title: yng_pdl1-6: Young_anti-PDL1_treated_mammary_tumor_replicate_6

first: Gregory

middle: James

last: Goreczny

address: 4 Blackfan Cir.

institute: Brigham & Women's Hospital

data_processing:
Pseudoalignment with salmon, version ,0.8.0
Import and summarize salmon generated counts with tximport, version 1.4.0
Analyze differential expression with DESeq2 BioConductor package, version 1.16.1
Genome_build: mm10
Supplementary_files_format_and_content: comma separated format, rawCounts matrix file contains raw counts as generated by Salmon and imported by tximport (these counts were used for the DESeq2 analysis), tpm matrix contains transcripts per million normalized counts as calculated by tximport

source_name: Mammary tumor

growth_protocol: 8-12 week old or >12 months old Balb/C mice were injected orthotopically with 100,000 4T1 cells into the 4th left mammary fat. All experiments were conducted in accordance with regulations of the Children’s Hospital Institutional Animal Care and Use Committee (protocol # 12-11-2308R) and the Brigham and Women’s Hospital (protocol # 2017N000056)

extract_protocol:
RNA was extracted from tumors no larger than ~150 mm3 and stored in 1 mL RNA Later (Qiagen, 1018087) at 4°C overnight before being transferred to -80°C. Tumors were homogenized using a homogenizer 150 (Fisher Scientific) in RLT buffer (Qiagen, 79216), processed through QIAshredder columns (Qiagen, 79656) and then total RNA isolated using an RNeasy Mini Kit (Qiagen, 74136) according to the manufacturer’s protocol. Quality of total RNA was determined using a 2100 Bioanalyzer (Agilent).
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

treatment_protocol: Three doses of 200µg anti-CTLA4 (clone 9D9, BioXCell, BE0164), anti-PD-L1 (clone 10F.9G2, BioXCell, BE0101), or isotype (clone LTF-2, BioXCell, BE0090) were injected intraperitoneally on days 7, 10, and 13 post tumor cell injection

value: Balb/C

tag: tissue

value: Mammary tumor

value: 8-10 weeks

tag: treatment

tag: biological replicate

tag: sequencing batch


title: yng_pdl1-9: Young_anti-PDL1_treated_mammary_tumor_replicate_9

status: Public on Apr 05 2020

type: SRA

city: Boston

state: MA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: age


title: yng_pdl1-7: Young_anti-PDL1_treated_mammary_tumor_replicate_7


title: yng_pdl1-8: Young_anti-PDL1_treated_mammary_tumor_replicate_8


title: pp2cf_WT

city: Ramat-Gan

first: Ofir

last: Hakim

address: Max and Anna Webb

country: Israel

institute: Bar-Ilan University

library_source: genomic

data_processing:
Sequenced reads were aligned to the TAIR10 Arabidopsis genome using bowtie.
SAM file was converted to BED using sam2bed python script.
Reads were assigned to restriction enzyme sites using bedtools intersect with -c parameter.
For raw data, the intersection resulted with a sgr file.
for pScore, pValue was calculated using a custom code available in Github: https://github.com/HakimLab/4SEE.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedgraph

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: All plants were grown in growth room under cool white LED light ~100 LUX for 16 hr/day at 22C. Surface sterilized seeds were sowed on agar-coated floats on 1/8 Murashige and Skoog (MS).

extract_protocol:
Frozen tissue was grinded in liquid nitrogen using mortar and pestle, and transferred into Nuclear Isolation Buffer 1 (10 mM HEPES pH=7.5, 0.4 M sucrose, 5 mM KCl, 5mM MgCl2, 5 mM EDTA, supplemented with 0.2 mM Spermine, 0.5 mM Spermidine and 0.6% Triton X-100) and incubated on a rotator at 4ºC for 30 min. The sample was then passed through 40µm mesh and centrifuged (2500g at 4°C). The pellet was resuspended with Nuclear Isolation Buffer 2 (10 mM HEPES pH=7.5, 0.25 M sucrose, 5 mM KCl, 5mM MgCl2 and 5 mM EDTA). The debris was further reduced by two rounds of gentle centrifugation at 300g at 4°C for 15 sec and collecting the supernatant. The supernatant was further centrifuged for 10 min, at 2000g at 4°C and the resulting nuclei pellet was re-suspended with NIB2. For crosslinking, the sample was incubated with 1% formaldehyde at room temperature for 10 min and neutralized with125mM glycine for 5 minutes at room temperature. 10^6 crosslinked nuclei were washed twice with Csp6I RE buffer (Thermo, #ER0211) and resuspended in 1.2X Csp6I RE 1.2X. SDS was added to a final concentration of 0.3% (v/v). After 30 minutes incubation at 65°C, triton X- 100 was added to final concentration of 1.8% and the sample was incubated for 1h in 37°C. 150 units of restriction enzyme Csp6I (Thermo, #ER0211) were added and the sample was incubated overnight at 37°C. Inactivation of Csp6I was achieved by incubating the samples at 65°C for 25 minutes. Ligation reaction was then done in 1.5ml of 1X ligase buffer with 25 units T4 ligase (Roche, #EL0011) and incubated over-night at 4°C followed by 30 minutes incubation at RT. To reverse the crosslinks the sample was supplemented with 50µg proteinase K (Invitrogene, #25530049) and incubated overnight at 65°C, followed by incubation with 150 µg RNAse (Thermo, EN0551) for 45 min at 37°C. The resulting proximity-ligated DNA was extracted by phenol-chloroform followed by ethanol precipitation and dissolved in 20 µl TE buffer. For generating DNA circles, DNA was then digested over-night with DpnII (NEB, #R0543T) at 37°C.  DNA was purified using Expin DNA clean up kit (GeneAll, 112-102) and DNA concentration was determined by Nanodrop 2000 (Thermo Scientific).Ligation junctions were amplified by inverse PCR with viewpoint primers and Phusion hot-start high fidelity Taq (Thermo, #F-549) and the following thermal cycles conditions: 30 sec at 98°C ; 25 cycles of 98°C for 10 sec, 60°C for 30 sec and 72°C for 2 min; 72°C for 5min. PCR products were purified on Expin columns. 30, 120, and twice 60 ng (in total four amplified libraries) DNA templates from SALK and ADF8p:NTF/ACT2p:BirA lines were amplified separately with primer-specific barcodes. For further varying the template amounts, the sequenced tags from these libraries were combined.
Libraries for Illumina sequencing were prepared using NEBNext Ultra II system (NEB, #E7645, #E7103) and sequenced on a NextSeq platform (Illumina). For multiplexing several samples on the same sequencing lane, 4-letter barcodes were added to the primers used for inverse PCR.
4C-seq

tag: strain/background


title: pp2cf_ADF


title: yng_pdl1-5: Young_anti-PDL1_treated_mammary_tumor_replicate_5


title: ADF_150ng_100K

description: 150ng used for library preparation. Total number of reads:100K.


title: EMB76_WT


title: shLacZ, EBd4

first: Aref

last: Ebrahimi

address: 1 Joslin Pl

department: Islet Cell and Regenerative Biology

institute: Harvard Medical School - Joslin

data_processing:
Quality control of the reads by fastqc
Mouse index built by Subread
Reads aligned by Subread
Gene quantification raw counts by FeatureCounts
Voom/Limma for differential expression
Genome_build: Ensembl v88 - GRCm38

molecule: polyA RNA

source_name: EB differentiated cells

growth_protocol: Undifferentiated mESCs were grown in LIF/2i condition

extract_protocol:
Cells were lyzed by Trizol, RNA was extracted by chloroform and precipitated by isopropanol.
Illumina

treatment_protocol: mESCs differentiation was induced by LIF/2i removal and hanging drop formation at the presence of serum to form embryoid bodies (EBs)

tag: cell type

value: ESC-derived EB differentiated cells

tag: day

tag: genotype/variation

value: shLacZ


title: shLacZ, 2i

source_name: mESC

value: Undifferentiated mouse ESCs


title: yng_pdl1-3: Young_anti-PDL1_treated_mammary_tumor_replicate_3


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 1_untreated

status: Public on Apr 06 2020

type: RNA

city: Amsterdam

first: Renske

middle: DM

last: Steenbergen

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Amsterdam UMC, location VUmc

description:
raw data file: US22502676_251485074085_S01_GE2_107_Sep09_1_1.txt
none
FK18BT1-

hyb_protocol: 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17h in a 65°C hybridization oven (G2545A, Agilent) set to 10rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction software. Raw expression data generated by the Feature Extraction software was imported into R using the LIMMA package in Bioconductor. The intensity distributions within and between arrays were normalized using the quantile scaling algorithm in LIMMA.

organism: Homo sapiens

source_name: primary human foreskin keratinocytes transfected with HPV18

label_protocol: 500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

growth_protocol: Establishment and culture of the HPV16 (FK16A and FK16B) and HPV18 (FK18A and FK18B) transformed keratinocyte cell lines was described previously (Steenbergen et al., Oncogene 1996).

extract_protocol: Total RNA was isolated using TRIzol Reagent according to the manufacturer’s instructions (ThermoFisher Scientific).

treatment_protocol: Cells were treated with either 5000nM 5-aza-2’-deoxycytidine (DAC; Sigma-Aldrich) dissolved in PBS or PBS only for 5 days. Medium with or without DAC was refreshed every day.

tag: transformation stage

value: extended lifespan

tag: timepoint

value: timepoint 1

value: no treatment


title: yng_pdl1-2: Young_anti-PDL1_treated_mammary_tumor_replicate_2


title: EMB76_ADF


title: myblike_ADF


title: COX11_ADF


title: COX11_WT


title: yng_pdl1-1: Young_anti-PDL1_treated_mammary_tumor_replicate_1


title: yng_iso-6: Young_isotype_treated_mammary_tumor_replicate_6

value: Isotype


title: yng_pdl1-4: Young_anti-PDL1_treated_mammary_tumor_replicate_4


title: C2H2C_WT


title: yng_iso-5: Young_isotype_treated_mammary_tumor_replicate_5


title: C2H2C_ADF


title: KO NSC 3

city: Madison

first: Christopher

last: Morrow

state: Wisconsin

address: 1111 Highlange Ave.

institute: University of Wisconsin - Madison

description:
Raw Sequences read and mapped to genome
5_isoforms_fpkm_expression

data_processing:
Transcripts Assembly: Firstly, Cutadapt[1] and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used Bowtie2[2] and Tophat2[3] to map reads to the genome of Mus musculus (Version: v88). The mapped reads of each sample were assembled using StringTie[4]. Then, all transcriptomes from 6 samples were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare (https://github.com/gpertea/gffcompare/). After the ﬁnal transcriptome was generated, StringTie[4] and Ballgown[5] was used to estimate the expression levels of all transcripts.
lncRNA ID: First of all, transcripts that overlapped with known mRNAs, known lncRNAs and transcripts shorter than 200 bp were discarded. Then we utilized CPC[6] and CNCI[7] to predict transcripts with coding potential. All transcripts with CPC score <-1 and CNCI score <0 were removed. The remaining transcripts with class code (I, j, o, u, x) were considered as lncRNAs.
Different expression analysis of transcripts: StringTie[4] was used to perform expression level for mRNAs and lncRNAs by calculating FPKM (FPKM=[total_exon_fragments/mapped_reads(millions)×exon_length(kB)]). The differentially expressed mRNAs and lncRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with parametric F-test comparing nested linear models (p value < 0.05) by R package Ballgown[5].
Target gene prediction and functional analysis of lncRNAs: To explore the function of lncRNAs, we predicted the cis-target genes of lncRNAs. lncRNAs may play a cis role acting on neighboring target genes. In this study, coding genes in 100,000 upstream and downstream were selected by perl script. Then, we showed functional analysis of the target genes for lncRNAs by using the scripts in house. Signiﬁcance was expressed as a p value < 0.05.
Localization of lncRNAs on genome: Two diagrams were generated to show the localization and abundance of lncRNAs in genome using the program Circos[8]. One diagram showed lncRNA expression level in different samples. The lncRNAs in the other diagram were subdivided into five categ ories according to their class code generated by StringTie: (i) a transfrag falling entirely within a reference intron (intronic); (j) potentially novel isoform or fragment at least one splice junction is shared with a reference transcript; (o) generic exonic overlap with a reference transcript; (u) unknown, intergenic transcript (intergenic); (x) Exonic overlap with reference on the opposite strand (antisense).
Genome_build: Mus musculus (Version: v88)
Supplementary_files_format_and_content: "5_iso…" XLSX, has a list of counts for each mapped gene, "Raw Seq…" .FA, has a list of all of the DNA sequences mapped to each transcript

source_name: Neural Stem Cell

growth_protocol: NSCs were cultured with 37°C/5% CO2 in serum-free media: DMEM/F12 GlutaMax (Invitrogen 10565018) with penicillin-streptomycin-fungizone (1:100, Invitrogen 15140122), B27 (1:50, Invitrogen 17504044), and 20 ng/mL FGF-2 and EGF (PeproTech 100-18B and AF-100-15). Cells grown as monolayers were additionally given 5ug/mL Heparin (Sigma H3149).

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA was used to remove ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA).
Following purification, the ribo-minus RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with a strand-specific library preparation by dUTP method. The average insert size for the paired-end libraries was 300±50 bp. And then we performed the pair-end 2×150bp sequencing on an illumina Hiseq 4000 platform housed in the LC Sciences (Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: All samples were untreated

value: vimentin knock out


title: KO NSC 2


title: salk_064627_90ng

description: 90ng used for library preparation


title: yng_iso-4: Young_isotype_treated_mammary_tumor_replicate_4


title: KO NSC 1


title: salk_064627_60ng

description: 60ng used for library preparation


title: salk_064627_30ng

description: 30ng used for library preparation


title: myblike_WT


title: yng_iso-7: Young_isotype_treated_mammary_tumor_replicate_7


title: salk_064627_150ng

description: 150ng used for library preparation


title: yng_ctla4-12: Young_anti-CTLA4_treated_mammary_tumor_replicate_12


title: salk_064627_180ng

description: 180ng used for library preparation


title: salk_064627_120ng

description: 120ng used for library preparation


title: yng_iso-3: Young_isotype_treated_mammary_tumor_replicate_3


title: yng_iso-1: Young_isotype_treated_mammary_tumor_replicate_1


title: salk_063720_90ng

description: 90ng used for library preparation


title: WT NSC 1

value: wild type


title: ADF_210ng_100K

description: 210ng used for library preparation. Total number of reads:100K.


title: yng_ctla4-11: Young_anti-CTLA4_treated_mammary_tumor_replicate_11


title: WT penis, rep 3

city: Notre Dame

first: Xin

last: Lu

state: IN

address: 100 Mason Center, Building GALVIN Department of Biological Sciences

department: Biological Sciences

institute: University of Notre Dame

data_processing:
The raw reads are aligned to the Mouse reference genome build mm10, using Tophat RNASeq alignment software.
The aligned reads verified for quality using FASTQC software.
HTseq software is used to summarize the gene expression counts from Tophat alignment data after sorting the BAM files.
Cluster analysis is performed on the most variable to verify any outlieers and overall similarity/differences among all samples.
The raw counts are normalized and differential expression analysis is performed on contrasts of interest using the DEseq2 package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene expression counts for each sample.

source_name: Penile epithelium (normal)

growth_protocol: Three 5-month-old SA  (PB-Cre+ Smad4L/L ApcL/L) mice were used for harvesting penile tumors. Age-matched WT (wild type) C57BL/6 mice were used for harvesting normal penile epithelium.

extract_protocol:
Total RNA from fresh tissues was extracted using Direct-zol RNA Miniprep Kit (Zymo Research). The quantity and quality of each sample were measured using an Agilent 2100 Bioanalyzer. RNA sequencing was performed at Sequencing and Microarray Facility at MD Anderson Cancer Center using standard stranded RNA-seq protocol on an Illumina HiSeq 4000 (76nt pair-end).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tumors formed spontaneously without any carcinogen treatment.

value: 5 month

tag: genotype

value: Wild type

value: Penile epithelium (normal)


title: WT NSC 2


title: yng_ctla4-10: Young_anti-CTLA4_treated_mammary_tumor_replicate_10


title: salk_063720_60ng

description: 60ng used for library preparation


title: salk_063720_180ng

description: 180ng used for library preparation


title: salk_063720_120ng

description: 120ng used for library preparation


title: BON2_ADF


title: yng_ctla4-9: Young_anti-CTLA4_treated_mammary_tumor_replicate_9


title: WT penis, rep 2


title: yng_iso-2: Young_isotype_treated_mammary_tumor_replicate_2


title: salk_063720_210ng

description: 210ng used for library preparation


title: WT penis, rep 1


title: yng_ctla4-8: Young_anti-CTLA4_treated_mammary_tumor_replicate_8


title: salk_041474_30ng

description: 30ng used for library preparation


title: salk_011436_90ng

description: 90ng used for library preparation


title: salk_011436_60ng

description: 60ng used for library preparation


title: salk_011436_30ng

description: 30ng used for library preparation


title: yng_ctla4-7: Young_anti-CTLA4_treated_mammary_tumor_replicate_7


title: SA tumor, rep 3

source_name: Penile epithelium (malignant)

value: PB-Cre+ Smad4L/L ApcL/L

value: Penile epithelium (malignant)


title: SA tumor, rep 2


title: salk_011436_120ng

description: 120ng used for library preparation


title: salk_011436_150ng

description: 150ng used for library preparation


title: salk_009469_30ng

description: 30ng used for library preparation


title: yng_ctla4-6: Young_anti-CTLA4_treated_mammary_tumor_replicate_6

value: Balb/C


title: SA tumor, rep 1


title: yng_ctla4-5: Young_anti-CTLA4_treated_mammary_tumor_replicate_5

value: Mammary tumor


title: salk_063720_30ng

description: 30ng used for library preparation


title: yng_ctla4-4: Young_anti-CTLA4_treated_mammary_tumor_replicate_4

value: 8-10 weeks


title: salk_005512_90ng

description: 90ng used for library preparation


title: salk_005512_60ng

description: 60ng used for library preparation


title: yng_ctla4-3: Young_anti-CTLA4_treated_mammary_tumor_replicate_3


title: salk_005512_30ng

description: 30ng used for library preparation


title: salk_005512_150ng

description: 150ng used for library preparation


title: salk_005512_120ng

description: 120ng used for library preparation


title: salk_005512_210ng

description: 210ng used for library preparation


title: salk_005512_180ng

description: 180ng used for library preparation


title: sbt4.12_2


title: sbt4.12_1


title: yng_ctla4-1: Young_anti-CTLA4_treated_mammary_tumor_replicate_1


title: yng_ctla4-2: Young_anti-CTLA4_treated_mammary_tumor_replicate_2


title: pif4_2


title: old_pdl1-8: Old_anti-PDL1_treated_mammary_tumor_replicate_8

value: >12 months


title: pif4_1


title: MBP1_2


title: old_pdl1-7: Old_anti-PDL1_treated_mammary_tumor_replicate_7


title: old_pdl1-6: Old_anti-PDL1_treated_mammary_tumor_replicate_6


title: MBP1_1


title: PD+PEG 15d

city: Yangling

first: bo

last: wang

state: Shaanxi

address: No. 3 Taicheng Road

country: China

institute: Northwest A&F University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Peltaster frucitcola whole genome (GenBank accession no. GCA_001592805.1) using TopHat v. 2.1.0 with parameters --bowtie1 -p 8 -g 1
A gene expression profile was created using cufflinks software.
Normalized read counts of transcripts with a significant P-value (< 0.05) and a greater than threefold change (log2) in transcript level were considered to be differently expressed. All P-values were corrected for false discoveries resulting from multiple hypothesis testing using the Benjamini-Hochberg procedure.
Genome_build: reference genome deposited at DDBJ/EMBL/GenBank under the accession GCA_001592805.1
Supplementary_files_format_and_content: tab-delimited text files include normalized read count values for each treatment.

organism: Peltaster fructicola

source_name: mycelium

extract_protocol:
Total RNA was extracted according to the instruction manual of the Trizol Reagent (Life technologies, California, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: mycelium

tag: growth

value: potato dextrose and PEG6000 for 15 days


title: PD 15d

value: potato dextrose for 15 days


title: old_pdl1-5: Old_anti-PDL1_treated_mammary_tumor_replicate_5


title: old_pdl1-4: Old_anti-PDL1_treated_mammary_tumor_replicate_4


title: old_pdl1-2: Old_anti-PDL1_treated_mammary_tumor_replicate_2


title: old_iso-7: Old_isotype_treated_mammary_tumor_replicate_7


title: PD 5d

value: potato dextrose for 5 days


title: shDis3l2, EBd4

value: ESC-derived EB differentiated cells


title: old_pdl1-3: Old_anti-PDL1_treated_mammary_tumor_replicate_3


title: old_pdl1-1: Old_anti-PDL1_treated_mammary_tumor_replicate_1


title: human_roundspermatid_input

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description:
hs_k4m1_rs_peaks.broadPeak
hs_k27ac_rs_peaks.broadPeak

data_processing:
ChIP-seq reads were filtered using fastq_quality_filter from FASTX Toolkit version 0.0.14 with parameters –q 20 –p80, and aligned to the hg19 genome build using bowtie2.2.9 using --end-to-end --fast mode with default parameters. Peaks were called using MACS version 2.1.1 with parameters -s 40 --broad --broad-cutoff 0.1.

Genome_build: mm10. hg19
Supplementary_files_format_and_content: bed files with peak coordinates

source_name: adult testis

growth_protocol: Human testis samples were obtained from patients undergoing vasectomy reversals at the Infertility Clinic of St. Louis. All donors had previous demonstrated fertility.

extract_protocol:
Pachytene spermatocyte and round spermatid fractions were collected by StaPut (Bellve et al 1993).  Purity was assessed under phase optics and was consistently >95% for each desired cell type.  Cells were washed once in PBS and then split into two aliquots.  One aliquot (for ChIP) was fixed in 1% formaldehyde then quenched with 2.5M glycine, while the second (for RNA) was left unfixed.  Both fixed and unfixed aliquots were snap frozen in liquid nitrogen, then stored at -80C.  ChIP was performed as previously described (Lesch et al 2013).
ChIP-seq libraries were prepared using a TruSeq ChIP sample prep kit (Illumina) according to the manufacturer’s instructions, except that size selection was performed after instead of before PCR amplification.

value: round spermatids

tag: chip antibody


title: human_roundspermatid_H3K4me1_ChIP

value: H3K4me1 (Abcam, ab8995)


title: old_iso-5: Old_isotype_treated_mammary_tumor_replicate_5

value: Isotype


title: human_pachytene_input

description:
hs_k4m1_ps_peaks.broadPeak
hs_k27ac_ps_peaks.broadPeak

value: pachytene spermatocytes


title: old_iso-3: Old_isotype_treated_mammary_tumor_replicate_3


title: human_roundspermatid_H3K27ac_ChIP

value: H3K27ac (Abcam, ab4729)


title: old_iso-4: Old_isotype_treated_mammary_tumor_replicate_4


title: old_iso-2: Old_isotype_treated_mammary_tumor_replicate_2


title: human_pachytene_H3K27ac_ChIP


title: KUL30-N

city: Seoul

first: Yourae

last: Hong

address: 81, Irwon-ro

department: Samsung Genome Institute

country: South Korea

institute: Samsung Medical Center

description:
GEO_processed_KUL3_CRC_10X_raw_UMI_count_matrix
GEO_processed_KUL3_CRC_10X_natural_log_TPM_matrix
GEO_processed_KUL3_CRC_10X_annotation

data_processing:
Using CellRanger 2.1.0 pipeline (10X Genomics), fastq data was aligned to a human genome reference (GRCh38) and the unique molecular identifier (UMI) counts was quantified .
The raw gene expression matrix from the CellRanger pipeline was filtered using the Seurat R package (version 2.3) and selected according to the following criteria: cells with > 1000 UMI counts, > 200 genes, and < 6,000 genes, and < 20% of mitochondrial gene expression in UMI counts.
After filtering step, the raw gene expression matrix was normalized to the total UMI counts per cell and transformed to the natural log scale.
We combined the Seurat multiCCA and RCA pipelines for initial clustering and cell type identification and removed discordant cells from 2 methods.
To eliminate doublets, cells with a number of genes exceeding the outliers were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-deliminated text file containing the raw gene expression and the normalized gene expression for QC filtered cells.

source_name: KUL30_Normal mucosa

extract_protocol:
An enzymatic manual tumor dissociation method was used for the KUL3 samples. After rinsing with cold PBS, the tumor specimens were minced to obtain < 1 mm3 pieces. The resulting pieces were incubated in digestion buffer (2 mg/mL Collagenase P and 0.2 mg/mL DNase I in 10 mL DMEM) for 10 minutes at 37C. The resulting suspension was filtered using a 40-µm nylon mesh, mixed with 30 mL ice cold PBS/FBS, and centrifuged at 300 ×g for 5 minutes at 4°C. The supernatant was removed, the pellet was resuspended in 1 mL RBC lysis buffer, and the suspension was incubated at RT for 5 minutes. The suspension was centrifuged at 150 ×g for 5 minutes at 4°C and the supernatant was removed. The pellet was resuspended in 0.04% BSA/PBS and filtered using a 40 µm tip strainer. The number of cells in the resulting cell suspension was determined using a LUNA Counter.
Following the manufacturer’s instructions, barcoded sequencing libraries were generated using Chromium Single Cell 3’ v2 kits. Sequencing was performed on Illumina NextSeq 500 and Illumina NovaSeq 6000 for quality control and coverage respectively.

tag: tumor stage

tag: tissue type

value: Normal mucosa


title: KUL31-N

source_name: KUL31_Normal mucosa


title: KUL28-N

source_name: KUL28_Normal mucosa


title: human_pachytene_H3K4me1_ChIP


title: old_ctla4-8: Old_anti-CTLA4_treated_mammary_tumor_replicate_8

tag: tissue


title: CyTRF#5_cAMP

city: Tokyo

first: Shoma

last: Matsumoto

address: 1-1-1 Yayoi, Bunkyo-ku

department: Department of Animal Resource Sciences

country: Japan

institute: The University of Tokyo

data_processing:
Basecalls performed using bcl2fastq v1.8.4.
Reads were mapped to the version 5.0 assembly (Ensembl) of the Macaca fascicularis genome using HISAT2 v2.0.1-beta, with using a transcript assembly to guide mapping.
Putative transcripts were identified in all samples using Stringtie v 1.2.2.
Reads from all samples were assigned to genes in the assembled genome model using FeatureCounts v.1.4.6 and the count table was loaded into DESeq2 for differential expression analysis.
Genome_build: macFas5

organism: Macaca fascicularis

source_name: Trophoblast progenitor cells

growth_protocol: CyTRF#1 and #2 were cultured in TS medium with Activin-A, FGF4, heparin, BMS493, Y-27632 (AFHBY) to maintain proliferative, undifferentiated state for 4days. CyTRF#3-5 were cultured in TS medium with FHBY for 4 days. All CyTRFs were cultured with dbcAMP to differentite multinucleated STB and invasive EVT for 6 days. For the control of cAMP treatment, CyTRF#1 and #2 were cultured in TS medium without all factors.

extract_protocol:
Total RNA was extracted from culture cells and placenta using TRIzol. TruSeq Stranded mRNA LT Sample Prep Kit was used for the construction of sequencing libraries of CyTRF#1, #2, fibroblast, placenta and ESC. TruSeq Stranded mRNA Sample Prep Kit was used for the construction of sequencing libraries of CyTRF#3-5.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Sample Preparation Guide Rev.E protocols

value: trophoblast progenitor cells

tag: passages/age


title: old_iso-6: Old_isotype_treated_mammary_tumor_replicate_6

tag: treatment

tag: biological replicate


title: KUL19-N

source_name: KUL19_Normal mucosa


title: old_ctla4-7: Old_anti-CTLA4_treated_mammary_tumor_replicate_7

tag: strain

tag: sequencing batch


title: CyTRF#5_FHBY


title: old_ctla4-6: Old_anti-CTLA4_treated_mammary_tumor_replicate_6

tag: age


title: KUL21-N

source_name: KUL21_Normal mucosa


title: CyTRF#4_cAMP

tag: cell type


title: KUL31-B

source_name: KUL31_Border region

value: I

value: Border region

tag: region

value: sigmoid

tag: pathologic

value: Well differentiated adenocarcinoma NST


title: CyTRF#4_FHBY


title: KUL01-N

source_name: KUL01_Normal mucosa


title: old_ctla4-4: Old_anti-CTLA4_treated_mammary_tumor_replicate_4

source_name: Mammary tumor

value: Balb/C

value: Mammary tumor

value: >12 months


title: old_iso-1: Old_isotype_treated_mammary_tumor_replicate_1


title: CyTRF#3_cAMP


title: old_ctla4-3: Old_anti-CTLA4_treated_mammary_tumor_replicate_3


title: yng_pdl1-10: Young_anti-PDL1_treated_mammary_tumor_replicate_10

value: 8-10 weeks


title: KUL28-B

source_name: KUL28_Border region

value: IIA


title: KUL30-B

source_name: KUL30_Border region

value: ascending


title: CyES

source_name: Embryonic stem cells

value: embryonic stem cells


title: old_ctla4-2: Old_anti-CTLA4_treated_mammary_tumor_replicate_2


title: BeWo Control Forskolin-treated [BeWoC FSK2]

city: Paris

first: Daniel

last: Vaiman

address: 24 rue du Faubourg St Jacques

department: Genetics and Development

country: France

institute: INSERM

description: BeWoC FSK2

hyb_protocol: Protocols of the genom'ic platform (Cochin Institute, https://www.institutcochin.fr/core_facilities/genome-sequencing-studies?set_language=en).

data_processing: Through the Transcriptome Analysis Console of Affymetrix (https://www.thermofisher.com/fr/fr/home/global/forms/life-science/download-tac-software.html).

source_name: BeWo Control Forskolin-treated

growth_protocol: Cells were grown in F12 medium with the relevant antibiotics (maintained selection pressure under Geneticin G-418).

extract_protocol: TrIZol extraction of RNA from cells using classical protocols, validation of concentration by Bioanalyzer. RIN >8.

treatment_protocol: Forskolin was added to part of the cells at 24 µM for three days.

tag: cell line

value: BeWo

tag: genotype/variation

value: Control

value: Forskolin


title: BeWo Control DMSO [BeWoC1]

scan_protocol: Protocols of the genom'ic platform (Cochin Institute, https://www.institutcochin.fr/core_facilities/genome-sequencing-studies?set_language=en).

source_name: BeWo Control DMSO

value: DMSO


title: BeWo overexpressing STOX1B Forskolin-treated [BeWOB FSK3]

description: BeWOB FSK3

label_protocol: Protocols of the genom'ic platform (Cochin Institute, https://www.institutcochin.fr/core_facilities/genome-sequencing-studies?set_language=en).

value: overexpressing STOX1B


title: KUL21-B

source_name: KUL21_Border region

value: IVA


title: old_ctla4-5: Old_anti-CTLA4_treated_mammary_tumor_replicate_5


title: BeWo Control DMSO [BeWoC3]


title: KUL19-B

source_name: KUL19_Border region

value: IIIB

value: rectosigmoid

value: Moderately differentiated adenocarcinoma NST


title: BeWo overexpressing STOX1B Forskolin-treated [BeWOB FSK2]

description: BeWOB FSK2


title: CyTRF#2_cAMP

value: trophoblast progenitor cells


title: CyTRF#2_TS


title: KUL01-B

source_name: KUL01_Border region

value: IIB

value: Border region

value: caecum

value: Global moderately differentiated adenocarcinoma with mixed glandulair, mucinous growth patern, moderate budding


title: BeWo Control Forskolin-treated [BeWoC FSK1]

description: BeWoC FSK1


title: KUL31-T

source_name: KUL31_Core region

value: I

value: Core region

value: sigmoid

value: Well differentiated adenocarcinoma NST


title: CyTRF#2_AFHBY


title: CyTRF#3_FHBY


title: mouse_roundspermatid_input

description:
mm_k4m1_rs_peaks.broadPeak
mm_k27ac_rs_peaks.broadPeak

data_processing:
ChIP-seq reads were filtered using fastq_quality_filter from FASTX Toolkit version 0.0.14 with parameters –q 20 –p80, and aligned to the mm10 genome build using bowtie2.2.9 using --end-to-end --fast mode with default parameters. Peaks were called using MACS version 2.1.1 with parameters -s 40 --broad --broad-cutoff 0.2.

Genome_build: mm10. hg19
Supplementary_files_format_and_content: bed files with peak coordinates

source_name: adult testis

growth_protocol: Testes were obtained from adult CD1 wild type male mice (Charles River Laboratories).

extract_protocol:
Populations of pachytene spermatocytes and round spermatids were recovered using a StaPut gradient as previously described (Bellve et al, 1993).  All isolated fractions were at least 95% pure.  Cells were washed once in PBS and then split into two aliquots.  One aliquot (for ChIP) was fixed in 1% formaldehyde then quenched with 2.5M glycine, while the second (for RNA) was left unfixed.  Both fixed and unfixed aliquots were snap frozen in liquid nitrogen, then stored at -80C.  ChIP was performed as previously described (Lee et al 2006).
ChIP-seq libraries were prepared using a TruSeq ChIP sample prep kit (Illumina) according to the manufacturer’s instructions, except that size selection was performed after instead of before PCR amplification.

value: round spermatids


title: mouse_roundspermatid_H3K27ac_ChIP

value: H3K27ac (Abcam, ab4729)


title: BeWo overexpressing STOX1B Forskolin-treated [BeWOB FSK1]

description: BeWOB FSK1

value: BeWo

value: Forskolin


title: Engineered Human Kidney Organoids

city: Pleasanton

first: Juan

middle: Pablo

last: Romero

state: CA

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics

data_processing:
Demultiplexing, alignment to the homo sapiens (hg38) genome and quantification was performed using 10X Genomics Cell Ranger (v3.0.1)
Further analysis steps (quality control filtering, normalization, clustering and differential expression) were performed using R package Seurat (v3.0.2)
Genome_build: hg38
Supplementary_files_format_and_content: HDF5 Feature Barcode Matrix. Gene x Cells UMI count matrix

source_name: Human Kidney Organoid

extract_protocol:
Cells were thawed and centrifuged at 1,500 RPM for 5 minutes. After that, cells were stained with sytox blue (Thermofisher) and sorted by FACS to remove the nonviable cells, generating a single cell suspension with greater than 90% viability analyzed using the cellometer K2 (Nexcelom Biocience).
Libraries were prepared using the Chromium Single Cell 3ʹ GEM, v3, (PN-1000075, 10X genomics) following the manufacturer´s instructions and sequenced with a NEXTseq500 (R1:28, R2: 55, i7:8) up to 30.000 reads per cell.

value: kidney organoid

tag: 10x barcode

value: 10X Barcode H3


title: KUL30-T

source_name: KUL30_Core region

value: IIA

value: ascending


title: BeWo overexpressing STOX1B DMSO [BeWoB3]

source_name: BeWo overexpressing STOX1B DMSO

value: overexpressing STOX1B

value: DMSO


title: old_ctla4-1: Old_anti-CTLA4_treated_mammary_tumor_replicate_1

value: Balb/C

value: Mammary tumor

value: >12 months


title: mouse_roundspermatid_H3K4me1_ChIP

value: H3K4me1 (Abcam, ab8995)


title: KUL28-T

source_name: KUL28_Core region

value: Core region


title: CyEF

source_name: Fibroblast

value: fibloblast


title: CyTRF#1_cAMP

source_name: Trophoblast progenitor cells

value: trophoblast progenitor cells


title: BeWo overexpressing STOX1B DMSO [BeWoB1]


title: mouse_pachytene_input

description:
mm_k4m1_ps_peaks.broadPeak
mm_k27ac_ps_peaks.broadPeak

value: pachytene spermatocytes


title: BeWo overexpressing STOX1A Forskolin-treated [BeWoA FSK3]

description: BeWoA FSK3

value: overexpressing STOX1A


title: KUL21-T

source_name: KUL21_Core region

value: IVA

value: sigmoid


title: mouse_pachytene_H3K27ac_ChIP

value: H3K27ac (Abcam, ab4729)


title: BeWo overexpressing STOX1A Forskolin-treated [BeWoA FSK2]

description: BeWoA FSK2

value: BeWo

value: Forskolin


title: KUL01-T

source_name: KUL01_Core region

value: IIB

value: caecum

value: Global moderately differentiated adenocarcinoma with mixed glandulair, mucinous growth patern, moderate budding


title: mouse_pachytene_H3K4me1_ChIP


title: BeWo overexpressing STOX1A Forskolin-treated [BeWoA FSK1]

description: BeWoA FSK1


title: CyTRF#1_TS


title: CyTRF#1_AFHBY


title: CyPL

source_name: Placenta

value: placenta

value: day 50


title: BON2_WT

source_name: Seedling

tag: strain/background


title: BeWo overexpressing STOX1A DMSO [BeWoA3]

source_name: BeWo overexpressing STOX1A DMSO

value: DMSO


title: Input_NC_cell_2

status: Public on Apr 04 2020

first: Jitendra

last: Badhai

address: Plesmanlaan 121

department: Division Molecular Genetics

institute: Netherlands Cancer Institute

data_processing:
Sequencing libraries were constructed with a TruSeq mRNA Library Preparation Kit using poly-A-enriched RNA (Illumina, San Diego, CA, USA). The Samples were run on a HiSeq 2500 Illumina sequencer generating 65 base-pair single end reads. The sequence reads were mapped to the mouse genome (mm10), using TopHat (2.0.12). TopHat was run with default. Reads with mapping quality less than 10 and non-primary alignments were discarded. Remaining reads were counted using HTSeq-count. Statistical analysis of the differential expression of genes was performed using DESeq2
DNA library preparation for Illumina sequencing was done with the TruSeq® DNA LT Sample Preparation kit (Illumina). Up to ten uniquely indexed samples were pooled equimolarly, and each pool was then sequenced as single end 65 bp run using an Illumina HiSeq2500 machine according to manufacturer's instructions.
Reads were aligned to the reference genome (mm10) using the Burrows-Wheeler Aligner (BWA 7.10). The CopywriteR program was adapted for low coverage sequencing without peak calling algorithm (Kuilman et al., 2015). A depth-of-coverage method was used for 20-kb bins, and the read count was normalized for GC content and mappability. Log2-transformed ratios were calculated for all tumor samples versus reference (normal tail) sample. The normalized and corrected profiles were further analyzed by CGHcall
Genome_build: mm10
Supplementary_files_format_and_content: normalised read counts for RNAseq/DNAseq data. Bigwig files for ChIpseq data

source_name: Mesothelioma tumor cells

extract_protocol:
for RNA se: RNA was isolated from tumor cell lines and mouse tumors with the Qiagen All Prep DNA/RNA kit. Quantification and quality assessment for RNA were performed with a Bioanalyzer (RIN >6.5) (Agilent, Santa Clara, CA, USA). For DNAseq: Genomic DNA were isolated from frozen tumor sample using the Allprep DNA/RNA/Protein mini kit (Qiagen) according to the manufacturer’s instructions. The amount of double stranded DNA in genomic DNA samples was quantified using the Qubit® dsDNA HS Assay Kit (Invitrogen). Subsequently, 250 ng of double stranded genomic DNA was fragmented by Covaris shearing and samples were purified with the Agencourt AMPure XP PCR Purification beads according to manufacturer's instructions (Beckman Coulter, cat no A63881). for ChIp seq: ChIP-Seq were performed for H3K27me3 and H2A119Ub1 with the protocol provided by Diagenode (iDeal ChIp-seq kit for histones Cat #C01010051). In brief, samples were crosslinked with formaldehyde for 10 minutes at room temperature and subsequently quenched with glycine. Samples lysed and sonicated for at least 20 cycles of 30 s On and 30 s Off using Diagenode Bioruptor Pico. For ChIP, 5 μg of antibody was conjugated with 50 μl of protein A magnetic beads. Immunoprecipitated DNA were processed for library preparation.
for RNAseq: Sequencing libraries were constructed with a TruSeq mRNA Library Preparation Kit using poly-A-enriched RNA (Illumina, San Diego, CA, USA). The Samples were run on a HiSeq 2500 Illumina sequencer generating 65 base-pair single end reads. , for DNAseq: DNA library preparation for Illumina sequencing was done with the TruSeq® DNA LT Sample Preparation kit (Illumina). Up to ten uniquely indexed samples were pooled equimolarly, and each pool was then sequenced as single end 65 bp run using an Illumina HiSeq2500 machine according to manufacturer's instructions., for ChIpseq: DNA were processed for library preparation. Libraries were sequenced using Illumina HiSeq2500 genome analyzed (65bp, single end) and aligned to mm10 using TopHat with the default setting. Reads with mapping quality >20 were selected, peak calling over input control was performed using MACS2 .

value: Mesothelioma tumor cells

tag: genotype

tag: antibody

value: input


title: Input_NC_cell_1


title: Input_BNC_cell_2


title: H2A119ub1_NC_cell_2


title: H2A119ub1_NC_cell_1


title: H2A119ub1_BNC_cell_1


title: H3K27me3_NC_cell_2


title: BeWo overexpressing STOX1A DMSO [BeWoA1]


title: H2A119ub1_BNC_cell_2


title: H3K27me3_NC_cell_1


title: H3K27me3_BNC_cell_1


title: H3K27me3_BNC_cell_2


title: NC_tumor_2

data_processing:
Library strategy: DNA-Seq
Sequencing libraries were constructed with a TruSeq mRNA Library Preparation Kit using poly-A-enriched RNA (Illumina, San Diego, CA, USA). The Samples were run on a HiSeq 2500 Illumina sequencer generating 65 base-pair single end reads. The sequence reads were mapped to the mouse genome (mm10), using TopHat (2.0.12). TopHat was run with default. Reads with mapping quality less than 10 and non-primary alignments were discarded. Remaining reads were counted using HTSeq-count. Statistical analysis of the differential expression of genes was performed using DESeq2
DNA library preparation for Illumina sequencing was done with the TruSeq® DNA LT Sample Preparation kit (Illumina). Up to ten uniquely indexed samples were pooled equimolarly, and each pool was then sequenced as single end 65 bp run using an Illumina HiSeq2500 machine according to manufacturer's instructions.
Reads were aligned to the reference genome (mm10) using the Burrows-Wheeler Aligner (BWA 7.10). The CopywriteR program was adapted for low coverage sequencing without peak calling algorithm (Kuilman et al., 2015). A depth-of-coverage method was used for 20-kb bins, and the read count was normalized for GC content and mappability. Log2-transformed ratios were calculated for all tumor samples versus reference (normal tail) sample. The normalized and corrected profiles were further analyzed by CGHcall
Genome_build: mm10
Supplementary_files_format_and_content: normalised read counts for RNAseq/DNAseq data. Bigwig files for ChIpseq data

source_name: Mesothelioma tumor

value: Mesothelioma tumor


title: BeWo overexpressing STOX1A DMSO [BeWoA2]


title: NC_tumor_1


title: NC_tumor_4


title: KUL19-T

source_name: KUL19_Core region

tag: tumor stage

value: IIIB

tag: tissue type

value: Core region

value: rectosigmoid

value: Moderately differentiated adenocarcinoma NST


title: BNC_tumor_9

tag: tissue


title: BNC_tumor_10


title: BNC_tumor_7


title: BNC_tumor_6


title: BNC_tumor_8


title: BNC_tumor_4


title: SMC13N-F

data_processing:
Using CellRanger 2.1.0 pipeline (10X Genomics), fastq data was aligned to a human genome reference (GRCh38) and the unique molecular identifier (UMI) counts was quantified.
The raw gene expression matrix from the CellRanger pipeline was filtered using the Seurat R package (version 2.3) and selected according to the following criteria: cells with > 1000 UMI counts, > 200 genes, < 6,000 genes, and < 20% of mitochondrial gene expression in UMI counts.
After filtering step, the raw gene expression matrix was normalized to the total UMI counts per cell and transformed to the natural log scale.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-deliminated text file containing the raw gene expression and the normalized gene expression for QC filtered cells.

source_name: SMC13_Normal mucosa with cryopreserved cell dissociates

extract_protocol:
For the assessment of 3 different dissociation protocols, both primary tumor and distant normal tissues were processed from a single patient.  First, samples using SMC tissue dissociation protocols used a tumor dissociation kit (Miltenyi Biotech, Germany), according to the manufacturer’s instructions. Briefly, tissues were cut into 2-4 mm pieces and transferred to C tubes containing an enzyme mix (Enzyme H, R, and A in RPMI1640 media). Gentle MACS programs (h_tumor_01, 02, and 03) were run in a MACSmix tube rotator, with two 30-min incubation periods at 37°C between each run. The digested samples were filtered through a 70-µm strainer, purified via a Ficoll-Paque PLUS (GE healthcare, USA) gradient, and cryopreserved in cell bank (Zenoaq, Japan) before sequencing.\  Second, samples using KUL3 tissue dissociation protocols were dissociated using an enzymatic manual tumor dissociation method. After rinsing with cold PBS, the tumor specimens were minced to obtain < 1mm3 pieces. The resulting pieces were incubated in the digestion buffer (2 mg/ml Collagenase P and 0.2 mg/ml DNase I in 10 ml DMEM) for 10 minutes at 37C. The resulting suspension was filtered using a 40 um nylon mesh, mixed with 30 ml ice cold PBS/FBS and centrifuged at 300xG for 5 minutes at 4°C. The supernatant was removed and the pellet was resuspended with 1 ml RBC lysis buffer and incubated at RT for 5 minutes. The resulting suspension was centrifuged at 150xG for 5 minutes at 4°C and the supernatant is removed. The pellet is resuspended in 0.04% BSA and filtered using a 40um tipstrainer. The number of cells in the resulting cell suspension was quantified by LUNA Counter.  Third, Singapore protocol consisted of tissue digestion by collagenase IV and DNases I in RPMI1640 media at 37°C for 1 h, followed by mechanical shearing with a 16 1/2 gauge needle, washing in PBS containing 1% BSA and 2 mM EDTA, and red blood cell lysis using ACK lysis buffer.  For the evaluation of fresh vs. frozen cell preparations, single cell suspension was generated using the SMC protocol, then subjected to single-cell RNA-seq in fresh or freeze-thaw states from a second patient.  For freshly prepared samples, we loaded the single cell suspension to Chromium system (10X genomics) immediately after cell dissociation targeting 5,000 cells per run. The cryopreserved single cell dissociates were loaded after a rapid thaw-wash cycle.
Following the manufacturer’s instructions, barcoded sequencing libraries were generated using Chromium Single Cell 3’ v2 kits and sequenced on a Hiseq 2500 platform (Illumina).

tag: dissociation protocol

value: SMC protocol

tag: cell preparation

value: Cryopreserved cell dissociates

value: Normal mucosa


title: BNC_tumor_5


title: WT NSC 3

source_name: Neural Stem Cell

tag: strain

value: wild type


title: SMC13N

source_name: SMC13_Normal mucosa with fresh cell dissociates

value: SMC protocol (with fresh cell dissociates)

value: Fresh cell dissociates


title: Input_BNC_cell_1


title: BNC_tumor_2


title: SMC13T

source_name: SMC13_Colorectal cancer with fresh cell dissociates

value: Colorectal cancer


title: NC_tumor_3


title: SMC171-N-SING

source_name: SMC171_Normal mucosa with Singapore protocol

value: Singapore protocol


title: NC_4


title: SMC13T-F

source_name: SMC13_Colorectal cancer with cryopreserved cell dissociates


title: SMC171-T-SING

source_name: SMC171_Colorectal cancer with Singapore protocol


title: NC_2


title: SMC171-T-BEL

source_name: SMC171_Colorectal cancer with KUL protocol

value: KUL protocol


title: BNC_5


title: SMC171-N-SGI

source_name: SMC171_Normal mucosa with SMC protocol


title: BNC_4


title: NC_1


title: SMC171-T-SGI

source_name: SMC171_Colorectal cancer with SMC protocol


title: BNC_3


title: BNC_tumor_3


title: BNC_tumor_1


title: BNC_2


title: BNC_1


title: NC_cell_2


title: NC_cell_3


title: NC_cell_1


title: Tcp- and Dex-treated H3K4me3 ChIP-Seq

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

institute: Fudan Univ, Shanghai, China

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v1.2.1.1 with parameters -m 1 -p 10
mapped data were smoothed with spp (http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial.html)
ChIP signal was normalizated by excluting Input signal
For histone modification ChIP-Seq, ChIP signal was further normalized with H3 signal.
GR peaks were identified using the Model based Analysis of ChIP-Seq (MACS v1.4) package regions of significant enrichment were determined against sample input at p < 1E-5.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using KentUtils

source_name: A549 cell line

growth_protocol: A549 cells were cultured in DMEM supplemented with 20% FBS for maintenance. For experiments cells were to being grown in media supplemented with charcoal striped serum for 16-24 hours to hormone deplete prior to ethanol or Dex treatment.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.

treatment_protocol: Cells were treated with 100nM Dex for 2 hours for ChIP-seq and for 24 hours for microarry. For TCP cells were treated with 150 uM for 24 hours.

value: lung adenocarcinoma

tag: passages

value: immortalized

tag: chip antibody

value: Millipore (07-473)


title: Tcp- and Dex-treated H3K4me1 ChIP-Seq

tag: cell type

value: Abcam (ab8895)


title: Tcp- and Dex-treated Input


title: Tcp- and Dex-treated H3K4me2 ChIP-Seq

value: Millipore (07-030)


title: Tcp- and Dex-treated GR ChIP-Seq

value: santa cruz (sc-8992)


title: BNC_cell_3

value: Mesothelioma tumor cells


title: BNC_cell_2


title: Tcp- and EtOH-treated H3K4me3 ChIP-Seq


title: Tcp- and Dex-treated H3 ChIP-Seq

value: Abcam (ab1791)


title: NC_3

value: Mesothelioma tumor


title: SMC171-N-BEL

source_name: SMC171_Normal mucosa with KUL protocol


title: Tcp- and EtOH-treated H3 ChIP-Seq


title: Tcp- and EtOH-treated Input


title: Tcp- and EtOH-treated H3K4me1 ChIP-Seq


title: Tcp- and EtOH-treated GR ChIP-Seq


title: Dex-treated KDM1A ChIP-Seq

value: Abcam ab17721)


title: BNC_cell_1


title: Dex-treated H3K9me2 ChIP-Seq

value: Abcam (ab1220)


title: Dex-treated H3K4me2 ChIP-Seq


title: Dex-treated H3K4me3 ChIP-Seq


title: Dex-treated H3K4me1 ChIP-Seq


title: Tcp- and EtOH-treated H3K4me2 ChIP-Seq


title: Dex-treated Input


title: Dex-treated H3K27ac ChIP-Seq

value: millipore (17-683)


title: Dex-treated H3 ChIP-Seq


title: Dex-treated H3K9me1 ChIP-Seq


title: Dex-treated GR ChIP-Seq


title: FT13

city: Miami

first: Sophia

middle: HL

last: George

state: FL

address: 1550 NW 10th Ave

department: Obstetrics and Gynecology

institute: University of Miami

hyb_protocol: not provided

scan_protocol: not provided

data_processing:
Expression arrays were preprocessed using the frma package (McCall et al., 2010) from  Bioconductor for hgu133plus2 arrays, and the oligo Bioconductor package (Carvalho and  Irizarry, 2010) for human genome HTA-2.0 arrays
Heat maps for data visualization were created using the  heatmap.2 function from the ggplot2 R package. Affymatrix Transcriptome Analysis software was used to analyze datasets. The data was normalized to oligo RMA gene level.

label: biotin

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Total RNA was isolated using Qiagen  RNeasy Micro. Quality and quantity of RNA was confirmed using the Agilent 2100  Bioanalyzer RNA 6000 Pico LabChip kit (Agilent Technologies, Inc.) and NanoDrop ND-  1000 Spectrophotometer (NanoDrop Technologies), respectively, before inclusion in the  study.

tag: tissue anatomy

value: AMPULLA

tag: menstrual phase

value: FOLLICULAR


title: FT11

value: LUTEAL


title: FIM6

description: This sample was removed from the analysis. No processed data are available.

value: FIMBRIA


title: EtOH-treated KDM1A ChIP-Seq


title: FIM12


title: FIM11


title: FIM10


title: FT10


title: EtOH-treated H3K9me2 ChIP-Seq


title: FIM13


title: FT12


title: FT8


title: EtOH-treated H3K9me1 ChIP-Seq


title: FIM7


title: FIM9


title: FT7


title: EtOH-treated H3K4me1 ChIP-Seq


title: EtOH-treated H3K4me2 ChIP-Seq


title: FT9


title: EtOH-treated Input


title: EtOH-treated H3K4me3 ChIP-Seq


title: EtOH-treated H3K27ac ChIP-Seq


title: EtOH-treated H3 ChIP-Seq


title: EtOH-treated GR ChIP-Seq


title: FIM8


title: P1-87

city: Houston

first: Mingfu

state: Texas

address: University of Houston College of Pharmacy, 4349 Martin Luther King Boulevard

department: Molecular and Cellular Physiology

institute: University of Houston

description: single ProEpiC

data_processing:
Kallisto pseudoalignment
Genome_build: hg38 transcriptome
Supplementary_files_format_and_content: counts of each gene in csv format

source_name: Tbx18Cre labeled ProEpiC

extract_protocol:
Tbx18Cre;mTmG labled PEO were dissected and digested to single cells; flow cytometry was used to sort pro-epicardial cells.
SMARTSeq V4 followed by Nextera XT.
full-length scRNAseq

value: pro-epicardial organ

tag: developmental stage

value: E9.5 embryo

value: pro-epicardial cells


title: P1-88

description: single ProEpiC


title: P1-86

description: single ProEpiC


title: H9 1 R+250 A

city: New York

first: Owen

middle: A

last: O"Connor

state: NY

address: 51 West 51st Street

department: enter for Lymphoid Malignancies

institute: Columbia University Medical Center

data_processing:
Alignment with STARv2.5.3
Gene-level raw counts summarization with STARTv2.5.3 quant-mode
Variance stabilization (normalization) with DESeq2 (R bioconductor package)
Gene expression signature generation with limma (R bioconductor package)
Genome_build: GRCh37.p2
Supplementary_files_format_and_content: Tab delimited text output of raw counts from STAR alignment and gene count quantification

source_name: H9 Cutaneous T-cell Lymphoma

growth_protocol: The cells grown in logarithomic phase during treatment

extract_protocol:
RNAs were extracted with using Qiagen Rneasy mini kit
Strand specific sequencing libraries were generated from rRNA depleted total RNAs using the TruSeq Stranded mRNA kit by Illumina
RNA Sequencing was performed on an Illumina NextSeq 500 sequencer.

treatment_protocol: All the samples were treated with indicated concentration of drugs for 96 hours. Romidepsin was added at time 0, 5-azacytidine sequentially every 24 hours.

tag: cell line

value: Cutaneous T-cell Lymphoma


title: FT5


title: H9 1 R+50 A


title: H9 1 R+125 A


title: P1-83

description: single ProEpiC


title: H9 250 nM azacitidine


title: H9 125 nM azacitidine


title: P1-82

description: single ProEpiC


title: H9 50 nM azacitidine


title: FIM3


title: FT4


title: FT2


title: H9  1 nM romidepsin


title: P1-81

description: single ProEpiC


title: FIM5


title: FIM4


title: FT1


title: FIM2


title: FT3


title: P1-80

description: single ProEpiC


title: H9 untreated


title: P1-79

description: single ProEpiC


title: P1-78

description: single ProEpiC


title: HH 1.25 R+250 A

source_name: HH Cutaneous T-cell Lymphoma

value: HH


title: P1-77

description: single ProEpiC


title: P1-76

description: single ProEpiC


title: P1-84

description: single ProEpiC


title: HH 250 nM azacitidine

source_name: HH Cutaneous T cell Lymphoma


title: P1-75

description: single ProEpiC


title: HH 1.25 R+125 A


title: HH 50 nM azacitidine


title: HH 125 nM azacitidine


title: P1-73

description: single ProEpiC


title: HH 1 nM romidepsin


title: P1-72

description: single ProEpiC


title: P1-71

description: single ProEpiC


title: HH untreated


title: P1-70

description: single ProEpiC


title: TLOm1 1 R+250 A

source_name: TLOm1 Adult T-cell leukemia

value: Adult T-cell leukemia


title: TLOm1 1 R+500 A


title: TLOm1 1 R+125 A


title: P1-67

description: single ProEpiC


title: HH 1.25 R+50 A


title: P1-66

description: single ProEpiC


title: TLOm1 500 nM azacitidine


title: TLOm1 125 nM azacitidine


title: P1-64

description: single ProEpiC


title: TLOm1 250 nM azacitidine


title: P1-63

description: single ProEpiC


title: PF382 1.25 R+500 A

source_name: PF382 T-cell Acute Lymphoblastic Leukemia

value: T-cell Acute Lymphoblastic Leukemia


title: TLOm1 untreated


title: PF382 1.25 R+125 A


title: FIM1


title: P1-85

description: single ProEpiC


title: PF382 1.25 R+250 A


title: P1-60

description: single ProEpiC


title: P1-59

description: single ProEpiC


title: P1-62

description: single ProEpiC


title: P1-58

description: single ProEpiC


title: PF382 500 nM azacitidine


title: P1-57

description: single ProEpiC


title: PF82 250 nM azacitidine


title: P1-68

description: single ProEpiC


title: P1-56

description: single ProEpiC


title: P1-65

description: single ProEpiC


title: PF382 untreated


title: PF382  1.25 nM romidepsin


title: PF382 125 nM azacitidine


title: P1-51

description: single ProEpiC


title: P1-52

description: single ProEpiC


title: P1-50

description: single ProEpiC


title: P1-45

description: single ProEpiC


title: TLOm1  1 nM romidepsin


title: 92.1BAP1KD_rep2

first: Matthew

middle: G.

last: Field

address: 1501 NW 10th Avenue

data_processing:
Raw RNA-Seq FASTQ files were assessed for quality using FastQC
Sequenced reads were aligned to the human genome (hg19) using STAR with the following settings --runThreadN 16 --genomeSAindexNbases 12 --genomeSAsparseD 2  --genomeDir  /nethome/mfield/ref_files/ENSEMBL/STAR_genomedirectory --readFilesIn /scratch/projects/hlab/newRNAseq/F46.fastq.gz --readFilesCommand zcat --outFileNamePrefix /scratch/projects/hlab/newRNAseq/STAR/F46 --outSAMtype BAM SortedByCoordinate --chimSegmentMin 12 --quantMode GeneCounts --alignIntronMax 200000 --alignMatesGapMax 200000 --alignSJDBoverhangMin 10 --chimJunctionOverhangMin 12 --twopassMode Basic --twopass1readsN -1
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file with gene count file output from STAR

source_name: 92.1 uveal melanoma, cell line

extract_protocol:
RNA was isolated using TriZol and the RNeasy Mini RNA isolation kit with RNAase-Free DNase treatment (Qiagen).
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA prep kit with Ribo-Zero Gold to remove cytoplasmic and mitochondrial rRNA according to the manufacturer's recommendation (Illumina, Inc.).

tag: agent

value: Induced with dox for 5D, BAP1KD


title: Mel202WT_rep1

source_name: Mel202 uveal melanoma, cell line

value: Uninduced


title: P1-46

description: single ProEpiC


title: P1-74

description: single ProEpiC


title: Mel202BAP1KD_rep1


title: P1-41

description: single ProEpiC


title: 92.1WT_rep2


title: P1-38

description: single ProEpiC


title: 92.1WT_rep1


title: KO_RPF_2

first: Qi

last: Liu

state: MASSACHUSETTS

address: Boston, 02115.USA

institute: Boston Children's Hospital

description:
KO_RPF_2
RiboZero mRNA

data_processing:
After adapter-trimming and quality-filtering, the sequences were further filtered to exclude rRNA and tRNA reads by aligning to mouse rRNA and tRNA sequence which were retrieved from Ensembl (Release 91) (https://useast.ensembl.org/Mus_musculus/Info/Index) and GtRNAdb databases (Chan and Lowe, 2016), respectively. The cleaned ribosome-protected fragments (RPFs) were aligned to the mouse canonical known gene models (UCSC, mm10) using Bowtie with a maximum one mismatch allowed (Langmead et al., 2009). For codon occupancy analysis, the A site were inferred using an offset of 15 nt from 5’ end of 28-31nt fragments which were unique mapped and translated in the zero-frame of CDS (Nedialkova and Leidel, 2015). The codon occupancy of an A-site was further normalized by its basal occupancy which is the average codon occupancy among +1, +2 and +3 downstream of A-site. The translation efficiency (TE) was calculated by dividing RPF abundancy on CDS by its mRNA abundancy. We used 1.5 fold change of TE to define the differential translation genes (Zinshteyn and Gilbert, 2013). For the metagene analysis, we divided each CDS region into 50 equal bins and counted the RPF occupany in each bin, which were then normalized by total number of RPFs of respective gene.
Genome_build: mm10
Supplementary_files_format_and_content: RPF occupany in each bin, which were then normalized by total number of RPFs of respective gene

source_name: mESC

growth_protocol: Undifferentiated mESCs were grown in LIF/Setum condition

extract_protocol:
Cells were treated by cyclohexamide to pause translation and lyzed in Mammalian Polysome Buffer (Illumina). Input mRNAs and RPFs were isolated, ribosomal RNAs were depleted and cDNA libraries were prepared according to the TruSeq Ribo Profile pipeline (Illumina)
TruSeq Ribo Profile pipeline (Illumina)

treatment_protocol: Dis3l2 knockout mESCs were generated by CRISPR/Cas9-mediated gene editing

value: Undifferentiated mouse ESCs

tag: sample type

value: RPF


title: KO_RPF_1

description:
KO_RPF_1
RiboZero mRNA

tag: genotype


title: P1-42

description: single ProEpiC


title: P1-37

description: single ProEpiC


title: P1-35

description: single ProEpiC


title: Control_RPF_2

description:
Control_RPF_2
RiboZero mRNA


title: P1-55

description: single ProEpiC


title: P1-34

description: single ProEpiC


title: KO_input_2

description:
KO_input_2
RiboZero mRNA

value: Input


title: Control_RPF_1

description:
Control_RPF_1
RiboZero mRNA


title: P1-32

description: single ProEpiC


title: KO_input_1

description:
KO_input_1
RiboZero mRNA


title: P1-31

description: single ProEpiC


title: Control_input_2

description:
Control_input_2
RiboZero mRNA


title: P1-33

description: single ProEpiC


title: P1-44

description: single ProEpiC


title: P1-30

description: single ProEpiC


title: Control_input_1

description:
Control_input_1
RiboZero mRNA


title: P1-29

description: single ProEpiC


title: P1-25

description: single ProEpiC


title: P1-27

description: single ProEpiC


title: P1-23

description: single ProEpiC


title: Ctrl_sgRNA_Wnt_Rep2

first: Chen

last: Chu

address: 450 Brookline Ave, Smith 914

institute: Dana-Farber Cancer Institute

description: processed data file: Dot1l KO_Wnt.csv

data_processing:
Basecalling performed using bcl2fastq v2.18.
For Thio-ChIP-seq, sequencing reads were aligned to mm9 using Bowtie (default parameter, except: -k 1 -m 1 --best). The thiopeaks were called using MACS v1.4.2 with the corresponding input control (default parameter, except: -p 1e-9).
For H3K79me2 ChIP-seq, sequencing reads were aligned to mm9 using Bowtie 2 v2.2.9, and peak calling was performed using MACS2 v2.1.1 with corresponding input controls (default parameter, except: --broad).
For RNA-seq, sequencing reads were aligned to the GRCm38 using STAR v2.5.4a, and differential gene expression analysis was performed using the Cuffdiff function in the Cufflinks v2.2.1.
Genome_build: mm9 (Thio-ChIP-seq, H3K79me2 ChIP-seq), GRCm38 (RNA-seq)
Supplementary_files_format_and_content: bed (peak files for Thio-ChIP-seq and H3K79me2 ChIP-seq) and csv (for RNA-seq).

source_name: ES cells

growth_protocol: Mouse embryonic stem cells were maintained on a monolayer of mitotically inactivated mouse embryonic fibroblasts in SL medium consisting of Knockout DMEM medium (Invitrogen), 15% HyClone fetal bovine serum (Invitrogen), 100 U/ml leukemia inhibitory factor (LIF) (Millipore), 1% MEM non-essential amino acids, 1% penicillin/streptomycin, 1% glutamine and 0.1 mM 2-mercaptoethanol.

extract_protocol:
For Thio-ChIP-Sequencing, cells were scraped and collected by centrifugation at 1350 rpm for 5 min at 4o C, resuspended in 6 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1, Halt phosphatase and protease inhibitors) and sonicated for 10 cycles 30 s ON and 30 s OFF, using Diagenode Bioruptor Pico. The lysates were then cleared by centrifugation at 16000 x g for 5 min, the pH was adjusted to 6.0 with formic acid, and p-nitrobenzyl mesylate was added to 1.5 mM for 30 min. Two percent of the labeled and control alkylated lysates volume were saved as input controls and the rest was incubated with 10 μl of anti-thiophosphate ester antibody overnight at 4o C. Fifty μl of protein G Dynabeads (Invitrogen) were then added and the reactions incubated for another 5 h. Beads were then washed twice with RIPA buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.1% sodium deoxycholate), twice with RIPA buffer with 0.3 M NaCl, twice with LiCl buffer (250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and two times with TE buffer (1 mM EDTA, 10 mM Tris-HCl pH 8.0, 0.1% Triton X-100). The beads and the previously saved input controls were then rotated with 300 μl elution buffer (1% SDS, 0.1 M NaHCO3) overnight, 65o C. Next day, the beads were discarded and DNA recovered by adding 1.5 µl RNase A (10 mg/ml) and incubated for 30 min at 37o C. Next, 2.4 μl EDTA (0.5 M), 4.8 μl Tris-HCl (1 M), 2 μl glycogen (20 mg/ml) and 3 μl proteinase K (20 mg/ml) were added, followed by 2 h incubation at 62o C. DNA was then extracted using phenol/chloroform, washed with 75% ethanol, air dried and reconstituted in 24 μl TE buffer.
For H3K79me2 ChIP-sequencing, cell pellets were thawed into Nuclei EZ lysis buffer (Sigma) with protease inhibitor cocktail (Roche), incubated for 30 min on ice, centrifuged as above, and the nuclei resuspended in 3 ml of sonication buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, protease inhibitors). Nuclei were then sonicated 10x 30 s ON (output level 3, 24W) / 60 s OFF cycles with probe sonicator, on ice. Sonicated nuclear extracts were then cleared by centrifugation at 16000 x g, 15 min, 4o C. Twenty five microliters of the nuclear extracts were saved as input material. Chromatin was immunoprecipitated from nuclear extracts with anti-histone H3 Lys79me2 antibody beads (obtained by binding ab3594 antibody to protein G Dynabeads, Novex), overnight at 4o C. The beads were collected using magnetic separator, washed, and chromatin was eluted for 30 min at 65o C with 200 μl of buffer containing 50 mM Tris-HCl, pH 8.0, 10 mM EDTA and 1% SDS. Crosslinking of ChIP and input samples was reversed for 16 h at 65o C. Samples were treated with RNase A at 0.5 mg/ml for 2 h at 37o C, supplemented with 5 mM CaCl2 and 0.3 mg/ml Proteinase K and digested for 30 min at 55o C. DNA was next purified with phenol-chloroform-isoamyl alcohol mix (Qiagen) and 2 ml MaXtract gel tubes (Qiagen). After 10 min centrifugation at 16000 x g, DNA was precipitated by adding 16 μl of 5 M NaCl, 1 μl of 20 mg/ml glycogen (Fermentas) and 900 μl ethanol, centrifuged at 16000 x g, 4o C, and dissolved in 25 μl of TE buffer.
For RNA-seq, total RNA was purified using RNeasy Mini Kit (Qiagen).
DNA libraries were prepared according to Illumina's standard protocols.
RNA libraries were prepared using Roche Kapa mRNAseq Hyper prep according to manufacturer's protocol.

treatment_protocol:
To differentiate the cells, the ES cells were trypsinized and plated at 3 x 10e4/cm2 on gelatin-coated dishes in N2B27 medium (Knockout DMEM, 1% N2 and 2% B27 without vitamin A (Invitrogen), 1% MEM non-essential amino acids, 1% penicillin/streptomycin, 1% glutamine, 0.1 mM 2-mercaptoethanol and 10 μM Y-27632 (Selleckchem). Two days later medium was changed to N2B27 with 50 ng/ml Wnt3a (R&D Systems, 5036-WN) and 10 ng/ml Activin A (R&D Systems, 330-AC). Cells were usually harvested after 24 h for gene expression, or allowed to differentiate for 4 and 7 days to follow changes in Cdk1/2 activity and H3K79me2 mark.
For Thio-ChIP-Sequencing, Cdk1AS/AS ES cells were plated in N2B27 medium. Two days later, cells were co-treated for 16 h with 500 nM retinoic acid and 1 μM 3-MB-PP1 to obtain cells synchronized at G2/M phase with peak Cdk1 activity. The inhibitor was then washed off with PBS and 2 ml of the labeling buffer, modified from ref. 53 (20 mM HEPES pH 7.5, 100 mM KOAc, 5 mM NaOAc, 2 mM MgOAc2, 1 mM EGTA, 10 mM MgCl2, 0.5 mM DTT, 45 μg/ml digitonin, 5 mM GTP, 0.2 mM ATP, 0.1 mM N6-furfuryl ATPγS (Biolog), Roche protease inhibitors cocktail) were added for 25 min. Control cells were treated the same way except that N6-furfuryl ATPγS was omitted. Formaldehyde was then added to 0.5% final concentration and plates were incubated for 15 min, followed by quenching with 150 mM glycine.
For H3K79me2 ChIP-sequencing, Cdk1AS/AS ES cells were grown without feeders and treated with 1 μM 3-MB-PP1 or DMSO for 4 days. Cells were crosslinked with 1% formaldehyde for 20 min, glycine (0.125 M final concentration) was added, cells were scraped, collected by centrifugation at 1350 x g, 10 min, 4o C, flash frozen in liquid nitrogen and stored at -70o C.

value: WT

value: ES cells

tag: treatment

value: Wnt3a and activin A


title: Ctrl_sgRNA_Wnt_Rep3

description: processed data file: Dot1l KO_Wnt.csv


title: Dot1l_KO_LIF_Rep3

description: processed data file: Dot1l KO_LIF.csv

value: Dot1l KO


title: Dot1l_KO_Wnt_Rep1

description: processed data file: Dot1l KO_Wnt.csv


title: Dot1l_KO_LIF_Rep2

description: processed data file: Dot1l KO_LIF.csv


title: P1-22

description: single ProEpiC


title: Ctrl_sgRNA_Wnt_Rep1

description: processed data file: Dot1l KO_Wnt.csv


title: Dot1l_KO_Wnt_Rep2

description: processed data file: Dot1l KO_Wnt.csv


title: P1-20

description: single ProEpiC


title: 92.1BAP1KD_rep1


title: P1-19

description: single ProEpiC


title: Ctrl_sgRNA_LIF_Rep3

description: processed data file: Dot1l KO_LIF.csv


title: Ctrl_sgRNA_LIF_Rep2

description: processed data file: Dot1l KO_LIF.csv


title: P1-18

description: single ProEpiC


title: P1-21

description: single ProEpiC


title: mESC_Rep_3

description: processed data file: Transcriptome of mESC.csv


title: P1-16

description: single ProEpiC


title: mESC_Rep_2


title: P1-28

description: single ProEpiC


title: Ctrl_sgRNA_LIF_Rep1

description: processed data file: Dot1l KO_LIF.csv


title: mESC_Rep_1


title: P1-15

description: single ProEpiC


title: P1-13

description: single ProEpiC


title: CL_HDL_LPS-3

first: David

middle: G

last: Thomas

department: Medicine

institute: Columbia University

description:
hdl_counts.txt
hdl_effect_inCL_1-5F.csv

data_processing:
Nextseq 500 lanes were merged using gunzip/cat
Adaptor contamination was removed using cutadapt
Reads were aligned to mouse genome mm10 using HISAT2
Feature assignment was performed using Subread-featureCounts
Statistical comparison of read counts was performed using DESeq2
Differentially expressed gene lists were prepared by filtering for q<0.05 (5% FDR)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with counts for each gene; comma-delimited text file with differentially expressed gene lists

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow-derived macrophages (BMDMs) were obtained by isolating bone marrow cells from femurs and tibias of mice and incubated in DMEM (Corning) 10% FBS (Thermo), 1% pen-strep (Thermo) supplemented with 20% L929-conditioned medium in tissue culture plates (Thermo). Fresh medium was added on day 3 and day 5. After 7 days, macrophages were fully differentiated and the culturing media were replaced with DMEM, 1% pen-strep supplemented with 4% L929-conditioned medium to normalize exposure to serum-derived lipoproteins.

extract_protocol:
Macrophages were washed twice with cold PBS and lysed in TRIzol reagent (Thermo). RNA was isolated from the aqueous phase using RNeasy kits (Qiagen).
RNA with RIN > 8 was subjected to poly-dT pulldown using magnetic beads (NEB) before preparation for RNA-Seq using RNA Ultra kits (NEB).

treatment_protocol: On day 8, macrophages were treated with reconstituted HDL CSL111 (CSL Behring) with an APOA1 to soybean phosphatidylcholine ratio of 1:150 1 for 20 hours. The BMDMs were washed twice with PBS, fresh DMEM, 1% pen-strep supplemented with 4% L929-conditioned medium was added with or without LPS (Cell signaling) for the indicated time. For cholesterol loading experiments, macrophages were incubated with POPC/cholesterol-liposomes prior to rHDL treatment.

value: Bone marrow-derived macrophages

value: Chol. Liposomes+HDL+LPS


title: CL_HDL_LPS-2

description:
hdl_counts.txt
hdl_effect_inCL_1-5F.csv


title: P1-11

description: single ProEpiC

value: pro-epicardial organ

value: E9.5 embryo


title: CL_HDL_LPS-1

description:
hdl_counts.txt
hdl_effect_inCL_1-5F.csv


title: CL_Ctrl_LPS-3

description:
hdl_counts.txt
hdl_effect_inCL_1-5F.csv

value: Chol. Liposomes+LPS


title: P1-9

description: single ProEpiC

value: pro-epicardial cells


title: P1-12

description: single ProEpiC


title: P1-7

description: single ProEpiC


title: CL_Ctrl_LPS-1

description:
hdl_counts.txt
hdl_effect_inCL_1-5F.csv


title: P1-8

description: single ProEpiC


title: P1-5

description: single ProEpiC


title: HDL_LPS-2

description:
hdl_counts.txt
hdl_effect_1-5F.csv

value: HDL+LPS


title: HDL_LPS-3

description:
hdl_counts.txt
hdl_effect_1-5F.csv


title: HDL_LPS-1

description:
hdl_counts.txt
hdl_effect_1-5F.csv


title: P1-4

description: single ProEpiC


title: P1-1

description: single ProEpiC


title: LPS_Ctrl-3

description:
hdl_counts.txt
hdl_effect_1-5F.csv

value: LPS only


title: P1-2

description: single ProEpiC


title: P1-3

description: single ProEpiC


title: LPS_Ctrl-2

description:
hdl_counts.txt
hdl_effect_1-5F.csv


title: LPS_only-3


title: P1-24

description: single ProEpiC


title: CL_Ctrl_LPS-2

description:
hdl_counts.txt
hdl_effect_inCL_1-5F.csv


title: LPS_only-1


title: Notr_Ctrl-3

value: No treatment


title: Notr_Ctrl-2


title: Notr_Ctrl-1


title: LPS_Ctrl-1

description:
hdl_counts.txt
hdl_effect_1-5F.csv


title: Macrophages_exposed_to_CoMtb_rep4

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

hyb_protocol: We performed hybridization with 2.0 ug of Cy3-cDNA and the hybridization kit (Roche NimbleGen). The samples were then incubated for 5 min at 65°C, and 5 min at 42°C before loading for 17h at 42°C, according to manufacturer's protocol.

scan_protocol: After washing, the microarrays were scanned with MS200 microarray scanner (Roche NimbleGen), and using Feature Extraction software, the Agilent raw files were extracted and then processed through Bioconductor (version 3.1) in the R statistical environment (version 3.6.0)

data_processing: Using the limma package, raw expression values were background corrected in a ‘normexp’ fashion and then quantile normalized and log2 transformed. Density plots, boxplots, principal component analyses, and hierarchical clustering assessed the quality of the hybridizations.

label_protocol: cDNA was labeled with Cy3-dCTP using One-color DNA labeling kit (Roche NimbleGen). Gene expression was analyzed using the Agilent Human GE 4x44 vs (G4845A) microarray kit.

growth_protocol: Human monocytes were isolated from healthy subject buffy coat and differentiated towards macrophages under M-CSF and conditioned media for 3 days

extract_protocol: Conditioned cells (approximately 1.5 million) were treated with TRIzol Reagent (Invitrogen) and stored at -80°C. Total RNA was extracted from the TRIzol samples using the RNeasy mini kit (Qiagen). RNA amount and purity (absorbance at 260/280 nm) was measured with the Nanodrop ND-1000 apparatus (Thermo Scientific). According to the manufacturer's protocol, complementary DNA was then reverse transcribed from 1 µg total RNA with Moloney murine leukemia virus reverse transcriptase (Invitrogen), using random hexamer oligonucleotides for priming

treatment_protocol: Conditioned media was generated from human macrophages infected with Mycobacterium tuberculosis (coMtb) or mock control (coCtlr). The cells were then treated with 40% of conditioned media and 60% of RPMI-media supplemented with M-CSF (10 ng/ml) and 10% (fetal calf serum).

tag: donor status

value: healthy subject

value: Macrophages

tag: conditioned media source

value: Mycobacterium tuberculosis-infected (coMtb) macrophages


title: Macrophages_exposed_to_CoMtb_rep2


title: LPS_only-2


title: Macrophages_exposed_to_CoMtb_rep3


title: Macrophages_exposed_to_CoCtrl_rep4

value: non-infected (coCtrl) macrophages


title: Dot1l_KO_Wnt_Rep3

description: processed data file: Dot1l KO_Wnt.csv


title: JEV Injection group BP2 (mRNA)

city: Hohhot

first: Yang

last: yang

state: Inner Mongolia Autonomous Region

address: No. 24 Zhaojun Road, Yuquan District

department: School of Life Sciences

institute: Inner Mongolia University

description: mRNA expression after the injection medium

hyb_protocol: Prepare the fragmented mixture according to the formula, and then incubate at 60 ° C for 30 min to perform fragmentation. Including: Cy3 cRNA 875ng, 10XBlocking Agent 11µl, 25X Fragmentation Buffer 2.2µl, and add the corresponding Nuclease-free water to a total volume of 55µl, then add 55µl 2X GEx Hybridization Buffer, take 100µl 65 ℃, 10rpm rolling hybridization for 17 hours.After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scan in an Agilent scanner with a resolution of 5 μm. The scanner automatically scans once at 100% and 10% PMT, and the Agilent software can automatically merge the results twice.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Mouse brain,JEV Injection

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the QIAGEN RNeasy Mini Kit according to the manufacturer's recommendations. This protocol uses an RNeasy column to separate RNA samples treated with Buffer RLT and absolute ethanol, and then quantifies RNA using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Four week old healthy C57BL / 6 mice were selected. One group was injected with JEV virus as the experimental group. A group of injection medium was used as a control group. After the experimental group showed the corresponding symptoms, the two groups of mice were sacrificed immediately, the brain tissue was separated from the liquid nitrogen and sent to the company for detection of gene expression levels.

tag: infection

value: JEV

tag: tissue

value: brain

tag: age

value: four weeks


title: Macrophages_exposed_to_CoCtrl_rep2


title: Dot1l_KO_LIF_Rep1

city: Boston

description: processed data file: Dot1l KO_LIF.csv

tag: strain

value: Dot1l KO

value: ES cells


title: JEV Injection group BP3 (miRNA)

description: MiRNA expression after the injection JEV

hyb_protocol: The dried sample was re-dissolved in 18 μL of nuclease-free water. Add 4.5 μL of prepared 10 × GE Blocking Agent and 22.5 μL of 2 × Hi-RPM Hybridization Buffer to each tube, mix by vortexing gently, and place in a 100 ° C metal bath for 5 minutes, then quickly transfer it to an ice-water bath Cool for 5 minutes. The reaction solution was collected by centrifugation, and about 45 μL was slowly pipetted onto a cover slip placed on the base of an Agilent SureHyb chamber, and hybridized in a hybridization oven at a temperature of 55 ° C. and a rotation speed of 20 rpm for 20 minutes. After hybridization, the chip was washed with 2 mL of 10% Triton X-102 at room temperature.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner （Agilent p/n G2565BA）using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with  Feature Extraction (FE) software version 9.5.3 (Agilent) using default parameters (protocol miRNA-v1_95_May07) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: According to the manufacturer's instructions, using the miRNA Complete Labeing and Hyb Kit, first dilute the RNA sample to 50 ng / μL with 1 × TE (pH 7.5) or DNase / RNase-free water, and then pipette 2 μL of the dilution with the The phosphorylated mixture is mixed for dephosphorylation. Take 2 μL of the dephosphorylated mixture, add 2.8 μL of 100% DMSO to it, heat it in a 100 ° C metal bath for 5-10 minutes for denaturation, and then take 4.5 μL of Cy3 10 × T4 RNA Ligase Buffer, T4 RNA Ligase mixed solution and sample were mixed and incubated at 16 ° C for 2 hours. After the reaction, place the sample in a vacuum concentrator and completely dry it for later use.

extract_protocol: Total RNA was extracted from mouse brain tissue by Shanghai bohao biotechnology co., LTD. According to the mir Vana ™ RNA Isolation Kit (Applied Biosystem p/n AM1556)

treatment_protocol: Four week old healthy C57BL / 6 mice were selected. One group was injected with JEV virus as the experimental group. A group of injection medium was used as a control group. After the experimental group showed the corresponding symptoms, the two groups of mice were sacrificed immediately, the brain tissue was separated from the liquid nitrogen and sent to the company for detection of miRNA levels.


title: JEV Injection group BP3 (mRNA)


title: Medium injection control group BD3 (mRNA)

source_name: Mouse brain,Medium injection

value: control


title: Medium injection control group BD2 (mRNA)


title: JEV Injection group BP1 (mRNA)


title: Macrophages_exposed_to_CoMtb_rep1


title: ura3FLAGsta_WCE

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

description:
input control DNA (matched sample with ura3FLAGsta_IP)
HBT-ura3-cdrL-stat-pks.bed

data_processing:
50 bp single reads were assessed for quality using FastQC (www.bioinformatics.babraham.ac.uk)
adapter sequences trimmed using Trim Galore (www.bioinformatics.babraham.ac.uk) and Cutadapt
Resultant sequences were aligned to H. salinarum NRC-1 genome (RefSeq: NC_002607.1, NC_002608.1, NC_001869.1) using Bowtie2
Peaks were called using MOSAiCS with arguments: fragment length 200, bin size 200, read capping 0, analysis type IO, background estimate rMOM, signal model 2S, FDR 0.01.
Genome_build: GCF_000006805.1_ASM680v1
Supplementary_files_format_and_content: wig files were generated using the "generateWig()" command in the R MOSAiCs package; bed files were generated from peak calling with MOSAiCs

organism: Halobacterium salinarum

source_name: archaeal cells

growth_protocol: Triplicate cultures of strains AKS113 (CdrL tagged at the C-terminus with the FLAG epitope, Supplementary Table 4) and ∆ura3 control strain were grown until stationary phase and subcultured in rich media supplemented with 50 µg/ml uracil. At mid-log phase (OD600 ~0.15) and early stationary phase (OD600 ~1.8), cultures were crosslinked and immunoprecipitated.

extract_protocol: Libraries were constructed using the KAPA Hyper Prep kit and Illumina TruSeq adapters according to manufactuer's instructions. DNA library quality was assessed by Bioanalyzer using a High Sensitivity DNA chip (Agilent). Samples were pooled and run in a single lane on an Illumina HiSeq 4000 (Duke Sequencing and Genomics Technologies core).

treatment_protocol: Cells were crosslinked and immunopreciptated with FLAG antibody as described in Wilbanks et al., 2012 (doi: 10.1093/nar/gks063) with the following exceptions: cultures were crosslinked and immuniprecipitated as described (Wilbanks et al., 2012) with the following exceptions: cultures were crosslinked with 1% formaldehyde for 30 minutes at room temperature; immuoprecipitations were conducted using Dynabead magnetic beads (Thermo-Fisher product 10002D) conjugated with anti-FLAG (Abcam ab1162) anti-rabbit monoclonal antibody at 1:250 dilution. DNA concentration was determined by Nanodrop (Thermo Scientific).

value: [delta]ura3 cdrL::FLAG

tag: growth phase

value: stationary

tag: epitope tag

value: FLAG

tag: antibody


title: JEV Injection group BP2 (miRNA)


title: Macrophages_exposed_to_CoCtrl_rep1

tag: cell type


title: Medium injection control group BD1 (mRNA)


title: Macrophages_exposed_to_CoCtrl_rep3


title: ura3FLAGlog_IP

description:
DNA immunopreciptated control with no epitope tag
HBT-ura3-cdrL-log-pks.bed

value: logarithmic

value: anti-FLAG (Abcam ab1162) anti-rabbit monoclonal antibody


title: P1-14

description: single ProEpiC

value: pro-epicardial organ

value: E9.5 embryo

value: pro-epicardial cells


title: ura3FLAGsta_IP

description:
DNA immunopreciptated control with no epitope tag
HBT-ura3-cdrL-stat-pks.bed


title: 0195FLAG3sta_IP

description:
DNA immunopreciptated with the CdrL transcription protein
HBT-cdrL3-stat-pks.bed


title: 0195FLAG2sta_WCE

description:
input control DNA (matched sample with 0195FLAG2sta_IP)
HBT-cdrL2-stat-pks.bed


title: ura3FLAGlog_WCE

description:
input control DNA (matched sample with ura3FLAGlog_IP)
HBT-ura3-cdrL-log-pks.bed


title: Medium injection control group BD2 (miRNA)

description: MiRNA expression after the injection medium


title: 0195FLAG2sta_IP

description:
DNA immunopreciptated with the CdrL transcription protein
HBT-cdrL2-stat-pks.bed


title: 0195FLAG1sta_IP

description:
DNA immunopreciptated with the CdrL transcription protein
HBT-cdrL1-stat-pks.bed


title: Medium injection control group BD3 (miRNA)


title: 0195FLAG1sta_WCE

description:
input control DNA (matched sample with 0195FLAG1sta_IP)
HBT-cdrL1-stat-pks.bed


title: 0195FLAG3log_WCE

description:
input control DNA (matched sample with 0195FLAG3log_IP)
HBT-cdrL3-log-pks.bed


title: S348: K-sh_dex_rep2

data_processing:
Salmon quantification produced count data
DEseq2 differential expression analysis produced p-values and log2 fold change values

growth_protocol: Cultured in DMEM supplemented with 10% FBS, and changed to DMEM with 5% charcoal stripped FBS for 24 hours prior to Dex or ethanol treatment

extract_protocol:
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 100nM Dex or equal volume ethanol for 24 hours

value: 100nM Dex 24 hours


title: Medium injection control group BD1 (miRNA)


title: 0195FLAG3sta_WCE

description:
input control DNA (matched sample with 0195FLAG3sta_IP)
HBT-cdrL3-stat-pks.bed


title: 0195FLAG2log_WCE

description:
input control DNA (matched sample with 0195FLAG2log_IP)
HBT-cdrL2-log-pks.bed


title: Input_3MB

description: processed data file: H3K79me2_3MB_Peaks.bed

tag: chip antibody


title: 0195FLAG1log_WCE

description:
input control DNA (matched sample with 0195FLAG1log_IP)
HBT-cdrL1-log-pks.bed


title: S347: K-sh_dex_rep1


title: H3K79me2_3MB

value: Anti-histone H3 Lys79me2


title: S345: SC_dex_rep1

value: scramble


title: S346: SC_dex_rep2


title: 0195FLAG3log_IP

description:
DNA immunopreciptated with the CdrL transcription protein
HBT-cdrL3-log-pks.bed


title: 0195FLAG2log_IP

description:
DNA immunopreciptated with the CdrL transcription protein
HBT-cdrL2-log-pks.bed


title: Input_DMSO

description: processed data file: H3K79me2_DMSO_Peaks.bed

value: DMSO


title: H3K79me2_DMSO


title: JEV Injection group BP1 (miRNA)

description: MiRNA expression after the injection JEV

value: JEV

value: brain


title: Uveal melanoma, sample 89

type: genomic

description:
beta.201404481.01
MM89

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K array using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: ChAMP pipeline in R (2.12.4)

label: Cy5 and Cy3

source_name: primary uveal melanoma, enucleation

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using QIAamp DNA Mini Kit (Qiagen) according to standard instuctions.

value: Uveal melanoma

tag: gep

value: Class 1


title: S344: K-sh_etoh_rep2

value: ethanol


title: S343: K-sh_etoh_rep1


title: 0195FLAG1log_IP

description:
DNA immunopreciptated with the CdrL transcription protein
HBT-cdrL1-log-pks.bed

value: [delta]ura3 cdrL::FLAG


title: ThioChIP_Input

description: processed data file: ThioChIP_Peaks.bed

value: ES cells


title: Uveal melanoma, sample 16

description:
beta.201404476.01
MM16


title: ThioChIP

description: processed data file: ThioChIP_Peaks.bed

value: Anti-thiophosphate ester


title: Uveal melanoma, sample 93

description:
beta.201404482.01
MM93

value: Class 2


title: cdc7-7 OE Cse4 ChIP

city: Worcester

first: Richard

middle: E

last: Baker

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

data_processing:
50-base paired-end Illumina reads were aligned to the S. cerevisiae S288C reference (R64-2-1) using Bowtie version 1.0.0 with command line options -n2 -m1 -X 500.
Duplicate reads (20-89%) were removed using Samtools rmdup (version 0.1.19).
Input alignments were randomly down sampled to 10M alignments each. Peaks were called using MACS (ZHANG et al. 2008) version 2.1.1.20160226 in paired-end mode with default parameters and no additional down sampling.
Genome_build: sacCer3
Supplementary_files_format_and_content: narrowPeak files were generated during peak calling; scores are -10*log10qvalue
Supplementary_files_format_and_content: bedGraph files were generated by MACS during peak calling. Results are expressed as reads per million total reads.

organism: Saccharomyces cerevisiae S288C

growth_protocol: Cells were grown to logarithmic phase in glucose (endogenous Cse4) or raffinose/galactose (OE Cse4) media for 1.75 hours.

extract_protocol:
Cell suspension was distributed to screw top tubes with glass beads (0.4-0.65 mm diameter) and lysed three times for 40 seconds each, followed by a five-minute rest on ice, and lysed two times for 40 seconds each in an MP Bio FastPrep-24 5G. Lysates were collected, and the chromatin pellets  washed twice in FA lysis buffer, resuspended in FA lysis buffer, sonicated 24 times with repeated 15 seconds on/off at 20% amplitude using a Branson digital sonifer. After 3 minutes of centrifugation (13000 rpm, 4ºC), a portion of the supernatant was saved for input library constucation and the remainder incubated with anti-FLAG® M2 Affinity Gel (Sigma, A2220-5ML) overnight. The beads were washed with FA, FA-HS (500 mM NaCl), RIPA, and TE buffers twice each. The beads were resuspended in 25 mM Tris-HCl pH7.6, 100 mMNaCl, 0.5% SDS), incubated at 65°C overnight, treated with proteinase K (0.5 mg/ml) at 55°C for four hours followed by Phenol/Chloroform extraction and ethanol precipitation.
Following repair using the NEB Pre-PCR Repair Mix (New England Biolabs, M0309), paired-end libraries were prepared using the NEBNext® End Prep (New England Biolabs, E7370) and NEBNext® Multiplex Oligos for Illumina (New England Biolabs, E7335).

treatment_protocol: Cells were treated with formaldehyde (final 1%) for 20 minutes at 30°C followed by the addition of 2.5 M glycine for 10 minutes, then washed twice with 1 X PBS and resuspended in 2 mL FA Lysis Buffer (1 mM EDTA pH8.0, 50 mM HEPES-KOH pH7.5, 140 mM NaCl, 0.1% sodium deoxycholate, 1% Triton X-100) with 1 x protease inhibitors (Sigma) and 1 mM PMSF final concentration.

tag: genotype/variation

value: GAL-CSE4-FLAG cdc7-7

value: sonicated spheroplasts

value: anti-FLAG M2 Affinity Gel (Sigma, A2220)


title: cdc7-7 endogenous Cse4 ChIP

value: CSE4-HA cdc7-7


title: Wild-type OE Cse4 ChIP

source_name: WT-IP-OE


title: Uveal melanoma, sample 49

description:
beta.201404473.01
MM49


title: Uveal melanoma, sample 90

description:
beta.201404477.01
MM90


title: S341: SC_etoh_rep1


title: Wild-type endogenous Cse4 ChIP

source_name: WT-IP-endo


title: P1-17

description: single ProEpiC

source_name: Tbx18Cre labeled ProEpiC

value: pro-epicardial organ

tag: developmental stage

value: E9.5 embryo

value: pro-epicardial cells


title: T24 cells_Q63E2

city: Tianjin

first: Yaxiu

last: Guo

address: 22 Qi Xiangtai Road

department: Immunology

institute: Tianjin Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Index of the reference genome was built using Bowtie2 and paired-end clean reads was aligned to the reference genome using Hisat2 2.1.0.
String Tie are used for assembling transcripts and gene expression level is calculated by FPKM value. In each million sequences, each gene takes 1,000 bases as a unit, and FPKM is the number of the matched reads (The obtained fragments were interrupted when the library was built. When sequenced with PE, the same fragment contained two reads).
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample

source_name: bladder cancer cell line

extract_protocol:
After transduced with vector or RhoC-Q63E, T24 RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: T24 cells stably expressing vector or constitutively active RhoC mutant Q63E were constructed using lentiviral supernatant. The stably expressed cells were selected by puromycin

value: urinary bladder

tag: cell line

tag: disease state

value: transitional epithelial cell carcinoma

value: constitutively active RhoC mutant Q63E


title: Uveal melanoma, sample 10

description:
beta.201404478.01
MM10

value: Uveal melanoma


title: Uveal melanoma, sample 70

description:
beta.201404480.01
MM70


title: Uveal melanoma, sample 92

description:
beta.201404479.01
MM92

value: Class 1


title: Uveal melanoma, sample 176

description:
beta.201404475.01
MM176


title: T24 cells_Q63E3

tag: genotype


title: cdc7-7 OE Cse4 input

tag: sample type


title: T24 cells_Q63E1


title: Uveal melanoma, sample 50

description:
beta.201404474.01
MM50


title: cdc7-7 endogenous Cse4 input


title: T24 cells_VEC3

value: control (Vector)


title: Uveal melanoma, sample 100

description:
beta.201404483.01
MM100


title: Uveal melanoma, sample 28

description:
beta.201404472.01
MM28


title: 67_DCR_GLP1_trimmed_collapsed_AAGA

status: Public on Apr 03 2020

city: Ramat Gan

first: sivan

last: Korenblit

state: - None -

address: Life Sciences Building (212) , mailbox 63, Bar-Ian University

department: Faculty of Life Sciences

institute: Bar-Ilan University

description: 8N identifier AAGA barcode

data_processing:
Filter sequences with irrelevant barcodes, Split relevant sequences by barcode, Remove the linker from each sequence, DEseq package in R (http://www.r-project.org) was used from the data obtained from bowtie to identify differentially expressed siRNAs.
Genome_build: C. elegans WS220
Supplementary_files_format_and_content: DEseq results based on normalized read counts; excel

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: glp-1(e2144) or dcr-1(mg375) glp-1(e2144) eggs were incubated at 25°C for 50 hours to day-1 stage.

extract_protocol:
worms were washed several times to avoid contamination with bacteria, snap-freezed at liquid nitrogen, and grinded to powder in a liquid nitrogen -prechilled mortar and pestle. High-molecular weight and Low-molecular weight RNA fractions were isolated using miRVana miRNA isolation kit Applied Biosystems (Ambion).
QsRNA-seq (Fishman etl al., Genome Biology 2018)

treatment_protocol: Embryos were isolated from gravid N2 adults by treatment with sodium hypochlorite solution.

value: Adult day 1

tag: biological replicate no

tag: technical replicate no


title: T24 cells_VEC1

tag: tissue


title: 67_GLP1_trimmed_collapsed_GGGT

description: 8N identifier GGGT barcode


title: 58_GLP1_trimmed_collapsed_CTGG

description: 8N identifier CTGG barcode


title: T24 cells_VEC2


title: 30_GLP1_trimmed_collapsed_CTGG

description: 8N identifier CTGG barcode


title: 58_DCR_GLP1_trimmed_collapsed_GCAG

description: 8N identifier GCAG barcode


title: 30_DCR_GLP1_trimmed_collapsed_ACTT

description: 8N identifier ACTT barcode


title: Wild-type endogenous Cse4 input

source_name: WT-IN-endo