title: T19_10mM_MPE_(20211006_TB_Mv_T19_10uM_MPE_2SCU_20210831)

data_processing:
Library strategy:  MPE-seq
Genome_build: T19_genome.fasta
1. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map 25bp paired-end reads to the reference sequence (Drosophilia melanogaster dm6 or Marseillevirus marseillvirus strain T19 or Marseillevirus marseillvirus strain G648 or 3 copies of the artificial sequence Widom 601). 2. We extracted properly paired reads from the alignments to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz).  3. We used bedtools genomecov to make a normalized count bedgraph file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

source_name: MPE-seq of T19 10 uM H2O2

value: DNA from MPE-digested chromatin


title: shHif_N1

status: Public on Sep 27 2022

type: SRA

city: Wuhu

first: Xiaopeng

last: Shen

address: 1 East Beijing Rd.

country: China

institute: Anhui Normal University

library_source: transcriptomic

data_processing:
trim_galore
Hisat2
Stringtie
Assembly: GRCm38
Supplementary files format and content: csv files include read counts values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Embryonic stem cells

extract_protocol:
Total RNA samples were extracted using the Total RNA Isolation Reagent (Biosharp).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Embryonic stem cells

tag: cell line

tag: cell type

value: ESC

tag: treatment

value: shHif-1a normoxia


title: Hif1aOE_3

value: Hif1aOE normoxia


title: T19_100mM_MPE_(20211006_TB_Mv_T19_100uM_MPE_2SCU_20210831)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

library_source: genomic

molecule: genomic DNA

organism: Marseillevirus marseillevirus

source_name: MPE-seq of T19 100 uM H2O2

tag: strain

tag: type

value: viral DNA


title: CTL (3A)

city: S. Giovanni Rotondo (FG)

first: Tommaso

last: Mazza

address: Viale Cappuccini, 1

department: Bioinformatics

country: Italy

institute: IRCCS Casa Sollievo della Sofferenza

data_processing:
Basecalls were performed using Illumina's bcl2fastq tool
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie2 version 2.3.5.1. Using the following parameters : -q --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700.
Peaks were called uing MACS v2.2.6 with the following parameters : --broad -p 1e-5 -f BAMPE –keep-dup all
bigWig files were generated using the bamCoverage package of deepTools.
Assembly: hg38
Supplementary files format and content: bigWig (except for CTL samples)
Library strategy: CUT&Tag

organism: Homo sapiens

source_name: HUVEC

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVEC) were obtained from Thermo Fisher Scientific (Massachusetts, USA). Cells were cultured in Nunc EasYFlasks in Endothelial Cell Growth medium 2 (Promocell, Heidelberg, Germany).

extract_protocol:
Cells on the fourth day post-transfections were collected in 1.5mL tubes. Cut & Tag was performed according to the manufacturer’s protocol (Active Motif, California, USA). Briefly, cells were harvested and washed once using 1mL of 1x Wash buffer. In parallel, the Concanavalin A Beads were prepared. Each 500.000 cells, 20µL of the beads’ slurry were withdrawn and mixed with 1,6mL of 1x Binding buffer. Beads were harvested using a magnetic stand and washed twice with 1,5 mL of 1x Binding buffer. The pellet containing the cells previously harvested and the beads’ suspension were mixed in a 1.5 mL tube, rotating end-over-end for 10 minutes at room temperature. Cells were harvested by using a magnetic stand to clear and the supernatant was discarded. The pellet was resuspended in 50µL of Antibody Buffer and 1µL of Rabbit ab9108 Anti-6X His tag antibody (Abcam, Cambridge, United Kingdom) was added where needed. The mix was incubated overnight at 4oC with orbital mixing ensuring the liquid to stay together at the bottom of the tube. The Guinea Pig Anti-Rabbit Antibody secondary antibody was diluted 1:100 in Dig-Wash Buffer. The tubes were cleared using a magnetic stand and the liquid was discarded. 100µL of Guinea Pig Anti-Rabbit Antibody mix was added and tubes were incubated at room temperature for 60 minutes in an orbital rotator. Cells were cleared through a magnetic stand, and they were washed three times using 1mL of Dig-Wash Buffer. In parallel, the CUT&TAGTM Assembled pA-Tn5 Transposomes was diluted 1:100 with Dig-300 Buffer. For each immunoprecipitated samples, 100µL of CUT&TAGTM Assembled pA-Tn5 Transposomes was added, and the mix was placed on an orbital rotator for 60 minutes at room temperature. The cells were harvested using a magnetic stand and eventually washed three times using 1mL of Dig-300 buffer. In the following step each tube was supplemented with 125µL of Tagmentation Buffer and incubated at 37oC for 60 minutes. To isolate the DNA surrounding macroH2A1.1 and macroH2A1.2 deposition regions, the tagmentation was first stopped by addition of 4,2µL of 0,5M EDTA, 1,25µL of 10% SDS and 1,25µL of Proteinase K (10mg/mL) per each sample. The tubes were then vortexed at full speed and incubated for 60 minutes at 55oC to digest. The samples were cleared using a magnetic stand and 625µL of DNA Purification Buffer per each were added. The samples were transferred to DNA Purification Columns, centrifuged at 17000G for 1 minute. After the flow-through was discarded, 750µL of DNA Purification Wash Buffer was added to each sample, which was then centrifuged again at 17000G for 1 minute. The flow-through was discarded. To remove any DNA Purification Wash Buffer leftover, the empty columns were further centrifuged at 17000G for 2 minutes. To isolate the DNA, 35µL of DNA Purification Elution Buffer were added to each sample, which was then incubated at room temperature for 1 minute and eventually centrifuged at 17000G for 1 minute.
Library preparation for Cut & Tag samples was performed according to the manufacturer’s protocol (Active Motif, California, USA). Paired-end Illumina sequencing was obtained using Illumina Hiseq 2500 (Illumina, San Diego, CA,  USA), obtaining two FASTQ files for each of the two biological replicates of macroH2A1.1,  two for each of the three biological replicates of macroH2A1.2  and two for each of the three biological replicates of the control samples, for a total of 4.8, 8.1 and 7.2 million reads, respectively.

treatment_protocol: Cellular reprogramming was performed as already described (Giallongo et al. 2022). Briefly, cells were harvested using TrypLE express enzyme (Thermo Fisher Scientific, Massachusetts, USA) and transfected with Epi5 Episomal iPSC Reprogramming Kit (Thermo Fisher Scientific, Massachusetts, USA), using 10µL Neon Transfection System (Thermo Fisher Scientific, Massachusetts, USA). For this purpose, 10^5 living cells were resuspended in 10µL of R buffer and 1µL of the content of each vial from the reprogramming kit was added. Furthermore, 3mL of E buffer were added to the Neon transfection tube together with the vectors expressing macroH2A1.1-6His and macroH2A1.2-6His (Addgene, Massachusetts, USA), where needed [25]. Electroporation was performed using Pulse voltage 1400 V, Pulse Width 20 ms, Pulse number 2. Cells were seeded on 35mm Petri dishes coated by hESC-qualified MatriGel in endothelial medium, which was changed daily until day 4 post-transfection.

value: HUVEC

value: Human Umbilical Vein Endothelial Cells

value: control

tag: chip antibody

value: ab9108 Anti-6X His tag antibody


title: GMP.13.r1

city: Boston

first: Michael

middle: K.

last: Mansour

state: MA

address: 55 Fruit Street

institute: Massachusetts General Hospital

data_processing:
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of mm9 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Genome_build: mm9
Supplementary_files_format_and_content: htseq_output

source_name: granulocyte monocyte progenitor

growth_protocol: GMPs were maintained in culture in the presence of stem cell factor and β-estradiol (0.5 µM) which permits nuclear translocation of the ER-HoxB8 fusion protein, resulting in the conditional immortalization of the GMP.

extract_protocol:
Clonal naïve GMP and neutrophil total RNA was extracted from cells at 5x106 cells/ml using the Qiagen RNeasy Plus Mini Kit (Qiagen) with DNaseI treatment (RNase free DNase Set, Qiagen). RNA quality was confirmed by RNA Tapestration and quantified with Qbit. All samples showed RNA quality of >7.5 and RNA-seq libraries were prepared.
Sequencing was performed on Illumina HiSeq 2500 instrument, resulting in approximately 30 million of 50 bp reads per sample. Sequencing reads were mapped in a splice-aware fashion to the mouse reference transcriptome (mm9 assembly) using STAR. Read counts over transcripts were calculated using HTSeq based on the Ensembl annotation for NCBI37/mm9 assembly.

treatment_protocol: Removal of beta-estradiol from the media restores differentiation of the GMP into mature neutrophils. To remove β-estradiol completely, GMPs were washed twice with phosphate-buffered saline prior to seeding cells in complete RPMI containing stem cell factor.

value: C57Bl/6 CD45.1-STEM

tag: media type

value: Plus beta-estradiol (0.5 microM)

tag: replicate

value: replicate 1


title: shHif_H1

value: shHif-1a hypoxia


title: MacroH2A1.2 (2C)

value: over-expressing tagged macroH2A1.2


title: Hif1aOE_2


title: T19_1000mM_MPE_(20211006_TB_Mv_T19_1000uM_MPE_2SCU_20210831)

source_name: MPE-seq of T19 1000 uM H2O2


title: T19_128th_MNase_(20210610_TB_Mv_20210526_1_128x)

data_processing:
Genome_build: T19_genome.fasta
1. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map 25bp paired-end reads to the reference sequence (Drosophilia melanogaster dm6 or Marseillevirus marseillvirus strain T19 or Marseillevirus marseillvirus strain G648 or 3 copies of the artificial sequence Widom 601). 2. We extracted properly paired reads from the alignments to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz).  3. We used bedtools genomecov to make a normalized count bedgraph file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

source_name: MNase-seq of T19 1/512h MNase

value: DNA from MNase-digested chromatin


title: G648_no-MNase_(20210628_TB_Mv_G648_0x_06092021)

data_processing:
Genome_build: G648_genome.fasta
1. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map 25bp paired-end reads to the reference sequence (Drosophilia melanogaster dm6 or Marseillevirus marseillvirus strain T19 or Marseillevirus marseillvirus strain G648 or 3 copies of the artificial sequence Widom 601). 2. We extracted properly paired reads from the alignments to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz).  3. We used bedtools genomecov to make a normalized count bedgraph file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

source_name: MNase-seq of G648 no MNase


title: GMP.12.r2

value: replicate 2


title: MacroH2A1.2 (2B)


title: GMP.12.r1


title: Hif1aOE_1


title: shHif_N2


title: MacroH2A1.2 (2A)


title: CTL (3B)


title: G648_MPE40_(20211006_TB_Mv_G648_MPE40_20210924)

data_processing:
Library strategy:  MPE-seq
Genome_build: G648_genome.fasta
1. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map 25bp paired-end reads to the reference sequence (Drosophilia melanogaster dm6 or Marseillevirus marseillvirus strain T19 or Marseillevirus marseillvirus strain G648 or 3 copies of the artificial sequence Widom 601). 2. We extracted properly paired reads from the alignments to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz).  3. We used bedtools genomecov to make a normalized count bedgraph file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

source_name: MPE-seq of G648 replicate 4

value: DNA from MPE-digested chromatin


title: MacroH2A1.1 (1C)

value: over-expressing tagged macroH2A1.1


title: ctrl_3

value: Embryonic stem cells

value: ESC

value: control normoxia


title: ctrl_2


title: GMP.10.r1


title: GMP.13.r2


title: G648_MPE40_2S_(20211006_TB_Mv_G648_MPE40_2SCU_20210924)

source_name: MPE-seq of G648 replicate 5

value: viral DNA


title: GMP.10.r2


title: MacroH2A1.1 (1A)

value: HUVEC


title: GMP.7.r2


title: ctrl_1


title: G648_MPE10_(20211006_TB_Mv_G648_MPE10_20210924)

source_name: MPE-seq of G648 replicate 2


title: WT_3 (MX1-Cre_3)

city: San Diego

first: Dong-Er

last: Zhang

state: California

address: 3855 Health Sciences Dr

department: Pathology

institute: UCSD

data_processing:
Mouse LK and K562 reads were aligned to GRCm38 and GRCh38 references genomes, respectively, using STAR software package.
Differential Gene Expression analysis was conducted for Mouse LK and K562 using DESeq2 package in R. For K562, DEGs were defined by FC > 2, FC < 0.5, and adjusted p < 0.05. In Mouse LK, DEGs were defined by FC > 1.5 or FC < 0.667, and adjusted p-value < 0.05.
rMATs was used to identify alternative splicing. In K562, altered splice events were identified, requiring at least 5% inclusion ration (-cstat) with FDR < 0.05. In mouse LK cells, altered splicing events were identified requiring > 5% inclusion ratio and FDR < 0.01.
Assembly: GRCm38, GRCh38
Supplementary files format and content: Differentially expressed genes (DEG) from DESeq2 analysis between indicated samples (WT vs P95H, etc.) for both Murine LK cells and K562
Supplementary files format and content: Alternative splice events from rMATs analysis of RNA-seq data between indicated samples (WT vs RUNX1 KD, etc.) for both Murine LK and K562

source_name: hematopoeitic progenitors

extract_protocol:
Total RNA was extracted from mouse LK cells and K562 cells using the Trizol Reagent. Mouse LK cells (Lin- c-Kit+) were flow sorted from bone marrow.
PolyA-selected RNA was purified using Illumina TruSeq RNA Sample Preparation Kit according to manufacturer's protocol.

value: Lin- c-Kit+ (LK) cells

tag: genotype

value: Mouse LK WT


title: GMP.4.r2


title: G648_8th_MNase_(20210628_TB_Mv_G648_1_8x_06092021)

source_name: MNase-seq of G648 1/32nd MNase


title: GMP.7.r1


title: Runx1-KO_3 (Runx1-/-; MX1-Cre_3)

description:
cmpr_deg_p95_runx1_double.selected.xlsx
AS_runx1_default.001005.xlsx

value: Mouse LK WT SRSF2 RUNX1 KO


title: G648_64th_MNase_(20210628_TB_Mv_G648_1_64x_06092021)

source_name: MNase-seq of G648 1/256th MNase


title: WT_2 (MX1-Cre_2)


title: GMP.4.r1

value: C57Bl/6 CD45.1-STEM


title: WT_1 (MX1-Cre_1)


title: Runx1-KO_1 (Runx1-/-; MX1-Cre_1)


title: G648_4x_MNase_(20210628_TB_Mv_G648_4x_06092021)

source_name: MNase-seq of G648 1x MNase


title: GMP.3.r1

value: Plus beta-estradiol (0.5 microM)


title: G648_32th_MNase_(20210628_TB_Mv_G648_1_32x_06092021)

source_name: MNase-seq of G648 1/128th MNase


title: Runx1-KO_2 (Runx1-/-; MX1-Cre_2)


title: P95_4 (Srsf2P95H/+; MX1-Cre_4)

description:
cmpr_deg_p95_runx1_double.selected.xlsx
AS_P95_default.001005.xlsx

value: Mouse LK P95H SRSF2


title: RNA-seq cKO CB 3

city: Turku

first: Matthieu

last: Bourgery

address: Kiinamyllynkatu 10

country: Finland

institute: University of Turku

description:
mRNA_transcript_counts_ensembl_CB_RNAseq.txt
Tetranscripts_out_UCSC_CB_RNAseq.cntTable
counts_piRNA_precursors_CB_RNAseq.txt

data_processing:
RNA-seq: For transcript-level DE analysis, reads were trimmed off adapter contents using cutadapt (v2.8) and mapped to the mouse genome (Ensembl: Grcm38) using STAR (v2.7.1a) in two-pass mode. Then, reads were assigned and counted using FeatureCounts (v2.0.1) in paired-end mode. First, raw read counts were filtered in order to keep only transcripts with 20 or more normalized counts in at least three individual samples among six samples from a given cell type (3 x CTRL and 3 x cKO). Raw count reads were normalized and differential expression calculated using DESeq2 in R (v4.0.3). 2) To analyze transposable elements and piRNA precursors, reads were mapped to the mouse genome (UCSC: mm10) using STAR (v2.7.1a) in two-pass mode. For transposable elements, reads were assigned and counted using TEtranscripts in reverse stranded mode (v2.2.1). For piRNA precursor transcripts, reads were assigned and counted against the gtf file containing the 214 piRNA precursors using FeatureCounts. Raw count reads were filtered to keep only genes with at least 10 reads across all samples (Smg6-cKO and CTRL). Raw count reads were normalized and differential expression calculated using DESeq2 in R (v4.0.3).
Small RNA-seq: SPORTS1.1 was used to map small RNA reads successively rsRNA, miRNA, tsRNA and piRNA sequences extracted from mm10 UCSC genome files originating from rRNAdb, miRBase (v.22) GtRNAdb (v.2.0) and piRBase (v.2.0) using SPORTS default settings. Then, reads mapping to rsRNA, miRNA and tsRNA sequences were extracted from SPORTS output text file using R. Repeats from repeatMasker and piRNA precursor locations were mapped to the mouse genome (UCSC : mm10) using HISAT2 (v2.1.0); then, reads were assigned and counted using FeatureCounts (v2.0.1). Raw read counts were filtered to keep only genes with at least one occurrence found per sample. Raw read counts were normalized and differential expression calculated using DESeq2 (v4.0.3).
Genome_build: mm10
Supplementary_files_format_and_content: Raw read counts text files

source_name: testis

extract_protocol:
RNA was extracted from enriched fractions of Spc, RS or isolated CBs with the Trisure reagent (Bioline) using standard protocols. Isolated RNA was analyzed using NanoDrop (Thermo Scientific) and Bioanalyzer (Agilent).
1) CB RNA-seq: Total RNA libraries without ribosomal RNA removal were prepared by NEBNext® Ultra™ Directional RNA Library Prep Kit without fragmentation. Sequencing was performed with NovaSeq6000 (PE150) platform (Illlumina) at Novogene (www.en.novogene.com). 2) RNA-seq of Spc and RS samples: Libraries were constructed with Illumina TruSeq Stranded mRNA library preparation kit and sequenced with HiSeq3000 (read length 2 x 75 bp) sequencing system (Illumina, San Diego, CA, USA) at the Finnish Functional Genomics Centre (https://bioscience.fi/services/functional-genomics/services/). 3) SmallRNA-seq of Spc and RS samples: Libraries were constructed with QIAseq miRNA library preparation kit and sequenced with HiSeq2500 Rapid run sequencing platform (1 x 75bp) at the Finnish Functional Genomics Centre.

value: isolated CBs

value: mixed C57Bl/6J and SV129


title: GMP.3.r2


title: G648_4th_MNase_(20210628_TB_Mv_G648_1_4x_06092021)

source_name: MNase-seq of G648 1/16th MNase

value: DNA from MNase-digested chromatin


title: G648_MPE10_2S_(20211006_TB_Mv_G648_MPE10_2SCU_20210924)

source_name: MPE-seq of G648 replicate 3


title: P95_2 (Srsf2P95H/+; MX1-Cre_2)


title: G648_2x_MNase_(20210628_TB_Mv_G648_2x_06092021)

source_name: MNase-seq of G648 1/2 MNase


title: RNA-seq cKO CB 2


title: GMP.2.r2

value: replicate 2


title: GMP.1.r2


title: GMP.2.r1

value: replicate 1


title: P95_1 (Srsf2P95H/+; MX1-Cre_1)


title: GMP.1.r1


title: Double_3 (Srsf2P95H/+;Runx-/-; MX1-Cre_3)

description:
cmpr_deg_p95_runx1_double.selected.xlsx
AS_double_default.001005.xlsx

value: Mouse LK P95H SRSF2 and RUNX1 KO


title: G648_1x_MNase_(20210628_TB_Mv_G648_1x_06092021)

source_name: MNase-seq of G648 1/4th MNase


title: G648_1mM_MPE_(20211006_TB_Mv_G648_1uM_MPE_2SCU_20210831)

source_name: MPE-seq of G648 1 uM H2O2

value: DNA from MPE-digested chromatin


title: RNA-seq cKO CB 1


title: RNA-seq CTRL CB 4

value: control


title: G648_16th_MNase_(20210628_TB_Mv_G648_1_16x_06092021)

source_name: MNase-seq of G648 1/64th MNase


title: G648_2th_MNase_(20210628_TB_Mv_G648_1_2x_06092021)

source_name: MNase-seq of G648 1/8 MNase


title: Double_2 (Srsf2P95H/+;Runx-/-; MX1-Cre_2)


title: G648_128th_MNase_(20210628_TB_Mv_G648_1_128x_06092021)

source_name: MNase-seq of G648 1/512h MNase


title: RNA-seq CTRL CB 3


title: RNAseq_ESC_qko_mbd_cl2_3

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: processed data file: totalRNA_knownGene_mm10_esc.csv

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. RNA-seq reads were mapped to mm10 using QuasR in spliced alignment mode (splicedAlignment = TRUE) with the option (aligner="Rhisat2"), which internally uses hisat2 (Kim, Paggi, Park et al, Nature Biotech 2019)
Genome_build: mm10
Supplementary_files_format_and_content: Alignments (first read for paired-end) overlapping the opposite strand of any exon of a known gene (gene annotation from the Bioconductor package TxDb.Mmusculus.UCSC.mm10.knownGene, version 3.10.0) were counted using the qCount function from the QuasR Bioconductor package (Gaidatzis et al, Bioinformatics, 2015) with default parameters.

source_name: esc

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All ES cell experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma).

extract_protocol:
RNA for RNA-seq was isolated for ES cells with the RNeasy mini kit (Qiagen) using on- column DNA digestion or of neurons with Direct-zol RNA Microprep (Zymo research) with on-column DNA digestion.
Sequencing libraries were prepared from purified RNA for a minimum of two biological replicates per condition using TruSeq stranded total RNA Library Prep (Illumina)

treatment_protocol: For HA36 cells containing the pTRE-Ngn2 construct differentiation was carried out by inducing expression of NGN2 with doxycycline as previously described (Thoma et al., 2012) with modifications. In brief, cells were plated on poly-D-lysine/laminin coated plates and treated with DMEM/F12 with Glutamax (LifeTech, 31331-028) containing 1x B27 without VitaminA (LifeTech #12587-010), 1x N2 supplement (LifeTech #17502-048), 10 ng/ml hEGF (LifeTech, PHG0315), 10 ng/ml hFGF (LifeTech, CTP0261) and 1 μg/mL doxycycline (Sigma, D989) for three days with no media change. At day three after doxycycline induction, medium was exchanged to Neurobasal-Medium (LifeTech, 21103-049) supplemented with 1x B27 with Vitamin A (LifeTech, 17504-044) , 1x N2 (LifeTech #17502-048) and 10ng/ml BDNF (PeproTech, 450-02), 10ng/ml GDNF (PeproTech, 450-10) and 10ng/ml NT-3 (PeproTech, 450-03). Every second day half of the media was replaced with fresh media.

value: ebryonic stem cells

value: MBD quadruple knock-out

tag: cell line/strain background

value: HA36 cells (mixed 129-C57Bl/6 strain)


title: Double_1 (Srsf2P95H/+; Runx-/-; MX1-Cre_1)

value: Lin- c-Kit+ (LK) cells


title: RNAseq_ESC_qko_mbd_cl2_2


title: RNAseq_ESC_qko_mbd_cl2_1


title: HIBD-SB input2

city: beijing

first: shan

last: wang

address: 2yabao road

institute: Capital Institute of Pediatrics

description: rat brain tissue,H3K9cr,PTM

data_processing:
Raw data were generated after sequencing,  image analysis, base calling and quality filtering on Illumina NovaSeq 6000 sequencer. Firstly, Q30 was used to perform quality control. After adaptor-trimming and low quality reads removing by cutadapt (v1.9.1) software, high quality clean reads were generated. Then these clean reads were aligned to rat reference genome  (UCSC rn5) using bowtie2 software  (v2.2.4) with default parameters. Peak calling was performed with MACS software (v2.2.7.1).
Differentially enriched regions were identified by diffReps software (v1.55.4).
The  enriched peaks were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation. GO and KEGG Pathway analysis were performed on the peak-associated genes or differentially enriched peak-associated genes. And the enriched peaks were visualized in UCSC Genome Browser.
Assembly: RN5
Supplementary files format and content: chr: chromosome number of enrichment peak; Start: initial genomic coordinates of enrichment peak; End: terminating genome coordinates of enrichment peak; Peak ID: indicates the MACS peak ID.MACS uses sample VS Input for ChIP enrichment peak recognition, and the default peak with P <= 1E-5 is statistically significant enrichment peak.

organism: Rattus norvegicus

source_name: brain

growth_protocol: Wistar rats, 8–10 weeks old, SPF grade,  housed in a 12-h light/dark cycle, with free access to food and water.

extract_protocol:
Briefy, after deeply anesthetized with chloral hydrate(200 mg/kg), the rats pups in Sham, HIBD and HIBD+SB groups were perfused with physiological saline from the right auricle until the liver turns white. The brain of rats was removed on ice, put into an ice-cold PBS and rapidly separated the infarct side cerebral cortex
Illumina sequencing libraries were generated with NEBNext® Ultra™ DNA Library Prep Kit (New England Biolabs) by following the manufacturer’s manual. The library quality was determined by using Agilent 2100 Bioanalyzer (Agilent), and then, subjected to high-throughput 150 base paired-end sequencing on Illumina Novaseq sequencer according to the manufacturer’s recommended protocol.

value: brain

value: HIBD-SB

value: Wistar

value: none (input)


title: HIBD-SB input1

description: rat brain tissue,H3K9cr,PTM


title: RNA-seq CTRL CB 1


title: G648_10mM_MPE_(20211006_TB_Mv_G648_10uM_MPE_2SCU_20210831)

source_name: MPE-seq of G648 10 uM H2O2

value: viral DNA


title: RNAseq_ESC_qko_mbd_cl1_2


title: HIBD-SB IP2

description: rat brain tissue,H3K9cr,PTM

value: H3K9cr (PTM-525RM)


title: G648_100mM_MPE_(20211006_TB_Mv_G648_100uM_MPE_2SCU_20210831)

source_name: MPE-seq of G648 100 uM H2O2


title: RNAseq_ESC_qko_mbd_cl1_1


title: G648_1000mM_MPE_(20211006_TB_Mv_G648_1000uM_MPE_2SCU_20210831)

source_name: MPE-seq of G648 1000 uM H2O2


title: Oligodendrocyte-enriched cells from RalAB cKO mouse 3 at P10

city: Zurich

first: Jorge

middle: A.

last: Pereira

address: Otto-Stern-Weg 7

department: Dep. of Biology

institute: ETH Zurich

data_processing:
The raw reads were first cleaned by removing adapter sequences, trimming low quality ends, and filtering reads with low quality (phred quality <20) using Trimmomatic (Version 0.36).
Sequence alignment of the resulting high-quality reads to the mouse reference genome (build GRCm38.p6 with the gene annotations downloaded on 2019-11-05 from Gencode Release M23) and quantification of transcript level expression was carried out using Kallisto (Version 0.44).
The Kallisto options were "--bias --bootstrap-samples 10 --seed 42 --single --rf-stranded --fragment-length 170 --sd 50".
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: *.txt: Tab-delimited text files including Raw and normalized Transcript Counts from Kallisto.

source_name: oligodendrocyte-enriched cells extracted from spinal cord

extract_protocol:
Oligodendrocyte-enriched cells were isolated from P10 spinal cords of individual mice per genotype. Spinal cords were minced with a scalpel and the cells were enzymatically disaggregated with an enzymatic solution. The suspension of disaggregated cells was loaded into a FACS machine and the populations enriched in oligodendrocytes were selected by conditional expression of the tdTomato reporter gated for large forward scatter (FSC-A). Cells from each mouse were directly collected into individual tubes containing 0.5 ml of Trizol (Invitrogen). Tubes were stored at -80C until needed. RNA extraction was performed with Trizol as per manufacturer's instructions.
RNA libraries were prepared for sequencing using Illumina's TruSeq Stranded mRNA.

tag: age


title: Oligodendrocyte-enriched cells from RalAB cKO mouse 4 at P10

value: oligodendrocyte-enriched cells extracted from spinal cord


title: HIBD-SB IP1

description: rat brain tissue,H3K9cr,PTM

value: H3K9cr (PTM-524RM)


title: RNAseq_ESC_tko_3

value: Dnmt triple knock-out


title: RNAseq_ESC_qko_mbd_cl1_3


title: RNAseq_ESC_tko_2


title: HIBD input2

description: rat brain tissue,H3K9cr,PTM

value: HIBD


title: Oligodendrocyte-enriched cells from RalAB cKO mouse 2 at P10


title: Oligodendrocyte-enriched cells from RalAB cKO mouse 1 at P10


title: RNAseq_ESC_tko_1


title: Oligodendrocyte-enriched cells from control mouse 4 at P10


title: HIBD input1

description: rat brain tissue,H3K9cr,PTM


title: HIBD IP1

description: rat brain tissue,H3K9cr,PTM

value: H3K9cr (PTM-520RM)


title: RNA-seq CTRL CB 2

value: isolated CBs

value: mixed C57Bl/6J and SV129


title: HIBD IP2

description: rat brain tissue,H3K9cr,PTM

value: H3K9cr (PTM-521RM)


title: RNAseq_ESC_wt_3

value: ebryonic stem cells

value: wild-type


title: Sham input2

description: rat brain tissue,H3K9cr,PTM

value: sham


title: Sham input1

description: rat brain tissue,H3K9cr,PTM

value: brain


title: Oligodendrocyte-enriched cells from control mouse 1 at P10


title: RNAseq_ESC_wt_1

value: HA36 cells (mixed 129-C57Bl/6 strain)


title: Sham IP2

description: rat brain tissue,H3K9cr,PTM

value: Wistar

value: H3K9cr (PTM-517RM)


title: Oligodendrocyte-enriched cells from control mouse 3 at P10


title: Sham IP1

description: rat brain tissue,H3K9cr,PTM

value: H3K9cr (PTM-516RM)


title: Oligodendrocyte-enriched cells from RalA cKO mouse 3 at P10


title: Oligodendrocyte-enriched cells from control mouse 2 at P10


title: TCR for colon GF 3-4, colon PM 3-4, colon CR 3-4, colon EcN 3-4, colon kif 3-4, spleen CR1, spleen SPF 1

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description:
TotalSeq C1-10, Totalseq C1 + C2, Totalseq C3 + C4
10x lane of 12 individually hashed samples, 10 from colon, 2 from spleen. 2 Germfree colon biol reps, 2 GF + P. magnus colon biol reps, 2 GF + C. ramosum colon biol reps, 2 GF + E. coli Nissl colon biol reps, 2 GF + E. coli kifCD colon biol reps, 1 GF + C. ramosum spleen rep, 1 SPF spleen rep

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0 and hash libraries were processed using cite-seq-count
Data analsysis was performed using Seurat v3 pipeline. Low-quality cells were defined as those with less than 700 or more than 3000 unique genes, or those with >10% mitochondrial gene reads and were removed.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon, Spleen

extract_protocol:
Lymphocytes were prepared by either digestion with collagenase and dispase (intestine) or mechanical disruption (MLNs, spleen), followed by staining with floursecent antibodies, hashing with Totalseq-C antibodies against MHCI and CD45,  and flow sorting CD4 T cells into RPMI/2%FCS
Libraries were prepared according to the 10x 5' (samples 1-22) and 10x5'v2 (samples 23-42) GEX, TCR, and FBC protocols

value: Colon, Spleen

value: CD4+ CD44+  T cells

tag: Sex

value: Male

value: None, P. magnus, C. ramosum, E. coli Nissl, E. coli kifCD


title: Oligodendrocyte-enriched cells from RalA cKO mouse 2 at P10

value: oligodendrocyte-enriched cells extracted from spinal cord


title: RNAseq_ESC_wt_2


title: Oligodendrocyte-enriched cells from RalA cKO mouse 1 at P10


title: FBC for colon GF 3-4, colon PM 3-4, colon CR 3-4, colon EcN 3-4, colon kif 3-4, spleen CR1, spleen SPF 1


title: AB2.2_N4_3

data_processing:
trim_galore
Hisat2
Stringtie
Genome_build: GRCm38
Supplementary_files_format_and_content: matrix table and raw fastq sequencing data

source_name: AB2.2 mESC_normoxia

value: mESC

value: normoxia


title: GEX for colon GF 3-4, colon PM 3-4, colon CR 3-4, colon EcN 3-4, colon kif 3-4, spleen CR1, spleen SPF 1


title: AB2.2_N4_2


title: AB2.2_N4_1


title: AB2.2_H4_3

source_name: AB2.2 mESC_hypoxia

value: hypoxia


title: Grass puffer brain

city: Nagoya

first: Takashi

last: Yoshimura

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

data_processing:
Library strategy: Visium spatial gene expression reagent kits (10X Genomics)
~345 million of read pairs were obtained with 100 % of valid UMIs and 91.1% of them were mapped onto tiger puffer genome (assembly fTakRub1.2)
Count data and the HE image were integrated by Space Ranger pipeline (v1.1.0, 10X Genomics).
Genome_build: assembly fTakRub1.2
Supplementary_files_format_and_content: Raw matrix (including background GEMs) of UMI counts.
Supplementary_files_format_and_content: Image files
Supplementary_files_format_and_content: test files

organism: Takifugu alboplumbeus

growth_protocol: Wild male grass puffers were obtained from the spawning site, Minamichita, Japan.

extract_protocol:
Staining, permeabilization, reverse transcription, cDNA amplification, and library construction were conducted following Visium user guide (Rev. C) with Visium spatial gene expression reagent kits (10X Genomics).
Staining, permeabilization, reverse transcription, cDNA amplification, and library construction were conducted following Visium user guide (Rev. C) with Visium spatial gene expression reagent kits (10X Genomics). After HE staining, HE image was immediately captured (BZ-X800, Keyence). Time for permeabilization was 12 min with thermal cycler (T100, Bio Rad). The number of cycles for cDNA amplification was 14 with real-time qPCR system (Quant Studio 3, Applied Biosystems).

treatment_protocol: After bringing live puffers back to the laboratory, fresh brain of male grass puffer was dissected and frozen in the optimal cutting temperature compound with dry ice. Two sagittal sections with 10 µm thickness were cut onto one square of spatial transcriptomic slide by cryostat.

value: male


title: T19_NP40_MNase_PE50_(20220204_TB_Gv_1_P_NP40_Mnase_20210930)

data_processing:
Genome_build: T19_genome.fasta
1. We used cutadapt 2.9 with parameters "--nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters off 50bp paired-end reads. 2. We used Bowtie2 2.4.2 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the trimmed reads to the reference sequence (Marseillevirus marseillvirus strain T19 or Marseillevirus marseillvirus strain G648 or 3 copies of the artificial sequence Widom 601). 3. We extracted properly paired reads from the alignments with bedtools bamtobed  to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz).  4. We used bedtools genomecov to make a normalized count bigwig file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bigwig).

source_name: MNase-seq of T19

extract_protocol:
MNase-extraction_TB2021.pdf
viral DNA

tag: description

value: DNA from MNase-digested chromatin


title: AB2.2_H4_2


title: Oligodendrocyte-enriched cells from RalA cKO mouse 4 at P10


title: WT rep1

city: Tianjin

first: Jian

middle: ming

last: Yang

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

institute: Tianjin Medical University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default  parameters.
Then clean reads were separately aligned to reference genome with orientation mode  using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.
RSEM was used to quantify gene abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: Intestinal epithelial cells

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Colon

value: wild type


title: AB2.2_H4_1


title: G648_NP40_MPE_PE50_(20220324_TB_Mv_G648_10uM_MPE_2SCU_20210831)

data_processing:
Library strategy:  MPE-seq
Genome_build: G648_genome.fasta
1. We used cutadapt 2.9 with parameters "--nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters off 50bp paired-end reads. 2. We used Bowtie2 2.4.2 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the trimmed reads to the reference sequence (Marseillevirus marseillvirus strain T19 or Marseillevirus marseillvirus strain G648 or 3 copies of the artificial sequence Widom 601). 3. We extracted properly paired reads from the alignments with bedtools bamtobed  to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz).  4. We used bedtools genomecov to make a normalized count bigwig file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bigwig).

source_name: MPE-seq of G648

extract_protocol:
MPE-extraction_TB2021.pdf
viral DNA

value: DNA from MPE-digested chromatin


title: WT rep3


title: RhoB-/- rep3

value: RhoB-/-


title: WT rep4


title: RhoB-/- rep5


title: WT rep2


title: RhoB-/- rep1


title: RhoB-/- rep4


title: WT rep5


title: RhoB-/- rep2


title: Hulunbuir Short-tail Sheep embryo

city: Inner Mongolia

first: Hong

last: Su

state: Inner Mongolia

address: No. 306, Zhaowuda Road, Saihan District, Hohhot, Inner Mongolia Autonomous Region

institute: Inner MongoliaAgricultural University

description: RNA from single cells

data_processing:
Following sequencing, the raw data from each sample were demultiplexed, aligned to the Ovis_aries_genome_v1.0 reference genome, and UMI counts were quantified using the 10x Genomics Cell Ranger pipeline (v3.1.0, 10X Genomics). Then, we continued the data analysis with the raw barcode matrix files using the Seurat package (v3.2.0). Cells more than 100 detected genes and less than 10% mitochondrial reads were considered valid cells and were kept for downstream analysis. In order to prevent clusters from being biased by mitochondrial transcript content, gene expression values were scaled based on  the cell mitochondrial transcript content. Next, "LogNormalize" and "vst" was applied to normalize and find variable features within the single cell gene expression data. Clustering and differential expression analysis was performed using R package Seurat with default parameters. Based on the PC ElbowPlot, we picked a certain number of principal components (PCs) for the clustering analysis when the number reached the baseline of the standard deviation of PC. We generally used the cluster resolution that higher one did not result in increasing clusters linearly. Cell clusters were visualized using UMAP. For differential gene expression, we used model-based analysis of single-cell Transcriptomics (MAST) (log fc ≥0.25, min.pct = 0.1, min.diff.pct > -Inf) and only selected the genes with adjusting p value <0.05. In order to predict cellular differentiation, cells were ordered in pseudotime using Monocle2 (v2.14.0) with default parameters. All analyses were carried out in R 3.6.1 environment.
Genome_build: Ovis_aries_genome_v1.0
Supplementary_files_format_and_content: matrix table with gene counts for every gene and every cell
Supplementary_files_format_and_content: gene files
Supplementary_files_format_and_content: cell barcode files

molecule: polyA RNA

organism: Ovis aries

source_name: Hulunbuir Short-tail Sheep embryo

extract_protocol:
Briefly, tissues were cut into approximately 1-2 mm3 pieces in the RPMI-1640 medium (Gibco), and enzymatically digested with gentleMACS (Miltenyi) using program 37C_m_TDK_1 on a rotor at 37°C, according to manufacturer’s instruction. The dissociated cells were subsequently passed through a 100 µm SmartStrainer and centrifuged at 400 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi) and incubated on ice for 1-2 min to lyse red blood cells. After washing twice with 1× PBS (Gibco), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 2% fetal bovine serum (FBS, Gibco)).
Cells were loaded around 17,400 cells/chip position using the 10x Chromium Single cell 3’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, V3.0 barcoding chemistry) according to the manufacturer’s instructions.

tag: breed

value: Hulunbuir Short-tail

tag: developmental  stage

value: 16-day embryo


title: Ujumqin sheep embryo

description: RNA from single cells

source_name: Ujumqin sheep embryo

value: Ujumqin


title: lung_505s_P8

status: Public on Sep 26 2022

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

data_processing:
bcl2fastq - demultiplexing
sequenced reads were trimmed for adaptor sequence, and then mapped to the mouse reference genome (GRCm38 / mm10) using TapHat2, Bowtie1 or Bowtie2.
raw read counts per gene were calculated using featureCounts from subread
for analysis, all raw counts from all cells of each of the sample-plates were combined into one expression matrix file
counts data was processed and analyzed using SingleCellExperiment, pagoda2 and monocle packages in R-software
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

source_name: female mouse

extract_protocol:
FACS into 384well plate of single cells from dissociation of mouse heart in Miltenyi's skeletal muscle dissociation kit (supplemented with collagenase IV-S).
RNA libraries were prepared using standard Smart-Seq2 protocol

value: lung

value: 8-30 weeks


title: lung_505s_P20


title: lung_505s_P21


title: lung_505s_P4


title: lung_505s_P2


title: lung_505s_P19


title: lung_505s_P22


title: lung_505s_P7


title: lung_505s_P6


title: lung_505s_P18


title: lung_505s_P5


title: lung_505s_P3


title: lung_505s_P17


title: lung_505s_P9


title: lung_505s_P14


title: lung_505s_O4


title: lung_505s_O9


title: lung_505s_O5


title: lung_505s_O8


title: lung_505s_P11


title: lung_505s_P15


title: lung_505s_O7


title: lung_505s_O6


title: lung_505s_P12


title: lung_505s_P13


title: lung_505s_O23


title: lung_505s_O3


title: lung_505s_O22


title: lung_505s_O20


title: lung_505s_O2


title: lung_505s_O21


title: lung_505s_O19


title: lung_505s_P16


title: lung_505s_P1


title: lung_505s_P10


title: lung_505s_O18


title: lung_505s_O24


title: lung_505s_O14


title: lung_505s_O17


title: lung_505s_N5


title: lung_505s_N9


title: lung_505s_O11


title: lung_505s_O10


title: lung_505s_N8


title: lung_505s_O1


title: lung_505s_O16


title: lung_505s_O12


title: lung_505s_O15


title: lung_505s_N7


title: lung_505s_O13


title: lung_505s_N4


title: lung_505s_N22


title: lung_505s_N2


title: lung_505s_N3


title: lung_505s_N23


title: lung_505s_N24


title: lung_505s_N21


title: lung_505s_N20


title: lung_505s_N16


title: lung_505s_N17


title: lung_505s_N15


title: lung_505s_N19


title: lung_505s_N18


title: lung_505s_N14


title: lung_505s_N1


title: lung_505s_N10


title: lung_505s_N11


title: lung_505s_N12


title: lung_505s_M9


title: lung_505s_M8


title: lung_505s_M7


title: lung_505s_M6


title: lung_505s_M4


title: lung_505s_N13


title: lung_505s_M3


title: lung_505s_M24


title: lung_505s_M5


title: lung_505s_M22


title: lung_505s_M23


title: lung_505s_M21


title: lung_505s_M12


title: lung_505s_M16


title: lung_505s_M15


title: lung_505s_M2


title: lung_505s_M18


title: lung_505s_M20


title: lung_505s_M17


title: lung_505s_M19


title: lung_505s_M13


title: lung_505s_M14


title: lung_505s_M11


title: lung_505s_M1


title: lung_505s_M10


title: lung_505s_N6


title: lung_505s_L8


title: lung_505s_L5


title: lung_505s_L7


title: lung_505s_L24


title: lung_505s_L6


title: lung_505s_L3


title: lung_505s_L4


title: lung_505s_L9


title: lung_505s_L22


title: lung_505s_L23


title: lung_505s_L21


title: lung_505s_L20


title: lung_505s_L2


title: lung_505s_L19


title: lung_505s_L18


title: lung_505s_L14


title: lung_505s_L12


title: lung_505s_L15


title: lung_505s_L13


title: lung_505s_L16


title: lung_505s_L17


title: lung_505s_L10


title: lung_505s_L11


title: lung_505s_L1


title: lung_505s_K7


title: lung_505s_K6


title: lung_505s_K8


title: lung_505s_K9


title: A549_Smp9_Crizotinib_Repeat1

type: RNA

city: Seoul

first: Ju-Hong

last: Jeon

state: Seoul

address: 28 Yongon-Dong, Chongno-Gu

department: Department of Physiology and Biomedical Sciences

country: South Korea

institute: Seoul National University College of Medicine

description: Gene expression profile in A549 cells vehicle treated

hyb_protocol: Following fragmentation, 5.5 ug of framented cDNA were hybridized for about 17 hr at 45℃ on Human Gene 2.0 ST array. The hybridized probe arrays were stained and washed with GeneChip® Hybridization, Wash and Stain Kit using the Fluidics Station 450(Affymetrix).

scan_protocol: The stained GeneChips were scanned with a GeneChip® Scanner 3000+ 7G(Affymetrix) a 570 nm.

data_processing: Raw data were normalized using the Single Channel Array Normalization (Piccolo et al. 2012, PMID: 22959562) method. As part of the normalization process, a custom chip-definition file (hugene20sthsentrezgprobe_25.0.0.tar.gz) from the BrainArray resource was used to map genes based on updated genome mappings and excludes inaccurate or wrongly annotated probes. The microarray probests were mapped to 18,549 of protein coding genes.

label: biotin

source_name: Lung cancer cell line A549

label_protocol: The Affymetrix GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 300ng total RNA(GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Rev.5). Protocol performed  using the Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix 900652).

growth_protocol: The cells were maintained under RPMI1640 medium containing 10% FBS.

extract_protocol: Total RNA was extracted from the cells and processed according to the manufacturer’s guideline (Affymetrix).

treatment_protocol: TGFb was disolved in 4 mM HCl, Crizotinib was dissolved in DMSO and treated in A549 cells.

tag: disease state

value: Non-small cell lung carcinoma (A549) cell line

value: Crizotinib


title: A549_Smp13_TGFb_Crizotinib_Repeat1

description: Gene expression profile in A549 cells crizotinib treated


title: A549_Smp5_TGFb_Repeat1

value: TGFb


title: A549_Smp10_Crizotinib_Repeat2


title: A549_Smp7_TGFb_Repeat3


title: A549_Smp15_TGFb_Crizotinib_Repeat3


title: A549_Smp1_Vehicle_Repeat1

value: Non-small cell lung carcinoma

value: vehicle


title: A549_Smp16_TGFb_Crizotinib_Repeat4


title: A549_Smp2_Vehicle_Repeat2


title: lung_505s_K5

tag: tissue


title: lung_505s_K3


title: lung_505s_K4


title: A549_Smp8_TGFb_Repeat4


title: lung_505s_K22


title: lung_505s_K23


title: lung_505s_K24


title: lung_505s_K2


title: lung_505s_K20


title: lung_505s_K19


title: A549_Smp14_TGFb_Crizotinib_Repeat2


title: lung_505s_K18


title: A549_Smp3_Vehicle_Repeat3


title: A549_Smp11_Crizotinib_Repeat3


title: A549_Smp6_TGFb_Repeat2


title: lung_505s_K16


title: lung_505s_K17


title: lung_505s_K21


title: lung_505s_K14


title: lung_505s_K11


title: lung_505s_K13


title: lung_505s_K12


title: A549_Smp4_Vehicle_Repeat4


title: A549_Smp12_Crizotinib_Repeat4


title: lung_505s_J8


title: lung_505s_K10


title: lung_505s_K1


title: lung_505s_J9


title: lung_505s_J7


title: lung_505s_K15


title: lung_505s_J5


title: lung_505s_J23


title: lung_505s_J3


title: lung_505s_J4


title: lung_505s_J20


title: lung_505s_J22


title: lung_505s_J24


title: lung_505s_J21


title: lung_505s_J19


title: lung_505s_J17


title: lung_505s_J18


title: lung_505s_J16


title: lung_505s_J14


title: lung_505s_J15


title: lung_505s_J13


title: lung_505s_J6


title: lung_505s_J12


title: lung_505s_J11


title: lung_505s_J1


title: lung_505s_J10


title: lung_505s_I7


title: lung_505s_I9


title: lung_505s_I6


title: lung_505s_J2


title: lung_505s_I5


title: lung_505s_I24


title: lung_505s_I4


title: lung_505s_I8


title: lung_505s_I3


title: lung_505s_I22


title: lung_505s_I19


title: lung_505s_I2


title: lung_505s_I23


title: lung_505s_I20


title: lung_505s_I17


title: lung_505s_I21


title: lung_505s_I15


title: lung_505s_I18


title: lung_505s_I16


title: lung_505s_I14


title: lung_505s_I12


title: lung_505s_I10


title: lung_505s_I13


title: lung_505s_I1


title: lung_505s_H9


title: lung_505s_H7


title: lung_505s_H8


title: lung_505s_H6


title: lung_505s_H5


title: lung_505s_H22


title: lung_505s_H24


title: lung_505s_H23


title: lung_505s_H4


title: lung_505s_H19


title: lung_505s_H21


title: lung_505s_H17


title: lung_505s_H20


title: lung_505s_H14


title: lung_505s_I11


title: lung_505s_H13


title: lung_505s_H10


title: lung_505s_G9


title: lung_505s_H1


title: lung_505s_H15


title: lung_505s_H11


title: lung_505s_G8


title: lung_505s_G7


title: lung_505s_H3


title: lung_505s_G4


title: lung_505s_G3


title: lung_505s_H2


title: lung_505s_G5


title: lung_505s_H16


title: lung_505s_G24


title: lung_505s_G23


title: lung_505s_H18


title: lung_505s_G18


title: lung_505s_G19


title: lung_505s_G22


title: lung_505s_G20


title: lung_505s_G17


title: lung_505s_H12


title: lung_505s_G2


title: lung_505s_G16


title: lung_505s_G15


title: lung_505s_G12


title: lung_505s_G6


title: lung_505s_G13


title: lung_505s_G14


title: lung_505s_G21


title: lung_505s_G10


title: lung_505s_F15


title: lung_505s_F6


title: lung_505s_F13


title: lung_505s_F9


title: lung_505s_F20


title: lung_505s_G11


title: lung_505s_F16


title: lung_505s_F4


title: lung_505s_F19


title: lung_505s_F17


title: lung_505s_F24


title: lung_505s_F7


title: lung_505s_F3


title: lung_505s_F5


title: lung_505s_F2


title: lung_505s_F23


title: lung_505s_F8


title: lung_505s_F22


title: lung_505s_F14


title: lung_505s_F18


title: lung_505s_F21


title: lung_505s_E9


title: lung_505s_E20


title: lung_505s_F11


title: lung_505s_F10


title: lung_505s_E8


title: lung_505s_E23


title: lung_505s_E21


title: lung_505s_E16


title: lung_505s_E17


title: lung_505s_E6


title: lung_505s_E24


title: lung_505s_E19


title: lung_505s_E7


title: lung_505s_F12


title: lung_505s_E14


title: lung_505s_E2


title: lung_505s_E4


title: lung_505s_E5


title: lung_505s_E18


title: lung_505s_F1


title: lung_505s_E22


title: lung_505s_E15


title: lung_505s_E12


title: lung_505s_D8


title: lung_505s_E10


title: lung_505s_E1


title: lung_505s_D9


title: lung_505s_E11


title: lung_505s_E13


title: lung_505s_D7


title: lung_505s_D20


title: lung_505s_D21


title: lung_505s_D5


title: lung_505s_D18


title: lung_505s_D3


title: lung_505s_D19


title: lung_505s_D6


title: lung_505s_D24


title: lung_505s_D4


title: lung_505s_D17


title: lung_505s_D15


title: lung_505s_D14


title: lung_505s_D13


title: lung_505s_D16


title: lung_505s_C11


title: lung_505s_C22


title: lung_505s_C16


title: lung_505s_D11


title: lung_505s_C19


title: lung_505s_C4


title: lung_505s_C24


title: lung_505s_C18


title: lung_505s_C23


title: lung_505s_C7


title: lung_505s_D12


title: lung_505s_D1


title: lung_505s_C9


title: lung_505s_C17


title: lung_505s_D10


title: lung_505s_C14


title: lung_505s_C21


title: lung_505s_C13


title: lung_505s_C6


title: lung_505s_C8


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title: lung_505s_C3


title: lung_505s_B9


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title: lung_505s_B5


title: lung_505s_B4


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title: lung_505s_A5


title: lung_505s_A4


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title: lung_505s_A12


title: lung_505s_B14


title: lung_505s_A20


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title: lung_505s_A23


title: lung_505s_A22


title: lung_505s_A7


title: lung_505s_A21


title: lung_505s_A13


title: lung_131s_P8

source_name: male mouse


title: lung_505s_A3


title: lung_505s_A15


title: lung_505s_A10


title: lung_505s_A18


title: lung_505s_A1


title: lung_505s_A16


title: lung_505s_A11


title: lung_505s_B13


title: lung_505s_A8


title: lung_505s_A6


title: lung_131s_P6


title: lung_131s_P5


title: lung_131s_P7


title: lung_505s_B10


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title: lung_131s_P4


title: lung_131s_P3


title: lung_131s_P22


title: lung_131s_P20


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title: lung_131s_P18


title: lung_131s_P15


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title: lung_131s_O8


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title: lung_131s_O7


title: lung_131s_O24


title: lung_131s_P10


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title: lung_131s_O5


title: lung_131s_O6


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title: lung_131s_P17


title: lung_131s_O17


title: lung_131s_O14


title: lung_131s_O16


title: lung_131s_O18


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title: lung_131s_N21


title: lung_131s_N3


title: lung_131s_N6


title: lung_131s_N18


title: lung_131s_N24


title: lung_131s_N19


title: lung_131s_O1


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title: lung_131s_N4


title: lung_131s_N15


title: lung_131s_O10


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title: lung_131s_N2


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title: lung_131s_M8


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title: lung_131s_M6


title: lung_131s_M24


title: lung_131s_M7


title: lung_131s_M20


title: lung_131s_M5


title: lung_131s_M19


title: lung_131s_M23


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title: lung_131s_M3


title: lung_131s_M21


title: lung_131s_M15


title: lung_131s_M2


title: lung_131s_M17


title: lung_131s_M14


title: lung_131s_M13


title: lung_131s_M10


title: lung_131s_M12


title: lung_131s_M11


title: lung_131s_L9


title: lung_131s_L6


title: lung_131s_M1


title: lung_131s_L8


title: lung_131s_L5


title: lung_131s_L23


title: lung_131s_L4


title: lung_131s_L24


title: lung_131s_L3


title: lung_131s_L20


title: lung_131s_L17


title: lung_131s_L2


title: lung_131s_L18


title: lung_131s_K9


title: lung_131s_L16


title: lung_131s_L15


title: lung_131s_L10


title: lung_131s_K8


title: lung_131s_K5


title: lung_131s_L1


title: lung_131s_K6


title: lung_131s_K7


title: lung_131s_K3


title: lung_131s_K4


title: lung_131s_L14


title: lung_131s_K24


title: lung_131s_K21


title: lung_131s_K22


title: lung_131s_K2


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title: lung_131s_L19


title: lung_131s_K20


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title: lung_131s_K15


title: lung_131s_K16


title: lung_131s_K12


title: lung_131s_K14


title: lung_131s_K11


title: lung_131s_K1


title: lung_131s_K10


title: lung_131s_J3


title: lung_131s_J6


title: lung_131s_J8


title: lung_131s_K23


title: lung_131s_J9


title: lung_131s_J4


title: lung_131s_J21


title: lung_131s_J22


title: lung_131s_J5


title: lung_131s_J24


title: lung_131s_J20


title: lung_131s_J2


title: lung_131s_J23


title: lung_131s_J19


title: lung_131s_J15


title: lung_131s_J13


title: lung_131s_J14


title: lung_131s_J18


title: lung_131s_J10


title: lung_131s_J1


title: lung_131s_J12


title: lung_131s_J11


title: lung_131s_I9


title: lung_131s_I8


title: lung_131s_J7


title: lung_131s_I7


title: lung_131s_I6


title: lung_131s_I5


title: lung_131s_I3


title: lung_131s_I24


title: lung_131s_I23


title: lung_131s_I21


title: lung_131s_I20


title: lung_131s_I19


title: lung_131s_I18


title: lung_131s_I16


title: lung_131s_I15


title: lung_131s_I13


title: lung_131s_I11


title: lung_131s_I12


title: lung_131s_I10


title: lung_131s_I17


title: lung_131s_I1


title: lung_131s_H8


title: lung_131s_H9


title: lung_131s_H5


title: lung_131s_H6


title: lung_131s_H4


title: lung_131s_I22


title: lung_131s_H21


title: lung_131s_H20


title: lung_131s_H23


title: lung_131s_I2


title: lung_131s_I14


title: lung_131s_H2


title: lung_131s_H19


title: lung_131s_H17


title: lung_131s_H16


title: lung_131s_H3


title: lung_131s_H24


title: lung_131s_H22


title: lung_131s_H7


title: lung_131s_H18


title: lung_131s_H14


title: lung_131s_H12


title: lung_131s_H13


title: lung_131s_H11


title: lung_131s_H15


title: lung_131s_H1


title: lung_131s_G23


title: lung_131s_G14


title: lung_131s_G20


title: lung_131s_G2


title: lung_131s_G10


title: lung_131s_G15


title: lung_131s_G11


title: lung_131s_G13


title: lung_131s_G6


title: lung_131s_G19


title: lung_131s_G4


title: lung_131s_H10


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title: lung_131s_G16


title: lung_131s_G17


title: lung_131s_G5


title: lung_131s_G8


title: lung_131s_G3


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title: lung_131s_G21


title: lung_131s_G24


title: lung_131s_G9


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title: lung_131s_F8


title: lung_131s_F6


title: lung_131s_F7


title: lung_131s_F9


title: lung_131s_G1


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title: lung_131s_F23


title: lung_131s_F3


title: lung_131s_F2


title: lung_131s_F21


title: lung_131s_F24


title: lung_131s_F22


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title: lung_131s_E22


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title: lung_131s_F17


title: lung_131s_F13


title: lung_131s_E9


title: lung_131s_F18


title: lung_131s_F12


title: lung_131s_E20


title: lung_131s_F1


title: lung_131s_E8


title: lung_131s_E3


title: lung_131s_E5


title: lung_131s_F14


title: lung_131s_E23


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title: lung_131s_F19


title: lung_131s_E4


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title: lung_131s_D7


title: lung_131s_D8


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title: lung_131s_D4


title: lung_131s_D3


title: lung_131s_D24


title: lung_131s_D23


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title: lung_131s_C2


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title: lung_131s_C8


title: lung_131s_C9


title: lung_131s_D19


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title: lung_131s_D18


title: lung_131s_C4


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title: lung_131s_C15


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title: lung_131s_B20


title: lung_131s_B19


title: lung_131s_A2


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title: lung_046s_O8


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title: lung_046s_O23


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title: lung_131s_B12


title: lung_131s_A21


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title: lung_131s_A16


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title: lung_046s_F7


title: lung_046s_F3


title: lung_046s_F4


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