title: porcine_PG_2C_Smartseq_rep2


title: HMN83576_flu

status: Public on Nov 26 2021

type: SRA

city: Chicago

first: Luis

middle: B

last: Barreiro

address: 900 E 57th Street

country: USA

institute: University of Chicago

description:
bulk RNA library
bulk_PBMCs.Homo_sapiens_with_flu.GRCh38.kallisto.gene_level.ScaledTPM.txt

library_source: transcriptomic

data_processing:
Fastqs were trimmed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) in single-end mode (-q 20 --phred33)
Reads were pseudoaligned to GRCh38 and the IAV reference transcriptome using kallisto's quant function (Bray et al.) in single-end mode
Quantification estimates were obtained from abundance.h5 files using the R package tximport (Soneson et al.)
Genome_build: GRCh38.p12 and influenza A virus (A/California/04/09)
Supplementary_files_format_and_content: bulk_PBMCs.Homo_sapiens_with_flu.GRCh38.kallisto.gene_level.ScaledTPM.txt includes counts from abundance estimates scaled by library size

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMCs

growth_protocol: All samples were obtained from BioIVT. Blood was collected utilizing a standard protocol from 90 male African- (AFR) and European-American (EUR) donors between the ages of 21 – 69 using a sodium heparin anticoagulant from the same collection site in the United States. A signed, written consent was obtained from each participant. Briefly, PBMCs were extracted from whole blood using a density gradient, washed with HBSS, reconstituted in CryoStor CS10 to a concentration of 10 million (M) cells/ml, and subsequently cryopreserved.

extract_protocol:
Cells were collected, washed, and stored in Qiazol prior to RNA extraction.
RNA libraries were prepared for sequencing using TM3’seq, a 3’-enriched library preparation protocol (https://www.g3journal.org/content/10/1/143).

treatment_protocol: Per individual for each condition, 1 million (M) PBMCs were plated at a concentration of 1M/ml and infected with either mock-conditioned media (negative control) or Cal/04/09 IAV at an MOI of 0.5. After 30 minutes of IAV infection, the virus was washed from PBMC cultures, cells were replated, and cells were then incubated for 6hr at 37C in 5% CO2 and 20% O2.

tag: cell type

value: peripheral blood mononuclear cells

tag: treatment

value: flu-infected


title: HMN83577_flu


title: HMN83576_NI

value: mock


title: SIGAF8: CSBKO2 10X scRNA-seq

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

country: United Kingdom

institute: University of Cambridge

data_processing:
Demutiplexing with CASAVA
Processing with Cellranger
Genome_build: Mm10

molecule: total RNA

organism: Mus musculus

source_name: kidney

growth_protocol: Mice were housed in SPF conditions

extract_protocol:
Kidneys were taken and a single cell suspension produced following treatment with liberase, kidneys from up to 6 mice were combinded into one pool
10x libraries were made according to manufactuers protocols with each cell pool split over 2 lanes of 10x

treatment_protocol: Mice were given Methanol prior to sample collection

tag: genotype

value: CSB -/-

tag: tissue

value: kidney


title: porcine_PG_Bl_H3K4me3_CR_rep2

city: Beijing

first: Wei

last: Xie

address: Zhongguancun north street

country: China

institute: Tsinghua University

library_source: genomic

data_processing:
Library strategy: Cut&Run
Basecalls performed using CASAVA version 1.8
All STEM-seq datasets were firstly treated with cutadapt v1.11 (Martin, 2011) and the low-quality reads and adaptors were removed before mapping. Then all filtered reads were aligned to different genomes (rat, rn6; cow, bosTau8; pig, susScr11) using Bismark (v0.7.0；bowtie2 2.1.0) (Krueger and Andrews, 2011) with default parameters. Multi-mapped reads and PCR duplicates were removed also with the Bismark. The unique mapped reads were used for CpG methylation calling with bismark_methylation_extractor. For every single CpG site, only the CpG sites that were covered at least 3 times were used for further analysis. The spiked-in Lamda DNA (1:200) was used for conversation rate calculation.
All RNA-seq datasets were mapped to the different genomes (rat: rn6; cow: bosTau8; pig: susScr11). All genomes were downloaded from UCSC (citation) by Tophat v2.1.1 (Trapnell et al., 2009). Gene expression was then calculated according to refFlat database by cufflinks 2.2.1 (Trapnell et al., 2012).
All reads were firstly processed by TrimGalore (v.0.6.4) with default parameters to remove the poor qualitied reads and also the adapters. Then the filtered reads were mapped to different genomes (rat: Rn6; cow: bosTau8; pig: susScr11) by Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012) with the default parameters. All multiple mapped reads as well as the duplicates were removed with MarkDuplicates.jar. Then all unique mapped reads were used for the downstream RPKM (reads per kilobase per million of sequenced reads) calculation. The Pearson correlation was generated for each sample with two biological replicates with 10 kb bins. The replicates with good reproducibility were pooled for downstream analysis.
Supplementary_files_format_and_content: The cov txt files contains the chr, start positon, methylated CG count, unmethylated CG count. The txt files for FPKM contain gene names and the FPKM value for all stages.

molecule: genomic DNA

organism: Sus scrofa

source_name: embryo

extract_protocol: CUT&RUN library preparation and sequencing  CUT&RUN was performed as previously reported (Skene et al., 2018; Skene and Henikoff, 2017) with modifications. Briefly, after removing the zona pellucida with Tyrode’s solution (Sigma-Aldrich, T1788) or 0.5% (m/v) Protease from Streptomyces griseus (Sigma-Aldrich, P8811), mammalian oocytes and early embryos were incubated with Concanavalin-coated magnetic beads (Polyscience, 86057) for 10 min at room temperature on a thermomixer at 400 rpm. Samples were then incubated with primary antibody at a ratio of 1:100 at 4℃ overnight on a thermomixer at 400 rpm. The next day, after washing for one time, beads were incubated with pA-MNase (to a final concentration of 400-700ng/mL) (a gift from Steven Henikoff lab) at 4℃ for 3 hours on a thermomixer at 400 rpm. After two times of washing, targeted digestion was performed by adding 2μL of 100mM CaCl2 for 30 mins on ice, followed by termination by adding an equal volume of 2  × stop buffer. Samples were then incubated at 37℃ for 20 mins for fragment releasing. The total samples or supernatants were digested with Proteinase K (NEB, P8107S) and purified using phenol:chloroform:isoamyl alcohol (25:24:1, v/v) followed by ethanol purification at -80℃ overnight. The next day, DNA was purified and subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Sequencing was done using the HiSeq X Ten system (Illumina) according to the manufacturer’s protocol.

tag: developmental stage

tag: antibody


title: SIGAE8: CSBKO1 10X scRNA-seq


title: HMN83575_NI


title: porcine_PG_Bl_H3K4me3_CR_rep1


title: HMN83580_NI


title: porcine_PG_8C_H3K4me3_CR_rep2

value: parthenogenetically activated 8-cell embryo


title: SIGAC8: ADH5KO1 10X scRNA-seq


title: HMN83574_NI


title: porcine_PG_8C_H3K4me3_CR_rep1


title: HMN83573_NI


title: HMN83574_flu


title: porcine_FGO_Smartseq_rep1

data_processing:
Basecalls performed using CASAVA version 1.8
All STEM-seq datasets were firstly treated with cutadapt v1.11 (Martin, 2011) and the low-quality reads and adaptors were removed before mapping. Then all filtered reads were aligned to different genomes (rat, rn6; cow, bosTau8; pig, susScr11) using Bismark (v0.7.0；bowtie2 2.1.0) (Krueger and Andrews, 2011) with default parameters. Multi-mapped reads and PCR duplicates were removed also with the Bismark. The unique mapped reads were used for CpG methylation calling with bismark_methylation_extractor. For every single CpG site, only the CpG sites that were covered at least 3 times were used for further analysis. The spiked-in Lamda DNA (1:200) was used for conversation rate calculation.
All RNA-seq datasets were mapped to the different genomes (rat: rn6; cow: bosTau8; pig: susScr11). All genomes were downloaded from UCSC (citation) by Tophat v2.1.1 (Trapnell et al., 2009). Gene expression was then calculated according to refFlat database by cufflinks 2.2.1 (Trapnell et al., 2012).
All reads were firstly processed by TrimGalore (v.0.6.4) with default parameters to remove the poor qualitied reads and also the adapters. Then the filtered reads were mapped to different genomes (rat: Rn6; cow: bosTau8; pig: susScr11) by Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012) with the default parameters. All multiple mapped reads as well as the duplicates were removed with MarkDuplicates.jar. Then all unique mapped reads were used for the downstream RPKM (reads per kilobase per million of sequenced reads) calculation. The Pearson correlation was generated for each sample with two biological replicates with 10 kb bins. The replicates with good reproducibility were pooled for downstream analysis.
Supplementary_files_format_and_content: The cov txt files contains the chr, start positon, methylated CG count, unmethylated CG count. The txt files for FPKM contain gene names and the FPKM value for all stages.

source_name: oocyte

extract_protocol: RNA library preparation and sequencing  The RNA libraries for mammalian oocytes and preimplantation embryos were prepared using Smart-seq2 method as previously reported (Picelli et al., 2014).

value: full_grown oocyte


title: HMN83573_flu


title: SIGAB8: WT2 10X scRNA-seq

value: WT


title: porcine_PG_4C_H3K4me3_CR_rep2

value: parthenogenetically activated 4-cell embryo


title: HMN83572_NI


title: porcine_PG_4C_H3K4me3_CR_rep1


title: HMN83575_flu


title: HMN83572_flu


title: HMN83571_flu


title: SIGAD8: ADH5KO2 10X scRNA-seq


title: HMN83570_flu


title: HMN83569_NI


title: HMN83571_NI


title: HMN83569_flu


title: H3K4me3_14_2LJ-1

city: New Orleans

first: Francesca

last: Peruzzi

state: LA

address: 1700 Tulane Ave.

institute: LSU Health Sciences Center

data_processing:
Homo sapiens genome GRCh37/hg19 was used as the reference genome
Reads were aligned to the reference genome using BWA V.0.7.5a. Samples were filtered for regions blacklisted by the ENCODE project. PCR duplicates and multimapping reads were removed using samtools.
Alignment coordinates were converted to BED format using BedTools v.2.17 and peak calling was performed using SICER with optimized parameters for each histone mark
Genome_build: hg19
Supplementary_files_format_and_content: peak text files

extract_protocol:
CD14+ monocytes were isolated from blood using EasySep Direct human monocytes isolation kit (StemCell Technologies, cat#19669). For each sample, 8x106 cells were pelleted and resuspended in PBS containing formaldehyde (37%) followed by the addition of 1.25 M Glycine. Cells were washed twice with cold PBS and 2x10e6 aliquots were shipped to Diagenode for subsequent ChIP-Seq.
Libraries were generated and sequences were performed on an Illumina HiSeq 3000/4000 by Diagenode
ChIP-sequencing (Diagenode)

tag: hiv status

value: HIV+

value: blood

value: CD14+ monocyte

tag: chip antibody

value: H3K4me3- Diagenode, cat# C15410003


title: porcine_PG_2C_H3K4me3_CR_rep2

value: parthenogenetically activated 2-cell embryo


title: H3K4me3_12_1XU


title: porcine_IVM_MII_H3K4me3_CR_rep2

value: In vitro matured mataphase II oocyte


title: HMN83570_NI


title: porcine_PG_2C_H3K4me3_CR_rep1


title: H3K4me3_13_2LH-1


title: HMN83567_NI


title: porcine_IVM_MII_H3K4me3_CR_rep1


title: HMN83567_flu


title: HMN83566_NI


title: H3K4me3_8_1TF-4


title: HMN83566_flu


title: H3K4me3_10_Ctr10


title: porcine_FGO_H3K4me3_CR_rep2


title: HMN83565_NI


title: SIGAA8: WT1 10X scRNA-seq


title: porcine_FGO_H3K4me3_CR_rep1


title: HMN83564_flu


title: HMN83563_NI


title: porcine_CC_H3K36me3_STAR_rep1

source_name: cumulus cell

extract_protocol: STAR ChIP-seq library preparation and sequencing  STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system (Illumina) according to the manufacturer’s protocol.

value: cumulus cell


title: H3K4me3_11_272


title: H3K4me3_2_Ctr12

value: HIV- control


title: HMN83562_NI

value: peripheral blood mononuclear cells


title: HMN83562_flu

value: flu-infected


title: HMN83565_flu


title: HMN83561_flu


title: H3K4me3_3_Ctr4


title: H3K4me1_14_2LJ-1

value: H3K4me1- Diagenode, cat# C15410194


title: H3K4me3_6_1T3


title: HMN83568_NI

value: mock


title: HMN83560_NI


title: HMN83568_flu


title: HMN83561_NI


title: H3K4me1_13_2LH-1


title: H3K4me1_12_1XU


title: HMN83559_NI


title: HMN83563_flu


title: porcine_FGO_100_mESC_250_mix_H3K36me3_STAR_rep1

description:
pig_FGO_H3K36me3_cChIP_rep1.bw
mouse_ESC_H3K36me3_cChIP_with_pigFGO_rep1.bw

value: full_grown oocyte/ESC


title: porcine_CC_H3K36me2_STAR_rep2


title: HMN83560_flu


title: HMN83559_flu


title: HMN83564_NI


title: H3K4me1_11_272


title: HMN83558_NI


title: porcine_CC_H3K36me3_STAR_rep2


title: porcine_FGO_H3K36me3_STAR_rep1


title: porcine_FGO_H3K36me3_STAR_rep2


title: H3K4me1_10_Ctr10


title: HMN83557_flu


title: HMN83557_NI


title: porcine_CC_H3K36me2_STAR_rep1


title: porcine_FGO_H3K36me2_STAR_rep2


title: HMN83556_NI


title: HMN83555_NI


title: H3K4me1_6_1T3


title: porcine_FGO_100_mESC_250_mix_H3K36me2_STAR_rep1

description:
pig_FGO_H3K36me2_cChIP_rep1.bw
mouse_ESC_H3K36me2_cChIP_with_pigFGO_rep1.bw

source_name: oocyte/mESC


title: H3K4me1_8_1TF-4


title: HMN83555_flu


title: H3K4me1_3_Ctr4


title: porcine_CC_H3K27me3_CR


title: HMN83554_flu


title: H3K4me1_2_Ctr12


title: porcine_PG_Bl_H3K27me3_CR_rep2


title: HMN83553_NI


title: HMN83553_flu


title: HMN83552_NI


title: porcine_PG_Bl_H3K27me3_CR_rep1


title: DTP_04

city: Bangkok

first: Varodom

last: Charoensawan

address: 272 Rama VI Road, Ratchathewi District

department: Biochemistry

country: Thailand

institute: Mahidol university

description: single-cell cDNA library

data_processing:
Raw reads were aligned and UMI counts were obtained using CellRanger V5.0.0 (10x Genomics, USA) with the  human genome GRCh38 version 2020-A as reference genome.
The gene barcode matrices of  all samples were further analyzed in R (version 3.6) using the Read10x() function and converted to the Seurat V3 objects for further preprocessing and downstream analyses
To minimize apoptotic cells, only cells with percentages of mitochondrial genes lower than 25% were kept for further analysis. The droplets that contained potential  doublets were excluded using DoubletFinder
Genome_build: GChr38
Supplementary_files_format_and_content: gene-barcode matrix (filtered)

source_name: Isolated cells from dental pulp

extract_protocol:
Single-cell suspensions were incubated with lysis and RT buffer as provided by the manufacturer (10x Genomics)
The libraries were prepared with Chrominun Single-cell Chemistry V2 (10x Genomics) following manufacturer's instructions and sequenced on Illumina Hiseq

treatment_protocol: Dental pulp tissue was washed with 1X PBS before treated with 3mg/ml collagenase and 1U dispase for 1 hr at 37C with a vortexing interval of 15 minutes. The dissociated cells were washed twice with PBS before further single-cell library preparation.

tag: donor

value: Donor C

value: dental pulp

tag: disease stage

value: Enamel caries


title: HMN83552_flu


title: HMN83558_flu


title: HMN83551_NI


title: porcine_PG_8C_H3K27me3_CR_rep2

value: parthenogenetically activated 8-cell embryo


title: HMN83551_flu


title: HMN52561_NI


title: HMN52561_flu


title: porcine_FGO_H3K36me2_STAR_rep1

value: full_grown oocyte


title: HMN83556_flu


title: porcine_PG_8C_H3K27me3_CR_rep1


title: DTP_01

description: single-cell cDNA library

value: Donor A

value: Sound tooth


title: HMN52560_NI


title: HMN83554_NI


title: HMN52560_flu


title: porcine_PG_4C_H3K27me3_CR_rep2

value: parthenogenetically activated 4-cell embryo


title: HMN52559_NI


title: porcine_PG_4C_H3K27me3_CR_rep1


title: HMN52559_flu


title: rat_Bl_Smartseq_rep1

organism: Rattus norvegicus

value: in vivo blastocyst


title: DTP_05

description: single-cell cDNA library

value: Donor D

value: Deep dental caries


title: rat_Bl_Smartseq_rep2


title: HMN52558_NI


title: rat_8C_Smartseq_rep2

value: in vivo 8-cell embryo


title: HMN52557_NI

value: peripheral blood mononuclear cells


title: porcine_PG_2C_H3K27me3_CR_rep2

value: parthenogenetically activated 2-cell embryo


title: porcine_PG_2C_H3K27me3_CR_rep1


title: HMN52557_flu

value: flu-infected


title: porcine_IVM_MII_H3K27me3_CR_rep2

value: In vitro matured mataphase II oocyte


title: HMN52556_flu


title: HMN52556_NI

value: mock


title: DTP_02

description: single-cell cDNA library

value: Donor B


title: rat_8C_Smartseq_rep1


title: rat_4C_Smartseq_rep2

value: in vivo 4-cell embryo


title: HMN52555_NI


title: porcine_IVM_MII_H3K27me3_CR_rep1


title: porcine_FGO_H3K27me3_CR_rep2


title: rat_4C_Smartseq_rep1


title: HMN52554_flu


title: HMN52554_NI


title: HMN52555_flu


title: rat_2C_Smartseq_rep2

value: in vivo 2-cell embryo


title: HMN52553_NI


title: rat_2C_Smartseq_rep1


title: HMN52553_flu


title: HMN52552_NI


title: HMN52552_flu


title: HMN52551_NI


title: HMN52551_flu


title: HMN52558_flu


title: rat_1C_Smartseq_rep3

value: in vivo 1-cell embryo


title: rat_1C_Smartseq_rep4


title: porcine_CC_DNAme_rep1

extract_protocol: STEM-Seq library preparation  The whole genome bisulfite libraries for bovine and porcine FGO were constructed with STEM-seq as previously described (Zhang et al., 2018a). Briefly, the oocytes were firstly lysed with 10μL lysis buffer and 1μL protease K at 55°C for 3 hours. The protease K was inactivated at 72°C for 40 minutes. After lysis, the spike-in λ-DNA (Promega; D150A) was added with a mass ratio of 1:200. Then the mixture was treated and then purified with the bisulfite conversion reagent with the EpiTect Fast Bisulfite Conversion Kit (Qiagen; 59824) following the manufacture’s instruction, with a modified protocol: denature for 8 min at 95 °C, incubate at 60 °C for 25 min, and repeat the procedure once. Finally, the purified converted DNA was subject to TELP library construction process as previously reported (Peng et al., 2015).

value: cumulus cell


title: porcine_FGO_DNAme_rep3

description: Pig_FGO_DNAme_rep123_merge.rmdup.bismark.cov.gz

value: full_grown oocyte


title: porcine_CC_DNAme_rep2


title: HMN52550_flu


title: rat_1C_Smartseq_rep2


title: porcine_FGO_DNAme_rep2


title: HMN52549_NI


title: HMN52550_NI


title: HMN52549_flu


title: rat_1C_Smartseq_rep1


title: porcine_FGO_DNAme_rep1


title: HMN52548_flu


title: HMN52548_NI


title: rat_MII_Smartseq_rep4

value: In vivo matured mataphase II oocyte


title: HMN52547_flu


title: HMN52546_NI


title: HMN52547_NI


title: rat_MII_Smartseq_rep3


title: RNA extracted from batch 3 of embryos transfected only epiB:YFP

city: Aigaleo Athens

first: Vasileios

last: Papadogiannis

address: Solonos 2

department: Zoology

country: Greece

institute: University of Oxford

data_processing:
fastQC was used to assess sequencing quality
Trimmomatic was used to trim off adapters and Sickle to trim low quality reads
Remaining reads were then mapped to the Ciona robusta genome (KH2012) using STAR
Genome_build: Ciona robusta genome (KH2012)
Supplementary_files_format_and_content: ciHMXsequencing_countTable.csv (the gene IDs correspond to gene models of the KH2012 Ciona robusta genome. The models and genome can all be found in https://www.aniseed.cnrs.fr/aniseed/ and https://www.aniseed.cnrs.fr/aniseed/download/download_data)

organism: Ciona intestinalis

source_name: Transfected late tailbud embryos

extract_protocol:
Fluorescent transfected embryos were collected in 1.5ml tubes. Embryos were dissociated in TRIZOL, dissociating via gentling passing through a needle. RNA was subsequently extracted using phase separation with chlorofom, pricipitated with isopropanol, followed by ethanol washes and re-suspension in nuclease free water.
The mRNA fraction was selected from the total RNA provided before conversion to cDNA. Second strand cDNA  synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated. Prior to amplification,  samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and QC’ed before paired  end sequencing was carried out over four lanes.

value: Late tailbud

value: Whole embryos

value: control


title: RNA extracted from batch 2 of embryos transfected only epiB:YFP


title: rat_MII_Smartseq_rep2


title: HMN52546_flu


title: RNA extracted from batch 1 of embryos transfected only epiB:YFP


title: porcine_FGO_H3K27me3_CR_rep1


title: Lab_strain_control_2

city: Nottingham

first: WILLIAM

middle: RA

last: BROWN

state: NOTTS

address: Life Sciences Department, Queens Medical Centre

department: Life Sciences

institute: Nottingham University

description:
Generated by CHIP~seq
FASTA file:
Lab_strain.fasta

data_processing:
fastq files were not quality trimmed but aligned to customized fasta files (inlcluded) using the Burroughs Wheeler aligner in samtools. Bam files were filtered for  paired sequences using the 99, 147, 83 and 163 flags and then merged into  asingle bam file
Generation of the coverage vectors used in the figures used a Granges object using the R libraries, GenomicRanges, GenomicAlignments, rtracklayer, Rsamtools, limma,
Coverage vectors were normalized on the basis of read counts to the centromeres of chromosomes 1 and 3. Read counts were calculated using the samtools view command.
Coverage vectors were normalized on the basis of read counts to the centromeres of chromosomes 1 and 3. Read counts were calculated using the samtools view command.
Vectors were smoothed using a median smoothing ; using the runmed command on a vectorized derivative of the Rle object with a smoothing distance of either 101 or 1001 residues for either the centromere of whole chromsome coverage vectors
Genome_build: Not relevant used custom fasta files; FASTA files available on the series record.
Supplementary_files_format_and_content: coverage vectors that can be processed and inspected with simple text editors

organism: Schizosaccharomyces pombe

source_name: S. pombe modified by genome engineering

growth_protocol: Growth in YES to OD 0.7 at 600nm

extract_protocol: Material was quantified using Qubit (Invitrogen) and the size profile analysed on the 2200 or 4200 TapeStation (Agilent, dsDNA HS Assay). Input material was normalised to 5 ng or maximum available prior to library preparation. Automated library preparation was performed using the Apollo prep system (Wafergen, PrepX ILMN 32i, 96 sample kit) and standard Illumina multiplexing adapters following manufacturer’s protocol up to pre-PCR amplification. Libraries were PCR amplified (18 cycles) on a Tetrad (Bio-Rad) using the NEBNext High-Fidelity 2X PCR Master Mix (NEB) and in-house unique dual indexing primers (based on DOI: 10.1186/1472-6750-13-104). Individual libraries were normalised using Qubit, and the size profile was analysed on the 2200 or 4200 TapeStation. Individual libraries were normalised and pooled together accordingly. The pooled library was diluted to ~10 nM for storage. The 10 nM library was denatured and further diluted prior to loading on the sequencer. Paired end sequencing was performed using a HiSeq4000 75bp platform (Illumina, HiSeq 3000/4000 PE Cluster Kit and 150 cycle SBS Kit)

treatment_protocol: see supplementary data

tag: strain

value: Laboratory strain  derived

tag: modification

value: chromsome 2 centromere modified

tag: chip target and antibody

value: CENP_A modified by  amino terminal GFP tag and precipitated using Abcam Ab 290


title: rat_FGO_Smartseq_rep4


title: rat_MII_Smartseq_rep1


title: Lab_Strain_NeoCen_before_2

description:
Generated by CHIP~seq
FASTA file:
LS_NeoCen_II.fasta

value: chromsome II centromere modified


title: HMN52545_NI

value: peripheral blood mononuclear cells


title: RNA extracted from batch 3 of embryos transfected with epiB::ciHMX and epiB:YFP

value: ciHMX overexpression


title: Lab_Strain_NeoCen_before_1


title: rat_FGO_Smartseq_rep3


title: RNA extracted from batch 2 of embryos transfected with epiB::ciHMX and epiB:YFP


title: Cen_2_before_2

description:
Generated by CHIP~seq
FASTA file:
Not_76_Cen_2_before.fasta

value: Strain CBS 2777 derived


title: RNA extracted from batch 1 of embryos transfected with epiB::ciHMX and epiB:YFP


title: HMN52544_NI

value: mock


title: Cen_2_before_1


title: rat_FGO_Smartseq_rep2


title: HMN52544_flu

value: flu-infected


title: rat_FGO_Smartseq_rep1


title: HMN52543_NI


title: Cen_1_before_2

description:
Generated by CHIP~seq
FASTA file:
Not_76_Cen_1_before.fasta


title: rat_ESC_H3K4me3_CR_rep2

source_name: ESC

value: ESC


title: Lab_strain_control_1


title: HMN52543_flu


title: rat_ESC_H3K4me3_CR_rep1


title: HMN52545_flu


title: Cen_1_before_1


title: wee1_2

description:
Generated by CHIP~seq
FASTA file:
wee1_combined.fasta


title: rat_CC_H3K4me3_CR_rep1


title: HMN52540_NI


title: rat_Bl_H3K4me3_CR_rep2

value: in vivo blastocyst


title: rat_Bl_H3K4me3_CR_rep1


title: HMN52540_flu


title: Cen_29_after_2

description:
Generated by CHIP~seq
FASTA file:
Cen_29_after_combined.fasta


title: Cen_29_after_1


title: wee1_1


title: HMN52539_NI


title: rat_8C_H3K4me3_CR_rep2

value: in vivo 8-cell embryo


title: rat_8C_H3K4me3_CR_rep1


title: HMN52541_NI


title: Cen_29_before_2

description:
Generated by CHIP~seq
FASTA file:
Cen_29_before_combined.fasta


title: JK_JBK_C8C_4

city: Philadelphia

first: Apoorva

last: Babu

state: PA

address: SCTR, 3400 Civic Center Blvd

department: Cardiovascular Institute

institute: University of Pennsylvania

data_processing:
Fastq files were aligned to the mm10 reference genome using STAR and default parameters
Ensmebl gene annotations were used for gene counts. Gene counts were obtained using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method
Genome_build: mm10
Supplementary_files_format_and_content: Voom transformed abundance measurements

source_name: lung

extract_protocol:
A single cell suspension was obtained by instilling Dispase into perfused lungs, followed by mechanical dissociation, and treatment with DNAase I.  Differential adherence on plastic culture dishes negatively selected mesenchymal cells. CD45+ cells were depleted by negative selection using Dynabeads untouched mouse T cell kit and Dynabeads mouse DC enrichment kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 200mg/kg IP tamoxifen x 2 days with AEC2 isolation on day 7

tag: age

value: SP-C C185G

tag: Sex

value: F


title: JK_JBK_C8C_2


title: Cen_29_before_1


title: JK_JBK_C8C_3


title: rat_4C_H3K4me3_CR_rep2

value: in vivo 4-cell embryo


title: HMN52539_flu


title: KO3  TUNOR

type: RNA

city: shanghai

first: peng

last: xu

address: Yanchang Road 301，shanghai

institute: shanghai tenth  people’s  hospital

description: TPA induce  skin  tumor of P2RY6-/- mice

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE V2.0 (8*60K,Design ID:074809) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray  Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area  61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set  to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1  (Agilent) using default parameters to obtain background subtracted and spatially  detrended Processed Signal intensities as the raw data. Raw data were normalized  in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2  samples flagged as Detected were maintained.

source_name: P2RY6-/-  TUMOR 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color  Low RNA Input Linear Amplification PLUS kit (Agilent) according to the  manufacturer's instructions, followed by RNAeasy column purification (QIAGEN,  Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop  ND-1000 Spectrophotometer

growth_protocol: For the long-term two-stage carcinogenesis model, a single dose of 195 nmol of 7,12-dimethylbenz[a]anthracene (DMBA) with very high purity (> 99.8%) (Sigma, St. Louis, MO,USA) in 200 μL of acetone was applied to the shaved dorsal skin of P2ry6+/+ (n=12) and P2ry6-/- (n=12) mice. A week later, 16 nmol of TPA (Sigma) with very high purity (> 99.5%) in 200 mL of acetone was applied twice a week to the shaved back skin until the 22nd week. The tumors on the backs of the mice were counted weekly after becoming visible. The incidence of mouse tumors and multiplicity of tumors were also calculated.We took the skin tumors of P2RY6 +/+ mice and P2RY6-/- mice, and checked the differential genes through RNA extraction and gene chip technology .

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n  AM1556 ) following the manufacturer's instructions.

treatment_protocol: A single dose of 195 nmol of 7,12-dimethylbenz[a]anthracene (DMBA) with very high purity (> 99.8%) (Sigma, St. Louis, MO,USA) in 200 μL of acetone was applied to the shaved dorsal skin of P2ry6+/+ (n=12) and P2ry6-/- (n=12) mice. A week later, 16 nmol of TPA (Sigma) with very high purity (> 99.5%) in 200 mL of acetone was applied twice a week to the shaved back skin until the 22nd week. The tumors on the backs of the mice were counted weekly after becoming visible. The incidence of mouse tumors and multiplicity of tumors were also calculated.We took the skin tumors of P2RY6 +/+ mice and P2RY6-/- mice, and checked the differential genes through RNA extraction and gene chip technology .

value: skin  tumor

tag: gender

value: male


title: KO1  TUMOR

source_name: P2RY6-/-    TUMOR  1


title: KO2  TUMOR

source_name: P2RY6-/-  TUMOR  2


title: WT3 TUMOR

description: TPA induce  skin  tumor of P2RY6+/+ mice

source_name: P2RY6+/+  TUMOR  3


title: WT1 TUMOR

source_name: P2RY6+/+  TUMOR  1


title: HMN52541_flu


title: WT2 TUMOR

source_name: P2RY6+/+  TUMOR  2


title: HMN52538_NI

source_name: PBMCs


title: rat_4C_H3K4me3_CR_rep1


title: Cen_28_after_2

description:
Generated by CHIP~seq
FASTA file:
Cen_28_after_combined.fasta


title: JK_JBK_C8C_1


title: JK_JBK_C185G_4

value: SP-C C185Gneo


title: JK_JBK_C185G_3


title: rat_2C_H3K4me3_CR_rep2

value: in vivo 2-cell embryo


title: Cen_28_after_1

value: chromsome 2 centromere modified

value: CENP_A modified by  amino terminal GFP tag and precipitated using Abcam Ab 290


title: rat_2C_H3K4me3_CR_rep1


title: Cen_28_before_2

description:
Generated by CHIP~seq
FASTA file:
Cen_28_before_combined.fasta


title: HMN52538_flu

value: peripheral blood mononuclear cells


title: HMN52537_flu


title: HMN52537_NI


title: JK_JBK_C185G_2


title: rat_1C_H3K4me3_CR_rep2

value: in vivo 1-cell embryo


title: HMN52536_NI


title: rat_1C_H3K4me3_CR_rep1


title: Cen_28_before_1

value: Strain CBS 2777 derived


title: Cen_25_after_2

description:
Generated by CHIP~seq
FASTA file:
Cen_25_after.fasta


title: Cen_25_after_1


title: HMN52536_flu


title: JK_JBK_WT_4

value: SP-C WT


title: rat_MII_H3K4me3_CR_rep4

value: In vivo matured mataphase II oocyte


title: JK_JBK_C185G_1


title: HMN52535_NI

value: mock


title: JK_JBK_WT_3


title: Cen_25_before_2

description:
Generated by CHIP~seq
FASTA file:
Cen_25_before_combined.fasta


title: HMN52535_flu

description:
bulk RNA library
bulk_PBMCs.Homo_sapiens_with_flu.GRCh38.kallisto.gene_level.ScaledTPM.txt

value: flu-infected


title: rat_MII_H3K4me3_CR_rep3


title: Cen_25_before_1


title: HMN52534_NI


title: JK_JBK_WT_1


title: rat_MII_H3K4me3_CR_rep1


title: Lab_Strain_cen_25_before_2

description:
Generated by CHIP~seq
FASTA file:
LS_cen_25_before.fasta

value: Laboratory strain derived

value: chromsome II centromere modified


title: HMN52534_flu


title: rat_FGO_H3K4me3_CR_rep3

value: full_grown oocyte


title: Lab_Strain_cen_25_before_1


title: rat_FGO_H3K4me3_CR_rep2


title: HMN52533_flu


title: Lab_Strain_cen_25_after_2

description:
Generated by CHIP~seq
FASTA file:
LS_cen_25_after.fasta


title: Lab_Strain_cen_25_after_1


title: AKPS HX531 batch 2 rep 3 RNA

city: Nijmegen

first: Michiel

last: Vermeulen

state: Gelderland

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

data_processing:
RNA-seq: RNA-seq data was processed using seq2science using default options. In short, reads were first trimmed using Fastp. Sequencing reads were aligned to the mm10 (mouse) or hg38 (human) transcript assembly from UCSC using STAR, after which a count table is generated using HTSeq. For experiments without replicates (mouse experiments), counts per million reads were calculated for each sample and any transcript not detected in all samples was filtered, log2 values were calculated and genes were ranked. For experiments with replicates (human), differential gene expression analysis was performed with the DESeq2 package. The ‘rlogTransformation’ function in DESeq2 was used to normalize, log2 transform and noise‐stabilize the expression data for visualization purposes
ATAC-seq: Preprocessing of reads was done automatically with workflow tool seq2science v0.3.0. Reads were aligned to hg38 with bwa-mem v0.7.17 with option '-M' to discard reads mapping to the mitochondrial chromosome. Mapped reads were removed if they did not have a minimum mapping quality of 30, were a (secondary) multimapper or aligned inside the ENCODE blacklist and finally were tn5 bias shifted by seq2science. Afterwards, duplicate reads were removed with picard MarkDuplicates v2.21.2. Next, paired-end info was removed from reads with seq2science to utilize both mates during peak calling with macs2 v2.2.7 with options '--shift -100 --extsize 200 --nomodel --keep-dup 1 --buffer-size 10000' in BAM mode. The effective genome size was estimated by taking the number of unique kmers in the assembly of the same length as the average read length for each sample. Narrowpeak files of replicates belonging to the same condition were merged with fisher's method in macs2 v2.2.7. Raw counts for all samples under each peak, as determined by GimmeMotifs coverage_table function, were used to define differentially accessible regions with DESeq2 (adjusted p-value < 0.05).
Genome_build: Mouse: mm9; Human: hg38
Supplementary_files_format_and_content: RNA-seq: count per transcript tables, and log transformed and normalized tables. ATAC-seq: bigWig files

source_name: human colorectal cancer organoid

growth_protocol: Mouse small intestinal organoids: Mouse Lgr5GFPDTR/+ small intestinal organoids were cultured as described in Sato et al., 2009. Briefly, organoids are embedded in RGF BME Type 2 PathClear (Cultrex, R&D Systems) and cultured in ENR medium (advanced Dulbecco’s modified Eagles Medium/F12 (Gibco) supplemented with 1x Penicillin‐Streptomycin (Gibco), 10 mM HEPES (Gibco), and 1x GlutaMAX™ Supplement (Gibco)), 1x B27 (Gibco) or 1x B27 without Vitamin A (Gibco), 1,25 mM N‐acetylcysteine (Sigma Aldrich), 50 ng/mL mEGF (Gibco), 10% final volume noggin conditioned medium, 5% final volume R‐Spondin1 conditioned medium). For maintenance, organoids were split by mechanical shearing every 5 days and the culture medium was refreshed every 2-3 days. Human colorectal cancer organoids: TPO3APC‐/‐,P53‐/‐,KRAS(G12D) and TPO4APC‐/‐,P53‐/‐,KRAS(G12D)/SMAD4‐/‐ organoids were cultured as described in Drost et al., 2015, with the addition of 10% final volume noggin conditioned medium to the culture medium of TPO4, resulting in identical culture medium for both TPO3 and TPO4. Briefly, organoids were embedded in RGF BME Type 2 PathClear (Cultrex, R&D Systems) and cultured in media containing advanced Dulbecco’s modified Eagles Medium/F12 (Gibco) (supplemented with 1x Penicillin‐Streptomycin (Gibco), 10 mM HEPES (Gibco), and 1x GlutaMAX™ Supplement (Gibco)), 1x B27 (Gibco) or 1x B27 without Vitamin A (Gibco), 1,25 mM N‐acetylcysteine (Sigma Aldrich), 50 ng/mL mEGF (Gibco), 10% final volume noggin conditioned medium, 10 mM nicotinamide (Sigma Aldrich), 500 nM A83‐01 (Cayman Chemical), and 10 μM SB202190 (Cayman Chemical). For maintenance, organoids were split by mechanical shearing every 5 days and the culture medium was refreshed every 2-3 days.

extract_protocol:
RNA-seq: Pellets were snap frozen and stored at ‐80 ⁰C. RNA from snap frozen pellets of drug treated organoids was extracted using the RNeasy RNA extraction kit (Qiagen) with DnaseI treatment. ATAC-seq: Cells were pelleted and resuspended in Recovery Cell Culture Freezing Medium (GIBCO) at -80°C to maintain native chromatin. At the start of the experiment, cells were thawed quickly at 37°C and washed twice with PBS.
RNA-seq: A total amount of 1 µg RNA per sample was used for the preparation of RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems). In short, oligo hybridization and rRNA depletion, rRNA depletion cleanup, Dnase digestion, Dnase digestion cleanup, and RNA elution were performed according to protocol. Fragmentation and priming were performed at 94 ⁰C for 6:30 min. First strand synthesis, second strand synthesis, and A‐ tailing was performed according to protocol. For the adapter ligation, a 7 μM stock was used (NextFlex DNA barcodes, Bioo Scientific). First, and second post‐ligation cleanup was performed according protocol. For the library amplification, 6 cycli were used. The library amplification cleanup was performed using a 0.8x bead‐based cleanup. Library size was determined using the High Sensitivity DNA bioanalyzer (Agilent Technologies), library concentration was measured using the DeNovix dsDNA High Sensitivity Assay (DeNovix). Sequencing was performed using an Illumina NextSeq 500, 50‐bp paired‐end reads were generated. ATAC-seq: Nuclei isolated in hypotonic buffer were tagmented for 5 minutes with in-house generated Tn5 while shaking at 37°C and DNA was purified using 2x SPRI beads (Ampure) purification. DNA was subsequently PCR amplified by using KAPA HiFi Hotstart Ready Mix (KAPA Biosystems) and Nextera Index Kit (Illumina) primers followed by reverse phase 0.65 x SPRI beads purification and a QIAquick Spin Column (QIAGEN) purification. Amplified DNA libraries were sequenced with an Illumina NextSeq 500 at a read length of 38 bp.

treatment_protocol: 24 hours after splitting, organoids were treated with either 0.1% final volume DMSO, 5µM all‐trans‐Retinoic acid (ATRA, Cayman Chemical), 10µM 9‐ cis‐Retinoic acid (9‐cisRA, Cayman Chemical), 1µM AGN193109 (Sigma Aldrich), 1µM NRX194204 (Axon Medchem), 1µM HX531 (Sigma Aldrich) or 10 µM LG100268 (Sigma Aldrich). Drugs were stored under reduced light conditions and exposure to light was minimized. Media containing compounds was refreshed after 24h. Total treatment time was 48h for all drugs. All drugs were dissolved in DMSO and added to the culture medium at working concentration in 0.1% final volume DMSO. After treatment, organoids were harvested using Organoid Harvesting Solution (Cultrex, R&D Systems) and pelleted

tag: line

value: Tumor progression organoid 4

tag: celltype

value: human colon organoid

tag: mutations


title: HMN52532_NI

tag: cell type

tag: treatment


title: AKPS HX531 batch 2 rep 2 RNA


title: AKPS HX531 batch 2 rep 1 RNA


title: rat_FGO_H3K4me3_CR_rep1

tag: developmental stage


title: AKPS -VitA batch 2 rep 3 RNA

value: no Vit A


title: JK_JBK_WT_2

tag: genotype

value: F


title: HMN52532_flu


title: rat_CC_H3K36me3_STAR_rep1

value: cumulus cell

tag: antibody


title: rat_MII_H3K4me3_CR_rep2


title: rat_FGO_H3K36me3_STAR_rep2


title: AKPS -VitA batch 2 rep 2 RNA


title: bovine_IVF_Bl_Smartseq_rep2

organism: Bos taurus

source_name: embryo

value: in vitro fertilized blastocyst


title: AKPS -VitA batch 2 rep 1 RNA


title: bovine_IVF_Bl_Smartseq_rep3


title: rat_FGO_H3K36me3_STAR_rep1

source_name: oocyte


title: HMN52543_48hr

description:
bulk RNA library
time_course_PBMCs.Homo_sapiens_with_flu.GRCh38.kallisto.gene_level.ScaledTPM.txt

data_processing:
Fastqs were trimmed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) in single-end mode (-q 20 --phred33)
Reads were pseudoaligned to GRCh38 and the IAV reference transcriptome using kallisto's quant function (Bray et al.) in single-end mode
Quantification estimates were obtained from abundance.h5 files using the R package tximport (Soneson et al.)
Genome_build: GRCh38.p12 and influenza A virus (A/California/04/09)
Supplementary_files_format_and_content: time_course_PBMCs.Homo_sapiens_with_flu.GRCh38.kallisto.gene_level.ScaledTPM.txt includes counts from abundance estimates scaled by library size

treatment_protocol: Per individual for each condition, 1 million (M) PBMCs were plated at a concentration of 1M/ml and infected with either mock-conditioned media (negative control) or Cal/04/09 IAV at an MOI of 0.5. After 30 minutes of IAV infection, the virus was washed from PBMC cultures, cells were replated, and cells were then incubated for various time points at 37C in 5% CO2 and 20% O2.


title: HMN52533_NI


title: rat_CC_H3K36me2_STAR_rep1

source_name: cumulus cell


title: HMN52555_48hr


title: AKPS DMSO batch 2 rep 3 RNA

value: DMSO


title: bovine_IVF_Bl_Smartseq_rep1


title: AKPS DMSO batch 2 rep 2 RNA


title: HMN171223_48hr

value: peripheral blood mononuclear cells


title: rat_FGO_H3K36me2_STAR_rep1


title: HMN83561_48hr


title: bovine_IVF_16C_Smartseq_rep1

value: in vitro fertilized 16-cell embryo


title: bovine_IVF_8C_Smartseq_rep2

value: in vitro fertilized 8-cell embryo


title: AKP HX531 batch 2 rep 3 RNA

value: Tumor progression organoid 3


title: HMN83554_48hr


title: cow_CC_H3K36me2_STAR_rep3

tag: experiment type

value: STAR-ChIP-seq


title: rat_ESC_H3K27me3_CR_rep2

value: ESC


title: bovine_IVF_8C_Smartseq_rep1


title: rat_CC_H3K27me3_CR_rep1


title: bovine_IVF_4C_Smartseq_rep2

value: in vitro fertilized 4-cell embryo


title: AKP HX531 batch 2 rep 2 RNA


title: rat_ESC_H3K27me3_CR_rep1


title: rat_FGO_H3K36me2_STAR_rep2


title: bovine_IVF_4C_Smartseq_rep1


title: rat_Bl_H3K27me3_CR_rep2

value: in vivo blastocyst


title: rat_Bl_H3K27me3_CR_rep1


title: bovine_IVF_16C_Smartseq_rep2


title: bovine_IVM_MII_Smartseq_rep3

value: In vitro matured mataphase II oocyte


title: AKP -VitA batch 2 rep 3 RNA


title: HMN171232_48hr

value: flu-infected


title: HMN171238_48hr


title: HMN171233_48hr


title: AKP HX531 batch 2 rep 1 RNA


title: HMN171231_48hr


title: AKPS DMSO batch 2 rep 1 RNA

value: Tumor progression organoid 4


title: AKP -VitA batch 2 rep 1 RNA

value: human colon organoid


title: rat_8C_H3K27me3_CR_rep2

value: in vivo 8-cell embryo


title: bovine_IVM_MII_Smartseq_rep2


title: HMN83554_36hr


title: HMN83570_48hr


title: bovine_IVM_MII_Smartseq_rep1


title: rat_8C_H3K27me3_CR_rep1


title: AKP DMSO batch 2 rep 3 RNA


title: HMN52543_36hr


title: bovine_FGO_Smartseq_rep3

value: full_grown oocyte


title: rat_4C_H3K27me3_CR_rep2

value: in vivo 4-cell embryo


title: AKP DMSO batch 2 rep 2 RNA


title: HMN52555_36hr


title: AKP -VitA batch 2 rep 2 RNA

value: no Vit A


title: bovine_FGO_Smartseq_rep2


title: HMN171223_36hr


title: rat_2C_H3K27me3_CR_rep2

value: in vivo 2-cell embryo


title: HMN83561_36hr

value: peripheral blood mononuclear cells


title: bovine_FGO_Smartseq_rep1


title: AKP DMSO batch 2 rep 1 RNA

value: DMSO


title: HMN83570_36hr


title: rat_1C_H3K27me3_CR_rep2

value: in vivo 1-cell embryo


title: rat_2C_H3K27me3_CR_rep1


title: HMN171231_36hr


title: AKPS ATAC rep 2

description: TPO3-4-BulkATACseq-HN-JD-Jan2020-TPO4-2-17965

data_processing:
RNA-seq: RNA-seq data was processed using seq2science using default options. In short, reads were first trimmed using Fastp. Sequencing reads were aligned to the mm10 (mouse) or hg38 (human) transcript assembly from UCSC using STAR, after which a count table is generated using HTSeq. For experiments without replicates (mouse experiments), counts per million reads were calculated for each sample and any transcript not detected in all samples was filtered, log2 values were calculated and genes were ranked. For experiments with replicates (human), differential gene expression analysis was performed with the DESeq2 package. The ‘rlogTransformation’ function in DESeq2 was used to normalize, log2 transform and noise‐stabilize the expression data for visualization purposes
ATAC-seq: Preprocessing of reads was done automatically with workflow tool seq2science v0.3.0. Reads were aligned to hg38 with bwa-mem v0.7.17 with option '-M' to discard reads mapping to the mitochondrial chromosome. Mapped reads were removed if they did not have a minimum mapping quality of 30, were a (secondary) multimapper or aligned inside the ENCODE blacklist and finally were tn5 bias shifted by seq2science. Afterwards, duplicate reads were removed with picard MarkDuplicates v2.21.2. Next, paired-end info was removed from reads with seq2science to utilize both mates during peak calling with macs2 v2.2.7 with options '--shift -100 --extsize 200 --nomodel --keep-dup 1 --buffer-size 10000' in BAM mode. The effective genome size was estimated by taking the number of unique kmers in the assembly of the same length as the average read length for each sample. Narrowpeak files of replicates belonging to the same condition were merged with fisher's method in macs2 v2.2.7. Raw counts for all samples under each peak, as determined by GimmeMotifs coverage_table function, were used to define differentially accessible regions with DESeq2 (adjusted p-value < 0.05).
genome build: Mouse: mm9; Human: hg38
processed data files format and content: RNA-seq: count per transcript tables, and log transformed and normalized tables. ATAC-seq: bigWig files

source_name: TPO4 ATAC

growth_protocol: Mouse small intestinal organoids: Mouse Lgr5GFPDTR/+ small intestinal organoids were cultured as described in Sato et al., 2009. Briefly, organoids are embedded in RGF BME Type 2 PathClear (Cultrex, R&D Systems) and cultured in ENR medium (advanced Dulbecco’s modified Eagles Medium/F12 (Gibco) supplemented with 1x Penicillin‐Streptomycin (Gibco), 10 mM HEPES (Gibco), and 1x GlutaMAX™ Supplement (Gibco)), 1x B27 (Gibco), 1,25 mM N‐acetylcysteine (Sigma Aldrich), 50 ng/mL mEGF (Gibco), 10% final volume noggin conditioned medium, 5% final volume R‐Spondin1 conditioned medium). For maintenance, organoids were split by mechanical shearing every 5 days and the culture medium was refreshed every 2-3 days. Human colorectal cancer organoids: TPO3APC‐/‐,P53‐/‐,KRAS(G12D) and TPO4APC‐/‐,P53‐/‐,KRAS(G12D)/SMAD4‐/‐ organoids were cultured as described in Drost et al., 2015, with the addition of 10% final volume noggin conditioned medium to the culture medium of TPO4, resulting in identical culture medium for both TPO3 and TPO4. Briefly, organoids were embedded in RGF BME Type 2 PathClear (Cultrex, R&D Systems) and cultured in media containing advanced Dulbecco’s modified Eagles Medium/F12 (Gibco) (supplemented with 1x Penicillin‐Streptomycin (Gibco), 10 mM HEPES (Gibco), and 1x GlutaMAX™ Supplement (Gibco)), 1x B27 (Gibco), 1,25 mM N‐acetylcysteine (Sigma Aldrich), 50 ng/mL mEGF (Gibco), 10% final volume noggin conditioned medium, 10 mM nicotinamide (Sigma Aldrich), 500 nM A83‐01 (Cayman Chemical), and 10 μM SB202190 (Cayman Chemical). For maintenance, organoids were split by mechanical shearing every 5 days and the culture medium was refreshed every 2-3 days.

tag: cell line

value: human colorectal cancer organoid

tag: genotype/variation


title: bovine_CC_H3K4me3_CR_rep1

value: cumulus cell


title: bovine_IVF_Bl_H3K4me3_CR_rep2

value: in vitro fertilized blastocyst


title: rat_1C_H3K27me3_CR_rep1


title: HMN171233_36hr


title: AKP ATAC rep 4

description: TPO3-4-BulkATACseq-HN-JD-Jan2020-TPO3-4-17963

source_name: TPO3 ATAC

value: Tumor progression organoid 3


title: rat_4C_H3K27me3_CR_rep1


title: rat_MII_H3K27me3_CR_rep2


title: bovine_IVF_Bl_H3K4me3_CR_rep1


title: AKP ATAC rep 3

description: TPO3-4-BulkATACseq-HN-JD-Jan2020-TPO3-3-17962


title: HMN171238_36hr


title: bovine_IVF_16C_H3K4me3_CR_rep1

value: in vitro fertilized 16-cell embryo


title: AKPS ATAC rep 4

description: TPO3-4-BulkATACseq-HN-JD-Jan2020-TPO4-4-17967


title: bovine_CC_H3K4me3_CR_rep2


title: AKPS ATAC rep 3

description: TPO3-4-BulkATACseq-HN-JD-Jan2020-TPo4-3-17966


title: HMN171232_36hr


title: rat_MII_H3K27me3_CR_rep3

value: In vitro matured mataphase II oocyte


title: rat_MII_H3K27me3_CR_rep1


title: HMN83554_30hr

value: flu-infected


title: AKP ATAC rep 2

description: TPO3-4-BulkATACseq-HN-JD-Jan2020-TPO3-2-17961


title: bovine_IVF_8C_H3K4me3_CR_rep1

value: in vitro fertilized 8-cell embryo


title: HMN52543_30hr


title: AKP ATAC rep 1

description: TPO3-4-BulkATACseq-HN-JD-Jan2020-TPO3-1-17960


title: AKPS ATAC rep 1

description: TPO3-4-BulkATACseq-HN-JD-Jan2020-TPO4-1-17964

value: Tumor progression organoid 4


title: rat_FGO_H3K27me3_CR_rep2


title: rat_FGO_H3K27me3_CR_rep3


title: bovine_IVF_8C_H3K4me3_CR_rep2


title: HMN52555_30hr


title: AKPS HX531 batch 1 rep 3 RNA

source_name: TPO4 HX531 RNA


title: bovine_IVF_4C_H3K4me3_CR_rep2

value: in vitro fertilized 4-cell embryo


title: HMN83570_30hr


title: bovine_IVF_16C_H3K4me3_CR_rep2


title: rat_FGO_H3K27me3_CR_rep1

value: full_grown oocyte


title: AKPS HX531 batch 1 rep 2 RNA


title: bovine_IVF_4C_H3K4me3_CR_rep1


title: bovine_IVM_MII_H3K4me3_CR_rep1


title: J18-11_S20

city: Minneapolis

first: Katherine

middle: M

last: Satrom

state: MN

address: 516 Delaware St SE

institute: University of Minnesota

description: Postnatal day 6; Jaundiced + PT

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Tophat (v2.0.13) using the mouse (mm10 as a reference.
Counts were quantified via Feature counts (Subread Package).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
mm10

source_name: jj+PT

extract_protocol:
Invitrogen RNAqueous total RNA isolation kit extration protocol followed. RNA was isolated from the hippocampus
RNA libraries were prepared for sequencing using Illumina Truseq protocols

treatment_protocol: A subset of Jj and jj pups are subjected to receive phototherpy (PT) from P4-P6. The Jj+no PT and jj+no PT did not receive PT and serve as congrols.

tag: strain

value: Gunn rat

tag: genotype/disease state

value: Homozygous/Jaundiced

tag: tissue

value: P6 Hippocampus

value: Phototherapy


title: J18-10_S19

description: Postnatal day 6; Jaundiced + PT


title: HMN171231_30hr

value: peripheral blood mononuclear cells


title: AKPS HX531 batch 1 rep 1 RNA


title: AKPS NRX194204 batch 1 rep 2 RNA

source_name: TPO4 NRX194204 RNA


title: J18-9_S18

description: Postnatal day 6; Jaundiced + PT


title: bovine_FGO_H3K4me3_CR_rep2


title: bovine_IVM_MII_H3K4me3_CR_rep2


title: HMN83554_24hr


title: HMN171238_30hr


title: J18-8_S17

description: Postnatal day 6; Jaundiced + PT


title: J18-7_S16

description: Postnatal day 6; Jaundiced + PT


title: HMN171233_30hr


title: J18-5_S15

description: Postnatal day 6; Non-jaundiced + PT

source_name: Jj+PT

value: Heterozygous/Non-jaundiced


title: AKPS NRX194204 batch 1 rep 1 RNA

value: human colorectal cancer organoid


title: HMN52543_24hr


title: bovine_CC_H3K36me3_STAR_rep2

value: cumulus cell


title: AKPS 9-cis RA batch 1 rep 3 RNA

source_name: TPO4 9-cis RA RNA

value: 9-cis RA


title: bovine_CC_H3K36me3_STAR_rep1


title: J18-4_S14

description: Postnatal day 6; Non-jaundiced + PT


title: AKPS 9-cis RA batch 1 rep 1 RNA


title: AKPS NRX194204 batch 1 rep 3 RNA


title: HMN52555_24hr


title: bovine_FGO_H3K36me3_STAR_rep2


title: AKPS DMSO batch 1 rep 3 RNA

source_name: TPO4 DMSO RNA

value: DMSO


title: J18-3_S13

description: Postnatal day 6; Non-jaundiced + PT


title: bovine_FGO_H3K4me3_CR_rep1


title: HMN171223_24hr


title: AKPS DMSO batch 1 rep 2 RNA


title: bovine_FGO_H3K36me3_STAR_rep1


title: AKPS 9-cis RA batch 1 rep 2 RNA


title: HMN171232_30hr


title: J18-1_S11

description: Postnatal day 6; Non-jaundiced + PT


title: HMN83570_24hr


title: J17-13_S10

description: Postnatal day 6; Jaundiced/No PT

source_name: jj+no PT

value: Control/No Phototherapy (PT)


title: bovine_FGO_120_mESCs_500_mix_H3K36me3_STAR_rep1

description:
cow_FGO_H3K36me3_cChIP_rep1.bw
mouse_ESC_H3K36me3_cChIP_with_cowFGO_rep1.bw

source_name: oocyte/mESC

value: in vitro matured oocyte/mESC


title: HMN171231_24hr

value: flu-infected


title: bovine_CC_H3K36me2_STAR_rep2


title: bovine_CC_H3K36me2_STAR_rep1


title: AKPS DMSO batch 1 rep 1 RNA


title: AKP HX531 batch 1 rep 2 RNA

source_name: TPO3 HX531 RNA

value: Tumor progression organoid 3


title: AKP HX531 batch 1 rep 3 RNA


title: J17-11_S8

description: Postnatal day 6; Jaundiced/No PT


title: J17-12_S9

description: Postnatal day 6; Jaundiced/No PT


title: bovine_FGO_H3K36me2_STAR_rep3


title: HMN171238_24hr


title: J18-2_S12

description: Postnatal day 6; Non-jaundiced + PT


title: bovine_FGO_H3K36me2_STAR_rep1


title: HMN83561_24hr


title: HMN171233_24hr


title: bovine_CC_H3K27me3_CR_rep2


title: J15-10_S5

description: Postnatal day 6; Non-jaundiced/No PT

source_name: Jj+no PT


title: HMN52555_18hr

source_name: PBMCs


title: bovine_FGO_H3K36me2_STAR_rep2


title: J17-10_S7

description: Postnatal day 6; Jaundiced/No PT


title: AKP NRX194204 batch 1 rep 3 RNA

source_name: TPO3 NRX194204 RNA


title: HMN171232_24hr


title: AKP 9-cis RA batch 1 rep 3 RNA

source_name: TPO3 9-cis RA RNA


title: J17-9_S6

description: Postnatal day 6; Jaundiced/No PT


title: HMN52543_18hr


title: bovine_CC_H3K27me3_CR_rep1


title: AKP NRX194204 batch 1 rep 1 RNA


title: J15-8_S4

description: Postnatal day 6; Non-jaundiced/No PT


title: AKP 9-cis RA batch 1 rep 2 RNA


title: AKP NRX194204 batch 1 rep 2 RNA


title: J15-7_S3

description: Postnatal day 6; Non-jaundiced/No PT


title: HMN83570_18hr


title: bovine_IVF_16C_H3K27me3_CR_rep2

source_name: embryo

value: in vitro fertilized 16-cell embryo


title: AKP DMSO batch 1 rep 3 RNA

source_name: TPO3 DMSO RNA


title: AKP HX531 batch 1 rep 1 RNA


title: bovine_IVF_Bl_H3K27me3_CR_rep2

value: in vitro fertilized blastocyst


title: HMN171231_18hr


title: AKP 9-cis RA batch 1 rep 1 RNA


title: HMN171238_18hr


title: AKP DMSO batch 1 rep 2 RNA


title: bovine_IVF_Bl_H3K27me3_CR_rep1


title: J13-1_S1

description: Postnatal day 6; Non-jaundiced/No PT


title: bovine_IVF_16C_H3K27me3_CR_rep1


title: HMN171232_18hr


title: bovine_IVF_8C_H3K27me3_CR_rep2

value: in vitro fertilized 8-cell embryo


title: AKP DMSO batch 1 rep 1 RNA


title: PC3_siRNA_CTRL_rep3

city: Trento

first: Michela

middle: A.

last: Denti

address: Via Sommarive 9

department: Department of Cellular, Computational and Integrative Biology

country: Italy

institute: University of Trento

hyb_protocol: Hybridization was performed in miRNA Hybridization Solution (Agilent 5190-0456) for 20 hours ar 55°C

scan_protocol: Hybridized microarray slides were scanned with an Agilent DNA Microarray Scanner G2505C using one color scan setting

data_processing: Data was analysed with the Agilent ScanControl version 8.1.3 software. The scanned TIFF images were background corrected using the Agilent Feature Extraction Software version 10.7.7.1. The raw data were normalized to the 75th percentile signal intensity.

source_name: PC3 cells, transfected with Control siRNAs, 72 hrs, replicate 4

label_protocol: 100 nanograms of total RNA sample was labelled using the miRNA Microarray System labelling kit V2 (Agilent 5190-0456) following manufacturer's instructions

growth_protocol: Human  PC3 cell line (RRID:CVCL_0035)  was obtained from American type culture collection (ATCC, Manassas, VA, USA) and regularly tested for mycoplasma (N-GARDE Mycoplasma PCR Reagent set, EuroClone,  Milan, IT). Cells were cultured in RPMI 1640 (EuroClone) supplemented with 10% heat-inactivated foetal bovine serum (EuroClone), 2 mM glutammine and 100 U/ml penicillin/ streptomycin (EuroClone).

extract_protocol: Total RNA was extracted from cells using Trizol (Invitrogen) and treated with Turbo DNA-free™ Kit (Applied Biosystem, Thermo-Fisher Scientific).

treatment_protocol: hUHRF1 siRNAs (On-TARGETplus SMARTpool, Dharmacon RNA Technologies, Lafayette, CO, USA) and non-targeting Pool (Dharmacon) were transfected with INTERFERin siRNA transfection reagent (Polyplus transfection, Strasbourg, France) following the manufacturer’s recommendations.

value: prostate cancer cell line

tag: transfection

value: siRNA Control


title: HMN52543_12hr


title: HMN83554_12hr


title: bovine_IVF_8C_H3K27me3_CR_rep1


title: bovine_IVF_4C_H3K27me3_CR_rep2

value: in vitro fertilized 4-cell embryo


title: PC3_siRNA_CTRL_rep1

source_name: PC3 cells, transfected with Control siRNAs, 72 hrs, replicate 1


title: PC3_siRNA_CTRL_rep2

source_name: PC3 cells, transfected with Control siRNAs, 72 hrs, replicate 2


title: HMN52555_12hr


title: PC3_siRNA_UHRF1_rep3

source_name: PC3 cells, transfected with siRNA_UHRF1, 72 hrs, replicate 3

value: siRNA UHRF1


title: bovine_IVF_4C_H3K27me3_CR_rep1


title: J14-3_S2

description: Postnatal day 6; Non-jaundiced/No PT

value: Gunn rat

value: P6 Hippocampus


title: HMN171233_18hr

value: peripheral blood mononuclear cells


title: HMN171223_12hr


title: HMN83561_12hr


title: bovine_IVM_MII_H3K27me3_CR_rep2

source_name: oocyte

value: In vitro matured mataphase II oocyte


title: PC3_siRNA_UHRF1_rep1

source_name: PC3 cells, transfected with siRNA_UHRF1, 72 hrs, replicate 1


title: PC3_siRNA_UHRF1_rep2

source_name: PC3 cells, transfected with siRNA_UHRF1, 72 hrs, replicate 2


title: bovine_IVM_MII_H3K27me3_CR_rep1


title: HMN83570_12hr


title: IgG.HiChIP.Treg

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Library strategy: HiChIP
HiChIP paired-end reads were aligned to the mm10 genome using the HiC-Pro pipeline. Default settings were used for removal of duplicated reads, assignment to MboI restriction fragments and filtering for valid interactions.
Non-uniquely mapped reads were discarded.
HiChIP HiC-Pro valid pairs of replicates and processed as .hic files using the hicpro2juicebox function.
Genome_build: mm10
Supplementary_files_format_and_content: .hic contact matrix

source_name: spleen

extract_protocol: Libraries were prepared using Illumina Nextera DNA library preparation kit, size-selected using low-melt gel extraction and paired-end sequenced using NextSeq 500 Illumina platform.

treatment_protocol: HiChIP was optimized and performed in biological replicates for all conditions. Briefly, 5 x 10^6 Tregs were crosslinked for each FoxP3 HiChIP replicate, 2 x 10^6 million cells for H3K27Ac and Yy1 HiChIPs respectively. Additionally, 5 x 10^6 million Tregs and Tconvs were crosslinked to include a negative IgG isotype control HiChIP samples. Low input H3K27Ac HiChIP was performed on 2 x 10^5 crosslinked WT-GFP and KO-GFP Tregs respectively. DNA sonication of fragments to 200-600 bp following MboI digestion was performed using the Covaris M220. Sonicated DNA was pre-cleared using Protein A magnetic beads followed by overnight chromatin immunoprecipitations with 3 ug H3K27Ac (Abcam ab4729), 5 ug FoxP3 (Abcam ab150743), 3 ug Yy1 (Abcam ab109237) and 5 ug rabbit IgG (Cell Signaling 2729S), in a final concentration 0.07% SDS.

value: Treg

value: spleen

value: wt

tag: epitope

value: IgG

tag: chip antibody

value: IgG (Cell Signaling 2729S)


title: Yy1.HiChIP.Treg#1

value: Yy1 (Abcam ab109237)


title: IgG.HiChIP.Tcon

value: Tconv


title: FoxP3.HiChIP.Treg#2

value: FoxP3 (Abcam ab150743)


title: H3K27Ac.HiChIP.KOGFP#2

value: H3K27Ac (Abcam ab4729)


title: FoxP3.HiChIP.Treg#1


title: HMN171231_12hr

value: flu-infected


title: Yy.HiChIP.Treg#2


title: bovine_FGO_H3K27me3_CR_rep2

value: full_grown oocyte


title: HMN171233_12hr


title: bovine_FGO_DNAme_rep1

description: Cow_FGO_DNAme_merge.rmdup.bismark.cov.gz


title: H3K27Ac.HiChIP.KOGFP#1


title: H3K27Ac.HiChIP.WTGFP#1


title: H3K27Ac.HiChIP.Tconv#2


title: HMN83554_6hr


title: MDA-231-5Ca, biological rep4

city: Nashville

first: LaMonica

middle: V

last: Stewart

state: TN

address: 1005 DB Todd JR BLVD

department: School of Graduate Studies and Research (SOGSR)

institute: Meharry Medical College

description: Gene expression data from 5mM calcium containing tissue culture medium

hyb_protocol: Following fragmentation, 2.5 µg of cRNA were hybridized overnight in an Affymetrix Model 645 Hybridization Oven. After hybridization, the cartridge arrays were washed, and stained per standard Affymetrix protocols using an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G plus scanner.

data_processing: The data were analyzed by Applied Biosystems Transcriptome Analysis Console v4.0.2.15 using Gene Level Robust Multi-array Average (RMA)

label: biotin

source_name: MDA231 breast cancer tissue culture

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 130 ng total RNA, using the Affymetrix labeling reagents following the manufacturer’s protocols .

growth_protocol: Cells were cultured overnight in complete DMEM/F12 medium (supplemented with 10% FBS, 100, Penicillin and Streptomycin), in a humidified incubator at 37 °C, 5% CO2.

extract_protocol: Total RNA was extracted by using the RNeasy mini kits (Qiagen)

treatment_protocol: The cells were then treated with 3.0 mM or 5.0 mM Ca2+ in complete medium for 48 h.

tag: agent

value: 5mM calcium


title: bovine_FGO_H3K27me3_CR_rep1


title: HMN171232_12hr

extract_protocol:
Cells were collected, washed, and stored in Qiazol prior to RNA extraction.
RNA libraries were prepared for sequencing using TM3’seq, a 3’-enriched library preparation protocol (https://www.g3journal.org/content/10/1/143).


title: HMN52543_6hr


title: HMN52555_6hr


title: H3K27Ac.HiChIP.Treg#2


title: HMN83561_6hr


title: MDA-231-3Ca, biological rep4

description: Gene expression data from 3mM calcium containing tissue culture medium

value: 3mM calcium


title: HMN171223_6hr


title: MDA-231-5Ca, biological rep3


title: H3K27Ac.HiChIP.Treg#1


title: HMN171238_12hr


title: MDA-231-5Ca, biological rep1


title: H3K27Ac.HiChIP.Tconv#1


title: H3K27Ac.HiChIP.WTGFP#2


title: MDA-231-5Ca, biological rep2


title: scRNA-seq, brain parenchyma from C57BL/J mice

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

country: Germany

institute: University Hospital Muenster

description:
ctrl_pia
single-cell RNA seq data of brain parenchyma from C57BL/J mice

data_processing:
Raw bcl files were de-multiplexed using the cellranger mkfastq pipeline (cellranger v6.0)
Read alignments and transcript counting were done individually for each sample using the cellranger count pipeline with standard parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Standard cellranger output format

source_name: CD45iv-CD45+ leukocytes from pia mater

extract_protocol:
Mice were injected (intravenously; iv) with fluorochrome coupled anti-mouse CD45 antibody (clone 30-11F, Biolegend, 3 µg/mouse). Five minutes later, animals were intracardially perfused with cold PBS with 10 U/ml heparin under deep ketamine/xylazine anesthesia. During perfusion, blood was collected and transferred into a tube. To separate different CNS compartments, the forebrain and cerebellum were dissected from mice. Under binoculars, the dura was dissected from the calvaria and the pia was dissected from the brain parenchyma. All choroid plexuses were removed from the ventricles of the brain. Brain tissue was cut into pieces and digested with collagenase D (2.5 mg/ml, Roche Diagnostics) and DNase I (0.05 mg/ml, Sigma) at 37 °C for 20 min. Pia, dura, and CP were digested in medium containing 1 mg/ml Collagenase D (Roche) for 45 min at 37°C. Afterwards, digested tissue was passed through a 70 μm cell strainer. The parenchyma was centrifuged on a 70%/37% percoll gradient. The interphase was removed, washed and re-suspended in PBS with 2% FCS. Cells extracted from the CNS, pia and dura were sorted for CD45+CD45iv- cells.
Single cell suspensions were loaded onto the Chromium Single Cell Controller using the Chromium Single Cell 3' Library & Gel Bead Kit with v2 and 3 chemistry (both from 10X Genomics, #1000128, #1000157). Sample processing and library preparation was performed according to manufacturer's instructions using AMPure beads (Beckman Coulter, A63881). Sequencing was carried out on a Illumina Novaseq using NovaSeq 6000 S4 Reagent Kit (300 Cycles, #20028312) the a 150-8-8-150 read setup.
scRNA-seq

value: pia mater

value: CD45iv-CD45+ tissue-resident leukocytes (TRL)

tag: condition

value: control


title: scRNA-seq, brain parenchyma leukocytes from C57BL/J mice 72h after transient middle cerebral artery occlusion

description:
stroke_cns_72h
single-cell RNA seq data of brain parenchyma leukocytes from C57BL/J mice 72h after transient middle cerebral artery occlusion

source_name: CD45iv-CD45+ leukocytes from brain parenchyma

value: brain parenchyma

value: transient middle cerebral artery occlusion 72h


title: scRNA-seq, brain parenchyma leukocytes from C57BL/J mice 24h after transient middle cerebral artery occlusion, rep1

description:
stroke_cns_24h_1
single-cell RNA seq data of brain parenchyma leukocytes from C57BL/J mice 24h after transient middle cerebral artery occlusion

value: transient middle cerebral artery occlusion 24h


title: scRNA-seq, dura mater leukocytes from C57BL/J mice

description:
ctrl_dura
single-cell RNA seq data of dura mater leukocytes from C57BL/J mice

source_name: CD45iv-CD45+ leukocytes from dura mater

value: dura mater


title: HMN83570_6hr

description:
bulk RNA library
time_course_PBMCs.Homo_sapiens_with_flu.GRCh38.kallisto.gene_level.ScaledTPM.txt

source_name: PBMCs

value: peripheral blood mononuclear cells


title: MDA-231-3Ca, biological rep1


title: MDA-231-CM, biological rep2

description: Gene expression data from control complete tissue culture medium


title: scRNA-seq, brain parenchyma leukocytes from C57BL/J mice

description:
ctrl_cns
single-cell RNA seq data of brain parenchyma leukocytes from C57BL/J mice


title: MDA-231-3Ca, biological rep2


title: HMN171231_6hr


title: MDA-231-3Ca, biological rep3


title: HMN171233_6hr


title: Mouse3_neo

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
FASTQ files were mapped using STAR to  GRCm38 genome build
Gene counts were obtained using featureCounts on GENCODE vM22 annotations
Genome_build: GRCm38
Supplementary_files_format_and_content: gene_counts

growth_protocol: Not Applicable

extract_protocol:
Tissue lysed in trizol. RNA extracted using Qiagen RNAeasy mini kit.
libraries were constructed using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina

treatment_protocol: Not Applicable

tag: tissue type

value: neoplastic

value: tamoxifen induction

tag: timepoint

value: 3 month


title: MDA-231-CM, biological rep4


title: MDA-231-CM, biological rep3


title: Mouse3_inv

tag: treatment


title: MDA-231-CM, biological rep1


title: R7Astar_rep_B

city: Dunedin

first: Benjamin

middle: J

last: Perry

state: Otago

address: 720 Cumberland Street

department: Microbiology and Immunology

country: New Zealand

institute: University of Otago

description: rRNA-depleted whole cell RNA

data_processing:
Reads were aligned to the reference genome using Rsubread::subjunc, reporting the single best alignment for each read pair.
Count values for features were calculated using Rsubread::featureCounts. Briefly, mapped paired-reads were counted towards a feature if: both forward and reverse reads mapped, the mapping quality was greater than MQ=10, the transcript “fragment” bound by a mapped paired-read was >50bp and <800bp, the read pair orientation was concordant with the sense or antisense transcription being counted, and a fraction of the feature overlapped with the mapped fragment.
The merged feature count table was imported into DESeq2 and analysed for differential expression of features using the Wald test with FDR correction. Reads were normalised using DESeq2 standard scaling normalisation prior to statistical analysis.
Differential expression of features using the Wald test with FDR correction.
Genome_build: Reference genomes accession used: GCA_012913625.1
Supplementary_files_format_and_content: Tab-delimited text including sense and antisense transcription. Raw counts and normalized counts.

organism: Mesorhizobium japonicum

source_name: bacterial cell culture

growth_protocol: Early stationary phase TY-broth culture (48 hr) grown at 28C

extract_protocol:
Qiagen RNeasy Mini Kit
RNA was treated with Ribo-Zero rRNA Removal Kit (Illumina) and sequencing libraries were prepared using an NEBNext Ultra Directional RNA Library Prep  Kit for Illumina (NEB).
Libraries were sequenced on an Illumina MiSeq using 75bp paired end sequencing. Paired-end strand specific RNA-seq data (dUPT method).


title: R7A_rep_A

description: rRNA-depleted whole cell RNA


title: R7A_rep_B

description: rRNA-depleted whole cell RNA


title: Mouse2_inv


title: R7Astar_rep_A

description: rRNA-depleted whole cell RNA


title: HMN171238_6hr

city: Chicago

first: Luis

last: Barreiro

address: 900 E 57th Street

institute: University of Chicago

tag: cell type


title: HMN83554_2hr


title: Mouse2_neo


title: Not_76__control_2

description:
Generated by CHIP~seq
FASTA file:
Not_76_control.fasta

source_name: S. pombe modified by genome engineering

value: Strain CBS 2777 derived

tag: modification

value: chromsome 2 centromere modified

tag: chip target and antibody

value: CENP_A modified by  amino terminal GFP tag and precipitated using Abcam Ab 290


title: Mouse1_neo


title: HMN171232_6hr

value: flu-infected


title: Not_76__control_1


title: Cen_1_after_pools_last_time_point_2

description:
Generated by CHIP~seq
FASTA file:
Not_76_combined_Cen_1_after_50p213.fasta


title: HMN52555_2hr


title: HMN52543_2hr


title: Mouse1_inv


title: HMN83561_2hr


title: Cen_1_after_pools_last_time_point_1


title: HMN171231_2hr


title: Cen_1_after_pools_1st_time_point_2


title: HMN171233_2hr


title: HMN83570_2hr


title: HMN171232_2hr


title: HMN171238_2hr


title: 841_842_Cen_8_at_native_cen _in_strain_with_neocen_2

description:
Generated by CHIP~seq
FASTA file:
Not_76_old_cen_Cen8_combined.fasta


title: Cen_1_after_pools_1st_time_point_1


title: 841_842_Cen_8_at_native_cen _in_strain_with_neocen_1


title: HMN83554_mock

value: mock


title: 839_840_Cen_8_at_neocen_in_strain_with_neocen_2

description:
Generated by CHIP~seq
FASTA file:
Not_76_combined_cen_8_839_840.fasta


title: 839_840_Cen_8_at_neocen_in_strain_with_neocen_1


title: HMN52543_mock


title: 772_NeoCen_before_2

description:
Generated by CHIP~seq
FASTA file:
772_combined_neocen_before.fasta


title: HMN52555_mock


title: mouse_Eed_mKO_FGO_H3K36me3_STAR

data_processing:
Basecalls performed using CASAVA version 1.8
All STEM-seq datasets were firstly treated with cutadapt v1.11 (Martin, 2011) and the low-quality reads and adaptors were removed before mapping. Then all filtered reads were aligned to different genomes (rat, rn6; cow, bosTau8; pig, susScr11) using Bismark (v0.7.0；bowtie2 2.1.0) (Krueger and Andrews, 2011) with default parameters. Multi-mapped reads and PCR duplicates were removed also with the Bismark. The unique mapped reads were used for CpG methylation calling with bismark_methylation_extractor. For every single CpG site, only the CpG sites that were covered at least 3 times were used for further analysis. The spiked-in Lamda DNA (1:200) was used for conversation rate calculation.
All RNA-seq datasets were mapped to the different genomes (rat: rn6; cow: bosTau8; pig: susScr11). All genomes were downloaded from UCSC (citation) by Tophat v2.1.1 (Trapnell et al., 2009). Gene expression was then calculated according to refFlat database by cufflinks 2.2.1 (Trapnell et al., 2012).
All reads were firstly processed by TrimGalore (v.0.6.4) with default parameters to remove the poor qualitied reads and also the adapters. Then the filtered reads were mapped to different genomes (rat: Rn6; cow: bosTau8; pig: susScr11) by Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012) with the default parameters. All multiple mapped reads as well as the duplicates were removed with MarkDuplicates.jar. Then all unique mapped reads were used for the downstream RPKM (reads per kilobase per million of sequenced reads) calculation. The Pearson correlation was generated for each sample with two biological replicates with 10 kb bins. The replicates with good reproducibility were pooled for downstream analysis.
Supplementary_files_format_and_content: The cov txt files contains the chr, start positon, methylated CG count, unmethylated CG count. The txt files for FPKM contain gene names and the FPKM value for all stages.

tag: experiment type

value: STAR-ChIP-seq

tag: developmental stage

value: Full grown oocyte


title: HMN171223_mock


title: mouse_Eed_Ctrl_FGO_H3K36me3_STAR


title: mouse_Eed_mCKO_MII_H3K4me3_CR_rep2

data_processing:
Library strategy: CUT&RUN
Basecalls performed using CASAVA version 1.8
All STEM-seq datasets were firstly treated with cutadapt v1.11 (Martin, 2011) and the low-quality reads and adaptors were removed before mapping. Then all filtered reads were aligned to different genomes (rat, rn6; cow, bosTau8; pig, susScr11) using Bismark (v0.7.0；bowtie2 2.1.0) (Krueger and Andrews, 2011) with default parameters. Multi-mapped reads and PCR duplicates were removed also with the Bismark. The unique mapped reads were used for CpG methylation calling with bismark_methylation_extractor. For every single CpG site, only the CpG sites that were covered at least 3 times were used for further analysis. The spiked-in Lamda DNA (1:200) was used for conversation rate calculation.
All RNA-seq datasets were mapped to the different genomes (rat: rn6; cow: bosTau8; pig: susScr11). All genomes were downloaded from UCSC (citation) by Tophat v2.1.1 (Trapnell et al., 2009). Gene expression was then calculated according to refFlat database by cufflinks 2.2.1 (Trapnell et al., 2012).
All reads were firstly processed by TrimGalore (v.0.6.4) with default parameters to remove the poor qualitied reads and also the adapters. Then the filtered reads were mapped to different genomes (rat: Rn6; cow: bosTau8; pig: susScr11) by Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012) with the default parameters. All multiple mapped reads as well as the duplicates were removed with MarkDuplicates.jar. Then all unique mapped reads were used for the downstream RPKM (reads per kilobase per million of sequenced reads) calculation. The Pearson correlation was generated for each sample with two biological replicates with 10 kb bins. The replicates with good reproducibility were pooled for downstream analysis.
Supplementary_files_format_and_content: The cov txt files contains the chr, start positon, methylated CG count, unmethylated CG count. The txt files for FPKM contain gene names and the FPKM value for all stages.

extract_protocol: CUT&RUN library preparation and sequencing  CUT&RUN was performed as previously reported (Skene et al., 2018; Skene and Henikoff, 2017) with modifications. Briefly, after removing the zona pellucida with Tyrode’s solution (Sigma-Aldrich, T1788) or 0.5% (m/v) Protease from Streptomyces griseus (Sigma-Aldrich, P8811), mammalian oocytes and early embryos were incubated with Concanavalin-coated magnetic beads (Polyscience, 86057) for 10 min at room temperature on a thermomixer at 400 rpm. Samples were then incubated with primary antibody at a ratio of 1:100 at 4℃ overnight on a thermomixer at 400 rpm. The next day, after washing for one time, beads were incubated with pA-MNase (to a final concentration of 400-700ng/mL) (a gift from Steven Henikoff lab) at 4℃ for 3 hours on a thermomixer at 400 rpm. After two times of washing, targeted digestion was performed by adding 2μL of 100mM CaCl2 for 30 mins on ice, followed by termination by adding an equal volume of 2  × stop buffer. Samples were then incubated at 37℃ for 20 mins for fragment releasing. The total samples or supernatants were digested with Proteinase K (NEB, P8107S) and purified using phenol:chloroform:isoamyl alcohol (25:24:1, v/v) followed by ethanol purification at -80℃ overnight. The next day, DNA was purified and subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Sequencing was done using the HiSeq X Ten system (Illumina) according to the manufacturer’s protocol.

value: Cut&Run

value: MII oocyte


title: 823_824_unbent before_1

description:
Generated by CHIP~seq
FASTA file:
Not_76_combined_unbent_before.fasta


title: 772_NeoCen_before_1


title: BM-MSCs from newly diagnosed AML patients, biological rep2

city: Tianjin

first: Jingying

last: Cheng

state: State...

address: 288 Nanjing Road, Heping District, Tianjin

institute: Institute of Hematology and Blood Diseases Hospital,Chinese Academy of Medical Sciences and Peking Union Medical College

description: Gene expression data from BM-MSCs of newly diagnosed AML patients

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Primeview. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: bone marrow, primary

label_protocol: Cyanine-3 (Cy3) labeled cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MSCs were isolated from fresh BM aspirates, and cultured in DMEM/F12 supplemented with 10% fetal bovine serum, 100 U/ml penicillin and 100μg/ml streptomycin at 37°C under 5% CO2. The medium was replaced every 3 days. Adherent, spindle-shaped cells appeared within 1-2 weeks, and were passaged at 80% confluency.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: MSCs from different resources were digested using enzymatic digestion with 0.125% trypsin/0.5 mM EDTA. Centrifuge and remove the trypsin solution by discarding the supernatant.

tag: fab subtype

value: BM-MSCs

tag: gender

value: male

tag: age


title: HMN83570_mock


title: BM-MSCs from newly diagnosed AML patients, biological rep3

value: female


title: BM-MSCs from relapsed AML patients, biological rep3

description: Gene expression data from BM-MSCs of relapsed AML patients

source_name: bone marrow, relapsed


title: mouse_Eed_mCKO_MII_H3K4me3_CR_rep1

city: Beijing

first: Wei

last: Xie

address: Zhongguancun north street

institute: Tsinghua University


title: BM-MSCs from relapsed AML patients, biological rep2


title: BM-MSCs from healthy donors, biological rep3

description: Gene expression data from BM-MSCs of healthy donors

source_name: bone marrow, healthy


title: BM-MSCs from relapsed AML patients, biological rep1


title: BM-MSCs from healthy donors, biological rep1


title: mouse_Eed_Ctrl_MII_H3K4me3_CR_rep2


title: HMN171231_mock


title: 860_861_HighGC bent before_2

description:
Generated by CHIP~seq
FASTA file:
Not76_combined_Bent_High_GC_before.fasta

tag: strain


title: HMN83561_mock


title: 823_824_unbent before_2


title: 801_802; Cen8 at neo_cen_2

description:
Generated by CHIP~seq
FASTA file:
Not_76_801_2_combined.fasta


title: HMN171238_mock


title: 860_861_HighGC bent before_1


title: BM-MSCs from newly diagnosed AML patients, biological rep1


title: BM-MSCs from healthy donors, biological rep2


title: CP_04_G2

city: Modena

first: Marika

last: Quadri

state: Modena

address: Via del Pozzo 71

institute: University of Modena and Reggio Emilia

hyb_protocol: As per Nanostring Technologies standard protocol

scan_protocol: NanoString cartridges were scanned on a digital analyzer under default setting set by the manufacturer.

data_processing: Data were nomalized using unique housekeeping gene for each RCM-subtypes, and comparison were performed between RCM-subtypes to obtain Fold-Change

label: Fluorescent barcode

source_name: primary melanoma

extract_protocol: Total RNA was extracted from Formalin-Fixed paraffin-Embedded primary melanoma sampley by using RNeasy FFPE kit (Quiagen). 10 slices of 10uM per patients were employed and only tumoral area was collected. NanoString nCounter technology was performed by PharmaDiagen team (Pordenone, Italy) and the analysis was focused on 770 genes (nCounter PanCancer Progression Panel).

tag: tissue

value: primary melanoma

tag: tumor stage

value: III

tag: rcm subtypes

value: CT


title: HMN171233_mock

value: peripheral blood mononuclear cells


title: 801_802; Cen8 at neo_cen_1

data_processing:
fastq files were not quality trimmed but aligned to customized fasta files (inlcluded) using the Burroughs Wheeler aligner in samtools. Bam files were filtered for  paired sequences using the 99, 147, 83 and 163 flags and then merged into  asingle bam file
Generation of the coverage vectors used in the figures used a Granges object using the R libraries, GenomicRanges, GenomicAlignments, rtracklayer, Rsamtools, limma,
Coverage vectors were normalized on the basis of read counts to the centromeres of chromosomes 1 and 3. Read counts were calculated using the samtools view command.
Coverage vectors were normalized on the basis of read counts to the centromeres of chromosomes 1 and 3. Read counts were calculated using the samtools view command.
Vectors were smoothed using a median smoothing ; using the runmed command on a vectorized derivative of the Rle object with a smoothing distance of either 101 or 1001 residues for either the centromere of whole chromsome coverage vectors
Genome_build: Not relevant used custom fasta files; FASTA files available on the series record.
Supplementary_files_format_and_content: coverage vectors that can be processed and inspected with simple text editors


title: HMN171232_mock


title: 4.4_Hot_concat_after_pools_2

description:
Generated by CHIP~seq
FASTA file:
Not_76_Chr_2_4.4_Hot_after_combined.fasta


title: 4.4_Hot_concat_after_pools_1


title: mouse_Eed_Ctrl_MII_H3K4me3_CR_rep1


title: B14_c2

description: multiplexed 10X single-cell capture

data_processing:
Sample preprocessing was performed using the count function in cellranger (v3.0.2).
We demultiplexed cells into individuals and respective infection conditions using souporcell (v2.0) (Heaton et al., 2020)
We excluded cells that featured: 1) a “singlet” status called by souporcell, 2) between 200 – 2500 genes detected (nFeature_RNA), and 3) a mitochondrial reads percentage < 10%
We calcualted pseudobulk estimates for each major immune cell cluster (5) by summing the raw UMI counts across all cells assigned to that sample for each gene using the sparse_Sums function in textTinyR (v1.1.3)
We filtered out lowly-expressed genes based on cluster-specific logCPM values (removed genes with a median logCPM < 1.5 in CD4+ T cells, monocytes, and PBMCs, < 2.5 in B cells and CD8+ T cells, and < 4.0 in NK cells)
We used the function voom from the R package limma (Ritchie et al., 2015) to normalize the pseudobulk data
Genome_build: GRCh38.p12 and influenza A virus (A/California/04/09)
Supplementary_files_format_and_content: .mtx files include count values for each multiplexed sample; .tsv files include the description of barcodes (cells) and features (genes)

source_name: multiplexed PBMCs

extract_protocol:
Cells were collected, washed, and prepared for single-cell capture using the 10X workflow. Immediately prior to the capture, cells from samples were combined into two pools (6 samples per pool), so that each pool was balanced for infection status and contained cells from each individual processed that day (either 4 EUR and 2 AFR individuals or 4 AFR and 2 EUR individuals) combined in an equal ratio.
Single-cell GEMs were generated using a Chromium Controller instrument (10x Genomics).
Sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kits (v2, 10x Genomics), according to the manufacturer’s instructions. Briefly, GEM-RT was performed in a thermal cycler: 53°C for 45 min, 85°C for 5 min. cDNA was cleaned up with DynaBeads MyOne Silane Beads (ThermoFisher Scientific) and amplified with a thermal cycler: 98°C for 3 min, cycled 11 x 98°C for 15 s, 67°C for 20s, 72°C for 1 min, and 72°C 1 min. After a cleanup with SPRIselect Reagent Kit, the libraries were constructed by performing the following steps: fragmentation, end-repair, A-tailing, SPRIselect cleanup, adaptor ligation, SPRIselect cleanup, sample index PCR, and SPRIselect size selection. Libraries were sequenced on NovaSeq S4 and SP flowcells with 100 bp paired-end reads.

treatment_protocol: Per individual for each condition, 1 million (M) PBMCs were plated at a concentration of 1M/ml and infected with either mock-conditioned media (negative control) or Cal/04/09 IAV at an MOI of 0.5. After 30 minutes of IAV infection, the virus was washed from PBMC cultures, cells were replated, and cells were then incubated for 6hrs at 37C in 5% CO2 and 20% O2.

value: mock- and IAV-infected


title: B15_c1

description: multiplexed 10X single-cell capture


title: B15_c2

description: multiplexed 10X single-cell capture


title: Hot_concat_before_2

description:
Generated by CHIP~seq
FASTA file:
Not_76_Chr_2_Hot_region_concatamer_before_combined.fasta

value: Strain CBS 2777 derived


title: 4.4_Hot_concat_Hot_before_1

description:
Generated by CHIP~seq
FASTA file:
Not_76_combined_4.4_Hot_before.fasta

value: chromsome 2 centromere modified


title: CP_11_G4

label_protocol: As per Nanostring Technologies standard protocol

value: IV


title: 4.4_Hot_concat_Hot_before_2

value: CENP_A modified by  amino terminal GFP tag and precipitated using Abcam Ab 290


title: CP_08_G4

value: V


title: CP_10_G4


title: CP_09_G4


title: Hot_concat_after_pools_2

description:
Generated by CHIP~seq
FASTA file:
Not_76_combined_Hot_region_concatamer_after.fasta


title: CP_06_G1

value: II


title: CP_12_G4


title: B11_c2

description: multiplexed 10X single-cell capture


title: B12_c1

description: multiplexed 10X single-cell capture


title: B13_c2

description: multiplexed 10X single-cell capture


title: Hot_concat_after_pools_1


title: CP_06_G4


title: Hot_concat_before_1


title: CP_04_G4


title: B14_c1

description: multiplexed 10X single-cell capture


title: Art_Cen after_pools_1

description:
Generated by CHIP~seq
FASTA file:
Not_76_Art_Cen_after_combined.fasta


title: Art_Cen after_pools_2


title: B13_c1

description: multiplexed 10X single-cell capture


title: B11_c1

description: multiplexed 10X single-cell capture


title: Art_Cen before_2

description:
Generated by CHIP~seq
FASTA file:
Not_76_Art_Cen_before_combined.fasta


title: Art_Cen before_1


title: CP_02_G3

value: DN


title: C. acetobutylicum A+T rich after; pools_2

description:
Generated by CHIP~seq
FASTA file:
Not_76_ATrich_after_combined.fasta


title: B12_c2

description: multiplexed 10X single-cell capture


title: C. acetobutylicum A+T rich after; pools_1


title: MSI-O HX531 RNA

source_name: MSI-O HX531 RNA

tag: cell line

value: line26 wild type

value: mouse small intestinal organoid

tag: genotype/variation

value: wild type


title: B10_c2

description: multiplexed 10X single-cell capture


title: B10_c1

description: multiplexed 10X single-cell capture


title: CP_05_G4


title: MSI-O -Vit A RNA

source_name: mouse small intestinal organoid

tag: line

value: no Vit A

tag: celltype

value: intestinal organoid

tag: mutations


title: CP_01_G3

value: primary melanoma


title: MSI-O NRX194204 RNA

source_name: MSI-O NRX194204 RNA

tag: cell type

tag: treatment


title: MSI-O LG100268 RNA

source_name: MSI-O LG100268 RNA


title: B9_c1

description: multiplexed 10X single-cell capture


title: B9_c2

description: multiplexed 10X single-cell capture


title: C. acetobutylicum A+T rich before_2

description:
Generated by CHIP~seq
FASTA file:
Not_76_Chr_2_AT_rich_before_combined.fasta

tag: modification

tag: chip target and antibody


title: B8_c2

description: multiplexed 10X single-cell capture


title: CP_09_G3


title: C. acetobutylicum A+T rich before_1


title: B8_c1

description: multiplexed 10X single-cell capture


title: CP_10_G3

value: III


title: MSI-O AGN193109 RNA

source_name: MSI-O AGN193109 RNA


title: CP_07_G2

value: RC


title: 376_cen_8_2

description:
Generated by CHIP~seq
FASTA file:
Not_76_Ade_6_cen_8_combined.fasta


title: B7_c2

description: multiplexed 10X single-cell capture

value: peripheral blood mononuclear cells


title: 376_cen_8_1


title: CP_12_G3


title: MSI-O 9-cis RA RNA RNA

source_name: MSI-O 9-cis RA RNA RNA

value: 9-cis RA


title: CP_08_G3


title: CP_03_G2


title: B7_c1

description: multiplexed 10X single-cell capture

value: mock- and IAV-infected


title: CP_01_G2


title: CP_12_G2


title: alphoid_unswapped_1

description:
Generated by CHIP~seq
FASTA file:
Not_76_alphoid_before_combined.fasta

value: Strain CBS 2777 derived

value: chromsome 2 centromere modified


title: Control_swapped_1

description:
Generated by CHIP~seq
FASTA file:
Not_76_empty_vector_after_combined.fasta

value: CENP_A modified by  amino terminal GFP tag and precipitated using Abcam Ab 290


title: alphoid_unswapped_2


title: B5_c1

description: multiplexed 10X single-cell capture


title: CP_11_G2


title: Cytoplasm poly(A)+ RNA-seq with METTL3 KD

city: Wuhan

first: Yu

last: Zhou

state: Hubei

address: Luojia Hill

department: College of Life Sciences

institute: Wuhan University

description: polyA+ RNA-seq of cytoplasm in METTL3-KD cells

data_processing:
Reads of total RNA-seq were mapped to hg19 and Gencode v19 using STAR with parameters --alignEndsType EndToEnd --outFilterMultimapNmax 1 --outFilterMismatchNoverReadLmax 0.04. Reads of poly(A)+ RNA-seq were mapped to hg19 and ENSEMBL v75 using STAR with parameters --alignEndsType EndToEnd --outFilterMultimapNmax 1 --outFilterMismatchNmax 10. Reads of nanopore were mapped to hg19 using minimap2 with parameters -ax splice -k 14 -uf --secondary=no. Reads of SLAM-seq were preprocessed to remove adapters, 3’poly(A) runs of read 2, 5’poly(A) runs of read 1 with cutadapt (v1.18) and corrected by fastp (v0.20.0). Then, these reads were mapped to hg19 and ENSEMBL v75 using STAR with parameters --alignEndsType EndToEnd --outFilterMultimapNmax 1 --outFilterMismatchNmax 10.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig file of coverage signals for rRNA-depleted RNA-seq, bedGraph file of normalized coverage (cpm) in genome for polyA RNA-seq, and Bed format file for mapped Nanopore long reads.

growth_protocol: HeLa cells  were maintained in DMEM (Gibco) supplemented with 10% FBS (Hyclone) and 100 U penicillin/streptomycin (Gibco) at 37°C with 5% CO2.

extract_protocol:
RNA from the lysates of different cellular fractionations  or total RNA was extracted by TRIZOL reagent.
Libraries of the RNA-seq were prepared according to NEB's protocol of the NEBNext® Ultra™ II directional RNA library prep kits. Libraries of the SLAM-seq were prepared according to Lexogen's instructions of QuantSeq 3'mRNA-seq library prep kit REV for Illumina. Naropore libraries were prepared and sequenced according to Oxford's instructions for direct RNA sequencing.
RNA-seq, SLAM-seq, Nanopore direct RNA-seq

treatment_protocol: For RNA metabolic labeling, three hours just before the 4-thiouridine was added into the medium, fresh medium was exchanged. Then, s4U (Sigma) was added to the medium at a final concentration of 1 mM and the cells were placed back into the incubator for another 30 mins.

value: HeLa

value: METTL3 KD

tag: fraction

value: cytoplasm


title: B6_c2

description: multiplexed 10X single-cell capture


title: CP_02_G2


title: B6_c1

description: multiplexed 10X single-cell capture


title: Cen_5_swapped_2

description:
Generated by CHIP~seq
FASTA file:
Not_76_Cen_5_after_combined.fasta

extract_protocol: Material was quantified using Qubit (Invitrogen) and the size profile analysed on the 2200 or 4200 TapeStation (Agilent, dsDNA HS Assay). Input material was normalised to 5 ng or maximum available prior to library preparation. Automated library preparation was performed using the Apollo prep system (Wafergen, PrepX ILMN 32i, 96 sample kit) and standard Illumina multiplexing adapters following manufacturer’s protocol up to pre-PCR amplification. Libraries were PCR amplified (18 cycles) on a Tetrad (Bio-Rad) using the NEBNext High-Fidelity 2X PCR Master Mix (NEB) and in-house unique dual indexing primers (based on DOI: 10.1186/1472-6750-13-104). Individual libraries were normalised using Qubit, and the size profile was analysed on the 2200 or 4200 TapeStation. Individual libraries were normalised and pooled together accordingly. The pooled library was diluted to ~10 nM for storage. The 10 nM library was denatured and further diluted prior to loading on the sequencer. Paired end sequencing was performed using a HiSeq4000 75bp platform (Illumina, HiSeq 3000/4000 PE Cluster Kit and 150 cycle SBS Kit)


title: MSI-O ATRA RNA RNA

source_name: MSI-O ATRA RNA RNA

value: line26 wild type

value: ATRA


title: CP_06_G2

value: II

value: DC


title: B5_c2

description: multiplexed 10X single-cell capture


title: Control_swapped_2


title: DRB SLAM RNA-seq rep2

description: 4sU polyA-seq rep2 in DRB treated cells

source_name: DRB SLAM RNA-seq rep2

value: WT

value: DRB


title: Cen_5_swapped_1


title: B4_c2

description: multiplexed 10X single-cell capture


title: Nuclear matrix poly(A)+ RNA-seq with METTL3 KD

description: polyA+ RNA-seq of nuclear matrix in METTL3-KD cells

value: nuclear matrix


title: DRB SLAM RNA-seq rep1

description: 4sU polyA-seq rep1 in DRB treated cells

source_name: DRB SLAM RNA-seq rep1


title: CP_10_G1

value: primary melanoma


title: MSI-O DMSO RNA

source_name: MSI-O DMSO RNA

value: mouse small intestinal organoid

value: wild type

value: DMSO


title: CP_09_G1


title: CP_11_G3

value: III

value: DN


title: B3_c2

description: multiplexed 10X single-cell capture

value: peripheral blood mononuclear cells

value: mock- and IAV-infected


title: Nucleoplasm poly(A)+ RNA-seq with METTL3 KD

description: polyA+ RNA-seq of nucleoplasm in METTL3-KD cells

value: HeLa

value: METTL3 KD

value: nucleoplasm


title: DMSO SLAM RNA-seq rep2

description: 4sU polyA-seq rep2 in DMSO treated cells

source_name: DMSO SLAM RNA-seq rep2


title: Cen_5_unswapped_1

description:
Generated by CHIP~seq
FASTA file:
Not_76_Cen_5_before_combined.fasta

source_name: S. pombe modified by genome engineering

value: Strain CBS 2777 derived

value: chromsome 2 centromere modified

value: CENP_A modified by  amino terminal GFP tag and precipitated using Abcam Ab 290


title: CP_08_G1

value: I

value: DC


title: Cen_8_swapped_2

description:
Generated by CHIP~seq
FASTA file:
Not_76_Cen_8_after_combined.fasta


title: Cen_8_swapped_1


title: DMSO SLAM RNA-seq rep1

description: 4sU polyA-seq rep1 in DMSO treated cells

source_name: DMSO SLAM RNA-seq rep1

value: WT


title: Nuclear matrix poly(A)+ RNA-seq

description: polyA+ RNA-seq of nuclear matrix

source_name: Nuclear matrix poly(A)+ RNA-seq

value: nuclear matrix


title: B2_c1

description: multiplexed 10X single-cell capture


title: B3_c1

description: multiplexed 10X single-cell capture


title: B2_c2

description: multiplexed 10X single-cell capture


title: Cen_8_unswapped_2

description:
Generated by CHIP~seq
FASTA file:
Not_76_Cen_8_before_combined.fasta


title: CP_07_G1

value: primary melanoma


title: B4_c1

description: multiplexed 10X single-cell capture


title: CP_04_G1


title: B1_c2

description: multiplexed 10X single-cell capture


title: Nucleoplasm poly(A)+ RNA-seq

description: polyA+ RNA-seq of nucleoplasm

source_name: Nucleoplasm poly(A)+ RNA-seq


title: Cytoplasm poly(A)+ RNA-seq

description: polyA+ RNA-seq of cytoplasm

source_name: Cytoplasm poly(A)+ RNA-seq

value: cytoplasm


title: B1_c1

description: multiplexed 10X single-cell capture

source_name: multiplexed PBMCs


title: Nuclear matrix rRNA-depleted RNA-seq

description: total RNA-seq

source_name: Nuclear matrix rRNA-depleted RNA-seq


title: CP_03_G1

source_name: primary melanoma

value: II


title: Cen_8_unswapped_1


title: Cen_5_unswapped_2


title: CP_01_G1

value: III


title: CP_02_G1