title: 128264: 12Z LINC01133 knockdown 3

status: Public on Aug 23 2021

city: Klosterneuburg

first: Florian

last: Pauler

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (IST Austria)

data_processing:
Index for alignments was prepared using STAR (2.7.6a_patch_2020-11-17 GRCh38.p13) with FASTA files from GRCh38.p13 assembly and Gencode (v36) gene annotation in GTF format.
Raw reads were supplied as BAM files and converted to fastq using samtools (v1.10) for alignment with STAR using parameters: --outFilterMultimapNmax 1 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 3000000000 --quantMode GeneCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited text files with read counts in genes as reported by the STAR aligner

molecule: polyA RNA

source_name: Endometriosis epithelial cell line

growth_protocol: 12Z cells were seeded in complete culture cell medium 12 hours prior transfection on 6-well culture plates (Nunc, Thermo Fisher Scientific, MA, USA) at a concentration of 1X10^5 cells per/well and allowed to grow to approximately 40% confluency.

extract_protocol:
Total RNA was isolated using the RNeasy® Mini Kit (Qiagen).
NEB polyA RNA-seq library, Illumina HiSeqV4 PE125 according to manufacturers protocols

treatment_protocol: Cells were then transfected with either the LINC0133 targeting siRNA oligo at a final concentration of 10nM (Cat. S444575, Ambion) or a non-targeting control siRNA oligo (Cat. 4390846, Ambion, USA) using Lipofectamine RNAiMAX transfection reagent according to the manufacturer’s protocol (Invitrogen by Life Technology, MA, USA). The cells were lysed and analyzed 72 hours after transfection.

value: 12Z epithelial endometriosis cell line

value: LINC01133a siRNA oligo (Cat. S444575, Ambion)

tag: timepoint

value: 72 hours after transfection


title: 128262: 12Z LINC01133 knockdown 1

type: SRA

middle: M

library_source: transcriptomic

organism: Homo sapiens

tag: cell line

tag: treatment


title: 128263: 12Z LINC01133 knockdown 2


title: 3InfectedVehicle

status: Public on Nov 24 2021

city: Bethesda

first: Joseph

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

country: USA

institute: NIH / National Cancer Institute

data_processing:
Sequences were trimmed for adapter sequences and mapped to reference human hg38 genome and gencode v24 transcripts using STAR software. Quantification was carried out with RSEM using transcriptome bam file created by star and gencode v24 transcriptome as index for RSEM.
Genome_build: hg19v24 with KSHV(NC_009333.1) and hg38v30 with EBV (NC_007605.1)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

source_name: human umbilical vein endothelial cells

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were obtained from Lonza and passaged in EGM2 medium (Lonza) for up to 5 passages, with passages 3 to 5 used for experiments.

extract_protocol:
HUVEC mRNA was extracted using the RNeasy kit (Qiagen) with DNAse treatment
Truseq Stranded RNA prep kit RS-122-2201

treatment_protocol: 25HC (H1015; Sigma) was reconstituted in ethanol at 5 mM and stored in single-use aliquots at 20°C for no more than 4 weeks. 25HC was diluted in EGM2 media (final: 5 uM 25HC) and added 2 hours prior to infection and again after infection. De novo infections in HUVECs were carried out by diluting concentrated BCBL-1 supernatant in EGM2 media at a multiplicity of infection (MOI) of 40, as determined by LANA copy number. Polybrene was added at 8 ug/ml. Virus supernatant were washed off after 6 h and replaced with fresh EGM2. HUVECs were harvested 2 days after infection.

tag: infection status

value: KSHV de novo infection

value: ethanol


title: 1MockVehicle

value: Uninfected


title: 128259: 12Z control 1

value: control non-targeting control siRNA oligo (Cat. 4390846, Ambion)


title: ExpLBM_PRRX1_high_rep2

status: Public on Jul 08 2021

city: okayama

first: Takeshi

last: Takarada

state: okayama

address: 2-5-1 Shikata-cho

department: Graduate School of Medicine, Dentistry and Pharmaceutical Sciences

country: Japan

institute: Okayama university

data_processing:
All sequence reads were extracted in FASTQ format using the CASAVA 1.8.4 pipeline.
Trimmomatic (version 0.36) was used to remove adapters and filter raw reads <36 bases as well as leading and trailing bases < quality 20.
Genome_build: Filtered reads were mapped to hg19 using HISAT2 (v2.1.0).

source_name: Stably expanded PRRX1 high LBM cells derived from hiPSC

growth_protocol: hPSCs were cultured or maintained with StemFit (Ajinomoto). Before reaching subconfluency, cells were stripped with TrypLE Select / 0.25 mM EDTA and suspended in StemFit containing 10 µM Y27632. Then 1x104 cells were suspended with StemFit containing 10 µM Y27632 and 8 µl iMatrix511-silk to seed them onto 6 cm dish. Next day culture media were replaced with fresh StemFit w/o 10 µM Y27632. Until next passage, culture media were changed every 2 days. LBM cells were stripped with Accutase and 2x105 cells were suspended with ExpLBM medium (CDM2 medium, 1 µM A-83-01, 0.5 µM LDN-193189, 3 µM CHIR99021, 150 nM Vismodegib, 10 µM Y27632) containing 16 µl iMatrix511-silk and seeded onto 6 cm culture dish. Culture media were replaced with fresh ExpLBM medium every 2 days. Before reaching subconfluency, cells were passaged as described.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN).
Sequencing libraries were KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems) and SeqCap Adapter Kit (Set A or Set B, Roche) following manufacture`s instruction. The initial amount of total RNA was 1000 ng.

treatment_protocol: 3x10~4 hPSCs were suspended in 1 ml of StemFit (Ajinomoto) containing 10 µM Y27632 (Fujifilm wako) and 4 µl iMatrix511-silk (Nippi) and seeded to 3.5 cm culture dish. Next day culture medium was replaced with fresh StemFit w/o 10 µM Y27632. After culturing for 2 days, cells were washed with PBS and differentiation was induced by changing culture media at each time point. CDM2 medium26 was used as basal culture medium and cytokines or chemicals were added to prepare each differentiation medium. The composition of chemicals or cytokines used in this study was as follows: mid primitive streak (30 ng/ml ACTIVIN A, 40 ng/ml BMP4, 6 µM CHIR99021, 100 nM PIK90, 10 µM Y27632), lateral plate mesoderm (1 µM A-83-01, 30 ng/ml BMP4, 1 µM C59, 10 µM Y27632), limb bud mesenchyme (1 µM A-83-01, 0.5 µM LDN-193189, 3 µM CHIR99021, 150 nM Vismodegib, 10 µM Y27632)

tag: cell type

value: iPSC

value: PRRX1 3`tomato reporter established with 414C2

tag: days after induction


title: ExpLBM_PRRX1_high_rep1


title: Input_DN-TLX3

status: Public on Apr 27 2021

city: Marseille

first: Salvatore

last: Spicuglia

state: France

address: Luminy

country: France

institute: Aix-Marseille University, INSERM, TAGC, UMR 1090

library_source: genomic

data_processing:
The ABI SOLiD v3.0 system was used to produce sequence files in colour space formats.
Reads were mapped onto the mm9 reference genome using SOLiD pre-processing pipeline.
To reduce the risk of potential bias, we discarded all tags with exactly the same coordinates.
Reads were then elongated to 300 bp and converted to bin format using a window of 10 bp or 100 bp.
Enriched regions (peaks) were isolated using CoCAS software with 7.5SD + mean for the main window and 5SD + mean for the extension window.
Artifacts were detected and removed by performing peak detection in CoCAS (using 7SD + mean and 5SD + mean as main and extension window thresholds, respectively) in reads originating from Input treatment.
Genome_build: mm9
Supplementary_files_format_and_content: peaks as bed file

molecule: genomic DNA

organism: Mus musculus

source_name: DN-TLX3 cells

growth_protocol: Thymi from 4- to 6-week old C57Bl/6 mice were extracted and mechanistically disrupted on a 75-µm nylon cell strainer (BD Biosciences Pharmingen). CD4-CD8- double-negative (DN) thymocytes were purified by the depletion of CD4+CD8+ double-positive (DP) cells, and CD4+CD8- and CD4-CD8+ single-positive (SP) cells, using the AutoMACS system (Miltenyi Biotec). Single-cell suspensions of thymocytes were stained with magnetic bead-conjugated anti-CD4 and anti-CD8 antibodies (Catalogue No: 130-117-043 and 130-104-075; Miltenyi Biotec) at 4 °C for 15 min and then sorted in AutoMACS. For maximum purity, sorting of DN cells was performed using a FACS Aria sorter (BD Biosciences). Sorted DN cells were transduced with pMSCV-GFP-TLX3 retroviral vectors were resuspended in vector supernatants in the presence of 10 µg/ml polybrene and spinoculated for 2 hours at 3500 rpm. Transduced thymocytes were seeded in 6-well plates in co-culture with OP9-DL1 g-irradiated cells for further T-cell differentiation in vitro over 5 weeks. The differentiation medium (referred to as IL-7/Flt3L medium) consisted of a-MEM medium supplemented with 10% FCS, 50 µM 2-ME, 2 mM glutamine, 10 mM HEPES (pH 7.5), 1 mM sodium pyruvate, 100 U/ml penicillin, 0.1 mg/ml streptomycin, 10 µg/ml gentamicin, 1% supernatant of rIL-7-secreting J558L cells, and 2.5% supernatant of rFlt3L-producing SP2.0 cells. A cell line, named DN-TLX3, was generated and maintenaed in co-culture with OP9-DL1 strom cells.

extract_protocol:
ChiP from DN-TLX3 cells was performed using a custom antibody as previously described (Blood Adv. 2017 May 4;1(12):733-747; Cancer Cell. 2012 Apr 17;21(4):563-76)
Single-end using ABI SOLiD platform version 4

treatment_protocol: No tratement was applied

value: DN-TLX3 cells

tag: antibody


title: Jurkat_RNA_DMSO

status: Public on Apr 16 2021

data_processing:
Base-calling with bcl2fastq v2.19.0.
Trimming with sickle v1.33 and "-t sanger -q 20" arguments
Alignement on hg19 with STAR v2.7 using Ensembl release 87 gtf annotations
Counting in protein-coding genes using subread featureCounts v2.0.0 with "-O" argument.
Genome_build: hg19
Supplementary_files_format_and_content: raw_counts: comma-separated raw counts produced by featureCounts

source_name: Jurkat T-cell line

extract_protocol:
The extraction of total RNA was performed using the RNeasy Plus Mini kit (Qiagen) according to the protocol recommended by the supplier. Total RNA was quantified using a Nanodrop 1000 spectrophotometer (Thermo Scientific) and stored at −80 °C until needed. Extracted RNA was used for the RNA-seq library preparation, using the TruSeq RNA Library Prep Kit v2 (Illumina). Libraries were paired-end sequenced on the Illumina NextSeq 500 sequencer.
Extracted RNA was used for the RNA-seq library preparation, using the TruSeq RNA Library Prep Kit v2 (Illumina). RNA-Seq libraries were paired-end sequenced (50+30 bp) on an Illumina NextSeq 500 sequencer.

treatment_protocol: Jurkat cells were treated with either DMSO or 10 μM PBIT for 5 and 24 hours

value: Jurkat

value: DMSO

tag: treatment duration


title: 1Mock25HC


title: 4Mock25HC


title: Jurkat_RNA_PBIT_24h

value: PBIT


title: ChIP_TLX3_DN-TLX3


title: B lymphocytes (D7_2 + VDJ_D4_2)

status: Public on May 29 2021

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description:
Multiplexed: Gene expression library (GEX)
Multiplexed: V(D)J library

data_processing:
Library strategy: RNA-seq + VDJ
Data were analyzed using Cell Ranger™ v3.1.0 pipelines which is available in 10xGenomics website.
Genome_build: mm10 3.0.0 for GEX and GRCm38 3.1.0 for V(D)J
Supplementary_files_format_and_content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix
Supplementary_files_format_and_content: csv;High-level descriptions of each clonotype and annotations of each high-confidence, cellular contig.

source_name: B lymphocytes

extract_protocol:
The heart samples were enzymatically digested in type II collagenase (1,000 IU/ml, Worthington Biochemical Corporation, Lakewood, NJ, USA) for 30 minutes at 37°C. The digested hearts and the med-LNs were gently filtered through a 30-µm mesh (Miltenyi Biotec, Bergisch Gladbach, Germany). Following a washing step, all samples were resuspended in FACS buffer (PBS containing 1% BSA, 0.1% sodium azide and 1 mM EDTA), and surface staining was performed in the presence of FC-blocking antibody (anti-CD16/CD32, clone 2.4G2, BD Pharmingen). The following fluorophore-conjugated antibodies (obtained from Biolegend [San Diego, CA, USA], unless otherwise indicated) were used for surface staining: anti-CD45 (clone 30-F11), anti-CD45.2 (clone 104), anti-CD19 (clone 6D5), anti-CD45/B220 (clone RA3-6B2), anti-CXCR5 (clone L138D7), anti-CD69 (clone H1.2F3), anti-CD95 (clone SA367H8), and anti-GL7 (clone GL7). Additionally, AmCyan Zombie Aqua fixable viability dye (Biolegend, San Diego, CA, USA) was used to exclude dead cells. Flow cytometry measurements were performed on an Attune-NxT (Thermo Scientific, Darmstadt, Germany) or on a FACS Canto (BD, Heidelberg, Germany). Cell sorting for single-cell RNA sequencing was performed using a FACS Aria III (BD, Heidelberg, Germany), and no sodium azide was included in the buffers used for sorting purposes. Post-sorting, the cells were washed once in PBS containing 1% FCS, and each sample was labelled separately with anti-CD45/H2-K hashtag antibody (Biolegend TotalSeq-C antibodies, San Diego, CA, USA). Following a washing step, all the samples were pooled and resuspended in 100 µl of PBS/0.05% BSA, filtered through a 40 µm cell strainer and loaded in the 10x Genomics Chromium system as one multiplexed sample.
Cells were loaded in the 10X Genomics Chromium with the aim of recovering 10,000 cells. Libraries were generated with the Chromium Next GEM Single Cell 5’ Reagents Kit v1.1 Chemistry according to manufacturer ´s instructions.
Chromium Next GEM Single Cell 5’ v1.1 (10xGenomics)

tag: tissue

value: heart

tag: strain

tag: kit

value: Chromium Next GEM Single Cell 5’ v1.1


title: 128260: 12Z control 2


title: Jurkat_Input

data_processing:
Base-calling with bcl2fastq v2.19.0.
Trimming with sickle v1.33 and "-t sanger -q 20" arguments
Alignement on both endogenous hg19 and exogenous BDGP6 genomes with bowtie v2.4.2
Filtering on mapping quality using samtools v1.11 and "view -q 30" argument
Bigwig files were produced using DeepTools bamCoverage and scaling the signal by 100,000 divided by the number of reads mapping to the drosophila exogenous BDGP6 genome.
Genome_build: hg19
Supplementary_files_format_and_content: bw : spikein-normalized bigwig files

extract_protocol:
ChIP was performed using anti-H3K4me3 (C15410003; Diagenode). 5x106 Jurkat cells were used for each treatment with PBIT (10 uM) or OICR-9429 (25 uM) for 5 hours. Briefly, cells were cross-linked with 1% formaldehyde for 10 min at room temperature before the reaction was quenched with 250 mM glycine. Cell pellets were washed twice with PBS and nuclear lysates sonicated for 6 cycles using a Bioruptor Pico (Diagenode). Immunoprecipitation was performed with 5x105 Jurkat cells, complemented with 10% of Drosophila chromatin from S2 cells as spike in control (Orlando et al. 2014). Antibody (1 ug) was added to each sample and immunoprecipitation performed overnight on a rotator at 4 °C. 20 uL of magnetic beads (Dynabeads protein G, Novex Life technologies) was added to each sample. After 5 washes with three different buffers according to the BLUEPRINT protocol (http://dcc.blueprint-epigenome.eu/#/md/methods). ChIP-bound fractions were extracted by incubation for 20 min at room temperature with elution buffer (1% SDS, 0.1M NaHCO3). Cross-linking was then reversed by incubation at 65°C. Proteinase K (10mg/mL) was added to eliminate protein from the samples. DNA was extracted using the QIAquick MinElute PCR purification kit (Qiagen) following manufacturer’s instructions.
ChIP-Seq libraries were generated with the MicroPlex Library Preparation Kit (Diagenode), according to the manufacturer instructions. The libraries were sequenced in paired-end 50+30 bp mode using the NextSeq® 500/550 (Illumina) according to manufacturer’s instructions.

treatment_protocol: 5-hour incubation with treatment (DMSO, PBIT 10 μM or OICR-9429 25 μM)

value: input


title: Jurkat_H3K4me3_PBIT_Spike


title: 128261: 12Z control 3


title: 3Mock25HC


title: CCRF-CEM_H3K4me3

data_processing:
Base calling was performed using RTA version 2.
Reads were trimmed with Sickle v1.33 and aligned to the hg38 genome assembly using Bowtie v2.3.4.3 and defaults parameters.
Coverage tracks were generated with deepTools v3.2.1.
Peaks were called using Macs2 v2.1.1 and –broad argument.
Genome_build: hg38
Supplementary_files_format_and_content: bw: RPKM-normalized coverage track
Supplementary_files_format_and_content: bed: peaks

source_name: T acute lymphoblastic cell line

growth_protocol: cell lines were cultured in RPMI-1640 medium (Thermo Fisher, Cat. 21875091) supplemented with 20%  FBS and 1% penicillin/streptomycin and 1x sodium pyruvate

extract_protocol:
H3K4me3 ChIP were performed following the BLUEPRINT protocol (http://dcc.blueprint-epigenome.eu/#/md/methods). For the Loucy and Jurkat cell lines, a 1% of Drosphila S2 chromatin was added as spike-in
Single-end sequencing 75bp was performed using Illumina NextSeq 500.

tag: chip target

value: CCRF-CEM


title: ALL-SIL_H3K4me3

value: ALL-SIL


title: RPMI_H3K4me3

value: RPMI


title: 790_BT15_H3K4me3

source_name: T acute lymphoblastic blasts


title: Jurkat_H3K4me3_Spike


title: 427_BT3_H3K4me3


title: 764_BT16_H3K4me3


title: Nodular goiters, biological replicate 2

status: Public on Mar 05 2022

type: genomic

city: Hangzhou

first: Lisong

last: Teng

address: Yuhangtang Road

country: China

institute: Zhejiang University

description:
Nodular goiters sample
N2

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Infnium MethylationEPIC Array using standard Illumina protocol

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

data_processing: The raw intensity data were loaded to a biocondutor package “minfi”. The raw data were normalized using the subset-quantile within array normalization (SWAN) method and probes with a detection p-value >= 0.01 in at least one sample were excluded from further analysis. Methylation values, referred to as β-values, were calculated as the ratio of the methylated signal intensity to the sum of the methylated and unmethylated signals after background subtraction. The β-values were reported as a DNA methylation score ranging from 0 (completely unmethylated) to 1 (fully methylated).

label: biotin (C,G), dinitrophenyl (A,T)

source_name: Nodular goiters

label_protocol: Standard Illumina Protocol

growth_protocol: not applicable

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: fixed paraffin-embedded

tag: sample type

value: FFPE

tag: disease state

value: Nodular goiters

value: Thyroid


title: V610_RNASeq

status: Public on Apr 06 2021

city: College Station

first: Monique

last: Rijnkels

state: Texas

address: 660 Raymond Stotzer Pkway

department: Department of Veterinary Integrative Biosciences

institute: Texas A&M University

data_processing:
aligned with HISAT2 v 2.0, using options  --rna-strandness RF --dta
converted to sorted bam using samtools
aligned reads were assembled into transcripts using Stringtie (version 1.3.2) including information on strandedness of reads with the reference annotation Ensembl v87 for the genome assembly UMD3.1 (ftp://ftp.ensembl.org/pub/release-87).
the resulting gtf annotation files for all samples were merged into a final gtf annotation file using the Stringtie merge option.
assigned transcripts to existing Ensembl 87 annotations with Gffcompare
counted reads per feature with featureCounts (Liao et al. 2014), v.1.5.2 Subread package, default settings
differential expression analysis on features with at least 10 reads in at least 4 samples (as determined by feature counts) in edgeR. Statistical significance of difference between virgin and lactating stages evaluated with a linear model, likelihood ratio test, and Bonferroni correction.
Genome_build: Bos taurus UMD 3.1
Supplementary_files_format_and_content: tab delimited text file of read counts for every feature with an identified Ensembl87 annotation in all samples
Supplementary_files_format_and_content: tab delimited text file containing sample RPKM, log 2 fold change (virgin / lactating), and corrected p values for every feature with an identified Ensembl87 annotation.

organism: Bos taurus

source_name: Mammary epithelial organoids

extract_protocol:
Tissue was minced to a fine slurry in freshly prepared Collagenase solution (0.2% Collagenase A (Roche), 0.05% Trypsin (1:250 powder, 100U/ ml  Gibco/life sciences), Hyaluronidase (Sigma, St Louis MO), 5% Fetal Calf serum, Pen/Strep/Fung (hyclone) or 5µg/ml Gentamycin (Sigma), in DMEM/F12 (Gibco/Life technologies) 10 ng/ml Insulin). Minced tissue was incubated in Collagenase solution (10 ml solution/g tissue) for 3.5 hours at 37C in 50 ml conical tube with slow shaking (120 rpm). Digested tissue was centrifuged for 10 minutes at 453xg at 4°C, supernatant and fat layer discarded, pellet was gently resuspended by pipetting in 5 ml DMEM/F12 without serum. A further 5 ml DMEM/F12 without serum was added and resuspended sample was centrifuged for 10 minutes at 453xg at 4°C, media was discarded and pellet resuspended gently in 10 ml DMEM/F12 and centrifuged for 10 minutes at 453xg at 4°C . Pellet was resuspend gently in 10 ml followed by brief pulls spins at 453xg (centrifuge set to 1 minute @ 453 x g, hit the brakes 2 seconds after 453 xg is reached). Pulls spins were repeated at least 4 time or until very few single cells and mainly epithelial organoid clusters were observed under a microscope. Organoid pellet for RNA-analysis was resuspended in 1 ml TRIzol and stored at -80C.   To Isolate RNA, Macherey-Nagel NucleoSpin miRNA kit for isolation of small and Large RNA was used according to manufacturers protocol (November 2011/rev.02). RNA was analyzed on Bioanlayzer (Agilent) all  RIN were ≥7.5 and stored at -80C till further use.
Whole-transcriptome RNA sequencing (RNA-seq) was performed using high quality total RNA (RIN>7) extracted from mammary epithelial organoids to prepare strand-specific, poly-A+ RNA-seq libraries for sequencing on the Illumina platform. To monitor sample and process variability, in addition to sequence metrics, RNA developed by the External RNA Controls Consortium (ERCC) which consists of a mix of 92 polyadenylated RNA transcripts was also added to total RNA at the beginning of the library preparation.  Briefly, poly-A+ mRNA was extracted from 1 μg total RNA using Oligo(dT)25 Dynabeads (Life Technologies, Cat. No. 61002) followed by fragmentation of the mRNA by heat at 94oC for 6 minutes. First strand cDNA was synthesized using the Superscript III reverse transcriptase (Life Technologies, Cat. No. 18080-044) and purified using Agencourt RNAClean XP beads (Beckman Coulter, Cat. No. A63987). During second strand cDNA synthesis, dNTP mix containing dUTP was used to introduce strand-specificity.  For Illumina paired-end library construction, the resultant cDNA was processed through end-repair and A-tailing, ligated with Illumina PE adapters, and then digested with 10 units of Uracil-DNA Glycosylase (NEB, Cat. No. M0280L).  Amplification of the libraries was performed for 13-14 PCR cycles using the Phusion High-Fidelity PCR Master Mix (NEB, Cat. No. M0531L); twelve such 6-bp molecular barcodes were also incorporated during this PCR amplification. The cDNA was purified with Agencourt AMPure XP beads after each enzymatic reaction, and after quantification using the Agilent Bioanalyzer 2100 DNA Chip 7500 (Cat. No. 5067-1506), libraries were pooled in equimolar amounts (6-7 libraries/pool).  The library pools were then loaded onto a HiSeq flowcell lane, and following amplification with Illumina’s cBot cluster generation system, sequencing runs were performed in paired-end mode (2 x 100-bp reads) using the Illumina HiSeq2000 platform. On average, 67 million reads were generated per sample.

tag: mammary develpoment stage

value: virgin


title: Nodular goiters, biological replicate 3

description:
Nodular goiters sample
N3


title: V598A_RNASeq


title: V507R_RNASeq


title: V509_RNASeq


title: V504_RNASeq


title: Jurkat_H3K4me3_OICR-9429_Spike


title: V468A_RNASeq


title: V502_RNASeq


title: L610_RNASeq

value: lactating


title: L598_RNASeq


title: Follicular thyroid carcinoma, biological replicate 1

description:
Follicular thyroid carcinoma sample
FTC1

source_name: Follicular thyroid carcinoma

value: Follicular thyroid carcinoma


title: Loucy_H3K4me3_Spike

value: Loucy


title: L507_RNASeq


title: L509_RNASeq


title: L504_RNASeq


title: P5424_WT_unstim_4C_Ikzf1

status: Public on Mar 31 2021

data_processing:
Library strategy: 4C-seq
Base calling was performed using RTA version 2.
Reads were trimmed with Sickle v1.33 and aligned to the GRCm38 genome assembly using Bowtie v2.3.4.3 and defaults parameters.
Individual 4C-seq experiments were demultiplexed according to bait primer sequence using sabre, with two mismatches permitted (-m 2). Reads were aligned using Bowtie (v1.0.0) with the settings -a -m 1 --best --strata. Mapped reads were filtered and mapped to DpnII restriction fragments, essentially as described in Ben Zouari et al., Frontiers Genetics 10: 1372 (2010).
Coverage tracks were generated with deepTools v3.2.1.
Peaks were called using Macs2 v2.1.1 and –broad argument.
Genome_build: GRCm38
Supplementary_files_format_and_content: bw: RPKM-normalized coverage track
Supplementary_files_format_and_content: bed: peaks
Supplementary_files_format_and_content: cis: 4See browser input, as described in Ben Zouari et al., Frontiers Genetics 10:1372 (2010)

source_name: P5424 cell line

growth_protocol: P5424 cells were passed every 2-3 days and routinely tested for mycoplasma contamination, and maintained in RPMI medium (Gibco) supplemented with 10% FBS (Gold, PAA) at 37 °C, 5% CO2. Primary DN3 cells were sorted from the thymus of WT c57/Bl6 mice. J1 mouse ES cells were grown on gamma-irradiated mouse embryonic fibroblast cells under standard conditions (4.5 g/L glucose-DMEN, 15% FCS, 0.1 mM non-essential amino acids, 0.1 mM beta-mercaptoethanol, 1 mM glutamine, 500 U/mL LIF, gentamicin), then passaged onto feeder-free 0.2% gelatin-coated plates for at least two passages to remove feeder cells.

extract_protocol:
Total 40 x106 of wt and ∆IkE120P5424 cells were crosslinked in 1% formaldehyde for 10 min at 20 °C, followed by quenching with glycine at a final concentration of 250 mM. Pelleted cells were washed twice with ice-cold PBS, and then re-suspended in lysis buffer (20 mM Hepes PH 7.6, 1% SDS, 1X PIC) at final cell concentration of 15 x 106 cells/ml. Chromatin was sonicated with Bioruptor (Diagenode) to an average length of 200-400 bp (5 pulses of 30 sec ON and 30 sec OFF). An aliquot of sonicated cell lysate equivalent to 0.5 x 106 cells was diluted with SDS-free dilution buffer (1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris PH 8.0, 167 mM NACL) for single immunoprecipitation. Specific antibodies (1 µg per ChIP) and proteinase inhibitor cocktail were added to the lysate and rotated overnight at 4 °C. The antibody used was as follow H3K27ac (C15410196, Diagenode). On the next day, Protein A magnetic beads (Invitrogen) were washed twice with dilution buffer (0.15% SDS, 1% Triton X-100,1.2 mM EDTA, 16.7 mM Tris pH 8.0, 167 mM NaCl and 0.1% BSA) and added to the lysate and rotated 1 hour at 4 °C. Then, beads were washed with each of the following buffers: once with Wash Buffer 1 (2 mM EDTA, 20 mM Tris pH 8.0, 1% Triton X-100, 01% SDS, 150 mM NaCl), twice with Wash Buffer 2 (2 mM EDTA, 20 mM Tris pH 8.0, 1% Triton X-100, 0.1% SDS, 500 mM NaCl), twice with Wash Buffer 3 (1 mM EDTA, 10 mM Tris pH 8.0). Finally, beads were eluted in Elution buffer (1% SDS, 0.1 M NaHCo3) and rotated at RT for 20 min. Eluted materials were then added with 0.2 M NaCl, 0.1 mg/ml of proteinase K and incubated overnight at 65 °C reverse cross-linking, along with the untreated input (10% of the starting material). The next day, DNA was purified with QIAquick PCR Purification Kit (Qiagen) and eluted in 30 µl of water. For 4C, cells were detached with trypsin (for ES cells), washed by centrifugation in PBS, and then fixed with 2% formaldehyde in mES culture medium for 10 min at 23°C. The fixation was quenched with cold glycine at a final concentration of 125 mM, then cells were washed with PBS and permeabilized on ice for 1 h with 10 mM Tris-HCl, pH 8, 100 mM NaCl, 0.1% NP-40 and protease inhibitors. Nuclei were resuspended in DpnII restriction buffer at 10 million nuclei/mL concentration, and 5 million nuclei aliquots were further permeabilized by treatment for 1 h with 0.4% SDS at 37°C, then a further 1h with 2.6% Triton-X100 at 37°C. Nuclei were digested overnight with 1000 U DpnII at 37°C, then washed twice by centrifuging and resuspending in T4 DNA ligase buffer. In situ ligation was performed in 400 μL T4 DNA ligase buffer with 20,000 U T4 DNA ligase overnight at 16°C. DNA was purified by reverse cross-linking with an overnight incubation at 65°C with proteinase K, followed by RNase A digestion, phenol/chloroform extraction and isopropanol precipitation. The DNA was digested with 5 U/μg Csp6I at 37°C overnight, then re-purified by phenol/chloroform extraction and isopropanol precipitation. The DNA was then circularized by ligation with 200 U/μg T4 DNA ligase under dilute conditions (5 ng/μL DNA), and purified by phenol/chloroform extraction and isopropanol precipitation. 50 ng aliquots of this DNA were used as template for PCR with bait-specific primers containing Illumina adapter termini (primer sequences and optimal PCR conditions available on request)
At least 1ng of ChIP was used for library preparation. Libraries for ChIPs against H3K27ac was prepared according to Illumina ChIP-Seq protocol and sequenced on a Nextseq500 (Illumina) according to the manufacturer's instructions. For 4C, PCR reactions were pooled, primers removed by washing with 1.8x AMPure XP beads, then quantified on a Bioanalyzer (Agilent) before sequencing with a HiSeq 4000 (Illumina).
Paired-end sequencing 50+30bp was performed using Illumina NextSeq 500. For 4C, single-end sequencing (50 nt) on Illumina HiSeq 4000.

treatment_protocol: P5424 stimulation was performed by incubating for 6 h with 20 µg/ml of PMA plus 0.5 µg/ml of ionomycin

tag: genotype/variation

value: WT


title: L502_RNASeq


title: L468_RNASeq


title: P5424_ΔIKE120_unstim_4C_Ikzf1


title: P5424_WT_PI_4C_Ikzf1


title: DN3_4C_Ikzf1

source_name: CD4-/CD8-/CD44lo/CD25+ Thymic T Cells (DN3)

value: CD4-/CD8-/CD44lo/CD25+ Thymic T Cells


title: Nodular goiters, biological replicate 4

description:
Nodular goiters sample
N4


title: Nodular goiters, biological replicate 5

description:
Nodular goiters sample
N5


title: P5424_ΔIKE120_H3K27ac

data_processing:
Base calling was performed using RTA version 2.
Reads were trimmed with Sickle v1.33 and aligned to the GRCm38 genome assembly using Bowtie v2.3.4.3 and defaults parameters.
Individual 4C-seq experiments were demultiplexed according to bait primer sequence using sabre, with two mismatches permitted (-m 2). Reads were aligned using Bowtie (v1.0.0) with the settings -a -m 1 --best --strata. Mapped reads were filtered and mapped to DpnII restriction fragments, essentially as described in Ben Zouari et al., Frontiers Genetics 10: 1372 (2010).
Coverage tracks were generated with deepTools v3.2.1.
Peaks were called using Macs2 v2.1.1 and –broad argument.
Genome_build: GRCm38
Supplementary_files_format_and_content: bw: RPKM-normalized coverage track
Supplementary_files_format_and_content: bed: peaks
Supplementary_files_format_and_content: cis: 4See browser input, as described in Ben Zouari et al., Frontiers Genetics 10:1372 (2010)


title: P5424_WT_H3K27ac


title: EA_100420_Mel_H2_1

status: Public on Feb 02 2021

city: Boston

first: Evan

middle: Michael

last: Appleton

state: MA

address: 75 Kneeland St.

institute: Colossal Biosciences

description:
mel_h2_fpkm.tsv
LIB047627_TRA00195780_S32_L001

data_processing:
Trim reads to 30bp using HOMER  v.4.9 (command: 'homerTools trim -len 30 -3 13 x.fastq.gz')
Bowtie2 alignment to hg38 using Bowtie2 v.2.2.9
Peak calling for FPKM values using HOMER v.4.9. (command: 'analyzeRepeats.pl')
Genome_build: hg38
Supplementary_files_format_and_content: FPKM files showing FPKM expression for all replicates of each differentiated cell type in one .tsv file

source_name: induced iPSCs

growth_protocol:
NK-cells: 6 wells of 3000 hiPSCs were plated into uncoated round-bottom plates in 200uL of StemDiff APEL2 media [StemCell Technologies] with Stem Cell Factor (SCF) (40 ng/mL) [R&D Systems], BMP4 (40 ng/mL) [R&D systems], and VEGF (40 ng/mL) [BioLegend] and spun at 1500 rpm at RT for 5 minutes. Cells were then incubated at 37C and 5% CO2 for 11 days. Half-media changes were performed on days 5, 7, and 9. On day 11, all 6 wells of spin EBs were aspirated without disturbing the structure of the EB and plated into a well of a 24-well plate in NK differentiation media consisting of StemDiff APEL2, SCF (20 ng/mL), IL-3 95 (5 ng/mL) (first week only) [R&D Systems], IL-7 (20 ng/mL) [R&D Systems], IL-15 (10 ng/mL) [R&D Systems], and FlT3l (10 ng/mL), [BioLegend]. Half media changes were performed once per week for 4 weeks.
Mammary Epithelial Cells (HMEC): 50,000 hiPSCs were plated on matrigel-coated plates and differentiated with 2ng/mL doxycycline [Sigma] for 8 days in mTeSR [StemCell Technologies] with full media changes daily.
Melanocytes: 50,000 hiPSCs were plated on matrigel-coated plates and differentiated with 2ng/mL doxycycline [Sigma] for 8 days in Melanocyte Growth Media [Sigma] with full media changes every other day.

extract_protocol:
Zymo Quick-RNA Microprep Kit (R1050) performed as described by the manufacturer's protocol
SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian User Manual (Cat. No. 634487) performed as described by manufacturer's protocol
Bulk RNA-seq

treatment_protocol: Cells reconstituted and lysed in Invitrogen TRIzol reagent (Cat. No. 15596026) and stored at -80C prior to RNA-prep

tag: cell culture conditions

value: iPSCs with induced TFs cultured for melanocyte differentiation

value: melanocyte

tag: tfome cassettes


title: EA_100420_Mel_L_3

description:
mel_l_fpkm.tsv
LIB047627_TRA00195779_S31_L001

tag: cell line


title: EA_100420_PGP1_2

description:
ips_ctrl_fpkm.tsv
LIB047627_TRA00195775_S27_L001

source_name: iPSCs

value: iPSC control

value: [NONE]


title: EA_100420_Mel_L_1

description:
mel_l_fpkm.tsv
LIB047627_TRA00195777_S29_L001


title: P5424_ΔIKE120_PI_4C_Ikzf1


title: Follicular thyroid carcinoma, biological replicate 3

description:
Follicular thyroid carcinoma sample
FTC3


title: ES_4C_Ikzf1

source_name: J1 embryonic stem cells

value: J1 ES


title: EA_100420_NK_5_4_1

description:
nk_5_4_fpkm.tsv
LIB047627_TRA00195773_S25_L001

value: iPSCs with induced TFs cultured for NK-cell differentiation

value: NK-cell


title: EA_100420_HMEC_6_1_3

description:
hmec_6_1_fpkm.tsv
LIB047627_TRA00195769_S21_L001

value: iPSCs with induced TFs cultured for mammary epithelial cell differentiation

value: mammary epithelial cell


title: EA_100420_PGP1_3

description:
ips_ctrl_fpkm.tsv
LIB047627_TRA00195776_S28_L001


title: EA_100420_HMEC_5_2_1

description:
hmec_5_2_fpkm.tsv
LIB047627_TRA00195764_S16_L001


title: EA_100420_HMEC_6_2_2

description:
hmec_6_2_fpkm.tsv
LIB047627_TRA00195762_S14_L001


title: EA_100420_NK_5_4_2

description:
nk_5_4_fpkm.tsv
LIB047627_TRA00195774_S26_L001


title: EA_100420_HMEC_6_3_1

description:
hmec_6_3_fpkm.tsv
LIB047627_TRA00195770_S22_L001


title: EA_100420_HMEC_6_2_1

description:
hmec_6_2_fpkm.tsv
LIB047627_TRA00195761_S13_L001


title: EA_100420_HMEC_6_1_1

description:
hmec_6_1_fpkm.tsv
LIB047627_TRA00195767_S19_L001


title: EA_100420_HMEC_5_2_3

description:
hmec_5_2_fpkm.tsv
LIB047627_TRA00195766_S18_L001


title: EA_100420_HMEC_6_3_2

description:
hmec_6_3_fpkm.tsv
LIB047627_TRA00195771_S23_L001


title: EA_100420_Mel_L_2

description:
mel_l_fpkm.tsv
LIB047627_TRA00195778_S30_L001


title: EA_100420_HMEC_6_2_3

description:
hmec_6_2_fpkm.tsv
LIB047627_TRA00195763_S15_L001


title: EA_100420_HMEC_6_3_3

description:
hmec_6_3_fpkm.tsv
LIB047627_TRA00195772_S24_L001


title: Follicular thyroid carcinoma, biological replicate 4

description:
Follicular thyroid carcinoma sample
FTC4

value: FFPE


title: EA_100420_HMEC_6_1_2

description:
hmec_6_1_fpkm.tsv
LIB047627_TRA00195768_S20_L001


title: EA_100420_HMEC_5_4_1

description:
hmec_5_4_fpkm.tsv
LIB047627_TRA00195758_S10_L001


title: EA_100420_HMEC_5_1_3

description:
hmec_5_1_fpkm.tsv
LIB047627_TRA00195757_S9_L001


title: EA_100420_HMEC_5_1_1

description:
hmec_5_1_fpkm.tsv
LIB047627_TRA00195755_S7_L001


title: EA_100420_HMEC_5_1_2

description:
hmec_5_1_fpkm.tsv
LIB047627_TRA00195756_S8_L001


title: EA_100420_HMEC_5_2_2

description:
hmec_5_2_fpkm.tsv
LIB047627_TRA00195765_S17_L001


title: EA_100420_HMEC_5_4_3

description:
hmec_5_4_fpkm.tsv
LIB047627_TRA00195760_S12_L001


title: EA_100420_Mel_med_ctrl_2

description:
mel_media_ctrl_fpkm.tsv
LIB047627_TRA00195753_S5_L001

value: iPSCs cultured for melanocyte differentiation


title: EA_100420_Mel_med_ctrl_3

description:
mel_media_ctrl_fpkm.tsv
LIB047627_TRA00195754_S6_L001


title: EA_100420_Mel_med_ctrl_1

description:
mel_media_ctrl_fpkm.tsv
LIB047627_TRA00195752_S4_L001


title: EA_100420_Mel_6_1_3

description:
mel_6_1_fpkm.tsv
LIB047628_TRA00195809_S61_L002


title: EA_100420_Mel_6_1_2

description:
mel_6_1_fpkm.tsv
LIB047628_TRA00195808_S60_L002


title: EA_100420_Mel_5_1_3

description:
mel_5_1_fpkm.tsv
LIB047627_TRA00195751_S3_L001


title: EA_100420_Mel_H2_2

description:
mel_h2_fpkm.tsv
LIB047628_TRA00195805_S57_L002


title: EA_100420_NK_5_2_1

description:
nk_5_2_fpkm.tsv
LIB047628_TRA00195799_S51_L002


title: EA_100420_Mel_H1_3

description:
mel_h1_fpkm.tsv
LIB047628_TRA00195812_S64_L002


title: EA_100420_Mel_5_1_1

description:
mel_5_1_fpkm.tsv
LIB047627_TRA00195749_S1_L001


title: EA_100420_Mel_H1_2

description:
mel_h1_fpkm.tsv
LIB047628_TRA00195811_S63_L002


title: EA_100420_NK_5_2_3

description:
nk_5_2_fpkm.tsv
LIB047628_TRA00195801_S53_L002


title: EA_100420_Mel_H1_1

description:
mel_h1_fpkm.tsv
LIB047628_TRA00195810_S62_L002


title: EA_100420_NK_5_2_2

description:
nk_5_2_fpkm.tsv
LIB047628_TRA00195800_S52_L002


title: EA_100420_NK_5_3_1

description:
nk_5_3_fpkm.tsv
LIB047628_TRA00195802_S54_L002


title: EA_100420_Mel_6_1_1

description:
mel_6_1_fpkm.tsv
LIB047628_TRA00195807_S59_L002


title: EA_100420_NK_6_4_3

description:
nk_6_4_fpkm.tsv
LIB047628_TRA00195798_S50_L002


title: EA_100420_Mel_H2_3

description:
mel_h2_fpkm.tsv
LIB047628_TRA00195806_S58_L002


title: EA_100420_NK_6_1_3

description:
nk_6_1_fpkm.tsv
LIB047628_TRA00195795_S47_L002


title: EA_100420_NK_6_4_1

description:
nk_6_4_fpkm.tsv
LIB047628_TRA00195796_S48_L002


title: EA_100420_NK_6_1_1

description:
nk_6_1_fpkm.tsv
LIB047628_TRA00195793_S45_L002


title: EA_100420_NK_6_1_2

description:
nk_6_1_fpkm.tsv
LIB047628_TRA00195794_S46_L002


title: EA_100420_NK_5_3_2

description:
nk_5_3_fpkm.tsv
LIB047628_TRA00195803_S55_L002


title: EA_100420_NK_5_1_2

description:
nk_5_1_fpkm.tsv
LIB047628_TRA00195791_S43_L002


title: EA_100420_NK_5_1_1

description:
nk_5_1_fpkm.tsv
LIB047628_TRA00195790_S42_L002


title: EA_100420_NK_6_2_3

description:
nk_6_2_fpkm.tsv
LIB047628_TRA00195789_S41_L002


title: EA_100420_NK_6_4_2

description:
nk_6_4_fpkm.tsv
LIB047628_TRA00195797_S49_L002


title: EA_100420_NK_5_5_2

description:
nk_5_5_fpkm.tsv
LIB047628_TRA00195785_S37_L002


title: EA_100420_NK_5_1_3

description:
nk_5_1_fpkm.tsv
LIB047628_TRA00195792_S44_L002


title: EA_100420_NK_6_2_2

description:
nk_6_2_fpkm.tsv
LIB047628_TRA00195788_S40_L002


title: EA_100420_NK_5_3_3

description:
nk_5_3_fpkm.tsv
LIB047628_TRA00195804_S56_L002


title: EA_100420_NK_6_2_1

description:
nk_6_2_fpkm.tsv
LIB047628_TRA00195787_S39_L002


title: EA_100420_NK_media_ctrl_1

description:
nk_media_ctrl_fpkm.tsv
LIB047628_TRA00195781_S33_L002

value: iPSCs cultured for NK-cell differentiation


title: EA_100420_NK_media_ctrl_2

description:
nk_media_ctrl_fpkm.tsv
LIB047628_TRA00195782_S34_L002


title: EA_100420_NK_5_5_3

description:
nk_5_5_fpkm.tsv
LIB047628_TRA00195786_S38_L002


title: EA_100420_NK_5_5_1

description:
nk_5_5_fpkm.tsv
LIB047628_TRA00195784_S36_L002


title: EA_100420_NK_media_ctrl_3

description:
nk_media_ctrl_fpkm.tsv
LIB047628_TRA00195783_S35_L002


title: RNA-seq_WT_limb_embryo_3

status: Public on Feb 01 2021

city: Santander

first: Marian

last: Ros

address: Albert Einstein, 22 (PCTCAN)

country: Spain

institute: Consejo Superior de Investigaciones Cientificas (CSIC) with Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC)

description:
sample name:
5.10_WT

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the mouse reference assembly, version GRCm38, using TopHat2
Read count means, fold-change (FC) and p-values were calculated with DEseq2
gene expression for the individual samples was calculated with Cufflinks as FPKMs.
Genome_build: GRCm38

source_name: Mouse embryo (E10.5) limb ectoderm

growth_protocol: For wild type embryos C57BL/6 inbred male and female mice were crossed. For Sp8 null embryos (Sp8-Cre-ERT2) heterozygous (Sp8+/-) male and female mice were crossed. E10.5 embryos were obtained from pregnant females by cesarean section. Genotype was performed by PCR from extraembryonic membranes.

extract_protocol:
Total RNA was extracted with RNeasy-Plus Micro Kit according to the manufacturer’s instructions (Qiagen). Libraries were prepared with the RNA sample preparation kit (TruSeq v2; Ilumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ectoderms were isolated with fine forceps from E10.5 forelimb buds after digestion with 0.25% trypsin for 20 min. on ince. The ectoderms of the two forelimbs of a single WT (C57Bl6J) or Sp8 null (Sp8-Cre-ERT2) embryo were used for each replicate.

value: limb ectoderm

tag: developmental stage

tag: mouse genotype

tag: background strain


title: RNA-seq_WT_limb_embryo_1

description:
sample name:
4.2_WT


title: RNA-seq_SP8KO_limb_embryo_1

description:
sample name:
4.7_HO

value: Sp8 KO


title: Flag-Sp8_input_rep2

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the mouse reference assembly, version GRCm38, using TopHat2
Normalized bedGraph files were generated using DeepTools
Peaks were called using MACS2
Genome_build: mm10

growth_protocol: Sp8-FLAG homozygous embryos male and female mice were crossed. E10.5 embryos were obtained from pregnant females by cesarean section. Genotype was confirmed by PCR from extraembryonic membranes.

extract_protocol:
ChIPmentation protocol was based on (Schmidl et al., 2015) with some modifications from A. Rada-Iglesias’s lab. Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the anti-FLAG M2 antibody (Sigma).
DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries.

treatment_protocol: Ectoderms were isolated with fine forceps from E10.5 forelimb buds of Sp8-FLAG homozygous embryos after digestion with 0.25% trypsin for 20 min. on ince. The ectoderms of 50 forelimb buds were used for each replicate.

value: Sp8FL KI

tag: chip antibody


title: Flag-Sp8_input_rep1


title: Flag-Sp8_ChIP-seq_rep2

value: FLAG M2 antibody- Sigma-Aldrich -Catalog No:F1804


title: Flag-Sp8_ChIP-seq_rep1


title: TNF_I_MKI5

status: Public on Jan 08 2021

first: Bing

last: Shui

address: 360 Longwood Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description:
TNF_Raw_gene_counts_matrix.txt
TNF_Normalized_gene_counts_matrix.txt

data_processing:
Salmon (salmon v0.14.1) pseudo-aligner was used for sequencing alignment and read count, with the Ensembl mm10 genome (Mus_musculus.GRCm38) as reference, using the following parameter: -l A --seqBias --useVBOpt --validateMappings
Normalized count was obtained using DESeq2, normalized across all samples from the same model
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: Intestine

growth_protocol: T cell transfer colitis was induced in Rag1 null mice as described before (Lyons et al., 2018; Strasser et al., 2019). Naïve and Bulk T cells were injected intraperitoneally in Rag1 null mice at 400,000 and 200,000 cells per animal, respectively. Naïve T injected mice developed colitis in an 8-12 week period after injection, whereas Bulk T injected mice served as uninflamed controls. TNF∆ARE mice were maintained in a heterozygous breeding scheme in order to generate inflamed (Tnf ∆ARE/+) and uninflamed littermate controls (Tnf +/+). When mice reached 16 weeks of age they were randomized into treatment groups for MK2 inhibition studies.

extract_protocol:
Distal colons and ileum tissues were snap-frozen and powderized in liquid nitrogen with a tissue homogenizer. RNA was extracted using the RNeasy Plus Universal kit from Qiagen, following the manufacturer's instructions. RNA concentration and quality were evaluated in Agilent Bioanalyzer/TapeStation.
1µg of RNA was used for RNA-Seq library preparation. Poly-A enrichment was performed to increase mRNA amount in the input RNA. RNA-Seq library was prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® following the manufacturer's instructions.

treatment_protocol: MK2 inhibitor ATI-450 was obtained from Aclaris Therapeutics. For transcriptomic studies, mice were dosed with 3mg/kg ATI450 or vehicle (0.5% methylcellulose/0.025% Tween20/PBS), and re-dosed 16 hours later. 90 min after the second dose, mice were euthanized and tissues harvested for RNA extraction.

value: Intestine

tag: model

value: TNF

tag: inflammation status

value: Inflamed

tag: treatment

value: ATI-450(MK2 inhibitor) treated

tag: batch


title: TNF_I_MKI1

tag: strain

tag: tissue


title: RNA-seq_WT_limb_embryo_2

description:
sample name:
5.6_WT

value: WT


title: TNF_I_MKI3


title: TNF_I_MKI2


title: TNF_NI_MKI3

value: Non-inflamed


title: RNA-seq_SP8KO_limb_embryo_3

description:
sample name:
5.8_HO


title: TNF_I_V4

value: Vehicle


title: TNF_NI_MKI4


title: TNF_I_V3


title: TNF_I_V2


title: TNF_I_V5


title: TNF_NI_V3


title: TNF_NI_V5


title: TNF_NI_MKI1


title: TNF_NI_V2


title: TNF_NI_MKI2


title: TNF_NI_V4


title: TNF_I_V1


title: TNF_NI_V1


title: TNF_I_MKI6


title: Jurkat_RNA_PBIT_5h

tag: cell type

value: Jurkat

value: PBIT

tag: treatment duration


title: TNF_NI_MKI5


title: TNF_I_MKI4


title: TCT_I_MKI5

description:
TCT_Raw_gene_counts_matrix.txt
TCT_Normalized_gene_counts_matrix.txt

value: TCT


title: TCT_I_MKI3


title: TCT_I_MKI1


title: TCT_I_MKI2


title: Jurkat_H3K4me3_DMSO_Spike

value: DMSO


title: TCT_NI_MKI4


title: TCT_NI_MKI6


title: TCT_NI_MKI1


title: TCT_NI_MKI5


title: TCT_NI_MKI2


title: TCT_I_V6


title: TCT_NI_MKI3


title: TCT_NI_V1


title: TCT_I_V5


title: TCT_I_V4


title: TCT_I_V2


title: TCT_NI_V7


title: TCT_I_MKI6


title: TCT_I_V1


title: TCT_I_V3


title: TH148_LC_ATAC

status: Public on Jul 09 2020

data_processing:
Base calling was performed using RTA version 2.
Reads were trimmed with Sickle v1.33 and aligned to the hg38 genome assembly using Bowtie v2.3.4.3 and defaults parameters.
Coverage tracks were generated with deepTools v3.2.1.
Peaks were called using Macs2 v2.1.1.
Genome_build: hg38
Supplementary_files_format_and_content: bw: RPKM_normalized coverage track
Supplementary_files_format_and_content: bed: peaks

source_name: late cortical thymic subpopulation

growth_protocol: Human thymic subpopulations were sorted using FACS ARIA III

extract_protocol:
DNA extraction with MinElute PCR Purification kit (Qiagen Cat#28004)
Single_end sequencing 75bp was performed using Illumina NextSeq 500.

treatment_protocol: Thymocytes were washed with cold PBS and lysed in 50µl cold lysis buffer (10 mM Tris HCL pH 7.4; 10 mM NaCl; 3m M MgCl2; 0.1% Igepal CA-630). Transposition reaction was performed in 50 µl of 1x TD reaction buffer supplemented with 2.5 µl of TDE1 Tn5 Transposase from Nextera DNA Library Prep Kit at 37°C for 30 minutes.

tag: donor

value: late cortical thymic subpopulation


title: TH148_EC_ATAC

source_name: early cortical thymic subpopulation

value: early cortical thymic subpopulation


title: TH149_EC_ATAC


title: TCT_I_MKI4


title: TCT_NI_V2


title: TH149_LC_ATAC


title: TH149_CD34pos_1apos_ATAC

source_name: CD34+1a+ thymic subpopulation

value: CD34+1a+ thymic subpopulation


title: TH148_CD34pos_1aneg_7pos_ATAC

source_name: CD34+1a-7+ thymic subpopulation

value: CD34+1a-7+ thymic subpopulation


title: TH125_SP4_H3K27ac

source_name: thymus

extract_protocol:
Lysates were clarified from sonicated nuclei of sorted thymic subpopulations and histone-DNA complexes were isolated with antibody.
Single-end sequencing 75bp was performed using Illumina NextSeq 500.

tag: Stage

value: single positive 4 thymic subpopulation


title: TH125_LC_H3K36me3


title: TCT_NI_V4


title: TH149_CD34pos_1aneg_7pos_ATAC


title: TH125_LC_H3K27ac


title: TH125_EC_H3K27ac


title: TH125_EC_H3K27me3


title: TCT_NI_V6


title: TH137_CD34_RUNX1

data_processing:
Base calling was performed using RTA version 2.
Reads were trimmed with Sickle v1.33 and aligned to the hg38 genome assembly using Bowtie v2.3.4.3 and defaults parameters.
Coverage tracks were generated with deepTools v3.2.1.
Peaks were called using Macs2 v2.1.1.
Genome_build: hg38
Supplementary_files_format_and_content: bw: RPKM-normalized coverage track
Supplementary_files_format_and_content: bed: peaks

source_name: CD34+ thymic subpopulation

extract_protocol:
Immunoprecipitated DNA was purified by QIAquick PCR Purification Kit (Qiagen, Cat#28104)
Single-end sequencing 75bp was performed using Illumina NextSeq 500.

treatment_protocol: tCD34+ thymocytes were crosslinked for 10 minutes with 1% formaldehyde at 20°C and sonicated using Branson 450 Sonifier Cell Disruptor. Chromatin immunoprecipitation was conducted with anti-RUNX1 (Abcam, Cat#ab23980) using Dynabeads Protein G for Immunoprecipitation (Thermo Fisher Cat#10003D).

value: CD34+ thymic subpopulation


title: TH117_LC_H3K27me3


title: TH125_LC_H3K4me1


title: EA_100420_Mel_5_1_2

description:
mel_5_1_fpkm.tsv
LIB047627_TRA00195750_S2_L001

tag: cell culture conditions

value: iPSCs with induced TFs cultured for melanocyte differentiation

value: melanocyte


title: EA_100420_HMEC_5_4_2

description:
hmec_5_4_fpkm.tsv
LIB047627_TRA00195759_S11_L001

value: iPSCs with induced TFs cultured for mammary epithelial cell differentiation

value: mammary epithelial cell

tag: tfome cassettes


title: TH148_CD34pos_1apos_ATAC


title: 40N: genomic DNA from thyroid normal tissue 32

status: Public on Jan 01 2020

city: daejeon

first: Jonglyul

last: Park

address: 52, Eoeun-dong, Yuseong-gu

department: Medical genomics

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: thyroid normal sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iSCAN using standard recommended Illumina scanner setting

data_processing: Each methylation signal was used to compute the β value, which is a quantitative measure of DNA methylation ranging from 0 (for completely unmethylated cytosines) to 1 (for completely methylated cytosines) (Bibikova et al., 2006).

label: Cy5 and Cy3

source_name: thyroid tissue

extract_protocol: genomic DNA was extracted and purified from 34 thyroid normal and tumor tissues samples using Qiagen DNeasy Kit according to standard instructions

value: normal thyroid

tag: disease state

value: Normal


title: 41T: genomic DNA from thyroid tumor tissue 34

description: thyroid tumor sample

value: thyroid tumor

value: Classic PTC


title: 38T: genomic DNA from thyroid tumor tissue 23

description: thyroid tumor sample

value: TCVPTC


title: 02T: genomic DNA from thyroid tumor tissue 25

description: thyroid tumor sample

value: IEFVPTC


title: 02N: genomic DNA from thyroid normal tissue 24

description: thyroid normal sample


title: 03T: genomic DNA from thyroid tumor tissue 26

description: thyroid tumor sample


title: 25T: genomic DNA from thyroid tumor tissue 14

description: thyroid tumor sample


title: 34T: genomic DNA from thyroid tumor tissue 20

description: thyroid tumor sample

value: NIFTP


title: 06T: genomic DNA from thyroid tumor tissue 28

description: thyroid tumor sample


title: Wild type HCT116, control, replicate 2

status: Public on Jul 15 2019

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

description:
HCT116_WT_DMSO-PBS_3
Nascent RNA (PRO-seq) from HCT116 cells.
processed data file: TSS_counts.txt
processed data file: body_counts.txt

data_processing:
Library strategy: PRO-Seq
Signal processing, base-calling, and quality scoring were carried out automatically by the NextSeq 500 RTA software (v2.4.11 Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (v2.20.0.422, Illumina).
FASTQC (v0.11.5) was used to assess sequence data quality.
Fastq files from 3 separate lanes were merged for each sample to obtain sufficient read depth.
Trimming and filtering of low-quality bases/reads were performed using BBDUK from BBTools (v37.99) and FASTQ-MCF from EAUtils (v1.05).
FastQ Screen (v0.9.1) was used to check for common sequencing contaminants.
Alignment to the Human reference genome (GRCh37/hg19) was carried out using Hisat2 (v2.1.0) in unpaired, no-spliced-alignment mode with a GRCh37/hg19 index.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data for transcription start site (TSS, -30 to +300) and gene body (+301 to end) regions were obtained using featureCounts from the Subread package (v1.6.2) with custom annotation files for single unique TSS and gene body regions per gene.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: *_counts.txt: Tab-delimited text files containing gene-level counts for unique TSS or gene body regions per gene for each sample.

source_name: Wild type HCT116 cells

growth_protocol: HCT116 cells were grown in McCoy media with pen/strep antibiotics and 5% FBS supplementation.

extract_protocol: Nuclear run-on experiments were performed as described previously (Mahat, D. B., Kwak, H., Booth, G. T., Jonkers, I. H., Danko, C. G., Patel, R. K., et al. (2016). Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nature Protocols, 11(8), 1455–1476. http://doi.org/10.1093/bioinformatics/btq033) with the following modification. The final concentration of non-biotinylated CTP was raised from 0.25uM to 25uM, and the final library clean up and size selection was accomplished using 1X AMPure XP (Beckman).

treatment_protocol: Cells were treated with IFNgamma (control PBS) and/or the ATP analog 3MB-PP1 (control DMSO) for 45 minutes.

tag: cell line

value: colorectal carcinoma

tag: genotype/variation

value: Wild-type

value: Control (PBS + DMSO)


title: 20T: genomic DNA from thyroid tumor tissue 10

description: thyroid tumor sample


title: 07T: genomic DNA from thyroid tumor tissue 29

description: thyroid tumor sample


title: 40T: genomic DNA from thyroid tumor tissue 33

description: thyroid tumor sample


title: 15T: genomic DNA from thyroid tumor tissue 8

description: thyroid tumor sample


title: 14T: genomic DNA from thyroid tumor tissue 7

description: thyroid tumor sample


title: 34N: genomic DNA from thyroid normal tissue 19

description: thyroid normal sample


title: 04T: genomic DNA from thyroid tumor tissue 27

description: thyroid tumor sample


title: 37T: genomic DNA from thyroid tumor tissue 22

description: thyroid tumor sample


title: 39T: genomic DNA from thyroid tumor tissue 31

description: thyroid tumor sample


title: 22T: genomic DNA from thyroid tumor tissue 11

description: thyroid tumor sample


title: 28T: genomic DNA from thyroid tumor tissue 17

description: thyroid tumor sample


title: 27T: genomic DNA from thyroid tumor tissue 16

description: thyroid tumor sample


title: 23N: genomic DNA from thyroid normal tissue 12

description: thyroid normal sample


title: 35T: genomic DNA from thyroid tumor tissue 21

description: thyroid tumor sample


title: 32T: genomic DNA from thyroid tumor tissue 18

description: thyroid tumor sample


title: 23T: genomic DNA from thyroid tumor tissue 13

description: thyroid tumor sample


title: 19T: genomic DNA from thyroid tumor tissue 9

description: thyroid tumor sample


title: 27N: genomic DNA from thyroid normal tissue 15

description: thyroid normal sample


title: 39N: genomic DNA from thyroid normal tissue 30

description: thyroid normal sample


title: 12T: genomic DNA from thyroid tumor tissue 5

description: thyroid tumor sample


title: Wild type HCT116, control, replicate 1

description:
HCT116_WT_DMSO-PBS_1
Nascent RNA (PRO-seq) from HCT116 cells.
processed data file: TSS_counts.txt
processed data file: body_counts.txt


title: 13T: genomic DNA from thyroid tumor tissue 6

description: thyroid tumor sample


title: 10T: genomic DNA from thyroid tumor tissue 3

description: thyroid tumor sample


title: TC-16

status: Public on Jan 01 2019

city: Singapore

first: Arnoud

last: Boot

state: Singapore

address: 8 college road

country: Singapore

institute: Duke-NUS Medical School

hyb_protocol: DNA was bisulfite converted using the EZ DNA methylation gold kit. Hybridization was performed according to the illumina protocol.

scan_protocol: Standard Illumina Protocol

data_processing: Data was normalized using the BMIQ function from the wateRmelon package in R with nfit=5000. probes with detection pval. ## 1370 sites were removed as beadcount <3 in 5 % of samples ## 5118 sites having 1 % of samples with a detection p-value greater than 0.05 were removed ## final filtering: sites with total intensity (methylated + unmethylated) <2000 were removed.

label: Cy3 and Cy5

source_name: Oncocytic follicular thyroid carcinoma

extract_protocol: DNA was isolated using the DNA isolation was performed using the Wizard Genomic DNA Purification Kit (Promega

value: Oncocytic follicular thyroid carcinoma

value: Yes


title: TC-25

source_name: Pappillary thyroid carcinoma

value: Pappillary thyroid carcinoma

value: No


title: 09N: genomic DNA from thyroid normal tissue 1

description: thyroid normal sample


title: 555T-A_tumor

status: Public on Oct 20 2017

city: Vejle

first: Mariana

last: Bisarro dos Reis

address: Kabbeltoft 25

country: Denmark

institute: Vejle Hospital

hyb_protocol: Bisulphite modified DNA was amplified, fragmented and hybridized in the Illumina Hybridization Oven according the standard Illumina protocol.

scan_protocol: Arrays were imaged using the HiScan system (Illumina).

data_processing: Methylation data were analyzed as β values. Probes were also filtered, using WateRmelon package, for low bead count (<3) and low quality (p detection >0.05). Samples having 1% of sites with a detection p-value > 0.05 were also removed. Data was adjusted for color bias, inter-sample normalization and corrected using BMIQ normalization. The batch effects were corrected using sva package.

source_name: tumor tissue

growth_protocol: Not applicable

extract_protocol: Tumor and non-neoplastic adjacent tissues were macro-dissected and genomic DNA extracted using a standard phenol/chloroform method.

treatment_protocol: Genomic DNA samples were bisulfite-modified using EZ DNA Methylation Gold kit D5006 (Zymo Research, Irvine, CA, USA) according to the Illumina recommendation.

tag: histology

value: follicullar thyroid cancer

tag: gender

value: Male

tag: race

tag: age

tag: variant


title: 09T: genomic DNA from thyroid tumor tissue 2

description: thyroid tumor sample


title: TC-24


title: TC-12


title: 544T_tumor

value: poorly differentiated thyroid carcinoma

value: Caucasian


title: 298T_tumor

value: anaplastic thyroid cancer

value: Female


title: TC-13


title: 551T-A_tumor

value: Hürthle cell carcinomas


title: 11T: genomic DNA from thyroid tumor tissue 4

description: thyroid tumor sample

value: thyroid tumor

value: TCVPTC


title: 548T_tumor

value: minimally invasive follicular carcinomas


title: TC-15


title: 550T_tumor

value: Non Caucasian


title: 541T_tumor


title: TC-01

source_name: Anaplastic thyroid carcinoma

value: Anaplastic thyroid carcinoma


title: 542T_tumor


title: 264T_tumor


title: TC-03


title: TC-14


title: TC-11


title: TC-09

source_name: Oncocytic follicular adenoma

value: Oncocytic follicular adenoma


title: 587T_tumor


title: 549T_tumor


title: TC-07


title: TC-08


title: 540T_tumor


title: 543T_tumor


title: TC-04


title: 410T_tumor

value: papillary thyroid cancer

value: Follicular + Classic


title: 344T_tumor

value: Classic


title: 345T_tumor


title: 320T_tumor

value: Sclerosing


title: 369T_tumor


title: 5424_tumor


title: 361T_tumor


title: 462T_tumor


title: 371T_tumor


title: 315T_tumor


title: 506T_tumor


title: 290T_tumor


title: 355T_tumor


title: 407T_tumor


title: 518T_tumor

value: Follicular


title: 495T_tumor

value: Male


title: 521T_tumor


title: 333T_tumor


title: 400T_tumor


title: 376T_tumor


title: 373T_tumor


title: 338T_tumor


title: 360T_tumor


title: 467T_tumor


title: 516T_tumor


title: 328T_tumor


title: 393T_tumor


title: 386T_tumor


title: 366T_tumor

value: Tall cell


title: 4869_tumor

value: Caucasian


title: 5049_tumor


title: 416T_tumor


title: 332T_tumor


title: 4955_tumor


title: 316T_tumor

value: Mcossecretor + Classic


title: 329T_tumor

value: Female


title: 473T_tumor


title: 522T_tumor


title: 367T_tumor


title: 365T_tumor


title: 382T_tumor


title: 507T_tumor


title: 339T_tumor


title: 358T_tumor

value: n inform


title: 423T_tumor


title: 318T_tumor


title: 354T_tumor


title: 334T_tumor


title: 343T_tumor


title: 395T_tumor


title: 4810_tumor


title: 346T_tumor


title: 43T_benign

source_name: benign lesion

value: nodular goiter


title: 384T_tumor


title: 27169_tumor


title: 379T_tumor


title: 350T_tumor


title: 287T_benign

value: follicular adenoma/Hürthle cell


title: 381T_tumor


title: 285T_benign

value: follicular adenoma


title: 267T_benign


title: 93T_benign


title: 48T_benign


title: 393N_normal

source_name: non-neoplastic adjacent tissue

value: non-neoplastic adjacent tissue


title: 348T_tumor


title: 275T_benign


title: 284T_benign


title: 88T_benign


title: 314T_benign


title: 337T_tumor


title: 286T_benign


title: 407N_normal


title: 5441_tumor


title: 534N_normal

value: Non Caucasian


title: 201T_benign


title: 294T_benign


title: 521N_normal


title: 371N_normal


title: 338N_normal


title: 518N_normal


title: 355N_normal


title: 369N_normal


title: 516N_normal


title: 328N_normal


title: 400N_normal


title: 333N_normal


title: 386N_normal


title: 316N_normal


title: 507N_normal


title: 583N-A_normal


title: 506N_normal


title: 339N_normal


title: 416N_normal


title: 373N_normal


title: 367N_normal


title: 545N_benign


title: 423N_normal


title: 376N_normal


title: 329N_normal


title: 365N_normal


title: 366N_normal


title: 332N_normal


title: 473N_normal


title: 395N_normal


title: 382N_normal


title: 522N_normal


title: Dehydrobrachylaenolide treated biological replicate2 after 12 hours drug exposure

status: Public on Nov 01 2011

type: RNA

city: Brummeria

first: John

middle: van Wyk

last: Becker

state: Gauteng

address: Meiring Naude Road

department: Biosciences

country: South Africa

institute: Council for Scientific and industrial Research

description: Co-hybridised with biological and technical experiment replicates

hyb_protocol: Probe labelling was estimated on a Nanodrop. Similar amounts of labelled probe (typically 100 picomoles) were hybridized to the microarray slides. Slides were prehybridized with a solution containing 5X SSC (from 20X SSC: 3 M NaCl, 1.5 M sodium citrate, pH 7.0), 0.1% SDS and 0.1 mg/mL BSA, prewarmed to 42ºC. Prehybridization proceeded in 50 mL Falcon tubes, incubated at 42ºC for 45-60 min. Following prehybridization, the slides were washed in three washes of 0.1X SSC before centrifugation for 5 min at 200 xg. The combined Cy-labelled probes (4 µl) were mixed with 36 µl of Operon hybridization buffer for a total volume of 40 µl. The probes were denatured at 95ºC for 5 min, and subsequently applied to the slide under Lifterslips (Erie Scientific Company). The microarray slides were enclosed in ArrayIt (Telechem International) hybridization chambers and submersed in a heated water bath and incubated for 16-20 h at 42ºC. The slides were successively washed in low stringency (2X SSC, 0.5% SDS; heated to 42ºC), medium stringency (1X SSC) and high stringency (0.1X SSC) wash buffers for 5 min each. Slides were then centrifuged (5 min, 200X g). Scanning was performed with an Axon GenePix 4000B scanner (Molecular Devices).

scan_protocol: Washed slides were scanned with a Genepix™ 4000B scanner (Axon Instruments, Foster City, CA, USA). Separate images were acquired for each fluorophore at a resolution of 10 μm per pixel.

data_processing: GenePix results (gpr) files were generated using GenePix 6.0 (Molecular Devices) software, without normalization. For clustering analyses, results files were normalized with DNMAD using print-tip loess. The normalized values were subsequently downloaded and analyzed with the Multiexperiment Viewer (MeV) in the TM4 software suite. Hierarchical Clustering (HCL, average linkage was performed to estimate technical and biological variation between samples and at which point cytostasis most likely occurred for comparative purposes in downstream analyses. Intensity data for individual slides were imported into LIMMA (linear models for microarray data) in the R computing environment (www.bioconductor.org). Pre- and post-normalization diagnostic plots were performed using MARRAY. Data from each microarray slide was normalized using print-tip loess. Data between microarrays was normalized using rquantile normalisation. Results from biological and slide replicates within each of the time points was collated, and linear models were computed to contrast gene expression between time points. A two-fold change in gene expression was used as cut-off, in conjunction with correction for false discovery (FDR = 5%). Analysis of differentially expressed genes was performed in MADIBA (Micro Array Data Interface for Biological Annotation; http://www.bi.up.ac.za/MADIBA/index.php).

organism: Plasmodium falciparum 3D7

source_name: Drug treated P. falciparum cultures 12 hpt

label_protocol: cDNA synthesis reactions of 12 µg each were set up for each sample or reference RNA in a total of 50 µl. Before denaturation at 70ºC for 10 min, 2 µl of oligo d(T) primer (2 µg/µl) and 8 µl of random nanomer primer (0.5 µg/µl) (both New England Biolabs) were added. cDNA synthesis proceeded overnight at 42ºC after the addition of an aminoallyl-dNTP mix (Fermentas), DTT, reaction buffer and 200 U of SuperScript III Reverse Transcriptase (Invitrogen). RNA was hydrolyzed by the addition of 10 µl each of 1 M NaOH and 0.5 M EDTA solutions and incubated at 65ºC for 10 min. Unincorporated aminoallyl dUTP was removed by purification using the Macherey-Nagel NucleoSpin Extract II Kit. The eluted cDNA was quantified using a Nanodrop and similar quantities of test and reference cDNA (typically 2 µg) were dried down to a volume of 2.5 µl in a vacuum drier. Five microliters of a 0.2 M Na2CO3 buffer, pH 9.0, was added to the cDNA and mixed well. Cy3 (sample) or Cy5 (reference) (2.5 µl) (GE Healthcare) ester was added and the coupling allowed to proceed for 2 h in the dark at room temperature. Uncoupled dyes were removed by purification with the RNeasy Mini Kit (Qiagen).

growth_protocol: P. falciparum isolate 3D7 parasites were cultured in 75cm2 flasks (Nalgene) in human erythrocytes (blood group A+) and RPMI 1640 medium supplemented with 25 mM HEPES, 0.0088% hypoxanthine, 40 ug/ml gentamycin (all Sigma) and 0.5 % Albumax (Invitrogen). Parasites were maintained in continuous culture in a 10 ml volume, and were scaled up to 50 ml for drug treatments. The parasitemia and morphological forms detected in the cultures were determined and estimated by Giemsa (Fluka) stained smears under 1000x light microscopy.

extract_protocol: Erythrocytes from harvested cultures were pelleted, washed once with 1X PBS to remove traces of culture medium, and then frozen at -80ºC until RNA extractions were performed. RNA was isolated from 15 ml culture samples with a Qiagen RNeasy kit, using a modified protocol including Qiazol (Qiagen) in the lysis step. Contaminating genomic DNA was removed with DNase I (Qiagen).

treatment_protocol: Fresh cultures were scaled up to 50 ml (5% hematocrit, 10% parasitemia), synchronized twice with 5% D-sorbitol for 5 min at 37ºC to select for parasites in the ring stage, and treated with 2 mM cyclohexylamine at invasion. Fifteen milliliters of culture was harvested at late ring/early trophozoite (18 hpi), mid trophozoite (25 hpi) and late trophozoite (30 hpi) stages. Similar volumes were harvested from untreated P. falciparum 3D7 control cultures at the same time points. Parallel drug treatments were conducted, serving as biological replicates.

tag: agent

value: Dehydrobrachylaenolide

tag: parasite isolate

tag: time point

value: 12 hpt

source_name: Universal RNA Reference

tag: sample type

value: Total RNA pooled from mixed stage in vitro Plasmodium falciparum isolate 3D7 cultured in human erythrocytes


title: Dehydrobrachylaenolide treated biological replicate1 after 12 hours drug exposure


title: Dehydrobrachylaenolide treated biological replicate2 after 6 hours drug exposure

source_name: Drug treated P. falciparum cultures 6 hpt

value: 6 hpt


title: Dehydrobrachylaenolide treated biological replicate1 after 6 hours drug exposure


title: 348N_normal


title: 585N_normal


title: 318N_normal


title: 346N_normal


title: 77N_normal


title: 347N_normal


title: 354N_normal


title: 379N_normal


title: Dehydrobrachylaenolide treated technical replicate after 6 hours drug exposure


title: Dehydrobrachylaenolide treated biological replicate2 after 2 hours drug exposure

source_name: Drug treated P. falciparum cultures 2 hpt

value: 2 hpt


title: 343N_normal


title: Dehydrobrachylaenolide treated biological replicate1 after 2 hours drug exposure


title: DMSO treated control technical replicate after 12 hours drug exposure

source_name: Control P. falciparum cultures 12 hpt

value: DMSO


title: DMSO treated control biological replicate2 after 12 hours drug exposure


title: DMSO treated control biological replicate1 after 6 hours drug exposure

source_name: Control P. falciparum cultures 6 hpt


title: DMSO treated control technical replicate after 6 hours drug exposure


title: DMSO treated control biological replicate2 after 6 hours drug exposure


title: DMSO treated control biological replicate1 after 12 hours drug exposure


title: 337N_normal


title: 350N_normal


title: DMSO treated control biological replicate1 after 2 hours drug exposure

source_name: Control P. falciparum cultures 2 hpt


title: DMSO treated control technical replicate2 after 2 hours drug exposure


title: 510N_normal


title: Dehydrobrachylaenolide treated technical replicate1 after 2 hours drug exposure


title: 334N_normal

value: Male


title: 360N_normal


title: DMSO treated control technical replicate1 after 2 hours drug exposure


title: 586N-A_normal


title: 381N_normal


title: 358N_normal


title: 384N_normal


title: Dehydrobrachylaenolide treated  technical replicate after 12 hours drug exposure


title: DMSO treated control biological replicate2 after 2 hours drug exposure