title: LECS_CM_WM164_MDK_3

first: David

last: Olmeda

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

institute: CNIO

description: 42551_CGTACG_C9ELMANXX_3_20160802B_20160802

data_processing:
RNA-seq processing:
RNA-seq data was analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
Reads are quality-checked with FastQC, and aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 20 multihits
Transcripts quantification and differential expression are calculated with Cufflinks 2.2.1, using the human GRCh37/hg19 transcript annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tabulated text file with gene FPKM values

growth_protocol: hLEC  were grown in EGM2-MV media according to manufactured instructions.

extract_protocol:
Total RNA was purified using RNeasy Mini kit (Qiagen) and digested with DNase (Qiagen).
1 µg of total RNA samples was used. Average sample RNA Integrity Number was 9.8 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (10 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina HiSeq2500 by following manufacturer's protocols.

treatment_protocol: hLEC cells were seeded at 40% confluency. 24 h after the media was substituted by 24h conditioned EGM-2MV media from the indicated cell lines. Cells were left to grow for 3 more day before being collected and processed for RNA-seq anlysis.

tag: cell type

value: Primary Human Lymphatic Endothilial cells (hLECs)

tag: conditioned media source

value: WM164 cell line overexpressing MDK (MDK)

tag: sample group

value: MDK gain of fuction


title: SF3B1 p.K700E 2

status: Public on Jun 27 2017

type: SRA

city: Cambridge

first: Silvia

last: Buonamici

state: MA

address: 300 Technology Square #5

country: USA

institute: H3 Biomedicine

library_source: transcriptomic

data_processing:
Raw data were aligned to hg19 using the STAR alignment package
Junction counts and reads across exon-intron boundaries are converted to percent spliced-in (PSI)
Genome_build: hg19
Supplementary_files_format_and_content: PSI values for each junction within each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: chronic lymphocytic leukemia (CLL)

extract_protocol:
Total RNA was harvested and Poly A selected
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: chronic lymphocytic leukemia (CLL)

tag: genotype/variation

value: SF3B1 K700E


title: LECS_CM_WM164_NEG_3

city: Madrid

state: Madrid

country: Spain

description: 42548_GTGAAA_C9ELMANXX_3_20160802B_20160802

value: WM164 cell line with empty vector (NEG)

value: MDK gain of fuction_Control


title: SF3B1 p.K700E 5


title: SF3B1 WT 2

value: wild type


title: LECS_CM_WM164_NEG_2

description: 42547_GTCCGC_C9ELMANXX_3_20160802B_20160802


title: LECS_CM_WM164_NEG_1

description: 42546_CCGTCC_C9ELMANXX_3_20160802B_20160802


title: LECS_CM_10_sHM5_2

description: 42544_AGTTCC_C9ELMANXX_3_20160802B_20160802

value: Cell line SK-Mel-147 KD for MDK (shMDK)

value: MDK loss of fuction


title: NHF1_CPD_10J_0h_A

city: Istanbul

first: Ogun

last: Adebali

address: Orta Mah. Universite Cad No 27

department: Faculty of Natural Sciences and Engineering

country: Turkey

institute: Sabanci University

library_source: genomic

data_processing:
adapter discarding
alignment
filtering duplicates
damage position locating
filtering rare dinucleotides
Genome_build: hg19
Supplementary_files_format_and_content: Bed files contain genomic locaions of damages of the most common two dinucleotides at the damage sites for (6-4)PP and CPD. Each interval length is 10 nt, and the pyrimidine dimer is located at the 4-5th positions.

molecule: genomic DNA

growth_protocol: Normal human fibroblast NHF1 was obtained from W.K. Kaufmann, UNC, Chapel Hill (1) and cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 2 mM glutamine. Human lymphocyte GM12878 was purchased from the NIGMS Human Genetic Cell Repository (Coriell Institute) and cultured in RPMI 1640 medium (no phenol red) supplemented with 15% fetal bovine serum. Cells were maintained at 37°C in a 5% CO2 humidified chamber.

extract_protocol:
Genomic DNA were extracted by PureLink Genomic DNA kit (Thermo).
Genomic DNA was sheared by sonication with Q800 Sonicator (Qsonica) to generate fragments averaging 600 bp in length and then purified by an equal volume of HighPrep PCR beads (MagBio). DNA fragments were eluted by 0.1xTE and the concentration was determined by Qubit (Thermo). Purified DNA fragments (1 µg) were used for end-repair by NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) following the manufacturer's instruction. Ad1 (100 pmol) was ligated to both ends at 16°C overnight, then purified by HighPrep PCR beads (60 µl) and eluted in 55 µL of 0.1x TE. Damaged DNA immunoprecipitation was performed as described previously with modification. DNA were denatured by adding 20 µL of 8M urea, boiling for 1 min and immediately putting in ice water for 1 min. Then 20 µg of denatured sonicated salmon sperm DNA (Thermo) and 11 µL 8x IP Buffer (1x IP Buffer: 20 mM Tris-Cl pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, and 0.5% sodium deoxycholate) were added, followed by incubation with antibody-coated beads which were prepared as described previously (4) at 4°C overnight.  The beads were then washed sequentially with Wash Buffer U (20 mM Tris-Cl pH 8.0, 2 mM EDTA, 1% Triton X-100, and 2M Urea), Wash Buffer II (20 mM Tris-Cl pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, and 0.1% SDS), Wash Buffer III (10 mM Tris-Cl pH 8.0, 1 mM EDTA, 150 mM LiCl, 1% NP-40, and 1% sodium deoxycholate), Wash Buffer IV (100 mM Tris-Cl pH 8.0, 1 mM EDTA, 500 mM LiCl, 1% NP-40, and 1% sodium deoxycholate) and TE (10 mM Tris-Cl pH 8.0 and 1 mM EDTA) at room temperature. The fragments containing damage were eluted by incubation with 100 µL of Elution Buffer (50 mM NaHCO3, 1% SDS) at 65°C for 10 min on a thermomixer at 1100 rpm. The eluted DNA was then isolated by phenol/chloroform extraction followed by ethanol precipitation.  Primer Bio3U was attached to IP purified DNA and extended by NEBNext Q5 DNA polymerase, followed by ExoI (New England Biolabs) treatment and  HighPrep PCR beads cleanup, then denatured and captured by Dynabeads MyOne Streptavidin C1 (Thermo) as described previously (2). After incubation at 4°C for 1 hr, the beads were washed by 1x B&W buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl) and 1x TE, followed by incubation with 2 µL of USER Enzyme (New England Biolabs) in 18 µL of 0.1x TE at 37°C on a thermomixer at 900rpm for 25 min. The supernatant was separated by the magnetic stand and transferred to a new tube. Then the beads were washed with 25 µL of 1x B&W Buffer and the supernatant was collected and combined with supernatant from the last step. For subtractive hybridization, 20 pmol of oligo SH were added, followed by boiling for 1 min and naturally cooling down to room temperature. Oligo SH was then captured by incubating with 10 µL of Dynabeads MyOne Streptavidin C1 for 1 hr at room temperature. After separating the liquid on a magnet and transferring supernatant to a new tube, the beads were washed with 35 µL of 1x B&W Buffer and the supernatant was transferred to the same tube. DNA were purified by phenol/chloroform extraction and ethanol precipitation.  The following ligation of Ad2 and PCR amplification were performed as described previously (2). Libraries were sequenced from both ends on Hiseq 2500 by the University of North Carolina High-Throughput Sequencing Facility.

treatment_protocol: UV irradiation of NHF1 cells was performed as described previously (3). Briefly, the culture medium was removed from ~80% confluent cells in one R150 dish, then cells were irradiated under a GE germicidal lamp emitting primarily 254-nm UV light (1 J/m2/s) connected with a digital timer for 20s (for (6-4)PP damage) or 10s (for CPD damage). Following irradiation, the dishes were put on ice immediately or incubated in a chamber for indicated time with culture medium. The cells were then washed once with ice-cold PBS and harvested with a cell scraper in PBS and collected by centrifugation. GM12878 cells were grown to ~8x105 cells/ml in colorless medium and 10ml of cells were transferred to one R150 dish and irradiated with 20J/ m2 UV-C as described above. Then cells were immediately transferred to a pre-chilled 15 ml tube on ice, collected by centrifugation, washed with ice-cold PBS. For UV irradiation of naked DNA, purified genomic DNA in 100 µl of 1xTE buffer were irradiated with 20J/ m2 UV-C and stored at -20°C for further use.

tag: uv product

value: CPD

tag: replicate

value: A

tag: treatment

tag: uv dose

tag: cell line


title: LECS_CM_10_sHM5_1

description: 42543_AGTCAA_C9ELMANXX_3_20160802B_20160802


title: LECS_CM_10_sHM1_3

description: 42542_CTTGTA_C9ELMANXX_3_20160802B_20160802


title: LECS_CM_10_sHM1_2

description: 42541_CAGATC_C9ELMANXX_3_20160802B_20160802


title: LECS_CM_10_sHC_2

description: 42538_TGACCA_C9ELMANXX_3_20160802B_20160802

value: Cell line SK-Mel-147 KD control (shCtrl)

value: MDK loss of fuction_Control


title: LECS_CM_10_sHM1_1

description: 42540_GCCAAT_C9ELMANXX_3_20160802B_20160802


title: LECS_CM_WM164_MDK_2

description: 42550_GTTTCG_C9ELMANXX_3_20160802B_20160802


title: DRIPseq_B1_4_LP_RH

city: San Antonio

first: Rong

last: Li

state: TX

address: 7703 Floyd Curl Drive

department: Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

description:
BSC127_LumPro_RH
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI. Digested DNA was treated with RNASEH1 overnight before DRIP.
No data processing was done on this sample.

data_processing:
Library strategy: DRIP-Seq
DRIP-seq and ChIP-seq data were aligned using BWA default parameters. Peak was called using macs14 using q value cutoff 0.01.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Bed files include peaks.

source_name: Normal breast tissue: Luminal Progenitor (EpCAMhigh CD49f+), BRCA1 mutation, RNase H

extract_protocol:
DRIP-seq: DRIP assay was performed following the established protocol. Briefly, cells were washed twice in PBS, and resuspended in TE (Sigma, T9285) containing 5μl of proteinase K (Roche, 03115828001) and a final concentration of 0.5% SDS and proteinase K (Roche, 03115828001). Samples were incubated overnight at 37C. Genomic DNA was extracted using phenol/chloroform (Sigma, P2069) in phase lock tubes (5PRIME, 2302840) and ethanol precipitated. DNA was digested using established restriction enzyme cocktail (HindIII, EcoRI, BsrGI, XbaI and SspI) overnight at 37C. Digested DNA was cleaned up by phenol-chloroform extraction and ethanol precipitation. For DRIP, digested DNA was incubated with S9.6 antibody (Kerafast, ENH001, lot# 101614) overnight at 4C in binding buffer (10 mM sodium phosphate, 140 mM sodium chloride, 0.05% Triton X-100 in TE). As a negative control for DRIP, digested DNA was treated overnight with RNase H (NEB, M0297S) and then precipitated for DRIP. Dynabeads were added the next day for 2 hours. Bound Dynabeads were then washed with binding buffer three times at room temperature. DNA was eluted, phenol-chloroform extracted, and ethanol precipitated. DRIP DNA was sonicated using Covaris (Model S220) before library preparation.
ChIP-seq: Cells were crosslinked with 1% formaldehyde at room temperature for 10 min, and the reaction was terminated with 125 mM Glycine at room temperature for 5 min. The crosslinking reagent was removed by spinning at 1,000 g at 4C for 5 min, and cells were washed with cold PBS three times. From this step on to ChIP elution, all buffers were prepared with freshly added cocktail of phosphatase and protease inhibitors (10 mM sodium fluoride, 10 mM sodium pyrophosphate tetrabasic, 2 mM sodium orthovanadate, 1 µg/ml leupeptin, 1 µg/ml aprotinin, 1 µg/ml pepstatin and 1 mM PMSF). Cells were lysed on ice for 10 min using lysis buffer (5 mM HEPES, pH 7.9, 85 mM KCl, 0.5% Triton-X-100). Supernatant was removed after spinning at 1600 g at 4C for 5 min, and pellet was resuspended with nuclei lysis buffer (50 mM Tris–HCl, pH 8.0, 10 mM EDTA, 1% (wt/vol) SDS). Chromosomal DNA was sonicated using a probe sonicator on ice, then centrifuged at 14,000 g for 15 min and the supernatant was saved. Antibodies used for ChIP include: anti-Pol II (Abcam ab817, lot# GR299078-2) and anti-NELF-A which was described previously (J Cell Biochem. 107, 131-139). Sonicated DNA was incubated with antibody at 4C overnight. Dynabeads Protein A (Thermo Fisher Scientific, 10002D) was added the following day and incubated for 4 hours. After incubation, Dynabeads was washed twice in TE Sarcosyl buffer (50 mM Tris-HCl pH 8.0, 2 mM EDTA, 0.2% sarcosyl), twice in TSE1 buffer (150 mM sodium chloride, 20 mM Tris-HCl pH 8.0, 2 mM EDTA, 0.1% (wt/vol) SDS, 1% Triton-X-100), twice in TSE2 buffer (500 mM sodium chloride, 20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 0.1% (wt/vol) SDS, 0.1% Triton-X-100), twice in TSE3 buffer (250 mM lithium chloride, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1% sodium deoxycholate, 1% NP-40), and twice in TE buffer (50 mM Tris-HCl pH 8.0, 2 mM EDTA). Samples were subsequently eluted and reverse-crosslinked and ethanol-precipitated.
DRIP-seq and ChIP-seq libraries were built following the instruction of MicroPlex library preparation kit (Diagenode, C05010011). A total of 15 cycles of PCR amplification was performed. After amplification, libraries were purified using Agencourt AMPure XP system (Beckman Coulter, A63880) following the product manual. Quantity of the libraries was measured with Qubit dsDNA HS Assay Kit (Life Technologies, Q32851), and quality of the libraries was verified using Bioanalyzer 2100. Libraries were pooled based on index sequences.

treatment_protocol: Normal breast tissue samples from four BRCA1 mutation carriers (B1) and four non-carriers (NC) were procured, digested into single cells, and sorted by flow cytometry using established cell surface markers (EpCAM and CD49f).

value: BRCA1 mutation

tag: tissue

value: Normal breast

tag: sorted cell type

value: Luminal progenitor

tag: antibody

tag: individual identifier


title: DRIPseq_B1_4_ML_RH

description:
BSC127_MatLum_RH
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI. Digested DNA was treated with RNASEH1 overnight before DRIP.
No data processing was done on this sample.

source_name: Normal breast tissue: Mature Luminal (EpCAMhigh CD49f-), BRCA1 mutation, RNase H

value: Mature luminal epithelial


title: LECS_CM_10_sHC_1

description: 42558_CGATGT_C9MRRANXX_2_20160811B_20160811

value: Primary Human Lymphatic Endothilial cells (hLECs)


title: LECS_CM_10_sHC_3

description: 42539_ACAGTG_C9ELMANXX_3_20160802B_20160802


title: Hypoxia 24h

city: Singapore

first: Jia

address: 8 College Road

country: Singapore

institute: Duke-NUS

data_processing:
RNA-seq aligned to hg19 genome and UCSC reference transcript using STAR (version 2.4.0).
Bigwig generated after normalization.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig

molecule: total RNA

source_name: Human breast cancer

growth_protocol: DMEM (Nacalai Tesque), supplemented with 10% fetal bovine serum (Sigma-Aldrich), 100 mM non-essential amino acids, 100 U/ml penicillin, 100 mg/ml streptomycin, 2 mM GlutaMAX-I (Invitrogen) and 55 mM β-mercaptoethanol (Sigma)

extract_protocol:
Total RNA was extracted from cells using the RNeasy Mini kit (Qiagen).
BGI RNA-Seq library construction (90bp paired-end sequencing)

treatment_protocol: MCF7 cells were seeded simultaneously into 6cm tissue culture dishes at a density of 0.6 million per dish and incubated in 21% O2 and 5% CO2 at 37°C in a Forma Steri-Cycle CO2 incubator overnight before treatment. All treatment conditions were carried out in parallel in the same 24 h window. For hypoxia treatments, these were carried out in 1% O2 and 5% CO2 at 37°C in an Invivo2 400 hypoxia workstation (Ruskinn Technology). For the acute phase hypoxia treatment, cells were cultured for 20h in normoxia (21% O2 and 5% CO2) followed by 4h of hypoxia while chronic hypoxia treatments consist of continuous culture for 24h in hypoxia. Normoxia controls were carried out simultaneously for 24h at 37°C in a Forma Steri-Cycle CO2 incubator.

value: breast cancer

tag: seeding density

value: 0.6 million per 6cm tissue culture dish

value: 24h hypoxia


title: Hypoxia 4h

value: normoxia 20h followed by 4h of hypoxia


title: Normoxia

value: 24h normoxia


title: LECS_CM_WM164_MDK_1

description: 42549_GTGGCC_C9ELMANXX_3_20160802B_20160802

value: WM164 cell line overexpressing MDK (MDK)

value: MDK gain of fuction


title: ChIPseq_NC_POLII

description:
BSC132L_POLII
RNAPII ChIP-seq using normal human breast tissue.
No data processing was done on this sample.

data_processing:
DRIP-seq and ChIP-seq data were aligned using BWA default parameters. Peak was called using macs14 using q value cutoff 0.01.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Bed files include peaks.

source_name: Normal breast tissue, unsorted, non-carrier, Pol II ChIP

value: Non-Carrier

value: Unsorted

value: anti-Pol II


title: ChIPseq_NC_NELF

description:
BSC132L_NELF
NELFA ChIP-seq using normal human breast tissue.
No data processing was done on this sample.

source_name: Normal breast tissue, unsorted, non-carrier, NELF-A ChIP

value: anti-NELF-A


title: DRIPseq_B1_4_ML

description:
BSC127_MatLum
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

source_name: Normal breast tissue: Mature Luminal (EpCAMhigh CD49f-), BRCA1 mutation


title: DRIPseq_B1_4_LP

description:
BSC127_LumPro
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

source_name: Normal breast tissue: Luminal Progenitor (EpCAMhigh CD49f+), BRCA1 mutation


title: DRIPseq_B1_4_Stromal

description:
BSC127_Stromal
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

source_name: Normal breast tissue: Stromal (EpCAM- CD49f-), BRCA1 mutation

value: Stromal


title: DRIPseq_B1_3_Basal

description:
BSC120_Basal
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

source_name: Normal breast tissue: Basal (EpCAMLow CD49fhigh), BRCA1 mutation

value: BRCA1 mutation

value: Basal epithelial


title: DRIPseq_B1_2_Basal

description:
BSC115_Basal
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

value: Normal breast


title: DRIPseq_B1_2_LP

description:
BSC115_LumPro
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

value: Luminal progenitor


title: DRIPseq_B1_1_ML

description:
BSC107_MatLum
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

value: Mature luminal epithelial


title: DRIPseq_B1_3_ML

description:
BSC120_MatLum
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.


title: DRIPseq_B1_2_ML

description:
BSC115_MatLum
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.


title: DRIPseq_B1_3_Stromal

description:
BSC120_Stromal
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.


title: DRIPseq_B1_1_LP

description:
BSC107_LumPro
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.


title: DRIPseq_B1_1_Basal

description:
BSC107_Basal
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.


title: DRIPseq_NC_4_ML

description:
BSC134_MatLum
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

source_name: Normal breast tissue: Mature Luminal (EpCAMhigh CD49f-), non-carrier


title: DRIPseq_B1_1_Stromal

description:
BSC107_Stromal
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.


title: DRIPseq_B1_3_LP

description:
BSC120_LumPro
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.


title: DRIPseq_NC_4_LP

description:
BSC134_LumPro
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

source_name: Normal breast tissue: Luminal Progenitor (EpCAMhigh CD49f+), non-carrier


title: DRIPseq_NC_3_LP

description:
BSC132_LumPro
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.


title: DRIPseq_NC_3_Stromal

description:
BSC132_Stromal
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

source_name: Normal breast tissue: Stromal (EpCAM- CD49f-), non-carrier


title: DRIPseq_NC_3_Basal

description:
BSC132_Basal
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

source_name: Normal breast tissue: Basal (EpCAMLow CD49fhigh), non-carrier


title: DRIPseq_NC_4_Basal

description:
BSC134_Basal
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.


title: DRIPseq_NC_4_Stromal

description:
BSC134_Stromal
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.


title: DRIPseq_NC_3_ML

description:
BSC132_MatLum
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.


title: DRIPseq_NC_2_ML

description:
BSC119_MatLum
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.


title: DRIPseq_NC_2_Basal

description:
BSC119_Basal
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.


title: LECS_CM_10_sHM5_3

description: 42545_ATGTCA_C9ELMANXX_3_20160802B_20160802

value: Primary Human Lymphatic Endothilial cells (hLECs)

value: Cell line SK-Mel-147 KD for MDK (shMDK)

value: MDK loss of fuction


title: RNA-Seq on wild-type of 32-64 cell embryos rep1

city: Irapuato

first: C.

middle: Stewart

last: Gillmor

state: Guanajuato

address: Km. 9.6 Libramiento Nte Carr Leon-Irapuato

country: Mexico

institute: National Laboratory of Genomics for Biodiversity

data_processing:
FastQC 0.11.5 was used to assess read quality
Mapping was done using HISAT2 v2.0.5 (--max-intronlen 900)
Cufflinks 2.2.1 was used to assemble pri-miRNA transcripts (merged from se-1 and Col reads alignments) (--overlap-radius 1 --library-type fr-unstranded). Araport11 miRNA annotation was used to guide the assembly process.
Quantification of reads was done using the function featureCounts in the Rsubread package in R
Genome_build: TAIR10 assembly
Supplementary_files_format_and_content: tab-delimited text files include assigned reads to genes

organism: Arabidopsis thaliana

source_name: early globular embryos

growth_protocol: Plants were grown in soil in a growth chamber under long-day conditions (22°C with 16h light / 8h dark), after incubation for at least 4 days at 4°C in the dark

extract_protocol:
Total RNA was extracted from each ecotype globular stage embryos following the protocol of RNAqueous-Micro kit (Ambion, Catalog# 1927). The mRNA amplification was conducted according to the protocol provided in the MessageAmp aRNA kit (Ambion, Catalog# 1750).
Illumina mRNA-seq libraries were prepared using the TruSeq RNA kit (version 1, rev A).

tag: ecotype background

value: Col

tag: genotype

value: wild type

value: embryo

tag: Stage

value: 32-64 cell (early to mid-globular) stage


title: RNA-Seq on se-1 early globular embryos rep1

value: se-1; serrate-1


title: Ileum IEC OGT-KO-3

city: Minneapolis

first: Hai-Bin

last: Ruan

state: MN

department: Integrative Biology and Physiology

institute: University of Minnesota

data_processing:
BaseSpace (Illumina) applications TopHat Alignment (Version 1.0.0), which runs Bowtie, TopHat, the Isaac Variant Caller, and Cufflinks, were used to procude aligned reads, variant calls and FPKM abundance estimates of reference genes and transcripts.
The BaseSpace apps TopHat Alignment and Cufflinks Assembly and Differential Expression, which includes the TopHat and Cufflinks apps derived from the Tuxedo suite, was used to perform novel transcript assembly and differential expression analysis.
Genome_build: Mus musculus UCSC mm10
Supplementary_files_format_and_content: Excel files with log2(FPKM) and log2(Ratio) values

organism: Mus musculus

source_name: Intestinal epithelial cells

extract_protocol:
IECs from ileum and colon were isolated by shaking intestinal tissue in PBS with 10 mM EDTA at 37°C for 30 minutes. Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instruction. RNA concentration and integrity of each sample was measured on an Agilent Bioanalyzer.
Equal amounts of RNA from the each sample were pooled for cDNA library construction using standard Illumina protocols.

value: IEC-OGT KO

value: Ileum

tag: age

value: 10 weeks


title: RNA-Seq on wild-type of 32-64 cell embryos rep2


title: Ileum IEC OGT-KO-1


title: Ileum IEC OGT-KO-2


title: DRIPseq_NC_2_Stromal

description:
BSC119_Stromal
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

value: Non-Carrier

value: Stromal


title: DRIPseq_NC_1_Stromal

description:
BSC117_Stromal
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.


title: DRIPseq_NC_2_LP

description:
BSC119_LumPro
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.


title: Ileum IEC WT-1

value: WT


title: colon IEC OGT-KO-2

value: Colon


title: colon IEC OGT-KO-1


title: colon IEC WT-2


title: colon IEC WT-3


title: RNA-Seq on se-1 early globular embryos rep2


title: DRIPseq_NC_1_LP

description:
BSC117_LumPro
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

value: Normal breast

value: Luminal progenitor


title: 50nM_CH3Hg_r3

city: Versoix

first: Rebecca

last: Beauvais-Flueck

address: 10 route de Suisse - CP 416

department: Institut F.-A. Forel

country: Switzerland

institute: University of Geneva

description:
Sample name: M10000.3
artificial exposure medium

data_processing:
Samples were aligned with TopHat2 to the Creiinhardtii 236 V.9.0 available at phytozome.org.
Reads were counted using the Python package HTSeq.
Genome_build: C. reinhardtii 236 V.9.0
Supplementary_files_format_and_content: The .txt files report raw counts

organism: Chlamydomonas reinhardtii

source_name: cell culture exposed to metal

growth_protocol: Algal cells were exposed in an artificial freshwater medium.

extract_protocol:
Total RNA was extracted using TRI Reagent® protocol.
RNA libraries were prepared using Illumina TruSeq Stranded mRNA kit.
RNA libraries were sequenced on a Illumina HiSeq 2500 System.

treatment_protocol: Algal pellets were frozen in liquid nitrogen and cells were broken using glass beads in the presence of TRI Reagent.

tag: strain

value: 50 nM CH3Hg

tag: time (exposure)


title: 0.5nM_CH3Hg_r1

description:
Sample name: M100.1
artificial exposure medium

tag: genotype/variation

value: 0.5 nM CH3Hg


title: 100nM_Hg_r2

description:
Sample name: H20000.2
artificial exposure medium

value: 100 nM Hg


title: colon IEC OGT-KO-3


title: 0.05nM_CH3Hg_r3

description:
Sample name: M10.3
artificial exposure medium

value: 0.05 nM CH3Hg


title: SF3B1 WT 4

source_name: chronic lymphocytic leukemia (CLL)

tag: disease state

value: chronic lymphocytic leukemia (CLL)

value: wild type


title: 50nM_CH3Hg_r1

description:
Sample name: M10000.1
artificial exposure medium


title: 5nM_CH3Hg_r2

description:
Sample name: M1000.2
artificial exposure medium

value: 5 nM CH3Hg


title: DRIPseq_NC_1_ML

description:
BSC117_MatLum
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

value: Mature luminal epithelial


title: 5nM_CH3Hg_r3

description:
Sample name: M1000.3
artificial exposure medium


title: 50nM_CH3Hg_r2

description:
Sample name: M10000.2
artificial exposure medium


title: 1nM_Hg_r2

description:
Sample name: H200.2
artificial exposure medium

value: 1 nM Hg


title: 5nM_CH3Hg_r1

description:
Sample name: M1000.1
artificial exposure medium


title: 1nM_Hg_r1

description:
Sample name: H200.1
artificial exposure medium


title: 0.1nM_Hg_r2

description:
Sample name: H20.2
artificial exposure medium

value: 0.1 nM Hg


title: 0.1nM_Hg_r1

description:
Sample name: H20.1
artificial exposure medium


title: 0.5nM_CH3Hg_r3

description:
Sample name: M100.3
artificial exposure medium


title: 0.1µM_Cu_r3

description:
Sample name: Cu.3
artificial exposure medium

value: 0.1 µM Cu


title: 0.5nM_CH3Hg_r2

description:
Sample name: M100.2
artificial exposure medium


title: 100nM_Hg_r3

description:
Sample name: H20000.3
artificial exposure medium


title: 0.1µM_Cu_r1

description:
Sample name: Cu.1
artificial exposure medium


title: 100nM_Hg_r1

description:
Sample name: H20000.1
artificial exposure medium


title: Control_r2

description:
Sample name: Co.2
artificial exposure medium

value: Control


title: w1118_2

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences using Cutadapt v1.2.1, and then mapped to Flybase r5.57 genome using TopHat v2.0.10 with parameters -r 0 --library-type fr-firststrand --mate-std-dev 100 --solexa-quals -p 24 --bowtie-n.
After removing duplicate reads, the number of reads mapped to gene features were counted using HTSeq v0.6.1.
The number of reads counted by HTseq were converted to log2-read counts after adding one to the read counts. The log2-read counts for the samples in each condition were then normalized using the quantile normalization method (MATLAB R2011b).
Genome_build: Flybase r5.57
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

organism: Drosophila melanogaster

source_name: heads of flies without expressing MJDtr-78Q

extract_protocol:
Total RNAs were extracted from the heads of Drosophila melanogaster with or without expressing MJDtr-78Q. Poly(A) mRNA isolation from total RNA (2 µg) and fragmentation were performed using the Illumina Truseq Stranded mRNA LT Sample Prep Kit with poly-T oligo-attached magnetic beads, according to the manufacturer’s instructions.
Libraries were prepared for multiplex sequencing using Illumina Truseq Stranded mRNA LT Sample Prep Kit, according to the manufacturer’s protocol.

value: head

value: without expressing MJDtr-78Q


title: MJDtr-78Q_2

source_name: heads of flies with expressing MJDtr-78Q

value: with expressing MJDtr-78Q


title: 1nM_Hg_r3

description:
Sample name: H200.3
artificial exposure medium


title: npc_rna_rep2

status: Public on Jun 26 2017

city: San Francisco

first: Stephen

middle: N.

last: Floor

state: CA

address: 513 Parnassus Ave, HSW 740

department: Cell and Tissue Biology

institute: University of California, San Francisco

description:
rRNA-depleted; ligation lib prep
processed data file: rp_gene_orf_tpms.tsv
processed data file: rp_orf_5utr_counts.tsv
Read adapter: NNNNNATCGTAGATCGGAAGAGCACACG

data_processing:
Library strategy: RNA-seq (ligation)
Basecalling was performed on-instrument and converted to FASTQ using bcl2fastq v2.17.
Adapters were trimmed using Cutadapt v1.13, reads aligning to the repeatmasker or Illumina iGenomes abundant sequences using Bowtie2 v2.2.6 were discarded. Unaligned reads were then aligned to the Ensembl release 84 transcriptome using HISAT2 v2.0.4.
Transcript isoform level abundances were calculated using Kallisto v0.43 and normalized between samples.
Transcript abundances were aggregated to the gene-level using tximport.
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV files include TPM (transcripts per million) for Ensembl transcripts from protein coding genes in release 84.

source_name: Neural progenitor cells (NPC)

growth_protocol: Cells were grown according to cell-type specific requirements and were actively growing when harvested

extract_protocol:
Libraries were prepared using a slightly modified version of the ribosome profiling protocol (Ingolia 2012). Protected footprints were generated by RNase digestion; fragmented RNA was generated using limited alkaline hydrolysis.
Polysomal RNA was extracted from sucrose gradient fractions by ethanol precipitation. RNA was then DNase treated, subjected to acid phenol:chloroform extraction, and ethanol precipitated. Cytoplasmic and nuclear RNA was extracted using TRIzol extraction (Life Technologies) and ethanol precipitation. Total RNA integrity was verified using a BioAnalyzer (Agilent).

treatment_protocol: Media was aspirated and replaced by PBS + 100 ug/ml cycloheximide and incubated at 37 °C for ten minutes. Cells were isolated with type-specific protease and lysed on ice in hypotonic buffer by ten strokes through a 26-gauge needle and nuclei were pelleted at 1,500g for 5 minutes. Lysate from ~10 million cells was layered on top of 10-50% (w/v) sucrose gradients (20 mM HEPES pH 7.6, 100 mM KCl, 5 mM MgCl2, 1 mM DTT and 100 ug/ml cycloheximide).  Gradients were centrifuged for 2 hours at 36,000 RPM in a SW-41 rotor, punctured, and manually peak fractionated using real-time A260 monitoring with a Brandel gradient fractionator and ISCO UA-6 detector.

tag: cell type

value: Neural progenitor cells (NPC)

tag: fraction

value: Cytoplasm

tag: molecule

value: Cytoplasmic RNA


title: neu14_rp_rep1

description:
Ribosome profiiling; rRNA-depleted
processed data file: rp_gene_orf_tpms.tsv
processed data file: rp_orf_5utr_counts.tsv
Read adapter: NNNNNATCGTAGATCGGAAGAGCACACG

data_processing:
Library strategy: Ribosome profiling
Basecalling was performed on-instrument and converted to FASTQ using bcl2fastq v2.17.
Adapters were trimmed using Cutadapt v1.13, reads aligning to the repeatmasker or Illumina iGenomes abundant sequences using Bowtie2 v2.2.6 were discarded. Unaligned reads were then aligned to the Ensembl release 84 transcriptome using HISAT2 v2.0.4.
Transcript isoform level abundances were calculated using Kallisto v0.43 and normalized between samples.
Transcript abundances were aggregated to the gene-level using tximport.
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV files include TPM (transcripts per million) for Ensembl transcripts from protein coding genes in release 84.

source_name: Neural cultures (14 days)

value: Neural cultures (14 days)

value: Ribosome protected footprints


title: neu14_rp_rep2


title: DRIPseq_NC_1_Basal

description:
BSC117_Basal
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

value: Non-Carrier

value: Normal breast

value: Basal epithelial


title: 0.1nM_Hg_r3

description:
Sample name: H20.3
artificial exposure medium

value: wild type

tag: treatment


title: 0.05nM_CH3Hg_r1

description:
Sample name: M10.1
artificial exposure medium

value: 0.05 nM CH3Hg


title: hesc_rna_rep2

source_name: Human embryonic stem cells (hESC)

value: Human embryonic stem cells (hESC)


title: neu14_rna_rep2


title: 0.05nM_CH3Hg_r2

description:
Sample name: M10.2
artificial exposure medium


title: hesc_rp_rep1


title: w1118_1

tag: tissue


title: MJDtr-78Q_1


title: neu50_poly_low_rep2

description:
rRNA-depleted
processed data file: tripseq_gene_tpms.tsv
processed data file: tripseq_transcript_tpms.tsv
Read 1 adapter: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Read 2 adapter: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

data_processing:
Basecalling was performed on-instrument and converted to FASTQ using bcl2fastq v2.17.
Adapters were trimmed using Cutadapt v1.13, reads aligning to the repeatmasker or Illumina iGenomes abundant sequences using Bowtie2 v2.2.6 were discarded. Unaligned reads were then aligned to the Ensembl release 84 transcriptome using HISAT2 v2.0.4.
Transcript isoform level abundances were calculated using Kallisto v0.43 and normalized between samples.
Transcript abundances were aggregated to the gene-level using tximport.
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV files include TPM (transcripts per million) for Ensembl transcripts from protein coding genes in release 84.

source_name: Neural cultures (50 days)

extract_protocol:
Libraries were prepared using the Illumina TruSeq Stranded Total RNA kit using 100ng RNA input and 13 PCR cycles.
Polysomal RNA was extracted from sucrose gradient fractions by ethanol precipitation. RNA was then DNase treated, subjected to acid phenol:chloroform extraction, and ethanol precipitated. Cytoplasmic and nuclear RNA was extracted using TRIzol extraction (Life Technologies) and ethanol precipitation. Total RNA integrity was verified using a BioAnalyzer (Agilent).

value: Neural cultures (50 days)

value: Low polysome (2-4 ribosomes)

value: Polysomal RNA


title: neu50_poly_high_rep2

value: High polysome (5-8+ ribosomes)


title: neu50_mono_rep2

value: Monosome (80S)

value: Monosomal RNA


title: Control_r1

description:
Sample name: Co.1
artificial exposure medium

value: Control


title: Control_r3

description:
Sample name: Co.3
artificial exposure medium


title: neu14_rna_rep1

value: Cytoplasm


title: neu50_poly_low_rep1


title: neu50_mono_rep1


title: npc_rna_rep1

value: Neural progenitor cells (NPC)

value: Cytoplasmic RNA


title: npc_rp_rep1

value: Ribosome protected footprints


title: 0.1µM_Cu_r2

description:
Sample name: Cu.2
artificial exposure medium

value: 0.1 µM Cu


title: neu50_cyto_rep2


title: neu50_cyto_rep1


title: neu50_poly_high_rep1


title: hesc_rp_rep2


title: neu14_poly_high_rep2

value: Neural cultures (14 days)


title: neu14_poly_low_rep2


title: neu50_nuc_rep2

value: Nucleus

value: Nuclear RNA


title: neu14_nuc_rep2


title: npc_poly_high_rep2


title: neu14_mono_rep2


title: neu14_cyto_rep2


title: npc_poly_low_rep2


title: npc_mono_rep2


title: DRIPseq_B1_4_Basal

description:
BSC127_Basal
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

value: BRCA1 mutation

value: Normal breast

tag: sorted cell type

value: Basal epithelial


title: npc_cyto_rep2


title: npc_nuc_rep2


title: hesc_poly_low_rep2

value: Human embryonic stem cells (hESC)

value: Low polysome (2-4 ribosomes)


title: hesc_poly_high_rep2

value: High polysome (5-8+ ribosomes)

value: Polysomal RNA


title: hesc_monosome_rep2

value: Monosome (80S)

value: Monosomal RNA


title: DRIPseq_B1_2_Stromal

description:
BSC115_Stromal
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

value: Stromal

tag: antibody


title: neu50_nuc_rep1

value: Neural cultures (50 days)


title: hesc_nuc_rep2


title: neu14_poly_low_rep1


title: neu14_mono_rep1


title: hesc_cyto_rep2

value: Cytoplasm

value: Cytoplasmic RNA


title: neu14_nuc_rep1


title: neu14_poly_high_rep1


title: neu14_cyto_rep1


title: hesc_rna_rep1


title: npc_poly_high_rep1

value: Neural progenitor cells (NPC)


title: npc_poly_low_rep1


title: npc_nuc_rep1


title: npc_cyto_rep1


title: npc_mono_rep1


title: hesc_poly_high_rep1


title: hesc_poly_low_rep1


title: hesc_monosome_rep1


title: hesc_cyto_rep1


title: control

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

country: France

institute: IRHS

data_processing:
mapping performed with BSMAP v 2.89
methylation call performed with BSMAP v 2.89
Genome_build: TAIR10
Supplementary_files_format_and_content: BSMAP standard output format

source_name: seedlings

growth_protocol: Prior to germination, Arabidopsis seeds were stratified for 2 days at 4 °C. Before and during stress treatments plants were grown under controlled conditions in a Sanyo MLR-350 growth chamber on solid ½ MS medium (1 % sucrose, 0.5 % Phytagel (Sigma), pH 5.8) under long day conditions (16 h light) at 24 °C (day) and 22 °C (night).

extract_protocol:
DNA from Arabidopsis plants was extracted with the DNeasy Plant Mini Kit (Qiagen) following the manufacturer’s recommendations.
Bisulfite treatment was applied to determine the cytosine methylation status using the Epitect bisulfite kit. Illumina library was then constructed following manufacturer's instructions

treatment_protocol: Surface sterilized seeds of Arabidopsis were germinated and grown on solid ½ MS medium that was supplemented with sterile filtrated zebularine (Sigma, 40 microM), α-amanitin (Sigma, 5 microM) or a combination of both chemicals.

tag: developmental stage

value: seedlings arial parts

value: Columbia

tag: agent


title: amanitin

value: amanitin


title: amanitin_and_zebularine


title: S47

city: Lebanon

first: Britton

middle: C

last: Goodale

state: NH

address: 1 Medical Center Drive

department: Dartmouth Cancer Center

institute: Geisel School of Medicine at Dartmouth

description: Barcode: ACTGAT

data_processing:
Libraries were sequenced on an Illumina HiSeq 2500 and initial data analysis/base calling/read quality analysis performed with HiSeq Control Software version 2.2.58
Reads were trimmed for quality (limit=0.01, max of 2 amibiguous bases) and aligned to Homo sapiens genome assembly GRCh38.82 in CLC Genomics Workbench version 8.0 (Qiagen) using paired read parameters.
Count tables of aligned paired reads per gene were exported from CLC Genomics Workbench version 8.0 were exported for analysis in R
Libraries were normalized and differentially expressed transcripts determined using R/EdgeR (Robinson et al. Bioinformatics (2010))
Genome_build: GRCh38.82
Supplementary_files_format_and_content: Comma-delimited csv file of counts per transcript per sample

source_name: Polarized bronchial epithelial cells

growth_protocol: Primary cells were seeded on 12-mm transwell filters and allowed to polarize for 3 weeks, fed basolaterally with Air-liquid interface (ALI) media every other day

extract_protocol:
HBE cells were rinsed with PBS and lysed in RNAzol. Total RNA was extracted following manufactuers instructions
Libraries were prepared for sequencing using the Illumina TruSeq stranded mRNA protocol
24 libraries were pooled per lane for RNAseq. Data were collected from 2 sequencing runs (2 lanes per run)

treatment_protocol:
[Arsenic] Arsenic was added to basolateral media (0, 5, 10 or 50 ug/L) and exchanged every other day for 6 days (antibiotic-free media was used starting on day 5)
[Pseudomonas aeruginosa] Following 6 days of arsenic exposure, Pseudomonas aeruginosa (strain PaO1, MOI of 25-30) or antibiotic-free media control was added to the apical surface and HBE cells were incubated for 6 hours

value: Polarized bronchial epithelial cells

tag: donor

value: A

tag: Sex

value: female

tag: arsenic (ug/l)

tag: pseudomonas aeruginosa infection


title: S48

description: Barcode: ATTCCT


title: zebularine

tag: genotype

value: zebularine


title: Ileum IEC WT-2

value: WT

value: Ileum

tag: age

value: 10 weeks


title: EM-mRNA-2

city: Beijing

first: xiaosu

last: zhou

address: Dong Dan San Tiao 9

country: China

institute: Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

description: Sample 4

data_processing:
For mRNA sequencing,low quality and adapter sequences were removed from the Illumina reads by an in-house Perl script.
For mRNA sequencing,high-quality reads were mapped onto the E. granulosus and E. multilocularis genome v3 downloaded from http://www.sanger.ac.uk/ by tophat v2.0.4.
mRNA transcript sequences were assembled by Cufflinks v2.0.2. Then Cuffdiff was used to find significant changes of expression.
Functional annotation and classification were analysed by using KEGG and Gene Ontology databases.
Genome_build: E. granulosus and E. multilocularis genome v3 downloaded from http://www.sanger.ac.uk/
Supplementary_files_format_and_content: The .xlsx file reports FPKMs.

organism: Echinococcus multilocularis

source_name: hydatid cyst

extract_protocol:
Total RNA from the parasites was purified with Trizol reagent and contaminating gemomic DNA was removed by the RNase-Free DNase Set. Polyadenylated RNA  were isolated from total RNA.
The mRNA was interrupted into short fragments by adding fragmentation buffer as described (Illumina RNA-seq kit, part no. 1004898). Taking these short fragments as templates, random hexamer primers were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I, respectively. Short fragments were purified and double strand cDNAs were end-repaired according to manufacturer-recommended protocols (https://icom.illumina.com/), and then were connected with Illumina adapters (Illumina RNA-seq kit, part no. 1004898). The fragments were first amplified by PCR. Purified cDNA fragments were pooled and indexed and were loaded onto one lane of an Illumina HiSeq™ 2000 instrument. Pair-end 100 sequencing cycles were carried out.

tag: larvel stage

value: protoscoleces


title: hesc_nuc_rep1

value: Human embryonic stem cells (hESC)

value: Nucleus

value: Nuclear RNA


title: S44

description: Barcode: GTTTCG


title: S45

description: Barcode: CGTACG


title: EM-mRNA-1

description: Sample 3


title: S46

description: Barcode: GAGTGG


title: S42

description: Barcode: GTGAAA


title: S41

description: Barcode: GTCCGC


title: S38

description: Barcode: GAGTGG

value: E


title: S37

description: Barcode: CGTACG


title: EM-smallRNA-1

description: Sample 3

data_processing:
For small RNA sequencing, the unique reads were mapped onto the E.granulosus and E.multilocularis genomes respectively, using the program Bowtie."Contaminations" were removed by screening the unique reads against non-coding RNA database (Release 10), using Bowtie.
To identify potential conserved miRNA sequences, the remaining perfectly matched reads were Blast-searched against the Metazoa mature miRNA of Sanger miRBase(Release 20) using the program Patscan.
For novel miRNA prediction,software Einverted of Emboss (v6.5.7.0) was used to find the inverted repeats the secondary structure of the inverted repeat was predicted by RNAfold (ViennaRNA, v1.8.5). Unique reads in the inverted repeats were evaluated by MirCheck.
IDEG6 was used to identify miRNAs showing statistically significant difference in relative abundance (as reflected by total count of individual sequence reads) between the two small RNA libraries from E.granulosus and E.multilocularis.
Genome_build: E. granulosus and E. multilocularis genome v3 downloaded from http://www.sanger.ac.uk/
Supplementary_files_format_and_content: The .xlsx file reports abundance measurements.

extract_protocol:
For small RNA sequencing, an RNA preparation enriched in < 200nt RNAs was obtained from each sample using the mirVana miRNA Isolation Kit (Ambion, USA).
The 18-30nt fraction of total RNA was excised and purified following 15% Tris-Borate-EDTA (TBE) denaturing polyacrylamide gel electrophoresis (PAGE). Subsequently, proprietary adapters were ligated to the 5’ and 3’ termini of the RNA using T4 RNA ligase respectively. The adaptor-ligated small RNAs were subjected to RT-PCR amplification, and after the cDNA was further amplified, the PCR products (90bp, small RNA+ adaptors) were purified using PAGE. Two biological replicate small RNA libraries were constructed for each species and were sequenced on Illumina HiSeq™ 2000 Sequencing System at the Beijing Genomics Institute (BGI), Shenzhen, P.R.China.


title: S36

description: Barcode: GTTTCG


title: S34

description: Barcode: GTGAAA


title: S33

description: Barcode: GTCCGC


title: S35

description: Barcode: GTGGCC


title: colon IEC WT-1

value: Colon


title: S31

description: Barcode: ATGTCA

value: C


title: S30

description: Barcode: AGTTCC


title: S39

description: Barcode: ACTGAT


title: S29

description: Barcode: AGTCAA


title: S32

description: Barcode: CCGTCC


title: S28

description: Barcode: CTTGTA


title: S27

description: Barcode: GGCTAC


title: S43

description: Barcode: GTGGCC


title: S25

description: Barcode: GATCAG


title: S26

description: Barcode: TAGCTT


title: EM-smallRNA-2

description: Sample 4


title: npc_rp_rep2

value: Neural progenitor cells (NPC)

value: Ribosome protected footprints


title: S24

description: Barcode: ACTTGA

value: B


title: S22

description: Barcode: GCCAAT

value: Polarized bronchial epithelial cells


title: S19

description: Barcode: TTAGGC


title: S20

description: Barcode: TGACCA


title: S40

description: Barcode: ATTCCT


title: S23

description: Barcode: CAGATC


title: S17

description: Barcode: ATCACG


title: S21

description: Barcode: ACAGTG


title: S15

description: Barcode: ATGTCA

value: F

value: male


title: S14

description: Barcode: AGTTCC


title: S16

description: Barcode: CCGTCC


title: S13

description: Barcode: AGTCAA


title: S12

description: Barcode: CTTGTA


title: S11

description: Barcode: GGCTAC


title: S10

description: Barcode: TAGCTT


title: MxCre H3K27me3

city: New York

first: Omar

last: Abdel-Wahab

state: NY

address: 1275 York Ave.

department: Medicine

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Low quality (< 15) bases were trimmed using cutadapt
Reads were aligned to genome assembly mm10 or hg19 using Bowtie2 with default paramters
Duplicate reads were removed using Picard MarkDuplicates
The coverage data was converted to bed format using a custom script, and then to BigWig format
Genome_build: mm10
Supplementary_files_format_and_content: BigWig format

source_name: cikit+ Bone marrow

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions

tag: strain

value: cikit+ Bone marrow

tag: drug

value: after pIpC injection

value: wildtype

tag: chip antibody

value: anti-H3K27me3 (Millipore 07-449)


title: MxCre Asxl2 fl/fl H3K27me3

value: Asxl2 -/-


title: S9

description: Barcode: GATCAG

tag: cell type


title: ATAC-seq ASXL2 KO BM ckit+

data_processing:
Library strategy: ATAC-Seq
Low quality (< 15) bases were trimmed using cutadapt
Reads were aligned to genome assembly mm10 using Bowtie2 with default paramters
Duplicate reads were removed using Picard MarkDuplicates
The coverage data was converted to bed format using a custom script, and then to BigWig format
only read fragments less than 100bp were used
Genome_build: mm10
Supplementary_files_format_and_content: BigWig format

source_name: Bone marrow

tag: cell markers

value: ckit+ selection

value: bone marrow


title: ATAC-seq Control KO BM ckit+

tag: tissue


title: S8

description: Barcode: ACTTGA

value: D


title: ATAC Seq Ckit Mice cells AE9a #402


title: S7

description: Barcode: CAGATC


title: ATAC Seq Ckit Mice cells AE9a ASXL2Ko (412)


title: S5

description: Barcode: ACAGTG


title: ATAC Seq Ckit Mice cells AE9a #401


title: S18

description: Barcode: CGATGT

value: female


title: S6

description: Barcode: GCCAAT


title: MX1CRE-Control-LSK3

data_processing:
The reads were aligned to genome assembly mm10 using STAR
Number of reads on each transcript was counted using featurecounts
Differentially expressed genes were determined using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Transcript read counts. 1st column is NCBI accession id, 2nd column is gene symbol, 3rd column is number of reads

source_name: LSK

extract_protocol:
BM cells were harvested, Lineage-ckit+ScaI+ fractions were sorted by flow cytometry, and RNA was harvested using RNAeasy micro kit. 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

value: Bone marrow

value: LSK

value: wild type


title: S4

description: Barcode: TGACCA


title: MX1CRE-Control-LSK1


title: S3

description: Barcode: TTAGGC


title: S1

description: Barcode: ATCACG


title: MX1CRE-Control-LSK2


title: MX1CRE-ASXL2-LSK1


title: Donor6_IL2OKT3ZA

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

data_processing:
BCL conversion was done with Casava 1.8 pipeline.
Read QC was checked using FastQC v0.11.4.
Sequenced reads were trimmed for adaptor sequence and mapped to hg19 whole genome using the default parameters of the STAR aligner.
Gene quantification was performed with the GeneCounts feature in STAR against GENCODE v19 GTF.
Differential Expression was calculated using GLM for paired samples in edgeR.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *tab: STAR GeneCounts raw gene count files.

source_name: Sorted regulatory T-cells with ZA

growth_protocol: Overnight culture of flow-cytometry-sorted human T regulatory cells.

extract_protocol:
Cells were resuspended and stored in RLT buffer (Qiagen) at -80˚C. RNA was purified using the RNeasy Micro Kit (Qiagen) to a final volume of 14µl.
RNA libraries were prepared for sequencing using the Clontech SMARTer library preparation kit.

treatment_protocol: Flow-cytometry-sorted human T regulatory cells were cultured overnight with IL-2 and OKT3 (anti-CD3) in the presence or absence of Zoledronic Acid.

tag: disease status

value: Healthy

value: Sorted regulatory T-cells

tag: treatment

value: IL-2, OKT3, ZA


title: Donor5_IL2OKT3ZA


title: MxCre Asxl1 fl/fl H3K27me3

value: Asxl1 -/-


title: MX1CRE-ASXL2-LSK2


title: Donor4_IL2OKT3ZA


title: MX1CRE-ASXL2-LSK3


title: Donor2_IL2OKT3ZA


title: S2

description: Barcode: CGATGT

value: Polarized bronchial epithelial cells

value: male


title: Donor6_IL2OKT3

source_name: Sorted regulatory T-cells without ZA

value: IL-2, OKT3


title: Donor3_IL2OKT3


title: Donor2_IL2OKT3


title: Donor1_IL2OKT3


title: SKNO1 control H3K27ac

data_processing:
Low quality (< 15) bases were trimmed using cutadapt
Reads were aligned to genome assembly mm10 or hg19 using Bowtie2 with default paramters
Duplicate reads were removed using Picard MarkDuplicates
The coverage data was converted to bed format using a custom script, and then to BigWig format
Genome_build: hg19
Supplementary_files_format_and_content: BigWig format

source_name: SKNO1 cells

tag: fusion protein

value: AML-ETO fusion

tag: cell line

value: AML cell line

value: H3K27Ac antibody (Abcam ab4729)


title: sKH1_GATA2_SIREVI1_ChIPseq

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Quality of reads was verified using FASTQC analysis
Sequences reads in fastq format were mapped onto the reference human genome version hg38, Genome Reference Consortium GRCh38. The Illumina reads were aligned to the human genome using Bowtie2
Reads that were uniquely aligned to chromosomal positions were retained and duplicate reads were removed from the aligned data using Picard tools.
The filtered aligned reads were used to generate density profiles using “genomeCoverageBed” function from bedtools and then converted to big wig file using "wigToBigWig" function
Genome_build: hg38
Supplementary_files_format_and_content: Wiggle

source_name: RUNX1-EVI1 KD SKH-1 cells

extract_protocol:
Each aliquot of 2x10^7 cells was resuspended in 600μl of sonication buffer (Tris-HCL pH8 25mM, NaCL 150mM, EDTA 2mM, Triton 100x 1%, SDS 0.25%, Protease inhibitior cocktail (PIC) 1x).  300 μl of nuclei in sonication buffer was placed in each polystyrene tube and sonicated at 75% amplitude, 26 cycles: 30s on and 30s off per cycle (Q800, Active Motif, USA).  Subsequently, 1.2ml of dilution buffer (Tris-HCL pH8 25mM, NaCL 150mM, EDTA 2mM, Triton 100x 1%, glycerol 7.5%, PIC 1x) was added to the pooled post sonication material.  This was divided equally between four immunoprecipitations (with 5% of input taken for validation).15 μl protein G beads (Diagenode, Belgium) were washed twice with 500 μl of 50mM citrate phosphate buffer and once with 100mM sodium phosphate).  2μg antibody (EVI-1, C50E12, Cell signalling, lot 3; or RUNX1, Ab23980, Abcam lot 144722) or 4µg antibody (C/EBPα, A2814 Santa Cruz) was added to 10 μl 100mM sodium phosphate, 0.5% BSA and incubated with protein G beads at 4°C for 1 hour.  Chromatin was then added to the protein G beads with antibody and returned to 4°C for 4 hours.  Unbound chromatin was separated from the beads by magnet and the attached beads were washed by buffer 1 (Tris HCL 20mM, NaCl 150mM, EDTA 2mM, Triton x100 1%, SDS 0.1%), twice with buffer 2 (Tris HCL 20mM, NaCl 500mM, EDTA 2mM, Triton x100 1%, SDS 0.1%), LiCL buffer (Tris HCL 10mM, LiCl 250mM, EDTA 1mM, NP40 0.5%, sodium deoxychlolate 0.5%) and finally twice with wash buffer 4 (Tris HCL pH8, 10mM, NaCl 50mM, EDTA 1mM).  The column was eluted twice with 50 μl buffer (NaHCO3 100mM and SDS 1%) and the eluant containing the chromatin was pooled.  Crosslinks were reversed by incubating the samples at 65°C overnight in 500mM NaCl, 500 μg/ml proteinase K.  DNA was purified by Ampure beads (Beckman Coulter, USA), as above, with the DNA eluted with 50 μl water.  Validation of the ChIP was performed by qPCR using a standard curve of genomic DNA from untreated SKH-1 cells (10ng/ μl followed by serial 1:5 dilutions).  The input material was diluted 1:5 with water and qPCR was performed as above with primers listed in SI.  Validation was analysed as a ratio of the qPCR signal from the ChIP material over the input.
Libraries for high throughput sequencing were prepared using the Tru-seq DNA sample preparation kit (Illumina, USA) or Kapa HyperPrep kit (Kapa biosystems, USA), as per manufacturer’s protocol.  18 cycles of PCR was performed and 200-350bp fragments were size selected by running the samples in an agarose gel.  Libraries were purified from the gel using a Minieluta Gel extraction kit (Qiagen, USA).  Libraries were validated by qPCR, with an analysis of the ChIP signal of a positive control region (e.g. PU.1 3H enhancer) over a negative control region (e.g. IVL).  Finally, libraries were quantified by Kapa library quantification kit (Kapa biosystems, USA) and run in a pool of four indexed libraries in one lane of a HiSeq 2500 (Illumina, USA) or 12 indexed libraries in one lane of a NextSeq 500 (Illumina, USA) using 50 cycle single-end reads.

tag: genotype/variation

value: RUNX1-EVI1 KD

tag: chip antibody vendor

value: RD Systems

tag: chip antibody cat. #

tag: chip antibody lot #


title: ATAC Seq Ckit Mice cells AE9a ASXL2Ko (413)

value: ckit+ selection

value: bone marrow


title: SKNO1 shASXL2-3 H3K27ac


title: sKH1_GATA2_CTRL_ChIPseq

source_name: mismatch control SKH-1 cells

value: mismatch control


title: SKNO1 shASXL2-2 H3K27ac


title: WT cells + pBY011-YOX1 vector - 4h galactose induction and HU treatment - replicate 2

city: Toronto

first: Raphael

last: Loll-Krippleber

state: Ontario

address: 160 College street

department: Biochemistry

country: Canada

institute: University of Toronto

data_processing:
50 bp sequenced reads were aligned on the sacCer3 version of the S. cerevisiae genome using Tophat2 (default parameters)
Transcripts were assembled using Cufflinks (default parameters)
Merged assembly files were generated using Cuffmerge (default parameters)
Differential expression was assessed using Cuffdiff (default parameters)
Genome_build: sacCer3
Supplementary_files_format_and_content: cufflinks output file containing FPKM values for each sample
Supplementary_files_format_and_content: cuffdiff output file containing mean FPKM values (between 2 biological replicates) for all samples as well as log2 expression ratios and statistical data

organism: Saccharomyces cerevisiae

source_name: WT cells

growth_protocol: growth in synthetic complete medium lacking uracil and containing raffinose as unique carbon source before adding galactose (2 % final concentration) and hydroxyurea (200 mM final concentration)

extract_protocol:
RNA extractions were performed using the yeast RiboPure kit (ThermoFischer scientific) according to the manufacturer’s instructions.
Prior to sequencing library preparation, rRNAs were removed from the RNA samples using the yeast RiboZero kit (Illumina). Sequencing libraries were prepared using the TruSeq RNA Library Prep v2 kit (Illumina) and ran on a HiSeq2500 using the v4 chemistry (Illumina).

value: BY4741 WT strain containing pBY011-YOX1 vector

value: 4h galactose induction + HU 200 mM


title: Donor5_IL2OKT3

value: Healthy

tag: donor


title: Donor4_IL2OKT3

value: Sorted regulatory T-cells


title: Donor3_IL2OKT3ZA

value: IL-2, OKT3, ZA


title: WT cells + pBY011 control vector - 4h galactose induction and HU treatment - replicate 1

value: BY4741 WT strain containing pBY011 control vector


title: WT cells + pBY011 control vector - 4h galactose induction and HU treatment - replicate 2


title: sKH1_siREVI1-D2-Replicate2

data_processing:
Quality of reads was verified using FASTQC analysis
RNA-Seq reads were aligned to the hg38 human genome build using STAR.
Separate density files for the positive and negative strand were generated for RNA-seq data and uploaded to the UCSC genome browser
Fragments per Kilobase of transcript per Million mapped reads (FPKM) values for each gene were extracted using Cufflinks
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

source_name: RUNX1-EVI1 KD  SKH-1 cells 2 days rep2

growth_protocol: 1x107 cells were electroporated using a EPI 3500 (Fischer, Germany) electroporation at 350v, 10ms.  siRNA sequences (Axolabs, Germany) specific for the translocation breakpoint of Runx1-Evi-1 were 5'-GAACCUCGAAAUAAUGAGUGU-3' (sense) and  5'-ACUCAUUAUUUCGAGGUUCUC-3' (antisense).  Control siRNA was 5’-CCUCGAAUUCGUUCUGAGAAG-3’ (sense) with 5’-UC UCAGAACGAAUUCGAGGUU-3’ (antisense).  siRNA was used at 200nM.  After electroporation, the cells remained in their cuvettes for 5 minutes before being directly added to RPMI-1640 with 10% FCS, supplemented with penicillin/streptomycin and glutamine at a concentration of 0.5 x106 cells per ml and returned to an incubator kept at 37°C and 5% CO2

extract_protocol:
RNA was isolated from SKH-1 cells by TrizolTM (Life Technologies, US) as by manufacturer’s instructions.  At the last step of the protocol RNA was resuspended in 17µl of RNAse free water to which was added 2µl of 10x buffer supplied with the Ambion Turbo DNaseI (Thermos Scientific, USA), of which 1 µl was added.  All of which was incubated at 37ºC for 30 minutes.  The RNA solution was then purified using a Nucleospin RNA clean up column (Machery Nagel, France), according to their instructions.   The quality of RNA from all methods was assessed using a spectrophotometer, by the ratio of the absorbance at 260nM and 280nM wavelengths. RNA has a greater absorbance in the 260nM wavelength, Eukaryotic Total RNA PICO Bioanalyser chip (Agilent technologies, USA) allows visualisation of the size of the RNA molecules and thus, demonstrates whether the sample is degraded or not
RNA-seq libraries were prepared with a Total RNA Ribo-zero library preparation kit (with ribosomal RNA depletion) (Illumina, USA) according to manufacturer’s instructions with the following alterations: 15 cycles of PCR was undertaken to amplify the library and adaptors for multiplexing were used at a 1:4 dilution. Library quality was checked by running the samples on a Bioanalyser and libraries were quantified using a Kapa library quantification kit (Kapa Biosystems, USA) and run in a pool of eight indexed libraries in two lane of a HiSeq 2500 (Illumina, USA) using rapid run chemistry with 100bp paired end reads.

value: SKH-1 cells

tag: genotype

value: RUNX1-EVI1 Knock down 2 days


title: WT cells + pBY011-YOX1 vector - untreated condition - replicate 2

value: no treatment


title: WT cells + pBY011-YOX1 vector - 2h galactose induction and HU treatment - replicate 1

value: 2h galactose induction + HU 200 mM


title: WT cells + pBY011 control vector - 2h galactose induction and HU treatment - replicate 1


title: sKH1_siREVI1-D10-Replicate2

source_name: RUNX1-EVI1 KD  SKH-1 cells 10 days rep2

value: RUNX1-EVI1 Knock down 10 days


title: WT cells + pBY011-YOX1 vector - 2h galactose induction and HU treatment - replicate 2


title: Donor1_IL2OKT3ZA


title: WT cells + pBY011-YOX1 vector - untreated condition - replicate 1


title: WT cells + pBY011 control vector - 2h galactose induction and HU treatment - replicate 2


title: sKH1_siREVI1-D2-Replicate1

source_name: RUNX1-EVI1 KD SKH-1 cells 2 days rep1


title: WT cells + pBY011 control vector - untreated condition - replicate 1


title: sKH1_siREVI1-D10-Replicate1

source_name: RUNX1-EVI1 KD SKH-1 cells 10 days rep1


title: sKH1_siMM-D4-Replicate1

source_name: mismatch control SKH-1 cells 4 days rep1

value: mismatch control 4 days


title: lsm1∆ cells - 4h HU 200 mM - replicate 2

source_name: lsm1∆ cells

growth_protocol: growth in YPD medium containing or not hydroxyurea at a final concentration of 200 mM.

value: lsm1-delta strain (BY4741 background)

value: 4h HU treatment


title: sKH1_siMM-D4-Replicate2

source_name: mismatch control SKH-1 cells 4 days rep2


title: lsm1∆ cells - 4h HU 200 mM - replicate 1


title: sKH1_siREVI1-D4-Replicate2

source_name: RUNX1-EVI1 KD  SKH-1 cells 4 days rep2

value: RUNX1-EVI1 Knock down 4 days


title: sKH1_siMM-D2-Replicate2

source_name: mismatch control SKH-1 cells 2 days rep2

value: mismatch control 2 days


title: WT cells - 4h HU 200 mM - replicate 2

source_name: wild type cells

value: BY4741 WT strain


title: lsm1∆ cells - 2h HU 200 mM - replicate 2

value: 2h HU treatment


title: lsm1∆ cells - 2h HU 200 mM - replicate 1


title: WT cells - 4h HU 200 mM - replicate 1


title: WT cells - 2h HU 200 mM - replicate 2


title: WT cells + pBY011-YOX1 vector - 4h galactose induction and HU treatment - replicate 1

value: BY4741 WT strain containing pBY011-YOX1 vector

value: 4h galactose induction + HU 200 mM


title: sKH1_siREVI1-D4-Replicate1

source_name: RUNX1-EVI1 KD  SKH-1 cells 4 days rep1


title: WT cells - 2h HU 200 mM - replicate 1


title: sKH1_siMM-D2-Replicate1

source_name: mismatch control SKH-1 cells 2 days rep1


title: Stalk organoid individual 10, passage 11

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

data_processing:
data was quality filtered using sickle and the fastx_trimmer (>Q20)
data was mapped to the hg19 genome using tophat 2.0.6 (UCSC RefSeq gtf)
RPKMs were calculated from the mapped data.
Genome_build: Human hg19 (UCSC)
Supplementary_files_format_and_content: RPKM files containing RPKM scores per transcript.

source_name: Cultured embryonic lung stalk epithelium

growth_protocol: Cultured samples were grown as organoids in Matrigel in the presence of FGF, WNT and EGF agonists and BMP and TGF-B antagionists

extract_protocol:
Fresh tissue was mmicrodissected, and cultured organoids were removed from Matrigel substrate, then RNA extraction was performed according to the PicoPure RNA Isolation Kit protocol. Reverse transcription and cDNA amplification was performed according to Ovation RNA-Seq Systems V2 protocol (NuGEN). For each sample a minimum total input RNA amount of 500 pg was used.
RNA-Seq library preparation was performed according to the NuGEN Ovation Rapid DR Multiplex System 1-8 protocol.

tag: embryo age

value: 7 post conception weeks (pcw)

tag: passage number


title: Stalk organoid individual 12, passage 1

value: Cultured embryonic lung stalk epithelium


title: H12812_t821_Patient1

source_name: AML t(8;21) paitent 1

growth_protocol: Initial analysis of AML patient samples was carried out by the Haematological Malignancy Diagnostic Service (St James’s Hospital, Leeds), where cytogenetic abnormalities and sample immunophenotype were determined at the time of disease diagnosis. Several sets of 6–colour FACS staining were performed on a FACSCanto or FACSCanto II flow cytometer using antibodies obtained from BD Bioscience (Oxford, UK) as follows: Anti-CD34 - APC / PerCP:Cy5.5 (clone 8G12), Anti-CD117 – PE / PE:Cy7 (clone 10402), Anti-CD45 – PerCP:Cy5.5 / APC:Cy7 (Clone 2D1), Anti-CD15 – FITC (clone MMA), Anti-CD13 – PE (clone L138), Anti-HLADR – APC:Cy7 (Clone L243 (G46-6)), Anti-CD33 – PE (clone P37.6), Anti-CD7 – FITC (clone M-T701), Anti-CD19 – PerCP:Cy5.5 (clone SJ25C1), Anti-CD56 – APC (clone NCAM16.2), Anti-CD14 – FITC (clone MφP9), Anti-CD38-PE:Cy7 (clone HB7) and Anti-CD64 – PE (clone MD22). The result of flow cytometry analysis is shown in Supplementary Table 2. The presence of the t(8;21) translocation and expression of mRNA encoding the RUNX1/ETO fusion protein were determined using RT-PCR, with the primers 5’-TCAAAATCACAGTGGATGGGC and 5’-CAGCCTAGATTGCGTCTTCACA. Mononuclear cells freshly obtained from patients #1 and #2 and from the control patient were prepared by differential centrifugation using Lymphoprep (Axis-Shield UK, Cambridgeshire, UK), and CD34+ blast cells were then isolated using MACS Micro Beads (Miltenyi Biotec GmbH ) staining and separation on magnetic columns according to the manufacturer’s guidelines. Purity of CD34+ cells was >85%

extract_protocol:
Pelleted cells from primary patient material were lysed by adding 1ml Trizol ™ (Life Technologies, US).  200µl of chloroform was added and the mixture was manually shaken for 15 seconds.  The mixture was incubated at room temperature for 3 minutes. The mixture was centrifuged at 12000 x g for 15 minutes at 4°C.  The top clear aqueous phase was removed and placed in a fresh tube.  0.5ml of 100% isopropanol was added to the isolated aqueous phase and incubated at room temperature for 10 minutes whichs was then transferred to a RNeasy MinElute column (Qiagen, USA) and centrifuged for 15s at 8000xg. 350µl of RWI buffer from the RNeasy Kit was added to the column and centrifuged for 15s at 8000xg.  DNaseI 10µl and 70µl RDD buffer (Qiagen, USA) were mixed and added to the column and incubated for 15 minutes at room temperature.  Afterwards, 350µl of RWI buffer from RNeasy Kit (Qiagen, USA) was added to the column and centrifuged for 15s at 8000xg.  Following this 500µl of RPE buffer was added and centrifuged for 15s at 8000xg. The column was washed with 500µl 80% ethanol and centrifuged at 2 minutes at 8000xg.  The column was dried by centrifuged at 5 minutes at 8000xg.  RNA was eluted from the column by adding 12µl of water to the column followed by centrifugation at 5 minutes at 8000xg.
RNA-seq libraries were prepared with a Total RNA Ribo-zero library preparation kit (with ribosomal RNA depletion) (Illumina, USA) according to manufacturer’s instructions with the following alterations: 15 cycles of PCR was undertaken to amplify the library and adaptors for multiplexing were used at a 1:4 dilution. Library quality was checked by running the samples on a Bioanalyser and libraries were quantified using a Kapa library quantification kit (Kapa Biosystems, USA) and run in a pool of eight indexed libraries in two lane of a HiSeq 2500 (Illumina, USA) using rapid run chemistry with 100bp paired end reads.

value: t(8;21) paitent


title: H18901_t821_Patient2

source_name: AML t(8;21) paitent 2


title: WT cells + pBY011 control vector - untreated condition - replicate 2

tag: strain

value: BY4741 WT strain containing pBY011 control vector


title: lsm1∆ cells - untreated condition - replicate 2


title: lsm1∆ cells - 1h HU 200 mM - replicate 2

value: 1h HU treatment


title: WT cells - 1h HU 200 mM - replicate 1


title: sKH1_siMM-D10-Replicate2

source_name: mismatch control SKH-1 cells 10 days rep2

value: SKH-1 cells

value: mismatch control 10 days


title: sKH1_siMM-D10-Replicate1

source_name: mismatch control SKH-1 cells 10 days rep1


title: lsm1∆ cells - untreated condition - replicate 1

value: no treatment


title: WT cells - untreated condition - replicate 1


title: sKH1_control_replicate1

source_name: untreated SKH-1 cells rep1

value: untreated control


title: lsm1∆ cells - 1h HU 200 mM - replicate 1

value: lsm1-delta strain (BY4741 background)


title: Tip organoid individual 7, passage 7

source_name: Cultured embryonic lung tip epithelium

value: Cultured embryonic lung tip epithelium


title: sKH1_control_replicate2

source_name: untreated SKH-1 cells rep2


title: Stalk organoid individual 11, passage 1


title: Tip organoid individual 5, passage 5


title: Microdissected fresh stalk individual 4

source_name: Fresh embryonic lung stalk epithelium

value: Embryonic lung stalk epithelium

value: 9 post conception weeks (pcw)


title: Microdissected fresh tip individual 4

source_name: Fresh embryonic lung tip epithelium

value: Embryonic lung tip epithelium


title: Tip organoid individual 8, passage 7

value: 6 post conception weeks (pcw)


title: Stalk organoid individual 9, passage 5


title: WT cells - 1h HU 200 mM - replicate 2

value: BY4741 WT strain


title: CD34plus-PBSCs_2

source_name: CD34+ human healthy donor 2

growth_protocol: CD34+ peripheral blood stem cells (PBSCs) from healthy adults identified by the NHS Blood and Transplant service (NHSBT) were mobilised into the peripheral circulation by administrating donors with pegylated G-CSF (trade name: Lenograstim, Chugai Pharmaceuticals, Japan). Cells were harvested from the patients by apheresis and stored by NHSBT in liquid nitrogen. Cryopreserved cells were thawed at 37ºC using a waterbath and eluted from storage bag with a PBS/Glucose/Citrate solution (0.09% glucose + 3.3% FCS + 1mM sodium citrate).  After centrifugation at 300xg for 5 minutes, the cell pellet was treated with DNAseI (Roche, Switzerland) at 0.6mg/ml concentration in PBS/Glucose/Magnesium/Calcium solution (PBS+0.5 mM MgCl2 + 1.2 mM CaCl2)  + 1 % FCS + 0.1 % glucose + 2 mM MgCl2) for 5 minutes at room temperature.  Following DNAseI treatment the cells were once again diluted with PBS/Glucose/Citrate solution and the mononuclear isolated by density gradient medium and CD34+ beads separation by MACS columns

value: CD34+ human


title: t321_Patient1

source_name: AML t(3;21) paitent 1

growth_protocol: Blood from t(3;21) patient 1 was diluted 1:1 with PBS and layered onto density gradient medium (Lymphoprep Stem Cell technology, USA).  The blood-PBS-lymphoprep mix was subsequently centrifuged at 592xg (acceleration setting 4, no brakes).  After centrifugation, the mixture had separated into two phases with the mononuclear cells separated into a layer in between. This midlayer was then isolated and incubated with  CD34+ microbeads (Miltenyi-Biotech, USA), according to the manufacturer instructions. The CD34+ expression on this fraction was confirmed by flow cytometry before either immediately use for DNaseI hypersensitivity site mapping or RNA extraction by Trizol

value: t(3;21) paitent


title: Microdissected fresh tip individual 3


title: WT cells - untreated condition - replicate 2


title: Tip organoid individual 6, passage 5


title: SKH1_SIREVI1_D10_DNAse1Seq

data_processing:
Quality of reads was verified using FASTQC analysis
Sequences reads in fastq format were mapped onto the reference human genome version hg38, Genome Reference Consortium GRCh38. The Illumina reads were aligned to the human genome using Bowtie2
Reads that were uniquely aligned to chromosomal positions were retained and duplicate reads were removed from the aligned data using Picard tools.
The filtered aligned reads were used to generate density profiles using “genomeCoverageBed” function from bedtools and then converted to big wig file using "wigToBigWig" function
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

source_name: RUNX1-EVI1 KD SKH-1 cells after 10 days

extract_protocol:
Prior to DNaseI digestion, apoptotic cells were removed using the Dead Cell Removal Kit (Miltenyl Biotech, UK) as per manufacturer’s instructions. 3x 107 SKH-1 cells were suspended in 1ml DNase I buffer (0.3M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 10 mM Tris pH7.4).  Digestion on 4.5x106 cells was performed with DNase I (Worthington, DPPF grade) at 80 units/ml in DNase I buffer with 0.4% NP-40 and 2mM CaCl2 at 22ºC for 3 minutes.  The reaction was stopped with cell lysis buffer (0.3M NaAcetate, 10mM EDTA pH 7.4, 1% SDS) with 1mg/ml Proteinase K and incubated at 45ºC overnight. For DHS mapping in CD34+ purified t(3;21) patient cells and in SKH-1 transfected with siRNA, lower cell numbers were available and therefore the DNaseI concentrations were reduced according to the cell numbers available.The digested DNAseI material was treated with RNAseA (Sigma Aldrich, Germany) at a final concentration of 100µg/ml at 37ºC for 1 hr.  Genomic DNA was extracted using phenol/chloroform method: an equal volume of phenol was added to the reaction and placed on a rotator wheel for 45 minutes.  This was centrifuged for 5 minutes at 16000 x g at room temperature. The top layer was transferred to a new tube and the process was repeated sequentially with phenol/chloroform and chloroform. After purification by chloroform extraction, genomic DNA was precipitated with ethanol. This was pelleted by centrifugation for 5 minutes, at 16000 x g at 4°C.  The pellet was resuspended with 70% ethanol and centrifugation for 5 minutes, at 16000 x g at 4°C.  The pellet was air-dried and dissolved by Tris-EDTA (40mM Tris Acetate 1mM EDTA).Digestion was checked visually by running the samples on a 0.7% agarose gel and by RT-PCR evaluating the ratio of open (TBP promoter) to closed regions of DNA (chromosome 18) and active gene body (beta-actin) to prevent selection of over digested samples (primers in Table S5B). Subsequently, between 2 to 10µg of DNaseI digested DNA (depending on material available) were run on a 1.2% agarose gel for selection of shorter fragments to increase the fraction of fragments captured from DHSs. Prior to loading on gel, the purified DNA was treated again with RNAseA (Sigma Aldrich, USA) at a final concentration of 100µg/ml at 37ºC for 1 hr.  50-300bp fragments were isolated and purified from the gel using a MinElute gel extraction kit (Qiagen, USA) as per manufacturer’s instructions and validated by qPCR. Following this, the size selected sample was validated again by RT-PCR, this time using shorter amplicons to enable detection of the shorter fragments enriched by the size selection process.
After size selection, a library was prepared using Tru-seq DNA sample preparation kit (Illumina, USA) or MicroPlex library preparation kit v2 (Diagenode, Belgium) as per manufacturer’s protocol.  After PCR a final size selection step was performed by running the library on 1.5% TAE gel, followed by excision of 190-250bp sized gel fragment.  The library was purified from the gel using a MinElute gel extraction kit (Qiagen, USA). The quality of the libraries was assessed on an Agilent 2100 bioanalyser.   Libraries were subsequently run on two lanes of an Illumina HiSeq 2500 flow-cell for transcription factor footprinting, or as part of 12 indexed libraries in one lane of a NextSeq500 (Illumina, USA) for DHS mapping alone.

value: RUNX1-EVI1 KD  after 10 days


title: Microdissected fresh stalk individual 3


title: Microdissected fresh stalk individual 2

value: 7 post conception weeks (pcw)


title: EG-mRNA-2

description: Sample 2

organism: Echinococcus granulosus

source_name: hydatid cyst

tag: larvel stage

value: protoscoleces


title: Microdissected fresh tip individual 2

tag: cell type


title: Microdissected fresh stalk individual 1


title: sKH1_JL24_6510_DNAse1Seq

source_name: untreated SKH-1 cells

value: untreated cells


title: EG-smallRNA-2

description: Sample 2


title: Sample_APP1x4x8moPFC_mm_rna_sr_Michael_D_6_S31_L005_R1_001

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

country: Germany

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Reads were mapped to mouse genome mm10.
In RNA-Seq reads were counted using FeaturesCount.
Genome_build: mm10
Supplementary_files_format_and_content: count files

source_name: Dentate gyrus

extract_protocol:
RNA was isolated using TRIZOL from whole tissue
Libraries for RNA-Seq were prepared using Illumina TruSeq RNA Sample Preparation v2 Kit.

tag: age

value: 4 months

value: wild type


title: EG-smallRNA-1

description: Sample 1


title: CD34plus-PBSCs_1

source_name: CD34+ human healthy donor 1


title: EG-mRNA-1

description: Sample 1


title: Microdissected fresh tip individual 1


title: t321_Patient1_DNAse1Seq

growth_protocol: Cells from t(3;21) patient 2 was previously isolated by density gradient medium and cryopreserved at the Erasmus University Medical Centre, Netherlands.  CD34+ cells were thawed with pre-warmed RPMI-1640 +10%FCS.  After centrifugation, the cell pellet was re-suspended in 750 µl MACS buffer (PBS with 0.5% BSA and 2mM EDTA) and 35µl CD34-PE, with a separate sample stained with IgG PE as an isotype control.  CD34+ cells were isolated by FACS using a MoFlo Astrios (Beckman Coulter, USA) and were then directly used for DNaseI hypersensitivity site mapping or underwent RNA extraction by Trizol

value: AML t(3;21) paitent


title: Sample_APP1x4x8moPFC_mm_rna_sr_Michael_D_4_S28_L005_R1_001


title: AML5354-t321_Patient2_DNAse1Seq

source_name: AML t(3;21) paitent 2


title: Sample_APP1x4x8moPFC_mm_rna_sr_Michael_D_5_S29_L005_R1_001


title: sKH1_Anti-CEBPA_SIREVI1_D10_ChIPseq

extract_protocol:
Each aliquot of 2x107 cells was resuspended in 600μl of sonication buffer (Tris-HCL pH8 25mM, NaCL 150mM, EDTA 2mM, Triton 100x 1%, SDS 0.25%, Protease inhibitior cocktail (PIC) 1x).  300 μl of nuclei in sonication buffer was placed in each polystyrene tube and sonicated at 75% amplitude, 26 cycles: 30s on and 30s off per cycle (Q800, Active Motif, USA).  Subsequently, 1.2ml of dilution buffer (Tris-HCL pH8 25mM, NaCL 150mM, EDTA 2mM, Triton 100x 1%, glycerol 7.5%, PIC 1x) was added to the pooled post sonication material.  This was divided equally between four immunoprecipitations (with 5% of input taken for validation).15 μl protein G beads (Diagenode, Belgium) were washed twice with 500 μl of 50mM citrate phosphate buffer and once with 100mM sodium phosphate).  2μg antibody (EVI-1, C50E12, Cell signalling, lot 3; or RUNX1, Ab23980, Abcam lot 144722) or 4µg antibody (C/EBPα, A2814 Santa Cruz) was added to 10 μl 100mM sodium phosphate, 0.5% BSA and incubated with protein G beads at 4°C for 1 hour.  Chromatin was then added to the protein G beads with antibody and returned to 4°C for 4 hours.  Unbound chromatin was separated from the beads by magnet and the attached beads were washed by buffer 1 (Tris HCL 20mM, NaCl 150mM, EDTA 2mM, Triton x100 1%, SDS 0.1%), twice with buffer 2 (Tris HCL 20mM, NaCl 500mM, EDTA 2mM, Triton x100 1%, SDS 0.1%), LiCL buffer (Tris HCL 10mM, LiCl 250mM, EDTA 1mM, NP40 0.5%, sodium deoxychlolate 0.5%) and finally twice with wash buffer 4 (Tris HCL pH8, 10mM, NaCl 50mM, EDTA 1mM).  The column was eluted twice with 50 μl buffer (NaHCO3 100mM and SDS 1%) and the eluant containing the chromatin was pooled.  Crosslinks were reversed by incubating the samples at 65°C overnight in 500mM NaCl, 500 μg/ml proteinase K.  DNA was purified by Ampure beads (Beckman Coulter, USA), as above, with the DNA eluted with 50 μl water.  Validation of the ChIP was performed by qPCR using a standard curve of genomic DNA from untreated SKH-1 cells (10ng/ μl followed by serial 1:5 dilutions).  The input material was diluted 1:5 with water and qPCR was performed as above with primers listed in SI.  Validation was analysed as a ratio of the qPCR signal from the ChIP material over the input.
Libraries for high throughput sequencing were prepared using the Tru-seq DNA sample preparation kit (Illumina, USA) or Kapa HyperPrep kit (Kapa biosystems, USA), as per manufacturer’s protocol.  18 cycles of PCR was performed and 200-350bp fragments were size selected by running the samples in an agarose gel.  Libraries were purified from the gel using a Minieluta Gel extraction kit (Qiagen, USA).  Libraries were validated by qPCR, with an analysis of the ChIP signal of a positive control region (e.g. PU.1 3H enhancer) over a negative control region (e.g. IVL).  Finally, libraries were quantified by Kapa library quantification kit (Kapa biosystems, USA) and run in a pool of four indexed libraries in one lane of a HiSeq 2500 (Illumina, USA) or 12 indexed libraries in one lane of a NextSeq 500 (Illumina, USA) using 50 cycle single-end reads.

value: SKH-1 cells


title: SKH1_SIMM_D10_DNAse1Seq

source_name: mismatch control SKH-1 cells after 10 days

value: mismatch control 10 days


title: sKH1_Anti-RUNX1_SIREVI1_D10_ChIPseq


title: Sample_APP1x4x8moPFC_mm_rna_sr_Michael_C_5_S61_L007_R1_001

value: APP


title: Sample_APP1x4x8moPFC_mm_rna_sr_Michael_D_2_S26_L005_R1_001


title: AML5354-t321_Patient2


title: Sample_APP1x4x8moPFC_mm_rna_sr_Michael_D_1_S25_L005_R1_001


title: Sample_APP1x4x8moPFC_mm_rna_sr_Michael_C_6_S62_L007_R1_001


title: Sample_APP1x4x8moPFC_mm_rna_sr_Michael_C_2_S58_L007_R1_001


title: R299-PBSCs_DNAse1Seq

source_name: CD34+ human healthy donor

value: CD34+ human healthy donor


title: sKH1_Anti-CEBPA_SIMM_D10_ChIPseq


title: Sample_APP1x4x8moPFC_mm_rna_sr_Michael_C_4_S60_L007_R1_001


title: Sample_APP1x4x8moPFC_mm_rna_sr_Michael_C_3_S59_L007_R1_001


title: Sample_741APPxFmn2_mm_rna_sr_Cemil_K_7_S70_L007_R1_001

value: 3 months

value: FMN2 +/+ APP


title: sKH1_Anti-RUNX1_SIMM_D10_ChIPseq


title: Sample_767APPxFmn2_mm_rna_sr_Cemil_K_9_S72_L007_R1_001


title: Sample_764APPxFmn2_mm_rna_sr_Cemil_K_8_S71_L007_R1_001


title: Sample_741APPxFmn2_mm_rna_sr_Cemil_K_7_S24_L004_R1_001


title: sKH1_Anti-EVI1_SIREVI1_D10_ChIPseq


title: Sample_729APPxFmn2_mm_rna_sr_Cemil_K_5_S66_L006_R1_001


title: Sample_727APPxFmn2_mm_rna_sr_Cemil_K_2_S60_L005_R1_001


title: sKH1_Anti-EVI1_SIMM_D10_ChIPseq


title: Anti-RUNX1_sKH1_ChIPseq


title: Anti-EVI1_sKH1_ChIPseq


title: SKNO1-a-ASLX2

data_processing:
Low quality (< 15) bases were trimmed using cutadapt
Reads were aligned to genome assembly hg19 using Bowtie2 with default paramters
Duplicate reads were removed using Picard MarkDuplicates
The coverage data was converted to bed format using a custom script, and then to BigWig format
Genome_build: hg19
Supplementary_files_format_and_content: BigWig format

source_name: SKNO1 cells

value: AML-ETO

value: AML cell line

tag: chip antibody

value: ASXL2 antibody (Bethyl A302-037A)


title: Sample_723APPxFmn2_mm_rna_sr_Cemil_K_6_S68_L006_R1_001


title: Sample_689APPxFmn2_mm_rna_sr_Cemil_K_3_S62_L005_R1_001


title: Sample_686APPxFmn2_mm_rna_sr_Cemil_K_1_S58_L005_R1_001


title: Cells_C_miRNA

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 12.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

growth_protocol: Simian virus 40-immortalized human osteoblast cells (SV-HFO cells) seeded at a density of 5 × 103 cells/ cm2 were cultured in α-MEM (GIBCO, Paisley, UK) supplemented with 20 mM HEPES, pH 7.5 (Sigma, St. Louis, MO, USA), streptomycin/ penicillin, 1.8 mM CaCl2 (Sigma), 10 mM β-glycerophosphate (Sigma) and 2% depleted (100,000g for 90 minutes at 4°C)-FCS (GIBCO) at 37°C in a humidified atmosphere of 5% CO2 for 14 days. The culture medium was replaced every 2-3 days.

extract_protocol:
Total cellular and EV-RNA was isolated using the TRIzol® reagent (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SV-HFOs were washed with 1X PBS and refreshed with serum-free medium 24 hours prior to EV isolation. EVs were isolated from SV-HFO conditioned medium by low speed centrifugation (1,500 rpm, 5 minutes; 4,500 rpm, 10 minutes) followed by ultracentrifugation (20,000g, 30 minutes; 100,000g, 1 hour at 4°C) using the SW32Ti rotor (Beckman Coulter, Fullerton, CA, USA).

tag: tissue

value: extracellular vesicles


title: EV_B_miRNA

source_name: Simian virus 40-immortalized human osteoblast cells (SV-HFO cells)


title: Sample_656APPxFmn2_mm_rna_sr_Cemil_W_5_S65_L006_R1_001


title: EV_A_miRNA

value: Simian virus 40-immortalized human osteoblast cells (SV-HFO cells)


title: Cells_B_miRNA


title: Sample_655APPxFmn2_mm_rna_sr_Cemil_W_7_S23_L004_R1_001


title: SKNO-1 H3k27me3 Empty Vector

value: H3K27me3 antibody (Millipore 07-449)


title: Sample_654APPxFmn2_mm_rna_sr_Cemil_W_6_S67_L006_R1_001


title: Sample_APP1x4x8moPFC_mm_rna_sr_Michael_C_1_S57_L007_R1_001


title: Sample_655APPxFmn2_mm_rna_sr_Cemil_W_7_S69_L007_R1_001


title: Sample_327APPxFmn2_mm_rna_sr_Cemil_W_4_S63_L006_R1_001


title: SKNO-1 H3K27me3 ASXL2 SH2


title: Sample_653APPxFmn2_mm_rna_sr_Cemil_W_3_S61_L005_R1_001


title: Sample_728APPxFmn2_mm_rna_sr_Cemil_K_4_S64_L006_R1_001


title: SKNO-1 H3K27me3 ASXL1 SH3


title: Sample_319APPxFmn2_mm_rna_sr_Cemil_W_2_S59_L005_R1_001


title: EV_C_miRNA


title: SKNO-1 H3K27me3 ASXL1 SH2


title: EV_C_mRNA


title: Sample_647APPxFmn2_mm_rna_sr_Cemil_W_1_S57_L005_R1_001


title: Sample_8moFmn2ko_mm_rna_sr_Roberto_D_4_1_S107_L007_R1_001

value: 8 months

value: FMN2 knock out


title: Sample_8moFmn2ko_mm_rna_sr_Roberto_D_5_1_S103_L007_R1_001


title: Sample_APP1x4x8moPFC_mm_rna_sr_Michael_D_3_S27_L005_R1_001

value: 4 months


title: EV_B_mRNA


title: SKNO-1 H3K27me3 ASXL2 SH3


title: Sample_8moFmn2ko_mm_rna_sr_Roberto_D_3_1_S106_L007_R1_001


title: Vector_H3K4me1

value: H3K4me1 antibody (AbCam ab8895)


title: EV_A_mRNA


title: Sample_8moFmn2ko_mm_rna_sr_Roberto_D_2_1_S105_L007_R1_001


title: Cells_A_miRNA


title: Sample_8moFmn2ko_mm_rna_sr_Roberto_D_1_1_S104_L007_R1_001


title: Sample_8moFmn2wt_mm_rna_sr_Roberto_C_3_1_S102_L007_R1_001

value: wild type


title: Sample_8moFmn2wt_mm_rna_sr_Roberto_C_2_1_S101_L007_R1_001


title: Sh3_ASXL2_h3K4me1


title: Sample_8moFmn2wt_mm_rna_sr_Roberto_C_1_1_S100_L006_R1_001


title: Cells_C_mRNA


title: Cells_B_mRNA


title: 3_Sh3_ASXL2_H3K4me3

value: H3K4me3 antibody (Cell Signaling 9751S)


title: Sample_3moFmn2ko_mm_rna_sr_Roberto_B_6_1_S99_L006_R1_001


title: 2_Sh_ASXL2_H3K4me3


title: Cells_A_mRNA


title: Sample_3moFmn2ko_mm_rna_sr_Roberto_B_2_1_S95_L006_R1_001


title: Sample_3moFmn2ko_mm_rna_sr_Roberto_B_4_1_S97_L006_R1_001


title: Sample_3moFmn2wt_mm_rna_sr_Roberto_A_5_1_S93_L005_R1_001


title: Sample_3moFmn2ko_mm_rna_sr_Roberto_B_1_1_S94_L005_R1_001


title: Sample_3moFmn2wt_mm_rna_sr_Roberto_A_4_1_S92_L005_R1_001


title: Sample_3moFmn2wt_mm_rna_sr_Roberto_A_3_1_S91_L005_R1_001


title: CBF54-BM-ASXLwt

data_processing:
The reads were aligned to genome assembly hg19 using STAR
Number of reads on each transcript was counted using featurecounts
Differentially expressed genes were determined using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Transcript read counts. 1st column is NCBI accession id, 2nd column is gene symbol, 3rd column is number of reads

source_name: Bone marrow

value: Bone marrow

tag: asxl1/2 genotype

value: wildtype

tag: cell markers

value: ckit+ScaI+


title: Sample_3moFmn2wt_mm_rna_sr_Roberto_A_2_1_S90_L005_R1_001

value: 3 months


title: CBF369-Blood-ASXL2

source_name: Peripheral blood

value: Peripheral blood

value: ASXL2 mutation


title: CBF376-Blood ASXL2


title: Sample_3moFmn2wt_mm_rna_sr_Roberto_A_1_1_S89_L005_R1_001


title: CBF337-BM-ASXLwt


title: Sh2_ASXL2_H3k4me1

tag: fusion protein

value: AML-ETO

tag: cell line

value: AML cell line


title: CBF124-BM-ASXLwt


title: 45565-BM-ASXL1

value: ASXL1 mutation


title: CBF234-BM-ASXLwt


title: Sample_3moFmn2ko_mm_rna_sr_Roberto_B_5_1_S98_L006_R1_001


title: 49060-2010-BM-ASXLwt


title: 48549-Blood-ASXL2


title: 41267-BM-ASXL2


title: 37582-BM-ASXLwt


title: 40810-BM-ASXLwt


title: CBF77-Blood-ASXL2


title: CBF370-BM-ASXL2


title: SKNO1 EV 25

extract_protocol:
BM cells were harvested, Liniage-ckit+ScaI+ fractions were sorted by flow cytometry, and RNA was harvested using RNAeasy micro kit. 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: SKNO1 EV 13


title: 35450-BM-ASXL2


title: SKNO1 EV 01


title: 08462-BM-ASXL1


title: SKNO1 ASXL2 SH3 25


title: SKNO1 ASXL2 SH3 13


title: SKNO1 ASXL2 SH3 1


title: Arid1b +/- replicate 2

city: Dallas

first: Hao

last: Zhu

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

description: HA422 - Arid1bHet2

data_processing:
Raw sequencing reads were trimmed to remove adaptor and low quality sequences (Phred score<20) using trim_galore package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Trimmed reads were aligned to mouse reference genome GRCm38/mm10 with HiSAT226. After duplicates removal by SAMtools27 and Picard (http://broadinstitute.github.io/picard.), read counts were generated for the annotated genes based GENCODE V2028 using featureCounts29. Differential gene analysis was performed use edgeR30, using FDR < 0.05 as cutoff. Enriched pathways were analyzed through the use of QIAGEN’s Ingenuity® Pathway Analysis (IPA®,QIAGEN RedwoodCity,www.qiagen.com/ingenuity). Heatmaps to visualize the data were generated by using GENE-E (www.broadinstitute.org/cancer/software/GENE-E).
Genome_build: mm10
Supplementary_files_format_and_content: RPKM values

source_name: frozen whole hippocampus_Arid1b +/-

extract_protocol:
Whole hippocampus was harvested using Trizol reagent and the Qiagen miRNeasy Mini kit.
RNA libraries were prepared for sequencing using standard Nugen library protocols.

treatment_protocol: Whole hippocampus was collected from 80 days old male mice to extract RNA.

tag: strain background

tag: genotype/variation

value: Arid1b +/-

tag: gender

value: male

value: postnatal day 80

value: hippocampus


title: Arid1b +/- replicate 3

description: HA426 - Arid1bHet3


title: Arid1b +/- replicate 4

description: HA430 - Arid1bHet4


title: Arid1b +/- replicate 1

description: HA416 - Arid1bHet1


title: SKNO1 ASXL2 SH2 13


title: GST RNAi Hi-C biological rep A

city: Freiburg

first: Thomas

last: Manke

address: Stuebeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
[processed data file:]
GST_merge_rf_corrected_score.bedgraph

data_processing:
mapping : each mate aligned separately to drosophla genome (dm3, ensembl) using bwa mem with parameters ` -E50 -L0`
build hic matrix : using hicBuildMatrix (HiCExplorer v1.7.0, using restriction fragment resoltiion) with parameters `-rs <dpn2.bed> `
correct hic Matrix : using hicCorrectMatrix (HiCExplorer v1.7.0)
find TADs : using hicFindTADs (HiCExplorer v1.7.0) with parameters `TAD_score --minDepth 10000 --maxDepth 40000 --step 2500` followed by `find_TADs --pvalue 0.001 --delta 0.01`
Genome_build: dm3
Supplementary_files_format_and_content: bedgraph format. The bedgraph files contain TAD separation scores in windows over the genome, calculated using HiCExplorer. A HiC matrix was created for each sample using HiCExplorer and matrices for replicates for each sample were merged. Matrices were then normalized using ICE correction and TAD separation score was calculated in windows.

growth_protocol: Drosophila S2 cells were cultured in Express Five SFM (Thermo Fisher Scientific) supplemented with glutamax, at 27°C at a density of 1-16 million/ml.

extract_protocol:
S2 cells have been fixed with 2% formaldehyde for 10 minutes at room temperature. Glycine at 125 mM final concentration has been added to the plates followed by 5 minutes incubation. After two washes in PBS, cells have been scraped off the plate and pelleted. Each pellet (10-50 million of cells) has been resuspended in 1 ml of lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% IGEPAL CA-630) and nuclei have been extracted by sonication (Arrigoni et al. 2016) using Covaris E220 sonicator (settings: 75W peak power, 2% duty factor, 200 cycles/burst), for 60-90 seconds until about 70% of intact nuclei have been released.
10-50 ng of DNA bound to beads have been used for library preparation using a modification of the NEBNext Ultra II DNA library preparation workflow (NEB, E7645). DNA bound to beads have been end-repaired, A-tailed, adaptor-ligated using manufacturer’s instruction. Beads were reclaimed on a magnet, washed once in EB and eluted at 98 °C for 10 minutes. DNA has been USER-treated to open the adapters in meantime to PCR amplification.

treatment_protocol: For knockdown experiments, 7.5 million cells transfected with 100μg of dsRNA on 10cm dishes, using Lipofectamine RNAiMAX Reagent (Thermo Fisher Scientific). The M1BP knockdown lasted for 7 days while that of Beaf-32 lasted for 4 days. For M1BP-Beaf-32 double knockdown, cells were first treated with M1BP dsRNA at day 1, followed by treatment with Beaf-32 dsRNA at day 3, and were collected at day 7. All knockdown experiments were carried out in duplicate.


title: M1BP RNAi Hi-C biological rep A technical rep 1

description:
[processed data file:]
M1BP_KD_merge_corrected_score.bedgraph


title: SKNO1 ASXL2 SH2 1


title: Beaf-32 + M1BP RNAi Hi-C biological rep B technical rep 1

description:
[processed data file:]
Beaf32_M1BP_KD_merge_rf_corrected_score.bedgraph


title: WT replicate2

description: HWT424 - WT2

source_name: frozen whole hippocampus_WT

value: WT


title: M1BP RNAi Hi-C biological rep B technical rep 1


title: WT replicate1

description: HWT421 - WT1


title: Beaf-32 + M1BP RNAi Hi-C biological rep A technical rep 2


title: WT replicate3

description: HWT425 - WT3


title: wild type Hi-C technical rep 1

description:
[processed data file:]
zscorev_min10_max40_step1.5_score.bedgraph