title: LK4804-14

description:
SP 300 cycle kit
LK4804-14

source_name: C57BL/6N mouse heart tissue, KO, vehicle treatment

value: Heart

value: KO

value: Vehicle (PBS, Sodium ascorbate)


title: SUM185_wt_dox_short_H3K27ac_ChIP_1

status: Public on Nov 10 2023

type: SRA

city: Boston

first: Daniel

last: Temko

address: 450 Brookline Ave.

country: USA

institute: Dana-Farber Cancer Institute

library_source: genomic

data_processing:
Reads were aligned to hg19 with BWA-mem v0.7.17 (http://bio-bwa.sourceforge.net).
Duplicates were removed using Picard MarkDuplicates v2.18.17 (http://broadinstitute.github.io/picard/), with parameters (REMOVE_DUPLICATES=TRUE, VALIDATION_STRINGENCY=LENIENT).
ChIP-signal was quantified and peaks were called using MACS2 v2.1.2 {Zhang, 2008, PMID:18798982}, with parameters (--SPMR -B --keep-dup=1 --extsize=146 --nomodel, -q 0.05).
Assembly: hg19
Supplementary files format and content: bigwig of signals
Supplementary files format and content: bed files of called peaks

molecule: genomic DNA

organism: Homo sapiens

source_name: breast cancer

growth_protocol: Cells were grown in their respective media prepared per provider's guidelines, at 37 degree C, 5% CO2.

extract_protocol:
Cells were cross-linked in fixing buffer (50 mM HEPES-NaOH (pH 7.5), 100 mM NaCl, 1mM EDTA) containing 1% paraformaldehyde (Electron Microscopy Sciences, 15714) for 10 min at 37 °C. Crosslinking was quenched by adding glycine to a final concentration of 0.125 M. The cells were washed with ice-cold PBS, harvested in PBS. The nuclear fraction was extracted by first resuspending the pellet in 1 ml of lysis buffer (50 mM HEPES-NaOH (pH 8.0), 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min at 4 °C. Cells were pelleted and washed in 1 ml of wash buffer (10 mM Tris-HCL (pH 8.0), 200 mM NaCl, 1 mM EDTA) for 10 min at 4 °C. Cells were then pelleted and resuspended in 1 ml of shearing buffer (10 mM Tris-HCl (pH 8), 1 mM EDTA, 0.1% SDS) and sonicated in a Covaris sonicator. Lysate was centrifuged for 5 min at 14,000 rpm to purify the debris. Then 100 µl of 10% Triton X-100 and 30 µl of 5M NaCl were added. The sample was then incubated with 20 µl of Dynabeads Protein G (LifeTechnologies,10003D) for 1 h at 4 °C. Primary antibodies were added to each tube, and immunoprecipitation (IP) was conducted overnight at 4 °C. Cross-linked complexes were precipitated with Dynabeads Protein G for 2 hr at 4 °C. The beads were then washed in low salt wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C, high salt wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C and LiCl wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C. DNA was eluted in elution buffer (100 mM sodium bicarbonate and 1% SDS). Cross-links were reversed overnight at 65 °C. RNA and protein were digested with 0.2 mg ml−1 RNase A for 30 min at 37 °C followed by 0.2 mg ml−1 Proteinase K for 1 h at 55 °C. DNA was purified with phenol-chloroform extraction and isopropanol precipitation.
ChIP-seq libraries were prepared using xGen DNA EZ Library Prep Kit from (IDT) with xGen™ UDI Primer Pairs according to manufacturers protocol.

treatment_protocol: cells were treated with (dox) or without (no_dox) Doxycyclin to induce TRE promoter gene expression

tag: tissue

value: breast cancer

tag: parental cell_line

tag: cell type

value: tumor cells

value: wild type

tag: condition

value: doxycycline

tag: time point

value: 7 days

tag: antibody

value: anti-H3K27ac (Diagenode, C15410196)


title: LK4804-13

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description:
SP 300 cycle kit
LK4804-13

library_source: transcriptomic

data_processing:
Libraries were sequenced using paired-end 150-bp reads on an Illumina Novaseq 6000.
The FASTQ sequence reads were aligned to the mouse genome GRC m38 using HISAT2 v2.1.0.
Mapped reads were quantified with FeatureCounts v1.6.3 (gencode.vM23.annotation.gtf).
Gene expression analysis was completed in R version 3.6.0 using the limma 3.40.6 package.
Assembly: GRCm38/M23
Supplementary files format and content: raw_counts_gene_based_featureCounts.csv contains raw counts

molecule: total RNA

organism: Mus musculus

growth_protocol: Mice were fed a standard NIH-31 diet.

extract_protocol:
Hearts were excised from mice, weighed, and flash-frozen using liquid nitrogen-chilled clamps. Frozen hearts were ground in to a fine powder in a chilled mortar and pestle. A small aliquot of heart powder was then used to extract RNA using Qiagen's RNeasy RNA extraction kit. Isolated RNA was stored at -80 until ready for sequencing analysis.
The library was constructed using Illumina's Truseq stranded total RNA library prep kit.

treatment_protocol: WT and OGFOD1-KO mice aged 3-5 months were treated with either vehicle (1X PBS and Sodium Ascorbate) or isoproterenol (1X PBS, Sodium Ascorbate, and Isoproterenol) for 2 weeks by osmotic minipump. Hearts were isolated from these mice and RNA was extracted and subjected to RNAsequencing.

tag: strain

tag: diet

tag: genotype

tag: treatment (2_weeks)


title: SUM185_wt_no_dox_short_H3K27ac_ChIP_1

value: no doxycycline


title: TTC642_8 weeks_shPRRX1_3_DOX

data_processing:
Raw RNA-seq reads were aligned to version hg19 of the human genome and gene count and FPKM values were obtained using the VIPER pipeline {Cornwell, 2018, PMID: 29649993}, with parameters (stranded: true, library_type: ‘fr-firststrand’, filter_mirna: true).
Assembly: hg19
Supplementary files format and content: TNBC_Cell_line_PRRX1_LT_KD_RNAseq_Gene_Counts.csv: Counts table
Supplementary files format and content: TNBC_Cell_line_PRRX1_LT_KD_RNAseq_Gene_FPKM.csv: FPKM table

molecule: polyA RNA

source_name: rhabdoid tumor

extract_protocol:
Total RNA was extracted using the Qiagen ALL Prep kit (cat#80204)
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to the manufacturer’s protocols.

treatment_protocol: Cells were treated with 3ug/ml doxycycline to induce shRNA expression

value: rhabdoid tumor

tag: cell line

value: 56 days

tag: shRNA


title: SUM185_wt_no_dox_short_H3K27ac_ChIP_2


title: RNAseq_wt_rep1

city: Los Angeles

first: Oliver

last: Bell

state: California

address: 1450 Biggy St, NRT6510

institute: USC

data_processing:
RNA-seq Data Analysis: Raw paired-end RNA-seq reads were aligned to the mm10 genome using STAR-2.6.1c (Dobin et al., 2013). Overlap of STAR-aligned reads with genes was performed using HTSeq count function (Anders et al., 2015) with stranded=reverse option and the GRCm38 version 94 GTF file. The HTseq count matrix was pre-filtered to exclude genes with a read count below 10. Differential gene expression analysis was performed using DESeq2 (Love et al., 2014) using the “apeglm” method (Zhu et al., 2019) for LFC shrinkage. We applied a threshold of p-adj < 0.05 and fold change > 0.5 or -0.5 for gene expression changes to be considered significant. Visualization of RNA-seq data was performed using custom R scripts and ggplot2. Gene ontology analysis for significantly deregulated genes was performed using custom R scripts and clusterProfiler reference (Wu et al., 2021; Yu et al., 2012).
ChIP-seq Data Analysis: Raw reads were mapped to the custom concatenated mouse (mm10) and spike-in human (hg38) genome sequences using bowtie 2 with “–no-mixed” and “no-discordant” options (Langmead and Salzberg, 2012). Subsequently, low quality reads were filtered using SAMtools (Li et al., 2009), duplicated reads were discarded with the Picard toolkit (http://broadinstitute.github.io/picard/) and only unique mapped reads were retained. For visualization uniquely mapped mouse reads were normalized by random subsampling with samtools using calibration factors calculated from the corresponding hg38 spike-in reads as described previously (Bonhoure et al., 2014; Fursova et al., 2019; Hu et al., 2015). High correlation between replicates was confirmed using multiBamSummary and plotCorrelation functions from deepTools (Ramírez et al., 2016) before merging for visualization and downstream analysis. Genome coverage tracks (bigWig files) were produced with MACS2’ pileup function (Zhang et al., 2008) and heatmaps and profile plots generated with deepTools (Ramírez et al., 2016). Peaks were called on each replicate independently using MACS2 (Zhang et al., 2008). Peaks overlapping with a custom-build blacklist were discarded to remove sequencing artifacts and only peaks called in both replicates were retained for downstream analysis.
Hi-C data analysis: Hi-C data were analyzed using the HiC-Pro (2.11.1) pipeline (Servant et al., 2015). Read mapping to the mm10 genome was performed using bowtie 2 (Langmead and Salzberg, 2012) within the HiC-Pro pipeline. PCR and optical duplicates as well as reads with MAPQ < 30 were removed. Filtered valid HiC contact data was binned and raw and ICE normalized .hic contact matrices were generated. We also produced balanced single and multi-resolution .cool and .mcool cooler files for visualization in HiGlass.
Genome_build: mm10; ChIPcapseq: amended mm9 genome build

source_name: mouse embryonic stem cells

growth_protocol: All mESCs were cultivated without feeders in high-glucose-DMEM (Corning 10-013-CV) supplemented with 13.5% fetal bovine serum (Corning 35-015-CV), 10 mM HEPES pH 7.4 (Corning, 25-060-CI), 2 mM GlutaMAX (Gibco, 35050-061), 1 mM Sodium Pyruvate (Corning 25-000-Cl), 1% Penicillin/Streptomycin (Sigma, P0781), 1X non-essential amino acids (Gibco, 11140-050), 50 mM β-mercaptoethanol (Gibco, 21985-023) and recombinant LIF. Cells were incubated at 37°C and 5% CO 2 and were passaged every 48 hours by trypsinization in 0.25% 1x Trypsin-EDTA (Gibco, 25200-056). In order to reverse of TetR-CBX7 fusion protein binding 1 µg/ml Doxycycline (Sigma, D9891) was added to cell culture medium.

extract_protocol:
RNA-seq: 5 million mESCs were trypsinized and collected by centrifugation. Resulting cell pellets were washed in 1x PBS and resuspended in 1x DNA/RNA protection reagent (Monarch Total RNA Miniprep Kit, NEB). Subsequently, cells were lysed and total RNA extracted following the mammalian cell protocol including optional on-column DNase I treatment. Calibrated ChIP-seq (cChIP) and ChIPCap-seq: 30 million mESCs and HEK293T cells were collected, washed once in 1x PBS and crosslinked for 7 min in 1% formaldehyde. The crosslinking was quenched by addition of 125 mM glycine and incubated on ice. The crosslinked cells were pelleted by centrifugation for 5 min at 1200g at 4 °C. Nuclei were prepared by washes with NP-Rinse buffer 1 (10 mM Tris pH 8.0, 10 mM EDTA pH 8.0, 0.5 mM EGTA, 0.25% Triton X-100) followed by NP-Rinse buffer 2 (10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl). Afterwards, the nuclei were washed twice with shearing buffer (1 mM EDTA pH 8.0, 10 mM Tris-HCl pH 8.0, 0.1% SDS) and subsequently resuspended in 900 µL shearing buffer with added 1× protease inhibitors complete mini (Roche). Chromatin was sheared by sonication in 15 ml Bioruptor tubes (Diagenode, C01020031) with 437.5 mg sonication beads (Diagenode, C03070001) for 6 cycles (1 min on/1 min off) on a Bioruptor Pico sonicator (Diagenode). For each ChIP reaction 4 % HEK293T-derived human spike-in lysate was combined with mESC lysate and incubated in 1x IP buffer (50 mM HEPES/KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS), with following appropriate antibodies at 4 °C o/n a rotating wheel: H3K27me3 (Diagenode, C15410195), RING1B (Cell Signaling, D22F2), PDS5a (Millipore Sigma #SAB2101764), SUZ12 (Cell Signaling D39F6), H2AK119ub (Cell Signaling D27C4), PCGF1 (Abcam ab202395), RAD21 (Abcam ab992), CTCF (Millipore 070729). Antibody-bound chromatin was captured using Dynabeads protein G beads (Thermofisher #10004D) for 4 hours at 4°C. ChIP washes were performed as described previously (Farcas et al., 2012). ChIPs were washed 5x with 1x IP buffer ( 50 mM HEPES/KOH pH 7.5, 300 mM NaCl, I mM EDTA, 1% Triton-X100, 0.1% DOC, 0.1% SDS), or 1.5x IP buffer for H3K27me3 and H2AK119ub, followed by 3x washes with DOC buffer (10 mM Tris pH 8, 0.25 mM LiCl, 1 mM EDTA, 0.5% NP40, 0.5% DOC) and 1x with TE/50 mM NaCl. ChIP DNA was eluted 2x in elution buffer (1% SDS, 0.1 M NaHCO3 ) at 65°C for 20 min, RNase A treated for 30 min at 37 °C, Proteinase K treated for 3 hrs at 55 °C and crosslinks were reversed o/n at 65 °C. The following day, ChIP samples and corresponding inputs were puriﬁed by PCI extraction and DNA precipitation. In Situ Hi-C: Hi-C was performed as previously described (Rao et al., 2014) with modifications described in (Boyle et al., 2020) as following: 5 million mESCs were crosslinked in 1% formaldehyde for 10 mins before the reaction was quenched by adding 0.2 M final glycine. Cells were permeabilized in lysis buffer (0.2% IGEPAL, 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 1x Halt Protease inhibitor cocktail) and nuclei isolated in NEBuffer 3 supplemented by 0.3% SDS at 62 °C for 10 min. SDS was quenched with 1% Triton X100 at 37°C for 60 min, the nuclei pelleted and resuspended in 250 µl of 1x DpnII buffer with 600 U DpnII (NEB). Following o/n digestion at 37°C, 200 U were added for 2 hrs. DpnII was inactivated for 20 min at 65°C before the DNA ends were filled-in and biotinmarked using Klenow, d(C/G/T)TPs and biotin-14-dATP for 90 min at 37°C. Proximity ligation was performed using T4 DNA ligase (NEB) for 4 hrs at room temperature. Subsequently, nuclei were spun down, resuspended in 200 µl mQ water and digested with proteinase K for 30 min at 55°C in presence of 1% SDS. For crosslink reversal 1.85 M final NaCl was added and samples incubated at 65°C o/n. The next day, sample DNA was ethanol precipitated and sheared in 500 µL sonication buffer (50 mM Tris pH 8.0, 0.1% SDS, 10 mM EDTA) on a Bioruptor Pico sonicator (Diagenode). DNA was then concentrated on Amicon ultra 0.5 30K ﬁlter units (Millipore), biotin-pulldown performed using MyOne Streptavidin T1 beads (Life technologies, 65602) and used for NGS library preparation.
RNA-seq: For RNA-seq library preparation, 1 µg of total RNA per sample was enriched for poly-A using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and final RNA-seq libraries generated using the NEBNext Ultra II Directional RNA Library Prep kit (NEB, E7760 and NEBNext Multiplex Oligos (NEB, E7335/E7500). cChIP-seq and ChIPCap-seq library preparation: Libraries were prepared using the NEXTflex ChIP-Seq kit (Bio Scientific) following the “No size-selection cleanup” protocol. Libraries were purified using Agencourt AMPure XP (Beckman Coulter) and amplified using the KAPA Real-Time Library Amplification Kit (KAPABiosystems) following the manufacturer’s instructions. ChIPCap-seq libraries were prepared identically to ChIP-seq libraries. After PCR amplification the libraries were enriched for loci of interest using the MYbaits kit DNA capture target enrichment system (Arbor Biosciences) according to manufacturer’s manual. 120 nucleotides long MYbaits sequence capture probes (Arbor Biosciences) were custom designed against 25 mm9 genomic loci (Table S3). Library quality control including determination of average size and concentration was performed prior to sequencing by commercial Next Generation Sequencing providers. NGS libaries were eventually sequenced as 150 bp paired-end reads on the Illumina HiSeq platform. In situ HiC: DNA ends were repaired, biotin removed from unligated ends and NEXTFLEX DNA barcoded adapters (Perkin Elmer) were ligated. Desired PCR cycle numbers were determined in test endpoint PCRs using Q5 DNA polymerase (NEB M0491L). Final HiC libraries were generated from 4-6 individual PCR reactions, which were pooled and subjected to cleanup and size-selection using AMPure beads (Beckman Coulter A63882). Samples were ﬁrst test sequenced to check library quality before selected Hi-C ibraries were sequenced at greater depth (Table S2).
NGS libaries were eventually sequenced as 50 bp single-end reads or 150 bp paired-end reads on Illumina platforms

value: embryonic stem cells


title: OTI_Ctrl_Veh_Rest_rep1

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

description:
replicate 1
5894_9_OT-I_Ctrl-1_Veh_Rest_rep1_ATGTCAG_S13_R1_001

data_processing:
Sequence samples were mapped to the mouse genome (GRCm38) using STAR(2.6.0c) using 2-pass mapping with default settings. Sequence reads were counted using HTSeq-count.
Genome_build: mm10
Supplementary_files_format_and_content: Un-processed read count data

source_name: Mouse T-cells

growth_protocol: B16F10 were maintained in DMEM/10%FCS/Penicillin (100U/mL)/Streptomycin (100ug/mL)/Puromycin (1ug/mL) and passaged 1:10 every two days. T cells were maintained in RPMI/10%FCS/Penicillin (100U/mL)/Streptomycin (100ug/mL) with IL-2 (10ng/mL), IL-7 (0.5ng/mL), IL-15 (1ng/mL), betamercaptoethanol (50uM) and puromycin (4ug/mL) and passaged every day at a density of 1*10^6/mL.

extract_protocol:
RNA was extracted using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For drug treatment, DMSO or thapsigargin (50ng/mL) was added to the culture where indicated. For activation, a 24-well non-tissue-culture-treated plate was coated with anti-CD3 antibodies overnight and on the day of the experiment, cells were seeded on this plate at a density of 1*10^6/mL where indicated.

value: OT-I/Cas9 CD8 T cells

value: Ctrl

tag: activation?

value: Resting

tag: treatment

value: DMSO


title: B16_Ccdc_TG_rep2

description:
replicate 2
5894_8_B16_Ccdc_TG_rep2_AGTTCCG_S23_R1_001

source_name: murine melanoma

value: Ccdc101 KO

value: Thapsigargin


title: OTI_Ctrl_Veh_Rest_rep2

description:
replicate 2
5894_10_OT-I_Ctrl-1_Veh_Rest_rep2_CCGTCCC_S15_R1_001


title: B16_Ccdc_TG_rep1

description:
replicate 1
5894_7_B16_Ccdc_TG_rep1_AGTCAAC_S22_R1_001


title: TTC642_8 weeks_shPRRX1_3_no_DOX


title: LK4804-12

description:
SP 300 cycle kit
LK4804-12

value: Heart

value: KO

value: Vehicle (PBS, Sodium ascorbate)


title: LK4804-11

description:
SP 300 cycle kit
LK4804-11

source_name: C57BL/6N mouse heart tissue, KO, isoproterenol treatment

value: Vehicle (PBS, Sodium ascorbate, isoproterenol)


title: RNAseq_wt_rep2


title: RNAseq_Pds5a_KO_rep1


title: DL1, Pp2A-29B dsRNA, Rep C

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (version 0.39, parameters: PE -threads 3 -phred33 TruSeq3PE-2.fa:2:30:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30)
Trimmed sequence reads were mapped to dm6/BDGP6.22 using (version 2.1.0, parameters: --no-softclip --score-min L,-16,0 --mp 7,7 --rfg 0,7 --rdg 0,7 --dta -k 1 --max-seeds 20)
Read count extraction were performed using featureCounts in a strand-specific manner based on the Ensembl D. melanogaster gene annotation (BDGP6.22.96) (version 2.0.1, parameters: -s 2 -p --fraction -O -T 16 -t exon -g gene_id)
Assembly: dm6
Supplementary files format and content: tab-delimited text file include gene read counts for samples

organism: Drosophila melanogaster

growth_protocol: Drosophila DL1 cells were cultured at 25°C in Schneider’s Drosophila medium (Thermo Fisher Scientific 21720024), supplemented with 10% (v/v) fetal bovine serum (HyClone SH30396.03), 1% (v/v) penicillin-streptomycin (Thermo Fisher Scientific 15140122), and 1% (v/v) L-glutamine (Thermo Fisher Scientific 35050061).

extract_protocol:
Total RNA was isolated using TRIzol (Thermo Fisher Scientific 15596018) according to the manufacturer’s instructions.
Illumina strand-specific RNA-seq with rRNA depletion performed by Genewiz.

treatment_protocol: To determine the effect of Integrator/PP2A subunit down-regulation on the endogenous transcriptome, 5 x 10^5 DL1 cells were bathed in 2 microgram of dsRNAs in 12-well plates in 0.5 mL Schneider’s Drosophila medium without FBS, penicillin/streptomycin, or L-glutamine. After incubating cells at 25°C for 45 min, 1 mL of complete Drosophila medium was added and cells were grown at 25°C for 3 d.

value: Pp2A-29B depletion


title: DL1, Mts dsRNA, Rep C

value: Mts depletion


title: LK4804-9

description:
SP 300 cycle kit
LK4804-9


title: B16_Ccdc_Veh_rep2

description:
replicate 2
5894_6_B16_Ccdc_Veh_rep2_CTTGTAA_S19_R1_001


title: TTC642_8 weeks_shPRRX1_1_no_DOX

value: tumor cells


title: B16_Ccdc_Veh_rep1

description:
replicate 1
5894_5_B16_Ccdc_Veh_rep1_CAGATCA_S21_R1_001


title: RNAseq_Pds5a_KO_rep2


title: LK4804-15

description:
SP 300 cycle kit
LK4804-15

source_name: C57BL/6N mouse heart tissue, WT, isoproterenol treatment

value: WT


title: LK4804-8

description:
SP 300 cycle kit
LK4804-8


title: DL1, IntS4 dsRNA, Rep C

value: IntS4 depletion


title: TTC642_8 weeks_nt_control_DOX

value: rhabdoid tumor

value: 56 days

value: non-targeting control

value: doxycycline


title: B16_Ctrl_TG_rep2

description:
replicate 2
5894_4_B16_Ctrl_TG_rep2_GCCAATA_S20_R1_001

value: Ctrl


title: LK4804-10

description:
SP 300 cycle kit
LK4804-10


title: LK4804-7

description:
SP 300 cycle kit
LK4804-7


title: DL1, B-gal dsRNA, Rep C


title: TTC642_8 weeks_nt_control_no_DOX

value: no doxycycline


title: B16_Ctrl_TG_rep1

description:
replicate 1
5894_3_B16_Ctrl_TG_rep1_ACAGTGA_S16_R1_001


title: B16_Ctrl_Veh_rep2

description:
replicate 2
5894_2_B16_Ctrl_Veh_rep2_TGACCAA_S17_R1_001

value: DMSO


title: TTC642_4 weeks_shPRRX1_3_DOX

value: 28 days


title: DL1, Mock, Rep C


title: B16_Ctrl_Veh_rep1

description:
replicate 1
5894_1_B16_Ctrl_Veh_rep1_CGATGTA_S14_R1_001


title: TTC642_8 weeks_shPRRX1_1_DOX


title: DL1, Pp2A-29B dsRNA, Rep B


title: LK4804-6

description:
SP 300 cycle kit
LK4804-6

value: Heart


title: LK4804-4

description:
SP 300 cycle kit
LK4804-4

source_name: C57BL/6N mouse heart tissue, WT, vehicle treatment


title: TTC642_4 weeks_shPRRX1_1_DOX


title: TTC642_4 weeks_shPRRX1_3_no_DOX


title: DL1, IntS6 dsRNA, Rep C

value: IntS6 depletion


title: TTC642_4 weeks_shPRRX1_1_no_DOX


title: Input

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

data_processing:
Data analysis was carried out using the web tool https://usegalaxy.org/. Briefly, Bowtie2 [http://bowtie-bio.sourceforge.net/] was used for fastq files alignments and, for peak detection, MACS software [http://liulab.dfci.harvard.edu/MACS/] with default parameters. The Integrative Genomics Viewer (IGV) [http://www.broadinstitute.org/igv] was used for a graphic illustration of ChIP-Seq peaks and ENCODE data (http://genome.ucsc.edu/ENCODE/) for information on chromatin organization. Raw data files from ChIP-seq assays were aligned to the GRCh38 reference genome with Bowtie2. MACS2 software was used for peak detection, with a q-value cutoff of 0.05. Peaks were annotated and merged with the annotatePeaks.pl and mergepeaks.pl functions, available within the HOMER software.
Assembly: GRCh38
Supplementary files format and content: bedgraph files

source_name: human dermal fibroblasts (HDFs)

extract_protocol:
Primary human dermal fibroblasts overexpressing ANKRD1 were previously cross-linked for protein-protein interactions with ethylene glycol bis succinimidyl succinate (EGS) at a final concentration of 1.5mM for 30 minutes. Formaldehyde was added to a final concentration of 1% for 10 min at RT. The reaction was quenched using the addition of glycine (final concentration 125 mM). Cells were washed with ice-cold PBS and collected by centrifugation. Next, cells  were lysed using the iDeal ChIP-seq kit (DIAGENODE) for Transcription Factors according to the manufacturer’s instructions DNA in the cross-linked chromatin was fragmented by sonication to 100-500 bp range using Diagenode Bioraptor. Samples were precleared using the beads included in the kit and incubated overnight at 4°C with 5 ug of commercially available V5 tag antibody from GENETEX targeting the V5 tag in ANKRD1 over-expressing fibroblasts. Incubations of parallel samples performed Non-immune controls with non-immune IgG. Antibody–chromatin complexes were pulled down using protein A- beads from the kit (DIAmag protein A-coated magnetic beads, DIAGENODE). Elution proceeded according to the manufacturer’s instructions. Chromatin was quantified using the Qubit Fluorometric Quantification Kit (Thermo Fisher Scientific).
ChIP-Seq library preparation and data analysis: as recommended by the manufacturer, a total of 10 ng of ChIPed DNA was used for library preparation using NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina. Sequencing was carried out at the Lausanne Genomic Technologies Facility (GTF) using the HiSeq 4000.

tag: chip antibody


title: DL1, Mts dsRNA, Rep B


title: LK4804-3

description:
SP 300 cycle kit
LK4804-3


title: DL1, IntS6 dsRNA, Rep B


title: TTC642_4 weeks_nt_control_DOX


title: LK4804-2

description:
SP 300 cycle kit
LK4804-2

value: Vehicle (PBS, Sodium ascorbate)


title: DL1, IntS4 dsRNA, Rep B


title: Anti-ANKRD1 antibody

value: antibody the V5 tag in ANKRD1


title: MitralValve M ctrl CAV901

city: Frederiksberg

first: Peter

last: Karlskov-Mortensen

state: Select One...

address: Grønnegårdsvej 3

department: IVH

country: Denmark

institute: University of Copenhagen

description: MitralValve M ctrl

data_processing:
Quality control using FastQC
Mapping using STAR, reference genome: CanFam4
Feature counting using featureCounts
Annotation file: NCBI-RefSeq CanFam4 annotation + non-overlapping human XenoRefSeq genes
DESeq2 analysis - differential expression
Assembly: CanFam4/UU_Cfam_GSD_1.0
Supplementary files format and content: tab delimited txt file with counts for each feature (rows) for each sample (columns)

organism: Canis lupus familiaris

source_name: Mitral valve

extract_protocol:
Qiagen RNeasy Fibrous Tissue Mini Kit
Libraries were constructed at E-GENE, Shenzhen, China
paired-end 150bp

value: Mitral valve

tag: breed

value: Cavalier King Charles Spaniel


title: LK4804-5

description:
SP 300 cycle kit
LK4804-5

value: KO

value: Vehicle (PBS, Sodium ascorbate, isoproterenol)


title: LK4804-1

description:
SP 300 cycle kit
LK4804-1

value: WT


title: Hs578T_8 weeks_shPRRX1_3_DOX

value: breast cancer

value: tumor cells


title: DL1, Mock, Rep B


title: DL1, B-gal dsRNA, Rep B


title: MitralValve M ctrl CAV865

description: MitralValve M ctrl


title: TTC642_4 weeks_nt_control_no_DOX

value: rhabdoid tumor

value: non-targeting control


title: Midgut, resistant, rep3, IP

city: Beijing

first: Zhaojiang

last: Guo

address: No. 12, Zhongguancun South Street, Haidian District, Beijing 100081; China

department: Department of Plant Protection

institute: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences

description:
NIL_R_IPVSNIL_R_input_peak.txt
NIL_R_3_IP

data_processing:
Reads that contained low-quality bases, adaptor contamination, or undetermined bases were removed using fastp (https://github.com/OpenGene/fastp) with default parameters.
The reads were mapped to the reference genome of P. xylostella deposited in GenBank database (https://www.ncbi.nlm.nih.gov/bioproject/PRJEB34571/) using HISAT2 (http://www.ccb.jhu.edu/software/hisat/).
R package exomePeak (https://bioconductor.org/packages/3.9/bioc/html/exomePeak.html) were used for peak calling
Assembly: GCF_905116875.1
Supplementary files format and content: Tab-delimited text file includs peak calling for each sample

organism: Plutella xylostella

source_name: midgut

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen), and Poly (A) RNA was extracted from 50 μg total RNA with Dynabeads Oligo (dT) 25-61005 (Thermo Fisher Scientific).
The poly (A) RNA was fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). Then, the fragmented RNAs were incubated with the m6A-specific antibody (Synaptic Systems). Then, the precipitated RNA was reverse-transcribed to generate cDNA using the SuperScript II Reverse Transcriptase (Invitrogen), and the obtained cDNA was used to synthesize U-labeled second-stranded DNAs with Escherichia coli DNA, RNase H (New England Biolabs), dUTP Solution (Thermo Fisher Scientific), and polymerase I (New England Biolabs). The indexed adapters were prepared using the blunt ends with an A-base. The A-tailed fragmented DNA was ligated to the adapter with a T-base, and the AMPureXP beads were used to select the size of index adapters. The U-labeled second-stranded DNAs were treated with heat-labile UDG enzyme (New England Biolabs), the ligated fragments were amplified using PCR

value: midgut

tag: phenotype

value: resistant


title: Midgut, resistant, rep3, input

description:
NIL_R_IPVSNIL_R_input_peak.txt
NIL_R_3_input

tag: tissue


title: DL1, Pp2A-29B dsRNA, Rep A

value: Pp2A-29B depletion


title: Hs578T_8 weeks_shPRRX1_3_no_DOX

value: 56 days

value: no doxycycline


title: Midgut, resistant, rep2, IP

description:
NIL_R_IPVSNIL_R_input_peak.txt
NIL_R_2_IP


title: Hs578T_8 weeks_nt_control_DOX

value: doxycycline


title: MitralValve F ctrl CAV748

description: MitralValve F ctrl


title: Midgut, resistant, rep2, input

description:
NIL_R_IPVSNIL_R_input_peak.txt
NIL_R_2_input


title: Hs578T_8 weeks_nt_control_no_DOX


title: DL1, Mts dsRNA, Rep A

value: Mts depletion


title: MitralValve M ctrl CAV749

description: MitralValve M ctrl


title: DL1, IntS4 dsRNA, Rep A

value: IntS4 depletion


title: MitralValve M case CAV648

description: MitralValve M case

value: Mitral valve


title: Midgut, resistant, rep1, IP

description:
NIL_R_IPVSNIL_R_input_peak.txt
NIL_R_1_IP


title: DL1, B-gal dsRNA, Rep A


title: Hs578T_4 weeks_shPRRX1_3_DOX

value: 28 days


title: Midgut, resistant, rep1, input

description:
NIL_R_IPVSNIL_R_input_peak.txt
NIL_R_1_input


title: Hs578T_4 weeks_shPRRX1_3_no_DOX


title: MitralValve M case CAV614

description: MitralValve M case

value: Cavalier King Charles Spaniel


title: MitralValve M case CAV828

description: MitralValve M case


title: MitralValve F ctrl CAV579

description: MitralValve F ctrl


title: Midgut, susceptible, rep3, input

description:
DBM1Ac_S_IPVSDBM5Ac_S_input_peak.txt
DBM1Ac_S_3_input

value: susceptible


title: Hs578T_4 weeks_shPRRX1_1_no_DOX


title: DL1, IntS6 dsRNA, Rep A

value: IntS6 depletion


title: Hs578T_4 weeks_shPRRX1_1_DOX

value: breast cancer


title: MitralValve F ctrl CAV576

description: MitralValve F ctrl


title: MitralValve M ctrl CAV743

description: MitralValve M ctrl


title: DL1, Mock, Rep A

value: WT


title: Hs578T_4 weeks_nt_control_DOX

value: tumor cells


title: Midgut, susceptible, rep1, IP

description:
DBM1Ac_S_IPVSDBM2Ac_S_input_peak.txt
DBM1Ac_S_1_IP


title: DL1 pMtnA IntS6 +24h Cu, Rep C

growth_protocol: Drosophila DL1 cell lines were cultured at 25°C in Schneider’s Drosophila medium (Thermo Fisher Scientific 21720024), supplemented with 10% (v/v) fetal bovine serum (HyClone SH30396.03), 1% (v/v) penicillin-streptomycin (Thermo Fisher Scientific 15140122), and 1% (v/v) L-glutamine (Thermo Fisher Scientific 35050061). To generate DL1 cells stably maintaining the inducible IntS6 or IntS12 transgenes, 2 x 10^6 cells were first plated in complete media in 6-well dishes. After 24 h, 2 micrograms of pMtnA FLAG-IntS6 puro or pMtnA FLAG-IntS12 puro plasmid was transfected using Effectene (Qiagen 301427; 16 microliter Enhancer and 30 microliter Effectene Reagent). On the following day, 5 microg/mL puromycin was added to the media to select and maintain the cell population.

extract_protocol:
Total RNA was isolated using Trizol
Illumina strand-specific RNA-seq with rRNA depletion performed by Genewiz.

treatment_protocol: To determine the effect of Integrator subunit over-expression on the endogenous transcriptome, DL1, DL1 pMtnA IntS6, and DL1 pMtnA IntS12 cells were seeded in 6-well plates (2 x 10^6 cells per well) in 2 mL complete Schneider’s Drosophila medium (with FBS, penicillin/streptomycin, and L-glutamine) and grown for 3 d. As indicated, a final concentration of 500 μM copper sulfate (Fisher BioReagents BP346-500) was added to cells for the last 24 h prior to RNA isolation using TRIzol (Thermo Fisher Scientific 15596018).

value: IntS6 overexpression

value: +24h Cu


title: Midgut, susceptible, rep2, input

description:
DBM1Ac_S_IPVSDBM3Ac_S_input_peak.txt
DBM1Ac_S_2_input

value: midgut


title: MitralValve F ctrl CAV494

description: MitralValve F ctrl


title: Midgut, susceptible, rep2, IP

description:
DBM1Ac_S_IPVSDBM4Ac_S_input_peak.txt
DBM1Ac_S_2_IP


title: Hs578T_4 weeks_nt_control_no_DOX

value: non-targeting control


title: MitralValve M ctrl CAV488

description: MitralValve M ctrl


title: UM-UC-3-DHCR24-3

city: 广东省广州市越秀区

first: jian

middle: cheng

address: 孙逸仙纪念医院沿江西路107号

institute: Sun Yat-sen Memorial Hospital

data_processing:
GSE219211_file.pdf
Supplementary files format and content: count, fpkm

source_name: human bladder cancer UM-UC-3 cells

growth_protocol: The human bladder cancer cell lines UM-UC-3 were purchased from American Type Culture Collection and cultured in an incubator with 5% CO2 at 37℃. UM-UC-3 cells were cultured in RPMI 1640 contained 10% fetal bovine serum.

extract_protocol:
The indicated UM-UC-3 cells were harvested and subjected into extracting the total RNA by TRIZOL (Invitrogen, Carlsbad, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The pcDNA3.1 expression vector with DHCR24 gene were purchased from Genepharma company (Shanghai, China) and used to overexpress the DHCR24 gene in UM-UC-3 cells. The transfections were conducted with assistance of lipofectamine 3000 (Invitrogen, Carlsbad, CA, USA) under manufacturer’s protocols.

value: human bladder cancer UM-UC-3 cells

tag: expression vector

value: transfected with DHCR24 overexpressing plasmids

value: total RNA


title: DL1 pMtnA IntS6, Rep C

value: no Cu treatment


title: MitralValve M case CAV487

description: MitralValve M case


title: Midgut, susceptible, rep3, IP

description:
DBM1Ac_S_IPVSDBM6Ac_S_input_peak.txt
DBM1Ac_S_3_IP


title: UM-UC-3-DHCR24-2

address: 孙逸仙纪念医院沿江西路107号


title: Midgut, susceptible, rep1, input

description:
DBM1Ac_S_IPVSDBM1Ac_S_input_peak.txt
DBM1Ac_S_1_input


title: MitralValve F ctrl CAV447

description: MitralValve F ctrl


title: UM-UC-3-DHCR24-1

address: 孙逸仙纪念医院沿江西路107号


title: DL1 pMtnA IntS12 +24h Cu, Rep C

value: IntS12 overexpression


title: MitralValve M ctrl CAV444

description: MitralValve M ctrl

value: Mitral valve


title: DL1 pMtnA IntS12, Rep C


title: DL1, Rep C


title: SD-HFD-rep3

type: RNA

city: Chicago

first: Monica

last: Lee

address: 835 S Wolcott

institute: University of Illinois at Chicago

hyb_protocol: Gene expression profiling was performed using NanoString PanCancer Immune Profile Mouse and nCounter instrument (Yale University) according to the manufacturer’s instructions.

scan_protocol: Standard protocol

data_processing: NanoString data were normalized based on NanoString housekeeping probes using the nCounter Advanced Analysis Software. Normalized expression counts were extracted from the NanoString nSolver software for further data analyses using Qlucore Omics Explorer® (Version 3.8). Samples were log2 transformed in Qlucore and assigned into their respective groups. Best clustering of the samples was achieved with multi-group (ANOVA) comparison of all 4 groups at a p-value ≤ 0.05 (corresponding q-value ≤ 0.125). No fold change cutoffs imposed given the limited number of input probes. Differential gene expression and pathway enrichment were considered significant with an adjusted p-value of ≤0.05.

source_name: aorta, S1176D, HFD

label_protocol: Unlabeled total mouse aorta tissue. RNA quality assessed via spectrophotometric  readings (A260/280 ratio ~2.0). No further label/purification step necessary.

extract_protocol: RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: eNOS S1176A ‘loss-of-function’ and eNOS S1176D ‘gain-of-function’ mice (Akt1;ApoE double knockout background) were maintained on a standard laboratory diet. At ~8wks of age, mice were fed either a standard laboratory diet or a high-fat, high-cholesterol Western Diet for 4weeks. Aortas were processed for mRNA collection.

tag: gender

value: male

tag: diet type

value: Western Diet 4wks


title: MitralValve M case CAV373

description: MitralValve M case

value: Cavalier King Charles Spaniel


title: DL1 pMtnA IntS12 +24h Cu, Rep B


title: UM-UC-3-Vector-3

address: 孙逸仙纪念医院沿江西路107号

value: transfected with Vector plasmids


title: MitralValve M ctrl CAV285

description: MitralValve M ctrl


title: UM-UC-3-Vector-2

address: 孙逸仙纪念医院沿江西路107号


title: MitralValve M case CAV2156

description: MitralValve M case


title: UM-UC-3-Vector-1

address: 孙逸仙纪念医院沿江西路107号


title: SD-HFD-rep2


title: DL1 pMtnA IntS6 +24h Cu, Rep B


title: DL1 +24h Cu, Rep C


title: DL1 pMtnA IntS6, Rep B


title: MitralValve M case CAV2102

description: MitralValve M case


title: SD-CHOW-rep3

source_name: aorta, S1176D, chow

value: Standard Chow


title: DL1 +24h Cu, Rep B

value: WT


title: SD-HFD-rep1


title: MitralValve M ctrl CAV1939

description: MitralValve M ctrl


title: FEZ1-null hESC cerebral organoid [FKO1-D60]

city: Singapore

first: John Chua

last: Jia En

address: 28 Medical Dr

department: Centre for Life Sciences

country: Singapore

institute: National University of Singapore

data_processing:
Clean reads were aligned to the reference human genome (hg19) by using STAR with default parameters.
The gene expression quantification was done by using HTSeq-count in strand-specific mode with "-s reverse" option and read counts only from the sense strand were used for each gene.
Differential gene expression analysis was performed by using DESeq2. The genes that did not express or in low expression (read counts less than 2 on average per sample) were removed from the analysis. After correction for multiple hypothesis testing (adjusted p value (Padj) < 0.05, using Benjamini- Hochberg method), 87 and 439 genes were identified with significant up- and down-regulation in the FEZ1-null group when compared to WT group. We identified differentially expressed genes by focusing on a subset of the samples ("contrast" parameter) to examine early development changes, i.e. only considering Day 10 FEZ1-KO vs corresponding controls, and excluded Day 60 samples from further analysis.
We further narrowed down the significant expressed genes by applying expression fold change (log2 KO/WT) cut off at +/- 1 as differentially expressed genes (DEGs, 42 and 383 genes were identified with significant up and down-regulation in the FEZ1-null group when compared to WT group) for the subsequent analysis, including Gene Ontology (GO) and pathway enrichment analysis by Metascape and disease related gene enrichment analysis by Enrichr.
Assembly: hg19
Supplementary files format and content: A spreadsheet including row counts, normalized counts and DESeq2 full output table for Differential Expression analysis FEZ1-null group compared to WT group

extract_protocol:
RNAs were harvested with the TRIzol™ reagent.
RNA libraries for RNA-seq were prepared by Novogene (Singapore).

tag: cell type

value: hESC (human embryonic stem cell)

value: Day 60


title: DL1, Rep B


title: wildtype hESC cerebral organoid [WT2-D60]

value: Wildtype


title: SD-CHOW-rep2


title: SD-CHOW-rep1


title: MitralValve F case CAV1876

description: MitralValve F case


title: SA-HFD-rep3

source_name: aorta, S1176A, HFD


title: DL1 pMtnA IntS12, Rep B


title: wildtype hESC cerebral organoid [WT1-D60]


title: DL1 pMtnA IntS12 +24h Cu, Rep A

value: +24h Cu


title: MitralValve F case CAV1872

description: MitralValve F case


title: SA-HFD-rep2


title: FEZ1-null hESC cerebral organoid [FKO2-D60]


title: DL1 pMtnA IntS12, Rep A


title: MitralValve F ctrl CAV1790

description: MitralValve F ctrl


title: FEZ1-null hESC cerebral organoid [FKO3]

value: Day 10


title: DL1 pMtnA IntS6 +24h Cu, Rep A

value: IntS6 overexpression


title: SA-HFD-rep1


title: DL1 pMtnA IntS6, Rep A


title: MitralValve M case CAV1784

description: MitralValve M case


title: wildtype hESC cerebral organoid [WT4]


title: MitralValve F ctrl CAV1732

description: MitralValve F ctrl


title: MitralValve F ctrl CAV1731

description: MitralValve F ctrl


title: SA-CHOW-rep1

source_name: aorta, S1176A, chow


title: DL1 +24h Cu, Rep A


title: FEZ1-null hESC cerebral organoid [FKO2]


title: SA-CHOW-rep2


title: MitralValve F case CAV1519

description: MitralValve F case


title: MitralValve F case CAV1259

description: MitralValve F case


title: Q0990YUC4_3_1

city: qingdao

first: Ting

middle: Ting

last: Ding

address: binhai street  NO.72

institute: shandong university

data_processing:
The RNA was purified by electrophoresis through a TBE_urea polyacrylamide gel. The gel regions harboring 18_30 nt fragments were excised and the RNA recovered. The resulting population of sRNAs was 5' and 3' RNA adapter_ligated using T4 RNA ligase, and amplified for 18 PCR cycles
The amplicons were purified and sequenced using an Illumina/Solexa Genome Analyzer (Beijing Genomics Institute, Shenzhen, China).
Raw reads were trimmed by removing low_quality and adaptor sequences, then aligned to the A. thaliana genome using SOAP2 software.
Transcript frequency was calculated using the reads per kilobase per million reads method. Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the P value and the false discovery rate (FDR) (Audic and Claverie, 1997).
Supplementary_files_format_and_content: fpkm

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: The seedlings grew on 1/2 MS for 5 days, the root of the seedlings were extracted for RNA sequencing.

extract_protocol:
Root were cut, flash frozen on liquid nitrogen, and total RNA was isolated using a RNeasy Mini Kit (TIANGEN Biotech).
First strand cDNA was generated using reverse transcriptase and random primers. The constructed cDNA libraries was qualified and quantified with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real_Time PCR System, and then sequenced via Illumina HiSeqTM 2000 or other sequencer when necessary at the Beijing Genomics Institute, Shenzhen, China.

tag: seedling age

value: Roots


title: Q0990YUC4_2_1


title: wildtype hESC cerebral organoid [WT2]


title: wildtype hESC cerebral organoid [WT3]


title: FEZ1-null hESC cerebral organoid [FKO4]


title: MitralValve F case CAV1196

description: MitralValve F case


title: FEZ1-null hESC cerebral organoid [FKO1]


title: Q0990YUC4_1_1


title: DL1, Rep A


title: wildtype hESC cerebral organoid [WT1]


title: MitralValve F ctrl CAV1114

description: MitralValve F ctrl


title: J0121YUC4_3


title: MitralValve M case CAV1097

description: MitralValve M case


title: MitralValve M ctrl CAV1049

description: MitralValve M ctrl


title: J0121YUC4_2


title: J0121YUC4_1


title: U937 CROPseq, replicate 2, scRNAseq

city: La Jolla

first: Karina

middle: Ofelia

last: Barbosa Guerra

state: CA

address: 10901 North Torrey Pines Rd, Deshpande Lab RM6210B

department: Tumor Initiation & Maintenance Program

institute: Sanford Burnham Prebys Medical Discovery Institute

description:
10x Genomics
JB_316

library_source: transcriptomic single cell

data_processing:
Cell Ranger Single-Cell Software Suite (v4.0.0; 10x Genomics) was used for sample demultiplexing, alignment, filtering, and UMI counting.
Barcode processing, gene counting and aggregation were made using a custom pipeline (see Methods).
Assembly: Hg38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: JB_BothRepsWgRNAs_processed_cell_by_gene_wgRNA_REAL_genes.txt.gz is a matrix-like object with unnormalized counts with features (genes) as rows and cells as columns. Required to generate a Seurat object (counts argument).
Supplementary files format and content: JB_BothRepsWgRNAs_gRNA_cell_file_wTargetGene.txt is a data frame cell-level metadata to add to the Seurat object. Rows are cell names and columns are gRNA, cell barcodes, target genes and UMI counts. Required to generate a Seurat object (meta.data argument).

source_name: Pleural effusion

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum, 2mM Glutamine and 100 U/ml penicillin/streptomycin.

extract_protocol:
Cells were provided in a single-cell suspension in culture medium to the UC San Diego Center for Epigenomics.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). cDNA was PCR-amplified and purified using SPRIselect Reagent Kit (Beckman Coulter). Sequencing was performed on the Illumina NovaSeq using the S4 200 kit and PE100 run configuration at the University of California San Diego Center for Epigenomics.

treatment_protocol: Cells were transduced at low MOI with a pooled virus containing an equimolar mix of CRISPR sgRNA lentiviral constructs targeting the top epigenetic regulators found in the Epigenetic CRISPR screen, as well as controls (MLLT10, KMT2A, CSNK2A1, KAT7, BRD4, MLLT6, CSNK2B, AFF4, NTC, MLLT3, DOT1L, AFF2, SGF29 and MLLT1).

value: Monocytes

value: Pleural effusion

tag: disease

value: Adult acute monocytic leukemia


title: MitralValve F case CAV1047

description: MitralValve F case

value: Mitral valve


title: 16-shANKRD1-36

hyb_protocol: RNA samples were hybridized to the human Clariom™ D Arrays (Thermo Fisher Scientific). Data  were analyzed using the Transcriptome Analysis Console (TAC) software (Thermo  Fisher Scientific) carried out at the Institute of Genetics and Genomics of Geneva  (iGE3).

scan_protocol: Arrays were scanned on GS300 scanner (Thermo Fisher Scientific) with AGCC Scan Control Software.

data_processing:
the analysis was performed with Transcriptome Analysis Console (TAC) Software (Thermo Fisher Scientific).
Clariom_D_Human.r1.pgf
Clariom_D_Human.na36.hg38.transcript.csv

label: biotin

source_name: CAF

label_protocol: samples were labelled with biotin

extract_protocol: RNA extraction and purification using Direct-zol RNA Miniprep Kit (Zymo  Research). GeneChip® WT PLUS Reagent Kit (Thermo Fisher Scientific) was used.  RNA samples were checked for purity (OD260/OD280 ≥ 1.8, RIN ≥ 8).

value: silencing of ANKRD1


title: 16-shANKRD1-67


title: U937 SGF29 FLAG overexpression, input [WT_F7_input]

data_processing:
Reads were trimmed using Cutadapt to remove Illumina Adaptors.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie2. Only uniquely mapping reads with at most two mismatches were retained.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum, 2mM Glutamine and 100 U/ml penicillin/streptomycin in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were fixed with 1% formaldehyde and chromatin was sheared using a Bioruptor™ (Diagenode Inc, NJ) in 15 cycles (each one in high-setting for 30 s on and 30 s off), at 4°C.  Chromatin was immunoprecipitated using antibodies listed.
Library preparation on eluted DNA was performed using the NEBNext Ultra II DNA library prep kit for Illumina (E7645S and E7600S) as per the manufacturer’s protocol. DNA libraries were sequenced in paired-end 150 bp reads in a NovaSeq600 sequencer (Illumina, San Diego, CA) in Novogene Corporation (Sacramento, CA).

treatment_protocol: U937 cells were transduced with FLAG-tagged SGF29-wild-type or SGF29_D196R mutant overexpression constructs for samples: Mutant_F3_Flag, Mutant_H2_Flag, Mutant_H2_input, WT_F7_input, WT_F7_Flag, WT_G2_Flag. For the remaining samples, U937 cells were transduced with sgRNAs expressing a non-targeting control or targeting SGF29.


title: 3-shANKRD1-67


title: 16-plko

value: control


title: Q2500YUC4_3


title: MitralValve F ctrl CAV1041

description: MitralValve F ctrl

value: Cavalier King Charles Spaniel


title: 3-shANKRD1-36


title: U937 SGF29 D196R FLAG mutant overexpression, input [Mutant_H2_input]


title: eyeRibo_nocteRNAi3

city: Baltimore

first: Weidong

last: Wang

address: 251 Bayview Blvd BRC, Suite 100 Rm10B014

institute: National Institute of Aging

data_processing:
library strategy: Ribo-seq
For RNA-seq of polyA RNA samples, fastq files are mapped to fly dm6 genome by Tophat to get bam flies. The bam files are sorted by samtools.v1.9 sort and index, and then converted to bed format files by bamtools.v1.8 with convert function. Bam files and bed files are used to get bedgraph and raw counts. Raw counts are normalized to get RNA expression levels.
For RNA-seq of total RNA samples, fastq files are mapped to fly dm6 genome by Tophat to get bam flies. The bam files are sorted by samtools.v1.9 sort and index. Sorted bam files are used to generate bigwig graph and get raw counts in CDS regions by Htseq. Raw counts are normalized to get RNA expression levels.
For Ribo-seq fastq files, adaptors are removed by fastx_clipper, ribosomal RNA sequences are removed by bowtie2. Following steps are the same to the analysis of RNA-seq of total RNA samples.

source_name: eye discs

extract_protocol:
RNA was extracted byTRizol following the product manual. For Ribo-seq, total RNA was digested with Mnase S7 and run using 15% TBE-urea gel, followed by cutting the 28 nt RNA fragments.
Library was constructed by standard Illumina protocol. Ribo-seq library was generated by NEBNext® Multiplex Small RNA Library Prep Set for Illumina (E7300S, New England BioLabs).

value: eye discs

value: ey-GAL4, UAS-nocte-RNAi

value: flies maintained at 25oC, eye discs with mouth hooks were dissected from late L3 larvae.

tag: molecule subtype

value: ribosome bound RNA fragments


title: 3-plko


title: Q2500YUC4_1


title: U937 CROPseq, replicate 1, scRNAseq

description:
10x Genomics
JB_315


title: U937 SGF29 D196R FLAG mutant overexpression, Flag antibody, Replicate 2 [Mutant_H2_Flag]

value: Anti-FLAG® M2 beads (Millipore Sigma, Cat. No. M8823)


title: J0571YUC4_3


title: eyeRibo_nocteRNAi2

tag: genotype


title: Q2500YUC4_2


title: U937 SGF29 FLAG overexpression, Flag antibody, Replicate 1 [WT_F7_Flag]


title: U937, SGF29 knockout, input  [SGF_R1_INPUT]


title: U937, non-targeting control, input  [NTC_R1_INPUT]


title: eyeRibo_WT2


title: 2-shANKRD1-36


title: 2-shANKRD1-67


title: J0571YUC4_1


title: 2-plko


title: 1-shANKRD1-67


title: 1-plko


title: 1-shANKRD1-36


title: U937, SGF29 knockout, H2K120Ub1, Replicate 2 [SGFKO2_H2B]

value: Histone H2BK120ub1 (Active Motif, 39623)


title: FEZ1-null hESC cerebral organoid

description: 10x Genomics

data_processing:
The Cell Ranger 3.1.0 pipeline (10x Genomics) was used to align reads from scRNA-seq to the GRCh38 human reference genome and the associated gene by cell count matrix was generated. The default parameters were used except for specifying the expected number of cells ("--expect-cells=10000"). The resulting matrices containing the unique molecular identifier (UMI) counts were merged from WT and FEZ1-null samples into a single object and analyzed by the Seurat R package v.3.1. Cells expressing a range of 1000-8000 genes and less than 20% of mitochondrial genes were retained based on the inspection 376 of feature distributions, and genes expressed in less than 10 cells were filtered out. UMI counts were normalized and variance-stabilized by using "SCTransform" function which employs a regularized negative binomial regression to remove technical differences between cells due to sequencing depth. This step was accompanied by regressing out variation due to proportion of mitochondrial gene expression and identifying top 3000 most variable genes. Principal component analysis (PCA) was performed on the normalized data for the variable genes, and the first 30 principal components were used for clustering. In this PCA space, the cells were clustered by finding the nearest 20 neighbors to each cell (FindNeighbors function with "dims=1:30"), building a Shared Nearest Neighbor (SNN) graph with edges between neighbor cells weighted by the Jaccard index, and performing Louvain algorithm on the resulting graph (FindClusters function with "resolution=0.8"). The clusters of cells were then visualized in two-dimensional space by using t-distributed Stochastic Neighbor Embedding (t-SNE) projection. The resulting 26 clusters were manually merged into 14 clusters and assigned to corresponding cell types based on the expression of known marker genes: vNE/vRG (ventricular neuroepithelium/ radial glia cells ): LIX1, NES, HMGA2, PAX6; Dividing vNE/vRG: MKI67, LIX1, PAX6, ASPM; tRG (truncated radial glia cells): CRYAB, EGR1, HMGA2; HOPX- oRG (HOPX- outer radial glia cells): FABP7, MOXD1, QKI, CLU; HOPX+ oRG (HOPX+ outer radial glia cells): FABP7, CLU, FEZF2, HOPX; Dividing oRG: MIK67, HJURP, FABP7, CLU, FEZF2, HOPX; CP (choroid plexus): TTR, OTX2; IP (intermediate progenitor): EOMES, DCX, BEUROG1; Dividing IP: EOMES, MKI67, BEUROG1; New born neuron: STMN2, DCX; Deep layer neuron: STMN2, NEUROD6, BCL11B; Upper layer neuron: POU3F2, BHLHE22; Interneuron: DLX5, GAD2, DLX1; Pericyte: COL3A1, LUM.
For each sample (WT and FEZ1-null), differentially expressed genes (DEGs) that were upregulated or downregulated in each cluster compared to the rest of the cells were identified and visualized by using Partek Flow and Bioturing (DEG filtering: false discovery rate (FDR)<0.01, log2FC>0.137 or <-0.137). Gene Ontology (GO) and pathway enrichment analysis 404 of DEG in specific clusters were visualized by Metascape, DAVID and g:Profiler (version e99_eg46_p14_f929183) with g:SCS multiple testing correction method, applying a significance threshold of 0.05. The trajectory analysis was perform using Partek Flow. In brief, maker genes (known as DEGs) from vNE/vRG, HOPX- oRG and HOPX+ oRG clusters (Table S4) were used as feature genes to generate the trajectory plot for both WT and FEZ1-null groups. Pseudotime plot was subsequently calculated and generated from the trajectory analysis by Partek Flow as well.
Assembly: hg19
Supplementary files format and content: Compressed files including tab-separated count values, i.e. filtered_feature_bc_matrix output

source_name: brain organoids

extract_protocol:
RNAs were harvested with the TRIzol™ reagent.
hCOs were dissected into smaller pieces by scalpel and trypsinized by Trypsin/EDTA solution for 25 min. Digestion was stopped by adding serum medium (Modified Eagle’s Medium supplemented with 5% fetal calf serum, 2 mM L-alanyl-L-glutamine, 1x MEM Vitamin Solution, 0.2x Mito+Serum extender and 21 mM D-glucose. The mixture were then gently triturated with a Pasteur pipette and the suspension spun down at 500x g for 5 min. Pelleted cells were resuspended in ESCAPETM buffer (provided by Proteona) and passed through a 40 um strainer.
Single cell sample library preparation and sequencing were done by Proteona (Singapore). Only QC passed single alive cells were used for library preparation using the 3’RNA V3 kit on 10X Genomics Chromium Controller. Cell suspensions were processed with the Chromium Controller (10x Genomics) using Chromium Single Cell 3’ Gem, Library & Gel Bead Kit v3 (10x Genomics, Cat# PN-1000078) and Chromium Single Cell B Chip Kit (10x Genomics, Cat# PN-1000074). RNA libraries that met QC criteria were sent for further sequencing using HiSeq X (Illumina) with 150 bp paired end reads.

value: H1 human embryonic stem cell

value: hESC

value: brain organoids

value: Day 28


title: J0951YUC4_3

value: Roots


title: control - rep3

source_name: Human dermal fibrloblasts


title: wildtype hESC cerebral organoid

description: 10x Genomics

value: Wildtype


title: J0951YUC4_2


title: U937, SGF29 knockout, H2K120Ub1, Replicate 1  [SGFKO1_H2B]

value: Monocytes


title: U937, SGF29 knockout, IGG  [SGFKO_IGG]

value: Normal rabbit IgG (Cell Signaling Technology, Cat. No, 2729)


title: U937, SGF29 knockout, H3K9AC, Replicate 1  [SGFKO1_K9AC]

value: Histone H3K9ac (Abcam, ab4441)


title: J0571YUC4_2


title: eyeRibo_WT3


title: J0951YUC4_1


title: Beta-glucan/anti-CD40_3

city: Philadelphia

first: Max

middle: M

last: Wattenberg

state: PENNSYLVANIA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
BGCD40a3
allsamples.deseq.normalized.counts.csv

data_processing:
FASTQ files were uploaded to the BaseSpace Suite (Illumina) and aligned using its RNA-Seq Alignment application (version 2.0.2), in which STAR was selected to align sequences with maximum mismatches set to 14 as recommended by Lexogen.
Differentially expressed genes were determined using the DESeq2 package.
Assembly: mm10
Supplementary files format and content: *.csv file with DESeq2 normalized counts of all samples

source_name: Tumor

extract_protocol:
Total RNA was extracted from 5μm serial sections obtained from FFPE tissues using the RNeasy FFPE kit (Qiagen).
3’ mRNA-seq libraries were generated from 100ng of DNAseI treated total RNA using the QuantSeq FWD Library Preparation kit (Lexogen), according to manufacturer’s directions.

value: Tumor

value: Polyclonal KPC derived mouse pancreatic ductal adenocarcinoma

value: WT

value: Beta-glucan + anti-CD40


title: Beta-glucan/anti-CD40_4

description:
BGCD40a4
allsamples.deseq.normalized.counts.csv


title: Beta-glucan/anti-CD40_5

description:
BGCD40a6
allsamples.deseq.normalized.counts.csv


title: U937, SGF29 knockout, H3K9AC, Replicate 2 [SGFKO2_K9AC]


title: C4

city: shantou

first: jichen

last: chen

address: university road

institute: shantou university

data_processing:
illuma casava 1.7 software  used for basecalling
Sequence reads were trimmed for adaptor sequence, and masked for low complexity or low-quality sequence then mapped to mm10 whole genome using bowtie V0.12.2 with parameters
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read per kilobase of exon per magabase of library size (readcount) were caculated using a protocol
Assembly: ftp://ftp.ensemblgenomes.org/pub/protists/release-51/fasta/phaeodactylum_tricornutum/
Assembly: phaeodactylum_tricornutum ASM15095v2

organism: Phaeodactylum tricornutum

source_name: cell

extract_protocol:
24h light
RNA was harvested using Trizol reagent illumina truseq RNA sample kit (Cat#FC-122-1001) was used with 1ug of total RNA for construction
RNA libraries for RNA-seq were prepared using standard illumia protocols

value: cell

tag: strain

value: CCAP 1055

value: Wild type

value: 64-75-5,Tetracycline hydrochloride for 4mg/L


title: J0951Col_3


title: B4


title: J0951Col_1


title: Beta-glucan/anti-CD40_2

description:
BGCD40a2
allsamples.deseq.normalized.counts.csv

tag: cell line


title: U937, non-targeting control, H2K120Ub1, Replicate 1  [NTC1_H2B]

value: Histone H2BK120ub1 (Active Motif, 39623)


title: A4


title: eyeRNA_WT2

data_processing:
For RNA-seq of polyA RNA samples, fastq files are mapped to fly dm6 genome by Tophat to get bam flies. The bam files are sorted by samtools.v1.9 sort and index, and then converted to bed format files by bamtools.v1.8 with convert function. Bam files and bed files are used to get bedgraph and raw counts. Raw counts are normalized to get RNA expression levels.
For RNA-seq of total RNA samples, fastq files are mapped to fly dm6 genome by Tophat to get bam flies. The bam files are sorted by samtools.v1.9 sort and index. Sorted bam files are used to generate bigwig graph and get raw counts in CDS regions by Htseq. Raw counts are normalized to get RNA expression levels.
For Ribo-seq fastq files, adaptors are removed by fastx_clipper, ribosomal RNA sequences are removed by bowtie2. Following steps are the same to the analysis of RNA-seq of total RNA samples.

value: eye discs

value: flies maintained at 25oC, eye discs with mouth hooks were dissected from late L3 larvae.


title: Beta-glucan/anti-CD40_1

description:
BGCD40a1
allsamples.deseq.normalized.counts.csv


title: U937, non-targeting control, H3K9Me3, Replicate 2 [NTC2_K9M3]

value: Histone H3K9me3 (Abcam, Cat. No. ab8898)


title: C0


title: control - rep2

value: control


title: ANKRD1 overepxression - rep2

value: ANKRD1 overexpression


title: ANKRD1 overepxression - rep3


title: anti-CD40_6

description:
CD40a6
allsamples.deseq.normalized.counts.csv

value: anti-CD40 (FGK45, 0.1mg IP x1)


title: eyeRNA_WT1


title: U937, non-targeting control, H3K9Me3, Replicate 1  [UB3_NTC1_K9M3]

value: Monocytes


title: control - rep1


title: ANKRD1 overepxression - rep1


title: anti-CD40_5

description:
CD40a5
allsamples.deseq.normalized.counts.csv


title: B0


title: U937, non-targeting control, H3K9AC, Replicate 2  [UB3_NTC2_K9AC]

value: Histone H3K9ac (Abcam, ab4441)


title: F-11-C

first: Libin

last: Song

address: 270 Dongan Road

institute: Fudan University Shanghai Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using HISAT2 with default parameters.
StringTie was used to quantify gene expression levels
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

extract_protocol:
Total RNA was collected using TRIzol Reagent (Invitrogen); then, rRNAs were removed by using the RiboMinus Eukaryote Kit (QIAGEN, Valencia, CA, USA). We next prepared the RNA-seq libraries using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Beverly, MA, USA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pancreatic cancer

tag: drug

value: Control


title: anti-CD40_3

description:
CD40a3
allsamples.deseq.normalized.counts.csv

value: Tumor

value: Polyclonal KPC derived mouse pancreatic ductal adenocarcinoma

value: WT


title: U937, non-targeting control, H3K9AC, Replicate 1 [UB3_NTC1_K9AC]


title: J0951Col_2

value: Roots


title: A0

value: cell

value: CCAP 1055

value: Wild type


title: Oocyte, Spermidine, 4

city: Nanjing

first: Zhang

last: Yu

address: No. 1 Weigang

institute: Nanjing Agricultural University

data_processing:
Data filtering raw data from sequencing was filtered using SOAPnuke (v1.5.6).
Variation detection uses HISTA2 (v2.1.0) software to match clean data to a reference genome.  Then, Ericscript (v0.5.5) was used for gene fusion detection and rMATS (V3.2.5) for variable splicing and differential variable splicing detection.
Differential gene analysis used Bowtie2(v2.3.4.3) to match clena data to a reference gene set.  The reference gene set is provided by the Dr. Tom multi-omics data Mining System. Differential gene testing is performed using DESeq2 (v1.4.5) (or DEGseq or PoissonDis) if Q value≤0.05 or FDR≤0.001.
RSEM (v1.3.1) software was used to quantify gene expression, and pheatmap (v1.0.8) was used to draw the clustering heatmap of gene expression in different samples.
KEGG and GO enrichment analysis further explored the gene functions related to phenotypic changes.   Based on hypergeometric test, Phyper was used to conduct GO and KEGG enrichment analysis for differential genes, with Qvalue≤0.05 as the threshold, and those meeting this condition were defined as significantly enriched in candidate genes.
Assembly: mm9
Supplementary files format and content: Tab-delimited text files include RESM values for each Sample.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

source_name: Ovary

extract_protocol:
Micro-transcriptomic sequencing uses the smart-seq2 method to reverse transcribe mRNA directly through oligo dT, and uses the reverse transcriptase MMLVRT to obtain a full-length single-stranded cDNA template containing fixed sequences at both ends, and then uses this cDNA as a template for extensive amplification.
RNA libraries were prepared for sequencing using standard DNBseq protocols

value: Ovary

value: Oocyte

value: Germ cell

value: Rescue


title: Oocyte, Spermidine, 2


title: Oocyte, Spermidine, 3


title: U937, non-targeting control, H2K120Ub1, Replicate 2 [NTC2_H2B]

value: Histone H2BK120ub1 (Active Motif, 39623)


title: anti-CD40_4

description:
CD40a4
allsamples.deseq.normalized.counts.csv

value: anti-CD40 (FGK45, 0.1mg IP x1)


title: F-09-b


title: anti-CD40_2

description:
CD40a2
allsamples.deseq.normalized.counts.csv


title: anti-CD40_1

description:
CD40a1
allsamples.deseq.normalized.counts.csv


title: Oocyte, Spermidine, 1


title: F-07-b


title: MCF10A-22-8h-Cis-3

city: Montreal

first: Meredyth

middle: Laurel Georgia

last: Elisseou

state: Quebec

address: 3999 ch de la Cote-Sainte-Catherine

department: Experimental Medicine

country: Canada

institute: McGill

data_processing:
Data processing annotations not provided by submitter.
Assembly: hg19
Supplementary files format and content: bw

source_name: Breast

growth_protocol: MCF10A cells were cultured in DMEM/F12 50/50 mix media (Wisent, cat# 319-085-CL) supplemented with 2% horse serum (Wisent, cat# 065150), 0.5μg/mL hydrocortisone (Sigma, cat# H0888-1G), 0.02μg/mL epidermal growth factor (Wisent, cat# 511-110-UM), 0.01mg/mL insulin (Wisent, cat# H511-016-U6) and 0.1μg/mL cholera toxin (Sigma, cat# C8052-2MG). MCF10A, cell cultures were maintained at 1:6 and discarded once they reach passage 8. 67NR cells were cultured in DMEM (Wisent, cat#319-005-CL) supplemented with 10% fetal bovine serum (Gibco, cat# 12483-020). 67NR cell cultures were maintained at 1:10 and discarded once they reach passage 8. For CTCF single copy loss cell lines previously generated by CRISPR/Cas9-mediated gene knockdown, single allele knockdown was confirmed by sanger sequencing and lower protein expression of CTCF was confirmed by western blot.

extract_protocol:
After ensuring the MCF10A cells are ideally 90-95% viable, the media was aspirated and washed with 5ml D-PBS (Wisent, 311-425-CL) which was aspirated and 2ml TRYPSIN/EDTA (Wisent, 325-043-EL) was added. The cells were placed in an incubator until the cells began to detach. Plates were removed from the incubator and 4ml of supplemented DMEM/F12 50/50 mix media (Wisent, cat# 319-085-CL) was added. 6ml of cells in media were transferred to a tube and centrifuged at 1200 RPM for 4 minutes. The supernatant was aspirated, and the cell pellet was resuspended in 6 mL of the supplemented DMEM/F12. Cells were counted and 50,000 viable cells were transferred to a 1.5 mL Eppendorf. For best results, the cells were used fresh and were not stored before proceeding to the transposition reaction.
Following transposition, a DNA purification reaction was performed using the Zymo DNA Clean and Concentrator-5 Kit (D4014). Following the kits instruction, In a 1.5 mL tube, add 5 volumes (~250 uL) of DNA binding buffer to each volume of DNA sample. Mix by vortexing briefly. Transfer the mixture to the provided Zymo-Spin Column in a collection tube. Centrifuge for 30 seconds at 12,000 RPM and discard flowthrough. Add 200 uL DNA wash buffer to the column. Centrifuge at 12,000 RPM for 30 second. The wash step was repeated. Transfer the column to a 1.5 mL tube and elute the DNA in 12 uL of elution buffer for 2 minutes. It was centrifuged for 1 minute at 12,000 RPM. The elution step was repeated. The eluted DNA (24 uL) was stored at -20°C until ready for amplification or used immediately. The PCR pre-amplification mixture was prepared using 2.5 uL of the 25 uM Primer Ad1 (IDT, Custom Illumina Adapters), 2.5 uL of the 25 uM Primer Ad2.x (A unique custom Ad2.x is used for each sample, IDT), 25 uL 2X NEBNext Master Mix (New England BioLabs, M0541S), and 20 uL of the transposed sample. The samples are amplified by PCR under the following conditions: 72C for 5 minutes, 98C for 30 seconds, then 5 cycles of 98C for 10 seconds, 63C for 30 seconds, 72C for 1 minute, and put on hold at 4C.According to Buenrostro et al. in 2015, In order to reduce size bias and GC bias in PCR, the number of additional PCR cycles was determined with qPCR to avoid stopping amplification prior to saturation. Using. the pre-amplified mixture, a qPCR amplification mixture was prepared with 4uL sterile water, 0.5 uL 25uM Primer Ad1 (IDT, custom adapters), 0.5 uL 25uM Primer Ad2.x (IDT, custom adapters), 2x GoTaq PCR mix (Promega, A600A), and 2 uL of the pre-amplified sample. The qPCR was run under the following cycling conditions:  72C for 5 minutes, 98C for 30 seconds; then 40 cycles of 98C for 10 seconds, 63C for 30 seconds, 72C for 1 minute, and put on hold at 4C. After qPCR amplification, manually assess the amplification profiles and determine the required number of additional cycles to amplify. To calculate the additional number of cycles needed, linear Rn versus cycle was plotted and used to determine the cycle number that corresponds to ¼ of the maximum fluorescent intensity. The remaining PCR pre-amplification mixture were amplified by PCR under the following conditions: 98C for 30 seconds, then N cycles of 98C for 10 seconds, 63C for 30 seconds, 72C for 1 minute, and put on hold at 4C. N is the number of cycles determined by qPCR. Following amplification, a DNA purification reaction was performed using the Zymo DNA Clean and Concentrator-5 Kit (D4014). Following the kits instruction, In a 1.5 mL tube, add 5 volumes of DNA binding buffer to each volume of DNA sample. Mix by vortexing briefly. Transfer the mixture to the provided Zymo-Spin Column in a collection tube. Centrifuge for 30 seconds at 12,000 RPM and discard flowthrough. Add 200 uL DNA wash buffer to the column. Centrifuge at 12,000 RPM for 30 second. The wash step was repeated. Transfer the column to a 1.5 mL tube and elute the DNA in 12 uL of nuclease-free water for 2 minutes. It was centrifuged for 1 minute at 12,000 RPM. The elution step was repeated. The eluted DNA was stored at -20C.
Samples were sequenced by The Hospital for Sick Children at The Center for Applied Genomics. DNA was sequenced using Illumina NovaSeq -S1 flow cell. The conditions were paired-end sequencing 2x150bp reads. We required a minimum of 50 million pairs of reads per sample and this service yielded ~ 70-88 million pairs of reads per library
Library prep was done using custom Illumina Adapters
Primer Name, Sequence
Ad1_noMX, AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG
Ad2.1_TAAGGCGA, CAAGCAGAAGACGGCATACGAGATTCGCCTTAGTCTCGTGGGCTCGGAGATGT
Ad2.2_CGTACTAG, CAAGCAGAAGACGGCATACGAGATCTAGTACGGTCTCGTGGGCTCGGAGATGT
Ad2.3_AGGCAGAA, CAAGCAGAAGACGGCATACGAGATTTCTGCCTGTCTCGTGGGCTCGGAGATGT
Ad2.4_TCCTGAGC, CAAGCAGAAGACGGCATACGAGATGCTCAGGAGTCTCGTGGGCTCGGAGATGT
Ad2.5_GGACTCCT, CAAGCAGAAGACGGCATACGAGATAGGAGTCCGTCTCGTGGGCTCGGAGATGT
Ad2.6_TAGGCATG, CAAGCAGAAGACGGCATACGAGATCATGCCTAGTCTCGTGGGCTCGGAGATGT
Ad2.7_CTCTCTAC, CAAGCAGAAGACGGCATACGAGATGTAGAGAGGTCTCGTGGGCTCGGAGATGT
Ad2.8_CAGAGAGG, CAAGCAGAAGACGGCATACGAGATCCTCTCTGGTCTCGTGGGCTCGGAGATGT
Ad2.9_GCTACGCT, CAAGCAGAAGACGGCATACGAGATAGCGTAGCGTCTCGTGGGCTCGGAGATGT
Ad2.10_CGAGGCTG, CAAGCAGAAGACGGCATACGAGATCAGCCTCGGTCTCGTGGGCTCGGAGATGT
Ad2.11_AAGAGGCA, CAAGCAGAAGACGGCATACGAGATTGCCTCTTGTCTCGTGGGCTCGGAGATGT
Ad2.12_GTAGAGGA, CAAGCAGAAGACGGCATACGAGATTCCTCTACGTCTCGTGGGCTCGGAGATGT
Ad2.13_GTCGTGAT, CAAGCAGAAGACGGCATACGAGATATCACGACGTCTCGTGGGCTCGGAGATGT
Ad2.14_ACCACTGT, CAAGCAGAAGACGGCATACGAGATACAGTGGTGTCTCGTGGGCTCGGAGATGT
Ad2.15_TGGATCTG, CAAGCAGAAGACGGCATACGAGATCAGATCCAGTCTCGTGGGCTCGGAGATGT
Ad2.16_CCGTTTGT, CAAGCAGAAGACGGCATACGAGATACAAACGGGTCTCGTGGGCTCGGAGATGT
Ad2.17_TGCTGGGT, CAAGCAGAAGACGGCATACGAGATACCCAGCAGTCTCGTGGGCTCGGAGATGT
Ad2.18_GAGGGGTT, CAAGCAGAAGACGGCATACGAGATAACCCCTCGTCTCGTGGGCTCGGAGATGT

treatment_protocol: Treated cells had 6uM cisplatin added in 10ml media for 8h

value: Breast

value: non-tumorigenic, Breast Epithelial Cell

tag: knockdown

value: CTCF+/-

value: 6uM Cisplatin, 8h


title: Oocyte, Aged, 3

tag: treatment

value: Treatment


title: Beta-glucan_6

description:
BG6
allsamples.deseq.normalized.counts.csv

value: Tumor

value: Polyclonal KPC derived mouse pancreatic ductal adenocarcinoma

value: Beta-glucan (1.2mg IV x1)


title: MCF10A-22-8h-Cis-2


title: Oocyte, Aged, 1


title: F-04-b

value: Pancreatic cancer

value: Control


title: Oocyte, Aged, 2


title: MCF10A-22-8h-Cis-1


title: Beta-glucan_5

description:
BG5
allsamples.deseq.normalized.counts.csv

value: WT


title: MCF10A-17-8h-Cis-3


title: U937, non-targeting control, IGG  [UB3_NTC1_IGG]

value: Monocytes

tag: chip antibody

value: Normal rabbit IgG (Cell Signaling Technology, Cat. No, 2729)


title: E-09-b

value: QYHJ treatment


title: Beta-glucan_4

description:
BG4
allsamples.deseq.normalized.counts.csv


title: E-08-c


title: Beta-glucan_3

description:
BG3
allsamples.deseq.normalized.counts.csv


title: Oocyte, Young, 2

value: Ovary

value: Oocyte

value: Germ cell


title: MCF10A-17-8h-Cis-2

value: Breast


title: Oocyte, Young, 3


title: Beta-glucan_2

description:
BG2
allsamples.deseq.normalized.counts.csv


title: Beta-glucan_1

description:
BG1
allsamples.deseq.normalized.counts.csv


title: MCF10A-17-8h-Cis-1

value: non-tumorigenic, Breast Epithelial Cell


title: Oocyte, Young, 1


title: E-03-b


title: F-01-C


title: E-01-C


title: MCF10A-WT-8h-Cis-3

value: Wild type


title: untreated_6

description:
control6
allsamples.deseq.normalized.counts.csv

value: untreated


title: MCF10A-WT-8h-Cis-2

value: 6uM Cisplatin, 8h


title: BES1-RNAi_Green_2

first: Yuhan

last: Hao

address: #300 Fenglin Road

institute: CAS Center for Excellence in Molecular Plant Science

data_processing:
Illumina software used for basecalling.
Sequenced reads were processed using Trimmomatic(Version0.36), The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2(Version2.2.1.0).
Then quantified read counts per gene and normalized Fragments Per Kilobase exon per Million reads mapped (FPKM) values using Cufflinks TopHat（version:2.2.1）
FPKM and read counts valueof each transcript (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using the DESeq(Version1.18.0)(2012) functions estimateSizeFactors and nbinomTest.
Assembly: TAIR10.1_NCBI
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: seedling

extract_protocol:
total RNA was isolated using RNAiso Plus kit (Takara Bio, Shiga, Japan)
The RNA library generation process followed the manufacturer’s protocol for the Illumina TruseqTM RNA sample prep Kit

value: seedling

tag: age

value: 3 DAY OLD


title: BES1-RNAi_Green_3


title: Retina, WT, 10X V3 Chemistry

city: Houston

first: John

last: O'Brien

state: Texas

address: 4401 Martin Luther King Blvd

department: Vision Science

institute: University of Houston College of Optometry

description: Pool of 3 adult zebrafish retinas between 4 and 8 months old

data_processing:
Sequences were run through the 10x Genomics CellRanger V3.1.2.0 pipeline. First, sequences were demultiplexed into FASTQ files through CellRanger mkfastq. FASTQ files were then aligned to the Zf reference genome (GCA_000002035.4_GRCz11) through CellRanger count. Output files were run through Babraham Bioinformatics’ FASTQC V0.11.9 to check on the quality of the sequences used for analysis. Sequences had a normal distribution of GC content as well as base call accuracy above 99%. Over 93% of reads mapped successfully to the genome. All computational analysis was performed through Texas Advanced Computing Center (TACC) Lonestar5 computing service. Scripts were written in Notepad++ v7.6.2 and uploaded to TACC through PuTTY V0.72.
After alignment, quality control was assessed through FASTQC. Aligned data were run through the Seurat V3.1.1 package [27] in R V3.6.1.
In the Seurat processing, any cell that was determined to be an outlier or contained greater than 10% mitochondrial genes was removed. Low-abundant genes (expressed in fewer than 10 cells) and cells of potentially low quality (percentage of mitochondrial genes >10%) were removed from downstream analysis.  P23H and WT datasets contained between 200 and 4,700 genes and 200 and 6,000 genes per cell, respectively (Table S4). PCElbowPlots were performed and 20 principal components were used for downstream analysis of each dataset. PC1 to PC20 were used to construct nearest neighbor graphs in the PCA space followed by Louvain clustering and non-linear dimensional reduction by tSNE to visualize and explore the clusters. Each cluster was assigned a cell type based on their expression of cell type-specific marker genes (Table S1). Dot plots, Heatmaps, Violin Plots and tSNE cluster maps were all generated through Seurat’s vignettes V3.2. Expression levels are expressed in a base 2 log scale.
Assembly: GCA_000002035.4_GRCz11
Supplementary files format and content: Tab Separated Values files
Supplementary files format and content: Matrix files

organism: Danio rerio

source_name: Whole retina

growth_protocol: Zebrafish fish were grown in 14hr light:10hr dark cycle conditions and collected between 4 and 8 months of age

extract_protocol:
3 fish of the same strain were collected in the morning between nine and eleven a.m., 2 to 4 hours after light onset in the fish room, in Falcon tubes containing 0.15% Tricaine/MS222 and incubated on ice for 10 minutes. Zebrafish were decapitated and eyeballs were detached and placed in dissecting medium containing Leibovitz's L-15 medium (Gibco 21083027). Each retina was then extracted and placed in a 1.5 mL microcentrifuge tube with 300 µL of dissociation solution containing L15 and Earle's Balanced Salt Solution (EBSS; Gibco 14155063) in a 3:1 ratio. After all retinas were collected, the dissociation solution was replaced with 200 µL of Papain solution (50 U/mL in EBSS; Worthington Biochemical LK003178) and retinas were incubated at 28˚C. After 20 minutes of incubation, retinas were gently triturated 20-30 times with fire-polished glass pipettes. Supernatants were collected and incubated with Papain for another 40 minutes with trituration performed every 10 minutes. Papain reaction was terminated by adding 2x volume of 0.1% BSA in L15: EBSS medium. Tubes were centrifuged at 400g for 5 minutes to pellet the cells. The supernatant was removed and washed again with 0.05% BSA. The supernatant was removed and cells were finally suspended in 100 µl of 0.05% BSA.
The cell samples were submitted for 3’ sc-RNA library preparation and sequencing through the Baylor College of Medicine Single Cell Genomics Core facility. Single-cell Gene Expression Libraries were prepared usingChromium Next GEM Single Cell 3’ Reagent Kits v2 and v3.1(10x Genomics, Pleasanton, CA). In brief, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single-cell GEMS (Gel Beads-In-Emulsions) where full-length cDNA was synthesized and barcoded for each single cell. Subsequently, the GEMS are broken and cDNA from every single cell is pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing and adaptor ligation. The final library was generated by amplification. cDNA libraries were sequenced on an Illumina HiSeq2500.
3' SC RNA Seq

value: Whole retina

tag: FISH line

value: WT AB; ZIRC_ZL1

value: 4 to 8 months old

tag: disease state

value: control

tag: 10x chemistry

value: 10X V3 Chemistry


title: BES1-RNAi_Green_1

tag: tissue


title: MCF10A-22-0h-Cis-3

value: CTCF+/-

value: No treatment


title: untreated_3

description:
control3
allsamples.deseq.normalized.counts.csv

value: Tumor

value: Polyclonal KPC derived mouse pancreatic ductal adenocarcinoma

value: WT


title: BES1-RNAi_Dark_3


title: Retina, P23H, 10X V2 Chemistry

value: P23H Positive

value: Retinitis Pigmentosa model

value: 10X V2 Chemistry


title: untreated_2

description:
control2
allsamples.deseq.normalized.counts.csv

value: untreated


title: MCF10A-22-0h-Cis-2

value: Breast

value: non-tumorigenic, Breast Epithelial Cell


title: untreated_1

description:
control1
allsamples.deseq.normalized.counts.csv


title: BES1-RNAi_Dark_2

value: seedling

value: 3 DAY OLD


title: E-02-C

value: Pancreatic cancer

value: QYHJ treatment


title: MCF10A-22-0h-Cis-1


title: WT_Green_3

value: Wild-type


title: En1cKO-rep2

first: Yana

middle: G

last: Kamberov

state: PA

address: 415 Curie Blvd CRB 535

department: Genetics

institute: University of Pennsylvania Perelman School of Medicine

description: Drop-seq

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Drop-seq Tools v1.12
Assembly: mm10
Supplementary files format and content: txt files of read counts and tagged DGE

source_name: skin (volar foot)

extract_protocol:
En1-cKO and Control pups were euthanized at P2.5 and volar hindlimb skin (right and left) was rapidly dissected on ice and snap frozen on dry ice and stored at -80ºC until nuclear isolation. Single nuclear suspensions were generated from the pooled volar hindlimb skin (right and left) from 5 mice of the same genotype, for a total of 10 pooled volar skins, as previously described (https://www.protocols.io/view/snucdrop-seq-protocol-n2bvjr36plk5/v2) with some modifications. Pooled samples were dissociated in homogenization buffer using a Polytron homogenizer (Kinematica Inc.) followed by dounce homogenization (20 times with loose pestle; 10 times with tight pestle). For P2.5 volar skin, we obtained ≥ 2.1x105 nuclei/ml for each sample. Sucrose gradient centrifugation was not performed on single nuclear suspensions. Biological replicates were prepared and sequenced in two separate batches; one replicate of each genotype (En1-cKO: tetO-Cre/+; Krt5-rtTA/+; En1flox/flox; Control: En1flox/flox, Krt5-rtTA/+; En1flox/flox) was processed and sequenced in the same batch to avoid autocorrelation of condition and batch effects
Single nuclei were co-encapsulated with barcoded beads and reverse transcription was performed as described here: https://www.protocols.io/view/snucdrop-seq-protocol-n2bvjr36plk5/v2
snRNA-seq (Drop-seq)

value: skin (volar foot)


title: MCF10A-17-0h-Cis-2

value: CTCF+/-


title: En1cKO-rep1

description: Drop-seq


title: BES1-RNAi_Dark_1


title: MCF10A-17-0h-Cis-3

value: No treatment


title: WT_Green_2


title: MCF10A-17-0h-Cis-1


title: untreated_5

description:
control5
allsamples.deseq.normalized.counts.csv

value: Tumor


title: MCF10A-WT-8h-Cis-1

value: Wild type

value: 6uM Cisplatin, 8h


title: rttaControl-rep2

description: Drop-seq


title: Retina, P23H, 10X V3 Chemistry

value: Whole retina

value: 4 to 8 months old

value: P23H Positive

value: 10X V3 Chemistry


title: WT_Green_1


title: MCF10A-WT-0h-Cis-3

value: Breast

value: WT


title: MCF10A-WT-0h-Cis-2

value: non-tumorigenic, Breast Epithelial Cell


title: rttaControl-rep1

description: Drop-seq


title: WT_Dark_3

value: seedling

value: 3 DAY OLD


title: WT_Dark_2


title: b_INP_13 vs b_NSCII_7

city: Plymouth

first: Claudia

last: Barros

state: Devon

address: The John Bull Building, Plymouth Science Park, 16 Research Way

department: School of Medicine

country: United Kingdom

institute: University of Plymouth

hyb_protocol: Add 140 µl of Ocimum hybridization buffer to the labelled mixture and heat at 100 ºC for 2 minutes on a hot-block. Centrifuge for 3 minutes at 13,000 rpm. Load 140 µl of the labelled sample to the microarray, and hybridize for 16 hours at 51 ºC. Perform post-hybridization washes as per PowerMatrix slides protocol (FMB). Pre-heat wash solution 1 (0.2 x SSC; 0.2% SDS) and wash solution 2 (0.2 x SSC) to 55 ºC using a water bath. Incubate slides in a slide staining dish with pre-heated wash solution 1 on an orbital shaker at 50 rpm for 20 minutes. Transfer the slides to a staining trough containing pre-heated wash solution 2. Gently dip the slides up and down for 1 minute in wash solution 2. Repeat step in fresh wash solution 2 twice. Rinse the slides 3 times with fresh deionized water at room temperature (dip the rack in MilliQ water for 3 seconds). Transfer the slides to a clean microscope slide box with tissue at the base and centrifuge at 1000 rpm for 5 minutes. The slides are now ready to be scanned.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains selected by the Auto-PMT function (0.005% saturation tolerance). Images are saved as Single-image TIFF.

data_processing:
Data pre-processing and normalization were carried out in R with additional Bioconductor packages. To remove background noise, the background correction method normexp implemented in the backgroundCorrect function of the limma package was applied with an offset of 50. Spots that were flagged by the scanner software or corresponding to spikes were removed. Lowly expressed genes were removed from further analysis by filtering genes with signals less than 100 in more than half of the samples (1402 genes remain). To balance both signal channel, the optimised intensity normalization method (OIN) of the OLIN package for normalization of two-color array data was applied.
Normalized log2 ratios (ch2/ch1) based on local intensity-dependent normalization (LIN) of two-color microarrays as implemented in the OLIN Bioconductor package. Log2 ratios between brat INPs vs control iINPs were based on reconstituted single channel expression values after intra- and inter-microarray normalization (i.e. OIN and quantile normalization).

source_name: Live brain

label_protocol: For cDNA PCR amplification, 2µl of nested primer (5´- AAGCAGTGGTATCAACGCAGAGT-3´, 10 µM), 2µl dNTPs (10mM), 5µl Roche buffer, 0.5µl Roche Long Expand polymerase and 34.5µl of µltrapure water were added. PCR program: one cycle (95ºC 3min, 50ºC 5min, 68ºC 15min) followed by 25 cycles (95ºC 20s, 60ºC 1min, 68ºC 7min). Individual cells showing clear banding patterns on agarose gels were used for microarray analysis. To label, take 1 µg double stranded DNA and make up to a total volume of 25 µl with DEPC-water. Add 20 µl 2.5x Random Primer Reaction Buffer (Invitrogen‚ BioPrime DNA Labelling Kit). Incubate at 100 ºC for 5 minutes, snap cool on ice. Add 1 µl 10 X low-C dNTP mix (5mM dATP,dGTP,dTTP, 2 mM dCTP), 2 µl 1 mM Cy3 or Cy5 dCTP (GE Healthcare) and 1 µl 40U/µl Klenow (Invitrogen‚ BioPrime DNA Labelling Kit). Incubate at 37ºC for 2 to 3 hours. Stop the reaction by adding 5 µl Stop Buffer (Invitrogen, BioPrime DNA Labelling Kit). Resuspend the resin in the AutoSeq G-50 column (GE Healthcare) by vortexing gently. Loosen the cap a quarter turn and snap off the bottom closure. Place the column in a collection tube. Pre-spin column at 5,000 rpm for 1 minute to remove the buffer. Remove the top cap and place column in a new 1.5 ml tube. Pipette half of the sample onto the centre of the angled surface of the compacted resin bed being carefµl not to disturb the resin. Spin for 1 minute at 5,000 rpm. Discard the column. Place a second column into the same 1.5 ml microfuge tube and then add the second half of the sample. Spin for 1 minute and 5,000 rpm. Reduce volume of probe to between 2 to 5 µl by placing in a speed vac with medium heat. Add 2 µl of 10 mg / ml sonicated salmon sperm DNA (Invitrogen).

growth_protocol: Individual brat mutant INPs and NSCII, and control iINPs, INP and NSCII, expressing CD8-GFP driven by pnt-Gal4 were manually harvested from 24h ALH live brains.

extract_protocol: Each single cell was expelled in its own Eppendorf tube containing annealing mix: 0.3µl anchored polyT primer (5´- AAGCAGTGGTATCAACGCAGAGTACT(26)VN-3´, 10µM), 0.3µl SM primer (5´-AAGCAGTGGTATCAACGCAGAGTACGCrGrGrG-3´, 10µM), 0.4µl RNase inhibitor (Superase, Ambion) and 2µl Lysis Mix (10% Nonidet P-40, 0.1M DTT in DEPC-treated µltrapure water), and processed in less than 20 min. Each sample was spun (14000rpm, 1min, 4ºC), primers annealed (3min, 70ºC) and snap-frozen in dry ice/ isopropanol. 1.5µl of mix 1 (1µl Invitrogen first strand buffer, 0.5µl 10mM dNTPs) and 0.5µl of mix 2 (3µl Invitrogen Superscript II reverse transcriptase, 0.5µl Ambion Superase RNase inhibitor) were added per sample. Samples were thawed during centrifugation (14000rpm, 1 min, 4ºC) and reverse transcribed (37ºC, 90min), followed by enzyme thermal inactivation (65ºC, 10 min). RNA was digested in 2µl digestion mix (0.7µl Roche RNase H buffer, 0.5µl Roche RNase H, 0.8µl µltrapure water) for 20min at 37ºC, followed by enzyme thermal inactivation (65ºC, 15 min).

value: INP

value: brat, UAS-mCD8-GFP; pnt-GaL4

value: CNS (brain)

value: 24 h ALH

value: NSCII


title: control-rep1

description: Drop-seq

value: skin (volar foot)


title: c_INP_89 vs c_NSCII_3

value: iINP

value: UAS-mCD8-GFP; pnt-GaL4 (control)


title: Hypoxia IP #3

status: Public on Nov 09 2023

city: Pittsburgh

first: Adam

last: Handen

state: Pennsylvania

address: 200 Lothrop Street

department: Vascular Medicine Institute

institute: University of Pittsburgh

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using STAR v2.7.9a
peaks were called using MACS2 v2.2.7.1
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak peak calls

source_name: Pulmonary arterial endothelial cells

growth_protocol: Primary HPAECs were grown in EBM-2 basal medium supplemented with EGM-2 MV BulletKit (Lonza).

extract_protocol:
Cells were fixed, crosslinked, and sonicated to get soluble chromatin for immunoprecipitation. 10% input of crosslinked DNA was saved while the remining DNA was precipitated with histone 3 lysine 4 antibody (H3K4Me3, Abcam, ab8580) or non-immune rabbit IgG (Pierce magnetic ChIP kit). Chromatin/antibody complex was then pulled down using Protein A/G Magnetic Beads (Pierece).
DNA samples were proceeded with ChIP-sequencing (sequencing platform: DNBSeqTM, 20M reads).

treatment_protocol: Experiments were performed at passages 5 to 8. Cultured HPAECs were either under normoxia or hypoxia (0.2% oxygen) for 24 hours.

value: Pulmonary arterial endothelial cells

value: Hypoxia

tag: control

value: No


title: WT_Dark_1

city: Shanghai

value: Wild-type


title: b_NSCII_9 vs b_INP_14

tag: cell type


title: c_NSCII_90 vs c_INP_92


title: Normoxia IP #2

value: Normoxia


title: Normoxia IP #3


title: Normoxia IP #1


title: c_NSCII_3b vs c_INPm


title: Hypoxia IP #1


title: c_INP_84 vs c_NSCII_2


title: Control

value: Yes


title: control-rep2

description: Drop-seq


title: MCF10A-WT-0h-Cis-1

value: Breast

value: non-tumorigenic, Breast Epithelial Cell

value: WT

value: Wild type

value: No treatment


title: Hypoxia IP #2


title: Infant 39 day 30

city: Memphis

first: Zhaohui

last: Xu

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

institute: St. Jude Children's Research Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with lumi in R

source_name: Human Whole blood

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total RNA was isolated with Tempus Spin RNA Isolation Kit and globin mRNA from total RNA was removed with GLOBINclear Whole Blood Globin Reduction Kit. Quality control was performed with Agilent Bioanalyser.

tag: subject

value: Whole blood

tag: time point

value: day 30


title: Infant 14 day 30


title: Infant 34 day 30


title: Infant 20 day 30


title: Infant 15 day 30


title: Infant 22 day 30


title: Infant 21 day 30


title: Infant 34 day 7

value: day 7


title: Infant 39 day 7


title: Infant 19 day 30


title: b_INP_12 vs b_NSCII_6

value: INP

value: brat, UAS-mCD8-GFP; pnt-GaL4

value: CNS (brain)

value: 24 h ALH

value: NSCII


title: Infant 42 day 30


title: Infant 1 day 30


title: Infant 4 day 30


title: Infant 25 day 7


title: Infant 42 day 7


title: Infant 21 day 7


title: Infant 8 day 30


title: Infant 22 day 7


title: Infant 30 day 30


title: Infant 6 day 30


title: Infant 25 day 30


title: Infant 26 day 7


title: Infant 30 day 7


title: Infant 3 day 30


title: Infant 26 day 30


title: Infant 17 day 30


title: Infant 5 day 30


title: Infant 12 day 30


title: Infant 20 day 7


title: Infant 11 day 30


title: Infant 17 day 7


title: Infant 4 day 7


title: Infant 14 day 7


title: Infant 12 day 7


title: Infant 13 day 7


title: Infant 11 day 7


title: Infant 19 day 7


title: Infant 6 day 7


title: Infant 30 day 0

value: day 0


title: Infant 1 day 7


title: Infant 39 day 0


title: Infant 15 day 7


title: Infant 21 day 0


title: Infant 2 day 7


title: Infant 3 day 7


title: Infant 26 day 0


title: Infant 13 day 0


title: Infant 5 day 7


title: Infant 34 day 0


title: Infant 15 day 0


title: Infant 19 day 0


title: Infant 20 day 0


title: Infant 12 day 0


title: Infant 14 day 0


title: Infant 31 day 0


title: Infant 17 day 0


title: Infant 8 day 7


title: Infant 22 day 0


title: Infant 25 day 0


title: Infant 42 day 0


title: NPE infected without OTI T cells, replicate 3, RNAseq

city: Bethesda

first: Katherine

last: Hornick

address: 10 Center Dr, Building 29B

department: Integrated Data Sciences Section (IDSS)

institute: NIAID

data_processing:
Raw fastq files were trimmed for quality and adapter contamination with Cutadapt v1.18 (Martin 2011). Trimmed reads were aligned to the mouse GRCm38.p6 reference genome and GENCODE release 21 reference transcriptome using STAR v2.7.0f run in two-pass mode (Dobin et al. 2013).  RSEM v.1.3.1 (Li and Dewey 2011) was used to compute the expected counts which were further converted to counts per million (CPM) by eVITTA (Cheng et al. 2021). Genes that were expressed with at least 1 CPM in a minimum of three samples were included in the principal component analysis (PCA) and differential expression testing by edgeR (v.3.40.2) (Robinson et al. 2010). Differential expression analysis compared samples in different conditions including transferred OT-I with NPS infection vs. no OT-I transfer with NPS, OT-I with NPE vs. transferred OT-I with NPS infection, OT-I with NPE vs. naïve tissue (control), and transferred OT-I with NPS infection vs. naïve tissue (control).
Assembly: GRCm38.p6 reference genome and GENCODE release 21
Supplementary files format and content: raw expression (expected counts) text file generated from RSEM

source_name: whole ear, right

extract_protocol:
Ears were collected on indicated day post-infection (dpi) and immediately placed in buffer RLT (Qiagen). Tissues were homogenized, and RNA was isolated using Lysing Matrix S (1/8”) metal beads (MPBiomedicals) and a FastPrep-24 Instrument (MPBiomedicals). RNA was then purified using a Qiagen RNAEasy Mini Kit (Qiagen) according to the manufacturer’s protocol. An on-column DNAse digestion was performed prior to RNA elution. RNA concentration and purity were accessed using an Agilent TapeStation 4200. Samples were sequenced on a NovoSeq 6000 S1 using Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus and paired-end sequencing.
Tissues were homogenized, and RNA was isolated using Lysing Matrix S (1/8”) metal beads (MPBiomedicals) and a FastPrep-24 Instrument (MPBiomedicals). RNA was then purified using a Qiagen RNAEasy Mini Kit (Qiagen) according to the manufacturer’s protocol. An on-column DNAse digestion was performed prior to RNA elution.

value: whole ear, right

value: infected, no OT-I


title: NPE infected without OTI T cells, replicate 2, RNAseq


title: NPE infected without OTI T cells, replicate 1, RNAseq


title: NPS infected without OTI T cells, replicate 3, RNAseq

source_name: whole ear, left

value: whole ear, left


title: NPS infected without OTI T cells, replicate 1, RNAseq


title: NPS infected without OTI T cells, replicate 2, RNAseq


title: NPE infected with OTI T cells, replicate 2, RNAseq

value: VACV infected with transferred OTI-CD8+ T-cells


title: NPE infected with OTI T cells, replicate 3, RNAseq


title: NPS infected with OTI T cells, replicate 3, RNAseq


title: NPS infected with OTI T cells, replicate 2, RNAseq


title: Infant 3 day 0


title: NPS infected with OTI T cells, replicate 1, RNAseq


title: NPE infected with OTI T cells, replicate 1, RNAseq


title: Infant 4 day 0


title: Infant 8 day 0


title: control, replicate 2, RNAseq

source_name: whole ear

value: whole ear

value: control


title: Infant 2 day 0


title: control, replicate 3, RNAseq


title: Infant 6 day 0


title: GFAP_Positive_Microglia [411O.AAGAGGCA_AGCTAGAA]

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

description: Sorted Microglia

data_processing:
The sample is aligned to GRCm38 reference genome using STAR, and then quantified using RSEM
Genome_build: GRCm38
Supplementary_files_format_and_content: .isoforms.results files from RSEM

source_name: Microglia

extract_protocol:
N/A
Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al 2014).

tag: Sex

value: Female

value: Adults


title: Infant 5 day 0

value: Whole blood


title: control, replicate 1, RNAseq


title: Infant 1 day 0


title: GFAP_Positive_Microglia [411O.CTCTCTAC_AGCTAGAA]

description: Sorted Microglia


title: GFAP_Negative_Microglia [411O.AGGCAGAA_AGCTAGAA]

description: Sorted Microglia


title: GFAP_Positive_Microglia [411O.TAGGCATG_AGCTAGAA]

description: Sorted Microglia


title: GFAP_Negative_Microglia [411O.GGACTCCT_AGCTAGAA]

description: Sorted Microglia


title: GFAP_Positive_Microglia [411O.CGAGGCTG_AGCTAGAA]

description: Sorted Microglia


title: GFAP_Negative_Microglia [411O.TCCTGAGC_AGCTAGAA]

description: Sorted Microglia


title: GFAP_Positive_Microglia [411O.GTAGAGGA_AGCTAGAA]

description: Sorted Microglia


title: GFAP_Positive_Microglia [411O.GCTCATGA_AGCTAGAA]

description: Sorted Microglia


title: GFAP_Negative_Microglia [411O.CGTACTAG_AGCTAGAA]

description: Sorted Microglia