title: H9_P4CNCC_INPUT_matchedToTWIST1_ChIPseq_replicate2

description: Input


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E2_ad012

status: Public on Sep 28 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: ACB

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E3_ad006


title: ImM1 SNS-seq replicate 1 part1

city: birmingham

first: ildem

last: akerman

address: BR Tower, 3rd Floor, Room 333, Edgbaston,

department: IMSR

country: United Kingdom

institute: University of Birmingham

description:
Imm1_127.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
Immortal_1

data_processing:
Library strategy: SNS-seq
base calling : base calling was done using RTA for illumina, quality controls were performed using the spike in PhiX at the MGX facility, Montpellier, France
QC and alignment : FastQ files were trimmed and low quality score reads removed. The remaining reads were aligned to the human genome hg38 using bowtie2 (--end-to-end --sensitive -N 0)
peak calling : Peaks were called using a combination of two peak calling programs, MACS2 and SICER. Peaks were first called using MACS2 (default parameters plus --bw 500 -p 1e-5 -s 60 -m 10 30 --gsize 2.7e9), followed by peak calling by SICER (parameters: redundancy threshold = 1, window size (bp) = 200, fragment size = 150 effective genome fraction = 0.85,  gap size (bp) = 600, FDR = 1e-3). MACS2 peaks that intersect SICER peaks from each sample were merged using bedtools intersect
quantification : Quantification of the SNS-seq signal on DNA replication origins was done using the R-package DiffBind (dba.sCore: TMM_minus_background), using all human origin coordinates
Differential gene expression : DGE was performed by MGX, using Deseq2 with default parameters and gencode v25 genes as annotation file
pipelines : can be found at https://github.com/iakerman/SNS-seq upon publication of the manuscript
Genome_build: hg38
Supplementary_files_format_and_content: .xlx, .txt and .bed

organism: Homo sapiens

source_name: Human mammary gland

growth_protocol: Tissue culture cells were grown as indicated in the manuscript

extract_protocol:
RNA was extracted using TriPure, following manufacturer's instructions
Truseq mRNA stranded sample preparation kit (for RNA) and TruSeq ChIP Library Preparation Kit
Stranded mRNA for RNA samples, and ChIP-seq for SNS-seq samples

treatment_protocol: some samples were treated with erythropoietinin (EPO). Please see manuscript for details.

tag: agent

value: no treatment


title: H9_Day9chond_RNAseq_replicate2

city: Stanford

first: Hannah

middle: Katherine

last: Long

address: Lokey Stem Cell Research Building

department: Chemical and Systems Biology

institute: Stanford University

library_source: transcriptomic

data_processing:
ChIP sequencing reads were trimmed using skewer and aligned to the human genome (hg19) using bowtie2. For normalization, bedgraph files were generated from aligned bam files using bedtools genomecov with -scale option to normalize to 1 million reads. For visualization, bigwig files were generated using bedgraphToBigWig.
ATAC sequencing reads were trimmed to remove Nextera adapter sequences using cutadapt and aligned to the human genome (hg19) using bowtie2. For normalization, bedgraph files were generated from aligned bam files using bedtools genomecov with -scale option to normalize to 1 million reads. For visualization, bigwig files were generated using bedgraphToBigWig.
RNA sequencing reads were trimmed using cutadapt and aligned to human gene models (hg38) using HISAT2. Read counts per gene were quantified using featureCounts, gene expression was normalized to fragments per million and plotted in R.
Capture-C analysis was performed using bespoke analysis scripts outlined here: http://userweb.molbiol.ox.ac.uk/public/telenius/captureManual/oligofile.html. For comparison across samples, Capture-C profiles were plotted as the number of unique interactions per restriction fragment normalized to 10,000 interactions in cis.
10X Linked-Read sequencing data was analyzed using Long Ranger (longranger-2.2.2) and visualized using the 10X loupe genome browser.
Genome_build: hg19 and hg38

molecule: polyA RNA

source_name: cranial neural crest cells

growth_protocol: To differentiate cNCCs to chondrocytes, passage 3 cNCCs were passaged to passage 4, and the following day (Day 1) were transitioned to chondrocyte media without TGFb3 (ChM). ChM: DMEM-HG, 5% FBS, 1x ITS premix, 1mM sodium pyruvate, 50 μg/mL ascorbic acid, 0.1 μM dexamethasone and 1x antibiotic/antimycotic. The following day (Day 2), cells were fed with chondrocyte media with TGFb3 (ChMT). ChMT: ChM + 10 ng/mL TGFb3. Cells were fed every subsequent 3 days with ChMT. Cells were harvested at day 9.

extract_protocol:
Total RNA was extracted from a 6-well of hESC, early (P1 and 2) and late (P3 and P4) hCNCCs and day 9 chondrocytes differentiated from hCNCCs using Trizol reagent (Invitrogen) for four independent differentiations.
10μg RNA was purified twice by Dyna1 oligo(dT) beads (Invitrogen) to enrich for poly(A)+ mRNA. The mRNA was then fragmented using 10X fragmentation buffer (Ambion) for exactly 5 min and purified by ethanol precipitation with sodium acetate and RNase-free glycogen. First strand synthesis was performed using Random Hexamer Primers (Invitrogen) and SuperScript II (Invitrogen), followed by second strand synthesis using DNA PolI and RNaseH (Invitrogen), and cDNA was purified using Nucleospin Gel and PCR Cleanup (Takara). All of the cDNA was used for library preparation by end repair, A-tailing and adapter ligation (NEB). The samples were treated with USER enzyme, purified using XP SPRI beads then subjected to dual size selection using XP SPRI beads using bead ratios 0.55x to remove >700bp followed by 0.85x to recover >200bp sized cDNA. Size-selected cDNA was amplified using NEBNext HiFi 2X PCR mix and Dual Index Primers (NEB, E7600) for 7-10 cycles (as determined by qPCR). Libraries were then purified using XP SPRI beads, and quantified using Qubit dsDNA HS assay kit and pooled for sequencing using average library size (bp) from Bioanalyzer and concentration from KAPA quantification (Kapa Biosystems). Libraries were sequenced using NextSeq 500 (2x 75 bp).

tag: cell type

value: H9 embryonic stem cell-derived chondrocytes (Day 9; A7 clone)

tag: genotype

value: wildtype

tag: cell line of origin

value: H9 ESCs (WA09)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E2_ad007


title: H9_Day9chond_RNAseq_replicate4

value: H9 embryonic stem cell-derived chondrocytes (Day 9; H9 clone)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E2_ad006


title: H9_ESC_INPUT_ChIPseq_replicate2

description: Input

source_name: human embryonic stem cells

growth_protocol: H9 human embryonic stem cells (hESCs) were obtained from ATCC and cultured in mTeSR (Stem Cell Technologies) and grown on Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix (Corning). hESCs were fed every day and passaged every 5-6 days using ReLeSR (Stem Cell Technologies).

extract_protocol:
5-15 million cells were cross-linked per ChIP experiment in 2mL PBS per 6-well with 1% methanol-free formaldehyde for 5-10 min and quenched with a final concentration of 0.125M glycine for 5 min with nutation. Cross-linked cells were washed with PBS, scraped and pelleted by centrifugation, flash-frozen in liquid nitrogen and stored at -80°C. Samples were defrosted on ice and resuspended in 5mL LB1 (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, with 1X cOmplete Protease Inhibitor Cocktail and optionally 1mM PMSF) and rotated vertically for 10 min at 4°C. Samples were centrifuged for 5 min at 1350 x g at 4°C, and resuspended in 5mL LB2 (10 mM Tris, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, with 1X cOmplete Protease Inhibitor Cocktail and optionally 1mM PMSF) and rotated vertically for 10 min at 4°C. Samples were centrifuged for 5 min at 1350 x g at 4°C, and resuspended in 1mL LB3 per 10 million cells (maximum concentration of cells for Covaris sonication), or 1 mL per ChIP. Samples were sonicated in 1mL AFA tubes for 5 min on E220 evolution Covaris with settings Peak power = 140, Duty Factor = 10, Cycles per burst = 200 to achieve chromatin sized approximately 500-2000bp. Following sonication, samples were re-combined (if aliquoted for sonication), Triton X-100 was added to the fragmented chromatin to a final concentration of 1%, and the chromatin divided for input (1-2%) and ChIP samples. 5μg anti-histone antibody or 5-9μg anti-transcription factor antibody was added per ChIP sample, and incubated overnight at 4°C.  Protein G Dynabeads (ThermoFisher) were first blocked with Block solution (0.5% BSA (w/v) in 1X PBS) and then added to cleared chromatin to bind antibody-bound chromatin for a 4-6 hour incubation. Chromatin-bound Dynabeads were washed at least 6 times with chilled RIPA wash buffer (50 mM Hepes-KOH pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate), followed by a wash with chilled TE + 50 mM NaCl. Chromatin was eluted for 15-30 min in Elution Buffer (50 mM Tris, 10 mM EDTA, 1% SDS) at 65°C with frequent vortexing. The ChIP and input samples were then incubated at 65°C overnight to reverse cross-links (12-16 hours). Samples were diluted and sequentially digested with RNase A (0.2 mg/mL) for 2 hours at 37°C followed by Proteinase K (0.2 mg/mL) for 2 hours at 55°C for 2-4 hours to digest protein. ChIP and input samples were purified by phenol-chloroform-isoamylalcohol extraction and precipitation with final concentration 70% ethanol, 0.3M NaOAc pH 5.2 and 1.5μL glycogen.
For library preparation, samples were quantified by Qubit dsDNA HS assay kit, and 10-30ng of ChIP DNA was used for library preparation with end repair, A-tailing, and adaptor ligation (NEB). Following USER enzyme treatment, samples were purified using Nucleospin Gel and PCR Cleanup (Takara) and separated by gel electrophoresis and size-selected for 220-500 bp by gel extraction. Libraries were then amplified to add indices using NEBNext HiFi 2X PCR mix and NEBNext Multiplex Oligos for Illumina kit (NEB, E7335S) with 9-15 cycles (as determined by qPCR). ChIP libraries were purified by two rounds of XP SPRI bead clean-up to deplete adaptors. Library concentration and quality was assessed by Bioanalyzer (to determine size) and KAPA qPCR was used to pool multiple libraries. Samples were sequenced using NextSeq or HiSeq 4000 platform (2x 75bp).

value: H9 human embryonic stem cells

tag: chip antibody


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E2_ad004


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E2_ad008


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E2_ad010


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E12_ad012


title: H9_ESC_CTCF_ChIPseq_replicate2

value: CTCF (Cell Signaling, 2899S)


title: H9_ESC_RAD21_ChIPseq_replicate2

value: RAD21 (Abcam, ab992)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E12_ad010


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E12_ad007


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E12_ad006


title: H9_Day9chond_RNAseq_replicate3

value: H9 embryonic stem cell-derived chondrocytes (Day 9; F2 clone)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E12_ad008


title: H9_ESC_INPUT_ChIPseq_replicate1

description: Input


title: H9_P4CNCC_RNAseq_replicate1

growth_protocol: hESCs were differentiated to cranial neural crest cells (CNCCs) using a protocol described previously (Prescott, 2015). Briefly, hESCs were grown for 5-6 days until large colonies formed, then were disaggregated using collagenase IV and gentle pipetting (Day 0). Clumps of ~200 hESCs were washed in PBS and transferred to a 10cm petri dish in neural crest differentiation media (NDM). NDM: 1:1 ratio of DMEM-F12 and Neurobasal, 0.5x Gem21 NeuroPlex Supplement With Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF (PeproTech, 100-18B), 20ng/ml EGF (PeproTech, AF-100-15) and 5ug/ml bovine insulin (Gemini Bio-Products, 700-112P). After 7-8 days, neural crest emerged from neuroectodermal spheres attached to the petri dish, and after 11 days, neural crest cells were passaged onto fibronectin-coated 6-well plates using accutase and fed with neural crest maintenance media (NMM). NMM: 1:1 ratio of DMEM-F12 and neurobasal, 0.5x Gem21 NeuroPlex Supplement with Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF, 20ng/ml bFGF EGF and 1mg/ml BSA (Gemini). After 2-3 days, neural crest cells were split 1:3 and the following day cells were fed with neural crest long-term media. Long term media: neural crest maintenance media + 50pg/ml BMP2 (PeproTech, 120-02) + 3uM CHIR-99021 (Selleck Chemicals, S2924) (BCh media). cNCCs were then passaged twice to passage 4.

value: H9 embryonic stem cell-derived neural crest (passage 4)


title: H9_P4CNCC_RNAseq_replicate2

value: H9 embryonic stem cell-derived neural crest (passage 4; A7 clone)


title: H9_P3CNCC_RNAseq_replicate4

growth_protocol: hESCs were differentiated to cranial neural crest cells (CNCCs) using a protocol described previously (Prescott, 2015). Briefly, hESCs were grown for 5-6 days until large colonies formed, then were disaggregated using collagenase IV and gentle pipetting (Day 0). Clumps of ~200 hESCs were washed in PBS and transferred to a 10cm petri dish in neural crest differentiation media (NDM). NDM: 1:1 ratio of DMEM-F12 and Neurobasal, 0.5x Gem21 NeuroPlex Supplement With Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF (PeproTech, 100-18B), 20ng/ml EGF (PeproTech, AF-100-15) and 5ug/ml bovine insulin (Gemini Bio-Products, 700-112P). After 7-8 days, neural crest emerged from neuroectodermal spheres attached to the petri dish, and after 11 days, neural crest cells were passaged onto fibronectin-coated 6-well plates using accutase and fed with neural crest maintenance media (NMM). NMM: 1:1 ratio of DMEM-F12 and neurobasal, 0.5x Gem21 NeuroPlex Supplement with Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF, 20ng/ml bFGF EGF and 1mg/ml BSA (Gemini). After 2-3 days, neural crest cells were split 1:3 and the following day cells were fed with neural crest long-term media. Long term media: neural crest maintenance media + 50pg/ml BMP2 (PeproTech, 120-02) + 3uM CHIR-99021 (Selleck Chemicals, S2924) (BCh media). cNCCs were then passaged once to passage 3.

value: H9 embryonic stem cell-derived neural crest (passage 3; H9 clone)


title: H9_P4CNCC_INPUT_matchedToTWIST1_ChIPseq_replicate1

description: Input


title: H9_Day9chond_RNAseq_replicate1

value: H9 embryonic stem cell-derived chondrocytes (Day 9)


title: H9_P4CNCC_RNAseq_replicate4

value: H9 embryonic stem cell-derived neural crest (passage 4; H9 clone)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E11_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E11_ad012


title: H9_ESC_CTCF_ChIPseq_replicate1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E12_ad004


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E12_ad002


title: d124_xrTestis

city: Philadelphia

first: Youngsun

last: Hwang

state: PA

address: 3800 Spruce Street Old Vet Quad 220E

institute: University of Pennsylvania

data_processing:
Raw data were demultiplexed using mkfastq command in cell Ranger (v3.1.0) to generate Fastq files.
Fastq files were trimmed using cutadapt (v.2.6). Trimmed sequence files were mapped on the reference genome for humans (GRCh38-3.0.0).
Genome_build: human (GRCh38-3.0.0)
Supplementary_files_format_and_content: Cellranger ouputs containg barcodes, features, and count matrices.

source_name: hPGCLC-derived cells

extract_protocol:
hiPSCs and iMeLCs were harvested. The d5 floating aggregates containing hPGCLCs were incubated with 0.1% Trypsin-EDTA (Gibco) in PBS for 15 min at 37 °C with periodical pipetting. After quenching the reaction by addition of FBS and pipetting, cells were strained through a 70 µm nylon cell strainer (Thermo Fisher Scientific). The AG+ cells were sorted by FACSAria Fusion (BD Biosciences) and collected in an Eppendorf tube. xrTestes were treated with 0.1% Trypsin-EDTA in PBS for 15 min at 37 °C with periodical pipetting.  After quenching the reaction by addition of FBS and pipetting, cell suspension was washed with 0.1% BSA fraction V in PBS and strained through a 70 µm nylon cell strainer. AG+/-VT+/-PC+/- cells were sorted by FACSAria Fusion and collected in CELLOTION (Amsbio). Fetal gonads were cut into small pieces (~1mm2), then digested with collagenase type IV for 8 min at 37 ºC. Tissues were centrifuged at 200 g for 5 min and washed with Hank’s Balanced Salt Solution (Thermo Fisher Scientific). Tissues were then digested with 0.25% trypsin/EDTA and DNase I for 8 min at 37 ºC. After the digestion was quenched by adding 10% of fetal bovine serum, cells were strained through nylon cell strainer (70μm in pore size). The cells were then pelleted by centrifugation at 200 g for 5 min, which were resuspended in the MACS buffer (PBS containing 0.5% BSA and 2 mM EDTA). Dead cells were subsequently removed by Dead cell removal microbeads (Miltenyi Biotec). Flow-through cells were pelleted by centrifugation at 600 g for 15 min and resuspended in PBS containing 0.1% BSA
Cells were loaded into Chromium microfluidic chips with Chromium Single cell 3ʼ v3 chemistry and used to generate single cell gelbead emulsions (GEMs) using Chromium controller (10x Genomics) according to manufacturer’s protocol. All subsequent cDNA amplification and library construction steps were performed according to manufacturer protocol.

tag: gestational age

value: hPGCLC-derived cells

tag: number of cells


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E11_ad001

value: ACB


title: H9_P4CNCC_RNAseq_replicate3

value: H9 embryonic stem cell-derived neural crest (passage 4; F2 clone)


title: d81_xrTestis


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E11_ad004

value: male


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E11_ad002


title: H9_ESC_INPUT_ChIPseq_matchedp300_replicate1

description: Input


title: H9_P3CNCC_RNAseq_replicate2

value: H9 embryonic stem cell-derived neural crest (passage 3; A7 clone)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E10_ad012


title: hPGCLCs-1

source_name: human primordial germ cell-like cells

value: human primordial germ cell-like cells


title: H9_P3CNCC_RNAseq_replicate1

value: H9 embryonic stem cell-derived neural crest (passage 3)

value: wildtype

value: H9 ESCs (WA09)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E10_ad006


title: H9_P2CNCC_RNAseq_replicate4

growth_protocol: hESCs were differentiated to cranial neural crest cells (CNCCs) using a protocol described previously (Prescott, 2015). Briefly, hESCs were grown for 5-6 days until large colonies formed, then were disaggregated using collagenase IV and gentle pipetting (Day 0). Clumps of ~200 hESCs were washed in PBS and transferred to a 10cm petri dish in neural crest differentiation media (NDM). NDM: 1:1 ratio of DMEM-F12 and Neurobasal, 0.5x Gem21 NeuroPlex Supplement With Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF (PeproTech, 100-18B), 20ng/ml EGF (PeproTech, AF-100-15) and 5ug/ml bovine insulin (Gemini Bio-Products, 700-112P). After 7-8 days, neural crest emerged from neuroectodermal spheres attached to the petri dish, and after 11 days, neural crest cells were passaged onto fibronectin-coated 6-well plates using accutase (passage 1) and fed with neural crest maintenance media (NMM). NMM: 1:1 ratio of DMEM-F12 and neurobasal, 0.5x Gem21 NeuroPlex Supplement with Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF, 20ng/ml bFGF EGF and 1mg/ml BSA (Gemini). After 2-3 days, neural crest cells were split 1:3 and continued to be fed with neural crest maintenance media until collection (passage 2).

value: H9 embryonic stem cell-derived neural crest (passage 2; H9 clone)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E10_ad002


title: iMeLCs

source_name: incipient mesoderm-like cells

value: incipient mesoderm-like cells


title: H9_P3CNCC_RNAseq_replicate3

value: H9 embryonic stem cell-derived neural crest (passage 3; F2 clone)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E10_ad001


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E1_ad001


title: hiPSCs

source_name: human induced pluripotent stem cells

value: human induced pluripotent stem cells


title: H9_P2CNCC_RNAseq_replicate3

value: H9 embryonic stem cell-derived neural crest (passage 2; F2 clone)


title: H9_P2CNCC_RNAseq_replicate2

value: H9 embryonic stem cell-derived neural crest (passage 2; A7 clone)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E1_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E1_ad010


title: H9_P4CNCC_CaptureC_KCNJ2_COG1_SDK2_promoters

data_processing:
Library strategy: Capture-C
ChIP sequencing reads were trimmed using skewer and aligned to the human genome (hg19) using bowtie2. For normalization, bedgraph files were generated from aligned bam files using bedtools genomecov with -scale option to normalize to 1 million reads. For visualization, bigwig files were generated using bedgraphToBigWig.
ATAC sequencing reads were trimmed to remove Nextera adapter sequences using cutadapt and aligned to the human genome (hg19) using bowtie2. For normalization, bedgraph files were generated from aligned bam files using bedtools genomecov with -scale option to normalize to 1 million reads. For visualization, bigwig files were generated using bedgraphToBigWig.
RNA sequencing reads were trimmed using cutadapt and aligned to human gene models (hg38) using HISAT2. Read counts per gene were quantified using featureCounts, gene expression was normalized to fragments per million and plotted in R.
Capture-C analysis was performed using bespoke analysis scripts outlined here: http://userweb.molbiol.ox.ac.uk/public/telenius/captureManual/oligofile.html. For comparison across samples, Capture-C profiles were plotted as the number of unique interactions per restriction fragment normalized to 10,000 interactions in cis.
10X Linked-Read sequencing data was analyzed using Long Ranger (longranger-2.2.2) and visualized using the 10X loupe genome browser.
Genome_build: hg19 and hg38

extract_protocol:
Capture-C was performed as previously described (Davies et al., 2015). Briefly, cells were crosslinked for 10 min in 2% formaldehyde in PBS, quenched with 125mM glycine for 5 min, scraped, collected and pelleted by centrifugation (500 rcf, 5 min, 4°C). Cells were washed with 5mL cold PBS, pelleted and resuspended in 5mL cold lysis buffer (10mM Tris pH8, 10mM NaCl, 0.2% Ipegal CA-630 in water with cOmplete Protease Inhibitor Cocktail) for 20 min. Cells were pelleted, washed with 5mL cold PBS, pelleted, resuspended in 1mL cold PBS, flash frozen in liquid nitrogen and stored at -80°C.
For 3C library preparation, samples were defrosted on ice, pelleted and resuspended in 1xDpnII digestion buffer before extended digestion with DpnII overnight with addition of extra enzyme. DpnII was then heat inactivated at 65°C and samples were ligated with T4 Ligase for ~22 hours. DNA was extracted by sequential Proteinase K and RNase digestion followed by phenol-chloroform isoamylalcohol extraction and precipitation with ethanol and sodium acetate. Efficiency of digestion and ligation was assessed by gel electrophoresis and digestion efficiency was further assessed by qPCR. For addition of Illumina sequencing adaptors, samples were sheared by Covaris sonication and purified by XP SPRI bead clean-up. Sequencing adaptors were annealed using NEB Ultra II kit. Libraries were PCR amplified using Herculase II polymerase (Agilent) in duplicate to add indexing primers and purified by XP SPRI bead clean-up. Samples were pooled and quantified using Qubit dsDNA BR assay kit.    Biotinylated oligos for capture were designed using the Capsequm online tool (http://apps.molbiol.ox.ac.uk/CaptureC/cgi-bin/CapSequm.cgi) and ordered from IDT. 1-2μg indexed 3C library was mixed with 5μg COT DNA, 1nmol TS-HE Universal Oligo and 1nmol of TS-HE Index Oligo (Nimblegen SeqCap EZ HE-oligo and Accessory kit) and dried by vacuum centrifugation at 55°C until completely dry. The 3C library plus blocking oligos were then carefully resuspended in 7.5μL 2X hybridization buffer and 3μL Hybridization buffer A and denatured at 95°C for 10min. The 3C library was then transferred into a preheated PCR tube at 47°C containing 4.5μL of pooled Biotinylated oligonucleotide capture probes at 2.9μM. After a brief mix and centrifugation, the 3C library oligo mix was incubated at 47°C for 18-20 hrs. Following this incubation, the 3C library was washed and recovered by streptavidin bead (M-270 Dynabeads, Invitrogen) pull down using the Nimblegen SeqCap EZ Hybridization and wash kit. Following the recovery of the captured material, the captured DNA was amplified on the streptavidin beads using KAPA HiFi HotStart ReadyMix and POST-LM PCR oligo 1&2 and purified by XP SPRI bead clean-up. For improved capture efficiency, a second round of capture was performed on the total amplified DNA from the first capture. Following the second round of capture, the library was quantified using KAPA library quantification kit using the average size calculated from Bioanalyzer. Libraries were then sequenced on Illumina HiSeq-4000 (2x 150bp).

value: H9 embryonic stem cell-derived neural crest (passage 4)

value: COG1 promoter, KCNJ2 promoter, SDK2 promoter


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E1_ad004


title: H9_P1CNCC_RNAseq_replicate3

growth_protocol: hESCs were differentiated to cranial neural crest cells (CNCCs) using a protocol described previously (Prescott, 2015). Briefly, hESCs were grown for 5-6 days until large colonies formed, then were disaggregated using collagenase IV and gentle pipetting (Day 0). Clumps of ~200 hESCs were washed in PBS and transferred to a 10cm petri dish in neural crest differentiation media (NDM). NDM: 1:1 ratio of DMEM-F12 and Neurobasal, 0.5x Gem21 NeuroPlex Supplement With Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF (PeproTech, 100-18B), 20ng/ml EGF (PeproTech, AF-100-15) and 5ug/ml bovine insulin (Gemini Bio-Products, 700-112P). After 7-8 days, neural crest emerged from neuroectodermal spheres attached to the petri dish, and after 11 days, neural crest cells were passaged onto fibronectin-coated 6-well plates using accutase (passage 1) and fed with neural crest maintenance media (NMM). NMM: 1:1 ratio of DMEM-F12 and neurobasal, 0.5x Gem21 NeuroPlex Supplement with Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF, 20ng/ml bFGF EGF and 1mg/ml BSA (Gemini). Neural crest cells continued to be fed with neural crest maintenance media until collection (passage 1).

value: H9 embryonic stem cell-derived neural crest (passage 1; F2 clone)


title: H9_P4CNCC_CaptureC_EC1.45enhancer

value: EC1.45 enhancer


title: H9_P1CNCC_RNAseq_replicate4

value: H9 embryonic stem cell-derived neural crest (passage 1; H9 clone)


title: H9_P2CNCC_RNAseq_replicate1

value: H9 embryonic stem cell-derived neural crest (passage 2)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D9_ad006

value: ACB

value: male


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D9_ad004


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E10_ad007


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D9_ad008


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D9_ad007


title: H9_P1CNCC_RNAseq_replicate2

value: H9 embryonic stem cell-derived neural crest (passage 1; A7 clone)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D8_ad001


title: H9_ESC_CaptureC_EC1.45enhancer

value: H9 human embryonic stem cells

value: wildtype


title: H9_P1CNCC_RNAseq_replicate1

value: H9 embryonic stem cell-derived neural crest (passage 1)

value: H9 ESCs (WA09)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D8_ad006


title: H9_P4CNCC_CaptureC_EC1.35enhancer

value: EC1.35 enhancer


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D8_ad004


title: H9_ESC_CaptureC_EC1.35enhancer


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E1_ad002


title: H9_P4CNCC_CaptureC_EC1.25enhancer

value: EC1.25 enhancer


title: H9_ESC_RNAseq_replicate3

value: H9 human embryonic stem cells (F2 clone)


title: H9_ESC_CaptureC_KCNJ2_COG1_SDK2_promoters


title: H9_ESC_RNAseq_replicate4

value: H9 human embryonic stem cells (H9 clone)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D8_ad008


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D7_ad012


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E1_ad008


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D8_ad002


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D7_ad010


title: H9_ESC_CaptureC_EC1.25enhancer


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D7_ad006


title: H9_ESC_RNAseq_replicate1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A10_ad012


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D7_ad004


title: H9_ESC_RNAseq_replicate2

value: H9 human embryonic stem cells (A7 clone)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D7_ad007


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D8_ad010


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D5_ad010


title: H9_Day9chond_ATACseq_replicate3

source_name: chondrocytes

extract_protocol:
ATAC-seq was performed as described previously (Buenrostro et al., 2013; Corces et al., 2017) Briefly, cells were dissociated and treated with DNaseI (Worthington) and 50,000 viable cells were sorted as DAPI negative. Cells were pelleted at 500 RCF for 5 min at 4°C and resuspended in ATAC-resuspension buffer containing 0.1% NP40, 0.1% Tween20, and 0.01% Digitonin and incubated on ice for 3 minutes. Following wash-out with cold ATAC-Resuspension Buffer (RSB, 10 mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2 in sterile water) containing 0.1% Tween20, cells were pelleted and resuspended in 50μL transposition mix (25 μL 2x TD buffer, 2.5 μL transposase (100nM final), 16.5 μL PBS, 0.5 μL 1% digitonin, 0.5 μL 10% Tween20, 5 μL H2O) and incubated for 30 minutes at 37°C with shaking.
The transposition reaction was purified using the Zymo DNA Clean and Concentrator Kit, and amplified using PCR primers defined in (Buenrostro et al., 2013). Libraries were purified using the Zymo DNA Clean and Concentrator Kit, quantified using the KAPA Library Quantification kit and quality assessed by Bioanalyzer (also used to determine average size for pooling libraries). Samples were sequenced on the HiSeq4000 platform (2x 75bp).

value: H9 embryonic stem cell-derived chondrocytes (Day 9)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D5_ad007


title: WT33_P4CNCC_CTCF_ChIPseq_replicate2

value: WT33 induced pluripotent stem cell-derived neural crest (passage 4)

value: WT33 iPSCs

value: CTCF (Cell Signaling, 2899S)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D5_ad006


title: H9_P4CNCC_CTCF_ChIPseq_replicate1

value: H9 embryonic stem cell-derived neural crest (passage 4)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D5_ad004

value: ACB


title: H9_Day9chond_ATACseq_replicate1


title: H9_Day5chond_ATACseq_replicate3

growth_protocol: To differentiate cNCCs to chondrocytes, passage 3 cNCCs were passaged to passage 4, and the following day (Day 1) were transitioned to chondrocyte media without TGFb3 (ChM). ChM: DMEM-HG, 5% FBS, 1x ITS premix, 1mM sodium pyruvate, 50 μg/mL ascorbic acid, 0.1 μM dexamethasone and 1x antibiotic/antimycotic. The following day (Day 2), cells were fed with chondrocyte media with TGFb3 (ChMT). ChMT: ChM + 10 ng/mL TGFb3. Cells were fed every subsequent 3 days with ChMT. Cells were harvested at day 5.

value: H9 embryonic stem cell-derived chondrocytes (Day 5)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D4_ad007

value: male


title: H9_Day9chond_ATACseq_replicate4


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D5_ad008


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D4_ad012


title: H9_P4CNCC_RAD21_ChIPseq_replicate1

value: RAD21 (Abcam, ab992)


title: H9_Day5chond_ATACseq_replicate2

value: wildtype


title: WT33_P4CNCC_RAD21_ChIPseq_replicate2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D3_ad012


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D4_ad004


title: H9_P4CNCC_ATACseq_replicate4


title: H9_Day9chond_ATACseq_replicate2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D4_ad002


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D3_ad007


title: H9_P4CNCC_ATACseq_replicate3


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D3_ad001


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D3_ad010


title: H9_P4CNCC_ATACseq_replicate2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D3_ad002


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D12_ad012


title: H9_P4CNCC_ATACseq_replicate1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D12_ad010


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D3_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D12_ad008


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D12_ad007


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D4_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D12_ad006


title: H9_P2CNCC_ATACseq_replicate4

value: H9 embryonic stem cell-derived neural crest (passage 2)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D12_ad004


title: H9_Day5chond_ATACseq_replicate1

value: H9 ESCs (WA09)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D11_ad007


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D11_ad010


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D11_ad002


title: H9_P2CNCC_ATACseq_replicate1


title: H9_P2CNCC_ATACseq_replicate2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D11_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D11_ad001


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D1_ad007


title: H9_ESC_ATACseq_replicate4

value: H9 human embryonic stem cells


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D1_ad004


title: Ex3_1m

city: London

first: Helen

middle: M.

last: Rowe

state: --- Select a state ---

address: 4 Newark St, Whitechapel

department: Blizard Institute, Barts and The London School of Medicine and Dentistry

institute: Queen Mary University of London

data_processing:
Illumina’ s bcl2fastq Conversion Software v2.19 was used to demultiplex data and generate fastq files
TrimGalore v0.4.12 was used to remove sequencing adapters
TopHat2.1.0 was used to align reads to the human genome UCSC build hg38 with default parameters. Gencode v30 gene annotation were also provided as a reference transcriptome.
HTSeq-count v 0.11.0 was used to obtain read counts per gene with --mode intersection-nonempty and -s reverse parameters
Gene counts were imported into R and used for the differential expression analysis with DESeq2_1.22.1
Genome_build: hg38
Supplementary_files_format_and_content: gene_dea_Supp_table.xlsx contains the result of the differential gene expression analysis from DESeq2. repeat_loci_dea_Supp_table.xlsx contains the result of the differential repeat loci expression analysis.

molecule: total RNA

source_name: HeLa_MPP8 shRNA

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco, Thermo Fisher Scientific) supplemented with 100U/ml penicillin/streptomycin (Gibco, Thermo Fisher Scientific) and 10% heat-inactivated fetal calf serum (FCS), and grown at 10% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using an RNeasy mini kit (Qiagen) and treated with DNase (Ambion AM1907). The RNA was quality checked on a 4200 Tapestation using the RNA ScreenTape assay (Agilent Technologies, Wokingham, UK) and the RNA concentration measured using a Qubit RNA Broad Range kit (Life Technologies, Paisley, UK).
Total RNA samples were then processed using KAPA’s stranded RNA HyperPrep RiboErase kit using an input of 500ng per sample. Samples were sequenced on a NextSeq 500 instrument (Illumina Cambridge, Chesterford, UK) after pooling libraries in equimolar quantities, using a 2x 151bp paired-end run resulting in over 15 million reads per sample.

treatment_protocol: VSV-G-pseudotyped lentiviral vectors were produced by co-transfecting 293T cells in 10cm plates with 1.5µg of the shRNA plasmid, 1µg p8.91 and 1µg pMDG2 encoding VSV-G. Media was changed one day post transfection and supernatant harvested 48h post-transfection and concentrated via ultracentrifugation (20,000rpm for 2h at 4°C) and used directly without puromycin selection.

tag: cell line

value: HeLa

tag: treatment

value: pHR-SIREN shRNA lentiviral vector against MPP8 (Tchasovnikarova et al., Science 2015)

tag: time-point

value: Day 3 post-tranduction (no selection)

tag: full name

value: Experiment 3:MPP8 shRNA


title: Ex3_1s

source_name: HeLa_MPP8 Control shRNA

value: pHR-SIREN lentiviral vector without hairpin (control) (Tchasovnikarova et al., Science 2015)

value: Experiment 3:Control shRNA


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D1_ad010


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D1_ad008


title: H9_ESC_ATACseq_replicate2


title: Ex2_1m

value: Experiment 2:MPP8 shRNA


title: Ex2_1s

value: Experiment 2:Control shRNA


title: H9_ESC_ATACseq_replicate1


title: Ex1_1s

value: Experiment 1:Control shRNA


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C9_ad012

value: ACB


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C8_ad010


title: H9_P4CNCC_TWIST1_ChIPseq_replicate2

value: H9 embryonic stem cell-derived neural crest (passage 4)

value: TWIST1 (Abcam, ab50887)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C9_ad006

value: male


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C8_ad002


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C8_ad006


title: Ex1_1m

value: Experiment 1:MPP8 shRNA


title: H9_P4CNCC_TWIST1_ChIPseq_replicate1

value: wildtype


title: CEMBA181218_5F_1_CEMBA181218_5F_2_D1_ad001


title: H9_P2CNCC_ATACseq_replicate3

value: H9 embryonic stem cell-derived neural crest (passage 2)

value: H9 ESCs (WA09)


title: H9_ESC_ATACseq_replicate3

value: H9 human embryonic stem cells


title: H9_ESC_p300_ChIPseq_replicate1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C7_ad012


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C7_ad007


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C9_ad008


title: EPZ_Input

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Avenue NE

institute: Van Andel Research Institute

data_processing:
Base-calls were made with RTA 2.0, and converted to fastq files with cl2fastq2 v2.20.
ChIP-seq reads were aligned to the human hg38 genome build using the following command in bowtie2 version 2.3.4.3: bowtie2 -I 0 -X 700 --end-to-end --sensitive -x /path_to_hg38_index -1 /path_to_first_paired_read.fastq.gz -2 /path_to_second_paired_read.fastq.gz -S sample.sam
Data were filtered using the following specifications applied to SAM files: SAM files were further processed with the following command to isolate paired reads with high mapping quality, correct pair orientation, and to calculate fragment length: awk -v MAQ=20 ‘$5>=MAQ && $2==99 || $5>=MAQ && $2==163 {print $3”\t”$4”\t”$4+$9-1} sample.sam | awk ‘$2<=$3{print $1”\t”$2”\t”$3”\t”$3-$2} | sort -k1,1 -k2,2n > outfile.bed
To call peaks, we used the following command from macs2 (v2.1.2): macs2 callpeak -t {IP_sample}.bam -c {Input_sample}.bam -f BAMPE -n {SAMPLE} –outdir /path_to_output_dir/ --broad -B
Processed samples were applied to our siQ-ChIP algorithm (method described in this manuscript) to calculate binding efficiencies at different genomic regions (*.ce files).
Genome_build: hg38
Supplementary_files_format_and_content: bed files were generated from SAM files with the following command: awk -v MAQ=20 ‘$5>=MAQ && $2==99 || $5>=MAQ && $2==163 {print $3”\t”$4”\t”$4+$9-1} sample.sam | awk ‘$2<=$3{print $1”\t”$2”\t”$3”\t”$3-$2} | sort -k1,1 -k2,2n > outfile.bed. Columns in the bed file are as follows: (1) chr of the read (2) start position of the read (3) stop position of the read (4) read length; bedGraph files represent the cumulative efficiency of antibody binding at each genome location, and the columns are as follows: (1) chr (2) start (3) stop (4) cumulative efficiency of antibody binding to location

source_name: HCT-116 colorectal carcinoma cell line

growth_protocol: HCT116 colorectal carcinoma cells were grown in McCoys 5A media supplemented with 10% FBS and penicillin/streptomycin (100 units/ml) at 37°C with 5% CO2.

extract_protocol:
To purify nuclei, thawed cells were washed 3x with PBS, 2x with Buffer N (15 mM Trizma Base pH 7.5, 15 mM NaCl, 60 mM KCl, 5 mM MgCl2, 1 mM CaCl2, 8.5% sucrose, 1 mM DTT, 200 uM PMSF, 50 ug/mL BSA, and protease inhibitor), and lysed with 2x Lysis Buffer (0.6% NP-40 in Buffer N). Nuclei were layered over a 30% sucrose cushion, pelleted at 1300 rcf, and resuspended in Buffer N. Crude chromatin concentration was determined by sonicating 2 uL of nuclei in 18 uL NaCl (2 M) and measuring DNA concentration with a Nanodrop; nuclei equivalent to 50 ug of DNA were aliquoted and spiked with 5 uL of a SNAP-ChIP k-MetStat panel (Epicypher). 1 U MNase (25U/uL) was added per 4.275 ug chromatin and incubated at 37°C for 12 minutes with shaking. Mnase digestion was stopped with 1/10 volume MNase Stop Buffer (10x, 0.1 M EGTA) followed by 1/8 volume NaCl (5 M) to lyse nuclei and release digested chromatin. After centrifugation, soluble chromatin was added to 33 mg of rehydrated ceramic hydroxyapatite (CHT) resin and rotated for 10 min at 4°C. The CHT Resin:Chromatin mix was added to a centrifugal filter unit and washed 4x with HAP Wash Buffer 1 (5 mM NaPO4 pH 7.2, 600 mM NaCl, 1 mM EDTA, and 200 uM PMSF), 4x with Hap Wash Buffer 2 (5 mM NaPO4 pH 7.2, 100 mM NaCl, 1 mM EDTA, and 200 uM PMSF), and eluted with three successive additions of HAP Elution Buffer (500 mM NaPO4 pH7.2, 100 mM NaCl, 1 mM EDTA, and 200 uM PMSF). DNA concentration was again measured by sonication and adjusted to 20 ug/mL with ChIP Buffer 1 (25 mM Tris pH 7.5, 5 mM MgCl2, 100 mM KCl, 10% glycerol, 0.1% NP-40, 200 uM PMSF and 50 ug/mL BSA). Antibody:bead conjugates were prepped by adding 5 or 10 uL of Cell Signaling Technology H3K27me3 antibody (CST #9733, clone C36B11, lot 14, 102 ug/mL) to 12.5 uL of Protein A Magnetic Dynabeads (Invitrogen) that had been washed with ChIP Buffer 1. Antibody:bead conjugates were incubated on a rotator for 3 hours at 4°C, washed 2x, and resuspended with ChIP Buffer 1. Purified digested chromatin (0.75 ug as measured by DNA concentration) was added to the antibody:bead conjugates while a volume equivalent to 10% was saved for input from the purified chromatin. The bead:antibody:chromatin mixture volume was brought to 100 uL with ChIP Buffer 1 and incubated on a rotator for 17 min at 4°C. Using a magnetic rack, the mixture was washed for 10 min on a rotator at 4°C 2x with ChIP Buffer 2 (25 mM Tris pH 7.5, 5 mM MgCl2, 300 mM KCl, 10% glycerol, 0.1% NP-40, 200 uM PMSF and 50 ug/mL BSA), 1x with ChIP Buffer 3 (10 mM Tris pH 7.5, 250 mM LiCl, 1 mM EDTA, 0.5% NaDeoxycholate, 0.5% NP-40, 200 uM PMSF and 50 ug/mL BSA), 1x with ChIP Buffer 1, 1x with TE Buffer (pH 8.0), and resuspended in 50 ul of ChIP Elution Buffer. This was incubated at 55°C for 5 min, and sample was eluted from beads on a magnetic rack. Finally, 2 uL NaCl (5M), 1 uL EDTA (0.5M), and 0.5 uL Proteinase K (100x) were added to ChIP and Input samples, which were incubated overnight at 55°C. DNA was recovered using KAPA Pure beads at a 1.5X ratio on a magnetic rack. After two washes with 75% EtOH, DNA was eluted in 50 uL dH20 and DNA concentration was measured with a Qubit.
Libraries were prepared according to KAPA's instructions accompanying the KAPA Hyper Prep Kit (Part# KR0961 ). Briefly, DNA was end-repaired, A-Tail extended, and KAPA adapters were ligated to DNA fragments. Adapter-ligated fragments were amplified with 11 cycles on a thermocycler, and DNA was purified using KAPA Pure Beads. Prepared libraries were submitted to the VARI Genomics Core for library QC and quantification using the Agilent 2100 Bioanalyzer and KAPA Library Quantification Kit, respectively. Libraries were sequenced on an Illumina NextSeq 500 with 2 X 75 bp paired-end reads.

treatment_protocol: HCT116 colorectal carcinoma cells were treated for 72 hours with either vehicle (0.02% DMSO and 0.03% PBS) or EZH2 inhibitor (EPZ6438, 1 uM). Cells were trypsinized, collected, flash frozen, and stored at -80°C.

value: EZH2 inhibitor (EPZ6438)

value: colorectal carcinoma cell line

tag: passages


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C7_ad010


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C8_ad001


title: H9_ESC_H3K27ac_ChIPseq_replicate2

value: H3K27ac (Active Motif, 39133)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C7_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C6_ad001


title: Veh_Input

value: vehicle


title: H9_ESC_H3K27ac_ChIPseq_replicate1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C6_ad006


title: EPZ2_H3K27me3

value: Cell Signaling H3K27me3 (CST#9733, clone C36B11, lot 14)


title: EPZ1_H3K27me3


title: H9_ESC_H3K4me3_ChIPseq_replicate2

value: H3K4me3 (Active Motif, 39159)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C5_ad012


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C6_ad004


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C5_ad001


title: H9_ESC_H3K4me3_ChIPseq_replicate1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C5_ad007


title: Veh1_H3K27me3


title: H9_ESC_H3K4me1_ChIPseq_replicate2

value: H3K4me1 (Active Motif, 39297)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C5_ad010


title: H9_ESC_H3K4me1_ChIPseq_replicate1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C5_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C5_ad004


title: Veh2_H3K27me3


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C7_ad004


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C5_ad008


title: WT Total Microsomal RNA 3

city: Chicago

first: Robert

last: Keenan

state: IL

address: 929 East 57th Street

department: Department of Biochemistry & Molecular Biology

institute: University of Chicago

description:
Total mRNA attached to membranes in Hek293 TRex Cells
BK.AA.8

data_processing:
Basecalls performed using bcl2fastq v2.20
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using STAR v2.6.1 with author recommemded parameters
Count table were built using featureCounts in Subread v1.6.3.
Genome_build: GRCh38
Supplementary_files_format_and_content: Count table as tab-delimited text file

source_name: Hek293 TRex Cells

growth_protocol: Hek293 TRex cells containing a 3xFlag-Cas9 construct were maintained in DMEM supplemented with 10% FBS (Gemini Foundation) and penicillin/streptomycin mixture (Invitrogen)

extract_protocol:
After cell harvesting by scraping, membranes were isolated by hypotonic lysis followed by low speed centrifugation. For samples SAA1-6, membranes were then digitonin solubilized, followed by Flag IP and ultracentrifugation to isolate TMCO1-attached ribosomes.
RNA libraries were prepared for sequencing using standard Illumina protocols, using RiboZero to deplete rRNA in samples SAA1-6 and poly-dT in samples RKAA1-10.

tag: antibody

value: Hek293 TRex cells


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C4_ad012

tag: brain region

value: ACB


title: G10_Lancaster_d45_rep7

city: Bern

first: Jie

last: Wu

state: Bern

address: Freiestrasse 3

country: Switzerland

institute: Department of Chemistry, Biochemistry and Pharmaceutical Sciences

description: RNA - poly A enriched

data_processing:
Reads were mapped to the human genome hg19 with TopHat2 aligner using default input parameters and with Ensembl (GRCh37.87) gene annotation
Read counts were generated using HTSeq-count with "–mode union –stranded no"
Genome_build: hg19
Supplementary_files_format_and_content: htseq-count generated counts

source_name: iPSC-derived organoids

extract_protocol:
To isolate RNA of single organoids we used the Direct-zol-96 RNA kit (Zymo Research) according to the manufacturer’s instructions. We assessed RNA concentration and purity using a NanoDrop 8000 spectrophotometer and RNA integrity with a Bioanalyzer (Agilent Technologies) per standard protocols.
mRNA was enriched using the NEBNext Poly(A) Magnetic Isolation Module (NEB) followed by strand-specific cDNA NGS library preparation (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB). The size of the resulting library was controlled by use of a D1000 ScreenTape (Agilent 2200 TapeStation) und quantified using the NEBNext Library Quant Kit for Illumina (NEB).

tag: starting cells

value: iPSCs

value: Day 45

value: Wild type


title: H10_Lancaster_d45_rep8

description: RNA - poly A enriched

tag: age


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C4_ad007

tag: Sex

value: male

tag: strain


title: WT Total Microsomal RNA 2

description:
Total mRNA attached to membranes in Hek293 TRex Cells
BK.AA.7

tag: cell type


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C4_ad010


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C4_ad004


title: WT Total Microsomal RNA 1

description:
Total mRNA attached to membranes in Hek293 TRex Cells
RK.AA.1


title: E10_Lancaster_d45_rep5

description: RNA - poly A enriched

tag: genotype


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C4_ad008


title: D10_Lancaster_d45_rep4

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C3_ad007


title: Control IP Elution Rep3

description:
Mock IP elution from untagged line
SAA5


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C3_ad012


title: 3xFlagIP Elution Rep3

description:
3Flag-IP elution from 3Flag-TMCO1 line
SAA6

source_name: Herk293 TRex 3Flag-TMCO1 Cells


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C3_ad001


title: B10_Lancaster_d45_rep2

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C3_ad010


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C3_ad002


title: A10_Lancaster_d45_rep1

description: RNA - poly A enriched


title: 3xFlagIP Elution Rep1

description:
3Flag-IP elution from 3Flag-TMCO1 line
SAA2


title: Control IP Elution Rep2

description:
Mock IP elution from untagged line
SAA3


title: 3xFlagIP Elution Rep2

description:
3Flag-IP elution from 3Flag-TMCO1 line
SAA4


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C3_ad008


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C2_ad007


title: Control IP Elution Rep1

description:
Mock IP elution from untagged line
SAA1


title: H09_Lancaster_d30_rep8

description: RNA - poly A enriched

value: Day 30


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C2_ad001


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C2_ad012


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C3_ad006


title: G09_Lancaster_d30_rep7

description: RNA - poly A enriched


title: F10_Lancaster_d45_rep6

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C4_ad002


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C2_ad008


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C2_ad010


title: F09_Lancaster_d30_rep6

description: RNA - poly A enriched


title: Free_N2_3 [Mnase-seeq]

city: Geneva

first: Florian

last: Steiner

address: 30, Quai Ernest-Ansermet

department: Department of Molecular and Cellular Biology

institute: University of Geneva

description: processed data file: N2_MNase.bed

data_processing:
The paired-end reads (length=50 bp) or single-end reads (length = 100 bp) were mapped with the novoalign (default parameters) software to the C. elegans reference genome (producing SAM format files).
Reads were transformed into bins of the desired size (JSON format) with a custom UNIX script.
JSON files were transformed into bedgraphs annotating maximum amount of reads present in each bin with a custom R script.
All files were normalized to the same number of reads. Experimental samples were then normalized by subtracting the number of reads present in the corresponding bin in the control file. The control samples were DNA from nuclei treated with Free MNase (ChEC-seq), genomic DNA from cells treated with HU (EdU-seq) and genomic DNA from cells without treatment (Repli-seq)
Experiment biological replicates that passed the quality control were merged on the level of aligned reads (SAM files), and the downstream pipline was performed again using the merged file to obtain the final normalized bedgraph for each experiment.
the data were smoothed with a sliding window averaging 5 consecutive bins using a custom R script
Genome_build: WBcel215
Supplementary_files_format_and_content: Processed data are bedgraphs containing normalized results. Bin sizes used in the analysis were 1 kb or 10 kb (for Repli-seq data).

organism: Caenorhabditis elegans

source_name: Embryonic nuclei

growth_protocol: Nematodes were cultured using standard procedures and harvested as young adults to isolate embryos

extract_protocol:
For ChEC: Worm cultures were synchronized by embryo isolation with sodium hypochlorite for 4 generations. Embryos were treated with chitinase (1h, RT , 2 U/ml), washed twice in buffer A (15 mM Tris pH 7.5, 0.1 mM EGTA, 0.34 M sucrose, 0.2 mM spermine, 0.5 mM spermidine, 0.5 mM PMSF) and then resuspend in buffer A supplemented with detergents (0.25% NP-40 and 0.1% Tx-100). Nuclei were released with a glass dounce homogenizer and 15 stokes using the loose inserting pestle and 15 stokes using the tight inserting pestle. Debris were spun down at 100 g for 2 minutes and the supernatant, containing nuclei, was saved. The debris were resuspended in buffer A supplemented with detergents and the nuclei isolation step was repeated. The supernatants containing the nuclei were pooled, and the nuclei were pelleted at 1000 g for 10 min. Nuclei were washed once in buffer A, once in buffer B (15 mM Tris pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine, 1 mM PMSF), and resuspended in buffer B. MNase was activated by addition of CaCl2 to a final concentration of 2 mM at 30°C. Samples were incubated for 5 to 10 minutes (for CDT-1 ChEC), 5 to 7 minutes (for TRES-1 ChEC) or for 1 h (free MNase control). MNase was inactivated by adding an equal volume of 2x Stop buffer (400 mM NaCl, 20 mM EGTA). Samples were treated overnight with Proteinase K and SDS at 55°C. Phenol-chloroform-isoamyl treatment was used to remove Proteinase K prior the RNase treatment (Roche, Cat. No. 11119915001) for 1h30 minutes at 37°C. After chloroform extraction, DNA was precipitated overnight with ethanol and NaCl. DNA was resuspended overnight in TE prior to constructing the libraries. For EdU-seq and repli-seq: Cells were extracted from embryos as described in (Bianchi and Driscoll, 2006). Briefly, embryos were isolated using sodium hypochlorite, treated with chitinase (1h, RT, 2U/ml), washed once in M9 and resuspend in 10ml of L-15 medium (supplemented with 50 ml FBS (heat inactivated, Gibco), 7.7 g sucrose and 5 ml pen/strep (1:100)). Cells were dissociated with three passes through a syringe with a 22 gauge needle and two passes through a syringe with 26 gauge needle. Debris were pelleted by spinning at 80 g for 1 min, and the supernatant, containing cells, was saved. Debris were resuspended in supplemented L-15 medium and cell extraction was repeated twice more. Supernatants were pooled together and filtered using 5 micron filters. Cells were pelleted at 500 g for 15 min and resuspend in supplemented L-15 medium.
Libraries were constructed using NEBNext® Ultra™ II DNA Library Prep
NEBNext® Ultra™ II DNA Library Prep

value: wildtype

tag: temperature


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C2_ad002


title: C10_Lancaster_d45_rep3

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C12_ad012


title: Free_N2_2 [Mnase-seeq]

description: processed data file: N2_MNase.bed


title: E09_Lancaster_d30_rep5

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C12_ad004


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C12_ad007


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C12_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C12_ad001


title: Free_H3_3 [Mnase-seeq]

description: processed data file: H3_MNase.bed


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C11_ad012


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C11_ad010


title: C09_Lancaster_d30_rep3

description: RNA - poly A enriched


title: Free_H3_2 [Mnase-seeq]

description: processed data file: H3_MNase.bed


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C11_ad008


title: B09_Lancaster_d30_rep2

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C10_ad008


title: Free_MNase_2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C10_ad012


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C10_ad007


title: F08_3_inside_rep8

description: RNA - poly A enriched

source_name: Automated midbrain organoids

value: smNPCs


title: A09_Lancaster_d30_rep1

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C11_ad001

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C10_ad004


title: Free_MNase_1


title: Free_N2_1 [Mnase-seeq]

description: processed data file: N2_MNase.bed


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C10_ad006


title: E08_3_inside_rep7

description: RNA - poly A enriched


title: Genomic_DNA

source_name: Embyonic cells


title: D08_3_inside_rep6

description: RNA - poly A enriched


title: D09_Lancaster_d30_rep4

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C1_ad012


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C10_ad002


title: C08_3_inside_rep5

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C1_ad007


title: Genomic_DNA_HU


title: H3_Repli_Late_2

data_processing:
Library strategy: Repli-seq
The paired-end reads (length=50 bp) or single-end reads (length = 100 bp) were mapped with the novoalign (default parameters) software to the C. elegans reference genome (producing SAM format files).
Reads were transformed into bins of the desired size (JSON format) with a custom UNIX script.
JSON files were transformed into bedgraphs annotating maximum amount of reads present in each bin with a custom R script.
All files were normalized to the same number of reads. Experimental samples were then normalized by subtracting the number of reads present in the corresponding bin in the control file. The control samples were DNA from nuclei treated with Free MNase (ChEC-seq), genomic DNA from cells treated with HU (EdU-seq) and genomic DNA from cells without treatment (Repli-seq)
Experiment biological replicates that passed the quality control were merged on the level of aligned reads (SAM files), and the downstream pipline was performed again using the merged file to obtain the final normalized bedgraph for each experiment.
the data were smoothed with a sliding window averaging 5 consecutive bins using a custom R script
Genome_build: WBcel215
Supplementary_files_format_and_content: Processed data are bedgraphs containing normalized results. Bin sizes used in the analysis were 1 kb or 10 kb (for Repli-seq data).


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B9_ad012


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B9_ad001


title: H08_3_inside_rep4

description: RNA - poly A enriched


title: Free_H3_1 [Mnase-seeq]

description: processed data file: H3_MNase.bed


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B9_ad007


title: H3_Repli_Late_1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B9_ad010


title: B08_3_inside_rep3

description: RNA - poly A enriched


title: G08_3_inside_rep2

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B9_ad004


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B9_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B9_ad002


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B8_ad008


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B8_ad006


title: H3_Repli_Early_2


title: A08_3_inside_rep1

description: RNA - poly A enriched


title: H3_Repli_Mid_2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B8_ad004


title: H3_Repli_Mid_1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B8_ad002


title: CEMBA181218_5F_1_CEMBA181218_5F_2_C1_ad001


title: H3_Repli_Early_1


title: F07_2_inside_rep8

description: RNA - poly A enriched


title: E07_2_inside_rep7

description: RNA - poly A enriched


title: Repli_Late_3


title: D07_2_inside_rep6

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B7_ad007


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B8_ad012


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B7_ad004


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B7_ad002


title: C07_2_inside_rep5

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B7_ad008


title: Repli_Late_1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B6_ad012


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B6_ad007


title: B07_2_inside_rep3

description: RNA - poly A enriched


title: Repli_Early_2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B6_ad010


title: Repli_Mid_1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B6_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B6_ad002


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B6_ad004


title: G07_2_inside_rep2

description: RNA - poly A enriched


title: A07_2_inside_rep1

description: RNA - poly A enriched


title: H07_2_inside_rep4

description: RNA - poly A enriched


title: H3_EdU_Fork_60min_25C_2

data_processing:
Library strategy: EdU-seq
The paired-end reads (length=50 bp) or single-end reads (length = 100 bp) were mapped with the novoalign (default parameters) software to the C. elegans reference genome (producing SAM format files).
Reads were transformed into bins of the desired size (JSON format) with a custom UNIX script.
JSON files were transformed into bedgraphs annotating maximum amount of reads present in each bin with a custom R script.
All files were normalized to the same number of reads. Experimental samples were then normalized by subtracting the number of reads present in the corresponding bin in the control file. The control samples were DNA from nuclei treated with Free MNase (ChEC-seq), genomic DNA from cells treated with HU (EdU-seq) and genomic DNA from cells without treatment (Repli-seq)
Experiment biological replicates that passed the quality control were merged on the level of aligned reads (SAM files), and the downstream pipline was performed again using the merged file to obtain the final normalized bedgraph for each experiment.
the data were smoothed with a sliding window averaging 5 consecutive bins using a custom R script
Genome_build: WBcel215
Supplementary_files_format_and_content: Processed data are bedgraphs containing normalized results. Bin sizes used in the analysis were 1 kb or 10 kb (for Repli-seq data).


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B7_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B5_ad001


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B5_ad006


title: Repli_Late_2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B5_ad012


title: Repli_Early_1


title: H06_1_outside_rep18

description: RNA - poly A enriched


title: H3_EdU_Fork_60min_25C_1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B4_ad012


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B4_ad001


title: H05_1_outside_rep17

description: RNA - poly A enriched


title: H04_1_outside_rep16

description: RNA - poly A enriched


title: H3_EdU_Fork_30min_25C_2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B4_ad007


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B5_ad004


title: H03_1_outside_rep15

description: RNA - poly A enriched


title: H3_EdU_Fork_0min_25C_2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B4_ad002


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B4_ad008


title: H3_EdU_Fork_0min_25C_1


title: H02_1_outside_rep14

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B3_ad007


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B5_ad008


title: G01_1_outside_rep12

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B4_ad004


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B3_ad012


title: H3_EdU_Fork_60min_20C_2


title: E01_1_outside_rep10

description: RNA - poly A enriched


title: H3_EdU_Fork_30min_25C_1


title: H01_1_outside_rep13

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B4_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B12_ad007


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B3_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B3_ad002


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B3_ad008


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B3_ad004


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B12_ad012


title: H3_EdU_Fork_30min_20C_1


title: F01_1_outside_rep11

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B12_ad002


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B11_ad012


title: D01_1_outside_rep9

description: RNA - poly A enriched


title: H3_EdU_Fork_0min_20C_2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B11_ad010


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B11_ad008


title: C01_1_outside_rep8

description: RNA - poly A enriched


title: H3_EdU_Fork_0min_20C_1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B11_ad007


title: H3_EdU_Fork_30min_20C_2


title: H3_EdU_Fork_60min_20C_1


title: B01_1_outside_rep7

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B11_ad006


title: EdU_Fork_60min_25C_2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B11_ad004


title: A06_1_outside_rep6

description: RNA - poly A enriched


title: A05_1_outside_rep5

description: RNA - poly A enriched


title: EdU_Fork_60min_25C_1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B10_ad012


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B10_ad007


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B10_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B10_ad010


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B10_ad004


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B11_ad001


title: A04_1_outside_rep4

description: RNA - poly A enriched


title: A02_1_outside_rep2

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B10_ad001


title: EdU_Fork_0min_25C_1


title: EdU_Fork_30min_25C_2


title: EdU_Fork_0min_25C_2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B10_ad002


title: EdU_Fork_60min_20C_2


title: EdU_Fork_60min_20C_1


title: G06_1_inside_rep30

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B1_ad001


title: G05_1_inside_rep29

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B1_ad012


title: A03_1_outside_rep3

description: RNA - poly A enriched


title: EdU_Fork_30min_25C_1


title: EdU_Fork_30min_20C_2


title: G04_1_inside_rep28

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B1_ad007


title: EdU_Fork_30min_20C_1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B1_ad010


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B1_ad006


title: G03_1_inside_rep27

description: RNA - poly A enriched


title: G02_1_inside_rep26

description: RNA - poly A enriched


title: A01_1_outside_rep1

description: RNA - poly A enriched


title: F06_1_inside_rep25

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B1_ad004


title: EdU_20C_4


title: F05_1_inside_rep24

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B1_ad002


title: F04_1_inside_rep23

description: RNA - poly A enriched


title: EdU_Fork_0min_20C_2


title: EdU_20C_3


title: F03_1_inside_rep22

description: RNA - poly A enriched


title: EdU_Fork_0min_20C_1


title: F02_1_inside_rep21

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A9_ad010


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A9_ad007


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A9_ad012


title: E06_1_inside_rep20

description: RNA - poly A enriched


title: H3_TRES1_25C_3

data_processing:
Library strategy: ChEC-seq
The paired-end reads (length=50 bp) or single-end reads (length = 100 bp) were mapped with the novoalign (default parameters) software to the C. elegans reference genome (producing SAM format files).
Reads were transformed into bins of the desired size (JSON format) with a custom UNIX script.
JSON files were transformed into bedgraphs annotating maximum amount of reads present in each bin with a custom R script.
All files were normalized to the same number of reads. Experimental samples were then normalized by subtracting the number of reads present in the corresponding bin in the control file. The control samples were DNA from nuclei treated with Free MNase (ChEC-seq), genomic DNA from cells treated with HU (EdU-seq) and genomic DNA from cells without treatment (Repli-seq)
Experiment biological replicates that passed the quality control were merged on the level of aligned reads (SAM files), and the downstream pipline was performed again using the merged file to obtain the final normalized bedgraph for each experiment.
the data were smoothed with a sliding window averaging 5 consecutive bins using a custom R script
Genome_build: WBcel215
Supplementary_files_format_and_content: Processed data are bedgraphs containing normalized results. Bin sizes used in the analysis were 1 kb or 10 kb (for Repli-seq data).


title: EdU_20C_1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_B1_ad008


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A9_ad004


title: H3_TRES1_25C_2


title: EdU_20C_2


title: E05_1_inside_rep19

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A9_ad008


title: TRES1_25C_3

value: tres-1(uge102[MNase::tres-1]) I


title: E04_1_inside_rep18

description: RNA - poly A enriched


title: TRES1_25C_2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A8_ad001


title: TRES1_20C_4


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A8_ad010


title: E02_1_inside_rep16

description: RNA - poly A enriched


title: E03_1_inside_rep17

description: RNA - poly A enriched


title: TRES1_20C_3


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A8_ad008


title: D06_1_inside_rep15

description: RNA - poly A enriched


title: TRES1_20C_2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A8_ad004


title: colorectal adenoma_Tu15

type: RNA

city: Beijing

first: Rui

last: Chen

address: No.10 Xitoutiao, You An Men

country: China

institute: Capital medical university

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.a,The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min. b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated lncRNA and mRNAs were averaged and lncRNA and mRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. Discriminant lncRNA and mRNAs and differences between groups were analyzed using Bayes moderated t test (limma) with Benjamini Hochberg false discovery rate (FDR) at P < 0.05. A two-fold cut-off difference was applied to select the up- and down-regulated lncRNA and mRNAs.

source_name: primary colorectal adenoma

label_protocol: RNA labeling and array hybridization was according to Exiqon's manual.After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for lncRNA and mRNA labelling by following steps:  a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling reaction was incubated for 1 h at 16°C. c,Terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

tag: gender

tag: histology

value: tubulovillous adenoma


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A8_ad002


title: D04_1_inside_rep13

description: RNA - poly A enriched


title: colorectal adenoma_Tu16

value: female


title: TRES1_20C_1


title: colorectal adenoma_Tu9


title: CDT1_20C_5

value: cdt-1(uge34 [MNase::cdt-1]) I


title: D03_1_inside_rep12

description: RNA - poly A enriched


title: D05_1_inside_rep14

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A7_ad012


title: CDT1_20C_4


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A7_ad007


title: colorectal adenoma_Tu3


title: D02_1_inside_rep11

description: RNA - poly A enriched


title: CDT1_20C_2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A7_ad006


title: C06_1_inside_rep10

description: RNA - poly A enriched


title: CDT1_20C_3


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A7_ad004


title: colorectal adenoma_Tu8


title: colorectal cancer_Ca33

source_name: primary colorectal cancer

value: colorectal adenocarcinoma


title: C05_1_inside_rep9

description: RNA - poly A enriched


title: colorectal cancer_Ca25


title: colorectal adenoma_Tu10


title: colorectal cancer_Ca34


title: C04_1_inside_rep8

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A7_ad002


title: colorectal cancer_Ca23


title: Duct_1

type: genomic

city: Portland

first: Bin

last: Li

state: OR

address: 3181 SW Sam Jackson Pk Rd

department: Oregon Stem Cell Center

institute: Oregon Health and Science University

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

scan_protocol: Standard recommended Illumina scanner setting

data_processing: Methylation array data were processed with the minfi package in R. CpG sites were removed if the detection p-value (representing total fluorescence of the relevant probes) was >0.01 in any sample. Background correction and normalization were performed with the preprocessNoob function.

label: Cy5 and Cy3

source_name: Cholangiocytes

label_protocol: Standard Illumina Protocol

extract_protocol: NOT PROVIDED; REQUESTED

value: Female

tag: passage

value: no culture

tag: diagnosis

value: normal

value: Cholangiocytes


title: HC_2

source_name: normal hepatocytes

value: normal hepatocytes


title: normal mucosa_No34

source_name: adjacent normal mucosa

value: normal mucosa


title: C03_1_inside_rep7

description: RNA - poly A enriched


title: CDT1_20C_1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A7_ad008

value: ACB


title: Liv_Org_2

source_name: Liver Organoid

value: Liver Organoid


title: Liv_Org_3

value: Male


title: LiM_2

source_name: Cirrhotic liver cells

value: Alcoholic steatohepatitis

value: Cirrhotic liver cells


title: LiM_3

value: End stage liver disease


title: GB_Org_1

source_name: Gallbladder organoid

value: Gallbladder organoid


title: GB_Org_2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A6_ad010

value: male


title: B05_1_inside_rep4

description: RNA - poly A enriched

value: smNPCs

value: Day 30

value: Wild type


title: LiM_1


title: colorectal cancer_Ca5

value: colorectal adenocarcinoma


title: normal mucosa_No26


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A5_ad012


title: Liv_Org_1

value: Female

value: Autoimmune hepatitis


title: B04_1_inside_rep3

description: RNA - poly A enriched


title: Liv_Org_4

value: normal


title: B03_1_inside_rep2

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A5_ad001


title: B06_1_inside_rep5

description: RNA - poly A enriched


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A6_ad007


title: HC_1

value: no culture

value: normal hepatocytes


title: Naïve_control_rep4

city: Tianjin

first: Kaibin

last: Shi

address: 154 Anshan Rd

institute: Tianjin Medical University

description: HSCs were flow cytometric sorted from bone marrow of mice.

hyb_protocol: Each mRNA was hybridized with two ~50 base probes in the hybridization solution. The reporter probe carries the signal, the capture probe allows the complex to be immobilized for data collection.

scan_protocol: After hybridization, excess probes are removed and the probe/target complexes aligned and immobilized in the nCounter Cartridge. Sample cartridges are placed in the Digital Analyzer. Color codes on the surface of the cartridge are counted and tabulated for each target mRNA.

data_processing: Data were processed on the nSolver software. Data were normalized to the 14 reference genes including positive and negative controls and housekeeping genes probes using nSolver software.

label: not provided

source_name: HSCs

label_protocol: not provided

extract_protocol: HSC were sorted from femur bone marrow of ICH and sham mice at day 3 after surgery. Cells were directly sorted into Trizol LS (ThermoFisher)-containing tubes, and total RNA was then extracted.

value: Bone marrow hematopoietic stem cells

value: Healthy


title: Naïve_control_rep3


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A5_ad010

value: ACB


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A5_ad007


title: PBS_3

city: Kuala Lumpur

first: NADIAH

last: ABU

state: Kuala Lumpur

address: UKM Medical Molecular Biology, UMBI, UKM MEDICAL CENTER

country: Malaysia

institute: UKM MEDICAL MOLECULAR BIOLOGY INSTITUTE (UMBI)

description: Gene expression after 24h of treatment with phosphate buffered saline

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: PBS

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

growth_protocol: CD8+T cells were cultured in RPMI supplemented with 10% extracellular vesicle-free FBS and 1% penn-strep, alongside IL-2 and Immunoactivator (Stemcell technologies)

extract_protocol: Total RNA was isolated using the RNEasy Mini Kit  by Qiagen according to the manufacturers protocol

treatment_protocol: CD8+T cells were cultured with the respective extracellular vesicles (3-4 ug) from different groups for 24 hours

tag: tissue

value: Peripheral blood

value: CD8+T cells

tag: treatment

value: phosphate buffered saline

tag: timepoint

value: after 24h of treatment


title: PBS_1


title: colorectal cancer_Ca26

value: male


title: B02_1_inside_rep1

description: RNA - poly A enriched

value: smNPCs


title: normal mucosa_No25

value: female

value: normal mucosa


title: CRC_Obese_3

description: Gene expression after 24h of treatment with Evs from colorectal cancer patients with BMI >27 kg/m2


title: CRC_Obese_2

value: Evs from colorectal cancer patients with BMI >27 kg/m2


title: normal mucosa_No5


title: normal mucosa_No23


title: CRC_Obese_1


title: Naïve_control_rep2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A5_ad006

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column


title: UW mlaF_3

city: Athens

first: Matthew

last: Powers

state: GA

address: 501 DW Brooks Dr

institute: University of Georgia

data_processing:
Reads were trimmed to remove ambiguous nucleotides using CLC Genomics workbench software v12
Reads were mapped to the 17978 published genome using CLC Genomics workbench software v12
Differential expression was calculated using CLC Genomics Workbench Software v12
Genome_build: ATCC17978
Supplementary_files_format_and_content: RPKM values

organism: Acinetobacter baumannii

source_name: Bacterial

growth_protocol: Cultures were grown at 37C in LB until mid-log

extract_protocol:
Extraction was done using trizol. rRNA was depleted
Libraries were constructed for Illumina sequencing

treatment_protocol: Cultures were pelleted and resuspended in RNAlater prior to extraction

value: mlaF

tag: source

value: UW


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A5_ad004

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: UW mlaF_2


title: hpc_IFNb rep3

city: Vienna

first: Andreas

last: Bergthaler

address: Lazarettgasse 14 AKH BT25.3

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder.
Transcriptome analysis is performed using the Tuxedo suite. Reads are mapped on the mouse reference genome (Mus musculus, Ensembl e87, December 2016) using TopHat2 (v2.0.10).
Cufflinks (v2.2.1) is further used to assemble transcripts from spliced read alignments, using the Ensembl e87 transcriptome as the reference as well as de novo assembly of transcript models.
Differential expression is assessed with Cuffdiff (v2.2.1). Transcriptome sets of all replicates for each sample group will be combined with Cuffmerge.
Genome_build: Ensembl version e87(December 2016) of the Mus musculus genome.
Supplementary_files_format_and_content: tab-delimited text file of normalised cufflinks FPKM

source_name: hepatocytes

extract_protocol:
Total RNA was extracted after sample homogenisation using Qiazol lysis reagent according to manufacturer's instructions.
RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer).
Libraries will be pooled, diluted and sequenced on Illumina HiSeq 3000 using 50 bp single-read chemistry.

treatment_protocol: Primary murine hepatocytes were treated with 1000 U/mL IFN-b for 24h or left untreated.

value: IFNb


title: UW mlaF_1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A4_ad012


title: UW WT_3

value: WT


title: hpc_IFNb rep1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A4_ad007


title: Naïve_control_rep1


title: UW WT_2


title: hpc_ctl rep3

value: control


title: UW WT_1


title: hpc_ctl rep2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A4_ad010


title: hpc_IFNb rep2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A4_ad006


title: PBS_4


title: UGA mlaF_3

value: UGA


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A4_ad004


title: 293TT_rep3

city: Gwangjin-gu, Seoul

first: Nayoung

last: Park

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

description:
293TT_transcriptome_FPKM.xlsx
293TT_transcriptome_raw_readcount.xlsx
Baculovirus_FPKM.xlsx
Baculovirus_raw_readcount.xlsx

data_processing:
Sequenced RNA-sequencing reads were trimmed for adapter seuquence, and processed for eliminating artifacts such as contaminant DNA or PCR duplicates using Trimmomatic 0.38 with parameters SLIDINGWINDOW:4:15 TRAILING:3  LEADING:3 MINLEN:36.
Trimmed reads were mapped to reference genome (UCSC hg19 +  GCF_000838485.1_ViralProj14023) using the Bowtie2 2.3.4.1 aligner.
Fragments per kilobase of transcript per million mapped reads (FPKM) was estimated  with R package countToFPKM for viral genes, and with StringTie for human genes.
Fold change, and variance were calculated using edgeR.
Genome_build: UCSC hg19, GCF_000838485.1_ViralProj14023
Supplementary_files_format_and_content: Matrix table with raw read counts for every gene and every samples

source_name: embryonic kidney cells

growth_protocol: Human embryonic kidney 293TT cells were grown at 37°C in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Spodoptera frugiperda 9 (Sf9) insect cells were maintained at 27°C in Sf-900 medium containing 3% FBS and 1% antibiotic-antimycotic.

extract_protocol:
After 72 hours of virus infection, supernatants were removed, and cells were lysed for RNA isolation.
total RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA LT Sample Prep Guide

treatment_protocol: 293TT and Sf9 cells were infected with recombinant AcHERVenv-CMV-GFP at a multiplicity of infection (MOI) of 30.

value: AcHERVenv-CMV-GFP infected

tag: cell line


title: UGA mlaF_2


title: CRC_Lean_2

description: Gene expression after 24h of treatment with Evs from colorectal cancer patients with BMI >18.5 kg/m2 and <23 kg/m2


title: UGA mlaF_1


title: 293TT_rep2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A3_ad012

tag: brain region

value: ACB


title: UGA WT_3


title: 293TT_rep1


title: C02_1_inside_rep6

description: RNA - poly A enriched

tag: starting cells

value: Day 30

value: Wild type


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A5_ad002

tag: age


title: PBS_2

value: Peripheral blood

value: CD8+T cells

value: phosphate buffered saline


title: hpc_ctl rep1


title: NonCRC_Obese_2

description: Gene expression after 24h of treatment with Evs from healthy individuals with BMI >27 kg/m2

value: after 24h of treatment


title: CRC_Lean_1

value: Evs from colorectal cancer patients with BMI >18.5 kg/m2 and <23 kg/m2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A3_ad001

tag: Sex

value: male


title: UGA WT_2

tag: strain


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A3_ad007


title: NonCRC_Obese_3

tag: cell type

value: Evs from healthy individuals with BMI >27 kg/m2


title: 293TT_N_rep3

description:
293TT_transcriptome_FPKM.xlsx
293TT_transcriptome_raw_readcount.xlsx

value: uninfected


title: 293TT_N_rep2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A4_ad008


title: NonCRC_Lean_2

description: Gene expression after 24h of treatment with Evs from healthy individuals with BMI >18.5 kg/m2 and <23 kg/m2


title: NonCRC_Obese_1


title: NonCRC_Lean_1

value: Evs from healthy individuals with BMI >18.5 kg/m2 and <23 kg/m2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A3_ad004


title: normal mucosa_No33

value: female

value: normal mucosa


title: CNS_Treg_PD1cko_4

city: Boston

first: Peter

last: Sage

address: 221 Longwood Ave

department: Medicine/Renal

institute: Brigham and Women's Hospital

description: Sample 7

data_processing:
Briefly, reads were aligned (mismatch cost=2, insertion cost=3, deletion cost=3, length fraction=0.8, similarity fraction=0.8) to the mouse genome.
Analysis performed using CLC Genomics Workbench version 8.0.1 RNA-seq analysis software package (Qiagen).
Differential gene expression analysis performed (total count filter cutoff=5.0).
Results normalized to reads per million.
Genome_build: mm9
Supplementary_files_format_and_content: Reads Per Million

extract_protocol:
Treg cells were sorted from CNS preps. RNA isolation was performed using MyOne Silane Dynabeads (Thermo Fisher Scientific) followed by fragmentation and barcoding of RNA using 8bp barcodes in conjunction with standard Illumina adaptors.
Primers were removed using Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt) and samples were amplified with 14 PCR cycles. Libraries were gel purified. RNA-sequencing reactions were performed on  Illumina NextSeq sequencer (Illumina) according to the manufacturer’s instructions, sequencing 50bp reads.

tag: strain background

tag: genotype/variation

value: FoxHet PD1 fl/fl

tag: disease context/model

value: experimental autoimmune encephalomyelitis (EAE)

value: CNS

value: Treg cells


title: 293TT_N_rep1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A3_ad002

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

value: ACB


title: leaf_control_rep3 (S. exigua control)

city: Berlin

first: Tobias

last: Lortzing

state: Berlin

address: Haderslebener Str. 9

department: Biology

country: Germany

institute: Freie Universität Berlin

hyb_protocol: 600 ng of the cRNA were hybridised using the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) following the manufacturer’s protocol at 65°C for 17 h.

scan_protocol: Fluorescence signals were detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron per pixel.

data_processing: Data were analyzed using the “limma” software packages from Bioconductor in “R” (R Core Team; Ritchie et al. 2015). The uploaded data were background-corrected using the “normexp” method and normalized between microarrays using the “quantile” method and Log2-transformed. For the data-upload, all raw data were background-corrected and normalized across all arrays. In the publication, a detection limitwas set at 1.5 times the 10% quantile of fluorescence signal intensity of dark corner spots on each array. All structural spots, as well as oligos that were not above this detection limit in any of the arrays, were removed from further analysis. Subsequently, the expression levels were background-corrected after removal of the non-expressed genes using the normexp method and normalized between the arrays using quantile normalisation.

organism: Nicotiana attenuata

source_name: leaf control

label_protocol: Fluorescent cyanine 3-CTP-labelled cRNA was generated using the Low Input QuickAmp Labeling Kit (Agilent Technologies) using oligo-dT primer following the manufacture’s protocol.

growth_protocol: Nicotiana attanuata plants originated from a 15x WT inbred line collected in Utah and were grown from seed at a 16/8 h light/dark cycle and a photon irradiance between 190 - 250 µmol

extract_protocol: For each microarray sample, leaf material from three or four independent biological replicates was pooled. Leaf material was ground under liquid nitrogen and RNA was extracted with the NucleoSpin® RNA Plant kit (Macherey-Nagel GmbH & Co. KG) according to the manufacturer’s instructions using double the amount of RAP lysis buffer. RNA was DNase digested using TURBO DNA-free™ (AmbionTM) according to the manufacturer’s instructions.

treatment_protocol: Plants received oviposition by S. exigua (1-2 egg clutches). After 4 days, tissue from the next younger (systemic) leaf, or from the respective leaf position of a control plant without eggs, was harvested for RNA extraction.

tag: genotype location

value: rosette plant


title: CNS_Treg_PD1cko_3

description: Sample 6


title: leaf_S.exigua_eggs_rep_3

source_name: leaf S. exigua eggs


title: leaf_S.exigua_eggs_rep_1


title: CNS_Treg_PD1cko_2

description: Sample 5


title: leaf_S.exigua_eggs_rep_2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A2_ad012

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56


title: CNS_Treg_PD1cko_1

description: Sample 4


title: UGA WT_1

tag: genotype

value: WT

value: UGA


title: leaf_control_rep2 (S. exigua control)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A2_ad001


title: iPSCs (UNC0638) rep3

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

description:
MS7
iPSCs derived MEFs with UNC0638 replicate 3 for the first 48 hours

data_processing:
Raw sequencing data were aligned to mouse genome version mm10 with the tophat algorithm (version 2.1.0)(Kim et al., 2013) and the use of «--b2-very-sensitive» parameter.
Samtools (version 1.8) (Li et al., 2009b) was used for data filtering and file format conversion
Aligned reads were assigned to exons with the use of the HT-seq count (version 0.5.4p3) algorithm (Anders et al., 2015) and the following parameters «-m intersection -nonempty». (MarkDuplicates option)
Differentially expressed genes were identified with the use of DESeq R package (R.3.4.4) (Anders and Huber, 2010), excluding  genes with RPKM<1
Genome_build: MM10
Supplementary_files_format_and_content: csv tab delimited / rna-seq raw reads

source_name: iPSCs derived MEFs with UNC0638 for the first 48 hours

growth_protocol: MEF cultures were established by trypsin digestion of midgestation (embryonic day (E) 13.5–E15.5) embryos and maintained in DMEM supplemented with 10% FBS, L-glutamine, penicillin/streptomycin, nonessential amino acids and β-mercaptoethanol. Reprogrammable MEFs were heterozygous Rosa26-rtTA and for Oct4-GFP and either heterozygous for a DOX-inducible OKSM allele (Stadtfeld et al., 2010b) or homozygous for an inducible OKS allele.

extract_protocol:
Total RNA was extracted from cells with the RNeasy Plus Kit (Qiagen).  Total RNA with RIN values > 8 were subjected to Automated TruSeq stranded total RNA with RiboZero Gold library preparation (Illumina).
TruSeq stranded total RNA with RiboZero Gold library preparation (Illumina).

treatment_protocol: Indicated samples were treated with 1μM UNC0638. All samples were harvested after 48h reprogramming.

value: iPSC cells


title: CNS_Treg_WT_3

description: Sample 3


title: iPSCs (UNC0638) rep2

description:
MS6
iPSCs derived MEFs with UNC0638 replicate 2 for the first 48 hours


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A2_ad007


title: iPSCs (DMSO) rep3

description:
MS4
iPSCs derived MEFs replicate 1  with DMSO

source_name: iPSCs derived MEFs with DMSO

value: DMSO


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A2_ad010


title: CNS_Treg_WT_2

description: Sample 2


title: NonCRC_Lean_3

value: Peripheral blood

value: CD8+T cells

value: after 24h of treatment


title: iPSCs (DMSO) rep2

description:
MS2
iPSCs derived MEFs replicate 3  with DMSO


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A2_ad006

value: male


title: CNS_Treg_WT_1

description: Sample 1