title: BLD_GSH_10_rep3

status: Public on Jul 16 2022

city: Memphis

first: Yong

last: Cheng

state: Tennessee

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St. Jude Children's Research Hospital

data_processing:
transcript level quantification was calculated using default parameter of Kallisto quant (version 0.43.1) with bootstrap value set to 100
transcript to gene level quantification was carried out using ensembl gene annotation version 75 for hg19
Differential gene expression analysis carried out using Sleuth
Assembly: hg19

growth_protocol: Cells were expanded in StemSpan serum-free expansion medium (SFEM; Stem Cell Technologies) supplemented with 1 µM dexamethasone, 1 µg/mL doxycycline, 50 ng/mL human stem cell factor (SCF), 3 units/mL erythropoietin (EPO), and 1% penicillin–streptomycin

extract_protocol:
quick-RNA MiniPrep from Zymo Research (R1054) was used to extract RNA
TruSeq Stranded mRNA Library Prep Kit (Illumina) was used to create libraries for sequencing

treatment_protocol: CRISPR GFP integration was carried out using 3xNLS Cas9 protein and RL48-hGOLGA4-EGFP plasmid containing GFP expression cassettee

value: Human Umbilical cord blood-Derived Erythroid Progenitor-27

tag: sample type

value: GFP inserted HUDEP2


title: BLD_GSH_10_rep4

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

value: Human Umbilical cord blood-Derived Erythroid Progenitor-28

tag: cell line


title: BLD_GSH_10_rep2

value: Human Umbilical cord blood-Derived Erythroid Progenitor-26


title: AAVS1_rep1

value: Human Umbilical cord blood-Derived Erythroid Progenitor-21


title: BLD_GSH_10_rep1

value: Human Umbilical cord blood-Derived Erythroid Progenitor-25


title: AAVS1_rep2

value: Human Umbilical cord blood-Derived Erythroid Progenitor-22


title: BLD_GSH_10-R_rep4

value: Human Umbilical cord blood-Derived Erythroid Progenitor-20


title: BLD_GSH_10-R_rep1

value: Human Umbilical cord blood-Derived Erythroid Progenitor-17


title: BLD_GSH_15_rep4

value: Human Umbilical cord blood-Derived Erythroid Progenitor-16


title: HBEC, KRASG12V, RNA, 2 [intra.hbec.2.wt2_kras_v12]

status: Public on Jul 19 2022

city: Santa Cruz

first: Daniel

last: Kim

state: California

address: McLaughlin Dr

department: Biomolecular Engineering

institute: UC Santa Cruz

description:
hbec_intra_gencode_norm_counts.csv
hbec_intra_gencode+rmsk_norm_counts.csv

data_processing:
Basecalled by relevant sequencing centers
Trimmed with Trimmomatic 0.39, quality assessed with FastQC and MultiQC
Reads quantified with Salmon 1.3.0 for RNA-seq, Reads aligned with nf-core ATAC pipeline for ATAC-seq
Assembly: hg38
Supplementary files format and content: bigWig format for UCSC genome browser integration
Supplementary files format and content: DESeqII normalized counts in CSV format with reference name included as gencode or gencode+rmsk

molecule: polyA RNA

source_name: Bronchus Epithelial

extract_protocol:
the bulk RNA was extracted using Direct-Zol RNA Miniprep Kit (Zymo Research)
UC Davis DNA Technologies and Expression Analysis Core Laboratory for poly-A strand specific library preparation. 2x150 PE reads

tag: tissue

value: Bronchus Epithelial

value: HBEC

value: Human immortalized Lung Epithelial

tag: genotype

value: KRAS G12V


title: BLD_GSH_10-R_rep2

value: Human Umbilical cord blood-Derived Erythroid Progenitor-18


title: BLD_GSH_15_rep3

value: Human Umbilical cord blood-Derived Erythroid Progenitor-15


title: BLD_GSH_15_rep1

value: Human Umbilical cord blood-Derived Erythroid Progenitor-13


title: MEI_chr1_769_INS_rep4

value: Human Umbilical cord blood-Derived Erythroid Progenitor-12


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_F01P1_Run1

city: Summit

first: Rida

last: Khan

state: NJ

address: 556 Morris Ave

department: Knowledge Science Research, IPS

institute: Bristol-Myers Squibb

data_processing:
Data quality assessment and principal component analysis (PCA) were performed to understand the main source of variability.
Differential expression analysis was performed using the limma package (v3.42.2) in R (v3.6.1)  to identify differentially expressed genes (DEGs) across subgroups. Adjusted P_x0002_values were calculated using the Benjamini-Hochberg method; a gene was considered differentially expressed if the absolute fold change was >2 or <0.5 and the false discovery rate-adjusted P-value was <0.05.
Assembly: GRCh37ERCC-ensembl75
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: PBMC

growth_protocol: Not Applicable

extract_protocol:
RNA was extracted from 11 formalin-fixed (4%), paraffin-embedded tissue sections (4μm) per biopsy. After scraping the tissue from the slides and deparaffinization, tissue was digested in buffer PKD (Qiagen, USA). RNA was extracted using the RNAeasy FFPE kit, according to manufacturer’s protocol (Qiagen, USA). For RNA extraction from PBMCs, 3x10^6 cells were thawed and rested for 1h in RPMI medium supplemented with 10%FBS and Antibiotic-Antimycotic (all from Gibco, UK) at 37°C. After resting, cell lysis and RNA isolation were performed using the RNAeasy Mini kit, according to manufacturer’s protocol (Qiagen, USA). RNA was immediately stored at -80°C until further use.
Complementary DNA library preparation was performed using TruSeq Stranded Total RNA Library Prep Gold (Illumina, USA, Cat#20020598), following manufacturer’s recommendations. Prepared libraries were sequenced on a HiSeq 2500 System (Illumina, USA)

treatment_protocol: Not Applicable

tag: sjnumber

tag: acr eular

value: Positive

tag: parotid infiltration phenotype

value: Group IV

tag: labial infiltration phenotype

tag: blood mxa


title: MEI_chr1_769_INS_rep3

value: Human Umbilical cord blood-Derived Erythroid Progenitor-11

value: GFP inserted HUDEP2


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_G03P1_Run1


title: Batch1_sorted_normal_P0_1

status: Public on Jul 21 2022

city: Los Angeles

first: Yen-Wei

last: Chen

address: 650 Charles E. Young Dr. South  16-035 Center for Health Sciences

department: IDP Molecular Toxicology

institute: University of California, Los Angeles

library_source: transcriptomic single cell

data_processing:
Data quality checks were performed using the Cellranger tool
Reads passing quality control were further aligned to pre-mRNA reference transcriptome generated by replacing “transcript” to “exon” in annotation GTF file.
Assembly: ce10
Supplementary files format and content: filtered_feature_bc_matrix produced by Cellranger

organism: Caenorhabditis elegans

source_name: C. elegans whole worm body

growth_protocol: Worms were maintained on standard nematode growth medium (NGM) plates streaked with single colony Harvard OP50 E. coli. All experiments were grown at 20°C up until the generation right before sequencing during which they were moved at the L1 stage to 25°C and grown until day 2 of adulthood (i.e. 48 hours at 25°C). The JK560 (fog-1(q253) I.) strain used in this study was obtained from the C. elegans Genetics Center (CGC). This strain was chosen due to its defect in the last step of spermatogenesis. These mutants were observed to have a fully developed germline but not fertilized embryos.

extract_protocol:
All reagents except for Triton-X100, PBS-BSA 1%, and inhibitors were prepared the night before and all low retention 1.5mL microcentrifuge tubes were clearly labeled. The bench space and equipment used in this protocol were thoroughly sanitized with 70% ethanol and cleaned with RNaseZAP (AM9780 Fisher) before starting the dissociation. Reagents were prepared using RNase free water (BP2484100 Fisher). The FA lysis buffer was made using the following reagents: 50mM HEPES/NaOH pH 7.5, 1mM EDTA, 0.1% Triton X-100, 150mM NaCl, Protease inhibitor 0.5X (Roche 11697498001), RNase inhibitor 0.2U/μL (Thermo Fisher 10777019), and RNase free water and stored at 4°C or on ice. BSA was prepared to a final concentration of 1% in pH 7.4 1X PBS (AM9624 Thermo Fisher) using RNAse free water and RNAse free PBS. This solution was filtered using a 0.22μm pressure filter (Thermo Scientific 03-377-26, Fisher SLGP033RS). All equipment and reagents were moved to a 4°C cold room and subsequent steps were performed at 4°C.Homogenizers were stored pre-chilled in -20°C when not in use and moved to the 4°C room before starting the extraction. Each wheaton 1.5mL Dounce homogenizers (Z378623-1EA Sigma) was cleaned using 70% ethanol, RNaseZAP, and RNase free water. Homogenizers were rinsed twice with ethanol, twice with RNaseZAP, and 5 times with 1-2mL of RNase free water. The compact 30μL pellet of adult C. elegans was transferred to the dounce homogenizer and 400μL of ice cold FA buffer was used to rinse any remaining worms from the 1.5mL low bind microcentrifuge tube and 1000μL low bind pipette tip and added to the homogenizer. Worms were homogenized with 10 strokes of the dounce homogenizer using a corkscrew motion with a B (tight) pestle. Homogenized worms were transferred to a new low bind 1.5ml microcentrifuge tube and centrifuged at 100g for 1 minute to pellet debris. The supernatant containing the dissociated nuclei was removed using a 1000μL low bind tip and transferred to a fresh low bind 1.5mL microcentrifuge tube labeled pooled nuclei. 300μL of FA buffer was added to the debris remaining in the first microcentrifuge tube and homogenized using 10 strokes in a corkscrew fashion with an Eppendorf Dounce homogenizer. The newly homogenized sample was then centrifuged at 100g for 1 minute to pellet debris. The supernatant containing the newly dissociated nuclei was pooled with the previously dissociated nuclei and the previous steps with the Eppendorf Dounce homogenizer were repeated once more to further homogenize the sample. In total, worms were homogenized with 30 strokes: 10 strokes with the 1.5mL Wheaton Dounce homogenizer and 20 strokes with the Eppendorf dounce homogenizer. Between each homogenization step, debris was pelleted using 100g for 1 minute and the supernatant containing the dissociated nuclei was removed and added to a single 1.5mL microcentrifuge tube labeled pooled nuclei. Dissociated nuclei were removed after each set of 10 homogenization strokes to prevent overdigestion of nuclei. After homogenization, the pooled supernatant containing the dissociated nuclei was centrifuged at 100g for 1 minute to pellet any remaining or accidentally transferred debris. The top 900μL of supernatant containing nuclei was transferred to a clean low bind 1.5mL microcentrifuge tube, being careful not to disturb the debris pellet. These pooled nuclei were pelleted at 500g for 4 minutes. After pelleting, approximately 800μL of FA buffer was removed, being careful not to disrupt the nuclei pellet, and the pelleted nuclei was resuspended with 1000μL of PBS-BSA 1%. The nuclei was again centrifuged at 500g for 4 minutes and 1000μL of the PBS-BSA 1% supernatant was removed. Lastly, the nuclei pellet was resuspended in 750-850μL of PBS-BSA 1% (final volume was determined by examining the size of the nuclei pellet). After resuspension, the nuclei was filtered using a 40μm Flowmi tip filter (BAH136800040-50EA Sigma Aldrich). Filtered nuclei were transferred to a 1.5mL low retention microcentrifuge tube for FACS sorting or 10X sequencing.
Library preparation was performed by UCLA Technology Center for Genomics & Bioinformatics. Nuclei were isolated into single droplets and barcoded using the 10X platform. We sequenced using 50bp long paired end reads with the NovaSeq 6000 .

treatment_protocol: Worms were synchronized using a 10μm nylon mesh filter (NY1102500 EDM Millipore and SX00025000 EDM Millipore) which only allowed L1 staged worms to pass. The L1 worms were washed twice with M9 and centrifuged at 100g for 1 minute. These pellets were plated on fresh NGM plates and transferred to 25°C. Worms were grown for 62 hours at 25°C and were washed 5 times with M9. Between each wash, adult worms were centrifuged at 1300g for 1 minute to remove bacteria. After washing, worms were placed in 1mL of M9 in a 1.5mL low retention microcentrifuge tube and incubated in a rotator at 20°C for 30 minutes to remove residual OP50 from the worms gut. These microcentrifuge tubes were then set upright and the worms were allowed to settle by gravity for 5 minutes. The M9 supernatant was discarded and the final compact worm pellet volume was adjusted to 30μL.

tag: experitment design

value: normal

tag: treatment group

tag: treatment details

value: Worms were synchronized using a 10Œºm nylon mesh filter (NY1102500 EDM Millipore and SX00025000 EDM Millipore) which only allowed L1 staged worms to pass. The L1 worms were washed twice with M9 and centrifuged at 100g for 1 minute. These pellets were plated on fresh NGM plates and transferred to 25¬∞C. Worms were grown for 62 hours at 25¬∞C and were washed 5 times with M9. Between each wash, adult worms were centrifuged at 1300g for 1 minute to remove bacteria. After washing, worms were placed in 1mL of M9 in a 1.5mL low retention microcentrifuge tube and incubated in a rotator at 20¬∞C for 30 minutes to remove residual OP50 from the worms gut. These microcentrifuge tubes were then set upright and the worms were allowed to settle by gravity for 5 minutes. The M9 supernatant was discarded and the final compact worm pellet volume was adjusted to 30ŒºL.

value: whole worm body

tag: generation


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_C01P1_Run1

value: Negative

value: Group I


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_F08P1_Run1


title: MEI_chr1_769_INS_rep2

value: Human Umbilical cord blood-Derived Erythroid Progenitor-10


title: AAVS1_rep4

value: Human Umbilical cord blood-Derived Erythroid Progenitor-24


title: MEI_chr1_769_INS_rep1

value: Human Umbilical cord blood-Derived Erythroid Progenitor-9


title: AAVS1_rep3

value: Human Umbilical cord blood-Derived Erythroid Progenitor-23


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_C08P1_Run1

value: Group III


title: BLD_GSH_15_rep2

value: Human Umbilical cord blood-Derived Erythroid Progenitor-14


title: BRN_GSH_4_rep4

value: Human Umbilical cord blood-Derived Erythroid Progenitor-8


title: BRN_GSH_4_rep3

value: Human Umbilical cord blood-Derived Erythroid Progenitor-7


title: BLD_GSH_10-R_rep3

value: Human Umbilical cord blood-Derived Erythroid Progenitor-19


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_F02P1_Run1

value: Positive

value: Group IV


title: BRN_GSH_4_rep1

value: Human Umbilical cord blood-Derived Erythroid Progenitor-5

value: GFP inserted HUDEP2


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_C03P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_E02P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_G07P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_G02P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_C02P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_A05P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_B05P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_A06P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_D05P1_Run1


title: BLD_GSH_14_rep4

value: Human Umbilical cord blood-Derived Erythroid Progenitor-4


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_E08P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_C06P1_Run1


title: BLD_GSH_14_rep3

value: Human Umbilical cord blood-Derived Erythroid Progenitor-3


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_D06P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_H04P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_E06P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_F03P1_Run1


title: BLD_GSH_14_rep2

value: Human Umbilical cord blood-Derived Erythroid Progenitor-2


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_E01P1_Run1


title: BLD_GSH_14_rep1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_D03P1_Run1

value: Negative

value: Group I


title: MEI_chr3_3707_INS_rep4


title: BRN_GSH_4_rep2

value: Human Umbilical cord blood-Derived Erythroid Progenitor-6


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_D02P1_Run1


title: MEI_chr3_3707_INS_rep3


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_B06P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_E04P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_F05P1_Run1


title: WT_HUDEP2_clone3

value: Human Umbilical cord blood-Derived Erythroid Progenitor-31

value: wild HUDEP2 clone


title: MEI_chr3_3707_INS_rep1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_G04P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_F07P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_B07P1_Run1


title: WT_HUDEP2_clone1

value: Human Umbilical cord blood-Derived Erythroid Progenitor-29


title: MEI_chr3_3707_INS_rep2


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_D04P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_B04P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_G05P1_Run1

value: Group III


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_G06P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_B01P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_C04P1_Run1


title: WT_HUDEP2_clone2

value: Human Umbilical cord blood-Derived Erythroid Progenitor-30


title: WT_HUDEP2_rep4

value: wild type


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_A04P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_H05P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_H02P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_A01P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_B02P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_A03P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_A02P1_Run1


title: Ago2_WT_cytoplasm_1_CLIPinput

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description: whole testis cytoplasmic eCLIP input rep 1

data_processing:
AGO2 IP and size-matched input control (SMInput) samples were demultiplexed as previously described using the script demux_paired_end.py (Van Nostrand et al., 2016). 3’ and 5’ adapters were trimmed using Cutadapt v1.18 (Martin, 2011) with default parameters. To eliminate artifacts from rRNA and other repetitive sequences, trimmed reads were then mapped to RepBase (mouse mm10 RepeatMasker, last modified time: 05-May-2017 06:32) using STAR software v.2.6.1d (Dobin et al., 2013). Unmapped reads recovered after the RepeatMasker step were then mapped to the mouse mm10 genome assembly with options --outFilterScoreMin 0 --outFilterScoreMinOverLread 0.33 --outFilterMatchNminOverLread 0.33 --alignEndsType Local. The script barcode_collapse_pe.py (Van Nostrand et al., 2016) was used to remove PCR duplicates based on unique molecular identifiers (UMIs). Peaks were called using the tag2peak.pl script from the CLIP Tool Kit (CTK) software (Shah et al., 2017) with an adjusted p-value threshold of 0.01 and normalized to the mm10 background model. Each AGO2 eCLIP replicate was also normalized to the corresponding SMInput data using the Peak_input_normalization_wrapper.pl script from (Van Nostrand et al., 2016). CTK was also used to track cross-link-induced mutation sites (CIMS) and cross-link-induced truncation sites (CITS) with a resolution of ±50nt at an empirical false discovery rate (FDR) of 0.01. Specific types of mutations, including deletions, substitutions and insertions, were detected by analysis of unique CLIP tags (trimmed mapped reads). Results were confirmed using an independent analysis pipeline.
Library strategy: eCLIP

organism: Mus

source_name: whole testis

extract_protocol:
Cytoplasmic fractions from adult mouse testes were crosslinked with 254nm UV light. Nuclei were lysed and sonicated in a Bioruptor sonicator (Diagenode) at 4C, 5 min, 30sec on/30sec off. The nuclear lysate was then digested with RNase I (AM2295, Thermo) and Turbo DNase (AM2239, Thermo), and immunoprecipitated using anti-AGO2 antibody (04-642, Millipore). Next, the protein-bound RNAs were ligated with 3’ end adapters. Protein-RNA complexes were subjected to gel electrophoresis and transferred to a membrane, and RNA was isolated by cutting the membrane at the expected size range.
Libraries were prepared as described in van Nostrand et al, 2016 and Biancon et al, 2022. cDNA was generated by reverse transcription, DNA adapter was ligated to the 3' end of the cDNA, and the library was amplified by PCR. Screening of subclones prior to high-throughput sequencing was performed for quality control.

tag: ip antibody

tag: condition

tag: genome build

value: .bed file with peaks


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_E07P1_Run1

value: Positive


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_E05P1_Run1

value: Group IV


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_H03P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_B03P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_A07P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_F06P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_C05P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_A08P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_F04P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_D08P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_H06P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_C07P1_Run1


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_B08P1_Run1


title: M_KSR5_after_FBS_swap_5620 [IMPLICON]

status: Public on Jul 15 2022

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: genomic

data_processing:
IMPLICON-seq
Standard Illumina base-calling pipeline.
As first step in the processing, the first 8 bp of Read 2 were removed and written into the readID of both reads as an in-line barcode, or UMI (Unique Molecular Identifier). This UMI was then later used during the de-duplication step with "deduplicate bismark --barcode mapped_file.bam".
Raw sequence reads were then trimmed to remove both poor quality calls and adapters using Trim Galore (v0.6.5, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Cutadapt version 2.3; parameters: --paired). Trimmed reads were aligned to the mouse genome in paired-end mode. Alignments were carried out with Bismark v0.22.3 (Krueger and Andrews, 2011)  CpG methylation calls were extracted from the mapping output using the Bismark methylation extractor. Deduplication was then carried out with deduplicate_bismark, using the --bacode option to take UMIs into account (see above)). For hybrid mouse strain experiments, the data was aligned to a hybrid genome of C57Bl/6 (genome 1)/CAST (genome 2)(the genome was prepared with the SNPsplit package (v0.3.4, https://github.com/FelixKrueger/SNPsplit)). Following alignment and deduplication, reads were split allele-specifically with SNPsplit.
Assembly: GRCm38
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

molecule: genomic DNA

organism: Mus musculus

source_name: induced pluripotent stem cell

extract_protocol:
Genomic DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen) or the AllPrep DNA/RNA Micro Kit (Qiagen) according to manufacturer’s instructions and eluted into TE buffer or H2O.
The IMPLICON protocol consists of 2 PCR reactions. In the first reaction each sample is amplified with each primer pair in individual reactions: 30ng (2μl of 66μl eluted bisulfite treated DNA) of bisulfite treated DNA is amplified with 1.2μl of 10μM primer pool (final 1.5μM) containing both forward and reverse primers in 4μl of 2x KAPA HiFi Uracil+ ReadyMix in a final volume of 8μl. DNA was amplified using the following conditions: initial denaturation at 95°C for 5min, 30 cycles of 98°C denaturation for 20 seconds, variable annealing temperature for 15 seconds and extension at 72°C for 60 seconds; followed by a final extension at 72°C for 10 minutes. All PCR reactions for each individual sample were pooled together and samples cleaned-up using 1.5x AMPure XP beads and eluted in 20μl H2O. In the second PCR reaction, barcoded Illumina adapters are attached to the pooled PCR samples ensuring that each sample pool receives a unique reverse barcoded adapter. The 20μl PCR pool was amplified using 1μl of 10μM Illlumina PE1.0 primer (same for all samples) and 1μl of 10μM Illumina iTAG primer (distinct for each sample) and 25μl 2x KAPA HiFi Uracil+ ReadyMix in a 50μl volume reaction using the following conditions: initial denaturation at 98°C for 45 seconds, 5 cycles of 98°C denaturation for 15 seconds, 65°C annealing for 30 seconds and extension at 72°C for 30 seconds; followed by a final extension at 72°C for 5 minutes. Reactions were cleaned-up with 1x AMPure XP beads and eluted in 20μl. Libraries were verified by running 1:30 dilutions on Agilent bioanalyser.

treatment_protocol: 1μg of genomic DNA was bisulfite converted using the EZ DNA methylation Gold kit (Zymo Research) according to manufacturer’s instructions with either magnetic bead or column clean-up and eluted/resuspended in 66μl elution buffer to obtain a final concentration of ~15ng/μl bisulfite converted DNA.

value: induced pluripotent stem cell

tag: Sex

value: male

tag: group

value: Male KSR-iPSCs cultured in FBS medium for 10 days


title: M_FBSplusVitC3_5620 [IMPLICON]

tag: cell type

value: Male miPSC line generated using FBS with 0.5uM of VitC


title: M_FBSplusVitC4_5620 [IMPLICON]


title: M_KSR_FBS3_5620 [IMPLICON]

value: Male miPSC line generated using KSR/FBS formulation 1:1


title: M_KSR_FBS4_5620 [IMPLICON]


title: M_KSR_FBS1_5620 [IMPLICON]


title: M_KSR_FBS5_5620 [IMPLICON]


title: M_KSR_FBS6_5620 [IMPLICON]


title: M_FBSplusVitC6_5620 [IMPLICON]


title: M_FBSplusVitC2_5620 [IMPLICON]


title: M_FBSplusVitC5_5620 [IMPLICON]


title: M_FBS_day24_cl_A_5620 [IMPLICON]

source_name: day 24 reprogramming intermediate

value: day 24 reprogramming intermediate

value: Male reprogramming intermediate harvested at day 24 of reprogramming under FBS condition


title: M_FBS_day24_cl_B_5620 [IMPLICON]


title: GRCh37ERCC-ensembl75-genes-T_20171128SC_D01P1_Run1


title: M_FBSplusVitC1_5620 [IMPLICON]


title: M_FBS_day12_Tminus_Splus_5620 [IMPLICON]

source_name: day 12 reprogramming intermediate

value: day 12 reprogramming intermediate

value: Male reprogramming intermediate sorted at day 12 of reprogramming under FBS condition


title: M_FBS5_after_KSR_swap_5620 [IMPLICON]

value: Male FBS-iPSCs cultured in KSR medium for 10 days


title: F_FBS_day24_Tplus_Sminus_cl_C_5620 [IMPLICON]

source_name: day 24 non-reprogramming intermediate

value: day 24 non-reprogramming intermediate

value: female

value: Female non-reprogramming intermediate sorted at day 24 of reprogramming under FBS condition


title: M_FBS1_after_KSR_swap_5620 [IMPLICON]


title: M_KSR_FBS2_5620 [IMPLICON]


title: F_FBS_day24_cl_A_5620 [IMPLICON]

value: Female reprogramming intermediate harvested at day 24 of reprogramming under FBS condition


title: F_FBS_day12_Tminus_Splus_2_5620 [IMPLICON]

value: Female reprogramming intermediate sorted at day 12 of reprogramming under FBS condition


title: M_KSR4_miPSCs_5482 [IMPLICON]

source_name: Mouse induced pluripotent stem cell

value: Mouse induced pluripotent stem cell

value: Male miPSC line generated using KSR


title: M_KSR5_miPSCs_5482 [IMPLICON]


title: TX_2i_mESCs_5482 [IMPLICON]

source_name: embryonic stem cell

value: embryonic stem cell

value: Female control mESC line generated in 2i conditions


title: M_KSR6_miPSCs_5482 [IMPLICON]

value: male


title: M_KSR3_miPSCs_5482 [IMPLICON]


title: M_KSR2_miPSCs_5482 [IMPLICON]


title: M_FBS_day12_Tplus_Sminus_5620 [IMPLICON]

source_name: day 12 non-reprogramming intermediate

value: day 12 non-reprogramming intermediate

value: Male non-reprogramming intermediate sorted at day 12 of reprogramming under FBS condition


title: M_FBS5_NPC_5482 [IMPLICON]

source_name: neuronal precursor cell

value: neuronal precursor cell

value: Neuronal precursor cell generated from a male iPSCs


title: F_KSR6_miPSCs_5482 [IMPLICON]

value: Female miPSC line generated using KSR


title: M_KSR1_miPSCs_5482 [IMPLICON]


title: F_FBS_day12_Tplus_Sminus_1_5482 [IMPLICON]

value: Female non-reprogramming intermediate sorted at day 12 of reprogramming under FBS condition


title: F_FBS5_NPC_5482 [IMPLICON]

value: Neuronal precursor cell generated from a female iPSCs


title: F_KSR3_miPSCs_5482 [IMPLICON]


title: F_KSR2_miPSCs_5482 [IMPLICON]


title: F_KSR4_miPSCs_5482 [IMPLICON]


title: F_FBS_day12_Tminus_Splus_1_5482 [IMPLICON]

value: day 12 reprogramming intermediate


title: Male_MEFs_5069 [IMPLICON]

source_name: Mouse embryonic fibroblasts

value: Mouse embryonic fibroblasts

value: Parental male mouse embryonic fibroblasts


title: F_KSR1_miPSCs_5482 [IMPLICON]

value: female


title: F_KSR5_miPSCs_5482 [IMPLICON]


title: F_FBS_day24_Tminus_Splus_cl_C_5620 [IMPLICON]

value: day 24 reprogramming intermediate

value: Female reprogramming intermediate sorted at day 24 of reprogramming under FBS condition


title: fas1-4 rep1 (RNAseq)

status: Public on Jul 12 2022

first: Emma

middle: Tung

last: Corcoran

address: 260 Whitney Ave

department: Molecular, Cellular, and Developmental Biology

data_processing:
RNA-seq: Paired-end reads were filtered and trimmed using Trim Galore! (version 0.5.0) with default options for quality. The resulting data sets were aligned to The Arabidopsis Information Resource (TAIR10) genome using STAR (version 2.7.2a) allowing 2 mismatches (--outFilterMismatchNmax 2). Protein-coding genes were defined as described in the TAIR10 annotation gff3 file. The program featureCounts (version 1.6.4) was used to count the paired-end fragments overlapping with the annotated protein-coding genes. Differential expression analysis of protein-coding genes was performed using DESeq2 version 1.26 on raw read counts to obtain normalized fold changes and Padj-values for each gene. Genes were considered to be differentially expressed if they showed > +1.5-fold-change and Padj-value < 0.05.
Assembly: RNA-seq: TAIR10
Supplementary files format and content: RNA-seq bigwig: BPM of RNAseq over the genome using deeptools.

organism: Arabidopsis thaliana

source_name: 6-week-old unopened flowers

growth_protocol: Arabidopsis plants were grown under cool‐white fluorescent lights (~100 μmol m−2 s−1) in long‐day conditions (16 h light/8 h dark).

extract_protocol: Unopened flowers from 6-week-old plants grown in long-day conditions were frozen in liquid nitrogen, ground with a pestle, and then RNA was extracted using the Direct-zol RNA Miniprep Plus Kit (Zymo Research, Irvine, CA). For each biological replicate, pooled tissue collected simultaneously from three different plants was used. RNA quality was confirmed through analysis of Agilent Bioanalyzer 5300 electropherograms (Supp. Fig. 12A). For the library preparation, mRNA was purified from 500 ng of total RNA with oligo-dT beads and sheared by incubation at 94°C in the presence of Mg (KAPA mRNA Hyper Prep). Following first-strand synthesis with random primers, second strand synthesis and A-tailing were performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs were ligated to library insert fragments. Library amplification amplified fragments carrying the appropriate adapter sequences at both ends. Strands marked with dUTP were not amplified. Indexed libraries that met appropriate cut-offs for both were quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution was determined with LabChip GX or Agilent Bioanalyzer.

tag: ecotype

tag: tissue

value: unopened flowers

tag: age

value: 6 weeks

value: wild type


title: H4 septuple rep2 (RNAseq)

tag: genotype


title: H4 septuple rep1 (RNAseq)


title: fas1-4 rep2 (RNAseq)


title: Wildtype Col0 rep2 (RNAseq)


title: Single cell RNA-seq - embryonic tdTomato MPs, Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/tdTomato Embryonic Day 16.5 distal

city: Vancouver

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

country: Canada

institute: University of British Columbia

data_processing:
Samples were demultiplexed using cellranger mkfastq with bclfastq2.
Samples were aligned and output matrices generated using cellranger count for alignment.
cellranger aggregate was used to aggregate multiple samples for combined analysis
Assembly: mm10 with appended tdTomato and EGFP sequences
Supplementary files format and content: gene matrices, cell barcode and gene list are included as .mtx, .tsv and .tsv files, respectively

source_name: Mesenchymal Progenitors

growth_protocol: Mice were bred and raised using standard approved animal care committee methodology.

extract_protocol:
FACS purified cells were counted and inspected by hemocytometer before input to the 10X chromium library preparation pipeline and subsequent NGS.
10X Chromium Single Cell 3' v2 or v3

treatment_protocol: To label mesenchymal progenitors of the murine forelimb, adult dams >7 weeks of age were paired in timed matings and subsequently gavaged with 7.5mg tamoxifen in 300uL sunflower oil at embryonic day ten before forelimbs were dissociated and reporter positive cells isolated for interrogation.

tag: strain

value: Embryonic forelimb segment of the distal zeugopod and autopod

tag: developmental stage

value: Embryonic Day 16.5


title: Wildtype Col0 rep1 (RNAseq)

growth_protocol: Arabidopsis plants were grown under cool‐white fluorescent lights (~100 μmol m−2 s−1) in long‐day conditions (16 h light/8 h dark).


title: HCC1806_2D_1xSRSF7_1

status: Public on Jul 11 2022

city: Farmington

first: Olga

last: Anczukow

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

data_processing:
Read filtering and cropping of reads to same length using Trimmomatic (v0.39)
Mapping of reads to Gencode GRCh38 v.32 reference transcript annotation using STAR in 2-pass mode (v2.7.3a)
Transcript assembly and quantification with Stringtie (v2.1.3b)
Differential splicing using rMATS (v4.1.0)
Assembly: GRCh38.p13 v32
Supplementary files format and content: Csv with raw gene counts.

growth_protocol: 2D-grown HCC1806 cells were maintained in DMEM (Gibco) supplemented with 15% FBS and 1% penicillin streptomycin (Sigma) and were harvested by scraping adherent cells in PBS once ~90% confluence was reached.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) including DNase I treatment per manufacturer instructions.
Barcoded RNA libraries were prepared starting with 500ng of total RNA using the TrueSeq stranded mRNA kit with polyA selection (Illumina), and quantified using a Bioanalyzer DNA 1000 chip (Agilent).
Libraries were sequenced as 150bp paired-end reads at 100-200 million reads per library on an Illumina NovaSeq, equal amounts of 18 libraries were pooled per lane.

tag: cell line

value: human triple negative breast cancer cells

value: SRSF7 OE


title: HCC1806_2D_1xSRSF3_1

value: SRSF3 OE


title: HCC1806_2D_1xSRSF7_3


title: HCC1806_2D_1xSRSF3_2


title: HCC1806_2D_1xSRSF7_2


title: HCC1806_2D_1xSRSF3_3


title: HCC1806_2D_1xSRSF2_3

value: SRSF2 OE


title: HCC1806_2D_1xSRSF2_1


title: HCC1806_2D_1xSRSF2_2


title: HCC1806_2D_1xCtrl_3

value: single plasmid control


title: Female_MEFs_5069 [IMPLICON]

value: Parental female mouse embryonic fibroblasts


title: HCC1806_2D_1xCtrl_1


title: HCC1806_2D_1xCtrl_2


title: Tumor_+CACS_rep12

status: Public on Jul 09 2022

city: New York

first: Charles

last: Murphy

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

description:
Goncalves-MG-7833_2019_10_25_HTSeq.gene.counts.csv
Goncalves-MG-7833_2019_10_25_genes-fpkm.csv

data_processing:
Raw sequenced reads were aligned to the mouse reference GRCm38 using STAR (v2.4.1d, 2-pass mode) aligner and Raw counts were obtained using HTSeq (v0.6.1) (Engström et al., 2013; Teng et al., 2016). The principal component analysis (PCA) was performed using R Studio Version 3.6.3 and DEBrowser shinny application (Kucukural et al., 2019). Genes with <10 CPM were filtered out and batch effect correction was achieved using the Combat method (Johnson et al., 2007). The differentially expressed genes (DEG) were obtained using DESeq2 and were considered statistically significant when FDR < 0.05 and Log2(FC) > 1.5. The list of DEG was then used for KEGG pathway enrichment analysis using the R package clusterProfiler (Yu et al., 2012). The probability of browning in the WAT was assessed using the online webtool BATLAS (Perdikari et al., 2018).
Assembly: GRCm38
Supplementary files format and content: Files ending in "genes-fpkm.csv" are comma-delimited file containing FPKM values for each sample. Files ending in "HTSeq.gene.counts.csv" are comma-delimited file containing per-gene counts for each sample.

source_name: Tumor

extract_protocol:
Total RNA was extracted from gastrocnemius (whole muscle) and WAT (whole depot) using TRIzol (Thermo Fisher), followed up by a clean-up step using RNeasy kit (Qiagen).
One microgram of total RNA of each sample was submitted to the WCM Genomics Resources Core Facility.

value: M

tag: cacs status

value: Positive

tag: weight loss

tag: sequencing batch


title: Tumor_-CACS_rep10

value: Negative


title: Tumor_+CACS_rep10


title: Tumor_+CACS_rep8

description:
Marcus5291_2017_11_HTSeq.gene.counts.csv
Marcus5291_2017_11_genes-fpkm.csv

value: F


title: Tumor_+CACS_rep7


title: Tumor_+CACS_rep6


title: Tumor_-CACS_rep9


title: Tumor_+CACS_rep1


title: Tumor_+CACS_rep11


title: Tumor_+CACS_rep4


title: Tumor_+CACS_rep5


title: Tumor_+CACS_rep2


title: Tumor_+CACS_rep3


title: Tumor_-CACS_rep6


title: Tumor_-CACS_rep7


title: Tumor_-CACS_rep4


title: Tumor_-CACS_rep2


title: Tumor_-CACS_rep3


title: Tumor_-CACS_rep1


title: Tumor_+CACS_rep9


title: mTEChi, WT, ATAC, rep1

city: Tsurumi-ku, Yokohama

first: Hideyuki

last: Yoshida

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN IMS

data_processing:
trimming adapter sequences and low-quality reads by fastp
mapping to the mm10 reference genome by bowtie2 with options -X 1000 -fr
filtering nonuniquely mapped reads by samtools view -q 30
removing chrM mapped reads by samtools
removing duplicated reads by samtools
piling up the fragments defined by paired reads using macs2 with the SPMR option
Converting bedgraph into bigwig files using bdg2bw (https://gist.github.com/taoliu/2469050)
Assembly: mm10
Supplementary files format and content: bigWig files: read coverage across the whole genome (fragment pileup per million reads)

source_name: thymus

extract_protocol:
Mouse thymus was enzymatically digested and then DAPI-CD45-EpCAM+Ly51-MHCII-high or MHCII-low cells were sorted by FACSAria into 100 uL of BAMBANKER (GC LYMPHOTEC) and kept frozen until library constructions.
ATAC-seq libraries were constructed as previously reported by Corces et al. (Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat. Genet. 2016). Specifically, frozen samples were thawed, split into two tubes, and washed with 1 ml of ice-cold PBS containing protease inhibitors (cOmplete ULTRA, EDTA-free; Merck). Cell pellets were resuspended in 35 uL of Tn5 transposase mixture (10 mM TAPS-NaOH pH 8.5, 5 mM MgCl2, 10% DMF, 0.2 mg/ml digitonin, and in-house Tn5) on ice. Then, the cells were incubated at 37C for 30 min with agitation followed by DNA isolation using the Monarch PCR & DNA Cleanup Kit (New England Biolabs) according to the manufacturer’s instructions. The tagmented DNA was amplified using KAPA HiFi DNA Polymerase (Roche) with a set of primers designed by Buenrostro et al. (Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 2015) with the following thermal cycles: 5 min at 72C, 30 s at 95C followed by 17 cycles (98C for 20 s, 63C for 10 s), and a final extension at 72C for 3 min. The PCR products were purified using a 1.8x volume of AMPure XP beads (Beckman Coulter) and eluted in EB (Qiagen).

value: thymus

value: NOD

value: MHCII-high epitherial cells

value: WT

value: 8weeks old

value: female


title: mTEChi, WT, ATAC, rep2


title: mTEChi, 3xAireKI,ATAC, rep2


title: Tumor_-CACS_rep8


title: mTEClo, WT, ATAC, rep1

value: MHCII-low epitherial cells


title: LUAD_rna_3

status: Public on Jul 08 2022

city: Tampa

first: Alex

middle: M

last: Jaeger

state: FL

address: 12902 Magnolia Dr

department: Molecular Oncology

institute: Moffitt Cancer Center

data_processing:
raw fastq files were adapter trimmed and compressed prior to pipeline submission
compressed fastq files were submitted to the RiboToolKit pipeline
RiboToolKit outputs were used for further analysis and data interpretation
Supplementary files format and content: kallisto alignments

source_name: lung adenocarcionoma organoids

growth_protocol: Organoids were grown in custom lung organoid media and plated on matrigel washed tissue culture plates for 48 hours prior to harvest

extract_protocol:
Ribosome protected RNA fragments (RPFs) were extracted according to the RiboLace Protocol
Libraries were constructed from RPFs using the Takara SMARTer small RNA Library construction Kit; successfully generated libraries were pooled prior to sequencing

treatment_protocol: cells were treated with 100 µM cycloheximide for 5 min

value: lung adenocarcionoma organoids

tag: tag

value: RiboLace Protocol


title: LUAD_rna_2


title: LUAD_rna_1


title: AT2_rna_3

source_name: alveolar type 2 organoids

value: alveolar type 2 organoids


title: mTEChi, 3xAireKI, ATAC, rep1


title: LUAD_ribo_2


title: LUAD_rna_4


title: Tumor_-CACS_rep5


title: AT2_ribo_2


title: LUAD_ribo_1


title: LUAD_ribo_3


title: AT2_rna_1


title: AT2_ribo_1


title: RL3022_WGBS_DoxWD_3days_rep2

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

data_processing:
CASAVA v1.8.2
The WGBS sequenced reads were first trimmed using bbduk, and overlapping pairs were merged using BBMerge(Bushnell, Rood, and Singer 2017). The reads were mapped to the hg19 genome including the lambda and pUC19 sequences using BS-Seeker2 with Bowtie 2 as back-end aligner (-e 300 -X 2000)(Guo et al. 2013). The duplicated reads were removed using Sambamba markdup for paired-end reads and PALEOMIX for merged reads(Schubert et al. 2014). We then used CGmapTools to generate methylation calls(Guo et al. 2018).
Sequenced ATAC-seq reads were then trimmed with bbduk for Nextera adapters and mapped to the genome using Bowtie 2. Duplicated reads were removed and blacklisted regions filtered as with ChIP-seq, and peaks were called using MACS2 with “--nomodel -f BAM --keep-dup all” parameters. Replicates were merged using IDR, and each sample was validated visualising the insert size distribution following nucleosome periodicity
ChIP-seq reads were trimmed with bbduk(Bushnell, n.d.) and mapped to the genome using Bowtie 2(Langmead and Salzberg 2012) allowing for an insert site of 2000 bp, reads were deduplicated using Sambamba markdup function(Tarasov et al. 2015) and reads mapping to blacklisted genomic regions were filtered out using SAMtools(H. Li et al. 2009). We then used MACS2 to call peaks with the matched chromatin input sample as background for each ZF-D3A HA ChIP-seq experiment, specifying the parameters “-f BAMPE -q 0.05 --down-sample”(Feng et al. 2012). The peaks for replicate pairs were merged using IDR (https://github.com/nboley/idr)(Q. Li et al. 2011).
The RNA-seq reads were trimmed using fastp with default parameters(Chen et al. 2018), then mapped with HISAT2 (--rna-strandness RF) to an index including hg19 genome assembly and ERCC spike-in sequences(Sirén, Välimäki, and Mäkinen 2014). Then, RNA-seq read-pair counts were read into R using summarizeOverlaps function within the GenomicAlignments package and mapped to the UCSC hg19 gtf(Lawrence et al. 2013).
Assembly: hg19 UCSC
Supplementary files format and content: Bisulfite-seq files (CGmap files) are the direct output from BSseeker2/CGmaptools (https://github.com/BSSeeker/BSseeker2), they contain chromosome position, (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C / (#_of_C + #_of_T). (7) #_of_C (methylated C, the count of reads showing C here) (8) = #_of_C + #_of_T (all Cytosines, the sum of reads showing C or T in that position).
Supplementary files format and content: NarrowPeak files are the output of MACS2 software, ZF_Counts_table_GEO.tsv.gz was computed mapping RNA-seq with HISAT2 and extracting the counts with "featureOverlaps" in R.

source_name: MCF-7 cell line - ZF-D3A-wt

growth_protocol: complete media with 1000 ng/ml doxycyline for 3 days, then just complete media for 3 days

extract_protocol:
Qiagen DNeasy Blood & Tissue Kit
500 ng of genomic DNA was spiked with 0.5% (w/w) of unmethylated lambda phage DNA (Promega) for calculation of the bisulfite non-conversion rate, and sheared with a Covaris S2 sonicator to an average length of 300 bp. The sheared DNA was end-repaired, A-tailed and ligated to methylated adapters (NEXTflex Bisulfite-Seq Barcodes, PerkinElmer) using the NxSeq AmpFREE Low DNA Library Kit (Lucigen). Adapter ligated libraries were subject bisulfite conversion using the EZ DNA Methylation-Direct Kit (Zymo) following the manufacturer’s instructions and subjected to 6 cycles of PCR amplification using KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).


title: LUAD_ribo_4


title: AT2_ribo_3


title: AT2_rna_2


title: RL3021_WGBS_DoxWD_3days_rep1


title: RL3020_ATACseq_DoxWD_3days_rep2

extract_protocol:
50,000 FACS purified cells were resuspended in 50 µl cold ATAC resuspension buffer 1 (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) NP40, 0.1% (v/v) Tween-20, 0.01% (v/v) Digitonin) and incubated on ice for 3 minutes to lyse cells. The lysis reaction was stopped by adding 1 ml of cold ATAC resuspension buffer 2 (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Tween-20) and inverting the tube for 3 times to mix. The nuclei were pelleted by centrifugation at 500xg for 10 minutes at 4℃ in a fixed angle centrifuge.
The supernatant was removed and the nuclei were resuspended in transposition mix containing 25 µl of 2x TD buffer (20 mM Tris-HCl pH 7.5, 10 mM MgCl2, 20% (v/v) Dimethyl Formamide), 2.5 µl of 100 nM Tn5, 16.5 µl PBS, 0.5 µl of 1% (v/v) digitonin, 0.5 µl of 10% (v/v) Tween-20, and 5 µl H2O. The transposition reaction was incubated at 55°C for 30 minutes in a thermomixer with 1000 RPM mixing. Transposed DNA was cleaned up using the Qiagen MinElute PCR Purification kit following manufacturer’s instructions. 20 µl of eluted DNA was subject to 8-10 cycles of PCR amplifications using NEBNext 2x MasterMix.


title: mTEClo, 3xAireKI,ATAC, rep1


title: RL3033_Input_noDox_rep3

growth_protocol: complete media

extract_protocol:
Cells were washed two times with 10 ml of PBS and crosslinked for 5 minutes in 50 mM HEPES-KOH, pH 7.5, 100 mM NaCl, 1mM EDTA, 1% formaldehyde. The crosslinking reaction was quenched by the addition of glycine to a final concentration of 125 mM and washed twice with phosphate buffered saline (PBS). All subsequent solutions were supplemented with a protease inhibitor cocktail (Sigma Cat. # P8340). Cells were scraped off the plates with a rubber policeman in 10 ml of PBS and centrifuged at 3,000 rpm for 5 minutes in a swinging bucket rotor. The cell pellets were resuspended in 10 ml of 50 mM HEPES-KOH, pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, incubated on ice for 10 minutes and centrifuged at 3,000 rpm for 10 minutes in a swinging bucket rotor. Cell pellets were washed twice by gently adding 10 mM Tris-HCl, pH 8.1, 200 mM NaCl, 1 mM EDTA to the cell pellets, trying not to disturb the pellets, and centrifuged at 3,000 rpm for 5 min. Finally the cell pellets were resuspended in 0.1% SDS, 1 mM EDTA and transferred to a Covaris TC12x12 tube. The chromatin was sheared using a Covaris S2 sonicator with the following settings: time 12 min, duty cycle 5%, intensity 4, cycles per burst 200, temperature 4˚C, power mode frequency sweeping. Triton X-100 and NaCl were added to a final concentration of 1% and 150 mM respectively. The sheared chromatin was centrifuged at maximum speed in a microfuge for 15 minutes at 4˚C and the supernatant was transferred to a new tube.
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, bisulfite converted and subjected to 7 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).


title: RL3032_Input_DoxMut_rep3

source_name: MCF-7 cell line - ZF-D3A-mut

growth_protocol: complete media with 1000 ng/ml doxycyline for 3 days


title: RL3031_Input_Dox_rep3


title: RL3030_ChIPseq_noDox_H3K27me3


title: RL3029_ChIPseq_noDox_H3K9me3


title: RL3028_ChIPseq_DoxMut_HAflag_rep3


title: RL3027_ChIPseq_DoxMut_H3K27me3


title: mm_rna_immatureb_cd45.2.2

status: Public on Jul 06 2022

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

data_processing:
Raw reads were mapped to the reference genome using STAR. Gene expression levels were quantifed using featureCounts.
Assembly: mm9
Supplementary files format and content: Tab-delimited text of read counts per gene

source_name: Bone Marrow

extract_protocol:
FACS sorted cells from small pre-B and immature B cells isolated from mice and total RNA isolated using  Qiagen RNeasy Cat 74104
Libraries were generated TruSeq® Stranded mRNA Sample Prep” kit from Illumina and the associated user manual

value: Bone Marrow

value: Ev Vivo

value: Immature B


title: mm_rna_immatureb_cd45.2.1


title: mm_rna_spreb_cd45.2.2

value: Small Pre-B


title: mm_rna_lpreb_cd45.2.1

value: Large Pre-B


title: mm_rna_lpreb_cd45.2.2


title: mm_rna_spreb_cd45.2.3


title: mm_rna_spreb_cd45.1.1


title: mm_rna_spreb_cd45.2.1


title: mm_rna_spreb_cd45.1.2


title: mm_rna_lpreb_cd45.1.2


title: RL3026_ChIPseq_DoxMut_H3K9me3


title: RL3019_ATACseq_DoxWD_3days_rep1


title: DLD1asyn_Aux_H3K27me3_rep2

status: Public on Jul 05 2022

city: goettingen

first: Shu

last: Zhang

address: Robert-Koch-Strasse 40

department: Institute of Pathology

country: Germany

institute: University Medical Center Göttingen

data_processing:
library strategy: CUT&TAG
Pair-end reads were aligned to reference hg38 using offical cut&tag analysis pipline, https://yezhengstat.github.io/CUTTag_tutorial/
Mapping to human and E. Coli genome (Bowtie2); Peak calling with SEACR
Assembly: hg38
Supplementary files format and content: bigwig file

source_name: colorectal adenocarcinoma cell lines

growth_protocol: POLR2A-mAID-mClover DLD-1 (previously described; Nagashima et al, 2019) were passaged in RPMI-1640 medium supplemented with 10% FBS under 5% CO2.

extract_protocol:
Cut&Tag experiment was carried out with CUT&Tag-IT Assay Kit (Active Motif) according to manufacturers instructions.
Cut&Tag libraries were constructed as a part of CUT&Tag-IT Assay Kit (Active Motif) according to manufacturers instructions.

treatment_protocol: Inducible depletion of RPB1 initiated via treatment with doxycycline for 24 h to induce TIR1 expression, before addition of 500 µM indole-3-acetic acid solution (“auxin”, Sigma-Aldrich). Then treated with 14h auxin to RNAPll degradation.

value: colorectal adenocarcinoma cell line

tag: treatment

value: 1ug/ml doxycycline treatment 24h then 500uM Auxin treatment with 14h

tag: cut&tag antibody

value: anti-H3K27me3:39155 Active Motif SA


title: mm_rna_immatureb_cd45.1.1


title: RL3023_ChIPseq_Dox_H3K9me3


title: mm_rna_spreb_cd45.1.3


title: DLD1asyn_Aux_H3K27me3_rep1


title: mm_rna_immatureb_cd45.1.2


title: RL3025_ChIPseq_Dox_HAflag_rep3


title: DLD1asyn_Aux_SMC1A_rep2

value: anti-SMC1a ab9262 Abcam


title: DLD1asyn_Aux_H3K27ac_rep1

value: anti-H3K27ac:39134 Active Motif SA


title: DLD1asyn_Ctrl_H3K27me3_rep1

value: untreated


title: DLD1asyn_Ctrl_H3K27me3_rep2


title: DLD1asyn_Ctrl_H3K27ac_rep1


title: DLD1asyn_Aux_SMC1A_rep1


title: DLD1asyn_Ctrl_SMC1A_rep2


title: RL3024_ChIPseq_Dox_H3K27me3


title: DLD1asyn_Aux_CTCF_rep2

value: anti-CTCF:61311 Active Motif SA


title: mm_rna_lpreb_cd45.1.1


title: DLD1asyn_Ctrl_CTCF_rep2


title: DLD1asyn_Ctrl_CTCF_rep1


title: micro_C_async_control

data_processing:
Pair-end reads were separately aligned to reference hg38 using BWA through the pipeline offered by Dovetail to generate cool file (https://micro-c.readthedocs.io/en/latest/fastq_to_bam.html)
Genome_build: hg38
Supplementary_files_format_and_content: cool file

extract_protocol:
Micro-C experiments were carried out by company names Dovetail GENOMICS using Micro-C Kit
Libraries  were carried out by company names Dovetail GENOMICS using Micro-C Kit

tag: cell cycle

value: asynchronous


title: micro_C_async_degron

value: 14h auxin treatment


title: H3K27ac_E8.25_DKO_FHF_rep2

status: Public on Jul 03 2022

city: Beijing

first: Yaxi

last: Liu

address: 5 Yiheyuan Road

country: China

institute: Peking University

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Sequenced reads were trimmed and filtered by cutadapt (v 1.11) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Peaks were called by MACS2 (v 2.1.1), with parameter of "--broad".
Bigwig files were generated from bam files using deeptools (v 2.2.3) bamCoverage. All samples were normalized to 10 million reads with binsize as 50 bp by “--scaleFactor, --binSize 50” parameters.
Assembly: mm10
Supplementary files format and content: The processed files were bigwig files.

source_name: E8.25 first heart field

extract_protocol:
The E8.25 hearts were firstly fixed with 0.25% formaldehyde, then FHF/SHF were separated by forceps followed by methyl alcohol fixation. FHF/SHF were then subjected to H3K27ac in situ ChIP.
Libraries were constructed following the Illunima Nextera lib preperation kit. After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

value: E8.25 first heart field

tag: chip antibody


title: Mouse WT3

first: Neville

last: Dusaj

description: ATAC Fragments

library_source: genomic single cell

data_processing:
Pre-processing was performed using 10x Genomics Cell Ranger ARC (v1.0.1). Reads were de-multiplexed using the cellranger-arc mkfastq function. Single cell feature counts for each sample were then generated using the cellranger-arc count function. The gene expression information for these libraries exhibited exceedingly low UMI and genes per cell consistent with lower quality RNA in single-cell nuclei Multiome data; as such, we moved forward utilizing only the ATAC data for analysis. ATAC data was processed using the ArchR package (v1.0.1) using the atac_fragments.tsv.gz file generated by the cellranger-arc count function as input. Arrow files were created using a minimum TSS enrichment score of 5 and a minimum number of unique nuclear fragments of 1,000. Doublet scores were calculated using the addDoubletScores function with k = 10, knnMethod = “umap” and LSImethod = 1. Doublets were removed using the filterDoublets function with default parameters. Dimensionality reduction was performed through iterative semantic index (LSI) using the cell by genomic window (500 bp) matrix as input, using the addIterativeLSI function with the following parameters: iterations = 3, resolution = 0.2, sampleCells = 1,000, var.features = 25,000 and dimsToUse = 1:30. Cell clusters were identified using the addClusters function using the iterative latent semantic index (LSI) dimensions as input, with method = “Seurat”, resolution = 0.8. For visualization, UMAP dimensionality reduction was performed using the LSI dimensions as input, using the addUMAP function with: nNeighbors = 30, minDist = 0.5 and metric = “cosine”. Cell identities were assigned based on gene accessibility scores of known marker genes. Custom motif accessibility deviations were calculated as follows: position weight matrices in HOMER format (P < 0.001) were downloaded from the HOCOMOCO v11 mouse database. Motif occurrences were identified using the scanGenomeWide function of the HOMER package. To include only high confidence motif sites, we applied a minimum odds ratio score threshold of 6. We next created custom peakAnnotations using ArchR and performed ChromaVar analysis using the addDeviationsMatrix function with default parameters.
snATAC-seq data for CH05 was generated as described above using the Multiome platform (10x Genomics) and GoT performed as described above using the cDNA generated from the Multiome workflow. The gene expression information for these libraries exhibited very low UMI and genes per cell consistent with lower quality RNA in single-cell nuclei Multiome data; as such, we moved forward utilizing only the ATAC data for analysis. For the analysis, fragment files were generated by processing the fastq files using cell-ranger-ARC (v.1.0.0). Downstream analysis was performed using the ArchR (v1.0.1) pipeline. Based on the distribution of total fragments and TSS enrichment per cell, empty droplets were filtered out by requiring a minimum of 3,000 fragments per cell and a TSS enrichment score of 7.5. Potential doublets were detected using the addDoubletScores function, using KNN on the UMAP dimensionality reduction with k = 10. Cell barcodes with high enrichment for doublet scores were removed using the filterDoublets function with default parameters. Next, we performed dimensionality reduction through iterative latent semantic indexing (LSI) using the top 25,000 variable features. Cell clustering was performed using the addClusters function, with the following parameters: reduceDims = “IterativeLSI”; method = “Seurat”; resolution =1. For visualization, further dimensionality reduction was performed by applying UMAP to the iterative LSI space using the addUMAP function with the following parameters: nNeighbors = 30; minDist = 0.5; metric = “cosine”. Cell type identification was performed by manually inspecting the genes showing up-regulated gene accessibility scores (FDR < 0.01 and log2(fold change) > 1.25) for each of the defined clusters (Extended Data Fig. 13c). Motif occurrences were defined using the position weight matrices (PWMs) obtained from the Hocomoco (v.11.0) motif database or our custom PWMs for hypo-methylated and shuffled motifs using HOMER (v4.9), requiring a minimum enrichment score above 6. Transcription factor, hypo-methylated and shuffled motif accessibility was calculated using ChromVAR within the ArchR (v1.0.1) pipeline. Supervised pseudotime trajectories for either erythroid or lymphoid fates were defined within the ArchR (v1.0.1) pipeline applying the addTrajectory function.
Assembly: mm10
Supplementary files format and content: Processed 10X data is a fragments file of ATAC-seq fragments for each cell barcode.
Supplementary files format and content: Output matrices processed from amplicon data have two columns for cell barcode and assigned genotype

source_name: Bone marrow from mouse

extract_protocol:
All animal procedures were completed in accordance with the Guidelines for the Care and Use of Laboratory Animals and were approved by the Institutional Animal Care and Use Committees at MSKCC. The Dnmt3a R878H mouse model has been described previously (Guryanova et al., 2016), and was crossed to the Tal1-creERT2 transgenic model to allow for inducible control of the R878H mutation within the hematopoietic system. To induce recombination of the conditional alleles, age and gender-matched 10-16 week old Tal1-creERT2 control mice and Dnmt3a R878H Tal1-creERT2 mice were treated with tamoxifen (4 mg/kg/day; Cayman Chemical, Ann Arbor, Michigan) for 2 doses, separated 2 days apart. The mice were sacrificed 4-8 weeks after tamoxifen-induction. Primary mouse bone marrow (BM) cells were isolated into cold phosphate-buffered saline (PBS), without Ca2+ and Mg2+, and supplemented with 2% bovine serum albumin (BSA) to generate single cell suspensions. Red blood cells (RBCs) were removed using ammonium chloride-potassium bicarbonate (ACK) lysis buffer, resuspended in PBS/2% BSA, and filtered through a 40μm cell strainer. Total nucleated cells were quantified by Vi-Cell XR cell counter (Beckman Coulter, Brea, CA) and used for downstream data production.  Cryopreserved patient samples approved by the Institutional Review Board of the University of Chicago were thawed and stained using standard procedures (10 min, 4°C) with the surface antibody CD34-PE-Vio770 (clone AC136, Miltenyi Biotec) and DAPI (Sigma-Aldrich). Cells were then sorted for DAPI-negative, CD34+ and CD34-negative cells using BD Influx.
Hematopoietic progenitors (Lin-1-, c-Kit+) were sorted from wildtype (n = 3 mice) or Dnmt3a R878H (n = 3 mice) via c-Kit enrichment as directed by the manufacturer (CD117 Microbeads, clone 3C1, Miltenyi, Auburn, CA; LS Columns (Cat. No. #130-042-401), Miltenyi) followed by FACS (Lin-1 BV421 (Cat. No. #133311), Biolegend, San Diego, CA; CD117 APC (clone 2B8, Invitrogen, Waltham, MA). Nuclei isolation was performed as suggested by the manufacturer (10x Genomics, Pleasanton, CA). Briefly, single cell suspensions were centrifuged at 300 rcf for 5 minutes and cell pellets were resuspended in 100 μl of lysis buffer (Tris-HCl pH 7.4, 10mM; NaCl 10mM; MgCl2 3mM; Tween-20 0.1%; Nonidet P40 substitute (Sigma-Aldrich, St. Louis, MO) 0.1%; Digitonin 0.01%; BSA 1%; DTT 1 mM; RNase inhibitor 1 U/µL (Sigma-Aldrich, St. Louis, MO)) and kept on ice for 3 minutes. Then, 1 ml of wash buffer (Tris-HCl pH 7.4, 10mM; NaCl 10mM; MgCl2 3mM; BSA 1%; Tween-20 0.1%; DTT 1 mM; Sigma Protector RNase inhibitor 1 U/µL) was added. The isolated nuclei were centrifuged for 5 min at 500 rcf, and pellets were resuspended in Diluted Nuclei Buffer (10x Genomics Nuclei Buffer 1X; DTT 1 mM; Sigma Protector RNase inhibitor 1 U/µL). Nuclei concentration was determined by hemocytometer and processed as indicated by the manufacturer (10x Genomics User Guide: Chromium Next GEM Single Cell Multiome ATAC + Gene Expression, CG000338). Single nucleus ATAC and Gene Expression (GEX) libraries were constructed in parallel and assessed for quality control metrics using Agilent Bioanalyzer 2100 and Qubit respectively. ATAC libraries were sequenced to a depth of 25,000 read pairs per nucleus (paired-end, dual indexing: Read 1N 50 cycles, i7 Index 8 cycles, i5 Index 24 cycles, Read 2N 49 cycles) and GEX libraries were sequenced to a depth of 20,000 read pairs per nucleus (paired-end, dual indexing: 28 cycles for Read 1, 10 cycles for i7 Index, 10 cycles for i5 Index, 90 cycles for Read 2).
Multiome Single-nucleus ATAC + RNA-seq (10X) with targeted amplification of a mutation of interest for the patient sample.

value: Bone marrow


title: H3K27ac_E8.25_DKO_FHF_rep1


title: control_mutant_sample_3

status: Public on Jul 01 2022

city: Paris

first: Lasse

middle: van

last: Wijlick

address: 25-28 Rue du Dr Roux

department: Mycology

country: France

institute: Institut Pasteur

data_processing:
Reads were mapped on the available C. albicans genome sequence assembly 22 (candiagenome.org) using Hisat2
DEseq2 was used for differential expression analysis assuming a fold-change of 1.5 with P-adj < 0.05 as significant
Assembly: Candida genome databse assembly 22
Supplementary files format and content: tab-delimited text files include DE values for each Sample

organism: Candida albicans

source_name: SN76 parental strain

extract_protocol:
Cells were mechanically opened in lysis buffer provided by the RNA extraction kit from Qiagen, with 0.5mm glasbeads during 6 rounds of 45s on a FasPrep at 6.5m speed.
Libraries were prepared with the TruSeq stranded mRNA library kit from Illumina.

value: SN76 parental strain

value: wild-type

value: YPD


title: H3K27ac_E8.25_DKO_SHF_rep2

source_name: E8.25 second heart field

value: E8.25 second heart field


title: H3K27ac_E8.25_WT_SHF_rep3


title: control_mutant_sample_2


title: H3K27ac_E8.25_WT_SHF_rep4


title: Mouse WT2

description: ATAC Fragments


title: DLD1asyn_Ctrl_SMC1A_rep1


title: control_mutant_sample_1


title: H3K27ac_E8.25_DKO_SHF_rep1


title: mutant_sample_1, IRF1


title: Mouse MUT3

description: ATAC Fragments


title: mutant_sample_3, IRF1


title: Mouse MUT1

description: ATAC Fragments


title: Mouse WT1

description: ATAC Fragments


title: mutant_sample_2, IRF1


title: 4h control_sample_2

source_name: BWP17 parental strain

value: BWP17 parental strain

value: YPD+aTC


title: 4h control_sample_3


title: 4h overexpression, TET-promoter, IRF1, 3


title: 4h control_sample_1


title: DLD1asyn_Aux_CTCF_rep1

value: colorectal adenocarcinoma cell line


title: 4h overexpression, TET-promoter, IRF1, 2


title: 4h overexpression, TET-promoter, IRF1, 1


title: Mouse MUT2

description: ATAC Fragments


title: 2h control_sample_3


title: 2h control_sample_1


title: 2h overexpression, TET-promoter, IRF1, 2


title: 2h overexpression, TET-promoter, IRF1, 3


title: v2.Line584_ACRYL

status: Public on Jun 30 2022

city: Nashville

first: Amanda

middle: Jeanne

last: Lea

state: TN

address: Box 351634 Station B

institute: Vanderbilt University

description: Lymphoblastoid cell line from the 1000 Genomes study

data_processing:
trimmed each FASTQ file for low quality bases and adapter contamination using "cutadapt"
mapped the trimmed reads to the human reference genome (hg38) using "STAR"
extracted counts of reads mapped to genes using "HTSeq"
removed samples with fewer than 250,000 reads mapped to protein coding genes; if a sample was sequenced twice, kept the sample with the most mapped reads
filtered the per-gene counts matrix to exclude lowly expressed genes, normalized the count data using the R package "limma", and identified 3 surrogate variables that were then regressed out using the R package "sva"
Assembly: hg38
Supplementary files format and content: TXT file of the gene expression values processed as described above

growth_protocol: Lymphoblastoid cell lines (LCLs) were obtained for 544 unrelated individuals included in the 1000 Genomes study. All cells were ordered from Coriell Institute, and live cultures were shipped overnight to Princeton University in randomized batches of 25. Cells were cultured in parallel for 5-11 days until 12 million cells were available to seed (at a density of 1 million cells/2.5mL of media in a 12 well plate).

extract_protocol:
Zymo Quick-RNA
TM3'seq as in PMCID: PMC6945013

treatment_protocol: After an overnight incubation period, 1 of 12 environmental treatments were added to each of the 12 wells.  After 4 hours, cells were washed, harvested, and preserved in lysis buffer for downstream RNA work.

value: Lymphoblastoid

value: ACRYL


title: v3.Line584_PFOA

value: PFOA


title: v2.Line584_ETOH

value: Ethanol


title: v2.Line584_BPA

value: BPA


title: v3.Line584_TUNIC

value: Tunicamycin


title: 2h overexpression, TET-promoter, IRF1, 1


title: v3.Line584_BAFF

value: B-cell activating factor


title: v3.Line584_DEX

value: Dexamethasone


title: v3.Line584_IGF

value: Insulin-like Growth Factor 1


title: v2.Line584_WATER

value: Water


title: v3.Line578_TUNIC


title: v3.Line584_FSL1


title: v2.Line584_IFNg

value: Interferon Gamma


title: v3.Line578_IGF


title: v3.Line584_GARD

value: Gardiquimod


title: v2.Line578_BAFF


title: v3.Line578_BPA


title: v2.Line578_IFNg


title: v3.Line578_DEX


title: v3.Line578_WATER


title: v3.Line578_PFOA


title: v2.Line578_GARD


title: v3.Line575_DEX


title: 2h control_sample_2

value: wild-type


title: v2.Line575_WATER


title: v2.Line575_ACRYL


title: v2.Line575_IGF


title: v2.Line578_FSL1


title: v3.Line575_BAFF


title: v3.Line578_ACRYL


title: v3.Line575_PFOA


title: v3.Line575_TUNIC


title: v3.Line575_FSL1


title: v3.Line573_WATER


title: v3.Line575_GARD


title: v2.Line575_IFNg


title: v2.Line573_GARD


title: v3.Line573_BAFF


title: v2.Line575_BPA


title: v2.Line578_ETOH


title: v3.Line573_FSL1


title: v3.Line573_ETOH


title: v3.Line573_TUNIC


title: v2.Line573_DEX


title: v3.Line573_IGF


title: v2.Line573_ACRYL


title: v2.Line572_GARD


title: v3.Line573_BPA


title: v3.Line572_BAFF


title: v2.Line575_ETOH


title: v3.Line572_BPA


title: v3.Line572_IGF


title: v3.Line572_PFOA


title: v3.Line572_ETOH


title: v3.Line572_TUNIC


title: v3.Line572_FSL1


title: v3.Line573_IFNg


title: v3.Line573_PFOA


title: v2.Line565_ACRYL


title: v2.Line565_IFNg


title: v3.Line565_BPA


title: v2.Line572_IFNg


title: v3.Line565_BAFF


title: v2.Line565_FSL1


title: v3.Line565_WATER


title: v3.Line565_IGF


title: v2.Line565_GARD


title: v2.Line565_PFOA


title: v2.Line560_IGF


title: v2.Line565_TUNIC


title: v3.Line560_TUNIC


title: v2.Line560_DEX


title: v2.Line560_IFNg


title: v2.Line565_ETOH


title: v3.Line560_PFOA


title: v2.Line572_WATER


title: v3.Line560_FSL1


title: v3.Line560_ETOH


title: v2.Line560_GARD


title: v3.Line572_ACRYL


title: v2.Line572_DEX


title: v3.Line560_BAFF


title: v2.Line560_WATER


title: v2.Line551_ETOH


title: v3.Line565_DEX


title: v2.Line551_IGF


title: v3.Line551_FSL1


title: v3.Line551_BAFF


title: v2.Line560_ACRYL


title: v3.Line560_BPA


title: v2.Line551_ACRYL


title: v2.Line551_WATER


title: v2.Line551_BPA


title: v3.Line551_GARD


title: v3.Line551_DEX


title: Line544_DEX


title: v2.Line551_PFOA


title: CHIP-seq CD44 HIGH rep 2

city: Rome

first: Antonella

last: Sistigu

state: Rome

address: Viale Francesco Vito, 1

department: Translational Medicine and Surgery

country: Italy

institute: University of Rome Tor VergataUniversità Cattolica del Sacro Cuore

description:
CD133+ CD24+ CD44+ Cancer Stem Cells
CD44_H.consensus_peaks.chr.txt

data_processing:
Alignment: the ATAC-seq paired-end sequencing reads generated by Illumina sequencing (using NextSeq 500) were mapped to the genome using the BWA MEM algorithm, version 0.7.17, with default settings.
Processing: duplicate reads (“PCR duplicates”) are removed.
Peak Finding: the peak caller used for ATAC-Seq at Active Motif is MACS 2.1.0, using both Paired End reads from each aligned fragment.
Annotations: After defining the Intervals and Merged Regions, their genomic locations along with their proximities to gene annotations and other genomic features are determined.
Alignment CHIP-seq: the CHIP-seq paired-end sequencing reads generated by Illumina sequencing (using NextSeq 500) were mapped to the genome using the bowtie algorithm, version 2.4.1.
Peak Finding: the peak caller used for CHIP-Seq at Active Motif is MACS 2.1.0, using both Paired End reads from each aligned fragment.
Assembly: mm10
Supplementary_files_format_and_content: peaks

source_name: FACS-sorted sarcoma cancer cells (MCA205)

growth_protocol: MCA205 PARENTAL mouse fibrosarcoma cell line was cultured in a Roswell Park Memorial Institute 1640 (RPMI 1640) growth medium supplemented with 10% (v/v) fetal bovine serum (FBS), 2 mM L-glutamine, 100 IU/mL penicillin G sodium salt and 100 µg/mL streptomycin sulfate.  FACS-sorted MCA205 CD44L and CD44 H IFN-CSCs were cultured in DMEM/F12-based culture medium was supplemented with 4 mg/mL bovine serum albumin (BSA), 1X Penicillin-Streptomycin-Amphotericin B (PSF), 0.13% NaHCO3, 6 mM Hepes, 2 mM L-glutamine, 0.1 mg/mL apotransferrin, 0.4 units heparin sodium salt, 1.1% glucose, 25 µg/mL insulin, 6.3 ng/mL progesterone, 9.7 µg/mL putrescine dihydrochloride, and 5.2 ng/mL sodium selenite and supplemented with 20 ng/mL human epidermal growth factor (EGF), 10 ng/mL human basic fibroblast growth factor (bFGF), and 10 mM nicotinamide. CSCs were passaged once/twice a week at dilution 1:2 by mechanical dissociation, through a micropipette, and incubated in standard culture conditions in ultra-low attachment tissue culture flasks.

extract_protocol:
ATAC-seq: 1 x 10^5 parental MCA205 cells and their IFN-CSC counterparts were treated with DNase I at 37°C for 30min. Cells were then washed and cryopreserved in culture medium containing FBS and 5% DMSO in 1,5 mL eppendorf microtubes. Cryopreserved cells were sent to Epigenetics Services Active Motif, Inc. (Carlsband, CA) to perform the ATAC-seq assay. Cells were thawed in a 37°C water bath, pelleted, washed with cold PBS, and tagmented. In details, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit. Tagmented DNA was then purified using the MinElute PCR purification kit, amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads. Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms, and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina). RNA-seq: 2.5 x 10^5 parental MCA205 cells and their IFN-CSC counterparts were harvested, washed and cryopreserved in 1,5 mL eppendorf microtubes. As above, RNA-seq analysis was performed by Epigenetics Services Active Motif, Inc. Total RNA was isolated from cells by using the RNeasy Mini Kit. For each sample, 2 µg of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit.
Analysis of ATAC-seq data was performed as follows. Reads were aligned to the mouse genome (mm10) using the BWA algorithm. Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality ≥1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations. A peak re-calling strategy was used to reduce false positives. Analysis of RNA-seq: libraries were sequenced on Illumina NextSeq 500 as paired-end 42-nt reads. Sequence reads were analyzed with the STAR alignment – DESeq2, edgeR, limma-voom software pipelines. Analysis of CHIP-seq: reads were aligned to the mouse genome (mm10) using the BWA algorithm. Duplicate reads were removed. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm.

treatment_protocol: To induce putative-CSCs (CD44H and CD44L IFN-CSCs), 1 x 10^5 MCA205 PARENTAL cells were cultured in 6-well plates in 2 mL of growth medium and treated 72h with purified mouse IFN-α/β (6000 U/mL)

value: sarcoma cancer cells

tag: cd44 status

value: CD44 HIGH

value: Non-GMO. MCA-205 was derived from 3-methylcholanthrene-induced fibrosarcoma in C57BL/6 mice

value: PARENTAL


title: HHP87Y

status: Public on Jun 29 2022

first: Qiang

last: Ma

address: Datun Road, #15

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to macaca mulatta (release 95) pre-mRNA genome and GRCh38 pre-mRNA genome by Cell Ranger count(v3.0.2)
Alignment results of macaque data and human data were separately aggragated by Cell Ranger aggr(v3.0.2).
Aggragated data of macaque and human were separately read into scanpy.
Assembly: macaca mulatta release 95
Assembly: GRCh38
Supplementary files format and content: The file MHP_year4_11_23_raw.h5ad is formatted by h5ad (created by scanpy) and contains 3 macaque samples; the file HHP_gene_expression _matrix.txt is a tab-separated contains  4 human samples.

source_name: human hippocampus

extract_protocol:
hippocampal formation samples were homogenized in nuclei lysis buffer, isolated nuclei were loaded on 10X Genomics system.
Chromium Single Cell 3' Reagent Kits v3

value: 87 years old


title: CHIP-seq CD44 HIGH rep 1

tag: cell type


title: ATAC-seq MCA Kdm1bOVER

description: in vitro engineered with LVs to overexpress Kdm1b

value: Kdm1b overexpression


title: HHP85Y

value: 85 years old


title: ATAC-seq MCA Kdm1bKD

description: in vitro engineered with LVs to silence Kdm1b

value: Kdm1b knockdown


title: MDA-MB-231_Bottom5_HiC

city: Knoxville

first: Rachel

middle: Patton

last: McCord

address: 309 Mossman Bldg. 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee

description: collection method: HiC libraries prepared as described in Golloshi et al. (2018)

data_processing:
Data Pipeline: cMapping
Sequenced reads were mapped to the hg19 genome using bowtie2
For A375 clones, mapping, filtering, iterative correction, and binning were performed using the Hi-C pro pipeline available at: https://github.com/nservant/HiC-Pro
For MDA-MB-231 subpopulations, filtering, iterative correction, and binning were performed using the method described by Imakaev et al. and implemented in the cMapping package on GitHub (https://github.com/dekkerlab/cMapping)
All processed Hi-C contact maps were scaled to a sum of 1 million
Assembly: hg19
Supplementary files format and content: Each .tar.gz file contains the iteratively corrected and raw matrix.gz files for 20 kb, 40 kb, 100 kb, 250 kb, 1 Mb, and 2.5 Mb in their respective directories.  Bin size indicated as “C-40000” for example.  All matrices are for individual chromosomes except for the 1 Mb and 2.5 Mb bin size

source_name: Breast cancer (MDA-MB-231)

growth_protocol: Melanoma Clones (A375)  and Breast Cancer (MDA-MB-231) cells were grown to confluency under normal conditions. For the transwell experiments, 100000 cells suspended in media with no supplements were pippetted into the transwell and incubated for a 24 hr period. After incubation, migration efficiency was measured and highly migratory (Bottom) and non-migratory (Top) were isolated and grown until confluency. This experiment was repeated in tranwells with 5μm pore sizes for 10 rounds.

extract_protocol:
5 million cells of each Clonal condition were processed using the Arima-HiC+ Kit (Mammalian Cell Lines A160134v01) protocol. 5 MDA-MB-231 subpopulation cells were fixed with 1% formaldehyde, suspended in cell lysis buffer for permeabilization, and homogenized by douncing.
Biotinylated DNA was pulled down using streptavidin coated magnetic beads and prepared for multiplex sequencing on an Illumina platform using the NEBNext Ultra II kit (NEB). All end preparation, adaptor ligation, and PCR amplification steps were carried out on bead bound DNA libraries.

treatment_protocol: A375 Clonal and MDA-MB-231 subpopulations were grown to confluency and were crosslinked with 1% formaldehyde for subsequent Hi-C experiments

value: Breast cancer

tag: condition

value: Bottom  10 rounds - 5um

tag: media

value: DMEM, 10%FBS


title: MDA-MB-231_Control_HiC

value: Control


title: MDA-MB-231_Top5_HiC

value: Top  10 rounds - 5um


title: A375_Clone4_Bottom5_HiC

description: collection method: Arima-HiC+ Kit (Mammalian Cell Lines A160134v01)

data_processing:
Data Pipeline: HiCPro
Sequenced reads were mapped to the hg19 genome using bowtie2
For A375 clones, mapping, filtering, iterative correction, and binning were performed using the Hi-C pro pipeline available at: https://github.com/nservant/HiC-Pro
For MDA-MB-231 subpopulations, filtering, iterative correction, and binning were performed using the method described by Imakaev et al. and implemented in the cMapping package on GitHub (https://github.com/dekkerlab/cMapping)
All processed Hi-C contact maps were scaled to a sum of 1 million
Assembly: hg19
Supplementary files format and content: Each .tar.gz file contains the iteratively corrected and raw matrix.gz files for 20 kb, 40 kb, 100 kb, 250 kb, 1 Mb, and 2.5 Mb in their respective directories.  Bin size indicated as “C-40000” for example.  All matrices are for individual chromosomes except for the 1 Mb and 2.5 Mb bin size

source_name: Melanoma (A375)

value: Melanoma


title: A375_Clone4_Top5_HiC


title: A375_Clone3_Top5_HiC


title: A375_Clone3_Bottom5_HiC


title: v3.Line551_IFNg

value: Lymphoblastoid

value: Interferon Gamma


title: A375_Clone4_Control_HiC


title: A375_Clone3_Control_HiC


title: A375_Clone2_Bottom5_HiC

value: Bottom 10 rounds - 5um


title: A375_Clone1_Bottom5_HiC

value: Bottom 10 rounds- 5um


title: A375_Clone2_Top5_HiC


title: A375_Clone1_Control_HiC


title: v2.Line551_TUNIC

value: Tunicamycin


title: H9

status: Public on Jun 28 2022

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

description: 10x Genomics

data_processing:
Data were analyzed using Cell Ranger™ v2.0.2 pipeline which is available on the 10x Genomics website.
Assembly: mm10
Supplementary files format and content: tar.gz; gene barcode matrices and feature barcode matrix
Supplementary files format and content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis

source_name: brain

extract_protocol:
Blood was thoroughly removed by transcardial perfusion with PBS containing heparin. Brains including optic nerves, leptomeninges and choroid plexus were dissected, collected in ice‐cold PBS and cut into small pieces. Tissue was digested in 1 ml of Accutase (Merck Millipore) per brain at 37 °C for 30 min and triturated through 100-μm cell strainers, which were rinsed with 10% FCS in PBS. Cells were purified by a linear 40% Percoll (GE Healthcare) centrifugation step at 650 g without brakes for 25 min and the myelin top layer and supernatant were discarded. Mononuclear cells were resuspended in fluorescence-activated cell sorting buffer (1% BSA and 0.1% sodium azide in PBS) and isolated cells were counted for each brain. For scRNA-seq, cells from the brains of 5 adult (12-month-old), 4 aged (24-month-old), and 4 PLPmut (12-month-old) mice were pooled into 3 separate samples. Viable cells were identified by LIVE/DEAD stain (catalog no. L34965; Thermo Fisher Scientific), Fc receptors were blocked for 15 min with rat anti‐CD16/32 (1:100, catalog no. 553141; BD Biosciences) and cells were washed and labeled with the following antibodies for 30 min at 4 °C: rat anti-CD8 APC (1:100, catalog no. 553035; BD Biosciences); rat anti-CD45 PE (1:100, BioLegend 103105). Cells were washed twice, single viable cells were gated and CD45highCD8+ cells were collected using a FACSAria III and corresponding software (FACSDiva, v.6; BD Biosciences). Around 15,000 CD45highCD8+ single cells  were sorted per sample before being encapsulated into droplets with the Chromium Controller (10x Genomics) and processed according to the manufacturer’s specifications.
Complementary DNA libraries ready for sequencing on Illumina platforms were generated using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10x Genomics) according to the detailed protocol provided by the manufacturer. Libraries were quantified by Qubit 3.0 Fluorometer (Thermo Fisher Scientific) and quality was checked using a 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent Technologies).

value: CD8+ T cells

tag: tissue

value: brain

value: PLPmut

tag: age


title: A375_Clone1_Top5_HiC

value: Top 10 rounds - 5um


title: STAR, STA, REP3

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

description:
STAR_vs_GLU_STA.xlsx
STAR_EXP_vs_STAR_STA.xlsx
star_STA - 18

data_processing:
RNA sequencing was performed using an Illumina HiSeq2500 (50bp single-end reads; >10 million reads per sample) by GeneWiz.
The FASTQ files were uploaded to the GALAXY web-based platform for analysis. Aligments of the reads against the C. japonicus genome was perfomed using the HISAT2 and the transcript quantification was performed with HTSeq.
These counts were then used to generate the differential expression analyses using DESeq2.
Assembly: GCA_000019225.1
Supplementary files format and content: Excel Sheet (The following parameters were calculated: base mean, log2 (fold change), standard error of the log2(fold change), and a Benjamini-Hochberg adjusted p-value).

organism: Cellvibrio japonicus

source_name: bacterial cell

growth_protocol: MOPS defined medium

extract_protocol:
Standard extraction protocols
Standard Illumina protocols

treatment_protocol: 95%EtOH:5%Phenol to stop cellular metabolism

value: bacterial cell

tag: strain

tag: genotype

value: WT

value: starch (STAR)

tag: phase

value: Stationary phase (STA)


title: STAR, EXP, REP3

description:
STAR_vs_GLU_EXP.xlsx
STAR_EXP_vs_STAR_STA.xlsx
star_LOG - 15

value: Exponential growth (EXP)


title: STAR, STA, REP1

description:
STAR_vs_GLU_STA.xlsx
STAR_EXP_vs_STAR_STA.xlsx
star_STA - 16


title: STAR, EXP, REP2

description:
STAR_vs_GLU_EXP.xlsx
STAR_EXP_vs_STAR_STA.xlsx
star_LOG - 14


title: STAR, EXP, REP1

description:
STAR_vs_GLU_EXP.xlsx
STAR_EXP_vs_STAR_STA.xls
star_LOG - 13


title: MAN, STA, REP3

description:
MAN_vs_GLU_STA.xlsx
MAN_EXP_vs_MAN_STA.xlsx
man_STA - 42

value: mannan (MAN)


title: MAN, STA, REP2

description:
MAN_vs_GLU_STA.xlsx
MAN_EXP_vs_MAN_STA.xlsx
man_STA - 41


title: MAN, STA, REP1

description:
MAN_vs_GLU_STA.xlsx
MAN_EXP_vs_MAN_STA.xlsx
man_STA - 40


title: MAN, EXP, REP3

description:
MAN_vs_GLU_EXP.xlsx
MAN_EXP_vs_MAN_STA.xlsx
man_LOG - 39


title: MAN, EXP, REP2

description:
MAN_vs_GLU_EXP.xlsx
MAN_EXP_vs_MAN_STA.xlsx
man_LOG - 38


title: MAN, EXP, REP1

description:
MAN_vs_GLU_EXP.xlsx
MAN_EXP_vs_MAN_STA.xlsx
man_LOG - 37


title: 10x: Jurkat and Raji cDNA

first: Hoang Van

last: Phan

state: Illinois

address: 5640 S Ellis Ave

department: Priztker School of Molecular Engineering

institute: The University of Chicago

description: Prox-seq analysis of Jurkat and Raji cells using 10x pipeline

data_processing:
cDNA sequencing data was aligned using cellranger (v6.1.1). PLA sequencing data was aligned using a custom Java program (https://github.com/tay-lab/Prox-seq) and antibody barcode file Proxseq_probe_barcodes.xlsx to identify the Prox-seq probe barcodes.
Jurkat and Raji count data was analyzed in Python3 and R (v4.2.0). For mRNA data, we removed cells with fewer than 2,000 or more than 100,000 UMIs, and cells with more than 8,000 detected genes. We then removed genes detected in fewer than 10 cells. For PLA product data, we only kept cells with more than 50 or fewer than 10,000 UMIs, and kept PLA products detected in at least 1 cell.
Gene count and PLA product count data were used to cluster the cells in Seurat (v4.1.0)
Assembly: Human GRCh38
Supplementary files format and content: tab-separated text file

source_name: Jurkat and Raji cell lines

growth_protocol: Jurkat and Raji cells are kept in RPMI media with 10% FBS

extract_protocol:
PLA products were extracted from single cells following 10x pipeline
Sequencing library was prepared from PLA products using PCR

value: Human-derived T and B cells

tag: donor type

tag: passages


title: A375_Clone2_Control_HiC

tag: cell line

value: Melanoma

value: Control

value: DMEM, 10%FBS


title: 10x: Jurkat and Raji PLA

library_source: other

molecule: other


title: no Ab CUT&RUN wt mESC day 2.5 line 1

status: Public on Jun 27 2022

city: Parkville

first: Natalia

last: Benetti

state: Victoria

address: 1G Royal Parade

institute: WEHI

description: male

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using Bowtie2 v2.3.4.1 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth and library size using Seqmonk.
FPKM reads were called over defined MACS2 peaks (determined by calling peaks between all H3K27me3 sample libraries and all input (no Ab) libraries) using the features over probes pipeline in Seqmonk
FPKM reads were calculated over genes +/- 10kb using the features over probes pipeline in Seqmonk, then were normalised to the geometric average of FPKM reads over MACS peaks in Microsoft Excel
Differential genome-wide peaks were called using the csaw v1.24.3 package between wt and maternal null samples at each day, as well as between days each for wt and maternal null
Assembly: GRCm38.p6
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_diff_FPKM_over_MACS_peaks.txt: tab-delimited text file containing FPKM reads over defined MACS2 peaks (determined by calling peaks between all H3K27me3 sample libraries and all input (no Ab) libraries)
Supplementary files format and content: benetti_CUT_RUN_diff_FPKM_values_for_probes_over_Hox.txt: tab-delimited text file containing FPKM reads calculated over genes +/- 10kb, and normalised to the geometric average of FPKM reads over MACS peaks (in benetti_H3K27me3_CUT_RUN_diff_FPKM_over_MACS_peaks.txt)
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_d2_wt_vs_matdel.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw at day 2 of differentiation between Smchd1 wildtype and maternal null samples
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_d2.5_wt_vs_matdel.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw at day 2.5 of differentiation between wt and maternal null samples
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_d3_wt_vs_matdel.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw at day 3 of differentiation between Smchd1 wildtype and maternal null samples
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_matdel_d2_vs_d2.5.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw in Smchd1 maternal null samples between days 2 and 2.5 of differentiation
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_matdel_d2_vs_d3.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw in Smchd1 maternal null samples between days 2 and 3 of differentiation
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_matdel_d2.5_vs_d3.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw in Smchd1 maternal null samples between days 2.5 and 3 of differentiation
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_wt_d2_vs_d2.5.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw in Smchd1 wildtype samples between days 2 and 2.5 of differentiation
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_wt_d2_vs_d3.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw in Smchd1 wildtype samples between days 2 and 3 of differentiation
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_wt_d2.5_vs_d3.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw in Smchd1 wildtype samples between days 2.5 and 3 of differentiation
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_2i_wt_vs_matdel.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw ain mESCs grown in 2i + LIF medium between Smchd1 wildtype and maternal null samples.
Library strategy: CUT&RUN

source_name: primary mouse embryonic stem cell line

growth_protocol: mESCs derived, and cultured as described in Jansz et al., Nature Structural Molecular Biology 2018 DOI:10.1038/s41594-018-0111-z

extract_protocol:
CUT&RUN was performed as described in Skene and Henikoff eLife 2017;6:e21856 DOI: 10.7554/eLife.21856 DNA was purified by phenol/chloroform/isoamylalcohol extraction followed by glycogen/ethanol precipitation
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: primary mouse embryonic stem cell line

value: mouse embryonic stem cells in a differentiation time course to neural mesodermal progenitors

value: Smchd1[fl/+] (wild-type)

tag: time

value: day 2.5 differentation

tag: antibody

value: H3K27me3 (Cell Signalling Technologies, C36B11)


title: STAR, STA, REP2

description:
STAR_vs_GLU_STA.xlsx
STAR_EXP_vs_STAR_STA.xlsx
star_STA - 17

tag: treatment


title: H3K27me3 CUT&RUN mat del mESC day 3 line 1 rep 1

description: male

value: Smchd1[del/+] (maternally deleted)

value: day 3 differentation


title: H3K27me3 CUT&RUN mat del mESC day 2 line 2 rep 2

description: male

value: day 2 differentation


title: H3K27me3 CUT&RUN mat del mESC day 2 line 2 rep 1

description: male


title: H3K27me3 CUT&RUN mat del mESC day 3 line 2 rep 2

description: male


title: H3K27me3 CUT&RUN wt mESC day 3 line 2 rep 2

description: male


title: H3K27me3 CUT&RUN mat del mESC day 2.5 line 1 rep 1

description: male


title: no Ab CUT&RUN wt mESC day 3 line 1

description: male


title: H3K27me3 CUT&RUN mat del mESC day 2.5 line 2 rep 2

description: male


title: H3K27me3 CUT&RUN wt mESC day 3 line 2 rep 1

description: male


title: H3K27me3 CUT&RUN mat del mESC day 3 line 2 rep 1

description: male


title: H3K27me3 CUT&RUN mat del mESC day 2 line 1 rep 1

description: male


title: H3K27me3 CUT&RUN wt mESC day 3 line 1 rep 2

description: male


title: H3K27me3 CUT&RUN wt mESC day 3 line 1 rep 1

description: male


title: H3K27me3 CUT&RUN wt mESC day 2.5 line 2 rep 2

description: male


title: H3K27me3 CUT&RUN wt mESC day 2.5 line 2 rep 1

description: male


title: H3K27me3 CUT&RUN wt mESC day 2.5 line 1 rep 1

description: male


title: H3K27me3 CUT&RUN wt mESC day 2 line 2 rep 1

description: male


title: H3K27me3 CUT&RUN wt mESC day 2 line 1 rep 2

description: male


title: H3K27me3 CUT&RUN wt mESC day 2.5 line 1 rep 2

description: male


title: H3K27me3 CUT&RUN wt mESC day 2 line 1 rep 1

description: male


title: no Ab CUT&RUN wt mESC day 2 line 1

description: male


title: H3K27me3 CUT&RUN mat del mESC day 2.5 line 2 rep 1

description: male


title: H3K27me3 CUT&RUN mat del mESC day 2 line 1 rep 2

description: male