title: FBXL19fl_ES_TAM_rep1_CapC_set1

description:
processed data file:
Tpm4_id2969160_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Megf10_id5749717_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ckap2_id2847141_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ccdc177_id4213506_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ankrd6_id1387983_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Pdp2_id3050157_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Kdm7a_id2153561_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
AW146154_id2537634_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Slc47a2_id3871357_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Asic2_id3923197_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Tmco1_id411517_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Evi5l_id2802851_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Arrdc3_id4506220_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Cep126_id3124148_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
C77370_id6243560_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Lonrf1_id2881524_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ermp1_id5897272_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Polr3a_id4659089_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ccdc142_id2265006_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Stat5b_id3969874_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Tiam2_id5387471_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ednrb_id4854605_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Syce1_id2788219_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ppfia4_id331310_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
1500009L16Rik_id3612757_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Dnajc13_id3362998_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Adamtsl3_id2641148_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Pak3_id6344953_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
E030018B13Rik_id2596176_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Sema6d_id778751_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Inafm2_id765330_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Cabp1_id1973991_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Prdx3_id5973264_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Aplp1_id2508467_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Arg1_id3465762_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Rhob_id4035130_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Casp2_id2161600_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Cdh6_id4930340_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Cnn2_id3603335_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Col8a1_id5290658_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Epha5_id1896100_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Mpzl2_id3218449_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Fasn_id4018679_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Fzd7_id142589_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Fzd8_id5631876_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Gas1_id4452406_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Hoxb1_id3958722_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Hoxb5_id3958568_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Hpgd_id2929245_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Klf2_id2969645_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Lfng_id2036913_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Mapkapk2_id323408_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Mcm3_id47198_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Mmp15_id3027407_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Mmp2_id3020918_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Gadd45b_id3605594_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Pla2r1_id622128_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ptprn_id180345_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ptrf_id3970218_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
S100a10_id1149986_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Nkx1-2_id2768203_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Scd1_id5933791_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Supt4a_id3937444_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Tal2_id1439711_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Hnf1a_id1973455_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ttf1_id545321_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Vipr2_id4301021_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Abcg1_id5455875_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Asic1_id5143940_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Capn2_id449358_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Cd24a_id3512611_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Cdh11_id3045509_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Chat,Slc18a3_id4678235_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
S1pr3_id4431509_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Efs_id4735760_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ephb3_id5201786_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Fhl3_id1618914_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Gsto1_id5942000_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Hoxb3_id3958676_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Igfbp5_id174464_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Itga5_id5153214_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Lama3_id5639740_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Large_id2972265_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ndufa4_id2086878_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Nfkbia_id4151479_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Numbl_id2500220_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Pou3f1_id1618825_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Prlr_id4923288_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Pros1_id5303530_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ptprd_id1501257_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Scnn1g_id2741113_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
St8sia1_id2413404_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Sox2_id1003349_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Tcea3_id1647459_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Tubb5_id5468158_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ercc5_id104061_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Amfr_id3024072_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
C1ql1_id3975329_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Creg1_id407574_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Twf2_id3367775_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
St6galnac5_id1294639_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Asns_id2075943_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Fkbp9_id2196958_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Cpt1a_id5832120_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Frg1_id2894123_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Hebp1_id2394582_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Lrpap1_id1775334_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Atp5l_id3218128_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Tnfrsf19_id4750989_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Scly_id220349_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Gipc2_id1292782_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Insm1_id832241_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ctnnal1_id1447659_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ntsr1_id917074_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Slc1a4_id3770078_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ppie_id1615141_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Htra1_id2764107_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Arl10_id4439192_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Angptl4_id5462755_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Egr4_id2270850_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Snrpb2_id824501_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Shank3_id5119599_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Isl1_id4592795_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Slc4a8_id5146726_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Foxj2_id2362399_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Paqr4_id5438307_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Tbc1d20_id847836_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Rexo2_id3226797_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Tomm7_id1746923_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Llph_id3700641_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Tma16_id2954862_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Mrps14_id394136_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Isoc1_id5753246_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Polr2e_id3603475_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Mrps25_id2287411_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Sorcs3_id5942915_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Uqcrfs1_id4380171_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Tril_id2189634_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Eef1g_id5846437_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Snrpd3_id3591800_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Map1lc3b_id3091625_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Pkp2_id5188447_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Dph2_id1601224_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ufm1_id1050580_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Tmem86a_id2552408_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Mrpl19_id2261989_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Cdc42ep3_id5577780_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ndufb4_id5241422_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
1110007C09Rik_id4425616_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Mocos_id5670125_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Dus1l_id4018609_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Slc52a3_id847064_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Rhpn2_id2522257_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Nkd2_id4487550_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Wdr89_id4201123_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Lrpprc_id5590892_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Phykpl_id3847043_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Zfp493_id4472135_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Ptchd4_id5486398_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Zbtb8a_id1630475_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Irak3_id3700588_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Zfp819_id2543728_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Pck2_id4737370_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Pcdh1_id5703772_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Fam101b_id3908213_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Sgpp1_id4201286_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Hspa8_id3208123_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Kcnn1_id2965914_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Spred2_id3769103_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Tshz2_id890477_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Acss1_id843594_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Nphs2_id384824_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Arhgef5_id2164246_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Abhd17c_id2645639_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Cdcp1_id3409272_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Cisd1_id3581396_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Hoxb2_id3958685_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Smim3_id5757976_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Socs7_id3961207_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Nlgn1_id982921_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Susd4_id449923_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Zswim6_id4572766_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Zfp503_id4652828_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Pim3_id5118011_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Lace1_id3510061_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Lrrc3b_id4635973_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Cpped1_id5177046_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Aars_id3066336_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Prss50_id3379869_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Slc1a3_id4919615_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Rbm17_id500778_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Cd109_id3300227_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Cadm4_id2492585_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Gpr156_id5242053_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Cmtm4_id3049681_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Acsf2_id3954253_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Nfkbid_id2508402_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Oscp1_id1622319_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Rbm34_id3104231_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Sh3rf3_id3550886_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Tbcel_id3212157_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Galnt18_id2716596_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Mamdc2_id5882597_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Fbxl22_id3270912_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Mael_id408645_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Mroh1_id5086983_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Zfp770_id754414_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Prtg_id3286160_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Aard_id5025738_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Rab11fip4_id3917225_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Pld5_id434386_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Nwd2_id1845589_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Samd12_id5030415_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Arl4c_id214048_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Arap2_id1843354_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Tagln2_id424572_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Zfp365_id3573106_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Mapkapk3_id3370575_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Champ1_id2826164_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Tnrc6c_id4011171_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Dagla_id5850122_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Bahcc1_id4017212_FBXL19_ES_TAM_bg.bed_bg_sorted.bw
Mex3d_id3604301_FBXL19_ES_TAM_bg.bed_bg_sorted.bw

value: tamoxifen (OHT)

value: 96 hr


title: Lung.hv.T5

status: Public on Jan 21 2020

type: SRA

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
T5poumonHV
c-myc Igh transgenic mouse.
processed data file: kallisto_tpm.txt

library_source: transcriptomic

data_processing:
Reads quality control using fastQC and Fastq-scren.
Kallisto v0.43 quantification versus cdna and ncrna from Ensembl release 91 of mm10 build.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: kallisto_tpm.txt: Matrix text file with tpm estimates; rows are transcripts, columns are samples.

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
Trizol extraction.
500ng of total RNA were depleted of ribosomal RNA, ligated, reverse transcribed and amplified (12 cycles) with the reagents from the TruSeq Stranded Total RNA kit (Illumina). Libraries were quantified with the Bioanalyzer 2100 Kit (Agilent) and Qubit (Thermo Fisher). 4nM of libraries were then diluted and denatured according to the Illumina recommendations. Paired-end 2x150bp reads were sequenced on an Illumina Nextseq 500 sequencer.

tag: cell type

value: Malignant B cells

tag: genotype/variation

value: hv


title: Ctl.hv.s

description:
sample8
c-myc Igh transgenic mouse.
processed data file: kallisto_tpm.txt

source_name: Spleen

value: Non-malignant B cells

tag: treatment

value: LPS


title: Lung.hv.T1

description:
T1poumonHV
c-myc Igh transgenic mouse.
processed data file: kallisto_tpm.txt


title: Ctl.cr.s

description:
sample6
c-myc Igh transgenic mouse.
processed data file: kallisto_tpm.txt

value: cr


title: Ctl.hv.ns

description:
sample4
c-myc Igh transgenic mouse.
processed data file: kallisto_tpm.txt


title: Ctl.co.s

description:
sample7
c-myc Igh transgenic mouse.
processed data file: kallisto_tpm.txt

value: co


title: Ctl.cr.ns

description:
sample2
c-myc Igh transgenic mouse.
processed data file: kallisto_tpm.txt


title: Ctl.co.ns

description:
sample3
c-myc Igh transgenic mouse.
processed data file: kallisto_tpm.txt


title: Ctl.wt.s

description:
sample5
processed data file: kallisto_tpm.txt

value: wt


title: Ctl.wt.ns

description:
sample1
processed data file: kallisto_tpm.txt


title: Shh-/-_ATAC_rep1

city: Seattle

first: Rachel

last: Lex

state: WA

address: 1100 Fairview Ave N

country: USA

institute: Fred Hutchinson Cancer Center

library_source: genomic

data_processing:
Base calling was done using Illumina bcl2fasq version 1.8.4 or version 2.17.1.
Raw sequencing reads were mapped to mouse mm10 genome using Bowtie2 (version 2.2.5).
Peak calling was done using MACS (version 2.1.0) with default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: narrowPeak files: Peaks called by MACS.

molecule: genomic DNA

source_name: posterior forelimb bud

extract_protocol:
Limb buds were dissected, dissociated using 100ug/mL Liberase (Roche 05401119001) in PBS at 37 degrees for 6 minutes, and cells were counted. 5,000 cells per sample were lysed and immediately added to a transpose reaction for 30 min at 37C (Illumina FC-121-1030).
After the transposase reaction was complete, the entire reaction was put into a PCR library amplification reaction. Barcoded primers, specific to the inserted transposon sequence, amplified accessible chromatin fragments. Fragments were amplified for 18 PCR cycles using NEBNext High Fidelity 2x PCR Master Mix (M0541S). Excess primers were removed from PCR reactions using AmpureXP beads (A63880) at a ratio of 0.8x beads.

tag: strain/background

value: Swiss Webster

value: Shh-/-

tag: tissue

value: posterior forelimb bud

tag: age

value: E10.5 (35 somites)


title: WT_ATAC_rep1

value: wild type


title: WT_ATAC_rep2


title: Shh-/-_ATAC_rep2


title: Shh-/-_H3K27me3 rep 2

city: Austin

first: Steven

last: Vokes

state: Texas

address: 2500 Speedway, Stop A4800

department: Department of Molecular Biosciences, Institute for Cellular & Molecular Biology

institute: The University of Texas at Austin

data_processing:
Base calling was done using Illumina bcl2fasq version 1.8.4 or version 2.17.1
Raw sequencing reads are mapped to mouse mm10 genome using Bowtie2 (version 2.2.5).
Peak calling was done using Cisgenome with default parameters.  When available, Input data was incorporated in the peak calling.
For differential H3K27ac and H3K4me2 peak analysis and peak classifications, Cisgenome was used to call peaks for Wild Type and Shh-/- (or control and Purmorphamine treated NIH3T3 cells) respectively.  For the union of peaks from Wild Type and Shh-/-, we calculated the number of H3K27ac reads for WT H3K27ac, WT input, Shh-/- H3K27ac and Shh-/- input samples that overlap with each of the union peaks. The read counts are then divided by library size and log2 transformed after adding a pseudo count of 1 to generate the normalized read counts. We use Limma [2] to perform differential analysis in order to independently compare WT H3K27ac vs WT input, Shh-/- H3K27ac vs Shh-/- input, and WT H3K27ac vs Shh-/- H3K27ac to obtain adjusted p-values.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files: aligned sequencing reads to mm10 genome using Bowtie2 and converted to bedgraph
Supplementary_files_format_and_content: txt files: peaks called by Cisgenome

source_name: forelimb bud

extract_protocol:
Cells were fixed for 15 minutes at room temperature with 1% formaldehyde then lysed.  After cell lysis, chromatin was sheared in shearing buffer containing 0.25% SDS using a Covaris S2 focused ultrasonicator.   Sheared chromatin was incubated with antibody coated dynabead preparations (1ug antibody with 20ul beads) overnight.  Beads were washed 5 times with RIPA buffer (1% NP40, 0.7% Sodium Deoxycholate, 1mM EDTA pH8, 50mM Hepes-KOH pH7.5, 2% w/v Lithium Chloride) and then eluted at 70°C for 15 minutes in elution buffer (50mM TRIS pH 8, 10mM EDTA  pH 8, 1% SDS).  Crosslinks were reversed overnight at 70°C and chromatin was purified and concentrated by phenol chloroform extraction and EtOH precipitation.
One third of each ChIP sample was used for library preparation.  Library preparation was done according to the Broad Pond method, (PMCID: PMC3091298) using the NEBNext library preparation kit (NEB E6040L) using non-standard 15 cycles of PCR amplification.

treatment_protocol: limbs were dissociated using 100ug/mL Liberase (Roche 05401119001) in PBS at 37 degrees for 6 minutes.

tag: strain background

tag: tissue/chip rxn

value: ~400,000 cells/ChIP

tag: chip antibody

value: H3K27me3 (abcam ab6002)

tag: genotype or treatment


title: Shh-/-_H3K27me3 rep 2_input


title: HDAC_ChIP_2

data_processing:
Base calling was done using Illumina bcl2fasq version 1.8.4 or version 2.17.1
Raw sequencing reads are mapped to mouse mm10 genome using Bowtie2 (version 2.2.5).
Peak calling was done using CisGenome with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files: peaks called by CisGenome

source_name: 3 litters FL+ HL

extract_protocol:
Limb buds were dissected and limbs were dissociated using 100ug/mL Liberase (Roche 05401119001) in PBS at 37 degrees for 6 minutes.
ChIP libraries were prepared with NEBNext Ultra II Library Prep Kit or Diagenode MicroPlex Library Prep, with 15 cycles of library amplifications. Excess primers were removed from PCR reactions using AmpureXP beads (A63880) at a ratio of 0.8x beads.

value: forelimb and hindlimb buds

tag: Stage

value: HDAC1 antibody (Abcam ab7028)


title: Shh-/-_H3K27me3 rep 1_input


title: Shh-/-_H3K27me3 rep 1


title: Lung.co.T34

description:
T34poumonCo
c-myc Igh transgenic mouse.
processed data file: kallisto_tpm.txt


title: FBXL19fl_ES_UNT_rep1_CapC_set1

city: Oxford

first: Angelika

last: Feldmann

state: England

address: South Parks Road

country: United Kingdom

institute: University of Oxford, Department of Biochemistry

description:
processed data file:
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Lfng_id2036913_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Mapkapk2_id323408_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
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Itga5_id5153214_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Lama3_id5639740_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Large_id2972265_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Ndufa4_id2086878_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Nfkbia_id4151479_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Numbl_id2500220_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Pou3f1_id1618825_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Prlr_id4923288_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Pros1_id5303530_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Ptprd_id1501257_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Scnn1g_id2741113_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
St8sia1_id2413404_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Sox2_id1003349_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Tcea3_id1647459_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Tubb5_id5468158_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
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Amfr_id3024072_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
C1ql1_id3975329_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Creg1_id407574_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
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St6galnac5_id1294639_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Asns_id2075943_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Fkbp9_id2196958_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Cpt1a_id5832120_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Frg1_id2894123_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Hebp1_id2394582_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Lrpap1_id1775334_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Atp5l_id3218128_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Tnfrsf19_id4750989_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Scly_id220349_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Gipc2_id1292782_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Insm1_id832241_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Ctnnal1_id1447659_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Ntsr1_id917074_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
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Isl1_id4592795_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
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Paqr4_id5438307_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
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Rhpn2_id2522257_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
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Wdr89_id4201123_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Lrpprc_id5590892_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Phykpl_id3847043_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Zfp493_id4472135_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Ptchd4_id5486398_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Zbtb8a_id1630475_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Irak3_id3700588_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Zfp819_id2543728_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Pck2_id4737370_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Pcdh1_id5703772_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Fam101b_id3908213_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Sgpp1_id4201286_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Hspa8_id3208123_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Kcnn1_id2965914_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
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Tshz2_id890477_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Acss1_id843594_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Nphs2_id384824_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Arhgef5_id2164246_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Abhd17c_id2645639_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Cdcp1_id3409272_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Cisd1_id3581396_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Hoxb2_id3958685_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Smim3_id5757976_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Socs7_id3961207_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Nlgn1_id982921_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Susd4_id449923_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Zswim6_id4572766_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Zfp503_id4652828_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Pim3_id5118011_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Lace1_id3510061_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Lrrc3b_id4635973_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Cpped1_id5177046_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Aars_id3066336_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Prss50_id3379869_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Slc1a3_id4919615_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Rbm17_id500778_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Cd109_id3300227_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Cadm4_id2492585_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Gpr156_id5242053_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Cmtm4_id3049681_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Acsf2_id3954253_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Nfkbid_id2508402_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Oscp1_id1622319_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Rbm34_id3104231_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Sh3rf3_id3550886_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Tbcel_id3212157_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Galnt18_id2716596_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Mamdc2_id5882597_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Fbxl22_id3270912_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Mael_id408645_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Mroh1_id5086983_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Zfp770_id754414_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Prtg_id3286160_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Aard_id5025738_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Rab11fip4_id3917225_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Pld5_id434386_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Nwd2_id1845589_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Samd12_id5030415_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Arl4c_id214048_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Arap2_id1843354_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Tagln2_id424572_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Zfp365_id3573106_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Mapkapk3_id3370575_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Champ1_id2826164_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Tnrc6c_id4011171_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Dagla_id5850122_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Bahcc1_id4017212_FBXL19_ES_UNT_bg.bed_bg_sorted.bw
Mex3d_id3604301_FBXL19_ES_UNT_bg.bed_bg_sorted.bw

data_processing:
library strategy: CaptureC
For CaptureC, paired-end reads were aligned and filtered for HiC artefacts using HiCUP (Wingett S, et al. (2015)) and Bowtie2 (Langmead and Salzberg, 2012) with fragment filter set to 100-800bp. Read counts of reads aligning to captured gene promoters and interaction scores (=significant interactions) were then called  by CHiCAGO (Cairns et al., 2016).
For visualisation of CaptureC data weighted pooled read counts from chicago data files were normalized to total read count aligning to captured gene promoters in the sample and further to the number of promoters in the respective capture experiment. Bigwig files were generated from these normalized read counts.
For comparative boxplot analysis interactions called by chicago (score >= 5) across all samples were aggregated and interactions with a distance of less than 4 DpnII fragments were merged to a single interaction peak. For each interaction peak we then quantified mean normalized read count and chicago score of all overlapping DpnII fragments.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files showing the genome coverage of normalized read counts for each sample and each promoter were generated from chicago data object.

source_name: mESCs_untreated control, CaptureC

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor. Human HEK293T cells used for calibrated ChIP-seq were grown at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), and 0.5 mM beta-mercaptoethanol (Life Technologies). Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin solution (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech).

extract_protocol:
CaptureC libraries were prepared as described previously (Hughes et al., Nature Genetics 2014). Briefly, 10 Million mouse ES cells were trypsinized, collected in 50ml falcon tubes in 9.3ml media and crosslinked with 1.25ml 16% formaldehyde for 10min at room temperature. Cells were quenched with 1.5M glycine, washed with PBS and lysed for 20 minutes at 4oC lysis buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40, supplemented with complete proteinase inhibitors) prior to snap freezing in 1ml lysis buffer at -80oC.
Lysates were then thawed on ice, pelleted and resuspended in 650µl 1x DpnII buffer (NEB). Three 1.5ml tubes with 200µl lysate each were treated in parallel with SDS (0.28% final concentration, 1hr, 37 oC, interval shaking 500rpm, 30sec on/30sec off), quenched with trypsin (1.67% final concentration, 1hr, 37 oC, interval shaking 500rpm, 30sec on/30sec off) and subjected to a 24 hour digestion with 3x10µl DpnII (homemade, 37 oC, interval shaking 500rpm, 30sec on/30sec off). Each chromatin aliquot was independently ligated with 8 µl T4 Ligase (240 U) in a volume of 1440µl (20 hours, 16oC). Following this, the nuclei containing ligated chromatin were pelleted to remove any non-nuclear chromatin, reverse-crosslinked and the ligated DNA was phenol-chloroform purified. The sample was resupended in 300µl water and sonicated 13x (Pico Bioruptor, 30sec on, 30sec off) or until a fragment size of approximately 200bp was reached. Fragments were size selected using AmpureX beads (Beckman Coulter: A63881, selection ratios: 0.85x / 0.4x). 2x 1-5µg of DNA were adaptor ligated and indexed using the NEBNext DNA library Prep Reagent Set (New England Biolabs: E6040S/L) and NEBNext Multiplex Oligos for Illumina Primer sets 1 (New England: E7335S/L) and 2 (New England: E7500S/L). The libraries were amplified 7x using Herculase II Fusion Polymerase kit (Agilent: 600677). Libraries were hybridized in teh following way: Probes were designed using the online tool by the Hughes lab (CapSequm: http://apps.molbiol.ox.ac.uk/CaptureC/cgi-bin/CapSequm.cgi) to be either 120bp (Sox2) or 70bp long each, two probes for each promoter of interest. The probes were pooled at a 2.9nM each and the samples were multiplexed by mass prior to hybridization. Hybridization was carried out using the Nimblegen SeqCap system (Roche, Nimblegen SeqCap EZ HE-oligo kit A # 06777287001, Nimblegen SeqCap EZ HE-oligo kit B # 06777317001, Nimblegen SeqCap EZ Accessory kit v2 # 07145594001, Nimblegen SeqCap EZ Hybridisation and wash kit # 05634261001) according to Roche protocol for 72 hours followed by a 24 hours hybridization (double Capture). The captured libraries were sequenced on Illumina NextSeq.

treatment_protocol: To induce conditional removal of the Fbxl19 CxxC domain or Med13 and Med13l in FBXL19fl and MED13/13lfl ESC lines, cells were treated with 800nM 4-hydroxytamoxifen (TAM) for 96 hours. To induce differentiation, ES cells were treated with 1uM retinoic acid (RA) for 72 hours.

value: Mouse embryonic stem cells

tag: cell line background

tag: cell line

tag: genotype

value: Fbxl19-CxxCfl/fl; Rosa26::ERT2-Cre

tag: replicate

tag: treatment agent

tag: treatment time point

value: 0 hr


title: FBXL19fl_RA_UNT_rep1_CapC_set2

description:
processed data file:
Fli1_id3186524_FBXL19_RA_UNT_bg.bed_bg_sorted.bw
Mn1_id1964984_FBXL19_RA_UNT_bg.bed_bg_sorted.bw
Kif26b_id440003_FBXL19_RA_UNT_bg.bed_bg_sorted.bw
Dlk1_id4283906_FBXL19_RA_UNT_bg.bed_bg_sorted.bw
Spry1_id1010657_FBXL19_RA_UNT_bg.bed_bg_sorted.bw
Igdcc3_id3267532_FBXL19_RA_UNT_bg.bed_bg_sorted.bw
Col26a1_id2027715_FBXL19_RA_UNT_bg.bed_bg_sorted.bw
Samd14_id3955395_FBXL19_RA_UNT_bg.bed_bg_sorted.bw
Atoh8_id2237664_FBXL19_RA_UNT_bg.bed_bg_sorted.bw

source_name: mESCs_control, retinoic-acid treated (72hr RA), CaptureC

tag: cell type

value: retinoic acid (RA)

value: 72 hr


title: LCH015-14C

type: RNA

city: Houston

first: Carl

last: Allen

state: TX

address: 1102 Bates Street, C1024.25

department: Department of Pediatrics- Cancer

institute: Baylor College of Medicine

description: gene expression data from sorted subpopulations

hyb_protocol: Fragmented and biotinylated cDNA was hybridized to GeneChip™ Human Transcriptome Array 2.0 according to the manufacturer’s procedures.

scan_protocol: Chips were scanned using the Affymetric Gene Chip Scanner 3000

data_processing: Raw data from all samples were normalized using the SST-RMA algorithm implemented in the Affymetrix Expression Console

label: Biotin

organism: Homo sapiens

source_name: CD207 low

label_protocol: Amplified cDNA was fragmented and abeled with the FL-ovation cDNA Biotin module V2.

extract_protocol: Total RNA was purified from sorted subpopulations from peripheral blood and lesion specimens according to the Arcturus PicoPure RNA Isolation Kit protocol. RNA quality was verified using the Pico Chip and all samples have RIN>6. cDNA amplification was performed using the Ovation Pico WTA V2 System according to the manufacturer’s protocol.

tag: disease state

value: Langerhans cell histiocytosis

value: bone

tag: cell subtype

value: CD207 low

tag: individual

value: lesion disease patient 17


title: Lung.cr.T16

description:
T16poumonCr
c-myc Igh transgenic mouse.
processed data file: kallisto_tpm.txt

value: Malignant B cells

tag: genotype/variation

value: cr


title: LCH015-13C

source_name: CD207 high

tag: tissue

value: CD207 high


title: LCH014-13C

value: lesion disease patient 16


title: LCH013-15C

value: lymphocytes

value: lesion disease patient 15


title: LCH015-12C


title: LCH014-15C


title: LCH011-13C

value: lesion disease patient 13


title: LCH010-15C

value: lesion disease patient 12


title: LCH009-15C

value: lesion disease patient 11


title: LCH010-14C


title: LCH014-14C


title: LCH012-13C

value: lesion disease patient 14


title: LCH008-15C

value: lesion disease patient 10


title: LCH008-14C


title: LCH009-13C


title: LCH012-14C


title: LCH012-15C


title: LCH012-12C


title: LCH013-14C


title: LCH011-15C


title: LCH010-13C


title: LCH009-14C


title: LCH010-12C


title: LCH008-13C


title: LCH013-13C


title: LCH014-12C


title: Lung.hv.T16

description:
T16_POU_HV
c-myc Igh transgenic mouse.
processed data file: kallisto_tpm.txt

value: hv


title: LCH011-14C


title: LCH006-12D

value: lung

value: lesion disease patient 8


title: LCH007-15C

value: Langerhans cell histiocytosis

value: bone

value: lesion disease patient 9


title: LCH006-13D


title: LCH008-12C


title: LCH007-13C


title: HD0004-06B

source_name: epidermal langerhans cells

value: healthy

value: skin

value: epidermal langerhans cells

value: PBMC healthy patient 4


title: LCH001-13C

value: CD207 high

value: lesion disease patient 7


title: HD0006-06B

value: PBMC healthy patient 5


title: HD0002-03A

value: blood

value: monocyte

value: PBMC healthy patient 2


title: HD0003-04A

value: myeloid dendritic cells

value: PBMC healthy patient 3


title: HD0005-06B


title: LCH007-14C

value: CD207 low


title: LCH001-15C

value: lymphocytes


title: HD0003-01A


title: HD0001-03A

value: PBMC healthy patient 1


title: HD0003-03A


title: HD0001-04A


title: HD0003-05A

source_name: plasmacytoid dendritic cell

value: plasmacytoid dendritic cell


title: HD0002-05A

value: plasmacytoid dendritic cells


title: HD0002-02A

value: healthy


title: LCH001-14C

value: Langerhans cell histiocytosis

value: bone


title: LCH001-12C


title: LCH006-14D

value: lung

value: lesion disease patient 8


title: HD0003-02A


title: HD0001-02A


title: LCH006-15D


title: intact animal, replicate 3

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to mm10 using STAR2.4.0
Count read using HT-seq0.6.1 using mm10 RefSeq as reference
Normalization (TMM), and differential expression analysis using EdgeR
Genome_build: mm10

source_name: TRAPed mRNA from motor cortex

extract_protocol:
Three adult mice were pooled for each sample and three biological replicates were collected for each condition. All polysome puriﬁcations and mRNA extractions were carried out as described previously (Heiman, Schaefer et al. 2008).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For mouse-donor studies, grafting was performed 1 week after T1 dorsal column wire-knife lesion. Embryonic day 12 (E12) spinal cords from transgenic GFP-mice were dissected in ice cold HBSS, digested in 0.25% Trypsin for 20 min at 37C, washed 3 times with 10% FBS in Neurobasal medium, triturated in 5 ml Neurobasal medium + B27, filtered with 70 um mesh, spun at 200g for 5 min at room temperature, resuspended in 2 ml Neurobasal + B27 and kept on ice. Before grafting cells were spun at 200g for 3 min at room temperature, supernatant was aspirated and cell pellets were resuspended at a concentration of 200,000 cells/μl in a fibrin matrix (25 mg/ml fibrinogen and 25 U/ml thrombin, Sigma F6755 and T5772) containing growth factors to support graft survival (Kadoya, Lu et al. 2016): BDNF (50 μg/ml, Peprotech, 452-02), neurotrophin-3 (NT-3; 50 μg/ml, Peprotech, 450-03), platelet-derived growth factor (PDGF-AA; 10 μg/ml, Sigma, P3076), insulin-like growth factor 1 (IGF-1; 10 μg/ml, Sigma, I8779), epidermal growth factor (EGF; 10 μg/ml, Sigma, E1257), basic fibroblast growth factor (bFGF; 10 μg/ml, Sigma, F0291), acidic fibroblast growth factor (aFGF; 10 μg/ml, Sigma, F5542), glial-cell-line-derived neurotrophic factor (GDNF; 10 μg/ml, Sigma, G1401), hepatocyte growth factor (HGF; 10 μg/ml, Sigma, H9661), and calpain inhibitor (MDL28170, 50 μM, Sigma, M6690). Thrombin and Fibrinogen cell suspensions were injected separately to allow for fibrin matrix formation within the spinal cord. Fibrinogen suspension was injected in all sites prior to thrombin suspension. The graft mixture was microinjected into the lesion cavity at T1 and into the intact spinal cord at C4 and C6 in 2 locations each. Each injection site received 0.83 μl total cell suspension, and subjects survived for either 3, 7 or 14 days post-grafting. Lesion only animals received growth factors in fibrinogen/thrombin mixture without cells. N = 24 animals surviving 3 days (9 with NPC graft, 9 without graft, 6 for histology), N = 24 animals surviving 7 days (9 with NPC graft, 9 without graft, 6 for histology), and N = 33 animals surviving 14 days post-grafting (9 with NPC graft, 9 with MSC graft, 9 without graft, 6 for histology).

tag: grafted

value: no

value: motor cortex


title: intact animal, replicate 1


title: intact animal, replicate 2


title: lesion only, 10 days post lesion, replicate 2

tag: time point

value: 10 days


title: lesion only, 10 days post lesion, replicate 1


title: lesion only, 3 weeks post lesion, replicate 1

value: 3 weeks


title: lesion only, 3 weeks post lesion, replicate 2


title: lesion only, 3 weeks post lesion, replicate 3


title: lesion only, 2 weeks post lesion, replicate 1

value: 2 weeks


title: lesion only, 2 weeks post lesion, replicate 2


title: lesion only, 2 weeks post lesion, replicate 3


title: grafted animal, 10 days post lesion, replicate 1

value: yes


title: grafted animal, 3 weeks post lesion, replicate 2


title: grafted animal, 10 days post lesion, replicate 2


title: grafted animal, 10 days post lesion, replicate 3


title: grafted animal, 3 weeks post lesion, replicate 1


title: HD0002-04A

value: blood

value: myeloid dendritic cells

value: PBMC healthy patient 2


title: grafted animal, 3 weeks post lesion, replicate 3


title: grafted animal, 2 weeks post lesion, replicate 2


title: HD0001-05A

value: PBMC healthy patient 1


title: HD0002-01A

value: monocyte


title: HD0001-01A


title: grafted animal, 2 weeks post lesion, replicate 3


title: 13 day T3 leg

city: Ceske Budejovice

first: Barbora

last: Konopova

address: Branisovska 31

department: Institute of Entomology

country: Czech Republic

institute: Biology Centre CAS

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
LEG_13d

data_processing:
The quality of the sequenced reads was assessed using the FastQC software. All samples consistently showed a Per base sequence quality of >30. Reads were mapped to the reference transcriptome with Bowtie2 (version 2.2.5) using default parameter and the –local alignment mode (Langmead et al., 2009). The trimmed pairs of reads were concatenated for each stage and treated as single reads.
Sample 8-9 days: Prior to mapping, the 75bp PE reads were trimmed to 50 bp, using Trimmomatic in the paired-end mode (version 0.36) using the CROP function (CROP:50).
The R package HTSFilter (Rau et al., 2013) was used with default parameters to filter constantly low expressed genes
Differential gene expression analysis on active pleuropodia ("highly secreting"), samples 10 days, 11 days, 12 days: The differential expression analysis was performed with the NOISeq R package (2.22.1; Tarazona et al., 2011). Reads were first normalized using the RPKM method (Mortazavi et al., 2008). Samples from day 10, 11 and 12 were treated as replicate and analyzed using the NOISeq-real algorithm with the following parameters: k=0.5, norm="n", factor="type", nss=0, lc=1, replicates = "technical".
Genome_build: Reads were mapped to a reference embryonic transcriptome prepared by us. This Transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank under the accession GHHP00000000. The version used in the study is the first version, GHHP01000000.
Supplementary_files_format_and_content: Excel (xlsx) files. File "Sgre_pleuropodia_CountMatrix_filtered.xlsx" contains a count matrix for each sample after filtering using the HTSFilter (see "data processing"). File "Sgre_secreting_pleuropodia_DEGs.xlsx" contains output from differential expression analysis performed using NOISeq on samples from highly secreting pleuropodia and similarly aged legs. This includes "RPKM" that measures the transcript abundance.

organism: Schistocerca gregaria

source_name: embryonic T3 legs

growth_protocol: Eggs were incubated at 30 degrees Celsius.

extract_protocol:
Legs and pleuropodia were dissected from embryos of Schistocerca gregaria at indicated age (day) in phosphate buffer saline (PBS), then frozen in liquid nitrogen. Total RNA was extracted using Trizol, quantified using Nanodrop and sent to BGI (Hong Kong) (samples from stages 4, 5, 6, 7, 8, 10, 11, 12 and 13 days) or delivered to EASIH (Cambridge) (sample 8-9 days) for library preparation and sequencing.
Libraries were prepared according to Illumina protocol. The total RNA was enriched in mRNA by using the oligo(dT) magnetic beads.

value: embryo

tag: age

value: 13 days

value: T3 leg


title: 13 day pleuropodium

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
PLP_13d

source_name: pleuropodia

value: pleuropodium


title: MSC grafted animal, 3 weeks post lesion, replicate 3


title: 12 day T3 leg

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
Sgre_secreting_pleuropodia_DEGs.xlsx
LEG_12d

value: 12 days


title: grafted animal, 2 weeks post lesion, replicate 1


title: 11 day pleuropodium

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
Sgre_secreting_pleuropodia_DEGs.xlsx
PLP_11d

value: 11 days


title: MSC grafted animal, 3 weeks post lesion, replicate 1


title: MSC grafted animal, 3 weeks post lesion, replicate 2


title: 10 day pleuropodium

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
Sgre_secreting_pleuropodia_DEGs.xlsx
PLP_10d


title: 11 day T3 leg

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
Sgre_secreting_pleuropodia_DEGs.xlsx
LEG_11d


title: 8 day T3 leg

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
LEG_8d

value: 8 days


title: SAM24335311 C57Bl/6 tumor-associated macrophage anti-MerTK

city: South San Francisco

first: Robert

last: Piskol

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

molecule: polyA RNA

source_name: Purified TAMs from MC-38 tumor-bearing mice

extract_protocol: Purified TAMs were collected in RLT lysis buffer and total RNA was extracted with the RNeasy Plus Micro kit (Qiagen). The concentration and integrity of RNA samples was determined with the NanoDrop 8000 (Thermo Scientific) and the Bioanalyzer RNA 6000 Pico Kit (Agilent), respectively.

tag: strain

value: tumor

value: tumor-associated macrophage

tag: treatment

value: anti-MerTK


title: 7 day pleuropodium

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
PLP_7d

tag: Stage

value: 7 days


title: SAM24335309 C57Bl/6 tumor-associated macrophage anti-MerTK


title: 10 day T3 leg

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
Sgre_secreting_pleuropodia_DEGs.xlsx
LEG_10d

value: 10 days


title: 8 day pleuropodium

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
PLP_8d


title: SAM24335307 C57Bl/6 tumor-associated macrophage anti-MerTK


title: SAM24335308 C57Bl/6 tumor-associated macrophage anti-MerTK


title: 7 day T3 leg

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
LEG_7d


title: SAM24335306 C57Bl/6 tumor-associated macrophage anti-gp120


title: 12 day pleuropodium

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
Sgre_secreting_pleuropodia_DEGs.xlsx
PLP_12d


title: 6 day pleuropodium

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
PLP_6d

value: 6 days


title: SAM24335310 C57Bl/6 tumor-associated macrophage anti-MerTK


title: 6 day T3 leg

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
LEG_6d


title: SAM24335303 C57Bl/6 tumor-associated macrophage anti-gp120


title: SAM24335304 C57Bl/6 tumor-associated macrophage anti-gp120


title: SAM24335305 C57Bl/6 tumor-associated macrophage anti-gp120


title: 5 day pleuropodium

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
PLP_5d

value: 5 days


title: 5 day T3 leg

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
LEG_5d


title: 4 day pleuropodium

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
PLP_4d

value: 4 days


title: 4 day T3 leg

description:
Sgre_pleuropodia_CountMatrix_filtered.xlsx
LEG_4d


title: Shh-/-_H3K27ac input

tag: strain background

value: Swiss Webster

tag: tissue/chip rxn

value: ~400,000 cells/ChIP

tag: chip antibody

tag: genotype or treatment

value: Shh-/-


title: Shh-/-_H3K27ac rep 2

value: H3K27ac (Diagenode C15200184)


title: WT_H3K27ac rep 2

value: wild type


title: WT leg 1d rep 2

city: Kansas City

first: Maria

middle: Lynn

last: Spletter

state: MO

address: 5009 Rockhill Rd

department: Biological and Biomedical Systems

institute: University of Missouri Kansas City

description:
mRNA
leg1d_3
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

data_processing:
Basecalling and demultiplexing by IMP sequencing core facility (Vienna, Austria) using Illumina software.
Quality assessment of the raw data using fastqc v.011.2.
Filtering and trimming of adapter residues and low quality reads with the FASTX toolkit v.0.0.14 and cutadapt v1.4.1.
Sequenced reads were mapped to the Ensembl BDGP6.80 whole genome using STAR v2.4.2a.
Mapped reads were sorted and indexed using samtools v1.2.
Bam files were converted into bigwig for visualisation on the UCSC server.
Counting the mapped reads on the gene and exon level using featureCounts v1.4.6.
Run the differential gene expression analysis using the R package DESeq2 v1.8.2.
Calculate the differential exon usage with the R package DEXSeq.
Genome_build: BDGP6.80 from ENSEMBL
Supplementary_files_format_and_content: Tab-delimited text files including raw counts calculated by featureCount for all libraries

organism: Drosophila melanogaster

source_name: whole leg

growth_protocol: Flies were grown on standard medium using standard fly husbandry protocol.

extract_protocol:
Total RNA isolated in Tri-Pure reagent (phenol-chloroform), mRNA selected via 3 passes over Invitrogen oligo-dT magnetic beads, mRNA was fragmented using heat and fragmentation buffer, RT was performed with Invitrogen SSIII first strand synthesis system and second-strand labeled with dUTP.
RNA libraries were prepared for sequencing by the IMP sequencing core facility (Vienna, Austria) using standard Illumina protocols.

treatment_protocol: Dissected for up to 30 min. in PBS, spun-down at 2000xg for 5 min. to remove buffer and stored in Tri-Pure (Roche) reagent at -80C until extraction.

value: whole leg

tag: muscle type

value: tubular

tag: developmental stage

value: 1d adult

tag: genotype

value: Mef2-Gal4, UAS:GMA::GFP

tag: growth protocol

value: grown at 27C from cross until eclosion


title: salmIR IFM 1d rep_1

description:
mRNA
salm1d_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

source_name: indirect flight muscle

value: indirect flight muscle

value: tubular converted

value: Mef2-Gal4, UAS-T3029 (salmIR)


title: FRTsalmFRT mut IFM 1d rep_1

description:
mRNA
salm1d_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: UAS-Flp;mef2-Gal4,salm1/ FRT-salm-FRT

value: grown at 18C, shifted to 30C at crawling 3rd instar stage until eclosion


title: WT_H3K27ac rep 1


title: WT jump muscle 1d rep 1

description:
mRNA
jump1d_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

source_name: tergal depressor of the trochanter muscle


title: WT jump muscle 1d rep 2

description:
mRNA
jump1d_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: tergal depressor of the trochanter muscle


title: CastDrug_3

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

data_processing:
Single-end 50 bp reads generated on Illumina HiSeq were aligned to the murine genome version GRCm38 using TopHat v2.0.4 (Trapnell et al., 2009).
Read counts were obtained using HTSeq-count, normalised and tested for differential gene expression using the DESeq package in Bioconductor 2.11.
Genome_build: GRCm38
Supplementary_files_format_and_content: HTSeq-count gene counts

source_name: Pten-null tumour tissues

extract_protocol:
Pten-null tumours were removed, flash frozen on dry ice, and RNA was harvested using Qiagen Rnesy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB

value: Prostate tumour tissue

tag: age (month)

value: Surgical castration + AZD2014 (15mg/kg/day)


title: WT wing disc hinge rep1 (Myo1)

description:
mRNA
IFM_Myoblast_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

source_name: wing imaginal disc hinge

value: wing imaginal disc hinge

value: myoblast

value: 3rd instar

value: Mef2-Gal4, UAS-GMA-GFP

value: grown at 27C, staged 0h white pre-pupae


title: WT IFM 72h APF rep_1

description:
mRNA
IFM72h_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: fibrillar

value: 72h APF


title: CastDrug_1


title: Cast_3

value: Surgical castration + Vehicle (1% polysorbate 80)


title: CastDrug_4


title: WT IFM 72h APF rep_2

description:
mRNA
IFM72h_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: indirect flight muscle

value: Mef2-Gal4, UAS:GMA::GFP


title: SAM24335302 C57Bl/6 tumor-associated macrophage anti-gp120

value: tumor

value: tumor-associated macrophage


title: Cast_2


title: WT IFM 48h APF rep1

description:
mRNA
IFM48h_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: 48h APF


title: Cast_1


title: Shh-/-_H3K27ac rep 1

source_name: forelimb bud

value: Swiss Webster

value: ~400,000 cells/ChIP

value: H3K27ac (Diagenode C15200184)

value: Shh-/-


title: WT_H3K27ac input

value: wild type


title: WT IFM 30h APF rep_1

description:
mRNA
IFM30h_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: 30h APF


title: Drug_5

value: FVB

value: Prostate tumour tissue

value: AZD2014 (15mg/kg/day)


title: WT IFM 24h APF rep1

description:
mRNA
IFM24h_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: fibrillar

value: 24h APF

value: Mef2-Gal4, UAS-GMA-GFP

value: grown at 27C, staged 0h white pre-pupae


title: CastDrug_2

value: Surgical castration + AZD2014 (15mg/kg/day)


title: Drug_4


title: WT leg 1d rep 1

description:
mRNA
leg1d_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: whole leg

value: tubular

value: 1d adult

value: Mef2-Gal4, UAS:GMA::GFP

value: grown at 27C from cross until eclosion


title: WT IFM 1d rep_2

description:
mRNA
IFM1d_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: indirect flight muscle


title: Drug_3


title: Cast_4

value: Surgical castration + Vehicle (1% polysorbate 80)


title: Drug_1


title: WT IFM 1d rep_1

description:
mRNA
IFM1d_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt


title: WT IFM 30h APF rep_2

description:
mRNA
IFM30h_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt


title: aretIR IFM 72hAPF rep 2

description:
mRNA
aret72h_3
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: 72h APF

value: Mef2-Gal4, UAS:GMA::GFP, UAS-T41568 (aretIR)


title: aretIR IFM 72hAPF rep 1

description:
mRNA
aret72h_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt


title: aretIR IFM 30hAPF rep 2

description:
mRNA
aret30h_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: 30h APF


title: WT IFM 16h APF rep1

description:
mRNA
IFM16h_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: 16h APF


title: Veh_1

value: FVB

value: Prostate tumour tissue

value: Vehicle (1% polysorbate 80)


title: aretIR IFM 1d rep 1

description:
mRNA
aret1d_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: fibrillar


title: Veh_4


title: Veh_3


title: aretIR IFM 1d rep 2

description:
mRNA
aret1d_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt


title: Drug_2

value: AZD2014 (15mg/kg/day)


title: aretIR IFM 30hAPF rep 1

description:
mRNA
aret30h_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: grown at 27C, staged 0h white pre-pupae


title: Veh_2


title: JHH4_WT_rep3

city: Yokohama

first: Hidewaki

last: Nakagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
STAR aligner (ver. 2.5.3a) was used to map RNA-Seq reads onto the reference human genome GRCh37. The featureCounts software was employed to count reads per gene, using GENCODE release 19 as a gene model. Fragments per kilobase of exon per million fragments mapped (FPKM) with upper-quartile normalization was computed using in-house R script.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: Wildtype JHH4 were purchased from Health Science Research Resources Bank (Osaka, Japan). CRISPR-Cas9-mediated knockout of ARID2 was performed as previously described (Oba et al., J Hepatol. 2017 66(5):942-951). Cells were maintained in Dulbecco's modified Eagle's medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Sigma-Aldrich, St. Louis, MO), 100 U/ml penicillin, and 100 μg/ml streptomycin (Invitrogen). All cell lines were cultivated in a humidified incubator at 37 °C in 5% carbon dioxide and collected with 0.05% trypsin-0.02% EDTA solution (Invitrogen).

extract_protocol:
Cells were lysed, and total RNA was extracted using QIAGEN RNeasy Plus Mini Kit.
Illumina TruSeq Stranded mRNA Sample Prep Kit was used for the construction of sequencing libraries.

tag: cell line

value: Wildtype


title: JHH4_WT_rep1


title: JHH4_ARID2KO_rep3

value: ARID2 knockout


title: JHH4_ARID2KO_rep2


title: Veh_5

tag: tissue


title: JHH4_ARID2KO_rep1


title: JHH4_WT_rep2


title: ASD patient 10 before CPB

city: Genova

first: Davide

last: Cangelosi

address: Via Gerolamo Gaslini 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

hyb_protocol: Fragmented cRNA was hybridized on Affymetrix Human Genome U133 Plus PM Array Strips  (Thermo Fisher) containing 54,675 probe sets coding for 47,000 transcripts and variants, including 38,500 unique human genes) on a single array. Chips were stained with streptavidin-phycoerythrin (Invitrogen Life Technologies, Milano).

scan_protocol: GeneChips were scanned using  an Affymetrix GeneChip Scanner 3000.

data_processing: Expression values were quantified, and data were processed by RMA normalization utilizing the ‘Affy’ R package. Statistical analysis using Student’s t-test was performed to identify differentially expressed genes (DEGs). Specifically, unpaired Student’s t-test was used to assess whether there were significant differentially expressed genes between ASD and ToF, whereas paired Student’s t-test was used to identify differences in the gene expression levels between Pre-CPB and Post-CPB in ASD or in ToF. We corrected the p value by Benjamini- Hochberg method for false discovery rate (FDR) control. Only gene differences that passed the test at a confidence level of 95% (P≤0.05) and a FDR ≤ 0.05 were considered significant. Fold-change (FC) was calculated to determine the magnitude of the difference. Genes were considered significantly differentially expressed if they exhibited p value ≤0.05 and FC≥2 or ≤0.5. We filtered out genes having a coefficient of variation (CV) lower than 0.7, because they did not substantially change between the two diseases under consideration, and those having an expression value lower than 100 in at least 20% of the samples because they were not sufficiently expressed in our data set to provide a reliable transcriptional level. Filtering was carried out by ‘GeneFilter’ R package. We converted the Affymetrix probe sets into the corresponding gene symbol by Netaffix tool. When multiple probe sets were associated with the same gene symbol, the probe set with the highest expression signal was considered.

label: biotin

source_name: patient with ASD before CPB

extract_protocol: Tissue specimens were mechanically homogenized in lysis reagent from Qiagen (Milano, Italy). The procedure of RNA isolation and cRNA synthesis has been previously described. Briefly, total RNA was purified and DNase treated using the RNeasy MiniKit (Quigen), controlled for integrity by nanoelectrophoresis using an Agilent 2100 Bioanalyzer  (Agilent Technologies Europe, Waldbroon, Germany), quantified by spectrophotometry using a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, USA), and reverse-transcribed into double-stranded cDNA on a GeneAmp PCR System 2700 thermal cycler (Applied Biosystems, Milano) using the one-cycle cDNA synthesis kit (Affymetrix, Milano). cDNA was purified, transcribed into cRNA, and biotin labeled using the GeneChip IVT kit (Affymetrix). Labeled cRNA was fragmented according to Affymetrix’s instructions.

treatment_protocol: Pre- and post-operative right atrium biopsy specimens were collected at the time of surgical defect correction. The first biopsy was harvested five minutes before AoXC (Pre-CPB), whereas the second biopsy was harvested fifteen minutes after AoXC removal (Post-CPB) (average CPB duration did not exceed 70 minutes). Specimens were harvested with cold sharp dissection, immediately snap-frozen in liquid nitrogen, and stored until use at -80°C in the Integrating Tissueomics Biobank (BIT)–Gaslini, which collects and stores tissue and genomic specimens for diagnostic and research functions under the approval of the Ethical Committee of the Gaslini Institute and the ratification of the Ethical Committee of the Regione Liguria. Atrial sampling was atraumatic, provided full-thickness specimens, and was clinically reproducible.

tag: disease state

value: ASD

tag: individual

value: patient 10

tag: time

value: before CPB

value: Myocardium (right atrium biopsy)


title: ASD patient 10 after CPB

source_name: patient with ASD after CPB

label_protocol: cDNA was purified, transcribed into cRNA, and biotin labeled using the GeneChip IVT kit (Affymetrix). Labeled cRNA was fragmented according to Affymetrix’s instructions.

value: after CPB


title: ASD patient 1 before CPB

value: patient 1


title: TOF patient 10 before CPB

source_name: patient with TOF before CPB

value: TOF


title: HCT116_Auxin6hr_Ribodep_Rep1

first: Shiyuan

middle: (Cynthia)

last: Chen

department: Computational Biology

institute: Stowers Institute for Medical Research

description: RNAseqTPM.csv

data_processing:
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
RNA-seq was aligned to genome hg38 from UCSC using STAR aligner
TPM was generated using RSEM
Genome_build: UCSC genome hg38, ensembl 87 gene model
Supplementary_files_format_and_content: RNA-seq TPM in csv file

growth_protocol: HCT116-OsTIR1-MED26AID cells were cultured in McCoy's-5A media supplemented with 10% (v/v) fetal bovine serum, 1x MEM non-essential amino acids, 100mcg/ml Hygromycin, 1mcg/ml Puromycin and 100U/ml Penicillin- 100mcg/ml Streptomycin at 37oC with 5% CO2.

extract_protocol:
total RNA was extracted using the Maxwell simplyRNA cells kit (Promega) on a Maxwell RSC instrument according to the manufacture's instructions.
Standard protocol using Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-zero Gold (Ribodep), or TruSeq Stranded mRNA Preparation Kit (PolyA)

treatment_protocol: Cells were seeded at a density of 5x10e5 cells on a 6-well plate and culture overnight. Auxin treatment was started by replacing cultured media to fresh completed media supplemented with Auxin final 500uM. Mock treatment (NT) was performed same as Auxin treatment by using completed media mock supplemented with no auxin solvent (water).  After incubated for 6 hrs in 37oC with 5% CO2, RNA was extracted for analysis.

value: Auxin

tag: spike-in

value: Drosophila melanogaster

value: HCT116 expressing F-box protein (OsTIR1) and Auxin-inducible degron (AID) tagged endogenous MED26

tag: protocol

value: Ribosome Depleted RNA-seq


title: TOF patient 10 after CPB

source_name: patient with TOF after CPB


title: ASD patient 1 after CPB


title: HCT116_Auxin6hr_PolyA_Rep3

description: RNAseqTPM.csv

tag: treatment

value: PolyA Selected RNA-seq


title: lesion only, 10 days post lesion, replicate 3

tag: grafted

value: no

tag: time point

value: 10 days

value: motor cortex


title: HCT116_NT_Ribodep_Rep2

description: RNAseqTPM.csv

value: NT


title: HCT116_NT_Ribodep_Rep3

description: RNAseqTPM.csv


title: HCT116_Auxin6hr_Ribodep_Rep3

description: RNAseqTPM.csv


title: HCT116_NT_Ribodep_Rep1

description: RNAseqTPM.csv


title: HCT116_Auxin6hr_PolyA_Rep2

description: RNAseqTPM.csv


title: HCT116_NT_PolyA_Rep3

description: RNAseqTPM.csv


title: ASD patient 9 after CPB

value: patient 9


title: ASD patient 9 before CPB

value: ASD


title: TOF patient 9 after CPB


title: HCT116_NT_PolyA_Rep2

description: RNAseqTPM.csv


title: TOF patient 8 before CPB

value: patient 8


title: ASD patient 8 before CPB

value: before CPB


title: ASD patient 8 after CPB

value: Myocardium (right atrium biopsy)


title: TOF patient 7 before CPB

value: patient 7


title: TOF patient 7 after CPB

value: after CPB


title: ASD patient 7 before CPB


title: ASD patient 7 after CPB


title: TOF patient 9 before CPB

value: TOF


title: HCT116_Auxin6hr_PolyA_Rep1

description: RNAseqTPM.csv

value: Auxin


title: Nuclear RNA-seq CPSF73-AID Plus auxin rep 2

city: Exeter

last: West

state: Devon

address: Stocker Rd

department: Living Systems Institute

institute: University of Exeter

description:
nuclear RNA
bigwig coverage file was generated for merged replicate total reads

data_processing:
Adapters were removed from nuclear RNA-seq reads using Trim Galore! v0.4.4 (wrapper tool for Cutadapt v1.9.1).
Alignment of nuclear RNA-Seq reads with Hisat2 v2.1.0 to ensembl GRCh38.
Properly mapped single-end reads were extracted using SAMtools v1.4.1.
Filtered mapped BAM replicates were merged using Bamtools v2.4.0.
bigWig files of nuclear RNA-seq reads were generated from merged replicate BAM files using bamCoverage from Deeptools v3.3.0.
GRCh38
bigWig files of nuclear RNA-seq reads represent merged replicate normalised read-coverage (RPKM) over single bp windows across the whole genome.

source_name: HCT116 Nuclear RNA-seq CPSF73-AID Doxycycline inducible (TIR1) plus auxin

growth_protocol: HCT116 cell lines were maintianed in DMEM with 10% fetal bovine serum, pen/strep at 37 °C and 5% CO2.

extract_protocol:
Nuclear RNA was extracted from isolated nuclei using Trizol reagent.
Nuclear RNA was depleted of ribosomal RNA using Illumina Ribo-Zero (Illumina #20020597). Library was constructed using Illumina TruSeq® Stranded Total RNA (Illumina #20020597).

treatment_protocol: TIR1 induction for 18 h (1 μg/ml doxycycline) followed by the addition of auxin to cell media at a final concentration of 500 µM for 3 h.

tag: genotype/variation

value: auxin treated Nuclear RNA

tag: molecule subtype

value: nuclear RNA


title: HCT116_Auxin6hr_Ribodep_Rep2

description: RNAseqTPM.csv

value: Drosophila melanogaster

value: HCT116 expressing F-box protein (OsTIR1) and Auxin-inducible degron (AID) tagged endogenous MED26

value: Ribosome Depleted RNA-seq


title: Nuclear RNA-seq CPSF73-AID Plus auxin rep 1


title: Nuclear RNA-seq CPSF73-AID Minus auxin rep 2

source_name: HCT116 Nuclear RNA-seq CPSF73-AID Doxycycline inducible (TIR1) minus auxin

treatment_protocol: Control: TIR1 induction for 18 h (1 μg/ml doxycycline) followed by the addition of ethanol for 3 h.

value: Control:auxin untreated Nuclear RNA


title: Nuclear RNA-seq CPSF73-AID Minus auxin rep 1


title: Chromatin-associated RNA-seq CPSF73-AID Minus auxin rep2

description:
other
bigwig coverage files were generated for each strand.

data_processing:
Adapters were removed from chromatin-associated RNA-seq reads using Trim Galore! v0.4.4 (wrapper tool for Cutadapt v.1.15).
Alignment of chromatin-associated RNA-seq reads with Hisat2 v2.0.5 to ensembl GRCH38.p10 release 91.
The primary alignments for single-end mapped reads (i.e. excluding SAM flag 260) were extracted using SAMtools v1.4.1 and coverted to BAM files.
bigWig files of chromatin-associated RNA-seq reads were generated for each strand using bamCoverage from Deeptools v3.0.1.
GRCh38
bigWig files of chromatin-associated RNA-seq reads were normalised using 'BPM' option (equivalent to TPM for RNA-seq data) over single bp windows across the whole genome.

source_name: HCT116 Chromatin-associated RNA-seq CPSF73-AID Doxycycline inducible (TIR1) minus auxin

extract_protocol:
Isolated nuclei were lysed into an insoluble chromatin pellet and soluble nucleoplamic supernatant. Chromatin-associated RNA was then purified from the insoluble chromatin pellet using Trizol reagent (see Eaton et al. 2018 for detailed method).
Chromatin-associated RNA was depleted of ribosomal RNA using Illumina Ribo-Zero (Illumina #20020597). Library was constructed using Illumina TruSeq® Stranded Total RNA (Illumina #20020597).

treatment_protocol: Control: Treated for 18 h with ethanol followed by a second 3 h treatment with ethanol. Additionally, the sample was transfected with a silencer select negative control siRNA 72h prior to collection in media without any pen/strep using Lipofectamine RNAiMAX (Life Technologies).

value: chromatin-associated RNA


title: 293T_WT_Ribodep_Rep4

data_processing:
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
Reads were then mapped to human genome hg38, with STAR aligner (version 2.5.3a) default settings, using Ensembl 87 annotation gene models.
Transcripts per kilobase millon (TPM) values were then generated using RSEM (version 1.3.0) function rsem-calculate-expression with option –estimate-rspd.
ChIP-seq reads were aligned to human genome hg38 using Bowtie2 (version 2.2.4) with default settings. Peaks were called using MACS2 callpeak (version 2.1.1), default parameter, based on the corresponding input samples. The peaks with qsocre < 1e-4 were then used for downstream analysis.
Bigwig files are normalized by the total reads of the spike-in genome and extended to fragment length for IP samples
Genome_build: UCSC genome hg38, ensembl 87 gene model
Supplementary_files_format_and_content: RNA-seq TPM in csv file, ChIP-seq in bigwig files

growth_protocol: Cells were cultured in 1X DMEM (Sigma-Aldrich) supplemented with 10% fetal bovine serum (Sigma-Aldrich), 1X Glutamine (ThermoFisher) and 1X penicillin/streptomycin (ThermoFisher) in a CO2 incubator (5% CO2) at 37°C.

extract_protocol:
For RNA-seq, total RNA was extracted using miRNeasy Mini Kit (Qiagen #217004) and quantified using RNA 6000 Nano Kit (Agilent Technologies) in Bioanalyzer. 1µg of total RNA was subjected to oligo-dT selection or removal of rRNA (Ribo-Zero rRNA removal kit ,Illumina, #MRZH11124). ERCC spike-ins from Ambion were added to RNA prior to library preparation.
For MED26 ChIP-seq, cells were crosslinked  with 2 mM DSG in PBS for 30 min and then 1% formaldehyde for 20 min. For Pol II ChIP-seq, human cells and mouse cells used for spike-in control were crosslinked with 1% formaldehyde for 20 min at room temperature. Human and mouse chromatin  were mixed in 10:1 ratio.  Crosslinked chromatin was sonicated to generate  fragments of 150-500 bp prior to immunoprecipitation.
For PRO-seq, around 25 million wild type or mutant HEK293T cells were mixed Drosophila Kc167 (10:1 ratio), permeabilised, and incubated with biotin-labeled NTPs. Biotinylated RNA was hydrolyzed with NaOH, and biotin containing RNA fragments were enriched by affinity purification using streptavidin-coated magnetic beads. A 3' sequencing adaptor was ligated to the biotinylated RNA, the 5'cap was removed,  5'OH was generated by base hydrolysis and converted to 5′ phosphate by treatment with T4 polynucleotide kinase, a 5′ sequencing adaptor was ligated to RNA. RNA was purified to enrich for biotinylated fragments with adaptor at both ends and reverse transcribed. Detailed methods are in PRO-Seq, Mahat et al Nat Protoc, 11:1455-76;  doi: 10.1038/nprot.2016.086.
Ribo-depleted RNA seq libraries were prepared using TruSeq Stranded Total RNA kit (Illumina, #20020596) following manufacturer's instructions. PolyA-selected RNA-seq libraries were prepared using TruSeq Stranded mRNA kit (Illumina, #20020594) following manufacturer's instructions. Both TruSeq kits add Illumina-compatible adapter and indexes for sequencing.  Libraries were checked for quality (Bioanalyzer) and quantity (Qubit). Equimolar concentrations of libraries were pooled, requantified and sequenced as 50bp single reads on the Illumina HiSeq 2500 instrument. ChIP-seq libraries were prepared using KAPA HTP kit (Roche, #KK8234) and stock adapters by Bioo Scientific NEXTflex DNA barcodes with 15 cycles of PCR. Libraries were purified using Agencourt AMPure XP system and quantified using Bioanalyzer and Qubit fluorometer. Post amplification size selection was performed on all libraries using Pippin-prep (Sage Science) instument. Equimolar concentrations of libraries were pooled, requantified and sequenced either as single reads on the Illumina HiSeq 2500 platform (polyA-selected RNA-seq and MED26 ChIP-seq) or as single read High Output on Illumina NextSeq 500 platform (ribo-depleted RNA-seq and Pol II ChIP-seq). PRO-seq libraries were generated essentially as described in Mahat et al., 2016 (Nat Protoc, 11:1455-76;  doi: 10.1038/nprot.2016.086). Primers RPI4, RPI5, RPI6 and RPI7 were used to barcode cDNAs from 293T_WT_Rep1 (Wild Type, replicate 1), 293T_WT_Rep2 (Wild Type, replicate 2), 293_D2G8-MED26-MUT_Rep1 (Mutant MED26-D2G8, replicate 1), and 293_D2G8-MED26-MUT_Rep2 (Mutant MED26-D2G8, replicate 2) respectively.

treatment_protocol: siRNAs specific for human MED26, AFF4, ICE1 and Non-target were purchased from Dharmacon (SMARTpool) or ThermoFisher (Silencer Select).


title: Chromatin-associated RNA-seq CPSF73-AID Minus auxin rep1

value: Control:auxin untreated


title: 293T_WT_Ribodep_Rep3


title: ASD patient 6 before CPB

value: patient 6


title: 293T_WT_Ribodep_Rep2


title: 293T_WT_Ribodep_Rep1


title: 293T_Control_Ribodep_Rep3

tag: sirna

value: ON-TARGETplus Non-targeting Pool, Dharmacon D-001810-10


title: ASD patient 6 after CPB

value: ASD


title: ASD patient 2 before CPB

value: patient 2

value: before CPB


title: Chromatin-associated RNA-seq CPSF73-AID Plus auxin rep2

source_name: HCT116 Chromatin-associated RNA-seq CPSF73-AID Doxycycline inducible (TIR1) plus auxin

treatment_protocol: TIR1 induction for 18 h (1 μg/ml doxycycline) followed by the addition of auxin to cell media at a final concentration of 500 µM for 3 h. Additionally, the sample was transfected with a silencer select negative control siRNA 72h prior to collection in media without any pen/strep using Lipofectamine RNAiMAX (Life Technologies).


title: Chromatin-associated RNA-seq CPSF73-AID Plus auxin rep1


title: ASD patient 3 after CPB

value: patient 3

value: Myocardium (right atrium biopsy)


title: ASD patient 5 before CPB

value: patient 5


title: 293T_Control_Ribodep_Rep2


title: ASD patient 4 before CPB

value: patient 4


title: 293T_Control_Ribodep_Rep1


title: TOF patient 6 before CPB

value: TOF


title: 293T_MED26_KD_Ribodep_Rep2

value: Silencer Select MED26 siRNA, ThermoFisher s18074


title: ASD patient 3 before CPB


title: 293T_MED26_KD_Ribodep_Rep3


title: TOF patient 6 after CPB

value: after CPB


title: TOF patient 5 before CPB


title: ASD patient 4 after CPB


title: ASD patient 5 after CPB


title: 293T_MED26_KD_Ribodep_Rep1


title: 293T_MED26_KD_polyA_Rep3

value: ON-TARGETplus Human MED26 siRNA - SMARTpool, Dharmacon L-011948-00

value: PolyA Selected RNA-seq


title: 293T_MED26_KD_polyA_Rep2


title: ASD patient 2 after CPB


title: TOF patient 4 after CPB


title: HCT116_NT_PolyA_Rep1

description: RNAseqTPM.csv

value: NT

value: Drosophila melanogaster

value: HCT116 expressing F-box protein (OsTIR1) and Auxin-inducible degron (AID) tagged endogenous MED26


title: TOF patient 3 before CPB


title: 293T_MED26_KD_polyA_Rep1


title: 293T-D2G8-MED26-MUT_Ribodep_Rep4

value: Ribosome Depleted RNA-seq


title: TOF patient 4 before CPB


title: TOF patient 3 after CPB


title: 293T-D2G8-MED26-MUT_Ribodep_Rep3


title: 293T_KIAA0947/ICE1_KD_polyA_Rep3

value: ON-TARGETplus Human ICE1 siRNA - SMARTpool, Dharmacon L-024272-02


title: SENSOR LOW_2

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

institute: Istituto Italiano di Tecnologia

data_processing:
Data were analyzed with the HTSFLOW (High-Throughput Sequencing flow) tool, that provides a framework for the management and analysis of NGS data.
FASTQ data of the RNA sequencing experiment were trimmed and aligned with Tophat
Gene expression and Differential gene expression was evaluated with FeatureCount and Deseq2 packages
Genome_build: hg38
Supplementary_files_format_and_content: Excel Spreadsheet containing the raw counts of each gene

source_name: HMLE

growth_protocol: HMLE cells were grown in MEGM medium, according to manufacturer's protocol.

extract_protocol:
Total RNA was isolated through the miRNeasy micro kit (Qiagen).
500 nanograms of total RNA were used to prepare total RNA libraries following the Illumina TruSeqTM Stranded RNA kit instructions

treatment_protocol: HMLE cells infected with lentiviral miR-146 sensor were FACS-sorted according to different endogenous levels of miR-146. miR-146high and miR-146 low cells were plated in adhesion. miR-146high cells  were treated with 100 nM power family inhibitor to KD miR-146 , then all the samples were collected 24hs after transfection. Two independent infections, sorting and transfection procedures were performed.

tag: infection

value: miR-146 sensor

tag: levels of mir-146

value: low

value: breast normal

value: Human Mammary Epithelial cell line (HMLE) cell line


title: SENSOR HIGH_KD_2

value: high

value: power family inhibitor to KD miR-146


title: TOF patient 5 after CPB

value: patient 5

value: Myocardium (right atrium biopsy)


title: 293T-D2G8-MED26-MUT_Ribodep_Rep2


title: SENSOR HIGH_1


title: TOF patient 2 after CPB

value: TOF

value: patient 2


title: SENSOR HIGH_KD_1


title: 293T_KIAA0947/ICE1_KD_polyA_Rep1


title: SENSOR HIGH_2


title: 293T-D2G8-MED26-MUT_Ribodep_Rep1


title: TOF patient 1 before CPB

value: patient 1

value: before CPB


title: TOF patient 1 after CPB

value: after CPB


title: 293T_KIAA0947/ICE1_KD_polyA_Rep2

value: PolyA Selected RNA-seq


title: SENSOR LOW_1


title: 293T_Control_polyA_Rep3

value: siGENOME non-targeting siRNA Pool #2, Dharmacon D-001206-14


title: SPHV_rep3

city: Candiolo

last: Cora'

state: TO

department: Dept. of Oncology

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute

description: HUVEC spheroids  stimulated with VEGF-A - miRNAs-seq, replicate_3

data_processing:
Base calling was performed by using CASAVA-1.8.2.
FASTX was used to trim adaptor sequences
The BWA program was used to align reads to miRBase v22, on mature miRs.
Genome_build: miRBase v22.
Supplementary_files_format_and_content: TAB-delimited text providing raw counts for mature miRNAs in all the samples.

source_name: Human Umbilical Vein Endothelial Cells cultured as spheroids, VEGF-A stimulated

growth_protocol: HUVEC were isolated from umbilical cord veins and maintained in M199, 20% FBS, supplemented with heparin and bovine brain extract.

extract_protocol:
RNA was extracted from SPHC and SPHV collected after collagen digestio using miRNeasy Mini Kit (Qiagen #217004) according to manufacturer's instructions.
Standard small RNA protocol based on the illumina TruSeq small RNA kit. Starting from total RNA a polyacrylamide gel to select small RNAs  was performed (including miRNAs, siRNAs and piRNAs) with 18-30 nt fragment size before the library preparation.

treatment_protocol: HUVEC aggregates (spheroids) were generated by culturing cells in hanging drops for 10 hours, then embedded in a collagen matrix. VEGF-A 20 ng/ml was used to trigger sprouting. Sprouted spheroids were collected after 15 hours VEGF-A treatment.

value: HUVEC spheroids

tag: vegf stimulation

value: yes


title: SPHV_rep2

description: HUVEC spheroids  stimulated with VEGF-A - miRNAs-seq, replicate_2


title: SPHC_rep3

description: HUVEC spheroids unstimulated - miRNAs-seq, replicate_3

source_name: Human Umbilical Vein Endothelial Cells cultured as spheroids, unstimulated

value: no


title: 293T_AFF4_KD_polyA_Rep2

value: ON-TARGETplus Human AFF4 siRNA - SMARTpool, Dharmacon L-020276-00


title: 293T_Control_polyA_Rep1


title: TOF patient 2 before CPB


title: 293T_AFF4_KD_polyA_Rep3


title: SPHV_rep1

description: HUVEC spheroids  stimulated with VEGF-A - miRNAs-seq, replicate_1


title: 293T_AFF4_KD_polyA_Rep1


title: SPHC_rep2

description: HUVEC spheroids unstimulated - miRNAs-seq, replicate_2


title: SPHC_rep1

description: HUVEC spheroids unstimulated - miRNAs-seq, replicate_1


title: 293T_Control_polyA_Rep2


title: 293T_Med26_ChIP_Rep2

tag: chip antibody

value: anti-MED26 H-228, Santa Cruz sc-48776 X


title: 293T_Med26_ChIP_Rep1

tag: cell line


title: HUVEC spheroids  stimulated with VEGF-A rep2

description: HUVEC spheroids  stimulated with VEGF-A, replicate_2

data_processing:
Base calling was performed by using CASAVA-1.8.2.
The Bowtie program was used to align reads to the reference human hg19 genome.
Ensembl gene annotations provided by UCSC (hg19) were set as reference for the RSEM computational pipeline  (Li et al., BMC Bioinformatics 2011) used for quantification of gene expression levels.
Genome_build: GRCh37 / hg19.
Supplementary_files_format_and_content: TAB-delimited text providing FPKM values for Ensembl genes for all the samples.

source_name: Human Umbilical Vein Endothelial Cells cultured as spheroids

extract_protocol:
RNA was extracted from SPHC and SPHV collected after collagen digestion using miRNeasy Mini Kit (Qiagen #217004) according to manufacturer's instructions.
Illumina TruSeq Stranded mRNA Library Prep kit.
Poly-A, paired end


title: HUVEC spheroids unstimulated rep3

description: HUVEC spheroids unstimulated, replicate_3


title: 293T_Input_MED26_ChIP_Rep2

value: none (input)


title: HUVEC spheroids  stimulated with VEGF-A rep1

description: HUVEC spheroids  stimulated with VEGF-A, replicate_1


title: HUVEC spheroids unstimulated rep2

description: HUVEC spheroids unstimulated, replicate_2


title: CC_D6_p53 ChIP

city: Bethesda

first: Paul

middle: M.

last: Hwang

state: MD

address: 10 Center Drive

department: NHLBI

institute: National Institutes of Health

data_processing:
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration:Windows (50), Gaps (50), FDR (1e-10). Signals from the p53 KO cells were filtered out.
Single-end reads of RNA-seq are aligned to the mm9 genome assembly using bowtie2.
SICER v1.1 was used to calculate the reads per kilo base per million (RPKM) on exonic regions as expression measurements for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using in-house script and the scores represent RPKM; tab-delimited text files include Gene, read count, and RPKM values for each gene.

source_name: primary adipocytes

extract_protocol:
For ChIP-seq samples, primary adipocytes  were cross-linked with 1.5% formaldehyde for 10 min, and the nuclear extracts were sonicated and immunoprecipitated with anti-p53 (FL393, Santa Cruz).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA sample prep kit (Cat no. FC-121-2001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15-18 cycles and library fragments of 200-400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: strain

tag: genotypes

tag: cell types

value: iWAT derived primary adipocytes

value: anti-p53 (Santa Cruz, FL393)


title: KO_D6_input DNA


title: salmIR IFM 72h APF rep 2

description:
mRNA
salm72h_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

source_name: indirect flight muscle

tag: tissue

value: indirect flight muscle

tag: muscle type

value: tubular converted

tag: developmental stage

value: 72h APF

tag: genotype

value: Mef2-Gal4, UAS-T3029 (salmIR)

tag: growth protocol

value: grown at 27C, staged 0h white pre-pupae


title: KO_D6_p53 ChIP


title: salmIR IFM 72h APF rep 1

description:
mRNA
salm72h_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt


title: HUVEC spheroids unstimulated rep1

description: HUVEC spheroids unstimulated, replicate_1


title: RNA_iWAT_p53KO3

source_name: Inguinal white adipose tissue

extract_protocol:
For RNA-seq samples, total tissue RNA was purified using the RNeasy kit (Qiagen), and mRNA was isolated using the Dynabead mRNA Purification Kit (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: RR_D6_p53 ChIP

value: p53178R/R (wild-type)


title: RR_D6_input DNA


title: 8-9 day pleuropodium

description:
paired-end reads were sequenced for this sample, but only reads in one direction, trimmed from 75 to 50 bases were used for the analysis
Sgre_pleuropodia_CountMatrix_filtered.xlsx
PLP_8_9d

source_name: pleuropodia

tag: Stage

value: embryo

tag: age

value: pleuropodium


title: 8-9 day T3 leg

description:
paired-end reads were sequenced for this sample, but only reads in one direction, trimmed from 75 to 50 bases were used for the analysis
Sgre_pleuropodia_CountMatrix_filtered.xlsx
LEG_8_9d

source_name: embryonic T3 legs

value: T3 leg


title: RNA_iWAT_p53KO1


title: RNA_iWAT_CC4


title: HUVEC spheroids  stimulated with VEGF-A rep3

description: HUVEC spheroids  stimulated with VEGF-A, replicate_3


title: salmIR IFM 30h APF rep 1

description:
mRNA
salm30h_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: 30h APF


title: PAS whole body NE579 37S rep 3

city: Paris

first: Guilhem

last: Janbon

address: 25 rue du Dr Roux

institute: Institut Pasteur

data_processing: QuantSeq 3’mRNA-Seq reads containing both the Sequencing and indexing primers (Lexogen) were sorted. The reads were then cleaned using cutadapt/1.18 and trimmed for polyA sequence in their 3’end. PolyA untrimmed and trimmed reads were mapped to the adapted Cryptococcus deneoformans JEC21 genome with Tophat2 using previously published setting (Gonzalez-Hilarion et al Sci Rep 2016). To eliminate the polyadenylated reads corresponding to genomic polyA stretches, we considered only the reads that aligned to the genomes only after polyA trimming. The 3’end position of these reads were considered as potential PAS. Wig files were constructed using the 3’ extremities of these reads Their coverage was normalized using the normalization alpha factor used for spiked in RNA-Seq.

organism: Cryptococcus deneoformans

source_name: cells

extract_protocol: Cells were grown on YPD at 30°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. QuantSeq 3’mRNA-Seq libraries were prepared following the manufacturer instructions (Lexogen GmbH, Austria). 100 base single end reads were obtained using an Illumina HiSeq2000 instrument according to the manufacturer’s instructions (Illumina).

value: NE579 upf1delta

tag: growth condition

value: exponential phase 30 degrees C

tag: protocol

value: QuantSeq 3-prime RNA-Seq

tag: sample id

value: Sample 27


title: RNA_iWAT_p53KO2


title: CC_D6_input DNA


title: RNA_iWAT_CC2


title: 293T_Input_MED26_ChIP_Rep1

value: none (input)


title: RNA_iWAT_CC1


title: RNA_iWAT_RR3


title: RNA_iWAT_RR4


title: TSS whole body NE579 37S rep 3

data_processing:
Library strategy: TSS-Seq
For TSS analysis we kept only the reads containing both the oligo 3665 (AGATCGGAAGAGCACACGTCTGAAC) and the 11NCGCCGCGNNN tag. These sequenced were removed using cutadapt/1.18 and the trimmed reads were mapped to the Cryptococcus deneoformans JEC21 genome using Tophat2 using previously published setting (Gonzalez-Hilarion et al Sci Rep 2016). Wig files were constructed using the 5’ extremities of each reads. Their coverage was normalized using the normalization factor used for spiked in RNA-Seq.

extract_protocol: Cells were grown on YPD at 30°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. TSS-Seq libraries preparations were performed starting with 75 µg of total RNA. Single 50 bases single end reads were obtained using an an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).

value: TSS-Seq


title: RNA whole body NE579 37S rep 3

data_processing: The reads were then cleaned using cutadapt/1.18. Trimmed reads were mapped to the C. deneoformans JEC21 and to the S. cerevisiae S288C genomes with Tophat2 using previously published setting (Gonzalez-Hilarion et al Sci Rep 2016). RNA Reads count were evaluated using HTSeq/0.6.1 (intersection-nonempty) normalized using the S. cerevisiae DNA/RNA spike in alpha factor and used to calculate FPKM values.

extract_protocol: Cells were grown on YPD at 30°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. Total RNA was extracted with Trizol. For RNA-Seq, strand-specific, paired-end cDNA libraries were prepared from 10 μg of total RNA by polyA selection using the TruSeq Stranded mRNA kit (Illumina) according to manufacturer’s instructions. cDNA fragments of ~400 bp were purified from each library and confirmed for quality by Bioanalyzer (Agilent). Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).

value: RNA-Seq


title: salmIR IFM 24h APF rep 1

description:
mRNA
salm24h_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: indirect flight muscle

value: 24h APF


title: WT leg 1d rep2poor

description:
mRNA
leg1d_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

source_name: whole leg

value: whole leg

value: tubular

value: 1d adult

value: Mef2-Gal4, UAS:GMA::GFP

value: grown at 27C from cross until eclosion


title: RNA_iWAT_RR1

value: p53178R/R (wild-type)


title: DNA NE579 37S rep 3

data_processing:
Library strategy: DNA-Seq
The reads were then cleaned using cutadapt/1.18. Trimmed reads were mapped to the C. deneoformans JEC21 and to the S. cerevisiae S288C  genomes with Bowtie2 using default settings. For each sample, total DNA and RNA reads counts aligned to each organism were used to calculate an alpha normalization factor. The file with the alpha noramlization factors is available on the series record: alpha_factor.txt

extract_protocol: Cells were grown on YPD at 30°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in stationary phase. Total DNA samples were used to prepare DNA-Seq libraries using the kit TruSeq DNA PCR-Free (Illumina).Then, 100 bases were sequenced from both ends using an Illumina HiSeq2500 instrument according to the manufacturer’s instructions (Illumina).

value: DNA-Seq


title: WT wing disc myoblast rep3 (Myo3)

description:
mRNA
IFM_Myoblast_3
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

source_name: wing disc myoblasts

extract_protocol:
Total RNA isolated in Tri-Pure reagent (phenol-chloroform), mRNA selected via 3 passes over Invitrogen oligo-dT magnetic beads, mRNA was fragmented using heat and fragmentation buffer, RT was performed with Invitrogen SSIII first strand synthesis system and second-strand labeled with dUTP.
RNA libraries were prepared for sequencing by the IMP sequencing core facility (Vienna, Austria) using standard Illumina protocols.

value: wing disc myoblasts

value: myoblast

value: 3rd instar

value: Him-Gal4, UAS-BBM (RFP); salmEGFP

value: grown at 25C, collected crawling 3rd instar larvae


title: RNA_iWAT_CC3


title: hypoxia/-TH [T30]

first: Kailtyn

middle: Yan-Yun

last: Liu

address: 10833 Le Conte Ave

department: Medicine

institute: UCLA/VA

data_processing:
IlluminaHiseq3000 for a single read 50 run.
Data quality check was done on Illumina SAV.
Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0
the gene expression level was estimated using RSEM v1.2.15.
TMM (trimmed mean of M-values) was used to normalize the gene expression.
Genome_build: MM10
Supplementary_files_format_and_content: tab-delimited text files

source_name: Primary cortical neurons

growth_protocol: mouse primary cortiall neuron were growth for 7days. Then cells were subjected to treatment.

extract_protocol:
Cultured primary cortical neurons were exposed to hypoxia (0.2% oxygen) for 7 hours, in either the presence or absence of T3 (5 nM)
RNA libraries were prepared for sequencing using standard Illumina protocols
KAPA Strand RNA-Seq kit

treatment_protocol: Controlat 21% oxgen, hypoxia at 0.2% oxgen

value: embryonic day-17 mice

value: Brain

tag: cell type

value: Primary cortical neurons

tag: treatment

value: hypoxia