title: TC32

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

institute: Faculdade de Medicina da Universidade de Sao Paulo

description:
Gene expression from thymus explant
E_T56

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The selected transcripts were used for analysis using the R software and considering none NA for each age interval (A to E groups).

source_name: thymus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: Thymus explants (3-4 mm3) were homogenized with TissueRupter (Qiagen) and total RNA was extracted from the homogenates using the RNeasy Lipid Tissue Kit (Qiagen)

treatment_protocol: Fresh ex-vivo explants of patients were obtained at the surgery room and immediately preserved with 600 uL of RNAlater (Qiagen).

value: F

tag: age at surgery (yr mo d)

value: 2y 6mo 10d


title: TC04

status: Public on Dec 27 2019

type: RNA

country: Brazil

description:
Gene expression from thymus explant
E_T55

molecule: total RNA

organism: Homo sapiens

tag: gender

value: 2y 5mo


title: TC59

description:
Gene expression from thymus explant
E_T57

value: M

value: 2y 7mo


title: FLANC overexpressing vector #1-1, biological rep1 vs empty vector

city: Houston

first: George

last: Calin

state: TX

address: 1881 East Road

department: Experimental Therapeutics

country: USA

institute: MD Anderson Cancer Center

description: Empty vector versus FLANC overexpressing vector, replicate 1

hyb_protocol: Hybridization done according to Agilent Gene expression hybridization kit. http://www.genomics.agilent.com/en/Gene-Expression-Hybridization-Wash-Reagents/Gene-Expression-Hybridization-Kits/?cid=AG-PT-133&tabId=AG-PR-1054

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: HCT116 cell line empty vector

label_protocol: Labeling was done according to Agilent Gene Expression Hybridization Kit. http://www.genomics.agilent.com/en/Gene-Expression-Hybridization-Wash-Reagents/Gene-Expression-Hybridization-Kits/?cid=AG-PT-133&tabId=AG-PR-1054

growth_protocol: The human colon cancer cell line HCT116 was obtained from the American Type Culture Collection (Manassas, VA, USA) and grown according to ATCC recommendations. Cells were cultured at 37°C in 5% CO2.

extract_protocol: Cell were transduce with lentivirus containing the specific vectors. Total RNA was extracted using Trizol following manufacturer's instructions

tag: cell line

tag: tissue

value: colon

source_name: HCT116 cell line FLANC overexpressing vector


title: TC03

description:
Gene expression from thymus explant
E_T52

value: 2y 1mo


title: MPBMyeD5 [re-analysis]

type: genomic

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

hyb_protocol: Standard NimbleGen protocol. Briefly, Cy3 and Cy5 labeled DNA samples (31 ug each) were co-hybridized to Nimblegen CGH arrays containing oligonucleotide probes across the entire human genome.

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: Genome-wide RT profiles were constructed by Repli-chip, Repli-seq, Capture Repli-seq and deep whole genome sequencing (WGS). Replication timing profiles were scaled and pooled for analysis as previously described (Ryba et al., 2011; Marchal et al., 2018). Briefly, Log2 transformed early/late replication timing ratios were quantile normalized and loess smoothed in R

molecule: genomic DNA

source_name: Early-replicating DNA

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as previously described (Ryba, T. et al., 2011. Nat Protoc 6: 870–895). Briefly, replication intermediates were prepared from cells pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245] and Ryba, T. et al [Nat Protoc (2011) 6: 870–895].

tag: differentiation stage

value: Myeloid differentiation day 5 from CD34+ peripheral blood stem and progenitor cells

source_name: Late-replicating DNA


title: input_CD3_U1

type: SRA

city: tyuo-ku

first: noriko

last: nishi

state: Tokyo

address: 5-11 hakozaki 5F Yunibasaru Bldg

country: Japan

institute: Axiohelix Co. Ltd.

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.0.1 with default.
peaks were called using MACS version 2.0.9 with default.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using https://github.com/daler/rdbio-scripts/blob/master/sequenceFiles/bed2wig.py;

source_name: CD3+ LPMC

extract_protocol:
Isolated cells were immediately cross-linked with 1% formaldehyde/PBS for 10 minutes at room temperature. After washing, the cell pellet was lysed in the lysis buffer having the following final concentration: 50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% sodium dodecyl sulfate (SDS), 1 mM phenylmethylsulfonyl fluoride (PMSF), 1x proteinase inhibitor complete cocktail (Roche). The lysed solution was subjected to chromatin shearing by using Covaris S2 System (Covaris, Woburn, MA) to shear the chromatin into 100300 bp fragments.
ChIP-seq libraries were prepared for sequencing using the SOLiD Fragment Library Construction Kit and multiplexed by using SOLiD™ Fragment Library Barcoding Kit Module 1-16 according to the manufacturer’s instructions.

tag: cell type

value: CD3+ LPMC

tag: strain

value: UC

tag: chip antibody


title: A549_IL1b_w30d_repC

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

description: Biological repication 3 of 3

library_source: transcriptomic

data_processing:
Basecalls, demultiplex and adapter trimming were performed with Illumina Bcl2fastq2 v 2.17
Sequenced reads were mapped to Human Ensemble GRCh37 genome by using tophat2 v.2.0.14 and bowtie2 v.2.2.5 with following parameters -p 4 -g 1 --no-coverage-search.
Gene counts were performed with htseq-count function in HTSeq v.0.6.1. Aligned sequences from tophat2 were sorted by name before subjected to htseq-count analysis with following parameters: -s no -a 10 -m intersection-strict -q
Genome_build: GRCh37 human genome
Supplementary_files_format_and_content: tab-delimited text files include raw feature counts for each sample

source_name: A549 cell line

growth_protocol: A549 cells were cultured in standard RPMI media with 10% FBS with or without IL-1beta (1ng/ml) for indicated days, and split every 3-4 days.

extract_protocol:
total RNA was extracted from the cells using the Qiagen RNeasy Mini Kit following the manufactural instruction
Libraries for RNA-Seq were prepared with KAPA Stranded mRNA-Seq Kit. Library preparation performed by Techonology Center for Genomics & Bioinformatics (TCGB) at UCLA.

value: lung

value: non-small cell lung cancer

tag: treatment

value: IL1beta treated

tag: time point

value: day 30 posttreatment


title: TC12

description:
Gene expression from thymus explant
E_T53


title: TC53

description:
Gene expression from thymus explant
E_T54


title: input_CD3_N1

value: Non-IBD


title: MPBMyeD3 [re-analysis]

value: Myeloid differentiation day 3 from CD34+ peripheral blood stem and progenitor cells


title: A549_IL1b_21d_repC

description: Biological repication 3 of 3

value: day 21


title: A549_Ctrl_w6d_repC

description: Biological repication 3 of 3

value: Control

value: day 6 posttreatment


title: A549_IL1b_w6d_repC

description: Biological repication 3 of 3


title: TC40

description:
Gene expression from thymus explant
E_T49

value: 1y 8mo


title: MPBEpoD5 [re-analysis]

value: Erythroid differentiation day 5 from CD34+ peripheral blood stem and progenitor cells


title: A549_Ctrl_w15d_repC

description: Biological repication 3 of 3

value: day 15 posttreatment


title: A549_Ctrl_21d_repC

description: Biological repication 3 of 3


title: MPBEpoD3 [re-analysis]

value: Erythroid differentiation day 3 from CD34+ peripheral blood stem and progenitor cells


title: TC60

description:
Gene expression from thymus explant
E_T50

value: M


title: TC33

description:
Gene expression from thymus explant
E_T51


title: A549_IL1b_w15d_repC

description: Biological repication 3 of 3


title: TC48

description:
Gene expression from thymus explant
E_T48

value: 1y 7mo


title: A549_Ctrl_w30d_repC

description: Biological repication 3 of 3


title: A549_IL1b_6d_repC

description: Biological repication 3 of 3

value: day 6


title: MPBCD34 [re-analysis]

value: CD34+ peripheral blood stem and progenitor cells


title: specimen 12-006 [X12006R1]

source_name: Early S Fraction

treatment_protocol: BrdU labeled

value: Female

tag: method

value: E/L

tag: replicate

source_name: Late S Fraction


title: A549_Ctrl_6d_repC

description: Biological repication 3 of 3

value: lung

value: non-small cell lung cancer


title: TC05

description:
Gene expression from thymus explant
D_T43

value: F

value: 1y 5mo


title: A549_Ctrl_w30d_repB

description: Biological repication 2 of 3

value: day 30 posttreatment


title: TC49

description:
Gene expression from thymus explant
D_T44


title: TC79

description:
Gene expression from thymus explant
D_T45

value: 1y 5mo 5d


title: A549_Ctrl_w15d_repB

description: Biological repication 2 of 3

value: Control


title: TC54

description:
Gene expression from thymus explant
D_T42

value: 1y 4mo


title: A549_IL1b_w6d_repB

description: Biological repication 2 of 3

value: IL1beta treated

value: day 6 posttreatment


title: A549_IL1b_w15d_repB

description: Biological repication 2 of 3

value: day 15 posttreatment


title: A549_Ctrl_w6d_repB

description: Biological repication 2 of 3


title: A549_IL1b_15d_repC

description: Biological repication 3 of 3

value: day 15


title: TC09

description:
Gene expression from thymus explant
D_T46

value: M

value: 1y 6mo 10d


title: TC44

description:
Gene expression from thymus explant
D_T47


title: A549_Ctrl_15d_repC

description: Biological repication 3 of 3


title: TC61

description:
Gene expression from thymus explant
D_T39

value: 1y 2mo


title: A549_IL1b_21d_repB

description: Biological repication 2 of 3

value: day 21


title: A549_Ctrl_21d_repB

description: Biological repication 2 of 3


title: TC08

description:
Gene expression from thymus explant
D_T37


title: specimen 10-799 [X10799R2]

value: Female

value: E/L


title: A549_IL1b_w30d_repB

description: Biological repication 2 of 3

value: lung

value: non-small cell lung cancer


title: A549_Ctrl_15d_repB

description: Biological repication 2 of 3


title: A549_IL1b_15d_repB

description: Biological repication 2 of 3


title: TC50

description:
Gene expression from thymus explant
D_T36

value: 1y 1mo 10d


title: specimen 10-795 [X10795R2]


title: specimen 11-253 [X11253F1D]

source_name: S Fraction

value: Male

source_name: G1 Fraction


title: specimen 11-202 [X11202R1]

value: not collected


title: A549_Ctrl_6d_repB

description: Biological repication 2 of 3

value: Control

value: day 6


title: A549_IL1b_w30d_repA

description: Biological repication 1 of 3

value: IL1beta treated

value: day 30 posttreatment


title: specimen 10-356 [X10356R2]


title: specimen PATXMJ [PATXMJ]


title: specimen 11-132 [X11132R2]


title: TC47

description:
Gene expression from thymus explant
D_T35

value: 1y 1mo


title: TC78

description:
Gene expression from thymus explant
C_T34


title: A549_Ctrl_w30d_repA

description: Biological repication 1 of 3


title: specimen PATNGJ [PATNGJ]


title: TC58

description:
Gene expression from thymus explant
D_T38

value: F


title: A549_Ctrl_w15d_repA

description: Biological repication 1 of 3

value: day 15 posttreatment


title: A549_IL1b_w15d_repA

description: Biological repication 1 of 3


title: A549_IL1b_w6d_repA

description: Biological repication 1 of 3

value: day 6 posttreatment


title: A549_Ctrl_w6d_repA

description: Biological repication 1 of 3


title: TC76

description:
Gene expression from thymus explant
C_T33


title: TC81

description:
Gene expression from thymus explant
C_T32


title: A549_IL1b_21d_repA

description: Biological repication 1 of 3


title: specimen PATMBG [PATMBG]


title: A549_Ctrl_21d_repA

description: Biological repication 1 of 3


title: specimen PATDVJ [PATDVJ]


title: A549_IL1b_6d_repB

description: Biological repication 2 of 3


title: TC31

description:
Gene expression from thymus explant
C_T30

value: 9mo 26d


title: specimen PASZMP [PASZMP]


title: A549_IL1b_15d_repA

description: Biological repication 1 of 3

value: day 15


title: TC07

description:
Gene expression from thymus explant
C_T29

value: M

value: 9mo 2d


title: TC27

description:
Gene expression from thymus explant
C_T28

value: 9mo 1d


title: A549_Ctrl_6d_repA

description: Biological repication 1 of 3

value: lung

value: non-small cell lung cancer


title: specimen PASXSA [PASXSA]

value: Female


title: specimen PASUWV [PASUWV]


title: TG_795_11M_FC mRNAseq

city: Yuseing-gu

first: JaeWoong

last: Min

state: Daejeon

address: 17 Techno 4-ro

country: South Korea

institute: Biorchestra

data_processing:
The mouse genome sequence was then indexed using the "rsem-prepare-reference" command.
Each fastq file was aligned to the mouse genome using the rsem-calculate-expression (version 1.2.31) command to calculate FPKM (fragments per kilobase of transcript per million mapped reads) values.
All the results have been generated by our standard pipelines utilizing STAR (version 2.7.1) as the aligner and RSEM as the tool for annotation and quantification at both gene and isoform levels.
The .txt files give normalized expression abundance in TPM (Transcripts Per Kilobase Million) and FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for all the available genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: *_FC.genes.results.txt: Tab-delimited text files include TPM and FPKM values for each Sample.

organism: Mus musculus

source_name: Frontal cortex

extract_protocol:
Total RNA was prepared with RNeasy kit (Qiagen) and libraries were constructed using 600 ng of total RNA from each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Frontal cortex of brain

tag: age

value: 11 months


title: TC73

description:
Gene expression from thymus explant
C_T26

value: 8mo 11d


title: TG_183_11M_FC mRNAseq


title: WT_774_11M_FC mRNAseq


title: TG_180_11M_FC mRNAseq


title: specimen PASKSL [PASKSL]

value: Male


title: WT_772_11M_FC mRNAseq


title: specimen PAPSSKR2 [PAPSSKR2]


title: WT_178_11M_FC mRNAseq


title: TC01

description:
Gene expression from thymus explant
C_T24

value: 7mo 17d


title: TG_970_6M_FC mRNAseq

value: 6 months


title: TG_967_6M_FC mRNAseq


title: specimen PALHWG [PALHWG]

value: not collected


title: specimen PAPSSK [PAPSSK]


title: A549_IL1b_6d_repA

description: Biological repication 1 of 3

value: IL1beta treated

value: day 6


title: WT_819_6M_FC mRNAseq


title: WT_817_6M_FC mRNAseq


title: WT_807_6M_FC mRNAseq


title: A549_Ctrl_15d_repA

description: Biological repication 1 of 3

value: Control


title: TC02

description:
Gene expression from thymus explant
B_T20

value: F

value: 6mo 10d


title: TC19

description:
Gene expression from thymus explant
B_T21

value: 6mo 9d


title: specimen PALCRG [PALCRG]


title: TC18

description:
Gene expression from thymus explant
B_T18

value: M

value: 6mo 6d


title: WT_806_6M_FC mRNAseq


title: specimen 10-795 [X10795R1]

value: E/L


title: TC24

description:
Gene expression from thymus explant
B_T17

value: 6mo 3d


title: TC17

description:
Gene expression from thymus explant
B_T22

value: 6mo 24d


title: specimen PAKXBW [PAKXBW]


title: TC83

description:
Gene expression from thymus explant
B_T19

value: 6mo 5d


title: Femoral_artery (single-cell RNA-seq)

city: Shanghai

first: Fei

last: Li

address: 320 Yue-Yang Road Shanghai

country: China

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

description: single cell RNA sequencing(collagenase I)

data_processing:
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
Aligned reads and gene-barcode matrices were then generated from FASTQ files  using Cell Ranger (v.2.1.1) processing pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: TSV data for genes and barcodes; MTX data for gene expression matrix

molecule: polyA RNA

source_name: Femoral artery

extract_protocol:
To generate single-cell suspensions, femoral arteries isolated from both male and female mice (8 weeks old) were further digested in collagenase I for 30-60 min as described. In detail, femoral arteries were cut into 1mm small pieces, and these small pieces were digested by 1.5 mg/ml collagenase (Gibco, 17018029) at 37°C, during this process, artery pieces was frequent stirred to ensure full digestion. After sufficient digestion, cells were filtered through a 40-μm cell strainer, and the collected cells were centrifuged 5 min at 600g speed. Subsequently, cell pellet was suspended in PBS or DEME for further experiments
Single cell library was generated using Chromium™ Single Cell 3’ Library Kit v2

value: Femoral artery

value: Sca1+ cells


title: H3K4m3_CD33_U3

source_name: CD33+ LPMC

value: CD33+ LPMC

value: UC

value: H3K4m3 (Millipore, clone 07-473)


title: xenograft from bone marrow case 1 passage 1 [Case1P1R2]

value: Male


title: specimen PAKUGY [PAKUGY]


title: specimen 10-764 [X10764R1]

value: Female


title: TG_968_6M_FC mRNAseq

value: Frontal cortex of brain

value: 6 months


title: H3K4m3_CD33_U2


title: specimen PAKTAL [PAKTAL]


title: specimen PAIXSD [PAIXSD]


title: H3K4m3_CD3_N2

value: CD3+ LPMC

value: Non-IBD


title: H3K4m3_CD3_U2


title: H3K4m3_CD33_N2


title: specimen PAKKCA [PAKKCA]


title: H3K4m3_CD3_U3


title: TC38

description:
Gene expression from thymus explant
B_T16

value: M

value: 6mo 1d


title: TC46

description:
Gene expression from thymus explant
B_T15

value: F

value: 5mo 10d


title: TC80

description:
Gene expression from thymus explant
B_T13

value: 3mo 26d


title: H3K27m3_CD33_U3

value: H3K27m3 (Millipore, clone 07-449)


title: H3K27m3_CD33_U2


title: specimen PAIXMD [PAIXMD]

value: not collected


title: Day 6 of megakaryocytic differentiation of CD34+ cells. [MPBTPOd6]

value: E/L


title: H3K27m3_CD33_N2

value: CD33+ LPMC


title: H3K27m3_CD3_U2

value: UC


title: input_CD33_U3


title: input_CD33_U2


title: input_CD3_U3


title: TC37

description:
Gene expression from thymus explant
B_T11

value: 3mo 19d


title: H3K27m3_CD3_U3


title: H3K27m3_CD3_N2


title: cord blood CD34+ cells expanded in vitro in serum-free media + 5 growth factors for 4 days [CD34posR2]

description: cord blood CD34+ cells expanded in vitro in serum-free media + 5 growth factors (IL-3, IL-6, FLT3L, GCSF, SCF) for 4 days [CD34posR2]

value: not applicable


title: cell line MOLM14 [MOLM14R1]

value: Male


title: cell line MOLM14 [MOLM14R2]


title: input_CD33_N2


title: TC39

description:
Gene expression from thymus explant
B_T12

value: 3mo 18d


title: TC26

description:
Gene expression from thymus explant
B_T10

value: 2mo 11d


title: input_CD3_U2

value: CD3+ LPMC


title: input_CD3_N2

value: Non-IBD


title: cord blood CD34+ cells expanded in vitro in serum-free media + 5 growth factors for 4 days [CD34posR1]

description: cord blood CD34+ cells expanded in vitro in serum-free media + 5 growth factors (IL-3, IL-6, FLT3L, GCSF, SCF) for 4 days [CD34posR1]


title: xenograft from bone marrow case 5 passage 3 [Case5P3R2]


title: TC29

description:
Gene expression from thymus explant
B_T9

value: M

value: 2mo 1d


title: TC35

description:
Gene expression from thymus explant
A_T7


title: xenograft from bone marrow case 5 passage 3 [Case5P3R1]


title: TC22

description:
Gene expression from thymus explant
B_T8

value: 1mo 26d


title: TC30

description:
Gene expression from thymus explant
A_T4


title: TC82

description:
Gene expression from thymus explant
A_T6

value: F


title: TC20

description:
Gene expression from thymus explant
A_T5


title: SJSA-1_400 nM THZ2_rep3

city: Guangzhou

first: Jiajun

last: Zhang

address: #58，Zhongshan 2nd Road

institute: the First Affiliated Hospital of Sun Yat-Sen University

description: Gene expression data from SJSA-1 treated with 400 nM THZ2 for 6 hours

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® PrimeView™ Human Gene Expression Array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: U2-OS and SJSA-1 were maintained in Dulbecco’s modified Eagle medium. All media were supplemented with 10% fetal bovine serum, penicillin (100 U/mL) and streptomycin (100 mg/mL). Cells were incubated at 37℃ with 5% CO2.

extract_protocol: Total RNA of parietal cortex of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: Plate the target cells in a 10-cm dish in 10 ml of DMEM supplemented with 10% fetal bovine serum, penicillin (100 U/mL) and streptomycin (100 mg/mL) 24 hours prior to treatment. Replace medium with fresh complete medium containing the various concentration of THZ2 or DMSO in the next day. Make sure the cells reach same confluent at the time of treatment. Continue incubation in the CO2 incubator at 37℃. Total RNA was extracted from U2-OS or SJSA-1 cells treated with DMSO (control) and different doses of THZ2, respectively, using TRIzol reagent according to manufacturer’s instructions.

value: bone

tag: disease

value: osteosarcoma


title: xenograft from bone marrow case 5 passage 2 [Case5P2R2]


title: SJSA-1_100 nM THZ2_rep3

description: Gene expression data from SJSA-1 treated with 100 nM THZ2 for 6 hours


title: SJSA-1_400 nM THZ2_rep2

source_name: SJSA-1 treated with 400 nM THZ2 for 6 hours


title: xenograft from bone marrow case 5 passage 2 [Case5P2R1]


title: TC77

description:
Gene expression from thymus explant
A_T2


title: xenograft from bone marrow case 5 passage 1 [Case5P1R2]


title: bone marrow case 4  [Case4PatR2]


title: xenograft from bone marrow case 5 passage 1 [Case5P1R1]


title: SJSA-1_100 nM THZ2_rep2

source_name: SJSA-1 treated with 100 nM THZ2 for 6 hours


title: bone marrow case 4  [Case4PatR1]


title: Primary non-cultured AEC2s 272k

city: Durham

first: Christina

middle: E

last: Barkauskas

state: NC

address: BOX 2629 DUMC

department: Medicine / Pulmonary

institute: Duke University

description:
Primary non-cultured AEC2s
No treatment

data_processing:
 Data QC - remove adaptor and low quality bases using cutadapt (Martin, 2011). e.g. cutadapt -a adaptor -m 25 -q 25 -o output.fastq -z input.fastq.gz
 Align reads to reference using tophat2 with strand specific and multiple hit options(Trapnell et al., 2009). e.g. tophat2 –p 10 -o tophat_out --library-type fr-firststrand -g 2000 -G \ genes.gtf genome output.fastq
 Differential expression analysis using cuffdiff (upper quartile normalization, multiple hit corrections and strand specific options)(Trapnell et al, 2012). e.g. cuffdiff –p 10 -o cuffdiff_out --library-type fr-firststrand -N –u \  –L label1,label2 genes.gtf sample.bam
 Pathway analysis using iPage (Goodarzi et al., 2009); e.g., page.pl --expfile=genes_expr --pathways=mouse_go_orf
tophat.bam - alignment files produced from tophat using the pass-QC fastq reads.  The tophat version is 2.0.9
Genome_build: mm9

source_name: Lung alveolar epithelial cells type 2

growth_protocol: For organoid cultures, AEC2s and niche fibroblasts were mixed together in transwell inserts 50:50 Matrigel:MTEC medium and grown for 16 days.

extract_protocol:
Rneasy Micro Kit - QIAGEN
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: IL13 added to MTEC at 10ngn/mL; IL4 added to MTEC at 10ng/mL

value: primary AEC2s

tag: passage

value: primary

tag: total number of cells


title: Primary non-cultured AEC2s 325k

description:
Primary non-cultured AEC2s
No treatment


title: TC71

description:
Gene expression from thymus explant
A_T1

source_name: thymus


title: TP-24-R4

city: LUGO

first: Belen

middle: G

last: Pardo

state: LUGO

address: Avda. Carballo Calero s/n

department: Zoology, Genetics and Physical Anthropology

country: Spain

institute: University of Santiago de Compostela

description: Gene expression of Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 24 hours, replicate 3.

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to turbot custom Oligo Microarrays (G2514F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent). A single pooled control was hybridized in two microarrays per slide as technical replicates. Twelve microarrays were used for the treatments across the time-series (1 h, 8 h and 24 h) including four replicates per time point.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565B) using one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Extended dynamic range implemented in the Agilent software was applied to avoid saturation in the highest intensity range. The Agilent feature extraction was used as raw data for further preprocessing. The processed signal (gProcessed-Signal) value was chosen for the statistical analysis.

organism: Perkinsus olseni

source_name: Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 24 hours, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA of each strain and time using the Low Input Quick Amp Labeling Kit, One-Color (Cy3) (Agilent Technologies, USA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: P. olseni trophozoites were obtained from the gills of parasitized R. decussatus clams, and in vitro cultured for 1–2 months following the procedure described by Casas et al. (2002). A volume of culture containing ~5x10e6 trophozoites was taken from each culture and centrifuged (1000g, 25C, 10 min) to concentrate cells. The concentrated trophozoites were resuspended in 2.5 mL filtered sea water and added to IWAKI 6-well plates.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy mini kit with DNase following manufacturer’s instructions.

treatment_protocol: P. olseni trophozoites were in vitro challenged with 2.5 mL of plasma (treatment) or FSW (control), added into a permeable insert (0.2 µm Anopore® membrane NUNC 25 mm) set in the plate-wells. Four pseudo-replicates (trophozoites from the same culture) for both control and treatment groups were collected at 1, 8 and 24 h since the onset of the challenge.

value: trophozoites

value: in vitro challenge with Manila clam plasma, 24 hours


title: TC25

description:
Gene expression from thymus explant
A_T3


title: xenograft from bone marrow case 4 passage 1 [Case4P1R6]


title: TP-24-R3

description: Gene expression of Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 24 hours, replicate 2b.

source_name: Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 24 hours, replicate 3


title: Primary non-cultured AEC2s 1.45 x 10^6

description:
Primary non-cultured AEC2s
No treatment


title: TP-24-R1

description: Gene expression of Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 24 hours, replicate 1.


title: U2-OS_400 nM THZ2_rep3

description: Gene expression data from U2-OS treated with 400 nM THZ2 for 6 hours


title: U2-OS_400 nM THZ2_rep2

source_name: U2-OS treated with 400 nM THZ2 for 6 hours


title: SJSA-1_25 nM THZ2_rep3

description: Gene expression data from SJSA-1 treated with 25 nM THZ2 for 6 hours


title: U2-OS_400 nM THZ2_rep1


title: TP-8-R4

description: Gene expression of Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 8 hours, replicate 3.

source_name: Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 8 hours, replicate 4

value: in vitro challenge with Manila clam plasma, 8 hours


title: xenograft from bone marrow case 4 passage 1 [Case4P1R5]

value: E/L


title: SJSA-1_DMSO_rep2

description: Gene expression data from SJSA-1 treated with DMSO(control) for 6 hours


title: SJSA-1_100 nM THZ2_rep1


title: SJSA-1_DMSO_rep1

source_name: SJSA-1 treated with DMSO(control) for 6 hours


title: IL4-exposed organoid-expanded AEC2s 645k

description:
IL4-exposed organoid-expanded AEC2s
Culture medium + IL4

value: organoid cultured AEC2s


title: SJSA-1_25 nM THZ2_rep2

source_name: SJSA-1 treated with 25 nM THZ2 for 6 hours


title: SJSA-1_DMSO_rep3


title: xenograft from bone marrow case 4 passage 1 [Case4P1R4]

value: Male


title: SJSA-1_400 nM THZ2_rep1


title: TP-24-R2

description: Gene expression of Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 24 hours, replicate 2.


title: SJSA-1_25 nM THZ2_rep1


title: TP-8-R3

description: Gene expression of Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 8 hours, replicate 2b.

source_name: Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 8 hours, replicate 3


title: U2-OS_100 nM THZ2_rep3

description: Gene expression data from U2-OS treated with 100 nM THZ2 for 6 hours


title: TP-8-R1

description: Gene expression of Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 8 hours, replicate 1.


title: Control organoid-expanded AEC2s 321k

description:
Control organoid-expanded AEC2s
Control culture medium


title: TP-8-R2

description: Gene expression of Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 8 hours, replicate 2.


title: U2-OS_100 nM THZ2_rep2

source_name: U2-OS treated with 100 nM THZ2 for 6 hours


title: IL4-exposed organoid-expanded AEC2s 257k


title: xenograft from bone marrow case 4 passage 1 [Case4P1R2]

source_name: S Fraction


title: xenograft from bone marrow case 4 passage 1 [Case4P1R1]

source_name: G1 Fraction


title: IL13-exposed organoid-expanded AEC2s 275k

description:
IL13-exposed organoid-expanded AEC2s
Culture medium + IL13


title: TP-1-R4

description: Gene expression of Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 1 hour, replicate 3.

source_name: Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 1 hour, replicate 4

value: in vitro challenge with Manila clam plasma, 1 hour


title: xenograft from bone marrow case 21 passage 3 [Case21P3]

source_name: Early S Fraction

source_name: Late S Fraction


title: Control organoid-expanded AEC2s 74k


title: xenograft from bone marrow case 4 passage 1 [Case4P1R3]


title: xenograft from bone marrow case 21 passage 2 [Case21P2]


title: U2-OS_25 nM THZ2_rep3

description: Gene expression data from U2-OS treated with 25 nM THZ2 for 6 hours


title: IL4-exposed organoid-expanded AEC2s 330k


title: U2-OS_25 nM THZ2_rep1

source_name: U2-OS treated with 25 nM THZ2 for 6 hours


title: U2-OS_100 nM THZ2_rep1


title: U2-OS_25 nM THZ2_rep2


title: TP-1-R2

description: Gene expression of Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 1 hour, replicate 2.


title: U2-OS_DMSO_rep3

description: Gene expression data from U2-OS treated with DMSO(control) for 6 hours


title: TP-1-R1

description: Gene expression of Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 1 hour, replicate 1.


title: TP-C-R4

description: Gene expression of Perkinsus olseni trophozoites in vitro challenge, control pool replicate 4.

source_name: Perkinsus olseni trophozoites in vitro challenge, control pool, replicate 4

value: in vitro challenge with filtered seawater, control pool


title: U2-OS_DMSO_rep1

source_name: U2-OS treated with DMSO(control) for 6 hours


title: Control organoid-expanded AEC2s 150k

source_name: Lung alveolar epithelial cells type 2


title: xenograft from bone marrow case 1 passage 1 [Case1P1R3]


title: genomic DNA from FFPE tumor section #49

city: Riyadh

first: Malak

last: Abedalthagafi

state: Ar Raid

address: King Abdullah Rd

department: Genomics Research

country: Saudi Arabia

institute: King Abdulaziz City for Science and Technology

description:
gross total resection
203219650170_R04C01

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina iScan scanner settings for Methylation EPIC Beadchips

data_processing:
Bioconductor Package in R using minfi
Average Beta

label: Cy3, Cy5

label_protocol: labelled based on study number sample used for methylation

extract_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchips using standard Illumina protocol

treatment_protocol: Genomic DNA was extracted and purified using the Promega Maxwell 16 FFPE Plus LEV DNA Purification Kit

tag: sample type

value: Classic Histology type

tag: disease state

value: Average risk

tag: group

value: medulloblastoma WNT

value: FFPE tumor


title: xenograft from bone marrow case 21 passage 1 [Case21P1]

tag: gender


title: TP-1-R3

description: Gene expression of Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 1 hour, replicate 2b.

source_name: Perkinsus olseni trophozoites-Ruditapes philippinarum plasma in vitro challenge, 1 hour, replicate 3

tag: tissue


title: genomic DNA from FFPE tumor section #50

description:
subtotal resection [51-90%]
203219650170_R03C01

value: Female

value: High risk

value: Plexus Tumor


title: Yap/Taz dKO ATAC seq

city: Irvine

first: Hosung

last: Bae

state: CA

address: 839 Health Sciences Road Sprague Hall, Room 150

institute: UC Irvine

data_processing:
First, adapter sequences were removed by cutadapt. Then, reads were aligned to the mouse mm10 reference genome by using bowtie2.
Following processing steps were performed using Genrich.
First, reads mapped to mitochondrial DNA and PCR duplicates were removed.
Then, peaks were called for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: Processed BED (Browser Extensible Data) files are uploaded

source_name: Lgr5+ stem cells

extract_protocol:
tdtomato+ stem cells in dermis were sorted by FACS
Briefly, sorted cells were suspended in lysis buffer and nucleus were collected.
Then, Tn5 transposes were added to perform transposition reaction.
Transposed DNA were eluted and amplified by PCR using barcoded primers. Final products were purified by using AMPure-XP beads.

value: B6/129 mixed

value: Dermis

value: Adult

tag: genotype

value: Lgr5-Cre-ERT2; tdT; Yap-fl/fl; Taz-fl/fl


title: Lats1/2 dKO ATAC seq

value: Lgr5-Cre-ERT2; tdT; Lats1-fl/fl; Lats2-fl/fl


title: TP-C-R2

description: Gene expression of Perkinsus olseni trophozoites in vitro challenge, control pool replicate 2.

source_name: Perkinsus olseni trophozoites in vitro challenge, control pool, replicate 2

value: trophozoites


title: TP-C-R3

description: Gene expression of Perkinsus olseni trophozoites in vitro challenge, control pool replicate 3.

source_name: Perkinsus olseni trophozoites in vitro challenge, control pool, replicate 3


title: IL13-exposed organoid-expanded AEC2s 292k

tag: cell type

value: organoid cultured AEC2s


title: TP-C-R1

description: Gene expression of Perkinsus olseni trophozoites in vitro challenge, control pool replicate 1.

source_name: Perkinsus olseni trophozoites in vitro challenge, control pool, replicate 1


title: genomic DNA from FFPE tumor section #47

description:
subtotal resection [51-90%]
203219650170_R02C01

value: No match


title: Lgr_high ATAC seq

tag: strain

value: Lgr5-Cre-ERT2; tdT


title: xenograft from bone marrow case 1 passage 1 [Case1P1R1]

value: Male

value: E/L


title: genomic DNA from FFPE tumor section #46

description:
Near- gross total resection [> 90%]
203219650170_R01C01

value: Desmoplastic/nodular Histology type

value: family Medulloblastoma SHH


title: 36 hpf JAK1-WT transgenic rep 2

city: Ottawa

first: Sergey

last: Prykhozhij

state: ON

address: Room 318/319 | CAREG, 20 Marie-Curie Private

country: Canada

institute: CHEO Research Institute/University of Ottawa

data_processing:
Read trimming: the raw reads had the adapters “ATCACCGAC” removed and filtered by the quality of 20 with the Trim Galore (v0.4.4).
Read mapping: The reads passed through the two-step mapping for RNA-Seq data from Ion proton: first with STAR (v2.7) and then mapping the unmapped reads from the first alignment using bowtie2. The two mapped files were merged with Picard tools (v2.5.0).
Read counting: The counts were extracted using HTSeq (V0.9.1).
Genome_build: danRer11
Supplementary_files_format_and_content: read counts

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish experiments and husbandry follows standard protocols in accordance with the standards of the University Committee on Laboratory Animals (UCLA) of Dalhousie University. Zebrafish embryos were maintained at 28.5 °C during development and as adults. Embryos were grown in egg water (1x E3 prepared from 60x E3 stock).

extract_protocol:
Each total RNA sample was extracted from 30-50 zebrafish embryos by homogenizing them in 500 µL Trizol reagent (Thermo Fisher Scientific, 15596026) using 1 mL syringe and 22G needle. Lysates were centrifuged at 12,000 g at 4ºC for 5 minutes and the supernatant was transferred to Phasemaker Tubes (Thermo Fisher Scientific, A33248) and RNA was purified according to the Phasemaker Tubes protocol manual.
Total RNA samples were measured and analyzed for integrity on Agilent Tape Station. Samples with RNA integration number ≥8 were selected for library preparation. Poly-A enrichment was performed from 20 µg of total RNA to enrich for mRNA (Dyna beads mRNA direct micro Kit). 100ng of poly-A enriched RNA was fragmented using RNase III and purified using magnetic bead clean up module (RNA Seq V2 kit, Life Technologies). The size distribution of the fragmented RNA was assessed on Agilent Tape Station using RNA HS screen tape assay and 50 ng of fragmented polyA-enriched RNA was used to prepare whole transcriptome library (RNA seq V2). Yield and size distribution of the library was analyzed on Agilent Tape Station using D1000 screen tape. Barcoded library was equally pooled and amplified onto Ion Sphere™ Particles (ISPs) from Ion Pi HiQ OT2 kit (Life Technologies). ISPs enriched with template library were loaded onto Ion PI chip V3 and sequenced on Ion Proton from Thermo Fisher.

tag: developmental stage

value: 36 hours post-fertilization

value: casper

value: whole embryo


title: 36 hpf JAK1-WT transgenic rep 3


title: genomic DNA from FFPE tumor section #45

description:
gross total resection
203219670008_R07C01

value: Female

value: Classic Histology type

value: High risk

value: family Medulloblastoma group 3 and 4

value: FFPE tumor


title: FcgRIIB_neg_3

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description:
FcgRIIB- T cells sorted from 3 pooled spleens.
PolyA RNA
processed data file: CD8.FcgRIIB.exon.RPKM.txt

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Tophat2 and the UCSC mm9 known gene reference transcriptome.
For each sample, reads that overlapped exons of unique ENTREZ genes were annotated using the GenomicRanges (v1.22.4) package in R/Bioconductor.
Genes with less than 3 reads per million in at least 3 samples were removed and the remaining genes normalized to RPKM using custom R scripts.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.sort.dupMark.fragNA.norm1000000.bw: bigWig files
Supplementary_files_format_and_content: CD8.FcgRIIB.exon.RPKM.txt: Tab-delimited text file includes RPKM normalized read counts for each detected gene for each sample.

source_name: FcgRIIB- Effector CD8 T cells

extract_protocol:
On day 14 post grafting, 1000 cells were FACS sorted into RLT+1%Bme using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research).
All purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara). Final libraries were constructed using 200 pg of cDNA as input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

treatment_protocol: 10^6 antigen-specific OT-I T cells were adoptively transferred 24hrs prior to skin transplantation with OVA-expressing skin.

value: CD8 T cells

tag: strain/background

value: OT-I

tag: sorting markers

value: FcgRIIB- CD44hi Thy1.1+ CD8+

tag: timepoint

value: Day 14 post OVA skin graft


title: genomic DNA from FFPE tumor section #44

description:
gross total resection
203219670008_R06C01

value: Average risk


title: FcgRIIB_neg_2


title: 36 hpf JAK1-A634D transgenic rep 3


title: genomic DNA from FFPE tumor section #43

description:
Near- gross total resection [> 90%]
203219670008_R04C01

value: Male


title: U2-OS_DMSO_rep2

value: bone

value: osteosarcoma

tag: cell line


title: FcgRIIB_neg_1


title: genomic DNA from FFPE tumor section #38

description:
gross total resection
200970090015_R08C01

value: Medulloblastoma group 3 and 4


title: 36 hpf JAK1-A634D transgenic rep 1

value: 36 hours post-fertilization


title: 36 hpf JAK1-A634D transgenic rep 2

value: casper


title: FcgRIIB_pos_4

description:
FcgRIIB+ T cells sorted from 3 pooled spleens.
PolyA RNA
processed data file: CD8.FcgRIIB.exon.RPKM.txt

source_name: FcgRIIB+ Effector CD8 T cells

value: FcgRIIB+ CD44hi Thy1.1+ CD8+


title: FcgRIIB_neg_4


title: genomic DNA from FFPE tumor section #39

description:
PR [10-50%]
200970090015_R07C01


title: FcgRIIB_pos_3


title: genomic DNA from FFPE tumor section #40

description:
gross total resection
200970090015_R06C01

value: Desmoplastic/nodular Histology type

value: Medulloblastoma SHH


title: TNF 0hr rep4

city: Toronto

first: Philip

last: Marsden

address: 209 Victoria St

institute: St. Michael's hospital/University of Toronto

hyb_protocol: Cy3 labeled cRNA was fragmented by adding 11ul 10x Blocking Agent and 2.2ul of 25X Fragmentation Buffer, then heated at 60C for 30min after which 55ul 2X GE Hybridization buffer was added. 100ul of hybridization solution was then despensed into the gasket slide and assembled to the LncRNA expression microarray slide. Slides were incubated for 17 hours at 65C in an Agilent Hybridization Oven.

scan_protocol: Hybridized arrays were washed, fixed and scanned using Agilent DNA Microarray Scanner (G2505B).

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using GeneSpring GX v11.5.1 software (Agilent Technologies)

source_name: HUVEC

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). mRNA was purified from 1 microgram of total RNA (mRNA-ONLY eukaryotic mRNA Isolation Kit, Epicentre)

growth_protocol: HUVEC were grown as in Marsden PA, et al. (1992) Molecular cloning and characterization of human endothelial nitric oxide synthase. FEBS Lett 307(3):287-293. HMVEC were purchased from Lonza and grown according to their instructions.

extract_protocol: RNA was extracted using Qiagen Rneasy plus mini kit® as per manufactures recommendations.

treatment_protocol: TNF(10ng/uL) treatment was performed for 0, 4 or 24hr. TNF(10ng/uL) treatment was performed for 4hr to generate VCAM1 high and low cells.

value: HUVEC

value: TNF 0hr


title: TNF 4hr rep4

value: TNF 4hr


title: 36 hpf wild-type rep2

value: wild-type

value: whole embryo


title: VCAM1 5% LOW rep4

value: VCAM1 5% LOW


title: 36 hpf wild-type rep1


title: FcgRIIB_pos_2

value: CD8 T cells

value: OT-I

value: Day 14 post OVA skin graft


title: 36 hpf JAK1-WT transgenic rep 1


title: genomic DNA from FFPE tumor section #41

description:
subtotal resection [51-90%]
200970090015_R05C01

value: Male

value: Classic Histology type

value: High risk

value: FFPE tumor


title: VCAM1 5% HIGH rep4

value: VCAM1 5% HIGH


title: TNF 24hr rep4

value: TNF 24hr


title: 36 hpf wild-type rep3

value: 36 hours post-fertilization

value: casper


title: FcgRIIB_pos_1

value: FcgRIIB+ CD44hi Thy1.1+ CD8+


title: 28 hpf JAK1-WT transgenic rep 3

value: 28 hours post-fertilization


title: genomic DNA from FFPE tumor section #22

description:
gross total resection
200970090015_R04C01

value: Female

value: Average risk

value: Medulloblastoma group 3 and 4


title: genomic DNA from FFPE tumor section #2

description:
gross total resection
200970090015_R03C01


title: VCAM1 5% HIGH rep3

value: HUVEC


title: 28 hpf JAK1-WT transgenic rep 2

value: whole embryo


title: 28 hpf JAK1-WT transgenic rep 1


title: genomic DNA from FFPE tumor section #36

description:
gross total resection
200970090015_R02C01


title: TNF 0hr rep3

value: TNF 0hr


title: TNF 4hr rep3

value: TNF 4hr


title: TNF 24hr rep3


title: 28 hpf JAK1-A634D transgenic rep 3


title: VCAM1 5% LOW rep2

value: VCAM1 5% LOW


title: genomic DNA from FFPE tumor section #35

description:
gross total resection
200970090015_R01C01

value: Male

value: Classic Histology type


title: genomic DNA from FFPE tumor section #37

description:
gross total resection
200928190163_R08C01

value: High risk

value: FFPE tumor


title: genomic DNA from FFPE tumor section #34

description:
gross total resection
200928190163_R07C01


title: 28 hpf JAK1-A634D transgenic rep 1


title: 28 hpf JAK1-A634D transgenic rep 2


title: SW620_F5446_2

city: Augusta

first: Kebin

last: Liu

address: 1410 Laney Walker Blvd

department: Biochemistry and Molecular Biology

institute: Medical College of Georgia

hyb_protocol: The labeled cDNAs were hybridized onto the arrays using Affymetrix GeneChip fluidics station 450 systems.

scan_protocol: Arrays were scanned on GeneChip 3000 G7

data_processing: The expression data were imported into Partek GS version 6.6 using a standard import tool with GeneChip robust multiarray analysis normalization. The differential expressions were calculated using ANOVA of Partek package.

label: biotin using GeneChip WT PLUS Reagent kit

label_protocol: Total RNA samples were processed using the Ambion WT expression kit (Life Technologies, Calsbad, CA) and a GeneChip WT terminal labeling kit (Affymetrix). The synthesized sense strand cDNAs were fragmented and biotin-labeled using a GeneChip WT terminal labeling kit.

growth_protocol: Human colon carcinoma SW620 cells were cultured in RPMI medium plus 10% FBS.

extract_protocol: Total RNA extracted using Trizol (invitrogen) following manufacturer's instructions

treatment_protocol: Cells were treated with small molecule SUV39H1-selective inhibitor F5446 (Lu et al., 2019, Cancer Immunol Res 7:414-427 ) at 50 nM for 2 days.

tag: treatment


title: VCAM1 5% HIGH rep2

value: VCAM1 5% HIGH


title: TNF 4hr rep2


title: TNF 24hr rep2

value: TNF 24hr


title: SW620_F5446_1


title: TC32

description:
microRNA expression from thymus explant
E_T56

hyb_protocol: Dried Cy3-labelled miRNA sample was resuspended with 17uL of nuclease-free water and mixed to Hyb Spike-In and 10x GE Blocking Agent solutions, and 2x Hi-RPM Hybridization buffer. The final volume was incubated at 100°C for 5 minutes and hybridized to Human miRNA Microarray slides (8x60K) -  (G4872A) - Agilent Technologies, for 20 hours at 55°C in a rotating Agilent hybridization oven (20rpm).

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 8x60k miRNA microarray slides.

data_processing: Data extraction was carried out with Feature Extraction Software 10.7.3 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The selected miRNA transcripts were used for analysis using the R software and considering up to 4 NA for each age interval (A to E groups).

source_name: thymus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.05 ug RNA using the microRNA Complete Labeling and Hyb Kit (Agilent Technologies), without column purification, according to the manufacturer's instructions.

extract_protocol: Thymus explants (3-4 mm3) were homogenized with TissueRupter (Qiagen) and total RNA was extracted from the homogenates using the RNeasy Lipid Tissue Kit (Qiagen).

value: F

tag: age at surgery (yr/mo/d)

value: 2y 6mo 10d


title: 28 hpf wild-type rep3

value: wild-type

value: 28 hours post-fertilization

value: casper


title: genomic DNA from FFPE tumor section #33

description:
Near- gross total resection [> 90%]
200928190163_R06C01

value: Female

value: Average risk

value: Medulloblastoma group 3 and 4


title: VCAM1 5% LOW rep3

value: HUVEC


title: TC04

description:
microRNA expression from thymus explant
E_T55

value: 2y 5mo


title: 28 hpf wild-type rep2

value: whole embryo


title: genomic DNA from FFPE tumor section #32

description:
gross total resection
200928190163_R05C01

value: Medulloblastoma SHH


title: SW620_Ctrl_2

value: control


title: 28 hpf wild-type rep1


title: RNA_Seq_OS_12_3_Brain

city: Kunming

first: Wansheng

last: Jiang

state: Yunnan

address: 32# East Jiaochang Road

institute: Kunming Institute of Zoology, Chinese Academy of Sciences

data_processing:
High-quality clean reads were obtained by removing the adaptor sequences, duplicated sequences, ambiguous reads (‘N’), and low-quality reads.
De novo assembly of clean reads was carried out using Trinity software (Grabherr et al. 2011) with the default settings.
The generated unigenes of the three species were annotated by using the Trinotate transcriptome annotation pipeline (Haas et al. 2013).
The Illumina reads for each individual library were mapped back to the appropriate transcriptome using Bowtie2 (Langmead et al. 2009) within the program RSEM (Li & Dewey 2011) to estimate the number of reads mapped to each contig.The normalization of gene expression levels was performed using expected count for each gene.
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample according to species

organism: Oreoglanis setiger

source_name: Brain removed from fresh sample and frozen immediately in liquid nitrogen

extract_protocol:
Total RNA of each sample was extracted from the tissue samples using TRlzol Reagent (Invitrogen) and conjunction with an RNase-free DNaseI (TaKaRa) according to the manufacturer’s protocols.
The transcriptome libraries were generated using Illumina TruSeqTM RNA Sample Preparation Kit (Illumina) following the manufacturer’s recommendations

value: Brain


title: TC40

city: Sao Paulo

first: Carlos

last: Moreira-Filho

institute: Faculdade de Medicina da Universidade de Sao Paulo

description:
microRNA expression from thymus explant
E_T49

value: M

value: 1y 8mo


title: TC60

description:
microRNA expression from thymus explant
E_T50


title: SW620_Ctrl_1


title: genomic DNA from FFPE tumor section #13

description:
subtotal resection [51-90%]
200928190163_R04C01

value: Male

value: Classic Histology type

value: High risk

value: FFPE tumor


title: RNA_Seq_OS_12_2_Muscle

source_name: Muscle removed from fresh sample and frozen immediately in liquid nitrogen

value: Muscle


title: genomic DNA from FFPE tumor section #24

description:
Near- gross total resection [> 90%]
200928190163_R02C01


title: RNA_Seq_OS_12_1_Liver

source_name: Liver removed from fresh sample and frozen immediately in liquid nitrogen

value: Liver


title: TNF 0hr rep2

value: TNF 0hr


title: VCAM1 5% LOW rep1

value: VCAM1 5% LOW


title: TC49

description:
microRNA expression from thymus explant
D_T44

value: 1y 5mo


title: VCAM1 5% HIGH rep1

value: HUVEC

value: VCAM1 5% HIGH


title: TNF 4hr rep1

value: TNF 4hr


title: TNF 0hr rep1


title: TNF 24hr rep1

value: TNF 24hr


title: TC05

description:
microRNA expression from thymus explant
D_T43

value: F


title: RNA_Seq_OS_11_2_Muscle


title: Self-renewing Macrophages

city: Kumamoto

first: Hesham

middle: Elsayed

last: Nasser

state: Kumamoto

address: 2-2-1 Honjo, Chou-ku

department: Infection and Hematopoiesis

institute: Joint Research Center for Human Retrovirus Infection, Kumamoto University

description: M-CSF bone marrow-derived self-renewing macrophages after passage 4

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray Ver2.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%)

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500

source_name: C57BL/6 Mouse bone marrow-derived self-renewing macrophages

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Total bone marrow cells, which were obtained from C57BL/6 mice.

extract_protocol: Total RNA was isolated using the ISOGEN II reagent (Nippon Gene, Tokyo, Japan), according to manufaturer's instructions.

treatment_protocol: Total bone marrow cells were suspended into RPMI1640 media supplemented with 10% heat-inactivated FCS and 100 ng/ml rhM-CSF, seeded onto non-coated 10-cm dishes at 3 x 105 cells/mlabd cultured for 5-7 days for primary macrophages and passaged four times for self-renewing macrophages.

value: Bone Marrow


title: TC42

address: Av. Dr. Eneas Carvalho de Aguiar 647

description:
microRNA expression from thymus explant
D_T40

value: 1y 2mo 19d


title: genomic DNA from FFPE tumor section #4

description:
gross total resection
200928190156_R07C01

value: Female

value: Average risk

value: medulloblastoma WNT


title: RNA_Seq_OS_11_1_Liver


title: genomic DNA from FFPE tumor section #12

description:
gross total resection
200928190163_R03C01

value: Male

value: Classic Histology type

value: High risk

value: Atypical teratoid/rhabdoid tumor


title: TC58

description:
microRNA expression from thymus explant
D_T38

value: 1y 2mo


title: RNA_Seq_OS_10_3_Brain

value: Brain


title: RNA_Seq_OS_11_3_Brain


title: TC08

description:
microRNA expression from thymus explant
D_T37


title: IL13-exposed organoid-expanded AEC2s 701k

description:
IL13-exposed organoid-expanded AEC2s
Culture medium + IL13

value: organoid cultured AEC2s

tag: passage


title: genomic DNA from FFPE tumor section #1

description:
gross total resection
200928190156_R06C01

value: Medulloblastoma group 3 and 4

value: FFPE tumor


title: RNA_Seq_OS_10_2_Muscle

value: Muscle


title: TC09

description:
microRNA expression from thymus explant
D_T46

value: M

value: 1y 6mo 10d


title: genomic DNA from FFPE tumor section #6

description:
gross total resection
200928190156_R08C01

value: Desmoplastic/nodular Histology type


title: genomic DNA from FFPE tumor section #27

description:
gross total resection
200928190156_R04C01

value: LC/Anplastic Histology type


title: Liver right lobe_12_GLU+GAL42

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent Gene Expression Hybridization Kit. Samples were applied to 8*60K v2 microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations and finally covered with an ozone-barrier slide.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (10.7.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. QC checks were done on raw data and all arrays passed. Spots with a mean signal higher than twice the background value over all arrays and both channels were considered to be expressed. Data was normalized according to Pellis et al. (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

source_name: Liver (right lobe)

label_protocol: 200 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously by van Schothorst et al. (Anal Biochem 2007;363:315-7). All Cy3-labeled samples  were used for the reference pool.

extract_protocol: Total RNA was isolated from the right lobe of the liver with the RNeasy kit (Qiagen), quantified using Nanodrop (IsoGen Life Science) and qualified using TapeStation (Agilent).

treatment_protocol: The C57BL/6JRcc female mice (3 weeks old) were individually housed (12h light–dark cycle, 23±1°C, 55±15% humidity), with ad libitum access to feed and water. A semi-synthetic diet (16% energy from fat, 20% energy from protein, 32% energy from starch, and 32 en% from monosaccharides: either glucose only (GLU) or glucose and galactose in a 1:1 ration (called GLU+GAL). After three weeks on the diets, animals were sacrificed in a food-deprived state in the light phase. Liver was immediately isolated, liver lobes were separated, snap-frozen in liquid nitrogen and stored at -80C until analysis.

value: C57BL/6JRcc, female, 6 weeks old, liver


title: genomic DNA from FFPE tumor section #28

description:
gross total resection
200928190156_R05C01

value: Average risk


title: genomic DNA from FFPE tumor section #7

description:
gross total resection
200928190163_R01C01


title: TC50

description:
microRNA expression from thymus explant
D_T36

value: 1y 1mo 10d


title: Liver right lobe_10_GLU+GAL42


title: RNA_Seq_OS_10_1_Liver

value: Liver


title: RNA_Seq_GM_7_3_Brain

organism: Glyptothorax macromaculatus


title: Primary Macrophages

description: M-CSF monocyte-derived macrophage at Day 5

source_name: C57BL/6 Mouse bone marrow monocyte-derived macrophages

value: Bone Marrow

value: Male


title: TC47

description:
microRNA expression from thymus explant
D_T35

value: 1y 1mo


title: TC66

description:
microRNA expression from thymus explant
C_T31


title: RNA_Seq_GM_7_2_Muscle


title: Liver right lobe_11_GLU+GAL42


title: Liver right lobe_8_GLU+GAL42


title: TC31

description:
microRNA expression from thymus explant
C_T30

value: F

value: 9mo 26d


title: genomic DNA from FFPE tumor section #25

description:
gross total resection
200928190156_R02C01

value: Classic Histology type

value: High risk

value: Medulloblastoma WNT


title: Liver right lobe_9_GLU+GAL42


title: genomic DNA from FFPE tumor section #21

description:
subtotal resection [51-90%]
200928190156_R01C01

value: Medulloblastoma group 3 and 4

value: FFPE tumor


title: RNA_Seq_GM_7_1_Liver


title: Liver right lobe_7_GLU+GAL42


title: genomic DNA from FFPE tumor section #19

description:
gross total resection
200928190094_R08C01


title: Liver right lobe_6_GLU+GAL42


title: TC07

description:
microRNA expression from thymus explant
C_T29

value: M

value: 9mo 2d


title: TC27

description:
microRNA expression from thymus explant
C_T28

value: 9mo 1d


title: genomic DNA from FFPE tumor section #26

description:
gross total resection
200928190156_R03C01


title: RNA_Seq_GM_6_2_Muscle

value: Muscle


title: RNA_Seq_GM_6_1_Liver


title: Liver right lobe_4_GLU+GAL42

value: C57BL/6JRcc, female, 6 weeks old, liver


title: Liver right lobe_5_GLU+GAL42


title: TC55

description:
microRNA expression from thymus explant
C_T25

value: 8mo 9d


title: genomic DNA from FFPE tumor section #17

description:
gross total resection
200928190094_R06C01


title: RNA_Seq_GM_5_3_Brain

value: Brain


title: TC01

description:
microRNA expression from thymus explant
C_T24

value: 7mo 17d


title: genomic DNA from FFPE tumor section #30

description:
subtotal resection [51-90%]
200928190094_R05C01

value: Female

value: Desmoplastic/nodular Histology type


title: RNA_Seq_GM_6_3_Brain


title: TC19

description:
microRNA expression from thymus explant
B_T21

value: F

value: 6mo 9d


title: RNA_Seq_GM_5_2_Muscle


title: RNA_Seq_GM_5_1_Liver

value: Liver


title: genomic DNA from FFPE tumor section #16

description:
gross total resection
200928190094_R04C01

value: Male

value: Classic Histology type

value: Average risk


title: TC18

description:
microRNA expression from thymus explant
B_T18

value: 6mo 6d


title: TC02

description:
microRNA expression from thymus explant
B_T20

value: 6mo 10d


title: RNA_Seq_BY_3_3_Brain

organism: Bagarius yarrelli


title: TC24

description:
microRNA expression from thymus explant
B_T17

value: M

value: 6mo 3d


title: RNA_Seq_BY_3_2_Muscle

value: Muscle


title: genomic DNA from FFPE tumor section #18

description:
gross total resection
200928190094_R07C01

value: LC/Anplastic Histology type

value: High risk

value: Medulloblastoma group 3 and 4

value: FFPE tumor


title: Liver right lobe_12_GLU42

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: C57BL/6JRcc, female, 6 weeks old, liver


title: genomic DNA from FFPE tumor section #15

description:
gross total resection
200928190094_R03C01

value: Medulloblastoma SHH


title: TC46

description:
microRNA expression from thymus explant
B_T15

value: F

value: 5mo 10d


title: Liver right lobe_2_GLU+GAL42


title: Liver right lobe_1_GLU+GAL42


title: Liver right lobe_3_GLU+GAL42


title: Liver right lobe_10_GLU42


title: RNA_Seq_BY_3_1_Liver

value: Liver


title: genomic DNA from FFPE tumor section #42

description:
gross total resection
200970090025_R07C01

value: Female


title: Liver right lobe_9_GLU42


title: TC39

description:
microRNA expression from thymus explant
B_T12

value: 3mo 18d


title: RNA_Seq_BY_2_3_Brain

value: Brain


title: TC37

description:
microRNA expression from thymus explant
B_T11

value: 3mo 19d


title: RNA_Seq_BY_2_2_Muscle


title: TC26

description:
microRNA expression from thymus explant
B_T10

value: 2mo 11d


title: Liver right lobe_7_GLU42


title: Liver right lobe_11_GLU42


title: RNA_Seq_BY_2_1_Liver


title: TC29

description:
microRNA expression from thymus explant
B_T9

value: M

value: 2mo 1d


title: RNA_Seq_BY_1_3_Brain


title: RNA_Seq_BY_1_2_Muscle

value: Muscle


title: genomic DNA from FFPE tumor section #29

description:
gross total resection
200928190094_R01C01

value: Classic Histology type

value: Average risk

value: medulloblastoma WNT


title: genomic DNA from FFPE tumor section #14

description:
gross total resection
200928190094_R02C01

value: Male

value: Desmoplastic/nodular Histology type

value: FFPE tumor


title: RNA_Seq_BY_1_1_Liver


title: TC30

description:
microRNA expression from thymus explant
A_T4


title: TC25

description:
microRNA expression from thymus explant
A_T3

value: F


title: O. mekongensis de novo transcriptome

city: Bangkok

first: Arin

last: Ngamniyom

address: 114 Sukumvit 23

department: Major in Environment, Faculty of Environmental Culture and Eco-tourism

country: Thailand

institute: Srinakharinwirot University

data_processing:
Base Quality and Phred score relationship with the Illumina CASAVA v1.8 software
Trinity (Grabherr et al., 2011) is the software chosen to complete the transcriptome reconstruction process.
Using InterProscan software to annotate the Unigenes with InterPro database. Category and annotate Unigenes according to the protein domain
PFAM, the prediction of protein structure domain: HMMER 3.0 package,hmmscan, the evalue threshold is 0.01
GO: based on the protein annotation results of NR and Pfam: Blast2GO v2.5 (Götz et al., 2008)

organism: Oryzias mekongensis

source_name: whole body

extract_protocol:
RNeasy Mini Kit (Qiagen, Germany)
RNA libraries sequencing using standard Illumina protocols

treatment_protocol: treated with DNase I

value: whole body

tag: origin

value: Thailand


title: fresh_hepatocytes_isolation_1

status: Public on Dec 26 2019

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

institute: Utrecht University

description: freshly isolated primary hepatocytes

data_processing:
RNA-seq reads were aligned to the reference genome using STAR version 2.4.2a
Read groups were added to the BAM files with Picard's AddOrReplaceReadGroups
The BAM files are sorted with Sambamba v0.4.5 and transcript abundances were quantified with HTSeq-count version 0.6.1p1, using the union mode.
Genome_build: GRCh37

source_name: primary hepatocytes

extract_protocol:
Cells were stored in RLT. Total RNA was isolated using a RNeasy Mini Kit (Qiagen).
Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex)

value: primary hepatocytes

tag: growth


title: fresh_hepatocytes_isolation_2

description: freshly isolated primary hepatocytes


title: human_3_SF_DM_d5

description: liver organoids, donor 3, 5 days in differentiation medium, spinner flask

source_name: adult stem cell-derived liver organoids

value: adult stem cell-derived liver organoids


title: human_3_SF_EM

description: liver organoids, donor 3, expansion medium, spinner flask

value: expansion medium, spinner flask


title: human_3_SF_DM_d12

description: liver organoids, donor 3, 12 days in differentiation medium, spinner flask


title: human_3_SC_EM

description: liver organoids, donor 3, expansion medium, static control

value: expansion medium, static control


title: Liver right lobe_4_GLU42

value: C57BL/6JRcc, female, 6 weeks old, liver


title: human_3_SC_DM_d12

description: liver organoids, donor 3, 12 days in differentiation medium, static control


title: human_3_SC_DM_d5

description: liver organoids, donor 3, 5 days in differentiation medium, static control


title: human_2_SF_EM

description: liver organoids, donor 2, expansion medium, spinner flask


title: human_2_SF_DM_d5

description: liver organoids, donor 2, 5 days in differentiation medium, spinner flask


title: Liver right lobe_8_GLU42

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: human_2_SC_EM

description: liver organoids, donor 2, expansion medium, static control


title: Liver right lobe_5_GLU42


title: human_2_SF_DM_d12

description: liver organoids, donor 2, 12 days in differentiation medium, spinner flask


title: human_2_SC_DM_d5

description: liver organoids, donor 2, 5 days in differentiation medium, static control


title: human_2_SC_DM_d12

description: liver organoids, donor 2, 12 days in differentiation medium, static control


title: Liver right lobe_6_GLU42


title: human_1_SF_EM

description: liver organoids, donor 1, expansion medium, spinner flask


title: Liver right lobe_3_GLU42


title: human_1_SF_DM_d5

description: liver organoids, donor 1, 5 days in differentiation medium, spinner flask


title: Liver right lobe_1_GLU42


title: Liver right lobe_2_GLU42


title: human_1_SC_EM

description: liver organoids, donor 1, expansion medium, static control


title: human_1_SF_DM_d12

description: liver organoids, donor 1, 12 days in differentiation medium, spinner flask


title: human_1_SC_DM_d5

description: liver organoids, donor 1, 5 days in differentiation medium, static control


title: cryopreserved_hepatocytes

description: cryopreserved primary hepatocytes


title: human_1_SC_DM_d12

description: liver organoids, donor 1, 12 days in differentiation medium, static control


title: REX556 BFP+ rep2

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
Sequence reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped read pairs (fragments) were retained.
Genewise counts were obtained using featureCounts. Fragments overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped fragments) value of 0.5 or greater in at least two libraries. The immune globulin genes, the gene modules, the pseudo genes, the genes from non-primary chromosome assemblies, the ribosomal RNA genes and the genes that do not have official symbols were also removed from the analysis.
Counts were converted to log2 counts per million, quantile normalized and precision weighted with the "voom" function of the limma package, then normalized by the gene lengths. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.05 or less and had an expression change of two folds or greater. A minimum fold change of 1.2 was also required to call the DE genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file 'Raw_Read_Counts.txt' includes raw read counts for genes in each library.

source_name: FLt3-ligand derived pDCs

growth_protocol:
DCs were grown from BM precursors for 8 days in Flt3-ligand
sorting protocol: pDCs were sorted from culture based on SiglecH and CD11b and expression of CD11b

extract_protocol:
RNA purification was performed following the manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the SMART-Seq v4 Ultra low Input RNA kit(Clontech Laboratories) following the manufacturer’s instructions.

treatment_protocol: Cells were stimulated 24hr with IMQ 1ug/ml in cultured cell media

value: FLt3-ligand derived pDCs

value: pDC

tag: population


title: REX556 BFP- rep2


title: ANS+H3R #3_Heart

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

institute: University of Toyama

description:
Co-treatment of angiotensin II, nephrectomy, salt and H3R agonisit
Heart_Shamvs.H_ANSvs.H_ANS_H3a.xlsx

data_processing:
Reads were mapped on mm10 mouse reference genome and quantified using CLC Genomics Workbench version 9.5.1 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 9.5.1.
Filtering characteristics of fold-change -2 to 2 (false discovery rate (FDR) at P < 0.05) were used to identify the DEGs.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

source_name: Co-treatment of angiotensin II, nephrectomy, salt and H3R agonist

extract_protocol:
Kidney and heart were removed, flash frozen on dry ice, and total RNA was extracted from colon of mice using ISOGEN II reagent (Nippon Gene). 500 ng of total RNA were ribosomal RNA-depleted using NEBNext rRNA Depletion Kit (New England Biolabs), and converted to Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart

tag: age

value: 2 months

tag: Sex

value: male


title: REX550 BFP- rep1

tag: tissue


title: ANS+H3R #1_Heart


title: REX550 BFP+ rep1


title: ANS #2_Heart

description:
Co-treatment of angiotensin II, nephrectomy and salt
Heart_Shamvs.H_ANSvs.H_ANS_H3a.xlsx


title: ANS+H3R #2_Heart


title: ANS+H3R #4

description:
Co-treatment of angiotensin II, nephrectomy, salt and H3R agonisit
Kidney_Shamvs.ANSvs.ANS+H3R.xlsx

value: Kidney


title: ANS+H3R #1


title: Sham #2_Heart

source_name: sham


title: ANS #1_Heart

source_name: Co-treatment of angiotensin II, nephrectomy and salt


title: Sham #3_Heart


title: Sham #6


title: ANS+H3R #2


title: ANS #3_Heart


title: ANS #5

description:
Co-treatment of angiotensin II, nephrectomy and salt
Kidney_Shamvs.ANSvs.ANS+H3R.xlsx


title: Sham #1_Heart


title: ANS #4


title: ANS+H3R #5


title: ANS #1


title: ANS #2


title: Sham #5


title: ANS+H3R #3


title: Sham #4


title: ANS #3


title: Sham #3


title: Sham #2


title: Sham #1


title: H1975_TGFb_8h_1

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

hyb_protocol: 15 µg labelled cRNA were hybridized onto Human HuGene20-st  arrays (Affymetrix, CA, USA) for 16h at 45°C using Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 using the GeneChip Operating Software (Affymetrix).

data_processing: R/Bioconductor using RMA as implemented in the R/Bioconductor package 'oligo'

label: Biotin

source_name: Lung

label_protocol: Biotinylated cRNA was generated from 1.5 µg total RNA using the One-Cycle Target Labeling Assay (Affymetrix).

growth_protocol: The human lung adenocarcinoma cell line H1975 was purchased from ATCC and cultivated in Dulbecco's modified Eagle's Medium (DMEM, Lonza) supplemented with 10% FCS (Gibco) and 1% penicillin/streptomycin (Gibco).

extract_protocol: RNeasy Mini Plus Kit (Qiagen, Hilden, Germany)

treatment_protocol: Cells were starved over night before treatment and then supplemented with 2 ng/ml of human TGFβ1 (R&D Systems #240-B-010) and 80 ng/ul of human HGF (R&D Systems) was used for stimulation and RNA was extacted at the indicated time points.

tag: gender

value: female

tag: time

value: Lung

tag: stimulus

value: TGF-beta stimulation


title: H1975_TGFb_24h_2


title: H1975_HGF_48h_3

value: HGF stimulation


title: H1975_TGFb_6h_1


title: H1975_HGF_48h_1


title: H1975_HGF_48h_2


title: H1975_TGFb_4h_1


title: H1975_TGFb_48h_1


title: H1975_TGFb_24h_3


title: H1975_HGF_24h_1


title: H1975_TGFb_12h_1


title: H1975_TGFb_0.5h_2


title: H1975_TGFb_1h_1


title: H1975_HGF_8h_1


title: H1975_TGFb_48h_3


title: H1975_HGF_24h_2


title: H1975_TGFb_2h_1


title: H1975_HGF_18h_1


title: H1975_TGFb_18h_1


title: H1975_TGFb_0.5h_1


title: H1975_HGF_24h_3


title: H1975_HGF_12h_1


title: H1975_HGF_0.5h_1


title: H1975_HGF_6h_1


title: H1975_HGF_2h_1


title: H1975_HGF_4h_1


title: 1_primary colorectal carcinoma

city: Shanghai

first: DA

last: FU

state: Shanghai

address: Middle 301 Yanchang Road

institute: Shanghai Tenth People's Hospital

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: Data were analyzed with Chromosome Analysis Suite (ChAS) ChAS 3.1.

label: Cy3 and Cy5

source_name: primary colorectal carcinoma

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Biospecimens confirmed by two independent pathologists were collected from patients with CRC undergoing surgical resection. Primary CRC with (MT) or without liver metastasis (NM), matched hepatic metastatic focus (LM), and paracarcinoma normal colorectal tissues (PN) morphology was confirmed by using cryostat frozen sections stained with hematoxylin and eosin.

extract_protocol: Using a co-isolation protocol, DNA and RNA were purified simultaneously prepared with QIAGEN AllPrep DNA/RNA Micro Kit (Qiagen, CA, USA), according to manufacturer protocols.

treatment_protocol: None of the participants received chemotherapy, radiotherapy, or immunotherapy before surgical resection.

value: Female

value: colorectal

tag: tumor stage


title: H1975_Control_48h_1

value: Control


title: 1_normal colorectal tissue

source_name: normal colorectal tissue


title: H1975_HGF_1h_1


title: 2_synchronous matched liver metastasis

source_name: synchronous matched liver metastasis

value: Male

value: liver


title: H1975_Control_4h_1


title: H1975_Control_24h_3


title: H1975_Control_0.5h_1


title: H1975_Control_1h_1


title: H1975_TGFb_48h_2


title: H1975_Control_0h_1


title: H1975_Control_24h_1


title: H1975_Control_24h_2


title: H1975_Control_2h_1


title: Eed_matKO_TE_B6129xPWK_H3K4me3_rep1

city: Cincinnati

first: Zhiyuan

last: Chen

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description:
Sample 31
H3K4me3

data_processing:
Library strategy: CUT&RUN
RNA-seq datasets:
Low quality bases and sequencing adaptors of raw RNA-seq reads were trimmed using Trim Galore (version 0.4.5) with parameters “-q 20 –length 20bp”. Reads after trimming were then aligned to the mm9 reference genome using HISAT2 (version 2.1.0) with parameters “--sp 1000,1000 --dta-cufflinks --no-unal”.
Following reads mapping, uniquely aligned reads were retrieved by selecting the alignment records with “NH:i:1” tag and mapping quality greater than 30.
SNPsplit (version 0.3.2) was used separate parental-allele-specific reads and bamCoverage from deepTools (version 3.0.2) was used to generate bigwig tracks with parameters “--skipNonCoveredRegions --binSize 10 --scaleFactor 1”.
Raw read counts for each gene were generated using TEtranscripts (version 1.5.1) and statistical significance [i.e. false discovery rate (FDR)] was computed using the DESeq R package (version 1.34.1) . Only genes with RPKM > 1 in either group, FDR < 0.05 and fold change (FC > 2) were considered as differentially expressed. RPKM values were generated using Cufflinks (version 2.2.1) with default parameters.
WGBS datasets:
WGBS raw reads were trimmed using Trim Galore (version 0.4.5) with parameters “-q 20 –length 35bp -clip-R1 9 –three_prime_clip_R1 9”. Following reads trimming, Bismark (version 0.17.0) was used to align the reads to the mm9 reference genome.
Only uniquely aligned and non-PCR duplicate reads were used for downstream analyses. PCR-duplicates were identified using “MarkDuplicates” from Picard Tools (version 2.8.0). The DNA methylation level for each CpGs was computed as “reads containing methylated C / (reads containing methylated C + reads containing unmethylated C).
Parental-origins of the WGBS reads were determined using SNPsplit (version 0.3.2) and “bedGraphToBigWig” was used to convert bedGraph format to bigwig tracks. The minimum reads coverage for non-allelic and allelic DNA methylation tracks are five and three, respectively.
RRBS datasets:
RRBS reads were trimmed using Trim Galore (version 0.4.5) with parameters “--rrbs --paired -q 20 –length 35bp”. Bismark (version 0.17.0) was used to align the trimmed reads to the mm9 reference genome with default parameters. B6/DBA and PWK SNPs were masked as “N” for the reference assembly.
Uniquely aligned reads were used to compute methylation levels of each CpGs similar to the WGBS datasets. Generation of allelic DNA methylation tracks are the same as the WGBS datasets except that only CpGs with >5 reads coverage were used.
CUT&RUN datasets:
After quality trimming using Trim Galore version (0.4.5), the CUT&RUN reads were aligned to a custom mm9 reference genome (B6/129 and PWK SNPs masked as “N” for H3K4me3 and B6/DBA and PWK SNPs marked as "N" for H3K27me3) using Bowtie2 (version 2.2.9) with the following parameter: “-t -q -N 1 -L 25 --no-unal -I 150 -X 800 --no-mixed --no-discordant”.
After removing non-uniquely mapped reads and PCR duplicates, MACS2 (version 2.1.1) was used to call H3K4me3 and H3K27me3 peaks.
The CUT&RUN bigwig tracks were generated using BamCoverage in deepTools (version 3.0.2).
For allelic H3K27me3 and H3K4me3 enrichment analyses, the parental origins of the reads were determined using SNPsplit (version 0.3.2).
Genome_build: For datasets involved with Dnmt3l and Eed transgenic mouse lines, reference genome was the mm9 (MGSCv37) build with B6/129 and PWK SNPs masked as "N". For Dnmt3a/3b acute depletion experiments, mm9 (MGSCv37) build with B6/DBA and PWK SNPs masked as "N" was used.
Supplementary_files_format_and_content: *.bw: BigWig files that can be uploaded on a genome browser to view methylated cytosine, H3K27me3, H3K4me3, and RNA levels at different genomic locations.

source_name: Trophectoderm

extract_protocol:
As all libraries generated in this study involved low-input techniques, samples collected were directly put into lysis buffer for further library construction.
RNA-seq (Sample 1-13):
For low-input RNA-seq libraries, SMARTer Ultra Low Input RNA cDNA preparation kit (Clontech, 643890) was used for reverse transcription and cDNA amplification. cDNA were then fragmented, adaptor-ligated and amplified using Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s instructions. Single-end 100bp sequencing was performed on a HiSeq 2500 sequencer (Illumina).
Bisulfite-seq (Sample 24-25):
For low-input whole genome bisulfite sequencing (WGBS), the libraries were constructed using the PBAT method (Clark SJ et al., Nature Protocol. 2017 Mar; 12(3):534-547, PMID:28182018).
Bisulfite-seq (reduced representation) (Sample 14-19):
For low-input RRBS, the libraries were prepared as previously described (Shen L et al., Cell Stem Cell. 2014 Oct 2; 15(4):459-471. PMID:25280220).
H3K27me3 and H3K4me3 profiling using CUT&RUN (Sample 20-23, 26-31):
Eed CTR and matKO embryos H3K4me3 and H3K27me3 CUT&RUN libraries were constructed as previously described (Skene and Henikoff, 2017 eLife. 2017; 6: e21856, PMID: 28079019).

tag: strain/background

value: B6/129 x PWK

tag: parental genotype

value: Gdf9-Cre, Eed(fl/fl) x PWK

value: Trophectoderm


title: Eed_matKO_morula_B6129xPWK_H3K4me3_rep2

description:
Sample 29
H3K4me3

source_name: Morula embryos

value: Morula embryos


title: Eed_CTR_TE_B6129xPWK_H3K4me3_rep1

description:
Sample 30
H3K4me3

value: Eed(fl/fl) x PWK


title: Eed_CTR_morula_B6129xPWK_H3K4me3_rep2

description:
Sample 27
H3K4me3


title: H1975_Control_0h_3


title: H1975_Control_48h_3


title: Dnmt3ab_DKO_E65_ExE_B6DBAxPWK_H3K27me3_embryo5

description:
Sample 23
Acute depletion of Dnmt3a/3b by 1-cell CRIPSR/Cas9 injection.
H3K27me3

source_name: E6.5 extraembryonic ectoderm

value: B6/DBA x PWK

value: WT x WT

value: E6.5 extraembryonic ectoderm


title: Eed_CTR_morula_B6129xPWK_H3K4me3_rep1

description:
Sample 26
H3K4me3


title: Eed_matKO_morula_B6129xPWK_H3K4me3_rep1

description:
Sample 28
H3K4me3


title: Eed_CTR_E65_ExE_B6129xPWK_WGBS

description:
Sample 24
5mC

data_processing:
RNA-seq datasets:
Low quality bases and sequencing adaptors of raw RNA-seq reads were trimmed using Trim Galore (version 0.4.5) with parameters “-q 20 –length 20bp”. Reads after trimming were then aligned to the mm9 reference genome using HISAT2 (version 2.1.0) with parameters “--sp 1000,1000 --dta-cufflinks --no-unal”.
Following reads mapping, uniquely aligned reads were retrieved by selecting the alignment records with “NH:i:1” tag and mapping quality greater than 30.
SNPsplit (version 0.3.2) was used separate parental-allele-specific reads and bamCoverage from deepTools (version 3.0.2) was used to generate bigwig tracks with parameters “--skipNonCoveredRegions --binSize 10 --scaleFactor 1”.
Raw read counts for each gene were generated using TEtranscripts (version 1.5.1) and statistical significance [i.e. false discovery rate (FDR)] was computed using the DESeq R package (version 1.34.1) . Only genes with RPKM > 1 in either group, FDR < 0.05 and fold change (FC > 2) were considered as differentially expressed. RPKM values were generated using Cufflinks (version 2.2.1) with default parameters.
WGBS datasets:
WGBS raw reads were trimmed using Trim Galore (version 0.4.5) with parameters “-q 20 –length 35bp -clip-R1 9 –three_prime_clip_R1 9”. Following reads trimming, Bismark (version 0.17.0) was used to align the reads to the mm9 reference genome.
Only uniquely aligned and non-PCR duplicate reads were used for downstream analyses. PCR-duplicates were identified using “MarkDuplicates” from Picard Tools (version 2.8.0). The DNA methylation level for each CpGs was computed as “reads containing methylated C / (reads containing methylated C + reads containing unmethylated C).
Parental-origins of the WGBS reads were determined using SNPsplit (version 0.3.2) and “bedGraphToBigWig” was used to convert bedGraph format to bigwig tracks. The minimum reads coverage for non-allelic and allelic DNA methylation tracks are five and three, respectively.
RRBS datasets:
RRBS reads were trimmed using Trim Galore (version 0.4.5) with parameters “--rrbs --paired -q 20 –length 35bp”. Bismark (version 0.17.0) was used to align the trimmed reads to the mm9 reference genome with default parameters. B6/DBA and PWK SNPs were masked as “N” for the reference assembly.
Uniquely aligned reads were used to compute methylation levels of each CpGs similar to the WGBS datasets. Generation of allelic DNA methylation tracks are the same as the WGBS datasets except that only CpGs with >5 reads coverage were used.
CUT&RUN datasets:
After quality trimming using Trim Galore version (0.4.5), the CUT&RUN reads were aligned to a custom mm9 reference genome (B6/129 and PWK SNPs masked as “N” for H3K4me3 and B6/DBA and PWK SNPs marked as "N" for H3K27me3) using Bowtie2 (version 2.2.9) with the following parameter: “-t -q -N 1 -L 25 --no-unal -I 150 -X 800 --no-mixed --no-discordant”.
After removing non-uniquely mapped reads and PCR duplicates, MACS2 (version 2.1.1) was used to call H3K4me3 and H3K27me3 peaks.
The CUT&RUN bigwig tracks were generated using BamCoverage in deepTools (version 3.0.2).
For allelic H3K27me3 and H3K4me3 enrichment analyses, the parental origins of the reads were determined using SNPsplit (version 0.3.2).
Genome_build: For datasets involved with Dnmt3l and Eed transgenic mouse lines, reference genome was the mm9 (MGSCv37) build with B6/129 and PWK SNPs masked as "N". For Dnmt3a/3b acute depletion experiments, mm9 (MGSCv37) build with B6/DBA and PWK SNPs masked as "N" was used.
Supplementary_files_format_and_content: *.bw: BigWig files that can be uploaded on a genome browser to view methylated cytosine, H3K27me3, H3K4me3, and RNA levels at different genomic locations.


title: Dnmt3ab_DKO_E65_ExE_B6DBAxPWK_H3K27me3_embryo1

description:
Sample 22
Acute depletion of Dnmt3a/3b by 1-cell CRIPSR/Cas9 injection.
H3K27me3


title: 1_synchronous matched liver metastasis


title: 2_normal colorectal tissue


title: H1975_Control_48h_2

value: female


title: Dnmt3ab_WT_E65_ExE_B6DBAxPWK_H3K27me3_embryo7

description:
Sample 21
Water injected at 1-cell.
H3K27me3


title: Eed_matKO_E65_ExE_B6129xPWK_WGBS

description:
Sample 25
5mC


title: Dnmt3ab_WT_E65_ExE_B6DBAxPWK_H3K27me3_embry6

description:
Sample 20
Water injected at 1-cell.
H3K27me3


title: Dnmt3ab_DKO_E65_ExE_B6DBAxPWK_RRBS_embryo4

description:
Sample 17
Acute depletion of Dnmt3a/3b by 1-cell CRIPSR/Cas9 injection.
5mC


title: Dnmt3ab_WT_E65_ExE_B6DBAxPWK_RRBS_embryo5

description:
Sample 16
Water injected at 1-cell.
5mC


title: Dnmt3ab_WT_E65_ExE_B6DBAxPWK_RRBS_embryo4

description:
Sample 15
Water injected at 1-cell.
5mC


title: H1975_HGF_0.5h_2

value: Lung


title: Dnmt3ab_DKO_E65_ExE_B6DBAxPWK_RNAseq_embryo7

description:
Sample 13
Acute depletion of Dnmt3a/3b by 1-cell CRIPSR/Cas9 injection.
mRNA


title: Dnmt3ab_DKO_E65_ExE_B6DBAxPWK_RRBS_embryo7

description:
Sample 19
Acute depletion of Dnmt3a/3b by 1-cell CRIPSR/Cas9 injection.
5mC


title: Dnmt3ab_WT_E65_ExE_B6DBAxPWK_RRBS_embryo3

description:
Sample 14
Water injected at 1-cell.
5mC


title: H1975_TGFb_24h_1

value: TGF-beta stimulation


title: Dnmt3ab_DKO_E65_ExE_B6DBAxPWK_RNAseq_embryo4

description:
Sample 10
Acute depletion of Dnmt3a/3b by 1-cell CRIPSR/Cas9 injection.
mRNA


title: Dnmt3ab_DKO_E65_ExE_B6DBAxPWK_RNAseq_embryo5

description:
Sample 11
Acute depletion of Dnmt3a/3b by 1-cell CRIPSR/Cas9 injection.
mRNA


title: Dnmt3ab_DKO_E65_ExE_B6DBAxPWK_RNAseq_embryo3

description:
Sample 9
Acute depletion of Dnmt3a/3b by 1-cell CRIPSR/Cas9 injection.
mRNA


title: Dnmt3ab_DKO_E65_ExE_B6DBAxPWK_RNAseq_embryo6

description:
Sample 12
Acute depletion of Dnmt3a/3b by 1-cell CRIPSR/Cas9 injection.
mRNA


title: Dnmt3ab_WT_E65_ExE_B6DBAxPWK_RNAseq_embryo1

description:
Sample 5
Water injected at 1-cell.
mRNA


title: Dnmt3l_matKO_morula_B6129xPWK_RNAseq_rep2

description:
Sample 4
mRNA

value: Dnmt3l KO x WT


title: Dnmt3ab_WT_E65_ExE_B6DBAxPWK_RNAseq_embryo2

description:
Sample 6
Water injected at 1-cell.
mRNA


title: Dnmt3ab_DKO_E65_ExE_B6DBAxPWK_RNAseq_embryo1

description:
Sample 7
Acute depletion of Dnmt3a/3b by 1-cell CRIPSR/Cas9 injection.
mRNA


title: Dnmt3l_matKO_morula_B6129xPWK_RNAseq_rep1

description:
Sample 3
mRNA


title: 2_primary colorectal carcinoma


title: Dnmt3l_CTR_morula_B6129xPWK_RNAseq_rep1

description:
Sample 1
mRNA


title: Dnmt3l_CTR_morula_B6129xPWK_RNAseq_rep2

description:
Sample 2
mRNA


title: CAF-3

city: Seoul

first: Baek Gil

address: 50-1 Yonsei-Ro

institute: Yonsei University

hyb_protocol: Hybridization of NanoString probes was conducted according to the manufacturer's protocol.

scan_protocol: Sample cartridges were scaned and analyzed by nCounter digital analyzer (nanostring technologies inc.).

data_processing: The data were normalized and analyzed using nSolver 2.5.

label: oligonucleotide probe

source_name: Invasive ductal carcinoma

label_protocol: Specific oligonucleotide probe pairs that are bound to barcoded tags (nanostring technologies inc.) were conducted according to the manufacturer's protocol.

growth_protocol: Patient-derived fibroblasts were cultured in the DMEM/F12 medium supplemented with 1% penicillin/streptomycin and 10% FBS at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted from primary normal and cancer-associated fibroblasts using TRIzol according to the manufacturer's protocol.

tag: disease state

value: cancer-associated fibroblast


title: CAF-2


title: H1975_Control_6h_1

tag: cell line


title: NF-3

value: normal fibroblast


title: CAF-1


title: Dnmt3ab_DKO_E65_ExE_B6DBAxPWK_RNAseq_embryo2

description:
Sample 8
Acute depletion of Dnmt3a/3b by 1-cell CRIPSR/Cas9 injection.
mRNA


title: NF-2


title: NF-1


title: Single cells UP-8167 Tumor

city: Philadelphia

first: Daniel

last: Zhang

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

data_processing:
Raw sequencing data was demultiplexed with bcl2fastq2 with adapter trimming turned off. Additional processing was performed using drop-seq tools v.2.1.0 with GRCh38 as the reference genome, and gencode v.28 GTF was used as the annotation file.
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene counts matrix was constructed using drop-seq tools v2.1.0

source_name: Glioblastoma

growth_protocol: Glioblastoma organoids were generated by mincing fresh tumor tissue and cultured on an orbital shaker

extract_protocol: Drop-seq was performed as previously described with minor modifications (Macosko et al., 2015). Microfluidic chips were obtained from FlowJEM with plasma bonding and aquapel treatment using the same design as previously published. Each droplet co-encapsulation run was performed with 50% additional reagent volume to account for syringe and tubing dead volume as well as occasional microfluidic channel clogging and re-starts. Each sample was loaded onto 2-4 droplet generation runs, and cell suspensions and droplets were kept on ice prior to droplet encapsulation and droplet breakage. In the cDNA PCR amplification stage, between 4,000-8,000 beads were combined in a single PCR tube reaction and purified individually using 0.6x SPRI beads. cDNA across multiple runs of the same sample were pooled together and used as input for tagmentation, where the tagment reaction time was increased to 8 minutes. Final samples were purified once with 0.6x SPRI beads and a second time with 1.0x SPRI beads. Sequencing library fragment sizes were quantified by bioanalyzer, and concentrations were quantified by qPCR.

treatment_protocol: Multiple tumor pieces and GBOs were dissociated using a papain-based neural tissue dissociation kit (Miltenyi Biotech). Crude dissociates from parental tumor samples were treated with ammonium chloride based RBC lysis buffer for 5 minutes. All samples were washed three times by centrifugation at 200 g for 5 minutes and resuspension in 10 mL of calcium-free, magnesium-free DPBS. Cells were strained through a 70 µm filter (Miltenyi Biotech), analyzed for viability by trypan blue staining, and counted using an automatic cell counter.

tag: culture duration

value: 0 weeks


title: Single cells UP-8165PV 24wk

source_name: Glioblastoma organoid

value: 24 weeks


title: Single cells UP-8167 2wk

value: 2 weeks


title: Single cells UP-8167 24wk


title: Single cells UP-8165C 2wk


title: Single cells UP-8165C 24wk


title: Single cells UP-8165C Tumor


title: H1975_Control_0h_2

value: Control


title: Single cells UP-8036 GBO 8wk

value: 8 weeks


title: Single cells UP-8036 GBO 2wk


title: Single cells UP-8036 Tumor