title: B2020_44177_20201116_BC10

description:
B2020_44177
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_44609_20201119_BC01

status: Public on Jul 30 2022

type: SRA

city: Berlin

first: Luis

middle: Philipp

last: Kuschel

address: Robert-Koch-Platz 4

department: Abteilung für experimentelle Neurologie

country: Germany

institute: Charité Universitätsmedizin Berlin

description:
B2020_44609
Oxford Nanopore Technologies MinION Mk 1B

library_source: genomic

data_processing:
Basecalling was performed using guppy (Oxford Nanopore Technologies, UK) v3.1.5 (CPU-based, fast mode) or v3.4.3 (GPU-based)
Alignment to the hg19 human reference genome using minimap2 v.2.15
Methylation status of CpG sites (5mC) was called using nanopolish v0.13.2 and binarized using 0.6 as a cut-off value
Individual RData files containing binarized methylation status for CpG sites which overlap with the probeset of the 450k microarray are generated using R v4.0.2.
Individual BED files with genomic hg19 coordinates, binary methylation call and Illumina probe ID were generated and merged into a sparse table with sample ID as row header and Illumina probe IDs as column header
Assembly: hg19
Supplementary files format and content: .Rdata files containing binarized methylation status for CpG sites.
Supplementary files format and content: .bed files with hg19 coordinates and binary methylation status (cut-off 0.6)

molecule: genomic DNA

organism: Homo sapiens

source_name: brain tumor tissue

extract_protocol:
DNA was extraced either using spin columns (DNeasy Blood & Tissue Kit, Qiagen, NL) or using phenol chloroform procedure.
Library preparation was performed using the Rapid Barcoding Kit (RBK004, Oxford Nanopore Technologies, UK) according to manufacturers instructions.

tag: tissue

value: brain tumor tissue

tag: reference diagnosis

value: Pituitary adenoma gonadotropin producing

tag: nanopore methylation_call

value: PITAD, FSH LH

tag: nanopore methylation_class_family_call


title: B2020_44836_20201120_BC02

description:
B2020_44836
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma

value: MNG


title: B2020_47930_20201210_BC09

description:
B2020_47930
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_44083_20201116_BC11

description:
B2020_44083
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_43011_20201109_BC03

description:
B2020_43011
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_43562_20201111_BC12

description:
B2020_43562
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_45479_20201124_BC06

description:
B2020_45479
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype

value: GBM, MES

value: MCF GBM


title: B2020_43402_20201111_BC09

description:
B2020_43402
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_41723_20201030_BC02

description:
B2020_41723
Oxford Nanopore Technologies MinION Mk 1B

value: Pilocytic astrocytoma

value: GBM, RTK II


title: B2020_4841_20200204_BC03_FLO

description:
B2020_4841
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_42898_20201106_BC04

description:
B2020_42898
Oxford Nanopore Technologies MinION Mk 1B

value: LGG, PA PF

value: MCF PA


title: B2020_4108_20200131_BC08

description:
B2020_4108
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH wildtype, subclass midline*

value: DMG, K27


title: B2020_38197_20201008_BC02

description:
B2020_38197
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_38906_20201014_BC01

description:
B2020_38906
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_40280_20201021_BC01

description:
B2020_40280
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_46150_20201130_BC04

description:
B2020_46150
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_37024_20200929_BC10

description:
B2020_37024
Oxford Nanopore Technologies MinION Mk 1B

value: Anaplastic astrocytoma, IDH-mutant

value: A IDH

value: MCF IDH GLM


title: B2020_37911_20201006_BC08

description:
B2020_37911
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue


title: B2020_40210_20201021_BC06

description:
B2020_40210
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_37087_20200930_BC07

description:
B2020_37087
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_42358_20201104_BC03

description:
B2020_42358
Oxford Nanopore Technologies MinION Mk 1B

value: Schwannoma

value: LGG, SEGA


title: B2020_37322_20201001_BC09

description:
B2020_37322
Oxford Nanopore Technologies MinION Mk 1B

value: Anaplastic pilocytic astrocytoma


title: B2020_3404_20200129_BC03

description:
B2020_3404
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma

value: MNG


title: B2020_3661_20200129_BC06

description:
B2020_3661
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_32160_20200826_BC06

description:
B2020_32160
Oxford Nanopore Technologies MinION Mk 1B

value: SCHW


title: B2020_38372_20201009_BC03

description:
B2020_38372
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype

value: MCF GBM


title: B2020_35073_20200916_BC05

description:
B2020_35073
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_38628_20201009_BC04

description:
B2020_38628
Oxford Nanopore Technologies MinION Mk 1B

value: Pilocytic astrocytoma

value: LGG, PA MID


title: B2020_43014_20201109_BC08

description:
B2020_43014
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_36295_20200924_BC12

description:
B2020_36295
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK I


title: B2020_30698_20200817_BC02

description:
B2020_30698
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK II


title: B2020_32395_20200827_BC07

description:
B2020_32395
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma sparsely granulated GH/STH producing

value: PITAD, ACTH


title: B2020_32411_20200827_BC01

description:
B2020_32411
Oxford Nanopore Technologies MinION Mk 1B

value: Medulloblastoma, genetically defined, group 3

value: MB, G3

value: MCF MB G3G4


title: B2020_37284_20201001_BC01

description:
B2020_37284
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue


title: B2020_33363_20200903_BC10

description:
B2020_33363
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_33027_20200902_BC09

description:
B2020_33027
Oxford Nanopore Technologies MinION Mk 1B

value: PXA


title: B2020_31753_20200824_BC05

description:
B2020_31753
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma gonadotropin producing

value: PITAD, FSH LH


title: B2020_33657_20200907_BC03

description:
B2020_33657
Oxford Nanopore Technologies MinION Mk 1B

value: Anaplastic astrocytoma, IDH-mutant

value: A IDH

value: MCF IDH GLM


title: B2020_31572_20200821_BC04

description:
B2020_31572
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype

value: MCF GBM


title: B2020_30190_20200904_BC11

description:
B2020_30190
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, MES


title: B2020_296_20200107_FLO

description:
B2020_296
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_29478_20200807_BC10

description:
B2020_29478
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-mutant

value: A IDH, HG


title: B2020_29609_20200811_BC11

description:
B2020_29609
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma

value: MNG


title: B2020_3026_20200127_BC07

description:
B2020_3026
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_27641_20200727_BC04

description:
B2020_27641
Oxford Nanopore Technologies MinION Mk 1B

value: Schwannoma

value: SCHW


title: B2020_29191_20200806_BC09

description:
B2020_29191
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_28407_20200731_BC06

description:
B2020_28407
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK I


title: B2020_26726_20200720_BC03

description:
B2020_26726
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue

value: GBM, RTK II


title: B2020_27270_20200723_BC04

description:
B2020_27270
Oxford Nanopore Technologies MinION Mk 1B

value: Diffuse large B cell lymphoma (DLBCL)

value: LYMPHO


title: B2020_25637_20200710_BC07

description:
B2020_25637
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_24887_20200706_BC10

description:
B2020_24887
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_26370_20200716_BC01

description:
B2020_26370
Oxford Nanopore Technologies MinION Mk 1B

value: Anaplastic astrocytoma, IDH-mutant


title: P9_T_R3B2

city: Beijing

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling
scRNA-Seq:Read 2 was used to abtain the cell barcodes to further split the reads according to the cell IDs(barcode) and the same time recorded the UMI sequences;Read 1 was picked in each cell according to the cell ID in read2 and the UMI information was aligned to it,and then these raw reads were trimmed to remove TSO or polyA sequence;Adaptor contamination and low-quality reads were discarded from the trimmed Read 1 raw data;TopHat(version 2.0.14) with default settings were used for sequence alignment and uniquely mapped reads were kept.
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

molecule: polyA RNA

source_name: Patient 9 primary tumour

extract_protocol:
Single cells were picked into scRNA-seq lysis buffer by using mouth pipette. Then the cells in scRNA-seq lysis buffer were vortexed for 45 second and heated at 72℃for 3min to release RNA.
Modified STRT-Seq protocol: we modified the STRT-Seq protocol for application to a large number of cells. Briefly, the 8bp barcodes was used to label individual cells. So the cDNA of cells with different barcodes can be pooled together for library constructions. And we also enrich the 3’ cDNA by the affinity interaction between biotin and Dynabeads® MyOne™ Streptavidin C1 beads. Then the fragmented DNA inserts were library constructed according to the manufacturer procedures of KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series (KAPA, KK8054) and sequencing on Illumina 4000.

treatment_protocol: Normal and cancer colon tissues from six patients were dissected and washed by PBS for several times. Then the tissues were cut into small pieces by surgical scissors. Then the 2mg/mL Collagenase/Dispase was used to digest the tissues into single cells at 37℃ for 30-40 min after which the cell suspension was centrifuged at 800g  at 4℃ for 5min. The supernate was discarded and 1% HSA was used to re-suspended the cell pellet.

tag: disease state

value: liver metastasis

tag: type

value: adjacent normal colon tissue


title: B2020_26302_20200716_BC02

description:
B2020_26302
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_25796_20200713_BC08

description:
B2020_25796
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_26123_20200715_BC01

description:
B2020_26123
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_26225_20200715_BC01

description:
B2020_26225
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_26754_20200720_BC03

description:
B2020_26754
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype


title: P9_T_R2B1


title: B2020_24752_20200703_BC04

description:
B2020_24752
Oxford Nanopore Technologies MinION Mk 1B

value: Embryonal tumour with multilayered rosettes, C19MC-altered

value: ETMR


title: P9_T_R2B2


title: B2020_24230_20200701_BC08_

description:
B2020_24230
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_23959_20200629_BC07

description:
B2020_23959
Oxford Nanopore Technologies MinION Mk 1B

value: MCF GBM


title: B2020_28996_20200803_BC08

description:
B2020_28996
Oxford Nanopore Technologies MinION Mk 1B

value: Solitary fibrous tumour / haemangiopericytoma

value: SFT HMPC


title: P9_T_R3B1


title: B2020_23145_20200624_BC01

description:
B2020_23145
Oxford Nanopore Technologies MinION Mk 1B


title: P9_T_R1B2

value: primary tumour


title: B2020_24659_20200703_BC09

description:
B2020_24659
Oxford Nanopore Technologies MinION Mk 1B

value: Schwannoma


title: B2020_23068_20200624_BC05

description:
B2020_23068
Oxford Nanopore Technologies MinION Mk 1B

value: SCHW


title: P9_T_R1B1


title: P9_N_B1

source_name: Patient 9 adjacent normal colon tissue


title: P9_LyM_B2

source_name: Patient 9 lymph node metastasis


title: B2020_23683_20200626_BC06

description:
B2020_23683
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_21953_20200617_BC03

description:
B2020_21953
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma

value: MNG


title: B2020_21514_20200615_BC10

description:
B2020_21514
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue

value: Pituitary adenoma ACTH producing

value: PITAD, ACTH


title: P9_N_B2


title: B2020_26519_20200723_BC02

description:
B2020_26519
Oxford Nanopore Technologies MinION Mk 1B

value: Anaplastic astrocytoma, IDH-mutant

value: O IDH

value: MCF IDH GLM


title: B2020_22380_20200619_BC12

description:
B2020_22380
Oxford Nanopore Technologies MinION Mk 1B


title: P9_LM_R2B3

source_name: Patient 9 liver metastasis

value: liver metastasis


title: P9_LyM_B3


title: P9_LM_R2B2


title: P9_LyM_B1


title: B2020_24550_20200702_BC02

description:
B2020_24550
Oxford Nanopore Technologies MinION Mk 1B

value: Medulloblastoma, genetically defined, group 3

value: MB, G3

value: MCF MB G3G4


title: B2020_21333_20200612_BC09

description:
B2020_21333
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_20855_20200609_BC02

description:
B2020_20855
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype

value: GBM, RTK I

value: MCF GBM


title: B2020_2074_20200122_BC07

description:
B2020_2074
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma gonadotropin producing

value: PITAD, FSH LH


title: P9_LM_R1B2

value: lymph node metastasis


title: P9_LM_R2B1

value: primary tumour


title: B2020_19781_20200603_BC06

description:
B2020_19781
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue


title: P8_TR3_TR4

source_name: Patient 8 primary tumour


title: B2020_19952_20200603_BC01

description:
B2020_19952
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma

value: MNG


title: P9_LM_R1B1


title: P8_N

source_name: Patient 8 adjacent normal colon tissue


title: P8_TR1_TR2


title: B2020_2153_20200122_BC01

description:
B2020_2153
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_19050_20200527_BC02

description:
B2020_19050
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK II


title: B2020_19597_20200602_BC05

description:
B2020_19597
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_18609_20200522_RB01

description:
B2020_18609
Oxford Nanopore Technologies MinION Mk 1B


title: P8_LyMR1

source_name: Patient 8 lymph node metastasis


title: P8_LMR2

source_name: Patient 8 liver metastasis


title: P8_LyMR2


title: P8_LMR1


title: P7_W3

source_name: Patient 7 omentum metastasis

value: adjacent normal colon tissue


title: B2020_20060_20200604_BC07

description:
B2020_20060
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_20474_20200605_BC08

description:
B2020_20474
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, MES


title: B2020_17183_20200514_BC10

description:
B2020_17183
Oxford Nanopore Technologies MinION Mk 1B


title: P7_PT-C3-C4

source_name: Patient 7 primary tumour


title: P9_LM_R1B3


title: B2020_16871_20200513_BC09

description:
B2020_16871
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_15695_20200504_BC08

description:
B2020_15695
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_15617_20200504_BC04

description:
B2020_15617
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_15381_20200429_BC03

description:
B2020_15381
Oxford Nanopore Technologies MinION Mk 1B


title: P7_PT_C5


title: B2020_16112_20200506_BC05

description:
B2020_16112
Oxford Nanopore Technologies MinION Mk 1B

value: CONTR, REACT


title: B2020_14622_20200424_BC06

description:
B2020_14622
Oxford Nanopore Technologies MinION Mk 1B

value: Subependymal giant cell astrocytoma


title: P7_N

source_name: Patient 7 adjacent normal colon tissue


title: B2020_15288_20200429_BC12

description:
B2020_15288
Oxford Nanopore Technologies MinION Mk 1B

value: Schwannoma

value: SCHW


title: B2020_14523_20200422_BC05

description:
B2020_14523
Oxford Nanopore Technologies MinION Mk 1B

value: Medulloblastoma, genetically defined, SHH-activated and TP53-wildtype

value: MB, SHH CHL AD

value: MCF MB SHH


title: P7_PT-C1-C2


title: B2020_1925_20200122_BC07

description:
B2020_1925
Oxford Nanopore Technologies MinION Mk 1B


title: P7_LyM_1-2

source_name: Patient 7 lymph node metastasis


title: P7_LyM_1-3_1-4


title: B2020_1447_20200123_BC03

description:
B2020_1447
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma gonadotropin producing


title: P7_LM_2-3

source_name: Patient 7 liver metastasis

value: liver metastasis


title: P7_LM_N


title: P7_W1-W2

value: lymph node metastasis


title: P7_LM_2_1

value: primary tumour


title: B2020_13930_20200416_BC03

description:
B2020_13930
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue

value: Glioblastoma, IDH-wildtype

value: GBM, RTK I

value: MCF GBM


title: B2020_14119_20200417_BC11

description:
B2020_14119
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK II


title: B2020_1323_20200123_BC02

description:
B2020_1323
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma

value: MNG


title: B2020_13501_20200409_BC10

description:
B2020_13501
Oxford Nanopore Technologies MinION Mk 1B


title: P7_LM_1-2_2-2


title: P7_LM1-1


title: B2020_13090_20200408_BC09

description:
B2020_13090
Oxford Nanopore Technologies MinION Mk 1B

value: Ependymoma


title: P6_PT

source_name: Patient 6 primary tumour

value: adjacent normal colon tissue


title: B2020_11296_20200319_BC09

description:
B2020_11296
Oxford Nanopore Technologies MinION Mk 1B

value: Solitary fibrous tumour / haemangiopericytoma

value: SFT HMPC


title: B2020_11901_20200326_BC5

description:
B2020_11901
Oxford Nanopore Technologies MinION Mk 1B

value: PITAD, FSH LH


title: B2020_12186_20200327_BC05

description:
B2020_12186
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma ACTH producing

value: PITAD, ACTH


title: B2020_11635_20200324_BC12

description:
B2020_11635
Oxford Nanopore Technologies MinION Mk 1B

value: Schwannoma

value: SCHW


title: B2020_14171_20200417_BC04

description:
B2020_14171
Oxford Nanopore Technologies MinION Mk 1B

value: Anaplastic astrocytoma, IDH-mutant

value: A IDH

value: MCF IDH GLM


title: B2020_10955_BC11_FLO

description:
B2020_10955
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue

value: Glioblastoma, IDH-wildtype

value: GBM, RTK I


title: B2020_1034_20200122_BC01

description:
B2020_1034
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma


title: B2019_8351_20191021

description:
B2019_8351
Oxford Nanopore Technologies MinION Mk 1B

value: MNG


title: B2020_11435_20200320_BC10

description:
B2020_11435
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK II

value: MCF GBM


title: B2020_11127_20200318_BC08

description:
B2020_11127
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_10043_20200312_BC06

description:
B2020_10043
Oxford Nanopore Technologies MinION Mk 1B


title: B2019_52226_20191220_BC01

description:
B2019_52226
Oxford Nanopore Technologies MinION Mk 1B


title: B2019_52983_20191227

description:
B2019_52983
Oxford Nanopore Technologies MinION Mk 1B

value: Diffuse large B cell lymphoma (DLBCL)

value: LYMPHO


title: B2019_52905_20191224_BC05

description:
B2019_52905
Oxford Nanopore Technologies MinION Mk 1B


title: B2019_7334_07112019_FLO

description:
B2019_7334
Oxford Nanopore Technologies MinION Mk 1B


title: B2019_52753_20191224_BC04

description:
B2019_52753
Oxford Nanopore Technologies MinION Mk 1B


title: B2019_52517_20191223_BC03

description:
B2019_52517
Oxford Nanopore Technologies MinION Mk 1B


title: B2019_51391_20191216_FLO

description:
B2019_51391
Oxford Nanopore Technologies MinION Mk 1B


title: B2019_51171_20191212_BC09

description:
B2019_51171
Oxford Nanopore Technologies MinION Mk 1B

value: Anaplastic oligodendroglioma, IDH-mutant and 1p/19q-codeleted

value: O IDH


title: B2019_51597_20191217_BC11

description:
B2019_51597
Oxford Nanopore Technologies MinION Mk 1B

value: Pilocytic astrocytoma

value: LGG, PA PF

value: MCF PA


title: B2019_52083_20191219_BC12

description:
B2019_52083
Oxford Nanopore Technologies MinION Mk 1B


title: B2019_50666_20191211_BC08

description:
B2019_50666
Oxford Nanopore Technologies MinION Mk 1B

value: Anaplastic astrocytoma, IDH-mutant

value: A IDH, HG


title: B2020_13190_20200408_BC02

description:
B2020_13190
Oxford Nanopore Technologies MinION Mk 1B


title: B2019_50297_20191208_BC07

description:
B2019_50297
Oxford Nanopore Technologies MinION Mk 1B


title: B2019_5113_20191121_BC08

description:
B2019_5113
Oxford Nanopore Technologies MinION Mk 1B


title: B2019_50158_20191206_BC06

description:
B2019_50158
Oxford Nanopore Technologies MinION Mk 1B


title: B2019_48730_20191129_BC02

description:
B2019_48730
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_10539_20200316_BC07

description:
B2020_10539
Oxford Nanopore Technologies MinION Mk 1B


title: B2019_48500_20191126

description:
B2019_48500
Oxford Nanopore Technologies MinION Mk 1B

value: Ependymoma

value: EPN, SPINE


title: B2019_48565_20191127_BC01

description:
B2019_48565
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue


title: H3K9me3.DE.d14.Setdb1.Con.r2

city: Planegg-Martinsried

first: Gunnar

last: Schotta

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

data_processing:
ChIP-seq single end reads were aligned to the mouse genome mm10 using Bowtie(Langmead et al., 2009) with options “-q -n 2 --best --chunkmbs 2000 -p 32 -S”.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated from homer tag directories using makeBigWig.pl

organism: Mus musculus

source_name: setdb1 heterozygous cKO ES cells

growth_protocol: ES-derived definitive endoderm cells were generated by seeding 100K feeder-free ES cells in a 6-well FBS-coated plate with endoderm differentiation medium (EDM)+activinA (10ng/ml) and wnt3a (2ng/ml). After 7days differentiation, trypsinize the cells with StemPro™ Accutase™ Cell Dissociation Reagent,stop the reaction by adding EDM medium,seed cells in a ratio with 1:7 for d12 and 1:9 for d14 in a 6-well Biotechne Cultrex Stem Cell Qualified Reduced Growth Factor BME coated plate with endoderm differentiation medium (EDM)+activinA (10ng/ml) and wnt3a (2ng/ml).

extract_protocol:
Followed the Low cell ChIP protocol with minor modifications. Briefly formaldehyde-fixed cells (1% formaldehyde, 10min RT) were lysed in Buffer B (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0,5%SDS, 1x protease inhibitors -Roche) and sonicated in a microTUBE on a Covaris S220 until most of the DNA fragments were 200-500 base pairs long (settings: duty cycle 2%, peak incident power 105 Watts, cycles per burst 200). After shearing lysates were centrifuged (10min 4°C 12000g) and supernatant diluted with 1 volume of Dilution Buffer (1mM EGTA 300 mM NaCl, 2% Triton x-100, 0.2% DOC, 1x protease inhibitors-Roche). In parallel, Dynabeads (Protein A or Protein G dependent on the antibody used) were conjugated to the antibody in PCR tubes by rotating 2 hour at 4°C (30rpm). Antibody-conjugated magnetic beads were added to the tube containing the chromatin and incubated 4h at 4°C (30rpm). Beads were washed (20rpm; 10min) four times with 500 ul Buffer A (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 0.5 mM EGTA,1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl, 1x protease inhibitors) and once with 500 ul Buffer C (10 mM Tris-HCl, pH 8.0, 10 mM EDTA). Beads were then incubated with 70 μl elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris HCl pH 8.0) containing 2 μl of Proteinase K (20mg/ml) for 1 hour at 55°C and 8 hours at 65°C to revert formaldehyde crosslinking, and supernatant was transferred to a new tube. Another 30 μl of elution buffer was added to the beads for 1 minute and eluates were combined and incubated with another 1 μl of Proteinase K for 1 hour at 55°C. Finally, DNA was purified with SPRI AMPure XP beads (sample-to-beads ratio 1:2).
NEBNext Ultra II for Illumina, BioLabs E7335S

treatment_protocol: ES cells were cultured for 12/14days in EDM+activinA (10ng/ml) and wnt3a (2ng/ml)

tag: cell type

value: ES-derived DE cells

tag: genotype

value: Setdb1; Sox17-Cre; EGFP-Reporter | +/p; +/T, +/T

tag: sorting markers

value: yes (GFP positive)

tag: chip antibody

value: H3K9me3 (Active Motif  39161  lot13509002)


title: H3K9me3.DE.d14.Setdb1.KO.r2

source_name: setdb1 homozygous cKO ES cells

value: Setdb1; Sox17-Cre; EGFP-Reporter | p/p; +/T, +/T


title: H3K9me3.DE.d14.Setdb1.KO.r1


title: B2019_46617_20191118_FLO

description:
B2019_46617
Oxford Nanopore Technologies MinION Mk 1B

source_name: brain tumor tissue

value: Meningioma

value: MNG


title: H3K9me3.DE.d14.Setdb1.Con.r1


title: H3K9me3.DE.d12.Setdb1.KO.r2


title: H3K9me3.DE.d12.Setdb1.Con.r3


title: H3K9me3.DE.d12.Setdb1.KO.r1


title: B2019_46051_20191115_FLO

description:
B2019_46051
Oxford Nanopore Technologies MinION Mk 1B


title: H3K9me3.DE.d12.Setdb1.Con.r2


title: H3K9me3.DE.d12.Setdb1.Con.r1


title: B2019_45355_20191112_FLO

description:
B2019_45355
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype

value: GBM, RTK II

value: MCF GBM


title: B2019_49044_20191129_BC03

description:
B2019_49044
Oxford Nanopore Technologies MinION Mk 1B

value: Schwannoma

value: SCHW


title: B2019_44609_08112_FLO019

description:
B2019_44609
Oxford Nanopore Technologies MinION Mk 1B


title: H3K9me3.Suv39.DKO.ES.r1

description:
ES cells grow in a 6-well feeder-coated plate with serum+lif ES medium
GS1278_ES_Dn57_1_ATGTCA

source_name: Suv39 DKO ES cells

growth_protocol: feeder-dependent ES cells grow in a 6-well feeder-coated plate with serum+lif ES medium

treatment_protocol: trypsine+two time preplate to remove feeders

value: ES cells

value: Suv39 DKO

value: no


title: H3K9me3.Suv39.DKO.DE.r1

description:
ES-derived definitive endoderm cells were generated by seeding 100K feeder-free ES cells in a 6-well FBS-coated plate with endoderm differentiation medium (EDM). ES cells were cultured for 7days in EDM+activinA (10ng/ml) and wnt3a (2ng/ml)
GS1282_DE_Dn57_1_GTGGCC


title: H3K9me3.wt26.Con.ES.r1

description:
ES cells grow in a 6-well feeder-coated plate with serum+lif ES medium
GS1276_ES_wt26_1_AGTCAA

source_name: wt26 wildtype control ES cells

value: wildtype


title: B2019_46793_20191118_FLO

description:
B2019_46793
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue


title: H3K9me3.Suv39.DKO.ES.r2

description:
ES cells grow in a 6-well feeder-coated plate with serum+lif ES medium
GS1279_ES_Dn57_2_CCGTCC


title: H3K9me3.wt26.Con.DE.r1

description:
ES-derived definitive endoderm cells were generated by seeding 100K feeder-free ES cells in a 6-well FBS-coated plate with endoderm differentiation medium (EDM). ES cells were cultured for 7days in EDM+activinA (10ng/ml) and wnt3a (2ng/ml)
GS1280_DE_wt26_1_GTCCGC

value: ES-derived DE cells


title: H3K9me3.Suv39.DKO.DE.r2

description:
ES-derived definitive endoderm cells were generated by seeding 100K feeder-free ES cells in a 6-well FBS-coated plate with endoderm differentiation medium (EDM). ES cells were cultured for 7days in EDM+activinA (10ng/ml) and wnt3a (2ng/ml)
GS1283_DE_Dn57_2_GTTTCG


title: H3K9me3.wt26.Con.ES.r2

description:
ES cells grow in a 6-well feeder-coated plate with serum+lif ES medium
GS1277_ES_wt26_2_AGTTCC


title: H3K9me3.DE.d12.Setdb1.KO.r3


title: H3K9me3.Dnmt1.KO.DE.r4

description:
ES-derived definitive endoderm cells were generated by seeding 100K feeder-free ES cells in a 6-well FBS-coated plate with endoderm differentiation medium (EDM). ES cells were cultured for 7days in EDM+activinA (10ng/ml) and wnt3a (2ng/ml)
GS1145_Dnmt1-KO-DE-2_ATTCCT

source_name: Dnmt1 KO ES cells

value: Dnmt1 KO


title: H3K9me3.Dnmt1.KO.DE.r3

description:
ES-derived definitive endoderm cells were generated by seeding 100K feeder-free ES cells in a 6-well FBS-coated plate with endoderm differentiation medium (EDM). ES cells were cultured for 7days in EDM+activinA (10ng/ml) and wnt3a (2ng/ml)
GS1144_Dnmt1-KO-DE-1_ACTGAT


title: B2019_44272_08112019_FLO

description:
B2019_44272
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK I


title: H3K9me3.J1.Con.DE.r4

description:
ES-derived definitive endoderm cells were generated by seeding 100K feeder-free ES cells in a 6-well FBS-coated plate with endoderm differentiation medium (EDM). ES cells were cultured for 7days in EDM+activinA (10ng/ml) and wnt3a (2ng/ml)
GS1143_J1-DE-2_GAGTGG

source_name: J1 wildtype control ES cells

value: J1 wildtype

value: H3K9me3 (Active Motif  39161  lot13509002)


title: B2019_39582_20191009

description:
B2019_39582
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma


title: B2019_45842_20191112_FLO

description:
B2019_45842
Oxford Nanopore Technologies MinION Mk 1B

value: Pilocytic astrocytoma


title: B2019_45646_20191115_FLO

description:
B2019_45646
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype


title: H3K9me3.J1.Con.DE.r3

description:
ES-derived definitive endoderm cells were generated by seeding 100K feeder-free ES cells in a 6-well FBS-coated plate with endoderm differentiation medium (EDM). ES cells were cultured for 7days in EDM+activinA (10ng/ml) and wnt3a (2ng/ml)
GS1142_J1-DE-1_CGTACG


title: H3K9me3.Dnmt1.KO.XEN.r3

description:
ES-derived XEN cells were generated by seeding 100K ES cells in a 6-well gelatin-coated plate with serum+lif ES medium, select with ES medium plus puromycin after transduction and provide with XEN medium
GS1140_Dnmt1-KO-XEN-1_GTGGCC

value: ES-derived XEN cells


title: H3K9me3.J1.Con.XEN.r4

description:
ES-derived XEN cells were generated by seeding 100K ES cells in a 6-well gelatin-coated plate with serum+lif ES medium, select with ES medium plus puromycin after transduction and provide with XEN medium
GS1139_J1-XEN-2_GTGAAA


title: H3K9me3.Dnmt1.KO.XEN.r4

description:
ES-derived XEN cells were generated by seeding 100K ES cells in a 6-well gelatin-coated plate with serum+lif ES medium, select with ES medium plus puromycin after transduction and provide with XEN medium
GS1141_Dnmt1-KO-XEN-2_GTTTCG


title: H3K9me3.wt26.Con.DE.r2

description:
ES-derived definitive endoderm cells were generated by seeding 100K feeder-free ES cells in a 6-well FBS-coated plate with endoderm differentiation medium (EDM). ES cells were cultured for 7days in EDM+activinA (10ng/ml) and wnt3a (2ng/ml)
GS1281_DE_wt26_2_GTGAAA


title: B2019_39463_20191010

description:
B2019_39463
Oxford Nanopore Technologies MinION Mk 1B

value: MNG


title: H3K9me3.J1.Con.XEN.r3

description:
ES-derived XEN cells were generated by seeding 100K ES cells in a 6-well gelatin-coated plate with serum+lif ES medium, select with ES medium plus puromycin after transduction and provide with XEN medium
GS1138_J1-XEN-1_GTCCGC


title: H3K9me3.Dnmt1.KO.ES.r3

description:
ES cells grow in a 6-well feeder-coated plate with serum+lif ES medium
GS1136_Dnmt1-KO-ES-1_ATGTCA


title: H3K9me3.Dnmt1.KO.ES.r4

description:
ES cells grow in a 6-well feeder-coated plate with serum+lif ES medium
GS1137_Dnmt1-KO-ES-2_CCGTCC


title: B2019_3945_20191111_FLO

description:
B2019_3945
Oxford Nanopore Technologies MinION Mk 1B


title: H3K9me3.J1.Con.ES.r4

description:
ES cells grow in a 6-well feeder-coated plate with serum+lif ES medium
GS1135_J1-ES-2_AGTTCC


title: B2019_44605_07112019_FLO

description:
B2019_44605
Oxford Nanopore Technologies MinION Mk 1B

value: Ependymoma

value: EPN, PF B


title: B2019_36370_20191015

description:
B2019_36370
Oxford Nanopore Technologies MinION Mk 1B

value: A IDH

value: MCF IDH GLM


title: B2019_36764_20191008

description:
B2019_36764
Oxford Nanopore Technologies MinION Mk 1B

value: Diffuse large B cell lymphoma (DLBCL)

value: LYMPHO


title: RNA.Suv39.DKO.DE.r1

description:
ES-derived definitive endoderm cells were generated by seeding 100K feeder-free ES cells in a 6-well FBS-coated plate with endoderm differentiation medium (EDM). ES cells were cultured for 7days in EDM+activinA (10ng/ml) and wnt3a (2ng/ml)
GS1293_DE_Dn57_1_GAGTGG

data_processing:
RNA-seq reads were mapped to the mouse genome (mm10) using STAR (Dobin et al., 2013).
Expression of genes in FPKM was calculated with RSEM (Li et al., 2011).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_rsem.genes.results.txt: Tab-delimited text files were generated with RSEM.

molecule: total RNA

extract_protocol:
Trizol and RNA clean and concentrator kit (Zymo research)
NEBNext rRNA Depletion Kit(E6350),EBNext Ultra II Directional RNA Library Prep Kit (E7760S),BioLabs E7335S

value: Suv39 DKO

tag: sorting marker

value: no


title: RNA.Suv39.DKO.DE.r2

description:
ES-derived definitive endoderm cells were generated by seeding 100K feeder-free ES cells in a 6-well FBS-coated plate with endoderm differentiation medium (EDM). ES cells were cultured for 7days in EDM+activinA (10ng/ml) and wnt3a (2ng/ml)
GS1294_DE_Dn57_2_ACTGAT

value: ES-derived DE cells


title: RNA.Suv39.DKO.DE.r3

description:
ES-derived definitive endoderm cells were generated by seeding 100K feeder-free ES cells in a 6-well FBS-coated plate with endoderm differentiation medium (EDM). ES cells were cultured for 7days in EDM+activinA (10ng/ml) and wnt3a (2ng/ml)
GS1295_DE_Dn57_3_ATTCCT


title: B2019_40322_20191008

description:
B2019_40322
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue

value: Medulloblastoma, genetically defined, group 4

value: MB, G4

value: MCF MB G3G4


title: RNA.wt26.Con.DE.r3

description:
ES-derived definitive endoderm cells were generated by seeding 100K feeder-free ES cells in a 6-well FBS-coated plate with endoderm differentiation medium (EDM). ES cells were cultured for 7days in EDM+activinA (10ng/ml) and wnt3a (2ng/ml)
GS1292_DE_wt26_3_CGTACG

value: wildtype


title: H3K9me3.J1.Con.ES.r3

description:
ES cells grow in a 6-well feeder-coated plate with serum+lif ES medium
GS1134_J1-ES-1_AGTCAA

value: ES cells

value: J1 wildtype

value: H3K9me3 (Active Motif  39161  lot13509002)


title: RNA.wt26.Con.DE.r1

description:
ES-derived definitive endoderm cells were generated by seeding 100K feeder-free ES cells in a 6-well FBS-coated plate with endoderm differentiation medium (EDM). ES cells were cultured for 7days in EDM+activinA (10ng/ml) and wnt3a (2ng/ml)
GS1290_DE_wt26_1_GTGGCC


title: RNA.wt26.Con.DE.r2

description:
ES-derived definitive endoderm cells were generated by seeding 100K feeder-free ES cells in a 6-well FBS-coated plate with endoderm differentiation medium (EDM). ES cells were cultured for 7days in EDM+activinA (10ng/ml) and wnt3a (2ng/ml)
GS1291_DE_wt26_2_GTTTCG


title: B2019_29432_20200219_BC11

description:
B2019_29432
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype

value: GBM, MID

value: MCF GBM


title: B2019_32597_20191008

description:
B2019_32597
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma

value: MNG


title: RNA.wt26.Con.ES.r3

description:
ES cells grow in a 6-well feeder-coated plate with serum+lif ES medium
GS1286_ES_wt26_3_ATGTCA


title: B2019_2911_20190521

description:
B2019_2911
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, MES


title: B2019_22083_20191017

description:
B2019_22083
Oxford Nanopore Technologies MinION Mk 1B


title: RNA.Suv39.DKO.ES.r2

description:
ES cells grow in a 6-well feeder-coated plate with serum+lif ES medium
GS1288_ES_Dn57_2_GTCCGC

value: Suv39 DKO


title: B2019_17919_20190529

description:
B2019_17919
Oxford Nanopore Technologies MinION Mk 1B


title: RNA.wt26.Con.ES.r2

description:
ES cells grow in a 6-well feeder-coated plate with serum+lif ES medium
GS1285_ES_wt26_2_AGTTCC

value: no


title: B2019_16990_20190529

description:
B2019_16990
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-mutant

value: A IDH, HG

value: MCF IDH GLM


title: RNA.Suv39.DKO.ES.r3

description:
ES cells grow in a 6-well feeder-coated plate with serum+lif ES medium
GS1289_ES_Dn57_3_GTGAAA


title: RNA.Dnmt1.DE.KO.r1

description: ES-derived definitive endoderm cells were generated by seeding 100K feeder-free ES cells in a 6-well FBS-coated plate with endoderm differentiation medium (EDM). ES cells were cultured for 7days in EDM+activinA (10ng/ml) and wnt3a (2ng/ml)

source_name: Dnmt1 knockout ES cells

extract_protocol:
Trizol and RNA clean and concentrator kit (Zymo research)
Smarter ultra low input-v4 (Clontech 634888) and Microplex-v2 (Diagenode C05010012)

value: ES-derived DE cells

value: Dnmt1 homozygous knockout


title: RNA.Dnmt1.XEN.KO.r2

description: ES-derived XEN cells were generated by seeding 100K ES cells in a 6-well gelatin-coated plate with serum+lif ES medium, ES cells were transduced with virus generated from GS1582 plasmid, cells selected with 1ug/ml puromycin for 2days and 0.5ug/ml for 1day. Then replace with XEN medium for 1 day.

value: ES-derived XEN cells


title: RNA.wt26.Con.ES.r1

description:
ES cells grow in a 6-well feeder-coated plate with serum+lif ES medium
GS1284_ES_wt26_1_AGTCAA

value: ES cells

value: wildtype


title: RNA.J1.DE.Con.r2

source_name: J1 wildtipe ES cells


title: B2019_12943_20191008

description:
B2019_12943
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue


title: B2019_16481_20191022

description:
B2019_16481
Oxford Nanopore Technologies MinION Mk 1B


title: RNA.Dnmt1.DE.KO.r2


title: B2018_45932_20191112

description:
B2018_45932
Oxford Nanopore Technologies MinION Mk 1B


title: RNA.J1.XEN.Con.r2


title: RNA.J1.DE.Con.r1


title: RNA.Dnmt1.XEN.KO.r1


title: B2018_40845_20191111_FLO

description:
B2018_40845
Oxford Nanopore Technologies MinION Mk 1B


title: RNA.J1.XEN.Con.r1


title: RNA.Suv39.DKO.ES.r1

description:
ES cells grow in a 6-well feeder-coated plate with serum+lif ES medium
GS1287_ES_Dn57_1_CCGTCC


title: RNA.J1.ES.Con.r2

description: ES cells grow in a 6-well feeder-coated plate with serum+lif ES medium


title: RNA.Dnmt1.ES.KO.r2


title: RNA.Dnmt1.ES.KO.r1


title: RNA.J1.ES.Con.r1


title: B2018_41310_20191119_BC06

description:
B2018_41310
Oxford Nanopore Technologies MinION Mk 1B


title: B2018_30600_20191126_BC11

description:
B2018_30600
Oxford Nanopore Technologies MinION Mk 1B


title: H3K9me3.Dnmt1.DE.KO.r2

extract_protocol:
Followed the Low cell ChIP protocol with minor modifications. Briefly fixed cells were lysed in Buffer B (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0,5%SDS, 1x protease inhibitors -Roche) and sonicated in a microTUBE on a Covaris S220 until most of the DNA fragments were 200-500 base pairs long (settings: duty cycle 2%, peak incident power 105 Watts, cycles per burst 200). After shearing lysates were centrifuged (10min 4°C 12000g) and supernatant diluted with 1 volume of Dilution Buffer (1mM EGTA 300 mM NaCl, 2% Triton x-100, 0.2% DOC, 1x protease inhibitors-Roche). In parallel, Dynabeads (Protein A or Protein G dependent on the antibody used) were conjugated to the antibody in PCR tubes by rotating 2 hour at 4°C (30rpm). Antibody-conjugated magnetic beads were added to the tube containing the chromatin and incubated 4h at 4°C (30rpm). Beads were washed (20rpm; 10min) four times with 500 ul Buffer A (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 0.5 mM EGTA,1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl, 1x protease inhibitors) and once with 500 ul Buffer C (10 mM Tris-HCl, pH 8.0, 10 mM EDTA). Beads were then incubated with 70 μl elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris HCl pH 8.0) containing 2 μl of Proteinase K (20mg/ml) for 1 hour at 55°C and 8 hours at 65°C to revert formaldehyde crosslinking, and supernatant was transferred to a new tube. Another 30 μl of elution buffer was added to the beads for 1 minute and eluates were combined and incubated with another 1 μl of Proteinase K for 1 hour at 55°C. Finally, DNA was purified with SPRI AMPure XP beads (sample-to-beads ratio 1:2).
NEBNext Ultra II for Illumina, BioLabs E7335S

treatment_protocol: cells were fixed with 1* Foxp3 fixation/permeabilization(life technologies; 00552300) for 30min at 4 degree

value: Dnmt1 KO

value: yes (Sox17 positive)

value: H3K9me3 (Active Motif  39161  lot13509002)


title: H3K9me3.J1.DE.Con.r2

source_name: J1 wildtype ES cells

value: J1 wildtype


title: H3K9me3.Dnmt1.DE.KO.r1


title: B2018_34697_20191017

description:
B2018_34697
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma

value: MNG


title: H3K9me3.J1.XEN.Con.r1


title: H3K9me3.Dnmt1.XEN.KO.r2


title: B2018_22933_20191120_BC07

description:
B2018_22933
Oxford Nanopore Technologies MinION Mk 1B

value: Fibrous meningioma


title: H3K9me3.J1.DE.Con.r1


title: 8372T

description:
8372T
Oxford Nanopore Technologies MinION Mk 1B

value: Medulloblastoma, genetically defined, non-WNT/non-SHH

value: MB, G4

value: MCF MB G3G4


title: H3K9me3.Dnmt1.ES.KO.r1

value: yes (Sox17 negative)


title: H3K9me3.J1.ES.Con.r2


title: H3K9me3.J1.ES.Con.r1


title: H3K9me3.Dnmt1.ES.KO.r2


title: H3K9me3.Setdb1.DE.KO.r2

treatment_protocol: cells were fixed with 1% formaldehyde for 10min at RT

value: ES-derived DE cells

value: Setdb1 homozygous, Sox17-Cre heterozygous, EGFP-Reporter heterozygous

value: yes (GFP positive)


title: 8137T

description:
8137T
Oxford Nanopore Technologies MinION Mk 1B

value: Anaplastic oligodendroglioma, IDH-mutant and 1p/19q-codeleted

value: O IDH

value: MCF IDH GLM


title: H3K9me3.Setdb1.DE.Con.r2

value: Setdb1 heterozygous, Sox17-Cre heterozygous, EGFP-Reporter heterozygous


title: H3K9me3.Setdb1.DE.KO.r1


title: 7455T

description:
7455T
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue

value: Glioblastoma, IDH-wildtype

value: GBM, MES

value: MCF GBM


title: H3K9me3.Setdb1.XEN.KO.r2

value: ES-derived XEN cells

value: H3K9me3 (Active Motif  39161  lot13509002)


title: H3K9me3.Setdb1.XEN.KO.r1


title: H3K9me3.Setdb1.DE.Con.r1


title: 6228T

description:
6228T
Oxford Nanopore Technologies MinION Mk 1B

value: Diffuse midline glioma, H3 K27M-mutant

value: GBM, G34


title: H3K9me3.J1.XEN.Con.r2

value: J1 wildtype

value: yes (Sox17 positive)


title: B2018_30345_20191122_BC09

description:
B2018_30345
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma

value: MNG


title: H3K9me3.Dnmt1.XEN.KO.r1

description: ES-derived XEN cells were generated by seeding 100K ES cells in a 6-well gelatin-coated plate with serum+lif ES medium, ES cells were transduced with virus generated from GS1582 plasmid, cells selected with 1ug/ml puromycin for 2days and 0.5ug/ml for 1day. Then replace with XEN medium for 1 day.

value: Dnmt1 KO


title: H3K9me3.Setdb1.XEN.Con.r1

value: yes (GFP positive)


title: H3K9me3.Setdb1.ES.KO.r2

value: ES cells

value: Setdb1 homozygous, Sox17-Cre heterozygous, EGFP-Reporter heterozygous

value: yes (GFP negative)


title: 5337T

description:
5337T
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue

value: Glioblastoma, IDH wildtype, H3.3 G34 mutant*


title: H3K9me3.Setdb1.ES.KO.r1


title: H3K9me3.Setdb1.ES.Con.r1

value: Setdb1 heterozygous, Sox17-Cre heterozygous, EGFP-Reporter heterozygous


title: H3K9me3.Setdb1.ES.Con.r2


title: 8355T

description:
8355T
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype

value: PXA

value: MCF GBM


title: 374721_T

description:
374721_T
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK II


title: H3K9me3.Setdb1.XEN.KO.lnput

description:
ES-derived XEN cells were generated by seeding 100K ES cells in a 6-well gelatin-coated plate with serum+lif ES medium, ES cells were transduced with virus generated from GS1582 plasmid, cells selected with 1ug/ml puromycin for 2days and 0.5ug/ml for 1day. Then replace with XEN medium for 1 day.
GS124GS125_XEN_input_m1.ucsc.bigWig

value: ES-derived XEN cells

value: H3K9me3 (Active Motif  39161  lot13509002)


title: H3K9me3.Setdb1.XEN.Con.lnput


title: 373160_T

description:
373160_T
Oxford Nanopore Technologies MinION Mk 1B


title: 372712_T

description:
372712_T
Oxford Nanopore Technologies MinION Mk 1B


title: RNA.Setdb1.DE.KO.r3

description: ES-derived definitive endoderm cells were generated by seeding 100K feeder-free ES cells in a 6-well FBS-coated plate with endoderm differentiation medium (EDM). ES cells were cultured for 7days in EDM+activinA (10ng/ml) and wnt3a (2ng/ml)

value: ES-derived DE cells


title: RNA.Setdb1.DE.KO.r2


title: 7382T

description:
7382T
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK I


title: 371019_T

description:
371019_T
Oxford Nanopore Technologies MinION Mk 1B


title: RNA.Setdb1.DE.KO.r1


title: H3K9me3.Setdb1.XEN.Con.r2


title: RNA.Setdb1.DE.Con.r3


title: RNA.Setdb1.DE.Con.r2


title: RNA.Setdb1.XEN.KO.r2


title: RNA.Setdb1.DE.Con.r1


title: 369420_T

description:
369420_T
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, MES


title: 363839_T

description:
363839_T
Oxford Nanopore Technologies MinION Mk 1B


title: RNA.Setdb1.XEN.KO.r3


title: RNA.Setdb1.XEN.Con.r1


title: RNA.Setdb1.XEN.KO.r1


title: RNA.Setdb1.XEN.Con.r3


title: 362905_T

description:
362905_T
Oxford Nanopore Technologies MinION Mk 1B


title: RNA.Setdb1.XEN.Con.r2


title: 362322_T

description:
362322_T
Oxford Nanopore Technologies MinION Mk 1B


title: RNA.Setdb1.ES.KO.r2

description: ES cells grow in a 6-well feeder-coated plate with serum+lif ES medium


title: RNA.Setdb1.ES.KO.r1


title: RNA.Setdb1.ES.Con.r2


title: RNA.Setdb1.ES.Con.r1


title: RNA.Setdb1.ES.KO.r3


title: 363416_T

description:
363416_T
Oxford Nanopore Technologies MinION Mk 1B


title: 352565_T

description:
352565_T
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-mutant

value: A IDH, HG

value: MCF IDH GLM


title: 362254_T

description:
362254_T
Oxford Nanopore Technologies MinION Mk 1B


title: RNA.Setdb1.ES.Con.r3

value: ES cells


title: RNA.Setdb1.Embryo.Con.r2

description: Embryo endoderm cells were trypsinized from isolated embryos

source_name: setdb1 heterozygous cKO embryos

value: embryos

value: yes (GFP  positive )


title: RNA.Setdb1.Embryo.Con.r1


title: RNA.Setdb1.Embryo.KO.r3

source_name: setdb1 homozygous cKO embryos

value: Setdb1 homozygous, Sox17-Cre heterozygous, EGFP-Reporter heterozygous


title: RNA.Setdb1.Embryo.KO.r2


title: RNA.Setdb1.Embryo.Con.r3

value: Setdb1 heterozygous, Sox17-Cre heterozygous, EGFP-Reporter heterozygous


title: RNA.Setdb1.Embryo.KO.r1


title: MafB_R2

city: Durham

first: Anne (Maggie)

middle: M

last: Bara

state: NC

address: 307 Research Dr.

department: Cell Biology and Dermatology

country: USA

institute: Duke University

data_processing:
The adapter were trimmed by trimgalore (v0.6.6)
The reads were aligned to mm10 genome by bowtie2 (v 2.4.2)
The algnment coverage were created by deeptools (v 3.5.1)
Supplementary files format and content: bigwig files with coverage normalized by CPM
Library strategy: Cut & Run

source_name: Intestinal epithelium, P7

extract_protocol:
Single cells were isolated from medial intestinal epithelium of CD1 mice at postnatal day 7. CUT&RUN Assay Kit from Cell Signaling Technologies was used to perform the CUT&RUN. The MinElute PRC Purification Kit from Quiagen was used to isolate  the DNA.
Libraries were prepared as previously described (Meers et al., 2019; Skene and Henikoff, 2017).

value: Intestinal epithelium, P7

tag: cell line

value: Mixed primary intestinal epithelial

value: WT CD1

tag: antibody


title: input


title: HUVEC, p4, rep4

city: Guangzhou

first: lei

last: zeng

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Sequencing was performed on the DNBSEQ platform.
Raw reads were aligned to the human genome using hierarchical indexing for spliced alignment of transcripts 2 (HISAT2) and Bowtie2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include tpm values for all replicates.

source_name: HUVECs

growth_protocol: Human umbilical vein endothelial cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plus Kit. To obtain sufficient quantitation of RNA, and a total of four relicate experiments were performed.
RNA quality was evaluated via Agilent 2100 Bioanalyzer. One microgram of qualified RNA was used to construct mRNA sequencing libraries.

value: Human umbilical vein endothelial cells

value: HUVECs


title: PosCtl

value: Tri-methyl-histone H3(K4) (Cell signaling technology C42D8)


title: WT CD4 T cell Post-transplant Day 7 Rep3 Biol Rep3

city: Syracuse

first: Mobin

last: Karimi

state: NY

address: 766 Irving Ave Suite 2281

department: Microbiology/Immunology

institute: Suny Upstate Medical University

data_processing:
All data were processed and analyzed using the R programming language (Version 4.0.4), the RStudio interface (Version 1.4.1106), and Bioconductor
Transcript abundance of samples was computed by pseudoalignment with Kallisto (version 0.46.2). Transcript per million (TPM) values were then normalized for each pre and post transplant samples separately and fitted to a linear model by empirical Bayes method with the Voom and Limma R packages
Differential gene expression was defined as a FDR£10%, LogFC=1 for pre-transplant samples,FDR≤10% for Post-transplanted samples, after controlling for multiple testing using the Benjamini-Hochberg method  were used for hierarchical clustering and heatmap generation in R.
Gene Ontology enrichment analysis was conducted using the g: Profiler toolset; g:GOSt tool.
Supplementary files format and content: mm9
Supplementary files format and content: .tsv file

source_name: spleen

extract_protocol:
Total RNA was extracted with the Qiagen miRNeasy Mini kit. RNA quality and quantity were assessed with the Agilent 2100 Bioanalyzer. cDNA was prepared with the SMARTseq HT Kit (Takara Bio), using 1ng total RNA.
Dual indexed sequencing libraries were prepared using the Nextera XT DNA Library Prep kit (Illumina), using 250pg cDNA.

value: spleen

value: CD4 T cell

value: Wild type

tag: treatment

value: Post transplanted Day 7


title: HUVEC, p4, rep2


title: MafB_R1


title: homozygous MCP1 knockout tomato+ cells

city: Charlottesville

first: Katherine

last: Owsiany

state: VA

address: 415 Lane Rd

department: Biochemistry and Molecular Genetics

institute: University of Virginia

description:
10x Genomics
flox-tom

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: atherosclerotic plaque

growth_protocol: Lineage tracing was induced with tamoxifen injection at 6-8 weeks of age, followed by 18 weeks of Western diet before harvest

extract_protocol:
Individual plaques were microdissected from the brachiocephaic artery, miced and digested for 1 hour in Liberase plus actinomycin D to inhibit transcription during the digestion process. Samples were filtered and resuspended in PBS plsu 0.04% UltraPure non-acetylated BSA, counted, and submitted for sequecinging targeting 2,000 cells. Remaining cells were sorted on a FACS Aria fusion cell sorter and GFP+ and tomato+ cells were collected for each libary, again targeting 2,000 cells
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence and paired-end constructs with P5 and P7 sequences were added.

value: atherosclerotic plaque

value: tdTomato+ SMC

tag: strain

value: Myh11-DreERT2 Lgals3-Cre RosatdTomato-GFP ApoE MCP1 flox/flox

value: 18 wks Western diet feeding


title: homozygous MCP1 knockout gfp+ cells

description:
10x Genomics
flox-gfp

value: GFP+ SMC


title: HUVEC, p4, rep1


title: WT CD4 T cell Post-transplant Day 7 Rep1 Biol Rep1


title: WT CD4 T cell Post-transplant Day 7 Rep2 Biol Rep2


title: HFD IRI

type: RNA

city: Washington, DC

first: Alexander

last: Kroemer

state: DC

address: 3800 Reservoir Road NW, Pasquerilla Healthcare Center (PHC), 2nd Floor,

department: Center for Translational Transplant Medicine (CTTM)

institute: MedStar Georgetown Transplant Institute

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/us/
For the normalization, we used the manual selection method using B2m as a housekeeping gene.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt-based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

source_name: Mouse liver tissue

label_protocol: PCR assays were performed using mouse liver specimens stored in Allprotect Tissue Reagent (Qiagen) and the Mouse Cytokines & Chemokines PCR Array panel (Qiagen) following the manufacturer’s instructions. cDNA was synthesized utilizing RT² First Strand kit (Qiagen) using 1.25ug pooled total RNA from at least three separate mice livers in an equal proportion. Quantitative real-time PCR were performed using StepOnePlus (Applied Biosystems) thermocycler, the qPCR cycling conditions were 95°C for 10 minutes for 1 cycle, followed by 40 cycles of 95°C for 15 seconds and 60°C for 1 minute.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: Mixed

tag: diet

value: High fat diet (HFD)

tag: hepatic injury

value: Ischemia-reperfusion injury (IRI)

tag: n-acetylcysteine (nac)

value: No treatment


title: HFD + NAC Sham

description: Test

value: No injury

value: N-acetylcysteine (NAC)


title: TCF-7 cKO CD4 Tcell Post-transplant Day 7 Biol Rep1

tag: tissue

value: TCF-7 cKO


title: heterozygous gfp+ cells

description:
10x Genomics
het-gfp

value: Myh11-DreERT2 Lgals3-Cre RosatdTomato-GFP ApoE MCP1 wt/flox


title: HFD + NAC IRI

description: Test


title: TCF-7 cKO CD4 Tcell Post-transplant Day 7 Biol Rep3

value: spleen


title: ND + NAC IRI

description: Test

value: Normal diet (ND)


title: WT CD4 T cell Pre-transplant Biol Rep3

value: CD4 T cell

value: Wild type

value: Pre transplanted


title: WT CD4 T cell Pre-transplant Biol Rep1


title: homozygous MCP1 knockout unsorted plaque

description:
10x Genomics
flox-un

value: atherosclerotic plaque

value: endothelial cells, SMC, macropahges, monocytes, T cells, B cells


title: ND + NAC Sham

description: Test


title: HUVEC, p4, rep3

value: Human umbilical vein endothelial cells

value: HUVECs


title: heterozygous tomato+ cells

description:
10x Genomics
het-tom

value: tdTomato+ SMC

value: 18 wks Western diet feeding


title: wild type tomato+ cells

description:
10x Genomics
WT-tom

value: Myh11-DreERT2 Lgals3-Cre RosatdTomato-GFP ApoE MCP1 wt/wt


title: HFD Sham

description: Test

value: Mixed

value: High fat diet (HFD)

value: No treatment


title: TCF-7 cKO CD4 Tcell Post-transplant Day 7 Biol Rep2

value: TCF-7 cKO

value: Post transplanted Day 7


title: heterozygous unsorted plaque

description:
10x Genomics
het-un

value: Myh11-DreERT2 Lgals3-Cre RosatdTomato-GFP ApoE MCP1 wt/flox


title: wild type unsorted plaque

description:
10x Genomics
WT-un


title: -Asn+Fe RNA-seq rep2 [Z-8_S65]

city: Indianapolis

first: Ji

last: Zhang

state: IN

address: 1044 W Walnut Street, R4-170

department: Pediatrics

institute: Indiana University

description: -Asn+Fe RNA-seq rep2

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.7.2a) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to hg38 genes using featureCounts (from subread v1.6.5) with the following parameters: “-s2 –p –Q 10”.
Assembly: hg38
Supplementary files format and content: count

growth_protocol: RS4;11 cells were cultured in each condition for 24 hours. Around 10 million cells were used per collection.

extract_protocol:
For H3K4me3 ChIP-seq, we used the Covaris truChIP Chromatin Shearing Reagent Kit; for RNA-seq, we used Trizol for whole cell RNA extraction.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ferric Nitrate was added at 10 µM in the presence of 0.75 µM Hinokitiol

value: -Asn+Fe


title: -Asn RNA-seq rep3 [Z-6_S63]

description: -Asn RNA-seq rep3

value: -Asn


title: ND IRI

description: Test

value: Normal diet (ND)

value: Ischemia-reperfusion injury (IRI)


title: D7.5 mouse Visium spatial transcriptome, biological replicate 3

city: RTP

first: Franco

last: Demayo

address: 111 TW Alexander Drive

institute: NIEHS

data_processing:
library strategy: Spatial transcriptomics
Raw reads were processed by Cell Ranger with default setting.
Genome_build: mm10
Supplementary_files_format_and_content: The filtered feature count matrix was generated from Cell Ranger.

source_name: Uterus

growth_protocol: The female mice were fed with normal chow, and housed with its female littermates until 8 weeks old.

extract_protocol:
The frozen sections of mouse uterus were placed on 10X genomics Visium spatial transcriptomics slides.
RNA libraries were prepared according to the Visium spatial transcriptomic slide manual

treatment_protocol: The females were mated with stud males and dissected at pregnancy day 7.5

tag: tissue collection

value: Uterine sections

tag: timing

value: Pregnancy day 7.5


title: -Asn+Fe RNA-seq rep3 [Z-9_S66]

description: -Asn+Fe RNA-seq rep3


title: wild type gfp+ cells

description:
10x Genomics
WT-gfp

value: atherosclerotic plaque

value: GFP+ SMC


title: D7.5 mouse scRNA-seq

data_processing:
Raw reads were processed by Cell Ranger with default setting.
Genome_build: mm10
Supplementary_files_format_and_content: The filtered feature count matrix was generated from Cell Ranger.

extract_protocol:
The mouse uterus were incubated with Trypsin to dissociate into single cells. The single cell flows were loaded into the 10X genomics single cell chip.
RNA libraries were prepared by Chromium Single Cell 3’ Library & Gel Bead Kit v3.1

value: single cell isolation

value: Uterus


title: ND Sham

description: Control

value: No injury


title: WT CD4 T cell Pre-transplant Biol Rep2

value: spleen

value: CD4 T cell

value: Wild type

value: Pre transplanted


title: TCF-7 cKO CD4 Tcell Pre-transplant Biol Rep3

value: TCF-7 cKO


title: TCF-7 cKO CD4 Tcell Pre-transplant Biol Rep2


title: Relapse at recurrence 11086

city: Columbus

first: Carlo

middle: M.

last: Croce

state: Ohio

address: 460 West 12th Avenue

department: Department of Cancer Biology and Genetics

institute: The Ohio State University

description: MIRNA EXPRESSION FROM BM

hyb_protocol: 100ng of total RNA have been annealed with multiplexed DNA tags (miR-tag) and bridges target specifics. Mature microRNAs are bond to specific miR-tags using a Ligase enzyme and all the tags in excess have been removed by enzyme clean-up step. The tagged microRNAs product has been diluted 1 to 5 and 5 ul have been combined with 20 ul of Reported Probes in hybridization buffer and 5 ul of Capture probes. The overnight hybridization (16 to 20 hours) at 65°C allowed to complex the probes sequence specific with targets. Probes excess have been removed using two-step magnetic beads based purification on an automated fluidic handling system (nCounter Prep Station) and target/probe complexes are immobilized on the cartridge for data collection. The nCounter Digital Analyzer collected the data by taking images of immobilized fluorescent reporters in the sample cartridge with a CCD camera through a microscope objective lens. For each cartridge, a high-density scan encompassing 325 fields of view has been performed (Casadei et al.17)

scan_protocol: For each assay, a high density scan (600 fields of view) was performed.

data_processing: Nanostring data were normalized by using the Top-100 expressed miRNA normalization as implemented by the Nanostring nSolver software. P-values were calculated using the LIMMA package (Linear Models for Microarray Data) from the Bioconductor R project. Differential expressed miRNAs with an adjusted (B-H correction) P-value<0.05 and an expression of >50 counts in at least one condition (in each pair-wise analysis) were taken into consideration.

source_name: Bone Marrow

label_protocol: All sample preparations were performed according to the manufacturer’s instructions (NanoString Technologies).

extract_protocol: Mononuclear cells (MNC) were isolated by density gradient centrifugation, diluted in 90% fetal bovine serum (FBS) plus 10% dimethyl sulfoxide (DMSO) and stored in liquid nitrogen. CD34+ cells were magnetically separated using MACS CD34+ microbead kit (Miltenyi Biotech, Bergish Gladbach, DE).  Total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA, USA) and purified using RNA Cleanup and Concentration kit (Norgen, Thorold, ON, Canada). RNA quantification was performed using Nanodrop 2000 (Thermo-Scientific, Waltham, MA, USA) and RNA integrity and purity was assessed with RNA Bioanalyzer kit (Agilent Technologies, Santa Clara, CA, USA). MiR expression profile of CD34+ cells was performed using the nCounter Human v2 miRNA Expression Assay and nCounter Nanostring platform according to manufacturer’s protocol (NanoString Technologies).

tag: patient sample type

value: AML patient With Relapse at Recurrence

tag: gender

value: M

tag: molecular analysis


title: Relapse at recurrence 10584

description: MIRNA EXPRESSION FROM BM

value: F


title: D7.5 mouse Visium spatial transcriptome, biological replicate 4


title: SKOV3 cell line treated with 1 μM of BETi (JQ1) for 24 hours sample 4

city: Houston

first: Xubin

last: Li

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

data_processing:
The raw RNA sequencing reads were aligned using STAR with the reference genome GRCh38.d1.vd1.fa and annotation file gencode.v22.annotation.gtf.
The quality controls of raw reads and aligned reads were assessed using FastQC and RSeQC, respectively.
The gene counts are quantified using htseq-count from the aligned RNA reads in BAM files.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: breast

extract_protocol:
Total RNA was isolated and purified using the RNeasy Plus Mini Kit (Qiagen). After quantification with Qubit 2.0 (Life Technologies), the samples passed through quality control steps for sample integrity and purity with Agilent 2100 and Agarose Gel Electrophoresis.
After the sample QC, the cDNA library is constructed using the NEBNext Ultra II RNA Library Prep Kit (NEB) as follows: mRNA is enriched using oligo(dT) beads. The mRNA is then fragmented via sonication in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second strand synthesis buffer and enzyme mix are added to generate the second strand by nick translation. The final cDNA library is ready after a round of DNA purification, end-repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. For library QC, library concentration was quantified using a Qubit 2.0 fluorometer (Life Technologies) and then diluted to 1 ng/μl before checking insert size on an Agilent 2100. Libraries were then quantified to greater accuracy by quantitative PCR (Q-PCR) prior to sequencing.
RNA libraries were sequenced with 20M paired-end 150bp reads on the Illumina NovaSeq 6000 platform (Novogene Inc.).

treatment_protocol: Cells (HCC1954, SKOV3 and BT474) were collected after treating with 1 μM of BETi (JQ1) for 24 hours all in biological duplicates.

value: breast


title: -Asn+Fe RNA-seq rep1 [Z-7_S64]

description: -Asn+Fe RNA-seq rep1

value: -Asn+Fe


title: TCF-7 cKO CD4 Tcell Pre-transplant Biol Rep1

tag: cell type

tag: genotype


title: -Asn RNA-seq rep1 [Z-4_S61]

description: -Asn RNA-seq rep1

value: -Asn


title: RS-7 scATAC-seq

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
scRNA-seq libraries were sequenced using a NovaSeq6000 SP 100-cycle flow cell (Illumina). scRNA-seq libraries were sequenced using a NextSeq 500 150-cycle flow cell (Illumina).
For scATAC-seq, reads were aligned to the  human genomes (hg38), and peaks were called using the cellranger-atac count pipeline. Individual samples were merged using the cellranger-atac pipeline to generate the transcription factor activity matrix.
For scRNA-seq,  raw reads were aligned to the  human genomes (hg38), and the digital expression matrix was generated using cellranger count. Individual samples were merged to generate the digital expression matrix using cellranger aggr.
Genome_build: hg38
Supplementary_files_format_and_content: Transcription factor activity matrix for scATAC-seq and raw count expression matrix for scRNA-seq.

source_name: primary BM cells from SF3B1-mutant MDS-RS samples

growth_protocol: MACS-purified CD34+ cells were subjected to a 3-phase in vitro culture. Cells were maintained in phase 1 from the day of collection until day 8, at which time the cells underwent ribonucleoprotein-based gene editing and were transitioned to phase 2 medium. On day 13 of culture, the cells were transitioned to phase 3 medium. Samples for Western blot and cytospin analyses, and sample for flow cytometry were harvested on day 13 or 15 of culture, respectively.

extract_protocol:
BM MNCs were isolated from each sample using the standard gradient separation approach with Ficoll-Paque PLUS (GE Healthcare Lifesciences, Marlborough, MA). For cell sorting applications, MNCs were enriched in CD34+ cells using magnetic sorting (MACS) with the CD34 Microbead Kit (Miltenyi Biotec, Bergisch Gladbach, Germany) and further purified by fluorescence-activated cell sorting as described below.
For scATAC-seq, the scATAC Low Cell Input Nuclei Isolation protocol (10X Genomics) was used to isolate nuclei from FACS-purified cells. The trypan blue exclusion assay was performed to check for intact nuclei. The remaining extracted nuclei were used for the consecutive steps of the scATAC-seq library preparation protocol following 10X Genomics guidelines. Equal molar concentrations of uniquely indexed samples were pooled together. For scRNA-seq, sample preparation and sequencing were performed at MD Anderson Cancer Center’s Advanced Technology Genomics Core. Sample concentration and cell suspension viability were evaluated using a Countess II FL Automated Cell Counter (Thermo Fisher Scientific). Samples were normalized for input onto the Chromium Single Cell A Chip Kit (10X Genomics, Pleasanton, CA), and single cells were lysed and barcoded for reverse transcription. Equal amounts of each uniquely indexed sample library were pooled together.

tag: disease state

value: myelodysplastic syndrome with ringed sideroblasts (MDS-RS)

value: SF3B1 mutant

value: bone marrow


title: D7.5 mouse Visium spatial transcriptome, biological replicate 1, 2

value: Uterine sections

value: Pregnancy day 7.5


title: SKOV3 cell line treated with 1 μM of BETi (JQ1) for 24 hours sample 1


title: HCC1954 cell line treated with 1 μM of BETi (JQ1) for 24 hours sample 4


title: Relapse at recurrence 10121

description: MIRNA EXPRESSION FROM BM


title: +Asn RNA-seq rep2 [Z-2_S59]

description: +Asn RNA-seq rep2

value: +Asn


title: P1-N-2

description:
PolyA RNA
Single cell RNA-Seq.
processed data file: metastatic_Colon_TPM.txt

data_processing:
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling.
scRNA-Seq: Read 2 was used to obtain the cell barcodes to further split the reads according to the cell IDs (barcode) and the same time recorded the UMI sequences; Read 1 was picked in each cell according to the cell ID in read2 and the UMI information was aligned to it, and then these raw reads were trimmed to remove TSO or polyA sequence. Adaptor contamination and low-quality reads were discarded from the trimmed Read 1 raw data. TopHat (version 2.0.14) with default settings was used for sequence alignment and uniquely mapped reads were kept.
Whole genome sequencing: Quality control pipeline was firstly performed on paired-end sequencing data to remove low quality reads. The cleaned reads were mapped to human genome (hg19) by BWA. The total sequence reads of each 5M window were calculated and normalized by the total read depth of each samples. For each 5M window, they were normalized by dividing the average reads depth of all samples. Finally, the CNV values were visualized by ggplot2 package.
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly hg19.
Supplementary_files_format_and_content: metastatic_Colon_TPM.txt: Tab-delimited text file includes TPM values for each Sample.
Supplementary_files_format_and_content: 5M_Merge_Reads.txt: Tab-delimited text file includes read depth per 5M window for each bulk tissue.
Supplementary_files_format_and_content: The *.txt files provide the barcode sequences for the samples.

source_name: Patient 1 adjacent normal colon tissue

extract_protocol:
Single cells were picked into scRNA-seq lysis buffer by using mouth pipette. Then the cells in scRNA-seq lysis buffer were vortexed for 45 second and heated at 72℃ for 3min to release RNA. Bulk genomic DNA were extracted according to the manufacturer protocol of DNeasy Blood & Tissue Kit (QIAGEN).
Modified STRT-Seq protocol: we modified the STRT-Seq protocol for application to a large number of cells. Briefly, the 8bp barcodes was used to label individual cells. So the cDNA of cells with different barcodes can be pooled together for library constructions. And we also enrich the 3’ cDNA by the affinity interaction between biotin and Dynabeads® MyOne™ Streptavidin C1 beads. Then the fragmented DNA inserts were library constructed according to the manufacturer procedures of KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series (KAPA, KK8054) and sequenced on Illumina 4000. Bulk genomic DNA library construction protocol: The extracted genomic DNA was fragmented by sonication into 300bp and then library constructed according to the manufacturer procedures of KAPA Hyper Pre.

treatment_protocol: Normal and cancer colon tissues from six patients were dissected and washed by PBS for several times. Then the tissues were cut into small pieces by surgical scissors. Then the 2mg/mL Collagenase/Dispase was used to digest the tissues into single cells at 37℃ for 30-40 min after which the cell suspension was centrifuged at 800g at 4℃ for 5min. The supernate was discarded and 1% HSA was used to re-suspended the cell pellet.

tag: patient id

tag: patient disease

value: colorectal cancer, liver metastasis

value: adjacent normal colon tissue


title: HCC1954 cell line treated with 1 μM of BETi (JQ1) for 24 hours sample 3

tag: cell line


title: +Asn RNA-seq rep1 [Z-1_S58]

description: +Asn RNA-seq rep1

tag: treatment


title: Relapse at recurrence 09424

description: MIRNA EXPRESSION FROM BM


title: +Asn RNA-seq rep3 [Z-3_S60]

description: +Asn RNA-seq rep3


title: Relapse at recurrence 10577

description: MIRNA EXPRESSION FROM BM


title: P1-PT-2

source_name: Patient 1 primary tumour

value: primary tumour


title: SKOV3 cell line treated with 1 μM of BETi (JQ1) for 24 hours sample 3


title: HCC1954 cell line treated with 1 μM of BETi (JQ1) for 24 hours sample 1


title: -Asn RNA-seq rep2 [Z-5_S62]

description: -Asn RNA-seq rep2


title: RS-5 scATAC-seq


title: BT474 cell line treated with 1 μM of BETi (JQ1) for 24 hours sample 3


title: SKOV3 cell line treated with 1 μM of BETi (JQ1) for 24 hours sample 2


title: P2-N-2

source_name: Patient 2 adjacent normal colon tissue


title: Relapse at recurrence 09609

description: MIRNA EXPRESSION FROM BM


title: BT474 cell line treated with 1 μM of BETi (JQ1) for 24 hours sample 2


title: RS-4 scATAC-seq


title: HD-3 scATAC-seq

source_name: primary BM cells from healthy donor samples

value: healthy

value: SF3B1 wild type


title: Relapse at recurrence 08759

description: MIRNA EXPRESSION FROM BM

value: AML patient With Relapse at Recurrence


title: Relapse at recurrence 06080

description: MIRNA EXPRESSION FROM BM

value: M


title: P1-LM-2

source_name: Patient 1 liver metastasis

value: liver metastasis


title: Relapse at recurrence 08973

description: MIRNA EXPRESSION FROM BM

value: F


title: Relapse at recurrence 09011

description: MIRNA EXPRESSION FROM BM


title: P1-LM-1


title: P2-N-1


title: HCC1954 cell line treated with 1 μM of BETi (JQ1) for 24 hours sample 2

value: breast


title: HD-1 scATAC-seq


title: P2-LM-3

source_name: Patient 2 liver metastasis


title: SST K5

city: Basel

first: Geoffrey

last: Fucile

address: Spitalstrasse 41

department: sciCORE

country: Switzerland

institute: University of Basel

description: polyA-enriched RNA

data_processing:
adaptor removal and quality trimming with Trimmomatic
alignment and raw read count summary with STAR
Assembly: Ensembl GRCm38
Supplementary files format and content: tab delimited raw read counts from STAR

source_name: Brain, hippocampus

extract_protocol: NOT PROVIDED; REQUESTED

value: Brain, hippocampus

value: Somatostatin+ interneurons

value: SLM2 cKO


title: Relapse at recurrence 01140

description: MIRNA EXPRESSION FROM BM


title: P2-LM-2


title: SST W5

description: polyA-enriched RNA

value: SLM2 WT


title: BT474 cell line treated with 1 μM of BETi (JQ1) for 24 hours sample 4


title: Relapse at diagnosis 10290

description: MIRNA EXPRESSION FROM BM

value: AML patient With Relapse at Diagnosis


title: SST W3

description: polyA-enriched RNA


title: SST W2

description: polyA-enriched RNA


title: Relapse at recurrence 08011

description: MIRNA EXPRESSION FROM BM


title: A2780-DDP-2

city: Shanghai

first: Feng

last: Xing

address: 619 Zhonghua New Road, Zhabei District

department: gynecology

institute: Zhabei District Centre Hospital

data_processing:
SmallRNA_Pipline_V1.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (v0.20.0 parameter -q 20).
Trimmed sequence reads were mapped to GRCh38 using bwa aln(0.7.13 parameters- mismath: 0.04 Gap Extensions 3 Seed Length: 32 Maximum number of alignments: 50).
Read count extraction and normalization were performed using smallRNA_Pipline script.
Assembly: GRCh38
Supplementary files format and content: All_miRNA.mature.tpm.xlsx: Excel file includes TPM values for each Sample.

growth_protocol: All cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine and penicillin/streptomycin at 37 °C in a humidified circumstance containing 5% CO2.

extract_protocol:
RNA was harvested using TRIzol™ reagent. A minimum of 1ug RNA was used for the construction of sequencing libraries.
VAHTS Small RNA Library Prep Kit for Illumina.

treatment_protocol: No special treatment.

tag: phenotype

value: cisplatin-resistant


title: Relapse at recurrence 07679

description: MIRNA EXPRESSION FROM BM


title: SST K3

description: polyA-enriched RNA


title: A2780-DDP-1


title: SST W1

description: polyA-enriched RNA


title: P2-PT-2

source_name: Patient 2 primary tumour


title: Grik W6

description: polyA-enriched RNA

value: Excitatory pyramidal cells


title: P1-PT-1

value: colorectal cancer, liver metastasis


title: P1-N-1

value: adjacent normal colon tissue


title: Relapse at diagnosis 09211

description: MIRNA EXPRESSION FROM BM


title: SST K7

description: polyA-enriched RNA


title: BT474 cell line treated with 1 μM of BETi (JQ1) for 24 hours sample 1


title: Grik W5

description: polyA-enriched RNA


title: SST K4

description: polyA-enriched RNA


title: A2780-DDP-3


title: P2-LM-1


title: HRI10 scRNA-seq

value: myelodysplastic syndrome with ringed sideroblasts (MDS-RS)

value: CD34+ cells subjected to a 3-phase in vitro culture

value: SF3B1 mutant

value: bone marrow


title: P2-PT-3

value: primary tumour


title: A2780-3

value: cisplatin-sensitive


title: A2780-2


title: Relapse at diagnosis 08151

description: MIRNA EXPRESSION FROM BM

value: F


title: Relapse at diagnosis 08600

description: MIRNA EXPRESSION FROM BM

value: M


title: Relapse at diagnosis 09598

description: MIRNA EXPRESSION FROM BM


title: Relapse at diagnosis 08971

description: MIRNA EXPRESSION FROM BM


title: Grik K2

description: polyA-enriched RNA

value: Brain, hippocampus


title: Grik W4

description: polyA-enriched RNA


title: P6-LyM1-2

source_name: Patient 6 lymph node metastasis

value: colorectal cancer, lymph node metastasis

value: lymph node metastasis


title: CTR08 scRNA-seq


title: Relapse at diagnosis 08640

description: MIRNA EXPRESSION FROM BM


title: Grik K1

description: polyA-enriched RNA

value: SLM2 cKO


title: P2-PT-1


title: A2780-1


title: P6-LyM3-2


title: Grik W3

description: polyA-enriched RNA

value: SLM2 WT


title: Relapse at diagnosis 09468

description: MIRNA EXPRESSION FROM BM

value: AML patient With Relapse at Diagnosis


title: P6-PT2

source_name: Patient 6 primary tumour


title: Relapse at diagnosis 07612

description: MIRNA EXPRESSION FROM BM


title: P6-PT1


title: CamK W3

description: polyA-enriched RNA

value: Excitatory pyramidal cells


title: P6-LyM3-1


title: P5-PT3-4

source_name: Patient 5 primary tumour


title: Grik K4

description: polyA-enriched RNA


title: HRI08 scRNA-seq


title: CD34-UPN06 scRNA-seq


title: Relapse at diagnosis 05184

description: MIRNA EXPRESSION FROM BM


title: P6-LyM2-2


title: Grik K3

description: polyA-enriched RNA


title: HRI07 scRNA-seq


title: Relapse at diagnosis 00541

description: MIRNA EXPRESSION FROM BM


title: CD34-UPN04 scRNA-seq


title: Relapse at diagnosis 07916

description: MIRNA EXPRESSION FROM BM


title: P6-LyM2-1


title: CamK K6

description: polyA-enriched RNA


title: P5-PT1-2


title: CTR10 scRNA-seq


title: P6-LyM1-1


title: Relapse at diagnosis 06995

description: MIRNA EXPRESSION FROM BM


title: CTR07 scRNA-seq


title: CamK W5

description: polyA-enriched RNA


title: P5-N

source_name: Patient 5 adjacent normal colon tissue


title: CamK W2

description: polyA-enriched RNA


title: CamK W4

description: polyA-enriched RNA


title: CD34-UPN11 scRNA-seq


title: No Relapse 1111

description: MIRNA EXPRESSION FROM BM

value: AML patient With NO Relapse


title: CD34-UPN12 scRNA-seq


title: No Relapse 0808

description: MIRNA EXPRESSION FROM BM


title: No Relapse 0707

description: MIRNA EXPRESSION FROM BM


title: No Relapse 0909

description: MIRNA EXPRESSION FROM BM


title: CamK K5

description: polyA-enriched RNA


title: No Relapse 1010

description: MIRNA EXPRESSION FROM BM


title: CD34-Old5 scRNA-seq

value: healthy

value: SF3B1 wild type


title: No Relapse 0606

description: MIRNA EXPRESSION FROM BM


title: CD34-UPN03 scRNA-seq

value: myelodysplastic syndrome with ringed sideroblasts (MDS-RS)


title: P5-LyM1-2-lyM1-3

source_name: Patient 5 lymph node metastasis


title: P4-N

source_name: Patient 4 adjacent normal colon tissue

value: adjacent normal colon tissue


title: P4-PT1

source_name: Patient 4 primary tumour


title: CD34-UPN02 scRNA-seq

value: SF3B1 mutant

value: bone marrow


title: No Relapse 0303

description: MIRNA EXPRESSION FROM BM

source_name: Bone Marrow


title: CD34-UPN01 scRNA-seq

source_name: primary BM cells from SF3B1-mutant MDS-RS samples


title: CamK K4

description: polyA-enriched RNA


title: P5-LyM1-1-lyM2


title: P4-PT2

value: primary tumour


title: No Relapse 0202

description: MIRNA EXPRESSION FROM BM

value: F


title: No Relapse 0505

description: MIRNA EXPRESSION FROM BM

value: M


title: No Relapse 0101

description: MIRNA EXPRESSION FROM BM


title: BM-UPN11 scRNA-seq

value: bone marrow mononuclear cells


title: BM-UPN06 scRNA-seq


title: CD34-Old4 scRNA-seq


title: BM-UPN04 scRNA-seq


title: P4-LyM2

source_name: Patient 4 lymph node metastasis

value: colorectal cancer, lymph node metastasis


title: BM-UPN03 scRNA-seq


title: Healty Donor 7

description: MIRNA EXPRESSION FROM BM

value: Healty Donor


title: Healty Donor 8

description: MIRNA EXPRESSION FROM BM


title: Healty Donor 6

description: MIRNA EXPRESSION FROM BM


title: P4-LyM1

value: lymph node metastasis


title: P3-PT2

source_name: Patient 3 primary tumour

value: colorectal cancer, liver metastasis


title: P3-PT5


title: P3-PT4


title: MEF-RAS+shp53_3

city: Lyon

first: jean-michel

last: flaman

address: 28 rue Laennec

department: CRCL

country: France

institute: Inserm 1052

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. After fragmentation 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 4x44K v2  Microarrays (Agilent-026655) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried briefly in acetonitrile.

scan_protocol: Microarrays were scanned with an Agilent DNA microarray scanner G2565CA (Agilent Technologies).Fluorescent signals were extracted and normalized with the Feature Extraction software version 10.5.1.1 (Agilent Technologies),

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized to the 75th percentile signal intensity and the baseline was adjusted on control condition shp53 using GeneSpring GX 12.6 software (Agilent Technologies). Log2 values.

source_name: Mouse Embryonic Fibroblast transduced by RASV12 + shp53expressing viral vectors

label_protocol: cRNAs were synthesized and labeled with the Cy3 dye from 100 ng of total RNA using the one-color Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's recommandations, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mouse embryonic fibroblasts (MEFs) were isolated from E12.5-E13.5 embryos from pregnant C57BL/6 mice, and cultured in high glucose Dulbecco’s Modified Eagle’s Medium with GlutaMax, (DMEM, Life Technologies, Carlsbad, USA) supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich, Saint-Louis, USA), 1% penicillin-streptomycin (Life Technologies) and 1% MEM non-essential amino acid (Gibco™).

extract_protocol: Total RNA was extracted from the different MEFs using NucleoSpin® RNA (Macherey Nalgen) following the manufacturer's recommendations

value: MEF

tag: transduced with

value: RASV12 + shp53


title: MEF-shp53+RAS_1

source_name: Mouse Embryonic Fibroblast transduced by shp53 + RASV12 expressing viral vectors

value: shp53 + RASV12


title: Healty Donor 3

description: MIRNA EXPRESSION FROM BM


title: MEF-RAS_2

source_name: Mouse Embryonic Fibroblast transduced by RASV12 expressing viral vector


title: MEF-shp53+RAS_2


title: P3-PT1


title: MEF-RAS+shp53_1


title: MEF-RAS+shp53_2


title: BM-Old4 scRNA-seq

source_name: primary BM cells from healthy donor samples

value: healthy


title: P3-PT3


title: MEF-RAS_1


title: MEF-shp53+RAS_3


title: Healty Donor 5

description: MIRNA EXPRESSION FROM BM


title: BM-UPN02 scRNA-seq


title: MEF-RAS_3


title: Healty Donor 4

description: MIRNA EXPRESSION FROM BM


title: BM-UPN01 scRNA-seq


title: sgMiat-6-1

status: Public on Jul 29 2022

city: New York

first: Adam

last: Schmitt

state: New York

address: 417 E 68th St

institute: MSKCC

data_processing:
basepair https://app.basepairtech.com/
Sequence reads were trimmed for adaptor sequence/low-quality sequence using basepair QC, Trim
Trimmed sequence reads were mapped to GRCm38/mm10 using basepair STAR
Read count extraction and normalization were performed using basepair
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each Sample

source_name: cerebellum

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: cerebellum

value: stem-like medulloblastoma cells

value: Miat knockdown

value: Math1-Cre; SmoM2


title: MEF-shp53_1

source_name: Mouse Embryonic Fibroblast transduced by shp53 expressing viral vector


title: sgMiat-6-2


title: sgGal4-4-1

value: WT


title: P3-N

source_name: Patient 3 adjacent normal colon tissue

value: adjacent normal colon tissue


title: sgMiat-96-2


title: Healty Donor 2

description: MIRNA EXPRESSION FROM BM


title: sgMiat-96-1


title: BM-Old5 scRNA-seq

value: SF3B1 wild type

value: bone marrow


title: MEF-shp53_2


title: MEF-shp53_3


title: Healty Donor 1

description: MIRNA EXPRESSION FROM BM


title: sgGal4-4-2


title: prostate_cancer_primary_221

city: Tampa

first: Kosj

last: Yamoah

state: Florida

address: 12902 Magnolia Drive

institute: Moffitt Cancer Center

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)

label: biotin

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.

value: prostate cancer

tag: primary gleason

tag: secondary gleason

tag: pre-treatment psa (ng/ml)

tag: age

tag: race

value: NAAM


title: prostate_cancer_primary_220

tag: tissue


title: prostate_cancer_primary_216


title: prostate_cancer_primary_223

value: AAM


title: prostate_cancer_primary_224


title: prostate_cancer_primary_222


title: prostate_cancer_primary_226


title: prostate_cancer_primary_218


title: prostate_cancer_primary_225


title: prostate_cancer_primary_219


title: prostate_cancer_primary_210


title: prostate_cancer_primary_211


title: prostate_cancer_primary_213


title: prostate_cancer_primary_215


title: prostate_cancer_primary_209


title: prostate_cancer_primary_208


title: prostate_cancer_primary_205


title: prostate_cancer_primary_214


title: prostate_cancer_primary_207


title: prostate_cancer_primary_217


title: prostate_cancer_primary_212


title: prostate_cancer_primary_204


title: prostate_cancer_primary_203


title: prostate_cancer_primary_200


title: prostate_cancer_primary_202


title: prostate_cancer_primary_199


title: prostate_cancer_primary_201


title: prostate_cancer_primary_206


title: prostate_cancer_primary_198


title: prostate_cancer_primary_197


title: prostate_cancer_primary_195


title: prostate_cancer_primary_196


title: prostate_cancer_primary_193


title: prostate_cancer_primary_191


title: prostate_cancer_primary_190


title: prostate_cancer_primary_192


title: prostate_cancer_primary_194


title: prostate_cancer_primary_189


title: prostate_cancer_primary_180


title: prostate_cancer_primary_187


title: prostate_cancer_primary_181


title: prostate_cancer_primary_186


title: prostate_cancer_primary_188


title: prostate_cancer_primary_185


title: prostate_cancer_primary_178


title: prostate_cancer_primary_179


title: prostate_cancer_primary_184


title: prostate_cancer_primary_182


title: prostate_cancer_primary_173


title: prostate_cancer_primary_183


title: prostate_cancer_primary_177


title: prostate_cancer_primary_168


title: prostate_cancer_primary_165


title: prostate_cancer_primary_159


title: prostate_cancer_primary_162


title: prostate_cancer_primary_158


title: prostate_cancer_primary_160


title: prostate_cancer_primary_176


title: prostate_cancer_primary_172


title: prostate_cancer_primary_175


title: prostate_cancer_primary_174


title: prostate_cancer_primary_171


title: prostate_cancer_primary_169


title: prostate_cancer_primary_156


title: prostate_cancer_primary_167


title: prostate_cancer_primary_170


title: prostate_cancer_primary_155


title: prostate_cancer_primary_164


title: prostate_cancer_primary_166


title: prostate_cancer_primary_146


title: prostate_cancer_primary_144


title: prostate_cancer_primary_161


title: prostate_cancer_primary_153


title: prostate_cancer_primary_151


title: prostate_cancer_primary_163


title: prostate_cancer_primary_154


title: prostate_cancer_primary_152


title: prostate_cancer_primary_150


title: prostate_cancer_primary_157


title: prostate_cancer_primary_143


title: prostate_cancer_primary_138


title: prostate_cancer_primary_149


title: prostate_cancer_primary_136


title: prostate_cancer_primary_145


title: prostate_cancer_primary_147


title: prostate_cancer_primary_134


title: prostate_cancer_primary_131


title: prostate_cancer_primary_135


title: prostate_cancer_primary_142


title: prostate_cancer_primary_141


title: prostate_cancer_primary_148


title: prostate_cancer_primary_140


title: prostate_cancer_primary_139


title: prostate_cancer_primary_128


title: prostate_cancer_primary_129


title: prostate_cancer_primary_133


title: prostate_cancer_primary_132


title: prostate_cancer_primary_127


title: prostate_cancer_primary_137


title: prostate_cancer_primary_130


title: prostate_cancer_primary_125


title: prostate_cancer_primary_117


title: prostate_cancer_primary_121


title: prostate_cancer_primary_119


title: prostate_cancer_primary_126


title: prostate_cancer_primary_124


title: prostate_cancer_primary_116


title: prostate_cancer_primary_112


title: prostate_cancer_primary_122


title: prostate_cancer_primary_118


title: prostate_cancer_primary_113


title: prostate_cancer_primary_120


title: prostate_cancer_primary_123


title: prostate_cancer_primary_105


title: prostate_cancer_primary_110


title: prostate_cancer_primary_106


title: prostate_cancer_primary_114


title: prostate_cancer_primary_109


title: prostate_cancer_primary_103


title: prostate_cancer_primary_104


title: prostate_cancer_primary_115


title: prostate_cancer_primary_108


title: prostate_cancer_primary_101


title: prostate_cancer_primary_100


title: prostate_cancer_primary_102


title: prostate_cancer_primary_98


title: prostate_cancer_primary_96


title: prostate_cancer_primary_107


title: prostate_cancer_primary_97


title: prostate_cancer_primary_99


title: prostate_cancer_primary_95


title: prostate_cancer_primary_94


title: prostate_cancer_primary_92


title: prostate_cancer_primary_88


title: prostate_cancer_primary_86


title: prostate_cancer_primary_82


title: prostate_cancer_primary_89


title: prostate_cancer_primary_83


title: prostate_cancer_primary_87


title: prostate_cancer_primary_90


title: prostate_cancer_primary_85


title: prostate_cancer_primary_80


title: prostate_cancer_primary_93


title: prostate_cancer_primary_79


title: prostate_cancer_primary_69


title: prostate_cancer_primary_76


title: prostate_cancer_primary_75


title: prostate_cancer_primary_66


title: prostate_cancer_primary_74


title: prostate_cancer_primary_81


title: prostate_cancer_primary_73


title: prostate_cancer_primary_78


title: prostate_cancer_primary_77


title: prostate_cancer_primary_72


title: prostate_cancer_primary_70


title: prostate_cancer_primary_91


title: prostate_cancer_primary_84


title: prostate_cancer_primary_67


title: prostate_cancer_primary_68


title: prostate_cancer_primary_71


title: prostate_cancer_primary_111


title: prostate_cancer_primary_60


title: prostate_cancer_primary_65


title: prostate_cancer_primary_63


title: prostate_cancer_primary_62


title: prostate_cancer_primary_59