title: MPP4-ADA_2

value: Overexpressing MSI2-HyperADAR fusion


title: ST-HSC-ADA_1

status: Public on Mar 11 2020

type: SRA

city: New York

first: Diu

middle: Thi Thanh

last: Nguyen

state: New York

address: 417 East 68th street

country: USA

institute: Memorial Sloan Kettering Cancer Center

description:
Mouse_HSC_rnaseq_read_count_entrez_id.csv
mouse_hsc_snp_counts_dedupped.xlsx
mouse_hsc_snp_counts_dedupped_significant.csv

library_source: transcriptomic

data_processing:
The paired-end RNA-seq reads to mouse (mm10) genome using STAR aligner (Dobin et al., 2013)
All mutations (SNP) were identified for each RNA-seq library using the GATK (Van der Auwera et al., 2013) workflow for calling variants in RNA-seq
The mutations were then restricted to annotated mRNA transcripts, as well as restricted to A-to-G mutations in transcripts encoded by the forward strand and T-to-C mutations in transcripts encoded by the reverse strand.
Data were then filtered using mutations found in the dbSNP database since they are most likely DNA-level mutations.
The filtered sets of RNA editing events from all RNA-seq libraries of the same experiment were combined, and counted the number of reads containing reference (A/T) and alternative (G/C) alleles from each library at each site
Genome_build: mm10
Supplementary_files_format_and_content: "mouse_hsc_snp_counts_dedupped.xlsx" file includes coordinates of the editing sites, strand, entrez id, gene symbol, annotation, reference nucleotide, alternative nucleotide (edited nucleotide) for each RNA-seq library. "Mouse_hsc_snp_counts_dedupped_significant.xlsx" file includes also difference frequency (editing frequency of a site in MSI2_ADA sample subtracted to the average of editing frequency of the site in MSI2_DCD sample and MIG sample), p value, adjusted p value, number of edit sites per gene, fpkm in each sample for edited genes. "Mouse_HSC_rnaseq_read_count_entrez_id.csv" contains read counts for all genes that are mapped to the reference genome in each sample.

molecule: total RNA

organism: Mus musculus

source_name: Sorted ST-HSC from bone marrow of normal C57/B6J mice

growth_protocol: Bone marrow cells from 6-8 week-old C57BL/6 strain were processed for c-Kit enrichment by incubation with 50 μl of MACS CD117/c-Kit beads per mouse and then run on an AutoMACs (Miltenyi Biotec) following the manufacturer’s instructions. Cells were stained with Lineage antibody cocktail (CD3, CD4, CD8, Gr1, B220, CD19, TER119 conjugated with PeCy5), Sca1-Pacific Blue, and c-KIT-APC-Cy7. Lin-Sca+Kit+ cells (LSKs) were sorted using a BD FACS Aria II instrument. Sorted LSKs were grown overnight in SFEM medium containing 10ng/ml murine IL-3, 10ng/ml IL-6, 50ng/ml SCF, 10ng/ml thrombopoietin (TPO), and 20ng/ml FLT3l.

extract_protocol:
360-20,000 sorted cells were used for RNA extraction and sequencing.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 2ng total RNA with RNA integrity numbers ranging from 9.3 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification.Subsequently, 10ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR.

treatment_protocol: Cells were spinoculated with retrovirus expressing MSI2-ADA, MSI2-DCD or MIG controls and 4ug/mL polybrene on retronectin-coated plates at 2500rpm for 2 hours at 32oC. After 48 hours of transduction, all cells were collected and transplanted into lethally irradiated C57BL/6 mice (15,000 cells per mouse). Engraftment was checked after 6 weeks. After 7 weeks of transplantation, mice were sacrificed and c-Kit enriched bone marrow cells were stained with LSK markers as described above plus CD48-PE and CD150-APC. Cells were sorted into 4 populations GFP positive CD150+ CD48- (LT-HSC), CD150- CD48-  (ST-HSC or MPP1), CD150+ CD48+ (MPP2) and CD150- CD48+ (MPP4).

tag: cell type

value: Short-term hematopoietic stem cells

tag: overexpression

tag: time point

value: 7 weeks after transplantation


title: HEL_input

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

country: Germany

institute: Hannover Medical School

description: ChIP-input sample HEL cell line

library_source: genomic

data_processing:
Raw Illumina NextSeq BCL files converted to FASTQs using Illumina bcl2fastq v02.14.01.07 and reads trimmed using Trimmomatic v0.36 (phred quality threshold 33).
FastQ files were uploaded to the Basepair-server (basepairtech.com)
Alignment and ChIP-seq QC was performed using the basepair (Bowtie2) utilizing the default settings
Peak calling was performed using MACS (v.1.4) within the basepair platform utilizing the default settings
Genome_build: hg19
Supplementary_files_format_and_content: Sample signal files for visualization (.bigwig) and peak calling results as the original MACS output (.txt)

molecule: genomic DNA

organism: Homo sapiens

source_name: HEL cultured cell line

growth_protocol: HEL cells were cultured in PRMI1640 media supplemented with 10% Fetal bovine serum (v/v) (Gibco), 1x penicillin/streptomycin (Gibco), plasmocin (ThermoFisher).

extract_protocol:
The cells were collected and washed twice in ice-cold PBS followed by crosslinking in 1% formaldehide (methanol free) for 5 minutes. Excess of formaldehyde was quenched by addition of Tris pH 8.0 to 100nM final and Glycine 125 mM final. Chromatin was cheared using Covaris E220 for 20 min with power 140; duty 5; bursts 200/sec. We then used 5ul aliquote of sherared chromatin to decrosslink in order to test completeness of shearing. Chromatin was considered passed QC if fragments 100-600bp were >90%. For immunoprecipitation we used aproximately chromatin from 1-10x10^6 cells, 5-10ug of specific antibody and 10-20ul of Protein-A/G magnetic beads (Dynal). In 16 hours the immune complexes were wased in Mixed Micelle Buffer, buffer 500, LiCl/detergent solution and TE buffers. DNA was eluted from the beads using 100mM NaHCO3 100mM NaCl 1% SDS and purified using AmpureXP beads.
1-10 ng of ChIP'ed DNA was used for Illumina compatible library generation using ThruPlex DNA-seq kit with 10 to 14 cycles of amplification with single end barcodes

treatment_protocol: ChIPs were performed from steady-state cell cultures (no drug treatment)

tag: cell line

value: HEL

tag: chip target

value: none (input sample)


title: shRNF113A + cisplatin replicate 3

city: Liège

first: Alice

last: Mayer

address: GIGA, CHU, Sart-Tilman

country: Belgium

institute: University of Liège

description:
processed data files:
merged.gtf
isoforms.counts_tracking
isoforms.fpkm_tracking
isoforms.read_group_tracking
isoform_exp.diff
A3SS.MATS.ReadsOnTargetAndJunctionCounts.csv
A5SS.MATS.ReadsOnTargetAndJunctionCounts.csv
MXE.MATS.ReadsOnTargetAndJunctionCounts.csv
RI.MATS.ReadsOnTargetAndJunctionCounts.csv
SE.MATS.ReadsOnTargetAndJunctionCounts.csv
gencode.v19.GeneExonsProteinCoding.gtf

data_processing:
1. Illumina bcl2fastq v2.17 was used to generate fastq files with adapters trimmed
2. Trimming to 73bp per read with cutadapt
3.Removal of reads mapping to rRNA, tRNA, chrM with bowtie2
4. Mapping to hg19 reference genome using STAR v2.5.2b and ENCODE options
Additional Star option --outFilterIntronMotifs RemoveNoncanonical used for Cufflinks compatibility
Additional Star option --alignEndsType EndToEnd used for rMATS compatibility
5. Alignments were processed with cufflinks, transcriptome assembly was generated with cuffmerge, transcript abundance was evaluated with cuffquant and differential expression assessed with cuffdiff
6. Splicing analysis with rMATS v3.2.5 (with python 2.7.12)
7.Intron retention estimation using HTSeq count with options -m intersection-strict and -i gene_name with gencode.v19.GeneExonsProteinCoding.gtf. Option -t exon and -t gene used to generate *_exon.counts and *_gene.counts, respectively.
Genome_build: hg19
Supplementary_files_format_and_content: *_ReadsPerGene.out.tab = tab-delimited text files with gene raw counts from Star
Supplementary_files_format_and_content: merged.gtf and isoform* = tab-delimited text files with counts, fpkm and differential expression analysis from cuffdiff + transcriptome assembly from cuffmerge in gtf format (merged.gtf)
Supplementary_files_format_and_content: *.MATS.ReadsOnTargetAndJunctionCounts.csv = csv files with splicing analysis results from rMATS
Supplementary_files_format_and_content: *_exons.counts and *_genes.counts = tab-delimited text files with raw counts from HTSeq count for annotations in gencode.v19.GeneExonsProteinCoding.gtf

source_name: A549 Lung tumor cells

growth_protocol: DMEM with 10%FBS, 5%CO2, 37C°, split 1/10 every 4-5 days

extract_protocol:
Total RNA Rneasy Mini Kit Qiagen. Following manufacturer instructions.
Truseq stranded mRNA Sample Preparation Kits. Libraries were prepared following manufacturer instructions. Libraries were multipexed altogether and sequenced in two runs on Illumina NextSeq sequencers (2x 76bp)

treatment_protocol: 25ug/ml cisplatin for 20h in full growth media

value: A549 cell line after infection with lentivirus and puromicyn (1ug/ml) selection for 4 days.

tag: shRNA

tag: treatment

value: Cisplatin-treated


title: HEL_YBX1-ChIPseq_rep1

tag: antibody

value: anti-YBX1 (Abcam, EP2708Y, #ab76149)


title: HEL_YBX1-ChIPseq_rep2


title: H3Input_TESm rep2

city: Durham

first: Sara

middle: A.

last: Garcia-Moreno

state: North Carolina

address: Nanaline Bldg. Research Drive

institute: Duke University

data_processing:
Files were trimmed for quality using trim_galore with a stringency setting of 5
Reads were aligned to the mm9 genome with bowtie using the parameters -m 1 and --best
Unmapped reads were eliminated with samtools view using -F 4 settings
HOMER was used for calling peaks with the findPeaks function and settings “--style histone”, with a size of 5000 for H3K27me3. The setting “-C 0” was used in MNase ChIP to  disable fold enrichment limit of expected unique tag positions. H3K27me3 was used as treament (-t) and H3 as control (-c)
bigwig files were created from .bdg files using BedGraphToBigWig for visualization on the UCSC genome browser.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contain tracks for visualization on the UCSC genome browser.

source_name: FACS-sorted granulosa cells

extract_protocol:
Embryonic gonads were micro-dissected at according stage, removed from the mesonephros and incubated in 0.05% trypsin for 5 minutes at 37C. Gonads were then mechanically dissasociated in PBS/3% BSA and passed through a filter cap to obtain a single cell suspension. Fluorescently-labeled cells were collected by Fluorescence Activated Cell Sorting (FACS).  For ChIP-seq, ~100K cells were collected per replicate.
ChIP-seq libraries were prepared with no modifications according to Van Galen et al., 2016.

value: FACS-sorted granulosa cells

tag: strain

value: C57BL/6 x CD1

tag: embryonic stage

tag: Sex

value: female

tag: transgenic line

value: TESM-CFP

tag: chip antibody

value: H3 Active Motif 39763


title: LT-HSC-DCD_2

source_name: Sorted LT-HSC from bone marrow of normal C57/B6J mice

value: Long-term hematopoietic stem cells

value: Overexpressing MSI2-HyperADAR catalytic dead fusion


title: Sample64 hESC RetinalOrganoid

status: Public on Mar 12 2020

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: Noob normalization using preprocessNoob in the minfi R package

label: cy3, cy5

source_name: Human fetal retina

label_protocol: Bisulfite conversion was performed on 500 ng of DNA using the llumina Infinium Methylation Assay protocol in the EZ DNA Methylation kit (Zymo Research). Following the desulphonation and wash steps, converted DNA was eluted in 12 μl of the M-Elution buffer and then loaded onto the Infinium Human Methylation 450K BeadChip kit (Illumina, #WG-314-1003)

extract_protocol: Genomic DNA of the retinas was precipitated from the interphase and phenol  phase of the TRIzol solution using 100% ethanol. The DNA pellet was washed 3 times  with 0.1 M sodium citrate/10% ethanol solution and once with 75% ethanol. The pellet  was then resuspended in 8 mM NaOH buffer or concentrated using gDNA Clean and  Concentrator kit (Zymo Research, Irvine, CA).

tag: batch

tag: basename

tag: detailed location retina

value: whole but could be disorganized

tag: culture method

value: RetinalOrganoid

tag: externalsampleid

tag: humanid

value: Female

tag: gestational day

tag: days in vitro

tag: human expected days


title: shRNF113A + cisplatin replicate 2

tag: cell line

tag: shRNA


title: LT-HSC-ADA_2

tag: cell type

tag: overexpression

value: Overexpressing MSI2-HyperADAR fusion

tag: time point


title: shRNF113A + cisplatin replicate 1

tag: treatment


title: MPP2-DCD_2

source_name: Sorted MPP2 from bone marrow of normal C57/B6J mice

value: Myeloid-biased multipotent progenitor cells

value: 7 weeks after transplantation


title: MPP4-DCD_2

source_name: Sorted MPP4 from bone marrow of normal C57/B6J mice

value: Lymphoid-biased multipotent progenitor cells


title: shRNF113A untreated replicate 3

value: A549 cell line after infection with lentivirus and puromicyn (1ug/ml) selection for 4 days.

value: Untreated


title: shRNF113A untreated replicate 2


title: ST-HSC-DCD_2

value: Short-term hematopoietic stem cells


title: MPP4-DCD_1


title: ST-HSC-DCD_1


title: shControl + cisplatin replicate 3

value: shControl

value: Cisplatin-treated


title: shRNF113A untreated replicate 1


title: MPP2-ADA_1


title: LT-HSC_MIG_2

value: Overexpressing empty vector


title: shControl untreated replicate 3


title: MPP2-DCD_1


title: shControl + cisplatin replicate 1


title: shControl untreated replicate 1


title: shControl untreated replicate 2


title: LT-HSC-DCD_1


title: replicate 3, 4hr TCR stimulated T cells

city: Philadelphia

first: Joseph

middle: M

last: Dybas

state: PA

address: 3501 Civic Center Blvd

department: Department of Biomedical and Health Informatics

institute: Children's Hospital of Philadelphia

data_processing:
Alignments with STAR v2.5.2a
HTseq (-m intersection-strict)
Differential expression and FDR calculated with DEseq2
additional analysis and figures generated in R
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-separated table of raw HTseq counts for unstimulated samples 1,2,3 and stimulated samples 1,2,3

source_name: T cells

growth_protocol: Mouse primary CD4+ T cells were isolated from the spleen and lymph nodes of wildtype mice. The cells were stimulated with plate-bound anti-CD3/CD28 antibody for 3 days, removed from antibody stimulation, and proliferated in IL2 for 5 days. The cells were then left at rest or restimulated for 4 hours with anti-CD3/CD28 to induce Tcell Receptor stimulation.

extract_protocol:
Total RNA was isolated using the Qiagen Rneasy kit following the included protocol.
TruSeq RNA Sample prep

treatment_protocol: Mouse primary CD4+ T cells were left at rest or treated with anti-CD3/CD28 antibody for 4hr prior to RNA extraction.

value: primary CD4+ T cells

value: stim


title: replicate 3, unstimulated T cells

value: unstim


title: shControl + cisplatin replicate 2


title: AB6040

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: metadata2.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts

molecule: polyA RNA

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
Mice were housed under specific-pathogen-free conditions at the Animal Breeding Center of the Weizmann Institute of Science, and were used at 6 to 8 weeks of age. All animals were handled according to the regulations formulated by the Institutional Animal Care and Use Committee.
For the in vitro co-culture experiment, cells were isolated from spleens of C57BL/6 8 week old mice. DC derived from spleen tissues were enriched from the single cell suspension first by negative magnetic selection for CD19, and second by positive magnetic selection for CD11c. 2x106 DC were seeded in 6-well plate for 2h activation with 100ng/ml lipopolysaccharide (LPS; Sigma-Aldrich) and 2ug/ml OVA 323-339 (InvivoGen), at 37oC. In parallel, we isolated CD4+ T cells from spleens of OT-II mice. T cells were enriched by the CD4+ T cell Isolation Kit. For culture experiments CD11c+ DC and CD4+ T cells were plated on 96-well U-shape bottom, tissue culture plates. Co-cultured and mono-cultured cells were seeded in concentration of 1×106 cells/ml (1:1 ration in co-cultures), and harvested at different time points following cell plating (3h, 20h, 44h).
For the in vivo infection experiment, N. brasiliensis (Nb) infective L3 larvae were prepared, washed in sterile PBS and killed by three freeze-thaw cycles. Mice were anesthetized and antigen was administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals. Experiments were performed 48h following antigen injection.  To achieve single cell suspensions, auricular LN were digested in IMDM (Sigma-Aldrich) containing Liberase-TL (100μg/ml, Roche) and DNase-I (100μg/ml, Roche), and incubated with frequent agitation at 37oC for 20 min. Cells were washed with IMDM, filtered through a 100μm cell strainer, and centrifuged at 380g, 5min, 4oC.
In both experiments, prior to sorting, cells were stained with DAPI for evaluation of live/dead cells. For the sorting of T-DC PIC samples were gated for TCRβ+CD11c+, for sorting of T cells samples were gated for TCRβ+, and for the isolation of DC, samples were gated for CD11c+, after exclusion of dead cells (DAPI-), erythrocytes (TER119-) and B cells (CD19-).
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: Mice were sacrified by CO2

tag: strain

tag: organ

value: in vitro

tag: selection marker

value: Trbc+

value: Mono-culture

tag: replicate id

tag: age

value: 6-8 weeks


title: replicate 2, 4hr TCR stimulated T cells


title: ST-HSC_MIG_1


title: replicate 2, unstimulated T cells


title: MPP4_MIG_1


title: MPP4_MIG_2


title: LT-HSC_MIG_1

value: Long-term hematopoietic stem cells


title: replicate 1, 4hr TCR stimulated T cells


title: MPP2_MIG_1

value: Myeloid-biased multipotent progenitor cells


title: MPP2_MIG_2

value: 7 weeks after transplantation


title: Oregon-R rep2

city: Montpellier

first: Giacomo

last: Cavalli

address: IGH - CNRS, 141, rue de la Cardonille

country: France

institute: CNRS

data_processing:
Whole genome sequencing with overlapping (2x165nt) were generated for three biological replicates.
All three replicates were combined to call transposable elements (TEs) and reads were quality filtered with Trim galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). TEs were called by TIDALfollowing default parameters (R. Rahman et al; Nucreic Acids Res, 43, 10655-10672, 2015).
Supplementary_files_format_and_content: OR_123_S123_all_Inserts_Annotated.txt: use all pair-end reads as single-end (http://www.bio.brandeis.edu/laulab/Tidal_Fly/UserGuide_TIDAL_outputs.html#summary)  Chr : Chromosome  Chr_coord_5p : 5' genomic coordinate boundary of the reads forming the cluster of TE insertion reads.  Chr_coord_3p : 3' genomic coordinate boundary of the reads forming the cluster of TE insertion reads.  TE : name of TE family  TE_coord_start : deepest 5' end coordinate of the cluster of reads mapping in the TE's consensus sequence.  TE_coord_end : deepest 3' end coordinate of the cluster of reads mapping in the TE's consensus sequence.  Reads_collapsed : number of reads forming the read cluster demarcating new TE insertion (current minimum is 4 reads).  Chr_Coord_Dist : number of bases between the Chr_coord_5p and the Chr_coord_3p values. Should be no greater than 300bp (2x length of longest Illumina read, 150bp).  Symmetry : approximation of how many reads on either side of the TE insertion.  avg_blat_score : the average BLAT score for the cluster of reads marking the TE insertion. Entries are filtered so that false positives with average BLAT scores >83 are removed.  Norm_RefGen_Reads : approximation of the read coverage count for the reference genome mapping reads falling within the Chr_coord_5p and the Chr_coord_3p window, used in the calculation of the Coverage Ratio.  Coverage_Ratio : Calculation of TE insertion reads over reference genome reads plus a pseudocount. Insertion CR = (TE reads) / (RefGen reads+1). The "1" is a pseudocount.  classification : Type of functional genomic annotation based on the genomic coordinate (intron, exon, 3'UTR, 5'UTR, or intergenic)  comments : Name of the RefSeq gene nearest to the TE insertion coordinates, along with the genomic strand orientation of the gene. Note: the nearest gene is not necessarily the only gene with impacted expression; sometimes a more downstream gene exhibits an effect from the TE.  insert_code : A unique identifier string for SQL analyses. Combination of chromosome, reads_collapsed, and chromosome start coordinates rounded down to lowest 5kb interval.   loci_code : A unique identifier string for SQL analyses. Combination of chromosome, and chromosome start coordinates rounded down to lowest 5kb interval.   Sym_score : Decimal ratio of the text in the Symmetry field.  libname : Short name of the genome library.
Supplementary_files_format_and_content: OR_123_S123_trimmedto200bp_Inserts_Annotated.txt: merge pair-end and trimmed to 200bp (http://www.bio.brandeis.edu/laulab/Tidal_Fly/UserGuide_TIDAL_outputs.html#summary)  Chr : Chromosome  Chr_coord_5p : 5' genomic coordinate boundary of the reads forming the cluster of TE insertion reads.  Chr_coord_3p : 3' genomic coordinate boundary of the reads forming the cluster of TE insertion reads.  TE : name of TE family  TE_coord_start : deepest 5' end coordinate of the cluster of reads mapping in the TE's consensus sequence.  TE_coord_end : deepest 3' end coordinate of the cluster of reads mapping in the TE's consensus sequence.  Reads_collapsed : number of reads forming the read cluster demarcating new TE insertion (current minimum is 4 reads).  Chr_Coord_Dist : number of bases between the Chr_coord_5p and the Chr_coord_3p values. Should be no greater than 300bp (2x length of longest Illumina read, 150bp).  Symmetry : approximation of how many reads on either side of the TE insertion.  avg_blat_score : the average BLAT score for the cluster of reads marking the TE insertion. Entries are filtered so that false positives with average BLAT scores >83 are removed.  Norm_RefGen_Reads : approximation of the read coverage count for the reference genome mapping reads falling within the Chr_coord_5p and the Chr_coord_3p window, used in the calculation of the Coverage Ratio.  Coverage_Ratio : Calculation of TE insertion reads over reference genome reads plus a pseudocount. Insertion CR = (TE reads) / (RefGen reads+1). The "1" is a pseudocount.  classification : Type of functional genomic annotation based on the genomic coordinate (intron, exon, 3'UTR, 5'UTR, or intergenic)  comments : Name of the RefSeq gene nearest to the TE insertion coordinates, along with the genomic strand orientation of the gene. Note: the nearest gene is not necessarily the only gene with impacted expression; sometimes a more downstream gene exhibits an effect from the TE.  insert_code : A unique identifier string for SQL analyses. Combination of chromosome, reads_collapsed, and chromosome start coordinates rounded down to lowest 5kb interval.   loci_code : A unique identifier string for SQL analyses. Combination of chromosome, and chromosome start coordinates rounded down to lowest 5kb interval.   Sym_score : Decimal ratio of the text in the Symmetry field.  libname : Short name of the genome library.

organism: Drosophila melanogaster

source_name: adult female

growth_protocol: Oregon-R w1118 flies were raised in standard cornmeal yeast extract media at 25°C.

extract_protocol:
Genomic DNA was prepared from 100 Oregon-R w1118 adult female flies for each biological replicate with Gentra Puregene Cell kit (Qiagen cat#158388) according to the manufacturer’s instructions.
The library is prepared with an Illumina Truseq Nano DNA Library Preparation kit. The library validation is qualitatively and quantitatively done on Fragment Analyzer, as well as by qPCR.

value: Oregon-R w1118

tag: develpmental stage

value: adult

tag: Sex

value: female


title: Oregon-R rep3


title: Oregon-R rep1


title: roX2 thCHART (unprotected LNA) [RNA]

city: West Haven

first: Matthew

middle: D

last: Simon

state: CT

address: 600 West Campus Dr. MIC312

department: Molecular Biophysics & Biochemistry

institute: Yale University Chemical Biology Instiute

description: thCHART of roX2 was performed with unprotected LNA capture oligonucleotide, subjected to stringent rinses and eluted with respective elution oligonucleotide.

data_processing:
Library strategy: thCHART
Adaptor sequences were removed using Cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -m 3
Reads were aligned to refseq (dm6) transcriptome using tophat/bowtie2.
Genome coverage tracks from bam files were created using samtools.
Bedgraphs were converted to bigWig format.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: bigWig files contain genome coverage tracks of RNA reads from thCHART experiments.

source_name: S2 cell line

growth_protocol: S2 cells were grown in Schneider media supplemented with 1% penicillin/streptomycin and 10% heat-inactivated FBS at 27˚C until density of 4 million cells/ml.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min, followed by nuclei extraction and further crosslinking with 3% formaldehyde for 45 min. Crosslinked nuclei were sheared with covaries and cleared by centrifugation. Biotinylated antisense capture oligonucleotide was added to extract and left to hybridize over night at room temperature. Hybridized RNA complexes were captured on magnetic streptavidin beads and subjected to stringent rinses. Complexes were eluted by incubating beads with excess of elution oligonucleotide. Eluted molecules were de-crosslinked by incubating at 55˚C 1h and 65˚C 1h in the presence of proteinase K. RNA was isolated using RNeasy kit (Qiagen).
RNA libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina.


title: roX2 CHART [RNA]

description: CHART of roX2 performed with DNA capture oligonucleotide, subjected to mild wash conditions and eluted with RNaseH. As in Simon MD et al. (2011 PNAS).

data_processing:
Library strategy: CHART
Adaptor sequences were removed using Cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -m 3
Reads were aligned to refseq (dm6) transcriptome using tophat/bowtie2.
Genome coverage tracks from bam files were created using samtools.
Bedgraphs were converted to bigWig format.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: bigWig files contain genome coverage tracks of RNA reads from thCHART experiments.


title: replicate 1, unstimulated T cells


title: Input [RNA]


title: roX2 thCHART (control oligo) [RNA]

description: thCHART of roX2 was performed with unspecific protected toehold-LNA capture oligonucleotide, subjected to stringent rinses and eluted with respective elution oligonucleotide.


title: roX2 thCHART [RNA]

description: thCHART of roX2 was performed with protected toehold-LNA capture oligonucleotide, subjected to stringent rinses and eluted with respective elution oligonucleotide.


title: roX2 Heat shock rep3 [DNA]

description:
processed data file: HS_autosomal_peaks_summits.bed
processed data file: diff.HS_Full_peak_zscore10_down_FC.bed
processed data file: diff.HS_Full_peak_zscore10_up_FC.bed

data_processing:
Library strategy: thCHART
Adaptor sequences were removed using Cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -m 3
Reads were aligned to reference genome using bowtie2.
Aligned reads were filtered for MAPQ > 2 woth samtools.
Sample enrichment over input was calculated using MACS2.
Enrichment bedgraph files were converted to bigWig format.
roX2 enriched regions were detected with rseq using -i 20 option and pre-calculated dm6 dead zones for 76 nt reads.
CES summits were detected using MACS2 callpeak. Using custom R script, peaks were filtered for those that overlap between replicates and have -log10(q-value) > 100.
Autosomal peak summits were detected using MACS2 call peak and filtered with custom R script for those that overlap between replicates.
Differentially upregulated or downregulated roX2 regions upon heatshock were detected using Diffreps (-me nb --mode p --nsd 10) and filtered for those with more than 2 fold change.
Genome_build: Drosophila dm6 (Release 6 plus ISO1 MT); Mouse mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files contain track of sample enrichment over input.
Supplementary_files_format_and_content: thCHART_CO1-domains.bed contains roX2 thCHRT enriched regions detected by rseg.
Supplementary_files_format_and_content: CES_summits.bed contains position of CES summits.
Supplementary_files_format_and_content: HS_autosomal_peaks_summits.bed contains position of summits of heat shock induced roX2 autosomal peaks.
Supplementary_files_format_and_content: diff.HS_Full_peak_zscore10_down_FC.bed and diff.HS_Full_peak_zscore10_up_FC.bed contain coordinates of regions that were significantly down- or up-regulated, respectively, by more than 2-fold after heat shock.

growth_protocol: S2 cells were grown in Schneider media supplemented with 1% penicillin/streptomycin and 10% heat-inactivated FBS at 27˚C until density of 4 million cells/ml. MEF cells were grown in DMEM containing 1% penicillin/streptomycin, 10% FBS, at 37°C and 5% CO2 until 90% confluency.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min, followed by nuclei extraction and further crosslinking with 3% formaldehyde for 45 min. Crosslinked nuclei were sheared with covaries and cleared by centrifugation. Biotinylated antisense capture oligonucleotide was added to extract and left to hybridize over night at room temperature. Hybridized RNA complexes were captured on magnetic streptavidin beads and subjected to stringent rinses. Complexes were eluted by incubating beads with excess of elution oligonucleotide. Eluted molecules were de-crosslinked by incubating at 55˚C 1h and 65˚C 1h in the presence of proteinase K. DNA was isolated using PCR purification kit (Qiagen) and sheared with Covaris to 300bp range.
Libraries were constructed according to Bowman et al. (2012, BMC Genomics).

treatment_protocol: Ecdysone: Cells were incubated in growth media supplemented with 41 µM 20-Hydroxyecdysone (40 mM stock solution in DMSO) or equivalent volume of DMSO (Mock) for 24 h. DRB: Cells were incubated in growth media supplemented with 100 µM 5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside (75 mM stock solution in DMSO) or equivalent volume of DMSO (Mock) for 3 h. Heat shock: Cells were incubated 1 h at 37˚C.

tag: heat shock

value: yes


title: roX2 Heat shock rep2 [DNA]


title: condyloma acuminata, biological rep1

type: RNA

city: Wuhan

first: chao

middle: zhi

last: gu

state: Hubei

address: Liberation Road No. 1095

department: Department of Dermatology, Tongji Hospital

country: China

institute: Huazhong University of Science and Technology

hyb_protocol: Following fragmentation, 5 ug of cDNA was hybridized for 16 hr at 45C on GeneChip Human Transcriptome Array (HTA) 2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

label: biotin

source_name: keratinocytes from CA warts located at the skin of the patients’ penis

label_protocol: Extracted total RNA of each samples were reverse transcribed and amplified using the GeneChip WT PLUS Reagent Kit (WT PLUS Kit) (Affymetrix).

extract_protocol: Qiagen RNeasy with on-column DNase digestion

tag: tissue

value: skin

tag: source

value: condyloma acuminata warts

value: keratinocytes


title: condyloma acuminata, biological rep5


title: 14364454_C: Colorectal cancer tissue

city: shenyang

first: wu

last: huizhe

address: No.77, puhe avenue, shenbei new area

institute: Department of pharmacology, college of pharmacy, China medical university

description: Gene expression in  Human Colorectal cancer tissue

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 Human Gene Expression（8*60K）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.

CEL files for individual samples are not available (see combined files at foot of GSE137511)

source_name: Colorectal cancer tissue

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: The tissues were stored in liquid nitrogen before extraction

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

treatment_protocol: Total RNAs was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNAs integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNAs were transcribed to double strand cDNAs and then synthesized cRNAs. Next, 2nd cycle cDNAs were synthesized from cRNAs. Followed fragmentation and biotin labeling, the 2nd cycle cDNAs were hybridized onto the microarray. After washing and staining, the arrays were scanned by the Affymetrix Scanner 3000(Affymetrix).

value: Colorectal cancer tissue


title: condyloma acuminata, biological rep3


title: 14376075_C: Colorectal cancer tissue


title: roX2 Heat shock rep1 [DNA]


title: condyloma acuminata, biological rep2


title: roX2 Heat shock-mock rep2 [DNA]

description:
processed data file: CES_summits.bed
processed data file: diff.HS_Full_peak_zscore10_down_FC.bed
processed data file: diff.HS_Full_peak_zscore10_up_FC.bed

value: no


title: 841_RNASEQ

city: Ellicott city

first: Li

last: Zhang

state: Maryland

address: 733N Broadway

department: Department of Human Genetics

institute: The Johns Hopkins University

data_processing:
Sequencing reads were checked with the software Fastqc.
Reads were mapped to reference genome with the alignment tool Tophat 2 v.2.1.0 (Kim D et al, 2013).
The aligned reads were assembled with CLASS2 v.2.1.7 (Song L, et al, 2016) to create partial genes and transcript models (transfrags)
Transfrags from all samples were further merged with Cuffmerge and mapped to the GENCODE v. M17 gene models (Frankish A, et al, 2019), to create a unified set of gene annotations for  differential analyses.
Gene expression levels were computed, and differentially expressed genes were determined separately with the tools Cutdiff2 v.2.2.1. (Trapnell C, et al. 2013)
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression levels and differentially expressed genes

source_name: hippocampus

extract_protocol:
RNA were extracted from hippocampal tissue with Drirec-zol RNA micriprep kit (ZYMO Research).NEBNext Ultra RNA library prep kit for Illumina.
NEBNext UltraII RNA Library Prep kit for Illumina

treatment_protocol: Mice were  orally administered by gavaging with 1mg/kg/day of TAK-418-418 dissolved in vehicle(methylcellulose) or vehicle alone for 2 weeks starting at age of 2 weeks-old. At the end of two-week-treatment period, mice were sacrificed and hippocampi were harvested.

tag: genotype

value: Veh

value: 30-day old

value: hippocampus

tag: index

value: GATCAG


title: 14364454_N: Control colonic tissue

description: Gene expression in  Human Control colonic tissue

source_name: Control colonic tissue

value: Control colonic tissue


title: 14376075_N: Control colonic tissue


title: roX2 Heat shock-mock rep1 [DNA]

tag: cell line


title: 14364261_C: Colorectal cancer tissue


title: 840_RNASEQ

value: TGACCA


title: 839_RNASEQ

value: CTTGTA


title: roX2 Edysone [DNA]

tag: ecdysone


title: 14358758_N: Control colonic tissue


title: skin, biological rep1

source_name: keratinocytes from normal donors’ foreskins

value: foreskin

tag: cell type


title: skin, biological rep2


title: skin, biological rep3


title: spinal dorsal horn of vehicle-treated rats replicate 2

city: guangzhou

first: xiangcai

last: ruan

state: guangdong

address: 602 Renminbei Rd.

institute: Guangzhou First People's Hospital

description: Biological replicate 2 of 2. spinal dorsal horn of vehicle-treated rats on day 10

hyb_protocol: Scanned on an Agilent G2565AA scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Rattus norvegicus

source_name: spinal dorsal horn

label_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

growth_protocol: Preservation of spinal dorsal horn tissues in liquid nitrogen

extract_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

treatment_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: gender

value: male

value: 6 weeks

value: untreated

value: vehicle


title: 838_RNASEQ

tag: treatment

value: CAGATC


title: condyloma acuminata, biological rep4

value: skin

value: condyloma acuminata warts


title: 14364261_N: Control colonic tissue


title: spinal dorsal horn of vehicle-treated rats replicate 1

description: Biological replicate 1 of 2. spinal dorsal horn of vehicle-treated rats on day 10


title: spinal dorsal horn of oxaliplatin-treated rats replicate 1

description: Biological replicate 1 of 2. spinal dorsal horn of oxaliplatin-treated rats on day 10

value: oxaliplatin


title: 825_RNASEQ

tag: strain

value: ACTTGA


title: 835_RNASEQ

value: Veh

value: TTAGGC


title: 824_RNASEQ

value: 30-day old

value: hippocampus

value: TAGCTT


title: spinal dorsal horn of oxaliplatin-treated rats replicate 2

description: Biological replicate 2 of 2. spinal dorsal horn of oxaliplatin-treated rats on day 10


title: 14358758_C: Colorectal cancer tissue

value: Colorectal cancer tissue


title: roX2 thCHART CO2 [DNA]

description: CO protected with DNA PO.


title: roX2 DRB [DNA]

tag: drb

value: yes


title: 823_RNASEQ

value: ACAGTG


title: input S2 (single-end) [DNA]


title: 837_RNASEQ

value: CGATGT


title: roX2 thCHART CO1 [DNA]

description: CO protected with DNA PO.


title: 822_RNASEQ

value: AGTCAA


title: 821_RNASEQ

value: AGTTCC


title: 820_RNASEQ

value: GCCAAT


title: roX2 thCHART rep2 [DNA]


title: roX2 Edysone-mock [DNA]

value: no


title: roX2 thCHART rep1 [DNA]


title: 818_RNASEQ

value: GGCTAC


title: 819_RNASEQ

value: ATCACG


title: isp1_3

city: Koln

first: Jorge

last: Boucas

address: Joseph-Stelzmann-Str. 9b

department: Bioinformatics

institute: Max Planck Institute for Biology of Ageing

data_processing:
Trimming: flexbar 2.5; -n 18 -ao 10 -u 5 -q 20 -m 20 -f i1.8 -ae ANY
Alignment: Hisat 0.1.6-beta
Guided assembly: StringTie 1.0.4; -p 18 -G ORIGINAL_GTF -f 0.99
Merging assemblies: Cuffmerge 2.2.1; --min-isoform-fraction 1.0
Quantification: Cuffquant 2.2.1
Differential analysis: Cuffdiff 2.2.1; --dispersion-method per-condition
Genome_build: WBcel235
Supplementary_files_format_and_content: [gene.expression.tsv]  tab-separated values

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Worms were cultured at 20°C. Ad libitum (AL) bacteria conditions: Nematodes were cultured using standard techniques on nematode growth medium agar plates with the Escherichia coli strain OP50.

extract_protocol:
Samples were isolated using mRNAeasy Mini Kit (QIAGEN)
RNA-seq libraries were prepared with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: DAY1 adults of respective genotypes were washed in M9 (X3) and collected in Trizol

tag: diet

value: ad libitum bacteria

tag: developmental stage

value: Day 1


title: roX2 DRB-mock [DNA]


title: N2_3


title: nyfb1_isp1_3


title: nyfb1_3


title: 848_H3K4me1_CHIPSeq

data_processing:
Sequencing reads were trimmed 5bp at 5'end with software seqtk(https://github.com/ih3/seqtk)
Trimmed sequences were mapped to mouse reference genome (mm10) with the short sequence alignment tool boKMT2D+/+ie2(Langmead and Salzberg, 2012)
Peaks were subsequently called using MACS2(Zhang et al., 2008) with the condition of --broad, --nomodle, --nolamda
Merging the MACS peaks for all replicates in only one file per conditions; intersectBed used to determine the common and exclusive peaks between 2 conditions.
Detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates using THOR
Genome_build: mm10

extract_protocol:
Sonicated nuclear lysate were pre-cleared and histone-DNA complex were isolated with anti-H3K4me3 antibody (Abcam, ab8580) and anti-H3k4me1(Abcam, ab8895). After reverse cross-linking, DNA fragment were purified by DNA Clean and Concentrator (Zymo Research)
NEBNext UltraII DNA Library Prep kit for Illumina

treatment_protocol: Mice were  orally administered by gavaging with 1mg/kg/day of TAK-418-418 dissolved in vehicle(methylcellulose) or vehicle alone for 2 weeks. At the end of two-week-treatment period, mice were sacrificed and hippocampi were harvested.

value: Veh

tag: age

tag: chip antibody

value: CCGTCC


title: 847_H3K4me1_CHIPSeq

value: 30-day old

value: ATGTCA


title: LSC_MIG_B

data_processing:
The paired-end RNA-seq reads to mouse (mm10) genome using STAR aligner (Dobin et al., 2013)
All mutations (SNP) were identified for each RNA-seq library using the GATK (Van der Auwera et al., 2013) workflow for calling variants in RNA-seq
The mutations were then restricted to annotated mRNA transcripts, as well as restricted to A-to-G mutations in transcripts encoded by the forward strand and T-to-C mutations in transcripts encoded by the reverse strand.
Data were then filtered using mutations found in the dbSNP database since they are most likely DNA-level mutations.
The filtered sets of RNA editing events from all RNA-seq libraries of the same experiment were combined, and counted the number of reads containing reference (A/T) and alternative (G/C) alleles from each library at each site
Genome_build: mm10
Supplementary_files_format_and_content: "mouse_lsk_snp_counts_dedupped.xlsx" and "mouse_lsc_snp_counts_dedupped.xlsx" files include coordinates of the editing sites, strand, entrez id, gene symbol, annotation, reference nucleotide, alternative nucleotide (edited nucleotide) for each RNA-seq library. "Mouse_lsk_snp_counts_dedupped_significant.csv" and "mouse_lsc_snp_counts_dedupped_significant.csv" files include also difference frequency (editing frequency of a site in MSI2_ADA sample subtracted to the average of editing frequency of the site in MSI2_DCD sample and MIG sample), p value, adjusted p value, number of edit sites per gene, fpkm in each sample for edited genes. "lsk_rnaseq_read_count_entrez_id.csv" and lsc_rnaseq_read_count_entrez_id.csv" files contain read counts for all genes mapped to the reference genome in lsk and lsc, respectively.

source_name: Sorted c-Kit high (top 10%) from quaternary MLL-AF9 Actin-DsRed mice

growth_protocol: LSK cells were obtained from Flow cytometry sorting and grown in SFEM medium containing 10ng/ml murine IL-3, 10ng/ml IL-6, 50ng/ml SCF, 10ng/ml thrombopoietin (TPO), and 20ng/ml FLT3l. Quaternary MLL-AF9 leukemia model on Actin-dsRed background mice were generated as described before (Puram et al., 2016). Bone marrow cells from these mice were grown in BMT medium (RPMI 10%FBS 1%L-Glutamine PenStrep supplemented with 10ng/mL murine IL-3, 10ng/mL murine IL-6, 10ng/mL murine SCF and 10ng/mL murine GM-CSF).

extract_protocol:
Sorted GFP positive cells were harvested and frozen in TRIzol reagent. RNA was extracted using Phenol-Chloroform.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 2ng total RNA with RNA integrity numbers ranging from 9.3 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification.Subsequently, 10ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR.

treatment_protocol: LSKs were spinoculated with retrovirus expressing MSI2-ADA, MSI2-DCD or MIG controls and 4ug/mL polybrene on retronectin-coated plates at 2500rpm for 2 hours at 32oC. Cells were incubated for 48hrs and then sorted by flow cytometry for GFP positive (overexpressing the fusions). Bone marrow cells from MLL-AF9 Actin-DsRed mice were infected with MSI2-HyperTRIBE expressing virus in BMT medium for 48 hrs. LSC-enriched population was isolated by sorting dsRed+, GFP+ and c-Kit-APC-Cy7 high (top 10-12%) for library preparation and RNA-seq.

value: Leukemic stem cells

tag: overexpression

value: Overexpressing empty vector

tag: time point

value: 48hr after transduction


title: 846_H3K4me1_CHIPSeq

tag: tissue

value: hippocampus

value: GTGAAA


title: isp1_2


title: nyfb1_isp1_2


title: N2_2


title: nyfb1_2


title: 843_H3K4me1_CHIPSeq


title: 845_H3K4me1_CHIPSeq

value: GAGTGG


title: 842_H3K4me1_CHIPSeq

value: TAGCTT


title: 817_H3K4me1_CHIPSeq

value: CGTACG


title: 844_H3K4me1_CHIPSeq

value: GTCCGC


title: input S2 (paired-end) [DNA]


title: nyfb1_isp1_1


title: isp1_1


title: 814_H3K4me1_CHIPSeq

value: ACTGAT


title: nyfb1_1


title: N2_1


title: 805_H3K4me1_CHIPSeq

value: CGATGT


title: 813_H3K4me1_CHIPSeq

value: ATTCCT


title: 811_H3K4me1_CHIPSeq

value: TGACCA


title: 810_H3K4me1_CHIPSeq

value: TTAGGC


title: 801_H3K4me1_CHIPSeq

value: ATCACG


title: H3K27me3_TESm rep1

value: FACS-sorted granulosa cells

value: C57BL/6 x CD1

tag: embryonic stage

tag: Sex

value: female

tag: transgenic line

value: TESM-CFP

value: H3K27me3 CST 9733S


title: 848_H3K4me3_CHIPSeq

tag: genotype

value: Veh

value: 30-day old

value: hippocampus

tag: index

value: TAATCG


title: 847_H3K4me3_CHIPSeq

value: CCAACA


title: 846_H3K4me3_CHIPSeq

value: AGTTCC


title: 815_H3K4me1_CHIPSeq

value: GTGGCC


title: 844_H3K4me3_CHIPSeq

value: CTTGTA


title: Molm13_RRM(mut)MSI2_HyperADA_1

data_processing:
The paired-end RNA-seq reads to human (hg19) genome using STAR aligner (Dobin et al., 2013)
All mutations (SNP) were identified for each RNA-seq library using the GATK (Van der Auwera et al., 2013) workflow for calling variants in RNA-seq
The mutations were then restricted to annotated mRNA transcripts, as well as restricted to A-to-G mutations in transcripts encoded by the forward strand and T-to-C mutations in transcripts encoded by the reverse strand.
Data were then filtered using mutations found in the dbSNP database since they are most likely DNA-level mutations.
The filtered sets of RNA editing events from all RNA-seq libraries of the same experiment were combined, and counted the number of reads containing reference (A/T) and alternative (G/C) alleles from each library at each site
Genome_build: hg19
Supplementary_files_format_and_content: all processed files include coordinates of the editing sites, strand, entrez id, gene symbol, annotation, reference nucleotide, alternative nucleotide (edited nucleotide) for each RNA-seq library, difference frequency (editing frequency of a site in the indicated sample subtracted to the average of editing frequency of the site in MSI2_DCD sample and MIG sample), p value, adjusted p value, number of edit sites per gene, fpkm in each sample for edited genes.

source_name: Molm13 human leukemia cell line

growth_protocol: MOLM-13 cells (obtained from ATCC) were cultured in RPMI 10% FBS 1%L-Glutamine PenStrep.

extract_protocol:
0.5 million of sorted cells per sample were harvested and frozen in TRIzol reagent. RNA was extracted using Phenol-Chloroform.
After PicoGreen quantification and quality control by Agilent BioAnalyzer, 1ug RNA input was used for library preparation (TrueSeq Stranded mRNA LT Sample Prep Kit)

treatment_protocol: Cells were infected with virus expressing ADAR only (ADA only), RRM(del)MSI2-HyperADA or RRM(mut)MSI2-HyperADA fusions at 1:1 ratio (v/v) cell: virus at 0.5 million cells per mL (final density). Spinoculation was done with 10ug/mL Polybrene (Millipore #TR-1003-G) at 1500rpm for 1 hour at 32oC. Cells were incubated for 48hrs and then sorted by flow cytometry for GFP positive (overexpressing the fusions)

tag: cell line

tag: cell type

value: leukemia cell line

value: Overexpressing RRM1&2 mutated MSI2-ADA fusion

value: 48hr after transduction


title: Molm13_RRM(del)MSI2_HyperADA_3

value: Overexpressing RRM1&2 deleted MSI2-ADA fusion


title: Molm13_RRM(mut)MSI2_HyperADA_2


title: Molm13_RRM(del)MSI2_HyperADA_2


title: Molm13_RRM(mut)MSI2_HyperADA_3


title: Molm13_RRM(del)MSI2_HyperADA_1


title: Molm13_HyperADA_only_3

value: Overexpressing catalytic domain of hyperactive ADAR


title: Molm13_HyperADA_only_2


title: scRNAseq_Stage6C

city: Rochester

first: Caden

middle: Dale

last: Duffy

state: Minnesota

address: 11-20 Stabile 150 3rd St SW

department: Biomedical Engineering and Physiology

institute: Mayo Clinic

data_processing:
Libraries were sequenced at 60,000 fragment reads per cell following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cells were sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kit and HCS v3.3.52 collection software. Base-calling was performed using Illumina’s RTA version 2.7.3.
BCL files were converted into raw fastq files using Illumina's bcl2fastq function
Fastq files were processed into matrix files using CellRanger v. 3.0.2
Genome_build: Aligned with human genome GRCh38-3.0.0
Supplementary_files_format_and_content: Processed data format is .mtx and .tsv

source_name: Pancreatic alpha cells

extract_protocol:
Cells were dissociated with TrypLE, resuspended in 0.1% BSA, and filtered prior to 10X Chromium standard procedure
The cells were first counted and measured for viability using the Vi-Cell XR Cell Viability Analyzer (Beckman-Coulter).  The barcoded Gel Beads were thawed from -80C and the cDNA master mix was prepared according to the manufacture’s instruction for Chromium Single Cell 3’ v3 library kit (10x Genomics). The live cells were mixed with the cDNA master mix.  A per sample concentration of 500,000 cells per milliliter or better was required for the standard targeted cell recovery of 2000 cells.  The stock concentration requirements would not change for higher cell recovery numbers.  The cell suspension and master mix, thawed Gel Beads and partitioning oil were added to a Chromium Single Cell B chip.  The filled chip was loaded into the Chromium Controller, where each sample were processed and the individual cells within the sample were captured into uniquely labeled GEMs (Gel Beads-In-Emulsion).  The GEMs were collected from the chip and taken to the bench for reverse transcription, GEM dissolution, and cDNA clean-up.  The resulting cDNA was a pool of uniquely barcoded molecules.  A portion of the cleaned and measured pooled cDNA continued on to library construction, where standard Illumina sequencing primers and a unique i7 Sample index were added to each cDNA pool. All cDNA pools and resulting libraries were measured using Qubit High Sensitivity assays (Thermo Fisher Scientific), Agilent Bioanalyzer High Sensitivity chips (Agilent) and Kapa DNA Quantification reagents (Kapa Biosystems).

value: ES-derived pancreatic endocrine cells


title: Molm13_HyperADA_only_1


title: 843_H3K4me3_CHIPSeq

tag: treatment

value: CATGGC


title: 817_H3K4me3_CHIPSeq

tag: strain

value: CACTCA


title: 842_H3K4me3_CHIPSeq

value: CAGGCG


title: 146_001 HLHS

city: Palo Alto

first: Sharon

last: Paige

address: 265 Campus Drive

institute: Stanford University

data_processing:
The single cell library was sequencing with the Illumina HiSeq 4000 platform.
Sequencing reads were aligned to the human genome with CellRanger.
Genome_build: hg19

source_name: Blood

growth_protocol: iPSCs were thawed and plated on a 6-well Matrigel-coated plate with E8 media. Media was changed once daily. Cardiac directed differentiation was initiated when wells were confluent utilizing small molecule modulation of the canonical Wnt/β-catenin signaling pathway. Once differentiated, iPSC-derived cardiomyoctes were maintained in RPMI/B27 media until D30 of differentiation.

extract_protocol:
This step was done following the 10X genomics single cell preparation protocol.
This step was done following the 10X genomics single cell library preparation protocol.

value: iPSC-derived cardiomyocytes

tag: clone

value: D30 iPSC-CMs


title: 816_H3K4me3_CHIPSeq

value: 30-day old

value: hippocampus

value: CACGAT


title: scRNAseq_Stage5C

source_name: Pancreatic alpha progenitor cells


title: 814_H3K4me3_CHIPSeq

value: GCCAAT


title: 815_H3K4me3_CHIPSeq

value: CAACTA


title: Molm13_Hyper_dADAR_DCD_2

data_processing:
The paired-end RNA-seq reads to human (hg19) genome using STAR aligner (Dobin et al., 2013)
All mutations (SNP) were identified for each RNA-seq library using the GATK (Van der Auwera et al., 2013) workflow for calling variants in RNA-seq
The mutations were then restricted to annotated mRNA transcripts, as well as restricted to A-to-G mutations in transcripts encoded by the forward strand and T-to-C mutations in transcripts encoded by the reverse strand.
Data were then filtered using mutations found in the dbSNP database since they are most likely DNA-level mutations.
The filtered sets of RNA editing events from all RNA-seq libraries of the same experiment were combined, and counted the number of reads containing reference (A/T) and alternative (G/C) alleles from each library at each site
Genome_build: hg19
Supplementary_files_format_and_content: "molm13_snp_counts_dedupped.xlsx" file includes coordinates of the editing sites, strand, entrez id, gene symbol, annotation, reference nucleotide, alternative nucleotide (edited nucleotide) for each RNA-seq library. "Molm13_snp_counts_dedupped_significant.csv" file includes also difference frequency (editing frequency of a site in MSI2_ADA sample subtracted to the average of editing frequency of the site in MSI2_DCD sample and MIG sample), p value, adjusted p value, number of edit sites per gene, fpkm in each sample for edited genes. "MOLM13_rnaseq_read_count_entrez_id.csv" includes read counts for all genes that were mapped to the reference genome.

treatment_protocol: Cells were infected with virus expressing MSI2-HyperADAR (MSI2-ADA), MSI2-HyperADAR-DCD (MSI2-DCD) or MIG controls at 1:1 ratio (v/v) cell: virus at 0.5 million cells per mL (final density). Spinoculation was done with 10ug/mL Polybrene (Millipore #TR-1003-G) at 1500rpm for 1 hour at 32oC. Cells were incubated for 48hrs and then sorted by flow cytometry for GFP positive (overexpressing the fusions)

tag: transduction

value: Overexpressing MSI2-HyperADAR catalytic dead fusion


title: 813_H3K4me3_CHIPSeq

value: ACAGTG


title: 845_H3K4me3_CHIPSeq

value: Veh

value: CATTTT


title: 811_H3K4me3_CHIPSeq

value: CAAAAG


title: Molm13_MIG_3

value: leukemia cell line

value: Overexpressing empty vector

value: 48hr after transduction


title: Molm13_Hyper_dADAR_DCD_3


title: Molm13_Hyper_dADAR_3

value: Overexpressing MSI2-HyperADAR fusion


title: Molm13_Hyper_dADAR_2


title: WTC Control

value: Unknown


title: 805_H3K4me3_CHIPSeq

value: GGTAGC


title: Molm13_MIG_2


title: Molm13_Hyper_dADAR_1


title: 810_H3K4me3_CHIPSeq

value: ATGAGC


title: 801_H3K4me3_CHIPSeq

value: 30-day old

value: GTAGAG


title: AdNull-ATAC_1

city: La Jolla

first: John

last: Shyy

state: California

address: 9500 Gilman Dr., BRF2 Rm 1217 Bay LL

department: Medicine

institute: University of California, San Diego

description: HUVECs under PS, H3K27ac ChIP DNA, rep 1

data_processing:
Trimmomatic v0.35 was used to process the fastq files to remove poor-quality and  adapter reads
DNA reads were aligned to the pre-built UCSC hg19 reference human genome index by using bowtie2.
PCR duplicate reads were further removed by Picard-tools
Peak calling, annotation and bigwig generation were done with the homer suite. Homer-idr was used to process ChIP-seq data for high reroducibility among biological duplicates.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file showing DNA signal were generated with the homer suite using default parameters.

source_name: HUVEC

growth_protocol: HUVECs were cultured in medium M199 supplemented with 15% FBS, 3 ng/mL β-EC growth factor, 4 U/mL heparin, and 100 U/mL penicillin-streptomycin.

extract_protocol:
ECs were washed twice with cold PBS, and nuclei were isolated by resuspending ~5000 cells in 50 uL cold lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40). The nuclear pellets were resuspended in 50 uL transposition buffer (Nextera DNA Library Preparation Kit and 22.5 uL nuclease free water, and then incubated at 37°C for 30 min. After incubation, the DNA samples were purified by the Qiagen MinElute PCR purification kit.
Librariy preparation and Illumina sequencing were done by the IGM Genomics Core, University of California, San Diego.

treatment_protocol: ECs were infected with adenovirus-KLF4 or the empty vehicle (Ad-null) for 24 hr

tag: assay

value: ATAC


title: Molm13_MIG_1

city: New York

first: Diu

last: Nguyen

address: 417 East 68th street

institute: Memorial Sloan Kettering Cancer Center


title: Molm13_Hyper_dADAR_DCD_1


title: AdKLF4-ATAC_2

description: HUVECs transfected with KLF4 adnovirus for 24 hrs, rep2


title: AdNull-ATAC_2

description: HUVECs under PS, H3K27ac ChIP DNA, rep 2


title: AdKLF4-ATAC_1

description: HUVECs under OS, H3K27ac ChIP DNA, rep 1


title: RRBS_T60_Rep3

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
Reads were trimmed using  trim_galore v0.4.0 and cutadapt v1.9.1 using the –rrbs flag
Trimmed reads were mapped to mm10 and methylation levels estimated using Bismark v0.14.4 and Bowtie2 on default settings
Circadian rhythmicity of promoter methylation was determined using RAIN
Genome_build: mm10
Supplementary_files_format_and_content: Text file in tab separated format with DNA methylation levels

growth_protocol: Mouse C2C12 myoblasts were grown in DMEM with 10% FBS and 1% penicillin-streptomycin. Myoblasts were then seeded into 6 well plates with 50,000 cells per well. At approximately 90% confluence, cells were differentiated using DMEM with 2% horse serum and 1% penicillin-streptomycin

extract_protocol:
Qiagen RNA/DNA/miRNA AllPrep kit
DNA samples were incubated with MpsI enzyme (NEB #R0106L) and then bisulfite converted using the EZ DNA methylation Kit (Zymo Research). The DNA was PCR amplified and ligated to TruSeq (Illumina) sequencing adapters.

treatment_protocol: 50% horse serum shock for 2 hours

tag: replicate

tag: timepoint


title: RRBS_T60_Rep2


title: RRBS_T54_Rep2


title: RRBS_T54_Rep1


title: Input-ChIP-PS2

description: HUVECs under PS, Input DNA, rep 2

data_processing:
Trimmomatic v0.35 was used to process the fastq files to remove poor-quality and  adapter reads
DNA reads were aligned to the pre-built UCSC hg19 reference human genome index by using bowtie2.
PCR duplicate reads were further removed by Picard-tools
Peak calling, annotation and bigwig generation were done with the homer suite. Homer-idr was used to process ChIP-seq data for high reroducibility among biological duplicates.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file showing IP signal were generated with the homer suite using default parameters.

extract_protocol:
Cells were fixed at 37°C with 1% paraformaldehyde for 15 min, washed twice in cold phosphate buffered saline and scraped and pelleted at 3000 rpm for 5 min; cell pellets were resuspended in 50 uL lysis buffer, then diluted with 500 uL TE buffer for sonication.
20 ug chromatin, 3 ug antibody, and 11 uL dynabeads were incubated in ChIP buffer at 4°C overnight. The chromatin were eluted by 150 uL elution buffer followed by decrosslinking at 65℃ overnight. After incubation with RNase A and Proteinase K, DNA was precipitated by phenol:chloroform:isoamyl (25:24:1, v/v), dissolved in TE buffer, and stored at -80°C. Librariy preparation and Illumina HiSeq 2000 sequencing were done by the IGM Genomics Core, University of California, San Diego.

treatment_protocol: PS or OS was applied to endothelial cells (ECs) with a shear stress of 12 ± 5 dyn/cm2 or 1 ± 4 dyn/cm2 for 16 hr.

tag: flowpattern

value: pulsatile shear

tag: antibody

value: Input

value: ChIP


title: RRBS_T48_Rep3


title: Input-ChIP-PS1

description: HUVECs under PS, Input DNA, rep 1


title: RRBS_T48_Rep2


title: Input-ChIP-OS2

description: HUVECs under OS, Input DNA, rep 2

value: oscillatory shear


title: Input-ChIP-OS1

description: HUVECs under OS, Input DNA, rep 1


title: RRBS_T48_Rep1


title: H3K4me1-ChIP-PS1

description: HUVECs under PS, H3K4me1 ChIP DNA, rep 1


title: H3K4me1-ChIP-PS2

description: HUVECs under PS, H3K4me1 ChIP DNA, rep 2


title: RRBS_T42_Rep1


title: RRBS_T60_Rep1


title: RRBS_T36_Rep2


title: RRBS_T54_Rep3


title: RRBS_T42_Rep2


title: H3K27ac-ChIP-PS1


title: H3K4me1-ChIP-OS2

description: HUVECs under OS, H3K4me1 ChIP DNA, rep 2


title: H3K4me1-ChIP-OS1

description: HUVECs under OS, H3K4me1 ChIP DNA, rep 1


title: RRBS_T36_Rep3


title: H3K27ac-ChIP-PS2


title: RRBS_T30_Rep3


title: RRBS_T36_Rep1


title: H3K27ac-ChIP-OS2

description: HUVECs under OS, H3K27ac ChIP DNA, rep 2


title: RRBS_T30_Rep1


title: RRBS_T24_Rep3


title: H3K27ac-ChIP-OS1


title: RRBS_T30_Rep2


title: 4C_HEC-1-B_HS5-1_REV3_rep3

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

data_processing:
Library strategy: 4C-seq
Sequenced reads were trimmed for adaptor sequence and the bait sequence, then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1). The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3).
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files: the reads per million (RPM) value in 4C-seq experiments.

growth_protocol: Human endometrial HEC-1-B cells (ATCC) were cultured in MEM medium (Hyclone), supplemented with 10% (v/v) FBS (Gibco), 2 mM glutamine (Gibco), 1 mM sodium pyruvate (Sigma), and 1× penicillin-streptomycin (Gibco). Human K562 cells (ATCC) were cultured in DMEM medium (Hyclone) supplemented with 10% (v/v) FBS and 1× penicillin-streptomycin. Cells were maintained at 37 °C in a humidified incubator containing 5% (v/v) of CO2, and were passaged every three days.

extract_protocol:
After cross-linking with 2% formaldehyde, cells were lysed twice with cold lysis buffer, digested with DpnII, ligated with T4 DNA ligase.
4C libraries were generated by PCR.

value: human endometrial adenocarcinoma

tag: genotype/variation

value: R3 insertion

tag: restriction enzyme

value: DpnII


title: 4C_HEC-1-B_HS5-1_REV3_rep2


title: RRBS_T18_Rep3


title: RRBS_T24_Rep1


title: 4C_HEC-1-B_HS5-1_REV3_rep4


title: RRBS_T42_Rep3


title: 4C_HEC-1-B_HS5-1_REV3_rep1


title: 4C_HEC-1-B_HS5-1_REV3_mut_rep4

value: R3 mutation


title: RRBS_T18_Rep2


title: 4C_HEC-1-B_HS5-1_REV3_mut_rep3


title: 4C_HEC-1-B_HS5-1_REV3_mut_rep2


title: RRBS_T18_Rep1


title: 4C_HEC-1-B_HS5-1_REV3_mut_rep1


title: RRBS_T24_Rep2


title: 4C_HEC-1-B_HS5-1_REV2_rep2

value: R2 insertion


title: 4C_HEC-1-B_HS5-1_REV2_mut_rep2

value: R2 mutation


title: RRBS_T12_Rep2


title: RRBS_T12_Rep1


title: RNA-seq_T60_Rep3

data_processing:
Reads were trimmed using  trim_galore v0.4.0 and cutadapt v1.9.1 on default settings
Trimmed reads were mapped to mm10 with Rsubread and gene read coverages were computed with featureCounts and the Ensemble v84 gtf file
Circadian rhythmicity was determined using RAIN
Genome_build: mm10
Supplementary_files_format_and_content: Text file in tab separated format with gene coverages in units of read counts

extract_protocol:
Qiagen RNA/DNA/miRNA AllPrep kit
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold


title: RNA-seq_T60_Rep2


title: RNA-seq_T54_Rep1


title: RNA-seq_T54_Rep2


title: RNA-seq_T54_Rep3


title: RNA-seq_T48_Rep1


title: RNA-seq_T48_Rep2


title: RNA-seq_T48_Rep3


title: RNA-seq_T42_Rep3


title: RRBS_T12_Rep3


title: 4C_HEC-1-B_HS5-1_REV1_rep1

value: R1 insertion


title: 4C_HEC-1-B_HS5-1_REV1_mut_rep2

value: R1 mutation


title: 4C_HEC-1-B_HS5-1_REV2_mut_rep1


title: 4C_HEC-1-B_HS5-1_REV1_rep2


title: RNA-seq_T42_Rep2


title: 4C_HEC-1-B_HS5-1_REV-FWD_mut_rep3

value: RF mutation


title: RNA-seq_T42_Rep1


title: 4C_HEC-1-B_HS5-1_REV-FWD_rep2

value: RF insertion


title: 4C_HEC-1-B_HS5-1_REV1_mut_rep4


title: 4C_HEC-1-B_HS5-1_REV-FWD_rep1


title: 4C_HEC-1-B_HS5-1_REV2_rep1


title: 4C_HEC-1-B_HS5-1_REV1_mut_rep3


title: 4C_HEC-1-B_HS5-1_REV-FWD_mut_rep2


title: RNA-seq_T60_Rep1


title: RNA-seq_T36_Rep3


title: 4C_HEC-1-B_HS5-1_REV-FWD_mut_rep1


title: RNA-seq_T36_Rep2


title: 4C_HEC-1-B_HS5-1_FWD_rep2

value: F insertion


title: 4C_HEC-1-B_HS5-1_FWD_rep1


title: RNA-seq_T36_Rep1


title: 4C_HEC-1-B_HS5-1_REV1_mut_rep1


title: 4C_HEC-1-B_HS5-1_FWD_mut_rep2

value: F mutation


title: RNA-seq_T30_Rep2


title: 4C_HEC-1-B_HS5-1_FWD_mut_rep1


title: RNA-seq_T30_Rep1


title: RNA-seq_T24_Rep3


title: 4C_HEC-1-B_HS5-1_2REV-2FWD_rep4

value: RRFF insertion


title: RAL360315-IP2

city: Irvine

first: Grace

middle: Yuh Chwen

last: Lee

address: UCI

institute: University of California, Irvine

description: Processed data file is generated by contrasting IP to corresponding INPUT

data_processing:
raw reads were pre-processed with trim-galore to remove adatoprs and low quality bases
processed reads were mapped to reference genomes with bwa
reads with mapping quality score smaller than 30 were filtered using samtools
fold enrichment (IP with respect to matching INPUT) tracks were generated using MAC2
Genome_build: D. melanogaster release 6 (fly base)
Supplementary_files_format_and_content: bigWig

source_name: embryos

growth_protocol: Flies were reared on standard medium at 25C, 12hr/12hr light and dark cycle

extract_protocol:
Embryos were collected on standard apple juice plate. Before collection, pre-collection for 1hr was performed. Embryos were then collected for 2 hours and aged for 16 hours in 25C. ChIP was performed following standrad modEncode protocol.
Library was prepared using NEBNext® Ultra DNA Library Prep Kit for Illumina

tag: Stage

value: 16-18hr embryo

tag: chip-antibody


title: RAL360315-INPUT1


title: RAL360315-IP1


title: 4C_HEC-1-B_HS5-1_2REV-2FWD_rep3


title: 4C_HEC-1-B_HS5-1_2REV-2FWD_rep2


title: RAL315360-INPUT1


title: RAL315360-IP2


title: RAL315360-INPUT2


title: RAL315360-IP1


title: RNA-seq_T24_Rep1


title: 4C_HEC-1-B_HS5-1_2REV-2FWD_mut_rep2

value: RRFF mutation


title: 4C_HEC-1-B_HS5-1_2REV-2FWD_rep1


title: RNA-seq_T18_Rep3


title: RAL360-IP2


title: RAL360-INPUT2


title: RNA-seq_T30_Rep3


title: RAL360-INPUT1


title: RNA-seq_T18_Rep1


title: RNA-seq_T18_Rep2


title: RAL360-IP1


title: RAL360315-INPUT2


title: RNA-seq_T12_Rep3


title: RAL315-IP2


title: RAL315-INPUT2


title: RAL315-INPUT1


title: 4C_HEC-1-B_HS5-1_2FWD_rep4

value: FF insertion


title: 4C_HEC-1-B_HS5-1_2REV-2FWD_mut_rep1


title: RNA-seq_T24_Rep2


title: 4C_HEC-1-B_HS5-1_2FWD_rep3


title: RNA-seq_T12_Rep2


title: 4C_HEC-1-B_HS5-1_2FWD_rep 2


title: ORw1118-INPUT2


title: ORw1118-IP2


title: 4C_HEC-1-B_HS5-1_2FWD_rep 1


title: RNA-seq_T12_Rep1


title: ORw1118-INPUT1


title: ORw1118-IP1


title: 4C_HEC-1-B_HS5-1_2FWD_mut_rep2

value: FF mutation


title: TWIST1-TCF12 dimer induced_2

city: WESTMEAD

first: PIERRE

last: OSTEIL

state: NSW

address: 214 Hawkesbury Road

department: Embryology

country: Australia

institute: CMRI

data_processing:
FastQC package was used to assess data quality and adapter sequences and low-quality reads were trimmed from the original reads. A minimum of 50 bp read length filter was applied.
Alignment was performed using Tophat2 against mm10 genome.
Read count was obtained using htseq-count package, Genecode mouse basic genome assembly (GRCm38, vM10).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw count values

source_name: Embryoid Bodies

growth_protocol: The ESCs were cultured in complete mESC medium (high glucose DMEM (Gibco), 12.5 % (v/v) heat-inactivated FBS (Fisher Biotec Australia), 10 mM β-mercaptoethanol, 0.09 % (v/v), 1X non-essential amino acids (100X Thermo Fisher Scientific), 1 % (v/v) nucleosides (100X, Merck) and 10 mil U/mL ESGRO® mouse leukaemia inhibitory factor (Merck)). ESCs were passaged every 2–3 days.

extract_protocol:
Total RNA from snap frozen samples was extracted using ISOLATE II RNA Mini Kit following manufacturer protocol (Bioline, cat. #BIO-52073). In essence, samples were thawed on ice, lysed and column purified. Genomic DNA contaminants were removed by 15 mins DNase treatment at RT. Precipitated RNA was washed and eluted with RNase-free water. RNA concentration, and DNA and ethanol contamination, were measured using the NanoDrop
Libraries were prepared using TruSeq mRNA Prep Kit (Illumina)  by Macrogen Inc

treatment_protocol: Embryoid bodies (EB) were differentiated in EB-medium consisting of Dulbecco’s Modified Eagle’s Medium supplemented with 15% Fetal Calf Serum, 1% Non-essential amino-acid supplement and 0.1 µM 2-Mercaptoethanol. Single ES cells were seeded onto aggrewells in a 24 well plate (Stem Cell Technologies, Cat. No. 34411) at 1.5 × 10^6 cells per well in EB-medium. Cell aggregates were transferred to non-tissue culture treated 10 cm plates and EB-medium 24 hrs later, and placed on an orbital-shaker under slight rotation at 37 °C, 5% CO2, to prevent single EBs from attaching to each other or surfaces.  Media was refreshed every 48 hrs.

value: ESC-derived embroid body

tag: genotype

value: A2loxCre/ Twist1-Tcf12 dimer integrated

value: Doxycycline


title: TWIST1-TCF12 dimer induced_1


title: Heat shock TT-TimeLaps rep2

description: For the processed data files, reads were filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos):  LK180407.T.0.min.bedGraph  LK180407.T.0.pos.bedGraph  LK180407.T.1.min.bedGraph  LK180407.T.1.pos.bedGraph  LK180407.T.2.min.bedGraph  LK180407.T.2.pos.bedGraph  LK180407.T.3.min.bedGraph  LK180407.T.3.pos.bedGraph  LK180407.T.4.min.bedGraph  LK180407.T.4.pos.bedGraph  LK180407.T.5.min.bedGraph  LK180407.T.5.pos.bedGraph

data_processing:
Reads were filtered for unique sequences using FastUniq.
Reads were trimmed using cutadapt (--minimum-length=20).
Reads were aligned to the dm6 genome using STAR aligned with default parameters and --mp 4,2
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex.
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode).
T-to-C mutations were identified using Rsamtools and a custom R script (available upon request). Only mutations at positions with a base quality score of greater than 45 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph), and tracks were normalized based on number of reads containing at least 2 T-to-C mutations that mapped to 7SK transcript.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: bedGraph files

extract_protocol:
Cells were harvested with Trizol reagent, followed by chloroform extraction and ethanol precipitation. After DNase treatment and shearing, labelled RNA was enriched using MTS using a modified protocol from Duffy EE et al. Mol Cell (2015), as described in the methods section. Isolated RNA was subjected to oxidative-nucleophilic-aromatic-substitution chemistry and sequenced.
Libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian (Takara Bio USA, cat. 635005).

treatment_protocol: Cells were incubated 1 h at 37˚C. 8 min before end of incubation, medium was supplemented with 1 mM s4U.

tag: heat shock

value: yes


title: 4C_HEC-1-B_HS5-1_2FWD_mut_rep1

tag: cell line

value: human endometrial adenocarcinoma

value: DpnII


title: TWIST1-TCF12 dimer induced_3

tag: cell type


title: 4C_HEC-1-B_HS5-1_2FWD-2REV_rep2

value: FFRR insertion


title: Control TT-TimeLaps rep1

description: For the processed data files, reads were filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos):  LK180406.T.0.min.bedGraph  LK180406.T.0.pos.bedGraph  LK180406.T.1.min.bedGraph  LK180406.T.1.pos.bedGraph  LK180406.T.2.min.bedGraph  LK180406.T.2.pos.bedGraph  LK180406.T.3.min.bedGraph  LK180406.T.3.pos.bedGraph  LK180406.T.4.min.bedGraph  LK180406.T.4.pos.bedGraph  LK180406.T.5.min.bedGraph  LK180406.T.5.pos.bedGraph

value: no


title: dksA::cat+ greA::kan+ before stress

city: Birmingham

first: Michael

middle: Jeffrey

last: Gray

state: AL

department: Microbiology

institute: University of Alabama at Birmingham

description:
dksAgreA0
dksAgreA0vsdksAgreA5_transcripts.txt

data_processing:
Data were analyzed with Rockhopper 2, using the default parameters (Tjaden 2015 Genome Biol 16:1).
Genome_build: NCBI Reference Sequence: NC_000913.3
Supplementary_files_format_and_content: Rockhopper 2 verbose output files, comparing gene expression in each strain (WT, dksA, or dksAgreA) at 0 and 5 minutes after treatment. Columns: Transcription Start, Translation Start, Translation Stop, Transcription Stop, Strand, Name (Gene Symbol), Synonym (Locus Tag), Product, Raw Counts Before (0 min), Normalized Counts Before (0 min), RPKM Before (0 min), Expression Before (o min), Raw Counts After (5 min), Normalized Counts After (5 min), RPKM After (5 min), Expression After (5 min), p Value Before vs. After, q Value Before vs. After

organism: Escherichia coli

source_name: bacterial culture (A600=0.2-0.4)

growth_protocol: E. coli strains were grown in 10 ml LB at 37°C with shaking (200 rpm) to A600=0.2-0.4.

extract_protocol:
RNA was purified from 2 ml of cells harvested immediately before and 5 min after stress using the RiboPure™-Bacteria Kit (Ambion), according to the manufacturer’s instructions.
mRNA-sequencing was performed at the UAB Heflin Center for Genomic Sciences, using an Illumina NextSeq 500 as described by the manufacturer. Briefly, the quality of the total RNA was assessed using the Agilent 2100 Bioanalyzer. RNA with a RNA Integrity Number (RIN) of 7.0 or above was used for sequencing library preparation. We used the Agilent SureSelect Strand Specific mRNA library kit as per the manufacturer’s instructions (Agilent). Library construction began with ribosome reduction with the RiboMinus protocol for Gram-negative and Gram-positive bacteria as described by the manufacturer (Life Technologies). The resulting mRNA was randomly fragmented with cations and heat, followed by first strand synthesis using random primers with inclusion of Actinomycin D (2.4 ng µl-1 final concentration). Second strand cDNA production was done with standard techniques, the ends of the resulting cDNA were made blunt, A-tailed, and adaptors were ligated for amplification and indexing to allow for multiplexing during sequencing. The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for Illumina library quantitation (Kapa Biosystems) prior to cluster generation. Cluster generation was performed according to the manufacturers recommendations for onboard clustering (Illumina). We generated approximately 20 million single end 75 bp reads per sample.

treatment_protocol: To induce polyP synthesis by nutrient limitation, 5 ml of each culture was harvested by centrifugation (5 min at 4,696 x g at room temperature), resuspended in 5 ml phosphate-buffered saline (PBS) to rinse, then re-centrifuged and resuspended in 5 ml MOPS minimal medium containing 4 g l-1 glucose, 0.1 mM K2HPO4, and 0.1 mM uracil.

tag: treatment

value: rich media (0 min)


title: dksA::cat+ greA::kan+ after stress

description:
dksAgreA5
dksAgreA0vsdksAgreA5_transcripts.txt

tag: strain

value: minimal media (5 min) = nutrient limitation stress


title: 4C_HEC-1-B_HS5-1_2FWD-2REV_rep1


title: dksA::cat+ after stress

description:
dksA5
dksA0vsdksA5_transcripts.txt


title: TWIST1-TCF4 dimer induced_2

value: A2loxCre/ Twist1-Tcf4 dimer integrated


title: Control TT-TimeLaps rep2

description: For the processed data files, reads were filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos):  LK180408.T.0.min.bedGraph  LK180408.T.0.pos.bedGraph  LK180408.T.1.min.bedGraph  LK180408.T.1.pos.bedGraph  LK180408.T.2.min.bedGraph  LK180408.T.2.pos.bedGraph  LK180408.T.3.min.bedGraph  LK180408.T.3.pos.bedGraph  LK180408.T.4.min.bedGraph  LK180408.T.4.pos.bedGraph  LK180408.T.5.min.bedGraph  LK180408.T.5.pos.bedGraph

source_name: S2 cell line


title: dksA::cat+ before stress

description:
dksA0
dksA0vsdksA5_transcripts.txt


title: 4C_HEC-1-B_HS5-1_2FWD-2REV_mut_rep2

value: FFRR mutation


title: TWIST1-TCF4 dimer induced_3


title: TWIST1-TCF4 dimer induced_1


title: Heat shock TT-TimeLaps rep1

description: For the processed data files, reads were filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos):  LK180405.T.0.min.bedGraph  LK180405.T.0.pos.bedGraph  LK180405.T.1.min.bedGraph  LK180405.T.1.pos.bedGraph  LK180405.T.2.min.bedGraph  LK180405.T.2.pos.bedGraph  LK180405.T.3.min.bedGraph  LK180405.T.3.pos.bedGraph  LK180405.T.4.min.bedGraph  LK180405.T.4.pos.bedGraph  LK180405.T.5.min.bedGraph  LK180405.T.5.pos.bedGraph


title: RAL315-IP1


title: wild-type after stress

description:
WT5
WT0vsWT5_transcripts.txt


title: TWIST1-TCF3 dimer induced_3

value: A2loxCre/ Twist1-Tcf3 dimer integrated


title: 4C_HEC-1-B_a12_WT_rep4

value: wildtype


title: TWIST1-TCF3 dimer induced_2


title: 4C_HEC-1-B_a12_WT_rep3


title: P-H3K4me3-Cxxc1-Rep2

city: Hangzhou

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
ChIP–seq reads were trimmed to 50 bp and aligned to the mouse genome build mm9 using  bowtie2 (v2.3.4.1) with default parameters. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed.  H3K4me3 peaks were called using MACS2 (v 2.1.1.20160309) with the parameters -q 0.05 --nomodel --nolambda --broad --extsize 300 -B --SPMR -g mm and signal tracks for each sample were generated with wigToBigWig tool from UCSC.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig format for all ChIP-seq samples

source_name: Pachytene spermatocytes

growth_protocol: All mice have a C57BL/6J genetic background, and were maintained under specific pathogen-free conditions in a controlled environment of 20–22 oC, with a 12/12 h light/dark cycle, 50–70% humidity, and food and water provided ad libitum

extract_protocol:
Spermatocytes at different stages were isolated using FACS sorting. H3K4me3 ChIP-seq libraries were performed from ~10,000 spermatocytes using ULI-NChIP-seq protocol
The sequence libraries were generated using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645S) according to the manufacturer’s instructions.

treatment_protocol: Testes were prepared from adult male mice

value: Pachytene spermatocytes

tag: background strain

tag: chip antibody

value: anti-H3K4me3, CST#9727, lot6


title: 4C_HEC-1-B_a12_WT_rep2


title: P-H3K4me3-Cxxc1-Rep1


title: TWIST1 homodimer induced_3

value: A2loxCre/ Twist1 homodimer integrated


title: H3K27me3_ChIPSeq_VEH 33_D70

city: Houston

first: Cheryl

middle: L

last: Walker

state: TX

address: 1 Baylor Plaza

department: Center for Precision Environmental Health

institute: Baylor College of Medicine

data_processing:
The data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore.
ChIP-Seq reads were mapped to the rat genome build UCSC rn6 using bowtie2 and duplicate reads were removed.
ChIP-Seq tracks were prepared using bedtools, normalized to reads per million reads mapped (rpm).
Differential regions were determined using the diffReps software using the G-test with significance achieved for a fold change > 2 and an FDR-adjusted q-value < 0.01.
Genome_build: rn6
Supplementary_files_format_and_content: ChIP-Seq tracks represented normalized to reads per million mapped in WIG and TDF format

source_name: Rat liver

extract_protocol:
Frozen liver tissue was pulverized, followed by cross-linking of proteins to DNA with 37% formaldehyde, and then incubation with 10X glycine to stop the reaction. Cross-linked tissue was homogenized, and centrifuged at 1,500 rpm for 5 min at 4°C. The cell pellet was resuspended with cell lysis buffer (PBS with 0.5 mM EDTA and 0.05% Triton X-100), incubated on ice for 15 min, followed by centrifiugation at 5,000 rpm for 5 min at 4°C. The cell pellet was then resuspended with nuclear lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl at pH 8.1) and incubated on ice for 10 min. Chromatin was sonicated with a bioruptor (Diagenode, Denville, NJ) to obtain fragment sizes of 100-300 bp for ChIP-seq. ChIP was performed by incubating sheared chromatin with Magna ChIPTM Protein A+G magnetic beads, and antibodies against H3K4me3, H3K4me1, H3K27ac or H3K27me3 overnight at 4°.The next day, the beads were washed with low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, and 150 mM NaCl) high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, and 500 mM NaCl), lithium chloride wash buffer (0.25 M LiCl, 1% IGEPAL CA630, 1% sodium deoxycholate, 1 mM EDTA, and 10 mM Tris-HCl pH 8), and TE buffer (20 mM Tris-HCl pH 8 and 1 mM EDTA) for 5 minutes each at 4°. Immunoprecipitated DNA was recovered from the beads by incubation with ChIP elution buffer (1% SDS, 1 mM EDTA, 50 mM NaHCO3, and 50 mM Tris-HCl pH 8) and proteinase K for 2 hours at 62° with shaking, followed by incubation at 95° for 10 minutes. DNA was purified using the QIAquick PCR Purification kit (Qiagen) and DNA concetration was measured using a NanoDrop spectrophotometer (Thermo Scientific).
Sequencing librairies were prepared using Bioo Kit Option 2 protocol using 1.7-10 ng of DNA per sample.

treatment_protocol: Neonatal rats were treated with vehicle (VEH; sesame oil) or bisphenol A (BPA; 50 µg/kg dissolved in sesame oil) orally via pipette tip on post-natal days 1, 3, and 5. Littermates of the same sex were randomly assigned to the treatment groups. BPA was obtained from the National Instutite of Environmental Health Sciences (NIEHS). The dose and route of administration recapitulates human exposure to BPA. Rats were fasted overnight prior to tissue collection.Liver tissue was harvested on post-natal day 5 at 6 hours after treatment (PND5), and on day 70 (D70). Tissue was snap-frozen in liquid nitrogen for downstream epigenomic analyses.

value: H3K27me3 (Active Motif, 39155)

value: Sprague Dawley

value: Sesame oil (VEH)


title: H3K4me3_ChIPSeq_VEH 33_D70

value: H3K4me3 (Active Motif, 39915)


title: H3K4me1_ChIPSeq_VEH 33_D70

value: H3K4me1 (Abcam, ab8895)


title: TWIST1-TCF3 dimer induced_1

value: ESC-derived embroid body

value: Doxycycline


title: 4C_HEC-1-B_HS5-1_2FWD-2REV_mut_rep1

value: human endometrial adenocarcinoma

value: DpnII


title: P-H3K4me3-WT-Rep2

value: WT


title: P-H3K4me3-WT-Rep1


title: TWIST1 homodimer induced_2


title: 4C_HEC-1-B_a12_REV3_rep2

value: R3 insertion


title: LZ-H3K4me3-Cxxc1-Rep2

source_name: Leptotene/Zygotene spermatocytes

value: Leptotene/Zygotene spermatocytes


title: 4C_HEC-1-B_a12_REV3_rep1


title: TWIST1 homodimer induced_1


title: H3K27me3_ChIPSeq_VEH 29_D70


title: 4C_HEC-1-B_a12_REV3_mut_rep2

value: R3 mutation


title: H3K4me3_ChIPSeq_VEH 29_D70


title: H3K27ac_ChIPSeq_VEH 33_D70

value: H3K27ac (Abcam, ab4729)


title: LZ-H3K4me3-Cxxc1-Rep1


title: wild-type before stress

description:
WT0
WT0vsWT5_transcripts.txt

value: rich media (0 min)


title: TWIST1 monomer induced_3

value: A2loxCre/ Twist1 monomer integrated


title: TWIST1 monomer induced_2


title: CON-male, pool

city: Leipzig

first: Tobias

last: Polte

address: Permoserstrasse 15

institute: Helmholtz Centre for Environmental Research GmbH - UFZ

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) 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: 3 week old, spleen

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

growth_protocol: 3 week old offspring from mothers exposed toward BBP in perinatal period

extract_protocol: total RNA was extracted using Rneasy Mini Kit

treatment_protocol: pregnant mice were exposed to BBP via drinking water starting one week before mating until weaning when pups were 3 weeks old, Contols revceived normal drinking water.

tag: gender

value: male

tag: tissue

value: spleen

tag: maternal exposure

value: Control

tag: number of animals


title: 4C_HEC-1-B_a12_WT_rep1

value: wildtype


title: CON-female, pool

value: female


title: 4C_HEC-1-B_a12_REV3_mut_rep1


title: LZ-H3K4me3-WT-Rep2

value: anti-H3K4me3, CST#9727, lot6


title: BBP-male, pool

value: BBP


title: BBP-female, pool


title: TWIST1 monomer induced_1

value: ESC-derived embroid body

value: Doxycycline


title: LZ-H3K4me3-WT-Rep1


title: TWIST1 monomer uninduced_3

value: minus Doxycycline


title: H3K27ac_ChIPSeq_VEH 29_D70

value: Sprague Dawley

value: Sesame oil (VEH)


title: 4C_HEC-1-B_a12_REV2_mut_rep2

value: human endometrial adenocarcinoma

value: R2 mutation

value: DpnII


title: 4C_HEC-1-B_a12_REV2_rep1

value: R2 insertion


title: TWIST1 monomer uninduced_1

value: A2loxCre/ Twist1 monomer integrated


title: MII-Cxxc1-Rep2

data_processing:
RNA‐seq was performed with biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) with TopHat (v2.1.1) with default parameters. Uniquely mapped reads were subsequently assembled into transcripts guided by reference annotation (University of California at Santa Cruz [UCSC] gene models) with Cufflinks (v2.2.1). The expression level of each gene was quantified as fragments per kilobase of transcript per million mapped reads (FPKM) and FPKM values of replicates were averaged. Only expressed genes (FPKM > 1 in at least one sample) were considered in all analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples

source_name: Meiosis II spermatocytes

extract_protocol:
Spermatocytes at different stages were collected from indicated genotypes (500 cells per sample) using FACS sorting. Each sample was directly lysed with 4 μl lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers) and immediately used for cDNA synthesis using the Smart-seq2 method
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer's instructions

value: Meiosis II spermatocytes


title: TWIST1 monomer uninduced_2


title: A2loxCre_3


title: MII-Cxxc1-Rep1


title: 4C_HEC-1-B_a12_REV1_rep4

value: R1 insertion


title: H3K27me3_ChIPSeq_VEH 27_D70

value: H3K27me3 (Active Motif, 39155)


title: H3K27ac_ChIPSeq_VEH 27_D70

value: H3K27ac (Abcam, ab4729)


title: 4C_HEC-1-B_a12_REV2_mut_rep1


title: H3K4me1_ChIPSeq_VEH 29_D70

value: H3K4me1 (Abcam, ab8895)


title: A2loxCre_2


title: H3K4me3_ChIPSeq_VEH 27_D70

value: H3K4me3 (Active Motif, 39915)


title: D-Cxxc1-Rep2

source_name: Diplotene spermatocytes

value: Diplotene spermatocytes


title: Xist thCHART rep2 [DNA]

city: West Haven

first: Matthew

last: Simon

address: 600 West Campus Dr. MIC312

institute: Yale University Chemical Biology Instiute

data_processing:
Library strategy: thCHART
Adaptor sequences were removed using Cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -m 3
Reads were aligned to reference genome using bowtie2.
Aligned reads were filtered for MAPQ > 2 woth samtools.
Sample enrichment over input was calculated using MACS2.
Enrichment bedgraph files were converted to bigWig format.
roX2 enriched regions were detected with rseq using -i 20 option and pre-calculated dm6 dead zones for 76 nt reads.
CES summits were detected using MACS2 callpeak. Using custom R script, peaks were filtered for those that overlap between replicates and have -log10(q-value) > 100.
Autosomal peak summits were detected using MACS2 call peak and filtered with custom R script for those that overlap between replicates.
Differentially upregulated or downregulated roX2 regions upon heatshock were detected using Diffreps (-me nb --mode p --nsd 10) and filtered for those with more than 2 fold change.
Genome_build: Drosophila dm6 (Release 6 plus ISO1 MT); Mouse mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files contain track of sample enrichment over input.
Supplementary_files_format_and_content: thCHART_CO1-domains.bed contains roX2 thCHRT enriched regions detected by rseg.
Supplementary_files_format_and_content: CES_summits.bed contains position of CES summits.
Supplementary_files_format_and_content: HS_autosomal_peaks_summits.bed contains position of summits of heat shock induced roX2 autosomal peaks.
Supplementary_files_format_and_content: diff.HS_Full_peak_zscore10_down_FC.bed and diff.HS_Full_peak_zscore10_up_FC.bed contain coordinates of regions that were significantly down- or up-regulated, respectively, by more than 2-fold after heat shock.

source_name: immortalized MEFs (F1: 129S1/CastEiJ x 129S1)

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min, followed by nuclei extraction and further crosslinking with 3% formaldehyde for 45 min. Crosslinked nuclei were sheared with covaries and cleared by centrifugation. Biotinylated antisense capture oligonucleotide was added to extract and left to hybridize over night at room temperature. Hybridized RNA complexes were captured on magnetic streptavidin beads and subjected to stringent rinses. Complexes were eluted by incubating beads with excess of elution oligonucleotide. Eluted molecules were de-crosslinked by incubating at 55˚C 1h and 65˚C 1h in the presence of proteinase K. DNA was isolated using PCR purification kit (Qiagen) and sheared with Covaris to 300bp range.
Libraries were constructed according to Bowman et al. (2012, BMC Genomics).

treatment_protocol: Ecdysone: Cells were incubated in growth media supplemented with 41 µM 20-Hydroxyecdysone (40 mM stock solution in DMSO) or equivalent volume of DMSO (Mock) for 24 h. DRB: Cells were incubated in growth media supplemented with 100 µM 5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside (75 mM stock solution in DMSO) or equivalent volume of DMSO (Mock) for 3 h. Heat shock: Cells were incubated 1 h at 37˚C.

tag: strain/background

value: F1:129S1/CastEiJ x 129S1

value: immortalized MEFs


title: D-Cxxc1-Rep1


title: H3K27me3_ChIPSeq_BPA 25_D70

value: 50 microg/kg Bisphenol A (BPA)


title: H3K4me1_ChIPSeq_VEH 27_D70

value: Sprague Dawley


title: 4C_HEC-1-B_a12_REV1_rep2

tag: genotype/variation


title: MII-WT-Rep2

value: WT


title: A2loxCre_1

value: ESC-derived embroid body

value: Doxycycline


title: H3K4me1_ChIPSeq_BPA 25_D70


title: 4C_HEC-1-B_a12_REV1_rep1

value: human endometrial adenocarcinoma

tag: restriction enzyme

value: DpnII


title: 4C_HEC-1-B_a12_REV1_mut_rep4

value: R1 mutation


title: 4C_HEC-1-B_a12_REV1_rep3


title: D-WT-Rep2


title: Xist thCHART rep1 [DNA]


title: D-WT-Rep1


title: 4C_HEC-1-B_a12_REV1_mut_rep1


title: 4C_HEC-1-B_a12_REV1_mut_rep3


title: H3K27ac_ChIPSeq_BPA 25_D70


title: P-Cxxc1-Rep2

value: Pachytene spermatocytes


title: input MEF [DNA]


title: H3K4me3_ChIPSeq_BPA 25_D70


title: H3K4me3_ChIPSeq_BPA 23_D70


title: 4C_HEC-1-B_a12_REV1_mut_rep2


title: H3K27me3_ChIPSeq_BPA 23_D70


title: P-Cxxc1-Rep1


title: Mp3

city: Wuhan

first: Bang

address: No. 1 SHizishan St

institute: Huazhong Agricultural University

description: Mp _abundance measurements.txt

data_processing:
Illumina Casava 1.8 software was used for basecalling
sequenced reads were trimmed  for adaptor sequence, reads containing ploy-N and low quality reads. Then clean reads were mapped to Sus scrofa or Toxoplasma  reference genome by  using TopHat v2.0.12.
Genome_build: Sus scrofa reference genone for  alignment: ftp://ftp.ensembl.org/pub/current_fasta/sus_scrofa/dna/ ;  Me49 reference genome for alignment: ftp://ftp.ensemblgenomes.org/pub/release-23/protists//fasta/toxoplasma gondii/dna/
Supplementary_files_format_and_content: tab-delimited text files include reads counts values for each sample

organism: Sus scrofa

source_name: porcine alveolar macrophages

growth_protocol: the cells (porcine alveolar macrophages and HFF cells)  and Me49 tachyzoites were cultured in DMEM with 10% or 2% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin, respectively. Both maintained in incubator with 5% CO₂ and kept 37℃.

extract_protocol:
At indicated time, the samples were collected and  total RNA was harvested using Trizol reagent.   NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA)  was used with 3 µg total RNA per sample for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the purified Me49 tachyzoites from HFFs were counted and used to infect porcine alveolar macrophages (MOI=5) for 1 h, the extracellualr parasites were washed away with PBS. The infected porcine alveolar macrophages were cultured for further 15 h. the porcine alveolar macrophages and Me49 controls were maintained under same conditions.

value: porcine alveolar macrophages

tag: parasite strain

tag: culture time

value: at 70-80 percent confluency in T25 tissue culture flask, about 36 h


title: Mp2

description: Mp _abundance measurements.txt


title: MII-WT-Rep1

value: Meiosis II spermatocytes

tag: genotype


title: H3K4me1_ChIPSeq_BPA 23_D70

value: H3K4me1 (Abcam, ab8895)