title: kidney biopsy [GSM3525079 re-analysis]


title: kidney biopsy [GSM3524397 re-analysis]

status: Public on Sep 04 2024

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: kidney biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol:
All human heart biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.
Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

tag: rej7aaclust (nr, minor, tcmr1, tcmr2, eabmr, fabmr, labmr)

tag: tissue

value: kidney biopsy


title: kidney biopsy [GSM3524478 re-analysis]

value: LABMR


title: kidney biopsy [GSM3525378 re-analysis]

value: Minor


title: kidney biopsy [GSM3525369 re-analysis]


title: kidney biopsy [GSM3525259 re-analysis]

value: NR


title: kidney biopsy [GSM3524328 re-analysis]


title: kidney biopsy [GSM3524747 re-analysis]


title: kidney biopsy [GSM3523972 re-analysis]


title: kidney biopsy [GSM3524034 re-analysis]


title: kidney biopsy [GSM3524548 re-analysis]


title: kidney biopsy [GSM3524036 re-analysis]

value: EABMR


title: kidney biopsy [GSM3524532 re-analysis]


title: kidney biopsy [GSM3524647 re-analysis]


title: kidney biopsy [GSM3524421 re-analysis]

value: FABMR


title: kidney biopsy [GSM3525583 re-analysis]


title: kidney biopsy [GSM3525444 re-analysis]


title: kidney biopsy [GSM3524516 re-analysis]


title: kidney biopsy [GSM3525423 re-analysis]


title: kidney biopsy [GSM3524650 re-analysis]


title: kidney biopsy [GSM3524349 re-analysis]


title: kidney biopsy [GSM3524616 re-analysis]


title: kidney biopsy [GSM3524018 re-analysis]


title: kidney biopsy [GSM3524310 re-analysis]


title: kidney biopsy [GSM3525083 re-analysis]


title: kidney biopsy [GSM3525351 re-analysis]


title: kidney biopsy [GSM3524146 re-analysis]


title: kidney biopsy [GSM3525248 re-analysis]


title: kidney biopsy [GSM3525391 re-analysis]


title: kidney biopsy [GSM3524949 re-analysis]


title: kidney biopsy [GSM3523925 re-analysis]


title: kidney biopsy [GSM3524209 re-analysis]


title: kidney biopsy [GSM3524152 re-analysis]


title: kidney biopsy [GSM3524213 re-analysis]


title: kidney biopsy [GSM3524527 re-analysis]


title: kidney biopsy [GSM3523897 re-analysis]


title: kidney biopsy [GSM3524838 re-analysis]


title: kidney biopsy [GSM3524158 re-analysis]


title: kidney biopsy [GSM3525162 re-analysis]


title: kidney biopsy [GSM3525332 re-analysis]


title: kidney biopsy [GSM3525339 re-analysis]


title: kidney biopsy [GSM3524395 re-analysis]


title: kidney biopsy [GSM3524137 re-analysis]


title: kidney biopsy [GSM3525513 re-analysis]


title: kidney biopsy [GSM3525456 re-analysis]


title: kidney biopsy [GSM3524997 re-analysis]


title: kidney biopsy [GSM3524077 re-analysis]


title: kidney biopsy [GSM3524676 re-analysis]


title: kidney biopsy [GSM3524686 re-analysis]


title: kidney biopsy [GSM3525644 re-analysis]


title: kidney biopsy [GSM3523913 re-analysis]


title: kidney biopsy [GSM3524498 re-analysis]


title: kidney biopsy [GSM3524142 re-analysis]


title: kidney biopsy [GSM3524108 re-analysis]


title: kidney biopsy [GSM3525177 re-analysis]


title: kidney biopsy [GSM3524288 re-analysis]


title: kidney biopsy [GSM3524341 re-analysis]


title: kidney biopsy [GSM3523960 re-analysis]


title: kidney biopsy [GSM3524954 re-analysis]


title: kidney biopsy [GSM3524046 re-analysis]


title: kidney biopsy [GSM3525089 re-analysis]


title: kidney biopsy [GSM3524183 re-analysis]


title: kidney biopsy [GSM3525021 re-analysis]


title: kidney biopsy [GSM3524593 re-analysis]


title: kidney biopsy [GSM3525440 re-analysis]


title: kidney biopsy [GSM3524112 re-analysis]


title: kidney biopsy [GSM3524715 re-analysis]


title: kidney biopsy [GSM3524230 re-analysis]


title: kidney biopsy [GSM3524985 re-analysis]


title: kidney biopsy [GSM3525228 re-analysis]


title: kidney biopsy [GSM3524706 re-analysis]


title: kidney biopsy [GSM3525128 re-analysis]


title: kidney biopsy [GSM3524481 re-analysis]


title: kidney biopsy [GSM3524794 re-analysis]


title: kidney biopsy [GSM3524268 re-analysis]


title: kidney biopsy [GSM3524880 re-analysis]


title: kidney biopsy [GSM3525301 re-analysis]


title: kidney biopsy [GSM3525254 re-analysis]


title: kidney biopsy [GSM3525054 re-analysis]


title: kidney biopsy [GSM3524621 re-analysis]


title: kidney biopsy [GSM3524984 re-analysis]


title: kidney biopsy [GSM3525071 re-analysis]


title: kidney biopsy [GSM3524340 re-analysis]


title: kidney biopsy [GSM3524396 re-analysis]


title: kidney biopsy [GSM3524234 re-analysis]


title: kidney biopsy [GSM3525502 re-analysis]


title: kidney biopsy [GSM3524440 re-analysis]


title: kidney biopsy [GSM3523927 re-analysis]


title: kidney biopsy [GSM3524423 re-analysis]


title: kidney biopsy [GSM3525475 re-analysis]


title: kidney biopsy [GSM3524536 re-analysis]


title: kidney biopsy [GSM3524681 re-analysis]


title: kidney biopsy [GSM3525484 re-analysis]


title: kidney biopsy [GSM3524988 re-analysis]


title: kidney biopsy [GSM3524886 re-analysis]


title: kidney biopsy [GSM3524702 re-analysis]


title: kidney biopsy [GSM3524468 re-analysis]


title: kidney biopsy [GSM3525130 re-analysis]


title: kidney biopsy [GSM3523955 re-analysis]


title: kidney biopsy [GSM3523929 re-analysis]


title: kidney biopsy [GSM3525471 re-analysis]


title: kidney biopsy [GSM3524499 re-analysis]


title: kidney biopsy [GSM3524270 re-analysis]


title: kidney biopsy [GSM3524231 re-analysis]


title: kidney biopsy [GSM3524255 re-analysis]


title: kidney biopsy [GSM3524662 re-analysis]


title: kidney biopsy [GSM3524775 re-analysis]


title: kidney biopsy [GSM3524825 re-analysis]


title: kidney biopsy [GSM3524261 re-analysis]


title: kidney biopsy [GSM3525247 re-analysis]


title: kidney biopsy [GSM3524791 re-analysis]


title: kidney biopsy [GSM3525024 re-analysis]


title: kidney biopsy [GSM3524675 re-analysis]


title: kidney biopsy [GSM3525044 re-analysis]


title: kidney biopsy [GSM3525318 re-analysis]


title: kidney biopsy [GSM3524149 re-analysis]


title: kidney biopsy [GSM3525252 re-analysis]


title: kidney biopsy [GSM3525545 re-analysis]


title: kidney biopsy [GSM3524952 re-analysis]


title: kidney biopsy [GSM3525123 re-analysis]


title: kidney biopsy [GSM3524287 re-analysis]


title: kidney biopsy [GSM3524744 re-analysis]


title: kidney biopsy [GSM3524688 re-analysis]


title: kidney biopsy [GSM3524607 re-analysis]


title: kidney biopsy [GSM3523922 re-analysis]


title: kidney biopsy [GSM3524846 re-analysis]


title: kidney biopsy [GSM3525331 re-analysis]


title: kidney biopsy [GSM3524057 re-analysis]


title: kidney biopsy [GSM3524903 re-analysis]


title: kidney biopsy [GSM3524950 re-analysis]


title: kidney biopsy [GSM3524586 re-analysis]


title: kidney biopsy [GSM3525435 re-analysis]


title: kidney biopsy [GSM3524148 re-analysis]


title: kidney biopsy [GSM3525226 re-analysis]


title: kidney biopsy [GSM3524086 re-analysis]


title: kidney biopsy [GSM3524964 re-analysis]


title: kidney biopsy [GSM3524580 re-analysis]


title: kidney biopsy [GSM3524072 re-analysis]


title: kidney biopsy [GSM3523998 re-analysis]


title: kidney biopsy [GSM3525531 re-analysis]


title: kidney biopsy [GSM3523902 re-analysis]


title: kidney biopsy [GSM3525522 re-analysis]


title: kidney biopsy [GSM3524784 re-analysis]


title: kidney biopsy [GSM3524094 re-analysis]


title: kidney biopsy [GSM3524247 re-analysis]


title: kidney biopsy [GSM3525190 re-analysis]


title: kidney biopsy [GSM3524163 re-analysis]


title: kidney biopsy [GSM3525209 re-analysis]


title: kidney biopsy [GSM3525137 re-analysis]


title: kidney biopsy [GSM3524133 re-analysis]


title: kidney biopsy [GSM3524326 re-analysis]


title: kidney biopsy [GSM3525227 re-analysis]


title: kidney biopsy [GSM3525220 re-analysis]


title: kidney biopsy [GSM3524486 re-analysis]


title: kidney biopsy [GSM3524426 re-analysis]


title: kidney biopsy [GSM3524862 re-analysis]


title: kidney biopsy [GSM3525109 re-analysis]


title: kidney biopsy [GSM3523932 re-analysis]


title: kidney biopsy [GSM3524687 re-analysis]


title: kidney biopsy [GSM3524123 re-analysis]


title: kidney biopsy [GSM3524151 re-analysis]


title: kidney biopsy [GSM3524178 re-analysis]


title: kidney biopsy [GSM3524313 re-analysis]


title: kidney biopsy [GSM3524021 re-analysis]


title: kidney biopsy [GSM3525017 re-analysis]


title: kidney biopsy [GSM3525510 re-analysis]


title: kidney biopsy [GSM3524369 re-analysis]


title: kidney biopsy [GSM3524165 re-analysis]


title: kidney biopsy [GSM3524177 re-analysis]


title: kidney biopsy [GSM3525069 re-analysis]


title: kidney biopsy [GSM3525142 re-analysis]


title: kidney biopsy [GSM3525100 re-analysis]


title: kidney biopsy [GSM3524832 re-analysis]


title: kidney biopsy [GSM3524332 re-analysis]


title: kidney biopsy [GSM3524132 re-analysis]


title: kidney biopsy [GSM3525334 re-analysis]


title: kidney biopsy [GSM3524211 re-analysis]


title: kidney biopsy [GSM3525371 re-analysis]


title: kidney biopsy [GSM3524196 re-analysis]


title: kidney biopsy [GSM3525352 re-analysis]


title: kidney biopsy [GSM3525390 re-analysis]


title: kidney biopsy [GSM3523908 re-analysis]


title: kidney biopsy [GSM3524564 re-analysis]


title: kidney biopsy [GSM3525567 re-analysis]


title: kidney biopsy [GSM3525180 re-analysis]


title: kidney biopsy [GSM3525436 re-analysis]


title: kidney biopsy [GSM3524409 re-analysis]


title: kidney biopsy [GSM3525096 re-analysis]


title: kidney biopsy [GSM3525561 re-analysis]


title: kidney biopsy [GSM3524274 re-analysis]


title: kidney biopsy [GSM3525509 re-analysis]


title: kidney biopsy [GSM3524799 re-analysis]


title: kidney biopsy [GSM3525153 re-analysis]


title: kidney biopsy [GSM3525293 re-analysis]


title: kidney biopsy [GSM3525418 re-analysis]


title: kidney biopsy [GSM3525076 re-analysis]


title: kidney biopsy [GSM3525303 re-analysis]


title: kidney biopsy [GSM3525289 re-analysis]


title: kidney biopsy [GSM3524801 re-analysis]


title: kidney biopsy [GSM3524346 re-analysis]


title: kidney biopsy [GSM3524491 re-analysis]


title: kidney biopsy [GSM3525461 re-analysis]


title: kidney biopsy [GSM3524644 re-analysis]


title: kidney biopsy [GSM3525478 re-analysis]


title: kidney biopsy [GSM3524524 re-analysis]


title: kidney biopsy [GSM3525307 re-analysis]


title: kidney biopsy [GSM3524609 re-analysis]


title: kidney biopsy [GSM3525032 re-analysis]


title: kidney biopsy [GSM3524962 re-analysis]


title: kidney biopsy [GSM3524002 re-analysis]


title: kidney biopsy [GSM3523903 re-analysis]


title: kidney biopsy [GSM3524658 re-analysis]


title: kidney biopsy [GSM3524110 re-analysis]


title: kidney biopsy [GSM3523961 re-analysis]


title: kidney biopsy [GSM3524010 re-analysis]


title: kidney biopsy [GSM3525308 re-analysis]


title: kidney biopsy [GSM3524946 re-analysis]


title: kidney biopsy [GSM3524082 re-analysis]


title: kidney biopsy [GSM3524154 re-analysis]


title: kidney biopsy [GSM3525266 re-analysis]


title: kidney biopsy [GSM3525364 re-analysis]


title: kidney biopsy [GSM3525288 re-analysis]


title: kidney biopsy [GSM3524097 re-analysis]


title: kidney biopsy [GSM3524103 re-analysis]


title: kidney biopsy [GSM3525576 re-analysis]


title: kidney biopsy [GSM3524088 re-analysis]


title: kidney biopsy [GSM3524849 re-analysis]


title: kidney biopsy [GSM3525356 re-analysis]


title: kidney biopsy [GSM3524722 re-analysis]


title: kidney biopsy [GSM3524017 re-analysis]


title: kidney biopsy [GSM3524703 re-analysis]


title: kidney biopsy [GSM3525586 re-analysis]


title: kidney biopsy [GSM3524683 re-analysis]


title: kidney biopsy [GSM3524035 re-analysis]


title: kidney biopsy [GSM3525203 re-analysis]


title: kidney biopsy [GSM3524820 re-analysis]


title: kidney biopsy [GSM3524301 re-analysis]


title: kidney biopsy [GSM3525232 re-analysis]


title: kidney biopsy [GSM3525204 re-analysis]


title: kidney biopsy [GSM3524685 re-analysis]


title: kidney biopsy [GSM3524020 re-analysis]


title: kidney biopsy [GSM3524897 re-analysis]


title: kidney biopsy [GSM3523942 re-analysis]


title: kidney biopsy [GSM3524562 re-analysis]


title: kidney biopsy [GSM3525532 re-analysis]


title: kidney biopsy [GSM3524790 re-analysis]


title: kidney biopsy [GSM3525578 re-analysis]


title: kidney biopsy [GSM3524850 re-analysis]


title: kidney biopsy [GSM3525571 re-analysis]


title: kidney biopsy [GSM3523898 re-analysis]


title: kidney biopsy [GSM3525026 re-analysis]


title: kidney biopsy [GSM3524185 re-analysis]


title: kidney biopsy [GSM3524975 re-analysis]


title: kidney biopsy [GSM3524248 re-analysis]


title: kidney biopsy [GSM3525382 re-analysis]


title: kidney biopsy [GSM3524511 re-analysis]


title: kidney biopsy [GSM3524915 re-analysis]


title: kidney biopsy [GSM3525154 re-analysis]


title: kidney biopsy [GSM3524651 re-analysis]


title: kidney biopsy [GSM3525156 re-analysis]


title: kidney biopsy [GSM3525253 re-analysis]


title: kidney biopsy [GSM3525496 re-analysis]


title: kidney biopsy [GSM3525349 re-analysis]


title: kidney biopsy [GSM3524214 re-analysis]


title: kidney biopsy [GSM3525053 re-analysis]


title: kidney biopsy [GSM3525424 re-analysis]


title: kidney biopsy [GSM3524603 re-analysis]


title: kidney biopsy [GSM3524104 re-analysis]


title: kidney biopsy [GSM3524631 re-analysis]


title: kidney biopsy [GSM3523905 re-analysis]


title: kidney biopsy [GSM3525012 re-analysis]


title: kidney biopsy [GSM3525634 re-analysis]


title: kidney biopsy [GSM3524031 re-analysis]


title: kidney biopsy [GSM3524890 re-analysis]


title: kidney biopsy [GSM3525473 re-analysis]


title: kidney biopsy [GSM3525111 re-analysis]


title: kidney biopsy [GSM3524543 re-analysis]


title: kidney biopsy [GSM3525188 re-analysis]


title: kidney biopsy [GSM3525374 re-analysis]


title: kidney biopsy [GSM3525649 re-analysis]


title: kidney biopsy [GSM3525528 re-analysis]


title: kidney biopsy [GSM3524559 re-analysis]


title: kidney biopsy [GSM3524367 re-analysis]


title: kidney biopsy [GSM3524116 re-analysis]


title: kidney biopsy [GSM3525002 re-analysis]


title: kidney biopsy [GSM3524712 re-analysis]


title: kidney biopsy [GSM3524312 re-analysis]


title: kidney biopsy [GSM3524265 re-analysis]


title: kidney biopsy [GSM3525108 re-analysis]


title: kidney biopsy [GSM3524164 re-analysis]


title: kidney biopsy [GSM3524188 re-analysis]


title: kidney biopsy [GSM3524155 re-analysis]


title: kidney biopsy [GSM3525511 re-analysis]


title: kidney biopsy [GSM3524150 re-analysis]


title: kidney biopsy [GSM3525296 re-analysis]


title: kidney biopsy [GSM3525257 re-analysis]


title: kidney biopsy [GSM3525192 re-analysis]


title: kidney biopsy [GSM3524872 re-analysis]


title: kidney biopsy [GSM3525541 re-analysis]


title: kidney biopsy [GSM3524345 re-analysis]


title: kidney biopsy [GSM3525181 re-analysis]


title: kidney biopsy [GSM3524581 re-analysis]


title: kidney biopsy [GSM3525474 re-analysis]


title: kidney biopsy [GSM3525617 re-analysis]


title: kidney biopsy [GSM3525529 re-analysis]


title: kidney biopsy [GSM3524635 re-analysis]


title: kidney biopsy [GSM3525383 re-analysis]


title: kidney biopsy [GSM3525092 re-analysis]


title: kidney biopsy [GSM3524058 re-analysis]


title: kidney biopsy [GSM3524767 re-analysis]


title: kidney biopsy [GSM3524372 re-analysis]


title: kidney biopsy [GSM3525287 re-analysis]


title: kidney biopsy [GSM3525224 re-analysis]


title: kidney biopsy [GSM3524296 re-analysis]


title: kidney biopsy [GSM3524338 re-analysis]


title: kidney biopsy [GSM3525648 re-analysis]


title: kidney biopsy [GSM3524668 re-analysis]


title: kidney biopsy [GSM3524432 re-analysis]


title: kidney biopsy [GSM3525291 re-analysis]


title: kidney biopsy [GSM3524472 re-analysis]


title: kidney biopsy [GSM3524918 re-analysis]


title: kidney biopsy [GSM3524232 re-analysis]


title: kidney biopsy [GSM3525144 re-analysis]


title: kidney biopsy [GSM3525127 re-analysis]


title: kidney biopsy [GSM3524379 re-analysis]


title: kidney biopsy [GSM3524411 re-analysis]


title: kidney biopsy [GSM3525185 re-analysis]


title: kidney biopsy [GSM3524049 re-analysis]


title: kidney biopsy [GSM3525367 re-analysis]


title: kidney biopsy [GSM3524299 re-analysis]


title: kidney biopsy [GSM3524386 re-analysis]


title: kidney biopsy [GSM3524483 re-analysis]


title: kidney biopsy [GSM3524754 re-analysis]


title: kidney biopsy [GSM3524758 re-analysis]


title: kidney biopsy [GSM3525426 re-analysis]


title: kidney biopsy [GSM3525489 re-analysis]


title: kidney biopsy [GSM3524374 re-analysis]


title: kidney biopsy [GSM3524403 re-analysis]


title: kidney biopsy [GSM3524487 re-analysis]


title: kidney biopsy [GSM3525537 re-analysis]


title: kidney biopsy [GSM3524600 re-analysis]


title: kidney biopsy [GSM3525283 re-analysis]


title: kidney biopsy [GSM3524006 re-analysis]


title: kidney biopsy [GSM3524930 re-analysis]


title: kidney biopsy [GSM3524916 re-analysis]


title: kidney biopsy [GSM3525110 re-analysis]


title: kidney biopsy [GSM3523923 re-analysis]


title: kidney biopsy [GSM3524896 re-analysis]


title: kidney biopsy [GSM3525385 re-analysis]


title: kidney biopsy [GSM3525357 re-analysis]


title: kidney biopsy [GSM3525061 re-analysis]


title: kidney biopsy [GSM3524471 re-analysis]


title: kidney biopsy [GSM3525596 re-analysis]


title: kidney biopsy [GSM3524220 re-analysis]


title: kidney biopsy [GSM3523983 re-analysis]


title: kidney biopsy [GSM3524725 re-analysis]


title: kidney biopsy [GSM3524473 re-analysis]


title: kidney biopsy [GSM3524661 re-analysis]


title: kidney biopsy [GSM3524554 re-analysis]


title: kidney biopsy [GSM3525140 re-analysis]


title: kidney biopsy [GSM3524641 re-analysis]


title: kidney biopsy [GSM3525212 re-analysis]


title: kidney biopsy [GSM3525056 re-analysis]


title: kidney biopsy [GSM3525450 re-analysis]


title: kidney biopsy [GSM3524235 re-analysis]


title: kidney biopsy [GSM3524430 re-analysis]


title: kidney biopsy [GSM3524285 re-analysis]


title: kidney biopsy [GSM3524680 re-analysis]


title: kidney biopsy [GSM3524144 re-analysis]


title: kidney biopsy [GSM3524063 re-analysis]


title: kidney biopsy [GSM3525543 re-analysis]


title: kidney biopsy [GSM3525163 re-analysis]


title: kidney biopsy [GSM3525327 re-analysis]


title: kidney biopsy [GSM3525635 re-analysis]


title: kidney biopsy [GSM3525506 re-analysis]


title: kidney biopsy [GSM3523964 re-analysis]


title: kidney biopsy [GSM3525564 re-analysis]


title: kidney biopsy [GSM3524711 re-analysis]


title: kidney biopsy [GSM3525217 re-analysis]


title: kidney biopsy [GSM3525060 re-analysis]


title: kidney biopsy [GSM3525141 re-analysis]


title: kidney biopsy [GSM3524557 re-analysis]


title: kidney biopsy [GSM3524738 re-analysis]


title: kidney biopsy [GSM3524294 re-analysis]


title: kidney biopsy [GSM3524040 re-analysis]


title: kidney biopsy [GSM3525465 re-analysis]


title: kidney biopsy [GSM3525556 re-analysis]


title: kidney biopsy [GSM3525095 re-analysis]


title: kidney biopsy [GSM3524139 re-analysis]


title: kidney biopsy [GSM3525448 re-analysis]


title: kidney biopsy [GSM3524470 re-analysis]


title: kidney biopsy [GSM3525148 re-analysis]


title: kidney biopsy [GSM3525451 re-analysis]


title: kidney biopsy [GSM3524569 re-analysis]


title: kidney biopsy [GSM3524634 re-analysis]


title: kidney biopsy [GSM3524821 re-analysis]


title: kidney biopsy [GSM3524027 re-analysis]


title: kidney biopsy [GSM3525218 re-analysis]


title: kidney biopsy [GSM3524981 re-analysis]


title: kidney biopsy [GSM3525398 re-analysis]


title: kidney biopsy [GSM3524280 re-analysis]


title: kidney biopsy [GSM3524229 re-analysis]


title: kidney biopsy [GSM3524578 re-analysis]


title: kidney biopsy [GSM3525507 re-analysis]


title: kidney biopsy [GSM3524292 re-analysis]


title: kidney biopsy [GSM3525611 re-analysis]


title: kidney biopsy [GSM3524705 re-analysis]


title: kidney biopsy [GSM3525431 re-analysis]


title: kidney biopsy [GSM3524424 re-analysis]


title: kidney biopsy [GSM3525230 re-analysis]


title: kidney biopsy [GSM3524808 re-analysis]


title: kidney biopsy [GSM3525194 re-analysis]


title: kidney biopsy [GSM3525058 re-analysis]


title: kidney biopsy [GSM3524013 re-analysis]


title: kidney biopsy [GSM3524936 re-analysis]


title: kidney biopsy [GSM3525604 re-analysis]


title: kidney biopsy [GSM3524855 re-analysis]


title: kidney biopsy [GSM3524062 re-analysis]


title: kidney biopsy [GSM3525302 re-analysis]


title: kidney biopsy [GSM3524335 re-analysis]


title: kidney biopsy [GSM3524914 re-analysis]


title: kidney biopsy [GSM3524987 re-analysis]


title: kidney biopsy [GSM3525498 re-analysis]


title: kidney biopsy [GSM3523924 re-analysis]


title: kidney biopsy [GSM3524098 re-analysis]


title: kidney biopsy [GSM3524176 re-analysis]


title: kidney biopsy [GSM3525119 re-analysis]


title: kidney biopsy [GSM3525597 re-analysis]


title: kidney biopsy [GSM3525037 re-analysis]


title: kidney biopsy [GSM3524461 re-analysis]


title: kidney biopsy [GSM3524492 re-analysis]


title: kidney biopsy [GSM3524126 re-analysis]


title: kidney biopsy [GSM3524768 re-analysis]


title: kidney biopsy [GSM3524357 re-analysis]


title: kidney biopsy [GSM3525535 re-analysis]


title: kidney biopsy [GSM3524720 re-analysis]


title: kidney biopsy [GSM3524032 re-analysis]


title: kidney biopsy [GSM3525377 re-analysis]


title: kidney biopsy [GSM3524393 re-analysis]


title: kidney biopsy [GSM3524786 re-analysis]


title: kidney biopsy [GSM3525072 re-analysis]


title: kidney biopsy [GSM3525104 re-analysis]


title: kidney biopsy [GSM3525046 re-analysis]


title: kidney biopsy [GSM3524951 re-analysis]


title: kidney biopsy [GSM3523940 re-analysis]


title: kidney biopsy [GSM3524813 re-analysis]


title: kidney biopsy [GSM3525043 re-analysis]


title: kidney biopsy [GSM3524159 re-analysis]


title: kidney biopsy [GSM3525458 re-analysis]


title: kidney biopsy [GSM3525075 re-analysis]


title: kidney biopsy [GSM3525575 re-analysis]


title: kidney biopsy [GSM3524606 re-analysis]


title: kidney biopsy [GSM3524637 re-analysis]


title: kidney biopsy [GSM3523916 re-analysis]


title: kidney biopsy [GSM3525030 re-analysis]


title: kidney biopsy [GSM3525324 re-analysis]


title: kidney biopsy [GSM3524652 re-analysis]


title: kidney biopsy [GSM3525370 re-analysis]


title: kidney biopsy [GSM3523971 re-analysis]


title: kidney biopsy [GSM3523894 re-analysis]


title: kidney biopsy [GSM3525200 re-analysis]


title: kidney biopsy [GSM3524882 re-analysis]


title: kidney biopsy [GSM3525001 re-analysis]


title: kidney biopsy [GSM3524982 re-analysis]


title: kidney biopsy [GSM3525503 re-analysis]


title: kidney biopsy [GSM3525632 re-analysis]


title: kidney biopsy [GSM3525195 re-analysis]


title: kidney biopsy [GSM3525297 re-analysis]


title: kidney biopsy [GSM3524657 re-analysis]


title: kidney biopsy [GSM3525223 re-analysis]


title: kidney biopsy [GSM3525323 re-analysis]


title: kidney biopsy [GSM3525333 re-analysis]


title: kidney biopsy [GSM3525133 re-analysis]


title: kidney biopsy [GSM3524400 re-analysis]


title: kidney biopsy [GSM3524466 re-analysis]


title: kidney biopsy [GSM3525105 re-analysis]


title: kidney biopsy [GSM3524445 re-analysis]


title: kidney biopsy [GSM3524905 re-analysis]


title: kidney biopsy [GSM3524180 re-analysis]


title: kidney biopsy [GSM3524508 re-analysis]


title: kidney biopsy [GSM3525236 re-analysis]


title: kidney biopsy [GSM3524998 re-analysis]


title: kidney biopsy [GSM3524125 re-analysis]


title: kidney biopsy [GSM3524716 re-analysis]


title: kidney biopsy [GSM3524953 re-analysis]


title: kidney biopsy [GSM3525397 re-analysis]


title: kidney biopsy [GSM3525404 re-analysis]


title: kidney biopsy [GSM3524717 re-analysis]


title: kidney biopsy [GSM3525280 re-analysis]


title: kidney biopsy [GSM3524042 re-analysis]


title: kidney biopsy [GSM3524898 re-analysis]


title: kidney biopsy [GSM3524398 re-analysis]


title: kidney biopsy [GSM3525413 re-analysis]


title: kidney biopsy [GSM3524352 re-analysis]


title: kidney biopsy [GSM3524169 re-analysis]


title: kidney biopsy [GSM3524907 re-analysis]


title: kidney biopsy [GSM3525585 re-analysis]


title: kidney biopsy [GSM3525124 re-analysis]


title: kidney biopsy [GSM3525559 re-analysis]


title: kidney biopsy [GSM3524736 re-analysis]


title: kidney biopsy [GSM3524208 re-analysis]


title: kidney biopsy [GSM3524713 re-analysis]


title: kidney biopsy [GSM3524254 re-analysis]


title: kidney biopsy [GSM3525292 re-analysis]


title: kidney biopsy [GSM3524065 re-analysis]


title: kidney biopsy [GSM3524447 re-analysis]


title: kidney biopsy [GSM3524297 re-analysis]


title: kidney biopsy [GSM3524781 re-analysis]


title: kidney biopsy [GSM3524238 re-analysis]


title: kidney biopsy [GSM3523943 re-analysis]


title: kidney biopsy [GSM3524787 re-analysis]


title: kidney biopsy [GSM3525244 re-analysis]


title: kidney biopsy [GSM3524895 re-analysis]


title: kidney biopsy [GSM3525399 re-analysis]


title: kidney biopsy [GSM3523949 re-analysis]


title: kidney biopsy [GSM3525508 re-analysis]


title: kidney biopsy [GSM3525577 re-analysis]


title: kidney biopsy [GSM3525016 re-analysis]


title: kidney biopsy [GSM3525641 re-analysis]


title: kidney biopsy [GSM3524233 re-analysis]


title: kidney biopsy [GSM3524643 re-analysis]


title: kidney biopsy [GSM3524928 re-analysis]


title: kidney biopsy [GSM3523951 re-analysis]


title: kidney biopsy [GSM3524030 re-analysis]


title: kidney biopsy [GSM3524678 re-analysis]


title: kidney biopsy [GSM3524004 re-analysis]


title: kidney biopsy [GSM3524068 re-analysis]


title: kidney biopsy [GSM3524547 re-analysis]


title: kidney biopsy [GSM3523917 re-analysis]


title: kidney biopsy [GSM3524241 re-analysis]


title: kidney biopsy [GSM3524822 re-analysis]


title: kidney biopsy [GSM3525147 re-analysis]


title: kidney biopsy [GSM3525122 re-analysis]


title: kidney biopsy [GSM3525174 re-analysis]


title: kidney biopsy [GSM3524756 re-analysis]


title: kidney biopsy [GSM3525213 re-analysis]


title: kidney biopsy [GSM3524045 re-analysis]


title: kidney biopsy [GSM3524223 re-analysis]


title: kidney biopsy [GSM3524665 re-analysis]


title: kidney biopsy [GSM3524354 re-analysis]


title: kidney biopsy [GSM3525090 re-analysis]


title: kidney biopsy [GSM3525505 re-analysis]


title: kidney biopsy [GSM3525305 re-analysis]


title: kidney biopsy [GSM3524189 re-analysis]


title: kidney biopsy [GSM3524262 re-analysis]


title: kidney biopsy [GSM3525035 re-analysis]


title: kidney biopsy [GSM3524454 re-analysis]


title: kidney biopsy [GSM3524583 re-analysis]


title: kidney biopsy [GSM3524351 re-analysis]


title: kidney biopsy [GSM3524119 re-analysis]


title: kidney biopsy [GSM3525616 re-analysis]


title: kidney biopsy [GSM3524809 re-analysis]


title: kidney biopsy [GSM3524505 re-analysis]


title: kidney biopsy [GSM3525176 re-analysis]


title: kidney biopsy [GSM3524628 re-analysis]


title: kidney biopsy [GSM3525151 re-analysis]


title: kidney biopsy [GSM3525501 re-analysis]


title: kidney biopsy [GSM3524275 re-analysis]


title: kidney biopsy [GSM3524941 re-analysis]


title: kidney biopsy [GSM3523994 re-analysis]


title: kidney biopsy [GSM3524843 re-analysis]


title: kidney biopsy [GSM3524134 re-analysis]


title: kidney biopsy [GSM3523995 re-analysis]


title: kidney biopsy [GSM3524721 re-analysis]


title: kidney biopsy [GSM3524439 re-analysis]


title: kidney biopsy [GSM3525389 re-analysis]


title: kidney biopsy [GSM3525261 re-analysis]


title: kidney biopsy [GSM3524203 re-analysis]


title: kidney biopsy [GSM3523973 re-analysis]


title: kidney biopsy [GSM3523969 re-analysis]


title: kidney biopsy [GSM3524175 re-analysis]


title: kidney biopsy [GSM3524584 re-analysis]


title: kidney biopsy [GSM3523965 re-analysis]


title: kidney biopsy [GSM3525472 re-analysis]


title: kidney biopsy [GSM3525081 re-analysis]


title: kidney biopsy [GSM3525493 re-analysis]


title: kidney biopsy [GSM3525588 re-analysis]


title: kidney biopsy [GSM3524475 re-analysis]


title: kidney biopsy [GSM3524732 re-analysis]


title: kidney biopsy [GSM3524457 re-analysis]


title: kidney biopsy [GSM3525497 re-analysis]


title: kidney biopsy [GSM3525410 re-analysis]


title: kidney biopsy [GSM3525027 re-analysis]


title: kidney biopsy [GSM3523926 re-analysis]


title: kidney biopsy [GSM3524770 re-analysis]


title: kidney biopsy [GSM3525298 re-analysis]


title: kidney biopsy [GSM3525558 re-analysis]


title: kidney biopsy [GSM3524225 re-analysis]


title: kidney biopsy [GSM3525442 re-analysis]


title: kidney biopsy [GSM3523904 re-analysis]


title: kidney biopsy [GSM3525279 re-analysis]


title: kidney biopsy [GSM3524893 re-analysis]


title: kidney biopsy [GSM3525262 re-analysis]


title: kidney biopsy [GSM3525080 re-analysis]


title: kidney biopsy [GSM3524166 re-analysis]


title: kidney biopsy [GSM3524305 re-analysis]


title: kidney biopsy [GSM3524050 re-analysis]


title: kidney biopsy [GSM3525344 re-analysis]


title: kidney biopsy [GSM3524858 re-analysis]


title: kidney biopsy [GSM3525343 re-analysis]


title: kidney biopsy [GSM3525271 re-analysis]


title: kidney biopsy [GSM3525067 re-analysis]


title: kidney biopsy [GSM3525237 re-analysis]


title: kidney biopsy [GSM3523968 re-analysis]


title: kidney biopsy [GSM3524370 re-analysis]


title: kidney biopsy [GSM3524901 re-analysis]


title: kidney biopsy [GSM3525022 re-analysis]


title: kidney biopsy [GSM3524365 re-analysis]


title: kidney biopsy [GSM3524795 re-analysis]


title: kidney biopsy [GSM3524306 re-analysis]


title: kidney biopsy [GSM3525235 re-analysis]


title: kidney biopsy [GSM3525336 re-analysis]


title: kidney biopsy [GSM3525233 re-analysis]


title: kidney biopsy [GSM3524221 re-analysis]


title: kidney biopsy [GSM3524350 re-analysis]


title: kidney biopsy [GSM3524480 re-analysis]


title: kidney biopsy [GSM3524614 re-analysis]


title: kidney biopsy [GSM3525085 re-analysis]


title: kidney biopsy [GSM3524228 re-analysis]


title: kidney biopsy [GSM3525406 re-analysis]


title: kidney biopsy [GSM3525337 re-analysis]


title: kidney biopsy [GSM3525570 re-analysis]


title: kidney biopsy [GSM3524565 re-analysis]


title: kidney biopsy [GSM3524153 re-analysis]


title: kidney biopsy [GSM3524848 re-analysis]


title: kidney biopsy [GSM3525598 re-analysis]


title: kidney biopsy [GSM3524435 re-analysis]


title: kidney biopsy [GSM3524771 re-analysis]


title: kidney biopsy [GSM3524250 re-analysis]


title: intact_5

type: SRA

city: Cambridge

last: Whited

state: MA

address: 7 Divintiy Street, Sherman Fairchild - Whited Lab

country: USA

institute: Harvard University

description:
illumina
intactPeaks_peaks.narrowPeak
allsamppeaks_peaks.narrowPeak

library_source: genomic

data_processing:
ATAC-seq reads were aligned to ambMex60DD GCA_002915635.3 using bowtie2 (V2.3.2)
Peaks were called using MACS2
Assembly: ambMex60DD GCA_002915635.3
Supplementary files format and content: narrowPeak files containing the peak calls from MACS2

molecule: genomic DNA

organism: Ambystoma mexicanum

source_name: limb tissue

extract_protocol:
Cells were dissociated in dissociation buffer (100 mg/ml liberase diluted in 0.7X PBS with 0.5 U/ml DNase I) for 30 min at room temperature with gentle mixing. Cells were then stained with 1 mg/ml Hoecsht, calcein AM, and propidium iodide for isolation of alive, dividing (4C) and non-dividing (2C) cells by fluorescence activated cell sorting. The 4C cells were used for library preparation.
Ten thousand sorted 4C cells from homeostatic, systemically-activated, and regenerating limbs were resuspended in 5 μL PBS. 42.5 μL of transposition buffer (38.8mM tris-acetate, 77.6mM potassium acetate, 11.8mM magnesium acetate, 0.12% NP-40, 18.8% DMF, 0.47% protease inhibitor cocktail) was added to the cells, mixed, and incubated 10 min at room temperature. 2.5 μL of pre-loaded Tn5 (Diagenode cat# C01070012) was added to the reaction mixture. The transposition reaction was carried out at 37°C for 30 min with shaking at 300 rpm. Following transposition, the samples were purified through Direct-zol RNA MiniPrep kit (Zymo Research cat# R2050). Purified library fragments were amplified with custom primers 1 and 2 using the following conditions: 72°C for 5min; 98°C for 30s; and thermocycling at 98°C for 10s, 72°C for 30s and 72°C for 1min. The libraries were amplified for five cycles. Soon after, 5μL aliquot of the PCR reaction was added with 10μL of the PCR cocktail with SYBR Green (0.6Xfinal concentration). 20 cycles of PCR was performed to determine the additional number of cycles needed for the remaining 45 μL reaction. The libraries were purified using Direct-zol RNA MiniPrep kit.

value: limb tissue

tag: genotype

value: wild type


title: kidney biopsy [GSM3525614 re-analysis]


title: intact_4


title: kidney biopsy [GSM3524638 re-analysis]


title: intact_3


title: systemically activated_5

description:
illumina
contraPeaks_peaks.narrowPeak
allsamppeaks_peaks.narrowPeak


title: kidney biopsy [GSM3524999 re-analysis]


title: kidney biopsy [GSM3524682 re-analysis]


title: systemically activated_4


title: kidney biopsy [GSM3525405 re-analysis]


title: kidney biopsy [GSM3524989 re-analysis]


title: kidney biopsy [GSM3524802 re-analysis]


title: blastema_4

description:
illumina
blastemaPeaks_peaks.narrowPeak
allsamppeaks_peaks.narrowPeak

source_name: blastema and wound epidermis

value: blastema and wound epidermis


title: kidney biopsy [GSM3523962 re-analysis]


title: blastema_1


title: kidney biopsy [GSM3524694 re-analysis]


title: kidney biopsy [GSM3524957 re-analysis]


title: mRNA_SAHA_alignments_rep3

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

library_source: transcriptomic

data_processing:
Massively parallel sequencing was performed using a Genome Analyser IIx, and 36-cycle version 4 sequencing kit according to the manufacturers protocol. Sequence and quality data were extracted from cluster cycle imaging using Pipeline v1.6
mRNA-seq - RNA sequencing data were aligned to the human genome (hg19) using RNA-Aligner Mapsplice. Cufflinks was used for de novo transcriptome assembly, fragment length normalisation, annotation of the transcripts and differential expression analysis for RNA-Seq using the RefSeq (hg19) mRNA annotation set
ChIP-seq: reads were aligned to the human genome (hg19) using Burrows Wheeler Aligner (BWA), followed by MACS peak calling (v1.4.1)
Assembly: hg19
Supplementary files format and content: TSV files; ML16FB_hg19_HistoneMod_Peaks.tsv contains MACS peaks for ChIP data for all histone mod samples and contrasts.  RNA_gene_exp_diff.tsv contains differential expression as determined using cufflinks.

molecule: polyA RNA

growth_protocol: ML16 fibroblasts were maintained in DMEM medium

extract_protocol:
ChIP: Approximately 12 × 106 fibroblast cells were grown in four 150-mm cell culture dishes and to near confluency before VPA and SAHA stimulation. Media were decanted, and cells were incubated on the dish for 5 min with 20 ml ChIP fixation buffer (prepared fresh, 37% formaldehyde in PBS) with mild agitation on a platform mixer. ChIP fixation buffer was decanted and immediately replaced with 20 ml ChIP quenching buffer (Glycine prepared fresh in PBS), followed by 10-min incubation with mild agitation. After decanting the quenching buffer, cells were rinsed twice in ice-cold PBS and harvested by scraping in 5-ml ice-cold PBS. Cells were pelleted by centrifugation for 3 min at 300 × g, and supernatant was discarded. Cells were transferred into 1.5-ml safe-lock microcentrifuge tubes (Eppendorf) using 1-ml ice-cold PBS and pelleted for 10 min at 1000 × g, 4 °C. Cell pellets were resuspended in 300 µl of ChIP SDS-Lysis buffer at room temperature and sonicated for 30 min at high power at 4 °C using a Bioruptor (Diagenode). Samples were centrifuged for 10 min at 13.000 × g, 4 °C to remove insoluble chromatin. Soluble chromatin was transferred into a fresh 1.5-ml microcentrifuge tubes ready for the immunoprecipitation reaction.  DynaBeads Protein A magnetic beads (Invitrogen) (40 µl per ChIP reaction) were washed twice in 1 ml ChIP Dilution Buffer and resuspended. Up to 50 µl of soluble chromatin solution was reconstituted with 20 µl of pre-washed magnetic beads and 500 µl of ChIP Dilution Buffer and incubated for 2 h on a rotating wheel at 4 °C for pre-clearing. An equal aliquot of soluble chromatin was transferred to a separate 1.5-ml safe-lock microcentrifuge tube and kept at 4 °C to serve as input control sample at a later time. In parallel, 20 µl of pre-washed beads was incubated with 4 μg of ChIP grade antibody (H3K9/14ac 06-599 Sigma-Aldrich, H3K4me3 39,159 Active Motif and H3K9me3 8898 Abcam) in a total volume of 500 µl ChIP Dilution Buffer for 2 h, 4 °C, on a rotating wheel. Cleared soluble chromatin was incubated overnight on a rotating wheel at 4 °C, and the magnetic beads were washed consecutively with 1 ml of ChIP Low Salt Buffer, ChIP High Salt Buffer, ChIP LiCl Buffer, ChIP TE buffer and ChIP TE buffer containing 0.01% SDS using a rotation wheel at 4 °C for 5 min. To reverse cross-links, beads were incubated in 100 µl ChIP Elution Buffer including 2.5 µl proteinase K for 2 h at 62 °C in a thermo mixer (Eppendorf) at 1400 rpm. Similarly, the input control samples were combined with 100 µl ChIP Elution Buffer including 2.5 µl proteinase K and incubated alongside the ChIP samples. Input and ChIP samples were combined with 150 µl phenol/chloroform/isoamylalcohol and vortexed. Samples were centrifuged at 16.000 × g for 10 min at room temperature. The aqueous phase (~ 100 µl) was transferred to fresh 1.5-ml microcentrifuge tubes and DNA-purified using MinElute DNA extraction columns (Qiagen) according to manufacturer’s instructions. DNA concentration was determined using a Qubit QuantIt DNA quantitation kit (Invitrogen) according to the manufacturer’s instructions. Samples were stored at − 20 °C or used directly in next-generation sequencing library preparation.
RNA: Total RNA was isolated from cells grown to full confluency in 50-mm cell culture dishes using TRIzol reagent (Invitrogen) according to manufacturer’s instructions. Approximately 1 × 106 cells were washed once with 5 ml PBS. TRIzol (Invitrogen) was added directly to cells, vortexed for 20 s and incubated at RT for 5 min. 200 µl chloroform was added to each tube and vortexed for 10 s. The sample was incubated at RT for a further 3 min and centrifuged for 15 min at 13,200 rpm (4 °C) to separate the aqueous and organic phases. The upper, aqueous phase containing the RNA was transferred to a new 1.5-ml microcentrifuge tube and placed on ice to precipitate with ice-cold isopropanol for 15 min. Precipitated RNA was pelleted by centrifugation for 10 min at 13,200 rpm (4 °C) and washed in 200 µl ice-cold 75% ethanol. The pellet was resuspended in ice-cold nuclease-free water and subject to RNase-Free DNase Set (Qiagen, cat. no. 79254) according to the manufacturer’s instructions. RNA was prepared using RNeasy Mini Kit RNA Cleanup protocol (Qiagen), and the concentration was determined using a Qubit QuantIt RNA quantitation kit (Invitrogen). Samples were stored at -80 °C or used directly in next-generation sequencing library preparation.
ChIP enriched sequencing libraries were prepared as per the ChIP-Seq library preparation kit protocol using 5ng of enriched DNA. 10 Micrograms of total RNA per sample was used in construction of mRNA sequencing libraries, which were prepared using Illumina’s RNA-sequencing preparation kit.

treatment_protocol: Growth medium was decanted, and cells were exposed to Mock (vehicle), 5mM VPA or 2µM SAHA prepared in DMEM for 16h

tag: cell line

tag: cell type

value: Fibroblast

tag: treatment

value: 2uM SAHA


title: kidney biopsy [GSM3524961 re-analysis]


title: mRNA_Mock_alignments_rep2

value: Mock (vehicle)


title: kidney biopsy [GSM3524474 re-analysis]


title: kidney biopsy [GSM3524761 re-analysis]


title: mRNA_SAHA_alignments_rep2


title: mRNA_VPA_alignments_rep3

value: 5mM VPA


title: kidney biopsy [GSM3525396 re-analysis]


title: mRNA_VPA_alignments_rep2


title: kidney biopsy [GSM3525078 re-analysis]


title: mRNA_VPA_alignments_rep1


title: kidney biopsy [GSM3524973 re-analysis]


title: kidney biopsy [GSM3525290 re-analysis]


title: mRNA_Mock_alignments_rep1


title: Input_SAHA


title: kidney biopsy [GSM3524620 re-analysis]


title: kidney biopsy [GSM3524891 re-analysis]


title: mRNA_Mock_alignments_rep3


title: Input_VPA


title: Input_Mock


title: kidney biopsy [GSM3524673 re-analysis]


title: kidney biopsy [GSM3524284 re-analysis]


title: H3K4me3_Mock


title: H3K4me3_SAHA


title: H3K4me3_VPA


title: H3K9me3_SAHA


title: kidney biopsy [GSM3524718 re-analysis]


title: kidney biopsy [GSM3523928 re-analysis]


title: kidney biopsy [GSM3525258 re-analysis]


title: mRNA_SAHA_alignments_rep1


title: H3K9me3_VPA


title: kidney biopsy [GSM3523967 re-analysis]


title: kidney biopsy [GSM3525245 re-analysis]


title: kidney biopsy [GSM3524267 re-analysis]


title: H3K9me3_Mock


title: kidney biopsy [GSM3524789 re-analysis]


title: kidney biopsy [GSM3523958 re-analysis]


title: kidney biopsy [GSM3525178 re-analysis]


title: H3Ac_VPA


title: FFPE tissue of Ewing sarcoma, case 28

type: genomic

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

description: Case 28

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to either Illumina HumanMethylation450 BeadChip or Illumina Infinium MethylationEPIC v1 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan

data_processing:
RStudio (R package ChAMP v2.26.0)
Raw beta values obtained through function champ.load of R package ChAMP (with default parameters)

label: Cy5 and Cy30

source_name: Ewing sarcoma, M, 11 years old

label_protocol: Standard Illumina Protocol

extract_protocol: We extracted DNA from unstained sections of paraffin blocks containing at least 70% tumour cells, using MagPurix FFPE DNA Extraction Kit (Zzinexts).

tag: patient's gender

value: Ewing sarcoma

value: M

tag: patient's age (years)

tag: translocation

tag: translocation type

value: Canonical


title: kidney biopsy [GSM3525366 re-analysis]


title: H3Ac_Mock


title: kidney biopsy [GSM3524933 re-analysis]


title: WT, PBS

city: Pittsburgh

first: Wen

last: Xie

state: Pennsylvania

address: 335 Sutherland Dr

department: Center for Pharmacogenetics and Department of Pharmaceutical Sciences

institute: University of Pittsburgh

data_processing:
Reads were aligned using STAR.
Gene expression quantification and differential expression analysis were performed using cuffdiff.
Assembly: GRCm38
Supplementary files format and content: gene_exp.diff contains gene expression and detailed differential expression profile.

organism: Mus musculus

source_name: Primary hepatic stellate cell

growth_protocol: DMED with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated using an RNeasy Mini Kit (Qiagen).
Library were constructed using Illumina TruSeq Stranded Total RNA Sample Preparation kits following manufacturer's protocols.

treatment_protocol: HSCs were isolated from mice treated with 3 doses of PBS or TAA for every 3 days

value: Primary hepatic stellate cell

value: wild-type

value: PBS


title: WT, TAA

value: thioacetamide


title: FFPE tissue of Ewing sarcoma, case 27

description: Case 27

label: Cy5 and Cy29

source_name: Ewing sarcoma, M, 7 years old


title: KO, TAA

value: Cyp1b1 KO


title: KO, PBS


title: kidney biopsy [GSM3525504 re-analysis]

value: NR

value: kidney biopsy


title: kidney biopsy [GSM3524156 re-analysis]


title: FFPE tissue of Ewing sarcoma, case 25

description: Case 25

label: Cy5 and Cy27

source_name: Ewing sarcoma, M, 6 years old


title: FFPE tissue of Ewing sarcoma, case 24

description: Case 24

label: Cy5 and Cy26

source_name: Ewing sarcoma, M, 2 years old

value: Non-canonical


title: kidney biopsy [GSM3524207 re-analysis]


title: FFPE tissue of Ewing sarcoma, case 23

description: Case 23

label: Cy5 and Cy25

source_name: Ewing sarcoma, M, 1 years old


title: FFPE tissue of Ewing sarcoma, case 26

description: Case 26

label: Cy5 and Cy28

source_name: Ewing sarcoma, M, 9 years old


title: kidney biopsy [GSM3524443 re-analysis]


title: kidney biopsy [GSM3525549 re-analysis]


title: kidney biopsy [GSM3524191 re-analysis]

value: EABMR


title: H3Ac_SAHA


title: FFPE tissue of Ewing sarcoma, case 21

description: Case 21

label: Cy5 and Cy23

source_name: Ewing sarcoma, F, 16 years old

value: F


title: kidney biopsy [GSM3525445 re-analysis]


title: kidney biopsy [GSM3524064 re-analysis]

value: FABMR


title: LPDC + 5-HT + Htr7 antagnoist 3

city: boston

first: Hailong

last: Zhang

address: 181 longwood ave

institute: Brigham and Women's Hospital, Harvard Medical School

data_processing:
For data analysis, reads were trimmed using Trim Galore with automatic adapter sequence detection.
Then, trimmed reads were mapped to the mouse reference genome (mm10) and annotated using STAR v2.7.3a with default parameter.
The number of mapped reads to each gene were counted by featureCounts of the Subread package using mouse GENCODE annotation M25 (GRCm38.p6).
Assembly: mm10
Supplementary files format and content: Feature counts table

source_name: LPDC

extract_protocol:
Treated-LPDC were lysed in Trizol (15596018, Invitrogen), and RNA was extracted with the RNeasy mini Kit (74106, Qiagen) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using the KAPA mRNA HyperPrep kit (50-196-5308, Roche) or NEBNext Multiplex Oligos for Illumina kit (E7335L, NEB).

value: LPDC

value: 5-HT + Htr7 antagnoist


title: FFPE tissue of Ewing sarcoma, case 22

description: Case 22

label: Cy5 and Cy24

source_name: Ewing sarcoma, F, 10 years old


title: kidney biopsy [GSM3524489 re-analysis]


title: kidney biopsy [GSM3524993 re-analysis]


title: kidney biopsy [GSM3524330 re-analysis]

value: Minor


title: kidney biopsy [GSM3524162 re-analysis]


title: FFPE tissue of Ewing sarcoma, case 19

description: Case 19

label: Cy5 and Cy21

value: Ewing sarcoma


title: LPDC + 5-HT + Htr7 antagnoist 1


title: FFPE tissue of Ewing sarcoma, case 18

description: Case 18

label: Cy5 and Cy20

source_name: Ewing sarcoma, F, 27 years old


title: LPDC + 5-HT + Htr7 antagnoist 2


title: kidney biopsy [GSM3524394 re-analysis]


title: LPDC + 5-HT 3


title: LPDC + 5-HT 1


title: LPDC + 5-HT 2


title: kidney biopsy [GSM3524920 re-analysis]


title: FFPE tissue of Ewing sarcoma, case 17

description: Case 17

label: Cy5 and Cy19

source_name: Ewing sarcoma, F, 9 years old


title: WT 6TG 3

city: London

first: David

last: Heinrichs

state: ON

address: Microbiology and Immunology, 3014 Dental Sciences Building, 1151 Richmond Street

institute: University of Western Ontario

description: The processed data files has all 3 replicates combined and the calculations of differential expression/fold changesare based on the comparison with the appropriate control group. Each tab is named after what the comparisons are.

data_processing:
Sequencing reads were mapped to the reference S. aureus USA300 FPR3757 genome in Geneious Prime 2022.1 (https://www.geneious.com). Expression analysis and comparisons were performed using DESeq2 (Love MI et al Genome Biol 2014).
Assembly: Staphylococcus aureus USA300_FPR3757
Supplementary files format and content: xlsx file format, contains RPKM values and calculated differential expression, fold change and p-values for every transcript

organism: Staphylococcus aureus

growth_protocol: An overnight culture of WT USA300 was inoculated 1:100 into TSB and grown to an OD600 of 1.5 at 37oC with shaking. 3.125M of R91 was added to the treated cultures and all cultures were then grown for and additional 30 minutes.

extract_protocol:
To extract RNA from frozen S. aureus cell pellets were washed with TE buffer (pH 8.0) and re-suspended in a Tris-HCl mixture with 1 mg/mL lysostaphin (pH 7.5) to lyse for 1 hour at 37°C. RNA was extracted using an QIAGEN RNAEasy kit (QIAGEN ID: 74104)
RNA samples were processed by the Microbial Genome Sequencing Center in Pittsburgh, PA. Ribosomal RNA (rRNA) was depleted (Qiagen FastSelect5S/16S/23S) and cDNA libraries were generated (Qiagen Total Stranded RNA). cDNA libraries were sequenced using NextSeq 550 using a 75bp x 8bp x 8bp setup

treatment_protocol: Cells treated with the drug received 3.125μM R91 or and equal volume of DMSO for the vehicle control.


title: kidney biopsy [GSM3525581 re-analysis]


title: GBM39-ER_Paired_Hi-C_RNA

city: La Jolla

first: Yang

state: CA

address: Rm.2071, 9500 Gilman Dr

department: Department of Cellular and Molecular Medicine

institute: UC San Diego

description: 10XMultiome, gene expression

data_processing:
All sequencing were performed with an Illumina NextSeq 2000 or NovaSeq 6000 sequencer. Fastq files are demultiplexed using cellranger-arc v2.0.0. Hi-C and RNA modalities were preprocessed using cellranger-atac v2.0.0 and cellranger v6.1.2, respectively, and barcodes were manually paired with custom script using the matching relationship provided in cellranger-arc. To select high-quality nuclei from DNA modality, we filtered barcodes based on the per cell contacts number, and then further selected nuclei by pairing pass-filtered nuclei from both Hi-C and RNA modality.
Assembly: hg38
Supplementary files format and content: For Hi-C modality, processed data are provided in .pairs format, each line represents a unique contact, with cell barcodes corresponding to left- and right-side of the contacts being recorded as extra columns in pairs file. For RNA modality, raw cells-by-gene matrices are provided. Valid cells information is provided as metadata in the supplementary file.

molecule: nuclear RNA

growth_protocol: As described previously, patient-derived xenograft (PDX) model GBM39 (Mayo Clinic Hospital) was cultured in DMEM/F12 (ThermoFisher, 11320033), 20ng/mL EGF (STEMCELL Technologies, 78006), 20ng/ml FGF (STEMCELL Technologies, 78134.1), 10% B27 Supplement without Vitamin A (ThermoFisher, 12587010), and 1% penicillin-streptomycin solution at 37°C with 5% CO2. GBM39-ER was under continuous treatment with 5µM erlotinib (LC Laboratories, E-4007). GBM39 cell lines were cultured as neurospheres.

extract_protocol:
Cells were crosslinked in 1% formaldehyde, which was diluted from 37% formaldehyde with 1× PBS (pH=7.4), and incubated at room temperature for 10 min. After crosslinking, the reactions were quenched in 200 mM glycine and incubated at room temperature for 5 min. Quenched reactions were spun down at 1,000g for 5 min at 4°C, resuspended using 1% BSA in 1× PBS (pH=7.4) to wash twice, and then aliquoted 1 million cells into each tube. The cells were pelleted once again at 1,000g for 5 min, removed supernatant, and flash frozen in liquid nitrogen, and finally stored indefinitely at -80°C.
Following user guide of Chromium Next GEM Single Cell Multiome ATAC + Gene Expression.


title: FFPE tissue of Ewing sarcoma, case 20

description: Case 20

label: Cy5 and Cy22

source_name: Ewing sarcoma, F, 13 years old


title: kidney biopsy [GSM3524544 re-analysis]


title: FFPE tissue of Ewing sarcoma, case 15

description: Case 15

label: Cy5 and Cy17

value: M


title: WT 6TG 1


title: WT 6TG 2


title: GBM39_Paired_Hi-C_RNA

description: 10XMultiome, gene expression

growth_protocol: As described previously, patient-derived xenograft (PDX) model GBM39 (Mayo Clinic Hospital) was cultured in DMEM/F12 (ThermoFisher, 11320033), 20ng/mL EGF (STEMCELL Technologies, 78006), 20ng/ml FGF (STEMCELL Technologies, 78134.1), 10% B27 Supplement without Vitamin A (ThermoFisher, 12587010), and 1% penicillin-streptomycin solution at 37°C with 5% CO2. GBM39 cell lines were cultured as neurospheres.


title: FFPE tissue of Ewing sarcoma, case 14

description: Case 14

label: Cy5 and Cy16

source_name: Ewing sarcoma, F, 18 years old

value: Canonical


title: WT vehicle 2

value: Vehicle control; DMSO


title: kidney biopsy [GSM3525260 re-analysis]

source_name: kidney biopsy


title: WT vehicle 3


title: WT vehicle 1


title: kidney biopsy [GSM3524504 re-analysis]


title: FFPE tissue of Ewing sarcoma, case 13

description: Case 13

label: Cy5 and Cy15


title: kidney biopsy [GSM3525145 re-analysis]

value: LABMR


title: Hep3B cells, Control, DMSO

city: Jinju-si

first: Minyeong

last: Park

address: Jinju-daero

country: South Korea

institute: Gyeongsang National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastp), then mapped to GRCh38 (NCBI) whole genome using STAR.
Read count extraction using HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Liver

growth_protocol: The American Type Culture Collection (ATCC, Manassas, VA, USA) provided the Hep3B hepatocellular carcinoma cells, which were then grown in full DMEM with 10% FBS and supplemented with 100 U/mL penicillin and 100 µg/mL streptomycin (P/S). The cells were cultured in a humidified environment with 5% CO2 at 37 °C.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: For 12 h, Hep3B cells were planted in 96-well plates at a density of 1 × 104 cells per well. Next, for 24 h, the cells were exposed to varying doses of GLE (0, 10, 25, 50, 75, 100, 200, 300, 400, and 500 μg/mL). After treating each well with 10 μL of MTT solution (5 mg/mL) and 90 μL of media, the cells were grown at 37 °C for 4 h. It was decided that the insoluble formazan crystals should be dissolved using DMSO. Finally, each sample was run in triplicate, and a microplate reader (BioTek, Winooski, VT, USA) was used to read each well’s absorbance value at 450 nm.

value: Liver

value: human hepatoma

value: Liver Epith

value: WT

value: Cancer treatment


title: Hep3B cells, Test, GLE


title: FFPE tissue of Ewing sarcoma, case 12

description: Case 12

label: Cy5 and Cy14

source_name: Ewing sarcoma, M, 10 years old


title: kidney biopsy [GSM3525210 re-analysis]

label: biotin

value: NR

value: kidney biopsy


title: FFPE tissue of Ewing sarcoma, case 16

description: Case 16

label: Cy5 and Cy18

source_name: Ewing sarcoma, F, 4 years old

value: F


title: PC3_H3K4me3

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.3.3.1.
Duplication reads were removed from aligned file by using picard-tools-2.18.2
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER v4.7 makeUCSCfile command and comberted to bigwig by bedGraphToBigWig. BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: LNCaP,PC3 and DU145 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
Cells were fixed with 1% formaldehyde, and samples from sonicated nuclear fraction were incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol.

value: prostate cancer

tag: chip antibody

value: H3K4me3 (ACTIVE MOTIF,#39159)


title: FFPE tissue of Ewing sarcoma, case 11

description: Case 11

label: Cy5 and Cy13

source_name: Ewing sarcoma, F, 34 years old


title: kidney biopsy [GSM3525455 re-analysis]

value: FABMR


title: PC3_H3K27ac

value: H3K27ac (ACTIVE MOTIF,#91193)


title: PC3_H3K4me1


title: FFPE tissue of Ewing sarcoma, case 10

description: Case 10

label: Cy5 and Cy12

value: Ewing sarcoma


title: T8_Free4w_choline1

city: Bunkyo-ku

first: Eiko

last: SAIJOU

state: Tokyo

address: 1-1-1 Yayoi

department: Institute of Quantitative Bioscience

institute: The University of Tokyo

data_processing:
RumBall v0.5.0
STAR 2.7.10b
RSEM v1.3.3
DESeq2 v1.36.0
Assembly: GRCm38
Supplementary files format and content: bam files of each mapping results
Supplementary files format and content: count data and tpm data

extract_protocol:
RNA was harvested using TRIzol RNA Isolation Reagents.
RNA libraries were prepared by the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420; NEB) and NEBNext rRNA Depletion Kit (E6310; NEB).

value: oral TAA administration for 8w then recover 4w with choline chloride


title: kidney biopsy [GSM3524510 re-analysis]


title: FFPE tissue of Ewing sarcoma, case 9

description: Case 9

label: Cy5 and Cy11

source_name: Ewing sarcoma, F, 17 years old

value: Canonical


title: T8_Free1w_choline2

value: oral TAA administration for 8w then recover 1w with choline chloride


title: T8_Free2w_choline2

value: oral TAA administration for 8w then recover 2w with choline chloride


title: kidney biopsy [GSM3524991 re-analysis]


title: FFPE tissue of Ewing sarcoma, case 8

description: Case 8

label: Cy5 and Cy10

source_name: Ewing sarcoma, F, 12 years old


title: T8_Free4w_con2

value: Liver

value: oral TAA administration for 8w then recover 4w


title: T8_Free2w_choline1


title: T8_Free4w_choline2


title: kidney biopsy [GSM3524868 re-analysis]

value: EABMR


title: FFPE tissue of Ewing sarcoma, case 6

description: Case 6

label: Cy5 and Cy8

source_name: Ewing sarcoma, F, 5 years old


title: T8_Free4w_con1

value: WT


title: T8_Free2w_con1

value: oral TAA administration for 8w then recover 2w


title: T8_Free2w_con2


title: kidney biopsy [GSM3525242 re-analysis]

value: NR


title: T8_Free1w_con2

value: oral TAA administration for 8w then recover 1w


title: FFPE tissue of Ewing sarcoma, case 5

description: Case 5

label: Cy5 and Cy7

source_name: Ewing sarcoma, M, 12 years old

value: M


title: T8_Free1w_con1


title: FFPE tissue of Ewing sarcoma, case 4

description: Case 4

label: Cy5 and Cy6

source_name: Ewing sarcoma, M, 16 years old


title: kidney biopsy [GSM3525640 re-analysis]

value: kidney biopsy


title: kidney biopsy [GSM3524519 re-analysis]


title: TAA8w_1

value: oral TAA administration for 8w


title: TAA8w_2


title: kidney biopsy [GSM3524684 re-analysis]


title: WT_2

value: control


title: kidney biopsy [GSM3524512 re-analysis]


title: WT_1


title: FFPE tissue of Ewing sarcoma, case 3

description: Case 3

label: Cy5 and Cy5

source_name: Ewing sarcoma, F, 14 years old

value: F


title: FFPE tissue of Ewing sarcoma, case 2

description: Case 2

label: Cy5 and Cy4

source_name: Ewing sarcoma, F

value: Ewing sarcoma


title: MC_Paired_Hi-C_rep3_RNA

description: 10XMultiome, gene expression

data_processing:
All sequencing were performed with an Illumina NextSeq 2000 or NovaSeq 6000 sequencer. Fastq files are demultiplexed using cellranger-arc v2.0.0. Hi-C and RNA modalities were preprocessed using cellranger-atac v2.0.0 and cellranger v6.1.2, respectively, and barcodes were manually paired with custom script using the matching relationship provided in cellranger-arc. To select high-quality nuclei from DNA modality, we filtered barcodes based on the per cell contacts number, and then further selected nuclei by pairing pass-filtered nuclei from both Hi-C and RNA modality.
Assembly: mm10
Supplementary files format and content: For Hi-C modality, processed data are provided in .pairs format, each line represents a unique contact, with cell barcodes corresponding to left- and right-side of the contacts being recorded as extra columns in pairs file. For RNA modality, raw cells-by-gene matrices are provided. Valid cells information is provided as metadata in the supplementary file.

source_name: cortex

growth_protocol: All animal work described in this manuscript has been approved and conducted under the oversight of the Institutional Animal Care and Use Committee at the University of California, San Diego. Male C57BL/6J mice were purchased from the Jackson Laboratory (000664) at 7 weeks of age and were housed in the animal facility at University of California, San Diego, under a 12-h light/12-h dark cycle in a temperature-controlled room with ad libitum access to water and food until euthanasia and tissue collection at 8 weeks of age. The isocortex was dissected from 8-week-old male mice, snap-frozen in liquid nitrogen and stored at −80 °C before proceeding to nuclei extraction.

value: cortex


title: T8_Free1w_choline1


title: MC_Paired_Hi-C_rep2_RNA

description: 10XMultiome, gene expression


title: kidney biopsy [GSM3524894 re-analysis]


title: DoHH2 iCLIP rep4

first: Anne

middle: E

last: Willis

address: Gleeson Building, Tennis Court Road

department: MRC Toxicology Unit

country: United Kingdom

institute: University of Cambridge

data_processing:
iCLIP libraries were demultiplexed using JE demultiplex.
PCR duplicates were removed using dedupe.sh function from BBMAP package
Biological replicates with low read numbers were merged into 4 (for DoHH-2) or 2 (for GM01953) independent replicates.
Trimmed reads were mapped to ENSEMBL GRCh38 using HiSat2.
The iCount suite was used to determine crosslink sites, identify peaks of binding and cluster them into binding regions.
Assembly: ENSEMBL GRCh38
Supplementary files format and content: tab-separated values TSV file containing eIF4B binding sites for each sample

extract_protocol:
40x10^6 cells crosslinked using 150 mJ/cm2 UVC. RNA was partially digested with RNase I (0.6 U) prior to immunoprecipitation with 10 ug anti-eIF4B antibody. Immunoprecipitated RNA was 5’-end-labeled with 32P using T4 polynucleotide kinase and protein-RNA complexes were separated by SDS-PAGE and transferred to nitrocellulose membrane. RNA fragments bound to eIF4B were isolated by proteinase K digestion and phenol-chloroform separation.
Homemade with custom clip primers.


title: Microbiota of Tph2fl/fl; Hand2-Cre female 4

data_processing:
Raw sequencing data were analyzed by QIIME2
the data were imported into QIIME2
demultiplexed and the DADA2 pipeline was used for sequencing quality control
feature table was constructed
The feature table was used for alpha and beta diversity analysis as well as for taxonomic analysis and differential abundance testing.
Supplementary files format and content: Result.csv
Library strategy: 16S

source_name: Fecal

extract_protocol:
Fecal DNA was extracted from fecal pellets of the indicated mice with a QIAGEN QIAamp Fast DNA Stool Mini Kit (51604, Qiagen) according to the manufacturer’s instructions.
Purified DNA samples were amplificated with barcoded primer pairs: 341F and 805R.

value: Fecal

tag: Sex

value: female

value: Tph2fl/fl; Hand2-Cre

value: 16s rRNA


title: FFPE tissue of Ewing sarcoma, case 1

description: Case 1

label: Cy5 and Cy3

source_name: Ewing sarcoma, M, 5 years old

value: Non-canonical


title: kidney biopsy [GSM3524436 re-analysis]


title: kidney biopsy [GSM3525414 re-analysis]


title: Microbiota of Tph2fl/fl; Hand2-Cre female 2


title: Microbiota of Tph2fl/fl; Hand2-Cre female 1


title: Microbiota of Tph2fl/fl; Hand2-Cre female 3


title: DoHH2 iCLIP rep2


title: kidney biopsy [GSM3524038 re-analysis]


title: DoHH2 iCLIP rep1


title: Microbiota of Tph2fl/fl female 6


title: Microbiota of Tph2fl/fl female 5


title: kidney biopsy [GSM3525593 re-analysis]


title: kidney biopsy [GSM3525624 re-analysis]

value: FABMR


title: Microbiota of Tph2fl/fl female 4


title: FFPE tissue of Ewing sarcoma, case 7

description: Case 7

label: Cy5 and Cy9

source_name: Ewing sarcoma, M, 11 years old

value: Canonical


title: Microbiota of Tph2fl/fl female 2


title: Microbiota of Tph2fl/fl; Hand2-Cre female 6


title: Microbiota of Tph2fl/fl female 3


title: Microbiota of Tph2fl/fl female 1


title: MC_Paired_Hi-C_rep1_RNA

description: 10XMultiome, gene expression


title: Microbiota of Tph2fl/fl; Hand2-Cre female 5


title: Microbiota of Tph2fl/fl; Hand2-Cre male 6

value: male


title: kidney biopsy [GSM3525084 re-analysis]


title: Microbiota of Tph2fl/fl; Hand2-Cre male 5


title: DoHH2 iCLIP rep3


title: Microbiota of Tph2fl/fl; Hand2-Cre male 4


title: Microbiota of Tph2fl/fl; Hand2-Cre male 3


title: kidney biopsy [GSM3524465 re-analysis]

value: NR


title: 22RV1_Veh_3

city: Philadelphia

first: Christopher

last: McNair

state: PA

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University

data_processing:
Alignment with STAR
Count Table generation with Featurecounts
Differential expression with DESEq2
Supplementary files format and content: Count Table

extract_protocol:
Qiagen mRNA easy kit to DNAase treatment
Novagene - Directional mRNA library preparation (poly A enrichment)

value: human prostate carcinoma epithelial

value: vehicle


title: Microbiota of Tph2fl/fl; Hand2-Cre male 1


title: kidney biopsy [GSM3525446 re-analysis]

value: kidney biopsy


title: 22RV1_Veh_2


title: 22RV1_Veh_4


title: GM01953 iCLIP rep2


title: kidney biopsy [GSM3524929 re-analysis]

value: EABMR


title: 22RV1_Veh_1


title: GM01953 iCLIP rep1


title: Microbiota of Tph2fl/fl male 4


title: Microbiota of Tph2fl/fl male 5


title: kidney biopsy [GSM3524420 re-analysis]


title: kidney biopsy [GSM3525392 re-analysis]


title: Microbiota of Tph2fl/fl male 6


title: Microbiota of Tph2fl/fl male 1


title: Microbiota of Tph2fl/fl male 3


title: Microbiota of Tph2 KO female 6

value: KO


title: 22RV1_shP300_4


title: Microbiota of Tph2fl/fl male 2


title: kidney biopsy [GSM3524567 re-analysis]


title: kidney biopsy [GSM3524449 re-analysis]

value: LABMR


title: Microbiota of Tph2 KO female 5


title: 22RV1_shP300_3


title: 22RV1_shP300_2


title: Microbiota of Tph2 KO female 4


title: kidney biopsy [GSM3524128 re-analysis]


title: Microbiota of Tph2fl/fl; Hand2-Cre male 2


title: Microbiota of Tph2 KO female 2


title: 22RV1_shP300_1


title: Microbiota of Tph2 KO female 3


title: kidney biopsy [GSM3525463 re-analysis]


title: Microbiota of Tph2 KO female 1


title: 22RV1_shCON_4

value: shCON


title: Microbiota of Tph2 WT female 6

value: WT


title: Microbiota of Tph2 WT female 4

value: Fecal


title: 22RV1_shCON_3


title: kidney biopsy [GSM3525007 re-analysis]


title: kidney biopsy [GSM3524500 re-analysis]


title: 22RV1_shCON_2


title: Microbiota of Tph2 WT female 5

value: female


title: Microbiota of Tph2 WT female 2


title: Microbiota of Tph2 WT female 1


title: kidney biopsy [GSM3525412 re-analysis]


title: Microbiota of Tph2 KO male 5


title: Microbiota of Tph2 KO male 4


title: 22RV1_shCBP_4

value: shCBP


title: Microbiota of Tph2 KO male 3

value: 16s rRNA


title: Microbiota of Tph2 KO male 1


title: kidney biopsy [GSM3524955 re-analysis]


title: kidney biopsy [GSM3524477 re-analysis]


title: Microbiota of Tph2 KO male 2


title: 22RV1_shCBP_3


title: 22RV1_shCBP_2


title: kidney biopsy [GSM3525168 re-analysis]


title: Microbiota of Tph2 KO male 6


title: 22RV1_shCBP_1


title: kidney biopsy [GSM3524622 re-analysis]


title: Microbiota of Tph2 WT male 4


title: kidney biopsy [GSM3524596 re-analysis]


title: Microbiota of Tph2 WT male 3


title: Microbiota of Tph2 WT female 3


title: Microbiota of Tph2 WT male 2


title: 22RV1_shCON_1


title: Microbiota of Tph2 WT male 1


title: kidney biopsy [GSM3524356 re-analysis]


title: 22RV1_CCS_3

value: CCS1477 (CBP/p300 inhibitor)


title: bv12-3

city: Hangzhou

first: Junjie

last: Cheng

address: Huancheng East 208

department: Pharmacy

country: China

institute: Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the human genome (GRCh38) using HISAT2
FPKM of each gene was calculated using Cufflinks,  and the read counts of each gene were obtained by HTSeq count
Differential expression analysis was performed using the DESeq (2012) R package
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM value for each Samples

source_name: Brain

extract_protocol:
Total RNA was extracted using the TRIzol reagent. 1.0ug total RNA was used for the construction of sequencing libraries
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions

value: Brain

value: Microglia cells

value: LPS

tag: time


title: 22RV1_CCS_4


title: bv12-2


title: kidney biopsy [GSM3524835 re-analysis]

source_name: kidney biopsy


title: bv12-1


title: bv1-3


title: Microbiota of Tph2 WT male 6

value: male


title: kidney biopsy [GSM3525650 re-analysis]


title: 22RV1_CCS_1

value: human prostate carcinoma epithelial


title: 22RV1_CCS_2


title: Microbiota of Tph2 WT male 5


title: bv0-3

value: untreated


title: bv0-2


title: bv1-2


title: kidney biopsy [GSM3525003 re-analysis]

value: FABMR

value: kidney biopsy


title: bv1-1


title: Product IL15.CAR TCR Patient 10

city: Houston

first: Antonino

last: Montalbano

state: TX

address: 1102 Bates Ave

institute: Baylor School of Medicine

library_source: transcriptomic single cell

data_processing:
FASTQ files were analyzed with the 10× Genomics Cell Ranger (v7.1.0) software pipeline, including demultiplexing and read alignment to the CAR-augmented human reference genome GRCh38.p13 to detect endogenous and CAR RNAs.
Genes detected in less than 10 cells, cells with fewer than 200 profiled genes, and more than 10% of mitochondrial Raw unique molecular identifiers (UMIs) were removed to exclude low-quality or dying cells. Cells with more than 7,000 genes were excluded. Doublets were identified using DoubletFinder.
UMI counts were Log Normalized with a scale factor of 10,000. Feature variance was then calculated, and the top 2,000 highly variable features (genes) were retained and scaled (linear transformation). Samples were integrated using harmony.
Assembly: hg38
Supplementary files format and content: ProductsPBMCBx_Tcells_integrated.metadata.csv, contains cells metadata from the integrated Product, PBMC, and Bx samples used to analyze TCR clonality and CAR+ and CAR- cells
Supplementary files format and content: ProductsPBMCBx_Tcells_integrated.rawcounts.csv, contains cells raw counts from the integrated Product, PBMC, and Bx samples used to analyze TCR clonality  and CAR+ and CAR- cells
Supplementary files format and content: ProductsPBMCBx_Tcells_integrated.scaledcounts.csv, contains cells scaled data from the integrated Product, PBMC, and Bx samples used to analyze TCR clonality  and CAR+ and CAR- cells
Supplementary files format and content: ProductsPBMCBx_Tcells_integrated.umapcoordinates.csv, contains the UMAP coordinates from the integrated Product, PBMC, and Bx samples used to analyze TCR clonality  and CAR+ and CAR- cells
Supplementary files format and content: Bx_integrated.metadata.csv, contains cells meatadata from integrated Bx samples used to analyze CAR- cell abundances
Supplementary files format and content: Bx_integrated.rawcounts.csv, contains cells raw counts from integrated Bx samples used to analyze CAR- cell abundances
Supplementary files format and content: Bx_integrated.scaledcounts.csv, contains cells scaled data from integrated Bx samples used to analyze CAR- cell abundances
Supplementary files format and content: Bx_integrated.umapcoordinates.csv, contains the UMAP coordinates from integrated Bx samples used to analyze CAR- cell abundances

source_name: CAR-T cells

extract_protocol:
Cells were dissociated, and scRNA-seq libraries were prepared according to Chromium Next GEM Single Cell 5’ Reagent Kit v5.2 kit (10x Genomics).
scRNA-seq libraries were prepared according to Chromium Next GEM Single Cell 5' Reagent Kit v5.2 (10x Genomics). CAR transcript were amplified by PCR. Libraries were sequenced on NovaSeq6000.

value: CAR-T cells

value: CAR + IL15


title: bv0-1


title: kidney biopsy [GSM3524084 re-analysis]

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

value: EABMR


title: kidney biopsy [GSM3524779 re-analysis]


title: 22RV1 Input ChIP

description: FactorPath ChIP-Seq (by Active Motif) - sequenced on Illumina NovaSeq 6000 (75 bp, single end)

library_source: other

data_processing:
Bowtie2 Alignment
peak calling with MACS2
Assembly: GRCh38
Supplementary files format and content: BED files

molecule: other

extract_protocol:
FactorPath ChIP-Seq (by Active Motif) - lysis buffer, Dounce homogenizer, and EpiShear probe sonicator
FactorPath ChIP-Seq (by Active Motif) - Illumina sequencing library - standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation using automated system (Apollo 342, Wafergen Biosystems/Takara)

value: Vehicle


title: 22RV1 p300 Veh Replicate 2 ChIP


title: Product IL15.CAR TCR Patient 9


title: kidney biopsy [GSM3525206 re-analysis]

extract_protocol:
All human heart biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.
Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

value: NR


title: Product IL15.CAR TCR Patient 8


title: 22RV1 p300 Veh Replicate 1 ChIP


title: 22RV1 p300 CCS Replicate 2 ChIP


title: kidney biopsy [GSM3524672 re-analysis]


title: Product IL15.CAR TCR Patient 7


title: 22RV1 p300 CCS Replicate 1 ChIP


title: 22RV1 CBP Veh Replicate 2 ChIP


title: kidney biopsy [GSM3523966 re-analysis]


title: Product IL15.CAR TCR Patient 12


title: 22RV1 CBP Veh Replicate 1 ChIP


title: kidney biopsy [GSM3523981 re-analysis]


title: Product IL15.CAR TCR Patient 5


title: 22RV1 CBP CCS Replicate 1 ChIP


title: Product IL15.CAR TCR Patient 4


title: 22RV1 AR Veh Replicate 1 ChIP


title: kidney biopsy [GSM3525315 re-analysis]


title: 22RV1 AR Veh Replicate 2 ChIP


title: 22RV1 AR CCS Replicate 2 ChIP


title: PBMCs IL15.CAR TCR Patient 12


title: kidney biopsy [GSM3523896 re-analysis]


title: 22RV1 AR CCS Replicate 1 ChIP


title: PBMCs IL15.CAR TCR Patient 10


title: kidney biopsy [GSM3524101 re-analysis]


title: PBMCs IL15.CAR TCR Patient 9


title: SBC-3, ASO-NEAT1-1473, miRNA-seq rep.2

city: Montreal

first: Thomas

middle: Francis

last: Duchaine

state: Quebec

address: 3655 Promenade Sir-William-Osler

department: Biochemistry

institute: McGill University

data_processing:
Unique Molecular Identifiers (UMIs) of 12 nt were extracted from read pairs using UMI-tools.
5' adapter sequence and short reads (< 18 nt) were removed using Trimmomatic v0.39.
Reads were mapped to the hg38 Ensembl v104 genome assembly and the 52 QIAseq miRNA Library QC Spike-ins sequences using Bowtie v1.3.0.
Reads were deduplicated using UMI-tools v1.1.1.
miRNA counts were quantified using featureCounts (Subread v2.0.3) and using the human miRBase v22 annotation file.
Normalization and differential expression were performed using the R package DESeq2 v1.38.1
Assembly: hg38 Ensembl v104 for aligment and miRBasev22 for miRNA counts.
Supplementary files format and content: tab-delimimted text file contains gene information and counts for each sample.

growth_protocol: SBC-3 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % fetal bovine serum (FBS). Cells were incubated in a humidified environment at 37 °C with 5 % CO2.

extract_protocol:
Total RNA from mammalian cells was prepared using Trizol reagent according to the manufacturer’s instructions.
100 ng of RNA samples were spiked-in with 0.1 uL of QIAseq miRNA Library QC Spike-ins. Small RNA libraries were prepared with the QIAseq miRNA Library Kit according to the manufacturer’s instructions.

treatment_protocol: siRNAs and ASOs (10 nM) were reverse transfected into SBC-3 cells with Lipofectamine RNAiMAX according to the manufacturer’s instructions. Cells were harvested 72 h post-transfection.

value: Small cell lung cancer

value: NEAT1 knockdown

value: ASO NEAT1


title: SBC-3, ASO-NEAT1-1473, miRNA-seq rep.3


title: kidney biopsy [GSM3525166 re-analysis]


title: SBC-3, ASO-NEAT1-1473, miRNA-seq rep.1


title: SBC-3, ASO-NEAT1-1047, miRNA-seq rep.1


title: PBMCs IL15.CAR TCR Patient 8


title: PBMCs IL15.CAR TCR Patient 7


title: kidney biopsy [GSM3525074 re-analysis]


title: SBC-3, ASO-NEAT1-1047, miRNA-seq rep.3


title: SBC-3, ASO-Ctrl, miRNA-seq rep.2

value: WT

value: ASO Ctrl


title: SBC-3, ASO-Ctrl, miRNA-seq rep.1


title: kidney biopsy [GSM3524009 re-analysis]


title: 22RV1 CBP CCS Replicate 2 ChIP

value: CCS1477 (CBP/p300 inhibitor)


title: kidney biopsy [GSM3524521 re-analysis]


title: PBMCs IL15.CAR TCR Patient 5


title: PBMCs IL15.CAR TCR Patient 4


title: kidney biopsy [GSM3524731 re-analysis]


title: SBC-3, siNONO-4, miRNA-seq rep.3

value: NONO knockdown

value: siNONO


title: Biopsy IL15.CAR TCR Patient 10


title: SBC-3, siNONO-3, miRNA-seq rep.3


title: Biopsy IL15.CAR TCR Patient 12


title: kidney biopsy [GSM3525552 re-analysis]


title: SBC-3, siNONO-4, miRNA-seq rep.1


title: SBC-3, siNONO-3, miRNA-seq rep.2


title: kidney biopsy [GSM3524788 re-analysis]


title: SBC-3, siSFPQ-3, miRNA-seq rep.3

value: SFPQ knockdown

value: siSFPQ


title: Biopsy IL15.CAR TCR Patient 9


title: SBC-3, ASO-NEAT1-1047, miRNA-seq rep.2


title: SBC-3, siNONO-3, miRNA-seq rep.1


title: kidney biopsy [GSM3524135 re-analysis]

value: LABMR


title: SBC-3, ASO-Ctrl, miRNA-seq rep.3


title: SBC-3, siSFPQ-3, miRNA-seq rep.2


title: Biopsy IL15.CAR TCR Patient 8


title: kidney biopsy [GSM3524043 re-analysis]

value: kidney biopsy


title: Biopsy IL15.CAR TCR Patient 7

value: CAR-T cells


title: SBC-3, siSFPQ-2, miRNA-seq rep.3


title: SBC-3, siSFPQ-2, miRNA-seq rep.1


title: kidney biopsy [GSM3524884 re-analysis]


title: Biopsy IL15.CAR TCR Patient 5

value: CAR + IL15


title: kidney biopsy [GSM3525393 re-analysis]


title: SBC-3, siCtrl, miRNA-seq rep.3

value: siCtrl


title: Late_seed_2

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
BWA alignment 5',3' coordinate adjustment MACS2 peak calling Tn5 integration site intersection with ACRs binarization
Assembly: Oryza sativa MSU Release 7.0 of Nipponbare/ japonica
Supplementary files format and content: 1. rice_scATAC_atlas_cell_type_specific_ACRs.txt: chr of ACR (column 1), start position of ACR (column 2), end position of ACR (column 3), cell types (column 4).
Supplementary files format and content: 2. rice_scATAC_atlas_ACR_celltype_CPM.txt: a ACR by cell type matrix shows normalized read counts (CPM) per ACR per cell type.

organism: Oryza sativa

source_name: Seed

extract_protocol:
16,000 nuclei per library were extracted via FANS. 10x Genomics scATAC-seq v1
5 uL of nuclei (16,000 nuclei in total) were used as input for scATAC-seq library preparation. scATAC-seq libraries were prepared using the Chromium scATAC v1.1 (Next GEM) kit from 10X Genomics (Cat# 1000175), following the manufacturer's instructions

value: Seed

value: Nipponbare

value: Fresh


title: Biopsy IL15.CAR TCR Patient 4


title: SBC-3, siCtrl, miRNA-seq rep.2

value: Small cell lung cancer


title: Early_seed_2


title: Biopsy IL15.CAR TCR Patient 2


title: Late_seed_1


title: SBC-3, siCtrl, miRNA-seq rep.1


title: SBC-3, ASO-NEAT1-1473, RNA-seq rep.3

data_processing:
Adapter sequences, low-quality ends (phred quality < 15), and short reads (< 35 nt) were removed using Cutadapt v4.2.
Reads were mapped to the hg38 Ensembl v104 genome assembly using STAR v2.7.5a.
Gene-level stranded-reads counts were quantified using featureCounts (Subread v2.0.3).
Normalization and differential expression were performed using the R package DESeq2 v1.38.1.
Assembly: hg38 Ensembl v104
Supplementary files format and content: tab-delimimted text file contains gene information and counts for each sample

extract_protocol:
Total RNA from mammalian cells was prepared using Trizol reagent according to the manufacturer's instructions.
RNA libraries were prepared with the KAPA RNA HyperPrep Kit (Roche) according to the manufacturer’s instructions using 100 ng poly(A)-selected RNA for mRNA sequencing and Illumina universal adapters.

value: NEAT1 knockdown

value: ASO NEAT1


title: kidney biopsy [GSM3525365 re-analysis]

address: 250 Heritage Medical Research Centre

institute: University of Alberta


title: kidney biopsy [GSM3525006 re-analysis]

value: NR


title: SBC-3, siSFPQ-3, miRNA-seq rep.1


title: SBC-3, ASO-NEAT1-1473, RNA-seq rep.2


title: SBC-3, siSFPQ-2, miRNA-seq rep.2


title: kidney biopsy [GSM3524648 re-analysis]

value: FABMR


title: Panicle_2

source_name: Panicle

value: Panicle


title: PBMC_Paired_Hi-C_RNA

description: 10XMultiome, gene expression

data_processing:
gzipped pairs file, txt file with valid cells entry, and count matrix
Assembly: hg38
Supplementary files format and content: gzipped pairs file, txt file with valid cells entry, and count matrix
Library strategy: 10X Multiome

source_name: peripheral blood mononuclear cells

growth_protocol: Cryoperserved PBMC is purchased from ALLCELLS (Lot 3046679)

extract_protocol: Following user guide of Chromium Next GEM Single Cell Multiome ATAC + Gene Expression.

value: peripheral blood mononuclear cells


title: kidney biopsy [GSM3524797 re-analysis]


title: Panicle_1


title: PBMC_Droplet_Hi-C_10xATAC_v2

description: 10XATAC_v2, single-cell Hi-C

library_source: genomic single cell

data_processing:
gzipped pairs file, txt file with valid cells entry, and count matrix
Assembly: hg38
Supplementary files format and content: gzipped pairs file, txt file with valid cells entry, and count matrix

extract_protocol: Following user guide of Chromium Next GEM Single Cell ATAC Reagent Kits v2


title: kidney biopsy [GSM3524939 re-analysis]


title: SBC-3, ASO-NEAT1-1473, RNA-seq rep.1


title: kidney biopsy [GSM3524453 re-analysis]


title: SBC-3, ASO-NEAT1-1047, RNA-seq rep.3


title: Crown_root_2

source_name: Root

value: Root


title: Huh7_siMYCN_1

city: Shanghai

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters.
PCR duplicates were marked with the Picard “Mark Duplicates” utility and removed from further analysis.
Bam files were converted to BigWig files using deepTools.
Peaks were identified using the MACS2 peak caller with the following parameters: –f BAMPE –keep-dup all –g hs –q 0.01
Assembly: hg38
Supplementary files format and content: wig files were generated using deepTools.

source_name: liver

growth_protocol: Huh7 was cultured in DMEM (Invitrogen, CA, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, CA, USA) and antibiotics in an incubator at 37°C with 5% CO2.

extract_protocol:
ChIP-seq was performed as described previously (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT.  ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions.  Methods.2009;48:240-8)；CUT&Tag was performed according to the manufacturer’s protocol (Novoprotein, Shanghai, China).
Total RNA extracted using TRIzol was used for library preparation with an Illumina mRNA sequencing (mRNAseq) sample preparation kit.  Quality control of the RNA sequencing libraries was performed using a Bioanalyzer 2100 (Agilent, CA, USA) prior to paired-end sequencing on the HiSeq 3000 platform (Illumina, CA, USA);  CUT&Tag was performed according to the manufacturer’s protocol (Novoprotein, Shanghai, China).

treatment_protocol: siRNAs targeting HSF1, MYCN and negative control siRNAs (siNCs) were procured from RiboBio (Guangzhou, China).  Cells were transfected with the specified targeted or control siRNA  using Lipofectamine RNAiMAX reagent (Invitrogen, CA, USA).  After 48 hours of transfection, the cells were collected for further experiments

value: liver

value: HCC cells

value: MYCN knockdown

value: Huh7 cells transfected with siMYCN_1 using Lipofectamine RNAiMAX for 48 hours


title: SBC-3, ASO-NEAT1-1047, RNA-seq rep.2


title: Huh7_siMYCN_2

value: Huh7 cells transfected with siMYCN_2 using Lipofectamine RNAiMAX for 48 hours


title: Crown_root_1


title: SBC-3, ASO-NEAT1-1047, RNA-seq rep.1


title: Early_seed_1


title: Seminal_root_2


title: SBC-3, ASO-Ctrl, RNA-seq rep.3

value: WT

value: ASO Ctrl


title: Huh7_siHSF1_Input_ChIP

value: HSF1 knockdown

value: Huh7 cells transfected with siHSF1 using Lipofectamine RNAiMAX for 48 hours


title: Seminal_root_1

value: Nipponbare

value: Fresh


title: kidney biopsy [GSM3525118 re-analysis]

city: Edmonton

first: Jessica

last: Chang

value: kidney biopsy


title: PBMC_Paired_Hi-C_DNA

description: 10XMultiome, single-cell Hi-C


title: Leaf_2

source_name: Leaf

value: Leaf


title: Huh7_siHSF1_H3K27ac_ChIP


title: SBC-3, ASO-Ctrl, RNA-seq rep.2

value: Small cell lung cancer


title: Leaf_1


title: Huh7_siNC_Input_ChIP

value: Huh7 cells transfected with siNC using Lipofectamine RNAiMAX for 48 hours


title: kidney biopsy [GSM3524507 re-analysis]

value: NR


title: kidney biopsy [GSM3524633 re-analysis]

value: EABMR


title: Huh7_siNC_H3K27ac_ChIP

value: liver


title: SBC-3, siNONO-4, RNA-seq rep.3

value: NONO knockdown

value: siNONO


title: kidney biopsy [GSM3524971 re-analysis]


title: kidney biopsy [GSM3524986 re-analysis]


title: SBC-3, siNONO-4, RNA-seq rep.2


title: Huh7_HSF1_CUT&Tag

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters.
PCR duplicates were marked with the Picard “Mark Duplicates” utility and removed from further analysis.
Bam files were converted to BigWig files using deepTools.
Peaks were identified using the MACS2 peak caller with the following parameters: –f BAMPE –keep-dup all –g hs –q 0.01
Assembly: hg38
Supplementary files format and content: wig files were generated using deepTools.
Library strategy: CUT&Tag

value: HCC cells


title: Seedling_1

source_name: Seedling

value: Seedling


title: SBC-3, siNONO-4, RNA-seq rep.1


title: Huh7_siNC_MYCN

value: WT


title: kidney biopsy [GSM3525524 re-analysis]

value: FABMR


title: Huh7_H3K27ac_CUT&Tag


title: kidney biopsy [GSM3524100 re-analysis]


title: Early_seedling_2


title: kidney biopsy [GSM3524061 re-analysis]


title: Huh7_siHSF1_2

value: HSF1 knockdown

value: Huh7 cells transfected with siHSF1_2 using Lipofectamine RNAiMAX for 48 hours


title: SBC-3, siNONO-3, RNA-seq rep.3


title: kidney biopsy [GSM3524574 re-analysis]


title: Early_seedling_1

value: Nipponbare


title: Huh7_siHSF1_1

value: Huh7 cells transfected with siHSF1_1 using Lipofectamine RNAiMAX for 48 hours


title: kidney biopsy [GSM3524630 re-analysis]

value: LABMR

value: kidney biopsy


title: SBC-3, ASO-Ctrl, RNA-seq rep.1

value: Small cell lung cancer

value: ASO Ctrl


title: Axillary_bud_1

source_name: Axillary bud

value: Axillary bud

value: Fresh


title: SBC-3, siNONO-3, RNA-seq rep.1


title: Huh7_siNC_HSF1

value: liver

value: Huh7 cells transfected with siNC using Lipofectamine RNAiMAX for 48 hours


title: kidney biopsy [GSM3525613 re-analysis]

value: Minor


title: Seedling_2


title: SBC-3, siSFPQ-3, RNA-seq rep.3

value: SFPQ knockdown

value: siSFPQ


title: Normal_like_cell line mixing_Droplet_Hi-C_10xATAC_v2

description: 10XATAC_v2, single-cell Hi-C

data_processing:
Custom scripts for demultiplexing, mapping and extracting single cell contacts from Droplet Hi-C data were publicly available at https://github.com/Xieeeee/Droplet-Hi-C. First, depending on indexing primers used, Droplet Hi-C fastq files were demultiplexed using Illumina bcl2fastq (v2.19.0.316) or 10x Genomics cellranger-atac mkfastq (v2.0.0). After demultiplexing, a custom script was used to extract cellular barcode sequence from Read2, and barcodes are aligned to the whitelist provided by 10x Genomics using Bowtie (v1.3.0). Aligned barcode sequences were appended to the beginning of the read name to record cellular identity of each read. Next, sequencing adapters were detected and trimmed with Trim-Garole (v0.6.10). Cleaned reads were then mapped to the human (hg38) or mouse (mm10) reference genome using BWA-MEM (v0.7.17), with arguments ‘-SP5M’ specified. Finally, after mapping, valid contacts were parsed, sorted and deduplicated by Pairtools (v0.3.0), with barcodes information stored in a separated column in the pairs file. Contacts were balanced and stored in cool format using Cooler (v0.8.10) for visualization and downstream analysis84. High-quality cells were selected based on the number of total unique contacts per cell in each library.
Assembly: hg38
Supplementary files format and content: gzipped pairs file

growth_protocol: GM12878 cells were cultured at 37°C, 5% CO2 in RPMI-1640 supplemented with 1% Penicillin-Steptomycin-Glutamine and 15% FBS. WTC-11 iPSCs (a gift from the Yin Shen lab at UCSF) containing an inducible NGN2 cassette inserted into the AAVS1 safe harbor locus were maintained in Essential 8 Flex medium (Thermo Fisher, A2858501) on culture dishes coated with Matrigel (Corning, 354277). Cells were cultured with 10 uM ROCK inhibitor (STEMCELL Technologies, Y-27632) for 24h after seeding, and fed daily with fresh E8 Flex medium

extract_protocol:
Adherent cells were washed once with 1× PBS, trypsinized with 0.25% trypsin–EDTA (ThermoFisher Scientific, 25200056), spun down at 500× g for 5 min, resuspended in culture medium, and spun down again at 500 × g for 5 min. Suspension cells were spun down at 500× g for 5 min to be collected from the culture medium. The cell pellets were resuspended in 1 million cells/mL 1× PBS (pH=7.4) for crosslinking.
Following user guide of Chromium Next GEM Single Cell ATAC Reagent Kits v2


title: Treadmill muscle

city: Daejeon

first: Eui-Ju

last: Hong

state: Not Applicable

address: 99 Dahak-ro, #412, Veterinary Building, Daejeon, 34134

institute: Chungnam National University (CNU)

description: skeletal muscle with exercise

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using trimmomatic-0.39 and cutadapt 2.8), then mapped to mm10 whole genome using STAR-2.5.3a
The quantification of reads was processed using COMPSRA.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: skeletal muscle

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex Small RNA Library Prep kit (New England BioLabs, Inc., USA) according to the manufacturer’ instructions.

value: skeletal muscle

value: wild-type

value: Exercise


title: SBC-3, siSFPQ-3, RNA-seq rep.2


title: kidney biopsy [GSM3523975 re-analysis]

value: FABMR


title: Axillary_bud_2

value: Nipponbare


title: Control muscle

description: skeletal muscle without exercise

value: control


title: CP3

city: Xi'an

first: Xuzhao

last: Bian

state: Shaan'xi

address: No.28 Xianning West Road

institute: xi'an jiaotong university

data_processing:
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped. The formula is shown as follow:FPKM = {cDNA Fragments \over {Mapped Fragments(Millions) * TranscriptLength(kb)}}
Assembly: GRCh38 (hg38)
Supplementary files format and content: normalized_data.xls
Supplementary files format and content: raw_counts.xls

extract_protocol:
Peripheral blood was collected into an anticoagulant tube, and peripheral blood mononuclear cells (PBMCs) were isolated using a commercial Lymphocyte Separation Medium (Beyotime, China) by centrifugation at 700g for 30 minutes.
For library preparation and sequencing, each RNA sample, with an input quantity of 1 μg, underwent library construction using the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology, Shanghai, China), as per the provided protocol.

value: peripheral blood mononuclear cells

tag: disease

value: Hemorrhagic Fever with Renal Syndrome


title: kidney biopsy [GSM3524456 re-analysis]

value: NR

value: kidney biopsy


title: SBC-3, siSFPQ-3, RNA-seq rep.1

value: Small cell lung cancer


title: CP2


title: kidney biopsy [GSM3525073 re-analysis]


title: SBC-3, siNONO-3, RNA-seq rep.2

value: NONO knockdown

value: siNONO


title: Kidney, fibroblasts, Trf1flox/flox; Col1a2-CreERT2, RGQ00418

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

data_processing:
Obtained reads were single-end 86bp. Read adaptors and poly(A) tails were removed with bbduk.sh, following the Lexogen recommendations. Reads were then analysed with the nextpresso pipeline, as follows: Sequencing quality was checked with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse reference genome (GRCm39) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.19, allowing three mismatches and twenty multihits. Read counts were obtained with HTSeq-count v0.6.1, using the mouse gene annotation from GENCODE (vM26.GRCm39.Ensembl103). Differential expression was performed with DESeq2, using a 0.05 FDR.  GSEAPreranked was used to perform gene set enrichment analysis for several gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Assembly: GRCm39
Supplementary files format and content: Tabulated text file with DESeq2 normalized counts

source_name: Kidney

growth_protocol: Not applicable

extract_protocol:
Mice were euthanized after 8 weeks and kidneys were extracted.  To isolate fibroblasts populations in Col1a2 -CreERT2 mice, kidneys were collected in PBS, minced, and digested with 2.5 mg/ml type I collagenase (Thermo Fisher, 17100017), 2.5 mg/ml dispase II (Thermo Fisher, 17105041), and 50 ng/ml DNAse I (Roche, 10104159001) at 37 °C for 20 min to create a homogeneous cell suspension. Cell suspensions were passed through a 70 μm filter (Cultek, 45352350) to remove any undigested tissue. To remove erythroid cells, cell suspensions and blood samples were incubated for 10 min on ice in blood erythrocyte lysis buffer (Qiagen, 79217). Before analysis, cell suspensions were treated with PBS 0.04% Ultrapure BSA (Thermo Fisher, AM216). Cells were incubated at 4 °C for 30 min with anti-mouse CD29-PE (clone: HMB1-1, 1:00) (Milteneyi Biotec, 130-102-994)  and anti t-RFP (EVN-AB233, Evrogen; 1:00) for fibroblasts isolation respectively. Chicken anti-Rabbit Alexa 647 (A21443, Invitrogen;1:400) was used as a secondary control against t-RFP Thermo Fisher, A21443. Isolated cells were collected on a mix of NEBNext® Cell Lysis Buffer (New England Biolabs, E6428A) and Murine RNase Inhibitor (New England Biolabs, E6429A) in DNA LoBIND tubes (Eppendorf, 0030108051), using a BD FACSAria IIu cell sorter (BD Biosciences).
500 cells per sample were were processed with the "NEBNext Single Cell/Low Input RNA Library Prep" kit (NEB #E6420) by following manufacturer instructions. Briefly, extracts obtained by sample suspension in cell lysis buffer were submitted to an oligo(dT) primed reverse transcription with a template switching reaction. Double stranded cDNA production was performed by limited-cycle PCR. Sequencing libraries were completed with the "NEBNext Ultra II FS DNA Library Prep Kit for Illumina" (NEB #E7805). These libraries are non-directional or non-stranded. The resulting purified cDNA libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina NextSeq 550 (with v2.5 reagent kits) by following manufacturer's protocols.
Single read 86bp

treatment_protocol: Tamoxifen (TMX) (Sigma Aldrich, T-5648-1G) was intraperitoneally (i.p.) injected to six-to eight-week-old male and female Trf1+/+ KFP+/t Cre+/t and Trf1lox/lox KFP+/t Cre+/t mice for three times a week for 8 weeks

value: Kidney

value: fibroblasts

value: Trf1flox/flox; Col1a2-CreERT2

value: Tamoxifen


title: kidney biopsy [GSM3524699 re-analysis]


title: SBC-3, siNONO-4, miRNA-seq rep.2


title: SBC-3, siSFPQ-2, RNA-seq rep.3

value: SFPQ knockdown

value: siSFPQ


title: Kidney, fibroblasts, Trf1flox/flox; Col1a2-CreERT2, RGQ00372


title: CP1


title: SBC-3, siSFPQ-2, RNA-seq rep.2


title: Kidney, fibroblasts, Trf1flox/flox; Col1a2-CreERT2, RGQ00355


title: DP3


title: kidney biopsy [GSM3524571 re-analysis]

value: EABMR


title: SBC-3, siCtrl, RNA-seq rep.3

value: WT

value: siCtrl


title: DP1


title: kidney biopsy [GSM3524484 re-analysis]


title: SBC-3, siSFPQ-2, RNA-seq rep.1


title: DP2


title: Kidney, fibroblasts, Trf1+/+; Col1a2-CreERT2, RGQ00332

value: Trf1+/+; Col1a2-CreERT2