross-linked cChIP-seq.
To internally calibrate cChIP-seq experiments, we spiked-in a fixed number of control cells (Drosophila SG4 cells for native cChIP-seq and human HEK293T cells for cross-linked cChIP-seq) to each experimental sample. For annotation of genomic intervals and data visualisation, mm10 reads were randomly subsampled using factors that reflected the total number of dm6 (or hg19) reads in each sample. To account for any variation in spike-in cell mixing in different biological replicates, the downsampling factors were additionally corrected using the ratio of dm6 (or hg19)/mm10 total read counts in corresponding Input samples.
For each condition, biological replicates were merged for downstream applications. Genome coverage tracks were generated using the pileup function from MACS2 (Zhang et al. 2008).
RING1B and SUZ12 peak sets were generated with MACS2 (--broad) using corresponding Input samples for background normalisation. For each factor, a set of peaks identified in all biological replicates (intersection) was manually curated to remove sequencing artefacts. Classical Polycomb chromatin domains were identified by k-means clustering of ±10 kb windows centred on RING1B peaks based on their RING1B and SUZ12 chromatin occupancy using deeptools (v.3.0.1). This generated three clusters, two of which displayed high enrichment of both RING1B and SUZ12 and were combined into one set of genomic intervals.
Allele-specific analysis of H2AK119ub1 cChIP-seq was performed as described previously (Pintacuda et al. 2017). Briefly, paired-end reads were aligned using STAR (with “--outFilterMultimapNmax 1”, “--outFilterMismatchNmax 2”, “--alignEndsType EndToEnd” parameters) against the concatenated mm10+dm6 genome, in which polymorphic SNPs for 129S1 and CAST mouse strains were N-masked. Reads that were mapped more than once were discarded and PCR duplicates were removed with Sambamba. Reads mapping to mm10 genome were randomly subsampled using downsampling factors calculated based on spike-in calibration as described previously. To separate reads specifically mapping to the 129S1 and CAST alleles, we used SNPsplit (Krueger et al. 2016) with the paired-end mode.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files representing genome coverage for merged replicates of spike-in normalised cChIP-seq and Input profiles
Supplementary_files_format_and_content: bed files with enrichment peaks for RING1B and SUZ12 generated with MACS2 (--broad) from at least three biological replicates (intersection)

organism:
Homo sapiens
Mus musculus

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr), PCGF1 ChIP-seq

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor. Pcgf6fl/fl ESCs and Mus domesticus (129S1) x Mus castaneus F1 hybrid ESCs were grown on a monolayer of mitomycin-inactivated SNLP feeders (STO mouse fibroblasts expressing Neomycin, Puromycin resistance and Lif genes) in otherwise the same conditions as other mouse ESCs. Prior to harvesting these ES cells, the feeders were depleted by pre-plating trypsinised cells for 30 mins at 37°C on plates not coated with gelatin and discarding attached cells. Human HEK293T cells used for calibrated ChIP-seq were grown at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), and 0.5 Mm beta-mercaptoethanol (Life Technologies). Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin solution (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech).

extract_protocol:
For RING1B, SUZ12, PCGF1, PCGF2, CBX7 and PHC1 cChIP-seq, 5 x 10^7 mouse ESCs (both untreated and following 72 hours tamoxifen treatment) were mixed with 2 x 10^6 human HEK293T cells. Cells were resuspended in 10 ml phosphate buffered saline (PBS) and crosslinked at 25°C firstly with 2 mM DSG (Thermo Scientific) for 45 mins, and then with 1% formaldehyde (methanol-free, Thermo Scientific) for a further 15 minutes. Reactions were quenched by the addition of 125 mM glycine. Crosslinked cells were incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton-X100) for 10 min at 4˚C. The released nuclei were then washed (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 5 min at 4˚C. Chromatin was then resuspended in 1 ml of sonication buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine) and sonicated for 30 min using a BioRuptor Pico sonicator (Diagenode), shearing genomic DNA to an average size of approximately 0.5 kb. Following sonication, TritonX-100 was added to a final concentration of 1%. For ChIP, sonicated chromatin was diluted 10-fold in ChIP dilution buffer (1% Triton-X100, 1 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl) and pre-cleared for 1 hour using Protein A agarose beads (Repligen) blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA. For each ChIP reaction, 1ml of diluted and pre-cleared chromatin was incubated overnight with the appropriate antibody, anti-RING1B (CST D22F2, 3 ul), anti-SUZ12 (CST D39F6, 3 ul), anti-PCGF1 (in-house, 3 ul), anti-PCGF2 (sc-10744, 3 ul), anti-Cbx7 (ab21873, 4 ul), anti-Phc1 (CST 1F3F3, 6 ul). Antibody-bound chromatin was captured using blocked protein A agarose for 2 hours at 4°C and collected by centrifugation. ChIP washes were performed as described previously (Farcas et al. 2013). ChIP DNA was eluted in elution buffer (1% SDS, 0.1 M NaHCO3) and cross-links were reversed overnight at 65°C with 200 mM NaCl and 2 µl of RNase A (Sigma). A matched input sample (corresponding to 10% of original ChIP reaction) was identically treated. The following day ChIP samples and Inputs were incubated with Proteinase K (Sigma) for 1.5 hours at 56°C and purified using ChIP DNA Clean and Concentrator Kit (Zymo Research). For H2AK119ub1 and H3K27me3 native cChIP-seq, 5 x 10^7 mouse ESCs (both untreated and following 72 hours tamoxifen treatment) were mixed with 2 x 10^7 Drosophila SG4 cells in PBS. Mixed cells were pelleted and nuclei were released by resuspending in ice cold lysis buffer (10mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 5 mM N-ethylmaleimide). Nuclei were then washed, and resuspended in 1 ml of MNase digestion buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.25M sucrose, 3mM CaCl2, 10 mM N-ethylmaleimide, 1x protease inhibitors (Sigma)). Each sample was then incubated with 200 units of MNase (Fermentas) at 37°C for 5 min, followed by the addition of 4 mM EDTA to halt MNase digestion. Following centrifugation at 1500 g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300 µl of nucleosome release buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 1x protease inhibitors, 10 mM N-ethylmaleimide) at 4°C for 1 h, passed five times through a 27G needle using a 1 ml syringe, and spun at 1500 g for 5 min at 4°C. The second supernatant (S2) was collected and combined with corresponding S1 sample from above. A small amount of S1/S2 DNA was purified and visualized on a 1.5% agarose gel to confirm digestion to mostly mono-nucleosomes. For ChIP experiments, S1/S2 nucleosomes were diluted 10-fold in native ChIP incubation buffer (70 mM NaCl, 10 mM Tris pH 7.5, 2 mM MgCl2, 2 mM EDTA, 0.1% Triton, 1x protease inhibitor cocktail (Roche), 10 mM N-ethylmaleimide (NEM)), and 1 ml aliquots were made. Each ChIP reaction was then incubated overnight at 4°C with 5 ul of anti-H2AK119ub1 (CST D27C4) or anti-H3K27me3 (in-house). Antibody-bound nucleosomes were captured using protein A agarose (Repligen) beads, pre-blocked in native ChIP incubation buffer supplemented with 1 mg/ml BSA and 1 mg/ml yeast tRNA, for 1 hour at 4°C and collected by centrifugation. Immunoprecipitated material was washed four times with Native ChIP wash buffer (20 mM Tris pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% Triton-X100) and once with Tris-EDTA buffer (10 mM Tris pH 8, 1 mM EDTA). ChIP DNA was eluted using 100 ul of elution buffer (1% SDS, 0.1 M NaHCO3), and then purified using ChIP DNA Clean and Concentrator Kit (Zymo Research). For each individual ChIP sample, DNA from a matched Input control (corresponding to 10% of original ChIP reaction) was also purified.
Libraries for both ChIP and Input samples were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries was analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads on Illumina NextSeq 500 platform in biological triplicate unless otherwise specified. For allele-specific analysis in 129S1 x CAST hybrid ESC line with inducible fill-length Xist transgene, native cChIP-seq libraries were sequenced as 80 bp paired-end reads on Illumina NextSeq 500 platform to increase the number of reads overlapping allele-specific SNPs.

treatment_protocol: To induce conditional removal of distinct PRC1 complexes or their combinations in Pcgf4-/-; Pcgf2fl/fl, Pcgf1fl/fl, Pcgf3fl/fl, Pcgf5fl/fl, Pcgf6fl/fl, Pcgf3/5fl/fl, Pcgf1/3/5fl/fl, Pcgf1/3/5/2fl/fl, Pcgf1/3/5/6fl/fl and Ring1a-/-; Ring1bfl/fl ESC lines, cells were treated with 800 nM 4-hydroxytamoxifen (TAM) for 72 hours. To induce expression of Xist transgene, 129S1 x CAST ESCs were treated with 1.5 μg/mL doxycycline for 72 hours.

tag: replicate

tag: treatment agent

value: tamoxifen (OHT)

tag: treatment time point

value: 72 hr

tag: spike-in reference organism

value: Homo sapiens

tag: spike-in cell line

tag: ChIP

tag: antibody

value: In house (Blackledge et al., 2014)


title: PCGF135fl_UNT_PCGF1_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, PCGF1 ChIP-seq

value: 0 hr


title: LB3ZT22

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under ad-libitum feeding paradigm; sacrificed at ZT22

tag: strain

tag: genotype


title: PCGF135fl_TAM_PCGF1_rep3


title: NR1ZT22

description:
RAW_Table.txt
TPM_Table.txt


title: LB3ZT18

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under ad-libitum feeding paradigm; sacrificed at ZT18


title: NR2ZT02

description:
RAW_Table.txt
TPM_Table.txt


title: LB3ZT14

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under ad-libitum feeding paradigm; sacrificed at ZT14


title: PCGF135fl_UNT_PCGF1_rep2


title: PCGF2fl_TAM_XInput2_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr), gDNA-seq

tag: clone


title: LB3ZT10

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under ad-libitum feeding paradigm; sacrificed at ZT10


title: PCGF2fl_UNT_XInput2_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, gDNA-seq


title: PCGF2fl_TAM_XInput2_rep1


title: PCGF2fl_UNT_XInput2_rep2


title: LB3ZT02

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under ad-libitum feeding paradigm; sacrificed at ZT02


title: LB2ZT22

description:
RAW_Table.txt
TPM_Table.txt


title: MCF7 p21 rep 2

city: Chicago

first: Stephen

last: Kron

state: IL

department: MGCB

institute: University of Chicago

description: p21 rep2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GenomeStudio. The filtering is detection p-value less than 0.05.

label: biotin

source_name: breast cancer cell line

label_protocol: Biotinylated cRNA were prepared with the Illumina™ TotalPrep™ RNA Amplification Kit for Illumina arrays

growth_protocol: MCF7 cells grow in DMEM mediu with 4mM glutamine and 10% Tet system approved FBS and penicillin-streptomycin

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Bioanalyser.

treatment_protocol: The cells were irridated with 6 Gy or ectopic express p21

tag: treatment

value: ectopic express p21


title: shADRB2-2-3

city: Oslo

first: Peder

middle: Rustøen

last: Braadland

state: Oslo

address: Ullernchausseen 70

department: Tumor Biology

country: Norway

institute: Oslo University Hospital

description: Replicate 2

hyb_protocol: 750 ng of biotin labeled cRNA was hybridized to Illumina’s HumanHT-12 v4 Expression BeadChip using Illumina's Whole-Genome Gene Expression Direct Hybridization Assay (Part # 11286340 Rev. A)

scan_protocol: Following scanning, the iScan software was used to extract signal intensities and to save all files for each BeadChip. Raw data was imported to GenomeStudio V2011.1 Gene Expression module v. 1.9.0.

data_processing: HumanHT-12 expression BeadChip Data were quantile normalized, missing data imputed. The data were annotated using the HumanHT-12_V4_0_R2_15002873_B.bgx annotation file from Illumina.

source_name: LNCaP stably transfected with an ADRB2-targeting shRNA (shADRB2-2), maintained in RPMI supplemented with 10% FCS and 200 µg/mL G418.

label_protocol: 500ng of total RNA was amplified and labeled using the Illumina® TotalPrep™-96 RNA Amplification Kit. The quantity of the labeled cRNA was measured using the NanoDrop Spectrophotometer, and the quality and size distribution of the labeled cRNA assessed using the 2100 Bioanalyzer.

growth_protocol: Cells were incubated in 10% FCS

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit (Qiagen) according to manufacturer's protocol. Quality control and size distribution of the labeled cRNA was assessed using the 2100 Bioanalyzer.

treatment_protocol: Two short hairpin SureSilencingTM shRNA plasmids with insert sequences targeting ADRB2 mRNA, as well as a non-targeting shRNA as control, were stably transfected using Dharmafect Duo. Selection of transfected clones was acheived by adding 400 µg/mL G418-sulphate. Cells were maintained at  200 µg/mL G418.

tag: passage

value: Passage 25-27

tag: transfection

value: ADRB2-targeting shRNA (shADRB2-2)


title: LB2ZT18

description:
RAW_Table.txt
TPM_Table.txt

tag: Sex

tag: tissue


title: shADRB2-3-3

description: Replicate 3

source_name: LNCaP stably transfected with an ADRB2-targeting shRNA (shADRB2-3), maintained in RPMI supplemented with 10% FCS and 200 µg/mL G418.

value: ADRB2-targeting shRNA (shADRB2-3)


title: shADRB2-3-2

description: Replicate 2


title: shADRB2-3-1

description: Replicate 1


title: shCtrl-2

description: Replicate 3

source_name: LNCaP stably transfected with a non-targeting (scrambled) shRNA rep3, maintained in RPMI supplemented with 10% FCS and 200 µg/mL G418.

value: non-targeting (scrambled) shRNA


title: shCtrl-3

description: Replicate 1

source_name: LNCaP stably transfected with a non-targeting (scrambled) shRNA, maintained in RPMI supplemented with 10% FCS and 200 µg/mL G418.


title: shADRB2-2-2

description: Replicate 3


title: MCF7 p21 rep 1

description: p21 rep1

tag: cell line


title: MCF7 control2 rep 3

description: control rep3

value: control


title: MCF7 control2 rep 2

description: control rep2


title: shADRB2-2-1

description: Replicate 1


title: shCtrl-1

description: Replicate 2

source_name: LNCaP stably transfected with a non-targeting (scrambled) shRNA rep2, maintained in RPMI supplemented with 10% FCS and 200 µg/mL G418.


title: PCGF2fl_TAM_PHC1_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr), PHC1 ChIP-seq

value: Cell Signalling 1F3F3


title: PCGF2fl_TAM_XInput2_rep2


title: LB2ZT10

description:
RAW_Table.txt
TPM_Table.txt

value: Wild-type

value: male


title: PCGF2fl_UNT_XInput2_rep1


title: LB3ZT06

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under ad-libitum feeding paradigm; sacrificed at ZT06

value: Liver


title: MCF7 control2 rep1

description: control rep1


title: MCF7 IR rep 3

description: IR rep3

value: irridated with 6 Gy


title: PCGF2fl_TAM_PHC1_rep1


title: LB2ZT06

description:
RAW_Table.txt
TPM_Table.txt


title: shCN_253

city: Atlanta

first: Christopher

last: Porter

state: GA

address: 1760 Haygood Drive

department: Pediatrics

institute: Emory University

description: RNA-seq shNS v shCn - all - counts only

data_processing:
Bowtie for alignment to GRCm38
RPKM normalization
Genome_build: GRCm38
Supplementary_files_format_and_content: text file with cuffllinks output

source_name: murine BCR-ABL1+/Arf null lymphoblastic leukemia

extract_protocol:
Trizol
Illumina

tag: shRNA

value: shRNA against calcineurin B

tag: time point

value: sorted from recipient mouse at Day 7

value: lymphoblastic leukemia


title: PCGF2fl_TAM_PHC1_rep2

tag: replicate

tag: treatment agent

value: tamoxifen (OHT)

value: 72 hr

value: Homo sapiens


title: shCN_249

description: RNA-seq shNS v shCn - all - counts only


title: MCF7 IR rep 2

description: IR rep2


title: shNS_244

description: RNA-seq shNS v shCn - all - counts only

value: non-silencing shRNA


title: shCN_247

description: RNA-seq shNS v shCn - all - counts only


title: shNS_243

description: RNA-seq shNS v shCn - all - counts only


title: shCN_248

description: RNA-seq shNS v shCn - all - counts only


title: LB1ZT22

description:
RAW_Table.txt
TPM_Table.txt


title: LB2ZT02

description:
RAW_Table.txt
TPM_Table.txt


title: PCGF2fl_UNT_PHC1_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, PHC1 ChIP-seq

tag: treatment time point

value: 0 hr

tag: spike-in reference organism


title: MCF7 control rep1

description: control rep1


title: shNS_239

description: RNA-seq shNS v shCn - all - counts only


title: MCF7 control rep 3

description: control rep3


title: MCF7 control rep 2

description: control rep2


title: MCF7 IR rep 1

description: IR rep1


title: LB2ZT14

description:
RAW_Table.txt
TPM_Table.txt


title: PCGF2fl_UNT_PHC1_rep2

tag: spike-in cell line

tag: ChIP


title: shNS_241

description: RNA-seq shNS v shCn - all - counts only


title: PCGF2fl_UNT_PHC1_rep1

tag: antibody


title: PCGF2fl_TAM_CBX7_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr), CBX7 ChIP-seq

value: Abcam ab21873


title: LB1ZT18

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under ad-libitum feeding paradigm; sacrificed at ZT18

tag: strain

tag: genotype


title: 6E

city: Baton Rouge

first: Thanh

last: Dang

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

description:
WT HF 32.AVG_Signal
sample name:
6E
global knockout of Siah2

hyb_protocol: 750ng labeled RNA was hybridized to Illumina Mouse WG-6 v2 BeadChip arrays (Illumina) for females and Illumina MouseRef-8 v2.0 Expression BeadChip arrays for males according to manufacturer's protocol.

scan_protocol: Chips were scanned using Illumina iScan system with default settings

data_processing:
Raw data was analyzed using Illumina GenomeStudio with the Gene Expression Module v.1.0.6  Raw data were background-subtracted and normalized using the quantile normalization method using the preprocessCore package in R.
The "Matrix normalized" tab contains quantile normalized and background subtracted gene expression signals.  "Matrix non-normalized" contains background subtracted non-normalized data exported from GenomeStudio.

source_name: brown adipose tissue

label_protocol: 400ng total RNA was labeled with Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit for Illumina system

extract_protocol: The brown adipose tissue was quickly removed, frozen in liquid nitrogen and stored at -80C.  Total RNA was isolated using Tri-Reagent (Molecular Research Center, Inc. Cincinnati, Ohio) with modifications to remove DNA using Qiagen RNAeasy columns.

treatment_protocol: The mice were weaned at 4 weeks of age and randomized to either a low fat (10% fat) diet (Research Diets, New Brunswick, NJ, #D12450B) or high fat (45%) diet (Research Diets, D12451).  The mice remained on these diets until 20 weeks of age.

value: brown adipose tissue

tag: gender

value: Female

tag: diet

value: high fat diet

tag: age

value: 20 weeks

value: WT


title: Ccl5 promoter gRNA

city: Kyoto

first: Wooseok

last: Seo

address: Yoshida-Konoe-cho, Sakyo-ku

country: Japan

institute: Kyoto University Graduate School of Medicine

description:
Mouse T cell line
gRNA specific to the Ccl5 promoter was used

data_processing:
ChIP-seq sequences were aligned to mouse reference genome release mm10 using bowtie (v1.1.2) with default parameters. Fragment sizes were estimated and peaks were called by MACS2 (v.2.1.1) by using the following parameters; band width 300, model fold [5,50], qvalue cutoff 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 output files as bed files

source_name: 2B4 cell line

growth_protocol: 2B4 cells were cultured in RPMI supplemented with 10% FCS.

extract_protocol:
For ChIP-seq using anti-Flag (Sigma, F3165),  1x10^7 2B4 cells were washed with ice-cold PBS three times and  and were crosslinked by incubation with 1% formaldehyde containing 0.5 mM PMSF and protease inhibitor cocktail (Roche, 4693116001) on ice for 10 minutes. The crosslinking reaction was stopped by the addition of glycine to 0.125 M. Cells were incubated on ice for 5 minutes and then washed three times with ice-cold PBS. Cells were lysed by the incubation for 10 min on ice in 0.5 ml of 50 mM HEPES (pH 7.5), 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% TritonX-100 containing protease inhibitor cocktail. Nuclei were pelleted and lysed by resuspending in 10 mM Tris-Cl (pH 8.0), 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA containing protease inhibitor cocktail. Pelleted chromatin was resuspended in 400 μl of 10 mM Tris-Cl (pH 8.0), 300 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% TritonX-100, 0.1% sodium deoxycholate and 0.5% N-laurylsarcosine containing protease inhibitor cocktail, and was sonicated using a model XL2000 ultrasonic cell disruptor (MICROSON) to approximately 350 bp of DNA fragments. Sonicated chromatin was incubated at 4 °C overnight with anti-Flag antibody preconjugated to magnetic beads (Dynabeads). Beads were washed by RIPA buffer 6 times and DNA was eluted and reverse-crosslinked at 65 °C in 50 mM Tris-Cl (pH 8.0), 10 mM EDTA, 1% SDS overnight.
Library construction was conducted by using NEBNext ChIP-seq Library Prep Reagent Set for Illumina according to the manufacture’s protocol. Libraries were sequenced to 50 bp read length on a HiSeq2000 (Illumina).

treatment_protocol: Plat-E packaging cells were transfected with Mock_gRNA or Ccl5-promoter_gRNA in addition to dCas9 which have hCD2 or GFP as markers, respectively. After selection of Plat-E expressing both hCD2 and GFP, the culture supernatant was used to infect 2B4 cells. 2B4 cells were selected for hCD2 and GFP. Before ChIP-seq, 2B4 was stimulated by 50 ng/mL PMA and 1 ug/mL ionomycin for 24 hours.

tag: chip antibody

value: Anti-Flag M2

tag: transfection

value: gRNA specific to the Ccl5 promoter


title: mock gRNA

description:
Mouse T cell line
Mock gRNA was used as a control

tag: cell line

value: Mock gRNA


title: LB1ZT14

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under ad-libitum feeding paradigm; sacrificed at ZT14

value: Wild-type

tag: Sex

value: male

tag: tissue

value: Liver


title: LAN-6-input-3496_S45

city: houston

first: Wenting

last: Liao

address: 1881 east road

institute: md anderson

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to a reference genome (UCSC mm9; Assembly http://hgdownload.cse.ucsc.edu/downloads. html#mouse) using the Burrows–Wheeler Aligner.
Reads mapping to more than two genomic loci were ignored.
The peaks are called with p-value 1e-6, corresponding to the Peak score column: 10*log10(pvalue)
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using deeptools bamCoverage 2.3.3

source_name: Primarily cultured iKAP CRC cells

growth_protocol: Primarily cultured iKAP CRC cells were routinely cultured in DMEM plus 10% FBS (Tetracycline-Free) and 1ug/ml Doxycycline.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Immune complexes were then washed three times with RIPA buffer, once with RIPA-500 (RIPA with 500 mM NaCl), and once with LiCl wash buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA [pH 8.0], 250 mM LiCl, 0.5% NP-40, 0.5% deoxycholic acid). Elution and reverse-crosslinking were performed in direct elution buffer (10 mM Tris-Cl [pH 8.0], 5 mM EDTA, 300 mM NaCl, 0.5% SDS) with proteinase K (20 mg/ml) at 65°C overnight. Eluted DNA was purified using AMPure beads (Beckman-Coulter). Libraries were prepared using NEBNext Ultra DNA Library kit (E7370).

tag: cell type

value: Primarily cultured iKAP CRC cells

tag: passage

tag: antibdoy

value: input


title: LB1ZT10

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under ad-libitum feeding paradigm; sacrificed at ZT10


title: NR1ZT18

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under night-restricted feeding paradigm; sacrificed at ZT18


title: 5E

description:
WT HF 31.AVG_Signal
sample name:
5E
global knockout of Siah2


title: LAN-6-IRF2-3496plusDOX_S39

value: IRF2 (Bethyl, A303-381A)


title: PCGF2fl_TAM_CBX7_rep1

tag: replicate

tag: treatment agent

value: tamoxifen (OHT)

tag: treatment time point

value: 72 hr

tag: clone

tag: spike-in reference organism

value: Homo sapiens


title: LB1ZT02

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under ad-libitum feeding paradigm; sacrificed at ZT02

tag: strain

tag: genotype


title: LB1ZT06

description:
RAW_Table.txt
TPM_Table.txt


title: 2E

description:
SKG HF 6.AVG_Signal
sample name:
2E
global knockout of Siah2

value: brown adipose tissue

tag: gender

tag: diet

value: Siah2 knockout


title: 4E

description:
WT HF 30.AVG_Signal
sample name:
4E
global knockout of Siah2

value: Female

value: high fat diet

tag: age


title: 3E

description:
SKG HF 33.AVG_Signal
sample name:
3E
global knockout of Siah2

value: 20 weeks


title: PCGF2fl_UNT_CBX7_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, CBX7 ChIP-seq

value: 0 hr

tag: spike-in cell line

tag: ChIP

tag: antibody

value: Abcam ab21873


title: DR3ZT22

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under arrhythmic feeding paradigm (did not adapt fully); sacrificed at ZT22

tag: Sex

tag: tissue


title: PCGF2fl_UNT_CBX7_rep1

tag: cell line


title: DR3ZT18

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under arrhythmic feeding paradigm (did not adapt fully); sacrificed at ZT18


title: saP5

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description:
P5_S15_L003
processed data file: f2.glyphosate.csv.gz

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs, the reference genome was broken into 100 bp windows. Genomic windows with less than 40 mapped reads summed across all samples were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between control and exposure sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window. The PBS and DMSO controls were added together into a single control goup.
Windows with an edgeR p-value less than 10-6 were considered DMRs. The DMR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

source_name: F2_DMSO control_sperm

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley®™SD®™ (Harlan) at 70 to 100 days of age were fed ad lib with a standard rat diet and ad lib tap water. The gestating female rats treated were designated as the F0 generation. Subsequent generations were derived from the F0 generation. F1- F3 generation control and glyphosate lineages were housed in the same room and racks with lighting. There was a founder effect observed in the offspring of a specific male from the control population treated with PBS, manifesting as abnormally high rates of obesity in decedents. Therefore, a portion of original control colony was excluded from the study due to the obesity founder effects identified. These animals were replaced with offspring from DMSO-treated controls from a concurrent study.

extract_protocol:
The epididymis from each rat was dissected free of fat and connective tissue, a small cut made to the cauda and the tissue placed in 6 ml of phosphate buffer saline (PBS) for 20 minutes at room temperature and then kept at 4ºC to immobilize the sperm.  The epididymal tissue was coarsely minced and the released sperm centrifuged at 4ºC 3,000 x g for 10 min and pellet resuspended in fresh NIM buffer and stored at -80ºC until processed further. Twenty–fifty to 50 μl of rat sperm suspension were used for DNA extraction. The suspension was sonicated for five seconds (Fisher Sonic Dismembrator, model 300, power 25), then centrifuged 5 min at 6000 x g, supernatant discarded and sperm washed again to remove somatic cells and debris. Then the pellet was resuspended in 820 μL DNA extraction buffer and 80 μl 0.1M DTT added. The sample was incubated at 65°C for 15 minutes. Following this incubation 80 μl proteinase K (20 mg/ml) was added and the sample was incubated at 55°C for at least 2 hours under constant rotation. Then 300 μl of protein precipitation solution (Promega Genomic DNA Purification Kit, A795A) were added, the sample mixed thoroughly and incubated for 15 min on ice. The sample was centrifuged at 13,500 rpm for 30 minutes at 4°C. One ml of the supernatant was transferred to a 2 ml tube and 2 μl of glycoblue (Invitrogen, AM9516) and 1 ml of cold 100 % isopropanol were added. The sample was mixed well by vortexing the tube then left in -20°C freezer for at least one hour. After precipitation, the sample was centrifuged at 13,500 x g for 30 min at 4°C. The supernatant was taken off and discarded without disturbing the (blue) pellet. The pellet was washed with 70% cold ethanol, then tube was spun again briefly to collect residual ethanol at bottom of tube and then as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes). Pellet was then resuspended in 100 μl of nuclease free water. For all generations equal amounts of DNA from each individual’s sample was used to produce 6 different DNA pools per lineage and the pooled DNA used for methylated DNA immunoprecipitation (MeDIP). Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: The genomic DNA was sonicated using the Covaris M220 as follows: 6μg of pooled or individual animal sperm genomic DNA was diluted to 130 μl with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) into the appropriate Covaris tube. Covaris was set to 300 bp program and the program was run for each tube in the experiment. 10 μl of each sonicated DNA was run on 1.5% agarose gel to verify fragment size. The sonicated DNA was then diluted with TE buffer to 400 μl, heat-denatured for 10min at 95˚C, then immediately cooled on ice for 10 min. Then 100μl of 5X IP buffer and 5μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured (single-stranded) sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4˚C. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; Life Technologies 11201D) were pre-washed per manufacturer’s instructions and 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4˚C. After the incubation, the bead-DNA-antibody samples were washed three times with 1X IP buffer using a magnetic rack. The washed samples are then resuspended in 250μl digestion buffer (5mM Tris PH 8, 10.mM EDTA, 0.5% SDS) with 3.5μl Proteinase K (20mg/ml) and incubated for 2-3 hours on a rotator at 55˚. Samples were then extracted with Phenol-Chloroform-Isoamyalcohol and the final supernatant precipitated with 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol in -20˚C freezer for >1 hour to overnight.  The DNA precipitate was centrifuged at 14,000rpm for 20min at 4˚C, the pellet was washed with 500μl cold 70% ethanol and then air-dried at RT (about 5 minutes). It was resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA from the single-stranded DNA resulting from MeDIP. After this step the manufacturer’s protocol was followed. Each pool received a separate index primer.

treatment_protocol: Timed-pregnant females on days 8 through 14 of gestation were administered daily intraperitoneal injections of glyphosate (25 mg/kg BW/day dissolved in PBS)(Chem Service, Westchester PA) or dimethyl sulfoxide (DMSO) or Phosphate Buffered Saline (PBS). Only the F0 generation was treated with glyphosate, DMSO, or PBS.

tag: strain background

value: an outbred strain Hsd:Sprague Dawley SD (Harlan) strain

tag: generation

tag: treatment

value: DMSO control

value: sperm


title: PCGF2fl_TAM_CBX7_rep2

tag: replicate

tag: treatment agent

tag: treatment time point


title: saP3

description:
P3_S13_L003
processed data file: f1.glyphosate.csv.gz

source_name: F1_DMSO control_sperm


title: saP2

description:
P2_S12_L003
processed data file: f1.glyphosate.csv.gz


title: DR3ZT14

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under arrhythmic feeding paradigm (did not adapt fully); sacrificed at ZT14

tag: strain

value: Wild-type

value: male

value: Liver


title: PCGF2fl_TAM_PCGF2_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr), PCGF2 ChIP-seq

tag: clone

tag: spike-in reference organism

value: Santa Cruz (Mel18, sc-10744)