title: Suc-2

city: Shenzhen

first: Conghui

last: You

state: Guangdong

address: No. 1066 Xueyuan Road

department: College of Life Sciences and Oceanology

institute: Shenzhen University

description: Suc.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, unknown bases(N) are more than 10% and low-quality sequence, then mapped to NCM3722 whole genome using bowtie2 v2.3.2 with parameters --sensitive -I 100 -X 500 --end-to-end --no-unal
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. To avoid counting reads from the neighbor genes, the number of reads falling in the middle of 70% of the genes  were counted and normalized by the size of the 70% of the gene and by the size of the total library.
Genome_build: NCM3722 (NZ_CP011495.1 and NZ_CP011496.1) with minor updates following MG1655 (NC_000913.3)
Supplementary_files_format_and_content: Tab-delimited text files with raw gene counts and RPKM values for every gene and every sample

organism: Escherichia coli

source_name: E. coli

growth_protocol: in N-C- minimal medium plus NH4Cl and one specific carbon source aerobically at 37°C water bath, 250rpm

extract_protocol:
All samples were quick freezed in liquid nitrogen and stored at -80 °C for RNA extraction. Total RNA was extract by RNAiso plus (Takara) and PureLink RNA Mini Kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: culture

value: Batch culture in Suc at 37°C, OD600≈0.4

value: Wild Type


title: Suc-3

status: Public on Mar 02 2021

type: SRA

country: China

description: Suc.txt

library_source: transcriptomic

molecule: total RNA

treatment_protocol: no treatment

tag: strain

tag: genotype


title: KOcrp&cyaA-2

description: KOcrp&cyaA.txt

value: Batch culture in Glc at 37°C, OD600≈0.4

value: crp- & cyaA-


title: KOcrp&cyaA-3

description: KOcrp&cyaA.txt


title: BD_2

city: Beijing

first: Bo

last: He

state: Beijing

address: Yiheyuan Road 5th.

department: School of Life Science

institute: Peking University

library_source: genomic

data_processing:
Library strategy: CATCH-Seq
Low-quality bases (trim_galore v.0.4.1,using options: -q 30, --stringency 3) , adaptor (cutadapt v.1.16, using options: -a CCCCCCCCCCCCCCCCCCCCCCCCCC -g GATCTGGGGGGGGG -m 40) and PCR duplicates(FASTX Toolkit v 0.0.13) were removed.
Unique reads were trimmed for the poly-C sequence at the 3’ end of reads. Reads with minimum length of 40 bp were mapped to the human (hg38) reference genome by bismark(v.0.15.0) using options –bowtie2 -N 1 -L 30.
Read visualization was done with IGV(v.2.3.90).
The identification of 5hmC-enriched regions (peaks) in each sample was performed using MACS.
Genome_build: hg38
Supplementary_files_format_and_content: bw files contain genome-wide read coverage data.

molecule: genomic DNA

organism: Homo sapiens

source_name: bladder

extract_protocol:
Genomic DNA was isolated from frozen tissues by TIANamp Genomic DNA Kit(TIANGEN).
The AI-labeled ssDNA was used directly for library preparation with the TELP protocol except PCR amplification. Click chemistry was performed by adding the DBCO-S-S-PEG3-Biotin (Click Chemistry Tools, Cat. No. A112-10) to a final concentration of 400 mM, and incubated in the thermomixer (Eppendorf) for 1 h at 37°C (800 rpm). Purification steps were performed with DNA Clean & Concentrator 5 (Vistech) with the help of carrier RNA (Thermo Fisher Scientific).

treatment_protocol:
block endogenous 5fC using O-ethylhydroxylamine
oxidation reaction using K2RuO4
labeling of the newly generated 5fC

tag: tissue

value: bladder


title: Suc-1

description: Suc.txt


title: KOcrp&cyaA-1

description: KOcrp&cyaA.txt


title: Sor-2

description: Sor.txt

value: Batch culture in Sor at 37°C, OD600≈0.4


title: WT_plasmid_KRAB_plasmid

city: Santa Cruz

first: Sergio

last: Covarrubias

state: CA

address: Thimann Receiving/Department Carpenter Lab/Biomed 125, 1156 High St., Thimann Labs

department: MCD

country: USA

institute: UCSC

data_processing:
RNAseq 1: fastq.gz files were analyzed using the https://github.com/quasiben/gRNA_Tool
RNAseq 2: all guide RNA (sgRNA) + barcode reads were collapsed to obtain sgRNA counts
RNAseq 3: Counts were normalized to the median sgRNA count
RNAseq 4: Fold changes were calculated for for each sgRNA
Genome_build: custom whole-genome nuclease Cas9 mouse sgRNA library
Supplementary_files_format_and_content: Phenotypes_sgRNAs_NFKB screen
Supplementary_files_format_and_content: Phenotypes_sgRNAs_viability_screen

organism: synthetic construct

source_name: library plasmid

growth_protocol: Cells were maintained ~1-2 millions cells/ml in DMEM supplemented with 10% Fetal Calf Serum and Penicillin/Streptomycin.

extract_protocol:
Cell pellets from samples were resuspended in 20 mL P1 buffer (Qiagen) with 100 μg/mL RNase A and 0.5% SDS followed by incubation at 37C for 30 min. After that, Proteinase K was added (100 μg/mL final) followed by incubation at 55C for 30 min. After digest, samples were homogenised by passing them three times through a 18G needle followed by three times through a 22G needle. Homogenised samples were mixed with 20 mL Phenol:Chlorophorm:Isoamyl Alcohol (Invitrogen #15593–031), transferred into 50 mL MaXtract tubes (Qiagen) and thoroughly mixed. Samples were then centrifuged at 1500 g for 5 min at room temperature (RT). The aqueous phase was transferred into ultracentrifuge tubes and thoroughly mixed with 2 mL 3 M sodium acetate plus 16 mL isopropanol at RT before centrifugation at 15,000 g for 15 min. The gDNA pellets were carefully washed with 10 mL 70% ethanol and dried at 37C. Dry pellets were resuspended in H2O and gDNA concentration was adjusted to 1 μg/uL. The degree of gDNA shearing was assessed on a 1% agarose gel and gDNA was sheared further by boiling at 95C until average size was between 10 and 20 kb.
Multiple PCR reactions were prepared to allow amplification of the total harvested gDNA from a 1000x cell coverage for each sample. For the first round of two nested PCRs, the total volume was 100 μL containing 50 μg sheared gDNA, 0.3 μM forward (5′-ggcttggatttctataacttcgtatagca-3) and reverse (5′-cggggactgtgggcgatgtg-3′) primer, 200 μM each dNTP, 1x Titanium Taq buffer and 1 μL Titanium Taq (Clontech). PCR cycles were: 1x (94C - 3 min), 16x (94C - 30 s, 65C – 10 s, 72C – 20 s), 1x (68C – 2 min). All first round PCRs were pooled and a fraction was used as template for the second round PCR. The total volume of the second round PCR was 100 μL containing 2 μL pooled first round PCR, 0.5 μM forward (5’-AATGATACGGCGACCACCGAGATCCACAAAAGGAAACTCACCCTAAC-3′) and reverse (5’-CAAGCAGAAGACGGCATACGAGAT-(N)6-GTGACTGGAGTTCAGACGTG-3′) primer where (N)6 is a 6 nt index for sequencing on the Illumina HiSeq platform, 200 μM each dNTP, 1x Titanium Taq buffer and 1 μL Titanium Taq (Clontech). PCR cycles were: 1x (94C - 3 min), 16x (94C - 30 s, 55C – 10 s, 72C – 20 s), 1x (68C – 2 min). The resulting PCR product (344 bp) was extracted from a 1% agarose gel. Gel extracted bands were submitted for sequencing on an Illumina HiSeq 2500 platform using paired end 50 kits with the custom sequencing primer 5’-GAGACTATAAGTATCCCTTGGAGAACCACCTTGTTGG-3′ for reading the sgRNA sequence and the standard Truseq Illumina reverse primer to read out 20 nt unique barcode sequences and library IDs.
sequencing of amplicon

treatment_protocol: iBMDM-NFKB-Cas9 cells were infected with the sgRNA genome-scale library at a at low multiplicity of infection (moi=3) with an initial library coverage of >100X.  Three days post infection, cells were puromycin-selected (10ug/ml) for 5 days obtain cherry-positive (sgRNA) cells and were maintained at >1000X coverage at all times. For the NFKB screen, cells were stimulated with 200ng/ml LPS for 24h prior to FACS-based sorting

tag: mouse strain

tag: cells


title: Sor-3

description: Sor.txt


title: LN_4

source_name: lung

value: lung


title: Lac-3

description: Lac.txt

value: Batch culture in Lac at 37°C, OD600≈0.4


title: HR_4_LV

source_name: heart

value: heart


title: Lac-1

description: Lac.txt


title: Gly-3

description: Gly.txt

value: Batch culture in Gly at 37°C, OD600≈0.4


title: Gly-2

description: Gly.txt


title: Glc-3

description: Glc.txt


title: Sor-1

description: Sor.txt


title: Gly-1

description: Gly.txt


title: Glc-2

description: Glc.txt


title: Glc-1

description: Glc.txt


title: G6P-1

value: Batch culture in G6P at 37°C, OD600≈0.4


title: Lac-2

description: Lac.txt


title: Ace-3

description: Ace.txt

value: Batch culture in Ace at 37°C, OD600≈0.4


title: Ace-2

description: Ace.txt


title: G6P-2


title: MDA-MB-231 cells, ADR3

city: Nanjing

first: Jing

last: Yu

address: No.101 Longmian Avenue, Jiangning District

institute: Nanjing Medical University, China P.R

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl  scripts
Index of the reference genome was built using HISAT2 v2.0.4 and  paired-end clean reads were aligned to the reference genome using  HISAT2(Langmead, B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default.
The mapped reads of each sample were assembled by StringTie (v1.3.3) (Mihaela  Pertea.et al. 2016) in a reference-based approach
We used phyloFit to compute  phylogenetic models for conserved and non-conserved regions among species and  then gave the model and HMM transition parameters to phyloP to compute a set of  conservation scores of lncRNA and coding transcripts.
StringTie (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding  transcripts in each sample (Mihaela Pertea et al. 2016). FPKM means fragments per  kilo-base of exon per million fragments mapped, calculated based on the length of the  fragments and reads count mapped to this fragment.
Genome_build: Homo_sapiens_Ensemble_94
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: breast cancer cell

extract_protocol:
RNA  was isolated using TRIZOL.RNA purity was checked using the NanoPhotometer® spectrophotometer  (IMPLEN, CA, USA).RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0  Flurometer.RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the  Bioanalyzer 2100 system
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wild-type MDA-MB-231 cell, DOC resistant MDA-MB-231 cell，ADR resistant MDA-MB-231 cell

tag: cell line

tag: phenotype

value: ADR (Adriamycin) resistant breast cancer cell


title: MDA-MB-231 cells, ADR1


title: MDA-MB-231 cells, ADR2


title: MDA-MB-231 cells, DOC2

value: DOC (docetaxel) resistant breast cancer cell


title: MDA-MB-231 cells, DOC3


title: MDA-MB-231 cells, WT3

value: Wild-type breast cancer cell


title: MDA-MB-231 cells, WT1


title: TS22

city: Los Angeles

first: Peter

last: Tontonoz

address: 675 Charles E Young

department: Pathology

institute: UCLA

description:
HR_vs_LR.txt
HR_vs_NS.txt

data_processing:
RNA was harvested from Trizol and used for RNA-Seq library construction using the TruSeq V2 kit (illumina) and samples were sequenced paired end 2 x 100bp on a HiSeq2000. Reads were aligned using TopHat to the Hg19 genome with >85% matching base percentage and 1 allowable mismatched base. Total read counts were used as input for differential gene expression using edgeR with samples separated by risk status. Reads that failed to map to the reference human genome or transcriptome (i.e. unmapped reads) are stored in <fastq> format. We used ROP protocol v1.0.4  to profile viruses among the unmapped reads. ROP first filters out: (a) low quality reads, (b) low complexity reads and (c) rRNA reads. ROP also filters out ‘lost human reads’. Lost human reads are defined as unmapped reads aligned to human references using Megablast (BLAST+ 2.2.30).  The remaining high-quality non-human reads are used for viral profiling. ROP uses Megablast (BLAST+ 2.2.30) to align the reads onto viral genomes downloaded from NCBI ftp://ftp.ncbi.nih.gov/ on February 1, 2015.
The alignment profiles of the viral reads were scan through a Microbiome Coverage Profiler (MCP v1.0, distributed with ROP,  https://github.com/JRotman/mcp ). MCP reports coverage plots of viral genomes passed the stringent criteria.  MCP first filters out reads mapped due to sequencing and/or PCR artifacts.  MCP handles reads mapped to the multiple location of the same viral genome by randomly choosing one of the alignments. In case reads are mapped to the multiple genomes, MCP consider the average coverage of each genome (obtained from uniquely mapped reads) to randomly assign the read to one of the viral genomes. Each viral genome was then analyzed by its coverage. Genomes with less than 20 reads were rejected considering to have insufficient coverage. Any partially covered genomes were run through BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi) to determine if the covered regions are unique to the virus. Viral genomes passing the above criteria are reported as present in the samples. Coverage plots for reported viral genomes are generates using the Matplotlib 1.5.1 (http://matplotlib.org/users/installing.html).
Genome_build: hg19
Supplementary_files_format_and_content: DESeq output files comparing the three risk groups: High-Risk (HR), Low-Risk (LR), and Normal Skin (NS). For each gene there is an assigned fold difference and p-value.

source_name: Human Skin Biopsy

extract_protocol:
Human skin was biopsied and placed in RNA-Later (Thermo) until total RNA was purified using QIAshredder (Qiagen) and RNeasy (Qiagen) purification columns used according to manufacturer's protocol.
All total RNA libraries were generated using the Illumina Trueseq v.2 kit according to manufacturer's protocol.

value: skin

tag: risk-group

value: High-Risk


title: TS20

description:
HR_vs_LR.txt
HR_vs_NS.txt


title: TS15

description:
HR_vs_LR.txt
HR_vs_NS.txt


title: TS14

description:
HR_vs_LR.txt
HR_vs_NS.txt


title: TS16

description:
HR_vs_LR.txt
HR_vs_NS.txt


title: TS18

description:
HR_vs_LR.txt
HR_vs_NS.txt


title: G6P-3


title: TS10

description:
HR_vs_LR.txt
HR_vs_NS.txt


title: TS4

description:
HR_vs_LR.txt
HR_vs_NS.txt


title: TS13

description:
HR_vs_LR.txt
HR_vs_NS.txt


title: TS6

description:
HR_vs_LR.txt
LR_vs_NS.txt

value: Low-Risk


title: S4

description:
HR_vs_LR.txt
HR_vs_NS.txt


title: Ace-1

description: Ace.txt

value: Wild Type


title: CC01

description:
HR_vs_LR.txt
LR_vs_NS.txt


title: S2A

description:
HR_vs_LR.txt
LR_vs_NS.txt


title: S5

description:
HR_vs_LR.txt
LR_vs_NS.txt


title: S1A

description:
HR_vs_LR.txt
LR_vs_NS.txt


title: MDA-MB-231 cells, DOC1


title: MDA-MB-231 cells, WT2


title: TS5

description:
HR_vs_LR.txt
LR_vs_NS.txt


title: NSCC03

description:
HR_vs_NS.txt
LR_vs_NS.txt

value: Normal Skin


title: NS1

description:
HR_vs_NS.txt
LR_vs_NS.txt


title: Limbal Epithelial SCs- WT

city: Haifa

first: Anna

last: Altshuler

address: 1, Efron Street

department: Genetics & Developmental Biology

country: Israel

institute: Technion

data_processing:
Illumina NextSeq500
Cell ranger (version 2.2.0)
Alignment, filtering, barcode counting, and UMI counting was performed using the count function
Downstream analyses were performed using two R packages developed for analyzing single cell gene expression data - Seurat (version 2.3.4)
Genome_build: mm10

organism: Mus musculus

source_name: Cornea

extract_protocol:
Ten eyes of 2.5 months old Krt15-GFP mice were enucleated, the limbus (with marginal conjunctiva and peripheral cornea) was dissected (~0.5 mm), tissues were pooled and incubated in trypsin (X10 Biological Industries) for 10 min 37°C 300 μl. Supernatant was collected into 10 ml (RPMI (Biological Industries) 10% chelated fetal calf serum). Trypsinization was repeated for 10 cycles adding fresh trypsin in each cycle. Cell suspension was centrifuged (8 min at 300g), re-suspended and filtered using Cell strainer (Danyel Biotech) to achieve 1200 cells/μL.
An RNA library was produced according to the 10x Genomics protocol (Chromium Single Cell 3’ Library & Gel Bead Kit v2, PN-120237) using 18000 input cells.
scRNA-seq

value: Cornea

tag: age

value: post natal day 75


title: TS11

description:
HR_vs_LR.txt
LR_vs_NS.txt


title: CC05

description:
HR_vs_LR.txt
LR_vs_NS.txt


title: NPC_KO3

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L51438_Track-92535

data_processing:
Fastq reads were trimmed using Trim Galore 0.4.0 and the function Cutadapt 1.8.1. To remove cytosines that were filled in during ends preparation, an additional 2 bp were cut off from every sequence with detected adapter.
Trimmed reads were mapped against mm10 using Bismark 0.16.1
Base calling performed using MethylKit 1.12.0
Genome_build: mm10
Supplementary_files_format_and_content: Methylation percentages of cytosines for individual samples. Tab-delimited .txt file exported from Methylkit.

source_name: Dnmt3a/b (-/-)_NPC in vitro cultures from dentate gyrus

growth_protocol: NPCs were cultured in growth medium (Neurobasal; Gibco) supplemented with gluatamax (1x; Gibco), B-27 supplement (1x; Gibco), Pen/Strep (10,000 U/ml; Gibco), hEGF (20 mg/ml; PeproTech), hFGF-2 (20 mg/ml; Peprotech). Cells were maintained in a cell culture incubator at 37°C, 21% O2.

extract_protocol:
NPCs were covered with DNA lysis buffer and harvested using a cell scratcher. Neurons were isolated by FACS based on incorporation of the dye NeuroFluor (Stem Cell Technologies).
Genomic DNA was isolated using the QIAamp DNA Micro Kit (QIAGEN) following the manufacturer’s manuals. RRBS libraries were prepared using the Premium RRBS Kit (Diagenode) and purified twice using Agencourt AMPure XP beads (Beckman Coulter; 1X bead volume). Quality and concentration of RRBS libraries were determined using the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical) and a fragment analyzer with capillary size of 33 cm (Advanced Analytical).

treatment_protocol: During differentiation cells were cultured in the absence of hEGF and hFGF-2.

tag: genotype/variation

tag: Sex

value: Female

value: 2 months

tag: cell type


title: Neuron_KO2

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L51443_Track-92543

source_name: Dnmt3a/b (-/-)_Neurons differentiated from NPC in vitro cultures


title: NPC_WT3

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L51435_Track-92533

source_name: Dnmt3a/b (+/+)_NPC in vitro cultures from dentate gyrus


title: NPC_KO2

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L51437_Track-92534

value: NPC in vitro cultures from dentate gyrus


title: Neuron-ENR3

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32755_Track-66680
L32755_Track-66271

data_processing:
Fastq reads were trimmed using Trim Galore 0.4.0 and the function Cutadapt 1.8.1. To remove cytosines that were filled in during ends preparation, an additional 2 bp were cut off from every sequence with detected adapter.
Trimmed reads were mapped against mm10 using Bismark 0.16.1
Base calling was performed using MethylKit 1.5.2.
Genome_build: mm10
Supplementary_files_format_and_content: Methylation percentages of cytosines for individual samples. Txt file exported from Methylkit.

source_name: Neuron-ENR_dentate gyrus

growth_protocol: Mice housed in 12:12 light:dark cycle under SPF conditions and given ad libitum access to mouse chow and water.

extract_protocol:
Isolation of cells from the hippocampus by FACS for Nestin-Gfp (NSPCs; nestin::Gfp mice), Dcx-Gfp (lPCs; dcx::Gfp) or Neuro-Fluor.
Genomic DNA was isolated using the QIAamp DNA Micro Kit (QIAGEN) following the manufacturer’s manuals. RRBS libraries were prepared using the Premium RRBS Kit (Diagenode) and purified twice using Agencourt AMPure XP beads (Beckman Coulter; 1X bead volume). Quality and concentration of RRBS libraries were determined using the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical) and a fragment analyzer with capillary size of 33 cm (Advanced Analytical).

treatment_protocol: Mice were housed in either standard cages or in an enriched environment.

tag: strain/genotype

value: 3 months

tag: housing

value: enriched environment for five weeks

value: Dentate gyrus


title: NPC_KO1

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L51436_Track-92532


title: Neuron_WT2

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L51440_Track-92541

source_name: Dnmt3a/b (+/+)_Neurons differentiated from NPC in vitro cultures


title: NPC_WT1

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L51433_Track-92536


title: Neuron_WT3

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L51441_Track-92540

value: Neurons differentiated from NPC in vitro cultures


title: Neuron-ENR5

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32759_Track-66274


title: Neuron_KO1

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L51442_Track-92539


title: Neuron_WT1

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L51439_Track-92538


title: Neuron-ENR4

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32758_Track-66273


title: CC03

description:
HR_vs_LR.txt
LR_vs_NS.txt


title: Neuron-ENR2

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32754_Track-66681
L32754_Track-66272


title: CC02

description:
HR_vs_LR.txt
LR_vs_NS.txt


title: Neuron-ENR1

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32753_Track-66679
L32753_Track-66270


title: NS20

description:
HR_vs_NS.txt
LR_vs_NS.txt


title: Neuron_KO3

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L51444_Track-92542


title: Neuron-STD3

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32751_Track-66677
L32751_Track-66267

source_name: Neuron-STD_dentate gyrus

value: Standard housing


title: lPC-ENR6

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L26071_Track-58386

source_name: lPC-ENR_dentate gyrus


title: Neuron-STD2

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32750_Track-66678
L32750_Track-66268


title: Neuron-STD1

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32756_Track-66276


title: lPC-ENR4

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L26069_Track-58384


title: lPC-STD6

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L26067_Track-58382

source_name: lPC-STD_dentate gyrus


title: lPC-STD5

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L26066_Track-58381


title: NPC_WT2

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L51434_Track-92537


title: lPC-STD4

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L26065_Track-58380


title: NSPC-ENR4

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32768_Track-66300

source_name: NSPC-ENR_dentate gyrus


title: Neuron-STD4

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32752_Track-66676
L32752_Track-66269


title: NSPC-STD3

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32767_Track-66301

source_name: NSPC-STD_dentate gyrus


title: NSPC-STD5

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32762_Track-66307
L32762_Track-66280


title: NSPC-ENR1

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32763_Track-66305
L32763_Track-66282


title: NSPC-ENR3

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32765_Track-66304
L32765_Track-66278


title: NSPC-ENR2

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32764_Track-66309
L32764_Track-66281


title: NSPC-STD1

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32766_Track-66303


title: NSPC-STD4

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32761_Track-66308
L32761_Track-66279


title: NSPC-ENR5

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32769_Track-66298


title: X7_D24

data_processing:
Quality control with FASTQC
Data were demultiplexed using bcl2fastq2 v2.20 and aligned to the mouse reference transcriptome mm10 using kallisto v0.44.0 with default parameters.
Transcript levels were quantified as transcripts per million reads (TPM) and then summarized to the gene level.
Cells with fewer than 10 reads for at least  500 genes were removed from further analysis.
The pagoda2 package was used for variance normalisation (gam.k = 10), identification of cell clusters (PCA: nPcs = 100,  n.odgenes = 3e3; k-nearest neighbor: k = 50, perplexity = 30, min.group.size = 10) and t-distributed stochastic neighbor embedding (t-SNE). Log-transformed normalised gene expression values were then exported from pagoda2 for further analyses.
Genome_build: mm10
Supplementary_files_format_and_content: tsv: tab-delimited transcript abundances; csv: matrix of normalised and log-transformed expression values summarised by gene.

source_name: WT_dentate gyrus; adult-born neural precursor cell_T1

growth_protocol: Mice were housed in standard polycarbonate cages (Type II, Tecniplast) and maintained on a 12 h light/dark cycle. Food and water were provided ad libitum.

extract_protocol:
Single cells from dissociated hippocampus tissue were sorted by fluorescence cell cytometry and collected into a 384-well plates pre-loaded with 2.3 µl lysis buffer (50 mM guanidine hydrochloride, 17.4 mM dNTPs, 2.2 µM SMART dT30VN primer).
Smart-Seq2 libraries were generated using Tecan Freedom EVO and Nanodrop II (Bionex) systems.

value: WT

tag: animal id

tag: tissue/cell type


title: X7_H24

source_name: KO_dentate gyrus; adult-born neural precursor cell_T1

value: KO


title: X7_I24

source_name: KO_dentate gyrus; adult-born neural precursor cell_T4b


title: X7_E24

value: dentate gyrus; adult-born neural precursor cell


title: X7_G24

source_name: KO_dentate gyrus; adult-born neural precursor cell_T4


title: lPC-ENR5

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L26070_Track-58385


title: X7_J24


title: X7_C24

source_name: WT_dentate gyrus; adult-born neural precursor cell_T1b


title: NSPC-STD2

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L32760_Track-66306
L32760_Track-66277


title: X7_J23


title: X7_B24


title: X7_D23

source_name: WT_dentate gyrus; adult-born neural precursor cell_T4


title: X7_F24

source_name: WT_dentate gyrus; adult-born neural precursor cell_T2


title: X7_G23


title: X7_B23


title: X7_J22


title: X7_H22


title: X7_F22


title: X7_D22


title: X7_J21

source_name: KO_dentate gyrus; adult-born neural precursor cell_T3


title: X7_H21


title: X7_G21


title: X7_F21


title: X7_H20

source_name: KO_dentate gyrus; adult-born neural precursor cell_T1b


title: X7_G20


title: X7_I20


title: X7_C20


title: X7_F19


title: X7_G19


title: X7_B19


title: X7_C19


title: X7_J18


title: X7_H19


title: X7_B21


title: X7_D21


title: X7_I19


title: X7_J19


title: X7_I18


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title: X7_H18


title: X7_D18


title: X7_F18


title: X7_J17


title: X7_H17


title: X7_G17


title: X7_I21


title: X7_I17


title: X7_H16


title: X7_A20


title: X7_G16


title: X7_D16


title: X7_B20


title: X7_B16


title: X7_J15


title: X7_A16


title: X7_H15


title: X7_G15


title: X7_C15


title: X7_A15


title: X7_J14


title: X7_H13


title: X7_D14


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title: X7_B14


title: X7_D13


title: X7_I14


title: X7_F14


title: X7_G13


title: X7_I13


title: X7_E13


title: X7_I12


title: X7_G12


title: X7_F12


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title: X7_E12


title: X7_J10


title: X7_G11


title: X7_G10


title: X7_C10


title: X7_E10


title: X7_J9


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title: X7_C9


title: X7_I9


title: X7_H8


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title: X7_I3


title: X7_G4


title: X7_E4


title: X7_C7


title: X7_C4


title: X7_K3


title: X7_E8


title: X7_J4


title: X7_G7


title: X7_E6


title: X7_H3


title: X7_K2


title: X7_B3


title: X7_G2


title: X7_J3


title: X7_J2


title: X7_B2


title: X7_K1


title: X7_C2


title: X5_O24


title: X5_N24


title: X7_G1


title: X7_J1


title: X7_I1


title: X5_I24


title: X5_L24


title: X5_E24


title: X5_D24


title: X5_P23


title: X5_A24

source_name: WT_dentate gyrus; adult-born neural precursor cell_T3


title: X5_C24


title: X5_B24


title: X5_O23


title: X5_M23


title: X5_N23


title: X5_L23


title: X5_K23


title: X5_C23


title: X5_J23


title: X5_E23


title: X5_P22


title: X5_I23


title: X5_B23


title: X5_M22


title: X5_N22


title: X5_O22


title: X5_J22


title: X5_I22


title: X5_E22


title: X5_H22


title: X5_K22


title: X5_A22


title: X5_C22


title: X5_P21


title: X5_O21


title: X5_E21


title: X5_D21


title: X5_O20


title: X5_L21


title: X5_A23


title: X5_C21


title: X5_P20


title: X5_N20


title: X5_M20


title: X5_E20


title: X5_H20


title: X5_D20


title: X5_L20


title: X5_I20


title: X5_K20


title: X5_A20


title: X5_B22


title: X5_C20


title: X5_N19


title: X5_M19


title: X5_P19


title: X5_O19


title: X5_L19


title: X5_H19


title: X5_G19


title: X5_M21


title: X5_E19


title: X5_F19


title: X5_D19


title: X5_B20


title: X5_O18


title: X5_P18


title: X5_C19


title: X5_M18


title: X5_A19


title: X5_L18


title: X5_N18


title: X5_D18


title: X5_E18


title: X5_C18


title: X5_M17


title: X5_A18


title: X5_O17


title: X5_L17


title: X5_K17


title: X5_E17


title: X5_B17


title: X5_A17


title: X5_C17


title: X5_P17


title: X5_N17


title: X5_H17


title: X5_P16


title: X5_B19


title: X5_O16


title: X5_N16


title: X5_M16


title: X5_B18


title: X5_D16


title: X5_C16


title: X5_B16

source_name: WT_dentate gyrus; adult-born neural precursor cell_T4b


title: X5_E16


title: X5_P15

source_name: KO_dentate gyrus; adult-born neural precursor cell_T2


title: X5_N15


title: X7_A14


title: X5_F15


title: X5_D15


title: X5_A15


title: X5_M15


title: X5_C15


title: X5_P14


title: X5_E15


title: X5_C14


title: X5_O15


title: X5_M14


title: X5_E14


title: X5_B14


title: X5_A16


title: X5_O14


title: X5_N14


title: X5_A14


title: X5_P13


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title: X5_E13


title: X5_D13


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title: X5_P12


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title: X5_A12


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title: X5_P11


title: X5_C12


title: X5_M11


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title: X5_A11


title: X5_O10


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title: X5_B11


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title: X5_B10


title: X5_C11


title: X5_E11


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title: X5_O13


title: X5_K9


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title: X5_D8


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title: X5_G8


title: X5_A10


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title: X5_A8


title: X5_P7


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title: X5_D7


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title: X5_F6


title: X5_B6


title: X5_I6


title: X5_D6


title: X5_C6


title: X5_A6


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title: X5_H6


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title: X5_C7


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title: X5_C5


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title: X5_F4


title: X5_G4


title: X5_J4


title: X5_D4


title: X5_M3


title: X5_C4


title: X5_P3


title: X5_B4


title: X5_L3


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title: X5_H3


title: X5_J3


title: X5_N4


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title: X5_D3


title: X5_A4


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title: X5_G2


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title: X5_H2


title: X5_C2


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title: X5_N1


title: X5_B2


title: X5_P1


title: X5_A2


title: X5_K1


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title: X5_J1


title: X5_I1


title: X5_F1


title: X5_G1


title: X5_D1


title: X5_L2


title: X5_E1


title: X5_C1


title: X5_A1


title: X6_O24


title: X6_M24


title: X6_L24


title: X6_K24


title: X6_B24


title: X6_A24


title: X6_E24


title: X6_D24


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title: X5_B21


title: X6_P22


title: X6_O22


title: X5_B1


title: X6_A23


title: X6_M22


title: X6_L22


title: X6_F22


title: X6_E22


title: X6_M23


title: X6_H24


title: X6_P21


title: X6_C22


title: X6_N21


title: X6_K21


title: X6_O21


title: X6_G21


title: X6_H21


title: X6_A22


title: X6_I21


title: X6_H23


title: X6_F21


title: X6_E21


title: X6_D21


title: X6_C21


title: X6_B21


title: X6_P20


title: X6_A21


title: X6_O20


title: X6_N20


title: X6_L20


title: X6_K20


title: X6_J20


title: X6_I20


title: X6_H20


title: X6_F20


title: X6_E20


title: X6_B22


title: X6_D20


title: X6_M21


title: X6_C20


title: X6_A20


title: X6_B20


title: X6_O19


title: X6_K19


title: X6_N19


title: X6_J19


title: X6_I19


title: X6_H19


title: X6_G19


title: X6_E19


title: X6_F19


title: X6_D19


title: X6_M18


title: X6_F18


title: X6_H18


title: X6_I18


title: X6_O18


title: X6_B19


title: X6_E18


title: X6_D18


title: 3734

city: Ann Arbor

first: Stephen

middle: J.

last: Gurczynski

state: MI

address: 109 Zina Pitcher Pl, Room 4062

department: Internal Medicine

institute: University Of Michigan

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fall within exon regions were counted.  After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as  GENEWIZ  115 Corporate Boulevard  South Plainfield, NJ 07080  p (877) GENEWIZ (436-3949)  f (908) 333-4511  www.genewiz.com  Page 2 of 2  differentially expressed genes for each comparison. A gene ontology analysis was performed on the statistically significant set of genes by implementing the software GeneSCF. The GO list was used to cluster the set of genes based on their biological process and determine their statistical significance. A PCA analysis was performed using the "plotPCA" function within the DESeq2 R package. The plot shows the samples in a 2D plane spanned by their first two principal components. The top 500 genes, selected by highest row variance, were used to generate the plot.
Genome_build: Mus musculus GRCm38 reference genome available on ENSEMBL
Supplementary_files_format_and_content: File diffexp.csv contains differential expression analysis data from DESEQ comparing the average expresion of M1 macrophages (samples 3729 and 3730) with that of M2 macrophages (samples 3733 and 3734).  File raw_counts.csv contains raw count expression data supplied from genewiz.

source_name: Lyz2Cre+ BMDM

growth_protocol: bone marrow stem cells were harvested from tibias and femurs of Lyz2Cre+ or C57Bl/6 mice and grown in DMEM suplemented with 10% FBS and 30% L-cell supernatant (6ml volume per plate). Additional medium was added at 2 days and added/replaced at 4 days to maintain 10ml plate volume. BMDMs were gently scraped and replated at 6 days. Next day (day 7), BMDMs were used for downstream experiments.

extract_protocol:
RNA was harvested using RNAeasy columns
RNA samples received were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
The sequencing libraries were clustered on lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

treatment_protocol: 7 days post isolation, BMDMs were treated with either M1-conditioned media (serum-free DMEM with LPS+IFNg) or M2-conditioned media (SFM DMEM with IL-4+IL-13) with or without Erlotinib (1uM) for 24 hours.

tag: polarization

value: Lyz2Cre+ BMDM


title: X6_A19


title: X6_C18


title: 3733


title: 3730


title: X6_A18


title: 3729


title: X6_B18


title: X6_O17


title: X6_L17


title: RNAP2pSer5 ChIP-Seq Method 2 rep 2

city: Davis

first: Commodore

middle: Perry

last: St. Germain

address: One Shields Avenue

department: Microbiology and Molecular Genetics

institute: University of California, Davis

data_processing:
Sequenced reads were trimmed using Trimmomatic v0.36, mapped to the mm10 whole genome using bowtie2 v2.2.8
Unpaired, unmapped, and PCR duplicates were removed with samtools v1.9, Converted to bedGraph and normalized to RPM using bedtools genomecov, and converted to bigwig using wigToBigWig
Genome_build: mm10
Supplementary_files_format_and_content: bigwigs for each sample

source_name: Spleen

growth_protocol: B cells were isolated from mice spleen, stimulated with IL4, LPS, and anti-CD180 in B cell media and grown at 37C, 5% CO2 for 72 hours

extract_protocol:
Lysates were clarified from sonicated cells and RNAP2-DNA or RNA-DNA complexes were isolated with antibody. The crosslinks were reversed for the RNAP2 enriched material, purified, and for the TRIPn-Seq samples - sequencing adapters were ligated before the BrdU immunoprecipitation.
Libraries were prepared according to NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: The TRIPn-Seq experimental cells were treated with 10 uM BrdU for 30 minutes before harvesting, crosslinked with formaldehyde, quenched with glycine, washed, and snap frozen in EtOH/dry ice and stored at -80C. The DRIP-Seq samples were not crosslinked.

tag: strain

value: spleen

value: 4-6 months

value: wild type

tag: antibody


title: X6_C19

tag: genotype


title: X6_I17


title: X6_H17


title: 4C-seq Individual 12

city: Cambridge

first: Anne

last: Ferguson-Smith

address: 20 Downing Place

department: Genetics

country: United Kingdom

institute: Cambridge University

data_processing:
Library strategy: 4C-seq
ChIP-seq: The resulting ChIP-seq data was trimmed by Trim Galore and aligned using bwa 0.7.15. Using only reads with MAPQ≥10, bedgraph files were generated by bamCompare 3.3.1 (deeptools), ChIP peaks and summits were called by MACS2 2.1.0 as described in (Thorvaldsdottir et al. 2013) and were visualized using IGV and custom R scripts (see Data Access).
4C-seq: The sequencing data for each viewpoint were processed using the smoothCounts method from the R Bioconductor package FourCSeq (Klein et al. 2015). Read counts for each restriction fragment were then normalized and log transformed. The trend line and its 95% confidence interval were generated by the loess.sd method from the R package msir using span=0.01 (Scrucca 2011). ChromHMM data is from mouse liver, and was downloaded from a public GitHub repository https://github.com/gireeshkbogu/chromatin_states_chromHMM_mm9/blob/master/liver_cStates_HMM.zip and lifted over to mm10 (Bogu et al. 2015). Gene tracks are from the R Bioconductor package EnsDb.Mmusculus.v79.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized 4C-seq fragment counts: contain coordinates of 4C-seq fragments and corresponding log normalized read counts
Supplementary_files_format_and_content: bedgraphs were generated using bamCompare 3.1.1.  All_indivs.CTCFChIP.mapq_ge_10.log2ratio.BEDGRAPH (Processed data is derived from a merged fastq file that contains all eight CTCF ChIP-seq fastq files).
Supplementary_files_format_and_content: narrowPeaks were generated using macs2 2.1.0

source_name: Liver

extract_protocol:
Immediately following dissection, C57BL/6J livers were snap frozen in liquid nitrogen and manually pulverised. ChIP-seq: Chromatin immunoprecipitation (ChIP) was performed as previously described with some modifications (Imbeault et al. 2017). 100mg of powdered frozen mouse liver was crosslinked in 1% formaldehyde for 10 minutes and subsequently quenched with Tris pH 8.0 (250mM final) for 10 minutes. The quenched cells were washed twice with ice-cold PBS supplemented with a protease inhibitor cocktail (EDTA-free cOmpleteTM, Sigma Aldrich), flash frozen in liquid nitrogen, and stored at -80°C. Crosslinked cells were thawed on ice and then lysed sequentially on ice and for 10 minutes at each step in each of the following buffers: LB1 (50 mM HEPES- KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton-X-100 and EDTA-free cOmpleteTM), LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and EDTA-free cOmpleteTM), and SDS shearing lysis buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.15% SDS and EDTA-free cOmpleteTM). The lysates were sonicated (Bioruptor) at 4°C to generate DNA fragments of 100 – 500 bp (3 repetitions of 5 sonication cycles of 30 seconds on and 30 seconds off) and the sonicated lysates were subsequently clarified by centrifugation (15,000 rpm for 15 min at 4 ̊C). The sonicated lysate was divided into 1.5-mL Eppendorf tubes based on the number of ChIPs performed and topped up to 1mL with Lysis Buffer 500NaCl (20 mM Tris-HCl, pH 7.5, 500 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton-X-100, 0.1% Sodium deoxycholate, 0.1% SDS and EDTA-free cOmpleteTM). This mixture was incubated overnight at 4°C with beads (Protein A Dynabeads, Invitrogen) that had been pre-blocked with 0.5% BSA and mixed with polyclonal CTCF antibody (C15410210-50 Diagenode). To remove non-specifically bound proteins, beads were washed five times with RIPA Buffer (50 mM HEPES-KOH, pH 7.4, 500 mM LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Sodium deoxycholate) and once with TE Buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA) at 4°C. The DNA-protein complex was eluted from the beads in Elution Buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA and 1% SDS) for 20 min at 65°C, and reverse-crosslinked overnight at 65°C. The eluted samples were then treated with RNase A (Wako) and Proteinase K (Roche), and purified using a PCR purification kit (NEB). 4C-seq: 4C-seq was performed as previously described with some modifications (Splinter et al. 2012). Tissues were fixed as outlined in the ChIP protocol above. DpnII (New England Biolabs) was used as the primary restriction enzyme and NlaIII (New England Biolabs) as the secondary restriction enzyme. Prior to library preparation, samples were purified by the Monarch PCR & DNA Cleanup Kit (New England Biolabs).
ChIP-seq: ChIP-seq libraries were prepared using KAPA Adapters, KAPA HyperPrep Kit (KAPA Biosystems), and AMPure XP Beads (Beckman Coulter) and quality checked using Qubit, Bioanalyzer, and Tapestation. The libraries were sequenced as 150bp paired-end reads on the Illumina HiSeq4000. 4C-seq: 16 individual PCR reactions were performed for each sample per viewpoint with reverse primers containing indexes. The 16 PCRs were combined and purified using 0.8x Agencourt AMPure XP beads (Beckman Coulter). Five libraries for each of the five tested viewpoints were multiplexed, quality checked using Qubit and Bioanalyzer, and sequenced as 150bp paired-end reads on the Illumina HiSeq4000.

treatment_protocol: Each experiment was performed on an individual mouse liver.

tag: developmental stage

value: adult

tag: 4c-seq primary and secondary enzymes

value: DpnII/NlaIII


title: 4C-seq Individual 11


title: 4C-seq Individual 10


title: CTCF input Individual 8

data_processing:
ChIP-seq: The resulting ChIP-seq data was trimmed by Trim Galore and aligned using bwa 0.7.15. Using only reads with MAPQ≥10, bedgraph files were generated by bamCompare 3.3.1 (deeptools), ChIP peaks and summits were called by MACS2 2.1.0 as described in (Thorvaldsdottir et al. 2013) and were visualized using IGV and custom R scripts (see Data Access).
4C-seq: The sequencing data for each viewpoint were processed using the smoothCounts method from the R Bioconductor package FourCSeq (Klein et al. 2015). Read counts for each restriction fragment were then normalized and log transformed. The trend line and its 95% confidence interval were generated by the loess.sd method from the R package msir using span=0.01 (Scrucca 2011). ChromHMM data is from mouse liver, and was downloaded from a public GitHub repository https://github.com/gireeshkbogu/chromatin_states_chromHMM_mm9/blob/master/liver_cStates_HMM.zip and lifted over to mm10 (Bogu et al. 2015). Gene tracks are from the R Bioconductor package EnsDb.Mmusculus.v79.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized 4C-seq fragment counts: contain coordinates of 4C-seq fragments and corresponding log normalized read counts
Supplementary_files_format_and_content: bedgraphs were generated using bamCompare 3.1.1.  All_indivs.CTCFChIP.mapq_ge_10.log2ratio.BEDGRAPH (Processed data is derived from a merged fastq file that contains all eight CTCF ChIP-seq fastq files).
Supplementary_files_format_and_content: narrowPeaks were generated using macs2 2.1.0

tag: chip antibody


title: X6_G17


title: 4C-seq Individual 9


title: X6_E17


title: X6_D17


title: CTCF input Individual 7


title: X6_F17


title: X6_A17


title: X6_B17


title: CTCF ChIP-seq Individual 8

value: CTCF (Diagenode C15410210-50, polyclonal)


title: CTCF input Individual 6


title: X6_L16


title: X6_K16


title: 4C-seq Individual 13


title: X6_J17


title: X6_J16


title: CTCF input Individual 5


title: X6_G16


title: CTCF ChIP-seq Individual 6


title: CTCF ChIP-seq Individual 5


title: X6_F16


title: CTCF ChIP-seq Individual 4


title: CTCF input Individual 4


title: CTCF input Individual 3


title: X6_C16


title: X6_B16


title: CTCF input Individual 2


title: X6_A16


title: CTCF ChIP-seq Individual 7


title: CTCF ChIP-seq Individual 2


title: CTCF input Individual 1


title: X6_P15


title: X6_N15


title: X6_K15


title: CTCF ChIP-seq Individual 1


title: ES-f2

city: Vienna

first: Martin

last: Leeb

address: Dr.-Bohr-Gasse 9/3

department: Max Perutz Labs

country: Austria

institute: University of Vienna

description: Micro whole genome bisulfite sequencing (uWGBS) of dipoloid female 129/B6 F1 hybrid ESCs grown in ESDMEM/2i

data_processing:
Adapter trimming with Trimmomatic v0.32 (Bolger et al., 2014).
Alignment with Bismark v0.12.2 (Krueger and Andrews, 2011) with parameters: --minins 0 --maxins 6000 --bowtie2
Removal of duplicate reads and reads with a bisulfite conversion rate <90% or with fewer than three cytosines outside a CpG context
Identification of differentially methylated regions (DMRs) with dmrseq (Korthauer et al., 2018)
Additional annotation with neighbouring genes, etc.
Genome_build: mm10
Supplementary_files_format_and_content: CSV (methylation levels per DMR and additional annotations)

growth_protocol:
diploid ESCs were grown in ESDMEM/2i for the indicated number of passages.
ESCs: diploid ESCs were grown in ESDMEM/2i for the indicated number of passages; androgenetic haploid ES cells were derived from androgenetic haploid embryos and cultured in ESDMEM/2i medium; parthenogenetic haploid ESCs were derived from parthenogenetic haploid blastocysts and cultured in ESDMEM/2i medium (Leeb et al., 2012; Leeb and Wutz, 2011). Embryos: to generate androgenetic haploid embryos, sperm from 129/Sv-J-eGFP+/- hemizygous males were injected using a piezo-actuated micromanipulator (Prime Tech Ltd., Japan) into B6D2F1 mII oocytes enucleated as described previously (Wakayama et al., 1998): mII oocytes were placed in M2 medium containing 5 µg/ml cytochalasin B and spindles were removed. At least 1 h post-enucleation, sperm heads were injected followed by culture in KSOM for 6 h (37°C, humidified 5% CO2 [v/v] in air) before recording the morphology of the resultant embryos. Embryos were separated according to whether they possessed a single second polar body (Pb2) and pronucleus (pn). Parthenogenetic embryos were derived by strontium chloride triggered oocyte activation in calcium free medium followed by in vitro culture to the blastocyst stage in KSOM.

extract_protocol:
The cells were sampled in lysis buffer as described in the workflow of the µWGBS protocol in Farlik et al. Cell Reports 2015. Lysed cells were bisulfite converted as described. Bisulfite converted and extracted DNA was purified and subjected to library preparation.
The library preparation protocol was conducted following the workflow detailed in Farlik et al. Cell Reports 2015. Briefly, converted DNA was transcribed using a random primer. The newly synthesized strand was further extended using the terminal tagging oligo step from the Illumina Epignome DNA methylation Kit solution and the resulting construct was amplified with no more than 16 PCR cycles. Resulting Library was purified and sequenced on an Illumina HiSeq 3000/400 platform in 75bp paired-end setup.

tag: passage

tag: tissue

value: embryonic stem cell


title: pES3

description: Micro whole genome bisulfite sequencing (uWGBS) of dipoloid female 129 dtTomato ESCs grown in ESDMEM/2i

growth_protocol:
parthenogenetic haploid ESCs were derived from parthenogenetic haploid blastocysts and and cultured in ESDMEM/2i medium
ESCs: diploid ESCs were grown in ESDMEM/2i for the indicated number of passages; androgenetic haploid ES cells were derived from androgenetic haploid embryos and cultured in ESDMEM/2i medium; parthenogenetic haploid ESCs were derived from parthenogenetic haploid blastocysts and cultured in ESDMEM/2i medium (Leeb et al., 2012; Leeb and Wutz, 2011). Embryos: to generate androgenetic haploid embryos, sperm from 129/Sv-J-eGFP+/- hemizygous males were injected using a piezo-actuated micromanipulator (Prime Tech Ltd., Japan) into B6D2F1 mII oocytes enucleated as described previously (Wakayama et al., 1998): mII oocytes were placed in M2 medium containing 5 µg/ml cytochalasin B and spindles were removed. At least 1 h post-enucleation, sperm heads were injected followed by culture in KSOM for 6 h (37°C, humidified 5% CO2 [v/v] in air) before recording the morphology of the resultant embryos. Embryos were separated according to whether they possessed a single second polar body (Pb2) and pronucleus (pn). Parthenogenetic embryos were derived by strontium chloride triggered oocyte activation in calcium free medium followed by in vitro culture to the blastocyst stage in KSOM.


title: X6_J15


title: ES-f1

description: Micro whole genome bisulfite sequencing (uWGBS) of dipoloid female Rex1::GFPd2 ESCs grown in ESDMEM/2i


title: X6_H15


title: pES2

description: Micro whole genome bisulfite sequencing (uWGBS) of haploid parthenogenetic P1 ESCs grown in ESDMEM/2i


title: X6_G15


title: X6_L15


title: X6_F15


title: ES-m2

description: Micro whole genome bisulfite sequencing (uWGBS) of dipoloid male 129 ESCs grown in ESDMEM/2i


title: ES-f3

description: Micro whole genome bisulfite sequencing (uWGBS) of diploid parthenogenetic Mekl_2_C_ER ESCs grown in ESDMEM/2i


title: X6_C15


title: CTCF ChIP-seq Individual 3


title: pES1

description: Micro whole genome bisulfite sequencing (uWGBS) of haploid parthenogenetic Rex1::GFP ESCs grown in ESDMEM/2i


title: X6_E16


title: X6_D15


title: Kidney

description: Micro whole genome bisulfite sequencing (uWGBS) of somatic kidney tissue (control)

growth_protocol:
gDNA was extracted from kidney of a nude mouse
ESCs: diploid ESCs were grown in ESDMEM/2i for the indicated number of passages; androgenetic haploid ES cells were derived from androgenetic haploid embryos and cultured in ESDMEM/2i medium; parthenogenetic haploid ESCs were derived from parthenogenetic haploid blastocysts and cultured in ESDMEM/2i medium (Leeb et al., 2012; Leeb and Wutz, 2011). Embryos: to generate androgenetic haploid embryos, sperm from 129/Sv-J-eGFP+/- hemizygous males were injected using a piezo-actuated micromanipulator (Prime Tech Ltd., Japan) into B6D2F1 mII oocytes enucleated as described previously (Wakayama et al., 1998): mII oocytes were placed in M2 medium containing 5 µg/ml cytochalasin B and spindles were removed. At least 1 h post-enucleation, sperm heads were injected followed by culture in KSOM for 6 h (37°C, humidified 5% CO2 [v/v] in air) before recording the morphology of the resultant embryos. Embryos were separated according to whether they possessed a single second polar body (Pb2) and pronucleus (pn). Parthenogenetic embryos were derived by strontium chloride triggered oocyte activation in calcium free medium followed by in vitro culture to the blastocyst stage in KSOM.

value: kidney


title: X6_B15


title: X6_A15


title: Partheno 1

description: Micro whole genome bisulfite sequencing (uWGBS) of haploid parthenogenetic E4.5 blastocyst

growth_protocol:
parthenogenetic haploid blastocysts were generated by oocyte activation and cultured in ESDMEM/2i medium
ESCs: diploid ESCs were grown in ESDMEM/2i for the indicated number of passages; androgenetic haploid ES cells were derived from androgenetic haploid embryos and cultured in ESDMEM/2i medium; parthenogenetic haploid ESCs were derived from parthenogenetic haploid blastocysts and cultured in ESDMEM/2i medium (Leeb et al., 2012; Leeb and Wutz, 2011). Embryos: to generate androgenetic haploid embryos, sperm from 129/Sv-J-eGFP+/- hemizygous males were injected using a piezo-actuated micromanipulator (Prime Tech Ltd., Japan) into B6D2F1 mII oocytes enucleated as described previously (Wakayama et al., 1998): mII oocytes were placed in M2 medium containing 5 µg/ml cytochalasin B and spindles were removed. At least 1 h post-enucleation, sperm heads were injected followed by culture in KSOM for 6 h (37°C, humidified 5% CO2 [v/v] in air) before recording the morphology of the resultant embryos. Embryos were separated according to whether they possessed a single second polar body (Pb2) and pronucleus (pn). Parthenogenetic embryos were derived by strontium chloride triggered oocyte activation in calcium free medium followed by in vitro culture to the blastocyst stage in KSOM.

value: blastocyst


title: Partheno 2


title: ICSI 2

description: Micro whole genome bisulfite sequencing (uWGBS) of diploid E4.5 blastocyst

growth_protocol:
ICSI embryos were generated using standard protocols
ESCs: diploid ESCs were grown in ESDMEM/2i for the indicated number of passages; androgenetic haploid ES cells were derived from androgenetic haploid embryos and cultured in ESDMEM/2i medium; parthenogenetic haploid ESCs were derived from parthenogenetic haploid blastocysts and cultured in ESDMEM/2i medium (Leeb et al., 2012; Leeb and Wutz, 2011). Embryos: to generate androgenetic haploid embryos, sperm from 129/Sv-J-eGFP+/- hemizygous males were injected using a piezo-actuated micromanipulator (Prime Tech Ltd., Japan) into B6D2F1 mII oocytes enucleated as described previously (Wakayama et al., 1998): mII oocytes were placed in M2 medium containing 5 µg/ml cytochalasin B and spindles were removed. At least 1 h post-enucleation, sperm heads were injected followed by culture in KSOM for 6 h (37°C, humidified 5% CO2 [v/v] in air) before recording the morphology of the resultant embryos. Embryos were separated according to whether they possessed a single second polar body (Pb2) and pronucleus (pn). Parthenogenetic embryos were derived by strontium chloride triggered oocyte activation in calcium free medium followed by in vitro culture to the blastocyst stage in KSOM.


title: X6_P14


title: X6_M14


title: X6_L14


title: ICSI 1


title: Andro 2

description: Micro whole genome bisulfite sequencing (uWGBS) of haploid androgenetic E4.5 blastocyst

growth_protocol:
To establish androgenic haploid embryos, sperm from 129/Sv-J-eGFP+/- hemizygous males were injected using a piezo-actuated micromanipulator (Prime Tech Ltd., Japan) into B6D2F1 mII oocytes enucleated as described previously (Wakayama et al., 1998): mII oocytes were placed in M2 medium containing 5 µg/ml cytochalasin B and spindles were removed. At least 1 h post-enucleation, sperm heads were injected followed by culture in KSOM for 6 h (37°C, humidified 5% CO2 [v/v] in air) before recording the morphology of the resultant embryos. Embryos were separated according to whether they possessed a single second polar body (Pb2) and pronucleus (pn) and culture was continued for 3-4 days to be utilised for ahES cell derivation.
ESCs: diploid ESCs were grown in ESDMEM/2i for the indicated number of passages; androgenetic haploid ES cells were derived from androgenetic haploid embryos and cultured in ESDMEM/2i medium; parthenogenetic haploid ESCs were derived from parthenogenetic haploid blastocysts and cultured in ESDMEM/2i medium (Leeb et al., 2012; Leeb and Wutz, 2011). Embryos: to generate androgenetic haploid embryos, sperm from 129/Sv-J-eGFP+/- hemizygous males were injected using a piezo-actuated micromanipulator (Prime Tech Ltd., Japan) into B6D2F1 mII oocytes enucleated as described previously (Wakayama et al., 1998): mII oocytes were placed in M2 medium containing 5 µg/ml cytochalasin B and spindles were removed. At least 1 h post-enucleation, sperm heads were injected followed by culture in KSOM for 6 h (37°C, humidified 5% CO2 [v/v] in air) before recording the morphology of the resultant embryos. Embryos were separated according to whether they possessed a single second polar body (Pb2) and pronucleus (pn). Parthenogenetic embryos were derived by strontium chloride triggered oocyte activation in calcium free medium followed by in vitro culture to the blastocyst stage in KSOM.


title: X6_K14


title: Andro 1


title: aES1

description: Micro whole genome bisulfite sequencing (uWGBS) of haploid androgenetic A6GFP ESCs grown in ESDMEM/2i

growth_protocol:
androgenetic haploid ES cells were derived from androgenetic haploid embryos and cultured in ESDMEM/2i medium
ESCs: diploid ESCs were grown in ESDMEM/2i for the indicated number of passages; androgenetic haploid ES cells were derived from androgenetic haploid embryos and cultured in ESDMEM/2i medium; parthenogenetic haploid ESCs were derived from parthenogenetic haploid blastocysts and cultured in ESDMEM/2i medium (Leeb et al., 2012; Leeb and Wutz, 2011). Embryos: to generate androgenetic haploid embryos, sperm from 129/Sv-J-eGFP+/- hemizygous males were injected using a piezo-actuated micromanipulator (Prime Tech Ltd., Japan) into B6D2F1 mII oocytes enucleated as described previously (Wakayama et al., 1998): mII oocytes were placed in M2 medium containing 5 µg/ml cytochalasin B and spindles were removed. At least 1 h post-enucleation, sperm heads were injected followed by culture in KSOM for 6 h (37°C, humidified 5% CO2 [v/v] in air) before recording the morphology of the resultant embryos. Embryos were separated according to whether they possessed a single second polar body (Pb2) and pronucleus (pn). Parthenogenetic embryos were derived by strontium chloride triggered oocyte activation in calcium free medium followed by in vitro culture to the blastocyst stage in KSOM.


title: X6_G14


title: X6_F14


title: X6_E14


title: pES4

description: Micro whole genome bisulfite sequencing (uWGBS) of haploid parthenogenetic H129-1 ESCs grown in ESDMEM/2i


title: X6_I15


title: WT_GFP_hi_KRAB_GFP_hi

source_name: gDNA from library infected iBMDM-NFKB-Cas9

tag: mouse strain

tag: cells

tag: modifications

value: NFKB-GFP reporter and Cas9


title: X6_D14

tag: cell type


title: X6_L13


title: ES-m1

description: Micro whole genome bisulfite sequencing (uWGBS) of dipoloid male E14TG2a ESCs grown in ESDMEM/2i


title: WT_GFP_lo_KRAB_GFP_lo


title: aES3

description: Micro whole genome bisulfite sequencing (uWGBS) of haploid androgenetic A11 ESCs grown in ESDMEM/2i


title: X6_A14


title: KRAB_LPS


title: X6_K13


title: WT_noLPS_KRAB_noLPS


title: X6_H13


title: thp1_ctrl_unstim_sc004

description: deseq.results.thp1unstim.thp1p3csk4_final

data_processing:
RNAseq 1: the 100x100bp pairedEnd reads were trimmed by 50bp at the 3prime end to 100x100bp
RNAseq 2: reads mapping (by bowtie2) to mouse repeatMasker elements were discarded
RNAseq 3: reads were mapped to mm10 by STAR (2.5.3a), aided by a gtf file based on Gencode VM9basic with 100bp overlap
RNAseq 4: duplicate read mappings of the same start and end position were discarded using samtools rmdup.
RNAseq 5: bam files were converted to mm10 genomic coverage using bedtools genomeCoverageBed
RNAseq 6: the dup-removed coverage was used to extract coverage of all exonic positions for each gene in UCSC KnownGenes for mm10.
RNAseq 7: the exonic coverage (from paired-end 100x100bp reads) for each gene was divided by 200 to get read counts per gene for input to DESeq2
RNAseq 8: DESeq2 was run using the read counts for UCSC KnownGenes.
RNAseq 9: DESeq2 pairwise comparisons were separately performed for lung tissue samples and spleen tissue samples.
RNAseq 10: Within each tissue, wild-type samples were compared to mutant and knockout samples. Mutant and knockout samples were compared to each other.
Genome_build: hg19
Supplementary_files_format_and_content: txt files with normalized counts for all  samples and DESeq2 text file with all pairwise comparisons

source_name: THP-1-GFP unstimulated

extract_protocol:
THP1s were Pam3CSK4-stimulated for 6h or unstimulated and placed in Trizol. RNA was extracted and 1ug was used to prepare libraries using illumna mRNA isolation kits
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Pam3CSK4 100ng/ml for 6h

value: monocyte

value: peripheral blood

tag: disease

value: acute monocytic leukemia


title: X6_G13


title: X6_F13


title: thp1_ctrl_p3csk4_sc003

source_name: THP-1-GFP P3C4


title: X6_E13


title: aES2

description: Micro whole genome bisulfite sequencing (uWGBS) of haploid androgenetic A7 ESCs grown in ESDMEM/2i


title: thp1_cox2_unstim_sc002

source_name: THP-1-GFP-lincRNA-Cox2 unstimulated


title: h9_ESC_rep1

city: Nashville

first: Emily

last: Hodges

state: TN

address: 2215 Garland Ave

department: Department of Biochemistry

institute: Vanderbilt University

description:
chromatin
NPCdiffATACme0hr_genrich.narrowPeak

data_processing:
Library strategy: ATAC-Me
Fastqs were trimmed using trimgalore.
Reads were mapped to a reference genome index using walt (MethPipe).
Methylation levels and other methylation analysis of CpGs were calculated using MethPipe.
Peaks were called on mapped reads using Genrich, ATAC mode.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: .narrowPeak file contains consensus peak regions using both replicates.
Supplementary_files_format_and_content: .meth.txt files contain the methylation levels of symmetric CpG sites.

source_name: embryonic stem cells

growth_protocol: hESCs were routinely cultured on Matrigel (Corning) coated plates in mTeSR (STEMCell Technologies) media. They were passaged in clumps when cultures reached ~80% confluency.

extract_protocol:
Cells were dissociated using Accutase and a single cell suspension was generated. Cells were pelleted and resuspended in lysis buffer to isolate chromatin.
Libraries were assembled using the protocol outlined in the manuscript.

tag: cell line

value: pluripotent stem cells


title: h9_ESC_rep2


title: X6_A13

source_name: KO_dentate gyrus; adult-born neural precursor cell_T4

value: KO

tag: animal id


title: thp1_cox2_p3csk4_sc001

source_name: THP-1-GFP-lincRNA-Cox2 P3C4


title: X6_J12

source_name: WT_dentate gyrus; adult-born neural precursor cell_T1

value: WT

tag: tissue/cell type


title: X6_I12

source_name: WT_dentate gyrus; adult-born neural precursor cell_T2


title: X6_K12

value: dentate gyrus; adult-born neural precursor cell


title: X6_H12


title: X6_C12


title: X6_F12

source_name: WT_dentate gyrus; adult-born neural precursor cell_T1b


title: X6_B13


title: X6_L12


title: X6_N11


title: X6_K11


title: X6_J11


title: DCB4

city: Seoul

first: Kyung Hwan

last: Kim

address: 50-1 Yonsei-ro

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
Reads were aligned to the human genome (hg19) using TopHat v2.1.1
The number of mapped reads for each gene was quantified using StringTie
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Tumor

extract_protocol:
RNeasy FFPE Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: cervical cancer

tag: sample type

value: durable clinical benefit


title: X6_H11


title: DCB1


title: NDB2

value: no durable benefit


title: NDB4


title: DCB2


title: X6_F11


title: NDB3


title: DCB3


title: X6_G12


title: DCB5


title: Allstars_Control_1

type: RNA

city: NEWCASTLE UPON TYNE

first: David

last: Young

address: Centre For Life

institute: Newcastle University

description: SAMPLE 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were processed and normalised using the lumi package

label: biotin

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: SW1353 chondrosarcoma cells were seeded in a standard six-well plate (30 x 10E6 cells/well) in standard growth medium (DMEM/F-12,  10% (v/v) foetal bovine serum (FBS), 100 IU/ml penicillin, 100 μg/ml streptomycin and 2 mM L-glutamine.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The next day following seeding, the medium was replaced with medium as described but without the 10% FBS (serum starved).  Approx 20 hours later cells were stimulated as indicated +/- interleukin-1aplha (0.5 ng/ml) for 6 hours. After this cells were washed in PBS and RNA extracted

tag: treatment

value: control

value: chondrosarcoma


title: Allstars_IL-1_2

description: SAMPLE 5


title: Sample13_Control

description: SAMPLE 3


title: Allstars_IL-1_1

description: SAMPLE 4


title: X6_D11

tag: genotype


title: Allstars_Control_2

description: SAMPLE 2


title: Sample14_IL1

description: SAMPLE 6


title: H6.iBMEC.Day 16

city: New York

first: Tyler

last: Lu

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

data_processing:
RNA libraries were prepared and multiplexed using Illumina TruSeq RNA Library Preparation Kit v2 (non-stranded and poly-A selection)
cDNA was used as the input for high-throughput sequencing via Illumina’s HiSeq 2500 platform
Samples were analyzed via the Digital Expression Explorer 2 pipeline Docker container.
Resulting gene counts were processed in R package edgeR and a Log2 counts per million matrix was calculated after filtering and quality control.
Principal component analysis was subsequently performed. Gene set over-representation analysis with WebGestalt was run using the greatest and least 75 gene loading scores from the first three principal components.
Genome_build: GRCh38
Supplementary_files_format_and_content: gene counts tsv file

source_name: hPSC-Derived

growth_protocol: Cells were grown in 10cm coated tissue culture dishes using media specific for each cell type.

extract_protocol:
Total RNA, greater than 100ng, from cultured cells was isolated in TRIzol L and purified using Qiagen RNeasy Mini Kit per manufacturer’s protocols.
RNA libraries were prepared and multiplexed using Illumina TruSeq RNA Library Preparation Kit v2 (non-stranded and poly-A selection).

value: hPSC-Derived cell


title: X6_O11


title: X6_C11


title: H1.iBMEC.Day 16


title: X6_A12


title: X6_B11


title: X6_I11


title: H6.iBMEC.Day 11


title: X6_P10


title: IMR90.iBMEC.Day 16


title: H1.iBMEC.Day 11


title: NDB1


title: H1.iEC

value: hPSC-Derived endothelial cell


title: X6_O10


title: X6_N10


title: IMR90.EEF-rEC


title: H6.iEC


title: IMR90.iEC


title: X6_I10


title: T1

city: Chengdu

first: Zhenyu

last: Bai

address: 211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: http://www.mbkbase.org/Pinku1/
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Chrysanthemum x morifolium

source_name: leaves

growth_protocol: Chrysanthemum “jinba” grown in the greenhouse (16 h photoperiod, 23±2℃ temperature)

extract_protocol:
Chrysanthemums' leaves were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
The Iso-Seq library was prepared according to the Isoform Sequencing protocol (Iso-Seq) using the Clontech SMARTer PCR cDNA Synthesis Kit and the BluePippin Size Selection System protocol as described by Pacific Biosciences

treatment_protocol: The buds raised from tissue-cultured seedlings were grown on MS medium (16 h photoperiod, 25 °C/22 °C day/night temperature) for thirty days. Then thirty-day old chrysanthemum seedlings were transferred to pots filled with a 1:1 mixture of peat and perlite, and acclimated for five days at normal condition. Then the seedlings were subjected to following treatments: (CK) normal condition as control, (T) 4 °C for 24 h, followed by − 4 °C for 4 h. Each treatment collected a mixture of three biologically replicated leaves, then samples rapidly frozen with liquid nitrogen and stored at − 80 °C. There were two samples in total used for RNA-Seq.

tag: strain

value: tissue

value: leaves

tag: age


title: X6_H10


title: T3

value: 4 °C for 24 h, followed by − 4 °C for 4 h


title: CK3


title: IMR90.iBMEC.Day 11


title: T2


title: CK2


title: X6_F10


title: X6_A11


title: BMEC

source_name: Brain

value: Primary human endothelial cell


title: HUVEC

source_name: Human Umbilical Vein


title: X6_E10


title: CK1


title: X6_J10


title: X6_B10


title: Protoplast 2

city: Duesseldorf

first: Margaret

middle: G

last: Bezrutczyk

state: NRW

address: Universitatstrasse 1

department: Molecular Physiology

institute: Heinrich Heine Universitat

data_processing:
BCL to FASTQ conversion was performed by Novogene (California, USA)
Reads were trimmed using TrimGalore (v 0.6.5) with the parameters --paired -j 8 -o
Reads were aligned using STAR (v 2.5.1b) to B73 RefGen 4 with the parameters  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000  --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
Counts were generated using Subread featureCounts (v 2.0.1) with the parameters -T 8 -M -p -a
Genome_build: B73 RefGen 4 (Jiao et al., 2017)
Supplementary_files_format_and_content: tab delineated file

molecule: polyA RNA

organism: Zea mays

source_name: maize (B73)  leaf 2

growth_protocol: Zea mays L. B73 seeds were germinated on filter paper with deionized, distilled water in darkness at 22-25 °C and transferred to soil upon coleoptile emergence. Plants were subsequently grown at 28-30 °C in a greenhouse supplemented by sodium lamps (400 µmol m-2 s-1) from 8:00-20:00.

extract_protocol:
RNA was extracted using the RNEasy Plant Kit (Qiagen)
cDNA libraries were generated using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, MA, USA) with modifications to select for 250-500 bp fragments

treatment_protocol: Whole leaf RNA vs pooled protoplasted leaf RNA: Protoplasts  were generated from the last 6 cm of the distal portion of V2 leaf 2. For each pool of protoplasts tested, leaf segments from six concurrently grown plants were used. For bulk leaf tissue, the same portion of leaves selected for protoplast released were homogenized in liquid nitrogen. Pooled protoplast samples did not require homogenization beyond vortexing in RNEasy kit-provided extraction buffer.

value: B73 inbred line

value: V2 seedling leaf 2, distal 6cm

value: protoplasts derived from leaf segment


title: IRF4-eGFP-Input-rep2

city: reykjavik

first: Ramile

last: Dilshat

address: Sturlugata 8

department: Biochemistry and Molecular biology

country: Iceland

institute: University of Iceland

data_processing:
RNA-seq reads were aligned using Kallisto with --bootstrap 100
Differential expressed genes were called using Sleuth
Reads from ChIP-seq were aligned using Bowtie2 and Peaks were called using MACS
Genome_build: GRCh38 for RNA-seq and hg19 for ChIP-seq
Supplementary_files_format_and_content: bed
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: count matrix

source_name: skin melanoma cell line

extract_protocol: ChIP-seq DNA libraries were prepared from the purified ChIP DNA and input DNA using the NEBNext ChIP-seq Library Prep Kit (E6200, NEB). Libraries were prepared from 8-15 ng of fragmented ChIP and input DNA and 10 PCR cycles used for amplification. The amplified libraries were purified using Agencourt AMPure XP beads (A63881, Beckman Coulter) and then paired-end sequenced.


title: IRF4eGFP-ChIP-rep2


title: IRF4-eGFP-Input-rep1


title: X6_A10


title: Leaf 2

value: whole leaf segment


title: X6_P9

value: WT


title: IRF4eGFP-ChIP-rep1


title: Maize single cell sequencing dataset 2

description: Maize2_CKDL200156990-1a-SI_GA_E12_HC7FMBBXX_S1_L004

data_processing:
BCL to FASTQ conversion was performed by Novogene (California, USA)
Cellranger count (10x Genomics) was used to process FASTQ files, with read 1 trimmed to 26 bp (r1-length=26)
A formatted reference genome was generated using Cellranger mkref using the maize B73 RefGen 4 whole genome sequence and annotation (fasta and gff3 downloaded from Ensembl B73 RefGen V4)
Reads were aligned using STAR algorithm wrapped in Cellranger (10x Genomics)
For the manuscript associated with this dataset, the Seurat R package (v3.1)(Butler et al., 2018) was used for dimensionality reduction analysis and dataset filtering. The processed files included here are not normalized, but we recommend creating a Seurat object from the filtered feature barcode matrix files and performing normalization and scaling with Seurat SCTransform (Hafemeister and Satija, 2019).
Genome_build: B73 RefGen 4 (Jiao et al., 2017)
Supplementary_files_format_and_content: Filtered feature barcoded matrix files: .tsv; .mtx

extract_protocol:
RNA was extracted using the 10x Genomics Chromium Single Cell 3ʹ v3 Chemistry, according to the manufacturer's instructions
Single cell 3' RNAseq: cDNA libraries were generated using the 10x Genomics Chromium Single Cell 3ʹ v3 Chemistry, according to the manufacturer's instructions

treatment_protocol: Protoplasts for scRNA-seq were generated from the last 6 cm of the distal portion of V2 leaf 2. For each pool of protoplasts tested, leaf segments from six concurrently grown plants were used. 6 µL of the protoplast suspension with an estimated 1,200 cells/µL was applied to the 10x Genomics Chromium microfluidic chip.


title: PHH_D7_HCV72h

city: Hannover

first: Birthe

middle: Maren

last: Tegtmeyer

address: Feodor-Lynen-Str. 7

institute: TWINCORE - Centre for Experimental and Clinical Infection Research

description:
BT20_12
72hpi NI vs. Jc1 Expression Browser
Canonical pathways PHH 72hpi
Upstream regulators_PHH 72hpi NI vs Jc1_List

data_processing:
Transcriptomic analyses were performed using CLC Genomics Workbench (Qiagen, Aarhaus)
Generated Fastq files were mapped against the hg38 human reference genome with annotated gene and mRNA tracks.
Gene expression was calculated for individual transcripts as reads per kilobase per million bases mapped (RPKM).
Genome_build: hg38
Supplementary_files_format_and_content: xlsx documents include total counts & RPKM values for each gene and each condition and additionally, fold change and statistical values

source_name: hepatocytes

extract_protocol:
Cells were either lysed in 350 μl RA1 buffer supplemented with β-mercaptoethanol (Macherey-Nagel) or in 1 ml Trizol reagent (Invitrogen) (PHH D1-3 samples) and lysates stored at -80°C until processing. We extracted the total RNA and DNA according to the manufacturer's instructions.
RNA sequencing library generated with ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, Illumina)

tag: hcv

value: infected

tag: phh donor

tag: time

value: 72 hours


title: PHH_D7_UV72h

description:
BT20_11
72hpi NI vs. UV Expression Browser

value: UV-inactivated HCV control


title: X6_N9

value: dentate gyrus; adult-born neural precursor cell


title: Leaf 1

tag: tissue


title: X6_L9


title: LM low HLA-DR cd14 high 77k

first: Young

middle: J

address: 1215 21st Avenue South, Suite 7209

department: Otolaryngology

institute: Vanderbilt University Medical Center

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.    Transcript annotation was subsequently updated.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.na32.hg19.transcript.csv

source_name: peripheral blood

label_protocol: The NuGEN Ovation Pico WTA Exon Module ver 2.0 system was used according to the manufacturer's protocol in the JHMI DeepSequencing & Microarray Core facility.

growth_protocol: Monocytic MDSC (characterized as CD11b hi, CD14 hi, HLA-Dr low, CD15 low) and Polymorphonuclear (PMN) MDSC (characterized as CD11b hi, CD14 low, HLA-Dr low, CD15 hi) populations were isolated from freshly obtained peripheral blood of HNSCC patients undergoing surgical treatments or diagnostic procedures (such as biopsies) at Johns Hopkins Hospital and Johns Hopkins Bayview Hospital.

extract_protocol: Equal amounts of Monocytic MDSCs and Polymorphonuclear MDSCs where isolated and then spun down to which 1ml of Trizole was added and pipetted up and down several times until pellet disappeared. Samples were frozen in -80 and delivered to Johns Hopkins Deep Sequencing and Microarray Core Facility.

treatment_protocol: From PB, leukocytes were separated from the rest of the sample using a Ficoll gradient prior to addition FC blocking prior to staining and sorting. MDSC and lymphocyte cells were isolated on a MoFlo MLS sorter (Beckman Coulter) or a FACSAria II cell sorter (Beckton Dickinson), at JHH Cell Cytometry Core Facility. Multicolor cell analysis was performed using the following antibodies: αCD14, αCD11b, αCD15, and anti HLA-DR. Cell surface staining was performed as indicated in the manufacturer’s data sheet. Flowjo software (TreeStar, INC, Ashland, OR) was used for analysis.

tag: individual

value: patient 3

value: squamous cell carcinoma of the head and neck

value: Monocytic MDSC

tag: marker used for cell sorting

value: CD11b hi

value: CD14 hi

value: HLA-Dr low

value: CD15 low


title: Maize single cell sequencing dataset 1

description: Maize1_CKDL200150284-1a-SI_GA_D9_H7TLJBBXX_S1_L001


title: PBMC p3 (grn) 50k

value: patient 4

tag: cell type

value: Granulocytic MDSC

value: CD14 low

value: CD15 hi


title: PHH_D7_mock72h

description:
BT20_10
72hpi NI vs. Jc1 Expression Browser
72hpi NI vs. UV Expression Browser
Canonical pathways PHH 72hpi
Upstream regulators_PHH 72hpi NI vs Jc1_List

value: mock control, conditioned medium


title: RP 14+15-73K

value: patient 2


title: X6_D10

data_processing:
Quality control with FASTQC
Data were demultiplexed using bcl2fastq2 v2.20 and aligned to the mouse reference transcriptome mm10 using kallisto v0.44.0 with default parameters.
Transcript levels were quantified as transcripts per million reads (TPM) and then summarized to the gene level.
Cells with fewer than 10 reads for at least  500 genes were removed from further analysis.
The pagoda2 package was used for variance normalisation (gam.k = 10), identification of cell clusters (PCA: nPcs = 100,  n.odgenes = 3e3; k-nearest neighbor: k = 50, perplexity = 30, min.group.size = 10) and t-distributed stochastic neighbor embedding (t-SNE). Log-transformed normalised gene expression values were then exported from pagoda2 for further analyses.
Genome_build: mm10
Supplementary_files_format_and_content: tsv: tab-delimited transcript abundances; csv: matrix of normalised and log-transformed expression values summarised by gene.

value: WT


title: RP 15+14-73K


title: AP 15+14-90K

value: patient 1


title: PBMC p4 (monocyte) 50k


title: Protoplast 1

value: B73 inbred line

value: V2 seedling leaf 2, distal 6cm

value: protoplasts derived from leaf segment


title: LM low HLA-DR cd14 low 77k

value: patient 3

value: squamous cell carcinoma of the head and neck


title: AP 14+15-90k

value: Monocytic MDSC

value: CD11b hi


title: X6_K9

value: dentate gyrus; adult-born neural precursor cell


title: F50 N2

city: Zhenjiang

first: Pingzhen

last: Xu

state: Jiangsu

address: sibaidu road 16

department: School of Biotechnology,

institute: Jiangsu University of Science and Technology

data_processing:
Quality analysis was conducted for the original data obtained using the Illumina HiSeqTM2500 system
Clean reads were screened by filtering out low-quality reads
A second quality analysis for alignment, analysis of the distribution and coverage of the clean reads on the reference sequence was conducted
The sequences were aligned to the silkworm genome database SilkDB.
FPKM of each gene were calculated based on the length of the gene and read count mapped to a given gene. The clean reads were mapped to the B. mori genome. Genes with a FPKM ≥1.0 were identified as expressions. A ratio (log2 fold change) between the infected and control groups of ≥1.5 was identified as the determinant of differentially expressed genes (DEGs).
Genome_build: SilkDB (http://silkworm.swu.edu.cn/silkdb/)
Supplementary_files_format_and_content: All files are named with sample name followed by content name using files format of excel. The gene and its log2 Ratio of TPM among all time points would be selected if it is a DEG in any comparison. The expression patterns were clustered using hierarchical cluster analysis. The Pearson's correlation of log2 Ratio among the genes is being used as the distance for clustering.

organism: Bombyx mori

source_name: F50 silkworm

growth_protocol: The silkworm strain F50 was provided by The Sericulture Research Institute, Chinese Academy of Agricultural Sciences (Zhenjiang, China). Then they were reared under standard conditions until spawning (25˚C and 70% humidity). Prothoracic glands (PGs) were carefully removed from the day-6 fifth instar larvae were of the infected and control groups after BmNPV infection 48 h. All samples were immediately stored in liquid nitrogen.

extract_protocol:
Total RNA was extracted from PGs using TRIzol reagent (Invitrogen, New York, NY, USA) in accordance with the manufacturer’s instructions. The mRNA was purified by Oligo(dT) magnetic beads (Invitrogen, USA), then used as templates for cDNA synthesis.
Poly (A)-tailed RNA prepared using magnetic oligo (dT) beads was broken into short fragments using a fragment buffer and was then reverse-transcribed to synthesize the first-strand cDNA with a random primer, and then DNA polymerase I was mixed with RNase H, dNTP, and the buffer solution to synthesize the complementary strand. The libraries were constructed using the Illumina methods and protocols, following the manufacturer’s instructions. The insert size and concentration of the cDNA library were both checked and quantified by an Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA) and Qubit® RNA Assay Kit (Life Technologies, CA, USA), respectively. RNA-seq was carried out with an Illumina HiSeq 2500 instrument (Illumina, San Diego, CA, USA). In order to ensure the quality of information analysis, the raw reads were cleaned by removing the adapter sequences, empty reads, unknown nucleotides (ratio ≥10%), and low-quality reads with a basic mass value of Q ≤ 20 which accounted for more than 50% of the whole read length.

tag: tag

value: day-6 fifth instar larvae

value: BmNPV infecting

value: prothoracic glands


title: X6_J9

growth_protocol: Mice were housed in standard polycarbonate cages (Type II, Tecniplast) and maintained on a 12 h light/dark cycle. Food and water were provided ad libitum.

extract_protocol:
Single cells from dissociated hippocampus tissue were sorted by fluorescence cell cytometry and collected into a 384-well plates pre-loaded with 2.3 µl lysis buffer (50 mM guanidine hydrochloride, 17.4 mM dNTPs, 2.2 µM SMART dT30VN primer).
Smart-Seq2 libraries were generated using Tecan Freedom EVO and Nanodrop II (Bionex) systems.


title: PHH_D7_HCV6h

description:
BT20_9
6hpi NI vs. Jc1 Expression Browser

value: infected

value: 6 hours


title: PHH_D7_UV6h

description:
BT20_8
6hpi NI vs. UV Expression Browser

value: UV-inactivated HCV control


title: F50 N1


title: X6_H9


title: X6_I9


title: F50 C2

value: Control


title: PHH_D7_mock6h

description:
BT20_7
6hpi NI vs. Jc1 Expression Browser
6hpi NI vs. UV Expression Browser

value: mock control, conditioned medium


title: PHH_D6_HCV72h

description:
BT20_6
72hpi NI vs. Jc1 Expression Browser
Canonical pathways PHH 72hpi
Upstream regulators_PHH 72hpi NI vs Jc1_List

value: 72 hours


title: F50 C1


title: cast_x_B6_1xE3_5_bla_7

data_processing:
Reads were aligned using STAR (version 2.5.2b)
Mapped reads of different lanes were merged and sorted using samtools (version 1.9-92)
The Allelome.Pro pipeline was used to retrieve strain specific counts from intermediate results
Mapped reads were converted to bedgraphs using the genomecov function from bedtools (version: v2.28.0-33-g0f45761)
Bedgraphs were converted to bigwig files using the bedGraphToBigWig function from UCSC
Genome_build: mm10
Supplementary_files_format_and_content: CSV (strain specific reads for each sample from forward and reverse cross)

source_name: E3.5 blastocyst reverse cross (cast x B6)

extract_protocol:
Single E3.5 blastocysts were derived from Mus musculus musculus C57BL/6 (B6) x Mus musculus castaneus (cast) reciprocal natural matings and directly lysed for RNA extraction without in vitro culture.
SMART-Seq2


title: PHH_D6_UV72h

description:
BT20_5
72hpi NI vs. UV Expression Browser


title: PHH_D6_mock72h

description:
BT20_4
72hpi NI vs. Jc1 Expression Browser
72hpi NI vs. UV Expression Browser
Canonical pathways PHH 72hpi
Upstream regulators_PHH 72hpi NI vs Jc1_List


title: sm_BL_Km_pET_rep1

city: Moscow

first: Anton

last: Kuzmenko

email: dr.ant.kuz@gmail.com, antonk@img.ras.ru

address: Akademika Kurchatova square 2

country: Russia

institute: Institute of Molecular Genetics, Russian Academy of Sciences

description:
E. coli B F– ompT gal dcm lon hsdSB(rB–mB–) λ(DE3 [lacI lacUV5-T7p07 ind1 sam7 nin5]) [malB+]K-12(λS) pET28b_KmAgo
small DNA

data_processing:
All libraries were quality checked before further processing using FastQC (v. 0.11.8).
The 3’-adaptor sequence (5’-TGGAATTCTCGGGTGCCAAGGC-3’) was trimmed and reads with length less than 14 nt were removed using cutadapt (v. 2.7). Example usage: cutadapt -j 4 -a 'TGGAATTCTCGGGTGCCAAGGC' -m 14 path_to_fastq
Reads were aligned onto the reference genome allowing zero mismatches via bowtie (v. 1.2.3). Example usage: bowtie -p 4 -v 0 -m 1 -S --un path_to_the_file_with_unalligned_reads --max path_to_the_file_with_multimappers path_to_the_reference_fasta path_to_the_file_trimmed_fastq > file_name.bam
Alligned .sam files were converted to binary .bam, sorted and indexed using samtools (v. 1.9).
Genome coverage in the 1 Kb windows (RPKM) for uniquely mapped reads (total or strand-specific) were calculated using bedtools (v. 2.28.0). Example usage: bedtools coverage -counts -a path_to_the_bed -b path_to_the_sorted_bam > file_name.bedGraph
Genome_build: Reference genome: NC_012971.2
Supplementary_files_format_and_content: bedGraph files including count data for the 1kb genomic windows

source_name: Bacterial Cell Lysates

growth_protocol: Cells were grown in LB media supplemented with 50 ug/ml of kanamycin at 25˚C until OD 600 = 0.4. At this point, the temperature was adjusted to 16˚C and after 20 min KmAgo expression was induced by the addition of 0.2mM IPTG. After overnight growth cells were collected for subsequent smDNA isolation and cloning.

extract_protocol:
All purification steps were carried out at 4˚C. The cell pellet was resuspended in lysis buffer (50 mM Tris-HCl, 250 mM NaCl, 5% glycerol, 0.5 mM β-mercaptoethanol, pH 7.4 at 23˚C) supplemented with EDTA-free protease inhibitor cocktail (Roche) at approximately 7 ml per gram of wet weight and subjected to 3 rounds of disruption on a high-pressure homogenizer (Avestin) at 12000 psi. The cell lysate was clarified for 30 min at 35,000 g. KmAgo was pulled down on Talon metal affinity resin (Takara) charged with Co 2+ for 2 hours at 4˚C (300 ul of bead suspension per sample) with constant rocking. The beads were collected by centrifugation (300 g, 3 min) and washed one time with lysis buffer and three times with lysis buffer supplemented with 10 mM imidazole (140 ml in total). KmAgo-smDNA complexes were eluted in 500 ul of lysis buffer supplemented with 300 mM imidazole. Nucleic acids associated with KmAgo were extracted with phenol:chloroform:isoamyl alcohol (PCI) mixture (25:24:1, pH 8.0) according to a standard procedure. Briefly, the protein sample was mixed with an equal volume of PCI, vortexed intensively for 30 seconds and centrifuged at 13000 g for 3 min. The upper aqueous phase was carefully collected and treated twice with an equal volume of chloroform to eliminate any remaining traces of phenol. Nucleic acids were precipitated with three volumes of ethanol in the presence of a co-precipitating agent (PINK, Bioline) and dissolved in 20 ul of milliQ-grade water.
Libraries for high throughput sequencing of smDNAs were prepared according to the previously described bridged (splinted) ligation protocol. For the purpose of visualization, a 5 ul aliquot of the smDNA sample (1/4 of total volume) was dephosphorylated and radiolabeled as described above. Unlabeled DNA was mixed with the radiolabeled aliquot and 2x urea sample buffer (8 M urea, 20 mM EDTA, 0.005% Bromophenol Blue, 0.005% Xylene Cyanol and resolved under denaturing conditions in a 15% polyacrylamide-urea gel. Gel bands corresponding to 14-25 nt smDNAs were crashed and DNA was eluted in 0.4 M NaCl solution overnight at 21˚C with constant agitation. After ethanol precipitation, DNA was resuspended in 20 ul of milliQ-grade water. Illumina-compatible adaptors were ligated to both ends of smDNA. For this purpose, 8 ul of 5 x Rapid Ligation buffer (ThermoFisher), 2 ul of 100 uM 5’-adaptor, 2 ul of 100 uM of 3’-linker, 2 ul of 100 uM oligonucleotide bridge 1, 2 ul of 100 uM oligonucleotide bridge 2 and 2 units of T4 PNK (ThermoFisher) were added to 20 ul of the purified smDNA solution. The reaction mixture was incubated overnight at room temperature. Ligated DNA fragments were recovered by 10% denaturing PAGE. The libraries were amplified and indexed according to the standard protocol (small RNA sequencing kit, NEB), except that PCR conditions were adjusted in order to prevent library over amplification. A series of test PCR were performed to optimize the amount of adaptor-ligated smDNA to achieve the desired amplification level in 3-4 cycles. smDNA libraries were sequenced using the HiSeq2500 platform (Illumina) in the rapid run mode (50 nt single-end reads).

value: E. coli B F- ompT gal dcm lon hsdSB(rB-mB-) lambda(DE3 [lacI lacUV5-T7p07 ind1 sam7 nin5]) [malB+]K-12(lambdaS) pET28b_KmAgo


title: sm_BL_kM_pET_rep2


title: X6_F9

value: WT


title: X6_D9


title: Bcl-xAS-transfected 786-O cells_replicate 4_Cy5 vs. Control empty vector-transfected 786-O cells_replicate 4_Cy3

first: Angela

middle: A.

last: Fachel

address: 1300 York Ave

description:
Bcl-xAS_rep4_Cy5/Ctl_rep4_Cy3
Bcl-xAS-transfected 786-O cells, biological replicate 4 of 4, Cy5 labelled vs. empty vector-transfected 786-O cells, biological replicate 4 of 4, Cy3 labelled.

hyb_protocol: 300 ng of cRNA was hybridized following the Agilent Two-color Low Input Quick Amp Labeling Protocol Version 6.5.

scan_protocol: Scanned on an Agilent G2565CA Microarray Scanner System.

data_processing: Linear and lowess-normalized data (Processed Signal Column by Feature Extractor Agilent Software v.10.7.1.1) was transformed to log2 ratios for test/reference samples.

source_name: Bcl-xAS-transfected 786-O cells

label_protocol: 200 ng of total RNA was labelled following the Agilent Two-color Low Input Quick Amp Labeling Protocol Version 6.5.

growth_protocol: 786-O cells were cultivated in 147.8 cm2 cell culture plates with Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% FBS. To perform four biological replicates, we cultivated four plates in parallel.

extract_protocol: Total RNA was extracted with Trizol reagent following the manufacturer's instructions. Total RNA was DNase-I-treated and purified using the Illustra RNAspin Mini kit (GE Healthcare) following the manufacturer's instructions.

treatment_protocol: Cells were transfected with 6 μg of Bcl-xAS expression construct or with 6 μg of empty vector (pCEP) as control using 3:1 FuGENE HD reagent (Promega). At 24 h after transfection, total RNA was extracted.

tag: cell line

tag: original tissue

value: clear cell renal cell cancer (CCRCC)

tag: transfection

value: Bcl-xAS

value: control


title: Bcl-xAS-transfected 786-O cells_replicate 2_Cy3 vs. Control empty vector-transfected 786-O cells_replicate 2_Cy5

description:
Bcl-xAS_rep2_Cy3/Ctl_rep2_Cy5
Bcl-xAS-transfected 786-O cells, biological replicate 2 of 4, Cy3 labelled vs. empty vector-transfected 786-O cells, biological replicate 2 of 4, Cy5 labelled.


title: Bcl-xAS-transfected 786-O cells_replicate 2_Cy5 vs. Control empty vector-transfected 786-O cells_replicate 2_Cy3

description:
Bcl-xAS_rep2_Cy5/Ctl_rep2_Cy3
Bcl-xAS-transfected 786-O cells, biological replicate 2 of 4, Cy5 labelled vs. empty vector-transfected 786-O cells, biological replicate 2 of 4, Cy3 labelled.


title: Bcl-xAS-transfected 786-O cells_replicate 3_Cy5 vs. Control empty vector-transfected 786-O cells_replicate 3_Cy3

description:
Bcl-xAS_rep3_Cy5/Ctl_rep3_Cy3
Bcl-xAS-transfected 786-O cells, biological replicate 3 of 4, Cy5 labelled vs. empty vector-transfected 786-O cells, biological replicate 3 of 4, Cy3 labelled.


title: cast_x_B6_1xE3_5_bla_5

value: E3.5 blastocyst reverse cross (cast x B6)