title: U251 treated whit cyclodextrin as vehicle, technical rep. 2

city: CIUDAD DE MÉXICO

first: DIANA

middle: ELISA

last: VELÁZQUEZ

state: CIUDAD DE MÉXICO

address: CIRCUITO ESCOLAR 33, C.U., COYOACÁN

department: FACULTAD DE QUÍMICA

country: Mexico

institute: UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO

hyb_protocol: The labelled RNA was hybridized 16-18 h along with the hybridization controls, with the GeneChip miRNA 4.0 Array Affymetrix.

scan_protocol: GeneChips were digitized on the GeneChip Scanner 3000 7G scanner.

data_processing: The fluorescence intensity values in “.CEL” format, were loaded into Expression ConsoleTM 1.4.1.46 software where they were preprocessed with Robust Multiarray Analysis (RMA) and normalized by quartiles.

source_name: U251 cell line derived from a human GBM, treated whit cyclodextrin as vehicle for 6h

label_protocol: A total of 250 ng of total RNA were labeled with the FlashTag™ Biotin RNA Labeling kit, according to the manufacturer´s instructions.

growth_protocol: The U251 cell line derived from a human GBM was maintained in Dulbecco's Modified Eagle Medium with high glucose, phenol red, supplemented with 10% fetal bovine serum, 1 mM sodium pyruvate, 0.1 mM of non-essential amino acids and 1 mM antibiotic (Streptomycin 10 g / L, Penicillin G 6.028 g / L and Amphotericin B 0.025 g / L), at 37 ° C in a humid atmosphere with 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The DMEM medium with phenol red was replaced by DMEM without phenol red with SFB without hormones (charcoal stripped) 12 h before the treatments. Then, the cells were treated with P4 (10 nM), RU486 (10 µM), P4 (10 nM) + RU486 (10 µM) and vehicle (cyclodextrin, 0.02%) for 6 h.

value: male

value: brain

tag: disease

value: Glioma

tag: disease grade

value: astrocytoma grade IV, glioblastoma (GBM)


title: U251 treated whit cyclodextrin as vehicle, technical rep. 3

status: Public on Jan 25 2020

type: RNA

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: gender

tag: tissue


title: TN09-29_infected_Rep3 (MethylC-Seq)

type: SRA

city: Knoxville

first: Sarbottam

last: Piya

state: Tennessee

address: 2431 Joe Johnson Dr.

department: Plant Science

country: USA

institute: University of Tennessee

library_source: genomic

data_processing:
Adapters and low quality reads below phred threshold of 33 were removed using Trimmomatic.
Reads were aligned to the soybean reference genome (Wm82.a2.v1) using Bismark.
Differentially methylated cytosines were identified using R bioconductor package methylKit.
Differentially methylated regions were mapped to various genic regions using R Bioconductor package rtracklayer.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: methlyation calls

molecule: genomic DNA

organism: Glycine max

source_name: Root

growth_protocol: Soybean seeds of TN09-16, TN09-29, Fowler and Anand were washed under running water for 30 minutes followed by soaking in 10% bleach for 10 minutes. After surface sterilization, the seeds were washed again for 30 minutes to remove bleach remnants. The seeds were germinated on wet germination paper by keeping in dark at 26 degrees for three days.

extract_protocol:
Genomic DNA of root tissues were extracted using DNeasy Plant Mini Kit (Qiagen).
Whole genome methylC-seq libraries were constructed following the protocol from Illumina TruSeq Library Prep kit (Illumina, San Diego, CA)

treatment_protocol: Soybean seedlings of 3-days old TN09-16 and TN09-29 were treated with 3000 freshly hatched second stage juveniles (J2s) of SCN HG type 0 (race 3) by spreading the nematodes across the whole root of a seedling. Control plants were set up in the exact same way, except mock inoculations were performed using 0.1% (w/v) agarose per seedling. The two parental lines (Fowler and Anand) were only mock-inoculated. Root tissues of all in the samples were collected five days after nematode treatment.

tag: line

tag: phenotype

value: Soybean cyst nematode  resistant

value: Root

tag: age

value: 8 days

tag: infection

value: Soybean cyst nematode infected root tissue


title: MTAI1 [miRNA-seq]

city: Tianjin

first: Ming

last: Cui

address: 238 Baidi Road

department: Institute of Radiation Medicine,

country: China

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

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Position 2~8 of a mature miRNA were called seed region which were highly conserved. The target of a miRNA might be different with the changing of nucleotides in this region. In our analysis pipeline, miRNA which might have base edit could be detected by aligning all the sRNA tags to mature miRNA, allowing one mismatch.
Exploring the occurrence of miRNA families identified from the samples in other species. In our analysis pipeline, known miRNA used miFam.dat (http://www.mirbase.org/ftp.shtml) to look for families; novel miRNA precursor was submitted to Rfam (http://rfam.sanger.ac.uk/search/) to look for Rfam families.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010):Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Genome_build: ensembl 90
Supplementary_files_format_and_content: Excel file include TPM values for each Sample.

organism: Mus musculus

source_name: MTAI_small intestine

extract_protocol:
Small intestine were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.)

tag: strain

tag: genotype/variation

value: wild type

tag: Sex

tag: treatment

value: total abdominal irradiation

value: small intestine


title: Anand_noninfected_Rep1 (MethylC-Seq)

value: Anand

value: parental

value: Mock treated root tissue


title: Anand_noninfected_Rep2 (MethylC-Seq)


title: U251 treated whit P4+RU486, technical rep. 2

source_name: U251 cell line derived from a human GBM, treated whit P4+RU486 for 6h


title: U251 treated whit P4+RU486, technical rep. 3


title: U251 treated whit RU486, technical rep. 3

source_name: U251 cell line derived from a human GBM, treated whit RU486 for 6h


title: U251 treated whit P4+RU486, technical rep. 1


title: TN09-29_infected_Rep2 (MethylC-Seq)


title: U251 treated whit cyclodextrin as vehicle, technical rep. 1


title: U251 treated whit RU486, technical rep. 2


title: Spleen WT rep 2

city: Helsinki

first: Juha

middle: Mikael

last: Saarikettu

address: Viikinkari 1

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalization

source_name: Spleen

label_protocol: Standard Illumina protocol

extract_protocol: Trizol extraction

value: Female

value: 8-12 week-old


title: U251 treated whit RU486, technical rep. 1


title: U251 treated whit P4, technical rep. 3

source_name: U251 cell line derived from a human GBM, treated whit P4 for 6h


title: Spleen Snd1 KO rep 1


title: Spleen WT rep 1


title: Spleen Snd1 KO rep 2


title: U251 treated whit P4, technical rep. 1


title: TN09-29_infected_Rep1 (MethylC-Seq)


title: TN09-29_noninfected_Rep2 (MethylC-Seq)


title: TN09-29_noninfected_Rep3 (MethylC-Seq)


title: TN09-16_infected_Rep3 (MethylC-Seq)

value: Soybean cyst nematode susceptible


title: TN09-29_noninfected_Rep1 (MethylC-Seq)


title: TN09-16_noninfected_Rep3 (MethylC-Seq)


title: TN09-16_infected_Rep1 (MethylC-Seq)


title: TN09-16_noninfected_Rep2 (MethylC-Seq)


title: N-myc_KO_RNAseq_2

city: Rio de Janeiro

first: Rodrigo

middle: A. P.

last: Martins

state: RJ

address: Av. Pedro Calmon, 550

department: Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas

country: Brazil

institute: Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil

data_processing:
After trimming adapter with Trim Galore (v. 0.3.7), RNA-Seq reads were aligned back to mouse genome (mm10) with tophat (v. 2.0.13) (Trapnell et al., 2009).
Counts number was calculated with HTseq (v.0.6.1) (Anders et al., 2015 bioinformatics) using gene annotation file vM8 from GENCODE database.
The Cufflinks (v. 2.2.1) (Trapnell et al., 2010) was used to calculate FPKM values of the genes.
We further focused on 14850 genes that have mean FPKM value >1 in all samples. Deseq2 (Love et al., 2014) was used to determine the differentially expressed genes and the genes with FDR smaller than 0.05 were chosen as differentially expressed genes.

source_name: E14 mouse lens

growth_protocol: All Cre transgenes were kept in heterozygosity by crossing mice heterozygous for a Cre transgene with a wild-type. Control group consisted Cre -/- mice with Myc genes flanked by loxP sites: N-mycloxP/loxP (N-mycCtrl) and N-mycloxP/loxP;c-mycloxP/loxP (N-myc; c-mycCtrl). N-mycMlr10-Cre stands for Mlr10-Cre+/-; N-mycloxP/loxP.

extract_protocol:
After pooling, chloroform was added and samples were centrifuged at 15000g at 4°C for 15 minutes. Aqueous phase mixed with 1.5 volume of EtOH and processed in RNeasymini columns (Qiagen cat#74104) following manufacturer’s protocol. Genomic DNA (gDNA) contamination was verified by a PCR that amplified genomic non-transcribed region. RNA samples contaminated with gDNA were treated with DNase I (Ambion cat#: 1906) following manufacturer’s instructions.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Lenses from single animals were isolated in cold PBS, lysed in TRIzol reagent (ThermoFisher cat#15596026) and stored at -80°C.

tag: developmental stage

value: lens


title: Ctrl3_RNAseq


title: N-myc_KO_RNAseq_1


title: TN09-16_noninfected_Rep1 (MethylC-Seq)


title: U251 treated whit P4, technical rep. 2

value: male

value: brain


title: Ctrl1_RNAseq


title: MT3

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned to the reference genome using HISAT2(Langmead, B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default.
The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
The Ballgown suite includes functions for interactive exploration of the transcriptome assembly, visualization of transcript structures and feature-specific abundances for each locus, and post-hoc annotation of assembled features to annotated features(Alyssa C. Frazee et al.2014). Transcripts with an P-adjust <0.05 were assigned as differentially expressed.Cuffdiff provides statistical routines for determining differential expression in digital transcript or gene expression data using a model based on the negative binomial distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned as differentially expressed.
Genome_build: ensembl 90
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample.

source_name: MT_small intestine

extract_protocol:
Small intestine were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: total abdominal irradiation combined with simvastatin treatment

value: Small intestine


title: Ctrl2_RNAseq


title: MT2


title: MT1


title: MTAI2


title: MTAI3


title: Low protein diet3_liver sample_rep1

city: Zama

first: Yosuke

last: Komatsu

state: Kanagawa

address: 5-1-83 Higashihara

department: Wellness & Nutrition Science Institute

country: Japan

institute: Morinaga Milk Industry Co., Ltd.

hyb_protocol: Cyanine 3-labeled cRNA (600 ng) was fragmented in a reaction mixture containing Agilent fragmentation buffer and GE blocking agent for 30 min at 60°C. Next, Agilent GE hybridization buffer HI-RPM was added to the sample and hybridized to a SurePrint G3 Rat GE microarray 8 × 60K (Agilent Technologies) for 17 h rotated at 10 rpm in a hybridization oven at 65°C.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green at 20 bit).

data_processing: Raw data from the Feature Extraction Software were exported to GeneSpring GX ver. 14.9 (Agilent Technologies) using parameters (protocol GE1_1200_Jun14 and Grid: 074036_D_F_20190102) 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: Low protein diet3,liver sample,week4

label_protocol: Complementary RNA was generated and labeled with cyanine 3 using a Low Input QuickAmp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. Labeled cRNA was purified using an RNeasy mini kit (QIAGEN) and then RNA concentration was measured and labeling efficiency (> 6 pmol/μg) validated using a NanoDrop ND-1000 (Nano-Drop Technologies).

extract_protocol: Total RNA was extracted according to the instructions from the manufacturer. RNA samples were purified with an RNeasy mini kit (Qiagen, Hilden, Germany).

treatment_protocol: Liver tissues were homogenized in TRIzol reagent (LifeTechnologies, Carlsbad, CA) using glass homogenizer tubes.

value: liver

tag: condition

value: Rat fed low protein diet for 4 weeks


title: MTAI1


title: Low protein diet5_liver sample_rep1

source_name: Low protein diet5,liver sample,week4


title: Low protein diet6_liver sample_rep1

source_name: Low protein diet6,liver sample,week4


title: TN09-16_infected_Rep2 (MethylC-Seq)

value: Root

value: 8 days

value: Soybean cyst nematode infected root tissue


title: Low protein diet2_liver sample_rep1

source_name: Low protein diet2,liver sample,week4


title: Low protein diet4_liver sample_rep1

source_name: Low protein diet4,liver sample,week4


title: Mcon3

source_name: Mcon_small intestine

value: wild type

value: without irradiation


title: Control diet5_liver sample_rep1

source_name: Control diet5,liver sample,week4

value: Rat fed control diet for 4 weeks


title: Mcon2


title: Control diet4_liver sample_rep1

source_name: Control diet4,liver sample,week4


title: Mcon1


title: Ffat2

source_name: Ffat_small intestine

value: total abdominal irradiation combined with high fat diet


title: Low protein diet1_liver sample_rep1

source_name: Low protein diet1,liver sample,week4


title: Ffat3


title: Control diet2_liver sample_rep1

source_name: Control diet2,liver sample,week4


title: Control diet3_liver sample_rep1

source_name: Control diet3,liver sample,week4


title: Ffat1


title: Germline Deplete Replicate 3

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description:
File_S2_v1.xlsx
File_S3_v1.xlsx

data_processing:
Reads were trimmed with  Trim Galore (v0.6.0) and cutadapt (v1.18).
Trimmed reads were mapped to the WBcel235/ce11 build of the C. elegans genome with STAR (v2.7.2a).
Mapped reads were indexed and sorted with samtools v1.7.
Gene quantification and deferential expression was performed using Ensembl release 97 gene annotations with the Rsubread (v1.28.1) and DESeq2 (v1.26.0) packages in Bioconductor.
Genome_build: WBcel235/ce11
Supplementary_files_format_and_content: scaled bigWig

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Cell lysate from young adult animals

growth_protocol: Experimental (DG4700 and DG4703) and control strains (CA1352 and CA1200) were grown on peptone-enriched nematode growth medium with NA22 as a food source. Embryos were isolated by alkaline hypochlorite treatment (20% bleach and 0.5 N NaOH), washed in M9 buffer and allowed to hatch overnight in the absence of food. For each of three biological replicates, 60,000 L1-stage larvae were cultured on two 150- by 15-mm petri dishes containing peptone-enriched medium with OP50.

extract_protocol:
Total RNA was isolated using TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and the RNeasy Micro Kit (QIAGEN, Valencia, CA).
Poly(A)+ RNA was selected from 1 μg of total RNA using the NEBNext Ultra Kit (New England Biolabs, Ipswitch, MA).

treatment_protocol: The worms were grown to the young adult stage and harvested by washing off the plates with M9 and then placed on fresh plates containing peptone-enriched medium and 2 mM auxin seeded with OP50. Plates were cultured in the dark at 20°C for 24 hours. The worms were then harvested and washed with M9 repeatedly to reduce the presence of E. coli.

value: young adult animals

value: 2mM auxin at 20oC for 24hrs

value: sacy-1(tn1880[aid::gfp::myc::sacy-1]) I; ieSi64[gld-1p::TIR1::mRuby::gld-1 3'utr + Cb unc-119(+)] II


title: Germline Deplete Replicate 1

description:
File_S2_v1.xlsx
File_S3_v1.xlsx


title: Germline Control Replicate 3

description:
File_S2_v1.xlsx
File_S3_v1.xlsx

value: ieSi64[gld-1p::TIR1::mRuby::gld-1 3'utr + Cb unc-119(+)] II; unc-119(ed3) III


title: Germline Control Replicate 2

description:
File_S2_v1.xlsx
File_S3_v1.xlsx


title: FTAI2

source_name: FTAI_small intestine

value: total abdominal irradiation


title: FTAI3


title: Control diet6_liver sample_rep1

source_name: Control diet6,liver sample,week4

value: male


title: Control diet1_liver sample_rep1

source_name: Control diet1,liver sample,week4


title: Germline Control Replicate 1

description:
File_S2_v1.xlsx
File_S3_v1.xlsx


title: Soma Deplete Replicate 3

description:
File_S2_v1.xlsx
File_S3_v1.xlsx

value: sacy-1(tn1880[aid::gfp::myc::sacy-1]) I; ieSi57[eft-3p::TIR1::mRuby::unc-54 3'utr + Cb unc-119(+)] II


title: FTAI1

value: Small intestine


title: Fcon3

source_name: Fcon_small intestine


title: Soma Deplete Replicate 2

description:
File_S2_v1.xlsx
File_S3_v1.xlsx


title: Fcon2


title: Fcon1


title: Grp78KO_3

status: Public on Jan 24 2020

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

data_processing:
Reads were quality trimmed using CLC Genomics Workbench Tool (v 11.0.1). Trim using quality scores: yes, limit=0.05, Trim ambiguous nucleotides: yes, maximum number of ambiguities =2.
Reads were mapped using CLC Genomics Workbench Tool (v. 11.0.1) allowing intergenic mapping. Parameters: min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=30, Count paired reads as two=no, Expression value= Total counts.
Normalization and differential gene expression analysis was performed using edgeR, Version 3.7. Genes of which the sum of the read counts of all samples was under 100 were filtered out.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each sample.

source_name: alveolar epithelial type II (AT2) cells

growth_protocol: Lungs were digested with dispase.

extract_protocol: Libraries for your project were prepared using the NEBNext Ultra RNA Library Preparation kit according to manufacturer’s protocol. Libraries were multiplexed and loaded in an equimolar concentration and sequenced on the Illumina HiSeq 4000 or equivalent with a configuration of 2x150bp.

treatment_protocol: AT2 were obtained by MACS sorting of CD45- and EPCAM+ cells.

value: Lung

value: Sftpc+/creERT2; Grp78f/f with Tmx

tag: days

value: 10 days following Tmx injection


title: Germline Deplete Replicate 2

description:
File_S2_v1.xlsx
File_S3_v1.xlsx


title: Soma Control Replicate 3

description:
File_S2_v1.xlsx
File_S3_v1.xlsx

value: ieSi57[eft-3p::TIR1::mRuby::unc-54 3'utr + Cb unc-119(+)] II; unc-119(ed3) III


title: Soma Control Replicate 1

description:
File_S2_v1.xlsx
File_S3_v1.xlsx


title: Grp78KO_1


title: Grp78KO_2


title: Control_3

value: Sftpc+/creERT2; Grp78f/f without Tmx


title: Control_2


title: Control_1


title: Long_RNA_fragments

city: Hong Kong

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
The 3' adapter in the raw reads was removed using cutadapt (cutadapt -a TGGAATTCTCGGGTGCCAAGG). We then removed low quality reads and deduplicated the reads with the same barcodes using fastq_quality_filter (-q 20 -p 90) and fastx_collapser (default parameter) from FASTX-Toolkit, respectively. After trimming the barcode sequences (4 random nucleotides from both ends), the trimmed reads were mapped to the reference containing 19 pri-miRNAs sequence using BWA.
Genome_build: n/a
Supplementary_files_format_and_content: Tab-delimited text files, containing the raw read counts.

molecule: other

organism: synthetic construct

source_name: synthetic

extract_protocol:
Illumina adapter sequences were incorporated to the libraries using PCR.
The DNA sequences encoding pri-miRNAs were amplified from human HCT116 genomic DNA using specific primers. Pri-miRNAs were synthesized by in vitro transcription (IVT),  visualized on 10% UREA-PAGE and gel-eluted followed by isopropanol precipitation. The NLS Microprocessor complex (composed of NLS-D3 fragment of DROSHA and DGCR8) or minimal Microprocessor complex (composed of D3 fragment of DROSHA and G4 dimer of DGCR8)  was co-expressed and purified in HEK293E cells. Purified Microprocessor complex was used in in vitro processing assay for pri-miRNAs. After visualized in 10% UREA-PAGE, the fragments from the reaction mixture which are longer than pre-miRNAs, 5p and 3p basal segments were sliced from the gel and cloned to construct a DNA library for next generation sequencing.

tag: barcode

value: GGAACT


title: Soma Deplete Replicate 1

description:
File_S2_v1.xlsx
File_S3_v1.xlsx


title: MCF-7/TxR [dataset 2]

city: Goyang-si

first: sung bin

last: park

state: Gyeonggi-do

address: 32, Dongguk-ro, Ilsandong-gu

department: Department of Life Science

country: South Korea

institute: Dongguk University-Seoul

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

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing:
Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1
Array probes that have Flag A in samples were filtered out. Selected gProcessedSignal value was transformed by logarithm and normalized by quantile method.

source_name: Mammary Gland; Breast

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: RNA was extracted and purified from MCF-7/TxR and CAP treated MCF-7/TxR using ZR Dyet DNA/RNA kit (Zymo research) according

tag: cell line

tag: cell type

value: breast cancer cell; epithelial

tag: gender source

value: female

value: paclitaxel (Tx)-resistant MCF-7 (MCF-7/TxR)


title: MCF-7/TxR [dataset 3]

extract_protocol: RNA was extracted and purified from MCF-7 and MCF-7/TxR using ZR Dyet DNA/RNA kit (Zymo research) according


title: Multiple Myeloma_Replicate42 (mRNA)

city: New Delhi

first: Ritu

last: Gupta

state: Delhi

address: Dr. B.R.A.IRCH, Ansari Nagar

department: Laboratory Oncology

country: India

institute: All India Institute of Medical Sciences, New Delhi

description:
Gene expression data
SM72

hyb_protocol: Samples with specific activity≥ 6pmolCy3/ µg cRNA were considered for hybridization. 600ng of Cy-3 labeled cRNA mixed with blocking agent, fragmentation buffer and hybridization buffer was applied to a microarray slide, (Agilent technologies, CA, USA), and incubated for 17 hours at 65°C in a hybridization oven.

scan_protocol: After hybridization microarrays were washed with Gene Expression Wash Buffer Kit and scanned using SureScan microarray scanner D (Agilent Technologies, CA, USA).

data_processing: Quantitative data values were obtained from the images using Feature Extraction software ver 11.5.1.1 (Agilent, CA ,USA) using default parameters.

source_name: Bone marrow

label_protocol: cDNA was transcribed to cRNA by the low input quick amp labelling kit (Agilent Technologies, CA, USA) using T7 RNA polymerase and NTP mix and labelled with Cyanine3 using Cy3-CTP.  The labeled cRNA was purified according to manufacturer’s protocol using RNAeasy extraction kit (Qiagen, Hilden Germany).

extract_protocol: Plasma cells were obtained from the bone marrow aspirates by magnetic bead separation using the human CD138 RosetteSep kit (Stem Cell Technologies, Vancouver, British Columbia, Canada.The cells were stored in TRIZOL at  −80°C until analysis. Total RNA was isolated from CD138+ sorted cells of myeloma patients using the miRVana RNA isolation kit according to manufactures’ instructions (Ambion, USA).

tag: disease state

value: Multiple Myeloma

value: Plasma Cells

tag: gender

value: Male


title: Multiple Myeloma_Replicate40 (mRNA)

description:
Gene expression data
SM52


title: MCF-7/TxR CAP 30s x 10 [dataset 2]

tag: phenotype

value: CAP treated 10 times for 30 seconds


title: MCF-7/TxR CAP 30s X 10  [dataset 1]

description:
biotin
Tx_RP.gProcessedSignal

extract_protocol: RNA was extracted and purified from MCF-7 and MCF-7/TxR and CAP treated MCF-7/TxR using ZR Dyet DNA/RNA kit (Zymo research) according


title: Multiple Myeloma_Replicate45 (mRNA)

description:
Gene expression data
SM351

tag: age


title: Multiple Myeloma_Replicate38 (mRNA)

description:
Gene expression data
SM133


title: MCF-7 [dataset 3]


title: Multiple Myeloma_Replicate43 (mRNA)

description:
Gene expression data
SM21

value: Female


title: Multiple Myeloma_Replicate41 (mRNA)

description:
Gene expression data
SM69


title: Multiple Myeloma_Replicate34 (mRNA)

description:
Gene expression data
SM343


title: Multiple Myeloma_Replicate44 (mRNA)

description:
Gene expression data
SM24


title: Multiple Myeloma_Replicate39 (mRNA)

description:
Gene expression data
SM19


title: Control_Replicate3 (mRNA)

description:
Gene expression data
HD Pooled3

value: Control

value: Mononuclear cells


title: Multiple Myeloma_Replicate32 (mRNA)

description:
Gene expression data
SM197


title: Multiple Myeloma_Replicate33 (mRNA)

description:
Gene expression data
SM98


title: Multiple Myeloma_Replicate37 (mRNA)

description:
Gene expression data
SM167


title: Control_Replicate2 (mRNA)

description:
Gene expression data
HD Pooled2


title: Multiple Myeloma_Replicate31 (mRNA)

description:
Gene expression data
SM224


title: Multiple Myeloma_Replicate36 (mRNA)

description:
Gene expression data
SM339


title: Multiple Myeloma_Replicate35 (mRNA)

description:
Gene expression data
SM94


title: MCF-7  [dataset 1]

description:
biotin
MCF_7.gProcessedSignal


title: Uterus-GD5.5-GEN-3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from Uterus-GD5.5-GEN

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNA was fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: Uterus-GD5.5-GEN Rep 3

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Rneasy (Qiagen) with DNaseI cleanup on the column

tag: agent

value: genistein

tag: organ

value: Uterus


title: Multiple Myeloma_Replicate29 (mRNA)

description:
Gene expression data
SM267


title: MCF-7/TxR  [dataset 1]

description:
biotin
Tx_R.gProcessedSignal


title: Multiple Myeloma_Replicate30 (mRNA)

description:
Gene expression data
SM188


title: Uterus-GD5.5-GEN-4

description: Gene expression from Uterus-GD5.5-GEN

source_name: Uterus-GD5.5-GEN Rep 4

tag: strain


title: Uterus-GD5.5-GEN-2

description: Gene expression from Uterus-GD5.5-GEN

source_name: Uterus-GD5.5-GEN Rep 2


title: Multiple Myeloma_Replicate28 (mRNA)

description:
Gene expression data
SM5


title: Multiple Myeloma_Replicate26 (mRNA)

description:
Gene expression data
SM321


title: Uterus-GD5.5-GEN-1

description: Gene expression from Uterus-GD5.5-GEN

source_name: Uterus-GD5.5-GEN Rep 1


title: Multiple Myeloma_Replicate23 (mRNA)

description:
Gene expression data
SM67


title: Uterus-GD4.5-GEN-2

description: Gene expression from Uterus-GD4.5-GEN

source_name: Uterus-GD4.5-GEN Rep 2


title: Multiple Myeloma_Replicate20 (mRNA)

description:
Gene expression data
SM7


title: Uterus-GD5.5-CON-4

description: Gene expression from Uterus-GD5.5-CON

source_name: Uterus-GD5.5-CON Rep 4

value: corn oil


title: Uterus-GD4.5-CON-3

description: Gene expression from Uterus-GD4.5-CON

source_name: Uterus-GD4.5-CON Rep 3


title: Multiple Myeloma_Replicate24 (mRNA)

description:
Gene expression data
SM170


title: Uterus-GD4.5-GEN-3

description: Gene expression from Uterus-GD4.5-GEN

source_name: Uterus-GD4.5-GEN Rep 3


title: Uterus-GD3.5-GEN-4

description: Gene expression from Uterus-GD3.5-GEN

source_name: Uterus-GD3.5-GEN Rep 4


title: Uterus-GD4.5-CON-4

description: Gene expression from Uterus-GD4.5-CON

source_name: Uterus-GD4.5-CON Rep 4


title: Multiple Myeloma_Replicate22 (mRNA)

description:
Gene expression data
SM34


title: Uterus-GD3.5-GEN-3

description: Gene expression from Uterus-GD3.5-GEN

source_name: Uterus-GD3.5-GEN Rep 3


title: Uterus-GD4.5-GEN-4

description: Gene expression from Uterus-GD4.5-GEN

source_name: Uterus-GD4.5-GEN Rep 4


title: Uterus-GD5.5-CON-1

description: Gene expression from Uterus-GD5.5-CON

source_name: Uterus-GD5.5-CON Rep 1


title: Multiple Myeloma_Replicate21 (mRNA)

description:
Gene expression data
SM91


title: Multiple Myeloma_Replicate17 (mRNA)

description:
Gene expression data
SM100


title: Multiple Myeloma_Replicate25 (mRNA)

description:
Gene expression data
SM126


title: Multiple Myeloma_Replicate19 (mRNA)

description:
Gene expression data
SM87


title: Uterus-GD4.5-CON-1

description: Gene expression from Uterus-GD4.5-CON

source_name: Uterus-GD4.5-CON Rep 1


title: Multiple Myeloma_Replicate15 (mRNA)

description:
Gene expression data
SM201


title: Uterus-GD4.5-GEN-1

description: Gene expression from Uterus-GD4.5-GEN

source_name: Uterus-GD4.5-GEN Rep 1


title: Multiple Myeloma_Replicate14 (mRNA)

description:
Gene expression data
SM330


title: Uterus-GD5.5-CON-2

description: Gene expression from Uterus-GD5.5-CON

source_name: Uterus-GD5.5-CON Rep 2


title: Uterus-GD3.5-GEN-1

description: Gene expression from Uterus-GD3.5-GEN

source_name: Uterus-GD3.5-GEN Rep 1


title: Uterus-GD4.5-CON-2

description: Gene expression from Uterus-GD4.5-CON

source_name: Uterus-GD4.5-CON Rep 2


title: Control_Replicate1 (mRNA)

description:
Gene expression data
HD Pooled1

source_name: Bone marrow


title: Multiple Myeloma_Replicate16 (mRNA)

description:
Gene expression data
SM15


title: Multiple Myeloma_Replicate13 (mRNA)

description:
Gene expression data
SM18


title: Multiple Myeloma_Replicate18 (mRNA)

description:
Gene expression data
SM62


title: Uterus-GD5.5-CON-3

description: Gene expression from Uterus-GD5.5-CON

source_name: Uterus-GD5.5-CON Rep 3


title: Uterus-GD1.5-GEN-3

description: Gene expression from Uterus-GD1.5-GEN

source_name: Uterus-GD1.5-GEN Rep 3


title: Multiple Myeloma_Replicate5 (mRNA)

description:
Gene expression data
SM10


title: Uterus-GD3.5-CON-1

description: Gene expression from Uterus-GD3.5-CON

source_name: Uterus-GD3.5-CON Rep 1


title: Uterus-GD3.5-CON-3

description: Gene expression from Uterus-GD3.5-CON

source_name: Uterus-GD3.5-CON Rep 3


title: Multiple Myeloma_Replicate4 (mRNA)

description:
Gene expression data
SM96


title: Multiple Myeloma_Replicate3 (mRNA)

description:
Gene expression data
SM64


title: Multiple Myeloma_Replicate8 (mRNA)

description:
Gene expression data
SM15


title: Multiple Myeloma_Replicate6 (mRNA)

description:
Gene expression data
SM226


title: Uterus-GD3.5-CON-2

description: Gene expression from Uterus-GD3.5-CON

source_name: Uterus-GD3.5-CON Rep 2


title: Uterus-GD1.5-GEN-2

description: Gene expression from Uterus-GD1.5-GEN

source_name: Uterus-GD1.5-GEN Rep 2


title: Donor 4 (condition 2)

city: San Francisco

first: David

middle: E.

last: Gordon

state: California

address: 1700 4th Street, Byers Hall 309

institute: UCSF

description:
CNOT1.4
subread.featureCounts.counts.txt

data_processing:
Alignment of the samples to hg38 reference assembly was performed using STAR 2.5.2a.
Reads were assigned to genes using "featureCounts" by Liao et al., Bioinformatics, 30(7):923-30, 2014. featureCounts is part of the Subread suite (http://subread.sourceforge.net/). Gene-level counts were arrived at using Ensembl gene annotation, in GTF format.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited file with counts.

source_name: CD4+ T-cells

growth_protocol: Primary CD4+ T-cells were harvested from healthy donor blood using a Fabian CD4+ positive selection kit.  Cells were stimulated using adherent anti-CD3 and suspension anti-CD28 antibodies for 72 hours.  Cells were electroporated with Cas9-RNPs complexed with non-targeting guide RNA, or guide RNA targeting CNOT1 or CNOT10.  Following electroporation cells were restimulated using Miltenyi T-cell stimulation beads and maintained in complete RPMI media with 20 U/mL IL-2 for one week.

extract_protocol:
mRNA was purified using an Rneasy Mini kit (Qiagen) with on-column DNAse digestion.
RNA-Seq libraries were prepared with ovation RNA-seq Universal (NuGEN).   cDNA was fragmented with the Covaris S-series System and barcoded libraries were sequenced on a HiSeq4000.

value: CNOT1 knockout


title: Multiple Myeloma_Replicate10 (mRNA)

description:
Gene expression data
SM237


title: Multiple Myeloma_Replicate11 (mRNA)

description:
Gene expression data
SM208


title: Multiple Myeloma_Replicate2 (mRNA)

description:
Gene expression data
SM47


title: Multiple Myeloma_Replicate12 (mRNA)

description:
Gene expression data
SM325


title: Uterus-GD1.5-CON-2

description: Gene expression from Uterus-GD1.5-CON

source_name: Uterus-GD1.5-CON Rep 2


title: Multiple Myeloma_Replicate9 (mRNA)

description:
Gene expression data
SM78


title: Donor 4 (condition 1)

description:
NT1.4
subread.featureCounts.counts.txt

value: Non-targeting (negative control)


title: Donor 3 (condition 3)

description:
CNOT10.3
subread.featureCounts.counts.txt

value: CNOT10 knockout


title: Multiple Myeloma_Replicate7 (mRNA)

description:
Gene expression data
SM48


title: Uterus-GD1.5-GEN-1

description: Gene expression from Uterus-GD1.5-GEN

source_name: Uterus-GD1.5-GEN Rep 1


title: PDA30364_tumor cells_72h_GDC-0623-3

city: Heidelberg

first: Michael

last: Volkmar

state: BW

address: Im Neuenheimer Feld 280

department: D200 Molecular Oncology of Gastrointestinal Tumors

country: Germany

institute: German Cancer Research Center (DKFZ)

description: Gene expression data from tumor cells

hyb_protocol: After fragmentation, 11ug of cRNA were hybridized for 16h to the Affymetrix mouse 430 2.0 Gene Chip® array (GPL1261).

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000.

data_processing: Raw data was exported as cell intensity (CEL) files and analyzed using Chipster (Kallio et al., 2011; BMC Genomics 12, 507, doi:19.1186/1471-2164-12-507). After quality control, samples were normalized by applying the Robust Multichip Averaging (RMA) normalization method.

source_name: PDA30364 cell line pellet, snap frozen, RNA isolated from treated cells

label_protocol: Labeling was performed by the DKFZ's Genomics and Proteomics Core Facility using 200ng total RNA (RIN=>8.0) with  a GeneChip™ 3’IVT Plus Reagent Kit (Affymetrix).

growth_protocol: Murine tumor cell lines were passaged at least four times after thawing and grown as a monolayer with a maximal confluency of 70-80% and a viability of >90%. Cells were detached using 0.25% trypsin-EDTA solutions.

extract_protocol: RNA extraction was performed using the RNeasy Mini kit (Qiagen) according to the manufacturer’s instructions with on-column DNase I digestion. Amount of isolated RNA was measured using a Nanodrop spectrophotometer, while RNA quality was determined using a Agilent 2100 Bioanalyzer.

treatment_protocol: Cells were seeded at a densitiy of 450.000 cells in 22 ml medium. The next day, GDC-0623 was added five times concentrated to reach a final concentration of 100 nM. DMSO at the same cocentration served as control.

tag: tissue

value: Tumor cells

tag: treatment groups

tag: treatment period


title: PDA30364_tumor cells_24h_GDC-0623-3

description: Gene expression data from tumor cells


title: Multiple Myeloma_Replicate1 (mRNA)

description:
Gene expression data
SM77


title: PDA30364_tumor cells_24h_GDC-0623-2

description: Gene expression data from tumor cells


title: Uterus-GD1.5-CON-1

description: Gene expression from Uterus-GD1.5-CON

source_name: Uterus-GD1.5-CON Rep 1


title: Donor 3 (condition 1)

description:
NT1.3
subread.featureCounts.counts.txt


title: Donor 2 (condition 3)

description:
CNOT10.2
subread.featureCounts.counts.txt


title: PDA30364_tumor cells_72h_GDC-0623-2

description: Gene expression data from tumor cells


title: Donor 1 (condition 2)

description:
CNOT1.1
subread.featureCounts.counts.txt


title: PDA30364_tumor cells_24h_GDC-0623-1

description: Gene expression data from tumor cells


title: PDA30364_tumor cells_72h_GDC-0623-1

description: Gene expression data from tumor cells


title: Donor 2 (condition 1)

description:
NT1.2
subread.featureCounts.counts.txt


title: Donor 1 (condition 1)

description:
NT1.1
subread.featureCounts.counts.txt


title: Donor 1 (condition 3)

description:
CNOT10.1
subread.featureCounts.counts.txt


title: PDA30364_tumor cells_24h_DMSO-3

description: Gene expression data from tumor cells

value: 24h DMSO


title: N-DVP-2

city: Baltimore

first: Yiouli

last: Ktena

state: MD

address: 1800 Orleans Street

department: SOM Onc Pediatric Oncology

institute: JHU; School of Medicine

data_processing:
polyA RNA extraction with Qiagen rneasy kit per manufacturer protocol
Stranded mRNA libraries were sequenced on an Illumina HiSeq4000 instrument using 47bp paired-end dual indexed reads
Reads were aligned to GRCh38 using STAR version 2.7.2b
We generated summarized experiment objects using the gtf file Homo_sapiens.GRCh38.97.gtf and the following command from the Bioconductor package ‘GenomicAlignments’: summarizeOverlaps
Differential expression analysis and statistical testing was performed using DESeq2 software
Counts generated using built in DEseq2 functions normalized counts()
Genome_build: GRCh38.97
Supplementary_files_format_and_content: counts

source_name: vascular progenitor -induced pluripotent stem cell-derived (diabetic) (naïve)

growth_protocol: hiPSC and hESC were grown in either. conventional (E8) and LIF-3i naïve reversion media

extract_protocol: RNA-Seqstudies,strand specific mRNA libraries were generated using the NEBNext Ultra II Directional RNA library prep Kit for Illumina (New England BioLabs #E7760), mRNA was isolated using Poly(A) mRNA magnetic isolation module (New England BioLabs#E7490). Preparation of libraries followed the manufacturer’s protocol (Version 2.2 05/19). Input was 1microgram.

tag: passage

value: E1CA2 -N-DVP


title: N-DVP-1

value: E1CA1 -N-DVP


title: PDA30364_tumor cells_72h_DMSO-1

description: Gene expression data from tumor cells

value: 72h DMSO


title: Uterus-GD1.5-GEN-4

description: Gene expression from Uterus-GD1.5-GEN

source_name: Uterus-GD1.5-GEN Rep 4

value: female


title: N-VP (hiPSC-2)

source_name: vascular progenitor -induced pluripotent stem cell-derived (naïve)


title: N-VP (hiPSC-1)

value: E5C3 -N-VP


title: PDA30364_tumor cells_72h_DMSO-3

description: Gene expression data from tumor cells


title: PDA30364_tumor cells_72h_DMSO-2

description: Gene expression data from tumor cells


title: PDA30364_tumor cells_24h_DMSO-2

description: Gene expression data from tumor cells


title: N-VP (hESC-2)

source_name: vascular progenitor -embryonic stem cell-derived (naive)

value: RUES01 -N-VP


title: N-VP (hESC-1)

value: H9 -N-VP


title: N-VP (hiPSC-3)

value: C2 -N-VP


title: MC38_tumor cells_72h_GDC-0623-1

description: Gene expression data from tumor cells

source_name: MC38 cell line pellet, snap frozen, RNA isolated from treated cells


title: Multiple Myeloma_Replicate27 (mRNA)

description:
Gene expression data
SM119

source_name: Bone marrow

value: Multiple Myeloma

value: Plasma Cells

value: Male


title: MC38_tumor cells_72h_GDC-0623-3

description: Gene expression data from tumor cells


title: MC38_tumor cells_24h_GDC-0623-3

description: Gene expression data from tumor cells


title: MC38_tumor cells_72h_GDC-0623-2

description: Gene expression data from tumor cells


title: MC38_tumor cells_24h_GDC-0623-1

description: Gene expression data from tumor cells


title: PDA30364_tumor cells_24h_DMSO-1

description: Gene expression data from tumor cells


title: MC38_tumor cells_72h_DMSO-2

description: Gene expression data from tumor cells


title: DVP-1

source_name: vascular progenitor -induced pluripotent stem cell-derived (diabetic) (primed, conventional)

value: E1CA1 -DVP


title: N-VP (hESC-3)

value: RUES02 -N-VP


title: VP (hiPSC-3)

source_name: vascular progenitor -induced pluripotent stem cell-derived (primed, conventional)

value: C2 -VP


title: MC38_tumor cells_72h_DMSO-1

description: Gene expression data from tumor cells


title: MC38_tumor cells_24h_GDC-0623-2

description: Gene expression data from tumor cells


title: MC38_tumor cells_24h_DMSO-3

description: Gene expression data from tumor cells


title: MC38_tumor cells_24h_DMSO-1

description: Gene expression data from tumor cells


title: MC38_tumor cells_72h_DMSO-3

description: Gene expression data from tumor cells


title: VP (hESC-3)

source_name: vascular progenitor -embryonic stem cell-derived (primed, conventional)

value: RUES02 -VP


title: VP (hiPSC-1)

value: E5C3 -VP


title: VP (hESC-2)

value: RUES01 -VP


title: VP (hiPSC-2)

source_name: vascular progenitor -induced pluripotent stem cell-derived (primed, conventional


title: VP (hESC-1)

value: H9 -VP


title: MC38_tumor cells_24h_DMSO-2

description: Gene expression data from tumor cells

value: Tumor cells

value: 24h DMSO


title: Uterus-GD1.5-CON-3

description: Gene expression from Uterus-GD1.5-CON

source_name: Uterus-GD1.5-CON Rep 3

value: corn oil

value: female

value: Uterus


title: N-DhiPSC-2

source_name: induced pluripotent stem cell (diabetic) (naïve)

value: E1CA2 N-DhiPSC


title: N-hiPSC-2

source_name: induced pluripotent stem cell (naïve)

value: (P27 MEF+1LIF5i+6L3i)

value: C1.2 N-hiPSC


title: N-hiPSC-3

value: (P9 MEF+1LIF5i+7L3i)

value: C2 N-hiPSC


title: B16-OVA_tumor cells_24h_GDC-0623-3

description: Gene expression data from tumor cells

source_name: B16-OVA cell line pellet, snap frozen


title: B16-OVA_tumor cells_72h_GDC-0623-3

description: Gene expression data from tumor cells


title: B16-OVA_tumor cells_72h_DMSO-3

description: Gene expression data from tumor cells

value: 72h DMSO


title: B16-OVA_tumor cells_72h_GDC-0623-1

description: Gene expression data from tumor cells


title: N-hiPSC-1

value: E5C3 N-hiPSC


title: N-hESC-2

source_name: embryonic stem cell (naïve)

value: RUES01 N-hESC


title: B16-OVA_tumor cells_24h_GDC-0623-2

description: Gene expression data from tumor cells


title: N-hESC-1

value: H9 N-hESC


title: B16-OVA_tumor cells_24h_DMSO-2

description: Gene expression data from tumor cells


title: B16-OVA_tumor cells_72h_DMSO-2

description: Gene expression data from tumor cells


title: DVP-2

value: E1CA2 -DVP


title: B16-OVA_tumor cells_72h_GDC-0623-2

description: Gene expression data from tumor cells


title: B16-OVA_tumor cells_24h_DMSO-1

description: Gene expression data from tumor cells


title: B16-OVA_tumor cells_24h_GDC-0623-1

description: Gene expression data from tumor cells


title: N-hESC-3

value: RUES02 N-hESC


title: DhiPSC-1

source_name: induced pluripotent stem cell (diabetic) (primed, conventional)

value: E1CA1 DhiPSC


title: hiPSC-1

source_name: induced pluripotent stem cell (primed, conventional)

value: E5C3 hiPSC


title: hiPSC-2

value: C1.2 hiPSC


title: hiPSC-3

value: C2 hiPSC


title: B16-OVA_tumor cells_24h_DMSO-3

description: Gene expression data from tumor cells

value: Tumor cells

value: 24h DMSO


title: PDA30364_tumor_9947_MEKi+CD40-4

description: Gene expression data from tumor biopsy

source_name: PDA30364 whole tumor, snap frozen, RNA isolated from tumor

growth_protocol: Murine tumor cell lines were passaged at least four times after thawing and grown as a monolayer with a maximal confluency of 70-80%. Cells were detached using 0.25% trypsin-EDTA solutions, centrifuged and washed once with cell culture medium. 0.5 x 10^6 PDA30364 tumor cells were injected in PBS/Matrigel (1:1, Corning) subcutaneously into the flank of six to twelve weeks old C57BL/6-Ly5.1 mice. Tumor growth was measured twice a week with a caliper. The tumor volume was calculated by multiplying length by width by height.

extract_protocol: Tumor material was homogenized in RLT buffer (Qiagen) supplemented with beta-mercaptoethanol with 2.8 mm steel beads (Precellys) using a tissue homogenizer (TissueLyzer sample disrupter, Qiagen) at 30 Hz, 30 sec for 3 times. Subsequent RNA extraction was performed using the RNeasy Mini kit (Qiagen) according to the manufacturer’s instructions with on-column DNase I digestion. Amount of isolated RNA was measured using a Nanodrop spectrophotometer, while RNA quality was determined using a Agilent 2100 Bioanalyzer.

treatment_protocol: Mice were treated daily with 30 mg/kg GDC-0623 or vehicle solution (MCT) for approximately two weeks. Anti-CD40 and control Ab were administered intraperitoneally on treatment days 3, 5, 7 as well as 1 day prior to biomarker analyses. Four-Five mice per treatment group were sacrificed at the end of the MEK inhibitor treatment and subjected to whole transcriptome analyses (day 26 after tumor inoculation).

value: Whole tumor

value: MEKi+CD40 mIgG1


title: PDA30364_tumor_9943_MEKi+CD40-2

description: Gene expression data from tumor biopsy


title: PDA30364_tumor_9942_MEKi+CD40-1

description: Gene expression data from tumor biopsy


title: hESC-3

source_name: embryonic stem cell (primed, conventional)

value: RUES02 hESC


title: B16-OVA_tumor cells_72h_DMSO-1

description: Gene expression data from tumor cells


title: DhiPSC-2

value: E1CA2 DhiPSC


title: PDA30364_tumor_9945_MEKi+CD40-3

description: Gene expression data from tumor biopsy


title: hESC-2

value: RUES01. hESC


title: PDA30364_tumor_10029_MEKi-1

description: Gene expression data from tumor biopsy

value: MEKi+control IgG


title: hESC-1

value: H9 hESC


title: g1_ifn_tun_B

city: Evanston

first: Behram

middle: Sarosh

last: Radmanesh

state: IL

address: 633 Clark St

institute: Northwestern University

description:
g1_ifn_tun_B
cell barcode suffix in processed data file:
-2_6
10X chromium single-cell RNA-seq

data_processing:
cellranger v2.2 count
cellranger v2.2 aggr
Seurat v3.0
Monocle v2.1
PAGA v1.4.4
Genome_build: hg38
Supplementary_files_format_and_content: Seurat Raw Count Matrix

source_name: human kidney organoid cells

growth_protocol: iPSCs (1016SevA parent cells from Harvard Stem Cell Institute) were differentiated into kidney organoids following the previously published Freedman et al. protocol. Briefly, genome-edited APOL1-G0 and APOL1-G1 iPSCs were dissociated with 1:3 Accutase and plated onto 24-well plates pre-coated with 0.5% GelTrex in mTeSR1 supplemented with 10uM Y-27632 ROCK Inhibitor. 24 hours later another layer of GelTrex at 1.5% was added in mTeSR1 media. At the end of the fourth day the medium was replaced with Advanced RPMI supplemented with 12 uM CHIR-99021. Approximately 60 hours later, the medium was changed to Advanced RPMI with B27 (Gibco). Organoids were cultured in this medium until collection at day 25.

extract_protocol:
Kidney organoids were dissociated into single-cell suspensions using TrypLe reagent at 37 degrees C, with gentle agitation x 15 minutes
10X Genomics 5 prime chemistry per manufacturer's protocol

treatment_protocol: Day 24 APOL1-G0 and APOL1-G1 kidney organoids were treated with vehicle, 25ng/mL IFN gamma, or 25ng/mL IFN gamma + 5uM tunicamycin

value: iPSC-derived kidney organoid cells

tag: iPSc passage number


title: g1_ifn_tun_A

description:
g1_ifn_tun_A
cell barcode suffix in processed data file:
-1_6
10X chromium single-cell RNA-seq


title: PDA30364_tumor_10018_CD40-4

description: Gene expression data from tumor biopsy

value: Vehicle+CD40 mIgG1


title: PDA30364_tumor_10042_MEKi-2

description: Gene expression data from tumor biopsy


title: PDA30364_tumor_10014_CD40-3

description: Gene expression data from tumor biopsy


title: Donor 4 (condition 3)

description:
CNOT10.4
subread.featureCounts.counts.txt

source_name: CD4+ T-cells

tag: condition

value: CNOT10 knockout


title: PDA30364_tumor_9971_CD40-2

description: Gene expression data from tumor biopsy


title: PDA30364_tumor_9969_CD40-1

description: Gene expression data from tumor biopsy


title: g1_ifn_B

description:
g1_ifn_B
cell barcode suffix in processed data file:
-2_4
10X chromium single-cell RNA-seq


title: g0_ifn_tun_B

description:
g0_ifn_tun_B
cell barcode suffix in processed data file:
-2_5
10X chromium single-cell RNA-seq


title: g1_ifn_A

description:
g1_ifn_A
cell barcode suffix in processed data file:
-1_4
10X chromium single-cell RNA-seq


title: PDA30364_tumor_10043_MEKi-3

description: Gene expression data from tumor biopsy


title: Donor 3 (condition 2)

description:
CNOT1.3
subread.featureCounts.counts.txt

value: CNOT1 knockout


title: g0_ifn_B

description:
g0_ifn_B
cell barcode suffix in processed data file:
-2_3
10X chromium single-cell RNA-seq


title: g0_ifn_tun_A

description:
g0_ifn_tun_A
cell barcode suffix in processed data file:
-1_5
10X chromium single-cell RNA-seq


title: g0_ifn_A

description:
g0_ifn_A
cell barcode suffix in processed data file:
-1_3
10X chromium single-cell RNA-seq


title: PDA30364_tumor_10016_Ctrl-4

description: Gene expression data from tumor biopsy

value: Vehicle+control IgG


title: PDA30364_tumor_9966_Ctrl-1

description: Gene expression data from tumor biopsy


title: PDA30364_tumor_9967_Ctrl-2

description: Gene expression data from tumor biopsy


title: g1_ctrl_D

description:
g1_ctrl_D
cell barcode suffix in processed data file:
-4_2
10X chromium single-cell RNA-seq


title: g1_ctrl_A

description:
g1_ctrl_A
cell barcode suffix in processed data file:
-1_2
10X chromium single-cell RNA-seq


title: g1_ctrl_C

description:
g1_ctrl_C
cell barcode suffix in processed data file:
-3_2
10X chromium single-cell RNA-seq


title: g0_ctrl_D

description:
g0_ctrl_D
cell barcode suffix in processed data file:
-4_1
10X chromium single-cell RNA-seq


title: g0_ctrl_C

description:
g0_ctrl_C
cell barcode suffix in processed data file:
-3_1
10X chromium single-cell RNA-seq


title: MC38 tumor_7686_MEKi+CD40-3

description: Gene expression data from tumor biopsy

source_name: MC38 whole tumor, snap frozen, RNA isolated from tumor

growth_protocol: Murine tumor cell lines were passaged at least four times after thawing and grown as a monolayer with a maximal confluency of 70-80%. Cells were detached using 0.25% trypsin-EDTA solutions, centrifuged and washed once with cell culture medium. 0.5 x 10^6 MC38 tumor cells were injected in PBS/Matrigel (1:1, Corning) subcutaneously into the flank of six to twelve weeks old C57BL/6-Ly5.1 mice. Tumor growth was measured twice a week with a caliper. The tumor volume was calculated by multiplying length by width by height.

treatment_protocol: Mice were treated daily with 30 mg/kg GDC-0623 or vehicle solution (MCT) for approximately two weeks. Anti-CD40 and control Ab were administered intraperitoneally on treatment days 3, 5, 7 as well as 1 day prior to biomarker analyses. Four-Five mice per treatment group were sacrificed at the end of the MEK inhibitor treatment and subjected to whole transcriptome analyses (day 22 after tumor inoculation).


title: MC38 tumor_7688_MEKi+CD40-4

description: Gene expression data from tumor biopsy


title: PDA30364_tumor_9968_Ctrl-3

description: Gene expression data from tumor biopsy


title: Donor 2 (condition 2)

description:
CNOT1.2
subread.featureCounts.counts.txt


title: g0_ctrl_B

description:
g0_ctrl_B
cell barcode suffix in processed data file:
-2_1
10X chromium single-cell RNA-seq


title: g0_ctrl_A

description:
g0_ctrl_A
cell barcode suffix in processed data file:
-1_1
10X chromium single-cell RNA-seq


title: MC38 tumor_7547_CD40-4

description: Gene expression data from tumor biopsy


title: g1_ctrl_B

description:
g1_ctrl_B
cell barcode suffix in processed data file:
-2_2
10X chromium single-cell RNA-seq


title: MC38 tumor_7810_MEKi-4

description: Gene expression data from tumor biopsy


title: MC38 tumor_7809_MEKi-3

description: Gene expression data from tumor biopsy


title: MC38 tumor_7512_MEKi-1

description: Gene expression data from tumor biopsy


title: MC38 tumor_7542_CD40-1

description: Gene expression data from tumor biopsy


title: MC38 tumor_7544_CD40-2

description: Gene expression data from tumor biopsy


title: MC38 tumor_7685_MEKi+CD40-2

description: Gene expression data from tumor biopsy


title: MC38 tumor_7684_MEKi+CD40-1

description: Gene expression data from tumor biopsy


title: MC38 tumor_7545_CD40-3

description: Gene expression data from tumor biopsy


title: MC38 tumor_7696_Ctrl-1

description: Gene expression data from tumor biopsy


title: MC38 tumor_7862_Ctrl-5

description: Gene expression data from tumor biopsy


title: control-4(sham)

city: Beijing

first: Chuan

last: Qin

address: No.95,yong an road.

department: Department of Urology

institute: Beijing Friendship Hospital, Capital Medical University

description: tRNA-Derived Small RNAs

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Raw data files in FASTQ format were generated from the Illumina sequencer. To examine the sequencing quality, the quality score plot of each sample was plotted.
Trimmed reads in FASTA format are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software
The abundance of tRF & tiRNA are evaluated using their sequencing counts and is normalized as counts per million of total aligned reads (CPM).
The tRFs & tiRNAs  differentially expressed are screened based on the count value with R package edgeR
Genome_build: rn5
Supplementary_files_format_and_content: fasta files contain sequence counts

source_name: spinal cord

extract_protocol:
At 1day post-surgery, rats in all groups were euthanized with an overdose of 2% 2% Sodium pentobarbital solution, and a 1-cm long segment of spinal cord, including the injury epicenter, was quickly dissected and collected without transcardial perfusion in advance and was then fresh frozen in liquid nitrogen.sequencing libraries are size-selected for the RNA biotypes to be sequenced using an automated gel cutter.  Sequencing library was determined by Agilent 2100 Bioanalyzer using the Agilent DNA 1000 chip kit (Agilent, part # 5067-1504).
The libraries were denatured and diluted to a loading volume of 1.3ml and loading concentration of 1.8pM. Diluted libraries were loaded onto reagent cartridge and forwarded to sequencing run on Illumina NextSeq 500 system using NextSeq 500/550 V2 kit (#FC-404-2005, Illumina), according to the manufacturer’s instructions

value: Sprague-Dawley

value: spinal cord

tag: weight and gender


title: control-3(sham)

description: tRNA-Derived Small RNAs


title: control-2(sham)

description: tRNA-Derived Small RNAs


title: MC38 tumor_7513_MEKi-2

description: Gene expression data from tumor biopsy


title: MC38 tumor_7860_Ctrl-3

description: Gene expression data from tumor biopsy


title: control-1(sham)

description: tRNA-Derived Small RNAs


title: test-2(SCI)

description: tRNA-Derived Small RNAs


title: test-4(SCI)

description: tRNA-Derived Small RNAs


title: IgG control

city: Nankoku

first: Keisuke

last: Taniuchi

address: Kohasu

institute: Kochi Medical School

description: IgG

data_processing:
IlluminaCASAVA ver.1.8.1 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to SeqNovaTMCS (DNANexus).
We approximate the density of each RNA by the RPKM measure (Reads per kilobase per Million of mapped reads) (Mortazavi A et al, Nat. Methods 5, 621-628, 2008). We normalized RPKM estimates using adjusting the mean and standard deviation of each sample’s log2(RPKM) values.
Genome_build: hg19
Supplementary_files_format_and_content: EXCEL files include RPKM values for each Sample

source_name: pancreatic cancer

extract_protocol:
Fibronectin-stimulated S2-013 cells were lysed in NP2 buffer containing 50 mM Tris (pH 7.4), 150 mM NaCl, 1 mM MgCl2, 0.5% NP-40 and protease and RNAse inhibitors.
RIP protocol: Cell lysates were immunoprecipitated with anti-KHSRP antibody or with normal rabbit IgG and Dynabeads Protein G (Dynal, Oslo, Norway) for 2 h at 4ºC. Beads were pelleted on a magnetic rack (Dynal). The immunoprecipitation products were treated with proteinase K, extracted with phenol-chloroform, and precipitated with ethanol. Purified RNAs were subsequently treated with DNase I (Promega, Madison, WI) and extracted using the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. Finaly, RNAs were fragmented and purified using an Illumina TruSeq RNA Sample Prep Kit (San Diego, CA) according to the manufacturer’s instructions.
The KHSRP-associated RNAs were identified using a next generation sequencer, Illumina HiSeq 2000 (Hokkaido System Science, Sapporo, Japan).

tag: cell line

value: pancreatic cancer cell line

tag: antibody

value: normal rabbit IgG


title: test-1(SCI)

description: tRNA-Derived Small RNAs


title: MC38 tumor_7861_Ctrl-4

description: Gene expression data from tumor biopsy


title: RIP-Sequencing data from KHSRP RIP

description: Immunoprecipitated messenger RNA

tag: cell type

value: Anti-KHSRP (Abcam catalog number ab140648)


title: ZNF587-Tinput_rep3

city: Lausanne

first: Delphine

last: Grun

address: route Cantonale

country: Switzerland

institute: EPFL

data_processing:
Alignement for ChIP-seqs were done with bowtie2
Filtering of bam files was done using blacklist fom UCSC and greylist derived from TI using GreyListChIP Bioconductor package
Peak calling for ChIP-seqs were done using MACS
Genome_build: hg19
Supplementary_files_format_and_content: A bed file containing the output of the peak called by MACS is provided.

source_name: H1 human embryonic stem cells (WA01)

growth_protocol: H1 cells were maintained in mTesRI (StemCell Technologies) on hES-qualified Matrigel (BD Biosciences). For transduction, hES were detached using TryPLE Express (Invitrogen), split at 40,000 cells/cm2 and maintained at least 12 hrs with ROCK inhibitor (Y-27632)

extract_protocol:
Libraries were prepared according to Illumina's instructions
Chromatin was prepared from 3.10E+7 fixed H1 cells sonicated with Covaris Focus ultra-sonicator and KZFP-DNA complexes were isolated by immunoprecipitation with anti-HA antibody

treatment_protocol: Cells were transduced with lentivectors at a MOI of 100 and collected for ChIP.

value: H1 human embryonic stem cells (WA01)

tag: culture

value: mTESRI, matrigel


title: MC38 tumor_7700_Ctrl-2

description: Gene expression data from tumor biopsy

value: Whole tumor


title: kap1_chip

source_name: H1 human embryonic stem cells (WA01), p75

growth_protocol: Turelli et al., 2014

extract_protocol: Turelli et al., 2014

treatment_protocol: Turelli et al., 2014

tag: chip ab

value: polyclonal, home made


title: ZNF587-Tinput_rep2


title: total_input

value: H1 human embryonic stem cells (WA01), p75

value: none (input)


title: ZNF587-HA_ChIP_rep3


title: cca_stat_2

city: Hamburg

first: Andreas

last: Czech

address: Martin-Luther-King-Platz 6

institute: University of Hamburg

data_processing:
Read trimming with fastx-toolkit (0.0.13.2; quality threshold: 20)
Adapter cutting with cutadapt (1.2.1; minimal overlap: 1 nt)
Mapping against 10 nt upstream of CCA, sequences from genomic tRNA database (Escherichia coli K12)
Genome_build: tRNAscan-SE 1.3 Analysis of Escherichia coli K12 (http://gtrnadb2009.ucsc.edu/Esch_coli_K12/)
Supplementary_files_format_and_content: txt-file containing mapping sequences and raw reads for different tRNA sub-populations (CCA, CC, C, -, others)

organism: Escherichia coli

source_name: E. coli CA244 cca K.O.

growth_protocol: Cells were grown in LB-medium at 37°C and 250rpm

extract_protocol:
Total RNA was extracted by Hot Phenol or TriZol extraction, tRNA was PAGE-purified
3'-adapter ligation, alkaline fragmentation, 5'-adapter ligation, reverse transcription, PCR
3'-terminus RNAseq

tag: growth phase

value: stationary phase

tag: genotype

value: cca KO


title: cca_stat_1


title: In_Situ_HiC_in DMSO treated CD34+

city: Houston

first: Xiaotian

last: Zhang

state: TX

address: 6431 Fannin St

department: Biochemistry and Molecular Biology

institute: The University of Texas Health Science Center at Houston

data_processing:
Data are process by HiC-Pro to align to genome and generate ICED normalized contact matrix
Contact matrix is visualzied by converting the contact matrix to .HiC for visulization with hicpro2juicebox.sh
Genome_build: hg19
Supplementary_files_format_and_content: HiC

source_name: hematopietic progenitor and stem cells

growth_protocol: Cord Blood derived CD34+ HSPCs are cutlrued in SFEM II medium supplemented with 100ng/mL human TOP, SCF and FLT3L for 7 days, CD34+ CD38- cells are isolated with Miltenyl CD38 CD34 isolation kit

extract_protocol:
Cells were fixed by 1% formaldehyde, then isolated nucleus were cutted by MboI for 4hours, then isolated nuclear were end-filled with bio-dATP. Liagation was then performed overnight. Biotin enrichment was then performed with strepvadin beads. After washes, beads were tagmented by Tn5 enzyme for 10min at 55 degree.
Libraries are amplified off the beads by PCR for 5 cycles, additional PCR is then applified with libraries under BioRad CF96 qPCR machine.

treatment_protocol: DMSO is added to medium to 1:1000 dilution, EPZ6438 is added to medium to 0.5μM HSPCs are cultured for 7 days

tag: treatment

value: DMSO


title: In_Situ_HiC_ in EPZ6438 treated CD34+

value: EZH2 inhibitor EPZ6438


title: PET32_B

city: Wien

first: Klaus

last: Kratochwill

address: Lazarettgasse 14

country: Austria

institute: Medical University of Vienna

description: Gene expression data from cells isolated from peritoneal effluent following a single 4 h peritoneal dialysis dwell without added AlaGln in a patient who had previously suffered from peritonitis.

hyb_protocol: Affymetrix GeneChip® Human Gene 1.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0007).

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1.

data_processing: Samples were normalized via the Comprehensive R based Microarray Analysis web frontend CARMAweb (https://carmaweb.genome.tugraz.at/carma) using the Robust Multiarray Analysis (RMA) algorithm. The algorithm consists of: background correction (subtract the minimal signal intensity), normalization (quantile-quantile normalization) and summarizing the probe set values.

source_name: cells from peritoneal dialysis effluent, previous peritonitis, without AlaGln

label_protocol: 100ng of total RNA were amplified and labeled using the Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix GeneChip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA).

growth_protocol: No cell culturing was performed. The used cell material was freshly isolated from peritoneal dialysis effluents.

extract_protocol: Total RNA was isolated from peritoneal cells (4 h PET) using RNeasy columns (Qiagen), using 350 µl of RLT buffer (Qiagen) and following the manufacturer's instructions without modifications.

treatment_protocol: No in-vitro treatment was performed. The differential treatment of the isolated cells resulted from treatment with different peritoneal dialysis solutions in the course of the clinical study.

value: cells isolated from peritoneal effluent of peritoneal dialysis patient

value: treatment B - without AlaGln

value: yes

tag: patient


title: PET27_B


title: PET36_A

description: Gene expression data from cells isolated from peritoneal effluent following a single 4 h peritoneal dialysis dwell with added AlaGln in a patient who had previously suffered from peritonitis.

source_name: cells from peritoneal dialysis effluent, previous peritonitis, with AlaGln

value: treatment A - with AlaGln


title: PET11_A

description: Gene expression data from cells isolated from peritoneal effluent following a single 4 h peritoneal dialysis dwell with added AlaGln in a patient who had no peritonitis before.

source_name: cells from peritoneal dialysis effluent, no previous peritonitis, with AlaGln

value: no


title: PET6_B

description: Gene expression data from cells isolated from peritoneal effluent following a single 4 h peritoneal dialysis dwell without added AlaGln in a patient who had no peritonitis before.

source_name: cells from peritoneal dialysis effluent, no previous peritonitis, without AlaGln


title: ZNF587-Tinput_rep1


title: MC38 tumor_7811_MEKi-5

description: Gene expression data from tumor biopsy

value: MEKi+control IgG


title: test-3(SCI)

description: tRNA-Derived Small RNAs

tag: strain

value: Sprague-Dawley

value: spinal cord


title: cca_exp_2

value: exponential phase


title: cca_exp_1


title: PET31_A


title: ZNF587-HA_ChIP_rep1

tag: tissue

value: H1 human embryonic stem cells (WA01)

value: mTESRI, matrigel


title: ZNF417-Tinput_rep2


title: wt, stat_3

source_name: E. coli CA244 wt

value: wt


title: rnt_exp_1

source_name: E. coli CA244 rnt K.O.

value: rnt KO


title: rnt_exp_2


title: wt, stat_2

value: stationary phase


title: wt, stat_1


title: wt_exp_3


title: ZNF417-Tinput_rep1


title: ZNF587-HA_ChIP_rep2


title: ZNF417-HA_ChIP_rep2


title: ZNF417-HA_ChIP_rep3


title: wt_exp_2


title: ZNF417-HA_ChIP_rep1


title: ZNF417-Tinput_rep3


title: Tinput_H1_shZNF587_B

data_processing:
Alignement for ChIP-seqs were done with bowtie2
Filtering of bam files were done using blacklist fom UCSC and greylist derived from TI using GreyListChIP Bioconductor package
Peak calling for ChIP-seqs were done using EPIC
Genome_build: hg19
Supplementary_files_format_and_content: A bed file containing the output of the peak called by EPIC is provided.

extract_protocol:
Libraries were prepared according to Illumina's instructions
Chromatin was prepared from fixed H1 cells sonicated with Covaris Focus ultra-sonicator and histone-DNA complexes were isolated by immunoprecipitation with anti-histones antibodies

treatment_protocol: Cells were transduced with lentivectors delivering the sh at a MOI of 4 and selected with puromycin (0.5 µg/ml) for 3 days before being amplified for ChIP.


title: wt_exp_1


title: ChIP_H3K4me1_H1_shZNF587_B


title: Tinput_H1_shE


title: Tinput_H1_shZNF587_A


title: Tinput_H1_shLuc_B


title: ChIP_H3K4me1_H1_shLuc_B


title: JH21_WT_retina_scRNAseq_R1

first: Jacob

middle: S

last: Heng

address: 725 North Wolfe Street

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: Dissociated retinal cells

data_processing:
scRNA-seq data were pre-processed using the Cell Ranger pipeline (v2.2.0; 10x Genomics) with default settings.  Cell barcodes were determined using the DropletUtils R/Bioconductor package. The normalized gene x cell matrix was used as input for the Monocle R/Bioconductor package (Trapnell et al., 2014).  Log-normalized expression estimates (with a pseudocount of 1) were used as input for a modified dpFeature analysis.  For preliminary cell clustering, PCA was performed on the high variance genes, and appropriate components were visualized in two dimensions using UMAP.  Initial clusters were identified from the 2-D embedding using k-means clustering.  Cell type identity was determined by cross-referencing clusters with expression of multiple known cell type markers.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: adult dissociated WT retina

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
Dissociated single cells were processed through the GemCode Single Cell Platform using the GemCode Gel Bead, Chip, and Library Kits (10X Genomics, Pleasanton) as per the manufacturer’s protocol.  In brief, single cells were sorted into 0.4% BSA–DPBS.  Approximately 14,000 single retinal cells were added to a channel.  The cells were then partitioned into Gel Beads in Emulsion in the 10x Genomics Chromium Controller, where cell lysis occurred
Cell lysis was followed by barcoded oligo-DT priming and reverse transcription of poly-adenylated RNA, amplification, shearing and 5′ adaptor and sample index attachment.

value: WT

tag: disease grade

tag: age

value: 16 weeks

tag: Sex

value: Female

value: retina

tag: treatment protocol


title: ChIP_H3K4me1_H1_shZNF587_A


title: Wild-type Control Rep3

city: Philadelphia

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Fastq files were align to the mm9 reference genome using STAR and default parameters
Ensmebl v67 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method
Genome_build: mm9
Supplementary_files_format_and_content: Voom transformed abundance measurements

source_name: Lung

extract_protocol: Lung were harvested from E12.5 wild-type littermate and ShhCre-Dnmt1KO mice.

tag: genotype/variation

value: Wild-type


title: ChIP_H3K9me3_H1_shZNF587_B


title: Wild-type Control Rep2


title: ChIP_H3K4me1_H1_shE


title: Wild-type Control Rep1


title: JH22_AireKO_retina_scRNAseq_R1

description: Dissociated retinal cells

source_name: adult dissociated AireKO retina

value: AireKO


title: Tinput_H1_shLuc_A


title: ShhCre-Dnmt1KO Rep3


title: ShhCre-Dnmt1KO Rep1


title: ChIP_H3K9me3_H1_shZNF587_A


title: ChIP_H3K4me1_H1_shLuc_A


title: ChIP_H3K9me3_H1_shLuc_B


title: P12 retina Crx KO

city: Suita

first: Takahisa

last: Furukawa

state: Osaka

address: 6-2-4 Furuedai

department: Developmental Biology

institute: Osaka Bioscience Institute

description: Gene expression in the Crx KO retina at P12

hyb_protocol: The labeled cDNA samples were hybridized using Gene Expression Hybridization Kit to the SurePrint G3 Mouse Gene Expression 8x60K microarray (Agilent Technology).

scan_protocol: Hybridized arrays were scanned using an Agilent DNA Microarray Scanner (G2565CA).

data_processing: Microarray analysis was performed by Takara Bio. The data analyses were performed using Feature Extraction software (Agilent Technology).

source_name: P12 retina Crx KO

label_protocol: The isolated total RNA was amplified and labeled with Cy3 using a Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies).

extract_protocol: Total RNA was purified using QIAzol reagent (Invitrogen).

treatment_protocol: Mouse retinas at P12 were dissected using fine forceps.

value: Crx KO

tag: developmental stage


title: P12 retina Otx2 KI

description: Gene expression in the Otx2 KI retina at P12

source_name: P12 retina Otx2 KI

value: Otx2 KI


title: ChIP_H3K9me3_H1_shE


title: Mm_retina_Input mRNA

first: Dwight

middle: Edward

last: Stambolian

address: 422 Curie Blvd.

department: Opthalmalogy

institute: University of Pennsylvania

data_processing:
The 10X pipeline used was Cell Ranger 2.0.0.
Seurat software was used to normalize gene counts and process the raw data
Genome_build: mm8
Supplementary_files_format_and_content: txt file (gene x cells)

source_name: Retina (spanning 11 cell types)

extract_protocol:
Ten-week old wild type C57BL/6J male mouse was purchased from Jackson Laboratory (Bar Harbor, ME, USA). The mouse was sacrificed with cervical dislocation under anesthesia, and an eyeball was immediately removed and placed in cold phosphate buffered saline (PBS). The mouse retina was carefully removed under a dissecting microscope, and the retina tissue was dissociated straightaway using the Papain dissociation system (Worthington, Lakewood, NJ, USA) following the manufacturer's instructions. Briefly, the mouse retina was incubated at 37°C for 30 min in Earle's Balanced Salt Solution (EBSS) with DNase followed by tissue trituration with a 10 ml pipette. Cell pellet was collected after centrifugation at 300g for 5 minutes, and then re-suspended in DNase dilute albumin-inhibitor solution.The cell suspension was carefully layered on top of the albumin-inhibitor solution, and then centrifuged at 70g for 6 minute. Similar procedure was followed for post-morten human eye tissue   Next, the cell pellet was washed and re-suspended in 1 : 1DMEM/F12 + 10% FBS. All centrifugation steps were performed at room temperature. The final cell suspension was filtered with 40 μm cell strainer (Falon, Corning, NY, USA) to remove large clump and debris. All experimental procedures approved by University of Pennsylvania Animal Care and Use Committee.
To assess cell viability, cells were stained with 0.4% trypan blue (Mediatech, Inc., Manassas, VA, USA) and counted using a hemocytometer. Retinal Horizontal Cells (RHCs) were identified by means of Lhx1+ and Prox1+ expression. sc-RNA seq was carried out on the viable cells using Chromium 10x Genomics as per the manufacturer’s recommendations.

value: mixed sample (non-demultiplexed)

value: post natal week 10

value: wild type

tag: gender

value: male


title: N-DhiPSC-1

source_name: induced pluripotent stem cell (diabetic) (naïve)

tag: cell line

tag: passage

value: (P17 MEF+1LIF5i+4L3i)

value: E1CA1 N-DhiPSC


title: D day6 rep 3

city: Aurora

first: Yu

last: Han

address: 12700 E. 19th Ave Mail Stop-B139

institute: University of Colorado

description:
HTSeq_gene_count.txt
FeatureCounts_annotation.txt
FeatureCounts_gene_counts.txt
all_samples_TPM.txt
DESeq2_gene_Dday6_Rday1.txt

data_processing:
The first ten bases of all reads were trimmed from each separate fastq file in a single-end fashion with trimmomatic (v0.32)
Trimmed fastq files were mapped in a paired-end fashion with tophat2 (v2.0.6, bowtie2 v2.0.2) with the parameters --b2-fast -p 12 -r 24 --mate-std-dev 105, as well as including the mm10 genome GTF file. Resultant BAM files were indexed with samtools (v0.1.18)
Mapped reads were counted using HTSeq (version 0.6.1) with the options {-f -r -s -m intersection-strict)
Differential expression analysis was performed pairwise between conditions with the R package DESeq2 (v1.16.1). All gene-level counts for all samples were loaded into a dds object, then analyzed. Pairwise comparisons were then extracted.
To count read for TPM calculation, mapped reads were counted using FeatureCounts within the R package Rsubread (v1.24.2, R v3.3.0) to generate FeatureCounts_gene_counts file with the option GTF.featureType = “exon”, GTP.attrType = “gene_id”, useMetaFeatures = TRUE, allowMultiOverlap = FALSE, largestOverlap =FALSE, strandSpecifc = 2, isPairedEnd = TRUE, requireBothEndsMapped = TRUE, checkFragLength = TRUE, minFragLength = 50, maxFragLength = 60000, countChimericFragments = FALSE, autosort=TRUE).
Genome_build: mm10 (fasta and gtf files were downloaded from NCBI)
Supplementary_files_format_and_content: 1) HTSeq_gene_count.txt is a tab-delimited text file containing the counts for all samples from HTSeq for DESeq2.  2) All_samples_TPM.txt is a tab-delimited text file containing transcripts per million (TPM) values for all genes and all samples.  3) DESeq2 files are tab-delimited text files containing the differential expression output from DESeq2.                     4) FeatureCounts_annotations.txt is a tab-delimited text file containing the annotation information extracted by featureCounts. This includes a portion of the gene GTF file input, including gene name, chromosomal positions of features (in this case exons), strand, and total gene length (used to calculate TPM). 5) FeatureCounts_gene_counts.txt is a tab-delimited text file containing counts for all files extracted from FeatureCounts. Counts are used for TPM calculation.

source_name: HC11 mouse epithelial cells

growth_protocol: HC11 cells were grown and maintained in proliferation (P) medium (RPMI supplemented with 10% (v/v) fetal bovine serum (FBS), 1% (v/v) penicillin/streptomycin (pen/strep), 10 ng/mL EGF and 5 μg/mL insulin).

extract_protocol:
Cells were lysed and RNA extracted following instructions of the Rneasy Mini Kit (QIAGEN, Catalog No. 74106)
Libraries were generated from RNA samples according to the Bioo NextFlex Dir RNA kit

treatment_protocol: To induce cell differentiation, 4 x 105 cells were plated in a 35-mm dish (or 1 x 106 cells in a 10-cm dish) in proliferation medium. Cells reached confluency after 3 days. Cells were maintained in resting (R) medium containing RPMI, 2% FBS (v/v), 1% pen/strep (v/v), 5 μg/mL insulin for one additional day, then treated with differentiation (D) medium containing 2% FBS, 1% pen/strep, 5 μg/mL insulin, 5 μg/mL prolactin, and 1 μM hydrocortisone for up to 6 days. Differentiation medium was changed every 2 days.

value: Cells cultured in differentiation media for 6 days


title: P12 retina  WT

description: Gene expression in the wild-type retina at P12

source_name: P12 retina  WT

value: wild-type


title: ShhCre-Dnmt1KO Rep2


title: D day6 rep 2


title: ChIP_H3K27ac_H1_shZNF587_A

source_name: H1 human embryonic stem cells (WA01)

value: H1 human embryonic stem cells (WA01)

tag: culture

value: mTESRI, matrigel


title: D day6 rep 1


title: D day1 rep 3

description:
HTSeq_gene_count.txt
FeatureCounts_annotation.txt
FeatureCounts_gene_counts.txt
all_samples_TPM.txt
DESeq2_gene_Dday1_Rday1.txt

value: Cells cultured in differentiation media for 1 day


title: ChIP_H3K27ac_H1_shLuc_B


title: D day1 rep 2


title: ChIP_H3K9me3_H1_shLuc_A


title: D day1 rep 1


title: ChIP_H3K27ac_H1_shLuc_A


title: R day1 rep 2

description:
HTSeq_gene_count.txt
FeatureCounts_annotation.txt
FeatureCounts_gene_counts.txt
all_samples_TPM.txt
DESeq2_gene_Dday1_Rday1.txt
DESeq2_gene_Dday6_Rday1.txt

value: Cells cultured in resting media for 1 day


title: ChIP_H3K27ac_H1_shE


title: ChIP_H3K27ac_H1_shZNF587_B


title: 4h MDI

city: Seoul

first: Jae-woo

last: Kim

address: 50 Yonsei-ro, Seodaemun-gu

department: Biochem and Mol Bio

institute: Yonsei University College of Medicine

description: 4 h after MDI treatment

data_processing:
Tophat v2.0.13
FPKM
cuffdiff v2.2.0

source_name: 3T3-L1 cell

growth_protocol: cell culture

extract_protocol:
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: differentiation medium MDI (IBMX, Dexa, insulin) or conditioned medium (MDI media from 48 h differentiating 3T3-L1 cells)

tag: cell type

value: adipocyte


title: Pro-CM

description: Preconfluent, CM treatment


title: mR5 rep2 resequencing [SAM3760523]

city: South San Francisco

first: Anneleen

last: Daemen

state: CA

address: 1 DNA Way

institute: GENENTECH, INC.

data_processing:
RNA sequencing (RNAseq) data were analyzed with HTSeqGenie [Pau and Reeder, R package, 2012] in BioConductor [Huber et al, Nat Methods 2015] as follows: reads were trimmed to 75 bp, filtered for quality and rRNA/adapter contamination, and aligned to the reference genome hg19
Gene expression was quantified as Reads Per Kilobase of exon model per Million mapped reads normalized by size factor (nRPKM), defined as number of reads aligning to a gene in a sample / (total number of uniquely mapped reads for that sample x gene length x size factor).
Genome_build: hg19
Supplementary_files_format_and_content: Tables of read counts for all genes and replicates

source_name: LNCaP MK2206 acquired resistant clone, MK2206 treated

growth_protocol: Cells (parental or resistant clones) were plated in duplicate in complete RPMI medium

extract_protocol:
Total RNA was extracted from duplicates using Qiagen RNeasy kit as per manufacturer’s protocol and quality control of RNA samples was done to determine their quantity and quality.
Approximately 500 ng of total RNA was used as an input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). In addition, RNA input of 100 ng was used for library preparation using TruSeq Stranded Total RNA Library Prep Kit (Illumina)
The libraries were multiplexed and then sequenced on Illumina HiSeq2500 (Illumina) to generate 50M of paired-end 75 base pair reads

treatment_protocol: The following day, cells were treated with DMSO, 5uM GDC-0068 or 5uM MK2206 for 14 hours

tag: cell line background

value: LNCaP

tag: clone

value: MK2206 resistant clone 5

tag: concentration

tag: cell line source age

tag: cell line source gender

value: Male


title: gR1 rep2 resequencing [SAM3760517]

source_name: LNCaP GDC-0068 acquired resistant clone, GDC-0068 treated

value: GDC-0068 resistant clone 1

tag: treatment


title: gR3 rep2 [SAM3760519]

value: GDC-0068 resistant clone 3


title: mR7 rep2 resequencing [SAM3760525]

value: MK2206 resistant clone 7


title: mR5 rep2 [SAM3760523]


title: mR7 rep2 [SAM3760525]


title: 24h CM

description: 24 h after CM treatment


title: R day1 rep 3


title: 24h MDI

description: 24 h after MDI treatment


title: gR1 rep2 [SAM3760517]


title: gR3 rep2 resequencing [SAM3760519]


title: Par_MK2206 rep2 [SAM3760514]

source_name: LNCaP parental cells, MK2206 treated

value: Parental


title: 0h Control

description: Before differentiation, confuent


title: Par_MK2206 rep2 resequencing [SAM3760514]


title: sh587_9_S7_b2

description: sh587 (#5+6), 16.11.15

data_processing:
hisat2 -k 5 --seed 42 -p 6 -x
htseq-count (with options -f bam -s reverse -t exon -i gene_id) for genes and bedtools multicov (with option -split -q 0) for eres
Genome_build: hg19
Supplementary_files_format_and_content: The .txt files contain read counts on genes or TEs

growth_protocol: mTESRI

extract_protocol:
high pure RNA kit (Roche)
As recommended by illumina (TruSeq stranded mRNA sample preparation kit)

treatment_protocol: puromycin

tag: tissue

value: Human pluripotent stem cells

value: mTESRI


title: R day1 rep 1


title: Par_DMSO rep2 resequencing [SAM3760512]

source_name: LNCaP parental cells, untreated

value: DMSO


title: Par_GDC0068 rep2 resequencing [SAM3760513]

source_name: LNCaP parental cells, GDC-0068 treated


title: Par_GDC0068 rep2 [SAM3760513]


title: Pro-MDI

description: Preconfluent, MDI treatment


title: sh587_7_S5_b2

description: sh587 (#6), 16.11.15


title: Par_DMSO rep2 [SAM3760512]


title: mR7 rep1 [SAM3760501]


title: mR7 rep1 resequencing [SAM3760501]


title: sh587_16_S6_b1

description: sh587 (#6), 16.10.07


title: shE_2_S4_b1

description: shE, 16.10.07


title: shE_12_S3_b2

description: shE, 16.10.15


title: mR5 rep1 resequencing [SAM3760499]


title: mR5 rep1 [SAM3760499]


title: gR3 rep1 resequencing [SAM3760495]


title: gR3 rep1 [SAM3760495]


title: d4_SH587_P47_S8

data_processing:
hisat2 -k 5 --seed 42 -p 6 -x
featureCounts -p -T 4 -t exon -g gene_id -Q 10 -a
Genome_build: hg19
Supplementary_files_format_and_content: The .txt files contain read counts on genes or TEs

source_name: KD iN

extract_protocol:
RNeasy kit (Qiagen)
As recommended by illumina (TruSeq stranded mRNA sample preparation kit)

treatment_protocol: w puromycin, w/wo doxycyclin

value: pluripotent stem cells-induced neurons

tag: passages


title: d4_SHE_P47_S7

source_name: WT iN


title: sh587_10_S1_b2

description: sh587 (#5+6), 16.11.15


title: gR1 rep1 [SAM3760493]


title: d4_SH587_P45_S6


title: shE_11_S2_b2

description: shE, 16.10.15


title: d4_SHE_P45_S1


title: Par_MK2206 rep1 [SAM3760490]


title: gR1 rep1 resequencing [SAM3760493]


title: d0_SHE_P47_S3

source_name: WT hiPS

value: induced pluripotent stem cells


title: d0_SHE_P45_S1


title: Par_GDC0068 rep1 resequencing [SAM3760489]


title: d0_SH587_P45_S2

source_name: KD hiPS


title: Par_GDC0068 rep1 [SAM3760489]


title: d0_SH587_P47_S4


title: Par_DMSO rep1 resequencing [SAM3760488]


title: Par_MK2206 rep1 resequencing [SAM3760490]


title: Par_DMSO rep1  [SAM3760488]


title: iN_Ctrl_2

description: iNGN dCas9KRAB E.2 (Ctrl)

data_processing:
hisat2 -k 5 --rna-strandness RF --seed 42 -p 7 -x
featureCounts -p -s 2 -T 4 -t exon -g gene_id -Q 10 -a
Genome_build: hg19
Supplementary_files_format_and_content: The .txt.gz files contain read counts on genes or TEs

source_name: iN

extract_protocol:
nucleospin RNA XS  (Macherey-Nagel)
As recommended by illumina (TruSeq stranded mRNA sample preparation kit)

value: mTESRI + doxycyclin


title: iN_Ctrl_1

description: iNGN dCas9KRAB E.1 (Ctrl)


title: 253J_negative_rep2

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

description:
Benny_processed_253J.xlsx
sample name:
Benny12

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome using STAR  v2.4.2a (using options outFilterMismatchNmax 2 and alignEndsType EndToEnd)
Counting proceeded over genes annotated in Ensembl release 83, using htseq-count
Normalization was performed using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file includes the normalized counts

source_name: Bladder-Human transitional cell carcinoma

growth_protocol: Cells were growth in MEM completed with 10 % FCS, antibiotics, puruvate, glutamine and vitamines.

extract_protocol: Inhouse poly A based RNA seq

treatment_protocol: Generation of two sub-cell populations originated from a single cell line, differing by their capacity to uptake 2.4 µm beads, was done by the FACS sorter. Each FACS sorting procedure separated cells that did not uptake any particles (“negative”, FL2Low) from the rest of the cells (“positive”, uptake of at least one bead, FLhigh). Therefore, after the first sorting, in each cycle we obtained four different sub-sets of cells: positive-positive; positive-negative, negative-positive, negative-negative. Only the positive-positive and negative-negative were kept for further sorting. In each cycle the sorting enrichment, Δ, was defined as  ∆≡J_+^+-J_+^- where J_+^+ was the percent of positive cells obtained in a sorting procedure on the positive-positive population of the previous cycle, and J_+^- was the percent of positive cells obtained in a sorting procedure on the negative-negative population of the previous cycle. An exception to this definition is the first cycle where both of the percent values of positive cells were calculated relative to the same origin population of cells, yielding J_+^+-J_+^-=0. Each sorting included the flowing steps. Cells were cultured for five generations and incubated with 2.4 µm beads for 24 h. Cells were then washed thoroughly with PBS and detached with trypsin, centrifuged, counted and diluted to 1.0x10^7 cells/ml in PBS. Using a BD-FACSAria-III cell sorter, cells were analyzed and sorted based on the fluorescence intensity distribution (FL-2). The levels of fluorescence intensity indicated accurately on the number of internalized particles, allowing for a highly sensitive uptake-based sorting.

tag: parental cell line

tag: cell population

value: 253J negative

tag: aggressiveness sorting

value: 5 times


title: 253J_negative_rep3

description:
Benny_processed_253J.xlsx
sample name:
Benny24

value: Bladder-Human transitional cell carcinoma


title: iN_KRAB_2

description: iNGN dCas9KRAB G4.2 (KRAB)


title: 253J_negative_rep1

description:
Benny_processed_253J.xlsx
sample name:
Benny11


title: iN_KRAB_1

description: iNGN dCas9KRAB G4.1 (KRAB)


title: 253J_positive_rep3

description:
Benny_processed_253J.xlsx
sample name:
Benny23

value: 253J positive


title: iPS_Ctrl_2

description: hIPS dCas9KRAB E.2 (Ctrl)

source_name: hIPS


title: iPS_Ctrl_1

description: hIPS dCas9KRAB E.1 (Ctrl)


title: 253J_positive_rep2

description:
Benny_processed_253J.xlsx
sample name:
Benny9


title: 253J_positive_rep1

description:
Benny_processed_253J.xlsx
sample name:
Benny8


title: iPS_KRAB_1

description: hIPS dCas9KRAB G4.1 (KRAB)


title: iPS_KRAB_2

description: hIPS dCas9KRAB G4.2 (KRAB)


title: A375_negative_rep2

description:
Benny_processed_A375.xlsx
sample name:
Benny21

source_name: Human Skin melanoma

value: A375 negative

value: Human Skin melanoma


title: A375_negative_rep1

description:
Benny_processed_A375.xlsx
sample name:
Benny5


title: A375_positive_rep3

description:
Benny_processed_A375.xlsx
sample name:
Benny19

value: A375 positive


title: RNA-seq in DMSO treated CD34+ duplicate #2

data_processing:
RNA-seq reads is aligned to genome by STAR and bigwig file is generated by RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: hematopietic progenitor and stem cells

extract_protocol:
RNA was extracted by Qiagen Allprep DNA/RNA micro kit.
RNA-seq libraries is build by NEB NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®


title: RNA-seq in 0.5uM EPZ6438 treated CD34+ duplicate #1

value: EZH2 inhibitor EPZ6438


title: A375_positive_rep2

description:
Benny_processed_A375.xlsx
sample name:
Benny3


title: AML-7, primitive

first: Shanshan

last: Pei

state: CO

data_processing:
Raw reads generated from the Illumina HiSeq2500 sequencer were demultiplexed using bcl2fastq version 2.19.0.
Quality filtering and adapter removal are performed using Trimmomatic-0.36 with the following parameters: "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35".
Processed/cleaned reads were then mapped to the Homo sapiens reference sequence (GRCh38, hg38) with STAR-2.6.0c given the following parameters: "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
The subread-1.6.1 package (featureCounts) was used to derive gene counts given the following parameters: “-s 2 -t exon -g gene_name”.
Differential expression analysis and data normalization was performed using DESeq2-1.16.1 with an adjusted p-value threshold of 0.05 within an R-3.4.1 environment. A batch factor was given to the differential expression model in order to control for batch differences.
Genome_build: GRCh38, hg38
Supplementary_files_format_and_content: raw counts produced by deSeq2 analysis provided in txt file

source_name: AML Patient L

growth_protocol: Freshly thawed and sorted, no growth involved

extract_protocol:
QIAGEN RNeasy Plus Kit
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols.
Briefly, mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA). Single end reads of 100nt were generated for each sample on the Illumina HiSeq2500 platform.

treatment_protocol: Freshly thawed and sorted, no treatment involved

value: Primary human AML patient specimen

tag: group

value: primitive

tag: sub-fraction

value: ROSlow enriched LSCs


title: H3K27me3 ChIP-seq in EPZ6438 treated CD34+

data_processing:
ChIP-seq is aligned to genome with BWA-mem to generate the BAM file
Bigwig file is generated with bedtools genomecov and converted to bigwig by bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
cells were fixed with 1% formaldehyde and sonicated with Covaris E220. Sonicated chromatin were then incubated with antibody against H3K27me3(Cell Signaling, #9733), H3K4me3(Cell Signaling, #9571) overnight. Protein A/G beads (ThermoFisher) were added to the sonicated chromatin for 2 hours. After washes with low-salt, high-salt and LiCl wash buffer. Following washes, beads were tagmented by Illumina tagmentation enzyme mix for 10 mins at 37 °C. After the tagmentation reaction stopped and the wash of beads, pull-downed DNA was de-crosslinked with Proteinase K (Zymo Research) at 55 °C for 3 hours. Pull-downed DNA was extracted by DNA clean and concentration kit (Zymo Research).
PCR amplification was directly performed, and libraries were cleaned by home made SeraMag beads and sequenced with Illumia NextSeq Platform.

tag: antibody


title: H3K4me3 ChIP-seq in EPZ6438 treated CD34+


title: A375_positive_rep1

description:
Benny_processed_A375.xlsx
sample name:
Benny2


title: AML-6, primitive

source_name: AML Patient K


title: AML-5, primitive

source_name: AML Patient J


title: H3K27me3 ChIP-seq in DMSO treated CD34+


title: AML-4, primitive

source_name: AML Patient I


title: AML-3, primitive

source_name: AML Patient H


title: RNA-seq in DMSO treated CD34+ duplicate #1


title: 4h CM

description: 4 h after CM treatment

source_name: 3T3-L1 cell

value: adipocyte


title: H3K4me3 ChIP-seq in DMSO treated CD34+


title: AML-4, monocytic

source_name: AML Patient D

value: monocytic


title: AML-1, primitive

source_name: AML Patient F


title: AML-5, monocytic

source_name: AML Patient E