title: g1.S39

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S39_XJ3969-2_S15


title: g1.S38

status: Public on Jun 26 2020

type: SRA

city: Cambridge

first: Xin

last: Jin

state: MA

address: 415 Main Street

country: USA

institute: Broad Institute of MIT and Harvard

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S38_XJ3969-2_S14

library_source: transcriptomic

data_processing:
Basecalling and sample demultiplexing were performed in Illumina NextSeq Control Software.
Potential mouse contaminating reads were removed by competitive mapping to the human/mouse hybrid genome using BBSplit (https://sourceforge.net/projects/bbmap/).
Reads that uniquely mapped to the human genome were then used as input for mapping and gene-level counting with RSEM (https://deweylab.github.io/RSEM/).
Barcode reads corresponding to cell line fractions were mapped to the barcode reference using Bowtie 2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
Genome_build: hg19, mm8
Supplementary_files_format_and_content: Tab-delimited text files that contain estimated count values and annotations for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: in vivo

growth_protocol: Breast cancer cell lines were individually barcoded using lentiviral barcode vectors. Cell lines were pooled and injected into NSG mice through intracardiac route. Five weeks post injection, organs were harvested, and purified for GFP+ cancer cells.

extract_protocol:
Individual cell lines, cell line pools prior to injection, and cells isolated from metastases were subjected to RNA-Seq. RNA extraction was performed using Quick-RNA MicroPrep according to instructions (Zymo Research). RNA was quantified using RNA 6000 Pico Kit on a 2100 Bioanalyzer (Agilent). RNA samples from cell numbers lower than 500 were not measured but all were used as input for library preparation.
cDNA was synthesized using Clontech SmartSeq v4 reagents from up to 2 ng RNA input. Full length cDNA was fragmented to a mean size of 150bp with a Covaris M220 ultrasonicator and Illumina libraries were prepared from 2 ng of sheared cDNA using Rubicon Genomics Thruplex DNAseq reagents. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on Illumina NextSeq500 runs with paired-end 75bp reads.

tag: pool

value: group 1 (g1)

tag: tissue/cell type

value: lung

tag: cancer cell line composition


title: g1.S34

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S34_XJ3969-2_S12

value: liver


title: g1.S58

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S58_XJ3969-3_S14

source_name: in vitro

value: BT549_BREAST:0; HDQP1_BREAST:0; JIMT1_BREAST:0; MDAMB157_BREAST:0; MDAMB436_BREAST:0; HCC1806_BREAST:1; HMC18_BREAST:0; MDAMB468_BREAST:0; DU4475_BREAST:0


title: g1.S33

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S33_XJ3969-2_S11

value: brain


title: g1.S32

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S32_XJ3969-2_S10


title: g1.S35

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S35_XJ3969-2_S13

value: kidney


title: g1.S62

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S62_XJ3969-3_S18

value: BT549_BREAST:0; HDQP1_BREAST:0; JIMT1_BREAST:0; MDAMB157_BREAST:0; MDAMB436_BREAST:0; HCC1806_BREAST:0; HMC18_BREAST:0; MDAMB468_BREAST:1; DU4475_BREAST:0


title: g2.S01

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S01_XJ4276-1_S1

value: group 2 (g2)

value: bone


title: g1.S30

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S30_XJ3969-2_S8


title: g1.S28

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S28_XJ3969-2_S6


title: g1.S29

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S29_XJ3969-2_S7


title: g1.S27

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S27_XJ3969-2_S5


title: g1.S26

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S26_XJ3969-2_S4

value: BT549_BREAST:0; HDQP1_BREAST:0; JIMT1_BREAST:0; MDAMB157_BREAST:0; MDAMB436_BREAST:0; HCC1806_BREAST:0; HMC18_BREAST:0; MDAMB468_BREAST:0; DU4475_BREAST:1


title: g1.S31

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S31_XJ3969-2_S9

value: BT549_BREAST:0; HDQP1_BREAST:0; JIMT1_BREAST:1; MDAMB157_BREAST:0; MDAMB436_BREAST:0; HCC1806_BREAST:0; HMC18_BREAST:0; MDAMB468_BREAST:0; DU4475_BREAST:0


title: g1.S23

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S23_XJ3969-2_S2


title: g1.S22

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S22_XJ3969-2_S1


title: g1.S16

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170315_S16_XJ3969-1_S14


title: g1.S10

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170315_S10_XJ3969-1_S9


title: g1.S14

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170315_S14_XJ3969-1_S12


title: g1.S12

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170315_S12_XJ3969-1_S11


title: g1.S20

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170315_S20_XJ3969-1_S18


title: g1.S06

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170315_S06_XJ3969-1_S6


title: g1.S17

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170315_S17_XJ3969-1_S15


title: g1.S19

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170315_S19_XJ3969-1_S17


title: g1.S11

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170315_S11_XJ3969-1_S10


title: g1.S05

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170315_S05_XJ3969-1_S5


title: g1.S04

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170315_S04_XJ3969-1_S4


title: g1.S02

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170315_S02_XJ3969-1_S2


title: pilot.S70

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160915_70_XJ3334-3_S17

value: pilot


title: g1.S01

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170315_S01_XJ3969-1_S1


title: pilot.S68

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160915_68_XJ3334-3_S15


title: pilot.S69

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160915_69_XJ3334-3_S16


title: pilot.S67

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160915_67_XJ3334-3_S14


title: g1.S03

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170315_S03_XJ3969-1_S3


title: pilot.S65

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160915_65_XJ3334-3_S12

value: MDAMB231_BREAST:0; HCC1954_BREAST:0; BT549_BREAST:0; CAL851_BREAST:1


title: pilot.S62

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160915_62_XJ3334-3_S9

value: MDAMB231_BREAST:0; HCC1954_BREAST:0; BT549_BREAST:1; CAL851_BREAST:0


title: pilot.S63

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160915_63_XJ3334-3_S10


title: g1.S25

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S25_XJ3969-2_S3


title: pilot.S64

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160915_64_XJ3334-3_S11


title: pilot.S66

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160915_66_XJ3334-3_S13


title: pilot.S61

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160915_61_XJ3334-3_S8


title: g1.S09

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170315_S09_XJ3969-1_S8


title: g1.S07

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170315_S07_XJ3969-1_S7


title: pilot.S60

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160915_60_XJ3334-3_S7


title: g1.S18

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170315_S18_XJ3969-1_S16


title: pilot.S59

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160915_59_XJ3334-3_S6


title: pilot.S58

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160915_58_XJ3334-3_S5

value: MDAMB231_BREAST:0; HCC1954_BREAST:1; BT549_BREAST:0; CAL851_BREAST:0


title: pilot.S57

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160915_57_XJ3334-3_S4


title: pilot.S52

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160914_52_XJ3334-2_S16

value: MDAMB231_BREAST:1; HCC1954_BREAST:0; BT549_BREAST:0; CAL851_BREAST:0


title: pilot.S51

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160914_51_XJ3334-2_S15


title: pilot.S43

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160914_43_XJ3334-2_S13


title: pilot.S54

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160915_54_XJ3334-3_S1


title: pilot.S44

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160914_44_XJ3334-2_S14


title: pilot.S39

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160914_39_XJ3334-2_S9


title: pilot.S34

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160914_34_XJ3334-2_S4


title: pilot.S38

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160914_38_XJ3334-2_S8


title: pilot.S36

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160914_36_XJ3334-2_S6


title: pilot.S37

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160914_37_XJ3334-2_S7


title: pilot.S35

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160914_35_XJ3334-2_S5


title: pilot.S31

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160914_31_XJ3334-2_S1


title: pilot.S33

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160914_33_XJ3334-2_S3


title: pilot.S32

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160914_32_XJ3334-2_S2


title: pilot.S06

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160907_6_XJ3334-1_S6


title: pilot.S05

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160907_5_XJ3334-1_S5


title: pilot.S30

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160907_30_XJ3334-1_S16


title: pilot.S53

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160914_53_XJ3334-2_S17


title: pilot.S29

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160907_29_XJ3334-1_S15


title: pilot.S03

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160907_3_XJ3334-1_S3


title: pilot.S28

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160907_28_XJ3334-1_S14


title: pilot.S26

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160907_26_XJ3334-1_S12


title: pilot.S42

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160914_42_XJ3334-2_S12


title: pilot.S55

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160915_55_XJ3334-3_S2


title: pilot.S27

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160907_27_XJ3334-1_S13


title: pilot.S18

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160907_18_XJ3334-1_S10


title: pilot.S17

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160907_17_XJ3334-1_S9


title: pilot.S41

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160914_41_XJ3334-2_S11


title: pilot.S02

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160907_2_XJ3334-1_S2


title: pilot.S16

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160907_16_XJ3334-1_S8


title: pilot.S15

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160907_15_XJ3334-1_S7


title: pilot.S04

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160907_4_XJ3334-1_S4


title: pilot.S25

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160907_25_XJ3334-1_S11


title: MED08A_YBX1_KD_rep2

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

country: Germany

institute: Helmholtz Centre for Infection Research

data_processing:
Read alignment: STAR aligner version 2.7.3a was used to map reads against the reference genome hg38. Only uniquely mapping reads were kept (specific parameters: --trim5p=13, --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.05)
Read counting: Reads were counted using the STAR-integrated method (special parameter during alignment: --quantMode GeneCounts)within annotated exons downloaded from Ensembl Genes V85. Only reads mapping the reverse strand (column 4 of the resulting counts-file) were used for further processing.
Normalization: edgeR version 3.16.5 was used to normalize read counts per sample and genes were filtered for counts-per-million > 1. CDS length from Ensembl Genes V85 was used to calculate FPKM values for filtered genes.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM table

extract_protocol:
RNA was extracted using the RNeasy Mini Kit using Qiagen kit (Catalog no: 74106) folllowing manufacturer's guidelines.
The libraries were prepared using TruSeq Small RNA Sample Prep Kit from Illumina (Catalog no: RS-200-0024) folllowing manufacturer's guidelines.

treatment_protocol: Cells were either infected with non-targeting (NT) control siRNAs or a pool of 30 siRNAs targeting YBX1 purchased from siTOOLs Biotech (50nM final concentration; cells were collected 24h after knockdown).

tag: cell line

tag: cell type

value: Medulloblastoma cell line

tag: sirna

value: YBX1-targeting (YBX1 KD)


title: UW228-3_NT_rep1

value: non-targeting (NT)


title: UW228-3_YBX1_KD_rep1


title: UW228-3_NT_rep2


title: MED08A_YBX1_KD_rep3


title: UW228-3_YBX1_KD_rep3


title: MED08A_NT_rep1


title: DAOY_YBX1_KD_rep3

value: DAOY


title: HEK293_PARCLIP_YBX1_rep1

data_processing:
library strategy: PAR-CLIP
Trimming: Adapter sequences and low quality ends were trimmed using cutadapt (version 1.4.1), keeping all reads longer than 16bp.
Alignment: All remaining reads were aligned againts hg38 genome and CDS database (Ensembl Genes V82) using PARA-suite pipeline (version 1.0.0).
Binding site detection: Only uniquely aligned reads were used for binding site detection using Bmix (version XX) with default parameters.
Annotation: All identified binding sites were annotated using homer annotatePeaks.pl function
Visualization: For visualization, we created a bigwig track using DeepTools (version 2.5.7) with special parameters --binSize 25 and --smoothLength 75
Genome_build: hg38
Supplementary_files_format_and_content: tsv (annotated binding sites)

extract_protocol:
Library was prepared according to Spitzer et al. (PMID 24581442; PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation):
a step-by-step protocol to the transcriptome-wide identification of binding sites of RNA-binding proteins; Methods Enzymology 2014). Antibody: YBX1 (D2A11; Cell Signaling Technology; catolog no. 9744S).

tag: antibody

value: YBX1 (D2A11; Cell Signaling Technology; Cat. no. 9744S)


title: UW228-3_NT_rep3


title: DAOY_YBX1_KD_rep2


title: DAOY_NT_rep1


title: DAOY_NT_rep2


title: DAOY_YBX1_KD_rep1


title: MED08A_NT_rep2


title: SEM_3

city: Boston

first: Henry

last: Long

address: 450 Brookline ave

institute: Dana Farber Cancer Institute

description: Immunoprecipitated DNA

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bw files were generated using MACS2 within the chilin pipeline.
Supplementary_files_format_and_content: bed files

molecule: genomic DNA

source_name: FFPE seminoma

extract_protocol:
FFPE blocks were histologically examined and accordingly sectioned, macrodissected or cored. Samples were deparaffinized, rehydrated and homogenized by heating at 65C in 1% SDS detergent buffer overnight. Next samples were sonicated and solubilized chromatin was immunoprecipitated following a low-input protocol.
Libraries were prepared with Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) or SMARTer® ThruPLEX® DNA-Seq Kit (Takara Bio USA Inc), amplified for 14 cycles.

tag: tissue type

value: testis

tag: biopsy year

tag: storage years

tag: sample collection

value: macrodissection

tag: chip antibody


title: HEK293_PARCLIP_YBX1_rep2


title: SEM_2

description: Immunoprecipitated DNA


title: MED08A_NT_rep3


title: DAOY_NT_rep3


title: UW228-3_YBX1_KD_rep2


title: RT4_OMNI-ATAC

description: Transposed DNA

source_name: bladder cancer cell line

extract_protocol:
OMNI-ATAC protocol was performed on 100000 RT4 cells.
Library was prepared according to OMNI-ATAC protocol and amplified for 11 cycles.

value: bladder cell line


title: lesion from epidemic KS patient c3032

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
c3032a
processed data file: KS_RNAseq.txt

data_processing:
The RNA-seq data was aligned against human (hg19 genome, Ensembl v75 transcriptome) or KSHV (NC_009333.1) genomes and transcriptomes using the bowtie2 algorithm, and RSEM v1.2.31 software was used to estimate read counts and FPKM values at the gene level.
DESeq2 was used for differential expression analysis.
Genome_build: Human: hg19 (GRCh37); KSHV: NC_009333.1
Supplementary_files_format_and_content: KS_RNAseq.txt: Processed data file contains the raw counts for each gene from human and KSHV transcriptome.

source_name: lesion from KS patient

growth_protocol: A 4 mm cylindrical single-use punch was used to collect biopsy samples from a representative KS lesion and a second identical punch biopsy was collected from an uninvolved ipsilateral /contralateral site on the same individual. The collected tissues were treated overnight in RNALater (Ambion) to facilitate subsequent DNA/RNA extraction. RNALater was removed prior to freezing at -80˚C.

extract_protocol:
Genomic RNA was extracted from the homogenized sample with miRNeasy mini kit with on-column DNase I treatment according to the manufacturer’s protocol (Qiagen, Hilden, Germany).
Library preparation was performed using the TruSeq™ RNA Library Prep Kit v2.

treatment_protocol: Fresh frozen biopsies from KS lesions and ipsilateral/contralateral normal sites were homogenized by cryo-cracking (pulverizing) in liquid nitrogen.

tag: diagnosis

value: Kaposi's Sarcoma

tag: origin

value: epidemic

tag: patient

tag: tissue

value: lesion

tag: gender

value: male

tag: hiv

value: yes

tag: batch


title: lesion from epidemic KS patient c3022

description:
c3022a
processed data file: KS_RNAseq.txt


title: lesion from epidemic KS patient 21083

description:
21083a
processed data file: KS_RNAseq.txt


title: pilot.S01

description:
The pilot pool contains MDAMB231_BREAST, HCC1954_BREAST, BT549_BREAST, CAL851_BREAST
20160907_1_XJ3334-1_S1

tag: pool

value: pilot

tag: tissue/cell type

value: brain

tag: cancer cell line composition


title: control skin from epidemic KS patient 21083

description:
21083b
processed data file: KS_RNAseq.txt

source_name: control skin from KS patient

value: control skin


title: MED08A_YBX1_KD_rep1

tag: cell line

tag: cell type

tag: sirna


title: control skin from epidemic KS patient c3022

description:
c3022b
processed data file: KS_RNAseq.txt


title: SEM_1

description: Immunoprecipitated DNA

tag: tissue type

tag: biopsy year


title: MEL_3

description: Immunoprecipitated DNA

source_name: FFPE melanoma

value: skin

tag: storage years

tag: sample collection


title: PNET3

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

source_name: FFPE pancreatic neuroendocrine tumor

extract_protocol:
FFPE blocks were histologically examined and accordingly sectioned, macrodissected or cored. Samples were deparaffinized, rehydrated and homogenized  by heating at 65C in 1% SDS detergent buffer overnight. Next samples were sonicated and solubilized chromatin was immunoprecipitated following a low-input protocol.
Libraries were prepared with Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) or SMARTer® ThruPLEX® DNA-Seq Kit (Takara Bio USA Inc), amplified for 14 cycles.

value: pancreas

tag: chip antibody


title: PNET2


title: MEL_2

description: Immunoprecipitated DNA


title: MEL_1

description: Immunoprecipitated DNA


title: BrCaBM_1

description: Immunoprecipitated DNA

source_name: FFPE breast cancer brain metastasis

value: brain metastasis

value: full section


title: PNET1


title: BlCa_2

description: Immunoprecipitated DNA

source_name: FFPE urothelial cell carcinoma

value: bladder


title: NPC_H3K9me3

city: Cleveland

first: Xiaoxiao

last: Liu

state: Ohio

address: 10900 Euclid Ave

department: Genetics and Genomes Sciences

institute: Case Western Reserve University

data_processing:
The paired-end Hi-C reads were mapped to human genome hg19 using BOWTIE. Only first 36 bases were used for mapping when reads is longer. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed. Easy Hi-C reads were mapped to hg19 using BOWTIE. Because nearly all the mappable reads start with HindIII sequence AGCTT, we trimmed the first 5 bases from every read, took the next 36 bases, and added the 6-base sequence AAGCTT to the 5’ of every read before mapping using the whole 42 bases.
For Hi-C, we focus on cis-interactions and therefore only kept Hi-C paired-end reads which both ends are mapped to the same chromosome. Out of all the intra-chromosome paired-end reads, we also discard the reads with both ends mapped to the same HindIII fragments. Since cut-and-ligation events are expected to generate reads within 500bp upstream of HindIII cutting sites due to the size selection (“+” strand reads should be within 500bp upstream of a HindIII site, and “-“ strand reads should be within 500bp downstream a HindIII site), we only keep reads pairs with both ends satisfying this criteria. For eHi-C library, the only type of invalid cis- pairs are self-circles with two ends within the same HindIII fragment facing each other
We next split all these reads into three classes based on their strand orientations (“same-strand”, “inward”, or “outward”), and generated the resulting lists of fragment pairs (with Hi-C read counts) from each class of reads.
There are total ~840k fragments in human genome. They are assembled into ~335k anchors after short fragments (<5kb) are merged into neighboring anchors. For every anchor, we first count Hi-C/eHi-C reads from the anchor to every fragment within 2Mb range.
We estimated a background frequency between any two fragments based on the average reads count of all fragment pairs that have similar lengths, similar gap distance, GC content, and visibility. The fragment-to-fragment data can be then converted to anchor-to-anchor data by adding the read counts and background frequencies together based on the assignment of fragments to anchors. P values of the enrichment of Hi-C reads over the background frequency can be calculated using a negative binomial model. The statistical method has been described in previous publication (Jin, F. et al. Nature 2013, 503:290-294)
Genome_build: hg19
Supplementary_files_format_and_content: For each Hi-C and easy Hi-C data set, the fragment-to-fragment frequency are provided in the txt file (columns 3 to 5: observed_reads, expected_reads, and p_value). For each Chip-Seq replicate, peak-calling results are provided in the bed file.

source_name: neural progenitor cells

growth_protocol: Fibroblasts were grown in DMEM medium supplemented with 10% FBS (Hyclone), Glutamax (Thermo Fisher Scientific) and NEAA (Thermo Fisher Scientific) and subcultured at a ratio of 1:3 when they reach 90% confluence. H1 cells were cultured on the hESC-qualified Matrigel (Corning, #354277) coated plates in mTeSR1 medium (StemCell Technologies, #05850). iPS cells were cultured on Matrigel with a daily change of E8 medium and passaged by collagenase. To generate iPSC-derived NPCs, detached iPSC colonies were suspended in embryoid body (EB) medium (DMEM:F12 with 20% KOSR, 2?M dorsomorphin and 2 ?M A 83-01) for 7 days. Floating EBs were attached on Matrigel and cultured in NPC medium (DMEM/F12, N2 supplement, NEAA and 2 uM cyclopamine). After 14 days, neural tube-like rosettes were mechanically picked and dissociated into single NPCs by Accutase. NPCs were maintained as monolayer in NPC medium with medium change every two days. For neuronal differentiation, NPCs were plated on Matrigel and cultured in Neurobasal medium supplemented with 2%B27, 2 mM L-glutamine, 10 ng/ml BDNF and 10 ng/ml GDNF.

extract_protocol:
For Hi-C, nuclei were extraced after fixing using a cell lysis buffer. For ChIP-seq, nuclei were extracted and chromatins were fragmented by sonication. The TF/histone-DNA complexes were isolated by antibody.
All Hi-C libraries were constructed following illumina insctructions accompanying Truseq sample preparation kit.  Random indexes were introduced for eHi-C libraries to remove PCR duplication. Generally, PCR amplification was done with 7-9 cycles. All ChIP-seq libraries were generated following a ChIPmentation protocol with Nextera adapters.

tag: treatment

value: induced from hIPS

value: H3K9me3 (Abcam,ab8898)


title: NPC_H3K4me3

value: H3K4me3 (Abcam, ab8580)


title: SN28: Substantia Nigra parkinson's disease

city: Jerusalem

first: Hermona

last: Soreq

address: The Edmond J. Safra Campus, Givat Ram

department: Department of Biological Chemistry

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
bcl2fastq
adapter trimmimg and sample splitting
rRNA-depletion using bowtie2
alignment using STAR
read count using htseq
Genome_build: hg19
Supplementary_files_format_and_content: raw counts of sequencing reads

source_name: Substantia Nigra parkinson's disease

extract_protocol:
miRNeasy kit QIAGEN
Stranded ligation-based libraries were prepared using a modified protocol from (Engreitz et al., 2013)

tag: diagnosis

value: Parkinson's disease

value: substantia nigra (SN)


title: SN26: Substantia Nigra parkinson's disease

tag: tissue


title: SN22: Substantia Nigra parkinson's disease


title: SN23: Substantia Nigra parkinson's disease


title: NPC_H3K27me3


title: SN20: Substantia Nigra parkinson's disease


title: NPC_H3K36me3

value: H3K36me3 (Abcam, ab9050)


title: SN15: Substantia Nigra parkinson's disease


title: NPC_CTCF

value: CTCF (Abcam, ab70303)


title: SN18: Substantia Nigra parkinson's disease


title: Neuron_H3K9me3

source_name: neuron cells

value: induced from hNPC which is induced from hIPS


title: SN12: Substantia Nigra parkinson's disease


title: control skin from epidemic KS patient c3032

description:
c3032b
processed data file: KS_RNAseq.txt

value: Kaposi's Sarcoma

tag: origin

value: epidemic

tag: patient

tag: gender

value: male

value: yes


title: Neuron_H3K36me3


title: Neuron_H3K4me3


title: SN21: Substantia Nigra parkinson's disease


title: Neuron_H3K27me3


title: Neuron_H3K27AC

value: H3k27Ac (Abcam, ab4729)


title: SN11: Substantia Nigra parkinson's disease


title: SN10: Substantia Nigra parkinson's disease


title: Neuron_CTCF


title: iPS_H3K9me3

source_name: induced pluripotent stem cells

value: no treat


title: SN8: Substantia Nigra parkinson's disease


title: iPS_H3K36me3


title: iPS_H3K4me3


title: SN7: Substantia Nigra parkinson's disease


title: NPC_H3K27AC


title: SN3: Substantia Nigra parkinson's disease


title: SN29: Substantia Nigra control

source_name: Substantia Nigra control

value: Control


title: iPS_H3K27ac


title: SN27: Substantia Nigra control


title: iPS_H3K27me3


title: iPS_CTCF


title: Hi-C Neuron

description: eHi-C

tag: restriction enzyme

value: HindIII


title: Hi-C IPS

description: eHi-C


title: SN5: Substantia Nigra control


title: SN14: Substantia Nigra control


title: SN25: Substantia Nigra control


title: SN6: Substantia Nigra control


title: MTG23: MTG parkinson's disease

source_name: MTG parkinson's disease

value: medil temporal gyrus (MTG)


title: Hi-C NPC

description: eHi-C

value: induced from hIPS


title: SN24: Substantia Nigra control


title: Thymic epithelial INS2hi

city: Montreal

first: Marie

last: Coutelier

address: 845 Rue Sherbrooke Ouest

country: Canada

institute: McGill University

data_processing:
Cellranger was used to align the reads to an adapted mm10 reference including the transgene (Cellranger v3.0.1)
Seurat was used to filter cells based on QC metrics, scale and normalize data, apply PCA and UMAP (Seurat v2.3)
Genome_build: mm10
Supplementary_files_format_and_content: tsv files containing the barcodes output by Cellranger
Supplementary_files_format_and_content: tsv files containing the genes output by Cellranger
Supplementary_files_format_and_content: matrix output by Cellranger
Supplementary_files_format_and_content: tsv files containing the cells metadata, together with transgene, Crp and Ins2 log-normalized counts; and labels attached to them with gene markers described in the paper

organism: Mus musculus

source_name: Thymus

extract_protocol:
For isolation of the thymic epithelial cells, the thymus was first cut in small pieces and pipetted up and down with a wide bore 1000 ul tip until cell release was no longer detectable. The remaining tissue was digested in RPMI media supplemented with 10% FBS, 10 mM HEPES, 0.25 mg/ml papain, 0.25 mg/ml collagenase D, 0.1 mg/ml DNase for 15 min at 37ºC. The TEC were then enriched using EpCAM magnetic microbeads (Miltenyi Biotec) and sorted using a BD FACS Aria III with an 85 uM nozzel.
Thymic epithelial cells (CD45-EpCAM+) were sorted from CRP, CRPlo and INS2 Tg mice, and a 10X Genomics Single-Cell 3' transcriptome library was prepared (Génome Québec). The libraries were sequenced using the Illumina HiSeq4000 PE100

value: Thymic epithelial cells

tag: gating strategy

value: gated on EpCAM+CD45-


title: SN13: Substantia Nigra control


title: Thymic epithelial CRPlo


title: SN2: Substantia Nigra control


title: SN4: Substantia Nigra control


title: Thymic epithelial CRPhi


title: MTG22: MTG parkinson's disease

value: Parkinson's disease


title: MTG21: MTG parkinson's disease


title: SN9: Substantia Nigra parkinson's disease

value: substantia nigra (SN)


title: MTG20: MTG parkinson's disease


title: NPC-3 RNA-Seq

data_processing:
The paired-end Hi-C reads were mapped to human genome hg19 using BOWTIE. Only first 36 bases were used for mapping when reads is longer. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed. Easy Hi-C reads were mapped to hg19 using BOWTIE. Because nearly all the mappable reads start with HindIII sequence AGCTT, we trimmed the first 5 bases from every read, took the next 36 bases, and added the 6-base sequence AAGCTT to the 5’ of every read before mapping using the whole 42 bases.
For Hi-C, we focus on cis-interactions and therefore only kept Hi-C paired-end reads which both ends are mapped to the same chromosome. Out of all the intra-chromosome paired-end reads, we also discard the reads with both ends mapped to the same HindIII fragments. Since cut-and-ligation events are expected to generate reads within 500bp upstream of HindIII cutting sites due to the size selection (“+” strand reads should be within 500bp upstream of a HindIII site, and “-“ strand reads should be within 500bp downstream a HindIII site), we only keep reads pairs with both ends satisfying this criteria. For eHi-C library, the only type of invalid cis- pairs are self-circles with two ends within the same HindIII fragment facing each other
We next split all these reads into three classes based on their strand orientations (“same-strand”, “inward”, or “outward”), and generated the resulting lists of fragment pairs (with Hi-C read counts) from each class of reads.
There are total ~840k fragments in human genome. They are assembled into ~335k anchors after short fragments (<5kb) are merged into neighboring anchors. For every anchor, we first count Hi-C/eHi-C reads from the anchor to every fragment within 2Mb range.
We estimated a background frequency between any two fragments based on the average reads count of all fragment pairs that have similar lengths, similar gap distance, GC content, and visibility. The fragment-to-fragment data can be then converted to anchor-to-anchor data by adding the read counts and background frequencies together based on the assignment of fragments to anchors. P values of the enrichment of Hi-C reads over the background frequency can be calculated using a negative binomial model. The statistical method has been described in previous publication (Jin, F. et al. Nature 2013, 503:290-294)
For RNAseq, basecalls/demultiplexing performed using Illumina CASAVA 1.8.2. Reads were aligned to Hg38 using STAR2.4.0. Read counting was done using HT-seq0.6.1 with Hg38 RefSeq as reference. Low count genes were filtered. Normalization by TMM. Differential expression analysis was done using EdgeR.
Genome_build: hg19
Supplementary_files_format_and_content: For each Hi-C and easy Hi-C data set, the fragment-to-fragment frequency are provided in the txt file. For each Chip-Seq replicate, peak-calling results are provided in the bed file.

source_name: Neural progenitor cells

extract_protocol:
For Hi-C, nuclei were extraced after fixing using a cell lysis buffer. For ChIP-seq, nuclei were extracted and chromatins were fragmented by sonication. The TF/histone-DNA complexes were isolated by antibody.     Total RNA was isolated from samples by RNeasy Mini Kit (Qiagen) according to the manufacturer?s instructions.
For eHi-C, briefly, the cells and tissues were first fixed with 1% formaldehyde and then quenched with 150mM glycine. The fixed samples were lysed using a cell lysis buffer or a tissue specific buffer. And nuclei were isolated and then digested with HindIII. After that, in situ proximity ligation was done by  ligating the digested chromatin in a large volume. Ligation products were then reverse-linked with proteinase K and purified using phenol-chloroform. The purified DNA was then digested with DpnII and then self ligated using T4 DNA ligase. After purification, the DNA products were then re-linearized with HindIII followed by DNA purification. The resulting DNA were used for library construction. First, the DNA were end-repaired using End-it kit (Epicentre). Second, the end repaired DNA was A-tailed by Klenow fragment (3??5? exo?; NEB). Then, a customized Illumina truseq Adapter was ligated and the resulting DNA was then PCR amplified. The final libraries were quantified and sequenced on Illumina Hiseq platform.
All Hi-C libraries were constructed following illumina insctructions accompanying Truseq sample preparation kit.  Random indexes were introduced for eHi-C libraries to remove PCR duplication. Generally, PCR amplification was done with 7-9 cycles. All ChIP-seq libraries were generated following a ChIPmentation protocol with Nextera adapters.

value: iPSC-derived neural progenitor cells


title: MTG19: MTG parkinson's disease


title: NPC-2 RNA-Seq


title: NPC-1 RNA-Seq


title: Neuron-3 RNA-Seq

source_name: Neurons

value: iPSC-derived neurons


title: MTG18: MTG parkinson's disease


title: MTG17: MTG parkinson's disease


title: MTG16: MTG parkinson's disease


title: Neuron-1 RNA-Seq


title: Neuron-2 RNA-Seq


title: MTG15: MTG parkinson's disease


title: iPSC-3 RNA-Seq

source_name: Induced pluripotent stem cells

value: Induced pluripotent stem cells derived from CCD-1079Sk fibroblasts


title: iPSC-2 RNA-Seq


title: MTG13: MTG parkinson's disease


title: MTG11: MTG parkinson's disease


title: Fibroblast-3 RNA-Seq

source_name: Fibroblasts

value: CCD-1079Sk newborn foreskin fibroblasts


title: MTG14: MTG parkinson's disease


title: iPSC-1 RNA-Seq


title: MTG12: MTG parkinson's disease


title: MTG9: MTG control

source_name: MTG control


title: Fibroblast-2 RNA-Seq


title: Fibroblast-1 RNA-Seq


title: MTG8: MTG control


title: MTG7: MTG control


title: MTG6: MTG control


title: MTG5: MTG control


title: MTG4: MTG control


title: Patient 7, normal tissue

type: RNA

city: Cologne

first: Christoph

last: Arolt

address: Kerpener Strasse 62

department: Institute of Pathology

institute: University of Cologne

description:
selected RNA, probe-based (Nanostring PanCancer Pathways Panel)
Nanostring pan Cancer Pathways Panel

hyb_protocol: The nCounter Nanostring analysis was carried out with 150 ng RNA according to the manufacturer’s instructions. The PanCancer Pathways Panel (Nanostring, Seattle, WA, USA) was used following the manufacturer´s recommendations. In brief, the RNA was denatured at 85 °C, followed by incubation with both probes (reporter and capture probe) for 12 hours at 65 °C.

scan_protocol: The barcoded hybrids were purified with the Prepstation platform and quantified using the Digital Analyzer (both Nanostring, Seattle, WA, USA).

data_processing: Raw expression counts of tumor samples and normal tissue were imported into the nSolver 4.0 Software (Nanostring, Seattle, WA, USA) for quality control and normalization procedures. Normalization was done using the geometric mean of the CodeSet Content housekeeping genes and positive controls. Background noise threshold was set to the maximum of all negative controls. All values below a background noise threshold were floored to this value.

label: reporter and capture probe

source_name: primary salivary gland carcinoma

label_protocol: not applicable

extract_protocol: Tumor areas with at least 70% tumor cell count as well as corresponding normal tissue were marked on H&E slides. After scraping off the respective tissue of the FFPE blocks, RNA isolation was carried out using the RNA FFPE kit from Promega on the Maxwell® 16 LEV (Promega AS1260, Heidelberg) according to the manufacturer’s instructions. RNA concentrations were quantified by the QuantiFluor® RNA System as recommended by the supplier (Promega, E6090) and adjusted to 30 ng / µl.

value: normal salivary gland tissue

tag: patient diagnosis

value: salivary gland carcinomas

tag: histology

value: mucoepidermoid carcinoma


title: Patient 8, normal tissue


title: Patient 5, tumor tissue

value: salivary gland carcinoma

value: adenoid cystic carcinoma


title: Patient 5, normal tissue


title: amy23: Amygdala parkinson's disease

source_name: Amygdala parkinson's disease

value: amygdala (AMG)


title: MTG3: MTG control

value: Control


title: Patient 58, tumor tissue


title: Patient 7, tumor tissue


title: Patient 58, normal tissue


title: P-269_biopsy1

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in BeadStudio 3.1.3.0

label: biotin

source_name: Cervical tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: 1-4 tumor biopsies were collected from each patient at the time of diagnosis

extract_protocol: RNA was extracted with Trizol reagent, followed by double precipitation with isopropanol and final precipitation with 5M lithium chloride, or using the miRNeasy mini kit. RNA from different biopsies of the same tumor was pooled, or analyzed separately. Quality control was performed with the Agilent Bioanalyzer.

treatment_protocol: The biopsies were immediately snap-frozen in liquid nitrogen and stored at -80 C until used for analysis.

value: Squamous cell carcinoma

tag: gene-based hypoxia

value: More hypoxic

tag: imaging-based hypoxia

value: Less hypoxic

tag: combined hypoxia biomarker

tag: figo stage

tag: rna isolation method

value: miRNeasy

tag: biopsy

value: Single biopsy


title: P-269_biopsy2


title: P-201_biopsy3


title: P-201_biopsy2


title: P-266_biopsy3


title: P-266_biopsy2


title: P-119_biopsy4


title: Patient 8, tumor tissue


title: MTG1: MTG control

value: medil temporal gyrus (MTG)


title: P-201_biopsy1


title: Patient 57, tumor tissue

value: salivary duct carcinoma


title: amy22: Amygdala parkinson's disease

value: Parkinson's disease


title: P-266_biopsy1


title: P-119_biopsy1


title: P-088_biopsy2


title: amy21: Amygdala parkinson's disease


title: Patient 57, normal tissue


title: P-088_biopsy1


title: amy20: Amygdala parkinson's disease


title: P-119_biopsy3


title: amy19: Amygdala parkinson's disease


title: amy18: Amygdala parkinson's disease


title: Patient 56, tumor tissue


title: P-072_biopsy2

value: Trizol


title: P-072_biopsy1


title: Patient 56, normal tissue


title: Patient 55, normal tissue


title: Patient 55, tumor tissue


title: amy17: Amygdala parkinson's disease


title: 180502-68

city: Brussels

first: Grégoire

last: de Streel

state: Woluwe-Saint-Lambert

address: 75 Avenue Hippocrate

department: de Duve Institute

country: Belgium

institute: UCLOUVAIN

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to GRCm38 genome using STAR-2.5.3a aligner
Bam files were sorted with Samtools 1.6
Gene counts were obtained using HTSeq 0.9.1 htseq-count with union mode
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CT26 tumor bearing mice

extract_protocol:
Tumor fragments were collected and stored at -80°C until processing. After tissue disruption with the Tissue Lyser (Quiagen), total RNA was extracted using Nucleospin Mini Columns (Macherey Nagel).
Library construction were done by Macrogen following their internal pipeline - Illumina TruSeq Stranded mRNA

treatment_protocol: On days 6, 9 and 12 after tumor implentation, mice received intraperitoneal (i.p.) injections of the following mAbs, administered alone or combined : isotype control (motavizumab), anti-GARP:TGF-β1 (clone 58A2, mIgG2a WT or FcD), anti-PD-1 (FcSilent), or anti-TGF-β (clone 1D11)

value: CT26 tumor

tag: tag

value: anti-TGFb + anti-PD1 FcS


title: Patient 54, tumor tissue

value: salivary gland carcinomas


title: 180502-80

value: anti-GARP:TGFb FcD + anti-PD1 FcS


title: 180502-62


title: 180502-53


title: 180502-66


title: P-044_biopsy1

value: Adenocarcinom


title: P-052_biopsy1


title: P-044_biopsy2


title: P-005_biopsy4


title: P-005_biopsy3


title: P-005_biopsy2


title: Patient 54, normal tissue

value: normal salivary gland tissue

value: mucoepidermoid carcinoma


title: P-052_biopsy2


title: amy16: Amygdala parkinson's disease

value: amygdala (AMG)


title: 180502-71


title: amy15: Amygdala parkinson's disease


title: 180502-60


title: 180502-50


title: amy14: Amygdala parkinson's disease


title: 180502-57


title: 180502-44


title: amy13: Amygdala parkinson's disease


title: 180502-77

value: anti-GARP:TGFb WT + anti-PD1 FcS


title: Patient 53, normal tissue

value: adenoid cystic carcinoma


title: Patient 53, tumor tissue

value: salivary gland carcinoma


title: 180502-64


title: amy12: Amygdala parkinson's disease


title: Patient 50, tumor tissue


title: amy11: Amygdala parkinson's disease


title: P-119_biopsy2

value: Squamous cell carcinoma

value: Less hypoxic

value: miRNeasy


title: P-005_biopsy1

value: Single biopsy


title: 180502-75

value: anti-GARP:TGFb FcD


title: 180502-45


title: 180502-55


title: 180502-70


title: 180502-61


title: amy10: Amygdala parkinson's disease

value: Parkinson's disease


title: 180502-58

value: CT26 tumor


title: 180502-41


title: Patient 50, normal tissue


title: Patient 4, tumor tissue


title: amy9: Amygdala parkinson's disease


title: 180502-73

value: anti-GARP:TGFb WT


title: amy8: Amygdala control

source_name: Amygdala control

value: Control


title: 180502-65


title: 180502-56


title: 180502-69


title: amy7: Amygdala control


title: Patient 4, normal tissue

value: salivary gland carcinomas


title: Patient 46, tumor tissue

value: salivary duct carcinoma


title: Patient 46, normal tissue

value: normal salivary gland tissue


title: amy6: Amygdala control


title: 180502-79

value: anti-TGFb


title: 180502-72


title: 180502-42


title: Patient 44, tumor tissue


title: amy5: Amygdala control

value: amygdala (AMG)


title: Patient 44, normal tissue


title: 180502-59


title: amy4: Amygdala control


title: 180502-43


title: 180502-76

value: anti-PD1 FcS


title: amy3: Amygdala control


title: Patient 43, tumor tissue

value: adenoid cystic carcinoma


title: 180502-49


title: WT-mESC-chase-0

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

country: China

institute: Institute of Biophysics, CAS

description: Enrich EdU-labeled DNA, add hairpin, and BS-seq

data_processing:
Basecalls performed by Annoroad Gene Technology Co. Ltd.
Raw reads from Illumina platforms were processed by HBS-Tools. In brief, preprocessing of raw reads, including bad quality bases trimming, sequencing adaptor, and hairpin adaptor removal were performed with the module of ‘hbs_process’. And then each preprocessed read pair was aligned pairwise using Smith-Waterman algorithm and only aligned parts were kept to recover the original genomic sequence. The recovered original sequences were then mapped to the genome assembly, with which the methylation information was extracted into the result SAM output. The original sequence recovery and mapping was performed with the module ‘hbs_mapper’ of HBS-Tools.  The aligned SAM files, that contain both strands of the hairpin read, were then de-duplicated based on the following criteria: the two strands were firstly concatenated with the one with higher-methylation as head and the lower as tail, and strand pairs with the same concatenated sequence were regarded as duplication and only one copy was retained.  Based on the de-duplicated aligned reads (in SAM file), reads of each pair were discriminated as parent (higher) or daughter (lower) strand according to the No. of methylated CpGs, with equally methylated reads randomly distributed to parent or daughter. Read pairs with no methylated CpGs on both strands were discarded. Then, methylation maintenance events were called based on parent/daughter read pairs, among which maintained methylation, un-maintained methylation, maintained un-methylation and de novo methylation were designated as MM, MU, UU, UM, respectively. All events were summed up for each genomic CpG site by chromosome coordinates, so now we have 4 numbers indicating 4 kinds of events of MM/MU/UU/UM for each CpG site.
Genome_build: hg19
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are provided as gzipped text files, that contain methylation mainenance events called for covered CpG sites. All events were summed up for each genomic CpG site by chromosome coordinates, so we have 4 numbers indicating 4 kinds of events of MM/MU/UU/UM for each CpG site. Maintenance events are also asigned into individual arm of the replication fork. Upper arm indicates parental Waston and daughter Crick strand, and lower arm indicates parental Crick and daughter Watson strand. All coloumns are indicated by the first row of the files.

source_name: EdU labeled WT mouse ES cells with chasing 0 min

growth_protocol:
HeLa-S3 Cells were cultured at 37 °C with 5% CO2. Culture medium contains DMEM High Glucose (HyClone, SH30022), 10% FBS (BI, 04-010-1ACS) and 1X Penicillin-Streptomycin (Gibco, 15140122). Cells were passed every two days. Detached from plates with 0.25% Trypsin at 37 °C for 2 to 3 min. The sub-cultivation is about 1:5 to 1:6.
Mouse embryonic stem cells were cultured on gelatin coated dishes in ES culture medium containing DMEM (ThermoFisher 11995), supplemented with 15% fetal bovine serum (Hyclone 30070.03), 1% None essential amino acids (Merck M7145), 1% L-glutamine (BBI Life Sciences E607004), 0.1% β-mercaptoethanol (Gibco 21985023), 0.01 % LIF (107 U/ml), and 1% Penicillin-Streptomycin (Gibco, 15140122).

extract_protocol:
Harvest cells and extract DNA with phenol-chloroform.
Fragment DNA with sonication (Covaris M200) or restrictive enzyme AluI (NEB, R0137). Size select DNA fragments ranging from 100 bp to 200 bp with AMPure beads (1.05X to 2.8X) (Beckman, A63881). Click it reaction to conjugate biotin to EdU labeled DNA: (Tris pH7.5 buffer 15 mM; Biotin azide (Sigma, 762024) 400 uM; CuSO4 (Sigma, 209198)/THPTA (Sigma, 762342) mix (1:5) (100 uM: 500 uM); Sodium ascorbate (freshly prepared, Sigma, A4034) 5 mM). Reaction at 34 °C for 20 min. DNA was purified with MinElute PCR purification kit (Qiagen, 28004). The click it reaction system is modified from (1) (2). End repair (NEB, E6050), dA-tailing (NEB, E6053) and adaptor ligation (NEB, E6056). Hairpin adapter and methylated sequencing adapter were pre-mix at the molar ratio of 3:1 before adapter ligation. After ligation, 1.4X AMPure beads were added to remove un-ligated adapters. Dissolve adapter ligated DNA in 1X TE buffer. Incubate DNA with M280 streptavidin beads (Thermo Fisher, 11205D) in 1X Binding & Washing buffer (5 mM Tris-Cl (pH 7.5), 1M NaCl, 0.5 mM EDTA (pH 8.0)) for 20 min. Wash with 1X Binding & Washing buffer containing 0.5% IGEPAL CA-630 (Sigma, I3021) for 6 times, and then wash with ddH2O once. Dissolve beads in 40 ul ddH2O. Perform bisulfite conversion (Qiagen, 59104) with DNA on beads. PCR amplification (KAPA KR0413) with bisulfite converted DNA. PCR product was running on a 2% agarose-gel and the larger band ranging from 300 bp to 400 bp was hairpin-ligated sample. Recover this band with gel-extraction kit (TIANGEN, DP208). Clean up with AMPure beads (0.9X). Dissolve DNA in 0.1X TE buffer. The HAMMER-seq library is ready for Next Generation Sequencing.

treatment_protocol: HeLa-S3 cells were synchronized at G1/S entrance with thymidine/aphidicolin double block (2 mM thymidine (Sigma, T1895) for 18 h; remove thymidine and continue to culture for 9 h; 1ug/ml aphidicolin (Abcam, 38966-21-1) for another 14 h). Remove aphidicolin. Pulse labeling with 20 uM EdU (Thermo Fisher, E10187) for 4 min. Remove EdU and chase with 20 uM thymidine for a series of desired time length (0 min to 24 h).

tag: strain background

tag: cell line

value: WT R1 mES Cell line (ATCC SCRC-1011)

tag: cell type

value: embryonic stem cell

tag: genotype/variation

value: WT

value: inner cell mass

tag: developmental stage

value: embryo, blastocyst


title: amy2: Amygdala control

tag: diagnosis

tag: tissue


title: 180502-52


title: 180502-54


title: amy1: Amygdala control


title: Patient 43, normal tissue


title: FFPE_input

description: Input DNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to mm9 using BWA.
For peak calling MACS2 was used.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline.
Supplementary_files_format_and_content: bed files

source_name: FFPE normal mouse liver

extract_protocol:
FFPE block was histologically examined and sectioned. Sample was deparaffinized, rehydrated and homogenized  by heating at 65C in 1% SDS detergent buffer overnight. Next sample was sonicated for 5 minutes and an aliquot of solubilized chromatin (2.5% of the sample) was used to prepare input DNA by reverse cross-link overnight at 65C with proteinase K.
Libraries were prepared with Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) or SMARTer® ThruPLEX® DNA-Seq Kit (Takara Bio USA Inc).

value: liver

tag: sample collection

value: full section

tag: chip antibody


title: Patient 42, tumor tissue

value: salivary gland carcinoma

tag: patient diagnosis

tag: histology


title: 180502-47

value: CT26 tumor


title: Patient 42, normal tissue


title: Patient 41, tumor tissue

value: mucoepidermoid carcinoma


title: FiTAc-seq_80°C_40min

description: Immunoprecipitated DNA

extract_protocol:
FFPE blocks were histologically examined and sectioned. Samples were deparaffinized, rehydrated and homogenized by heating at 50C, 65C or 80C in 1% SDS detergent buffer overnight. Next samples were sonicated for either 5 or 40 minutes and solubilized chromatin was immunoprecipitated following a low-input protocol. The optimal condition (65C and 5 minute sonication) was done in replicate.
Libraries were prepared with Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) or SMARTer® ThruPLEX® DNA-Seq Kit (Takara Bio USA Inc).


title: 180502-48


title: Patient 41, normal tissue

value: salivary gland carcinomas


title: WT-mESC-chase-2h

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
mESC-J1-2hC-0518_L1_A028

data_processing:
Basecalls performed by Annoroad Gene Technology Co. Ltd.
Raw reads from Illumina platforms were processed by HBS-Tools. In brief, preprocessing of raw reads, including bad quality bases trimming, sequencing adaptor, and hairpin adaptor removal were performed with the module of ‘hbs_process’. And then each preprocessed read pair was aligned pairwise using Smith-Waterman algorithm and only aligned parts were kept to recover the original genomic sequence. The recovered original sequences were then mapped to the genome assembly, with which the methylation information was extracted into the result SAM output. The original sequence recovery and mapping was performed with the module ‘hbs_mapper’ of HBS-Tools.  The aligned SAM files, that contain both strands of the hairpin read, were then de-duplicated based on the following criteria: the two strands were firstly concatenated with the one with higher-methylation as head and the lower as tail, and strand pairs with the same concatenated sequence were regarded as duplication and only one copy was retained.  Based on the de-duplicated aligned reads (in SAM file), reads of each pair were discriminated as parent (higher) or daughter (lower) strand according to the No. of methylated CpGs, with equally methylated reads randomly distributed to parent or daughter. Read pairs with no methylated CpGs on both strands were discarded. Then, methylation maintenance events were called based on parent/daughter read pairs, among which maintained methylation, un-maintained methylation, maintained un-methylation and de novo methylation were designated as MM, MU, UU, UM, respectively. All events were summed up for each genomic CpG site by chromosome coordinates, so now we have 4 numbers indicating 4 kinds of events of MM/MU/UU/UM for each CpG site.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: Processed data files are provided as gzipped text files, that contain methylation mainenance events called for covered CpG sites. All events were summed up for each genomic CpG site by chromosome coordinates, so we have 4 numbers indicating 4 kinds of events of MM/MU/UU/UM for each CpG site. Maintenance events are also asigned into individual arm of the replication fork. Upper arm indicates parental Waston and daughter Crick strand, and lower arm indicates parental Crick and daughter Watson strand. All coloumns are indicated by the first row of the files.

source_name: EdU labeled WT mouse ES cells with chasing 2 hours

growth_protocol:
HeLa-S3 Cells were cultured at 37 °C with 5% CO2. Culture medium contains DMEM High Glucose (HyClone, SH30022), 10% FBS (BI, 04-010-1ACS) and 1X Penicillin-Streptomycin (Gibco, 15140122). Cells were passed every two days. Detached from plates with 0.25% Trypsin at 37 °C for 2 to 3 min. The sub-cultivation is about 1:5 to 1:6.
Mouse embryonic stem cells were cultured on gelatin coated dishes in ES culture medium containing DMEM (ThermoFisher 11995), supplemented with 15% fetal bovine serum (Hyclone 30070.03), 1% None essential amino acids (Merck􀀂M7145), 1% L-glutamine (BBI Life Sciences􀀂E607004), 0.1% β-mercaptoethanol (Gibco 21985023), 0.01 % LIF (107 U/ml), and 1% Penicillin-Streptomycin (Gibco, 15140122).


title: FiTAc-seq_65°C_40min

description: Immunoprecipitated DNA


title: GFP_A

city: Tallahassee

first: Nicholas

middle: James

last: Waddell

state: FL

address: 319 Stadium Dr

department: Biological Sciences

institute: Florida State University

data_processing:
Base-calling was performed by RTA3.  Resulting sequencing reads were demultiplexed using bcl2fastq_v1.8.4.
Sequencing Reads were processed with trim_galore v0.4.4 to remove low-quality base-calls, adapter contamination in reads, and 5' sequence composition bias. Read length limit was 20bp, quality score limit was 20 (phread score).
Processed reads were aligned to the GRCm38 genome using STAR v2.7.0 using default parameters.
Aligned reads were assigned to gene features using featureCounts v1.5.0-p3 counting on the meta-feature level.  Multi-mapping reads and multi-overlapping reads were ignored.
Differential gene expression was calculated using EdgeR v3.20.9.  Genes passed filtering criteria if at least 3 samples had at minimum .5 counts per million.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Unnormalized gene count files.  Last column is the unnormalized gene count information, the remaining columns contain information about the genes.

source_name: Brain

growth_protocol: Adult 8 weeks old male mice were purchased from Jackson Lab and housed on a reverse 12-hour light/dark cycle with food and water available ad libitum.

extract_protocol:
Total RNA was extracted from frozen NAc tissue by homogenization in Trizol (Ambion Carlsbad, CA) according to manufacturer’s protocol. RNA was then DNase-treated and column-purified using the Zymo RNA Clean and Concentrate Kit (Zymo Research, Irvine, CA).  RNA was quantified using the NanoDrop Spectrophotometer (Thermo Scientific, Waltham, MA), and the RNA integrity number (RIN) of isolated total RNA was assessed for each individual HSV-treated sample using an Agilent RNA 6000 Nano Kit on an Agilent 2100 Bioanalyzer instrument (Agilent, Santa Clara, CA).
100 ng of total RNA was applied to the NEBNext® rRNA Depletion Kit (New England Biolabs, Inc., Ipswich, MA) to remove ribosomal RNAs (rRNAs) according to manufacturer’s protocol. The resulting rRNA-depleted samples were then used to generate RNA sequencing libraries by using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, Inc., Ipswich, MA). Briefly, RNA samples were fragmented, and cDNA was synthesized from the first and second strands, consecutively. The ends of the libraries were ligated to universal Illumina adaptors included in the kit. RNA-seq libraries were individually indexed with NEBNext® Multiplex Oligos for Illumina (New England Biolabs, Inc., Ipswich, MA) and amplified through 12 cycles of PCR amplification.

treatment_protocol: Each sample received a mico-injection of Gas5-EGFP or EGFP alone delivered via Herpes-simplex viral p1005+ vector

tag: strain

value: Nucleus Accumbens

tag: Sex

value: Male


title: GFP_C


title: 180502-74

value: mIgG2a - Isotype control


title: Patient 40, tumor tissue

value: salivary duct carcinoma


title: 180502-67

value: anti-PD1 FcS


title: Gas5_C


title: 180502-63


title: Gas5_B


title: Patient 3, tumor tissue


title: FiTAc-seq_65°C_5min_rep1

description: Immunoprecipitated DNA


title: FiTAc-seq_50°C_40min

description: Immunoprecipitated DNA


title: 180502-78


title: Gas5_A


title: GFP_B


title: FiTAc-seq_50°C_5min

description: Immunoprecipitated DNA


title: Patient 3, normal tissue

value: normal salivary gland tissue


title: FiT-seq_H3K4me2

description: Immunoprecipitated DNA

extract_protocol:
FFPE block was histologically examined and sectioned. Samples were deparaffinized, rehydrated and homogenized by proteinase K treatment and sonication in 1% SDS detergent buffer. Solubilized chromatin was immunoprecipitated following a low-input protocol.
Libraries were prepared with Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) or SMARTer® ThruPLEX® DNA-Seq Kit (Takara Bio USA Inc).

value: H3K4me2 (Millipore, cat. no. 07-030, lot no. 2477948)


title: Patient 38, tumor tissue


title: Patient 38, normal tissue


title: WT rep3

city: Seoul

first: Joon Yong

last: An

address: 145 Anam-ro, Anam-dong, Seongbuk-gu

country: South Korea

institute: Korea University

description:
WT-3_S84_L007
processed data file: table.raw_counts.WT.xlsx

data_processing:
Illumina Casava1.8 software used for basecalling.
Read count and transcript per million reads mapped (TPM) were determined using Salmon software version 0.12.0.
Read counts were summarized using txtimport in DESeq2
Genome_build: BDGP6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: wild type

extract_protocol:
RNA was extracted from the adult heads (5-7 days post-pupation) of heterozygous mutants of four genotypes (ASH1L/+ and WDFY3/+ and CHD2/+ and CHD8/+) and wild types with four biological replicates per group by using Lexogen’s RNA Extraction Kit (Lexogen).
RNA quality was checked with Bioanalyzer (Agilent Technologies Inc.) prior to library amplification. 3’mRNA-Seq Library Prep Kit for Illumina (FWD) from Lexogen was used for first strand cDNA, second strand synthesis, dsDNA purification, i7 single indexing, library amplification and final library purification. To estimate the PCR cycle numbers for library amplification, qPCR was done by using PCR Add-On Kit (Lexogen). Purified final libraries were quality tested by using Agilent Bioanalyzer 2100 with High Sensitivity DNA chips (Agilent Technologies Inc.). Qubit fluorometer (ThermoFisher Scientific) was used to quantify the concentration of the final library.

value: Wild type

tag: age

value: 5-7 days post-pupation

value: adult heads


title: WT rep1

description:
WT-1_S74_L007
processed data file: table.raw_counts.WT.xlsx


title: WT rep2

description:
WT-2_S79_L007
processed data file: table.raw_counts.WT.xlsx


title: WT rep4

description:
WT-4_S90_L007
processed data file: table.raw_counts.WT.xlsx


title: FiTAc-seq_65°C_5min_rep2

description: Immunoprecipitated DNA


title: 180502-51


title: Patient 37, normal tissue


title: FF_H3K27Ac

description: Immunoprecipitated DNA

source_name: Fresh frozen normal mouse liver

extract_protocol:
Frozen tissue was histologically examined and sectioned. Sample was crosslinked for 10 minutes at room temperature with 1% formaldehyde, lysed and sonicated. Solubilized chromatin was immunoprecipitated following a standard ChIP-seq protocol.
Libraries were prepared with Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) or SMARTer® ThruPLEX® DNA-Seq Kit (Takara Bio USA Inc).


title: Patient 37, tumor tissue


title: CHD8-PP2R5D_3

description:
KIS-WRD_3_S124
processed data file: table.raw_counts.CHD8-PP2R5D.xlsx

source_name: CHD8-PP2R5D (kis-wrd) double het

value: double heterozygous (CHD8/+, PP2R5D/+)


title: 180502-46


title: T6: IL17KO_SEB_4

city: Blacksburg

first: Shiv

middle: D.

last: Kale

state: VA

address: 1015 Steger Hall, Life Science Circle

department: Biocomplexity Institute

institute: Virginia Tech

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequences were trimmed for residual adaptors and poor quality bases  (sliding window 4, phred score 25)  and length (> 36) using Trimmomatic-0.35. Non-paired reads were also filtered out.
Filtered paired end reads were alligned to mouse reference genome (GRCm38.94) using HiSAT2
Transcript Assemble and quantification of RNA-Seq was done via Stringtie, with output specific for DESeq2
DESeq2 analysis was conducted to determine normalized gene counts and differential expression. Differential expression was conducted in a pair-wise manner between genotypes or treatments
Genome_build: GRCm38.94
Supplementary_files_format_and_content: Raw_Counts.txt: Counts from Stringtie in a appropriate format for DeSeq2.  Normalized_Counts.txt: Normalized counts generated post DESeq2, no-filtering has been performed for low or zero counts. Diff_Exp*.txt files: Files containing lists of genes considered to be differentially expressed.

molecule: polyA RNA

source_name: DR3+ IL17a KO with SEB

growth_protocol: Age-matched, wild-type, IFN-gamma knockout and IL-17 knockout mice of either sex, transgenically expressing HLA-DR3 were used in the study

extract_protocol:
Small intestinal tissues were collected and stored in RNAlater untill processing. RNA from tissue samples was extracted using Trizol and further purified using Qiagen columns following manufacturers' instructions.
Total RNA with RIN ≥ 8.0, was converted into a strand-specific library using Illumina’s TruSeq Stranded mRNA HT Sample Prep Kit (Illumina, RS-122-2103), for subsequent cluster generation and sequencing on Illumina's NextSeq. The library was enriched by 13 cycles of PCR, validated using Agilent TapeStation and quantitated by qPCR. Individually indexed cDNA libraries were pooled and sequenced on NextSeq

treatment_protocol: Age-matched, wild-type, IFN-gamma knockout and IL-17 knockout mice of either sex, transgenically expressing HLA-DR3 were challenged intraperitoneally with 50 micrograms of staphylococcal enterotoxin B. Experimental animals were euthanized at indicated time points, small intestines were collected for RNA Sequencing

value: DR3+ IL17a KO

value: small intestine


title: FiT-seq_H3K27Ac

description: Immunoprecipitated DNA

value: liver

value: full section


title: T5: IL17KO_SEB_3


title: Patient 36, tumor tissue

value: salivary gland carcinoma

value: mucoepidermoid carcinoma


title: Patient 36, normal tissue

value: salivary gland carcinomas


title: CHD8-PP2R5D_1

description:
KIS-WRD_1_S91
processed data file: table.raw_counts.CHD8-PP2R5D.xlsx


title: CHD8-PP2R5D_2

description:
KIS-WRD_2_S102
processed data file: table.raw_counts.CHD8-PP2R5D.xlsx


title: Patient 40, normal tissue


title: T4: IL17KO_SEB_2


title: Patient 35, tumor tissue


title: Patient 35, normal tissue


title: CHD8 rep4

description:
KIS-4_S89_L007
processed data file: table.raw_counts.CHD8.xlsx

source_name: CHD8 het

value: heterozygous (CHD8)


title: CHD8 rep3

description:
KIS-3_S86_L007
processed data file: table.raw_counts.CHD8.xlsx


title: S8: IL17KO_SEB_1


title: PC-3_Anoikis-resistant_rep3

city: Wuhan

first: Peng

state: Hubei

address: 1277 Jiefang Ave.

department: Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Gene expression of anoikis-resistant cells

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

source_name: Anoikis-resistant PC-3 cells, replicate 3

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Human PCa PC-3 cell lines were obtained from Shanghai Cell Bank, Chinese Academy of Sciences (Shanghai, China) and maintained in RPMI 1640 medium (Hyclone, GE Healthcare Life Sciences, Logan, UT, USA) with 10% fetal bovine serum (FBS; Biological Industries, Kibbutz Beit Haemek, Israel) containing 1% penicillin/streptomycin (Beyotime Institute of Biotechnology, Nanjing, China) at 37˚C with 5% CO2 and 95% humidified air.

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

treatment_protocol: To establish anoikis-resistant cell model, cells were continuously suspension cultured in ultra-low attachment 6-well plates (Corning, Acton, MA, USA) for 7 days, then transferred into normal plates with attachment culture for 2 days and the re-adherent cells were regarded as anoikis-resistant.

value: anoikis-resistant cell model


title: T13: IFNgKO_SEB_4

source_name: DR3+ IFNg KO with SEB

value: DR3+ IFNG KO


title: PC-3_Anoikis-resistant_rep1

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

source_name: Anoikis-resistant PC-3 cells, replicate 1


title: Patient 34, tumor tissue

source_name: primary salivary gland carcinoma


title: CHD8 rep2

description:
KIS-2_S82_L007
processed data file: table.raw_counts.CHD8.xlsx


title: CHD8 rep1

description:
KIS-1_S76_L007
processed data file: table.raw_counts.CHD8.xlsx


title: S6: IFNgKO_SEB_2


title: PC-3_Anoikis-resistant_rep2

source_name: Anoikis-resistant PC-3 cells, replicate 2


title: PC-3_contral_rep1

description: Gene expression of parental cells

source_name: Parental PC-3 cells, replicate 1


title: PC-3_contral_rep3

description: Gene expression of parental cells

source_name: Parental PC-3 cells, replicate 3


title: Patient 34, normal tissue


title: Patient 31, tumor tissue

value: salivary duct carcinoma


title: PC-3_contral_rep2

description: Gene expression of parental cells

source_name: Parental PC-3 cells, replicate 2


title: T12: IFNgKO_SEB_3


title: CHD2 rep4

description:
CHD-4_S94_L007
processed data file: table.raw_counts.CHD2.xlsx

source_name: CHD2 het

value: heterozygous (CHD2)


title: Patient 31, normal tissue

value: normal salivary gland tissue


title: CHD2 rep3

description:
CHD-3_S88_L007
processed data file: table.raw_counts.CHD2.xlsx


title: S3: DR3_SEB_3

source_name: DR3+ with SEB


title: Patient 2, tumor tissue

description:
selected RNA, probe-based (Nanostring PanCancer Pathways Panel)
Nanostring pan Cancer Pathways Panel


title: S2: DR3_SEB_2


title: S1: DR3_SEB_1


title: Patient 29, tumor tissue

value: adenoid cystic carcinoma


title: T7: IL17KO_PBS_3

source_name: DR3+ IL17a KO with PBS


title: Patient 2, normal tissue


title: S4: IFNgKO_SEB_1


title: WDFY3 rep4

description:
BCHS-4_S93_L007
processed data file: table.raw_counts.WDFY3.xlsx

source_name: WDFY3 het

value: heterozygous (WDFY3)

value: 5-7 days post-pupation


title: CHD2 rep1

description:
CHD-1_S78_L007
processed data file: table.raw_counts.CHD2.xlsx

value: adult heads


title: WDFY3 rep2

description:
BCHS-2_S80_L007
processed data file: table.raw_counts.WDFY3.xlsx


title: Patient 26, tumor tissue


title: Patient 29, normal tissue


title: S18: IL17KO_PBS_2

value: DR3+ IL17a KO


title: CHD2 rep2

description:
CHD-2_S81_L007
processed data file: table.raw_counts.CHD2.xlsx


title: PX_10wk_19_Inc_YES_BG_421

first: Aref

last: Ebrahimi

address: 1 Joslin Pl

department: Islet Cell and Regenerative Biology

institute: Harvard Medical School - Joslin

description: 4-5 Week Lewis Rat

data_processing:
fastqc
subread-buildindex
subread-align
featureCounts
limma
voom
Genome_build: Rnor6 ENSEMBLE v93

organism: Rattus norvegicus

source_name: Islets of Langerhans

extract_protocol:
miRNeasy Qiagen
Wafergreen Directional

value: Lewis Rats

tag: average bg pre-sac


title: Sham_10wk_27_Inc_YES_BG_88

description: 4-5 Week Lewis Rat


title: Sham_10wk_24_Inc_YES_BG_91

description: 4-5 Week Lewis Rat


title: Sham_10wk_25_Inc_YES_BG_96

description: 4-5 Week Lewis Rat


title: Sham_10wk_26_Inc_YES_BG_91

description: 4-5 Week Lewis Rat


title: Sham_10wk_23_Inc_YES_BG_88

description: 4-5 Week Lewis Rat


title: WDFY3 rep1

description:
BCHS-1_S77_L007
processed data file: table.raw_counts.WDFY3.xlsx


title: S15: IFNgKO_PBS_4

source_name: DR3+ IFNg KO with PBS

value: small intestine


title: PX_10wk_16_Inc_YES_BG_119

description: 4-5 Week Lewis Rat


title: Patient 25, tumor tissue


title: WDFY3 rep3

description:
BCHS-3_S87_L007
processed data file: table.raw_counts.WDFY3.xlsx


title: Patient 26, normal tissue


title: Patient 25, normal tissue


title: S11: DR3_PBS_2

source_name: DR3+ with PBS


title: ASH1L rep3

description:
ASH-3_S85_L007
processed data file: table.raw_counts.ASH1L.xlsx

source_name: ASH1L het

value: heterozygous (ASH1L)


title: PX_10wk_10_Inc_YES_BG_157

description: 4-5 Week Lewis Rat


title: S10: DR3_PBS_1


title: Patient 16, tumor tissue

value: salivary gland carcinoma


title: ASH1L rep4

description:
ASH-4_S91_L007
processed data file: table.raw_counts.ASH1L.xlsx


title: S13: IFNgKO_PBS_2


title: S17: IL17KO_PBS_1


title: P-301

source_name: Cervical tumor

value: Adenosquamous

tag: gene-based hypoxia

value: Less hypoxic

tag: imaging-based hypoxia

tag: combined hypoxia biomarker

tag: figo stage

tag: rna isolation method

value: Trizol

tag: biopsy

value: Pooled biopsies


title: PX_10wk_8_Inc_YES_BG_155

description: 4-5 Week Lewis Rat


title: PX_10wk_13_Inc_YES_BG_416

description: 4-5 Week Lewis Rat


title: S12: DR3_PBS_3

tag: genotype/variation


title: PX_10wk_11_Inc_YES_BG_211

description: 4-5 Week Lewis Rat


title: Patient 23, tumor tissue

value: salivary gland carcinomas


title: Patient 16, normal tissue

value: mucoepidermoid carcinoma


title: ASH1L rep2

description:
ASH-2_S83_L007
processed data file: table.raw_counts.ASH1L.xlsx


title: ASH1L rep1

description:
ASH-1_S75_L007
processed data file: table.raw_counts.ASH1L.xlsx


title: Oil and Pathogen Spleen 3

city: Ocean Springs

first: Maria

middle: L

last: Rodgers

state: Mississippi

address: 103 McIlwain Drive

department: Coastal Sciences

institute: University of Southern Mississippi

data_processing:
Bases called using Illumina CASAVA software
Read quality assessed using Illumina FastQC software; adpater trimming performed using Trimomatic software
Reads were aligned to the Fugu genome using CLC Genomics Workbench 10.1.1 (Qiagen, Hilden, Germany).
Gene expression (Total Counts) calculated using CLC Genomics Workbench 10.1.1 (Qiagen, Hilden, Germany)
Genome_build: Takifugu rubripes genome (NCBI genome ID 31033)
Supplementary_files_format_and_content: CSV text files including Total Count values

organism: Lutjanus campechanus

source_name: Spleen

growth_protocol: All organisms were kept at 30 ppt salinity, 23 degrees C, and dissolved oxygen greater than 6 ppm

extract_protocol:
Qiagen RNeasy kit using manufacturer's protocols
Illumina TruSeq Stranded mRNA kit to construct polyA libraries

treatment_protocol: Oil-exposed organisms were subject to exposure for 8 days

tag: oil concentration

tag: v. anguillarum concentration

value: 7.5 × 10^5 CFU/mL


title: Patient 19, normal tissue

tag: tissue

value: normal salivary gland tissue

value: salivary duct carcinoma


title: PX_10wk_4_Inc_YES_BG_152

description: 4-5 Week Lewis Rat


title: Patient 19, tumor tissue


title: siR_control-3

city: Indianapolis

first: Mircea

last: Ivan

state: IN

address: 980 W Walnut Street

institute: Indiana University School of Medicine

data_processing:
Sequencing and base-calling were performed with Torrent_Suite 4.0.2
Reads were aligned using STAR (v2.3.0)
Read coutns for each gene was created using bamutils count from the ngsutils and Gencode v19 as the annotation
Genome_build: hg19
Supplementary_files_format_and_content: read counts

source_name: breast cancer cell line

growth_protocol: MCF-7 cells were tested mycoplasma-free and maintained at 37°C in 5% CO2 with DMEM/High glucose medium supplemented with 10% (v/v) FBS and antibiotics

extract_protocol:
For RNA extraction, cells were lysed using QIAzol Lysis Reagent (QIAGEN) and total RNA was isolated using the RNeasy kit (QIAGEN) following manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For knockdown study, MCF-7 cells was transfected with lincNORS siRNA or control siRNA. After overnight incubation, medium was changed to growth media and the cells were further cultured for 24 hours under 1%O2 condition before RNA harvesting; For overexpression study, MCF-7 cells stably expressing lincNORS or pcDNA vector was cultured under normoxia (21% O2) condition for 24 hours beofore RNA harvesting.

tag: cell line

tag: transfection

value: negative control siRNA

tag: culture condition

value: hypoxia:1% O2


title: Oil and Pathogen Spleen 2


title: Patient 15, tumor tissue

tag: patient diagnosis

tag: histology

value: adenoid cystic carcinoma


title: siR_control-2


title: S14: IFNgKO_PBS_3

value: DR3+ IFNG KO


title: PX_10wk_15_Inc_YES_BG_464

description: 4-5 Week Lewis Rat

tag: strain

value: Lewis Rats


title: PX_10wk_2_Inc_YES_BG_132

description: 4-5 Week Lewis Rat

tag: average bg pre-sac


title: PX_10wk_14_Inc_YES_BG_104

description: 4-5 Week Lewis Rat


title: Oil and Pathogen Spleen 1


title: T11: IFNgKO_PBS_1

value: small intestine


title: siR_control-1


title: siNORS-3

value: NORS siRNA-s


title: Patient 15, normal tissue


title: Patient 23, normal tissue


title: 2 week leaf tissue digested with 10U/ml MNase, biological replicate 2

city: Manhattan

first: Eduard

last: Akhunov

state: Kansas

address: 1712 Claflin Road

department: Plant Pathology

institute: Kansas State University

data_processing:
Raw fastq files were run through quality control using Illumina NGSC Toolkit v2.3.3, and aligned to Chinese Spring RefSeqv1 genome using the HISAT2 v2.0.5 alignment program. Paired end reads were retained if 70% of the read length had a quality cutoff score of > 20. Only uniquely mapped reads were retained for further analysis.
BED files were made from each alignment, using the Bedtools v2.26.0 bamtobed conversion to get the coordinates where reads align, then depth of reads was measured in 10bp intervals using bedmap --count option. The read coverage (number of reads that map) for each 10bp interval was normalized by taking the total number of reads mapped for the whole genome and then dividing by million.
To get the differential MNase score for each 10bp interval, we subtracted the normalized depth of coverage of the heavy digest from the normalized depth of coverage of the light digest. For instance, for each 10 bp interval on a chromosome we obtain normalized depth of coverage for both light and heavy digests for each replicate, and then calculate the differential depth for each replicate (2 reps).
We performed a segmentation analysis using the iSeg algorithm to identify distinctly accessible (hypersensitive) and inaccessible (hyper-resistant) regions of the genome. A biological cutoff for genome-wide significance of sd = 1.5, was used to identify regions either accessible or inaccessible to MNase digest. Replicates were run separately and regions that were found to surpass the biological cutoff in both replicates were considered either accessible (hypersensitive, MSF), or inaccessible (hyper-resistant, MRF).
Supplementary_files_format_and_content: All processed files are in bigWig format. MSF.bw has MNase susceptible footprints detected by iSeg. MRF.bw has MNase resistant footprints detected by iSeg. MNase_score_rep1.bw has MNase differential score between library 1 and library 2. MNase_score_rep2.bw has MNase differential score between library 3 and library 4.

organism: Triticum aestivum

growth_protocol: Wheat cultivar Chinese Spring was grown in greenhouse conditions with 16:8-hour light:dark cycle

extract_protocol:
Two-week old leaf tissue was collected and immediately flash frozen in liquid nitrogen. Nuclei were isolated using a modified protocol by Vera et al. Briefly 4 g of frozen tissue were ground using mortar and pestle under liquid nitrogen and were cross linked for 10 minutes in ice cold fixation buffer (15 mM PIPES-NaOH, pH 6.8, 80 mM KCl, 20 mM NaCl, 0.32mM sorbitol, 2 mM EDTA, 0.5 mM EGTA, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 0.2 200 µM PMSF, and 200 µM phenanthroline, and 1% formaldehyde). The cross-linking was stopped by adding glycine to a final concentration of 125 mM and incubating at room temperature for 5 minutes. Nuclei were isolated by adding Triton-X 100 to a final volume of 1% and rotated for 5 minutes, then filtered through 1 layer of miracloth. Nuclear suspensions were divided in 2 aliquots and then suspended in 15mL of 50% volume:volume Percoll:PBS cushion, then centrifuged for 15 minutes at 4°C at 3,000 x g. Nuclei were transferred from the Percoll interphase to a new tube, diluted 2X in PBS buffer, and pelleted by centrifugation for 15 minutes at 4°C 2,000 x g. Pellets were resuspended in 15mL of ice cold MNase digestion buffer (50 mM HEPES-HCl, pH 7.6, 12.5% glycerol, 25mM KCl, 4mM MgCl2, 1mM CaCl2), and pelleted again by centrifugation for 15 minutes at 4°C 2,000 x g. Pellets were resuspended in 2 mL of MNase digestion buffer. A 100 µL aliquot of the resuspended nuclei were stained with 1µg/mL DAPI in PBS buffer, and quantified using hemacytometer on a confocal microscope. The remaining nuclei were split into 60µL aliquots containing 3,000 nuclei each and flash frozen in liquid nitrogen. Nuclei were digested by micrococcal nuclease (NEB) using 100 U/mL (heavy) and 10 U/mL (light) for 20 minutes at room temperature. Digestion was terminated by adding 10mM EGTA. To break the cross-links, digestions were treated overnight at 65°C in 1% SDS and 100 µg/mL proteinase K. DNA was extracted using phenol-chloroform extraction and precipitated in ethanol. Digested DNA was resuspended in 40 µg/mL RNaseA (Qiagen), and run on a 1% agarose gel to confirm the heavy and light digest.
Two separate biological replicates of nuclei were thawed to room temperature and split into 8 separate 60ul aliquots. For each replicate, 4 separate light digestions (10 U/ml) and 4 separate heavy digestions (100U/ml) were carried out for 20 minutes at room temperature. Digestions were stopped with the addition of 0.5M EGTA. DNA was extracted in the same manner described above, and then the 4 samples of each like digestion were combined to produce 2 replicate light digestions, and 2 replicate heavy digestions, resulting in 4 total libraries. Prior to library preparation digested DNA samples were subjected to 100-200 bp size selection using the Pippin prep system (Sage Science). The DNA-seq libraries were constructed from 500 ng of size selected DNA with the GeneRead DNA library I core kit (Qiagen, cat #180434) and GeneRead Adapter I set B (Qiagen, cat # 180986) according to Qiagen protocol with one exception: seven PCR cycles were performed for the library enrichment. The sizes of resulting libraries were validated on the 7500 DNA Bioanalyzer chip. To test the quality of library preparations, two out of four barcoded libraries prepared using the high and low concentrations of MNase were pooled in the equimolar amounts and sequenced with 2 x 75 bp Illumina MiSeq run using MiSeq 150 cycles reagent kit v3. Then each of the four libraries was sequenced on 2 lanes of HiSeq 2500 system (8 lanes total) using a 2 x 50 bp sequencing run producing a total of 1,749,823,029 reads.

tag: Stage

value: 2 week

value: leaf

tag: cultivar

value: chinese spring


title: Oil Only Spleen 2

value: 0 cfu/mL


title: Patient 11, tumor tissue

value: salivary gland carcinoma


title: Oil Only Spleen 1


title: siNORS-2


title: siNORS-1


title: 2 week leaf tissue digested with 10U/ml MNase, biological replicate 1


title: 2 week leaf tissue digested with 100U/ml MNase, biological replicate 2


title: Patient 11, normal tissue

value: salivary gland carcinomas


title: Oil Only Spleen 3


title: Patient 10, tumor tissue

value: mucoepidermoid carcinoma


title: Pathogen Only Spleen 3

value: 7.5 × 10^5 CFU/mL


title: 2 week leaf tissue digested with 100U/ml MNase, biological replicate 1


title: Sham_4wk_74_Inc_YES_BG_89

description: 4-5 Week Lewis Rat

data_processing:
fastqc
subread-buildindex
subread-align
featureCounts
limma
Genome_build: voom
Supplementary_files_format_and_content: Rnor6 ENSEMBLE v93


title: pcDNA3-3

value: pcDNA3 only

value: normoxia:21% O2


title: dilp_fatbody_day10_Polysome_3

first: Carina

middle: Marianne

last: Weigelt

address: Joseph-Stelzmann-Str 9b

institute: Max Planck Institute for Biology of Ageing

description: CircCoordinates_Polysome.tsv,CircRNACount_Polysome.tsv,LinearCount_Polysome.tsv,bbTest.total.Fatb_dilp_10_Polysome.tsv

data_processing:
Primary data analysis is done by Illumina’s real-time analysis software (RTA)
raw reads were mapped using STAR version 2.5.2b(circRNA)
circRNAs were detected using DCC version 0.4.4.
differential circRNA expression was analyzed using R’s ibb package
raw reads were mapped using HISAT version 2.0.4 (isoform expression)
transcripts were assembled using StringTie version 1.3.0
differential isoform expression was analyzed using cufflinks/cuffdiff version 2.2.1
Genome_build: BDGP6 Ensembl build 90
Supplementary_files_format_and_content: tab separated tables were generated representing circRNA coordinates, circRNA counts, linearRNA counts, differential circRNA statistics and isoform fpkm table

source_name: manually dissected fruit fly tissues

growth_protocol: Female flies were kept at 25°C and 65% humidity on standard sugar-yeast-agar food. Fly tissues were dissected manually with fine forceps in PBS and frozen in dry ice.

extract_protocol:
Total RNA extraction with Trizol and DNase treatment. For samples 73-78: Polysome-bound RNA was enriched.
RNA libraries were prepared for sequencing using standard Illumina protocols based on rRNA depleted RNA samples

treatment_protocol: Dissected tissues: brain, thorax (without gut), gut (without crop, but including maphigian tubules), fat body (without gut and without ovaries)

tag: rna

value: Polysome-enriched RNA

tag: age

value: Day 10

tag: genotype

value: fat body


title: Pathogen Only Spleen 2


title: Patient 10, normal tissue

source_name: primary salivary gland carcinoma

extract_protocol: Tumor areas with at least 70% tumor cell count as well as corresponding normal tissue were marked on H&E slides. After scraping off the respective tissue of the FFPE blocks, RNA isolation was carried out using the RNA FFPE kit from Promega on the Maxwell® 16 LEV (Promega AS1260, Heidelberg) according to the manufacturer’s instructions. RNA concentrations were quantified by the QuantiFluor® RNA System as recommended by the supplier (Promega, E6090) and adjusted to 30 ng / µl.

value: normal salivary gland tissue


title: dilp_fatbody_day10_Polysome_2


title: Pathogen Only Spleen 1


title: Sham_4wk_73_Inc_YES_BG_97

description: 4-5 Week Lewis Rat

value: Lewis Rats


title: pcDNA3-1


title: PX_4wk_70_Inc_YES_BG_108

description: 4-5 Week Lewis Rat


title: dilp_fatbody_day10_Polysome_1


title: PX_4wk_66_Inc_YES_BG_108

description: 4-5 Week Lewis Rat


title: wt_fatbody_day10_Polysome_3

description: CircCoordinates_Polysome.tsv,CircRNACount_Polysome.tsv,LinearCount_Polysome.tsv,bbTest.total.Fatb___wt_10_Polysome.tsv

value: wDah (wildtype)


title: Control Spleen 2


title: Control Spleen 1


title: wt_fatbody_day10_Polysome_2


title: PX_4wk_65_Inc_YES_BG_174

description: 4-5 Week Lewis Rat


title: wt_fatbody_day10_Polysome_1


title: PX_4wk_62_Inc_YES_BG_110

description: 4-5 Week Lewis Rat


title: oeNORS-2


title: HFD617_liver

city: Oxford

first: Rui

last: Gao

address: Old Road

department: Oxford Centre for Diabetes, Endocrinology and Metabolism

country: United Kingdom

institute: Churchill Hospital

data_processing:
The sequencing raw reads were filtered for low-quality, adaptor-polluted, high content of unknown base reads by SOAPnuke (v1.5.2).
We used Trinity (v2.0.6) to perform de novo assembly, and Tgicl (v2.0.6) on cluster transcripts to remove redundancy and get unigenes. The high-quality clean reads were then mapped to the mouse reference genome (GRCm38) via HISAT2 (v2.0.4) 25 and full-length transcriptome database via Bowtie2 (v2.2.5)
The gene expression levels were then quantified by RSEM (v1.1.12) and were normalized by the method of fragments per kilobase of exon model per million reads mapped (FPKM).
The DEseq2 (fold change≥2 and adjusted P-value≤0.05) package was applied to identify differentially expressed genes (DEGs) between HFD and CD groups at each time point.
Ingenuity Pathway Analysis (IPA, Qiagen, Redwood City, CA, USA, www.qiagen.com/ingenuity) was conducted to determine enriched canonical pathways, upstream regulators, mechanistic networks, and diseases and functions. Kyoto Encyclopedia Genes and Genomes (KEGG) analyses of DEGs were also performed according to the gene annotations provided by DAVID online tool (v6.8).
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Matrix table with fragments per kilobase per million (FPKM) for every gene and every sample

source_name: high-fat diet mice liver

growth_protocol: Four-week-old C57BL/6N male mice were purchased from GemPharmatech Co., Ltd. and were maintained at 22°C on a 12 h light/dark cycle with ad libitum access to food.

extract_protocol:
Islets extraction: After clamped with a hemostat at the duodenal opening, the bile duct was cannulated and perfused with 2 mL collagenase P (Roche Diagnostics, Germany, 1 mg/mL in Hanks' balanced salt solution (HBSS)). Pancreatic tissue was digested at 37 °C for 10 min. The reaction was stopped by adding cold HBSS with 10% fetal bovine serum (FBS), followed by 10 seconds of vigorous shaking. Islets were separated onto a gradient composed of HBSS and Histopaque (11191 and 10771, Sigma Aldrich, USA) layers and were hand-picked for 2 times under a dissection microscope to minimize acinar cells. The purity of islets for RNA-sequencing was evaluated by the expression of Amy1a (a marker of acinar cells) and Krt19 (a marker of ductal cells). In our transcriptome dataset, Amy1a and Krt19 showed no statistical difference at mRNA level from any time points, which indicates the contaminants were fairly minimized. Liver extraction: The same region of the liver were removed and flash frozen in liquid nitrogen. Total RNA was isolated from handpicked islets and homogenized liver tissue using TRIzol reagent (Invitrogen, CA, USA) in accordance with the manufacturer’s instructions. The quality and quantity of extracted RNA were measured by on-chip electrophoresis utilizing the Agilent RNA 6000 Nano Kit and Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). Samples exhibited 1.9≤A260/A280 ≤ 2.2, RNA integrity number>8.0 and 28S/18S>1.0 were selected for library preparation.
The total RNA was purified by enriching poly (A) mRNA with magnetic oligo (dT) beads. After reverse transcription by using the random hexamer (N6) primers, double-stranded cDNA fragments were synthesized and subjected to end repair and adapter ligation. The cDNA libraries were then constructed by PCR amplification, and finally sequenced on BGISEQ-500 sequencing platform by the Beijing Genomics Institute (Shenzhen, China).

treatment_protocol: Mice were fed either CD (LabDiet 5001, 13.5% fat) or HFD (Research Diets D12492, 60% fat) for 4−24 weeks.

value: liver

tag: diet

value: high-fat diet

tag: weeks on diet

value: 24 weeks


title: HFD617_islet

source_name: high-fat diet mice islets

value: islets


title: oeNORS-3


title: DNMT3A3B-DKO-chase-0

description: Enrich EdU-labeled DNA, add hairpin, and BS-seq

source_name: EdU labeled DNMT3A/3B double KO HeLa cells with chasing 0 min

tag: strain background

value: Adult female

value: HeLa-S3 with DNMT3A/3B double KO

tag: cell type

value: epithelial adenocarcinoma

tag: genotype/variation

value: DNMT3A/3B DKO

value: cervix

tag: developmental stage

value: 31 years