title: H3K27me3_Bex

city: Ottawa

first: Qiao

last: Li

address: 451 smyth road

department: Cellular and Molecular Medicine

institute: University of Ottawa

data_processing:
For H3K27me3, sequencing reads were mapped to the mouse genome build mm9 using Bowtie, allowing for 3 mismatches and reporting the single best alignment per 50bp read. Picard was used to filter out replicated reads and BAM files were converted into BED files after which aligned reads were extended by 125 bp at their 3’ end, and converted to bedgraph format using the bedtools2 package. The bedgraphtobigwig package was used for visualization of experiment results.
Genome_build: mm9
Supplementary_files_format_and_content: BAM files were converted into bedgraph format via extension of reads by 125 bp at their 3’ end using the bedtools2 package.

source_name: C2C12 myoblasts

growth_protocol: Cells of the murine myoblasts cell line C2C12 (ATCC) were maintained in growth medium (GM), Dulbecco’s Modified Eagle Medium (D-MEM) supplemented with 10% Fetal Bovine Serum, at 37ºC with 5% CO2. To induce differentiation, the medium of 80% confluent cell cultures was changed to differentiation medium (DM), D-MEM supplemented with 2% horse serum, and 50 nM of bexarotene was added for treatment conditions.

extract_protocol:
Cells were crosslinked in formaldehyde and sonicated with a Bioruptor (Diagenode). DNA was precipitated with the appropriate antibody and sent for sequencing to the McGill University Genome Quebec Innovation Centre.
Genomic DNA libraries were prepared for sequencing by McGill University Genome Quebec Innovation Centre using standard Illumina protocols.

treatment_protocol: For treatment conditions, 50 nM of bexarotene was added at the induction of differentiation.

tag: chip antibody

value: H3K27me3 (Abcam_ab6002 )

tag: cell line

tag: agent

value: 50 nM of bexarotene


title: H3K27me3_Ctl

status: Public on Jun 24 2020

type: SRA

state: Ontario

country: Canada

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT_mouse977CH_RNAPT08)

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

country: USA

institute: National Cancer Institute, NIH

description: RNA-seq data from snap frozen tissue or cultured cells

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the mouse mm9 genome assembly using TopHat Software
differentially expressed genes were determined using DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

molecule: total RNA

source_name: Primary Mammary Tumor

growth_protocol: cells were grown in tissue culture or isolated from mice and snap frozen

extract_protocol:
RNA was isolated from flash-frozen tissue. First the tissue was mechanically dissociated using a tissue grinder while submerged in 1 ml of TriPure (Roche). 200 µl of chloroform (Sigma-Aldrich) was then added and the soluble fraction was isolated by centrifugation at 12,000 rpm for 15 minutes at 4°C. RNA was then precipitated with the addition of 500 µl isopropanol and incubation of the sample at -20°C for 2 hours. Pure RNA was then extracted using the RNA: DNA mini-prep kit (Zymogen) and finally samples were eluted in 100 µl (PT) or 50 µl (metastases) of DEPC water (Quality Biological). RNA was isolated from cell lines using TriPure as described above but following isopropanol precipitated RNA was washed with 75% ethanol (Sigma-Aldrich), and then again with 95% ethanol before being resuspended in 100 µl DEPC water.
Preparation of mRNA libraries and mRNA sequencing was performed by the Sequencing Facility using the HiSeq2500 instrument with Illumina TruSeq v4 chemistry.

treatment_protocol: all samples are untreated

tag: mouse strain

value: FVB

tag: oncogenic driver

value: PyMT

tag: cell line name

tag: model

value: GEMM


title: FC57 fin clipped at 20 weeks during normal aging

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2fastq v1.8.4. Then, they were quality-trimmed and filtered for low complexity using preprocess from the SGA assembler 0.10.13 (-q 30 -m 50 --dust). The passed reads were mapped to the repeat-masked N. furzeri reference genome (assembly version Nfu_20150522, "hardmasked"; gene annotation version 150922) with TopHat2 2.1.0 under conservative settings (--b2-sensitive --no-coverage-search --no-novel-juncs --no-novel-indels --transcriptome-max-hits=1). For each gene, reads that map uniquely to one genomic position were counted with FeatureCounts 1.5.0 (multi-mapping or multi-overlapping reads were not counted).
Genome_build: Genome Nfu_20150522 and annotation 20150922 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (https://nfingb.leibniz-fli.de/).
Supplementary_files_format_and_content: csv (comma-separated values) file containing the gene id in the 1st column and the number of assigned reads (=counts) in the remaining 228 columns.

organism: Nothobranchius furzeri

source_name: fin clip

growth_protocol: Animal maintenance was performed as described in Baumgart et al. 2012. (PMID:22487494)

extract_protocol:
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
Library preparation was done using Illumina's TruSeq RNA v2 sample preparation kit following the manufacturer's instructions.

tag: animal id

tag: Sex

value: male

tag: tissue

value: fin clip

tag: age at fin clip (weeks)

tag: age at death (days)

tag: condition

value: normal aging


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT_mouse956CH_RNAPT07)


title: C2C12_p300_Bex

data_processing:
For p300, sequencing reads were mapped to the mouse genome build mm9 using Bowtie, allowing for 3 mismatches and reporting the single best alignment per 50bp read. For myogenin, sequence reads were aligned to the mouse mm9 reference genome build using BWA-Mem with default parameters. Picard was used to filter out replicated reads and BAM files were converted into BED files after which aligned reads were extended by 125 bp at their 3’ end, and converted to bedgraph format using the bedtools2 package. The bedgraphtobigwig package was used for visualization of experiment results.
Peak calling was performed with Hypergeometric Optimization of Motif EnRichment (Homer) v4.10 with -style factor and FDR of 1.0 x 10-4.
Genome_build: mm9
Supplementary_files_format_and_content: Myogenin and p300 peaks were called by HOMER and represent significant enrichment of aligned reads compared to input control.

value: C2C12 myoblasts

value: p300 (Santa Cruz_sc-584 )


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT-ING_mouse9716_sample1011-09)


title: C2C12_p300_Ctl


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT-ING_mouse9715_sample1011-08)


title: FC56 fin clipped at 20 weeks during normal aging


title: MMTV-neu GEMM FVB lung met RNA (PyMT-Neu_LuMet3_mouse472CH_sample1011-36)

source_name: lung metastasis

value: Neu


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT-ING_mouse978_sample1011-07)


title: C2C12_Input_p300_Histones


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT-ING_mouse974_sample1011-10)


title: FC56 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM MOLF lung met RNA (PyMT-MOLFJ_LM1_9944_KS137)

value: MOLF


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT_mouse9742_KS40)


title: FC55 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT_mouse9738_KS45)


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT_mouse9725_KS53)


title: FC55 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT_mouse9715_KS48)


title: FC54 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT_mouse9703_KS43)


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT_mouse9674_KS37)


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT_mouse9716_KS51)


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT_mouse947CH_RNAPT10)


title: FC57 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT_mouse974_KS56)


title: FC54 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT-AX_mouse978_sample1010-36)


title: FC53 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet4_mouse9470_RNALM15)


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet3_mouse974_KS36)


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet2_mouse9742_KS42)


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet3_mouse9470_RNALM17)


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet2_mouse9738_KS47)


title: FC53 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet2_mouse9725_KS55)


title: FC52 fin clipped at 10 weeks during normal aging


title: FC51 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet2_mouse9674_KS39)


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet2_mouse9715_KS50)


title: FC51 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet2_mouse974CH_RNALM30)


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet2_mouse977CH_RNALM09)


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet2_mouse9336_RNALM12)


title: FC50 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet2_mouse956CH_RNALM08)


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet1_mouse9742_KS41)


title: FC50 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet1_mouse9725_KS54)


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet1_mouse9738_KS46)


title: miR29 mimic C

type: RNA

city: London

first: David

middle: Jonathan

last: Fear

address: 5th Floor, Tower Wing, Great Maze Pond

department: Respiratory Medicine and Allergy

country: United Kingdom

institute: Kings College London

description:
SAMPLE 5
miR29 OE Sample C

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using RMA normalization using Illumina’s Genome Studio Suite v1.0

label: Biotin

organism: Homo sapiens

source_name: In vitro cultured tonsillar B cells

label_protocol: cDNA was synthesized and amplified from 40ng RNA using the Ovation Pico WTA system V2 (NuGEN). 4 ug of amplified cDNA was biotin labeled with Encore Biotin Module (NuGen)

growth_protocol: RPMI culture in humidified incubator

extract_protocol: total RNA from fixed and permeabilized cultured human tonsil B cells was isolated using the PureLink FFPE total RNA isolation kit (Invitrogen)

treatment_protocol: Transfect followed by 24 hours culture with IL-4 and anti-CD40 stimulation

tag: cell type

value: Germinal Centre B cell

tag: transfection

value: miR-29 mimic transfection

tag: donor id

value: C


title: miR29 mimic B

description:
SAMPLE 3
miR29 OE Sample B

value: B


title: miR29 mimic A

description:
SAMPLE 1
miR29 OE Sample A

value: A


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet1_mouse9716_KS52)


title: Negative control C

description:
SAMPLE 6
negative control Sample C

value: negative control transfection


title: FC49 fin clipped at 10 weeks during normal aging


title: Negative control B

description:
SAMPLE 4
negative control Sample B


title: Negative control A

description:
SAMPLE 2
negative control Sample A


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet1_mouse9715_KS49)


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet1_mouse9703_KS44)


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet1_mouse9674_KS38)


title: FC52 fin clipped at 20 weeks during normal aging


title: FC48 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet2_mouse9470_RNALM14)


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet1_mouse974CH_RNALM19)


title: MMTV-PyMT GEMM CAST primary tumor RNA (PyMT-CAST_PT_9802_KS140)

value: CAST


title: MMTV-PyMT GEMM CAST primary tumor RNA (PyMT-CAST_PT_9801_KS138)


title: MMTV-PyMT GEMM CAST lung met RNA (PyMT-CAST_LM1_9801_KS139)


title: MMTV-PyMT GEMM CAST lung met RNA (PyMT-CAST_LM1_9802_KS141)


title: FC47 fin clipped at 20 weeks during normal aging


title: FC48 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM BL10J primary tumor RNA (PyMT-C57BL10J_PT_9896_KS132)


title: MMTV-PyMT GEMM BL10J primary tumor RNA (PyMT-C57BL10J_PT_9895_KS130)


title: FC49 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM BL10J primary tumor RNA (PyMT-C57BL10J_PT_9891_KS128)


title: FC47 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM BL10J primary tumor RNA (PyMT-C57BL10J_PT_9786_KS124)


title: FC46 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM BL10J primary tumor RNA (PyMT-C57BL10J_PT_9839_KS126)


title: MMTV-PyMT GEMM BL10J lung met RNA (PyMT-C57BL10J_LM2_9891_KS129)


title: MMTV-PyMT GEMM BL10 lung met RNA (PyMT-C57BL10_LuMet1_mouse9788_sample1011-22)


title: FC44 fin clipped at 20 weeks during normal aging


title: FC44 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM BL10J lung met RNA (PyMT-C57BL10J_LM3_9786_KS125)


title: FC46 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM FVB lung met RNA (PyMT-FVB_LuMet1_mouse9336_RNALM11)

value: FVB


title: MMTV-PyMT GEMM BL10J lung met RNA (PyMT-C57BL10J_LM1A_9839_KS127)

value: PyMT


title: MMTV-PyMT GEMM BL6N lung met RNA (PyMT-C57BL6N_LM1_9783_KS122)

value: GEMM


title: MMTV-PyMT GEMM BL10J lung met RNA (PyMT-C57BL10J_LM1_9896_KS133)


title: MMTV-PyMT GEMM BL6N primary tumor RNA (PyMT-C57BL6N_PT_9873_KS123)


title: FC43 fin clipped at 10 weeks during normal aging

value: male


title: MMTV-PyMT GEMM BL10 primary tumor RNA (PyMT-C57BL10_PT-AX_mouse9788_sample1011-21)


title: MMTV-PyMT GEMM BL6N lung met RNA (PyMT-C57BL6N_LM1A_9780_KS121)


title: FC43 fin clipped at 20 weeks during normal aging

value: fin clip


title: MMTV-PyMT GEMM BL6N primary tumor RNA (PyMT-C57BL6N_PT_9780_KS120)


title: MMTV-PyMT GEMM BL6 lung met RNA (PyMT-C57BL6_LuMet3_mouse9792_sample1011-33)


title: MMTV-PyMT GEMM BL6 lung met RNA (PyMT-C57BL6_LuMet3_mouse9791_sample1011-30)


title: FC41 fin clipped at 20 weeks during normal aging

value: normal aging


title: MMTV-PyMT GEMM BL6 primary tumor RNA (PyMT-C57BL6_PT-AX_mouse9781_sample1011-25)


title: MMTV-PyMT GEMM BL10J lung met RNA (PyMT-C57BL10J_LM2_9895_KS131)


title: MMTV-PyMT GEMM BL6 primary tumor RNA (PyMT-C57BL6_PT-AX_mouse9792_sample1011-31)


title: MMTV-PyMT GEMM BL6 primary tumor RNA (PyMT-C57BL6_PT-AX_mouse9791_sample1011-28)


title: FC45 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM BL6 primary tumor RNA (PyMT-C57BL6_PT-AX_mouse9777_sample1011-23)


title: FC42 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM BL6 lung met RNA (PyMT-C57BL6_LuMet3_mouse9781_sample1011-27)


title: MMTV-PyMT GEMM BL6 lung met RNA (PyMT-C57BL6_LuMet1_mouse9777_sample1011-24)


title: MMTV-Neu GEMM PT RNA (Neu_PT_522_KS142)


title: FC45 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM BL6 lung met RNA (PyMT-C57BL6_LuMet2_mouse9792_sample1011-32)


title: MMTV-Neu GEMM lung met RNA (Neu_LM1A_522_KS143)


title: FC39 fin clipped at 20 weeks during normal aging


title: MMTV-Myc GEMM PT RNA (MycFVB_PT_mouse12358_RNAPT19)

value: cMYC


title: MMTV-PyMT GEMM BL6 lung met RNA (PyMT-C57BL6_LuMet1_mouse9791_sample1011-29)


title: MMTV-Myc GEMM PT RNA (MycFVB_PT_mouse12364_RNAPT22)


title: FC41 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM BL6 lung met RNA (PyMT-C57BL6_LuMet1_mouse9781_sample1011-26)


title: FC40 fin clipped at 20 weeks during normal aging


title: MMTV-Neu GEMM lung met RNA (Neu_LM2A_522_KS144)


title: MMTV-Myc GEMM PT RNA (MycFVB_PT_mouse11533_RNAPT20)


title: FC38 fin clipped at 20 weeks during normal aging


title: FC38 fin clipped at 10 weeks during normal aging


title: FC37 fin clipped at 20 weeks during normal aging


title: FC40 fin clipped at 10 weeks during normal aging


title: MMTV-Myc GEMM PT RNA (MycFVB_PT_mouse12621_RNAPT23)


title: Met1 Allograft TV injection lung met RNA (Mvt1-tailvein_LuMet1_mouse4_KS16)

value: cMYC / VEGF

value: Allograft tail vein injection


title: FC42 fin clipped at 20 weeks during normal aging


title: FC39 fin clipped at 10 weeks during normal aging


title: MMTV-Myc GEMM PT RNA (MycFVB_PT_mouse11036_RNAPT18)


title: Mvt1 Allograft orthotopic injection primary tumor RNA (Mvt1-ortho_PT_mouse6_KS06)

value: Allograft orthotopic injection


title: Met1 Allograft TV injection lung met RNA (Mvt1-tailvein_LuMet6_mouse2_KS14)


title: Met1 Allograft TV injection lung met RNA (Mvt1-tailvein_LuMet2_mouse3_KS15)


title: Mvt1 Allograft orthotopic injection primary tumor RNA (Mvt1-ortho_PT_mouse4_KS04)


title: Met1 Allograft TV injection lung met RNA (Mvt1-tailvein_LuMet1_mouse7_KS18)


title: FC35 fin clipped at 10 weeks during normal aging


title: FC34 fin clipped at 20 weeks during normal aging


title: MMTV-Myc GEMM PT RNA (MycFVB_PT_mouse11842_RNAPT21)


title: Mvt1 Allograft orthotopic injection primary tumor RNA (Mvt1-ortho_PT_mouse2_KS02)


title: Met1 Allograft TV injection lung met RNA (Mvt1-tailvein_LuMet1_mouse6_KS17)


title: FC34 fin clipped at 10 weeks during normal aging


title: FC33 fin clipped at 20 weeks during normal aging


title: FC36 fin clipped at 20 weeks during normal aging


title: FC32 fin clipped at 20 weeks during normal aging


title: Mvt1 Allograft orthotopic injection lung met RNA (Mvt1-ortho_LuMet2_mouse4_KS10)


title: FC31 fin clipped at 20 weeks during normal aging


title: FC37 fin clipped at 10 weeks during normal aging


title: Met1 Allograft TV injection lung met RNA (Mvt1-tailvein_LuMet1_mouse1_KS13)


title: FC35 fin clipped at 20 weeks during normal aging


title: Mvt1 Allograft orthotopic injection primary tumor RNA (Mvt1-ortho_PT_mouse5_KS05)


title: FC36 fin clipped at 10 weeks during normal aging


title: Mvt1 Allograft orthotopic injection lung met RNA (Mvt1-ortho_LuMet7_mouse1_KS07)


title: Mvt1 Allograft orthotopic injection primary tumor RNA (Mvt1-ortho_PT_mouse1_KS01)


title: Ast_D21_rep3

city: Daejeon

first: Jeongsu

last: B

address: Gwahak-ro

country: South Korea

institute: KRIBB

description: 3 Set D21

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Human Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: Astrocyte, day 21

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: Please refer to our papers about astrocyte differentiation.(Neurosci Lett. 2020 Jan 18;716:1346812020, Rapid Differentiation of Astrocytes From Human Embryonic Stem Cells)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: cell line background

value: Astrocyte progenitor cells

tag: treatment

value: CD44 sorting


title: Mvt1 Allograft orthotopic injection lung met RNA (Mvt1-ortho_LuMet3_mouse3_KS09)


title: FC33 fin clipped at 10 weeks during normal aging


title: Mvt1 Allograft orthotopic injection primary tumor RNA (Mvt1-ortho_PT_mouse3_KS03)


title: Ast_D21_rep1

description: 1 Set D21


title: Ast_D28_rep2

description: 2 Set D28

source_name: Astrocyte, day 28

value: Mature astrocyte


title: Ast_D21_rep2

description: 2 Set D21


title: Ast_D28_rep1

description: 1 Set D28


title: Mvt1 Allograft orthotopic injection lung met RNA (Mvt1-ortho_LuMet2_mouse6_KS12)


title: Ast_D28_rep3

description: 3 Set D28


title: Met1 Allograft TV injection lung met RNA (Met1_TV_LuMet1_KS92)


title: NP_D0_rep2

description: 2 Set NP

source_name: Neural progenitor cells, day 0

value: Neural progenitor cells

value: No sorting


title: FC32 fin clipped at 10 weeks during normal aging


title: Mvt1 Allograft orthotopic injection lung met RNA (Mvt1-ortho_LuMet2_mouse2_KS08)


title: Mvt1 Allograft orthotopic injection lung met RNA (Mvt1-ortho_LuMet1_mouse5_KS11)


title: FC31 fin clipped at 10 weeks during normal aging


title: CCRF-CEM WT high (2 mM) folate rep3

city: Haifa

first: Tomer

last: Shlomi

address: 7-2 Emerson Building, Technion

country: Israel

institute: Technion - Israel Institute of Technology

data_processing:
Library quality control: FASTQC version 0.11.5
Quality and adapter trimming: trim_galore (uses cutadapt version 1.10)
Mapping: Tophat2 version 2.1.0 (uses Bowtie2 version 2.2.6)
Gene counting: HTseq-count version 0.6.1
Normalization and differential expression analysis: DESeq2 R package version 1.18.1
Genome_build: GRCh37

source_name: T lymphoblast

growth_protocol: Cell lines were grown in RPMI 1640 supplemented with 10% (v/v) heat-inactivated dialyzed fetal bovine serum, 2 μM or 200 nM folic acid, 100 U/ml penicillin, and 100 μg/ml streptomycin in a 5% CO2 incubator at 37 °C.

extract_protocol:
RNA was isolated using Trizol
mRNA libraries were prepared using the TruSeq RNA Library Preparation kit v2 (Illumina).

value: peripheral blood

tag: disease

value: acute lymphoblastic leukemia

value: T lymphoblast

tag: culture media

value: RPMI 1640 supplemented with 10% (v/v) heat-inactivated dialyzed fetal bovine serum, 2 μM folic acid, 100 U/ml penicillin, and 100 μg/ml streptomycin


title: FC30 fin clipped at 20 weeks during normal aging

tag: strain


title: Met1 Allograft orthotopic injection lung met RNA (Met1_13_LuMet2_KS84)

tag: mouse strain

value: FVB

tag: oncogenic driver

value: PyMT


title: FC29 fin clipped at 20 weeks during normal aging

value: male

value: fin clip


title: CCRF-CEM WT low (0.2 mM) folate rep3

value: RPMI 1640 supplemented with 10% (v/v) heat-inactivated dialyzed fetal bovine serum, 200 nM folic acid, 100 U/ml penicillin, and 100 μg/ml streptomycin


title: FC30 fin clipped at 10 weeks during normal aging

value: normal aging


title: Met1 Allograft orthotopic injection resected primary tumor RNA (Met1_13_reOrtho_KS82)

tag: cell line name

tag: model

value: Allograft orthotopic injection and resection


title: Met1 Allograft orthotopic injection primary tumor RNA (Met1_13_Ortho_KS81)

value: Allograft orthotopic injection


title: FC29 fin clipped at 10 weeks during normal aging

tag: animal id

tag: Sex


title: CCRF-CEM WT low (0.2 mM) folate rep2

tag: tissue


title: Met1 Allograft orthotopic injection lung met RNA (Met1_13_LuMet1_KS83)


title: FC28 fin clipped at 20 weeks during normal aging

tag: age at fin clip (weeks)

tag: age at death (days)


title: NP_D0_rep3

description: 3 Set NP

tag: cell type


title: FC28 fin clipped at 10 weeks during normal aging

tag: condition


title: Met1 Allograft orthotopic injection resected primary tumor RNA (Met1_10_reOrtho_KS78)


title: CCRF-CEM WT high (2 mM) folate rep1


title: NP_D0_rep1

description: 1 Set NP


title: CCRF-CEM WT low (0.2 mM) folate rep1


title: FC27 fin clipped at 20 weeks during normal aging


title: Met1 Allograft orthotopic injection lung met RNA (Met1_10_LuMet2_KS80)


title: FC27 fin clipped at 10 weeks during normal aging


title: DamID_AML12_shCtrl_1

type: genomic

city: Shanghai

first: Luzhang

last: Ji

address: 1239 Siping Rd.

country: China

institute: Tongji University

description: Replicate 1 of 2 shCtrl treated AML12 cells

hyb_protocol: Hybridized to Agilent-027414 arrays.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization. we also smoothed the probe signals using a moving average approach with a window size of 40k bps. The smoothing procedure takes into consideration of the spatial correlation of signals.

label_protocol: Genomic DNA samples were differentially labeled with Invitrogen’s BioPrime Total for Agilent aCGH labeling kit.

growth_protocol: AML12 cells were cultured in  DMEM/F12 supplemented with 10% fetal bovine serum,  ITS Liquid Media Supplement, and 0.1μM dexamethasone at 37 °C and 5% CO2.

extract_protocol: 2×106 AML12 cells were planted in 6-well plates, and infected with lenti-virus expressing Dam or Dam-Lamin B1 after 48 hours. gDNA was isolated with the Dneasy Tissue kit (Qiagen) per the manufacturers protocol after 72 hours. 2.5 μg of gDNA was digested with DpnI (New England Biolabs), adapters were ligated with T4 ligase (New England Biolabs), and the ligation reaction was subsequently digested with DpnII (New England Biolabs). 500 ng of the DpnII digested material was used as input for a PCR amplification of methylated fragments (MePCR),see Vogel et al., 2008, Nature Protocols for details.

treatment_protocol: The shRNA lentiviruses were prepared as previously described (Fu et al., 2015). Then AML12 cells were infected with 200 μl of virus concentrate in a well of six-well-plates. Medium was changed 24 hours after transfection, and then collect cells 5 days after transfection.

tag: cell line

value: AML12 cells

tag: lenti-virus expression

value: Dam-only


title: DamID_AML12_shCtrl_2

description: Replicate 2 of 2 shCtrl treated AML12 cells


title: Met1 Allograft orthotopic injection primary tumor RNA (Met1_10_Ortho_KS77)


title: DamID_AML12_shTopors_2

description: Replicate 2 of 2 shTopors treated AML12 cells


title: ChIP_BAP1_shNONT_H1963

city: Chicago

first: Lu

last: Wang

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

description: Cells treated with non-targeting shRNA

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

source_name: small cell lung cancer

growth_protocol: Cell medium was composed as follow: RPMI-1640, DMEM-F12, DMEM (Thermo Fisher), 10% serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life Technologies), cells were grown in a CO2 incubator (5% CO2) at 37˚C

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
RNA-seq: Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with an longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used. Samples were pooled and sequencing on a HiSeq with a read length configuration of 150 PE. ChIP-seq: ChIP-sequencing libraries were prepared using KAPA HyperPrep Kit (Kapa Biosystems) following manufacturer’s recommendation. In brief, 500ng of input DNA sheared by Covaris LE220 ultrasonicator or 10 ng of immunoprecipitated DNA was end-repaired and 3'-dA tailed. Adapter was then ligated to the DNA, and ligated product was PCR amplified and cleaned up using SPRIselect Reagent (Beckman Coulter).

treatment_protocol: Cells were treated with dBET6, JQ1 or I-BET-151 for 2, 4 and 8 hours. DMSO was used as control

value: small cell lung cancer

tag: passages

value: Low passages (6-10)

tag: treatment

value: non-targeting shRNA

tag: antibody


title: FC26 fin clipped at 20 weeks during normal aging

tag: strain


title: DamID_AML12_shTopors_1

description: Replicate 1 of 2 shTopors treated AML12 cells


title: Met1 Allograft orthotopic injection lung met RNA (Met1_10_LuMet1_KS79)

tag: mouse strain


title: FC26 fin clipped at 10 weeks during normal aging


title: Met1 Allograft orthotopic injection resected primary tumor RNA (Met1_3_reOrtho_KS86_resent)

tag: oncogenic driver


title: ChIP_BAP1_shASXL3_H1963

description: Cells treated with ASXL3 shRNA

value: ASXL3 shRNA


title: Met1 Allograft orthotopic injection primary tumor RNA (Met1_3_Ortho_KS85)

tag: cell line name


title: CCRF-CEM WT high (2 mM) folate rep2

value: peripheral blood

tag: disease

value: acute lymphoblastic leukemia

tag: culture media


title: FC25 fin clipped at 20 weeks during normal aging

tag: animal id

tag: Sex


title: RNA_IBET-151_R2

tag: tissue

value: Cells treated with IBET-151


title: Met1 Allograft orthotopic injection lung met RNA (Met1_3_LuMet2_KS88)

value: FVB

tag: model


title: FC25 fin clipped at 10 weeks during normal aging

tag: age at fin clip (weeks)

tag: age at death (days)


title: RNA_JQ1_R2

tag: cell line

value: Cells treated with JQ1


title: Met1 Allograft orthotopic injection lung met RNA (Met1_3_LuMet1_KS87)

value: PyMT


title: FC24 fin clipped at 20 weeks during normal aging

value: male

value: fin clip

tag: condition


title: RNA_IBET-151_R1

tag: passages


title: NCI-H2066

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

institute: HiThru Analytics

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Average Beta values and detection p-values were obtained using the Bioconductor package minfi using default parameters

label: Cy3, Cy5

source_name: Small cell lung cancer cell line

label_protocol: Standard Illumina protocol

extract_protocol: Standard Illumina protocol


title: RNA_JQ1_R1

tag: treatment


title: Met1 Allograft orthotopic injection resected primary tumor RNA (Met1_1_reOrtho_KS74)


title: FC24 fin clipped at 10 weeks during normal aging

value: normal aging


title: RNA_dBET6_R2

value: Cells treated with dBET6


title: Met1 Allograft orthotopic injection primary tumor RNA (Met1_1_Ortho_KS73)

value: Allograft orthotopic injection


title: RNA_dBET6_R1


title: SPH77


title: FC23 fin clipped at 10 weeks during normal aging


title: FC23 fin clipped at 20 weeks during normal aging


title: Met1 Allograft orthotopic injection lung met RNA (Met1_1_LuMet2_KS76)


title: RNA_DMSO_R2

value: Cells treated with DMSO


title: Met1 Allograft orthotopic injection lung met RNA (Met1_1_LuMet1_KS75)


title: RNA_DMSO_R1


title: Met1 Allograft orthotopic injection primary tumor RNA (Met1-ortho_PT_mouse11_KS72)


title: NCI-H847


title: RNA_shASXL3_2_R2

value: Cells treated with ASXL3 shRNA


title: FC21 fin clipped at 20 weeks during normal aging


title: Met1 Allograft orthotopic injection primary tumor RNA (Met1-ortho_PT_mouse9_KS70)


title: FC19 fin clipped at 20 weeks during normal aging


title: RNA_shASXL3_2_R1

value: small cell lung cancer


title: NCI-H889


title: Met1 Allograft orthotopic injection lung met RNA (Met1-ortho_LuMet1_mouse9_KS71)


title: FC19 fin clipped at 10 weeks during normal aging


title: M6 Allograft orthotopic injection primary tumor RNA (M6_878_Ortho_KS105)

value: REAR


title: RNA_shASXL3_1_R1

value: Low passages (6-10)


title: NCI-H774


title: M6 Allograft orthotopic injection lung met RNA (M6_878_LuMet1_KS106)


title: NCI-H865


title: NCI-H841


title: NCI H82

value: NCI H82


title: FC18 fin clipped at 10 weeks during normal aging


title: FC21 fin clipped at 10 weeks during normal aging


title: FC18 fin clipped at 20 weeks during normal aging


title: M6 Allograft orthotopic injection liver met RNA (M6_878_LiverMet1_KS107)

source_name: Liver Metastasis


title: RNA_shNONT_R2

value: Cells treated with non-targeting shRNA


title: FC17 fin clipped at 20 weeks during normal aging


title: RNA_shNONT_R1


title: NCI-H748


title: RNA_shASXL3_1_R2


title: M6 Allograft orthotopic injection primary tumor RNA (M6_874_Ortho_KS102)


title: M6 Allograft orthotopic injection lung met RNA (M6_874_LuMet2_KS103)


title: ChIP_BRD4_2h_H1963

tag: antibody

value: anti-BRD4 (CST)


title: FC16 fin clipped at 20 weeks during normal aging

tag: strain


title: NCI-H720


title: M6 Allograft orthotopic injection primary tumor RNA (M6_873_Ortho_KS100_resent)

tag: mouse strain


title: ChIP_BRD4_shNONT_H1963


title: NCI-H711


title: NCI-H719


title: FC16 fin clipped at 10 weeks during normal aging


title: NCI-H735


title: FC15 fin clipped at 10 weeks during normal aging


title: NCI-H524


title: M6 Allograft orthotopic injection lung met RNA (M6_873_LuMet1_KS101)

tag: oncogenic driver


title: NCI-H69


title: ChIP_BRD4_shASXL3_2_H1963


title: ChIP_H3K27Ac_shASXL3_2_H1963

value: anti-H3K27Ac (CST)


title: FC17 fin clipped at 10 weeks during normal aging


title: ChIP_BRD4_shASXL3_1_H1963


title: M6 Allograft orthotopic injection liver met RNA (M6_874_LiverMet2_KS104)

tag: cell line name


title: FC14 fin clipped at 20 weeks during normal aging


title: NCI-H526

tag: disease


title: M6 Allograft orthotopic injection primary tumor RNA (M6_870_Ortho_KS97)


title: NCI-H510


title: M6 Allograft orthotopic injection lung met RNA (M6_870_LuMet1_KS98)


title: FC14 fin clipped at 10 weeks during normal aging


title: NCI-H28


title: ChIP_H3K27Ac_shNONT_H1963


title: ChIP_H3K27Ac_shASXL3_1_H1963


title: NCI-H446


title: M6 Allograft orthotopic injection liver met RNA (M6_870_LiverMet1_KS99)


title: FC13 fin clipped at 20 weeks during normal aging


title: NCI-H660


title: NCI-H220


title: M6 Allograft orthotopic injection primary tumor RNA (M6_823_Ortho_KS95_resent)


title: NCI-H345


title: FC13 fin clipped at 10 weeks during normal aging


title: FC15 fin clipped at 20 weeks during normal aging


title: ChIP_H3K4me1_H2171

value: anti-H3K4me1 (CST)

value: Parental cells


title: NCI-H250


title: M6 Allograft orthotopic injection primary tumor RNA (M6_820_Ortho_KS93_resent)


title: ChIP_H3K4me1_H1963


title: FC12 fin clipped at 10 weeks during normal aging


title: M6 Allograft orthotopic injection lung met RNA (M6_820_LuMet1_KS94)


title: FC12 fin clipped at 20 weeks during normal aging


title: M6 Allograft orthotopic injection lung met RNA (M6_823_LuMet1_KS96)


title: NCI-H378


title: ChIP_H3K27Ac_H1963


title: FC11 fin clipped at 20 weeks during normal aging


title: TSAE1 Allograft orthotopic injection primary tumor RNA (LW_TSAE1_ortho_PT5_sample1010-20)

value: BALB

value: unknown


title: FC11 fin clipped at 10 weeks during normal aging

value: male

value: fin clip


title: ChIP_H3K27Ac_H2171


title: ChIP_BRD4_H1963


title: NCI-H2330


title: TSAE1 Allograft orthotopic injection primary tumor RNA (LW_TSAE1_ortho_PT4_sample1010-19)


title: ChIP_Input_H1963

value: input


title: FC10 fin clipped at 10 weeks during normal aging

value: normal aging


title: FC10 fin clipped at 20 weeks during normal aging


title: ChIP_IgG_H1963

value: IgG control


title: TSAE1 Allograft orthotopic injection primary tumor RNA (LW_TSAE1_ortho_PT1_sample1010-17)

value: Allograft orthotopic injection


title: FC9 fin clipped at 20 weeks during normal aging


title: R3T Allograft orthotopic injection primary tumor RNA (LW_R3T_ortho_PT1-7_sample1010-12)


title: ChIP_ASXL3_Ab1_H1963

value: small cell lung cancer

value: anti-ASXL3-1 (homemade)


title: ChIP_ASXL3_Ab2_H1963

value: Low passages (6-10)

value: anti-ASXL3-2 (homemade)


title: FC9 fin clipped at 10 weeks during normal aging


title: NCI-H2171


title: NCI-H2141


title: R3T Allograft orthotopic injection primary tumor RNA (LW_R3T_ortho_PT1-6_sample1010-11)


title: FC8 fin clipped at 20 weeks during normal aging


title: NCI-H209


title: 2660501-1R-R_CGATGT_S112_L004

city: Kanchipuram

first: Subramaniam

last: Sivakumar

state: TamilNadu

address: Enathur

department: Biochemistry

country: India

institute: Sri Sankara Arts and Science College

data_processing:
These samples were run on a HiSeq 4000, 50bp single end.
The sequencing library was prepared with a BioScientific NEXT Flex small RNA v3 kit.
The initial processing was done by a pipeline HTSF uses to align and count miRNAs.
The differential expression analysis sets using DESeq2 in R.

source_name: Mouse gRhO

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.The sequencing library was prepared with a BioScientific NEXT Flex small RNA v3 kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Retina

value: treated with mouse rhodopsin gene

tag: age

value: post natal day 90


title: NCI-H2198


title: R3T Allograft orthotopic injection primary tumor RNA (LW_R3T_ortho_PT1-3_sample1010-10)


title: ChIP_Input_H2171


title: 2655176-2R-L_GACGAC_S95_L004


title: R3T Allograft orthotopic injection primary tumor RNA (LW_R3T_ortho_PT1-1_sample1010-09)


title: 2655176-3R-L_CGGAAT_S97_L004


title: FC7 fin clipped at 20 weeks during normal aging

tag: animal id


title: FC8 fin clipped at 10 weeks during normal aging

tag: Sex


title: SW1271


title: HRM1 Allograft orthotopic injection primary tumor RNA (LW_HRM1_ortho_PT1-11_sample1010-16)

value: FVB


title: FC6 fin clipped at 20 weeks during normal aging

tag: tissue


title: HRM1 Allograft orthotopic injection primary tumor RNA (LW_HRM1_ortho_PT1-9_sample1010-15)

tag: model


title: 2655176-1L-L_CTAGCT_S94_L004


title: NCI-H2107


title: NCI-H211


title: 2655174-1R-R_TCATTC_S92_L004


title: FC6 fin clipped at 10 weeks during normal aging

tag: age at fin clip (weeks)


title: HRM1 Allograft orthotopic injection primary tumor RNA (LW_HRM1_ortho_PT1-7_sample1010-14)


title: NCI-H2029


title: NCI-H196


title: HRM1 Allograft orthotopic injection primary tumor RNA (LW_HRM1_ortho_PT1-6_sample1010-13)


title: NCI-H2081


title: FC5 fin clipped at 20 weeks during normal aging

tag: age at death (days)


title: 2655176-3R-R_CTCAGA_S98_L004


title: F311 Allograft orthotopic injection primary tumor RNA (LW_F311_ortho_PT5_sample1010-31)


title: 2660501-1R-L_TTAGGC_S111_L004


title: NCI-H1963

tag: cell line


title: FC5 fin clipped at 10 weeks during normal aging

tag: condition


title: 2660501-1L-R_ATCACG_S110_L004


title: F311 Allograft orthotopic injection primary tumor RNA (LW_F311_ortho_PT4_sample1010-30)


title: FC4 fin clipped at 20 weeks during normal aging


title: FC4 fin clipped at 10 weeks during normal aging


title: 2655176-2R-R_CTATAC_S96_L004


title: NCI-H1836


title: F311 Allograft orthotopic injection primary tumor RNA (LW_F311_ortho_PT3_sample1010-29)


title: F311 Allograft orthotopic injection primary tumor RNA (LW_F311_ortho_PT1_sample1010-28)


title: FC3 fin clipped at 20 weeks during normal aging


title: 2660501-1L-L_TCGGCA_S109_L004


title: 2655174-2R-L_CCAACA_S93_L004


title: TSAE1 Allograft orthotopic injection primary tumor RNA (LW_TSAE1_ortho_PT2_sample1010-18)


title: NCI-H1876


title: EMT6 Allograft orthotopic injection primary tumor RNA (LW_EMT6_ortho_PT5_sample1010-04)


title: NCI-H1688


title: NCI-H187


title: NCI-H1930


title: 2655183-1R1L-L_TGACCA_S99_L004

source_name: Human gRHO

value: treated with human rhodopsin gene


title: EMT6 Allograft orthotopic injection primary tumor RNA (LW_EMT6_ortho_PT3_sample1010-03)

value: BALB


title: NCI-H1882


title: FC2 fin clipped at 20 weeks during normal aging


title: FC7 fin clipped at 10 weeks during normal aging


title: 2655183-2R1L-L_TCGAAG_S101_L004


title: FC2 fin clipped at 10 weeks during normal aging


title: EMT6 Allograft orthotopic injection primary tumor RNA (LW_EMT6_ortho_PT2_sample1010-02)

value: unknown


title: NCI-H1522


title: NCI-H1694


title: FC1 fin clipped at 20 weeks during normal aging

value: male


title: NCI-H1672


title: NCI-H1650


title: NCI-H1618


title: E0771 Allograft orthotopic injection primary tumor RNA (LW_E0771_ortho_PT1-6_sample1010-24)


title: 2660488-1R1L-R_CATTTT_S103_L004

source_name: Saline Injected

value: treated with saline


title: FC1 fin clipped at 10 weeks during normal aging

value: fin clip


title: E0771 Allograft orthotopic injection primary tumor RNA (LW_E0771_ortho_PT1-5_sample1010-23)


title: EMT6 Allograft orthotopic injection primary tumor RNA (LW_EMT6_ortho_PT1_sample1010-01)


title: 2660488-1R1L-L_CATGGC_S102_L004


title: NCI-H1436


title: Topors_input

data_processing:
We aligned paired-end reads to the mm9 reference using Bowtie2.
We annotated broad H3K9me3 domains using RSEG with the parameter "-i 20".
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contain ChIP-seq signal for each replicate.

source_name: Topors input

extract_protocol:
H3K9me3 ChIP was done as previously described (Wen et al., 2008) from 5×10^6 cells.
Illumina sequencing library were prepared according to the standard Illumina protocol.

value: AML12 cells

tag: genotype

value: Topors knockdown


title: 2660497-2R-L_GCCAAT_S107_L004

source_name: Un-injected P23H+/-

tag: treatment

value: untreated


title: E0771 Allograft orthotopic injection primary tumor RNA (LW_E0771_ortho_PT1-2_sample1010-22)

value: Allograft orthotopic injection


title: NCI-H146

value: small cell lung cancer


title: Control_input

value: Control


title: 2660497-2R-R_TATAAT_S108_L004


title: Topors_2_H3K9me3

source_name: Topors knockdown


title: 2660497-1R-L_CAGATC_S106_L004


title: FC3 fin clipped at 10 weeks during normal aging

value: normal aging


title: E0771 Allograft orthotopic injection primary tumor RNA (LW_E0771_ortho_PT1-1_sample1010-21)

source_name: Primary Mammary Tumor


title: D2A1 Allograft orthotopic injection primary tumor RNA (LW_D2A1_ortho_PT5_sample1010-35)


title: 2655183-1R1L-R_ACAGTG_S100_L004

value: Retina


title: Topors_1_H3K9me3


title: D2A1 Allograft orthotopic injection primary tumor RNA (LW_D2A1_ortho_PT4_sample1010-34)


title: NCI-H1105


title: NCI-H1417


title: Control_2_H3K9me3

source_name: Control


title: 2660497-1L-L_ACTTGA_S104_L004


title: 2660497-1L-R_TCCCGA_S105_L004


title: NCI-H128


title: D2A1 Allograft orthotopic injection primary tumor RNA (LW_D2A1_ortho_PT3_sample1010-33)


title: WT-L-25_TACAGC_S113_L004

source_name: Wild Type C57B


title: Control_1_H3K9me3


title: D2A1 Allograft orthotopic injection primary tumor RNA (LW_D2A1_ortho_PT2_sample1010-32)


title: Topors_2_H3K27ac

data_processing:
We aligned paired-end reads to the mm9 reference using Bowtie2.
We used MACS2 to call peaks with the command: macs2 callpeak -g mm -q 0.01. To define super-enhancers, we used Rank Ordering of Super-enhancers (ROSE) algorithm.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contain ChIP-seq signal for each replicate.

extract_protocol:
H3K27ac ChIP was done as previously described (Wen et al., 2008) from 5×10^6 cells.
Illumina sequencing library were prepared according to the standard Illumina protocol.


title: WT-R-24_TAATCG_S114_L004


title: Met1 Allograft orthotopic injection lung met RNA (LW_1_PT_KS89)

value: PyMT


title: Topors_1_H3K27ac


title: Met1 Allograft orthotopic injection lung met RNA (LW_1_LuMet2_KS91)

source_name: lung metastasis


title: AKP dox 72h rep2

city: Boston

first: Priscilla

last: Cheung

state: MA

address: 1 Blackfan Circle

department: Stem Cell Program

institute: Boston Children's Hospital

data_processing:
Salmon v0.14.1 with options “--useVBOpt --seqBias --gcBias --numBootstraps 30 --validateMappings" was used to perform quasi-mapping and transcript abundance estimation.
Genome_build: mm10
Supplementary_files_format_and_content: Quantification file output of Salmon as a tab-separated text file with the following columns: Name (name of transcript), Length (length of transcript in base pairs), EffectiveLength (effective length of transcript, taking into account sample-specific biases), TPM (abundance of transcript in Transcripts Per Million), and NumReads (estimated number of reads originating from this transcript given the transcript's relative abundance and length).

source_name: colon organoid

growth_protocol: Organoids were grown in Matrigel overlaid with culture media composed of Advanced DMEM/F12 supplemented with 10% FBS, 1x N2, 1x B-27, 1% Pen/Strep, 2 mM L-glutamine, 10 mM HEPES, 0.1 mg/mL primocin, 1 uM N-acety-L-cysteine, and 100 ng/mL noggin. Media for Apc knockout organoids were additionally supplemented with 50 ng/ml EGF.

extract_protocol:
Total RNA was isolated from organoids using the NucleoSpin RNA XS kit, and 100 ng were used for construction of sequencing libraries with the Illumina TruSeq RNA Library Preparation kit v2.
RNA libraries were prepared for sequencing using standard Illumina protocols as part of the TruSeq RNA Library Preparation kit v2.

treatment_protocol: Organoids were treated with 1 ug/ml doxycycline one day following passaging for the indicated hours.

value: colon

value: Apc-/- KrasG12D p53-/- tetO-Yap5SA rtTA

tag: agent

value: dox


title: Control_2_H3K27ac


title: Met1 Allograft orthotopic injection lung met RNA (LW_1_LuMet1_KS90)

value: FVB


title: Control_1_H3K27ac


title: AKP ctrl 72h rep2


title: AKP dox 72h rep1


title: C3Tag GEMM primary tumor RNA (C3TAg_17337_PT)

source_name: Primay mammary tumor

value: GEMM


title: RNA-seq_shTopors-2

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end reads from RNA-seq were aligned to the mouse mm10 reference assembly by using HISAT2 with parameters "--rna-strandness RF". Not uniquely mapped reads were removed.
For differential gene expression analysis, we counted reads mapped to Ensembl genes using HTSeq with the following command: htseq-count -f bam -r pos -s reverse -a 10 -t exon -i gene_id -m union. Fold-change and p values were calculated by the R package DESeq2.
To quantify the expression level of genes, we acquired the transcripts per million (TPM) using StringTie with options '-e -B -A –rf'.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including TPM values for each replicate.

source_name: shTopors

extract_protocol:
Total RNA was prepared with TRIzol reagents (Life Technologies).
Ribosomal RNA depleted and strand-specific libraries were constructed with the Ribo-zero gold (Epicentre) and TruSeq Stranded Total RNA Sample Prep kit (Illumina), and the libraries were sequenced using the HighSeq system (lllumina).

tag: genotype/variation

value: shTopors


title: LXFS 650L

value: LXFS 650L


title: AKP ctrl 72h rep1


title: NCI-H1092


title: 67NR Allograft orthotopic injection primary tumor RNA (67NR_ortho_mouse7_KS113)

tag: mouse strain

value: BALB

value: unknown


title: 67NR Allograft orthotopic injection primary tumor RNA (67NR_ortho_mouse4_KS111)

tag: oncogenic driver


title: RNA-seq_shCtrl-2

source_name: shCtrl

value: AML12 cells

value: shCtrl


title: Apc 96h rep1

value: Apc-/- tetO-YapS127A rtTA

tag: time point


title: Apc 72h rep2


title: 67NR Allograft orthotopic injection primary tumor RNA (67NR_ortho_mouse3_KS110)

tag: cell line name

value: Allograft orthotopic injection


title: Cocaine_F_S2

city: Birmingham

first: Jeremy

middle: Jason

last: Day

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: UAB

data_processing:
Cell demultiplexing and genome alignment in Cell Ranger using Emsemble pre-mRNA (v95) reference assembly GTF file. Raw count data obtained in Cell Ranger.
Genome_build: rn6
Supplementary_files_format_and_content: Cell Ranger output matrices for barcodes, features, and gene expression counts are provided for each sample.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Nucleus accumbens

growth_protocol: Sprague-Dawley 90-120-day-old male or female rats were purchased from Charles River Laboratories. Male or female adult rats were co-housed in pairs in plastic filtered cages with nesting enrichment in an AAALAC-approved animal care facility maintained between 23-24°C on a 12-hour light/dark cycle with ad libitum food (Lab Diet Irradiated rat chow) and water. Bedding and enrichment were changed weekly by animal resources program staff. Animals were randomly assigned to experimental groups.

extract_protocol:
1mm brain sections were taken at the level of the nucleus accumbens, and nucleus accumbens tissue was dissected using a 1mm punch tool centered on the nucleus accumbens core subregion. Frozen tissue punches were thawed slowly on ice prior to being chopped by scalpel 100 times in 2 orthogonal directions. Tissue from 4 animals in the same treatment condition was then combined and transferred to 5mL of chilled (4°C) Lysis Buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2 (Thermo Fisher, BP214-500), 0.1% Igepal in Nuclease-Free Water (Sigma, 18896-50ML)) for 15 min, mixing the tissue by inversion every 2 min. Lysis was quenched immediately at 15 min with 5mL of complete Hibernate-A (Thermo Fisher, A1247501) supplemented with B27 and Glutamax (Life Technologies, 35050-061)). Tissue was then triturated by fire-polished Pasteur pipette (2 pipettes of decreasing diameter; 8-10 passes per pipette) for 35 min and passed through a 40µm pre-wet filter. The samples were then pelleted at 500rcf for 10 min at 4°C followed by a wash in 10mL of Nuclei Wash & Resuspension Buffer (1X PBS, 1% BSA, 0.2U/ul NxGen RNase inhibitor (Lucigen, 30281-2)). Supernatant was then removed and the pellet was gently resuspended in a total volume of 800µl prior to 7-AAD (Thermo Fisher, 00-6993-50) staining and FACS to further purify the nuclei for sequencing. Immediately after FACS, nuclei were washed a final time at 200rcf in 10mL supplemented Hibernate-A containing 1% BSA for 10 minutes at 4°C to remove any remaining fine debris and nascent RNA. Nuclei were brought to a concentration of 1,700 nuclei/µl and an average total of 2,400 nuclei pooled from 4 rats were loaded per sex and treatment group.
FACS-sorted nuclei were subject to 10X GEM generation and barcoding, GEM-RT cleanup and cDNA amplication, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry). Libraries were quantified and underwent sequencing (~500M total 75bp paired-end reads) on an Illumina sequencing platform (NextSeq 500).

treatment_protocol: Rats were injected with either cocaine (20mg/kg, dissolved in physiological saline) intraperitoneally or equal volumes of physiological saline and placed in an open field for behavioral tracking. 1hr after injections, rats were sacrificed and the brain was removed ad flash frozen.

tag: strain

value: Sprague-Dawley

tag: age

value: Cocaine

value: Female


title: RNA-seq_shCtrl-1


title: PML_ChIP-seq_shTopors-2

data_processing:
We aligned paired-end reads to the mm9 reference using Bowtie2.
We utilized Enhanced Domain Detector (EDD) to call broad domains using the following flags: -g 8 --fdr 0.1.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contain ChIP-seq signal for each replicate.

extract_protocol:
PML ChIP was done as previously described (Lund et al., 2014) from 5×10^6 cells.
Illumina sequencing library were prepared according to the standard Illumina protocol.

tag: chip antibody


title: Cocaine_M_S4

tag: Sex

value: Male


title: NCI-H1048

source_name: Small cell lung cancer cell line

tag: disease

value: small cell lung cancer


title: Saline_M_S3

value: Saline


title: 67NR Allograft orthotopic injection primary tumor RNA (67NR_ortho_mouse2_KS109)

tag: model


title: Saline_F_S1


title: PML_ChIP-seq_shTopors-1


title: 67NR Allograft orthotopic injection primary tumor RNA (67NR_ortho_mosue5_KS112)


title: Apc 24h rep2

tag: tissue

value: colon

value: dox


title: KCL_S4

source_name: Striatal neuron culture

growth_protocol: Neurons were removed from striatal tissue at embryonic day 18, and maintained in vitro for 11 days prior to collection of RNA. Each culture well contained ~250,000 cells.

extract_protocol:
Neurons were treated with described stimuli for 1hr, washed, and harvested in lysis buffer prior to isolation of nuclei via centrifugation and FACS sorting.
FACS-sorted nuclei were subject to 10X GEM generation and barcoding, GEM-RT cleanup and cDNA amplication, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry). Libraries were quantified and underwent sequencing (~500M total 75bp paired-end reads) on an Illumina sequencing platform (NextSeq 500).

treatment_protocol: DIV 11 rat primary striatal neurons were treated with vehicle (neurobasal media), dopamine (50µM), the Drd1 agonist SKF-38393 (1µM), and potassium chloride (25mM) for 1hr.

value: Embryonic day 18, 11 DIV

value: KCL


title: PML_ChIP-seq_Input-2

tag: cell line

value: none (input)


title: NCI-H1341


title: 67NR Allograft orthotopic injection primary tumor RNA (67NR_1_Ortho_KS108)

value: BALB


title: 6DT1 Allograft TV injection lung met RNA (6DT1-tailvein_LuMet3_mouse9543_RNALM38)

value: FVB

value: cMyc

value: Allograft tail vein injection


title: Apc 12h rep2

value: Apc-/- tetO-YapS127A rtTA


title: PML_ChIP-seq_Input-1

value: AML12 cells

value: shCtrl


title: DMS 79

value: DMS 79


title: Apc 24h rep1


title: SKF_S3

value: Sprague-Dawley

value: SKF


title: NCI-H69/LX10

value: small cell lung cancer


title: DMS 237

value: DMS 237


title: NCI-H69/VCR


title: DA_S2

value: DA


title: 6DT1 Allograft TV injection lung met RNA (6DT1-tailvein_LuMet3_mouse9540_RNALM39)


title: PML_ChIP-seq_shCtrl-2


title: DMS 53

value: DMS 53


title: Apc 12h rep1

value: colon

value: dox


title: LXFS 605L

value: LXFS 605L


title: RNA-seq_shTopors-1

value: shTopors


title: PML_ChIP-seq_shCtrl-1


title: 6DT1 Allograft TV injection lung met RNA (6DT1-tailvein_LuMet2_mouse9543_RNALM40)

value: FVB


title: 106_7_S11

description: Experiment 2

data_processing:
Pre-trimming QC with FastQC (version build within trim-galore=0.4.5)
Trimming of low quality bases (Phred score <20) and Illumina adapter with trim-galore=0.4.5
Post-trimming QC with FastQC
Splice-aware alignment with star=2.6.0c. The genome utilized was: /data/project/daylab/Genome-Reference/Genomes/rn6-Ensembl/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa
Merging of BAM files and index generation with samtools=1.6
Count generation with bioconductor-rsubread=1.26.1 (R version: r-base=3.4.1). The GTF file utilized was: Rattus_norvegicus.Rnor_6.0.90.gtf
Genome_build: rn6
Supplementary_files_format_and_content: Matrix with of gene expression values (raw counts) for each gene in each sample. Genes are in rows, and columns contain the Ensembl ID, chromosome, start, end, and sample names.

extract_protocol:
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.0) and library construction for polyA+ RNA sequencing.
Directional polyA+ RNA llibraries were constructed at the UAB Helfin Genomics Core. Libraries were quantified and underwent sequencing (~25M total 75bp paired-end reads) on an Illumina sequencing platform (NextSeq 500).

treatment_protocol: Neurons were treated as described with CRISPR sgRNAs and dCas9-VPR fusion lentiviruses on DIV 4. Media was removed and RNA was extracted on DIV 11.

value: Striatal neuron culture

value: Embryonic day 18, 11 DIV

value: LacZ


title: Apc 96h rep2

value: Apc-/- tetO-YapS127A rtTA


title: 6DT1 Allograft TV injection lung met RNA (6DT1-tailvein_LuMet2_mouse9540_RNALM36)

data_processing:
RNA-seq reads were aligned to the mouse mm9 genome assembly using TopHat Software
differentially expressed genes were determined using DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

extract_protocol:
RNA was isolated from flash-frozen tissue. First the tissue was mechanically dissociated using a tissue grinder while submerged in 1 ml of TriPure (Roche). 200 µl of chloroform (Sigma-Aldrich) was then added and the soluble fraction was isolated by centrifugation at 12,000 rpm for 15 minutes at 4°C. RNA was then precipitated with the addition of 500 µl isopropanol and incubation of the sample at -20°C for 2 hours. Pure RNA was then extracted using the RNA: DNA mini-prep kit (Zymogen) and finally samples were eluted in 100 µl (PT) or 50 µl (metastases) of DEPC water (Quality Biological). RNA was isolated from cell lines using TriPure as described above but following isopropanol precipitated RNA was washed with 75% ethanol (Sigma-Aldrich), and then again with 95% ethanol before being resuspended in 100 µl DEPC water.
Preparation of mRNA libraries and mRNA sequencing was performed by the Sequencing Facility using the HiSeq2500 instrument with Illumina TruSeq v4 chemistry.

value: cMyc

value: Allograft tail vein injection


title: 106_6_S10

description: Experiment 2

value: Sprague-Dawley

value: Dopaplex


title: 6DT1 Allograft TV injection lung met RNA (6DT1-tailvein_LuMet1_mouse9543_RNALM37)


title: Apc 0h rep1


title: Apc 0h rep2


title: C2C12_Myog_Bex

source_name: C2C12 myoblasts

extract_protocol:
Cells were crosslinked in formaldehyde and sonicated with a Bioruptor (Diagenode). DNA was precipitated with the appropriate antibody and sent for sequencing to the McGill University Genome Quebec Innovation Centre.
Genomic DNA libraries were prepared for sequencing by McGill University Genome Quebec Innovation Centre using standard Illumina protocols.

value: C2C12 myoblasts

value: Myogenin (Santa Cruz_sc-12732X)


title: NCI-H69/CPR

value: small cell lung cancer


title: 6DT1 Allograft TV injection lung met RNA (6DT1-tailvein_LuMet1_mouse9540_RNALM35)


title: C2C12_Myog_Ctl


title: 106_5_S9

description: Experiment 2


title: 6DT1 Allograft orthotopic injection primary tumor RNA (6DT1-ortho_PT_mouse5_RNAPT17)

value: Allograft orthotopic injection


title: 106_3_S8

description: Experiment 2


title: DMS 114

value: DMS 114


title: Apc 72h rep1

value: colon

value: dox


title: COLO L47

value: COLO L47


title: H3

city: Suzhou

first: Yanfei

last: Bi

state: Jiangsu

address: Yulu NO.2

institute: Jiangsu Changshu National Agricultural Science and Technology Park Management Committee

description: growth in a high temperature enviroment at day / night temperature of 35°C / 25°C

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl  scripts
Index of the reference genome was built using HISAT2 v2.0.4 and  paired-end clean reads were aligned to the reference genome using  HISAT2(Langmead, B.et al) v2.0.4.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed
GO and KEGG enrichment analysis of differentially expressed genes
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/007/265/GCA_002007265.1_ASM200726v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Spinacia oleracea

source_name: Heat treatment3

growth_protocol: illumination incubator

extract_protocol:
RNA  was isolated using TRIZOL.RNA purity was checked using the NanoPhotometer® spectrophotometer  (IMPLEN, CA, USA).RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0  Flurometer.RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the  Bioanalyzer 2100 system
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: spinach in response to day / night temperature of 35°C / 25°C compared to 20°C / 15°C for 4 days

value: Heat treatment


title: H2

source_name: Heat treatment2


title: 103_6_S6

description: Experiment 1

value: Striatal neuron culture


title: COLO L32

value: COLO L32


title: 6DT1 Allograft orthotopic injection primary tumor RNA (6DT1-ortho_PT_mouse3_RNAPT15)

value: FVB


title: H1

source_name: Heat treatment1


title: ATAC-seq_shCtrl-2

data_processing:
Paired-end reads were aligned to the mouse genome (mm9) using Bowtie2 (Langmead and Salzberg, 2012) with parameters “-X 2000”.
Mitochondrial and PCR duplicate reads were removed after alignment.
Peaks were identified using MACS2 (Zhang et al., 2008) with a q value threshold of 0.01.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contain ATAC-seq signal for each replicate.

extract_protocol:
The ATAC-seq was performed as described (Buenrostro et al., 2015) with minor modifications: starting with 30,000 AML12 cells and transposition reaction at 37°C for 45 min.
Illumina sequencing library were prepared according to the standard Illumina protocol.

value: AML12 cells

value: shCtrl


title: 106_2_S7

description: Experiment 2

value: Embryonic day 18, 11 DIV


title: 103_5_S5

description: Experiment 1

value: Sprague-Dawley

value: LacZ


title: 103_4_S4

description: Experiment 1

value: Dopaplex


title: DMS 187

value: DMS 187


title: 6DT1 Allograft orthotopic injection primary tumor RNA (6DT1-ortho_PT_mouse2_RNAPT14)

value: cMyc


title: COLO 668

value: COLO 668

value: small cell lung cancer


title: 6DT1 Allograft orthotopic injection primary tumor RNA (6DT1-ortho_PT_mouse1_RNAPT13)

value: Allograft orthotopic injection


title: Veh_S1

value: Veh


title: ATAC-seq_shTopors-2

value: shTopors


title: C2

description: growth in  normal temperature enviroment at day / night temperature of 20°C / 15°C

value: Control


title: 103_3_S3

description: Experiment 1

value: Striatal neuron culture


title: 6DT1 Allograft orthotopic injection primary tumor RNA (6DT1-ortho_PT_mouse0_RNAPT12)


title: Tuber sample 4B

city: Mlochow

first: Dorota

last: Sołtys-Kalina

address: Platanowa 19

department: Mlochow Research Centre

country: Poland

institute: IHAR-PIB

data_processing:
Illumina Casava1.7 software used for basecalling.
The index of the reference genome (https://www.ncbi.nlm.nih.gov/assembly/GCF_000226075.1) was built using Bowtie v2.1.0.
Poor quality and to short reads (<30 nt) were removed from analysis.
Paired-end clean reads obtained for bulks H and L were aligned to the reference genome using TopHat v2.0.9
Genome_build: GCF_000226075.1
Supplementary_files_format_and_content: csv files were generated using DESeq2 package
Supplementary_files_format_and_content: csv files, abundance measurements

organism: Solanum tuberosum

source_name: Tubers

growth_protocol: Potato tubers were planted in plastic pots filled with soil. Plants grew under tent from May to October.

extract_protocol:
Total RNA was isolated using TRIZol method as described Chomczyński and Sacchi (1987).
The mRNA was isolated using the NEBNext Poly(A) mRNA magnetic Isolation Module (New England Biolabs, E7490), and cDNA libraries were prepared using the NEBNext Ultra Direction RNA Library Kit for Illumina (New England Biolabs, E7420S). The established cDNA libraries were sequenced on the Illumina HiSeq 4000 sequencing platform (Illumina Inc., San Diego, CA, USA) to generate 100-bp paired-end reads (PE100).

treatment_protocol: After harvest, tubers were ground in liquid nitrogen and freezed in -80°C untill use.

tag: population

value: Diploid hybrid 12-3

tag: developmental stage

value: Fully-developed tubers after harvest

tag: trait

value: Low starch, low AGPaseS-a expression

value: untreated


title: A549


title: C1

tag: treatment


title: 103_2_S2

description: Experiment 1

value: Embryonic day 18, 11 DIV


title: 6DT1 Allograft orthotopic injection lung met RNA (6DT1-ortho_LuMet6_mouse0_RNALM16)

value: FVB


title: Tuber sample 4A


title: 103_1_S1

description: Experiment 1

value: Sprague-Dawley

value: LacZ


title: 6DT1 Allograft orthotopic injection lung met RNA (6DT1-ortho_LuMet3_mouse4_RNALM27)


title: Tuber sample 3B

value: Low starch, high AGPaseS-a expression


title: ATAC-seq_shTopors-1

value: AML12 cells

tag: genotype/variation


title: COLO L279

value: COLO L279


title: Tuber sample 3A


title: 6DT1 Allograft orthotopic injection lung met RNA (6DT1-ortho_LuMet3_mouse3_RNALM25)

tag: mouse strain

value: cMyc


title: Human AF_loci (variant PCR) STARR_seq iAM1_isolated RNA_3

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

data_processing:
Reads were mapped to hg19 build of the human transcriptome using STAR (Dobin et al. 2013).
Signal was distributed over 500bp genomic bins. Putative enhancers were called when RNA>DNA (L2FC 0.8). Putative repressors were called when RNA<DNA (L2FC -0.8)
VarScan 2 was used to detect variants and  determine their allele specific occurrence. We used a minimum read depth of 100 and a minimum variant allele frequency threshold of 0.20  for variant detection.
Genome_build: hg19
Supplementary_files_format_and_content: BAC_STARR_putative_enhancers_hg19.bed and BAC_STARR_putative_repressors_hg19.bed contain the genomic coordinates of putative enhancers and repressors detected in the STARR-seq experiments.
Supplementary_files_format_and_content: Variant_allele_frequencies_STARR.xlsx contains the detected variants and their allele specific occurrence and relative enrichment between DNA and RNA samples.

source_name: human genetic material

growth_protocol: iAM1 cell line was generated an maintained as described in Liu et al., 2018 DOI: 10.1093/cvr/cvy134

extract_protocol:
RNA was isolated using RNeasy Maxi kit (Qiagen). DNA was isolated using short alkaline lysis method.
STARR-seq library was prepared as described in Arnold et al., 2013 DOI: 10.1126/science.1232542
STARR-seq

treatment_protocol: STARR-seq vector containing candidate sequences were transfected using lipofectamine 3000

tag: cell type

value: rat conditionally immortalized atrial myocyte (iAM1)


title: Human AF_loci (variant PCR) STARR_seq iAM1_isolated RNA_2


title: WT_3D7G7_S_GlcN+_RNAseq

first: Xinyu

last: Cui

address: Siping road

data_processing:
Low-quality and adaptor sequences were trimmed from the reads using cutadapt (v1.16) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Hisat2 strand-specific mode (v2.1.0) with parameters: --rna-strandness RF --dta --no-discordant --no-mixed --no-unal.
Mapped reads were subsequently assembled into transcripts guided by the PlasmoDB gff annotation files (Pf 3D7 v32) using featureCounts (v1.6.1) with parameters: -M -p -B -C for all; -s 2 for sense transcripts; -s 1 for antisense transcripts.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The raw counts were calculated by featureCounts as described above.

organism: Plasmodium falciparum

extract_protocol:
The experiment began to collect the highly synchronized Plasmodium, centrifuge and remove the supernatant, then the cells was lysed by adding 1:5 triazole. Next to depolymerize the proteins and nucleic acids in the cells to release them, and extract RNA according to reagent specification of Direct-zol RNA MiniPrep (R2052). The resullts of RNA extraction were verified on a 2% agarose gel.
The mRNA was enriched with magnetic beads with Oligo (dT). It has been optimized to isolate mature mRNA from total RNA by capturing twice using the KAPA mRNA Capture Beads. This experiment was performed using the KAPA Stranded mRNA-seq Kit. Here, the required fragment size for the experiment is 300-400 bp. It carried out the fragmentation and priming program as follows: 85°C 6min. In particular, some changes to the library amplification procedure have been made as follows: initial 98°C 45sec 1cycle; denaturation 98°C 15sec 14cycles; annealing 65°C 30sec 14cycles; extension 65°C 30sec 14cycles; final extension 65°C 5min 1cycle; hold 10°C 1cycle. Resuspend the dried beads in 22µl of RNase-free water to obtain the final library building results. The library were sequenced on an Illumina HiSeq Xten systerm with PE150 strategy.

value: Schizont

tag: genotype

tag: host

value: Homo sapiens


title: Tuber sample 2B

value: High starch, low AGPaseS-a expression


title: Human AF_loci (variant PCR) STARR_seq iAM1_isolated RNA_1


title: 6DT1 Allograft orthotopic injection lung met RNA (6DT1-ortho_LuMet2_mouse5_RNALM29)

tag: oncogenic driver

tag: cell line name

value: Allograft orthotopic injection


title: 6DT1 Allograft orthotopic injection lung met RNA (6DT1-ortho_LuMet3_mouse1_RNALM21)


title: Tuber sample 2A

value: Diploid hybrid 12-3


title: WT_3D7G7_T_GlcN+_RNAseq

value: Trophozoite


title: WT_3D7G7_T_RNAseq


title: Tuber sample 1B

value: Fully-developed tubers after harvest

value: High starch, high AGPaseS-a expression


title: 6DT1 Allograft orthotopic injection lung met RNA (6DT1-ortho_LuMet2_mouse2_RNALM23)


title: Human AF_loci (variant PCR) STARR_seq iAM1_isolated DNA_2


title: Tuber sample 1A

value: untreated


title: WT_3D7G7_R_GlcN+_RNAseq

value: Ring


title: PD-L1-lnc vector

city: Nanjing

first: HONGWEI

last: LIANG

state: Jiangsu Province

address: Qixia District, Xianlin Road No.163

institute: Nanjing University

hyb_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 µg total RNA using the One-Color Low RNA Input Amplification kit (Agilent) and QuickAmpLableling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. The minimum concentration and labeling efficiency were 60 ng/µl and 15pmol Cy3/µg cRNA, respectively.

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarry Scanner System using one color scan setting (AgilentG3_GX_1Color) for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Tiff 20 bit and Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Differentially expressed probes were identified by using R v3.4.3 and the Bioconductor package limma v3.34.8. Quality control of arrays were performed by checking distribution of ``bright corner'', ``dark corner'' probes, and unsupervised clustering of raw intensities.

source_name: PD-L1-lnc vector

growth_protocol: Human lung cancer cell lines A549 were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco, Carlsbad, CA, USA) supplemented with 10% (v/v) FBS (Gibco, Carlsbad, CA, USA), 1% (v/v) penicillin/streptomycin (Gibco, Carlsbad, CA, USA).

extract_protocol: Total RNAs were isolated from the A549 cells transfected with PD-L1-lnc overexpressed plasmid or control plasmid by TRIzol reagent and puriﬁed by RNeasy Mini Kit (Qiagen, USA).

treatment_protocol: A549 cells transfected with PD-L1-lnc overexpressed vector or control vector.

tag: knockdown

value: PD-L1-lnc vector


title: 6DT1 Allograft orthotopic injection lung met RNA (6DT1-ortho_LuMet2_mouse1_RNALM20)

value: FVB


title: Human AF_loci (variant PCR) STARR_seq iAM1_isolated DNA_1


title: WT_3D7G7_R_RNAseq


title: 6DT1 Allograft orthotopic injection lung met RNA (6DT1-ortho_LuMet1_mouse5_RNALM28)


title: WT_3D7G7_S_RNAseq


title: Human AF_loci (BAC) STARR_seq iAM1_ isolated RNA

description:
BAC_STARR_putative_enhancers_hg19.bed
BAC_STARR_putative_repressors_hg19.bed

source_name: human BAC


title: PfArp4_S_rep2_RNAseq


title: H4_ChIP_rep1_2

city: Stanford

first: Owen

middle: Kabnick

last: Smith

state: CA

address: 279 Campus Drive

institute: Stanford University School of Medicine

data_processing:
Remove PCR duplicates with BBtools Clumpify, bbmap v38.06
Trim adapters with trimmomatic, v0.38
Generate k-mers with KMC, v3.1.1
Identify CENP-A enriched k-mers
Align genome segments with enriched k-mers with bowtie2 v2.3.5
Align enriched k-mers with bowtie v1.2.2 with parameters -v 0 -a
Generate, sort ,index bam with Samtools, v1.9
Generate bigWig with deeptools, v2.5.7, -bs 5
Genome_build: X. laeivs v10.3
Supplementary_files_format_and_content: bigWig displaying mapping of CENP-A enriched k-mers

organism: Xenopus laevis

source_name: Red Blood Cells

extract_protocol:
Nuclei were isolated from cells through dounce nuclear extraction, incubated with MNase (300U 30min RT). Soluble mononucleosomes were extracted and precleared prior to use as input for antibody pulldowns.
Sequencing libraries were prepared with the NEBNext Ultra II DNA Library prep kit (E7645) with up to 1µg of input or ChIP eluate DNA following the manufacturer’s protocol

treatment_protocol: no treatement conditions

tag: strain

value: J-strain

value: Red Blood Cells

tag: chip antibody

value: Rb-anti-H4 Abcam ab7311


title: input_DNA_rep1_2


title: 6DT1 Allograft orthotopic injection lung met RNA (6DT1-ortho_LuMet1_mouse4_RNALM26)

first: Maxwell

last: Lee

address: Building 37, Room 5120

source_name: lung metastasis

value: cMyc

tag: model


title: input_DNA_rep4


title: 6DT1 Allograft orthotopic injection lung met RNA (6DT1-ortho_LuMet2_mouse3_RNALM31)


title: 6DT1 Allograft orthotopic injection lung met RNA (6DT1-ortho_LuMet1_mouse2_RNALM22)


title: control vector

source_name: control vector

value: control vector


title: PfArp4_T_GlcN+_rep2_RNAseq

value: Schizont


title: Striatal neuron culture, vehicle, S37-5

growth_protocol: Neurons were removed from striatal tissue at embryonic day 18, and maintained in vitro for 11 days prior to collection of RNA. Each culture well contained ~250,000 cells. Two culture wells were pooled at the time of extraction.

extract_protocol:
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.0) and library construction for polyA+ RNA sequencing.
Directional polyA+ RNA llibraries were constructed at HudsonAlpha Genomic Services Lab using NEBNext reagents (New England Biolabs) according to manufacturer's recommendations with minor modifications (including the use of custom library adapters and indexes). RNA libraries were quantified (Kapa Library Quant Kit, Kapa Biosystems), and underwent sequencing (25M total 50bp paired-end reads) on an Illumina sequencing platform (HiSeq v4).

treatment_protocol: Neurons were treated as described with neurobasal media (vehicle) or 1µM dopamine for 1hr on DIV 11. Media was removed and RNA was extracted.

value: Sprague-Dawley

tag: age

value: Embryonic day 18, 11 DIV

value: Striatal neurons

value: Vehicle

tag: time


title: PfArp4_T_rep2_RNAseq

value: Homo sapiens


title: input_DNA_rep2


title: Striatal neuron culture, dopamine, S37-4

value: Dopamine


title: 4T07 Allograft orthotopic injection primary tumor RNA (4T07_ortho_mouse9_KS119)

source_name: Primary Mammary Tumor

value: BALB

value: unknown

value: Allograft orthotopic injection


title: Striatal neuron culture, vehicle, S37-3


title: 4T07 Allograft orthotopic injection primary tumor RNA (4T07_ortho_mouse7_KS117)


title: Striatal neuron culture, dopamine, S37-6


title: Human AF_loci (BAC) STARR_seq iAM1_isolated DNA

value: rat conditionally immortalized atrial myocyte (iAM1)


title: 6DT1 Allograft orthotopic injection primary tumor RNA (6DT1-ortho_PT_mouse4_RNAPT16)

source_name: Primay mammary tumor

value: FVB


title: input_DNA_rep1

value: J-strain


title: PfArp4_R_rep2_RNAseq

value: Trophozoite


title: Striatal neuron culture, dopamine, S37-2


title: 4T07 Allograft orthotopic injection primary tumor RNA (4T07_ortho_mouse3_KS116)


title: 4T07 Allograft orthotopic injection primary tumor RNA (4T07_ortho_mouse2_KS115)


title: Striatal neuron culture, vehicle, S37-1


title: PfArp4_S_rep1_RNAseq


title: Human AF_loci (variant PCR) STARR_seq iAM1_isolated DNA_3


title: input_DNA_rep3

value: Red Blood Cells


title: H4_ChIP_rep4

value: Rb-anti-H4 Abcam ab7311


title: PfArp4_S_GlcN+_rep1_RNAseq


title: skpo_OP50_3

first: Daniel

middle: Martinez

last: Martinez

state: London

address: Hammersmith Hospital, Du Cane Road

institute: Medical Research Council

data_processing:
Illumina Real-Time-Analalysis (RTA2) software used for base calling
The sequencing reads were quality evaluated and adaptor trimmed using FastQC and Trimmomatic  (v.0.36), with a Phred cut-off value of 25
The resulting reads were mapped to the reference transcriptome (version WBcel235) using salmon (v.1.2.1), with options validateMappings and gcBias
Downstream differential expression analysis was performed in R (version 3.6.3) using DESeq2 (v.1.26.0), tximport (v.1.14.2) and tidyverse (v.1.3.0)  libraries, and Venn diagrams were produced using the VennDiagram library (v.1.6.20).
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited txt file including gene counts
Supplementary_files_format_and_content: tab-delimited txt file including normalised gene counts
Supplementary_files_format_and_content: complete_stats.xlsx: multi-univariate statistics (from DESeq2)

organism: Caenorhabditis elegans

source_name: Whole organism

extract_protocol:
Trizol/chloroform/isopropanol method
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: L4 stage worms were exposed to E. faecalis or E. coli for 16 hours and total RNA was extracted for 3 or 4 biological replicates

value: day1 adult

value: E. coli OP50


title: PfArp4_T_GlcN+_rep1_RNAseq

value: Ring


title: PfArp4_R_GlcN+_rep2_RNAseq


title: 4T07 Allograft orthotopic injection primary tumor RNA (4T07_ortho_mouse1_KS114)

institute: National Cancer Institute, NIH


title: H4_ChIP_rep2


title: 4T1 Allograft TV injection lung met RNA (4T1-tailvein_LuMet2_mouse5_KS66)

value: Allograft tail vein injection


title: PfArp4_T_rep1_RNAseq


title: 4T07 Allograft orthotopic injection primary tumor RNA (4T07_ortho_mouse8_KS118)


title: skpo_OP50_1


title: 4T1 Allograft TV injection lung met RNA (4T1-tailvein_LuMet2_mouse1_KS64)


title: PfArp4_R_GlcN+_rep1_RNAseq


title: skpo_OG1RF_4

value: E. faecalis OG1RF


title: skpo_OG1RF_3


title: 4T1 Allograft TV injection lung met RNA (4T1-tailvein_LuMet1_mouse9_KS69)


title: 4T1 Allograft TV injection lung met RNA (4T1-tailvein_LuMet1_mouse8_KS68)


title: ChIP-seq_PfArp4_H3K9ac_GlcN+_input

data_processing:
Low-quality and adaptor sequences were trimmed from the reads using cutadapt (v1.16) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Bowtie2 (v2.3.4.3) with parameters: -N 0 --no-discordant --no-mixed --no-unal.
The Samtools (v1.9) was used to transfer the mapping results from sam format to position sorted bam format. Next, the duplicated reads were removed by markdup from sambamba (v0.6.8).
Then, the bam files were converted to bigwig files using bamCoverage from the deeptools suite (v3.1.3) with parameters: --normalizeUsing RPKM --binSize 25. The bigwig files from ChIP sample were normalized to input sample by bigwigCompare from the deeptools suite (v3.1.3) with parameters: –operation log2 --pseudocount 1. The Integrative Genomics Viewer (IGV) was used to show the signal of histone modification in certain genomic region in a track view.
The histone modification peaks were called by MACS2 with parameters:-g 2.33e7 -f BAMPE.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: H3K9ac enrichment along the whole genome file  for different samples

extract_protocol:
In this experiment, highly synchronized infected red blood cells (iRBC) were collected and centrifuged to remove a portion of the supernatant. Parasites were extracted with 0.15% saponin and washed with pre-chilled PBS until the supernatant was clear. 2ml Lysis Buffer (containing 100× protease inhibitor and 100× DTT) was added to the sample, mixed well, and leave it on ice for 30min to lyse the body. The lysate was placed in a grinding tube and 50ul of 10% NP-40 was added. The cell debris was subjected to liquid phase ultrasound, after centrifuging the ultrasound product, took the supernatant and took 20ul of the supernatant as input (input was stored at -80°C). 100µl of salmon sperm DNA Agrose magnetic beads (50µl/ml) and protease inhibitor were added to the remaining supernatant, samples were incubated overnight. After overnight incubation, 3ug of anti-H3K9ac antibody and IgG antibody were added and incubated at 4°C for 2h. The buffers were added in the following order to wash the magnetic beads: the first step is to use 1ml of low-salt wash buffer, followed by the high-salt wash buffer, and finally add the LiCl wash buffer to the EP tube, the sample was incubated at 4°C for 5min, and let stand on ice for 2min. Samples were centrifuged at 1000rpm and 4°C for 1min, discard the supernatant after centrifugation. In the second step, 1ml of TE buffer was added to the EP tube and the EP tube was incubated at 37°C for 5min. Samples were centrifuged at 1000rpm and 37°C for 1min. Discard the supernatant and wash twice. The beads and Input (stored at -80°C) were eluted with 250µl of Elution Buffer, 10µl of 5M NaCl was added to the eluate, and samples were incubated at 65°C overnight. The DNA was extracted by phenol/chloroform and phenol/chloroform/isoamyl alcohol (25:24:1, pH7.8). DsDNA was then extracted by immunoprecipitation and decrosslinking. Take 14µl of RNase-free water to dissolve the extraction product.
The dsDNA was extracted by immunoprecipitation and de-crosslinking, and the dsDNA stored at -80°C was taken out. The END-IT kit was used to repair the sticky ends to blunt ends. The reaction procedure is as follows: ChIP DNA 8ng, 10x NEB Next end repair buffer 1.5µl, dNTP mix 1.5µl, ATP 1.5µl, NEB NEXT end repair enzyme mix 0.5µl, dH2O up to 15µl. Incubate the reaction tube in a thermal cycler at 25°C for 45 minutes. Then add A-tailing to the blunt end of DNA. The reaction procedure is as follows: End repaired DNA 10µl, NEB Next A-tailing buffer 1.5µl, Klenow (3-5’ exo-) 0.5µl, 2.5mM dATP 2µl, dH2O 1µl. Incubate the reaction tube in a thermal cycler at 37°C for 30 minutes. The third step is to connect the adapter to the DNA. The reaction procedure is as follows: End-Repaired A-tailed DNA 7µl, Indexed adaptor (diluted 1/10 in buffer EB) 1µl, NEB quick ligase 1µl, 10xT4 DNA ligase buffer 1µl. Incubate the reaction tube in a thermal cycler at 20°C for 10 minutes. The size of the DNA fragments was selected using Ampure beads. The required fragment size for the experiment is 300-600 bp. Finally, 10µl RNase-free water was used to dissolve the DNA fragment of the target size. The procedure for adaptor-ligated DNA amplification is as follows: DNA from previous step 10µl, 5x HF buffer 6µl, 10Mm dNTP 0.9µl, primer mix 0.5µl, KAPA HiFi enzyme 0.6µl, dH2O 12µl. Run program: 95°C 3min 1cycle, 98°C 20sec 14cycles, 65°C 30sec 14cycles, 65°C 30sec 14cycles, 65°C 3min 1cycle, 10°C 1cycle. The PCR products were cleaned up and eluted with 14µl EB, and the eluted products were sent for sequencing. The library were sequenced on an Illumina HiSeq Xten systerm with PE150 strategy.

tag: development stage

tag: chip target


title: H4_ChIP_rep3


title: skpo_OG1RF_2


title: 4T1 Allograft TV injection lung met RNA (4T1-tailvein_LuMet1_mouse6_KS67)


title: 4T1 Allograft TV injection lung met RNA (4T1-tailvein_LuMet1_mouse4_KS65)


title: ChIP-seq_PfArp4_H3K9ac_input


title: skpo_OG1RF_1


title: ChIP-seq_PfArp4_GlcN+_H3K9ac


title: N2_OP50_4

value: wild type


title: skpo_OP50_2


title: 1773_1_WT_Cold4h

city: Albany

first: Sneha

last: Damal Villivalam

address: 485 Ohlone Ave, Apt 210

department: NST

institute: UC Berkeley

data_processing:
RNA-seq reads were aligned to UCSC mm10 using STAR aligner and uniquely aligned reads were retained for downstream analysis. After filtering rRNA and mitochondrial reads, gene expression levels were measured using featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: excel file containing raw read count and RPKM-normalized count for each gene

source_name: Inguinal white adipose tissue

growth_protocol: Tet floxed mice or Tet1 KO mice were maintained on chow diet

extract_protocol:
Tissues were removed, flash frozen on liquid nitrogen. For RNA seq,  RNA was harvested using Trizol reagent. Qiagen Rneasy mini kit Sample Prep Kit (Cat#74106) was used with 1 ug of total RNA for the construction of sequencing libraries.  and sequencing was performed on the BGISEQ.
Libraries were prepared by the genome sequencing facility following manufacturers instructions for BGILibrary prep kit for RNA seq.

treatment_protocol: Mice were kept at room temperture or exposed to cold temperature 4 C for 4 hours.

value: C57BL/6 Tet1 adipose specific Floxed WT control mice

value: WT

tag: tissue

value: Inguinal white adipose tissue


title: H4_ChIP_rep1


title: 1814_1_KO_RT

value: C57BL/6 Tet1 adipose specific KO mice

value: Tet1 KO

tag: treatment

value: RT


title: 4T1 Allograft orthotopic injection primary tumor RNA (4T1-ortho_PT_mouse11_KS23)

city: Bethesda

value: BALB

value: unknown

value: Allograft orthotopic injection


title: PfArp4_R_rep1_RNAseq

tag: developmental stage

value: Homo sapiens


title: ChIP-seq_PfArp4_H2A.Z_GlcN+_input

data_processing:
Low-quality and adaptor sequences were trimmed from the reads using cutadapt (v1.16) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Bowtie2 (v2.3.4.3) with parameters: -N 0 --no-discordant --no-mixed --no-unal.
The Samtools (v1.9) was used to transfer the mapping results from sam format to position sorted bam format. Next, the duplicated reads were removed by markdup from sambamba (v0.6.8).
Then, the bam files were converted to bigwig files using bamCoverage from the deeptools suite (v3.1.3) with parameters: --normalizeUsing RPKM --binSize 25. The bigwig files from ChIP sample were normalized to input sample by bigwigCompare from the deeptools suite (v3.1.3) with parameters: –operation log2 --pseudocount 1. The Integrative Genomics Viewer (IGV) was used to show the signal of histone modification in certain genomic region in a track view.
The H2A.Z peaks were called by MACS2 with parameters:-g 2.33e7 -f BAMPE.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: H2A.Z enrichment along the whole genome file  for different samples

extract_protocol:
In this experiment, highly synchronized infected red blood cells (iRBC) were collected and centrifuged to remove a portion of the supernatant. Parasites were extracted with 0.15% saponin and washed with pre-chilled PBS until the supernatant was clear. 2ml Lysis Buffer (containing 100× protease inhibitor and 100× DTT) was added to the sample, mixed well, and leave it on ice for 30min to lyse the body. The lysate was placed in a grinding tube and 50ul of 10% NP-40 was added. The cell debris was subjected to liquid phase ultrasound, after centrifuging the ultrasound product, took the supernatant and took 20ul of the supernatant as input (input was stored at -80°C). 100µl of salmon sperm DNA Agrose magnetic beads (50µl/ml) and protease inhibitor were added to the remaining supernatant, samples were incubated overnight. After overnight incubation, 4ug of anti-HA antibody and IgG antibody were added and incubated at 4°C for 2h. The buffers were added in the following order to wash the magnetic beads: the first step is to use 1ml of low-salt wash buffer, followed by the high-salt wash buffer, and finally add the LiCl wash buffer to the EP tube, the sample was incubated at 4°C for 5min, and let stand on ice for 2min. Samples were centrifuged at 1000rpm and 4°C for 1min, discard the supernatant after centrifugation. In the second step, 1ml of TE buffer was added to the EP tube and the EP tube was incubated at 37°C for 5min. Samples were centrifuged at 1000rpm and 37°C for 1min. Discard the supernatant and wash twice. The beads and Input (stored at -80°C) were eluted with 250µl of Elution Buffer, 10µl of 5M NaCl was added to the eluate, and samples were incubated at 65°C overnight. The DNA was extracted by phenol/chloroform and phenol/chloroform/isoamyl alcohol (25:24:1, pH7.8). DsDNA was then extracted by immunoprecipitation and decrosslinking. Take 14µl of RNase-free water to dissolve the extraction product.
The dsDNA was extracted by immunoprecipitation and de-crosslinking, and the dsDNA stored at -80°C was taken out. The END-IT kit was used to repair the sticky ends to blunt ends. The reaction procedure is as follows: ChIP DNA 8ng, 10x NEB Next end repair buffer 1.5µl, dNTP mix 1.5µl, ATP 1.5µl, NEB NEXT end repair enzyme mix 0.5µl, dH2O up to 15µl. Incubate the reaction tube in a thermal cycler at 25°C for 45 minutes. Then add A-tailing to the blunt end of DNA. The reaction procedure is as follows: End repaired DNA 10µl, NEB Next A-tailing buffer 1.5µl, Klenow (3-5’ exo-) 0.5µl, 2.5mM dATP 2µl, dH2O 1µl. Incubate the reaction tube in a thermal cycler at 37°C for 30 minutes. The third step is to connect the adapter to the DNA. The reaction procedure is as follows: End-Repaired A-tailed DNA 7µl, Indexed adaptor (diluted 1/10 in buffer EB) 1µl, NEB quick ligase 1µl, 10xT4 DNA ligase buffer 1µl. Incubate the reaction tube in a thermal cycler at 20°C for 10 minutes. The size of the DNA fragments was selected using Ampure beads. The required fragment size for the experiment is 300-600 bp. Finally, 10µl RNase-free water was used to dissolve the DNA fragment of the target size. The procedure for adaptor-ligated DNA amplification is as follows: DNA from previous step 10µl, 5x HF buffer 6µl, 10Mm dNTP 0.9µl, primer mix 0.5µl, KAPA HiFi enzyme 0.6µl, dH2O 12µl. Run program: 95°C 3min 1cycle, 98°C 20sec 14cycles, 65°C 30sec 14cycles, 65°C 30sec 14cycles, 65°C 3min 1cycle, 10°C 1cycle. The PCR products were cleaned up and eluted with 14µl EB, and the eluted products were sent for sequencing. The library were sequenced on an Illumina HiSeq Xten systerm with PE150 strategy.


title: 4T1 Allograft orthotopic injection primary tumor RNA (4T1-ortho_PT_mouse10_KS22)

tag: mouse strain


title: 1810_1_WT_RT


title: 4T1 Allograft orthotopic injection primary tumor RNA (4T1-ortho_PT_mouse9_KS21)


title: 1788_1_WT_RT


title: N2_OP50_1


title: N2_OP50_3


title: N2_OG1RF_3


title: N2_OP50_2


title: ChIP-seq_PfArp4_GlcN+_H2A.Z


title: ChIP-seq_PfArp4_H2A.Z_input


title: ChIP-seq_PfArp4_H3K9ac


title: N2_OG1RF_2


title: 4T1 Allograft orthotopic injection primary tumor RNA (4T1-ortho_PT_mouse12_KS24)


title: 4T1 Allograft orthotopic injection primary tumor RNA (4T1-ortho_PT_mouse2_KS20)


title: 4T1 Allograft orthotopic injection primary tumor RNA (4T1-ortho_PT_mouse1_KS19)


title: 1786_1_KO_Cold4h


title: 4T1 Allograft orthotopic injection lung met RNA (4T1-ortho_LuMet4_mouse11_KS29)


title: ChIP-seq_PfArp4_H2A.Z


title: 4T1 Allograft orthotopic injection lung met RNA (4T1-ortho_LuMet7_mouse12_KS30)


title: N2_OG1RF_1


title: 1782_1_KO_Cold4h


title: 1783_1_WT_Cold4h


title: 1781_1_KO_RT


title: ChIP-seq_PfArp6_IgG

data_processing:
Low-quality and adaptor sequences were trimmed from the reads using cutadapt (v1.16) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Bowtie2 (v2.3.4.3) with parameters: -N 0 --no-discordant --no-mixed --no-unal.
The Samtools (v1.9) was used to transfer the mapping results from sam format to position sorted bam format. Next, the duplicated reads were removed by markdup from sambamba (v0.6.8).
Then, the bam files were converted to bigwig files using bamCoverage from the deeptools suite (v3.1.3) with parameters: --normalizeUsing RPKM --binSize 25. The bigwig files from ChIP sample were normalized to input sample by bigwigCompare from the deeptools suite (v3.1.3) with parameters: –operation log2 --pseudocount 1. The Integrative Genomics Viewer (IGV) was used to show the signal of histone modification in certain genomic region in a track view.
The peaks were called by MACS2 with parameters:-g 2.33e7 -f BAMPE.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: Arp4 and Arp6 enrichment along the whole genome file  for different samples

extract_protocol:
In this experiment, highly synchronized infected red blood cells (iRBC) were collected and centrifuged to remove a portion of the supernatant. Parasites were extracted with 0.15% saponin and washed with pre-chilled PBS until the supernatant was clear. 2ml Lysis Buffer (containing 100× protease inhibitor and 100× DTT) was added to the sample, mixed well, and leave it on ice for 30min to lyse the body. The lysate was placed in a grinding tube and 50ul of 10% NP-40 was added. The cell debris was subjected to liquid phase ultrasound, after centrifuging the ultrasound product, took the supernatant and took 20ul of the supernatant as input (input was stored at -80°C). 100µl of salmon sperm DNA Agrose magnetic beads (50µl/ml) and protease inhibitor were added to the remaining supernatant, samples were incubated overnight. After overnight incubation, 4ug of anti-Ty1 antibody and IgG antibody were added and incubated at 4°C for 2h. The buffers were added in the following order to wash the magnetic beads: the first step is to use 1ml of low-salt wash buffer, followed by the high-salt wash buffer, and finally add the LiCl wash buffer to the EP tube, incubate at 4°C for 5min, and let stand on ice for 2min. Samples were centrifuged at 1000rpm and 4°C for 1min, discard the supernatant after centrifugation. In the second step, 1ml of TE buffer was added to the EP tube and the sample was incubated at 37°C for 5min. Samples were centrifuged at 1000rpm and 37°C for 1min. Discard the supernatant and wash twice. The beads and Input (stored at -80°C) were eluted with 250µl of Elution Buffer, 10µl of 5M NaCl was added to the eluate, and samples were incubated at 65°C overnight. The DNA was extracted by phenol/chloroform and phenol/chloroform/isoamyl alcohol (25:24:1, pH7.8). DsDNA was then extracted by immunoprecipitation and decrosslinking. Take 14µl of RNase-free water to dissolve the extraction product.
The dsDNA was extracted by immunoprecipitation and de-crosslinking, and the dsDNA stored at -80°C was taken out. The END-IT kit was used to repair the sticky ends to blunt ends. The reaction procedure is as follows: ChIP DNA 8ng, 10x NEB Next end repair buffer 1.5µl, dNTP mix 1.5µl, ATP 1.5µl, NEB NEXT end repair enzyme mix 0.5µl, dH2O up to 15µl. Incubate the reaction tube in a thermal cycler at 25°C for 45 minutes. Then add A-tailing to the blunt end of DNA. The reaction procedure is as follows: End repaired DNA 10µl, NEB Next A-tailing buffer 1.5µl, Klenow (3-5’ exo-) 0.5µl, 2.5mM dATP 2µl, dH2O 1µl. Incubate the reaction tube in a thermal cycler at 37°C for 30 minutes. The third step is to connect the adapter to the DNA. The reaction procedure is as follows: End-Repaired A-tailed DNA 7µl, Indexed adaptor (diluted 1/10 in buffer EB) 1µl, NEB quick ligase 1µl, 10xT4 DNA ligase buffer 1µl. Incubate the reaction tube in a thermal cycler at 20°C for 10 minutes. The size of the DNA fragments was selected using Ampure beads. The required fragment size for the experiment is 300-600 bp. Finally, 10µl RNase-free water was used to dissolve the DNA fragment of the target size. The procedure for adaptor-ligated DNA amplification is as follows: DNA from previous step 10µl, 5x HF buffer 6µl, 10Mm dNTP 0.9µl, primer mix 0.5µl, KAPA HiFi enzyme 0.6µl, dH2O 12µl. Run program: 95°C 3min 1cycle, 98°C 20sec 14cycles, 65°C 30sec 14cycles, 65°C 30sec 14cycles, 65°C 3min 1cycle, 10°C 1cycle. The PCR products were cleaned up and eluted with 14µl EB, and the eluted products were sent for sequencing. The library were sequenced on an Illumina HiSeq Xten systerm with PE150 strategy.


title: ChIP-seq_PfArp6_rep2


title: ChIP-seq_PfArp6_rep1


title: ChIP-seq_PfArp4_input_rep3


title: 4T1 Allograft orthotopic injection lung met RNA (4T1-ortho_LuMet1_mouse9_KS27)


title: 4T1 Allograft orthotopic injection lung met RNA (4T1-ortho_LuMet2_mouse1_KS25)


title: 4T1 Allograft orthotopic injection lung met RNA (4T1-ortho_LuMet1_mouse2_KS26)


title: ChIP-seq_PfArp4_input_rep2