title: Plasma_cells_Multiple_Myeloma [T15436]


title: Plasma_cells_Multiple_Myeloma [T15469]

status: Public on Dec 14 2022

type: genomic

city: Toulouse

first: Laura

last: Do Souto Ferreira

address: 1 Av. Irène Joliot-Curie

country: France

institute: IUCT

hyb_protocol: Cytoscan HD arrays (Affymetrix)

scan_protocol: Scanner Affymetrix  GCS 3000 7G

data_processing: analysis with the logarithm of ChAS software

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: sorted Plasma cells, from bone marrow of newly diagnosed multiple myeloma patients

label_protocol: Cytoscan Affymetrix Label (DNA labeling reagent)

extract_protocol: Nucleospin Tissue Macherey Nagel

treatment_protocol: sorted plasma cells (CD138+) then frozen (-80°C)

tag: subject id

tag: diagnosis

value: multiple myeloma

tag: Sex

value: female

tag: age

tag: del1p32 status

tag: treatment

tag: tissue

value: bone marrow

tag: cell type

value: sorted plasma cells (CD138+)


title: Plasma_cells_Multiple_Myeloma [T15371]


title: Plasma_cells_Multiple_Myeloma [T15375]


title: Plasma_cells_Multiple_Myeloma [T15349]

value: male

value: VD


title: Plasma_cells_Multiple_Myeloma [T15347]


title: Plasma_cells_Multiple_Myeloma [T15586]


title: Plasma_cells_Multiple_Myeloma [T15329]


title: Plasma_cells_Multiple_Myeloma [T15325]


title: Plasma_cells_Multiple_Myeloma [T15328]


title: Plasma_cells_Multiple_Myeloma [T15312]

value: MPV


title: Plasma_cells_Multiple_Myeloma [T15313]

value: VCD


title: Plasma_cells_Multiple_Myeloma [T15451]


title: Plasma_cells_Multiple_Myeloma [T15269]

value: VRD-RD


title: Plasma_cells_Multiple_Myeloma [T15264]


title: Plasma_cells_Multiple_Myeloma [T15288]


title: Plasma_cells_Multiple_Myeloma [T15287]


title: Plasma_cells_Multiple_Myeloma [T15259]

value: VTD


title: Plasma_cells_Multiple_Myeloma [T15247]


title: Plasma_cells_Multiple_Myeloma [T15244]


title: Plasma_cells_Multiple_Myeloma [T15231]


title: Plasma_cells_Multiple_Myeloma [T15246]

value: RD


title: Plasma_cells_Multiple_Myeloma [T15379]

value: VRD-R


title: Plasma_cells_Multiple_Myeloma [T15187]


title: Plasma_cells_Multiple_Myeloma [T15171]


title: Plasma_cells_Multiple_Myeloma [T15182]


title: Plasma_cells_Multiple_Myeloma [T15167]


title: Plasma_cells_Multiple_Myeloma [T15129]


title: Plasma_cells_Multiple_Myeloma [T15179]


title: Plasma_cells_Multiple_Myeloma [T15157]


title: Plasma_cells_Multiple_Myeloma [T15341]


title: Plasma_cells_Multiple_Myeloma [T15169]


title: Plasma_cells_Multiple_Myeloma [T15318]


title: Plasma_cells_Multiple_Myeloma [T15110]


title: Plasma_cells_Multiple_Myeloma [T15132]


title: Plasma_cells_Multiple_Myeloma [T15109]


title: Plasma_cells_Multiple_Myeloma [T15098]


title: Plasma_cells_Multiple_Myeloma [T15083]


title: Plasma_cells_Multiple_Myeloma [T15128]


title: Plasma_cells_Multiple_Myeloma [T15217]


title: Plasma_cells_Multiple_Myeloma [T14990]


title: Plasma_cells_Multiple_Myeloma [T15037]


title: Plasma_cells_Multiple_Myeloma [T15029]


title: Plasma_cells_Multiple_Myeloma [T14970]


title: Plasma_cells_Multiple_Myeloma [T15104]


title: Plasma_cells_Multiple_Myeloma [T14973]


title: Plasma_cells_Multiple_Myeloma [T14987]

value: VCD-HDM


title: Plasma_cells_Multiple_Myeloma [T14995]


title: Plasma_cells_Multiple_Myeloma [T15026]


title: Plasma_cells_Multiple_Myeloma [T14962]


title: Plasma_cells_Multiple_Myeloma [T15017]


title: Plasma_cells_Multiple_Myeloma [T14991]


title: Plasma_cells_Multiple_Myeloma [T14901]


title: Plasma_cells_Multiple_Myeloma [T14916]


title: Plasma_cells_Multiple_Myeloma [T14924]


title: Plasma_cells_Multiple_Myeloma [T14926]


title: Plasma_cells_Multiple_Myeloma [T14889]


title: Plasma_cells_Multiple_Myeloma [T14851]


title: Plasma_cells_Multiple_Myeloma [T14883]


title: Plasma_cells_Multiple_Myeloma [T14849]


title: Plasma_cells_Multiple_Myeloma [T14847]


title: Plasma_cells_Multiple_Myeloma [T14841]


title: Plasma_cells_Multiple_Myeloma [T15072]


title: Plasma_cells_Multiple_Myeloma [T14843]


title: Plasma_cells_Multiple_Myeloma [T14810]


title: Plasma_cells_Multiple_Myeloma [T14830]


title: Plasma_cells_Multiple_Myeloma [T14808]


title: Plasma_cells_Multiple_Myeloma [T14949]


title: Plasma_cells_Multiple_Myeloma [T14783]


title: Plasma_cells_Multiple_Myeloma [T14930]


title: Plasma_cells_Multiple_Myeloma [T14765]


title: Plasma_cells_Multiple_Myeloma [T14718]


title: Plasma_cells_Multiple_Myeloma [T14686]


title: Plasma_cells_Multiple_Myeloma [T14699]


title: Plasma_cells_Multiple_Myeloma [T14697]


title: Plasma_cells_Multiple_Myeloma [T14688]


title: Plasma_cells_Multiple_Myeloma [T14729]


title: Plasma_cells_Multiple_Myeloma [T14681]


title: Plasma_cells_Multiple_Myeloma [T14668]


title: Plasma_cells_Multiple_Myeloma [T14621]


title: Plasma_cells_Multiple_Myeloma [T14860]


title: Plasma_cells_Multiple_Myeloma [T14620]


title: Plasma_cells_Multiple_Myeloma [T14592]


title: Plasma_cells_Multiple_Myeloma [T14591]


title: Plasma_cells_Multiple_Myeloma [T14616]


title: Plasma_cells_Multiple_Myeloma [T14462]


title: Plasma_cells_Multiple_Myeloma [T14448]


title: Plasma_cells_Multiple_Myeloma [T14542]


title: Plasma_cells_Multiple_Myeloma [T14567]


title: Plasma_cells_Multiple_Myeloma [T14446]


title: Plasma_cells_Multiple_Myeloma [T14588]


title: Plasma_cells_Multiple_Myeloma [T14426]


title: Plasma_cells_Multiple_Myeloma [T14414]


title: Plasma_cells_Multiple_Myeloma [T14434]


title: Plasma_cells_Multiple_Myeloma [T14412]


title: Plasma_cells_Multiple_Myeloma [T14721]


title: Plasma_cells_Multiple_Myeloma [T14411]


title: Plasma_cells_Multiple_Myeloma [T14407]


title: Plasma_cells_Multiple_Myeloma [T14384]


title: Plasma_cells_Multiple_Myeloma [T14667]


title: Plasma_cells_Multiple_Myeloma [T14344]


title: Plasma_cells_Multiple_Myeloma [T14349]


title: Plasma_cells_Multiple_Myeloma [T14350]


title: Plasma_cells_Multiple_Myeloma [T14363]


title: Plasma_cells_Multiple_Myeloma [T14333]


title: Plasma_cells_Multiple_Myeloma [T14298]


title: Plasma_cells_Multiple_Myeloma [T14341]


title: Plasma_cells_Multiple_Myeloma [T14334]


title: Plasma_cells_Multiple_Myeloma [T14381]


title: Plasma_cells_Multiple_Myeloma [T14308]


title: Plasma_cells_Multiple_Myeloma [T14288]


title: Plasma_cells_Multiple_Myeloma [T14332]


title: Plasma_cells_Multiple_Myeloma [T14281]


title: Plasma_cells_Multiple_Myeloma [T14229]

value: VRD


title: Plasma_cells_Multiple_Myeloma [T14231]


title: Plasma_cells_Multiple_Myeloma [T14234]


title: Plasma_cells_Multiple_Myeloma [T14227]


title: Plasma_cells_Multiple_Myeloma [T14183]


title: Plasma_cells_Multiple_Myeloma [T14216]


title: Plasma_cells_Multiple_Myeloma [T14196]


title: Plasma_cells_Multiple_Myeloma [T14119]


title: Plasma_cells_Multiple_Myeloma [T14137]


title: Plasma_cells_Multiple_Myeloma [T14106]


title: Plasma_cells_Multiple_Myeloma [T14116]


title: Plasma_cells_Multiple_Myeloma [T14312]


title: Plasma_cells_Multiple_Myeloma [T14068]

description: The .CEL file is not available for this sample.


title: Plasma_cells_Multiple_Myeloma [T14061]


title: Plasma_cells_Multiple_Myeloma [T14261]


title: Plasma_cells_Multiple_Myeloma [T14033]


title: Plasma_cells_Multiple_Myeloma [T13860]


title: Plasma_cells_Multiple_Myeloma [T13886]


title: Plasma_cells_Multiple_Myeloma [T13867]


title: Plasma_cells_Multiple_Myeloma [T14242]


title: Plasma_cells_Multiple_Myeloma [T13840]


title: Plasma_cells_Multiple_Myeloma [T13811]


title: Plasma_cells_Multiple_Myeloma [T13839]


title: Plasma_cells_Multiple_Myeloma [T13841]


title: Plasma_cells_Multiple_Myeloma [T13810]


title: Plasma_cells_Multiple_Myeloma [T13812]


title: Plasma_cells_Multiple_Myeloma [T13747]


title: Plasma_cells_Multiple_Myeloma [T13725]


title: Plasma_cells_Multiple_Myeloma [T13769]


title: Plasma_cells_Multiple_Myeloma [T13763]


title: Plasma_cells_Multiple_Myeloma [T13785]


title: Plasma_cells_Multiple_Myeloma [T13712]


title: Plasma_cells_Multiple_Myeloma [T14100]


title: Plasma_cells_Multiple_Myeloma [T13661]


title: Plasma_cells_Multiple_Myeloma [T13701]


title: Plasma_cells_Multiple_Myeloma [T13596]


title: Plasma_cells_Multiple_Myeloma [T13625]


title: Plasma_cells_Multiple_Myeloma [T13564]


title: Plasma_cells_Multiple_Myeloma [T13543]


title: Plasma_cells_Multiple_Myeloma [T13579]


title: Plasma_cells_Multiple_Myeloma [T13512]


title: Plasma_cells_Multiple_Myeloma [T14015]


title: Plasma_cells_Multiple_Myeloma [T13535]


title: Plasma_cells_Multiple_Myeloma [T13489]


title: Plasma_cells_Multiple_Myeloma [T13474]


title: Plasma_cells_Multiple_Myeloma [T13449]


title: Plasma_cells_Multiple_Myeloma [T13430]


title: Plasma_cells_Multiple_Myeloma [T13471]


title: Plasma_cells_Multiple_Myeloma [T13475]


title: Plasma_cells_Multiple_Myeloma [T13322]


title: Plasma_cells_Multiple_Myeloma [T13395]


title: Plasma_cells_Multiple_Myeloma [T13394]


title: Plasma_cells_Multiple_Myeloma [T13485]


title: Plasma_cells_Multiple_Myeloma [T13272]


title: Plasma_cells_Multiple_Myeloma [T13274]


title: Plasma_cells_Multiple_Myeloma [T13413]


title: Plasma_cells_Multiple_Myeloma [T13260]


title: Plasma_cells_Multiple_Myeloma [T13181]


title: Plasma_cells_Multiple_Myeloma [T13218]


title: Plasma_cells_Multiple_Myeloma [T13220]


title: Plasma_cells_Multiple_Myeloma [T13360]


title: Plasma_cells_Multiple_Myeloma [T13146]


title: Plasma_cells_Multiple_Myeloma [T13588]


title: Plasma_cells_Multiple_Myeloma [T13122]


title: Plasma_cells_Multiple_Myeloma [T13006]


title: Plasma_cells_Multiple_Myeloma [T13097]


title: Plasma_cells_Multiple_Myeloma [T13060]


title: Plasma_cells_Multiple_Myeloma [T12902]


title: Plasma_cells_Multiple_Myeloma [T12954]


title: Plasma_cells_Multiple_Myeloma [T12976]


title: Plasma_cells_Multiple_Myeloma [T12964]

value: MPT


title: Plasma_cells_Multiple_Myeloma [T12943]


title: Plasma_cells_Multiple_Myeloma [T12897]


title: Plasma_cells_Multiple_Myeloma [T12877]


title: Plasma_cells_Multiple_Myeloma [T12886]


title: Plasma_cells_Multiple_Myeloma [T12863]


title: Plasma_cells_Multiple_Myeloma [T12866]


title: Plasma_cells_Multiple_Myeloma [T12763]


title: Plasma_cells_Multiple_Myeloma [T12801]


title: Plasma_cells_Multiple_Myeloma [T12750]


title: Plasma_cells_Multiple_Myeloma [T12887]


title: Plasma_cells_Multiple_Myeloma [T12900]


title: Plasma_cells_Multiple_Myeloma [T12788]


title: Plasma_cells_Multiple_Myeloma [T12734]


title: Plasma_cells_Multiple_Myeloma [T12787]


title: Plasma_cells_Multiple_Myeloma [T12864]


title: Plasma_cells_Multiple_Myeloma [T12665]


title: Plasma_cells_Multiple_Myeloma [T12664]


title: Plasma_cells_Multiple_Myeloma [T12764]


title: Plasma_cells_Multiple_Myeloma [T12720]


title: Plasma_cells_Multiple_Myeloma [T12708]


title: Plasma_cells_Multiple_Myeloma [T13049]


title: Plasma_cells_Multiple_Myeloma [T12744]


title: Plasma_cells_Multiple_Myeloma [T12554]


title: Plasma_cells_Multiple_Myeloma [T12654]


title: Plasma_cells_Multiple_Myeloma [T12598]


title: Plasma_cells_Multiple_Myeloma [T12659]


title: Plasma_cells_Multiple_Myeloma [T12564]


title: Plasma_cells_Multiple_Myeloma [T12530]


title: Plasma_cells_Multiple_Myeloma [T12521]


title: Plasma_cells_Multiple_Myeloma [T12802]


title: Plasma_cells_Multiple_Myeloma [T12486]


title: Plasma_cells_Multiple_Myeloma [T12584]


title: Plasma_cells_Multiple_Myeloma [T12445]


title: Plasma_cells_Multiple_Myeloma [T12439]

value: MPR


title: Plasma_cells_Multiple_Myeloma [T12442]


title: Plasma_cells_Multiple_Myeloma [T12520]


title: Plasma_cells_Multiple_Myeloma [T12295]


title: Plasma_cells_Multiple_Myeloma [T12252]


title: Plasma_cells_Multiple_Myeloma [T12459]


title: Plasma_cells_Multiple_Myeloma [T12441]


title: Plasma_cells_Multiple_Myeloma [T12418]


title: Plasma_cells_Multiple_Myeloma [T12400]


title: Plasma_cells_Multiple_Myeloma [T12203]


title: Plasma_cells_Multiple_Myeloma [T12433]


title: Plasma_cells_Multiple_Myeloma [T12316]


title: Plasma_cells_Multiple_Myeloma [T12402]


title: Plasma_cells_Multiple_Myeloma [T12100]


title: Plasma_cells_Multiple_Myeloma [T12256]


title: Plasma_cells_Multiple_Myeloma [T12225]


title: Plasma_cells_Multiple_Myeloma [T12294]


title: Plasma_cells_Multiple_Myeloma [T12249]


title: Plasma_cells_Multiple_Myeloma [T12217]


title: Plasma_cells_Multiple_Myeloma [T12128]


title: Plasma_cells_Multiple_Myeloma [T12176]


title: Plasma_cells_Multiple_Myeloma [T12080]


title: Plasma_cells_Multiple_Myeloma [T12473]


title: Plasma_cells_Multiple_Myeloma [T12073]


title: Plasma_cells_Multiple_Myeloma [T12062]


title: Plasma_cells_Multiple_Myeloma [T12063]


title: Plasma_cells_Multiple_Myeloma [T12152]


title: Plasma_cells_Multiple_Myeloma [T12002]


title: Plasma_cells_Multiple_Myeloma [T12034]


title: Plasma_cells_Multiple_Myeloma [T11967]


title: Plasma_cells_Multiple_Myeloma [T11902]


title: Plasma_cells_Multiple_Myeloma [T11913]


title: Plasma_cells_Multiple_Myeloma [T11824]


title: Plasma_cells_Multiple_Myeloma [T11834]


title: Plasma_cells_Multiple_Myeloma [T11877]


title: Plasma_cells_Multiple_Myeloma [T11786]


title: Plasma_cells_Multiple_Myeloma [T11766]


title: Plasma_cells_Multiple_Myeloma [T11724]


title: Plasma_cells_Multiple_Myeloma [T11704]


title: Plasma_cells_Multiple_Myeloma [T11634]


title: Plasma_cells_Multiple_Myeloma [T12058]


title: Plasma_cells_Multiple_Myeloma [T11722]


title: Plasma_cells_Multiple_Myeloma [T11623]


title: Plasma_cells_Multiple_Myeloma [T11591]


title: Plasma_cells_Multiple_Myeloma [T11572]


title: Plasma_cells_Multiple_Myeloma [T11516]


title: Plasma_cells_Multiple_Myeloma [T11576]


title: Plasma_cells_Multiple_Myeloma [T11468]

value: RD-Dara


title: Plasma_cells_Multiple_Myeloma [T11947]

value: multiple myeloma


title: Plasma_cells_Multiple_Myeloma [T11493]


title: Plasma_cells_Multiple_Myeloma [T11526]

value: female


title: Plasma_cells_Multiple_Myeloma [T11452]

value: bone marrow


title: Plasma_cells_Multiple_Myeloma [T11866]

value: sorted plasma cells (CD138+)


title: Plasma_cells_Multiple_Myeloma [T11817]

value: male


title: Plasma_cells_Multiple_Myeloma [T11425]


title: Plasma_cells_Multiple_Myeloma [T11936]


title: Plasma_cells_Multiple_Myeloma [T11422]


title: Plasma_cells_Multiple_Myeloma [T11411]


title: Plasma_cells_Multiple_Myeloma [T11731]


title: Plasma_cells_Multiple_Myeloma [T11409]


title: Plasma_cells_Multiple_Myeloma [T11388]


title: Plasma_cells_Multiple_Myeloma [T11390]


title: Plasma_cells_Multiple_Myeloma [T11355]


title: Plasma_cells_Multiple_Myeloma [T11333]


title: Plasma_cells_Multiple_Myeloma [T11305]


title: Plasma_cells_Multiple_Myeloma [T11313]

value: Dara-RD


title: Plasma_cells_Multiple_Myeloma [T11301]


title: Plasma_cells_Multiple_Myeloma [T11266]


title: Plasma_cells_Multiple_Myeloma [T11232]


title: Plasma_cells_Multiple_Myeloma [T11201]

value: MPV


title: Plasma_cells_Multiple_Myeloma [T11210]


title: Plasma_cells_Multiple_Myeloma [T11177]


title: Plasma_cells_Multiple_Myeloma [T11445]


title: Plasma_cells_Multiple_Myeloma [T11204]


title: Plasma_cells_Multiple_Myeloma [T11156]


title: Plasma_cells_Multiple_Myeloma [T11166]


title: Plasma_cells_Multiple_Myeloma [T11142]


title: Plasma_cells_Multiple_Myeloma [T11076]


title: Plasma_cells_Multiple_Myeloma [T11140]


title: Plasma_cells_Multiple_Myeloma [T11118]


title: Plasma_cells_Multiple_Myeloma [T11080]


title: Plasma_cells_Multiple_Myeloma [T11061]


title: Plasma_cells_Multiple_Myeloma [T11116]


title: Plasma_cells_Multiple_Myeloma [T11134]


title: Plasma_cells_Multiple_Myeloma [T11391]


title: Plasma_cells_Multiple_Myeloma [T11024]


title: Plasma_cells_Multiple_Myeloma [T11006]


title: Plasma_cells_Multiple_Myeloma [T11260]


title: Plasma_cells_Multiple_Myeloma [T10996]


title: Plasma_cells_Multiple_Myeloma [T11011]


title: Plasma_cells_Multiple_Myeloma [T11032]


title: Plasma_cells_Multiple_Myeloma [T11219]


title: Plasma_cells_Multiple_Myeloma [T10961]


title: Plasma_cells_Multiple_Myeloma [T10973]


title: Plasma_cells_Multiple_Myeloma [T10957]


title: Plasma_cells_Multiple_Myeloma [T10941]


title: Plasma_cells_Multiple_Myeloma [T10946]


title: Plasma_cells_Multiple_Myeloma [T10925]


title: Plasma_cells_Multiple_Myeloma [T10837]


title: Plasma_cells_Multiple_Myeloma [T10865]


title: Plasma_cells_Multiple_Myeloma [T10860]


title: Plasma_cells_Multiple_Myeloma [T10828]


title: Plasma_cells_Multiple_Myeloma [T10845]


title: Plasma_cells_Multiple_Myeloma [T10799]


title: Plasma_cells_Multiple_Myeloma [T10819]


title: Plasma_cells_Multiple_Myeloma [T10783]


title: Plasma_cells_Multiple_Myeloma [T10793]


title: Plasma_cells_Multiple_Myeloma [T10784]


title: Plasma_cells_Multiple_Myeloma [T10712]


title: Plasma_cells_Multiple_Myeloma [T10719]


title: Plasma_cells_Multiple_Myeloma [T10718]


title: Plasma_cells_Multiple_Myeloma [T11060]


title: Plasma_cells_Multiple_Myeloma [T10671]


title: Plasma_cells_Multiple_Myeloma [T10646]


title: Plasma_cells_Multiple_Myeloma [T10672]


title: Plasma_cells_Multiple_Myeloma [T10959]


title: Plasma_cells_Multiple_Myeloma [T10619]


title: Plasma_cells_Multiple_Myeloma [T10537]


title: Plasma_cells_Multiple_Myeloma [T10600]


title: Plasma_cells_Multiple_Myeloma [T10575]


title: Plasma_cells_Multiple_Myeloma [T10521]


title: Plasma_cells_Multiple_Myeloma [T10559]


title: Plasma_cells_Multiple_Myeloma [T10469]


title: Plasma_cells_Multiple_Myeloma [T10478]


title: Plasma_cells_Multiple_Myeloma [T10508]


title: Plasma_cells_Multiple_Myeloma [T10449]


title: Plasma_cells_Multiple_Myeloma [T10770]


title: Plasma_cells_Multiple_Myeloma [T10471]


title: Plasma_cells_Multiple_Myeloma [T10444]


title: Plasma_cells_Multiple_Myeloma [T10389]


title: Plasma_cells_Multiple_Myeloma [T10362]


title: Plasma_cells_Multiple_Myeloma [T10372]


title: Plasma_cells_Multiple_Myeloma [T10664]


title: Plasma_cells_Multiple_Myeloma [T10400]


title: Plasma_cells_Multiple_Myeloma [T10371]


title: Plasma_cells_Multiple_Myeloma [T10337]


title: Plasma_cells_Multiple_Myeloma [T10326]


title: Plasma_cells_Multiple_Myeloma [T10642]


title: Plasma_cells_Multiple_Myeloma [T10325]


title: Plasma_cells_Multiple_Myeloma [T10316]


title: Plasma_cells_Multiple_Myeloma [T10271]


title: Plasma_cells_Multiple_Myeloma [T10210]


title: Plasma_cells_Multiple_Myeloma [T10307]


title: Plasma_cells_Multiple_Myeloma [T10207]


title: Plasma_cells_Multiple_Myeloma [T10291]

value: VD


title: Plasma_cells_Multiple_Myeloma [T10254]


title: Plasma_cells_Multiple_Myeloma [T10330]

value: VTD-Dara


title: Plasma_cells_Multiple_Myeloma [T10205]


title: Plasma_cells_Multiple_Myeloma [T10516]


title: Plasma_cells_Multiple_Myeloma [T10150]

value: VCD


title: Plasma_cells_Multiple_Myeloma [T10459]


title: Plasma_cells_Multiple_Myeloma [T10048]


title: Plasma_cells_Multiple_Myeloma [T10137]


title: Plasma_cells_Multiple_Myeloma [T10035]


title: Plasma_cells_Multiple_Myeloma [T10115]


title: Plasma_cells_Multiple_Myeloma [T10075]


title: Plasma_cells_Multiple_Myeloma [T10024]


title: Plasma_cells_Multiple_Myeloma [T09978]


title: Plasma_cells_Multiple_Myeloma [T09963]


title: Plasma_cells_Multiple_Myeloma [T09945]


title: Plasma_cells_Multiple_Myeloma [T09957]


title: Plasma_cells_Multiple_Myeloma [T09916]


title: Plasma_cells_Multiple_Myeloma [T10012]


title: Plasma_cells_Multiple_Myeloma [T09929]


title: Plasma_cells_Multiple_Myeloma [T09842]


title: Plasma_cells_Multiple_Myeloma [T09823]


title: Plasma_cells_Multiple_Myeloma [T09907]


title: Plasma_cells_Multiple_Myeloma [T09874]


title: Plasma_cells_Multiple_Myeloma [T09799]


title: Plasma_cells_Multiple_Myeloma [T09839]


title: Plasma_cells_Multiple_Myeloma [T09791]


title: Plasma_cells_Multiple_Myeloma [T09781]


title: Plasma_cells_Multiple_Myeloma [T09728]


title: Plasma_cells_Multiple_Myeloma [T09742]

value: RD


title: Plasma_cells_Multiple_Myeloma [T09726]


title: Plasma_cells_Multiple_Myeloma [T09753]


title: Plasma_cells_Multiple_Myeloma [T09724]


title: Plasma_cells_Multiple_Myeloma [T09930]

value: VTD


title: Plasma_cells_Multiple_Myeloma [T09686]


title: Plasma_cells_Multiple_Myeloma [T09699]


title: Plasma_cells_Multiple_Myeloma [T09655]


title: Plasma_cells_Multiple_Myeloma [T09696]


title: Plasma_cells_Multiple_Myeloma [T09855]


title: Plasma_cells_Multiple_Myeloma [T09870]


title: Plasma_cells_Multiple_Myeloma [T09620]

value: KMP


title: Plasma_cells_Multiple_Myeloma [T09780]


title: Plasma_cells_Multiple_Myeloma [T09626]


title: Plasma_cells_Multiple_Myeloma [T09654]


title: Plasma_cells_Multiple_Myeloma [T09571]


title: Plasma_cells_Multiple_Myeloma [T09622]


title: Plasma_cells_Multiple_Myeloma [T09580]


title: Plasma_cells_Multiple_Myeloma [T09528]


title: Plasma_cells_Multiple_Myeloma [T09557]


title: Plasma_cells_Multiple_Myeloma [T09565]


title: Plasma_cells_Multiple_Myeloma [T09526]


title: Plasma_cells_Multiple_Myeloma [T09481]


title: Plasma_cells_Multiple_Myeloma [T09465]


title: Plasma_cells_Multiple_Myeloma [T09507]


title: Plasma_cells_Multiple_Myeloma [T09476]


title: Plasma_cells_Multiple_Myeloma [T09701]


title: Plasma_cells_Multiple_Myeloma [T09450]


title: Plasma_cells_Multiple_Myeloma [T09443]


title: Plasma_cells_Multiple_Myeloma [T09452]


title: Plasma_cells_Multiple_Myeloma [T09434]


title: Plasma_cells_Multiple_Myeloma [T09422]


title: Plasma_cells_Multiple_Myeloma [T09382]


title: Plasma_cells_Multiple_Myeloma [T09444]


title: NT_DEX_mock_3 [OE404]

type: SRA

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

library_source: transcriptomic

data_processing:
Read quality control was performed using FastQC (Andrews, 2010).
The presence of contaminant organism reads was determined using Centrifuge (Kim et al., 2016).
Reads were mapped to the reference potato genome and counted using STAR (Dobin et al., 2013) with default parameters.
Differential expression analysis was performed in R using the limma package (Smyth et al., 2018).
Genome_build: Phureja DM1-3 potato genome v4.04 (Xu et al., 2011) using the merged PGSC and ITAG genome annotation (Petek et al., 2020)
Supplementary_files_format_and_content: differential gene expression statistics, normalized and raw read counts table in Excel spreadsheet format

molecule: total RNA

organism: Solanum tuberosum

source_name: leaf

growth_protocol: Plants were propagated from stem node tissue cultures and transferred to soil two weeks after node segmentation, where they were kept in growth chambers under controlled environmental conditions at 22/20 °C with a long-day (16 h) photoperiod of light (light intensity 4000 lm/m2) and 60-70% relative humidity.

extract_protocol:
Early visible lesions and their immediate surrounding area were sampled from PVY-inoculated leaves four days post inoculation. Sections of comparable size were sampled from mock-inoculated leaves as controls. Three plants per genotype per treatment were analysed, pooling together all lesions or mock-sections from one leaf per plant. Tissue sections were stored in RNA-later RNA Stabilization Solution (ThermoFisher Scientific) and then homogenized using Tissue Lyser (Qiagen). Total RNA was isolated with TRIzol (Invitrogen) and Direct-zol RNA MicroPrep Kit, DNAse treated and purified with RNA Clean & Concentrator kit (both Zymo Research) according to the manufacturer’s instructions.
Strand-specific library preparation was performed by Novogene (HongKong) using standard Illumina protocol.

treatment_protocol: Three to four weeks old potato plants were inoculated with GFP-tagged infectious PVY clones or mock inoculum. To induce gene overexpression, plants were treated with dexamethasone (DEX) foliar spray solution, containing 30 mM DEX and 0.01 % (v/v) Tween-20, or control spray solution without DEX (control), 3 h prior to virus inoculation, 3 h after virus inoculation and every day post inoculation until sampling.

tag: genotype

value: NT

tag: transgenic line

value: nd

value: DEX

tag: inoculation

value: mock

tag: sampling

value: mock sections

tag: number of sections in pool


title: NT_DEX_mock_2 [OE403]


title: Plasma_cells_Multiple_Myeloma [T09642]

value: multiple myeloma


title: Plasma_cells_Multiple_Myeloma [T09350]

value: female

value: bone marrow


title: Plasma_cells_Multiple_Myeloma [T09347]

value: male

value: sorted plasma cells (CD138+)


title: Plasma_cells_Multiple_Myeloma [T09977]


title: NT_DEX_PVY_3 [OE400]

value: PVY

value: lesions with surrounding area


title: NT_DEX_mock_1 [OE402]


title: Plasma_cells_Multiple_Myeloma [T09320]


title: Plasma_cells_Multiple_Myeloma [T09325]

value: MPV


title: NT_DEX_PVY_1 [OE394]


title: Plasma_cells_Multiple_Myeloma [T09215]


title: NahG_DEX_mock_1 [OE386]

value: NahG


title: NT_DEX_PVY_2 [OE396]


title: Plasma_cells_Multiple_Myeloma [T09190]


title: Plasma_cells_Multiple_Myeloma [T09300]


title: Plasma_cells_Multiple_Myeloma [T09306]


title: Plasma_cells_Multiple_Myeloma [T09186]

value: RD-Dara


title: Plasma_cells_Multiple_Myeloma [T09167]


title: NahG_DEX_mock_2 [OE387]


title: NahG_DEX_PVY_1 [OE378]


title: NahG_DEX_PVY_2 [OE379]


title: Plasma_cells_Multiple_Myeloma [T09164]


title: Plasma_cells_Multiple_Myeloma [T09142]

value: RD


title: TGA2.1-NahG_control_mock_1 [OE372]

value: control


title: Plasma_cells_Multiple_Myeloma [T09091]

value: Dara-RD


title: TGA2.1-NahG_control_mock_2 [OE373]


title: TGA2.1-NahG_DEX_mock_2 [OE367]


title: TGA2.1-NahG_DEX_mock_3 [OE369]


title: Plasma_cells_Multiple_Myeloma [T09107]


title: TGA2.1-NahG_DEX_mock_1 [OE365]


title: NahG_DEX_mock_3 [OE390]

value: nd


title: Plasma_cells_Multiple_Myeloma [T09072]


title: Plasma_cells_Multiple_Myeloma [T09198]


title: TGA2.1-NahG_control_PVY_3 [OE362]


title: NahG_DEX_PVY_3 [OE383]

value: DEX


title: Plasma_cells_Multiple_Myeloma [T09016]


title: Plasma_cells_Multiple_Myeloma [T09031]


title: Plasma_cells_Multiple_Myeloma [T09009]


title: TGA2.1-NahG_DEX_PVY_3 [OE352]


title: Plasma_cells_Multiple_Myeloma [T08975]


title: Plasma_cells_Multiple_Myeloma [T08974]


title: Plasma_cells_Multiple_Myeloma [T08951]

value: VD


title: TGA2.1-NahG_control_PVY_2 [OE358]


title: Plasma_cells_Multiple_Myeloma [T08945]


title: TGA2.1-NahG_control_PVY_1 [OE357]


title: TGA2.1-NahG_DEX_PVY_2 [OE350]


title: 118_RAW_shKDM1A_IL4_GPS2_rp2

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

country: China

institute: Nanjing University

library_source: genomic

data_processing:
ChIP-seq raw files (fastq or txt files, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
ATAC-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
RNA-seq raw files (fastq, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition. Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
Cut and Tag raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.

organism: Mus musculus

growth_protocol:
ChIP-Seq: WT RAW264.7 cells, lentivirus-medicated knockdown cells and GPS2 CRISPR KO cells were maintained normal 10% FBS DMEM medium.
ATAC-Seq: WT RAW264.7 cells were maintained normal 10% FBS DMEM medium.
RNA-Seq: BMDM cells were maintained normal 10% FBS DMEM medium supplement with 30% L929 medium for one week.
Cut&Tag: WT RAW264.7 cells were maintained normal 10% FBS DMEM medium.

extract_protocol:
ChIP-Seq: Fresh cells were crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 30 min, followed by 1% formaldehyde for 10 min at room temperature. Nuclei were isolated, sonicated and incubated with magnetic bead-antibody complexes.
ChIP-Seq: ChIPed DNA was processed using Takara SMRTer ThruPLEX DNA-seq Kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.
ATAC-Seq: WT RAW264.7 cells were seeded with triplicates in the 12 wells plates with 2×10^5 cells one day before the experiments. Cells were harvested with IL4 1h treatment, washed with PBS and then resuspended in lysis buffer. Cell nuclei were spined down and transferred into the transposition reaction buffer and incubated at 37 °C for 30 minutes using 105 cells. Genomic DNA was extracted using Qiagen MinElute PCR Purification Kit. ATAC-seq library was done with the protocol as previously reported (Buenrostro et al., 2015). The Purified ATAC-seq DNA library mix was sequenced on NextSeq 550 (Illumina, 35 SE reads, paired-end) in BEA Core Facility (Karolinska Institutet, Huddinge, Sweden).
ATAC-Seq: The ATAC-seq Library preparation was performed through the manufacturer's introduction.
RNA-Seq: 2×10^5 WT and GPS2 KO BMDM cells were seeded one day before the treatment. The next day the cells were treatment with IL4 6h and the total RNA was extracted from the manufacturer's introduction.
RNA-Seq: The RNA-seq library preparation was followed by the instructions of the NEB Next Ultra II RNA Library kit (NEB, E7770S).
Cut&Tag: 2×10^5 shGFP and shKDM1A RAW cells were seeded one day before.
Cut&Tag: The Cut and Tag Library preparation was performed through the manufacturer's introduction (Steven Henikoff lab,Bench top CUT&Tag V.3 ).

treatment_protocol:
ChIP-Seq: RAW264.7 cells were treated with or without LPS (100ng/ml) or IL4 (20ng/ml) treatment for indicated time.
ATAC-Seq: RAW264.7 cells were treated IL4 (20ng/ml) for 1h .
RNA-Seq: BMDM cells were treated with or without IL4 (20ng/ml) treatment for 6h.
Cut&Tag: No treatment

value: Macrophage

tag: strain

value: BALB/c

value: IL4 1h

tag: chip antibody

tag: chip antibody vendor

value: Cell Signaling

tag: chip antibody cat.


title: TGA2.1-NahG_DEX_PVY_1 [OE348]


title: 117_RAW_shKDM1A_IL4_GPS2_rp1


title: Plasma_cells_Multiple_Myeloma [T09053]

tag: subject id

value: multiple myeloma

value: female

value: bone marrow


title: 120_RAW_shKDM1A_IL4_STAT6_rp2


title: TGA2.1-NahG_control_mock_3 [OE374]

value: mock

value: mock sections


title: 116_RAW_shGFP_IL4_STAT6_rp2

value: Home made

value: No


title: 119_RAW_shKDM1A_IL4_STAT6_rp1


title: Plasma_cells_Multiple_Myeloma [T08863]

tag: diagnosis

value: male

value: sorted plasma cells (CD138+)


title: Plasma_cells_Multiple_Myeloma [T08933]

tag: Sex

value: MPV


title: 115_RAW_shGFP_IL4_STAT6_rp1


title: Plasma_cells_Multiple_Myeloma [T08919]

tag: age


title: Plasma_cells_Multiple_Myeloma [T08849]

tag: del1p32 status


title: 114_RAW_shGFP_IL4_GPS2_rp2

tag: treatment


title: Plasma_cells_Multiple_Myeloma [T08760]

value: RD-Dara

tag: tissue


title: 90_RAW_CRISPR_WT_H3K9me3_rp2

data_processing:
ChIP-seq raw files (fastq or txt files, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Supplementary_files_format_and_content: ChIP-seq: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.
ATAC-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Supplementary_files_format_and_content: ATAC-seq: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.
4C-seq raw files (fastq, single-end) were performed by the standard 4Cseqpipe protocol. The primer sequences were trimmed from the raw reads. The trimmed reads were mapped to the mm9 reference fragmented genome. The contact intensity was normalized by the fragment counts. The cis-interacting DNA contact profiles around the baits were plotted in the same chromosome window. As the 4C-seq program only provides the heatmaps, only the list of the 4C primers which was used to amplified the signals is provided.
RNA-seq raw files (fastq, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition.  Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
Supplementary_files_format_and_content: RNA-seq: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.
Cut and Tag raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Supplementary_files_format_and_content: CUT&TAG: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.

growth_protocol:
ChIP-Seq: WT RAW264.7 cells, lentivirus-medicated knockdown cells and GPS2 CRISPR KO cells were maintained normal 10% FBS DMEM medium.
ATAC-Seq: WT RAW264.7 cells were maintained normal 10% FBS DMEM medium.
4C-Seq: WT RAW264.7 cells were maintained normal 10% FBS DMEM medium.
RNA-Seq: BMDM cells were maintained normal 10% FBS DMEM medium supplement with 30% L929 medium for one week.
Cut&Tag: WT RAW264.7 cells were maintained normal 10% FBS DMEM medium.

extract_protocol:
ChIP-Seq: Fresh cells were crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 30 min, followed by 1% formaldehyde for 10 min at room temperature. Nuclei were isolated, sonicated and incubated with magnetic bead-antibody complexes.
ChIP-Seq: ChIPed DNA was processed using Takara SMRTer ThruPLEX DNA-seq Kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.
ATAC-Seq: WT RAW264.7 cells were seeded with triplicates in the 12 wells plates with 2×105 cells one day before the experiments. Cells were harvested with IL4 1h treatment, washed with PBS and then resuspended in lysis buffer. Cell nuclei were spined down and transferred into the transposition reaction buffer and incubated at 37 °C for 30 minutes using 105 cells. Genomic DNA was extracted using Qiagen MinElute PCR Purification Kit. ATAC-seq library was done with the protocol as previously reported (Buenrostro et al., 2015). The Purified ATAC-seq DNA library mix was sequenced on NextSeq 550 (Illumina, 35 SE reads, paired-end) in BEA Core Facility (Karolinska Institutet, Huddinge, Sweden).
ATAC-Seq: The ATAC-seq Library preparation was performed through the manufacturer's introduction.
4C-Seq: Fresh cells were crosslinked with 2% formaldehyde for 10 min at room temperature. Cells were counted and aliquoted with 10x7 cells per tube. For each 4C sample, 1 ml lysis buffer was applied for 10 min. Nuclei were spined down and discarded the supernatant. The nuclei were treated with the first digestion enzyme (Dpn II) overnight. The next day, the cell nuclei were heat-inactivated at 65C for 20 min and then treated with the first ligation enzyme overnight at room temperature. The genomic DNA was extracted and followed with the second digestion enzyme (Bfa I) overnight. Then heat-inactivated the enzyme and applied with then second the ligation enzyme overnight. The genomic DNA was purified again by phenol-chloroform extraction.
4C-Seq: PCR purified DNA (by baits) was processed using Takara SMRTer ThruPLEX DNA-seq Kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.
RNA-Seq: 2×105 WT and GPS2 KO BMDM cells were seeded one day before the treatment. The next day the cells were treatment with IL4 6h and the total RNA was extracted from the manufacturer's introduction.
RNA-Seq: The RNA-seq library preparation was followed by the instructions of the NEB Next Ultra II RNA Library kit (NEB, E7770S).
Cut&Tag: 2×105 shGFP and shKDM1A  RAW cells were seeded one day before.
Cut&Tag: The Cut and Tag Library preparation was performed through the manufacturer's introduction (Steven Henikoff lab,Bench top CUT&Tag V.3 ).

treatment_protocol:
ChIP-Seq:RAW264.7 cells were treated  with or without LPS (100ng/ml) or IL4 (20ng/ml) treatment for indicated time.
ATAC-Seq: RAW264.7 cells were treated IL4 (20ng/ml)  for 1h .
4C-Seq: RAW264.7 cells were treated  with or without LPS (100ng/ml) or IL4 (20ng/ml) treatment for indicated time.
RNA-Seq: BMDM cells were treated  with or without IL4 (20ng/ml) treatment for 6h.
Cut&Tag: No treatment

tag: cell type

value: Control

value: Abcam


title: 89_RAW_CRISPR_WT_H3K9me3_rp1

value: Macrophage


title: 88_RAW_CRISPR_GPS2_KO_H3K9me3_rp2

value: BALB/c


title: Plasma_cells_Multiple_Myeloma [T08873]

value: Dara-RD


title: 86_RAW_CRISPR_GPS2_KO_H3K4me2_rp2


title: Plasma_cells_Multiple_Myeloma [T08820]


title: 113_RAW_shGFP_IL4_GPS2_rp1

value: IL4 1h


title: Plasma_cells_Multiple_Myeloma [T08714]

value: multiple myeloma


title: Plasma_cells_Multiple_Myeloma [T08800]


title: 87_RAW_CRISPR_GPS2_KO_H3K9me3_rp1


title: Plasma_cells_Multiple_Myeloma [T08941]


title: Plasma_cells_Multiple_Myeloma [T08751]

value: VTD


title: 85_RAW_CRISPR_GPS2_KO_H3K4me2_rp1


title: 83_RAW_WT_CRISPR_Con_H3K4me2_rp1


title: Plasma_cells_Multiple_Myeloma [T08689]

value: bone marrow


title: Plasma_cells_Multiple_Myeloma [T08681]

value: VD


title: Plasma_cells_Multiple_Myeloma [T08662]

value: female


title: Plasma_cells_Multiple_Myeloma [T08667]


title: 82_RAW_CRISPR_GPS2_KO_LSD1_rp2


title: 84_RAW_WT_CRISPR_Con_H3K4me2_rp2


title: Plasma_cells_Multiple_Myeloma [T08856]

value: RD


title: Plasma_cells_Multiple_Myeloma [T08612]


title: 80_RAW_WT_CRISPR_Con_LSD1_rp2


title: Plasma_cells_Multiple_Myeloma [T08626]


title: 78_RAW_CRISPR_GPS2_KO_H3K4me3_rp2


title: Plasma_cells_Multiple_Myeloma [T08608]


title: 79_RAW_WT_CRISPR_Con_LSD1_rp1


title: 76_RAW_WT_CRISPR_Con_H3K4me3_rp2


title: Plasma_cells_Multiple_Myeloma [T08564]

value: VCD


title: 77_RAW_CRISPR_GPS2_KO_H3K4me3_rp1


title: Plasma_cells_Multiple_Myeloma [T08527]

value: male


title: 75_RAW_WT_CRISPR_Con_H3K4me3_rp1


title: 73_RAW_CRISPR_GPS2_KO_H3K4me1_rp1


title: 74_RAW_CRISPR_GPS2_KO_H3K4me1_rp2


title: Plasma_cells_Multiple_Myeloma [T08661]

value: sorted plasma cells (CD138+)


title: Plasma_cells_Multiple_Myeloma [T08513]

value: MPV


title: 72_RAW_WT_CRISPR_Con_H3K4me1_rp2


title: Plasma_cells_Multiple_Myeloma [T08488]


title: Plasma_cells_Multiple_Myeloma [T08496]


title: 71_RAW_WT_CRISPR_Con_H3K4me1_rp1


title: 81_RAW_CRISPR_GPS2_KO_LSD1_rp1


title: Plasma_cells_Multiple_Myeloma [T08507]


title: 70_RAW_input

value: No antibody

value: No


title: Plasma_cells_Multiple_Myeloma [T08516]


title: Plasma_cells_Multiple_Myeloma [T08464]


title: Plasma_cells_Multiple_Myeloma [T08449]


title: Plasma_cells_Multiple_Myeloma [T08461]


title: 68_RAW_shSTAT6_IL4_H3K27ac_rp1

value: Abcam


title: 69_RAW_shSTAT6_IL4_H3K27ac_rp2

value: Macrophage


title: 65_RAW_shSTAT6_IL4_GPS2_rp2

value: BALB/c

value: Home made


title: 67_RAW_shGFP_IL4_H3K27ac_rp2

value: IL4 1h


title: Plasma_cells_Multiple_Myeloma [T08413]

value: multiple myeloma


title: Plasma_cells_Multiple_Myeloma [T08439]


title: 64_RAW_shSTAT6_IL4_GPS2_rp1


title: 66_RAW_shGFP_IL4_H3K27ac_rp1


title: Plasma_cells_Multiple_Myeloma [T08402]


title: 63_RAW_shGFP_IL4_GPS2_rp2


title: 62_RAW_shGFP_IL4_GPS2_rp1


title: Plasma_cells_Multiple_Myeloma [T08393]


title: Plasma_cells_Multiple_Myeloma [T08371]


title: Plasma_cells_Multiple_Myeloma [T08360]


title: 61_RAW_shSTAT6_IL4_STAT6_rp2

value: Cell Signaling


title: 60_RAW_shSTAT6_IL4_STAT6_rp1


title: Plasma_cells_Multiple_Myeloma [T08357]

value: bone marrow


title: Plasma_cells_Multiple_Myeloma [T08301]


title: 59_RAW_shGFP_IL4_STAT6_rp2


title: 58_RAW_shGFP_IL4_STAT6_rp1


title: Plasma_cells_Multiple_Myeloma [T08295]


title: Plasma_cells_Multiple_Myeloma [T08292]


title: 56_RAW_shNCOR_GPS2_rp1

value: Control


title: 57_RAW_shNCOR_GPS2_rp2


title: Plasma_cells_Multiple_Myeloma [T08277]


title: Plasma_cells_Multiple_Myeloma [T08278]

value: female


title: Plasma_cells_Multiple_Myeloma [T08411]


title: 55_RAW_shGPS2_GPS2_rp2


title: 54_RAW_shGPS2_GPS2_rp1


title: Plasma_cells_Multiple_Myeloma [T08275]


title: 53_RAW_shGFP_GPS2_rp2


title: 52_RAW_shGFP_GPS2_rp1


title: Plasma_cells_Multiple_Myeloma [T08249]


title: 51_RAW_shNCOR_NCOR_rp1

value: NCOR

value: Bethyl


title: 50_RAW_shNCOR_NCOR_rp1


title: 49_RAW_shGFP_NCOR_rp2


title: Plasma_cells_Multiple_Myeloma [T08216]

value: male


title: Plasma_cells_Multiple_Myeloma [T08207]

value: sorted plasma cells (CD138+)


title: Plasma_cells_Multiple_Myeloma [T08208]


title: Plasma_cells_Multiple_Myeloma [T08175]

value: MPV


title: Plasma_cells_Multiple_Myeloma [T08149]

value: RD


title: 46_RAW_CRISPR_GPS2_KO_IL4_1h_STAT6_rp1


title: 43_RAW_WT_CRISPR_Con_IL4_1h_STAT6_rp2


title: Plasma_cells_Multiple_Myeloma [T08168]


title: 47_RAW_CRISPR_GPS2_KO_IL4_1h_STAT6_rp2


title: Plasma_cells_Multiple_Myeloma [T08162]

value: VCD-HDM


title: Plasma_cells_Multiple_Myeloma [T08250]


title: 42_RAW_WT_CRISPR_Con_IL4_1h_STAT6_rp1


title: Plasma_cells_Multiple_Myeloma [T08255]

value: VD


title: 40_RAW_WT_CRISPR_Con_STAT6_rp1

value: Macrophage


title: Plasma_cells_Multiple_Myeloma [T08148]


title: 32_RAW_WT_IL4_1h_H3K27ac_rp2

value: BALB/c

value: Abcam


title: Plasma_cells_Multiple_Myeloma [T08093]


title: 48_RAW_shGFP_NCOR_rp1


title: 44_RAW_CRISPR_GPS2_KO_con_STAT6_rp1


title: Plasma_cells_Multiple_Myeloma [T08095]


title: Plasma_cells_Multiple_Myeloma [T08195]


title: Plasma_cells_Multiple_Myeloma [T08128]


title: 31_RAW_WT_IL4_1h_H3K27ac_rp1

value: IL4 1h


title: Plasma_cells_Multiple_Myeloma [T08170]

value: multiple myeloma


title: 45_RAW_CRISPR_GPS2_KO_con_STAT6_rp2

value: Cell Signaling


title: 30_RAW_WT_H3K27ac_rp2


title: Plasma_cells_Multiple_Myeloma [T08041]

value: VRD

value: bone marrow


title: Plasma_cells_Multiple_Myeloma [T08040]


title: 29_RAW_WT_H3K27ac_rp1

value: Control


title: 41_RAW_WT_CRISPR_Con_STAT6_rp2


title: Plasma_cells_Multiple_Myeloma [T08686]

value: female


title: Plasma_cells_Multiple_Myeloma [T08026]


title: Plasma_cells_Multiple_Myeloma [T08008]


title: 27_RAW_WT_IL4_1h_GPS2_rp1

value: Home made

value: No


title: Plasma_cells_Multiple_Myeloma [T08000]

value: sorted plasma cells (CD138+)


title: Plasma_cells_Multiple_Myeloma [T07991]

value: RD-Dara


title: 28_RAW_WT_IL4_1h_GPS2_rp2


title: 22_RAW_GPS2_CRISPR_KO_IL4_pSTAT6_rp2

value: Thermo


title: 25_RAW_WT_GPS2_rp1


title: 21_RAW_GPS2_CRISPR_KO_IL4_pSTAT6_rp1


title: 23_RAW_GPS2_CRISPR_KO_pSTAT6_rp1


title: 17_RAW_WT_CRISPR_Con_pSTAT6_rp1


title: 24_RAW_GPS2_CRISPR_KO_pSTAT6_rp2


title: Plasma_cells_Multiple_Myeloma [T07975]

value: male

value: MPV


title: Plasma_cells_Multiple_Myeloma [T07983]


title: Plasma_cells_Multiple_Myeloma [T07927]


title: Plasma_cells_Multiple_Myeloma [T07959]


title: 20_RAW_WT_CRISPR_IL4_pSTAT6_rp2

value: Macrophage


title: 19_RAW_WT_CRISPR_IL4_pSTAT6_rp1

value: BALB/c


title: Plasma_cells_Multiple_Myeloma [T07926]


title: Plasma_cells_Multiple_Myeloma [T07971]

value: VCD


title: 18_RAW_WT_CRISPR_Con_pSTAT6_rp2


title: 16_RAW_GPS2_CRISPR_KO_IL4_H3K27ac_rp2

value: IL4 1h

value: Abcam


title: Plasma_cells_Multiple_Myeloma [T07996]

value: multiple myeloma


title: Plasma_cells_Multiple_Myeloma [T07911]

value: RD


title: 15_RAW_GPS2_CRISPR_KO_IL4_H3K27ac_rp1


title: Plasma_cells_Multiple_Myeloma [T07910]

value: bone marrow


title: Plasma_cells_Multiple_Myeloma [T07862]

value: VCD-HDM


title: 14_RAW_GPS2_CRISPR_KO_Con_H3K27ac_rp2

value: Control


title: 13_RAW_GPS2_CRISPR_KO_Con_H3K27ac_rp1


title: Plasma_cells_Multiple_Myeloma [T07823]

value: female

value: VTD


title: 12_RAW_WT_CRISPR_IL4_H3K27ac_rp2


title: 11_RAW_WT_CRISPR_IL4_H3K27ac_rp1


title: Plasma_cells_Multiple_Myeloma [T07812]

value: sorted plasma cells (CD138+)


title: Plasma_cells_Multiple_Myeloma [T07776]


title: Plasma_cells_Multiple_Myeloma [T07785]


title: Plasma_cells_Multiple_Myeloma [T07760]


title: Plasma_cells_Multiple_Myeloma [T07739]


title: 7_RAW_GPS2_CRISPR_KO_IL4_PolII_rp1

value: Pol II

value: BioLegend


title: Plasma_cells_Multiple_Myeloma [T07687]


title: Plasma_cells_Multiple_Myeloma [T07770]

value: male


title: Plasma_cells_Multiple_Myeloma [T07751]


title: Plasma_cells_Multiple_Myeloma [T07837]


title: 8_RAW_GPS2_CRISPR_KO_IL4_PolII_rp2


title: 6_RAW_GPS2_CRISPR_KO_Con_PolII_rp2


title: 9_RAW_WT_CRISPR_Con_H3K27ac_rp1


title: Plasma_cells_Multiple_Myeloma [T07697]


title: Plasma_cells_Multiple_Myeloma [T07683]


title: 10_RAW_WT_CRISPR_Con_H3K27ac_rp2


title: 5_RAW_GPS2_CRISPR_KO_Con_PolII_rp1


title: 2_RAW_WT_CRISPR_Con_PolII_rp2


title: 9_RAW_shKDM1A_ATACseq_rp1


title: 1_RAW_WT_CRISPR_Con_PolII_rp1


title: 4_RAW_WT_CRISPR_IL4_PolII_rp2


title: 3_RAW_WT_CRISPR_IL4_PolII_rp1


title: Plasma_cells_Multiple_Myeloma [T07649]


title: Plasma_cells_Multiple_Myeloma [T07665]


title: 8_RAW_shGFP_ATACseq_rp2


title: 10_RAW_shKDM1A_ATACseq_rp2


title: Plasma_cells_Multiple_Myeloma [T07615]

value: VD


title: 7_RAW_shGFP_ATACseq_rp1

value: Macrophage


title: Plasma_cells_Multiple_Myeloma [T07679]

value: MPV


title: Plasma_cells_Multiple_Myeloma [T07602]


title: Plasma_cells_Multiple_Myeloma [T07614]


title: 6_RAW_ATACseq_WT_IL4_1h_3

value: BALB/c


title: Plasma_cells_Multiple_Myeloma [T07585]


title: 5_RAW_ATACseq_WT_IL4_1h_2

value: IL4 1h


title: Plasma_cells_Multiple_Myeloma [T07581]


title: 3_RAW_ATACseq_WT_3


title: Plasma_cells_Multiple_Myeloma [T07575]


title: Plasma_cells_Multiple_Myeloma [T07579]


title: 2_RAW_ATACseq_WT_2


title: Plasma_cells_Multiple_Myeloma [T07550]


title: Plasma_cells_Multiple_Myeloma [T07555]


title: 1_RAW_ATACseq_WT_1


title: Plasma_cells_Multiple_Myeloma [T07624]


title: RAW_CRISPR_KO_basal_Ptgs1_promoter_bait_4C_seq

description: library strategy: 4C-seq


title: Plasma_cells_Multiple_Myeloma [T07543]


title: Plasma_cells_Multiple_Myeloma [T07539]


title: RAW_WT_IL4_1h_Ptgs1_promoter_bait_4C_seq

description: library strategy: 4C-seq


title: RAW_WT_Con_Ptgs1_promoter_bait_4C_seq

description: library strategy: 4C-seq


title: RAW_CRISPR_GPS2_KO_basal_Ptgs1_promoter_bait_4C_seq

description: library strategy: 4C-seq


title: RAW_Con_Ptgs1_promoter_bait_4C_seq

description: library strategy: 4C-seq


title: RAW_LPS_1h_Ptgs1_promoter_bait_4C_seq

description: library strategy: 4C-seq

value: LPS 1h


title: Plasma_cells_Multiple_Myeloma [T07549]

value: multiple myeloma


title: Plasma_cells_Multiple_Myeloma [T07534]


title: BMDM_GPS2_KO_IL4_RNA_seq_3

source_name: BMDM cells

value: IL4 6h


title: Plasma_cells_Multiple_Myeloma [T07532]

value: bone marrow


title: 4_RAW_ATACseq_WT_IL4_1h_1


title: Plasma_cells_Multiple_Myeloma [T07519]


title: Plasma_cells_Multiple_Myeloma [T07517]


title: Plasma_cells_Multiple_Myeloma [T07506]


title: Plasma_cells_Multiple_Myeloma [T07545]


title: BMDM_GPS2_KO_IL4_RNA_seq_1


title: Plasma_cells_Multiple_Myeloma [T07503]

value: RD


title: BMDM_GPS2_KO_RNA_seq_4

value: Control


title: BMDM_GPS2_KO_RNA_seq_3


title: Plasma_cells_Multiple_Myeloma [T07462]

value: female


title: BMDM_GPS2_KO_IL4_RNA_seq_4


title: Plasma_cells_Multiple_Myeloma [T07451]


title: Plasma_cells_Multiple_Myeloma [T07478]


title: Plasma_cells_Multiple_Myeloma [T07415]


title: Plasma_cells_Multiple_Myeloma [T07417]


title: Plasma_cells_Multiple_Myeloma [T07453]


title: BMDM_WT_IL4_RNA_seq_4


title: BMDM_WT_IL4_RNA_seq_1


title: BMDM_GPS2_KO_RNA_seq_2


title: BMDM_WT_IL4_RNA_seq_3


title: BMDM_WT_RNA_seq_4


title: BMDM_WT_RNA_seq_3


title: Plasma_cells_Multiple_Myeloma [T07404]


title: Plasma_cells_Multiple_Myeloma [T07398]


title: Plasma_cells_Multiple_Myeloma [T07387]


title: BMDM_GPS2_KO_IL4_RNA_seq_2


title: Plasma_cells_Multiple_Myeloma [T07374]


title: BMDM_WT_RNA_seq_1


title: Plasma_cells_Multiple_Myeloma [T07372]


title: Plasma_cells_Multiple_Myeloma [T07367]


title: BMDM_GPS2_KO_RNA_seq_1


title: BMDM_WT_IL4_RNA_seq_2


title: Plasma_cells_Multiple_Myeloma [T07343]


title: Plasma_cells_Multiple_Myeloma [T07347]


title: Plasma_cells_Multiple_Myeloma [T07346]


title: Plasma_cells_Multiple_Myeloma [T07339]


title: Plasma_cells_Multiple_Myeloma [T07312]


title: Plasma_cells_Multiple_Myeloma [T07330]


title: Plasma_cells_Multiple_Myeloma [T07303]

value: VCD-HDM


title: Plasma_cells_Multiple_Myeloma [T07307]

value: sorted plasma cells (CD138+)


title: BMDM_WT_RNA_seq_2


title: Plasma_cells_Multiple_Myeloma [T07261]


title: Plasma_cells_Multiple_Myeloma [T07239]


title: Plasma_cells_Multiple_Myeloma [T07348]


title: Plasma_cells_Multiple_Myeloma [T07235]


title: Plasma_cells_Multiple_Myeloma [T07212]


title: HCT116_SHC6_1+d repeat2

type: RNA

city: Guangzhou

first: Boyu

last: zhang

state: Guangdong

address: Yuancun Road

institute: The Sixth Affiliated Hospital of Sun Yat-sen University

description:
SHC6_1_d_2_NS
Gene expression data from HCT116_SHC6_1+d_2

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Affy packages in R.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: All cell lines were cultured at 37°C and 5% CO2 in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone) .

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Cells were treated with ddH2O (HCT116_SHC6_1_1 and  HCT116_SHC6_1_2) or Doxycycline (HCT116_SHC6_1+d_1 and HCT116_SHC6_1+d_2) to induce CHD6 knock-down

tag: cell line

value: Colorectal cancer cells

tag: genotype/variation

value: Tet-on inducible CHD6 KD construct

value: doxycycline for 48hrs


title: 26_RAW_WT_GPS2_rp2

value: Home made

value: No


title: Plasma_cells_Multiple_Myeloma [T07208]


title: Plasma_cells_Multiple_Myeloma [T07153]

value: male


title: Plasma_cells_Multiple_Myeloma [T07164]


title: HCT116_SHC6_1+d repeat1

description:
SHC6_1_d_1_NS
Gene expression data from HCT116_SHC6_1+d_1


title: HCT116_SHC6_1 repeat2

description:
SHC6_1_2_NS
Gene expression data from HCT116_SHC6_1_2

value: vehicle


title: GFPtreat_3

city: shijiazhuang

first: Xinhua

last: Zhang

state: Hebei

address: ZhongshanRoad NO.361

department: Biochemistry and Molecular Biology

institute: Hebei Medical University

description: Gene expression GFPtreat_3

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the  RNA Purification kit (Tiangen, China) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: smooth muscle cells

value: GFP


title: SvbRep rep2

first: Cedric

last: Polesello

address: 118 Route de Narbonne

institute: Centre de Biologie Intégrative de Toulouse

data_processing:
Quality of sequencing was measured with fastQC (v0.11.5)
Reads were mapped on dm6 genome (r6.13 flybase) with bwa (v0.7.17- r1188) using default parameters, unique reads were filtered and peak calling was done on replicates merge files with MACS2 2 -f BAM --B --g dm --to-large --nomodel --q 0.0001 (Sensible condition) or --q 0.1 (Stringent condition)) for Svb forms
ChIPseq signal was normalized by taking into account the genome mapping with bamCoverage5 (--binSize 10 --normalizeUsing RPKM --effectiveGenomeSize 125464728),
then normalized for the noise due to the experiment with bigwigCompare (-b1 experiment file -b2 input file --scaleFactors 1:1 --operation "log2").
Because SvbREP is less expressed than SvbACT in S2 cells, we scaled peaks signal by the result of the ratio of logFC for svb in the two conditions (scaleFactors 1.41:1)
Assembly: dm6
Supplementary files format and content: bigwig files generated with bamCoverage --binSize 10 --normalizeUsing RPKM --effectiveGenomeSize 125464728 for replicates files
Supplementary files format and content: bigwig files generated with bamCoverage --binSize 10 --normalizeUsing RPKM --effectiveGenomeSize 125464728 and bigwigCompare -b1 bigwig IP file -b2 bigwig Input file --scaleFactors 1.41:1 (for SvbRep) 1:1 (for SvbAct) --operation "log2" for replicates merged files

organism: Drosophila melanogaster

source_name: FS

growth_protocol: Drosophila S2 cells were grown in Schneider medium supplemented with 10% fetal calf serum and 1% penicillin/streptomycin.

extract_protocol:
DNA fragments were purified by phenol- chloroform protocol and resuspended in TE.
ChIPseq of Control, SvbREP and SvbACT S2 cells (single-end 50 nt) were performed with HiSeq 2000 (Illumina) at BGI with standard protocols

treatment_protocol: We used cell lines stably transformed with the copper-inducible construct pMT-Svb::GFP and pMT-pri ("SvbACT condition") or pMT-Svb::GFP and pMT-pri1-4fs ("SvbREP condition"). Cells were treated with Copper during 24h

value: S2 cells

tag: gebotype

value: SvbREP

value: GFP:GFP-TRAP gta-20 (chromotek) Lot N° 70828001A

value: treated with Cu2+ for 24 hours


title: SvbRep Input


title: CLL patient 1 Treated vs Untreated

city: Liverpool

first: Joseph

last: Slupsky

state: Select State

address: Sherrington Building, Dept Molecular and Clinical Cancer Med

department: Molecular and Clinical Cancer Medicine

country: United Kingdom

institute: University of Liverpool

description: Biological Replicate 1

hyb_protocol: Hybridization and washing was performed according to the protocol provided by Agilent (Two-Color Microarray-Based Gene Expression Analysis, CAT# G4140-90050, Version 5.7)

scan_protocol: Arrays were scanned with an Agilent Array scanner according to the manufacturers protocols.

data_processing: Data was processed using Agilent software according to the manufacturer's protocols, and then analysed using limma in Bioconductor 2.10.

source_name: CLL cells

label_protocol: 10ug RNA from each condition was reverse transcribed and labelled with Cy5 or Cy3 according to the protocol provided by Agilent (Two-Color Microarray-Based Gene Expression Analysis, CAT# G4140-90050, Version 5.7)

growth_protocol: Primary human CLL cells were purified from 4 patient samples. These samples were cultured in RPMI 1640 + 0.5% BSA, pen/strep, L-Gln)

extract_protocol: RNA was extracted from CLL cell pellets using RNeasy Mini Kit from Qiagen according to the protocol provided by the manufacturer.

treatment_protocol: Cells were maintained for 24h in the presence (mithramycin-treated) or absence (untreated) of 200nM mithramycin.

value: Primary

value: malignant B lymphocytes

tag: condition

value: Untreated

value: Treated


title: control3

description: Gene expression control3

value: control


title: CLL patient 2 Treated vs Untreated

description: Biological Replicate 2


title: GFPtreat_1

description: Gene expression GFPtreat_1


title: KLF4 treat_1

description: Gene expression KLF4 treat_1

source_name: KLF4 treat_1


title: Plasma_cells_Multiple_Myeloma [T07143]

value: multiple myeloma

value: female

value: MPV

value: bone marrow

value: sorted plasma cells (CD138+)


title: CLL patient 4 Treated vs Untreated

description: Biological Replicate 4


title: CLL patient 3 Treated vs Untreated

description: Biological Replicate 3


title: KLF4 treat_2

description: Gene expression KLF4 treat_2

source_name: KLF4 treat_2


title: SvbRep rep1


title: SvbAct Input

value: SvbACT


title: Plasma_cells_Multiple_Myeloma [T07140]

value: male


title: HCT116_SHC6_1 repeat1

description:
SHC6_1_1_NS
Gene expression data from HCT116_SHC6_1_1

value: Colorectal cancer cells

value: Tet-on inducible CHD6 KD construct

value: vehicle


title: GFPtreat_2

description: Gene expression GFPtreat_2

value: smooth muscle cells

value: GFP


title: Plasma_cells_Multiple_Myeloma [T07127]


title: KLF4 treat_3

description: Gene expression KLF4 treat_3

source_name: KLF4 treat_3


title: Plasma_cells_Multiple_Myeloma [T07144]


title: control1

description: Gene expression control1


title: SvbAct rep1

value: S2 cells

value: GFP:GFP-TRAP gta-20 (chromotek) Lot N° 70828001A

value: treated with Cu2+ for 24 hours


title: Input Ctrl rep2

description: Input ChIPseq on S2 cells

data_processing:
Quality of sequencing was measured with fastQC (v0.11.5)
Reads were mapped on dm6 genome (r6.13 flybase) with bwa (v0.7.17- r1188) using default parameters, unique reads were filtered and peak calling was done on replicates merge files with MACS2 --nomodel --f BAMPE --g dm --B --q 1 e-05 --broad
ChIPseq signal was normalized by taking into account the genome mapping with bamCoverage5 (--binSize 10 --normalizeUsing RPKM --effectiveGenomeSize 125464728),
then normalized for the noise due to the experiment with bigwigCompare (-b1 experiment file -b2 input file --scaleFactors 1:1 --operation "log2").
Because SvbREP is less expressed than SvbACT in S2 cells, we scaled peaks signal by the result of the ratio of logFC for svb in the two conditions (scaleFactors 1.41:1)
Assembly: dm6
Supplementary files format and content: bigwig files generated with bamCoverage --binSize 10 --normalizeUsing RPKM --effectiveGenomeSize 125464728 for replicates files
Supplementary files format and content: bigwig files generated with bamCoverage --binSize 10 --normalizeUsing RPKM --effectiveGenomeSize 125464728 and bigwigCompare -b1 bigwig IP file -b2 bigwig Input file --scaleFactors 1:1 --operation "log2" for replicates merged files

source_name: Ctrl

extract_protocol:
DNA fragments were purified by phenol- chloroform protocol and resuspended in TE.
ChIPseq of Histones Marks on S2 cells (paired-end 50 nt) were performed with HiSeq 2000 (Illumina) at MGX with standard protocols
with NovaSeq Reagent Kits (300 cycles). The histones ChIPseq bank constructions were also done by Montpellier Genomix platform with TruSeq® ChIP Sample Preparation (Illumina)

tag: genotype

value: Input ChIPseq


title: Plasma_cells_Multiple_Myeloma [T07105]


title: Input Ctrl rep1

description: Input ChIPseq on S2 cells


title: Input Rep rep2

description: Input ChIPseq  on S2 cells expressing SvbREP form

value: S2 cells expressing SvbREP form


title: Plasma_cells_Multiple_Myeloma [T07103]

value: multiple myeloma

value: VCD-HDM


title: Plasma_cells_Multiple_Myeloma [T07087]

value: female

value: MPV


title: Plasma_cells_Multiple_Myeloma [T07120]

value: RD

value: bone marrow

value: sorted plasma cells (CD138+)


title: control2

description: Gene expression control2

value: control


title: Plasma_cells_Multiple_Myeloma [T07055]

value: male

value: VCD


title: Plasma_cells_Multiple_Myeloma [T07049]


title: Input Act rep1

description: Input ChIPseq on S2 cells expressing SvbACT form

value: S2 cells expressing SvbACT form


title: Plasma_cells_Multiple_Myeloma [T07019]


title: H3K27me3 Ctrl rep1

description: ChIPseq of H3K27me3 on S2 cells

value: H3K27me3:ab6002 (abcam)


title: Plasma_cells_Multiple_Myeloma [T07036]


title: H3K27me3 Rep rep 2

description: ChIPseq of H3K27me3 on S2 cells expressing SvbREP form

value: S2 cells


title: Plasma_cells_Multiple_Myeloma [T07015]


title: Input Act rep2


title: SvbAct rep 2

value: SvbACT

value: GFP:GFP-TRAP gta-20 (chromotek) Lot N° 70828001A


title: Plasma_cells_Multiple_Myeloma [T07009]


title: H3K27me3 Act rep 2

description: ChIPseq of H3K27me3 on S2 cells expressing SvbACT form

value: treated with Cu2+ for 24 hours


title: H3K27me3 Rep rep 1

value: S2 cells expressing SvbREP form


title: H3K27me3 Act rep 1


title: H3K27ac Ctrl rep1

description: ChIPseq of H3K27ac on S2 cells

value: H3K27ac:ab4729 (abcam)


title: Plasma_cells_Multiple_Myeloma [T06997]

value: multiple myeloma


title: Plasma_cells_Multiple_Myeloma [T06991]


title: H3K27ac Rep rep 2

description: ChIPseq of H3K27ac on S2 cells expressing SvbREP form


title: Plasma_cells_Multiple_Myeloma [T06990]

value: female


title: Input Rep rep1

description: Input ChIPseq on S2 cells expressing SvbREP form

value: Input ChIPseq


title: Plasma_cells_Multiple_Myeloma [T07038]

value: MPV


title: Plasma_cells_Multiple_Myeloma [T06984]

value: bone marrow


title: Plasma_cells_Multiple_Myeloma [T06983]

value: sorted plasma cells (CD138+)


title: H3K27ac Act rep 1

description: ChIPseq of H3K27ac on S2 cells expressing SvbACT form


title: Plasma_cells_Multiple_Myeloma [T06965]


title: H3K27ac Rep rep 1


title: H3K27ac Act rep 2


title: H3K4me3 Ctrl rep2

description: ChIPseq of H3K4me3 on S2 cells

value: H3K4me3 :  ab8580 (abcam)


title: Plasma_cells_Multiple_Myeloma [T06922]

value: male


title: H3K4me3 Ctrl rep1

description: ChIPseq of H3K4me3 on S2 cells


title: Plasma_cells_Multiple_Myeloma [T06917]


title: Plasma_cells_Multiple_Myeloma [T06921]

value: RD


title: Plasma_cells_Multiple_Myeloma [T06957]

value: VCD-HDM


title: H3K4me3 Act rep 2

description: ChIPseq of H3K4me3 on S2 cells expressing SvbACT form

value: S2 cells expressing SvbACT form


title: Plasma_cells_Multiple_Myeloma [T06911]


title: H3K4me3 Rep rep 2

description: ChIPseq of H3K4me3 on S2 cells expressing SvbREP form

value: S2 cells


title: H3K4me3 Rep rep 1


title: H3K4me3 Act rep 1


title: Plasma_cells_Multiple_Myeloma [T06892]


title: Plasma_cells_Multiple_Myeloma [T06890]


title: Plasma_cells_Multiple_Myeloma [T06875]

value: MLN-RD


title: H3K4me1 Rep rep 2

description: ChIPseq of H3K4me1 on S2 cells expressing SvbREP form

value: H3K4me1:  ab8895 (abcam)


title: H3K4me1 Ctrl rep1

description: ChIPseq of H3K4me1 on S2 cells

value: treated with Cu2+ for 24 hours


title: Plasma_cells_Multiple_Myeloma [T06873]


title: Plasma_cells_Multiple_Myeloma [T06861]


title: H3K4me1 Act rep 1

description: ChIPseq of H3K4me1 on S2 cells expressing SvbACT form


title: H3K4me1 Act rep 2


title: Plasma_cells_Multiple_Myeloma [T06833]

value: VRD


title: S2_SvbRep rep 2

data_processing:
Quality of sequencing was measured with fastQC (v0.11.5)
Sequenced reads were mapped on Drosophila genome (r6.13 Flybase) with STAR (v 2.5.2b default parameters)
Reads were counted with HTseq-count (v 0.6.0, parameter -t gene -r pos - i gene_symbol)
Statistical analysis were performed with edgeR using the negative binomial generalized log-linear model to the read counts ( gmLRT), the TMM normalization and decideTest were used to determine the differentially expressed genes.
Clustering analysis was performed on the matrix of the reads count average centrered and reduced for each condition previously filtered for the gene expression (difference of read > 50 between condition. n = 3556 gene
Two steps of clustering were done. The hierarchical ascendant clustering was performed with R function hclust() with the Spearman distance and the Ward.D2 option.
The k-means clustering was done with R function kmeans() with default options and k = 5. The kmeans clustering was repeated 15 times ( 5 times with predefined centroid and 10 with random centroids). The predefined centroids are genes of differents cluster defined by the hierarchical clustering.
Different k-means clusters obtained by each repetition were compared with cluster_similarity (Clusteval v 0.1). Clustering is similar if the score eaqual 1.
Assembly: dm6
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with normalized counts, logFC, Pvalue, LogCPM, status for expressed genes
Supplementary files format and content: Matrix table with logFC and Pvalue for  gene which had a difference of read > 50 between condition and every sample prepared for the clustering analysis

extract_protocol:
Cells were harvested and RNA extraction was made with Rneasy Kit (Qiagen).
Banks of reads and sequencing were done by HiSeq 2000 (Illumina) at BGI at single-end 50nt per replicate using standard Illumina protocols

treatment_protocol: We used cell lines stably transformed with the copper-inducibleconstruct pMT-Svb::GFP and pMT-pri ("SvbACT condition") or pMT-Svb::GFP and pMT-pri1-4fs ("SvbREP condition")

value: pMT Svb::GFP ; pMT pri 1-4fs::GFP


title: S2_SvbRep rep 1


title: S2_Ctrl rep 2

source_name: S2 Ctrl

value: wild type


title: S2_SvbAct rep 2

value: pMT Svb::GFP ; pMT pri wt::GFP


title: Plasma_cells_Multiple_Myeloma [T06834]

value: multiple myeloma

value: female

value: VRD-R


title: S2_SvbAct rep 1


title: Plasma_cells_Multiple_Myeloma [T06819]

value: bone marrow

value: sorted plasma cells (CD138+)


title: Plasma_cells_Multiple_Myeloma [T06815]


title: Plasma_cells_Multiple_Myeloma [T06818]

value: male

value: VCD


title: H3K4me1 Rep rep 1

value: S2 cells expressing SvbREP form


title: Plasma_cells_Multiple_Myeloma [T06807]


title: DRIP-seq WT biol rep 2

city: Davis

first: Frederic

last: Chedin

state: CA

address: 1 Shields Avenue

department: MCB

country: USA

institute: UC Davis

data_processing:
For LAMS-HTGTS, sequences were processed and analyzed as detailed in (Crowe et al., 2018; Hu et al., 2016; https://github.com/robinmeyers/transloc_pipeline) with minor adjustments. Briefly, sequences were aligned to custom genomes, substituting the mm9 sequence from (114, 494, 415–114, 666, 816) with sequence from the NG_005838.1 (Genbank accession no. NG_005838.1) C57BL/6 IgH sequence on chr 12 (to 11,172 to 183,818), or sequence from the AJ851868.3 (GenBank accession no AJ851868.3) 129 IgH sequence (1,415,966– 1,592,715).Junctions were analyzed by comparing sequences to both C57BL/6 and S129 backgrounds. A consensus genome was generated between C57BL/6 and S129, and if reads fell into either category they were deemed not mutated—this eliminated over-estimation of insertions, deletions, and mismatch mutations. Of note, no junctions aligned to S129 on one side and C57BL/6. Deletions are defined as regions missing nucleotides adjacent to prey-break site but having 100% homology in flanking regions. Insertions are defined as regions containing nucleotides that map to neither the bait nor the prey-break site. Microhomologies (MHs) are defined as regions of 100% homology between the bait and the prey-break site. Blunt junctions are considered to have no MHs or insertions. Additional scripts used to analysis can be found in github (https://github.com/srhartono/TCseqplus).
For DRIP-seq, raw sequencing reads were trimmed with fastq-mcf v2.4.4 and mapped to mm9 genome with bowtie2 v2.2.6. Wig files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30). Peak bed files were generated using HMM as previously described in (Sanz et al., 2016) and converted into bigBed using bedToBigBed.
Assembly: mm9
Supplementary files format and content: bigWig, bigBed, and tlx (tab-separated files containing translocation coodinates and information)
Library strategy: DRIP-Seq

source_name: Spleen

growth_protocol: Setx-/- , Rnaseh2bf/f, and CD19cre mice were previously described and used to generate Setx-/- Rnaseh2bf/f CD19cre mice (Becherel et al., 2013; Hiller et al., 2012; Rickert et al., 1997)

extract_protocol:
For LAMS-HTGTS, genomic DNA was isolated from WT, Setx-/- , Rnaseh2bf/f , and Setx-/- Rnaseh2bf/f cells 72 hours after stimulation to switch to IgG1 with 72 h LPS/IL-4/α-RP105.
For DRIP-seq, genomic DNA was gently extracted by SDS/Proteinase K treatment at 37°C followed by phenol-chloroform extraction and ethanol precipitation. The extracted genomic DNA was fragmented with restriction enzyme (Hindlll, Xbal, EcoRI, SspI, BrsGI), 4 micrograms of digested DNA were incubated with 2 micrograms of S9.6 antibody overnight at 4 ℃ in DRIP buffer (10 mM NaPO4 pH 7.0, 140 mM NaCl, 0.05% Triton X-100). In vitro RNase H digestion was used to generate a negative control. After incubation, antibody-DNA complexes were bound to Protein G Dynabeads and thoroughly washed, DNA was recovered with Chelex-100, the bound fraction was suspended in 0.1 ml 10% Chelex-100 (Bio-Rad), vortexed, boiled for 10 min, and cooled to room temperature. This sample was added to 4 μl of 20 mg/ml Proteinase K followed by incubation at 55°C for 30 min while shaking. Beads were boiled for another 10 min. Sample was centrifuged and supernatant collected. Beads were suspended with 100 μl 2× TE to the beads, vortexed, centrifuged, and supernatants pooled.
For LAMS-HTGTS, linear amplification-mediated high-throughput genome-wide translocation sequencing (LAM-HTGTS) libraries were prepared from genomic DNA as previously described (Hu et al., 2016; Yin, Liu, Liu, & Hu, 2019; Yin, Liu, Liu, Wu, et al., 2019).
For DRIP-seq, libraries were prepared as described in (Ginno et al., 2012; Sanz et al., 2016)

treatment_protocol:
CD43- resting B cells were isolated and cultured in B cell media (BCM, RPMI-1640 supplemented with 10% fetal calf serum, 1% L-glutamine, 50 IU/ml penicillin/streptomycin, 1% sodium pyruvate, 53 μM 2-mercaptoethanol, 10 mM HEPES).
B cells were stimulated with LPS, α-RP105 and interleukin 4 (IL-4) for IgG1, LPS/α-RP105/TGF-B for IgG2b and LPS/α-RP105/TGF-B/CD40L for IgA class switch recombination.

value: Spleen

value: primary B cells

value: WT


title: Plasma_cells_Multiple_Myeloma [T06816]


title: Plasma_cells_Multiple_Myeloma [T06796]

value: VCD-HDM


title: S2_Ctrl rep 1


title: Plasma_cells_Multiple_Myeloma [T06765]


title: Plasma_cells_Multiple_Myeloma [T06756]

value: MLN-RD


title: Plasma_cells_Multiple_Myeloma [T06853]


title: Plasma_cells_Multiple_Myeloma [T06768]


title: DRIP-seq rnaseh2b-/- biol rep 2


title: DRIP-seq rnaseh2b-/- setx-/- biol rep 2

value: rnaseh2b-/- setx-/-


title: DRIP-seq rnaseh2b-/- setx-/- biol rep 1


title: DRIP-seq setx-/- biol rep 2

value: setx-/-


title: Plasma_cells_Multiple_Myeloma [T06747]


title: DRIP-seq WT biol rep 1


title: Plasma_cells_Multiple_Myeloma [T06733]


title: Plasma_cells_Multiple_Myeloma [T06734]


title: DRIP-seq rnaseh2b-/- biol rep 1


title: DRIP-seq setx-/- biol rep 1


title: Plasma_cells_Multiple_Myeloma [T06709]


title: Plasma_cells_Multiple_Myeloma [T06708]


title: Plasma_cells_Multiple_Myeloma [T06699]


title: S2_2_96

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

data_processing:
Raw reads were aligned to the mouse reference genome GRCm39v26 downloaded from GENCODE using STAR-2.7.5a with default parameters.
Transcript quantification was performed with RSEM program version 1.3.0 and the mouse GENCODE gene annotation version M27
Quality control and outlier cell detection was performed using Seurat R package.
Assembly: GRCm39
Supplementary files format and content: tab delimited TPM table

source_name: CD8 T cells

extract_protocol:
cells were sorted in 96 well plates directly in lysis buffer with a FACS Aria III sorter (BD Biosciences)
SMARTSeq v2 protocol with Illumina Nextera XT

tag: strain

value: C57BL/6J (RRID:IMSR_JAX:000664)

value: CD8 T cells

tag: disease state

value: Zika


title: S2_2_95


title: Plasma_cells_Multiple_Myeloma [T06705]

value: multiple myeloma

value: VTD


title: Plasma_cells_Multiple_Myeloma [T06691]

value: female

value: bone marrow


title: S2_2_92


title: S2_2_93


title: S2_2_84


title: S2_2_88


title: Plasma_cells_Multiple_Myeloma [T06667]

value: male

value: sorted plasma cells (CD138+)


title: S2_2_91


title: S2_2_80


title: S2_2_85


title: Plasma_cells_Multiple_Myeloma [T06644]

value: MPV


title: S2_2_77


title: S2_2_86


title: Plasma_cells_Multiple_Myeloma [T06688]


title: S2_2_79


title: Plasma_cells_Multiple_Myeloma [T06625]


title: S2_2_87


title: S2_2_76


title: Plasma_cells_Multiple_Myeloma [T06590]


title: Plasma_cells_Multiple_Myeloma [T06650]


title: S2_2_78


title: Plasma_cells_Multiple_Myeloma [T06612]


title: Plasma_cells_Multiple_Myeloma [T06639]

value: RD


title: Plasma_cells_Multiple_Myeloma [T06641]


title: Plasma_cells_Multiple_Myeloma [T06574]


title: Plasma_cells_Multiple_Myeloma [T06638]


title: S2_2_94


title: S2_2_73


title: Plasma_cells_Multiple_Myeloma [T06558]


title: S2_2_72


title: Plasma_cells_Multiple_Myeloma [T06535]


title: Plasma_cells_Multiple_Myeloma [T06556]


title: S2_2_68


title: Plasma_cells_Multiple_Myeloma [T06549]


title: S2_2_69


title: S2_2_62


title: Plasma_cells_Multiple_Myeloma [T06469]


title: S2_2_71


title: S2_2_67R


title: S2_2_63


title: S2_2_70


title: S2_2_60


title: Plasma_cells_Multiple_Myeloma [T06518]


title: S2_2_61


title: S2_2_59


title: Plasma_cells_Multiple_Myeloma [T06527]


title: Plasma_cells_Multiple_Myeloma [T06482]


title: Plasma_cells_Multiple_Myeloma [T06450]


title: S2_2_56


title: Plasma_cells_Multiple_Myeloma [T06426]


title: S2_2_58


title: S2_2_54


title: Plasma_cells_Multiple_Myeloma [T06451]


title: S2_2_55


title: Plasma_cells_Multiple_Myeloma [T06422]


title: Plasma_cells_Multiple_Myeloma [T06425]

value: VCD


title: Plasma_cells_Multiple_Myeloma [T06530]


title: Plasma_cells_Multiple_Myeloma [T06508]


title: Plasma_cells_Multiple_Myeloma [T06454]


title: Plasma_cells_Multiple_Myeloma [T06420]


title: S2_2_49


title: Plasma_cells_Multiple_Myeloma [T06392]


title: S2_2_52


title: Plasma_cells_Multiple_Myeloma [T06390]


title: S2_2_47


title: R11444


title: NS2_93


title: NS2_94


title: Plasma_cells_Multiple_Myeloma [T06341]


title: Plasma_cells_Multiple_Myeloma [T06347]


title: Plasma_cells_Multiple_Myeloma [T06328]


title: NS2_95


title: Plasma_cells_Multiple_Myeloma [T06504]


title: NS2_92


title: NS2_90


title: NS2_96


title: Plasma_cells_Multiple_Myeloma [T06283]


title: S2_2_53


title: Plasma_cells_Multiple_Myeloma [T06264]

value: VD


title: NS2_89


title: NS2_88


title: Plasma_cells_Multiple_Myeloma [T06277]


title: Plasma_cells_Multiple_Myeloma [T06419]


title: S2_2_51


title: NS2_87


title: S2_2_48


title: Plasma_cells_Multiple_Myeloma [T06230]


title: Plasma_cells_Multiple_Myeloma [T06378]


title: Plasma_cells_Multiple_Myeloma [T06312]

value: VCD-HDM


title: Plasma_cells_Multiple_Myeloma [T06195]


title: Plasma_cells_Multiple_Myeloma [T06374]


title: Plasma_cells_Multiple_Myeloma [T06228]


title: NS2_85


title: Plasma_cells_Multiple_Myeloma [T06173]


title: NS2_86


title: NS2_84


title: NS2_81


title: Plasma_cells_Multiple_Myeloma [T06151]


title: NS2_82


title: Plasma_cells_Multiple_Myeloma [T06143]


title: Plasma_cells_Multiple_Myeloma [T06123]


title: Plasma_cells_Multiple_Myeloma [T06103]

value: 14 VCD-HDM


title: Plasma_cells_Multiple_Myeloma [T06102]


title: NS2_80


title: NS2_8


title: Plasma_cells_Multiple_Myeloma [T06073]


title: Plasma_cells_Multiple_Myeloma [T06074]


title: NS2_77


title: Plasma_cells_Multiple_Myeloma [T06054]


title: NS2_79


title: Plasma_cells_Multiple_Myeloma [T06060]


title: Plasma_cells_Multiple_Myeloma [T06053]


title: Plasma_cells_Multiple_Myeloma [T06049]

value: MLN-RD


title: NS2_74


title: Plasma_cells_Multiple_Myeloma [T06017]


title: Plasma_cells_Multiple_Myeloma [T06025]


title: NS2_83


title: NS2_76


title: NS2_72


title: NS2_73


title: Plasma_cells_Multiple_Myeloma [T06015]


title: NS2_70


title: Plasma_cells_Multiple_Myeloma [T06000]


title: NS2_69


title: NS2_71


title: NS2_67


title: Plasma_cells_Multiple_Myeloma [T05980]


title: NS2_78


title: Plasma_cells_Multiple_Myeloma [T05964]


title: Plasma_cells_Multiple_Myeloma [T05966]


title: NS2_62


title: NS2_64


title: NS2_60


title: Plasma_cells_Multiple_Myeloma [T05961]


title: NS2_65


title: NS2_6


title: NS2_59


title: Plasma_cells_Multiple_Myeloma [T05939]


title: NS2_58


title: Plasma_cells_Multiple_Myeloma [T05908]


title: NS2_57


title: Plasma_cells_Multiple_Myeloma [T05918]


title: Plasma_cells_Multiple_Myeloma [T05999]


title: Plasma_cells_Multiple_Myeloma [T05894]


title: Plasma_cells_Multiple_Myeloma [T05892]


title: NS2_54


title: NS2_56


title: Plasma_cells_Multiple_Myeloma [T05893]


title: NS2_55


title: Plasma_cells_Multiple_Myeloma [T05977]


title: NS2_53


title: NS2_52


title: Plasma_cells_Multiple_Myeloma [T05888]

value: MPT


title: Plasma_cells_Multiple_Myeloma [T05868]


title: Plasma_cells_Multiple_Myeloma [T05880]


title: NS2_51

value: C57BL/6J (RRID:IMSR_JAX:000664)


title: Plasma_cells_Multiple_Myeloma [T05858]


title: NS2_50

value: CD8 T cells


title: Plasma_cells_Multiple_Myeloma [T05839]


title: NS2_49

value: Zika


title: NS2_48


title: Plasma_cells_Multiple_Myeloma [T05814]

value: multiple myeloma


title: Plasma_cells_Multiple_Myeloma [T05785]


title: Plasma_cells_Multiple_Myeloma [T05755]


title: NS2_43


title: NS2_42


title: Plasma_cells_Multiple_Myeloma [T05764]


title: Plasma_cells_Multiple_Myeloma [T05881]


title: NS2_45


title: NS2_41


title: Plasma_cells_Multiple_Myeloma [T05749]


title: Plasma_cells_Multiple_Myeloma [T05711]


title: Plasma_cells_Multiple_Myeloma [T05743]


title: Plasma_cells_Multiple_Myeloma [T05729]


title: Plasma_cells_Multiple_Myeloma [T05856]


title: NS2_4


title: NS2_38


title: Plasma_cells_Multiple_Myeloma [T05634]


title: NS2_39


title: NS2_40


title: Plasma_cells_Multiple_Myeloma [T05682]


title: NS2_37


title: Plasma_cells_Multiple_Myeloma [T05589]

value: VTD


title: NS2_5


title: NS2_31


title: NS2_35


title: NS2_30


title: Plasma_cells_Multiple_Myeloma [T05522]


title: NS2_46


title: Plasma_cells_Multiple_Myeloma [T05498]


title: NS2_28


title: NS2_26


title: Plasma_cells_Multiple_Myeloma [T05448]

value: female


title: NS2_25


title: Plasma_cells_Multiple_Myeloma [T05429]

value: bone marrow


title: Plasma_cells_Multiple_Myeloma [T05471]


title: Plasma_cells_Multiple_Myeloma [T05452]


title: NS2_23


title: NS2_24


title: Plasma_cells_Multiple_Myeloma [T05427]


title: Plasma_cells_Multiple_Myeloma [T05387]

value: male


title: Plasma_cells_Multiple_Myeloma [T05528]

value: sorted plasma cells (CD138+)


title: Plasma_cells_Multiple_Myeloma [T05381]

value: MPV


title: NS2_21


title: NS2_2


title: NS2_20


title: Plasma_cells_Multiple_Myeloma [T05338]

value: VRD


title: NS2_18


title: NS2_3


title: Plasma_cells_Multiple_Myeloma [T05506]


title: NS2_19


title: Plasma_cells_Multiple_Myeloma [T05260]


title: NS2_17


title: Plasma_cells_Multiple_Myeloma [T05251]


title: NS2_15


title: NS2_16


title: Plasma_cells_Multiple_Myeloma [T05206]


title: NS2_14


title: Plasma_cells_Multiple_Myeloma [T05198]


title: NS2_12


title: Plasma_cells_Multiple_Myeloma [T05159]


title: NS2_11


title: NS2_10


title: Plasma_cells_Multiple_Myeloma [T05192]


title: Plasma_cells_Multiple_Myeloma [T05153]


title: Plasma_cells_Multiple_Myeloma [T05303]


title: Plasma_cells_Multiple_Myeloma [T05315]


title: Plasma_cells_Multiple_Myeloma [T05147]


title: Plasma_cells_Multiple_Myeloma [T05128]


title: NS1_95


title: Plasma_cells_Multiple_Myeloma [T05078]


title: NS1_94


title: Plasma_cells_Multiple_Myeloma [T05080]


title: NS1_9R


title: Plasma_cells_Multiple_Myeloma [T05066]


title: Plasma_cells_Multiple_Myeloma [T05037]


title: Plasma_cells_Multiple_Myeloma [T05039]


title: NS1_90


title: NS1_88


title: NS1_89


title: Plasma_cells_Multiple_Myeloma [T05072]


title: NS1_93


title: NS1_92


title: NS1_87


title: Plasma_cells_Multiple_Myeloma [T05029]


title: NS1_86


title: Plasma_cells_Multiple_Myeloma [T04991]


title: NS1_85


title: Plasma_cells_Multiple_Myeloma [T04918]


title: NS1_83


title: Plasma_cells_Multiple_Myeloma [T04916]


title: NS1_84


title: NS1_91


title: Plasma_cells_Multiple_Myeloma [T05097]

value: RCD


title: NS1_82


title: Plasma_cells_Multiple_Myeloma [T04857]


title: NS1_81


title: Plasma_cells_Multiple_Myeloma [T04789]


title: Plasma_cells_Multiple_Myeloma [T04798]


title: NS1_79


title: Plasma_cells_Multiple_Myeloma [T04949]


title: Plasma_cells_Multiple_Myeloma [T04790]


title: Plasma_cells_Multiple_Myeloma [T04787]


title: Plasma_cells_Multiple_Myeloma [T04782]


title: NS1_77


title: NS1_78


title: Plasma_cells_Multiple_Myeloma [T04774]


title: NS1_75


title: NS1_74


title: NS1_76


title: Plasma_cells_Multiple_Myeloma [T04770]


title: Plasma_cells_Multiple_Myeloma [T04758]

value: KMP


title: NS1_73


title: NS1_72


title: Plasma_cells_Multiple_Myeloma [T04717]


title: Plasma_cells_Multiple_Myeloma [T04756]


title: NS1_71


title: NS1_69


title: NS1_7


title: Plasma_cells_Multiple_Myeloma [T04644]


title: NS1_80


title: Plasma_cells_Multiple_Myeloma [T04693]


title: NS1_68


title: NS1_67


title: Plasma_cells_Multiple_Myeloma [T04781]


title: Plasma_cells_Multiple_Myeloma [T04617]


title: Plasma_cells_Multiple_Myeloma [T04621]


title: NS1_65


title: Plasma_cells_Multiple_Myeloma [T04616]

value: RD


title: Plasma_cells_Multiple_Myeloma [T04613]

value: VD


title: Plasma_cells_Multiple_Myeloma [T04694]


title: NS1_64


title: Plasma_cells_Multiple_Myeloma [T04614]


title: NS1_63


title: NS1_62


title: Plasma_cells_Multiple_Myeloma [T04535]


title: Plasma_cells_Multiple_Myeloma [T04554]


title: Plasma_cells_Multiple_Myeloma [T04514]


title: NS1_61


title: Plasma_cells_Multiple_Myeloma [T04526]

value: VCD


title: NS1_60


title: NS1_59


title: Plasma_cells_Multiple_Myeloma [T04503]


title: NS1_6


title: NS1_66


title: Plasma_cells_Multiple_Myeloma [T04492]

value: MLN-RD


title: NS1_56

value: C57BL/6J (RRID:IMSR_JAX:000664)


title: NS1_55

value: CD8 T cells


title: Plasma_cells_Multiple_Myeloma [T04496]

value: VCD-HDM


title: Plasma_cells_Multiple_Myeloma [T04454]

value: multiple myeloma


title: NS1_58

value: Zika


title: NS1_57


title: Plasma_cells_Multiple_Myeloma [T04381]

value: female


title: NS1_54


title: Plasma_cells_Multiple_Myeloma [T04432]

value: bone marrow


title: NS1_53


title: Plasma_cells_Multiple_Myeloma [T04413]

value: male


title: Plasma_cells_Multiple_Myeloma [T04234]

value: sorted plasma cells (CD138+)


title: Plasma_cells_Multiple_Myeloma [T04471]


title: NS1_52


title: Plasma_cells_Multiple_Myeloma [T04303]


title: Plasma_cells_Multiple_Myeloma [T04328]

value: MPV


title: NS1_51


title: Plasma_cells_Multiple_Myeloma [T04269]


title: NS1_50


title: NS1_44


title: Plasma_cells_Multiple_Myeloma [T04225]


title: Plasma_cells_Multiple_Myeloma [T04183]


title: NS1_49


title: NS1_47


title: Plasma_cells_Multiple_Myeloma [T04224]


title: Plasma_cells_Multiple_Myeloma [T04221]


title: NS1_5


title: Plasma_cells_Multiple_Myeloma [T04165]


title: NS1_42


title: NS1_43


title: NS1_41


title: Plasma_cells_Multiple_Myeloma [T04173]


title: NS1_40


title: Plasma_cells_Multiple_Myeloma [T04156]


title: NS1_38


title: Plasma_cells_Multiple_Myeloma [T04130]


title: Plasma_cells_Multiple_Myeloma [T04118]


title: NS1_39


title: NS1_4


title: Plasma_cells_Multiple_Myeloma [T04098]


title: Plasma_cells_Multiple_Myeloma [T04077]


title: NS1_48


title: Plasma_cells_Multiple_Myeloma [T04057]


title: NS1_36


title: NS1_37


title: Plasma_cells_Multiple_Myeloma [T04020]


title: NS1_34


title: NS1_35


title: Plasma_cells_Multiple_Myeloma [T04038]


title: NS1_33


title: Plasma_cells_Multiple_Myeloma [T04004]


title: Plasma_cells_Multiple_Myeloma [T04029]


title: Plasma_cells_Multiple_Myeloma [T04006]


title: NS1_32


title: Plasma_cells_Multiple_Myeloma [T04001]


title: NS1_31


title: NS1_27


title: Plasma_cells_Multiple_Myeloma [T04000]


title: NS1_25


title: NS1_26


title: Plasma_cells_Multiple_Myeloma [T03951]


title: Plasma_cells_Multiple_Myeloma [T03937]


title: Plasma_cells_Multiple_Myeloma [T03944]


title: Plasma_cells_Multiple_Myeloma [T03926]


title: NS1_23


title: NS1_24


title: Plasma_cells_Multiple_Myeloma [T03954]


title: Plasma_cells_Multiple_Myeloma [T04052]


title: Plasma_cells_Multiple_Myeloma [T03881]


title: NS1_20


title: Plasma_cells_Multiple_Myeloma [T03831]


title: NS1_19


title: Plasma_cells_Multiple_Myeloma [T03762]


title: NS1_2


title: Plasma_cells_Multiple_Myeloma [T03693]


title: NS1_30


title: NS1_17


title: NS1_28


title: Plasma_cells_Multiple_Myeloma [T03771]


title: NS1_13


title: NS1_14


title: NS1_16


title: Plasma_cells_Multiple_Myeloma [T03640]


title: NS1_12


title: Plasma_cells_Multiple_Myeloma [T03620]


title: NS1_11


title: NS1_1


title: S2_2_7


title: S2_2_6


title: Plasma_cells_Multiple_Myeloma [T03565]


title: Plasma_cells_Multiple_Myeloma [T03501]


title: S2_2_46


title: S2_2_45


title: Plasma_cells_Multiple_Myeloma [T03468]


title: Plasma_cells_Multiple_Myeloma [T03578]


title: Plasma_cells_Multiple_Myeloma [T03460]


title: Plasma_cells_Multiple_Myeloma [T03446]


title: S2_2_43


title: NS1_15


title: Plasma_cells_Multiple_Myeloma [T03417]


title: S2_2_42


title: Plasma_cells_Multiple_Myeloma [T03638]


title: S2_2_41


title: S2_2_40


title: Plasma_cells_Multiple_Myeloma [T03381]


title: Plasma_cells_Multiple_Myeloma [T03613]


title: S2_2_39


title: S2_2_37


title: Plasma_cells_Multiple_Myeloma [T03376]


title: Plasma_cells_Multiple_Myeloma [T03377]

value: MPT


title: S2_2_36


title: S2_2_35


title: Plasma_cells_Multiple_Myeloma [T03306]


title: S2_2_31


title: S2_2_44


title: Plasma_cells_Multiple_Myeloma [T03302]


title: S2_2_3


title: Plasma_cells_Multiple_Myeloma [T03465]


title: Plasma_cells_Multiple_Myeloma [T03393]


title: Plasma_cells_Multiple_Myeloma [T03292]


title: Plasma_cells_Multiple_Myeloma [T03366]


title: Plasma_cells_Multiple_Myeloma [T03384]


title: S2_2_33


title: S2_2_32


title: Plasma_cells_Multiple_Myeloma [T03364]


title: Plasma_cells_Multiple_Myeloma [T03294]


title: Plasma_cells_Multiple_Myeloma [T03318]


title: S2_2_34


title: S2_2_29


title: Plasma_cells_Multiple_Myeloma [T03237]


title: Plasma_cells_Multiple_Myeloma [T03268]


title: S2_2_28


title: Plasma_cells_Multiple_Myeloma [T03222]


title: S2_2_24


title: S2_2_26


title: S2_2_22


title: S2_2_27


title: Plasma_cells_Multiple_Myeloma [T03219]


title: S2_2_21


title: Plasma_cells_Multiple_Myeloma [T03186]

value: VTD


title: Plasma_cells_Multiple_Myeloma [T03197]


title: S2_2_20


title: Plasma_cells_Multiple_Myeloma [T03181]


title: S2_2_2


title: S2_2_18


title: S2_2_15


title: S2_2_16


title: Plasma_cells_Multiple_Myeloma [T03084]


title: Plasma_cells_Multiple_Myeloma [T03235]


title: S2_2_14


title: S2_2_1


title: Plasma_cells_Multiple_Myeloma [T03169]


title: Plasma_cells_Multiple_Myeloma [T03174]

value: MD


title: S2_2_10


title: Plasma_cells_Multiple_Myeloma [T03077]


title: Plasma_cells_Multiple_Myeloma [T03069]


title: S2_2


title: Plasma_cells_Multiple_Myeloma [T03041]


title: Plasma_cells_Multiple_Myeloma [T03068]


title: Plasma_cells_Multiple_Myeloma [T03026]


title: S2_1_92


title: S2_1_96


title: Plasma_cells_Multiple_Myeloma [T03210]


title: Plasma_cells_Multiple_Myeloma [T02943]


title: Plasma_cells_Multiple_Myeloma [T03005]


title: S2_2_12


title: S2_1_91


title: S2_1_88


title: Plasma_cells_Multiple_Myeloma [T02978]


title: Plasma_cells_Multiple_Myeloma [T02920]


title: S2_1_93


title: Plasma_cells_Multiple_Myeloma [T02946]


title: S2_1_9


title: Plasma_cells_Multiple_Myeloma [T02909]

value: RD


title: Plasma_cells_Multiple_Myeloma [T03033]

value: VD


title: S2_2_11


title: S2_1_86


title: S2_1_79


title: S2_1_78


title: S2_1_87


title: Plasma_cells_Multiple_Myeloma [T02756]


title: Plasma_cells_Multiple_Myeloma [T02740]


title: Plasma_cells_Multiple_Myeloma [T02698]


title: Plasma_cells_Multiple_Myeloma [T02872]

value: VCD


title: S2_1_85


title: S2_1_74


title: S2_1_71


title: Plasma_cells_Multiple_Myeloma [T02676]


title: Plasma_cells_Multiple_Myeloma [T02800]


title: Plasma_cells_Multiple_Myeloma [T02842]


title: Plasma_cells_Multiple_Myeloma [T02860]


title: S2_1_70


title: Plasma_cells_Multiple_Myeloma [T02852]


title: S2_1_84


title: Plasma_cells_Multiple_Myeloma [T02725]


title: Plasma_cells_Multiple_Myeloma [T02925]


title: S2_1_8


title: S2_1_72


title: Plasma_cells_Multiple_Myeloma [T02656]


title: Plasma_cells_Multiple_Myeloma [T02673]


title: S2_1_67


title: S2_1_7


title: S2_1_75


title: S2_1_82


title: S2_1_81


title: S2_1_65


title: Plasma_cells_Multiple_Myeloma [T02662]


title: Plasma_cells_Multiple_Myeloma [T02622]


title: S2_1_77


title: Plasma_cells_Multiple_Myeloma [T02780]


title: S2_1_68


title: Plasma_cells_Multiple_Myeloma [T02554]


title: Plasma_cells_Multiple_Myeloma [T02661]


title: S2_1_61


title: Plasma_cells_Multiple_Myeloma [T02553]


title: Plasma_cells_Multiple_Myeloma [T02641]


title: Plasma_cells_Multiple_Myeloma [T02521]


title: S2_1_66


title: S2_1_59


title: S2_1_64


title: S2_1_62


title: Plasma_cells_Multiple_Myeloma [T02551]


title: S2_1_63


title: Plasma_cells_Multiple_Myeloma [T02494]


title: Plasma_cells_Multiple_Myeloma [T02602]


title: S2_1_60


title: Plasma_cells_Multiple_Myeloma [T02498]


title: Plasma_cells_Multiple_Myeloma [T02483]

value: MLN-RD


title: Plasma_cells_Multiple_Myeloma [T02442]


title: S2_1_6

value: C57BL/6J (RRID:IMSR_JAX:000664)


title: S2_1_5

value: CD8 T cells


title: Plasma_cells_Multiple_Myeloma [T02624]


title: S2_1_55


title: S2_1_57


title: Plasma_cells_Multiple_Myeloma [T02489]


title: Plasma_cells_Multiple_Myeloma [T02485]

value: VCD-HDM


title: Plasma_cells_Multiple_Myeloma [T02576]

value: multiple myeloma


title: Plasma_cells_Multiple_Myeloma [T02440]


title: S2_1_51

value: Zika


title: S2_1_48


title: S2_1_50


title: Plasma_cells_Multiple_Myeloma [T02468]


title: S2_1_52


title: S2_1_54


title: Plasma_cells_Multiple_Myeloma [T02439]

value: female


title: S2_1_47


title: S2_1_44


title: Plasma_cells_Multiple_Myeloma [T02431]

value: bone marrow


title: Plasma_cells_Multiple_Myeloma [T02414]

value: male


title: S2_1_43


title: S2_1_46


title: Plasma_cells_Multiple_Myeloma [T02413]

value: sorted plasma cells (CD138+)


title: Plasma_cells_Multiple_Myeloma [T02418]


title: Plasma_cells_Multiple_Myeloma [T02411]


title: S2_1_41


title: Plasma_cells_Multiple_Myeloma [T02374]


title: Plasma_cells_Multiple_Myeloma [T02315]

value: MPV


title: Plasma_cells_Multiple_Myeloma [T02369]


title: S2_1_34


title: S2_1_35


title: S2_1_42


title: Plasma_cells_Multiple_Myeloma [T02406]


title: S2_1_33


title: Plasma_cells_Multiple_Myeloma [T02310]


title: Plasma_cells_Multiple_Myeloma [T02397]


title: Plasma_cells_Multiple_Myeloma [T02394]


title: Plasma_cells_Multiple_Myeloma [T02392]


title: S2_1_39


title: S2_1_4


title: Plasma_cells_Multiple_Myeloma [T02331]


title: S2_1_45


title: S2_1_31


title: Plasma_cells_Multiple_Myeloma [T02276]


title: S2_1_36


title: Plasma_cells_Multiple_Myeloma [T02309]


title: Plasma_cells_Multiple_Myeloma [T02273]


title: Plasma_cells_Multiple_Myeloma [T02379]


title: S2_1_30


title: Plasma_cells_Multiple_Myeloma [T02254]


title: Plasma_cells_Multiple_Myeloma [T02280]

value: MPT


title: S2_1_3


title: S2_1_37


title: S2_1_24


title: S2_1_38


title: S2_1_29


title: S2_1_27


title: S2_1_28


title: Plasma_cells_Multiple_Myeloma [T02211]


title: S2_1_25


title: Plasma_cells_Multiple_Myeloma [T02229]


title: Plasma_cells_Multiple_Myeloma [T02252]


title: S2_1_20


title: S2_1_18


title: Plasma_cells_Multiple_Myeloma [T02157]


title: S2_1_19


title: Plasma_cells_Multiple_Myeloma [T02201]


title: S2_1_17


title: Plasma_cells_Multiple_Myeloma [T02181]

value: VTD


title: Plasma_cells_Multiple_Myeloma [T02127]


title: Plasma_cells_Multiple_Myeloma [T02192]


title: Plasma_cells_Multiple_Myeloma [T02190]


title: Plasma_cells_Multiple_Myeloma [T02130]


title: S2_1_16


title: S2_1_2


title: S2_1_13


title: Plasma_cells_Multiple_Myeloma [T02120]


title: S2_1_12


title: Plasma_cells_Multiple_Myeloma [T02082]


title: S1_2_95


title: Plasma_cells_Multiple_Myeloma [T02092]


title: S2_1_14


title: S1_2_96


title: S2_1_10


title: S1_2_94


title: S2_1_15


title: S1_2_93


title: Plasma_cells_Multiple_Myeloma [T02061]


title: Plasma_cells_Multiple_Myeloma [T02038]


title: Plasma_cells_Multiple_Myeloma [T02035]


title: Plasma_cells_Multiple_Myeloma [T02057]


title: Plasma_cells_Multiple_Myeloma [T02054]


title: S1_2_92


title: S1_2_91


title: Plasma_cells_Multiple_Myeloma [T02036]


title: S1_2_85


title: Plasma_cells_Multiple_Myeloma [T02100]


title: S1_2_83


title: Plasma_cells_Multiple_Myeloma [T02004]


title: Plasma_cells_Multiple_Myeloma [T02031]


title: S1_2_81


title: Plasma_cells_Multiple_Myeloma [T01983]


title: S1_2_82


title: S1_2_80


title: Plasma_cells_Multiple_Myeloma [T02078]


title: Plasma_cells_Multiple_Myeloma [T01979]


title: S1_2_78


title: Plasma_cells_Multiple_Myeloma [T01977]


title: Plasma_cells_Multiple_Myeloma [T01975]


title: Plasma_cells_Multiple_Myeloma [T01964]


title: S1_2_77


title: Plasma_cells_Multiple_Myeloma [T01951]


title: S1_2_76


title: Plasma_cells_Multiple_Myeloma [T01940]


title: Plasma_cells_Multiple_Myeloma [T01950]


title: Plasma_cells_Multiple_Myeloma [T01948]


title: S1_2_75


title: S1_2_73


title: S1_2_72


title: S1_2_71


title: S1_2_69


title: Plasma_cells_Multiple_Myeloma [T01913]


title: Plasma_cells_Multiple_Myeloma [T01911]


title: S1_2_67


title: S1_2_68