title: peripheral blood, prostate cancer-r1 (RN0390)


title: peripheral blood, prostate cancer-r1 (PN0482)

status: Public on Aug 31 2024

type: RNA

city: Richmond

first: Adam

last: Dempsey

state: VA

address: 8751 Park Central Drive, Suite 200

country: USA

institute: StageZero Life Sciences

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) v1.1.1 using Affymetrix default analysis settings and global scaling (MAS 5.0) as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 701021 Rev. 4, Affymetrix).

extract_protocol: Trizol extraction of total RNA from the pelleted cells was performed according to the manufacturer's instructions.

treatment_protocol: Blood plasma was removed after centrifugation and a hypotonic buffer was added at a 3:1 volume ratio to lyse the red blood cells. The mixture was centrifuged to yield a pellet for subsequent total RNA isolation.

tag: tissue

value: peripheral blood

tag: gender

value: M

tag: age

tag: cancer dx

value: prostate cancer


title: peripheral blood, prostate cancer-r1 (RN0389)


title: peripheral blood, prostate cancer-r1 (RN0161)


title: peripheral blood, prostate cancer-r1 (RN0183)


title: peripheral blood, prostate cancer-r1 (RN0231)


title: peripheral blood, prostate cancer-r1 (RN0374)


title: peripheral blood, prostate cancer-r1 (RN0302)


title: peripheral blood, prostate cancer-r1 (RN058)


title: peripheral blood, prostate cancer-r1 (RN0176)


title: peripheral blood, prostate cancer-r1 (RN0113)


title: peripheral blood, prostate cancer-r1 (RN0107)


title: peripheral blood, prostate cancer-r1 (RN0100)


title: peripheral blood, prostate cancer-r1 (RN0349)


title: peripheral blood, prostate cancer-r1 (RN0105)


title: peripheral blood, prostate cancer-r1 (RN0087)


title: peripheral blood, prostate cancer-r1 (RN027)


title: peripheral blood, prostate cancer-r1 (PN0164)


title: peripheral blood, prostate cancer-r1 (RN023)


title: peripheral blood, prostate cancer-r1 (RN0115)


title: peripheral blood, prostate cancer-r1 (RN0243)


title: peripheral blood, prostate cancer-r1 (PN0204)


title: peripheral blood, prostate cancer-r1 (RN0079)


title: peripheral blood, prostate cancer-r1 (PN0134)


title: peripheral blood, prostate cancer-r1 (RN0065)


title: peripheral blood, prostate cancer-r1 (RN0263)


title: peripheral blood, prostate cancer-r1 (PN0130)


title: peripheral blood, prostate cancer-r1 (PN0107)


title: peripheral blood, prostate cancer-r1 (PN0114)


title: peripheral blood, prostate cancer-r1 (PN0131)


title: peripheral blood, prostate cancer-r1 (RN0076)


title: peripheral blood, prostate cancer-r1 (PN0103)


title: peripheral blood, prostate cancer-r1 (PN0104)


title: peripheral blood, prostate cancer-r1 (PN0058)


title: peripheral blood, prostate cancer-r1 (PN0089)


title: peripheral blood, prostate cancer-r1 (PN0077)


title: peripheral blood, prostate cancer-r1 (PN0048)


title: peripheral blood, prostate cancer-r1 (PN0062)


title: peripheral blood, prostate cancer-r1 (PN0095)


title: peripheral blood, ovarian cancer-r1 (SM0390)

value: F

value: ovarian cancer


title: peripheral blood, ovarian cancer-r1 (SM0406)


title: peripheral blood, prostate cancer-r1 (BT0015)


title: peripheral blood, ovarian cancer-r1 (SM0349)


title: peripheral blood, ovarian cancer-r1 (SM0354)


title: peripheral blood, ovarian cancer-r1 (SM0340)


title: peripheral blood, ovarian cancer-r1 (SM0291)


title: peripheral blood, ovarian cancer-r1 (SM0332)


title: peripheral blood, ovarian cancer-r1 (SM0405)


title: peripheral blood, ovarian cancer-r1 (SM0268)


title: peripheral blood, ovarian cancer-r1 (SM0345)


title: peripheral blood, ovarian cancer-r1 (SM0216)


title: peripheral blood, ovarian cancer-r1 (SM0346)


title: peripheral blood, ovarian cancer-r1 (SM0422)


title: peripheral blood, ovarian cancer-r1 (SM0174)


title: peripheral blood, ovarian cancer-r1 (SM0227)


title: peripheral blood, ovarian cancer-r1 (SM0166)


title: peripheral blood, ovarian cancer-r1 (SM0248)


title: peripheral blood, ovarian cancer-r1 (SM0284)


title: peripheral blood, ovarian cancer-r1 (SM0289)


title: peripheral blood, ovarian cancer-r1 (SM0164)


title: peripheral blood, ovarian cancer-r1 (SM0171)


title: peripheral blood, ovarian cancer-r1 (SM0165)


title: peripheral blood, prostate cancer-r1 (PN0223)


title: peripheral blood, ovarian cancer-r1 (SM0125)


title: peripheral blood, ovarian cancer-r1 (SM0369)


title: peripheral blood, ovarian cancer-r1 (SM0123)


title: peripheral blood, ovarian cancer-r1 (SM0120)


title: peripheral blood, ovarian cancer-r1 (SM0119)


title: peripheral blood, ovarian cancer-r1 (SM0118)


title: peripheral blood, ovarian cancer-r1 (SM0103)


title: peripheral blood, ovarian cancer-r1 (SM0110)


title: peripheral blood, ovarian cancer-r1 (SM0114)


title: peripheral blood, ovarian cancer-r1 (SM0115)


title: peripheral blood, ovarian cancer-r1 (SM0050)


title: peripheral blood, ovarian cancer-r1 (SM0084)


title: peripheral blood, ovarian cancer-r1 (SM0085)


title: peripheral blood, ovarian cancer-r1 (SM0117)


title: peripheral blood, ovarian cancer-r1 (SM0097)


title: peripheral blood, ovarian cancer-r1 (SM0112)


title: peripheral blood, ovarian cancer-r1 (SM0087)


title: peripheral blood, ovarian cancer-r1 (SM0116)


title: peripheral blood, ovarian cancer-r1 (SM0047)


title: peripheral blood, ovarian cancer-r1 (SM0109)


title: peripheral blood, ovarian cancer-r1 (SM0049)


title: peripheral blood, ovarian cancer-r1 (SM0086)


title: peripheral blood, ovarian cancer-r1 (SM0094)


title: peripheral blood, ovarian cancer-r1 (SM0122)


title: peripheral blood, ovarian cancer-r1 (SM0111)


title: peripheral blood, ovarian cancer-r1 (SM0046)


title: peripheral blood, ovarian cancer-r1 (SM0043)


title: peripheral blood, ovarian cancer-r1 (SM0099)


title: peripheral blood, ovarian cancer-r1 (SM0018)


title: peripheral blood, ovarian cancer-r1 (SM0124)


title: peripheral blood, ovarian cancer-r1 (SM0044)


title: peripheral blood, ovarian cancer-r1 (SM0016)


title: peripheral blood, prostate cancer-r1 (RN0082)


title: peripheral blood, ovarian cancer-r1 (SM0031)


title: peripheral blood, ovarian cancer-r1 (SM0015)


title: peripheral blood, ovarian cancer-r1 (SM0019)


title: peripheral blood, ovarian cancer-r1 (SM0013)


title: peripheral blood, ovarian cancer-r1 (SM0004)


title: peripheral blood, ovarian cancer-r1 (SM0011)


title: peripheral blood, nasopharyngeal cancer-r1 (20070515)

value: nasopharyngeal cancer


title: peripheral blood, ovarian cancer-r1 (SM0012)


title: peripheral blood, nasopharyngeal cancer-r1 (R1578)


title: peripheral blood, nasopharyngeal cancer-r1 (R1843)


title: peripheral blood, nasopharyngeal cancer-r1 (R2093)


title: peripheral blood, nasopharyngeal cancer-r1 (R1708)


title: peripheral blood, nasopharyngeal cancer-r1 (R1549)


title: peripheral blood, nasopharyngeal cancer-r1 (R1514)


title: peripheral blood, ovarian cancer-r1 (SM0014)


title: peripheral blood, nasopharyngeal cancer-r1 (R1602)


title: peripheral blood, ovarian cancer-r1 (SM0003)


title: peripheral blood, nasopharyngeal cancer-r1 (R1510)


title: peripheral blood, nasopharyngeal cancer-r1 (R1530)


title: peripheral blood, nasopharyngeal cancer-r1 (R1487)


title: peripheral blood, nasopharyngeal cancer-r1 (R1997)


title: peripheral blood, nasopharyngeal cancer-r1 (R1332)


title: peripheral blood, nasopharyngeal cancer-r1 (R1316)


title: peripheral blood, nasopharyngeal cancer-r1 (R1244)


title: peripheral blood, nasopharyngeal cancer-r1 (R1255)


title: peripheral blood, nasopharyngeal cancer-r1 (R1324)


title: peripheral blood, nasopharyngeal cancer-r1 (R1261)


title: peripheral blood, nasopharyngeal cancer-r1 (R1829)


title: peripheral blood, nasopharyngeal cancer-r1 (R1242)


title: peripheral blood, nasopharyngeal cancer-r1 (R1214)


title: peripheral blood, ovarian cancer-r1 (SM0121)


title: peripheral blood, nasopharyngeal cancer-r1 (R1600)


title: peripheral blood, nasopharyngeal cancer-r1 (R1203)


title: peripheral blood, nasopharyngeal cancer-r1 (R1164)


title: peripheral blood, nasopharyngeal cancer-r1 (R1076)


title: peripheral blood, nasopharyngeal cancer-r1 (R1085)


title: peripheral blood, nasopharyngeal cancer-r1 (R0989)


title: peripheral blood, nasopharyngeal cancer-r1 (R1198)


title: peripheral blood, nasopharyngeal cancer-r1 (R1077)


title: peripheral blood, nasopharyngeal cancer-r1 (R1170)


title: peripheral blood, nasopharyngeal cancer-r1 (R1088)


title: peripheral blood, nasopharyngeal cancer-r1 (R0959)


title: peripheral blood, nasopharyngeal cancer-r1 (R0886)


title: peripheral blood, nasopharyngeal cancer-r1 (R0835)


title: peripheral blood, nasopharyngeal cancer-r1 (R0820)


title: peripheral blood, nasopharyngeal cancer-r1 (R0839)


title: peripheral blood, nasopharyngeal cancer-r1 (R0897)


title: peripheral blood, nasopharyngeal cancer-r1 (R0826)


title: peripheral blood, nasopharyngeal cancer-r1 (R0977)


title: peripheral blood, nasopharyngeal cancer-r1 (R0804)


title: peripheral blood, nasopharyngeal cancer-r1 (R0829)


title: peripheral blood, nasopharyngeal cancer-r1 (R0787)


title: peripheral blood, nasopharyngeal cancer-r1 (R0782)


title: peripheral blood, nasopharyngeal cancer-r1 (R0822)


title: peripheral blood, nasopharyngeal cancer-r1 (R0983)


title: peripheral blood, nasopharyngeal cancer-r1 (R0796)


title: peripheral blood, nasopharyngeal cancer-r1 (R0767)


title: peripheral blood, nasopharyngeal cancer-r1 (R0729)


title: peripheral blood, nasopharyngeal cancer-r1 (R0768)


title: peripheral blood, nasopharyngeal cancer-r1 (R0780)


title: peripheral blood, nasopharyngeal cancer-r1 (R0722)


title: peripheral blood, nasopharyngeal cancer-r1 (R0726)


title: peripheral blood, nasopharyngeal cancer-r1 (R0709)


title: peripheral blood, nasopharyngeal cancer-r1 (R0715)


title: peripheral blood, nasopharyngeal cancer-r1 (R0701)


title: peripheral blood, nasopharyngeal cancer-r1 (R0702)


title: peripheral blood, nasopharyngeal cancer-r1 (R0798)


title: peripheral blood, nasopharyngeal cancer-r1 (R0698)


title: peripheral blood, nasopharyngeal cancer-r1 (R0790)


title: peripheral blood, nasopharyngeal cancer-r1 (R0688)


title: peripheral blood, nasopharyngeal cancer-r1 (R0696)


title: peripheral blood, nasopharyngeal cancer-r1 (R0697)


title: peripheral blood, nasopharyngeal cancer-r1 (R0665)


title: peripheral blood, nasopharyngeal cancer-r1 (R0686)


title: peripheral blood, nasopharyngeal cancer-r1 (R0677)


title: peripheral blood, nasopharyngeal cancer-r1 (R0636)


title: peripheral blood, nasopharyngeal cancer-r1 (R0639)


title: peripheral blood, nasopharyngeal cancer-r1 (R1536)


title: peripheral blood, liver cancer-r1 (PN0067)

value: liver cancer


title: peripheral blood, nasopharyngeal cancer-r1 (R0654)


title: peripheral blood, nasopharyngeal cancer-r1 (R0679)


title: peripheral blood, nasopharyngeal cancer-r1 (R0572)


title: peripheral blood, nasopharyngeal cancer-r1 (R0673)


title: peripheral blood, nasopharyngeal cancer-r1 (R0578)


title: peripheral blood, liver cancer-r1 (CTL224p)


title: peripheral blood, nasopharyngeal cancer-r1 (R0577)


title: peripheral blood, liver cancer-r1 (CTL214p)


title: peripheral blood, nasopharyngeal cancer-r1 (R0860)


title: peripheral blood, nasopharyngeal cancer-r1 (R0877)


title: peripheral blood, liver cancer-r1 (CTL0894)


title: peripheral blood, liver cancer-r1 (CTL272p)


title: peripheral blood, liver cancer-r1 (CTL0898)


title: peripheral blood, nasopharyngeal cancer-r1 (R1102)


title: peripheral blood, liver cancer-r1 (CTL0830)


title: peripheral blood, liver cancer-r1 (CTL0895)


title: peripheral blood, liver cancer-r1 (CTL0855)


title: peripheral blood, liver cancer-r1 (CTL0852)


title: peripheral blood, liver cancer-r1 (CTL0512)


title: peripheral blood, liver cancer-r1 (CTL0540)


title: peripheral blood, liver cancer-r1 (CTL0499)


title: peripheral blood, nasopharyngeal cancer-r1 (R0858)


title: peripheral blood, liver cancer-r1 (CTL0498)


title: peripheral blood, liver cancer-r1 (CTL0451)


title: peripheral blood, endometrial cancer-r1 (SM0241)

value: endometrial cancer


title: peripheral blood, endometrial cancer-r1 (SM0239)


title: peripheral blood, liver cancer-r1 (CTL0085)


title: peripheral blood, endometrial cancer-r1 (SM0242)


title: peripheral blood, endometrial cancer-r1 (SM0215)


title: nDLBCL-36

type: genomic

city: Ulm

first: Thomas

last: Barth

state: Baden-Württemberg

address: Albert Einstein Allee 23

department: Pathology

country: Germany

institute: Ulm University

description: FFPE nDLBCL-36

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina Infinium HD protocol

scan_protocol: Arrays were imaged using the NextSeq 550Dx instrument, using standard recommended Illumina scanner setting

data_processing: GenomeStudio software (v2011.1; methylation module 1.9.0)

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Lymph node FFPE resection

label_protocol: Standard Illumina Infinium HD Protocol

extract_protocol: A tumor cell content of at least 70% was ensured based on morphologic inspection in every sample analyzed herein. Extraction of DNA from FFPE tissue was performed using the GeneRead DNA FFPE Kit (Qiagen)

tag: sample type

value: genomic DNA

tag: disease state

value: Tumor


title: nDLBCL-46

description: FFPE nDLBCL-46


title: nDLBCL-34

description: FFPE nDLBCL-34


title: peripheral blood, endometrial cancer-r1 (SM0210)


title: peripheral blood, endometrial cancer-r1 (SM0214)


title: nDLBCL-47

description: FFPE nDLBCL-47


title: nDLBCL-12

description: FFPE nDLBCL-12


title: nDLBCL-3

description: FFPE nDLBCL-3


title: nDLBCL-31

description: FFPE nDLBCL-31


title: peripheral blood, endometrial cancer-r1 (SM0208)


title: nDLBCL-2

description: FFPE nDLBCL-2


title: nDLBCL-4

description: FFPE nDLBCL-4


title: peripheral blood, endometrial cancer-r1 (SM0168)


title: nDLBCL-32

description: FFPE nDLBCL-32


title: nDLBCL-35

description: FFPE nDLBCL-35


title: nDLBCL-27

description: FFPE nDLBCL-27


title: nDLBCL-8

description: FFPE nDLBCL-8


title: peripheral blood, endometrial cancer-r1 (SM0148)


title: nDLBCL-1.1

description: FFPE nDLBCL-1.1 second block


title: peripheral blood, endometrial cancer-r1 (SM0147)


title: nDLBCL-33

description: FFPE nDLBCL-33


title: peripheral blood, endometrial cancer-r1 (SM0150)


title: nDLBCL-17

description: FFPE nDLBCL-17


title: nDLBCL-1

description: FFPE nDLBCL-1


title: nMZoL-64

description: FFPE nMZoL-64


title: peripheral blood, endometrial cancer-r1 (SM0145)


title: nMZoL-7

description: FFPE nMZoL-7


title: nDLBCL-26

description: FFPE nDLBCL-26


title: nMZoL-76

description: FFPE nMZoL-76


title: peripheral blood, endometrial cancer-r1 (SM0144)


title: peripheral blood, endometrial cancer-r1 (SM0081)


title: peripheral blood, endometrial cancer-r1 (SM0083)


title: nMZoL-21

description: FFPE nMZoL-21


title: peripheral blood, endometrial cancer-r1 (SM0146)


title: peripheral blood, endometrial cancer-r1 (SM0082)


title: nMZoL-45

description: FFPE nMZoL-45


title: peripheral blood, endometrial cancer-r1 (SM0078)


title: peripheral blood, endometrial cancer-r1 (SM0080)


title: nMZoL-69

description: FFPE nMZoL-69


title: nMZoL-44

description: FFPE nMZoL-44


title: peripheral blood, endometrial cancer-r1 (SM0072)


title: peripheral blood, endometrial cancer-r1 (SM0071)


title: peripheral blood, endometrial cancer-r1 (SM0075)


title: nMZoL-1

description: FFPE nMZoL-69


title: peripheral blood, cervical cancer-r1 (SM0143)

value: cervical cancer


title: peripheral blood, endometrial cancer-r1 (SM0076)


title: peripheral blood, endometrial cancer-r1 (SM0074)


title: peripheral blood, cervical cancer-r1 (SM0142)


title: nMZoL-46

description: FFPE nMZoL-46


title: peripheral blood, endometrial cancer-r1 (SM0073)


title: peripheral blood, cervical cancer-r1 (SM0141)


title: nMZoL-37s

description: FFPE nMZoL-37s small cell area


title: peripheral blood, cervical cancer-r1 (SM0139)


title: nMZoL-11

description: FFPE nMZoL-11


title: SGT_362

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

institute: Ludwig Maximilians University Hospital Munich

hyb_protocol: Bisulphite converted (using the EpiTect Bisulfite Kit (Qiagen)) DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan or NextSeq 550 system with default settings

data_processing:
Statistical analysis was performed using RStudio Pro 2022.12.0+353.pro20 based on R version 4.1.2.
The 'matrix_preprocessed.csv' contains preprocessed beta values, normalized using the dasen function from the wateRmelon packages.

label: Cy5 and Cy3

source_name: Surgigcal resection specimen, FFPE

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction was performed on the Maxwell RSC Instrument using the Maxwell RSC FFPE Plus DNA Purification Kit (Custom, AX4920; Promega), according to the manufacturer’s instructions.

tag: diagnosis

value: Warthin tumor

tag: methylation class

value: WARTH

tag: focal cnvs

value: Balanced

tag: fusions

tag: mutations

tag: location

value: Parotid gland


title: nMZoL-67

description: FFPE nMZoL-67


title: peripheral blood, cervical cancer-r1 (SM0137)


title: nMZoL-86

description: FFPE nMZoL-86


title: peripheral blood, cervical cancer-r1 (SM0133)


title: nMZoL-28

description: FFPE nMZoL-28


title: peripheral blood, cervical cancer-r1 (SM0134)


title: SGT_359

value: Salivary duct carcinoma

value: SDCA

value: CDKN2A loss


title: SGT_361


title: nMZoL-29

description: FFPE nMZoL-29


title: SGT_363


title: nMZoL-27

description: FFPE nMZoL-27

value: M


title: peripheral blood, cervical cancer-r1 (SM0130)

value: peripheral blood


title: peripheral blood, cervical cancer-r1 (SM0135)

value: F


title: nMZoL-5

description: FFPE nMZoL-5


title: SGT_360


title: peripheral blood, cervical cancer-r1 (SM0068)


title: nMZoL-57

description: FFPE nMZoL-57


title: nMZoL-37

description: FFPE nMZoL-37


title: nMZoL-61

description: FFPE nMZoL-61


title: SGT_358


title: nMZoL-11s

description: FFPE nMZoL-11s small cell area


title: nMZoL-32

description: FFPE nMZoL-32


title: SGT_355

value: ERBB2 amplification


title: SGT_354


title: nMZoL-24

description: FFPE nMZoL-24


title: SGT_353


title: nMZoL-9

description: FFPE nMZoL-9


title: SGT_356


title: SGT_352


title: nMZoL-34

description: FFPE nMZoL-34


title: peripheral blood, cervical cancer-r1 (SM0066)


title: SGT_351


title: SGT_350


title: peripheral blood, cervical cancer-r1 (SM0064)


title: peripheral blood, cervical cancer-r1 (SM0067)


title: SGT_357


title: peripheral blood, cervical cancer-r1 (SM0065)


title: peripheral blood, cervical cancer-r1 (SM0063)


title: peripheral blood, cervical cancer-r1 (SM0061)


title: peripheral blood, cervical cancer-r1 (SM0060)


title: peripheral blood, cervical cancer-r1 (SM0058)


title: SGT_346

value: Sclerosing polycystic adenoma

value: SPA

value: PTEN


title: nMZoL-62

description: FFPE nMZoL-62

value: genomic DNA


title: nMZoL-48

description: FFPE nMZoL-48

value: Tumor


title: s8_causp_homo_mor_3_8

type: SRA

city: Philadelphia

first: Natalie

middle: Alyce

last: Trigg

state: Pennsylvania

address: 421 Curie Blvd

institute: Children's Hospital of Philadelphia

description:
LIm_s8_homo_mor_3_8_S64
Supplemental_Table_S6_7.xlsx

library_source: transcriptomic

data_processing:
Reads were mapped using RSEM and normalized to transcripts per million (tpm).
Supplementary files format and content: xlsx spreadsheet with one tab per tissue type/comparison

molecule: polyA RNA

organism: Mus musculus

source_name: preimplantation embryo

extract_protocol:
RNA was isolated using RNA-Clean XP beads
Illumina Nextera XT Kit

value: preimplantation embryo

tag: developmental stage

value: Morula

tag: fvb/nj donor egg fertilized by

value: Dgcr8fl/fl; Stra8-iCre cauda sperm

tag: genome build


title: SGT_349

value: Warthin tumor

value: WARTH

value: Balanced


title: SGT_344

value: Parotid gland


title: SGT_343


title: peripheral blood, cervical cancer-r1 (SM0057)

value: cervical cancer


title: peripheral blood, cervical cancer-r1 (SM0055)


title: s8_causp_homo_mor_3_7

description:
LIm_s8_homo_mor_3_7_S63
Supplemental_Table_S6_7.xlsx


title: nMZoL-79

description: FFPE nMZoL-79

value: M


title: SGT_342


title: SGT_348


title: SGT_341

value: Secretory carcinoma

value: SCA

value: No mutation


title: peripheral blood, cervical cancer-r1 (SM0059)

value: peripheral blood

value: F


title: nMZoL-52

description: FFPE nMZoL-52


title: nMZoL-10

description: FFPE nMZoL-10


title: SGT_340


title: s8_causp_homo_mor_3_6

description:
LIm_s8_homo_mor_3_6_S62
Supplemental_Table_S6_7.xlsx


title: nMZoL-70

description: FFPE nMZoL-70


title: peripheral blood, cervical cancer-r1 (SM0052)


title: peripheral blood, cervical cancer-r1 (SM0056)


title: SGT_339

value: Oral cavity


title: peripheral blood, cervical cancer-r1 (SM0053)


title: peripheral blood, cervical cancer-r1 (SM0030)


title: peripheral blood, cervical cancer-r1 (SM0051)


title: SGT_337


title: SGT_336


title: s8_causp_homo_mor_3_4

description:
LIm_s8_homo_mor_3_4_S60
Supplemental_Table_S6_7.xlsx


title: SGT_334


title: SGT_333


title: SGT_347


title: s8_causp_homo_mor_3_3

description:
LIm_s8_homo_mor_3_3_S59
Supplemental_Table_S6_7.xlsx


title: SGT_332

value: Palate


title: s8_causp_homo_mor_3_2

description:
LIm_s8_homo_mor_3_2_S56
Supplemental_Table_S6_7.xlsx


title: nMZoL-41

description: FFPE nMZoL-41

value: genomic DNA

value: Tumor


title: SGT_335


title: SGT_330


title: SGT_331


title: SGT_329


title: SGT_328

value: Polymorphous adenocarcinoma


title: SGT_345

value: Sclerosing polycystic adenoma

value: SPA

value: PTEN


title: peripheral blood, cervical cancer-r1 (SM0028)


title: peripheral blood, cervical cancer-r1 (SM0029)


title: s8_causp_homo_mor_2_8

description:
LIm_s8_homo_mor_2_8_S44
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo

value: Morula

value: Dgcr8fl/fl; Stra8-iCre cauda sperm


title: nMZoL-74

description: FFPE nMZoL-74

value: M


title: peripheral blood, cervical cancer-r1 (SM0026)

value: cervical cancer


title: peripheral blood, cervical cancer-r1 (SM0022)


title: nMZoL-54

description: FFPE nMZoL-54


title: SGT_327

value: Balanced


title: s8_causp_homo_mor_3_1

description:
LIm_s8_homo_mor_3_1_S55
Supplemental_Table_S6_7.xlsx


title: SGT_326


title: s8_causp_homo_mor_2_7

description:
LIm_s8_homo_mor_2_7_S43
Supplemental_Table_S6_7.xlsx


title: SGT_325


title: peripheral blood, cervical cancer-r1 (SM0021)


title: peripheral blood, cervical cancer-r1 (CTL240p)


title: s8_causp_homo_mor_3_5

description:
LIm_s8_homo_mor_3_5_S61
Supplemental_Table_S6_7.xlsx


title: SGT_324


title: SGT_338

value: Secretory carcinoma

value: SCA

value: No mutation

value: Parotid gland


title: s8_causp_homo_mor_2_4

description:
LIm_s8_homo_mor_2_4_S38
Supplemental_Table_S6_7.xlsx


title: SGT_322

value: Submandibular gland


title: SGT_323

value: Palate


title: SGT_321


title: s8_causp_homo_mor_2_3

description:
LIm_s8_homo_mor_2_3_S37
Supplemental_Table_S6_7.xlsx


title: peripheral blood, cervical cancer-r1 (CTL190p)

value: peripheral blood

value: F


title: SGT_320

value: Oncocytoma

value: ONCO


title: SGT_319

value: Salivary duct carcinoma

value: SDCA

value: HRAS


title: SGT_318

value: ERBB2 amplification


title: s8_causp_homo_mor_2_2

description:
LIm_s8_homo_mor_2_2_S36
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo

value: Morula

value: Dgcr8fl/fl; Stra8-iCre cauda sperm


title: s8_causp_homo_mor_2_1

description:
LIm_s8_homo_mor_2_1_S35
Supplemental_Table_S6_7.xlsx


title: peripheral blood, cervical cancer-r1 (CTL186p)

value: cervical cancer


title: SGT_317

value: Balanced


title: SGT_316


title: s8_causp_homo_mor_2_6

description:
LIm_s8_homo_mor_2_6_S40
Supplemental_Table_S6_7.xlsx


title: SGT_315


title: peripheral blood, cervical cancer-r1 (CTL182p)


title: s8_causp_homo_mor_1_8

description:
LIm_s8_homo_mor_1_8_S22
Supplemental_Table_S6_7.xlsx


title: SGT_313


title: SGT_312

value: Base of tongue


title: peripheral blood, colorectal cancer-r1 (RC0725)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.

value: M

value: colorectal cancer


title: SGT_314

value: Parotid gland


title: s8_causp_homo_mor_1_7

description:
LIm_s8_homo_mor_1_7_S21
Supplemental_Table_S6_7.xlsx


title: SGT_310


title: SGT_309


title: s8_causp_homo_mor_1_5

description:
LIm_s8_homo_mor_1_5_S19
Supplemental_Table_S6_7.xlsx


title: SGT_307


title: peripheral blood, cervical cancer-r1 (CTL185p)

value: peripheral blood


title: peripheral blood, colorectal cancer-r1 (RC348)


title: SGT_308


title: SGT_306


title: s8_causp_homo_mor_1_3

description:
LIm_s8_homo_mor_1_3_S14
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colorectal cancer-r1 (RC343)


title: peripheral blood, colorectal cancer-r1 (RC1172)


title: SGT_305


title: SGT_304


title: s8_causp_homo_mor_1_1

description:
LIm_s8_homo_mor_1_1_S12
Supplemental_Table_S6_7.xlsx


title: SGT_302

value: Oral cavity


title: SGT_303

value: CDKN2A loss

value: Nasal cavity & paranasal sinus


title: SGT_300

value: Salivary duct carcinoma


title: s8_causp_homo_mor_1_6

description:
LIm_s8_homo_mor_1_6_S20
Supplemental_Table_S6_7.xlsx


title: SGT_301

value: SDCA


title: SGT_299


title: SGT_311


title: s8_causp_het_mor_3_7

description:
LIm_s8_het_mor_3_7_S53
Supplemental_Table_S6_7.xlsx

value: Dgcr8+/fl; Stra8-iCre cauda sperm


title: SGT_298


title: peripheral blood, colorectal cancer-r1 (RC0937)


title: s8_causp_homo_mor_1_2

description:
LIm_s8_homo_mor_1_2_S13
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colorectal cancer-r1 (PN0120)

value: F


title: s8_causp_het_mor_3_6

description:
LIm_s8_het_mor_3_6_S52
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo


title: SGT_296


title: peripheral blood, colorectal cancer-r1 (RC2134)


title: s8_causp_het_mor_3_8

description:
LIm_s8_het_mor_3_8_S54
Supplemental_Table_S6_7.xlsx

value: Morula


title: SGT_295


title: SGT_294


title: s8_causp_het_mor_3_5

description:
LIm_s8_het_mor_3_5_S51
Supplemental_Table_S6_7.xlsx


title: SGT_293

value: No mutation


title: peripheral blood, colorectal cancer-r1 (PN0085)


title: peripheral blood, colorectal cancer-r1 (PN0072)


title: peripheral blood, colorectal cancer-r1 (RC0459)


title: peripheral blood, colorectal cancer-r1 (PN0080)


title: peripheral blood, colorectal cancer-r1 (PN0066)


title: peripheral blood, colorectal cancer-r1 (PN0063)


title: s8_causp_het_mor_3_4

description:
LIm_s8_het_mor_3_4_S48
Supplemental_Table_S6_7.xlsx


title: SGT_297


title: SGT_287

value: ERBB2 amplification

value: Submandibular gland


title: s8_causp_het_mor_3_2

description:
LIm_s8_het_mor_3_2_S46
Supplemental_Table_S6_7.xlsx


title: SGT_289


title: peripheral blood, colorectal cancer-r1 (PN0059)


title: SGT_286

value: Balanced


title: SGT_291


title: s8_causp_het_mor_3_3

description:
LIm_s8_het_mor_3_3_S47
Supplemental_Table_S6_7.xlsx


title: s8_causp_het_mor_2_7

description:
LIm_s8_het_mor_2_7_S31
Supplemental_Table_S6_7.xlsx


title: SGT_285


title: SGT_288


title: SGT_283


title: s8_causp_het_mor_2_6

description:
LIm_s8_het_mor_2_6_S30
Supplemental_Table_S6_7.xlsx


title: SGT_284

value: HRAS


title: SGT_292


title: SGT_282


title: SGT_281


title: SGT_280

value: Oncocytoma

value: ONCO


title: s8_causp_het_mor_2_5

description:
LIm_s8_het_mor_2_5_S29
Supplemental_Table_S6_7.xlsx


title: SGT_290

value: Parotid gland


title: s8_causp_het_mor_3_1

description:
LIm_s8_het_mor_3_1_S45
Supplemental_Table_S6_7.xlsx


title: SGT_279


title: peripheral blood, colorectal cancer-r1 (PN0045)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.

value: peripheral blood

value: colorectal cancer


title: peripheral blood, colorectal cancer-r1 (PN0044)

value: M


title: peripheral blood, colorectal cancer-r1 (PB1842)


title: peripheral blood, colorectal cancer-r1 (PB1517)


title: s8_causp_het_mor_2_4

description:
LIm_s8_het_mor_2_4_S28
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colorectal cancer-r1 (HZ0028)


title: SGT_278


title: SGT_276


title: SGT_277


title: peripheral blood, colorectal cancer-r1 (HZ0039)


title: s8_causp_het_mor_2_3

description:
LIm_s8_het_mor_2_3_S27
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colorectal cancer-r1 (HZ0031)


title: SGT_275


title: SGT_274


title: SGT_273


title: s8_causp_het_mor_1_8

description:
LIm_s8_het_mor_1_8_S11
Supplemental_Table_S6_7.xlsx


title: SGT_272

value: Normal salivary gland tissue

value: NOR

value: Sublingual gland


title: s8_causp_het_mor_2_1

description:
LIm_s8_het_mor_2_1_S23
Supplemental_Table_S6_7.xlsx

value: Dgcr8+/fl; Stra8-iCre cauda sperm


title: SGT_269


title: SGT_271


title: s8_causp_het_mor_1_4

description:
LIm_s8_het_mor_1_4_S4
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo


title: SGT_270


title: SGT_268


title: SGT_267


title: SGT_266


title: s8_causp_het_mor_1_3

description:
LIm_s8_het_mor_1_3_S3
Supplemental_Table_S6_7.xlsx

value: Morula


title: SGT_265


title: peripheral blood, colorectal cancer-r1 (CTL840)

value: F


title: peripheral blood, colorectal cancer-r1 (CTL868)


title: peripheral blood, colorectal cancer-r1 (CTL622)


title: peripheral blood, colorectal cancer-r1 (CTL505)


title: s8_causp_het_mor_1_7

description:
LIm_s8_het_mor_1_7_S10
Supplemental_Table_S6_7.xlsx


title: SGT_264


title: SGT_263


title: s8_causp_het_mor_1_1

description:
LIm_s8_het_mor_1_1_S1
Supplemental_Table_S6_7.xlsx


title: SGT_262


title: SGT_261


title: SGT_259

value: Myoepithelial carcinoma

value: MYOCA

value: Nasal cavity & paranasal sinus


title: SGT_256

value: Balanced

value: Submandibular gland


title: SGT_260


title: s8_causp_4_het_17

description:
het_4_1210_17_S67
Supplemental_Table_S6_7.xlsx


title: SGT_257


title: SGT_258


title: peripheral blood, colorectal cancer-r1 (CTL312)


title: s8_causp_4_het_19

description:
het_4_1210_19_S69
Supplemental_Table_S6_7.xlsx


title: s8_causp_4_het_16

description:
het_4_1210_16_S66
Supplemental_Table_S6_7.xlsx


title: s8_causp_het_mor_1_2

description:
LIm_s8_het_mor_1_2_S2
Supplemental_Table_S6_7.xlsx


title: SGT_254


title: SGT_253


title: SGT_252

value: CDKN2A loss


title: peripheral blood, colorectal cancer-r1 (CTL313)


title: peripheral blood, colorectal cancer-r1 (CTL178)


title: SGT_251

value: Pleomorphic adenoma

value: Parotid gland


title: peripheral blood, colorectal cancer-r1 (CTL177)

value: peripheral blood

value: colorectal cancer


title: SGT_250


title: s8_causp_4_het_18

description:
het_4_1210_18_S68
Supplemental_Table_S6_7.xlsx


title: s8_causp_4_het_14

description:
het_4_1208a_14_S47
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colorectal cancer-r1 (CTL267)


title: peripheral blood, colorectal cancer-r1 (CTL180)

value: M


title: peripheral blood, colorectal cancer-r1 (CTL239)


title: peripheral blood, colorectal cancer-r1 (CTL176)


title: s8_causp_4_het_13

description:
het_4_1208a_13_S46
Supplemental_Table_S6_7.xlsx


title: SGT_255


title: SGT_248


title: peripheral blood, colorectal cancer-r1 (CTL788)


title: SGT_249


title: s8_causp_4_het_12

description:
het_4_1208a_12_S45
Supplemental_Table_S6_7.xlsx


title: SGT_246


title: SGT_247


title: s8_causp_4_het_15

description:
het_4_1210_15_S65
Supplemental_Table_S6_7.xlsx


title: SGT_244


title: SGT_245


title: s8_causp_4_het_11

description:
het_4_1208a_11_S44
Supplemental_Table_S6_7.xlsx


title: SGT_243

value: Lip


title: s8_causp_4_het_10

description:
het_4_1208a_10_S43
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colorectal cancer-r1 (CTL171)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.


title: SGT_242

value: Palate


title: peripheral blood, colorectal cancer-r1 (CTL138)


title: SGT_241


title: s8_causp_4_het_9

description:
het_4_1101_9_S39
Supplemental_Table_S6_7.xlsx

value: Dgcr8+/fl; Stra8-iCre cauda sperm


title: peripheral blood, colorectal cancer-r1 (CTL0904)


title: s8_causp_4_het_8

description:
het_4_1101_8_S38
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo


title: SGT_239


title: peripheral blood, colorectal cancer-r1 (CTL0903)


title: SGT_238


title: SGT_237


title: s8_causp_4_het_6

description:
het_4_1101_6_S36
Supplemental_Table_S6_7.xlsx


title: SGT_236

value: Oral cavity


title: s8_causp_4_het_5

description:
het_4_1101_5_S35
Supplemental_Table_S6_7.xlsx


title: s8_causp_4_het_4

description:
het_4_1101_4_S34
Supplemental_Table_S6_7.xlsx


title: s8_causp_4_het_3

description:
het_4_1101_3_S33
Supplemental_Table_S6_7.xlsx


title: SGT_240


title: peripheral blood, colorectal cancer-r1 (CTL0901)

value: F


title: SGT_235


title: SGT_234


title: s8_causp_4_het_2

description:
het_4_1101_2_S32
Supplemental_Table_S6_7.xlsx


title: SGT_230

value: Myoepithelioma


title: SGT_229


title: SGT_231


title: SGT_233


title: SGT_228


title: peripheral blood, colorectal cancer-r1 (CTL0905)


title: SGT_232


title: peripheral blood, colorectal cancer-r1 (CTL0882)


title: peripheral blood, colorectal cancer-r1 (CTL0871)


title: SGT_226


title: s8_causp_4_het_1

description:
het_4_1101_1_S31
Supplemental_Table_S6_7.xlsx


title: SGT_227


title: SGT_225


title: peripheral blood, colorectal cancer-r1 (CTL0835)


title: peripheral blood, colorectal cancer-r1 (CTL0656)


title: peripheral blood, colorectal cancer-r1 (CTL0730)


title: SGT_223


title: SGT_224


title: peripheral blood, colorectal cancer-r1 (CTL0666)


title: peripheral blood, colorectal cancer-r1 (CTL0761)


title: s8_causp_4_dg_14

description:
dg_4_1210_14_S72
Supplemental_Table_S6_7.xlsx

value: Dgcr8fl/fl; Stra8-iCre cauda sperm


title: s8_causp_4_dg_13

description:
dg_4_1210_13_S71
Supplemental_Table_S6_7.xlsx


title: SGT_220


title: s8_causp_4_dg_12

description:
dg_4_1210_12_S70
Supplemental_Table_S6_7.xlsx


title: SGT_216

value: Microsecretory adenocarcinoma

value: MSADC


title: SGT_221

value: Balanced

value: Submandibular gland


title: SGT_222


title: SGT_217


title: s8_causp_4_dg_9

description:
dg_4_1208b_9_S49
Supplemental_Table_S6_7.xlsx


title: SGT_219


title: s8_causp_4_dg_15

description:
dg_4_1210_15_S73
Supplemental_Table_S6_7.xlsx


title: SGT_215


title: s8_causp_4_dg_8

description:
dg_4_1208b_8_S48
Supplemental_Table_S6_7.xlsx


title: SGT_214


title: SGT_213


title: SGT_212


title: peripheral blood, colorectal cancer-r1 (CTL0634)


title: SGT_211


title: SGT_218


title: SGT_210

value: Mucoepidermoid carcinoma

value: MC

value: MAML


title: peripheral blood, colorectal cancer-r1 (CTL0627)

value: peripheral blood

value: colorectal cancer


title: peripheral blood, colorectal cancer-r1 (CTL0651)

value: M


title: peripheral blood, colorectal cancer-r1 (CTL0422)


title: peripheral blood, colorectal cancer-r1 (CTL0534)


title: peripheral blood, colorectal cancer-r1 (CTL0425)


title: SGT_209

value: Parotid gland


title: SGT_205


title: SGT_208

value: Lung


title: SGT_206


title: SGT_207


title: s8_causp_4_dg_5

description:
dg_4_1101_5_S28
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo


title: s8_causp_4_dg_7

description:
dg_4_1101_7_S30
Supplemental_Table_S6_7.xlsx


title: s8_causp_4_dg_6

description:
dg_4_1101_6_S29
Supplemental_Table_S6_7.xlsx


title: s8_causp_4_dg_4

description:
dg_4_1101_4_S27
Supplemental_Table_S6_7.xlsx


title: s8_causp_4_dg_11

description:
dg_4_1208a_11_S64
Supplemental_Table_S6_7.xlsx


title: SGT_204

value: Base of tongue


title: SGT_203

value: Nasal cavity & paranasal sinus


title: s8_causp_4_dg_10

description:
dg_4_1208a_10_S63
Supplemental_Table_S6_7.xlsx


title: SGT_202


title: peripheral blood, colorectal cancer-r1 (CTL0345)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.

value: F


title: peripheral blood, colorectal cancer-r1 (CTL0350)


title: peripheral blood, colorectal cancer-r1 (CTL0339)


title: SGT_201


title: peripheral blood, colorectal cancer-r1 (CTL0134)


title: peripheral blood, colorectal cancer-r1 (CTL0209)


title: SGT_200

value: Palate


title: SGT_199


title: peripheral blood, colorectal cancer-r1 (CTL0130)


title: SGT_198


title: s8_causp_4_dg_1

description:
dg_4_1101_1_S24
Supplemental_Table_S6_7.xlsx

value: Dgcr8fl/fl; Stra8-iCre cauda sperm


title: peripheral blood, colorectal cancer-r1 (CTL0103)


title: SGT_195


title: s8_tssp_M_homo_9

description:
M_homo_9_S66
Supplemental_Table_S4_5.xlsx

value: Morula

value: Dgcr8fl/fl; Stra8-iCre testicular sperm


title: s8_causp_4_dg_2

description:
dg_4_1101_2_S25
Supplemental_Table_S6_7.xlsx


title: SGT_194

value: Balanced


title: SGT_192

value: Mucoepidermoid carcinoma

value: Submandibular gland


title: s8_tssp_M_homo_8

description:
M_homo_8_S65
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colorectal cancer-r1 (CTL0102)


title: SGT_190

value: MC


title: s8_causp_4_dg_3

description:
dg_4_1101_3_S26
Supplemental_Table_S6_7.xlsx


title: SGT_197


title: SGT_193


title: SGT_189


title: s8_tssp_M_homo_6

description:
M_homo_6_S47
Supplemental_Table_S4_5.xlsx


title: SGT_191


title: SGT_187

value: Intraductal carcinoma

value: IDC

value: No fusion


title: SGT_188

value: Parotid gland


title: SGT_196

value: Sublingual gland


title: s8_tssp_M_homo_7

description:
M_homo_7_S48
Supplemental_Table_S4_5.xlsx

value: preimplantation embryo


title: SGT_186

value: RET


title: s8_tssp_M_homo_5

description:
M_homo_5_S46
Supplemental_Table_S4_5.xlsx


title: SGT_185


title: peripheral blood, colorectal cancer-r1 (CD0686)

value: peripheral blood

value: M

value: colorectal cancer


title: peripheral blood, colorectal cancer-r1 (CTL0101B)

value: F


title: s8_tssp_M_homo_4

description:
M_homo_4_S45
Supplemental_Table_S4_5.xlsx

value: Morula


title: SGT_183


title: peripheral blood, colorectal cancer-r1 (BT0013)


title: SGT_184


title: peripheral blood, colorectal cancer-r1 (BT0010)


title: peripheral blood, colorectal cancer-r1 (BT0011)


title: peripheral blood, colorectal cancer-r1 (CD0629)


title: peripheral blood, colorectal cancer-r1 (CD0157)


title: s8_tssp_M_homo_3

description:
M_homo_3_S25
Supplemental_Table_S4_5.xlsx

value: Dgcr8fl/fl; Stra8-iCre testicular sperm


title: s8_tssp_M_homo_21

description:
M_homo_21_S96
Supplemental_Table_S4_5.xlsx


title: SGT_180

value: Epithelial-myoepithelial carcinoma

value: EPMYOC

value: Balanced

value: HRAS

value: Nasal cavity & paranasal sinus


title: SGT_178

value: Lip


title: SGT_181


title: SGT_176


title: s8_tssp_M_homo_2

description:
M_homo_2_S24
Supplemental_Table_S4_5.xlsx


title: SGT_175


title: SGT_179


title: s8_tssp_M_homo_20

description:
M_homo_20_S95
Supplemental_Table_S4_5.xlsx


title: SGT_177


title: SGT_174

value: Submandibular gland


title: SGT_173

value: Parotid gland


title: s8_tssp_M_homo_19

description:
M_homo_19_S94
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colorectal cancer-r1 (RC3467)


title: peripheral blood, colorectal cancer-r1 (RC3438)


title: s8_tssp_M_homo_18

description:
M_homo_18_S93
Supplemental_Table_S4_5.xlsx


title: SGT_171

value: Oral cavity


title: SGT_172


title: SGT_170


title: SGT_169


title: peripheral blood, colorectal cancer-r1 (RC2273)


title: s8_tssp_M_homo_16

description:
M_homo_16_S91
Supplemental_Table_S4_5.xlsx

value: preimplantation embryo


title: SGT_167


title: SGT_182

value: Intraductal carcinoma

value: IDC

value: No fusion


title: s8_tssp_M_homo_15

description:
M_homo_15_S90
Supplemental_Table_S4_5.xlsx


title: SGT_166


title: peripheral blood, colorectal cancer-r1 (RC171)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.

value: peripheral blood

value: M

value: colorectal cancer


title: peripheral blood, colorectal cancer-r1 (RC2145)


title: s8_tssp_M_homo_14

description:
M_homo_14_S89
Supplemental_Table_S4_5.xlsx

value: Morula

value: Dgcr8fl/fl; Stra8-iCre testicular sperm


title: peripheral blood, colorectal cancer-r1 (RC3095)

value: F


title: s8_tssp_M_homo_13

description:
M_homo_13_S70
Supplemental_Table_S4_5.xlsx


title: SGT_162

value: Clear cell carcinoma

value: CCC

value: Balanced


title: SGT_164

value: Epithelial-myoepithelial carcinoma

value: EPMYOC

value: HRAS


title: SGT_161

value: Oral cavity


title: SGT_160

value: Palate


title: s8_tssp_M_homo_17

description:
M_homo_17_S92
Supplemental_Table_S4_5.xlsx

value: preimplantation embryo


title: SGT_159


title: peripheral blood, colorectal cancer-r1 (CD0256)


title: SGT_158

value: Base of tongue


title: SGT_163

value: Parotid gland


title: peripheral blood, colorectal cancer-r1 (CD0371)

value: peripheral blood


title: s8_tssp_M_homo_11

description:
M_homo_11_S68
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colorectal cancer-r1 (CD0164)

value: M


title: peripheral blood, colorectal cancer-r1 (PB0227)

value: colorectal cancer


title: s8_tssp_M_homo_10

description:
M_homo_10_S67
Supplemental_Table_S4_5.xlsx

value: Morula


title: SGT_157


title: SGT_156


title: SGT_155


title: s8_tssp_M_homo_1

description:
M_homo_1_S23
Supplemental_Table_S4_5.xlsx

value: Dgcr8fl/fl; Stra8-iCre testicular sperm


title: SGT_154


title: peripheral blood, colorectal cancer-r1 (MH0093)

value: F


title: s8_tssp_M_homo_12

description:
M_homo_12_S69
Supplemental_Table_S4_5.xlsx


title: SGT_153

value: Clear cell carcinoma


title: s8_tssp_M_het_9

description:
M_het_9_S41
Supplemental_Table_S4_5.xlsx

value: Dgcr8+/fl; Stra8-iCre testicular sperm


title: s8_tssp_M_het_8

description:
M_het_8_S40
Supplemental_Table_S4_5.xlsx


title: SGT_150

value: Cribriform adenocarcinoma

value: CADC

value: Balanced


title: SGT_151

value: CCC


title: SGT_149


title: s8_tssp_M_het_7

description:
M_het_7_S39
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colorectal cancer-r1 (MH0022)


title: SGT_148

value: Lip


title: SGT_147

value: Palate


title: s8_tssp_M_het_6

description:
M_het_6_S22
Supplemental_Table_S4_5.xlsx

value: preimplantation embryo


title: SGT_145

value: Base of tongue


title: SGT_146


title: s8_tssp_M_het_5

description:
M_het_5_S21
Supplemental_Table_S4_5.xlsx


title: SGT_168

value: Epithelial-myoepithelial carcinoma

value: EPMYOC

value: HRAS

value: Parotid gland


title: peripheral blood, colorectal cancer-r1 (JH0059)

value: peripheral blood

value: M

value: colorectal cancer


title: SGT_142


title: SGT_141

value: Oral cavity


title: SGT_143


title: peripheral blood, colorectal cancer-r1 (NK2017)


title: peripheral blood, colorectal cancer-r1 (FC0022)


title: peripheral blood, colorectal cancer-r1 (JH0125)

value: F


title: s8_tssp_M_het_4

description:
M_het_4_S20
Supplemental_Table_S4_5.xlsx

value: Morula

value: Dgcr8+/fl; Stra8-iCre testicular sperm


title: SGT_144

value: Cribriform adenocarcinoma

value: CADC

value: Balanced


title: s8_tssp_M_het_3

description:
M_het_3_S19
Supplemental_Table_S4_5.xlsx


title: SGT_139


title: SGT_140


title: SGT_138


title: SGT_137

value: Nasal cavity & paranasal sinus


title: peripheral blood, colorectal cancer-r1 (MH0030)


title: s8_tssp_M_het_28

description:
M_het_28_S88
Supplemental_Table_S4_5.xlsx

value: preimplantation embryo


title: peripheral blood, colorectal cancer-r1 (MH0037)


title: peripheral blood, colorectal cancer-r1 (MH0024)


title: peripheral blood, colorectal cancer-r1 (PB2846)


title: peripheral blood, colorectal cancer-r1 (RC1595)


title: s8_tssp_M_het_27

description:
M_het_27_S87
Supplemental_Table_S4_5.xlsx


title: SGT_136


title: SGT_134

value: Canalicular adenoma

value: Lip


title: SGT_133


title: s8_tssp_M_het_26

description:
M_het_26_S86
Supplemental_Table_S4_5.xlsx


title: SGT_135


title: peripheral blood, colorectal cancer-r1 (PB0466)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.


title: SGT_132


title: peripheral blood, colorectal cancer-r1 (MH0009)


title: s8_tssp_M_het_25

description:
M_het_25_S85
Supplemental_Table_S4_5.xlsx


title: SGT_130


title: SGT_129


title: s8_tssp_M_het_23

description:
M_het_23_S83
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colorectal cancer-r1 (FC0016)


title: SGT_128


title: SGT_126

value: Basal cell adenoma


title: SGT_127


title: peripheral blood, colorectal cancer-r1 (FC0013)


title: s8_tssp_M_het_22

description:
M_het_22_S82
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colorectal cancer-r1 (DS0001)


title: s8_tssp_M_het_21

description:
M_het_21_S81
Supplemental_Table_S4_5.xlsx


title: s8_tssp_M_het_20

description:
M_het_20_S64
Supplemental_Table_S4_5.xlsx


title: SGT_131


title: s8_tssp_M_het_24

description:
M_het_24_S84
Supplemental_Table_S4_5.xlsx


title: SGT_165

value: Epithelial-myoepithelial carcinoma

value: EPMYOC

value: HRAS

value: Submandibular gland


title: s8_tssp_M_het_2

description:
M_het_2_S18
Supplemental_Table_S4_5.xlsx


title: SGT_122


title: peripheral blood, colorectal cancer-r1 (CD0180)

value: peripheral blood

value: M

value: colorectal cancer


title: SGT_123

value: Parotid gland


title: SGT_121


title: SGT_120


title: SGT_118


title: s8_tssp_M_het_19

description:
M_het_19_S63
Supplemental_Table_S4_5.xlsx

value: Morula

value: Dgcr8+/fl; Stra8-iCre testicular sperm


title: SGT_125


title: peripheral blood, colorectal cancer-r1 (RC0287)


title: peripheral blood, colorectal cancer-r1 (AN0015)

value: F


title: peripheral blood, colorectal cancer-r1 (NK2012)


title: SGT_124

value: Balanced


title: SGT_115

value: Basal cell adenocarcinoma

value: BC

value: No mutation


title: SGT_117


title: peripheral blood, colorectal cancer-r1 (MR1002)


title: s8_tssp_M_het_18

description:
M_het_18_S62
Supplemental_Table_S4_5.xlsx

value: preimplantation embryo


title: peripheral blood, colorectal cancer-r1 (PB1872)


title: s8_tssp_M_het_17

description:
M_het_17_S61
Supplemental_Table_S4_5.xlsx


title: SGT_119

value: Basal cell adenoma


title: peripheral blood, colorectal cancer-r1 (MH0097)


title: SGT_113

value: Palate


title: SGT_112


title: SGT_111


title: s8_tssp_M_het_16

description:
M_het_16_S60
Supplemental_Table_S4_5.xlsx


title: SGT_110


title: s8_tssp_M_het_15

description:
M_het_15_S59
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colorectal cancer-r1 (MH0039)


title: SGT_109

value: MDM2 amplification


title: SGT_116


title: s8_tssp_M_het_14

description:
M_het_14_S58
Supplemental_Table_S4_5.xlsx


title: SGT_114


title: SGT_106


title: peripheral blood, colorectal cancer-r1 (BT0003)


title: s8_tssp_M_het_13

description:
M_het_13_S57
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colorectal cancer-r1 (MH0035)


title: peripheral blood, colorectal cancer-r1 (MH0004)


title: peripheral blood, colorectal cancer-r1 (JM0019)


title: SGT_104


title: SGT_102

value: Adenoid cystic carcinoma

value: ADCCA


title: SGT_101


title: SGT_099

value: Oral cavity


title: SGT_098

value: MYB amplification


title: s8_tssp_M_het_11

description:
M_het_11_S43
Supplemental_Table_S4_5.xlsx


title: SGT_108


title: s8_tssp_M_het_12

description:
M_het_12_S44
Supplemental_Table_S4_5.xlsx


title: s8_tssp_4_homo_9

description:
4_homo_9_S32
Supplemental_Table_S4_5.xlsx

value: Dgcr8fl/fl; Stra8-iCre testicular sperm


title: SGT_103

value: Parotid gland


title: SGT_100


title: SGT_097

value: Submandibular gland


title: s8_tssp_4_homo_8

description:
4_homo_8_S16
Supplemental_Table_S4_5.xlsx


title: s8_tssp_M_het_10

description:
M_het_10_S42
Supplemental_Table_S4_5.xlsx

value: Morula

value: Dgcr8+/fl; Stra8-iCre testicular sperm


title: SGT_105

value: Balanced


title: SGT_094


title: peripheral blood, colorectal cancer-r1 (JH0069)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.

value: peripheral blood

value: F

value: colorectal cancer


title: SGT_095


title: peripheral blood, colorectal cancer-r1 (MH0031-2)

value: M


title: peripheral blood, colorectal cancer-r1 (RC3445)


title: peripheral blood, colorectal cancer-r1 (JH0046)


title: peripheral blood, colorectal cancer-r1 (JH0154)


title: peripheral blood, colorectal cancer-r1 (DES1002)


title: SGT_093

value: Nasal cavity & paranasal sinus


title: peripheral blood, colorectal cancer-r1 (RC467)


title: SGT_092


title: SGT_089


title: s8_tssp_4_homo_5

description:
4_homo_5_S13
Supplemental_Table_S4_5.xlsx

value: preimplantation embryo


title: SGT_088


title: SGT_152

value: Clear cell carcinoma

value: CCC

value: CDKN2A loss


title: SGT_091

value: Adenoid cystic carcinoma

value: ADCCA


title: SGT_090


title: s8_tssp_4_homo_23

description:
4_homo_23_S80
Supplemental_Table_S4_5.xlsx

value: Dgcr8fl/fl; Stra8-iCre testicular sperm


title: s8_tssp_4_homo_7

description:
4_homo_7_S15
Supplemental_Table_S4_5.xlsx


title: SGT_087

value: Parotid gland


title: s8_tssp_4_homo_4

description:
4_homo_4_S12
Supplemental_Table_S4_5.xlsx


title: SGT_084


title: SGT_086


title: s8_tssp_4_homo_3

description:
4_homo_3_S11
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colorectal cancer-r1 (RC1053)


title: s8_tssp_4_homo_6

description:
4_homo_6_S14
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colorectal cancer-r1 (PB3010)


title: peripheral blood, colorectal cancer-r1 (PB2818)


title: peripheral blood, colorectal cancer-r1 (PB1829)


title: SGT_083

value: Oral cavity


title: SGT_082


title: SGT_085


title: peripheral blood, colorectal cancer-r1 (PB1471)


title: SGT_081

value: Lung


title: s8_tssp_4_homo_21

description:
4_homo_21_S78
Supplemental_Table_S4_5.xlsx


title: SGT_080

value: MYB amplification

value: Palate


title: SGT_078

value: Balanced


title: s8_tssp_4_homo_20

description:
4_homo_20_S77
Supplemental_Table_S4_5.xlsx


title: s8_tssp_4_homo_19

description:
4_homo_19_S76
Supplemental_Table_S4_5.xlsx


title: SGT_079


title: SGT_075


title: SGT_073


title: SGT_076


title: peripheral blood, colorectal cancer-r1 (PB0293)

value: peripheral blood


title: s8_tssp_4_homo_2

description:
4_homo_2_S10
Supplemental_Table_S4_5.xlsx


title: SGT_077


title: s8_tssp_4_homo_22

description:
4_homo_22_S79
Supplemental_Table_S4_5.xlsx


title: SGT_072


title: s8_tssp_4_homo_18

description:
4_homo_18_S56
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colorectal cancer-r1 (NK2011)

value: colorectal cancer


title: peripheral blood, colorectal cancer-r1 (MH0091)

value: M


title: SGT_071

value: Nasal cavity & paranasal sinus


title: peripheral blood, colorectal cancer-r1 (MH0033)


title: s8_tssp_4_homo_17

description:
4_homo_17_S55
Supplemental_Table_S4_5.xlsx

value: preimplantation embryo


title: SGT_070

value: MYB

value: Lip


title: SGT_069


title: s8_tssp_4_homo_16

description:
4_homo_16_S54
Supplemental_Table_S4_5.xlsx


title: SGT_068


title: SGT_074


title: peripheral blood, colorectal cancer-r1 (MH0063)


title: SGT_067


title: peripheral blood, colorectal cancer-r1 (MH0028)

value: F


title: SGT_066

value: Adenoid cystic carcinoma

value: CDKN2A loss


title: SGT_064

value: ADCCA


title: SGT_065

value: Parotid gland


title: s8_tssp_4_homo_13

description:
4_homo_13_S36
Supplemental_Table_S4_5.xlsx

value: Dgcr8fl/fl; Stra8-iCre testicular sperm


title: SGT_063


title: s8_tssp_4_homo_14

description:
4_homo_14_S37
Supplemental_Table_S4_5.xlsx


title: SGT_062


title: SGT_061


title: SGT_060


title: SGT_059


title: peripheral blood, colorectal cancer-r1 (MH0001)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.


title: s8_tssp_4_homo_15

description:
4_homo_15_S38
Supplemental_Table_S4_5.xlsx


title: s8_tssp_4_homo_11

description:
4_homo_11_S34
Supplemental_Table_S4_5.xlsx


title: SGT_057


title: SGT_058


title: peripheral blood, colorectal cancer-r1 (MH0018)


title: peripheral blood, colorectal cancer-r1 (JH0121)


title: peripheral blood, colorectal cancer-r1 (JM0015)


title: SGT_055


title: SGT_056

value: No fusion


title: peripheral blood, colorectal cancer-r1 (JH0071)


title: s8_tssp_4_homo_10

description:
4_homo_10_S33
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colorectal cancer-r1 (JH0058)


title: s8_tssp_4_het_9

description:
4_het_9_S26
Supplemental_Table_S4_5.xlsx

value: Dgcr8+/fl; Stra8-iCre testicular sperm


title: SGT_054


title: peripheral blood, colorectal cancer-r1 (JH0054)


title: s8_tssp_4_het_8

description:
4_het_8_S8
Supplemental_Table_S4_5.xlsx


title: SGT_051


title: SGT_052


title: s8_tssp_4_homo_12

description:
4_homo_12_S35
Supplemental_Table_S4_5.xlsx


title: SGT_096


title: SGT_050


title: s8_tssp_4_het_7

description:
4_het_7_S7
Supplemental_Table_S4_5.xlsx


title: SGT_049


title: peripheral blood, colorectal cancer-r1 (JH0044)


title: s8_tssp_4_het_6

description:
4_het_6_S6
Supplemental_Table_S4_5.xlsx


title: SGT_048


title: SGT_053


title: SGT_047


title: SGT_044


title: SGT_045


title: peripheral blood, colorectal cancer-r1 (JH0041)


title: s8_tssp_4_het_5

description:
4_het_5_S5
Supplemental_Table_S4_5.xlsx


title: s8_tssp_4_het_4

description:
4_het_4_S4
Supplemental_Table_S4_5.xlsx


title: SGT_046


title: SGT_043


title: s8_tssp_4_het_24

description:
4_het_24_S75
Supplemental_Table_S4_5.xlsx


title: SGT_040


title: s8_tssp_4_het_23

description:
4_het_23_S74
Supplemental_Table_S4_5.xlsx


title: SGT_042


title: SGT_039


title: SGT_038


title: peripheral blood, colorectal cancer-r1 (FC0006)


title: peripheral blood, colorectal cancer-r1 (JH0043)


title: peripheral blood, colorectal cancer-r1 (MH0038)


title: peripheral blood, colorectal cancer-r1 (JGA0021)


title: SGT_037


title: s8_tssp_4_het_20

description:
4_het_20_S71
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colorectal cancer-r1 (NK2018)


title: peripheral blood, colorectal cancer-r1 (CD0028)


title: peripheral blood, colorectal cancer-r1 (JM0021)


title: SGT_034

value: Acinic cell carcinoma

value: ACC


title: SGT_032

value: Balanced

value: Sublingual gland


title: s8_tssp_4_het_2

description:
4_het_2_S2
Supplemental_Table_S4_5.xlsx


title: SGT_033


title: SGT_035

value: Oral cavity


title: SGT_030


title: s8_tssp_4_het_19

description:
4_het_19_S53
Supplemental_Table_S4_5.xlsx


title: peripheral blood, colorectal cancer-r1 (JH0072)

value: peripheral blood

value: M

value: colorectal cancer


title: SGT_041

value: MYB

value: Nasal cavity & paranasal sinus


title: s8_tssp_4_het_22

description:
4_het_22_S73
Supplemental_Table_S4_5.xlsx

value: preimplantation embryo


title: s8_tssp_4_het_17

description:
4_het_17_S51
Supplemental_Table_S4_5.xlsx


title: s8_tssp_4_het_18

description:
4_het_18_S52
Supplemental_Table_S4_5.xlsx


title: SGT_029

value: CDKN2A loss


title: peripheral blood, colorectal cancer-r1 (FS1013)

value: F


title: SGT_028

value: Parotid gland


title: SGT_107

value: Basal cell adenocarcinoma

value: BC

value: No mutation


title: SGT_036

value: Acinic cell carcinoma


title: SGT_027

value: ACC


title: peripheral blood, colorectal cancer-r1 (MH0016)


title: SGT_025

value: Balanced


title: s8_tssp_4_het_16

description:
4_het_16_S50
Supplemental_Table_S4_5.xlsx

value: Dgcr8+/fl; Stra8-iCre testicular sperm


title: peripheral blood, colorectal cancer-r1 (FS0001)


title: peripheral blood, colorectal cancer-r1 (FC0014)


title: s8_tssp_4_het_15

description:
4_het_15_S49
Supplemental_Table_S4_5.xlsx


title: SGT_026


title: peripheral blood, colorectal cancer-r1 (DS0007)


title: SGT_023


title: SGT_024


title: SGT_031


title: SGT_022


title: SGT_021


title: s8_tssp_4_het_14

description:
4_het_14_S31
Supplemental_Table_S4_5.xlsx


title: s8_tssp_4_het_12

description:
4_het_12_S29
Supplemental_Table_S4_5.xlsx


title: s8_tssp_4_het_13

description:
4_het_13_S30
Supplemental_Table_S4_5.xlsx


title: SGT_018


title: SGT_020


title: peripheral blood, colorectal cancer-r1 (CD0379)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.


title: SGT_019


title: SGT_017


title: SGT_016


title: s8_tssp_4_het_11

description:
4_het_11_S28
Supplemental_Table_S4_5.xlsx


title: s8_tssp_4_het_10

description:
4_het_10_S27
Supplemental_Table_S4_5.xlsx


title: SGT_012


title: SGT_013


title: peripheral blood, colorectal cancer-r1 (DC4002)


title: SGT_011


title: s8_tssp_4_het_1

description:
4_het_1_S1
Supplemental_Table_S4_5.xlsx


title: SGT_009

value: Myoepithelial carcinoma

value: No fusion

value: Submandibular gland


title: SGT_010


title: SGT_015


title: SGT_006

value: Epithelial-myoepithelial carcinoma


title: SGT_008


title: SGT_007

value: MDM2 amplification


title: SGT_005


title: defb_causp_m_homo_miR_4_6

description:
m_homo_miR_4_6_S72
Supplemental_Table_S6_7.xlsx

value: Morula

value: Dgcr8fl/fl; Defb41-iCre cauda sperm

tag: rna microinjection

value: microRNA purified from cauda epididymosomes


title: defb_causp_m_homo_miR_4_7

description:
m_homo_miR_4_7_S73
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo


title: peripheral blood, colorectal cancer-r1 (PB1761)

value: peripheral blood

value: M

value: colorectal cancer


title: peripheral blood, colorectal cancer-r1 (MH0092)


title: peripheral blood, colorectal cancer-r1 (MR1001)

value: F


title: peripheral blood, colorectal cancer-r1 (MIP2007)


title: defb_causp_m_homo_miR_4_5

description:
m_homo_miR_4_5_S71
Supplemental_Table_S6_7.xlsx


title: SGT_004


title: peripheral blood, colorectal cancer-r1 (MH0017)


title: peripheral blood, colorectal cancer-r1 (MH0014)


title: peripheral blood, colorectal cancer-r1 (MH0034)


title: peripheral blood, colorectal cancer-r1 (RC3062)


title: defb_causp_m_homo_miR_4_4

description:
m_homo_miR_4_4_S60
Supplemental_Table_S6_7.xlsx


title: defb_causp_m_homo_miR_4_8

description:
m_homo_miR_4_8_S74
Supplemental_Table_S6_7.xlsx


title: SGT_002

value: Adenoid cystic carcinoma

value: Oral cavity


title: SGT_001

value: Balanced

value: Parotid gland


title: defb_causp_m_homo_miR_4_3

description:
m_homo_miR_4_3_S69
Supplemental_Table_S6_7.xlsx


title: wild type, embryos, rep 2

city: Fort Collins

first: Taiowa

middle: A

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

description: 16-30 nt purified RNAs from cell lysate

data_processing:
Small RNA data processing was done using the default configuration in the tinyRNA pipeline (https://github.com/MontgomeryLab/tinyRNA)
Assembly: WS279
Supplementary files format and content: wild_type_embryos_adults_rpm_normalized_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in wild type gravid adult and mixed stage embryo sRNA-seq libraries.
Supplementary files format and content: GFP-RDE-1_co-IP_nrlf-1_rpm_normalized_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in GFP::RDE-1 co-IPs and cell lysate sRNA-seq libraries.
Supplementary files format and content: GFP-ALG-1_co-IP_nrlf-1_rpm_normalized_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in GFP::ALG-1 co-IPs and cell lysate sRNA-seq libraries.

organism: Caenorhabditis elegans

source_name: mixed stage embryos

growth_protocol: Worms were grown for 72-75 hours from synchronized L1 larvae at 20˚C on media containing E. coli (OP50 or HT115).

extract_protocol:
Worms were washed from plates and rinsed with M9 3 times and flash frozed in liquid nitrogen. RNA was isolated using trizol/chloroform and isopropanol precipitation.
Small RNAs (~16-30-nt) were purified from total RNA by size selection using 17% polyacrylamide gels and in some instances treated with NEB RNA 5' Pyrophosphohydrolase (RppH)to facilitate capture of 22G-RNAs. Libraries were then prepared according to the NEBNext Multiplex Small RNA kit protocol. PCR products (~134-148 bp) were size selected using 10% polyacrylamide gels. For mRNA-seq DNase-treated total RNA was depleted of rRNA using Ribo-Zero and libraries were prepared using the Illumina TruSeq Stranded Total RNA kit.

value: mixed stage embryos

tag: genotype

value: wild type (N2)

tag: treatment


title: wild type, embryos, rep 1

description: 16-30 nt purified RNAs from cell lysate

tag: tissue


title: defb_causp_m_homo_miR_4_2

description:
m_homo_miR_4_2_S68
Supplemental_Table_S6_7.xlsx


title: wild type, adults, rep 3

description: 16-30 nt purified RNAs from cell lysate

source_name: gravid hermaphroditic adult whole animals


title: SGT_003

value: No fusion


title: peripheral blood, colorectal cancer-r1 (JM0018)

tag: gender

tag: age


title: peripheral blood, colorectal cancer-r1 (JM0017)

tag: cancer dx


title: peripheral blood, colorectal cancer-r1 (JH0149)


title: wild type, adults, rep 2

description: 16-30 nt purified RNAs from cell lysate

value: gravid hermaphroditic adult whole animals


title: wild type, adults, rep 1

description: 16-30 nt purified RNAs from cell lysate


title: defb_causp_m_homo_miR_4_1

description:
m_homo_miR_4_1_S67
Supplemental_Table_S6_7.xlsx


title: defb_causp_m_homo_miR_3_8

description:
m_homo_miR_3_8_S51
Supplemental_Table_S6_7.xlsx


title: D-3

city: Shenyang

first: JIE

last: LU

state: Liaoning

address: 77 Puhe Road, Shenbei Xiqu

department: Human Anatomy

country: China

institute: China Medical University

description:
OE-F
all.fpkm_mRNA_anno.xls
all.fpkm_lncRNA_anno.xls
all.fpkm_miRNA.xls
all.fpkm_circRNA.xls

data_processing:
Bcl2fastq (v2.17.1.14) software was used for base-calling
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less than 0.05. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways.
All transcripts as the result of Cuffmerge, were filtered by known non-lincRNA annotation, non- lincRNA characters, ORFs and protein-coding potential methods. Known non-lincRNA includes known protein-coding RNA, miRNA, tRNA, snoRNA, rRNA and pseudogenes. There are three characters of non-lincRNA, such as transcripts of non-lincRNA contain more than one exon; their length must be longer than 200bp; and the coverage of each transcript must be more than 3. ORFs were predicted by software HMMER (v3.1b1). CPC (Coding Potential Calculator) was used to do protein-coding potential prediction. CNCI (Coding-Non-Coding Index), by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations. Transcriptional regulation by lncRNAs could work either in cis or in trans, and could negatively or positively control pc gene expression. lncRNAs work in cis when their effects are restricted to the chromosome from which they are transcribed, and work in trans when they affect genes on other chromosomes. The cis regulation by lncRNAs can be predicted by software Bedtools (v2.17.0). And regulation in trans was analyzed via Pearson correlation coefficient.
Assembly: ENSEMBLE GRCm38.100
Supplementary files format and content: xls file includes FPKM values for each sample

source_name: medial frontal cortex

extract_protocol:
The total RNA of each sample was extracted from the medial frontal cortex of mouse brain by using TRIzol reagent (Life Technologies, USA)/RNeasy Mini Kit (Qiagen, USA) following the manufacturer’s protocol. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The rRNA was depleted from total RNA using rRNA removal Kit. The ribosomal depleted RNA was then fragmented and reverse-transcribed. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase with random primers and Actinomycin D. The second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix (include dACG-TP/dUTP). The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, and fragments of ~400 bp (with the approximate insert size of 300 bp) were recovered. The dUTP-marked second strand was digested with Uracil-Specific Excision Reagent enzyme. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P5/P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA,USA). Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq/Novaseq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA) or a MGI2000 instrument according to manufacturer’s instructions (MGI, Shenzhen, China) . Sequencing was carried out using a 2x150 paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument，image analysis and base calling were conducted by the NovaSeq Control Software (NCS) + OLB + GAPipeline- 1.6 (Illumina) on the NovaSeq instrument，image analysis and base calling were conducted by the Zebeacall on the MGI2000 instrument.

value: medial frontal cortex

tag: development stage

tag: Sex

value: Female


title: peripheral blood, colorectal cancer-r1 (JH0067)


title: D-2


title: defb_causp_m_homo_miR_3_7

description:
m_homo_miR_3_7_S10
Supplemental_Table_S6_7.xlsx

value: Morula

value: Dgcr8fl/fl; Defb41-iCre cauda sperm


title: C-3

description:
OE-M
all.fpkm_mRNA_anno.xls
all.fpkm_lncRNA_anno.xls
all.fpkm_miRNA.xls
all.fpkm_circRNA.xls

value: Male


title: defb_causp_m_homo_miR_3_6

description:
m_homo_miR_3_6_S49
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo

value: microRNA purified from cauda epididymosomes


title: defb_causp_m_homo_miR_3_5

description:
m_homo_miR_3_5_S48
Supplemental_Table_S6_7.xlsx


title: D-1


title: In vivo panicle rep2

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

country: South Korea

institute: Pusan National University

data_processing:
Using FASTX-Toolkit, raw data derived from RNA-seq was filtered to a minimum phred quality score of 28.
The BWA-MEM algorithm was employed to align the filtered reads into the reference genome.
SAM files were converted to BAM files of binary format, and then sorted by chromosomal coordinates using the SAMtools program.
Mapped reads per annotated gene were counted by featureCounts tool in the Subread package.
Counted values were nomalised in the RPKM method.
Genome_build: Burkholderia glumae BGR1 GCF_000022645.2
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample

organism: Burkholderia glumae

source_name: Wild type strain infected in in vivo rice panicle

growth_protocol: B. glumae BGR1 was used to inoculate 2 ml of LB broth and then incubated at 37°C overnight with shaking, after which it was subcultured at 37°C for 4 to 5 h in 2 ml of fresh LB broth to reach the mid-logarithmic phase. Cultured bacteria cells were then collected by centrifugation, washed twice with sterile water and resuspended in distilled water, after which the suspension was adjusted to OD600 = 0.5 using a colorimeter (Biochrom WPA CO8000 Cell Density Meter, Biochrom). Next, panicles of rice at a flowering stage were inoculated with bacterial suspensions using an atomizer (Binks Wren, Glendale Heights, IL), and grown in a greenhouse for 15 days. In the cold room, rice panicles with symptoms of B. glumae BGR1 were collected.

extract_protocol:
The infected rice panicles were mixed with DEPC-treated water by grinding. The mixture was centrifuged at 4°C and 1,000 × g for 1 min in 15-ml conical tubes to obtain bacteria pellets. For later RNA extraction, the collected pellets, which was primarily composed of B. glumae BGR1, were suspended in 2 ml of RNAprotectTM Bacteria Reagent (Qiagen, Valencia, CA).
Three ibraries for RNA-seq were prepared using the Illumina TruSeqTM RNA sample prep kit with the standard low-throughput protocol. Sequencing was performed on an Illumina HiSeq2000 instrument.

tag: strain

value: wild type

tag: conditions

value: in vivo rice panicle


title: peripheral blood, colorectal cancer-r1 (JH0065)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.

value: peripheral blood

value: M

value: colorectal cancer


title: In vivo panicle rep3


title: In vivo panicle rep1


title: peripheral blood, colorectal cancer-r1 (JH0061)


title: C-2


title: C-1


title: B-3

description:
CON-F
all.fpkm_mRNA_anno.xls
all.fpkm_lncRNA_anno.xls
all.fpkm_miRNA.xls
all.fpkm_circRNA.xls


title: B-2


title: defb_causp_m_homo_miR_3_4

description:
m_homo_miR_3_4_S47
Supplemental_Table_S6_7.xlsx


title: defb_causp_m_homo_miR_3_3

description:
m_homo_miR_3_3_S43
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colorectal cancer-r1 (JH0060)


title: peripheral blood, colorectal cancer-r1 (JH0039)


title: B-1


title: peripheral blood, colorectal cancer-r1 (RC1403)


title: peripheral blood, colorectal cancer-r1 (JGA0015)

value: F


title: peripheral blood, colorectal cancer-r1 (MH0032)


title: defb_causp_m_homo_miR_3_2

description:
m_homo_miR_3_2_S28
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colorectal cancer-r1 (MH0027)


title: A-2

description:
CON-M
all.fpkm_mRNA_anno.xls
all.fpkm_lncRNA_anno.xls
all.fpkm_miRNA.xls
all.fpkm_circRNA.xls


title: A-1


title: defb_causp_m_homo_miR_3_1

description:
m_homo_miR_3_1_S7
Supplemental_Table_S6_7.xlsx


title: defb_causp_m_homo_miR_2_2

description:
m_homo_miR_2_2_S30
Supplemental_Table_S6_7.xlsx


title: defb_causp_m_homo_miR_2_1

description:
m_homo_miR_2_1_S29
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colorectal cancer-r1 (JH0066)


title: defb_causp_m_homo_miR_1_4

description:
m_homo_miR_1_4_S9
Supplemental_Table_S6_7.xlsx


title: A-3


title: GFP::rde-1, nrfl-1 RNAi, co-IP, rep 3

description: 16-30 nt purified RNAs from co-IPs

value: nrfl-1 RNAi


title: defb_causp_m_homo_miR_1_3

description:
m_homo_miR_1_3_S13
Supplemental_Table_S6_7.xlsx


title: defb_causp_m_homo_miR_1_2

description:
m_homo_miR_1_2_S12
Supplemental_Table_S6_7.xlsx


title: GFP::rde-1, nrfl-1 RNAi, co-IP, rep 2

description: 16-30 nt purified RNAs from co-IPs


title: GFP::rde-1, nrfl-1 RNAi, co-IP, rep 1

description: 16-30 nt purified RNAs from co-IPs


title: GFP::rde-1, nrfl-1 RNAi, input, rep 2

description: 16-30 nt purified RNAs from cell lysate


title: GFP::rde-1, nrfl-1 RNAi, input, rep 3

description: 16-30 nt purified RNAs from cell lysate


title: GFP::rde-1, nrfl-1 RNAi, input, rep 1

description: 16-30 nt purified RNAs from cell lysate


title: GFP::alg-1, nrfl-1 RNAi, co-IP, rep 3

description: 16-30 nt purified RNAs from co-IPs


title: defb_causp_m_homo_miR_1_1

description:
m_homo_miR_1_1_S11
Supplemental_Table_S6_7.xlsx


title: defb_causp_m_homo_con_4_7

description:
m_homo_con_4_7_S66
Supplemental_Table_S6_7.xlsx

value: Control RNA


title: GFP::alg-1, nrfl-1 RNAi, co-IP, rep 2

description: 16-30 nt purified RNAs from co-IPs


title: GFP::alg-1, nrfl-1 RNAi, co-IP, rep 1

description: 16-30 nt purified RNAs from co-IPs


title: GFP::alg-1, nrfl-1 RNAi, input, rep 2

description: 16-30 nt purified RNAs from co-IPs


title: defb_causp_m_homo_con_4_5

description:
m_homo_con_4_5_S64
Supplemental_Table_S6_7.xlsx


title: GFP::alg-1, nrfl-1 RNAi, input, rep 1

description: 16-30 nt purified RNAs from co-IPs


title: defb_causp_m_homo_con_4_4

description:
m_homo_con_4_4_S52
Supplemental_Table_S6_7.xlsx


title: Org_W_6.1_A

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

data_processing:
FASTQ files were quality assessed by FASTQC, filtered for low quality reads and adapter sequences using cut adapt. Cleaned reads were aligned using HISAT2 (2.2.1), against the human genome build GRCH37. Sam files were converted to BAM files, sorted and indexed using samtools (1.13, htlib 1.13+ds). R (4.1) scripts were used to create a count table from BAM files and the human transcriptome G (including coding and non-coding RNA species) using the featureCounts function of Rsubread (2.8.2). Differential expression was calculated using a pipeline of EdgeR (4.2.1), and Limma (3.60.3) packages. Gene set enrichment was calculated by the camera function in the limma package. Human gene ontology files were obtained from the enrichment map resource (download.baderlab.org/EM_Genesets/). Human placental ontologies were from supplemental files from Naismith and Cox, 2021. Barcode graphs were generated using the barcode function in limma. Removal of dNK gene expression was accomplished using the granulator package in R applying the detanglr algorithm to estimate the transcriptional contribution of the NK cells to the co-cultured bulk mRNA signal. The dNK and organoid samples were used to estimate the pure signal. The estimated mean contribution was removed in limma as a fitted model.
Assembly: GRCH37
Supplementary files format and content: table of raw counts

source_name: placenta

growth_protocol: Trophoblast organoids were cultured according to the protocol described by (Turco et al., 2018), with the following modifications: mouse HGF (Sino Biological 50038-MNAH) rather than human HGF was used, cultures were performed using reduced growth factor Cultrex basement membrane extract (R&D #3433), and cultures were maintained in hypoxia chambers (Billups-Rothenberg MIC-101) perfused with 2% O2, 5% CO2 for 5 minutes at a rate of 25 L/min. Media was pre-conditioned in the perfused hypoxia chamber in a 37oC incubator for one hour before being applied to cultures. Trophoblast organoid media was comprised of: 1X N2 supplement (Gibco 17502048), 1X B27 supplement minus vitamin A (Gibco 12587010), 2mM L-glutamine (R&D B90010), 1.25 mM N-Acetyl-L-Cysteine (Cayman Chemical 20261), 50ng/mL human EGF (Gibco PHG0311L), 100ng/mL human FGF2 (Sigma-Aldrich F0291), 50ng/mL mouse HGF (Sino Biological 50038-MNAH), 80ng/mL human R-spondin (R&D 4645-RS), 500nM A83-01 (Tocris 2939), 2.5uM prostaglandin E2 (Tocris 2296), 1.5uM CHIR99021 (Cell Signaling Technology #54290S), 2uM Y27632 (Cell Signaling Technology #13624), and  1X Antibiotic-Antimycotic (Gibco 15240062) added to Advanced DMEM/F12 (Gibco 12634010). Trophoblast organoid cultures were initiated by seeding each dome of Cultrex gel either with <50 000 of thawed primary trophoblast cells or with thawed cryopreserved organoids from previous cultures. 40mL domes of Cultrex gel containing cultures were prepared in 24-well plates, allowed to polymerize upside-down, and were then overlaid with 500mL of trophoblast organoid media per dome.

extract_protocol:
All samples were collected and snap frozen following seven days of culture, then processed according to the manufacturer’s instructions using the RNeasy Micro Kit (Qiagen 74004) for total RNA isolation. The sample disruption and homogenization steps were performed using QIAShredders (Qiagen 79654).
Libraries were prepared at the Donnelley Centre at the University of Toronto using Takara SMART-Seq v.4 Ultra Low Input RNA kits.

treatment_protocol: When co-cultures with dNKs or dNK monocultures were prepared, 50 000 dNKs were added to each 40mL Cultrex dome. This number of dNKs was selected because it was the largest number that could be accommodated before their presence caused the Cultrex gel to depolymerize.

value: placenta

tag: cell line

tag: cell type

value: trophoblast

value: whole

tag: batch


title: OrgNK_W_6.2_4


title: OrgNK_W_6.1_6.1


title: defb_causp_m_homo_con_4_3

description:
m_homo_con_4_3_S58
Supplemental_Table_S6_7.xlsx

tag: developmental stage


title: defb_causp_m_homo_con_4_6

description:
m_homo_con_4_6_S65
Supplemental_Table_S6_7.xlsx

tag: fvb/nj donor egg fertilized by


title: GFP::alg-1, nrfl-1 RNAi, input, rep 3

description: 16-30 nt purified RNAs from co-IPs

value: gravid hermaphroditic adult whole animals


title: peripheral blood, colorectal cancer-r1 (JH0042)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.


title: SS00070, ER5 neruons, 3 replicates

city: Ashburn

first: Gerald

middle: M

last: Rubin

address: 19700 Helix Drive

institute: Janelia Research Campus

data_processing:
Sequencing adapters were trimmed from the reads with Cutadapt (Martin, 2011) prior to alignment with STARsolo (Dobin et al., 2013) to the Drosophila r6.17 genome assembly (Flybase). The resulting transcript alignments were passed to RSEM (Li and Dewey, 2011) to generate gene expression counts.
Assembly: Drosophila r6.17
Supplementary files format and content: csv test file include raw counts for each Sample and Mean and S.D. for each group of replicates.

organism: Drosophila melanogaster

source_name: brain

extract_protocol:
For each sample, 60-100 brains were dissected in freshly prepared, ice cold Adult Hemolymph Solution (AHS, 108 mM NaCl, 5 mM KCl, 2 mM CaCl2, 8.2 mM MgCl2, 4 mM NaHCO3, 1 mM NaH2PO4, 5 mM HEPES, 6 mM Trehalose, 10 mM Sucrose), and the major tracheal branches removed. The brains were transferred to a 1.5 ml Eppendorf tube containing 500 μl 1 mg/ml Liberase DH (Roche, prepared according to the manufacturer's recommendation) in AHS, and digested for 1 h at room temperature. The Liberase solution was removed and the brains washed twice with 800 microliters ice cold AHS. The final wash was removed completely and 400 μl of AHS+2% Fetal Bovine Serum (FBS, Sigma) were added. The brain samples were gently triturated with a series of fire-polished, FBS-coated Pasteur pipettes of descending pore sizes until the tissue was homogenized, after which the tube was allowed to stand for 2-3 m so that the larger debris could settle. For hand sorting, the cell suspension was transferred to a Sylgard-lined Glass Bottom Dish (Willco Wells), leaving the debris at the bottom of the Eppendorf tube, and distributed evenly in a rectangular area in the center of the plate with the pipet tip. The cells were allowed to settle for 10-30 m prior to picking. Fluorescent cells were picked with a mouth aspirator consisting of a 0.8 mm Nalgene Syringe Filter (Thermo), a short stretch of tubing, a plastic needle holder, and a pulled Kwik-Fil Borosilicate Glass capillary (Fisher). Cells picked off the primary plate were transferred to a Sylgard-lined 35 mm Mat Tek Glass Bottom Microwell Dishes (Mat Tek) filled with 170 μl AHS+2%FBS, allowed to settle, and then re-picked. Three washes were performed in this way before the purified cells were picked and transferred into 50 μl buffer XB from the PicoPure RNA Isolation Kit (Life Technologies), lysed for 5 m at 42˚C, and stored at -80˚C. For FACS, the samples were triturated in AHS+2%FBS that was run through a 0.2 μm filter, and the cell suspension was passed through a Falcon 5 ml round-bottom tube fitted with a 35 μm cell strainer cap (Fisher). Samples were sorted on a SONY SH800 cell sorter gated for single cells with a fluorescence intensity exceeding that of a non-fluorescent control.
One microliter of harsh lysis buffer (50 mM Tris pH 8.0, 5 mM EDTA pH 8.0, 10 mM DTT, 1% Tween-20, 1% Triton X-100, 0.1 g/L Proteinase K (Roche), 2.5 mM dNTPs (Takara), and ERCC Mix 1 (Thermo-Fisher) diluted to 1e-7) and 1 μl10 μM barcoded RT primer were added, and the samples were incubated for 5 m at 50˚C to lyse the cells, followed by 20 m at 80˚C to inactivate the Proteinase K. Reverse transcription master mix (2 μL 5X RT Buffer (Thermo-Fisher), 2 μL 5M Betaine (Sigma-Aldrich), 0.2 μL 50 μM E5V6NEXT template-switch oligo (Integrated DNA Technologies), 0.1 μL 200 U/μL Maxima H-RT (Thermo-Fisher), 0.1 μL 40U/μL RNAsin (Lucigen), and 0.6 μL nuclease-free water (Thermo-Fisher) was added to the lysis reaction and incubated at 42˚C for 1.5 h, followed by 10 m at 75˚C to inactivate the reverse transcriptase. PCR was performed by adding 10 μL 2X HiFi PCR Mix (Kapa Biosystems) and 0.5 μL 60 μM SINGV6 primer and incubating at 98˚C for 3 m, followed by 20 cycles of 98˚C for 20 s, 64˚C for 15 s, 72˚C for 4 m, and a final extension of 5 m at 72˚C. Groups of 8 reactions were pooled to yield ~250 μL and purified with Ampure XP Beads (0.6x ratio; Beckman Coulter), washed twice with 75% Ethanol, and eluted in 40 μL nuclease-free water. The DNA concentration of each sample was determined using Qubit High-Sensitivity DNA kit (Thermo-Fisher). To prepare the Illumina sequencing library, 600 pg cDNA from each pooled sample was used in a modified Nextera XT library preparation (Illumina) (Soumillon et al., 2014) using the P5NEXTPT5 primer and extending the tagmentation time to 15 m. The resulting libraries were purified according to the Nextera XT protocol (0.6x ratio) and quantified by qPCR using Kapa Library Quantification (Kapa Biosystems).

value: brain


title: SS57656, FB6A neurons, 5 replicates


title: SS55888, FB7A neurons, 4 replicates


title: SS02748, hDeltaK neurons, 5 replicates

value: hDeltaK


title: SS54343, FB6A neurons, 4 replicates


title: SS56319, FB2I_a, FB2I_b, 9 replicates

value: FB2I_a, FB2I_b


title: SS56684, ExR1 neurons, 5 replicates


title: NK_W_A_6.1

source_name: decidua

value: decidua

value: dNK


title: defb_causp_m_homo_con_4_2

description:
m_homo_con_4_2_S57
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo

value: Morula

value: Dgcr8fl/fl; Defb41-iCre cauda sperm

tag: genome build


title: OrgNK_S_6.2_6.1

value: sorted


title: OrgNK_W_6.2_6.1


title: defb_causp_m_homo_con_4_1

description:
m_homo_con_4_1_S70
Supplemental_Table_S6_7.xlsx

tag: rna microinjection


title: OrgNK_S_6.1_4

tag: genotype


title: NK_W_A_4

tag: treatment


title: defb_causp_m_homo_con_3_5

description:
m_homo_con_3_5_S46
Supplemental_Table_S6_7.xlsx

tag: tissue


title: OrgNK_W_6.1_4


title: p53KO, Day 21 rep 2

city: New York

first: Rei

last: Kudo

state: NY

address: 417 E 68th Street

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file.
Assembly: GRCh38
Supplementary files format and content: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file.

growth_protocol: MCF7 cells were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was extracted by using Rneasy Mini kit (Qiagen).
NEBNext Ultra II RNA Library Prep Kit

treatment_protocol: MCF7 cells were treated with 50 nM abemaciclib (Selleck) for indicated days.

value: breast cancer cell

value: TP53 knockout

value: abemaciclib


title: p53KO, Day 21 rep 3


title: defb_causp_m_homo_con_3_4

description:
m_homo_con_3_4_S42
Supplemental_Table_S6_7.xlsx

value: Control RNA


title: defb_causp_m_homo_con_3_3

description:
m_homo_con_3_3_S41
Supplemental_Table_S6_7.xlsx


title: Org_W_6.2_A

value: placenta


title: SGT_014

tag: diagnosis

value: Acinic cell carcinoma

tag: methylation class

value: ACC

tag: focal cnvs

value: Balanced

tag: fusions

tag: mutations

tag: location

value: Parotid gland


title: Org_S_6.1_A

value: trophoblast


title: p53KO, Day 21 rep 1


title: p53KO, Day 14 rep 3


title: defb_causp_m_homo_con_3_2

description:
m_homo_con_3_2_S40
Supplemental_Table_S6_7.xlsx


title: p53KO, Day 14 rep 2


title: defb_causp_m_homo_con_3_1

description:
m_homo_con_3_1_S39
Supplemental_Table_S6_7.xlsx


title: p53KO, Day 14 rep 1


title: p53KO, Day 3 rep 3


title: peripheral blood, colorectal cancer-r1 (JH0040)

value: peripheral blood

tag: gender

value: M

tag: age

tag: cancer dx

value: colorectal cancer


title: p53KO, Day 3 rep 2

tag: cell line

tag: cell type


title: p53KO, Day 3 rep 1


title: peripheral blood, colorectal cancer-r1 (PB1681)


title: defb_causp_m_homo_con_2_5

description:
m_homo_con_2_5_S27
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo

tag: developmental stage

tag: fvb/nj donor egg fertilized by


title: peripheral blood, colorectal cancer-r1 (JGA0031)

value: F


title: peripheral blood, colorectal cancer-r1 (JM0011)


title: peripheral blood, colorectal cancer-r1 (MH0096)


title: peripheral blood, colorectal cancer-r1 (RC3277)


title: p53KO, Day 0 rep 3

value: DMSO


title: peripheral blood, colorectal cancer-r1 (MH0036)


title: peripheral blood, colorectal cancer-r1 (MH0023)


title: defb_causp_m_homo_con_2_4

description:
m_homo_con_2_4_S26
Supplemental_Table_S6_7.xlsx

value: Morula

value: Dgcr8fl/fl; Defb41-iCre cauda sperm

tag: rna microinjection

tag: genome build


title: peripheral blood, colorectal cancer-r1 (RC2919)


title: peripheral blood, colorectal cancer-r1 (MH0029)


title: peripheral blood, colorectal cancer-r1 (JGA0019)


title: p53KO, Day 0 rep 1

value: breast cancer cell

tag: genotype

value: TP53 knockout

tag: treatment


title: p53KO, Day 0 rep 2


title: defb_causp_m_homo_con_2_3

description:
m_homo_con_2_3_S25
Supplemental_Table_S6_7.xlsx

tag: tissue

value: Control RNA


title: peripheral blood, colorectal cancer-r1 (RC176)


title: peripheral blood, colorectal cancer-r1 (RC0986)


title: MCF7 parental, Day 21 rep 3

value: WT

value: abemaciclib


title: peripheral blood, colorectal cancer-r1 (RC2803)


title: peripheral blood, colorectal cancer-r1 (JH0145)


title: peripheral blood, colorectal cancer-r1 (JM0025)


title: peripheral blood, colorectal cancer-r1 (JM0030)


title: peripheral blood, colorectal cancer-r1 (JH0119)


title: MCF7 parental, Day 21 rep 1


title: MCF7 parental, Day 14 rep 3


title: peripheral blood, colorectal cancer-r1 (JH0146)


title: defb_causp_m_homo_con_2_1

description:
m_homo_con_2_1_S16
Supplemental_Table_S6_7.xlsx


title: peripheral blood, colorectal cancer-r1 (MH0026)


title: defb_causp_m_homo_con_2_2

description:
m_homo_con_2_2_S24
Supplemental_Table_S6_7.xlsx


title: MCF7 parental, Day 14 rep 1


title: MCF7 parental, Day 14 rep 2


title: MCF7 parental, Day 21 rep 2


title: MCF7 parental, Day 3 rep 3


title: MCF7 parental, Day 3 rep 2


title: peripheral blood, colorectal cancer-r1 (JH0112)


title: defb_causp_m_homo_con_1_6

description:
m_homo_con_1_6_S14
Supplemental_Table_S6_7.xlsx


title: 5xFAD, BHB-treated, female, microglia 3

city: Sacramento

first: Jacopo

last: Di Lucente

state: CA

address: 2805 50th Street

department: Pathology and Laboratory Medicine

institute: UC Davis

description: BHB 6

data_processing:
Glaxy version 24.0.3
Sequence reads were trimmed Trimmomatic (version 0.39)
Trimmed reads were allign to mm10 using HISAT2 (version 2.2.1)
Gene expression was measured using featureCounts (version 2.0.3)
Differentially expressed features were determined using DESeq2 (version 2.11.40.8)
Assembly: mm10
Supplementary files format and content: Normalized counts

extract_protocol:
RNA was harvested using Rneasy plus universal mini kit (quiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Following is the workflow of library construction. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: brain

value: microglia

value: BHB


title: defb_causp_m_homo_con_1_5

description:
m_homo_con_1_5_S8
Supplemental_Table_S6_7.xlsx


title: MCF7 parental, Day 0 rep 3


title: MCF7 parental, Day 3 rep 1


title: peripheral blood, colorectal cancer-r1 (JH0068)


title: defb_causp_m_homo_con_1_4

description:
m_homo_con_1_4_S44
Supplemental_Table_S6_7.xlsx


title: 5xFAD, BHB-treated, female, microglia 2

description: BHB 5


title: peripheral blood, colorectal cancer-r1 (JH0057)


title: defb_causp_m_homo_con_1_7

description:
m_homo_con_1_7_S50
Supplemental_Table_S6_7.xlsx


title: 5xFAD, BHB-treated, female, microglia 1

description: BHB 4


title: 5xFAD, BHB-treated, male, microglia 3

description: BHB 3


title: MCF7 parental, Day 0 rep 2


title: defb_causp_m_homo_con_1_2

description:
m_homo_con_1_2_S38
Supplemental_Table_S6_7.xlsx


title: 5xFAD, BHB-treated, male, microglia 2

description: BHB 2


title: MCF7 parental, Day 0 rep 1


title: peripheral blood, colorectal cancer-r1 (JH0048)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.


title: defb_causp_m_homo_con_1_3

description:
m_homo_con_1_3_S6
Supplemental_Table_S6_7.xlsx


title: 5xFAD, BHB-treated, male, microglia 1

description: BHB 1


title: defb_causp_m_het_4_8

description:
m_het_4_8_S59
Supplemental_Table_S6_7.xlsx

value: Dgcr8+/fl; Defb41-iCre cauda sperm


title: peripheral blood, colorectal cancer-r1 (JH0062)

value: peripheral blood


title: 5xFAD, Vehicle-treated, female, microglia 3

description: Vehicle 6

value: Vehicle


title: Normal thyroid tissue, Patient 13: Adults, 66-year-old female, ND6

city: Fuzhou

first: Bo Wang

last: Wang

state: Fujian province

address: 29 XinQuan Rd

department: Department of Thyroid and Parathyroid Surgery

institute: Fujian Medical University Union Hospital

library_source: transcriptomic single cell

data_processing:
Quality control. Raw data (raw reads) of fastq format were firstly processed through in-hous eperl scripts. In this step, clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data. At the same time, Q20, Q3 0 and GC content of the clean data were calculated. All the downstream analyses were performed based on the clean data with high quality.
Mapping to the reference genome. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired- end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selectedHisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level. The raw counts were first normalized using TPM (Zhou et al., 2010) Normalized expression level = (readCount*1,000,000) / libsize (libsize is the sum of circRNA readcount).
For the samples without biological replicates. Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold fbr significantly differential expression
Assembly: GRCh38.p14
Supplementary files format and content: Text file include FRKM values for each sample.

source_name: Normal thyroid tissue

extract_protocol:
Ribosomal RNA was removed by Epicentre Ribozer rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, the linear RNA was digested with 3 U of RNase R (Epicentre, USA) per µg of RNA.
The sequencing libraries were generated by NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370-420 bp in length, the library fragments were purified with AMPure XP system (Beverly, USA). Then 3 µL USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37° C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent 5400 system（Agilent，USA） and quantified by QPCR (1.5 nM). The Qualified libraries were pooled and sequenced on Illumina platforms with PE150 strategy, according to effective library concentration and data amount required.

value: Normal thyroid tissue

value: female

tag: histological type


title: Normal thyroid tissue, Patient 11: Adults, 63-year-old female, ND4


title: 5xFAD, Vehicle-treated, female, microglia 2

description: Vehicle 5


title: 5xFAD, Vehicle-treated, female, microglia 1

description: Vehicle 4


title: Normal thyroid tissue, Patient 10: Adults, 43-year-old female, ND3


title: defb_causp_m_het_4_6

description:
m_het_4_6_S61
Supplemental_Table_S6_7.xlsx

value: preimplantation embryo


title: defb_causp_m_homo_con_1_1

description:
m_homo_con_1_1_S4
Supplemental_Table_S6_7.xlsx