title: plasma_without_exosomes_cancer_9

city: Seattle

first: Kai

last: Wang

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: plasma_without_exosomes_cancer_DB380_L6_R1

data_processing:
Basecalls performed using CASAVA version X.X.X
The reads were processed by trimming off the adaptor sequences and removing low quality sequences, polyA sequences and adaptor-only sequences. We used a “map and remove” strategy to map the sequence reads to various databases as described.
The processed sequences were first screened against known human microRNA, human transcripts, followed by human genomic sequence. To get mapping results, the alignment tool Blast was used to search microRNA and Bowtie was used to search other large databases.
For the endogenous sequence mapping, except microRNA, we applied three different levels of error tolerance: 0 mismatch, 1 and 2 mismatches. Due to the high sequence similarity for microRNA, we did not allow any sequence mismatch.  After normalizing the mapping results with total number of reads, the number of reads mapped to a specific transcript should be proportional to its concentration in circulation.
Genome_build: miRBase21
Supplementary_files_format_and_content: tab-delimted text files include RPM values for each sample.

source_name: plasma without exosome

growth_protocol: EDTA Plasma samples stored at −80°C from 38 individuals with benign IPNs. Plasma from 7 early stage adenocarcinoma patients and 10 granuloma cases were used for biomarker discovery by next generation sequencing (NGS)

extract_protocol:
50 µl serum was mixed well with 12.6 µl ExoQuick exosome isolation solution, and incubated on ice for 30 min. Then the samples were centrifuged at 1000 g for 30 min at 4°C. The pellet was washed wish 1X DPBS and resuspended in 50 µl 1X DPBS. 20 µl samples were loaded onto the nanochip and incubated at 37ºC for 2 h. On each chip, two wells with 1XDPBS were used as negative control.
The NextGen sequencing libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencing kit (New England Biolabs). The 3’ and 5’ adapters and the reverse transcription primer were diluted in nuclease-free water to concentrations specified by the kit.  The adapter sequences were ligated to the 3’ and 5’ ends of the RNA isolated from 100 μL of plasma using T4 RNA ligase. Ligation reactions were performed overnight at 16oC to maximize efficiency. cDNA was then transcribed from the ligation product followed by PCR amplification with a unique barcode sequence for each sample. The fragment size of about 150 nts, was then extracted and purified from an acrylamide gel. The final purified and barcoded libraries were then pooled in equal molar for single-end 50 nt sequencing run using an Illumina HiSeq2500 instrument.

tag: tumor

value: cancer


title: WTetoh00

status: Public on Dec 31 2020

type: SRA

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

country: USA

institute: NIEHS

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the December 2011 mouse reference genome (GRCm38) using Novoalign short-read alignment software version 1.0A
SAM files were converted to BAM files using the SamTransctiptomeParser application from the USeq software package version 8.8.5
Differentially expressed genes were determined using the DefinedRegionDifferentialSeq application from the USeq software package version 8.8.5
Genome_build: mouse GRCm38
Supplementary_files_format_and_content: FPKM normalized values in Excel spreadsheet

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Zymo Research Direct-zol RNA Miniprep
Illumina TruSeq RNA Library Preparation Kit v2 with poly(A) Selection
RNA-seq, HiSeq 50 cycle single-read sequencing v3

treatment_protocol: 5% ethanol liquid diet

tag: tissue

value: Liver

tag: genotype/strain

value: Wild-type C57BL/6

tag: treatment

value: Control

tag: timepoint


title: plasma_without_exosomes_cancer_10

description: plasma_without_exosomes_cancer_DB381_L6_R1

organism: Homo sapiens


title: WTctrl182


title: plasma_without_exosomes_cancer_8

description: plasma_without_exosomes_cancer_DB379_L6_R1


title: E185_NBN_KO_1

city: Basel

first: Verdon

last: Taylor

address: Mattenstrasse 28

department: Department of Biomedizin

country: Switzerland

institute: University of Basel

description:
mRNA
Forebrain NBN at stage E185, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz

data_processing:
Reads mapped to the transcriptome (GENCODE Release M2 GRCm38.p2) with kallisto 0.43.0 with option --single -l 200.0 -s 100.0 –pseudobam. Last option is to obtain pseudoalignments to transcriptome in BAM files.
The reads mapping to multiple transcripts are uniformly distributed.
Expression per transcript normalized by first dividing the number of reads mapping to each transcript by the length of the transcript in nucleotides and then transform the length-normalized read counts in transcript per million (TPM).
Gene expression was obtained by summing for each gene the TPM of the transcripts corresponding to the gene.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: gene_tpm_BULK_KO.txt: Tab-delimited text file, TPM table, genes in rows and samples in columns.

source_name: dorsal cerebral cortex

extract_protocol:
Total RNA was isolated from FAC-sorted GFP positive cells from Hes5::GFP; Ski KO and Tbr2::GFP; Ski KO transgenic lines using TRIzol reagent. A time course was performed with NSCs, BPs and NBNs isolated at each time point during development from E10.5 to E18.5. Samples were analyzed for their integrity and concentration using Agilent 2100 Bioanalyzer and Quant-IT RiboGreen RNA Assay Kit. Sequencing libraries were prepared with the Illumina TruSeq RNA Library Prep Kit v2 according to Illumina’s instructions.
After quality control (Fragment Analyzer, AATI) libraries were pooled and loaded on an Illumina flow cell for cluster generation (HiSeq SR Cluster Kit v4 cBot). Libraries were sequenced SR50 on the HiSeq 2500 system (HiSeq SBS Kit V4) following the manufacturer’s protocols.

treatment_protocol: Dorsal cortices from embryonic day E11.5 to E18.5 were micro-dissected and dissociated into single cell suspensions using Papain and Ovo-mucoid mix (Giachino et al, 2009). Cells were washed with L15 medium and FAC-sorted for GFP positive NSCs using FACSariaIII (BD Biosciences) derived from Hes5::GFP; Ski KO transgenic embryos for NSCs and Tbr2::GFP; Ski KO transgenic embryos for BPs and NBNs.

tag: strain/background

tag: isolate

tag: genotype

value: Ski knock-out

value: Forebrain

tag: cell type

value: Newborn neuron

tag: Sex

value: Female

tag: age


title: E185_NBN_KO_3

description:
mRNA
Forebrain NBN at stage E185, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz


title: plasma_without_exosomes_cancer_6

description: plasma_without_exosomes_cancer_DB377_L6_R1


title: E175_NBN_KO_4

description:
mRNA
Forebrain NBN at stage E175, replicate 4
processed data file: gene_tpm_BULK_KO.txt.gz


title: E175_NBN_KO_3

description:
mRNA
Forebrain NBN at stage E175, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz


title: plasma_without_exosomes_cancer_7

description: plasma_without_exosomes_cancer_DB378_L6_R1


title: plasma_without_exosomes_cancer_5

description: plasma_without_exosomes_cancer_DB376_L6_R1


title: E175_NBN_KO_2

description:
mRNA
Forebrain NBN at stage E175, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: E175_NBN_KO_1

description:
mRNA
Forebrain NBN at stage E175, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz


title: E165_NBN_KO_3

description:
mRNA
Forebrain NBN at stage E165, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz


title: plasma_without_exosomes_cancer_2

description: plasma_without_exosomes_cancer_DB373_L5_R1


title: plasma_without_exosomes_cancer_1

description: plasma_without_exosomes_cancer_DB372_L5_R1


title: WTctrl181


title: E185_NBN_KO_2

description:
mRNA
Forebrain NBN at stage E185, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: E165_NBN_KO_2

description:
mRNA
Forebrain NBN at stage E165, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: plasma_without_exosomes_cancer_4

description: plasma_without_exosomes_cancer_DB375_L6_R1


title: plasma_without_exosomes_granuloma_8

description: plasma_without_exosomes_granuloma_DB370_L5_R1

value: granuloma


title: plasma_without_exosomes_granuloma_9

description: plasma_without_exosomes_granuloma_DB371_L5_R1


title: plasma_without_exosomes_granuloma_7

description: plasma_without_exosomes_granuloma_DB369_L5_R1


title: plasma_without_exosomes_granuloma_5

description: plasma_without_exosomes_granuloma_DB367_L5_R1


title: plasma_without_exosomes_granuloma_6

description: plasma_without_exosomes_granuloma_DB368_L5_R1


title: E185_BP_KO_3

description:
mRNA
Forebrain BP at stage E185, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz

value: Basal progenitor


title: E155_NBN_KO_1

description:
mRNA
Forebrain NBN at stage E155, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz


title: E185_BP_KO_2

description:
mRNA
Forebrain BP at stage E185, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: plasma_without_exosomes_granuloma_4

description: plasma_without_exosomes_granuloma_DB366_L5_R1


title: plasma_without_exosomes_granuloma_3

description: plasma_without_exosomes_granuloma_DB365_L5_R1


title: plasma_without_exosomes_granuloma_1

description: plasma_without_exosomes_granuloma_DB363_L4_R1


title: plasma_without_exosomes_granuloma_2

description: plasma_without_exosomes_granuloma_DB364_L4_R1


title: E175_BP_KO_4

description:
mRNA
Forebrain BP at stage E175, replicate 4
processed data file: gene_tpm_BULK_KO.txt.gz


title: Plasma_exosomes_cancer_10

source_name: plasma exosome


title: plasma_without_exosomes_cancer_3

description: plasma_without_exosomes_cancer_DB374_L6_R1


title: E185_BP_KO_1

description:
mRNA
Forebrain BP at stage E185, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz


title: E175_BP_KO_1

description:
mRNA
Forebrain BP at stage E175, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz


title: Plasma_exosomes_cancer_9


title: Plasma_exosomes_cancer_8


title: E165_NBN_KO_1

description:
mRNA
Forebrain NBN at stage E165, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz


title: E165_BP_KO_3

description:
mRNA
Forebrain BP at stage E165, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz


title: Plasma_exosomes_cancer_7


title: E165_BP_KO_2

description:
mRNA
Forebrain BP at stage E165, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: Plasma_exosomes_cancer_5


title: E155_BP_KO_3

description:
mRNA
Forebrain BP at stage E155, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz


title: E155_NBN_KO_2

description:
mRNA
Forebrain NBN at stage E155, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: E165_BP_KO_1

description:
mRNA
Forebrain BP at stage E165, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz


title: Plasma_exosomes_cancer_4


title: Plasma_exosomes_cancer_1


title: Plasma_exosomes_cancer_2


title: E145_BP_KO_6

description:
mRNA
Forebrain BP at stage E145, replicate 6
processed data file: gene_tpm_BULK_KO.txt.gz


title: E145_BP_KO_5

description:
mRNA
Forebrain BP at stage E145, replicate 5
processed data file: gene_tpm_BULK_KO.txt.gz


title: Plasma_exosomes_granuloma_9


title: E155_BP_KO_2

description:
mRNA
Forebrain BP at stage E155, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: E145_BP_KO_3

description:
mRNA
Forebrain BP at stage E145, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz


title: Plasma_exosomes_granuloma_7


title: Plasma_exosomes_granuloma_8


title: Plasma_exosomes_granuloma_6


title: E145_BP_KO_2

description:
mRNA
Forebrain BP at stage E145, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: E145_BP_KO_1

description:
mRNA
Forebrain BP at stage E145, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz


title: Plasma_exosomes_granuloma_4


title: Plasma_exosomes_cancer_3


title: E135_BP_KO_2

description:
mRNA
Forebrain BP at stage E135, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: Plasma_exosomes_granuloma_3


title: E135_BP_KO_1

description:
mRNA
Forebrain BP at stage E135, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz


title: E135_BP_KO_3

description:
mRNA
Forebrain BP at stage E135, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz


title: E175_BP_KO_2

description:
mRNA
Forebrain BP at stage E175, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: E125_BP_KO_2

description:
mRNA
Forebrain BP at stage E125, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: E155_NBN_KO_3

description:
mRNA
Forebrain NBN at stage E155, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz


title: Plasma_exosomes_granuloma_2


title: E125_BP_KO_1

description:
mRNA
Forebrain BP at stage E125, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz


title: E145_BP_KO_4

description:
mRNA
Forebrain BP at stage E145, replicate 4
processed data file: gene_tpm_BULK_KO.txt.gz


title: Plasma_exosomes_granuloma_1


title: E155_BP_KO_1

description:
mRNA
Forebrain BP at stage E155, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz


title: E185_NSC_KO_3

description:
mRNA
Forebrain NSC at stage E185, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz

value: Neural stem cell


title: plasma_cancer_10

source_name: plasma


title: Raw264.7_wt_LPS_aH3K4me1_rep1

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

country: Germany

institute: TU München

library_source: genomic

data_processing:
Reads were aligned to the mouse mm10 (GRCm38.6) or Drosophila melanogaster dm6 (BDGP6 release 78) reference genome using BWA-MEM version 0.7.13 with default parameter settings.
PCR duplicates were removed using Picard Tools version 2.0.1.
Peaks  were  called  using  MACS2 version  2.1.1.20160309 in paired-end mode with a FDR threshold of 0.05.
Blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed from the called peaks.
Peaks were annotated to the closest TSS using the ChiPpeakAnno R package v3.18.2. (doi: 10.1186/1471-2105-11-237)
Genome_build: mm10, dm6
Supplementary_files_format_and_content: The .txt files containing the annotated peak positions called with MACS2. The .bw files contain coverage data for visualization in the genome browser.

molecule: genomic DNA

growth_protocol: Raw264.7 cells were kept at subconfluent conditions in DMEM (Gibco) supplemented with 10% FBS (heat inactivated, Sigma) and 1% penicillin/streptomycin (Gibco). Cells were cultured at 5% CO2 at 37°C in humified incubators. Medium was changed every other day.

extract_protocol:
For ChIP-Seq, 40 mio cells per sample or 20 mio cells in case of H3K4me1/me2/me3 were fixed as mentioned in the sample section either for 30 min in 2 mM DSG (#C1104 ProteoChem) and 10 min 1% MeOH-free formaldehye (#2890, ThermoFisher) or 10 min 1% formaldehyde at room temperature. Remaining formaldehyde was quenched with 150 uM glycin, cells collected and washed 2x in ice-cold D-PBS. Pellets were stored at -80°C until ChIP was performed. For ChIP-Seq nuclei were extracted in Fast-IP buffer (150 mM NaCl, 5 mM EDTA (pH=7.5), 5 mM Tris (pH=7.5), 1% Triton X-100, 0.5% NP40), chromatin sonicated in shearing buffer (1% SDS, 10 uM EDTA (pH=8),50 mM Tris (pH=8)) using the Bioruptor Pico (Diagenode) for 10-15 cycles (30s on/off) at high settings. Sonicated chromatin was diluted 1:10 in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 uM EDTA (pH= 8), 16.7 uM Tris (pH=8), 167 mM NaCl) and the immunoprecipitation against the protein of interest was performed over night at 4°C. Antigen-antibody complexes were captured with protein A/G Dynabeads (Life Techn. #11202D or #11204D), 5x washed in Fast-IP buffer. Reverse crosslink was performed overnight at 65°C and proteins degraded with 100 uM proteinase K. The DNA was puriefied using Quiagen PCR purification kit according to manufacture‘s manual (#28006).
Library preperation was performed from 2 ng of ChIP DNA using the Kapa Hyper Prep Kit with PCR library amplification (#KK8504, KapaBiosystems) according to the manufactur's protocol. Shortly, ChIP DNA was end-repaired and A-tailed before adapter ligation. After adapter ligation, the ChIP DNA was purified with Agencourt AMPure XP beads (#A63880, Beckman Coulter) and size-selected for 360-600 bp using the Pippin Prep System from Saga Science. The size-selected library is amplified by PCR using the Kapa Hyper Prep Kit (#KK8504,KapaBiosystems) and purified terminally with Agencourt AMPure XP beads (#A63880, Beckman Coulter).

treatment_protocol: Raw264.7 cells were either treated with 1 uM dexamethason (Dex, Sigma #D4902) or 0.1% EtOH (=vehicle) for 16 h followed by 3h treatment with 100 ng/ul LPS (Sigma #L2630).

tag: strain

value: Balb/c

value: male

value: wt

tag: spike-in

value: Drosophila melanogaster

value: 16h 0.1% EtOH, 3h 100ng/ul LPS

tag: fixation

value: 10min 1% FA

tag: antibody

value: rabbit polyclonal a-H3K4me1 Diagenode #C15410194


title: E185_NSC_KO_1

description:
mRNA
Forebrain NSC at stage E185, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz


title: Raw264.7_wt_LPS_aH3K4me1_rep2


title: plasma_cancer_8

value: cancer


title: plasma_cancer_7


title: E185_NSC_KO_2

description:
mRNA
Forebrain NSC at stage E185, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: Raw_Setd1aDel_6hIFNb1LPS_rep2

description:
Raw264_wtDel_Ifnb1LPSoverLPS_unfiltered_GEO.txt
MUC20642

data_processing:
Gene level quantification was performed with Salmon version 0.10.2 (https://combine-lab.github.io/salmon/). Settings:  -libType A, -gcBias, -biasSpeedSamp 5
Gene count normalization and differential expression analysis was performed with DESeq2 (doi: 10.1186/s13059-014-0550-8) version 1.22.0 (R version 3.6.0) after import of gene-level estimates with tximport (doi: 10.12688/f1000research.7563.1) in R.
For gene annotation Ensembl Transcript Ids were mapped to mgi_symbol using the Bioconductor package biomaRt (  doi:10.1093/bioinformatics/bti525) version 2.38 and information from Ensembl (GRCm38.p6)
Genome_build: mm10 (GRCm38.p6)
Supplementary_files_format_and_content: .txt file containing lenght normalized TPMs (transcripts per million) and log2FoldChanges, adjP and p-values for Dex+LPS over LPS treatment or for IFNb+LPS over LPS treatment as indicated in the file name.

molecule: polyA RNA

source_name: Raw264.7 cells

growth_protocol: Macrophages were differentiated from the bone marrow of wild-type male mice. Shortly femur and tibia were dissected from mice and the bone marrow flushed into Falcon tubes with RPMI (ThermoFisher Scientific). AKC lysis was performed to remove erythrocytes and cells seperated from tissue residues by Ficoll gradient (Ficoll-Paque Premium; GE Healthcare #17-5442-02 ). The isolated bone marrow-derived cells were differentiated in DMEM (4.5 g/l glucose, Sigma) containing 30% of supernatant from L929 cells (producing M-CSF and GM-CSF), 20% heat-inactivated FBS and 1% Pen/Strep for 7 days on non-tissue culture treated plates. The medium was changed after 3 days. After 7 days the differentiated macrophages were dissociated using Versene (ThermoFischer Scientific #15040066) at RT and seeded at 2 mio cells/6-well in serum-free conditions (macrophage-SFM medium (ThermoFisher Scientific #12065074)) for treatment and RNA isolation. Raw264.7 cells were kept at subconfluent level in DMEM (Gibco) with 10% FBS at 37°C and 5% CO2.

extract_protocol:
RNA was extracted using the Quiagen Rneasy Mini Kit (Quiagen #74106) according to manufacture's manual.The quality of the RNA was verified by Agilent 2100 Bioanalyzer with RNA 6000Nano Reagents (Agilent Technologies).
Library preparation and rRNA depletion was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to manufacture's manual. 500 ng RNA were used as input for each sample.

treatment_protocol: Differentiated macrophages were treated for 16h with 0.1% EtOH and 0.1% D-PBS (veh), 16h with 0.1% EtOH and 6h 100 ng/ul LPS (LPS) or 16h with 1 uM Dex and 6h 100 ng/ul LPS (Dex+LPS) . Raw264.7 cells were either treated for 16 h as mentioned for macrophages or treated for 6h with 0.1% EtOH and 0.1% D-PBS (veh), 6h with 0.1% EtOH and 6h 100 ng/ul LPS (LPS), 6h with 1 uM Dex and 6h 100 ng/ul LPS (Dex+LPS), 6h with 1 uM Dex (Dex) or 6h with 100 ng/ml LPS and 10 ng/ml IFNB1 (IFNb1LPS). Treatment and timing as given in the sample discription.

value: BALB/c

value: 6h 100 ng/ml LPS + 10 ng/ml IFNb1


title: Raw_Setd1aDel_6hIFNb1LPS_rep3

description:
Raw264_wtDel_Ifnb1LPSoverLPS_unfiltered_GEO.txt
MUC20643


title: Raw_Setd1aDel_6hIFNb1LPS_rep1

description:
Raw264_wtDel_Ifnb1LPSoverLPS_unfiltered_GEO.txt
MUC20641


title: Plasma_exosomes_granuloma_5


title: plasma_cancer_6


title: Raw_Setd1aDel_6hLPS_rep2

description:
Raw264_wtDel_Ifnb1LPSoverLPS_unfiltered_GEO.txt
MUC20630

value: 6h 100 ng/ml LPS


title: E175_NSC_KO_1

description:
mRNA
Forebrain NSC at stage E175, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz

value: Ski knock-out

value: Forebrain


title: E175_NSC_KO_2

description:
mRNA
Forebrain NSC at stage E175, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz

value: Female


title: Raw_Setd1aDel_6hLPS_rep1

description:
Raw264_wtDel_Ifnb1LPSoverLPS_unfiltered_GEO.txt
MUC20629


title: plasma_cancer_9


title: Raw_wt_6hIFNb1LPS_rep3

description:
Raw264_wtDel_Ifnb1LPSoverLPS_unfiltered_GEO.txt
MUC20619

value: Wild-type


title: E165_NSC_KO_2

description:
mRNA
Forebrain NSC at stage E165, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: Plasma_exosomes_cancer_6


title: plasma_cancer_3


title: plasma_cancer_1


title: Raw_wt_6hIFNb1LPS_rep1

description:
Raw264_wtDel_Ifnb1LPSoverLPS_unfiltered_GEO.txt
MUC20617


title: E165_NSC_KO_1

description:
mRNA
Forebrain NSC at stage E165, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz


title: E155_NSC_KO_3

description:
mRNA
Forebrain NSC at stage E155, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz


title: plasma_granuloma_9

value: granuloma


title: E175_NSC_KO_3

description:
mRNA
Forebrain NSC at stage E175, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz

value: Neural stem cell


title: Raw_wt_6hLPS_rep3

description:
Raw264_wtDel_Ifnb1LPSoverLPS_unfiltered_GEO.txt
MUC20607


title: plasma_cancer_5


title: plasma_granuloma_8


title: E155_NSC_KO_1

description:
mRNA
Forebrain NSC at stage E155, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz


title: Raw_Setd1aDel_6hLPS_rep3

description:
Raw264_wtDel_Ifnb1LPSoverLPS_unfiltered_GEO.txt
MUC20631


title: plasma_cancer_4


title: E155_NSC_KO_2

description:
mRNA
Forebrain NSC at stage E155, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: Raw_wt_6hIFNb1LPS_rep2

description:
Raw264_wtDel_Ifnb1LPSoverLPS_unfiltered_GEO.txt
MUC20618


title: Raw_wt_6hLPS_rep1

description:
Raw264_wtDel_Ifnb1LPSoverLPS_unfiltered_GEO.txt
MUC20605


title: E165_NSC_KO_3

description:
mRNA
Forebrain NSC at stage E165, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz


title: plasma_cancer_2


title: E145_NSC_KO_4

description:
mRNA
Forebrain NSC at stage E145, replicate 4
processed data file: gene_tpm_BULK_KO.txt.gz


title: replicate5_female

city: Stanford

first: Aaron

last: Gitler

state: California

address: Beckman Center

department: Genetics

institute: Stanford University

data_processing:
single-nucleus RNA seq analysis
illumina basecalling
10X cellranger (STAR alignment, UMI calls, etc)
Mitochondrial read removal (Seurat)
Read depth normalization (Seurat)
Batch correction by integration (Seurat)
PCA, graph-based clustering, and UMAP projection (Seurat)
Differential expression among clusters (Seurat, DEseq2 algorithm)
full analysis pipeline available as Jupyter-R notebook at github.com/neurojacob/blum_et_al_2020
Genome_build: mm10 (mm10-3.0.0-premrna)
Supplementary_files_format_and_content: .h5d expression matrices (output from cellranger) and CSV count files (output from Seurat integration, etc).

source_name: FACS-sorted mouse spinal cord nuclei

extract_protocol:
Transgenic reporter mice were aged to P100-150
Nuclei were extracted and purified (see methods), then sorted using FACS fluorescence for GFP reporter at 60/40 ratio.
Nuclei were encapsulated in droplets using the 10X V3 oligo-dT kit.
Libraries prepared according to manufacturer (10X) instructions for V3 library.

value: Chat-Cre;ROSAnT-nG

value: spinal cord


title: E145_NSC_KO_1

description:
mRNA
Forebrain NSC at stage E145, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz


title: E145_NSC_KO_2

description:
mRNA
Forebrain NSC at stage E145, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: plasma_granuloma_5


title: plasma_granuloma_4


title: E145_NSC_KO_3

description:
mRNA
Forebrain NSC at stage E145, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz


title: MR-7-d5-HSV-2

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v3.0.2)
sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v3.0.2)
barcode processing, Cell Ranger Single Cell Software Suite (v3.0.2)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v3.0.2)
alignment, Cell Ranger Single Cell Software Suite (v3.0.2)
Genome_build: mm10_and_HSV
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

source_name: Sorted live vaginal tissue

extract_protocol:
The vaginal tissues were harvested at 5 days post infection, live cells were sorted by FACS.
Libraries were prepared using the 10x genomics single cell v3 protocol.

treatment_protocol: WT C57BL/6 mice were treated with DMPA 5-7 days before infection, and infected with 10000 PFUs of HSV1-McKrae, HSV2-186 or PBS (mock).

value: Vagina

value: Wild type

tag: infection


title: Raw_wt_6hLPS_rep2

description:
Raw264_wtDel_Ifnb1LPSoverLPS_unfiltered_GEO.txt
MUC20606

value: male


title: E135_NSC_KO_3

description:
mRNA
Forebrain NSC at stage E135, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz


title: plasma_granuloma_7


title: plasma_granuloma_2


title: E135_NSC_KO_2

description:
mRNA
Forebrain NSC at stage E135, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: plasma_granuloma_3


title: MR-2-d5_HSV-1_2


title: MR-3-d3_HSV-1


title: Macrophages from a NASH liver, High_Fat diet

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v3.0.2)
sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v3.0.2)
barcode processing, Cell Ranger Single Cell Software Suite (v3.0.2)
single-cell 5′ gene counting , Cell Ranger Single Cell Software Suite (v3.0.2)
alignment, Cell Ranger Single Cell Software Suite (v3.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

source_name: macrophages from a NASH liver

extract_protocol:
Cell-barcoded cDNA was generated from single cells via an oligo-dT priming approach. Single cells were captured into droplets utilizing the 10X Chromium system.  A sequencing library was generated from the 3' fragments containing the barcode.
NovaSeq S4

value: NASH liver

value: macrophages


title: plasma_granuloma_1


title: MR-11-d1_HSV-2


title: plasma_granuloma_6


title: E125_NSC_KO_4

description:
mRNA
Forebrain NSC at stage E125, replicate 4
processed data file: gene_tpm_BULK_KO.txt.gz


title: E135_NSC_KO_1

description:
mRNA
Forebrain NSC at stage E135, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz


title: E125_NSC_KO_2

description:
mRNA
Forebrain NSC at stage E125, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: MR-1-mock

value: Mock


title: E115_NSC_KO_3

description:
mRNA
Forebrain NSC at stage E115, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz


title: E115_NSC_KO_2

description:
mRNA
Forebrain NSC at stage E115, replicate 2
processed data file: gene_tpm_BULK_KO.txt.gz


title: E125_NSC_KO_3

description:
mRNA
Forebrain NSC at stage E125, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz


title: MR-9-d3_HSV-2


title: E115_NSC_KO_1

description:
mRNA
Forebrain NSC at stage E115, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz


title: PN_NBN_WT_2

description:
mRNA
Forebrain NBN at stage PN, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz

data_processing:
Reads mapped to the transcriptome (GENCODE Release M2 GRCm38.p2) with kallisto 0.43.0 with option --single -l 200.0 -s 100.0 –pseudobam. Last option is to obtain pseudoalignments to transcriptome in BAM files.
The reads mapping to multiple transcripts are uniformly distributed.
Expression per transcript normalized by first dividing the number of reads mapping to each transcript by the length of the transcript in nucleotides and then transform the length-normalized read counts in transcript per million (TPM).
Gene expression was obtained by summing for each gene the TPM of the transcripts corresponding to the gene.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: gene_tpm_BULK_WT.txt: Tab-delimited text file, TPM table, genes in rows and samples in columns.

extract_protocol:
Total RNA was isolated from FAC-sorted GFP positive cells from Hes5::GFP and Tbr2::GFP transgenic lines using TRIzol reagent. A time course was performed with NSCs, BPs and NBNs isolated at each time point during development from E10.5 to postnatal day 1 (PN). Samples were analyzed for their integrity and concentration using Agilent 2100 Bioanalyzer and Quant-IT RiboGreen RNA Assay Kit. Sequencing libraries were prepared with the Illumina TruSeq RNA Library Prep Kit v2 according to Illumina’s instructions.
After quality control (Fragment Analyzer, AATI) libraries were pooled and loaded on an Illumina flow cell for cluster generation (HiSeq SR Cluster Kit v4 cBot). Libraries were sequenced SR50 on the HiSeq 2500 system (HiSeq SBS Kit V4) following the manufacturer’s protocols.

treatment_protocol: Dorsal cortices from embryonic day E10.5 to postnatal day 1 (PN) were micro-dissected and dissociated into single cell suspensions using Papain and Ovo-mucoid mix (Giachino et al, 2009). Cells were washed with L15 medium and FAC-sorted for GFP positive NSCs using FACSariaIII (BD Biosciences) derived from Hes5::GFP transgenic embryos for NSCs and Tbr2::GFP transgenic embryos for BPs and NBNs.

value: Newborn neuron


title: PN_NBN_WT_1

description:
mRNA
Forebrain NBN at stage PN, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: E125_NSC_KO_1

description:
mRNA
Forebrain NSC at stage E125, replicate 1
processed data file: gene_tpm_BULK_KO.txt.gz


title: E185_NBN_WT_3

description:
mRNA
Forebrain NBN at stage E185, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz


title: E185_NBN_WT_2

description:
mRNA
Forebrain NBN at stage E185, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz


title: E185_NBN_WT_1

description:
mRNA
Forebrain NBN at stage E185, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: E14_H3K4me3_1

city: Cologne

first: Giuliano

last: Crispatzu

address: Joseph-Stelzmann-Straße 26

department: CECAD

institute: University of Cologne (UoC), Germany

description: biological replicate 1

data_processing:
Library strategy: HiChIP
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools 1.2
Reads were mapped to the human (hg19), mouse (mm10) or chicken (galgal6) genome reference assembly using Bowtie2 within the HiC-Pro 2.10 framework.
Normalized bedGraph files were generated using hichipper 0.7.3 and DeepTools 2.5.7
Peaks were called using MACS2.1.1.20160309 and used  as input for loop calling by FitHiChIP 7.0
Valid pairs were converted using cooler 0.8.7 and the custom scripts within HiC-Pro 2.10, then loops were visualized with coolpup.py 0.9.2, hicexplorer 3.0 and HiCPlotter 0.8.1.
Genome_build: hg19, galGa6, mm10

source_name: WT E14 mESC

growth_protocol: 10cm plates were coated in 0.1% gelatine generally overnight. Cells (E14 WT, EED−/− and RING1a−/−RING1bfl/fl mESC) were thawed and resuspended in 10ml of medium (serum + LIF). Standard serum + LIF medium contained 500 mL Knock-out DMEM (Gibco 10829-018), 95 mL of filtered ES FBS (Gibco 16141-061), 5.9 mL of antibiotics (Hyclone SV30079.01), 5.9 mL Glutamax (Gibco 35050-038), 5.9 mL MEM NEAA (Gibco 11140-035), 4.7 mL titrated LIF (Miltenyi Biotec 130-095-777), and 1.3 mL Beta-mercaptoethanol 55 mM (Gibco 21985-023). Cells were split once (1/3 or 1/4) every two days. When they reached 80-100% confluence protein was extracted using the abcam cell nuclear protein preparation protocol for western blot. RNA was was extracted with 400ul (for 6wp) or 1 mL (for 10cm plates) of Lysis Solution RL (Guanidinium Thiocyanate; analytik jena), stored at -80°C or then purified using the innuPREP DNA/RNA Mini Kit (analytik jena) according to the manufacturer’s instructions, and reverse transcribed with ProtoScript II First Strand cDNA Synthesis Kit (E6560L, NEB). For RING1a−/−RING1bfl/fl mESC cells we added 1000x Tamoxifen (OHT) for 72h right after first passage. Floxed deletion was assessed after ChIP / HiChIP lysis in electrophoresis gel using flanking primers. Deleted protein was assessed via standard Western blot (using plate reader).

extract_protocol:
Fertilized chicken eggs (white leghorn; Gallus gallus domesticus) were obtained from a local breeder (LSL Rhein-Main) and incubated at 37°C and 80% humidity in a normal poultry egg incubator (Typenreihe Thermo-de-Lux). Following microsurgical procedures, the eggs were re-incubated until the embryos reached the desired developmental stages. The developmental progress was determined according to the staging system of HH (Hamburger and Hamilton, 1992). Mice were housed and bred under standard conditions in the CECAD ivRF. The breedings described were approved by the Landesamt für Natur, Umwelt, und Verbraucherschutz Nordrhein-Westfalen (LANUV), Germany (animal application 84-02.04.2015.A405). Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies againts the specific proteins of interest in each case.
HiChIP was performed as described by Mumbach et al. 2016 Nat Methods with some modifications. We generally replaced the ChIP protocol with the one described above, we cut and ligated overnight (NEB T4 Ligase, instead of Invitrogen T4) and DNA was extracted with phenol-chlorophorm not a kit. For low cell numbers, we increased the centrifugation time to 30 minutes and 15 minutes after lysis, as well as 30 minutes after ligation to see a pellet more accurately. Generally 12 cycles were used for Tn5 Nextera PCR amplification (Illumina Nextera DNA UD Indexes Kit). We aimed for 100M read pairs for each run on a NovaSeq 6000 sequencer (Illumina).

treatment_protocol: A full E14 WT 10cmp vial was thawed and resuspended in 10 mL of serum + LIF. The next day, cells were washed with PBS and medium was changed and the day after cells were split ¼. We began the differentiation the day after (d0). First, we trypsinized cells with 2mL TrypLE Express (Life technologies). After 5 minutes, Trypsin was quenched using 4 mL of serum + LIF. We then took 400ul for RNA extraction and the residual cells for differentiation. Both vials were centrifugated (750 and 1000 RPM respectively). Supernatant was discarded and cell pellet for RNA extraction was resuspended in Lysis Solution RL. The other vial was heavily resuspended in 5 mL of N2B27 with 0.1% of BSA (Life Technologies) and 0.1% of bFgf (Life Technologies) to get single cells. Cell resuspension and count was assessed using the BioRad TC20. We placed droplets of 15000 cells / cm2 in 10 mL of N2B27 with 0.1% of BSA and 10 ng/mL of bFgf. On d1 of differentiation, we changed medium (10 mL of N2B27 with 0.004% of BSA and 10 ng/mL bFgf) without PBS washing. On d2 of differentiation, we changed medium (10 mL of N2B27 with 0.004% of BSA, 10 ng/mL bFgf and 5 μM Xav939/Wnt inhibitor) without PBS washing. On d3 of differentiation, we changed medium (10 mL of N2B27 with 0.004% of BSA and 5 μM Xav939/Wnt inhibitor) without PBS washing. On d4 of differentiation, we changed medium (10 mL of N2B27 with 0.004% of BSA and 5 μM Xav939/Wnt inhibitor) without PBS washing. On the last day of differentiation (d5), we washed 1-2 with PBS (depending on amount of dead cells), resuspended plate in 5 mL of N2B27, scratched off cells, then extracted RNA and crosslinked these. Differentiation was assessed using RT-qPCR on a Light Cycler 480II comparing AntNPC d5 vs. E14 WT d0 relative gene expression levels (using the 2ΔCt method) with house keeping gene (Eef1a1), pluripotency markers (Pou5f1/Oct4 and Nanog), mesoderm marker (T) and ectoderm markers (Six3 and Lhx5). Standard deviations were calculated from technical triplicate reactions and were represented as error bars. Primers used can be found in the Supplemental Table.

value: WT E14 mESC

value: WT

tag: chip antibody

value: H3K4me3 (39159, Active Motif)


title: E14_H3K27me3_2

description: biological replicate 2

value: H3K27me3 (39155, Active Motif)


title: E175_NBN_WT_2

description:
mRNA
Forebrain NBN at stage E175, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz

value: Forebrain

value: Female


title: DNGC27_T3_1_D153N_15 2019 (D153N_15)

city: Strasbourg

first: Damien

last: GARCIA

address: 12 rue du Général Zimmer

country: France

institute: CNRS

description: Arabidopsis WT, ucn mutant line, overexpressor of UCND153N and vcs mutant. Seedlings grown on plates for 14 days.

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
read mapping with hisat2-2.1.0
read quantification
differential gene expression analysis with DEseq2 analysis (v1.24.0)
read quantification with htseq-count Seq-0.10.0
Genome_build: TAIR10

organism: Arabidopsis thaliana

extract_protocol:
TRIZOL
Lexogen SENSE mRNA-Seq Library Prep Kit

value: seedlings

value: 14 days

tag: background ecotype

value: Col0 accession

tag: batch


title: DNGC26_T3_1_D153N_14 2019 (D153N_14)

tag: tissue


title: E14_AntNPC_H3K4me3_1

description: biological replicate 1

source_name: WT E14 mESC → AntNPC

tag: treatment

value: E14 mESC differentiation into AntNPC


title: MR-6-d1_HSV-1

value: Vagina

value: HSV-1 McKrae


title: E175_NBN_WT_1

description:
mRNA
Forebrain NBN at stage E175, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz

value: Wild-type


title: E165_NBN_WT_3

description:
mRNA
Forebrain NBN at stage E165, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz


title: DNGC20_Col0_8 2019 (WT_8)


title: E14_AntNPC_H3K27ac_2

description: biological replicate 2

value: H3K27ac (39133, Active Motif)


title: E165_NBN_WT_1

description:
mRNA
Forebrain NBN at stage E165, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: DNGC19_Col0_7 2019 (WT_7)


title: E165_NBN_WT_2

description:
mRNA
Forebrain NBN at stage E165, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz


title: E14_AntNPC_H3K27ac_1

description: biological replicate 1


title: RING_H3K4me3_2

description: biological replicate 2

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools 1.2
Reads were mapped to the mouse (mm10) and chicken (galGal6) genome reference assembly using BWA 0.7.7 and PCR dupicates were removed using Picard-Tools 2.5.0
Normalized bedGraph files were generated using DeepTools 2.5.7
Peaks were called using MACS2.1.1.20160309
Genome_build: mm10, galGal6

source_name: RINGko/fl E14 mESC

extract_protocol:
Fertilized chicken eggs (white leghorn; Gallus gallus domesticus) were obtained from a local breeder (LSL Rhein-Main) and incubated at 37°C and 80% humidity in a normal poultry egg incubator (Typenreihe Thermo-de-Lux). Following microsurgical procedures, the eggs were re-incubated until the embryos reached the desired developmental stages. The developmental progress was determined according to the staging system of HH (Hamburger and Hamilton, 1992). Mice were housed and bred under standard conditions in the CECAD ivRF. The breedings described were approved by the Landesamt für Natur, Umwelt, und Verbraucherschutz Nordrhein-Westfalen (LANUV), Germany (animal application 84-02.04.2015.A405). Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies againts the specific proteins of interest in each case.
Cells were crosslinked in 1% of formaldehyde for 20 minutes (rotating at RT) with subsequent quenching by glycine (0.125M; rotating at RT). Washed twice with PBS and 25x Roche protease inhibitor. Then flash frozen in liquid nitrogen and stored at -80°C. Afterwards cells were thawed for ~30 minutes and lysed for 10 minutes at 4°C rotating in 50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40 and 0.25% TX-100 together with protease inhibitor (Lysis Buffer 1). After centrifugation for 5 min at 2000rcf at 4°C and discarding the supernatant, pellet was resuspended in 10 mM Tris, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, protease inhibitor (Lysis Buffer 2) and lysed for 10 minutes at 4°C rotating. After centrifugation for 5 min at 2000rcf at 4°C and discarding the supernatant, pellet was resuspended in 10 mM Tris, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate and 0.5% N-lauroylsarcosine with protease inhibitor (Lysis Buffer 3). Cells were then sonicated with ActiveMotif Sonicatior (amplitude: 25%, on=20s, off=30s, 20 cycles). Debris was then centrifugated for 10 minutes, 16000rcf at 4°C. Supernatant was resuspended with 10% Triton X-100 and 10% of mixture taken for input sample. 5 ul antibody (1 ng/ul) was added to sonicated chromatin aliquot for each ChIP reaction and inverted to mix. Then rotated vertically at 4°C overnight (12-16 hrs) to bind antibody to chromatin. On the next day, 50ul (for low cell numbers) or 75ul (for higher cell numbers) of magnetic Dynabeads (Protein G) were washed three times (3X) in 1 mL cold Block Solution (0.5% BSA (w/v), 1x PBS). Antibody-bound chromatin was added to beads and inverted to mix. Then rotated vertically at 4°C for at least 4 hrs. Afterwards bound beads were washed 5X in 1 mL cold RIPA buffer (50 mM Hepes, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). Then washed once in 1 mL TE + 50 mM NaCl on ice and centrifugated for 3 minutes at 1000rcf at 4°C to remove all remaining TE. 210 uL Elution Buffer was added to beads and DNA was eluted for 15 min at 65°C, 900 RPM, before centrifugating beads 1 min at 16000rcf at RT, adding to magnet and transferring supernatant (~200 uL) to fresh microfuge tube once beads settled. Both sample and input were then reverse crosslinked in appropriate amount of TE wash buffer, 20 mg/mL of RNAse, then Proteinase K, before extracting the DNA by phenol-chlorophorm. DNA content was measured using Qubit and the HS DNA Kit. Enrichment was measured using technical triplicates (input: 1%) by ChIP-qPCR with custom-made primers (Suppl.) on a Light Cycler 480II (Roche). All antibodies used in this study have been previously reported as suitable for ChIP: H3K4me3 (39159, Active Motif), H3K27ac (39133, Active Motif), H3K27me3 (39155, Active Motif).

value: E14 RING1a-/- mESC were treated for 72 hours with Tamoxifen to flox RING1b


title: DNGC21_Col0_9 2019 (WT_9)


title: Mice_epiblast_Input

description: input

source_name: Epiblast from E6.5 mice

value: Epiblast from E6.5 mice


title: DNGC17_vcs6_5 2019 (vcs6)

value: vcs


title: DNGC18_vcs6_6 2019 (vcs6)


title: Mice_epiblast_H3K27ac


title: E155_NBN_WT_4

description:
mRNA
Forebrain NBN at stage E155, replicate 4
processed data file: gene_tpm_BULK_WT.txt.gz

value: Newborn neuron


title: E155_NBN_WT_3

description:
mRNA
Forebrain NBN at stage E155, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz


title: K4me_EED_dKO

description: biological replicate 1

source_name: EEDko E14 mESC

value: WT E14 mESC


title: E155_NBN_WT_1

description:
mRNA
Forebrain NBN at stage E155, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: DNGC16_vcs6_4 2019 (vcs6)


title: E14_H3K27me3_1

description: biological replicate 1

value: WT


title: E155_NBN_WT_2

description:
mRNA
Forebrain NBN at stage E155, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz


title: DNGC15_Col0_3 2019 (WT_6)


title: K4me3_WT

value: H3K4me3 (39159, Active Motif)


title: PN_BP_WT_2

description:
mRNA
Forebrain BP at stage PN, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz

value: Forebrain

value: Basal progenitor


title: DNGC25_T3_1_D153N_13 2019 (D153N_13)

value: seedlings


title: DNGC13_Col0_1 2019 (WT_4)

value: 14 days


title: DNGC14_Col0_2 2019 (WT_5)

value: Col0 accession


title: Input_1_perc

description: input


title: PN_BP_WT_1

description:
mRNA
Forebrain BP at stage PN, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz

value: Female


title: E185_BP_WT_3

description:
mRNA
Forebrain BP at stage E185, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz


title: EED_H3K4me3_2

description: biological replicate 2


title: DNGC12_T3_5_DNE1_WT_GFP_I_3 2018 (DNE1OE2_3)

description: libraries prepared with the Lexogen kit: SENSE mRNA-Seq Library Prep Kit


title: E185_BP_WT_2

description:
mRNA
Forebrain BP at stage E185, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz


title: DNGC11_T3_2_DNE1_WT_GFP_D_3 2018 (DNE1OE1_3)


title: E185_BP_WT_1

description:
mRNA
Forebrain BP at stage E185, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: DNGC10_Salk132521_3 2018 (dne1_3)


title: AntNPC_H3K4me3

value: E14 mESC differentiation into AntNPC


title: AntNPC_CTCF

value: CTCF (61311, Active Motif)


title: E175_BP_WT_2

description:
mRNA
Forebrain BP at stage E175, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz

value: Wild-type


title: Mouse_E6.5_ATAC-seq_rep1

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools 1.2
Reads were mapped to the mouse (mm10) and chicken (galGal6) genome reference assembly using BWA 0.7.7 and PCR dupicates were removed using Picard-Tools 2.5.0
Normalized bedGraph files were generated using DeepTools 2.5.7
Peaks were called using MACS2.1.1.20160309
Genome_build: galGal6, mm10

source_name: Epiblast from E6.5 mice embryos

extract_protocol:
Fertilized chicken eggs (white leghorn; Gallus gallus domesticus) were obtained from a local breeder (LSL Rhein-Main) and incubated at 37°C and 80% humidity in a normal poultry egg incubator (Typenreihe Thermo-de-Lux). Following microsurgical procedures, the eggs were re-incubated until the embryos reached the desired developmental stages. The developmental progress was determined according to the staging system of HH (Hamburger and Hamilton, 1992). Mice were housed and bred under standard conditions in the CECAD ivRF. The breedings described were approved by the Landesamt für Natur, Umwelt, und Verbraucherschutz Nordrhein-Westfalen (LANUV), Germany (animal application 84-02.04.2015.A405).
Tissue were extracted and resuspended to single cell level. ATAC-seq was essentially conducted following Buenrostro et al. Nat Methods 2013. In short, single cells were centrifugated at 5000 g for 5 min and supernatant was removed. Cells were then lysed with 100 µl cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0,1% IGEPAL CA-630) substituted with 4 µl of protease inhibitor (1 tablet/2 mL conc.) for at least 15 minutes on ice. Immediately after lysis, nuclei were centrifugated at 6000 g for 10 minutes at 4°C. Pellet was resuspended in transposase reaction mix (25µl 2x TD buffer, 10 µl transposase (Illumina), 15 µl nuclease-free H2O) and incubated for 30 min at 37°C. Finally sample was purified using Qiagen MinElute PCR purification kit according to the manufacturer’s protocol.

value: Epiblast from E6.5 mice embryos

value: ATAC


title: DNGC9_Col0_3 2018 (WT_3)


title: Mouse_E6.5_ATAC-seq_gDNA

description: input


title: DNGC8_T3_5_DNE1_WT_GFP_I_2 2018 (DNE1OE2_2)


title: E175_BP_WT_1

description:
mRNA
Forebrain BP at stage E175, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: E165_BP_WT_3

description:
mRNA
Forebrain BP at stage E165, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz


title: Sample_139354: shRNA_5bp_rep4_miRNAseq

city: Ann Arbor

first: Michigan

middle: CDB

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

data_processing:
Sequencing/Basecalls/demultiplexing performed using Illumina NovaSeqControlSoftware 1.6.0 / RTA 3.4.4 / Bcl2fastq v2.20.0.422
Trimmed using Trim Galore 0.6.0 / Cutadapt 1.15 - minimum length changed to 18 bp
Aligned using miRDeep2 2.0.1.2 (using Bowtie 1.1.1) with options -e -h -i -j -l 18 -m to genome GRCm38.p6
miRDeep2 used to count and annotate from mirbase v22
Normalization (TMM), quantitation and differential expression analysis using EdgeR
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited file of counts from miRDeep2

source_name: Primary forebrain neuronal cultures

growth_protocol: Perinatal neuronal culture

extract_protocol:
TRIzol isolation + miRNeasy Purification
Samples were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (catalog number E7300L). Adapters were ligated to 100ng of total RNA which then goes through 1st Strand Synthesis and 15 cycles PCR amplification. The products are purified and size selected by Pippin Prep according to NEB protocol recommendations.  Final libraries were checked for quality and quantity by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (catalog # KK4835) (Kapa Biosystems,Wilmington MA)

treatment_protocol: Lentiviral vector transduction

value: Primary forebrain neuronal cultures


title: E165_BP_WT_2

description:
mRNA
Forebrain BP at stage E165, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz


title: DNGC6_Salk132521_2 2018 (dne1_2)


title: Sample_139353: shRNA_5bp_rep3_miRNAseq


title: K4me3_RING1A_dKO_OHT

description: biological replicate 1

value: E14 RING1a-/- mESC were treated for 72 hours with Tamoxifen to flox RING1b


title: E165_BP_WT_1

description:
mRNA
Forebrain BP at stage E165, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: DNGC5_Col0_2 2018 (WT_2)


title: Sample_139352: shRNA_5bp_rep2_miRNAseq


title: DNGC4_T3_5_DNE1_WT_GFP_I_1 2018 (DNE1OE2_1)


title: E155_BP_WT_3

description:
mRNA
Forebrain BP at stage E155, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz


title: Sample_139351: shRNA_5bp_rep1_miRNAseq


title: E175_BP_KO_3

description:
mRNA
Forebrain BP at stage E175, replicate 3
processed data file: gene_tpm_BULK_KO.txt.gz

value: Ski knock-out


title: Sample_139350: shRNA_2bp_rep4_miRNAseq


title: DNGC3_T3_2_DNE1_WT_GFP_D_1 2018 (DNE1OE1_1)


title: Sample_139349: shRNA_2bp_rep3_miRNAseq


title: Sample_139348: shRNA_2bp_rep2_miRNAseq


title: DNGC2_Salk132521_1 2018 (dne1_1)


title: DNGC1_Col0_1 2018 (WT_1)


title: DNGC7_T3_2_DNE1_WT_GFP_D_2 2018 (DNE1OE1_2)


title: Sample_139347: shRNA_2bp_rep1_miRNAseq


title: E155_BP_WT_1

description:
mRNA
Forebrain BP at stage E155, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: E145_BP_WT_3

description:
mRNA
Forebrain BP at stage E145, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz


title: Sample_139346: shRNA_rep4_miRNAseq

value: shRNA


title: Sample_139345: shRNA_rep3_miRNAseq


title: E135_BP_WT_3

description:
mRNA
Forebrain BP at stage E135, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz


title: Sample_139343: shRNA_rep1_miRNAseq


title: Sample_139344: shRNA_rep2_miRNAseq


title: E145_BP_WT_1

description:
mRNA
Forebrain BP at stage E145, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: Sample_139342: Empty_Vector_rep4_miRNAseq


title: E125_BP_WT_2

description:
mRNA
Forebrain BP at stage E125, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz


title: E155_BP_WT_4

description:
mRNA
Forebrain BP at stage E155, replicate 4
processed data file: gene_tpm_BULK_WT.txt.gz


title: Sample_139341: Empty_Vector_rep3_miRNAseq


title: Sample_139339: Empty_Vector_rep1_miRNAseq


title: E125_BP_WT_1

description:
mRNA
Forebrain BP at stage E125, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: E155_BP_WT_2

description:
mRNA
Forebrain BP at stage E155, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz


title: E125_BP_WT_3

description:
mRNA
Forebrain BP at stage E125, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz


title: Sample_139340: Empty_Vector_rep2_miRNAseq


title: Sample_139338: shRNA_5bp_rep4_RNAseq

data_processing:
Sequencing/Basecalls/demultiplexing performed using Illumina NovaSeqControlSoftware 1.6.0 / RTA 3.4.4 / Bcl2fastq v2.20.0.422
Trimmed using Trim Galore 0.6.0 / Cutadapt 1.15
Aligned to GRCm38 using STAR 2.7.2b and standard gencode options for the version
Count read using featureCounts function from Rsubread 1.34.6 and Ensembl GRCm38.p6/gencode.vM23.annotation.gtf as reference
Normalization (TMM), quantitation and differential expression analysis using EdgeR
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited file of counts after featureCounts command

extract_protocol:
TRIzol isolation + RNeasy Purification
Samples were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (catalog number E7760L) Ribo depletion Module NEBNext rRNA Human/Mouse/Rat (catalog number E6310X) and NEBNext Multiplex Oligos for Illumina Unique dual (catalog number E6440L) (NEB, Ipswitch, MA). Where 100ng of total RNA was ribosomal depleted using rRNA Depletion module. The rRNA-depleted RNA is then fragmented 10 minutes determined by RIN (RNA Integrity Number) of input RNA as per protocol, and copied into first strand cDNA using reverse transcriptase and dUTP mix. Samples undergo end repair and dA-Tailing step followed by ligation of NEBNext adapters. The products are purified and enriched by 12 cycles PCR to create the final cDNA library. Final libraries were checked for quality and quantity by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (catalog # KK4835) (Kapa Biosystems,Wilmington MA)


title: GFP-wt_R7

city: Beijing

first: Qikun

last: Liu

state: Beijing

address: Haidian District, 5 Yiheyuan Rd., Zonghekeyan BLDG, Rm 502

department: School of Advanced Agricultural Sciences

country: China

institute: Peking University

description:
mRNAseq, control for GFP-ddc_R1/R2/R3
SxaQSEQsYB069L8_index_19
processed data file:
gene_exp_ddc_wt_request4369.diff

data_processing:
Reads were aligned using TopHat v2.1.0 with default settings.
Gene expression differential analysis was performed using cufflinks v2.1.1.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each genes generated by Cuffdiff.

growth_protocol: long data condition. Plants were grown on soil.

extract_protocol:
RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)
1ug of total RNA was used to prepare libraries using the TrueSeq Stranded mRNA-Seq kit and Neoprep system (Illumina).

treatment_protocol: no treatment

tag: genotype/varaition

value: GFP-wt

value: inflorescence


title: Sample_139337: shRNA_5bp_rep3_RNAseq


title: PN_NSC_WT_2

description:
mRNA
Forebrain NSC at stage PN, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz

tag: strain/background

value: Forebrain

value: Neural stem cell


title: GFP-wt_R6

description:
mRNAseq, control for GFP-ddc_R1/R2/R3
SxaQSEQsYB069L8_index_18
processed data file:
gene_exp_ddc_wt_request4369.diff


title: PN_NSC_WT_1

description:
mRNA
Forebrain NSC at stage PN, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz

tag: isolate


title: PN_NSC_WT_3

description:
mRNA
Forebrain NSC at stage PN, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz

tag: genotype

value: Basal progenitor


title: Sample_139336: shRNA_5bp_rep2_RNAseq


title: GFP-wt_R5

description:
mRNAseq, control for GFP-ddc_R1/R2/R3
SxaQSEQsYB069L8_index_16
processed data file:
gene_exp_ddc_wt_request4369.diff


title: E135_BP_WT_2

description:
mRNA
Forebrain BP at stage E135, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz

tag: cell type


title: GFP-ddc_R3

description:
mRNAseq, control for GFP-ddc/med12 and GFP-ddc/med13
SxaQSEQsYB069L8_index_15
processed data file:
gene_exp_ddc_wt_request4369.diff

value: GFP-ddc


title: Sample_139335: shRNA_5bp_rep1_RNAseq


title: E135_BP_WT_1

description:
mRNA
Forebrain BP at stage E135, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz

tag: Sex


title: E185_NSC_WT_3

description:
mRNA
Forebrain NSC at stage E185, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz

tag: age


title: GFP-ddc_R2

description:
mRNAseq, control for GFP-ddc/med12 and GFP-ddc/med13
SxaQSEQsYB069L8_index_14
processed data file:
gene_exp_ddc_wt_request4369.diff


title: E185_NSC_WT_1

description:
mRNA
Forebrain NSC at stage E185, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: E185_NSC_WT_2

description:
mRNA
Forebrain NSC at stage E185, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz


title: E145_BP_WT_2

description:
mRNA
Forebrain BP at stage E145, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz


title: E175_NSC_WT_3

description:
mRNA
Forebrain NSC at stage E175, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz


title: Sample_139332: shRNA_2bp_rep2_RNAseq


title: GFP-ddc/med13_R3

description:
mRNAseq
SxaQSEQsYB069L8_index_12
processed data file:
gene_exp_ddcmed13_ddc_request4369.diff


title: GFP-ddc_R1

description:
mRNAseq, control for GFP-ddc/med12 and GFP-ddc/med13
SxaQSEQsYB069L8_index_13
processed data file:
gene_exp_ddc_wt_request4369.diff


title: E175_NSC_WT_2

description:
mRNA
Forebrain NSC at stage E175, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz


title: GFP-ddc/med13_R2

description:
mRNAseq
SxaQSEQsYB069L8_index_7
processed data file:
gene_exp_ddcmed13_ddc_request4369.diff


title: E175_NSC_WT_1

description:
mRNA
Forebrain NSC at stage E175, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: GFP-ddc/med13_R1

description:
mRNAseq
SxaQSEQsYB069L8_index_6
processed data file:
gene_exp_ddcmed13_ddc_request4369.diff


title: GFP-ddc/med12_R3

description:
mRNAseq
SxaQSEQsYB069L8_index_5
processed data file:
gene_exp_ddcmed12_ddc_request4369.diff


title: E165_NSC_WT_4

description:
mRNA
Forebrain NSC at stage E165, replicate 4
processed data file: gene_tpm_BULK_WT.txt.gz


title: E165_NSC_WT_3

description:
mRNA
Forebrain NSC at stage E165, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz


title: GFP-ddc/med12_R2

description:
mRNAseq
SxaQSEQsYB069L8_index_4
processed data file:
gene_exp_ddcmed12_ddc_request4369.diff


title: E165_NSC_WT_1

description:
mRNA
Forebrain NSC at stage E165, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: GFP-ddc/med12_R1

description:
mRNAseq
SxaQSEQsYB069L8_index_2
processed data file:
gene_exp_ddcmed12_ddc_request4369.diff


title: Sample_139326: Empty_Vector_rep4_RNAseq


title: Sample_139328: shRNA_rep2_RNAseq


title: Sample_139330: shRNA_rep4_RNAseq


title: E155_NSC_WT_4

description:
mRNA
Forebrain NSC at stage E155, replicate 4
processed data file: gene_tpm_BULK_WT.txt.gz


title: GFP-wt_R3

description:
mRNAseq, control for GFP-morc1_R4/R5/R6
SxaQSEQsYA044L4_index_22
processed data file:
gene_exp_morc_wt.diff

source_name: GFP-wt_rosette leaves

tag: developmental stage

value: 3-week old

value: rosette leaves


title: Sample_139324: Empty_Vector_rep2_RNAseq


title: GFP-morc1_R6

description:
mRNAseq, control for GFP-morc1/med13_R1/R2/R3
SxaQSEQsYA044L4_index_16
processed data file:
gene_exp_med13morc_morc.diff

source_name: GFP-morc1_rosette leaves


title: Sample_139323: Empty_Vector_rep1_RNAseq


title: Sample_139333: shRNA_2bp_rep3_RNAseq


title: E155_NSC_WT_3

description:
mRNA
Forebrain NSC at stage E155, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz

value: Female


title: GFP-morc1_R5

description:
mRNAseq, control for GFP-morc1/med13_R1/R2/R3
SxaQSEQsYA044L4_index_9
processed data file:
gene_exp_med13morc_morc.diff


title: Sample_139334: shRNA_2bp_rep4_RNAseq


title: E155_NSC_WT_1

description:
mRNA
Forebrain NSC at stage E155, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: E155_NSC_WT_2

description:
mRNA
Forebrain NSC at stage E155, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz


title: E145_NSC_WT_3

description:
mRNA
Forebrain NSC at stage E145, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz


title: Sample_139329: shRNA_rep3_RNAseq


title: GFP-morc1_R4

description:
mRNAseq, control for GFP-morc1/med13_R1/R2/R3
SxaQSEQsYA044L4_index_3
processed data file:
gene_exp_med13morc_morc.diff


title: E145_NSC_WT_2

description:
mRNA
Forebrain NSC at stage E145, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz


title: AAV9-anti-miR-199a TuDs replicate-2

city: Chengdu

first: Hualin

last: Yan

state: Sichuan

address: No.37, Guoxuexiang,

institute: West China Hospital, Sichuan University

data_processing:
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)  and index codes were added to attribute sequences to each sample.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample.

source_name: myocardium

extract_protocol:
The hearts were frozen in liquid nitrogen and stored at -80°C.Total RNA was extracted from cardiac samples using Total RNA Kit II (Omega, Norcross, GA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: strain

value: myocardium

value: 18 weeks

value: wild type

value: AAV9-anti-miR-199a TuDs


title: GFP-wt_R4

description:
mRNAseq, control for GFP-morc1_R4/R5/R6
SxaQSEQsYA044L4_index_27
processed data file:
gene_exp_morc_wt.diff


title: Ctrl AAV9-EGFP replicate-3

value: Ctrl AAV9-EGFP


title: AAV9-anti-miR-199a TuDs replicate-1


title: Ctrl AAV9-EGFP replicate-2


title: E135_NSC_WT_4

description:
mRNA
Forebrain NSC at stage E135, replicate 4
processed data file: gene_tpm_BULK_WT.txt.gz

source_name: dorsal cerebral cortex

value: Wild-type


title: GFP-morc1/med13_R1

description:
mRNAseq
SxaQSEQsYA044L4_index_2
processed data file:
gene_exp_med13morc_morc.diff

source_name: GFP-morc1/med13_rosette leaves


title: E145_NSC_WT_1

description:
mRNA
Forebrain NSC at stage E145, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: GFP-wt_R1

description:
mRNAseq, control for GFP-morc1_R1/R2/R3
SxaQSEQsYA044L4_index_19
processed data file:
gene_exp_morc_wt.diff


title: GFP-wt_R2

description:
mRNAseq, control for GFP-morc1_R1/R2/R3
SxaQSEQsYA044L4_index_21
processed data file:
gene_exp_morc_wt.diff


title: E135_NSC_WT_2

description:
mRNA
Forebrain NSC at stage E135, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz


title: GFP-morc1/med13_R2

description:
mRNAseq
SxaQSEQsYA044L4_index_4
processed data file:
gene_exp_med13morc_morc.diff


title: GFP-morc1_R3

description:
mRNAseq, control for GFP-morc1/med12_R1/R2/R3
SxaQSEQsYA044L4_index_15
processed data file:
gene_exp_med12morc_morc.diff


title: AAV9-anti-miR-199a TuDs replicate-3


title: GFP-morc1_R2

description:
mRNAseq, control for GFP-morc1/med12_R1/R2/R3
SxaQSEQsYA044L4_index_14
processed data file:
gene_exp_med12morc_morc.diff


title: E135_NSC_WT_1

description:
mRNA
Forebrain NSC at stage E135, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: Sample_139327: shRNA_rep1_RNAseq

value: Primary forebrain neuronal cultures


title: Ctrl AAV9-EGFP replicate-1


title: GFP-morc1_R1

description:
mRNAseq, control for GFP-morc1/med12_R1/R2/R3
SxaQSEQsYA044L4_index_5
processed data file:
gene_exp_med12morc_morc.diff


title: E125_NSC_WT_2

description:
mRNA
Forebrain NSC at stage E125, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz


title: Abdominal aorta PSGL-1 KO (DOCA+HS)5

city: Beijng

first: Xianxian

last: Wu

address: 5 Panjiayuan Nanli Chaoyang District

institute: Institute of laboratory animal sciences, CAMS, PUMC

description: PSGL-1 KO (DOCA+HS)5

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Abdominal aorta

extract_protocol:
Abdominal aortas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Abdominal aorta

value: 10 month old


title: GFP-morc1/med12_R3

description:
mRNAseq
SxaQSEQsYA044L4_index_13
processed data file:
gene_exp_med12morc_morc.diff

source_name: GFP-morc1/med12_rosette leaves


title: E125_NSC_WT_1

description:
mRNA
Forebrain NSC at stage E125, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: Abdominal aorta PSGL-1 KO (DOCA+HS)4

description: PSGL-1 KO (DOCA+HS)4


title: GFP-morc1/med13_R3

description:
mRNAseq
SxaQSEQsYA044L4_index_7
processed data file:
gene_exp_med13morc_morc.diff


title: GFP-morc1/med12_R2

description:
mRNAseq
SxaQSEQsYA044L4_index_12
processed data file:
gene_exp_med12morc_morc.diff


title: E115_NSC_WT_3

description:
mRNA
Forebrain NSC at stage E115, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz


title: GFP-morc1/med12_R1

description:
mRNAseq
SxaQSEQsYA044L4_index_6
processed data file:
gene_exp_med12morc_morc.diff


title: E115_NSC_WT_2

description:
mRNA
Forebrain NSC at stage E115, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz


title: Abdominal aorta PSGL-1 KO (DOCA+HS)3

description: PSGL-1 KO (DOCA+HS)3


title: E135_NSC_WT_3

description:
mRNA
Forebrain NSC at stage E135, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz


title: Abdominal aorta PSGL-1 KO (DOCA+HS)2

description: PSGL-1 KO (DOCA+HS)2


title: E125_NSC_WT_3

description:
mRNA
Forebrain NSC at stage E125, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz


title: Abdominal aorta PSGL-1 KO (DOCA+HS)1

description: PSGL-1 KO (DOCA+HS)1


title: E105_NSC_WT_3

description:
mRNA
Forebrain NSC at stage E105, replicate 3
processed data file: gene_tpm_BULK_WT.txt.gz


title: E115_NSC_WT_1

description:
mRNA
Forebrain NSC at stage E115, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz


title: Abdominal aorta WT(DOCA+HS)2


title: med13(gct-2)_R1_lane2

description:
mRNAseq, sequenced on lane2
SxaQSEQsYB024L4_index_15
processed data file:
gene_exp_med13_wt.diff

source_name: med13(gct-2)_rosette leaves


title: med12(cct-2)_R4_lane2

description:
mRNAseq, sequenced on lane2
SxaQSEQsYB024L4_index_14
processed data file:
gene_exp_med12_wt.diff

source_name: med12(cct-2)_rosette leaves


title: Abdominal aorta WT(DOCA+HS)1


title: med12(cct-2)_R3_lane2

description:
mRNAseq, sequenced on lane2
SxaQSEQsYB024L4_index_12
processed data file:
gene_exp_med12_wt.diff


title: Hsh-B

city: Nanjing

first: Xiannan

last: Meng

address: Hankou Road 22

institute: Nanjing University

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
The reference genomes and the annotation file were downloaded from MM10. Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Mapping reads to mature miRNA and hairping which recorded in miRBase (release 21) to identiy known-miRNA. After excluded the reads mapped to known miRNA/ncRNA/repeat region/mRNA region, the remaining reads were used to predict novel miRNA, the keys of prediction is hairping structure and stability. The software for identification and prediction is miRDeep2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: sperm

extract_protocol:
Sperm were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent.NEBNext® Ultra™ RNA Library Prep Kit for Illumina®（ #E7530L， NEB） was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina

value: Balb/c

value: post natal month 8

tag: shRNA

value: Hsp90aa1 shRNA


title: med12(cct-2)_R2_lane2

description:
mRNAseq, sequenced on lane2
SxaQSEQsYB024L4_index_6
processed data file:
gene_exp_med12_wt.diff


title: Abdominal aorta WT5


title: Sample_139331: shRNA_2bp_rep1_RNAseq


title: Abdominal aorta WT4


title: med13(gct-2)_R2_lane2

description:
mRNAseq, sequenced on lane2
SxaQSEQsYB024L4_index_19
processed data file:
gene_exp_med13_wt.diff


title: Abdominal aorta WT(DOCA+HS)3


title: med12(cct-2)_R1_lane2

description:
mRNAseq, sequenced on lane2
SxaQSEQsYB024L4_index_5
processed data file:
gene_exp_med12_wt.diff


title: Abdominal aorta WT3


title: NC-B

value: negative control


title: E105_NSC_WT_1

description:
mRNA
Forebrain NSC at stage E105, replicate 1
processed data file: gene_tpm_BULK_WT.txt.gz

value: Forebrain

value: Neural stem cell


title: Columbia-0_R3_lane2

description:
mRNAseq, sequenced on lane2, control for med12(cct-2) and med13(gct-2)
SxaQSEQsYB024L4_index_20
processed data file:
gene_exp_med12_wt.diff, gene_exp_med13_wt.diff

source_name: Columbia-0_rosette leaves

value: 3-week old

value: rosette leaves


title: NC-A


title: MC-B

tag: agent

value: MC-LR-exposure


title: Columbia-0_R2_lane2

description:
mRNAseq, sequenced on lane2, control for med12(cct-2) and med13(gct-2)
SxaQSEQsYB024L4_index_10
processed data file:
gene_exp_med12_wt.diff, gene_exp_med13_wt.diff


title: med13(gct-2)_R3_lane2

description:
mRNAseq, sequenced on lane2
SxaQSEQsYB024L4_index_21
processed data file:
gene_exp_med13_wt.diff


title: Columbia-0_R1_lane2

description:
mRNAseq, sequenced on lane2, control for med12(cct-2) and med13(gct-2)
SxaQSEQsYB024L4_index_1
processed data file:
gene_exp_med12_wt.diff, gene_exp_med13_wt.diff


title: Abdominal aorta WT1


title: MC-A


title: Lgr5-2A-DTR 2

city: Singapore

first: Si Hui

last: Tan

address: 8A Biomedical Grove #06-06 Immunos

country: Singapore

institute: Institute of Medical Biology

data_processing:
FASTQ files containing the RNA-Seq reads were checked for quality control issues using FASTQC and MultiQC for which no issues were found.
The reads were then mapped to the mouse genome build mm10 using STAR based on GENCODE M22 annotations.
Gene counts were counted using featureCounts (part of the Subread package) based on GENCODE M22 annotations.
The gene counts were then used in edgeR for a differential expression of genes (DEG) analysis comparing DTR and WT samples with multiple testing correction done using the method of Benjamini and Hochberg.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM

source_name: small intestine

extract_protocol:
Whole small intestines were lysed in Trizol (Qiagen). RNA was subsequently isolated with RNeasy Universal Plus kit (Qiagen) and cDNA was generated with Superscript III (Life Technologies) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Adult mice (>8 weeks old) were injected with 20ug DT/kg daily for 4 days, and harvested 6 hours after the last DT dose

value: Diphtheria Toxin


title: Lgr5-2A-DTR 3


title: med13(gct-2)_R3_lane1

description:
mRNAseq, sequenced on lane1
SxaQSEQsYB024L3_index_21
processed data file:
gene_exp_med13_wt.diff


title: Abdominal aorta WT2


title: E105_NSC_WT_2

description:
mRNA
Forebrain NSC at stage E105, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz

value: Female


title: Con-B

value: control


title: Con-A


title: Lgr5-2A-DTR 1


title: med13(gct-2)_R1_lane1

description:
mRNAseq, sequenced on lane1
SxaQSEQsYB024L3_index_15
processed data file:
gene_exp_med13_wt.diff


title: Tet2+/+ KitD816V , Rep2 [11pos]

city: MARSEILLE

first: erinn

last: soucie

address: 27 Boulevard Lei Roure

institute: CRCM

data_processing:
Sequencing quality control was done with FastQC v.0.10.1.
Reads were mapped with the TopHat v2.0.11 software to the UCSC mouse (mm10) or human (GRCh38/hg38) reference genome, with on average 20 million aligned reads/sample (mouse, 25 million human).
Biological quality control and summarization were done with RSeQC v2.4, PicardTools v1.92 and SamTools v0.1.18 respectively.
Read coverages were determined to be uniform and the percentage of mRNA bases was on average 64%. The percentage of ribosomal bases was less than 5%.
The count data, prepared with HTSeq v.0.6.1p1 (htseq-count, default parameters).
The raw count data are filtered. We filtered out very lowly expressed genes, keeping genes that are expressed at a reasonable level. Since the group size average is 2, we kept genes that achieved 10 counts in at least 2 samples: genes 23,420 – 11,821 = 11,599 expression values for each sample- ~49% (mouse); 23,710- 14,298 = 9,412 - ~40% (human).
The normalization and differential expression analysis was performed with the R/Bioconductor edgeR package v.3.4.2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include raw and normalized counts for all samples

source_name: Tet2+/+ KitD816V

growth_protocol: Primary mast cells were derived from bone marrow of either Tet2+/+ or Tet2-/- C57BL/6J Tet2LacZ

extract_protocol:
RNA was isolated from sorted cell fractions using the RNAeasyPlus kit (Qiagen) for sequencing
8- indexed libraries were prepared using the Illumina TrueSeq protocol following ribodepletion and 100 single-end reads were run on a HiSeq2500 from Illumina

treatment_protocol: mice, isolated and cultured in OptiMEM/10% FCS (Life Technologies) media supplemented with 10 ng/ml IL3 (Peprotech), 50ug/ml Penicillin/streptomycin, and 1% beta-mercaptoethanol (both Life Technologies) on tissue culture treated plastic, at 37°C, 5% CO2. Non-adherent cells were selected for 15 days under these conditions, at which point cultures were infected with lenti-virus carrying the KitD816V allele and GFP (ires). For infection, we used a single 2h spinoculation in the presence of 6μg/ml polybrene. Infected cells were further expanded for 15 days, for a total of 30 days of in vitro culture, and then GFP-negative and positive fractions (cultures were 40-80% GFP-positive) were FACS sorted on FACSAria using DIVATM (Becton- Dickinson) software for direct lysis and RNA isolation.

value: C57BL/6J Tet2LacZ

tag: genotype/variation

value: Tet2+/+ KitD816V

value: Primary murine mast cells derived from bone marrow


title: med12(cct-2)_R4_lane1

description:
mRNAseq, sequenced on lane1
SxaQSEQsYB024L3_index_14
processed data file:
gene_exp_med12_wt.diff


title: WT3

value: Wildtype


title: Tet2+/+ KitD816V , Rep1 [9pos]


title: WT2


title: med12(cct-2)_R3_lane1

description:
mRNAseq, sequenced on lane1
SxaQSEQsYB024L3_index_12
processed data file:
gene_exp_med12_wt.diff


title: Tet2+/+ control, Rep2 [11neg]

source_name: Tet2+/+ control


title: WT1


title: med12(cct-2)_R2_lane1

description:
mRNAseq, sequenced on lane1
SxaQSEQsYB024L3_index_6
processed data file:
gene_exp_med12_wt.diff


title: Tet2+/+ control, Rep1 [9neg]


title: Tet2-/- KitD816V , rep2 [15pos]

source_name: Tet2-/- KitD816V

value: Tet2-/- KitD816V


title: med12(cct-2)_R1_lane1

description:
mRNAseq, sequenced on lane1
SxaQSEQsYB024L3_index_5
processed data file:
gene_exp_med12_wt.diff


title: ext_L17951-1_hom

city: Bonn

first: Peter

last: Krawitz

address: Venusberg-Campus 1

institute: University Hospital Bonn

data_processing:
Filtering, mapping and gene expression quantification using zUMIs v2.5.6
Filtering and normalization using Seurat v3.0.0 with sctransfrom normalization approach
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix tables (csv) with filtered and normalized (sctransformed) single-cell gene expression values

source_name: hippocampus

extract_protocol:
Hippocampal cells were mechanically dissociated from 8 hippocampi (n=4) per genotype at 4°C and directly used for librabry preparation.
From the prepared single-cell suspensions sequencing libraries were generated using the Chromium Single-cell Gene Expression Solution v3 (10X Genomics, Inc.), according to manufacturer's protocol and sequenced with the Illumina NovaSeq 6000.

value: Pigv341Ehomozygous knock-in

value: hippocampus


title: ext_L17950-1_wt

value: wild-type control


title: med13(gct-2)_R2_lane1

description:
mRNAseq, sequenced on lane1
SxaQSEQsYB024L3_index_19
processed data file:
gene_exp_med13_wt.diff


title: Tet2-/- KitD816V , Rep1 [6pos]


title: Columbia-0_R2_lane1

description:
mRNAseq, sequenced on lane1, control for med12(cct-2) and med13(gct-2)
SxaQSEQsYB024L3_index_10
processed data file:
gene_exp_med12_wt.diff, gene_exp_med13_wt.diff


title: Tet2-/- control, Rep2 [15neg]

source_name: Tet2-/- control


title: Columbia-0_R1_lane1

description:
mRNAseq, sequenced on lane1, control for med12(cct-2) and med13(gct-2)
SxaQSEQsYB024L3_index_1
processed data file:
gene_exp_med12_wt.diff, gene_exp_med13_wt.diff


title: RNASeq_S2.hs.rep2

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

description: Replica 2

data_processing:
Base calling and quality control were performed in real time with standard Illumina analysis pipeline using a phiX control.
Sequenced reads were trimmed from low quality and/or short sequences by trimmomatic v. 0.36 using the following options: LEADING:18 TRAILING:18 SLIDINGWINDOW:4:22 MINLEN:20
Trimmed reads were mapped to BDGP6.22.96 D.melanogaster genome by STAR aligner 2.6.1c with dm6 ENSEMBLE genome map v.98 ftp://ftp.ensembl.org/pub/release-98/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.22.98.gtf.gz. Alignment options were the following:  --outSAMtype BAM SortedByCoordinate --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM --twopassMode Basic
Wig files with unique mappings from each replica and strand were converted to bigWig by wigToBigWig tool from UCSC Kent Utilities http://hgdownload.soe.ucsc.edu/admin/exe/ and then averaged by wiggletools 1.2 with the following options: wiggletools write_bg rnaseq.str1.mean.bedGraph mean rnaseq.rep1.str1.bw rnaseq.rep2.str1.bw. The files with mean expression signal for each strand were then converted to bigWig by bedGraphToBigWig tool from UCSC Kent utilities.
Trimmed reads were quantified to dm6 BDGP6.22 genome with ENSEMBLE genome map v.98 by RSEM 1.3.1 using the following options: rsem-calculate-expression --star --output-genome-bam --calc-ci --num-threads 10 --ci-memory 4096 --star-gzipped-read-file. This operation was performed for both replicas separately and both replicas simultaneously.
genome build: Drosophila melanogaster dm6/BDGP6.22.96 genome build. Drosophila melanogaster dm6/BDGP6.22.98 ENSEMBL annotation in GTF format.
processed data files format and content: bigWig files contain normalized (RPM, reads per million) expression signal genomewide for each strand. Results files contain quantified expression values in TPM (Transcripts Per Million) and FPKM (Fragments Per Kilobase Million) for each gene.

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were grown in DMEM with 10% FBS in a humidified incubator at 27°C and 5% CO2 to 80% confluency.

extract_protocol:
Total RNA was extracted from cell lysed with Trisol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA Quality was checked with  BioAnalyser and  RNA 6000 Nano Kit(Agilent). Poly(A)+ RNA was isolated with Dynabeads® mRNA Purification Kit (Ambion).
Poly(A)+ RNA was isolated with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length.

treatment_protocol: RNA-Seq procedure was used for analysis of expression in S2 cells. Heat shock treatment was performed for 1 h at 37°C. Then heat-shock treated S2 cells were incubated for 1 h at 27°C. Then cells of each replicate were separately lysed with Trizol reagent (Invotrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with  BioAnalyser and  RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 10 millions of reads were generated for each sample.

value: late embryo

value: wild type

tag: stress

value: heatshock


title: Columbia-0_R3_lane1

description:
mRNAseq, sequenced on lane1, control for med12(cct-2) and med13(gct-2)
SxaQSEQsYB024L3_index_20
processed data file:
gene_exp_med12_wt.diff, gene_exp_med13_wt.diff

value: 3-week old


title: 4C_DM_HS-.rep1

description: Replica 1

data_processing:
Base calling and quality control were performed in real time with standard Illumina analysis pipeline using a phiX control.
Sequenced reads were trimmed for adaptor sequences and low quality sequences by cutadapt v. 1.16 using the following options: cutadapt --trim-n --times=5 --minimum-length 20 -q 26 -e 0.15 -g ACTGTTCACGATGAACTTG -g TTCAGTTCACAATCCCAAG -a CTTGGGATTGTGAACTGAA -a CAAGTTCATCGTGAACAGT
Trimmed reads were mapped to dm6.BDGP6.22.96 genome by bwa 0.7.12-r1039 using the mem algorithm. All non-aligned reads were removed from resulting alignment file by samtools 1.6: -b -S -F 4 -@ 10 allalign.sam > aligned.bam
Mapping and alignment results were converted to resulting tables using samtools 1.6 and ad hoc Perl scripts.
Each replica results table was converted to bedGraph file for further processing using reads amount as data value. Intersection file was built by bedtools v. 2.27.1 with the following command line: bedtools intersect -a 4C_dm0.rep1.bedGraph -b 4C_dm0.rep2.bedGraph -wb. Ad hoc Perl script was used to convert bedtools output file back to bedGraph file with averaging in the overlapped regions.
Intersection file was filtered from low complexity regions and transposable elements from the DFAM database by bedtools v. 2.27.1 with the following command line: bedtools intersect -sorted -v -f 1.0 -a 4C_dm0.intersect.bedGraph -b dm6_dfam.hits.bed > 4C_dm0.intersect.hc.bedGraph and ad hoc Perl script.
genome build: Drosophila melanogaster dm6/BDGP.6.22.96 genome build
processed data files format and content: Tab-delimited text file include the following features of each mapping: begin, end, length, coverage, number of reads, sequence. bedGraph files for each replica and intersection are supplied too.

growth_protocol: S2 cells were grown in GIBCO Drosophila medium with 10% FBS in a humidified incubator at 25°C to 80% confluency.

extract_protocol:
DNA samples were prepared as described before (Dekker et al., 2002; Osborne et al., 2004; http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=3978).  Cross-linking: To suspension containing about 34x106 S2 cells in 4 ml of the GIBCO medium formaldehyde solution was added to final concentration 1.5%. After mixing incubation of cell suspension was performed for 10 min at room temperature with mixing. The quenching with 2.75 ml of 2M glycin (final concentration 0.125M) was performed. After incubation at room temperature for 5 min the suspension was cooled for 15 min in ice bath and then cells were collected by centrifugation for 15 min at 3500 rpm at +2°C.  Lysis: The pellet of cells was resuspended at °C in 1ml of buffer containing 10 mM tris-HCl buffer, pH 8, 10 mM NaCl, 0.2% NP-40 and freshly added protease inhibitors – 0.1 mM PMSF and 1:500 protease inhibitor cocktail (Sigma). After incubation for 15 min cells were homogenized by passing through insulin syringe about 50 times into Eppendorf. Then nuclei were spin down by centrifugation for 5 min at 5000 rpm in Eppendorf centrifuge 5415 R at +2°C.  Digestion with EcoRI: The nuclei pellet was resuspended in 756 microl of solution containing 40 mM tris-HCl buffer, pH 7.4, 50 mM NaCl, 10 mM MgCl2 and 10 mM 2-mercaptoethanol. Then 20% SDS was added to final concentration 0.3% and incubation with shaking was performed for 1 h at +37°C. To sequester SDS 180 l of 10% Triton X-100 was added and the incubation for 1 h at +37°C was performed. Before digestion 1 l of BSA (5 mg/ml) was added with mixing. Then 50 l of EcoRI (10 u/l) was added and after mixing digestion was performed overnight at +37°C.   Ligation: To inactivate the restriction enzyme, 35 l of 20% SDS was added (final concentration 0.7%) and the probe was heated to 65°C for 30 min. Then the mixture was transferred into 15 ml Nunc tube and consequently 375 l of 20% Triton X-100 (to final concentration 1%), 750 l of 10x ligase buffer, 7,5 l of BSA (5 mg/ml), 80 l of 100 mM ATP, and 5241 l of milliQ water  were added and the final 7.5 ml solution was well mixed. Then 10 l of T4 DNA ligase (200 u/l) was added and after mixing incubation was performed for 5 h at +16°C and then for 30 min at room temperature. Usually during ligation DNA concentration was equal to 2 ng/l.    DNA purification: For isolation of DNA 50 l of proteinase K (10 mg/ml) was added (final concentration 50 g/ml) and after mixing incubation was performed at 55°C B1overnight. For RNA digestion 40 l of RNase A (10 mg/ml) was added (final concentration 0.5 g/ml) and after mixing incubation was performed for 30 min at +37°C. After extensive extraction with phenol-chloroform extraction (three times with 7 ml each) DNA was precipitated by 2.5 vol. of ethanol after addition of 40 l 10 mg/ml glycogen and 175 l 4M NaCl. The final DNA pellet was washed twice with 70% ethanol and then dissolved in 0.1xTE.   Digestion with FaeI: About 15 g of DNA was digested in 250 microl solution with 75 u of FaeI overnight at +37°C. Then the enzyme was inactivated by heating at 65°C for 30 min. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 100l of 0.1xTE.   Ligation: For circularization 15 g of DNA was incubated in 8 ml of T4 DNA ligase buffer containing 400 u of T4 DNA ligase for 5 h at +16°C. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 50 l of 0.1xTE.
One  round of  PCR was used as described below. The following primers were used: 5' ACTGTTCACGATGAACTTGGAATT 3' and 5' TTCAGTTCACAATCCCAAGCATG 3'. PCR products were purified using QIAqiuck PCR purification kit kit (Quigen). The libraries were prepared using TruSeq RNA Sample Preparation Kit v2 (Illumina). The samples were sequenced using HiSeq 1500 (Illumina) following the manufacturer's protocols.


title: RNASeq_S2.rep2

description: Replica 2


title: 4C_DM_HS+.rep1

description: Replica 1

data_processing:
Base calling and quality control were performed in real time with standard Illumina analysis pipeline using a phiX control.
Sequenced reads were trimmed for adaptor sequences and low quality sequences by cutadapt v. 1.16 using the following options: cutadapt --trim-n --times=5 --minimum-length 20 -q 26 -e 0.15 -g ACTGTTCACGATGAACTTG -g TTCAGTTCACAATCCCAAG -a CTTGGGATTGTGAACTGAA -a CAAGTTCATCGTGAACAGT
Trimmed reads were mapped to dm6.BDGP6.22.96 genome by bwa 0.7.12-r1039 using the mem algorithm. All non-aligned reads were removed from resulting alignment file by samtools 1.6: -b -S -F 4 -@ 10 allalign.sam > aligned.bam
Mapping and alignment results were converted to resulting tables using samtools 1.6 and ad hoc Perl scripts.
Each replica results table was converted to bedGraph file for further processing using reads amount as data value. Intersection file was built by bedtools v. 2.27.1 with the following command line: bedtools intersect -a 4C_dm0.hs.rep1.bedGraph -b 4C_dm0.hs.rep2.bedGraph -wb. Ad hoc Perl script was used to convert bedtools output file back to bedGraph file with averaging in the overlapped regions.
Intersection file was filtered from low complexity regions and transposable elements from the DFAM database by bedtools v. 2.27.1 with the following command line: bedtools intersect -sorted -v -f 1.0 -a 4C_dm0.hs.intersect.bedGraph -b dm6_dfam.hits.bed > 4C_dm0.hs.intersect.hc.txt and ad hoc Perl script.
genome build: Drosophila melanogaster dm6/BDGP.6.22.96 genome build
processed data files format and content: Tab-delimited text file include the following features of each mapping: begin, end, length, coverage, number of reads, sequence. bedGraph files for each replica and intersection are supplied too.

growth_protocol: S2 cells were grown in GIBCO Drosophila medium with 10% FBS in a humidified incubator at 25°C to 80% confluency. Heat shock treatment was performed by incubation of celles in the medium at 37°C for 1 h and then for 1 h at 27°C.

extract_protocol:
DNA samples were prepared as described before (Dekker et al., 2002; Osborne et al., 2004; http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=3978).  Cross-linking: To suspension containing about 34x106 S2 cells in 4 ml of the GIBCO medium formaldehyde solution was added to final concentration 1.5%. After mixing incubation of cell suspension was performed for 10 min at room temperature with mixing. The quenching with 2.75 ml of 2M glycin (final concentration 0.125M) was performed. After incubation at room temperature for 5 min the suspension was cooled for 15 min in ice bath and then cells were collected by centrifugation for 15 min at 3500 rpm at +2°C.  Lysis: The pellet of cells was resuspended at °C in 1ml of buffer containing 10 mM tris-HCl buffer, pH 8, 10 mM NaCl, 0.2% NP-40 and freshly added protease inhibitors – 0.1 mM PMSF and 1:500 protease inhibitor cocktail (Sigma). After incubation for 15 min cells were homogenized by passing through insulin syringe about 50 times into Eppendorf. Then nuclei were spin down by centrifugation for 5 min at 5000 rpm in Eppendorf centrifuge 5415 R at +2°C.  Digestion with EcoRI: The nuclei pellet was resuspended in 756 microl of solution containing 40 mM tris-HCl buffer, pH 7.4, 50 mM NaCl, 10 mM MgCl2 and 10 mM 2-mercaptoethanol. Then 20% SDS was added to final concentration 0.3% and incubation with shaking was performed for 1 h at +37°C. To sequester SDS 180 l of 10% Triton X-100 was added and the incubation for 1 h at +37°C was performed. Before digestion 1 l of BSA (5 mg/ml) was added with mixing. Then 50 l of EcoRI (10 u/l) was added and after mixing digestion was performed overnight at +37°C.   Ligation: To inactivate the restriction enzyme, 35 l of 20% SDS was added (final concentration 0.7%) and the probe was heated to 65°C for 30 min. Then the mixture was transferred into 15 ml Nunc tube and consequently 375 l of 20% Triton X-100 (to final concentration 1%), 750 l of 10x ligase buffer, 7,5 l of BSA (5 mg/ml), 80 l of 100 mM ATP, and 5241 l of milliQ water  were added and the final 7.5 ml solution was well mixed. Then 10 l of T4 DNA ligase (200 u/l) was added and after mixing incubation was performed for 5 h at +16°C and then for 30 min at room temperature. Usually during ligation DNA concentration was equal to 2 ng/l.    DNA purification: For isolation of DNA 50 l of proteinase K (10 mg/ml) was added (final concentration 50 g/ml) and after mixing incubation was performed at 55°C B1overnight. For RNA digestion 40l of RNase A (10 mg/ml) was added (final concentration 0.5 g/ml) and after mixing incubation was performed for 30 min at +37°C. After extensive extraction with phenol-chloroform extraction (three times with 7 ml each) DNA was precipitated by 2.5 vol. of ethanol after addition of 40 l 10 mg/ml glycogen and 175 l 4M NaCl. The final DNA pellet was washed twice with 70% ethanol and then dissolved in 0.1xTE.   Digestion with FaeI: About 15 g of DNA was digested in 250 microl solution with 75 u of FaeI overnight at +37°C. Then the enzyme was inactivated by heating at 65°C for 30 min. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 100 l of 0.1xTE.   Ligation: For circularization 15 microg of DNA was incubated in 8 ml of T4 DNA ligase buffer containing 400 u of T4 DNA ligase for 5 h at +16°C. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 50 microl of 0.1xTE.
One  round of  PCR was used as described below. The following primers were used: 5' ACTGTTCACGATGAACTTGGAATT 3' and 5' TTCAGTTCACAATCCCAAGCATG 3'. PCR products were purified using QIAqiuck PCR purification kit kit (Quigen). The libraries were prepared using TruSeq RNA Sample Preparation Kit v2 (Illumina). The samples were sequenced using HiSeq 1500 (Illumina) following the manufacturer's protocols.