title: mBL_26_hybridized to U133 plus 2.0 array


title: WR_2008_313d2_A006_1

status: Public on Mar 09 2021

type: SRA

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

country: USA

institute: US Dept. Agriculture

description: Grown in loess over glacial outwash, and the soil series was a Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls). The surface horizon contained approximately 110 g sand, 580 g silt, and 310 g clay kg-1. Total nitrogen in the 0-15 and 15-60 cm depths were approximately 5.1 and 10.2 mg N ha-1, respectively. Total C in the 0-15 and 15-60 cm depths were approximately 44.6 and 78.5 mg C ha-1, respectively. Additional information about soil at the site is available in Clay et al. (1994) and Clay et al. (1995). N-rate application of 236 kg/ha (based on SDSU soil test recommendations for a yield goal of 13,000 kg/ha) was applied to all plots, and supplemental water was added as needed based on the checkbook method of irrigation management (Werner 1993) to limit water stress by overhead sprayers. Irrigation was applied in four applications in 2007 and 2008, totaling approximately 10 cm each year.

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then the forward reads were mapped to the Zea Mays Enseble19 refernce genome using the tophat2 SE program in the iPlant (now CyVerse) dicovery environment with default perameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated usung the cuffdiff2 program in the iPlant (now CyVerse) dicovery environment with default perameters.
Genome_build: esnemble 19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

molecule: total RNA

organism: Zea mays

source_name: Mature leaf tip

extract_protocol:
leaf tips were cut from the plants and placed in 50 ml plastic tubes. Tubes were filled with liquid N2 and moved to storage at -80C prior to extraction. Tissues were ground in liquid N2 and RNA was extracted using a modified pine tree extraction protocol or were extracted using the trizol extraction procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: planted on May 1, 2007 or May 7, 2008 at a seeding rate of approximately 32,000 seeds ha−1, with row spacing of 76 cm. Plants were either left weed free as a controls or were grown with weeds. To determine weed effects that persist after weed growth during the CWFP, some plots had weeds removed at V4. For 2007 weedy and weed removed (WR) plots, endemic velvetleaf populations consisted of between 34-60 weeds m-1 row, whereas the 2008 weedy and WR plots, canola was drilled 10 cm from the maize row at 7 kg ha−1 at maize planting. Control plots were kept weed free with a pretreatment of Dual II Magnum at 1.5 pts/ac - May 3, 2007 and May 9, 2008 and Roundup WeatherMax at 32 oz/acre - June 18, 2007 and June 14. 2008. For weed removal at V4, WR plots were also treated with Roundup WeatherMax at 32 oz/acre.  Weedy plots were not treated with Roundup prior to harvest. A randomized complete block design was used with four replications.

tag: strain

value: commercially available 97-d maize hybrid that had glyphosate-resistance and maize rootworm/maize borer stacked traits

tag: tissue

value: pooled mature leaf tips from at least 4 individual plants

tag: age

tag: treament

value: weeds removed at V4 collected at V8

tag: collection date

tag: temperature at tme of collection

tag: collection time


title: WR_2008_404d2_A007_1

growth_protocol: Grown in loess over glacial outwash, and the soil series was a Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls). The surface horizon contained approximately 110 g sand, 580 g silt, and 310 g clay kg-1. Total nitrogen in the 0-15 and 15-60 cm depths were approximately 5.1 and 10.2 mg N ha-1, respectively. Total C in the 0-15 and 15-60 cm depths were approximately 44.6 and 78.5 mg C ha-1, respectively. Additional information about soil at the site is available in Clay et al. (1994) and Clay et al. (1995). N-rate application of 236 kg/ha (based on SDSU soil test recommendations for a yield goal of 13,000 kg/ha) was applied to all plots, and supplemental water was added as needed based on the checkbook method of irrigation management (Werner 1993) to limit water stress by overhead sprayers. Irrigation was applied in four applications in 2007 and 2008, totaling approximately 10 cm each year.


title: Weedy_2008_107d_A002_1

value: weedy through V8


title: control_2007_C1HN_Red_2_CGATGT_L001

value: control (weed free)


title: control_2008_209d_yellow12_CTTGTA_L003


title: mBL_25_hybridized to U133 plus 2.0 array

type: RNA

city: Omaha

first: Javeed

last: Iqbal

state: NE

address: 601 S 42nd St

institute: UNMC

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Affymetrix Genotyping console software. Log2 intensities were generated from genotyping console were exported for further processing using the DNAcopy package for R. For gene expression data profiled by Affymetrix U133 plus 2.0 array, the raw signal intensities were imported into BRB-ArrayTools (v 4.5.0)  and normalized by MAS 5.0 with default settings.

label: biotin

organism: Homo sapiens

source_name: tumor biopsy

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA and total RNA was extracted from cryopreserved lymphoma tissue using the Qiagen AllPrep DNA/RNA kit. DNA and RNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: tumor type

value: lymphoma

tag: age group

value: Pediatric


title: mBL_22_hybridized to U133 plus 2.0 array


title: mBL_24_hybridized to U133 plus 2.0 array


title: mBL_23_hybridized to U133 plus 2.0 array


title: control_2007_306_Red_5_ACAGTG_L001


title: Weedy_2007_304_Green_12_CTTGTA_L004


title: mBL_2_hybridized to U133 plus 2.0 array

value: Adult


title: mBL_20_hybridized to U133 plus 2.0 array


title: mBL_18_hybridized to U133 plus 2.0 array


title: mBL_19_hybridized to U133 plus 2.0 array


title: mBL_15_hybridized to U133 plus 2.0 array


title: mBL_13_hybridized to U133 plus 2.0 array


title: mBL_17_hybridized to U133 plus 2.0 array


title: mBL_12_hybridized to U133 plus 2.0 array


title: Weedy_2007_401_Yellow_7_CAGATC_L003


title: mBL_16_hybridized to U133 plus 2.0 array


title: control_2007_501_Green_4_TGACCA_L004


title: Weedy_2007_804_Red_6_GCCAAT_L001


title: Δnmr Nitrogen Starvation Biological Replicate 3

city: Ithaca

first: Lori

middle: B

last: Huberman

state: NY

address: 236 Tower Rd.

department: Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science

institute: Cornell University

data_processing:
Illumina Casava1.8 software used for base calling
Sequence reads were trimmed for adaptor sequence and aligned to the predicted transcripts from the N. crassa OR74A genome (v12) with HiSat2 v2.1.0 with the parameters --max-intronlen 5000 --dta-cufflinks
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Cufflinks v2.2.1 with the parameters --library-type fr-unstranded -u -b -G --compatible-hits-norm --max-bundle-frags=10000000
FPKMs in the FPKM_Metafile.txt were generated by running all samples through cuffmerge v2.2.1; then cuffquant v2.2.1 with the parameters --library-type fr-unstranded --max-bundle-frags=10000000; then cuffnorm v2.2.1 with the parameters --library-type fr-unstranded.
Genome_build: Neurospora crassa OR74A genome v12
Supplementary_files_format_and_content: tab-deliminated text files include FPKM values for each sample

organism: Neurospora crassa

source_name: Neurospora crassa mycelia

growth_protocol: N. crassa conidia were inoculated into 3ml of Vogel's minimal media + 2% sucrose and incubated at 25C in constant light with constant shaking at 200rpm for 24h

extract_protocol:
Mycelia were filtered using Whatman paper #1 and flash frozen using liquid nitrogen. RNA was isolated by bead beating in Trizol reagent and then cleaned up using the Qiagen RNeasy kit.
RNA were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mycelia were washed in media lacking a carbon source (for mannose or carbon starvation) or media lacking a nitrogen source (for all others) and then transferred to 3ml of Vogel's minimal media with thie indicated carbon or nitrogen source and incubated at 25C in constant light with constant shaking at 200rpm for 4h prior to harvesting for RNAseq.

tag: genotype

value: {delta}nmr

tag: media

value: Vogel's minimal medium with 2% Sucrose and lacking a nitrogen source


title: WR_2007_702_White_4_TGACCA_L002


title: Δnmr Nitrogen Starvation Biological Replicate 2


title: Δnmr Nitrogen Starvation Biological Replicate 1


title: WR_2007_505_Yellow_2_CGATGT_L003


title: WR_2007_408_White_5_ACAGTG_L002


title: Δnmr Vogel's Minimal Medium Biological Replicate 2

value: Vogel's minimal medium with 2% Sucrose and 25mM NH4NO3


title: Δnmr Vogel's Minimal Medium Biological Replicate 3


title: Δnmr Vogel's Minimal Medium Biological Replicate 1


title: Δnit-4 Nitrogen Starvation Biological Replicate 3


title: New-7-4

city: Xi’an, Shaanxi

first: Feng

last: Chen

address: Xi’an Jiaotong University, Xianning West Road, Xi’an, Shaanxi, P. R. China

country: China

institute: Xi’an Jiaotong University,

data_processing:
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome and then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: hg38
Supplementary_files_format_and_content: fpkm.txt includes FPKM values for each Sample

organism: Hominidae

source_name: MCF-7 (malignant adenocarcinoma cell line)

extract_protocol:
cells were cultured with 4sU for different time (0h, 1h, 4h, and 8h), and RNA was harvested using Trizol reagent.  Novogene RNA library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer. First strand cDNA was synthesized using random hexamer primer and RNase H. In order to select cDNA fragments of preferentially 100~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Adapter ligation at 25°C for 10min before PCR . Then PCR was performed with Phusion HighFidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: cell line

tag: cell type

value: Human breast cancer cells

tag: treatment

value: treated with 4sU for 4 hours


title: New-7-8

value: treated with 4sU for 8 hours


title: New-7-1

value: treated with 4sU for 1 hours


title: Old-7

value: untreated


title: Δnit-4 Nitrogen Starvation Biological Replicate 2


title: New-231-4

source_name: MDA-MB-231 (highly metastatic breast cell line)


title: New-231-8


title: Δnit-2 Vogel's Minimal Medium Biological Replicate 2


title: Old-231


title: Δnit-2 Vogel's Minimal Medium Biological Replicate 3


title: Δnit-4 Nitrogen Starvation Biological Replicate 1


title: THP-1 ABZ_0.2uM

city: Kyoto

first: Ken

last: Morita

address: 53 Kawahara-cho, Syogoin, Sakyo-ku

department: Human Health Sciences

country: Japan

institute: Kyoto University

description:
EA1544_02
Gene expression data from THP-1 cells treated with 0.2 μM albendazole.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the GeneChip Fluidics Station 450 using GeneChip Hybridization, Wash and Stain Kit.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using GeneChip 3'IVT PLUS Reagent Kit from 250 ng total RNA.

growth_protocol: Cells were cultured in RPMI1640 medium supplemented with heat-inactivated 10% FBS at 37 ℃, 5% CO2.

extract_protocol: Total RNA was performed according to the manufacturer's instructions (Qiagen RNeasy Mini Kit).

treatment_protocol: Cells were treated with doxycycline (Wako Pure Chemical Industries, Ltd) at 3 μM for 48 hours to induce KLF4 expressions (THP-1_KLF4), or cells were treated with either by DMSO or albendazole (Sigma) at the indicated concentrations for 24 hours before lysed for RNA extractions.

value: Leukemic cell line

value: 0.2 uM albendazole


title: THP-1 KLF4

description:
EA1544_04
Gene expression data from THP-1 cells transduced with KLF4.

source_name: THP-1 cells transduced with KLF4


title: Δnit-2 Vogel's Minimal Medium Biological Replicate 1


title: THP-1 Control

description:
EA1544_01
Gene expression data from control THP-1 cells.

source_name: Control THP-1 cells

value: DMSO control


title: Δamn-1 2mM Mannose Biological Replicate 2

value: Vogel's minimal medium with 2mM Mannose  and 25mM NH4NO3


title: A64h

city: Nanjing

first: Huiming

last: Guo

address: NO.30 Puzhu Road

institute: Nanjing Tech University

data_processing:
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package.
We used KOBAS software to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: no. CP021467.1
Supplementary_files_format_and_content: FPKM value of each gene in each sample

organism: Komagataeibacter europaeus

source_name: acetic acid bacteria

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels.RNA purity was checked using the NanoPhotometer® spectrophotometer.RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer.RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent   Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: CGMCC 20445

tag: fermentation time


title: C88h


title: C64h


title: B40h


title: B88h


title: C40h


title: Wild type Carbon Starvation Biological Replicate 2

value: FGSC 2489

value: Vogel's minimal medium 25mM NH4NO3 and lacking a carbon source


title: Wild type 2mM Mannose Biological Replicate 3


title: A40h


title: Wild type Carbon Starvation Biological Replicate 1


title: Wild type Carbon Starvation Biological Replicate 3


title: New-231-1


title: Δamn-1 2mM Mannose Biological Replicate 3


title: THP-1 ABZ_0.4uM

description:
EA1544_03
Gene expression data from THP-1 cells treated with 0.4 μM albendazole.

value: 0.4 uM albendazole


title: Wild type Nitrogen Starvation Biological Replicate 6


title: Wild type Nitrogen Starvation Biological Replicate 5


title: Wild type 2mM Mannose Biological Replicate 1


title: Δamn-1 2mM Mannose Biological Replicate 1


title: C10h


title: A10h


title: A88h


title: B10h


title: Wild type Nitrogen Starvation Biological Replicate 4


title: Wild type Nitrogen Starvation Biological Replicate 3


title: Wild type Nitrogen Starvation Biological Replicate 1


title: Wild type Nitrogen Starvation Biological Replicate 2


title: Wild type 2mM Mannose Biological Replicate 2


title: Wild type 50mM Glutamine Biological Replicate 2

value: Vogel's minimal medium with 2% Sucrose and 50mM Glutamine


title: Wild type 50mM Glutamate Biological Replicate 3

value: Vogel's minimal medium with 2% Sucrose and 50mM Glutamate


title: Wild type 200mM Glycine Biological Replicate 1

value: Vogel's minimal medium with 2% Sucrose and 200mM Glycine


title: Wild type 200mM Glycine Biological Replicate 2


title: Wild type 50mM Glutamine Biological Replicate 3


title: Wild type 200mM Glycine Biological Replicate 3


title: Wild type 344mM Arginine Biological Replicate 2

value: Vogel's minimal medium with 2% Sucrose and 344mM Arginine


title: Wild type 344mM Arginine Biological Replicate 3


title: Wild type 112mM Alanine Biological Replicate 2

value: Vogel's minimal medium with 2% Sucrose and 112mM Alanine


title: Wild type 50mM Glutamate Biological Replicate 2


title: run_10_reaction_2

city: San Francisco

first: George

middle: Christopher

last: Hartoularos

state: CA

address: 513 Parnassus Ave S965F

department: Graduate Division

institute: University of California, San Francisco

description:
MVIR1-POOL-SCG57
multiplexed droplet single-cell transcriptomes
JYCVPBMC10_merged.clust1.samples.gz
JYCVPBMC10_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv

data_processing:
Base-calling and read demultiplexing was done using the NovaSeq 6000's on-system BCL to FASTQ conversion tool.
FASTQs were aligned and unique-molecular identifiers were counted using 10x Genomics' cellranger (runs 1, 2, 3, 4, 5, 7 version 3.1.0; runs 8, 9, 10 version 4.0.0) using the standard GRCh38-3.0.0 transcriptome reference. This produces 1 binary sequence alignment map (BAM) file per droplet  reaction, as well as the cell count matrices (i.e. h5 files).
BAMs were inputted into freemuxlet in a batched fashion (one merged pileup file per pool) and was used to annotate filtered barcodes as either singlets or doublets and assign cell-containing droplets to nameless cell donors. This generates a VCF with nameless donors.
The freemuxlet-generated VCF with nameless donors was matched to an orthogonal VCF with patient data to assign singlet droplet barcodes to each named patient, and therefore further attach clinical covariates.
Genome_build: GRCh38
Supplementary_files_format_and_content: h5 files are 10x-formatted files using the HDF5 standard, containing cell barcodes in one dimension, and features (i.e. genes and surface proteins) in the other dimension. The provided files contain only the cell barcodes that were automatically annotated as cells by cellranger (i.e. filtered barcodes);
Supplementary_files_format_and_content: samples.gz files are tab-separated values files with the genetic information of each cell-containing droplet. This includes the anonymous donor id (i.e. CLUST##) as learned by freemuxlet, as well as number of reads/snps, singlet or doublet status, the log-likelihood of the cluster assignment, and associated probabilities;
Supplementary_files_format_and_content: vcf.gz files are variant-calling format files that contain genotype information for each cluster as learned by freemuxlet;
Supplementary_files_format_and_content: freemux_gem_group_map.csv is a comma-separated values file that maps the gem group cell barcode suffix in the samples.gz files to their respective samples. This is because for processing, the pile up files (derived from the BAM files) were merged across samples from the same pool of cells to leverage the full set of SNPs from the same individuals across multiple droplet reactions, potentially increasing the accuracy of the annotations;
Supplementary_files_format_and_content: covars.csv is a comma-separated values file containing clinical covariates for each sample and the mappings of freemuxlet clusters to patient IDs

molecule: polyA RNA

source_name: peripheral blood mononuclear cells

growth_protocol: PBMCs were isolated from blood samples using SepMate-15 and lymphoprep (STEMCELL). Cells were frozen in fetal bovine serum containing 10% (vol/vol) dimethyl sulfoxide. Cells were frozen and not thawed until the day of the experiment.

extract_protocol:
Cells were multiplexed into pools of cells from different patients with the intent of using in silico genetic demultiplexing tools to recover more single cells and reduce batch effect. No samples from the same person were multiplexed into the same pool. Pools were loaded onto the 10x Genomics Chromium Controller using several lanes per pool, and processed using standard protocols for the single-cell 5'v1 kit with TCR and BCR encrichment, which includes cell lysis, reverse transcription, amplification and library generation.
Libraries were constructed using standard protocols from 10x Genomics' single-cell gene expression and immune repertoire solution, chemistry 5'v1.

value: PBMC


title: Wild type 344mM Arginine Biological Replicate 1


title: run_10_reaction_4

description:
MVIR1-POOL-SCG59
multiplexed droplet single-cell transcriptomes
JYCVPBMC10_merged.clust1.samples.gz
JYCVPBMC10_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_10_reaction_3

description:
MVIR1-POOL-SCG58
multiplexed droplet single-cell transcriptomes
JYCVPBMC10_merged.clust1.samples.gz
JYCVPBMC10_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: Wild type 50mM Glutamate Biological Replicate 1


title: run_9_reaction_4

description:
MVIR1-POOL-SCG53
multiplexed droplet single-cell transcriptomes
JYCVPBMC9_merged.clust1.samples.gz
JYCVPBMC9_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_10_reaction_1

description:
MVIR1-POOL-SCG56
multiplexed droplet single-cell transcriptomes
JYCVPBMC10_merged.clust1.samples.gz
JYCVPBMC10_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_9_reaction_3

description:
MVIR1-POOL-SCG52
multiplexed droplet single-cell transcriptomes
JYCVPBMC9_merged.clust1.samples.gz
JYCVPBMC9_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_9_reaction_5

description:
MVIR1-POOL-SCG54
multiplexed droplet single-cell transcriptomes
JYCVPBMC9_merged.clust1.samples.gz
JYCVPBMC9_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: Wild type 112mM Alanine Biological Replicate 3


title: run_9_reaction_2

description:
MVIR1-POOL-SCG51
multiplexed droplet single-cell transcriptomes
JYCVPBMC9_merged.clust1.samples.gz
JYCVPBMC9_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: Wild type 112mM Alanine Biological Replicate 1


title: Wild type 50mM Glutamine Biological Replicate 1


title: Wild type Vogel's Minimal Medium Biological Replicate 3

value: Vogel's minimal medium with 2% Sucrose and 25mM NH4NO3


title: run_9_reaction_6

description:
MVIR1-POOL-SCG55
multiplexed droplet single-cell transcriptomes
JYCVPBMC9_merged.clust1.samples.gz
JYCVPBMC9_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: Wild type Vogel's Minimal Medium Biological Replicate 2


title: run_8_reaction_5

description:
MVIR1-POOL-SCG48
multiplexed droplet single-cell transcriptomes
JYCVPBMC8_merged.clust1.samples.gz
JYCVPBMC8_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: Wild type Vogel's Minimal Medium Biological Replicate 4


title: run_9_reaction_1

description:
MVIR1-POOL-SCG50
multiplexed droplet single-cell transcriptomes
JYCVPBMC9_merged.clust1.samples.gz
JYCVPBMC9_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: Wild type Vogel's Minimal Medium Biological Replicate 1


title: Wild type Vogel's Minimal Medium Biological Replicate 5


title: run_8_reaction_6

description:
MVIR1-POOL-SCG49
multiplexed droplet single-cell transcriptomes
JYCVPBMC8_merged.clust1.samples.gz
JYCVPBMC8_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_8_reaction_2

description:
MVIR1-POOL-SCG45
multiplexed droplet single-cell transcriptomes
JYCVPBMC8_merged.clust1.samples.gz
JYCVPBMC8_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_8_reaction_3

description:
MVIR1-POOL-SCG46
multiplexed droplet single-cell transcriptomes
JYCVPBMC8_merged.clust1.samples.gz
JYCVPBMC8_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: B64h


title: WSU-DLCL2_RNASeq_rep3_run3

city: Lausanne

first: Yuanlong

last: Liu

address: Quartier UNIL-Sorge

department: Department of Computational Biology

country: Switzerland

institute: University of Lausanne

description: processed data file: WSU_DMSO_Rep3_run123.htseq.counts.txt (linked to the WSU-DLCL2_RNASeq_rep3_run1 sample records)

data_processing:
Fastq files were processed using RSEM with STAR-2.5.3a as aligner and gencode v27lift37 for annotation.  Gene read counts were generated using HTSeq2 with the gene annotation file GRCh37 version 75 as reference
Genome_build: hg19
Supplementary_files_format_and_content: Gene read counts  generated using HTSeq2

growth_protocol: standard grwoth condition as described in Sungalee et al. 2021

extract_protocol:
standard protocol for RNA extraction as described in Sungalee et al. 2021
standard Illumina sequencing protocol for library prepraration

treatment_protocol: as described in Sungalee et al. 2021

value: treated with A-485 for 48 hours


title: run_8_reaction_4

description:
MVIR1-POOL-SCG47
multiplexed droplet single-cell transcriptomes
JYCVPBMC8_merged.clust1.samples.gz
JYCVPBMC8_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: WSU-DLCL2_RNASeq_rep2

value: untreated


title: run_7_reaction_6

description:
MVIR1-POOL-SCG43
multiplexed droplet single-cell transcriptomes
JYCVPBMC7_merged.clust1.samples.gz
JYCVPBMC7_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: WSU-DLCL2_RNASeq_rep3_run2


title: run_8_reaction_1

description:
MVIR1-POOL-SCG44
multiplexed droplet single-cell transcriptomes
JYCVPBMC8_merged.clust1.samples.gz
JYCVPBMC8_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: WSU-DLCL2_RNASeq_rep1


title: WSU-DLCL2_BCL11AKO_RNASeq_clone3

value: BCL11A knockout


title: run_7_reaction_5

description:
MVIR1-POOL-SCG42
multiplexed droplet single-cell transcriptomes
JYCVPBMC7_merged.clust1.samples.gz
JYCVPBMC7_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_7_reaction_4

description:
MVIR1-POOL-SCG41
multiplexed droplet single-cell transcriptomes
JYCVPBMC7_merged.clust1.samples.gz
JYCVPBMC7_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_7_reaction_3

description:
MVIR1-POOL-SCG40
multiplexed droplet single-cell transcriptomes
JYCVPBMC7_merged.clust1.samples.gz
JYCVPBMC7_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: WSU-DLCL2_BCL11AKO_RNASeq_clone2


title: run_7_reaction_2

description:
MVIR1-POOL-SCG39
multiplexed droplet single-cell transcriptomes
JYCVPBMC7_merged.clust1.samples.gz
JYCVPBMC7_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_7_reaction_1

description:
MVIR1-POOL-SCG38
multiplexed droplet single-cell transcriptomes
JYCVPBMC7_merged.clust1.samples.gz
JYCVPBMC7_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: WSU-DLCL2_BCL11AKO_RNASeq_clone1


title: WSU-DLCL2_A485_treated_RNASeq_rep3


title: run_5_reaction_6

description:
MVIR1-POOL-SCG37
multiplexed droplet single-cell transcriptomes
JYCVPBMC5_merged.clust1.samples.gz
JYCVPBMC5_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: WSU-DLCL2_A485_treated_RNASeq_rep2


title: WSU-DLCL2_A485_treated_RNASeq_rep1


title: Karpas-422_RNASeq_rep3


title: Karpas-422_RNASeq_rep2


title: WSU-DLCL2_RNASeq_rep3_run1


title: run_5_reaction_5

description:
MVIR1-POOL-SCG36
multiplexed droplet single-cell transcriptomes
JYCVPBMC5_merged.clust1.samples.gz
JYCVPBMC5_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_5_reaction_3

description:
MVIR1-POOL-SCG34
multiplexed droplet single-cell transcriptomes
JYCVPBMC5_merged.clust1.samples.gz
JYCVPBMC5_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_5_reaction_1

description:
MVIR1-POOL-SCG32
multiplexed droplet single-cell transcriptomes
JYCVPBMC5_merged.clust1.samples.gz
JYCVPBMC5_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: Karpas-422_RNASeq_rep1


title: run_5_reaction_2

description:
MVIR1-POOL-SCG33
multiplexed droplet single-cell transcriptomes
JYCVPBMC5_merged.clust1.samples.gz
JYCVPBMC5_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: Karpas-422_A485_treated_RNASeq_rep3


title: run_5_reaction_4

description:
MVIR1-POOL-SCG35
multiplexed droplet single-cell transcriptomes
JYCVPBMC5_merged.clust1.samples.gz
JYCVPBMC5_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_4_reaction_3

description:
MVIR1-POOL-SCG30
multiplexed droplet single-cell transcriptomes
JYCVPBMC4_merged.clust1.samples.gz
JYCVPBMC4_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_4_reaction_4

description:
MVIR1-POOL-SCG31
multiplexed droplet single-cell transcriptomes
JYCVPBMC4_merged.clust1.samples.gz
JYCVPBMC4_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: GC_Hi_C_rep2

description:
no control access needed
processed data file: GC_merged_rep12.hic

library_source: genomic

data_processing:
For each library replicate of A-485 treated WSU-DLCL2 or Karpas-422, coordinate-sorted (SAMtools v1.6) and PCR duplicates (Picard tools v2.5.0) cleaned bam files were generated following alignment of the reads to the human hg19 reference genome (Bowtie2-2.2.9) and filtering for uniquely mapping reads (SAMtools v1.6). Custom Python and R scripts were used to process chimeric pairs with ‘unambiguous’ reads, for which one of the two reads mapped to two different sub-sequences. Those were recovered in a second round of alignment using bwa mem v0.7.12 and processed as above. Read pairs for each replicate were combined and generated as .hic file using Juicer
Genome_build: hg19
Supplementary_files_format_and_content: hic contact counts were binned at various resolution using Juicer software

molecule: genomic DNA

source_name: Germinal Center B-cells

extract_protocol:
Protocol for HiC sample preprartion as described in Sungalee at al. 2021
standard Illumina sequencing protocol for library prepraration

value: normal B cells

tag: tissue type

value: lymphonode biopsy


title: run_4_reaction_2

description:
MVIR1-POOL-SCG29
multiplexed droplet single-cell transcriptomes
JYCVPBMC4_merged.clust1.samples.gz
JYCVPBMC4_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: GC_Hi_C_rep1


title: Patient_7_Hi-C_rep3

description:
no control access needed
processed data file: Patient_7_merged_rep1234.hic

source_name: DLBCL lymphoma

value: ABC-DLBCL tumor suntype


title: run_3_reaction_6

description:
MVIR1-POOL-SCG27
multiplexed droplet single-cell transcriptomes
JYCVPBMC3_merged.clust1.samples.gz
JYCVPBMC3_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: Patient_7_Hi-C_rep4


title: run_3_reaction_5

description:
MVIR1-POOL-SCG26
multiplexed droplet single-cell transcriptomes
JYCVPBMC3_merged.clust1.samples.gz
JYCVPBMC3_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_3_reaction_4

description:
MVIR1-POOL-SCG25
multiplexed droplet single-cell transcriptomes
JYCVPBMC3_merged.clust1.samples.gz
JYCVPBMC3_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_3_reaction_3

description:
MVIR1-POOL-SCG24
multiplexed droplet single-cell transcriptomes
JYCVPBMC3_merged.clust1.samples.gz
JYCVPBMC3_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: Patient_7_Hi-C_rep2


title: Patient_7_Hi-C_rep1


title: run_3_reaction_2

description:
MVIR1-POOL-SCG23
multiplexed droplet single-cell transcriptomes
JYCVPBMC3_merged.clust1.samples.gz
JYCVPBMC3_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: Karpas-422_A485_treated_RNASeq_rep2


title: mBL_11_hybridized to U133 plus 2.0 array

value: lymphoma

value: Adult


title: Karpas-422_A485_treated_RNASeq_rep1


title: Patient_1_Hi-C_rep2

description:
no control access needed
processed data file: Patient_1_merged_rep12.hic

value: DLBCL double hit


title: run_4_reaction_1

description:
MVIR1-POOL-SCG28
multiplexed droplet single-cell transcriptomes
JYCVPBMC4_merged.clust1.samples.gz
JYCVPBMC4_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: WSU-DLCL2_A485_treated_Hi-C_rep4

description: processed data file: WSU_A485_merged_rep1234.hic

source_name: WSU-DLCL2 cells

value: lymphonode


title: Patient_1_Hi-C_rep1


title: WSU-DLCL2_A485_treated_Hi-C_rep3


title: WSU-DLCL2_Hi-C_rep2

description: processed data file: WSU_DMSO_merged_rep12.hic


title: WSU-DLCL2_A485_treated_Hi-C_rep1


title: WSU-DLCL2_A485_treated_Hi-C_rep2


title: run_2_reaction_2

description:
MVIR1-POOL-SCG17
multiplexed droplet single-cell transcriptomes
JYCVPBMC2_merged.clust1.samples.gz
JYCVPBMC2_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_2_reaction_1

description:
MVIR1-POOL-SCG16
multiplexed droplet single-cell transcriptomes
JYCVPBMC2_merged.clust1.samples.gz
JYCVPBMC2_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_2_reaction_5

description:
MVIR1-POOL-SCG20
multiplexed droplet single-cell transcriptomes
JYCVPBMC2_merged.clust1.samples.gz
JYCVPBMC2_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: WSU-DLCL2_Hi-C_rep1


title: run_2_reaction_3

description:
MVIR1-POOL-SCG18
multiplexed droplet single-cell transcriptomes
JYCVPBMC2_merged.clust1.samples.gz
JYCVPBMC2_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: Karpas-422_A485_treated_Hi-C_rep2

description: processed data file: KARPAS_A485_merged_rep1234.hic

source_name: Karpas-422 cells


title: run_1_reaction_5

description:
MVIR1-POOL-SCG14
multiplexed droplet single-cell transcriptomes
JYCVPBMC1_merged.clust1.samples.gz
JYCVPBMC1_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_2_reaction_4

description:
MVIR1-POOL-SCG19
multiplexed droplet single-cell transcriptomes
JYCVPBMC2_merged.clust1.samples.gz
JYCVPBMC2_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: Karpas-422_A485_treated_Hi-C_rep4


title: run_1_reaction_6

description:
MVIR1-POOL-SCG15
multiplexed droplet single-cell transcriptomes
JYCVPBMC1_merged.clust1.samples.gz
JYCVPBMC1_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: Karpas-422_A485_treated_Hi-C_rep1


title: run_1_reaction_4

description:
MVIR1-POOL-SCG13
multiplexed droplet single-cell transcriptomes
JYCVPBMC1_merged.clust1.samples.gz
JYCVPBMC1_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_1_reaction_3

description:
MVIR1-POOL-SCG12
multiplexed droplet single-cell transcriptomes
JYCVPBMC1_merged.clust1.samples.gz
JYCVPBMC1_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_3_reaction_1

description:
MVIR1-POOL-SCG22
multiplexed droplet single-cell transcriptomes
JYCVPBMC3_merged.clust1.samples.gz
JYCVPBMC3_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: run_1_reaction_1

description:
MVIR1-POOL-SCG10
multiplexed droplet single-cell transcriptomes
JYCVPBMC1_merged.clust1.samples.gz
JYCVPBMC1_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: hPSC γOFF input

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

description: Every sample has then 8 fastq associated file to be merged for analysis (4 lines, 2 back to back runs per sample)

data_processing:
Results quality control were performed using FastQC
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 (sensitive local, no discordant, no mixed configuration) and dupliacetes removed by picard.
peaks were called using HOMER (gh38)  with the following setting: peak size 1000; mimimum distance between peaks: 1000; fold over imput required: 4.00
Genome_build: hg38
Supplementary_files_format_and_content: wig files
Supplementary_files_format_and_content: peak text files with annotation

source_name: embrionic stem cells

growth_protocol: hPSCs were cultured on Matrigel-coated (BD Biosciences) tissue culture plates in mouse embryonic fibroblast-conditioned media (MEF-CM) supplemented with 8ng/ml bFGF (Thermo Fisher Scientific).

extract_protocol:
For each ChIP experimental condition (day 0 for pluripotency, day 3 for neural and heamtopoietic differentiation protocols), 3×106 cells were collected and cross-linked using 1% formaldehyde. Chromatin was fragmented by sonication in buffer containing 1% NP-40 to obtain fragments of 250-500bp in length. Sonicated DNA was subjected to immunoprecipitation using anti-γH2A.X antibodies conjugated with Dynabeads® Protein G (Thermo Fisher Scientific). Immunoprecipitated DNA was further reverse cross-linked, purified and subjected to sequencing analyses.
Libraries were prepared according to Illumina's instructions accompanying NEBNext Ultra II DNA library prep kit and sequenced with HiSeq 2500 instrument (Illumina).

treatment_protocol: For neural differentiation, hPSCs clones were harvested by collagenase IV treatment and EBs were generated with EB medium without cytokines. 24 hours after suspension culture, EBs were plated onto poly-L-lysine/laminin-coated plates (BD Biosciences) in neural differentiation medium composed of DMEM/F12 supplemented with B27 and N2 (Thermo Fisher Scientific), EGF (25 ng/ml, R&D Systems), and bFGF (8 ng/ml).  For hematopoietic differentiaion, Confluent undifferentiated hiPSCs were treated with 200 U/ml collagenase IV for 5–10 min and then transferred to Ultralow attachment plates (Corning). Clumps of hiPSCs were incubated overnight to allow hEB formation in the hEB-differentiation medium supplemented with hematopoietic growth factors as follows: granulocyte colony-stimulating factor (G-CSF, 50ng/ml), stem cell factor (SCF 300 ng/ml), interleukin-3 (10 ng/ml), interleukin-6 (10 ng/ml), BMP4 (25 ng/ml) and  Flt-3 ligand (Flt-3L 300 ng/ml) (all R&D Systems)

value: H9 hESC - H2AX S136/139A mutated

tag: chip antibody


title: run_2_reaction_6

description:
MVIR1-POOL-SCG21
multiplexed droplet single-cell transcriptomes
JYCVPBMC2_merged.clust1.samples.gz
JYCVPBMC2_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv


title: hPSC γOFF Meso-Hem

value: anti-gamma H2A.X (phospho S139) - ChIP Grade Abcam Cat#Ab2893

value: Hematopoietic differentiation 3 days


title: hPSC γOFF Pluri

value: untreated - MEFCM media


title: paracarcinoma(papillary thyroid cancer) tissues [N7]

city: Hangzhou

first: Junjie

last: Chu

state: Zhejiang

address: 3 East Qingchun Road

department: Sir RUN RUN Shaw Hospital

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
After obtaining the initial raw data (Raw Data), it is first necessary to filter the data, remove the joint sequence and process the low-quality reads, then evaluate the quality, and repeat the test to obtain better data (Clean Data).
Advanced comparison with the reference genome, and then use the find_circ (official description address: https://github.com/marvin-jens/find_circ) software to compare and analyze the results.
Finally, the read count is equal to or equal to 2, there is a pointed cutting site, and the circRNA at the intersection can be uniquely aligned as the circRNA to be screened.
Prototype RNA is annotated, sequence is predicted, expression level is calculated and heatmaps are drawn, and subsequent analysis such as clustering is performed.
Genome_build: Homo_sapiens.GRCh38.94
Supplementary_files_format_and_content: Matrix table with circRNA TPMs for every circRNAs and every sample

source_name: paracarcinoma tissues from patient C

extract_protocol:
RNA extraction method: Trizol
The first step is to build a circular RNA library and remove ribosomes, using RiboMinus Human/Mouse Transcriptome Isolation Kit (invitrogen, thermofisher); the second step is to remove linear RNA, using RNase R enzyme (epicentre, illumina), and the third step is to construct Library, using KAPA Stranded mRNA-Seq Kit (roche)

treatment_protocol: All tissues were histologically characterized by pathologists in accordance with the criteria established by the World Health Organization and were stored in liquid nitrogen after surgery.

value: Thyroid

tag: gender

value: Female

tag: tumor size(cm)

tag: extrathyroidal extension

value: Positive

tag: clinical stage

value: III

tag: t classification

tag: n classification

tag: lymphnode metastasis (positive/total)


title: hPSC γON input

value: H9 hESC - H2AX S139E mutated

value: untreated


title: papillary thyroid cancer [T7]

source_name: papillary thyroid cancer tissues from patient C

tag: tissue

tag: age


title: paracarcinoma(papillary thyroid cancer) tissues [N5]

source_name: paracarcinoma tissues from patient B

value: Male

value: Negtive

value: I


title: Karpas-422_A485_treated_Hi-C_rep3

value: treated with A-485 for 48 hours


title: paracarcinoma(papillary thyroid cancer) tissues [N41]

source_name: paracarcinoma tissues from patient A


title: hPSC input

value: H9 hESC - empty vector control


title: 4C_PromSix2VP_inv110

city: Santander

first: Alvaro

last: Rada-Iglesias

state: Cantabria

address: Albert Einstein 22, PCTCAN

country: Spain

institute: Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria

data_processing:
Library strategy: 4C-seq
Reads were assigned to samples based on the first 10 bases of the read. Subsequently, the primer sequence was removed from the read and the remaining sequence starting before the restriction site for NlaIII (CATG) was trimmed to 41 bases. These 41 bases were aligned to the mouse reference genome (mm10) using HISAT2 (Kim et al., 2015). From these alignments, RPM (reads per million) normalized bedgraph files were generated for downstream visualization and analysis (Thongjuea et al., 2013).
Genome_build: mm10
Supplementary_files_format_and_content: rpm normalized bedGraph

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: ESC were cultured on gelatin-coated plates using Knock-out DMEM supplemented with 15% FBS and LIF.

extract_protocol:
Circular Chromatin Conformation Capture (4C) followed by sequencingwere performed as previously described (Laugsch et al., 2019).
4C samples were amplified by inverse PCR using primer for the PE Sox1, PE Six3 or Six2 promoter. The primer included illumina adaptor sequences and short barcodes. The inverse PCRs were performed with the expand long template PCR system and 30 amplification cycles (94°C 2 min, 30x [94°C 10 sec, 60°C 1 min, 68°C 3 min], 68°C 5 min). The inverse PCR primers were designed as previously described (Stadhouders et al., 2013). Once amplified, 4C-seq libraries were sequenced on the HiSeq2500.

value: 2i+LIF ESC

tag: genotype

value: wild type


title: papillary thyroid cancer [T41]

source_name: papillary thyroid cancer tissues from patient A


title: hPSC γON Pluri


title: run_1_reaction_2

description:
MVIR1-POOL-SCG11
multiplexed droplet single-cell transcriptomes
JYCVPBMC1_merged.clust1.samples.gz
JYCVPBMC1_merged.clust1.vcf.gz
freemux_gem_group_map.csv
covars.csv

value: PBMC


title: 4C_PESox1VP_oCGIdel


title: hPSC Ecto-Neu

value: anti-gamma H2A.X (phospho S139) - ChIP Grade Abcam Cat#Ab2893

value: Neural differentiation 3 days


title: hPSC Meso-Hem

value: Hematopoietic differentiation 3 days


title: 4C_PESix3VP_inv110


title: HT29_siHOXA-AS3_1

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

data_processing:
Gene expression levels were quantified using RSEM61 and a RefSeq gene annotation database.
Genome_build: hg19
Supplementary_files_format_and_content: RSEM gene-level quantification files

source_name: HOXA-AS3 siRNA, rep1

growth_protocol: HT-29 cell lines and were routinely cultured in DMEM containing 10% fetal bovine serum and 100 U penicillin/0.1 mg ml−1 streptomycin, at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted from different cell lines and mouse tissues, by using RNeasy (Qiagen)  according to the manufacturer’s protocol.
Lexogen Sense mRNA

treatment_protocol: siRNAs were transfected into HT-29 cells at 10 nM siRNA pool or with control pool (Dharmacon) by using DharmaFect 4 (Dharmacon,T-2004-01/03) following the manufacturer’s protocol. Cells were harvested after 48h of siRNA treatment.

tag: sirna

tag: replicate


title: HT29_siHOXB-AS3_2

source_name: HOXB-AS3 siRNA, rep2

tag: cell line


title: HT29_siNT_2

source_name: Nontargeting siRNA, rep2

value: NT


title: HT29_siHOXB-AS3_1

source_name: HOXB-AS3 siRNA, rep1


title: hPSC Pluri

tag: cell type

tag: treatment

value: untreated - MEFCM media


title: HT29_siNT_1

source_name: Nontargeting siRNA, rep1


title: hPSC γON Ecto-Neu


title: papillary thyroid cancer [T5]

source_name: papillary thyroid cancer tissues from patient B

value: Thyroid


title: VDAC2 KO [14818X9]

city: Salt Lake City

first: Stavros

middle: George

last: Drakos

state: Utah

address: 95 South 2000 East

department: Cardiovascular research and training institute

institute: University of Utah

description:
Bulk RNA sequencing
14818X9_180201_D00550_0494_ACBT5KANXX_S9_L002

data_processing:
The human GRCm38 FASTA and GTF files were downloaded from Ensembl release 90.
The reference database was created using STAR version 2.7.2c with splice junctions optimized for 50 base pair reads.
Optical duplicates removed from NovaSeq runs via Clumpify v38.34
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3
Non-coding features, histones, and ribosomal RNAs were removed and differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: FeatureCounts output files combined into a single tab-delimited matrix

source_name: VDAC2 KO

extract_protocol:
miRNeasy Mini Kit
Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold

tag: strain background

value: VDAC2 KO

value: CARDIAC LV


title: 4C_PESox1VP_WT


title: HAP1_2_94

city: Shenzhen

first: Guipeng

last: Li

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

data_processing:
peaks were called by macs2
peak-cell matrices were determined using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: txt file, peak-by-cell count matrix

source_name: HAP1 cells

extract_protocol:
Plate-based snATAC-seq
1)One day before the experiment, prepare the 96-well plates by adding 1µL 2X Lysis Buffer (100 mM NaCl pH 7.4, 100 mM Tris-HCl pH 8.0, 40 µg/mL proteinase K, 0.4 % SDS) to each well. Then add 1µL of 10 µM S5xx/N7xx Nextera Index Primer Mix (5 µM each) (TD202, Vazyme) to each well. Seal the plate and store in -80 ºC. Thaw plates at room-temperature before use.
2)Pre-coat 1.5 mL Eppendorf tubes with 500 µL 0.5% BSA/DPBS. Collect 5×105 cells in DPBS into 1.5 mL Eppendorf tube. Centrifuge at 300 g for 5 min at room-temperature. Wash the cells once with 200µL DPBS, then with 200 µL ATAC resuspension buffer (10 mM NaCl, 10 mM Tris-HCl pH 7.4, 3 mM MgCl2). Centrifuge condition is 600 g, 5 min at 4 ˚C.
3)After two steps wash, resuspend cells in 100 µL ATAC cell lysis buffer (10 mM NaCl, 10 mM Tris-HCl pH 7.4, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP40, 0.01% Digitonin), then add 2.5 µL assembled CASB complex (control group was only resuspended in ATAC cell lysis buffer). Mix thorough by pipette. Incubate on ice for 5 min, then add 950 µL ATAC wash buffer (10 mM NaCl, 10 mM Tris-HCl pH 7.4, 3 mM MgCl2, 0.1% Tween-20) to quench reaction.
4)Centrifuge nuclei at 1000 g for 5 min at 4 ˚C, discard the supernatant by pipette carefully. Resuspend nuclei in 1 mL ATAC wash buffer. Centrifuge again.
5)Resuspend nuclei in 50 µL tagmentation reaction (TD501, Vazyme). Incubate at 37 ˚C on a thermomixer (600 rpm) for 30 min. Then, stop the reaction by adding 50 µL tagmentation stop buffer (20 mM EDTA, 10 mM Tris-HCl pH 8.0). Incubate on ice for 10 min.
6)Add 300 µL 0.5% BSA/DPBS into nuclei. Then add DAPI according to manufacturer’s instruction. Use FACS (MA900, Sony) to sort single nucleus into each well of prepared 96-well plates.
7)Set lip temperature of PCR machine to 100 ˚C, then incubate plates at 65 ºC for 15 min.
8)Add 2 µL 10% Tween-20 into each well to quench SDS. Then add 6 µL PCR mix (from TD501, Vazyme). PCR reaction as follow: 72 ˚C 10 min, 98 ˚C 1 min, (98 ˚C 30 s, 63 ˚C 30 s, 72 ˚C 30 s) ×25, 72 ˚C 5 min, 10 ˚C hold.
9)Collect all products into a 15 mL conical centrifuge tube. Purify the product using ZYMO DNA clean & concentrator kit.
10)Perform size


title: HAP1_2_96


title: HAP1_2_9


title: HAP1_2_93


title: VDAC2 KO [14818X8]

description:
Bulk RNA sequencing
14818X8_180201_D00550_0494_ACBT5KANXX_S8_L002


title: RNA-seq GSC2

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

country: France

institute: GReD CNRS

data_processing:
RNA-seq were mapped to the human genome (hg19) using tophat2 (version 2.1.0) with a transcript annotation file from Gencode (Release 19)
The reads count per gene were obtained with the HTseq-count script on properly paired reads and Genecode V19 transcript annotation file
Differential expression analysis between groups was based on reads count using DESeq2 and edgeR R packages
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample.

source_name: Glioblastoma stem cells: GSC2

growth_protocol: Glioblastoma stem cells were cultured in Neurobasal Medium supplemented with B27 1%; N2 0.5%; bFGF 0.05% and EGF 0.005% at 37°C in 5% CO2 humidified incubator. Culture medium was replaced twice a week and when spheres became large and numerous, they were enzymatically dissociated with accutase. Glioblastoma stem cell cultures were characterized by assessing self renewal, differentiation and tumorigenic ability as well as their expression of stemness markers (CD133, SOX2). Finally, all cultures were also classified according to Verhaak's classification of glioblastomas using the method of classification to nearest centroids (ClaNC) with a 840 gene signature.

extract_protocol:
RNA were isolated from frozen  cells using the RNeasy Mini Kit (Qiagen, Hamburg, GmbH),
RNA-seq were performed on total RNA following ribosomal RNAs depletion (Ribo-zero removal kit, illumina). RNA processing, rRNA depletion, library preparation and running on illumina Hiseq 2500 were performed by Integragen, SA (Evry, France), according to the manufacturer's protocol.

tag: glioblastoma stem cell culture

value: glioblastoma stem cell


title: RNA-seq GSC1

source_name: Glioblastoma stem cells: GSC1


title: ELF153_144_DAC3

city: Freiburg

first: Gabriele

last: Greve

address: Hugstetter Str 55

department: Department of Internal Medicine 1

country: Germany

institute: University of Freiburg Medical Center

description:
AML cell line ELF-153 treated with 100 nM DAC for 144 h, replicate 3
AML1_ELF153_144_count_matrix.txt

data_processing:
Read quality was determined by FastQC (all samples Q>32)
Alignment to reference genome was peformed with Tophat2 (Library type FR frist strand). For TE analysis reads were mapped with RNA STAR.
Counting of reads was performed with htseq-count (Mode: Intersection (nonempty), Stranded:reverse). For TE analysis, counting was performed with htseq-count (How to count nonunique or ambiguous mapping reads: All - count nonuniquely or ambiguously mapped reads).
Differential expression analysis in each cell line was performed with DESeq2 (Factor levels: DAC versus ctrl, Type of fitting of dispersions to the mean intensity: parametric)
Genome_build: hg19 (for count matrix)
Genome_build: RepeatMasker modified by Hammell et at., 2015, Bioinforma. Oxf. Engl. (for TE count matrix)
Supplementary_files_format_and_content: Count matrix as tab-delimited .txt file, generated by DESeq2, with normalized read counts for every transcript in every samples.

source_name: AML cell line

growth_protocol: Cell were cultured in RPMI supplemented with 20 % FCS, 1 % penicillin/streptomycin and 5 ng/ml human GM-CSF.

extract_protocol:
Total RNA was extracted using the Macherey-Nagel NucleoSpin RNA Kit according to manufacturer's protocol. Concentration was measured with the Invitrogen Qubit Fluorometer and RNA integrity was determined using an Agilent TapeStation 2200 and the corresponding RNA Screen Tapes and reagents.
Total RNA was depleted for ribosomal RNA and paired-end libraries were prepared using the Illumina TruSeq Stranded Total RNA Kit accoding to manufacturer's protocol.

treatment_protocol: Cells were either untreated or treated with 100 nM DAC for 4 consecutive days, with daily medium changes and fresh administration of DAC.

value: AML cell line

value: 100 nM DAC


title: HAP1_2_95


title: HT29_siHOXA-AS3_2

source_name: HOXA-AS3 siRNA, rep2


title: HAP1_2_92


title: VDAC2 KO [14818X7]

description:
Bulk RNA sequencing
14818X7_180201_D00550_0494_ACBT5KANXX_S7_L002


title: HAP1_2_91


title: HAP1_2_90


title: VDAC2 KO [14818X6]

description:
Bulk RNA sequencing
14818X6_180201_D00550_0494_ACBT5KANXX_S6_L002


title: VDAC2 WT [14818X5]

description:
Bulk RNA sequencing
14818X5_180201_D00550_0494_ACBT5KANXX_S5_L001

source_name: VDAC2 WT

value: VDAC2 WT


title: VDAC2 WT [14818X4]

description:
Bulk RNA sequencing
14818X4_180201_D00550_0494_ACBT5KANXX_S4_L001


title: HAP1_2_86


title: HAP1_2_87


title: HAP1_2_88


title: ELF153_144_ctrl3

description:
AML cell line ELF-153 untreated 144 h, replicate 3
AML1_ELF153_144_count_matrix.txt

value: untreated


title: ELF153_144_ctrl2

description:
AML cell line ELF-153 untreated 144 h, replicate 2
AML1_ELF153_144_count_matrix.txt


title: HAP1_2_85


title: VDAC2 WT [14818X3]

description:
Bulk RNA sequencing
14818X3_180201_D00550_0494_ACBT5KANXX_S3_L001


title: ELF153_144_ctrl1

description:
AML cell line ELF-153 untreated 144 h, replicate 1
AML1_ELF153_144_count_matrix.txt


title: HAP1_2_84


title: HAP1_2_83


title: VDAC2 WT [14818X2]

description:
Bulk RNA sequencing
14818X2_180201_D00550_0494_ACBT5KANXX_S2_L001


title: AML1_144_DAC3

description:
AML cell line UCSD-AML1 treated with 100 nM DAC for 144 h, replicate 3
AML1_ELF153_144_count_matrix.txt


title: HAP1_2_8


title: VDAC2 WT [14818X1]

description:
Bulk RNA sequencing
14818X1_180201_D00550_0494_ACBT5KANXX_S1_L001


title: AML1_144_DAC2

description:
AML cell line UCSD-AML1 treated with 100 nM DAC for 144 h, replicate 2
AML1_ELF153_144_count_matrix.txt


title: ELF153_144_DAC2

description:
AML cell line ELF-153 treated with 100 nM DAC for 144 h, replicate 2
AML1_ELF153_144_count_matrix.txt


title: ELF153_144_DAC1

description:
AML cell line ELF-153 treated with 100 nM DAC for 144 h, replicate 1
AML1_ELF153_144_count_matrix.txt


title: HAP1_2_81


title: HAP1_2_79


title: HAP1_2_7


title: HAP1_2_89


title: HAP1_2_80


title: AML1_144_DAC1

description:
AML cell line UCSD-AML1 treated with 100 nM DAC for 144 h, replicate 1
AML1_ELF153_144_count_matrix.txt


title: HAP1_2_78


title: Hmx3-Cre/tdTomato/Dnmt1loxp_KO_E16_MeDIP_1

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Illumina's CASAVA-1.8.2 was used to convert the base calls in the per-cycle BCL files to the per-read FASTQ format from raw images. Along with base calling, adapter trimming and demultiplexing were performed.
Samples aligned to mm10 using Bowtie2 2.3.4.
Alignments were filtered for high-quality to keep those with MAPQ=1 or MAPQ>4.
Coverage files bigWig were created from the high-quality BAM files using bamCoverage 3.2.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_hq.bw: bigWig files

source_name: Hmx3-derived interneurons isolated from basal telencephalon at E16 after DNMT1 knockout

growth_protocol: The transgenic mice were established by breeding the Hmx3-Cre line (obtained from Oscar Marin, King´s College, London, UK and described in Gelman DM et al. (2009)) with the tdTomato transgenic reporter mice (obtained from Christian Hübner, University Hospital Jena, Germany and described in Madisen L et al. (2010)) and the Dnmt1 loxP2 mice (B6;129S-Dnmt1tm4Jae/J, Jaenisch laboratory, Whitehead Institute; USA). The Dnmt1 loxP2 mice have LoxP-sites flanking exons 4 and 5 of the Dnmt1 gene. Cre-mediated deletion leads to out-of-frame splicing from exon 3 to exon 6, resulting in a null Dnmt1 allele (Jackson-Grusby L et al. 2001). For staging of mouse embryos, the day of insemination was considered as embryonic day 1 (E1).

extract_protocol:
Mice were deeply anesthetized intraperitoneally with 10% chloral hydrate in phosphate-buffered saline (PBS; pH 7.4). Embryos of anesthetized timed pregnant dams were prepared as described in Zimmer et al. (2011). For FACS-mediated enrichment of tdTomato cells at E16, the whole basal telencephalon of living brains was subjected to cell dissociation. Briefly, embryonic brains were prepared in Krebs buffer (126mM NaCl, 2.5mM KCl, 1.2mM NaH2PO4, 1.2mM MgCl2, 2.1mM CaCl2, 10mM D-glucose, 12.5mM NaHCO3) and the basal telencephalon was dissected and collected in ice-cold Hanks balanced salt solution (HBSS; Invitrogen) supplemented with 0.65% glucose. After incubation with 0.025% trypsin (Invitrogen) in HBSS for 17 min at 37 °C, cells were dissociated by trituration and filtering through nylon gauze. Cells were washed with HBSS supplemented with 0.65% glucose prior to FACS. Following the addition of DAPI, cells were sorted using an ARIA III FACS sorter (BD Biosciences) with the maximal flow rate of 6. The tdTomato reporter was excited by a 561-nm yellow/green solid-state laser and emission signal was detected in a range of 579–593 nm. According to their FCS/SSC criteria followed by cell doublet exclusion via an FSC-H versus FSC-W criterium, DAPI-negative living cells were sorted based on a distinctive tdTomato signal. Cells of interest were collected in DMEM/F12, 10% FBS, 100 U/mL penicillin, 100 g/mL streptomycin at 4 °C and pelleted by centrifugation. Enriched tdTomato cells prepared from the E16 basal telencephalon were split for each brain to prepare RNA for RNA sequencing and DNA for methylation-specific DNA immunoprecipitation (MeDIP) sequencing in parallel from the same set of sample. For RNA isolation, pellets were dissolved in 500 μL Trizol Reagent (Life Technologies) and subsequentially frozen on dry ice. For MeDIP-Seq analysis, cell pellets were frozen at −80 °C until further use. For RNA isolation the samples were then subjected to standard RNA isolation procedure using Trizol Reagent (Life Technologies) with additional application of GlycoBlue (Thermo Fisher Scientific) to a final concentration of 0.2% during RNA precipitation for better visualization of the pellet, digested with RNase-free DNase (Qiagen) and checked for integrity by capillary gel electrophoresis (Bioanalyzer, Agilent Technologies, Inc.). DNA isolation of FACS-enriched tdTomato cells was performed using QIAamp DNA Micro Kit (Qiagen) according to manufacturer’s instruction.
For genome-wide methylation analysis, we applied immunoprecipitation methods for the enrichment of 5-methylcytosines. Specifically, 100 ng of genomic DNA was used as starting material. The Methylated-DNA IP Kit from Zymo (Cat. No. D5101) was applied according to manufacturer’s instructions. The product of the IP and control reaction was then used for preparation of Illumina compatible libraries according to the TruSeq Nano DNA Library Prep Kit (Cat. No. FC-121-4001). Libraries were sequenced on a HiSeq 2000 yielding 50 bp single end reads. The sequencing reads were demultiplexed using the Illumina CASAVA tool and sequence quality was checked using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads were then aligned to the genome of Mus musculus (mm10) using Bowtie 2 (versions 2.0.2) with standard parameters. Differentially methylated regions were identified using the MEDIPS package for R (version 1.16.0; Lienhard et al. 2014) with a window size of 700 bp and a minimum coverage of 5% of the window length. A detailed description of the analysis pipeline can be found in Halder et al. (2016). Gene Ontology term enrichment analysis was performed for genes that were assigned to differentially methylated regions between wild-type and knockout samples. Results of gene ontology (GO) enrichment analysis were visualized in a bar diagram including the respective Benjamini–Hochberg corrected P value.

tag: genotype/variation

value: Dnmt1 knockout

tag: developmental stage

value: brain

tag: region

value: basal telencephalon

value: premature Hmx3-derived interneurons

tag: enrichment

value: MeDIP


title: AML1_144_ctrl3

description:
AML cell line UCSD-AML1 untreated 144 h, replicate 3
AML1_ELF153_144_count_matrix.txt


title: HAP1_2_77


title: HAP1_2_76


title: AML1_144_ctrl2

description:
AML cell line UCSD-AML1 untreated 144 h, replicate 2
AML1_ELF153_144_count_matrix.txt


title: Hmx3-Cre/tdTomato/Dnmt1loxp_WT_E16_MeDIP_1

source_name: Hmx3-derived interneurons isolated from basal telencephalon at E16

value: wild type


title: HAP1_2_75


title: Hmx3-Cre/tdTomato/Dnmt1loxp_KO_E16_rna_2

description: mRNA

data_processing:
Illumina's CASAVA-1.8.2 was used to convert the base calls in the per-cycle BCL files to the per-read FASTQ format from raw images. Along with base calling, adapter trimming and demultiplexing were performed.
Samples aligned to mm10 using STAR 2.5.2a.
Reads quantified to mouse genes in gene version mm10 version 97 using featureCounts 1.5.0-p1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_geneCounts.txt: Tab-delimited text files include gene counts.

extract_protocol:
Mice were deeply anesthetized intraperitoneally with 10% chloral hydrate in phosphate-buffered saline (PBS; pH 7.4). Embryos of anesthetized timed pregnant dams were prepared as described in Zimmer et al. (2011). For FACS-mediated enrichment of tdTomato cells at E16, the whole basal telencephalon of living brains was subjected to cell dissociation. Briefly, embryonic brains were prepared in Krebs buffer (126mM NaCl, 2.5mM KCl, 1.2mM NaH2PO4, 1.2mM MgCl2, 2.1mM CaCl2, 10mM D-glucose, 12.5mM NaHCO3) and the basal telencephalon was dissected and collected in ice-cold Hanks balanced salt solution (HBSS; Invitrogen) supplemented with 0.65% glucose. After incubation with 0.025% trypsin (Invitrogen) in HBSS for 17 min at 37 °C, cells were dissociated by trituration and filtering through nylon gauze. Cells were washed with HBSS supplemented with 0.65% glucose prior to FACS. Following the addition of DAPI, cells were sorted using an ARIA III FACS sorter (BD Biosciences) with the maximal flow rate of 6. The tdTomato reporter was excited by a 561-nm yellow/green solid-state laser and emission signal was detected in a range of 579–593 nm. According to their FCS/SSC criteria followed by cell doublet exclusion via an FSC-H versus FSC-W criterium, DAPI-negative living cells were sorted based on a distinctive tdTomato signal. Cells of interest were collected in DMEM/F12, 10% FBS, 100 U/mL penicillin, 100 g/mL streptomycin at 4 °C and pelleted by centrifugation. Enriched tdTomato cells prepared from the E16 basal telencephalon were split for each brain to prepare RNA for RNA sequencing and DNA for methylation-specific DNA immunoprecipitation (MeDIP) sequencing in parallel from the same set of sample. For RNA isolation, pellets were dissolved in 500 μL Trizol Reagent (Life Technologies) and subsequentially frozen on dry ice. For MeDIP-Seq analysis, cell pellets were frozen at −80 °C until further use. For RNA isolation the samples were then subjected to standard RNA isolation procedure using Trizol Reagent (Life Technologies) with additional application of GlycoBlue (Thermo Fisher Scientific) to a final concentration of 0.2% during RNA precipitation for better visualization of the pellet, digested with RNase-free DNase (Qiagen) and checked for integrity by capillary gel electrophoresis (Bioanalyzer, Agilent Technologies, Inc.). DNA isolation of FACS-enriched tdTomato cells was performed using QIAamp DNA Micro Kit (Qiagen) according to manufacturer’s instruction.
RNA quality was further assessed by measuring the RIN (RNA Integrity Number) using the fragment analyzer from Advanced Analytical (U.S.A.). Library preparation for RNA-Seq was performed using the TruSeq™ RNA Sample Prep Kit v2 (Illumina, Cat. N°RS-122-2002, U.S.A.) starting from 50 ng of total RNA. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega, U.S.A.). The size range of final cDNA libraries was determined applying the DNA chip on the fragment analyzer (average 350 bp; Advanced Analytical). cDNA libraries were amplified and sequenced by using the cBot and HiSeq2000 from Illumina (SR; 1x50 bp; ~30-40 million reads per sample). Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA v1.8.2. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics, G.B.). Read alignment was performed using STAR (v2.3.0; Dobin A et al. 2013) to the mm10 reference genome. Data were converted and sorted by samtools 0.1.19 and reads per gene were counted via htseq version 0.5.4.p3. Data analysis was performed using R/Bioconductor (3.0.2/2.12; Gentleman RC et al. 2004) loading DESeq2 (Love MI et al. 2014). Candidate genes were filtered to a FDR-corrected pvalue<0.05.


title: HAP1_2_74


title: Hmx3-Cre/tdTomato/Dnmt1loxp_KO_E16_rna_1

description: mRNA


title: HAP1_2_73


title: AML1_144_ctrl1

description:
AML cell line UCSD-AML1 untreated 144 h, replicate 1
AML1_ELF153_144_count_matrix.txt


title: HAP1_2_82


title: HAP1_2_72


title: Hmx3-Cre/tdTomato/Dnmt1loxp_WT_E16_rna_2

description: mRNA


title: ELF153_96_DAC3

description:
AML cell line ELF-153 treated with 100 nM DAC for 96 h, replicate 3
AML1_ELF153_96_count_matrix.txt
AML1_ELF153_96_TE_count_matrix.txt


title: HAP1_2_71


title: HAP1_2_70


title: Hmx3-Cre/tdTomato/Dnmt1loxp_WT_E16_rna_1

description: mRNA


title: HAP1_2_69


title: ELF153_96_DAC2

description:
AML cell line ELF-153 treated with 100 nM DAC for 96 h, replicate 2
AML1_ELF153_96_count_matrix.txt
AML1_ELF153_96_TE_count_matrix.txt


title: HAP1_2_6


title: HAP1_2_67


title: ELF153_96_DAC1

description:
AML cell line ELF-153 treated with 100 nM DAC for 96 h, replicate 1
AML1_ELF153_96_count_matrix.txt
AML1_ELF153_96_TE_count_matrix.txt


title: HAP1_2_68


title: ELF153_96_ctrl2

description:
AML cell line ELF-153 untreated 96 h, replicate 2
AML1_ELF153_96_count_matrix.txt
AML1_ELF153_96_TE_count_matrix.txt


title: HAP1_2_64


title: HAP1_2_65


title: HAP1_2_66


title: ELF153_96_ctrl3

description:
AML cell line ELF-153 untreated 96 h, replicate 3
AML1_ELF153_96_count_matrix.txt
AML1_ELF153_96_TE_count_matrix.txt


title: HAP1_2_63


title: HAP1_2_62


title: ELF153_96_ctrl1

description:
AML cell line ELF-153 untreated 96 h, replicate 1
AML1_ELF153_96_count_matrix.txt
AML1_ELF153_96_TE_count_matrix.txt


title: AML1_96_DAC3

description:
AML cell line UCSD-AML1 treated with DAC for 96 h, replicate 3
AML1_ELF153_96_count_matrix.txt
AML1_ELF153_96_TE_count_matrix.txt


title: HAP1_2_5


title: HAP1_2_60


title: AML1_96_DAC2

description:
AML cell line UCSD-AML1 treated with DAC for 96 h, replicate 2
AML1_ELF153_96_count_matrix.txt
AML1_ELF153_96_TE_count_matrix.txt


title: HAP1_2_59


title: HAP1_2_58


title: HAP1_2_57


title: AML1_96_ctrl3

description:
AML cell line UCSD-AML1 untreated 96 h, replicate 3
AML1_ELF153_96_count_matrix.txt
AML1_ELF153_96_TE_count_matrix.txt


title: AML1_96_DAC1

description:
AML cell line UCSD-AML1 treated with DAC for 96 h, replicate 1
AML1_ELF153_96_count_matrix.txt
AML1_ELF153_96_TE_count_matrix.txt


title: HAP1_2_56


title: Patient #17, d8, technical replicate 1

description:
17_d8-1
gene expression data from AML patients at day 8 of DAC treatment

hyb_protocol: Samples were hybridized according to manufacturer's protocol (Affymetrix).

scan_protocol: Samples were scanned according to manufacturer's protocol (Affymetrix).

data_processing: Raw data was analyzed with the Partek Genomics Suite.

label: Biotin

source_name: isolated blasts from peripheral blood

label_protocol: Samples were labeled with Biotin according to manufacturer's protocol (Affymetrix).

growth_protocol: Mononuclear cells were isolated out of AML patients' whole blood samples by Pancoll density centrifugation. AML blasts were enriched by automated magnetic sorting using anti-CD34 and -CD117 beads.

extract_protocol: Total RNA was extracted with Trizol Reagent (ThermoScientific)/Chloroform followed by DNase I digestion and column clean-up with the Qiagen RNeasy MinElute Cleanup Kit according to manufacturers' protocols. The subsequent steps were performed in technical triplicates (data only available in duplicates for samples 02_d8, 04_d0, 17_d0 and 17_d8 due to array QC failure)

treatment_protocol: AML patients were treated within the DECIDER trial (NCT00867672) with decitabine (DAC; 0 mg/m2 intravenously over 1 hour for 5 days).

tag: disease state

value: AML

tag: individual

value: Patient #17

value: decitabine (DAC)

tag: time

value: day 8

value: peripheral blood


title: Patient #17, d8, technical replicate 2

description:
17_d8-2
gene expression data from AML patients at day 8 of DAC treatment

tag: tissue


title: AML1_96_ctrl2

description:
AML cell line UCSD-AML1 untreated 96 h, replicate 2
AML1_ELF153_96_count_matrix.txt
AML1_ELF153_96_TE_count_matrix.txt


title: HAP1_2_55


title: HAP1_2_53


title: Patient #17, d0, technical replicate 2

description:
17_d0-2
gene expression data from AML patients at day 0 of DAC treatment

value: control

value: day 0


title: Patient #17, d0, technical replicate 1

description:
17_d0-1
gene expression data from AML patients at day 0 of DAC treatment


title: Patient #16, d8, technical replicate 3

description:
16_d8-3
gene expression data from AML patients at day 8 of DAC treatment

value: Patient #16


title: Patient #16, d8, technical replicate 1

description:
16_d8-1
gene expression data from AML patients at day 8 of DAC treatment


title: Patient #16, d8, technical replicate 2

description:
16_d8-2
gene expression data from AML patients at day 8 of DAC treatment


title: AML1_96_ctrl1

description:
AML cell line UCSD-AML1 untreated 96 h, replicate 1
AML1_ELF153_96_count_matrix.txt
AML1_ELF153_96_TE_count_matrix.txt

value: AML cell line


title: HAP1_2_61


title: HAP1_2_51


title: HAP1_2_4


title: PthrpCE_ColGFP-3-25

city: Houston

first: Noriaki

last: Ono

state: Texas

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

description: FACS-sorted at P25

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of eGFP and tdTomato_WPRE to the mouse genome (mm10).
Further downstream analysis steps were performed using the Seurat R package.
We filtered out cells with less than 1000 genes per cell and with more than 15% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (PCA, and UMAP), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Genome_build: mm10_trans_nono
Supplementary_files_format_and_content: raw_feature_bc_matrix/barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz

source_name: Mandibular molars

extract_protocol:
Mandibular molars were extracted, and cells were enzymatically dissociated from the periodontal space. GFP+, tdTomato+ cells and GFP+tdTomato+ cells were FACS-isolated. ~15,000 cells were loaded onto 10X Genomic Chromium Single Cell Solution v3
10X Genomic Chromium Single Cell 3' v3 Libraries

tag: cells

value: GFP+, tdTomato+ and GFP+tdTomato+ mesenchymal cells in periodontal space

value: Postnatal day 25


title: HAP1_2_49


title: HAP1_2_52


title: HAP1_2_54


title: ldko_rep_3

city: Urbana

first: Sayeepriyadarshini

last: Anakk

state: IL

address: 506 S. Mathews

department: Molecular and Integrative Physiology

institute: University of Illinois at Urbana Champaign

description: hepatocyte-specific fxr and shp knockout replicate 3

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Adaptors were trimmed from the reads using trimmomatic
Reads were mapped to the genome using STAR_2.4.2a
Insert distribution calculated with Picard_1.119
FPKM values were generated and compared between sets of samples using CuffDiff_2.2.1
Gene Ontology was determined using DAVID_6.8
Genome_build: GRCm38 vM10 mm10 (mus musculus)
Supplementary_files_format_and_content: csv file of calculated gene level fpkm values and cuffdiff output for differential gene expression

source_name: Liver

growth_protocol: Mice were housed in flow cages, following the standard 12 hour light/dark cycle and fasted for 8-10 hours overnight

extract_protocol:
Harvested livers were flash frozen in liquid nitrogen, and total RNA was isolated using Qiagen RNAeasy Kit with manufacturer's protocol.
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for “TruSeq Stranded mRNAseq Sample Prep kit”.

treatment_protocol: Not applicable

tag: strain

value: liver

tag: age

value: 10-12 weeks old

tag: genotype

value: hepatocyte-specific fxr-/- shp-/-

tag: fed state

value: 8-10 hours fasted


title: HAP1_2_48

tag: cell line


title: Patient #16, d0, technical replicate 3

description:
16_d0-3
gene expression data from AML patients at day 0 of DAC treatment

tag: treatment


title: HAP1_2_47


title: Patient #16, d0, technical replicate 2

description:
16_d0-2
gene expression data from AML patients at day 0 of DAC treatment


title: HAP1_2_50


title: Patient #16, d0, technical replicate 1

description:
16_d0-1
gene expression data from AML patients at day 0 of DAC treatment


title: HAP1_2_46


title: ldko_rep_2

description: hepatocyte-specific fxr and shp knockout replicate 2


title: HAP1_2_44


title: HAP1_2_45


title: ldko_rep_1

description: hepatocyte-specific fxr and shp knockout replicate 1


title: Patient #15, d8, technical replicate 1

description:
15_d8-1
gene expression data from AML patients at day 8 of DAC treatment

value: Patient #15


title: HAP1_2_43


title: Patient #15, d8, technical replicate 3

description:
15_d8-3
gene expression data from AML patients at day 8 of DAC treatment


title: HAP1_2_42


title: ctrl_rep_2

description: double floxed homozygous Fxr and Shp replicate 2

value: Fxrfl/fl Shpfl/fl


title: HAP1_2_40


title: ctrl_rep_3

description: double floxed homozygous Fxr and Shp replicate 3


title: HAP1_2_3


title: Patient #15, d8, technical replicate 2

description:
15_d8-2
gene expression data from AML patients at day 8 of DAC treatment

value: AML


title: HAP1_2_41


title: HAP1_2_39


title: ctrl_rep_1

description: double floxed homozygous Fxr and Shp replicate 1


title: Patient #15, d0, technical replicate 2

description:
15_d0-2
gene expression data from AML patients at day 0 of DAC treatment


title: HAP1_2_37


title: 4su RNA MUT replicate 1

city: Basel

first: Ilya

middle: M.

last: Flyamer

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
For 4SU and Spike in RNA seq: Fastq files were quality controlled using FastQC and mapped to the mm9 genome using tophat (parameters: --library-type fr-firststrand -r 200). Homer was used to make tagdirectories (makeTagDirectory, parameters: -unique -sspe -flip -fragLength 150), and to make bedgraphs for visualisation on UCSC (makeUCSCfile, parameters: -strand separate -style rnaseq).
For ChIPseq: Fastq files were quality controlled using FastQC and mapped to the mm9 genome using Bowtie2 (parameters: default). Sam files were converted to bam files and sorted using SamTools. Homer was used to make tagdirectories (makeTagDirectory, parameters: –unique, fragLength 150) and bedgraphs (makeUCSCfile, parameters: default).
Genome_build: mm9
Supplementary_files_format_and_content: gzipped bedgraph

extract_protocol: 4sU RNA was generated and isolated as described previously (Pintacuda et al., 2017),  with the following changes:  cells were incubated at 37°C with 4sU-supplemented medium for 20 min. The reaction was incubated with Biotin-HPDP with rotation for 1.5 hours at RT. For recovery of biotinylated 4sU-RNA, 1 µl of streptavidin beads was added per μg of RNA. Columns were washed using 900 µl washing buffer and RNA was eluted by 2 sequential additions of 100 µl Elution Buffer (100 mM DTT) to the column and eluates combined. RNA was further purified using the RNAeasy MinElute Clean-up kit (Qiagen; 74204) according to the manufacturer’s guidelines, eluting in 20 µl water. 1 μl of 4sU-labeled RNA was quality-checked by running on a 2100 Bioanalyzer Instrument (Agilent). To make 4sU sequencing libraries, 4sU labelled RNA was first depleted of rRNA using the Low Input Ribominus Eukaryotic System V2 (ThermoFisher Scientific; A15027) as per the manufacturer’s instructions. 600 ng of 4sU labelled RNA was used as input, and eluted in 5 µl RNase free water. All of the resulting rRNA free RNA was used to prepare 4sU sequencing libraries, using NEBnext Ultra Directional RNA library prep kit of Illumina (NEB; E7420). RNA fragmentation was carried out at 94°C for 15 min, as suggested for intact RNA. Libraries were indexed with Multiplex Oligos for Illumina® (Index Primers Set 1) (NEBnext; E7335) and amplified by PCR for 13 cycles. Library concentration and correct size distribution was confirmed on the Agilent 2100 Bioanalyser with the DNA HS Kit. Libraries were sequenced at BGI (Hong Kong; 100-base paired-end reads) using the HiSeq 4000 system (Illumina). Fastq files were quality controlled using FastQC and mapped to the mm9 genome using tophat (parameters: --library-type fr-firststrand -r 200). Homer was used to make tagdirectories (makeTagDirectory, parameters: -unique -sspe -flip -fragLength 150), and to make bedgraphs for visualisation on UCSC (makeUCSCfile, parameters: -strand separate -style rnaseq).

tag: cell type

value: mESCs

value: BRD4 Y430C


title: 4su RNA MUT replicate 2


title: HAP1_2_34


title: HAP1_2_38


title: HAP1_2_33


title: HAP1_2_35


title: HAP1_2_36


title: Patient #15, d0, technical replicate 3

description:
15_d0-3
gene expression data from AML patients at day 0 of DAC treatment


title: HAP1_2_32


title: HAP1_2_31


title: HAP1_2_2


title: HAP1_2_30


title: Patient #15, d0, technical replicate 1

description:
15_d0-1
gene expression data from AML patients at day 0 of DAC treatment


title: HAP1_2_27


title: 4sU RNA WT replicate 1

value: wild type


title: input DNA Y430C replicate 2

description: genomic DNA

extract_protocol: Cells were harvested by trypsinising and fixed with 1% formaldehyde (Thermo Fisher; 28906) in media (25°C, 10 min). This reaction was quenched with 0.125 M glycine for 5 min. ChIP was performed as described previously (Olley et al., 2018). After purification, DNA was eluted in 20 μl and libraries were prepared for ChIP and input samples as previously described (Pradeepa et al., 2016). Samples were sequenced at BGI (Hong Kong; 50-bp single-end reads) using the HiSeq 4000 system (Illumina). Fastq files were quality controlled using FastQC and mapped to the mm9 genome using Bowtie2 (parameters: default). Sam files were converted to bam files and sorted using SamTools. Homer was used to make tagdirectories (makeTagDirectory, parameters: –unique, fragLength 150) and bedgraphs (makeUCSCfile, parameters: default). For visualisation of BRD4 data, bedgraphs were uploaded to the genome browser UCSC.


title: input DNA Y430C replicate 1

description: genomic DNA


title: HAP1_2_28


title: HAP1_2_26


title: Patient #14, d8, technical replicate 2

description:
14_d8-2
gene expression data from AML patients at day 8 of DAC treatment

value: Patient #14

value: decitabine (DAC)

value: day 8

value: peripheral blood


title: Patient #14, d8, technical replicate 1

description:
14_d8-1
gene expression data from AML patients at day 8 of DAC treatment


title: Patient #14, d8, technical replicate 3

description:
14_d8-3
gene expression data from AML patients at day 8 of DAC treatment


title: Patient #14, d0, technical replicate 2

description:
14_d0-2
gene expression data from AML patients at day 0 of DAC treatment

value: control

value: day 0


title: Patient #14, d0, technical replicate 3

description:
14_d0-3
gene expression data from AML patients at day 0 of DAC treatment


title: Patient #14, d0, technical replicate 1

description:
14_d0-1
gene expression data from AML patients at day 0 of DAC treatment


title: BRD4 ChIP seq Y430C replicate 2

description: genomic DNA

tag: chip antibody

value: BRD4 Bethyl A301-985A-M


title: HAP1_2_25


title: 4sU RNA WT replicate 2


title: HAP1_2_24


title: HAP1_2_22


title: BRD4 ChIP seq Y430C replicate 1

description: genomic DNA


title: HAP1_2_23


title: HAP1_2_29


title: HAP1_2_21


title: input DNA WT replicate 2

description: genomic DNA


title: Patient #13, d8, technical replicate 1

description:
13_d8-1
gene expression data from AML patients at day 8 of DAC treatment

value: Patient #13


title: HAP1_2_20


title: input DNA WT replicate 1

description: genomic DNA


title: HAP1_2_1


title: HAP1_2_18


title: Patient #13, d0, technical replicate 3

description:
13_d0-3
gene expression data from AML patients at day 0 of DAC treatment


title: Patient #13, d8, technical replicate 3

description:
13_d8-3
gene expression data from AML patients at day 8 of DAC treatment


title: HAP1_2_17


title: Patient #13, d0, technical replicate 2

description:
13_d0-2
gene expression data from AML patients at day 0 of DAC treatment


title: HAP1_2_15


title: HAP1_2_16


title: HAP1_2_19


title: Patient #13, d8, technical replicate 2

description:
13_d8-2
gene expression data from AML patients at day 8 of DAC treatment


title: Patient #13, d0, technical replicate 1

description:
13_d0-1
gene expression data from AML patients at day 0 of DAC treatment


title: BRD4 ChIPseq WT replicate 1

description: genomic DNA


title: HAP1_2_13


title: spiked in RNAseq Y430C replicate 2

description: total RNA and drosophila RNA for spike in

extract_protocol: S2 cells were cultured in Schneider’s Drosophila Medium (Invitrogen; 11720-034), supplemented with 10% heat-inactivated FCS and 5% penicillin-streptomycin. Cells were passaged once they reached a density of ~2x107 cells/ml and seeded at a density of ~4x106. Cells were grown at 28°C in a 5% CO2 humidified atmosphere. Cells were frozen at a density of ~1x107 cells/ml in 45% conditioned Schneider’s Drosophila Medium media (containing 10% FCS), 45% fresh Schneider’s Drosophila Medium supplemented with 10% FCS, and 10% DMSO, and stored in liquid nitrogen. mESCs and S2 cells were harvested and counted. 0.2 million S2 cells were mixed with 10 million mESCs, and RNA was extracted using the RNeasy Mini Kit (Qiagen; 74104) using spin technology, with an additional on-column DNA digestion using the RNase-Free DNase Set (Qiagen; 79254). RNA was depleted of rRNA and RNA-seq libraries prepared as for the 4sU-seq.


title: spiked in RNAseq Y430C replicate 3


title: HAP1_2_11


title: spiked in RNAseq Y430C replicate 1


title: HAP1_1_9


title: spiked in RNAseq WT replicate 3


title: BRD4 ChIPseq WT replicate 2

description: genomic DNA


title: HAP1_2_10


title: HAP1_1_96


title: HAP1_1_95


title: spiked in RNAseq WT replicate 2


title: HAP1_2_12


title: HAP1_2_14


title: HAP1_1_94


title: HAP1_1_93


title: spiked in RNAseq WT replicate 1


title: HAP1_1_91


title: HAP1_1_90


title: HAP1_1_8


title: Patient #12, d0, technical replicate 3

description:
12_d0-3
gene expression data from AML patients at day 0 of DAC treatment

value: Patient #12


title: TRL CUT&RUN Rep3

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

data_processing:
Library strategy: CUT&RUN
Cleaved DNA is isolated and subjected to paired-end Illumina sequencing to map the distribution of the chromatin epitope. CUT&RUN profiling with 1x10^6 S2 cells and library amplification with 14 cycles of PCR was performed as described (Skene and Henikoff, 2017). Libraries were sequenced for 25 cycles in paired-end mode on the Illumina HiSeq 2500 platform at the Fred Hutchinson Cancer Research Center Genomics Shared Resource.
Paired-end reads were mapped to the dm3 version of the D. melanogaster genome (FlyBase.org) using Bowtie2 with following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700
The fraction of reads less than 50 bp in length mapped at each nucleotide was multiplied by the total number of nucleotides mapped genome-wide, which was arbitrarily chosen as approximate size of the genome (139712364), to give a normalized count at that position.
The reads were then aggregated to 10 base-pair windows, and only paired-end reads of length less than 50 bp were used in the analysis as they usually represent areas of transcription factor binding.
Genome_build: dm3
Supplementary_files_format_and_content: bigwig files of coverage of paired end reads with insert size less than 50 bp

organism: Drosophila melanogaster

source_name: Drosophila S2 Cells

growth_protocol: Drosophila S2 cells were purchased from Invitrogen and grown to mid-log-phase in HyClone Insect SFX media (GE).

extract_protocol:
We used a primary antibody to Drosophila TRL (Melnikova et al., Proc Natl Acad Sci U S A 101, 14806-14811, 2004) (a gift from G Cavalli, Institute of Human Genetics, Université de Montpellier, France) and protein A-micrococcal nuclease fusion (Skene and Henikoff, Elife 6, 2017) (pAMNase, a gift from S. Henikoff, Fred Hutchinson Cancer Research Center, Seattle WA). We used an immuno-tethered strategy for profiling the binding of the TRL transcription factor in Drosophila cells. The CUT&RUN method uses an antibody to a specific chromatin epitope to tether pAMNase at chromosomal binding sites within permeabilized cells (Skene and Henikoff, Elife 6, 2017). The nuclease is activated by the addition of calcium and cleaves DNA around binding sites.
Cleaved DNA is isolated and subjected to paired-end Illumina sequencing to map the distribution of the chromatin epitope. CUT&RUN profiling with 1x10e6 S2 cells and library amplification with 14 cycles of PCR was performed as described (Skene and Henikoff, 2017). Libraries were sequenced for 25 cycles in paired-end mode on the Illumina HiSeq 2500 platform at the Fred Hutchinson Cancer Research Center Genomics Shared Resource. Paired-end reads were mapped to the dm3 version of the D. melanogaster genome (FlyBase.org) using Bowtie2.

value: Drosophila S2 Cells

tag: antibody

value: a primary antibody to Drosophila TRL


title: Patient #12, d8, technical replicate 2

description:
12_d8-2
gene expression data from AML patients at day 8 of DAC treatment


title: Patient #12, d0, technical replicate 2

description:
12_d0-2
gene expression data from AML patients at day 0 of DAC treatment


title: HAP1_1_89


title: Patient #12, d8, technical replicate 3

description:
12_d8-3
gene expression data from AML patients at day 8 of DAC treatment


title: Patient #12, d8, technical replicate 1

description:
12_d8-1
gene expression data from AML patients at day 8 of DAC treatment


title: TRL CUT&RUN Rep2


title: TRL CUT&RUN Rep1


title: Patient #12, d0, technical replicate 1

description:
12_d0-1
gene expression data from AML patients at day 0 of DAC treatment


title: HAP1_1_87


title: HAP1_1_88


title: HAP1_1_86


title: TEAD/TGF-β(12h)

city: Nanchang

first: Xiaohua

last: Yan

address: No. 1299, Xuefu Avenue, Honggutan

institute: Nanchang University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

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


title: HAP1_1_92


title: HAP1_1_85


title: Patient #11, d8, technical replicate 2

description:
11_d8-2
gene expression data from AML patients at day 8 of DAC treatment

value: Patient #11


title: HAP1_1_84


title: TEAD/TGF-β(4h)


title: Patient #11, d8, technical replicate 3

description:
11_d8-3
gene expression data from AML patients at day 8 of DAC treatment


title: Patient #11, d8, technical replicate 1

description:
11_d8-1
gene expression data from AML patients at day 8 of DAC treatment


title: Patient #11, d0, technical replicate 3

description:
11_d0-3
gene expression data from AML patients at day 0 of DAC treatment


title: TEAD/TGF-β(0h)


title: HAP1_1_82


title: Patient #11, d0, technical replicate 2

description:
11_d0-2
gene expression data from AML patients at day 0 of DAC treatment


title: HAP1_1_81


title: HAP1_1_80


title: HAP1_1_78


title: HAP1_1_79


title: HAP1_1_7


title: Patient #11, d0, technical replicate 1

description:
11_d0-1
gene expression data from AML patients at day 0 of DAC treatment


title: HAP1_1_83


title: HAP1_1_77


title: HAP1_1_76


title: vector/TGF-β(0h)


title: Patient #07, d8, technical replicate 3

description:
07_d8-3
gene expression data from AML patients at day 8 of DAC treatment

value: Patient #07


title: vector/TGF-β(4h)


title: T_2

city: shanghai

first: Yongli

last: Zhang

address: No.2699 Gaokexi Road, Shanghai

department: Obstetrics and Gynecology

institute: Shanghai First Maternity and Infant Hospital

description:
sample_cir_count_with_gene_symbol_cirbase.xls
transcript_sample_FPKM.xls

data_processing:
Paired-end 150 bp reads was sequenced by Illumina Hiseq sequencer. Trim Galore software (v0.4.2) was used to remove adaptor and low quality reads. FastQC software (v0.11.5) was used for quality control.  High quality reads was mapped to human hg38 reference sequence by STAR software (v2.5.3a).
For mRNA and lncRNA transcripts, FPKMs (Fragments Per Kilobase of transcript per Million fragments mapped) were calculated as the expression of transcript.
For circRNA, BackSplice reads were counted and  BSRP (Back Spliced Reads Per million mapped reads) were calculated as the expression of circRNAs.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM & COUNTS

growth_protocol: 10% Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum

extract_protocol:
Total RNA was extracted from cells using TRIzolTM Reagent (#15596026, Invitrogen, Carlsbad, CA, USA) per the manufacturer’s protocol, and ribosomal RNA was removed using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA).
Fragmented RNA (average length of ~200 bp) were subjected to first-strand and second-strand cDNA synthesis followed by adaptor ligation and enrichment with a low cycle per the instructions of the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit 2.0 (Life Technologies, USA).

tag: tag

value: tumor tissue from the second patient

value: uterine leiomyoma


title: T_1

value: tumor tissue from the first patient


title: HAP1_1_74


title: HAP1_1_71


title: HAP1_1_72


title: HAP1_1_6


title: HAP1_1_70


title: Normal_3

value: adjacent normal uterine tissue from the third patient


title: HAP1_1_69


title: vector/TGF-β(12h)


title: Patient #07, d8, technical replicate 1

description:
07_d8-1
gene expression data from AML patients at day 8 of DAC treatment

value: AML


title: Patient #07, d0, technical replicate 3

description:
07_d0-3
gene expression data from AML patients at day 0 of DAC treatment


title: Patient #07, d0, technical replicate 2

description:
07_d0-2
gene expression data from AML patients at day 0 of DAC treatment


title: Normal_2

value: adjacent normal uterine tissue from the second patient


title: HAP1_1_68


title: Patient #07, d0, technical replicate 1

description:
07_d0-1
gene expression data from AML patients at day 0 of DAC treatment


title: HAP1_1_75


title: Patient #06, d8, technical replicate 3

description:
06_d8-3
gene expression data from AML patients at day 8 of DAC treatment

value: Patient #06

value: decitabine (DAC)

value: day 8


title: HAP1_1_66


title: Patient #07, d8, technical replicate 2

description:
07_d8-2
gene expression data from AML patients at day 8 of DAC treatment

value: peripheral blood


title: HAP1_1_73


title: HAP1_1_65


title: HAP1_1_64


title: mRNA-seq: GSC11 NS

data_processing:
RNA-seq were mapped to the human genome (hg19) using tophat2 (version 2.1.0) with a transcript annotation file from Gencode (Release 19)
The reads count per gene were obtained with the HTseq-count script on properly paired reads and Genecode V19 transcript annotation file
Differential expression analysis between groups was based on reads count using DESeq2 and edgeR R packages
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample …

source_name: glioblastoma stem cell

extract_protocol:
The total RNA were extracted using the RNeasy Mini Kit (Qiagen, 74104) following the manufacturer's protocol. RNA samples were quality-checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies).
TruSeq Stranded mRNA library preparation and sequencing on illumina  HiSeq4000 were performed by Integragen, SA (Evry, France), according to the manufacturer's protocol.

treatment_protocol: SMART vector non targeting PGK-TurboGFP (VSC11713) was purchased from GE Healthcare (Little Chalfont, UK). Viral particles were produced and concentrated by the Vectorology platform of Montpellier (Biocampus, Montpellier, France). GSCs were infected using a multiplicity of infection of 10 and processed 120 h later for RNA-seq analysis

tag: glioblastoma stem cell culture

value: Glioblastoma stem cells

value: non targeting shRNA


title: HAP1_1_63


title: HAP1_1_61


title: HAP1_1_62


title: mRNA-seq: GSC6 NS


title: Normal_1

value: adjacent normal uterine tissue from the first patient


title: HAP1_1_5


title: Experimental cell RNA, rep 3

city: Orlando

first: Ratna

last: Chakrabarti

address: 12722 Research Parkway

institute: University of Central Florida

description:
E3
polyA+ mRNA
Expression_Gene.xlsx
Expression_Transcript.xlsx

data_processing:
Sequence quality was examined using the FastQC.
The raw sequences were trimmed off 5’, 3’-adaptor bases using cutadapt.
The trimmed sequences were aligned to reference genome using Hisat2 software.
The aligned reads were assembled to transcripts by StringTie and FPKMs were computed.
The differentially expression of the genes and transcripts were analyzed using Ballgown R package.
rMATS was used to analyze alternative splicing events.
Genome_build: GENCODE mouse GRCm38
Supplementary_files_format_and_content: Gene/transcript expression levels in FPKM.

source_name: Stably transfected C4-2B prostate cancer cells

growth_protocol: Stable sublines of C4-2B prostate cancer cells constitutively expressing LINC00888 or the empty vector were maintained in RPMI1640 with 10% FBS.

extract_protocol:
Total RNA was extracted using Zymo RNA extraction kit and used for RNA-seq analysis.
Libraries were prepared according to Roche KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Briefly, polyA+ mRNAs were enriched by oligo (dT) magnetic beads from the total RNA samples; RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific; The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute quantification qPCR method; The barcoded libraries were mixed, denatured to single strands in NaOH, captured on Illumina flow cell, amplified in situ, and sequenced for 150 cycles for paired-ends on an Illumina HiSeq 4000 system.

treatment_protocol: Overexpression of LINC00888 with a fold change in expression 15.27±2.4 (Mean±SD) was determined by qRT-PCR in the extracted total RNA used for RNA-seq analysis.

value: Prostate cancer cell line

tag: vector

value: pcDNA 3.1+LINC00888


title: Patient #06, d0, technical replicate 3

description:
06_d0-3
gene expression data from AML patients at day 0 of DAC treatment

tag: disease state

value: control

value: day 0


title: HAP1_1_67


title: Patient #06, d8, technical replicate 2

description:
06_d8-2
gene expression data from AML patients at day 8 of DAC treatment

tag: individual


title: Patient #06, d0, technical replicate 2

description:
06_d0-2
gene expression data from AML patients at day 0 of DAC treatment

tag: time


title: HAP1_1_59