title: LP_m6A_IP2

status: Public on Jun 03 2025

city: Guangzhou

first: Huilin

last: Huang

address: #651 East Dong-feng Road

institute: Sun Yat-Sen University Cancer Center

description:
Library name: sample16
LP_m6A_IP2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by by cutadapt v. 4.1 with parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q 20,20 --max-n 0.25 --trim-n.
The clean reads were then mapped to the human genome (hg38) with HISAT2 v.2.1.1 with “--rna-strandness RF” parameters, and supplying the GENCODE Release 45 gene annotation. A post-alignment filter was preformed to remove alignments to ribosomal RNA (rRNA), secondary alignment and non-concordant mate pairs.
m6A peaks on each transcripts of gene were called using homemade Perl scripts according to the strand, separated by “-f 83 (and 163)” or “-f 99 (and 147) with SAMtools v. 1.16.1.
Peaks were identified as regions concentrated with significantly more normalized reads (fold change > 1.5 and adjusted P-value < 0.05) in IP than their corresponding input samples.
Assembly: hg38
Supplementary files format and content: bigwig files were generated by deepTools v3.5.2. BedWig files can be uploaded to UCSC Genome Browser for visualization.

source_name: lung progenitor cell

growth_protocol: iPS cell line PB004 generated from peripheral blood mononuclear cells (PBMCs) were maintained with mTeSR medium in humidified atmosphere with 5% CO2 at 37℃. DE, AFE, and LP were differentiated from iPSC.

extract_protocol:
Total RNA of iPSC, DE, AFE and LP was isolated using the TRIzol reagent.
m6A-modified RNA from iPSC, DE, AFE, and LP was enriched using picoMeRIP, a sensitive, picogram-scale m6A mapping method that optimizes signal-to-noise ratio. Following picoMeRIP, input and IP samples were used to construct NGS libraries using the SMARTer® Stranded Total RNA-Seq Kit v2.

treatment_protocol: iPS cells were treated with Activin A (100μg/ml) and CHIR99021 (10mM) to differentiate into DE; DE was treated with DSM (2μM) and SB431542 (10μM) to induce to AFE; LP was induced from AFE by adding ATRA (100nM), BMP4 (10ng/ml) and CHIR99021 (3μM).

value: lung progenitor cell

value: IP


title: Subject_C19_Blood

status: Public on Jun 11 2025

type: SRA

city: Cambridge

first: Menna

last: Clatworthy

address: Cambridge Biomedical Campus, Francis Crick Ave, Trumpington

department: Department of Medicine

country: United Kingdom

institute: University of Cambridge

description:
Library name: Sample_Fq_8
GEX

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the Cell Ranger software v6.0.1 (10x Genomics)
Assembly: GRCH38
Supplementary files format and content: Compressed tab-separated values files, unfiltered single cell barcode gene expression matrix

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Nasal tissue samples were minced, digested in a DNAse/Liberase solution for 30 minutes, strained and washed to create a single cell suspension. Paired whole blood was centrifuged layered on Histopaque 1077, with PBMC layer extracted and washed. Nasal and PBMC samples were loaded as single cell suspensions without sorting
ScRNAseq gene expression libraries were contructed in accordance with the manufacturer protocol (Single cell 5' v2 protocol, 10x Genomics)

tag: tissue

value: Blood

tag: treatment

value: Healthy control


title: Subject_C20_Blood

description:
Library name: Sample_Fq_4
GEX


title: Subject_C20_Nasal

description:
Library name: Sample_Fq_5
GEX

source_name: Nasal

value: Nasal


title: ILC2, lung, infected 3

status: Public on Jun 12 2025

city: Denver

first: Richard

middle: Lee

last: Reinhardt

state: Colorado

address: 1400 Jackson Street, K817A

department: Biomedical Research

country: USA

institute: National Jewish Health

description: Library name: 5A Lung

data_processing:
Raw sequencing data was demultiplexed and converted to FASTQ files with Illumina DRAGEN bcl2fastq (v4.2.7). Quality check, adapter trimming, and alignment to the murine genome reference sequence mm10 (UCSC) was performed using CellRanger (v6.1.2) to generate a gene expression matrix for each sample containing the number of UMIs for each gene associated with each cell barcode.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

organism: Mus musculus

source_name: Lung

extract_protocol:
Intestine draining mesenteric lymph nodes, lung, and bone marrow were collected 5 days post infection with Nippostrongylus brasiliensis. ILC2 and ILC progenitors were enriched using EasySep™ Mouse Hematopoietic Progenitor Cell Isolation Kit (Stemcell, 19856) prior to cell sorting. Bone marrow cells were sorted for progenitor cell markers CD45+Lin- CD127+ a4b7+ Flt3-. These markers account for both the common helper-like ILC progenitors (CHILP) and ILC2 progenitors (ILC2p). Mesenteric lymph nodes and lung cells were sorted for conventional ILC2 markers CD45+ Lin- CD127+ and KLRG1low/+. Lung, mesenteric lymph node, and bone marrow cell suspensions from three mice were treated as 9 separate samples for scRNA-seq. Sorted cells were resuspended in 0.04% BSA in PBS and counted prior to GEM encapsulation using the 10x Genomics Chromium controller with a targeted cell recovery of 5,000 cells.
3′ mRNA-seq gene expression libraries were prepared per the Chromium Single Cell 3' User Guide (10x Genomics, CG000204). Library quality was verified using TapeStation 4200 (Agilent) and libraries were quantified by Qubit fluorometer (Thermo Fisher) prior to pooling. Library pools were sequenced at the National Jewish Health Genomics Facility on an Illumina NEXTSEQ 2000, 28x10x10x90 bp, paired-end sequencing.

treatment_protocol: Nippostrongylus brasiliensis infection

value: Lung

tag: cell type


title: DE_m6A_IP2

country: China

description:
Library name: sample12
DE_m6A_IP2

library_source: transcriptomic

source_name: definitive endoderm cell

value: definitive endoderm cell


title: AFE_m6A_IP1

description:
Library name: sample13
AFE_m6A_IP1

source_name: anterior foregut endoderm cell

value: anterior foregut endoderm cell


title: iPSC_m6A_IP1

description:
Library name: sample9
iPSC_m6A_IP1

source_name: Human induced pluripotent stem cell

value: Human induced pluripotent stem cell


title: LP_m6A_input2

description:
Library name: sample8
LP_m6A_input2

value: input


title: iPSC_m6A_IP2

description:
Library name: sample10
iPSC_m6A_IP2


title: AFE_m6A_input2

description:
Library name: sample6
AFE_m6A_input2


title: LP_m6A_input1

description:
Library name: sample7
LP_m6A_input1


title: AFE_m6A_input1

description:
Library name: sample5
AFE_m6A_input1


title: DE_m6A_input1

description:
Library name: sample3
DE_m6A_input1


title: iPSC_m6A_input2

description:
Library name: sample2
iPSC_m6A_input2


title: DE_m6A_input2

description:
Library name: sample4
DE_m6A_input2


title: iPSC_m6A_input1

description:
Library name: sample1
iPSC_m6A_input1


title: mm202C-sgNTC_RNA_steadystate_REP1_250408_TTTGAGTC_S37

status: Public on Jun 02 2025

city: Boston

first: Scott

last: Armstrong

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

description:
Library name: Sample 28
mouse leukemia

data_processing:
Reads (paired-end 37-mers) were aligned to the mouse (Gencode M24/mm10) reference genome using STAR (v2.7.5a, sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl).
Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
Assembly: M24/mm10
Supplementary files format and content: DESeq2 differential expression summary data (Excel .xlsx format) and .tdf files viewable in Broad IGV

source_name: mouse leukemia

growth_protocol: IMDM with 20% FBS, 1% penicillin/streptomycin (Gibco), 6 mg/mL mIL3, 10 mg/mL mIL6, and 10 mg/mL mSCF (Stemcell Technologies) at 37°C and 5% CO2.

extract_protocol:
For RNA isolation from cell lines, 1x10^6 cells were lysed in 350 µl of RLT buffer and RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions for cell line experiments.
1.2 ug RNA was used as the input quantity for library construction. Poly-A tail selection and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA).

treatment_protocol: NUP98-HOXA9 murine leukemia cells expressing CRISPR-Cas9 were transduced with lentivirus to deliver sgRNA targeting Kat6a/6b/7.

tag: sgrna

value: sgNTC

value: mouse leukemia


title: mm202C-sgKat7-3_RNA_steadystate_REP1_250408_ATCAAATC_S25

description:
Library name: Sample 25
mouse leukemia

tag: cell line


title: mm202C-sgKat7-2_RNA_steadystate_REP3_250408_CGAGTCAG_S24

description:
Library name: Sample 24
mouse leukemia


title: mm202C-sgKat7-2_RNA_steadystate_REP2_250408_CCAATGAA_S23

description:
Library name: Sample 23
mouse leukemia


title: mm202C-sgNTC_RNA_steadystate_REP2_250408_TCACTAAC_S38

description:
Library name: Sample 29
mouse leukemia


title: mm202C-sgNTC_RNA_steadystate_REP3_250408_TCCGATGG_S39

description:
Library name: Sample 30
mouse leukemia


title: mm202C-sgKat7-3_RNA_steadystate_REP2_250408_CTATCGAA_S26

description:
Library name: Sample 26
mouse leukemia


title: mm202C-sgKat6b-4_RNA_steadystate_REP2_250408_GCCGAATC_S20

description:
Library name: Sample 20
mouse leukemia


title: mm202C-sgKat7-3_RNA_steadystate_REP3_250408_AAGTATGC_S27

description:
Library name: Sample 27
mouse leukemia


title: LP_m6A_IP1

description:
Library name: sample15
LP_m6A_IP1


title: mm202C-sgKat6b-4_RNA_steadystate_REP1_250408_TCCTGGAC_S19

description:
Library name: Sample 19
mouse leukemia


title: mm202C-sgKat6b-4_RNA_steadystate_REP3_250408_TACTGTGA_S21

description:
Library name: Sample 21
mouse leukemia


title: AFE_m6A_IP2

description:
Library name: sample14
AFE_m6A_IP2


title: DE_m6A_IP1

description:
Library name: sample11
DE_m6A_IP1


title: mm202C-sgKat7-2_RNA_steadystate_REP1_250408_TAACACGC_S22

description:
Library name: Sample 22
mouse leukemia


title: mm202C-sgKat6b-3_RNA_steadystate_REP2_250408_GTGAGCTA_S17

description:
Library name: Sample 17
mouse leukemia


title: mm202C-sgKat6b-3_RNA_steadystate_REP3_250408_TACTAAGG_S18

description:
Library name: Sample 18
mouse leukemia


title: mm202C-sgKat6b-3_RNA_steadystate_REP1_250408_ATGTACGT_S16

description:
Library name: Sample 16
mouse leukemia


title: mm202C-sgKat6a-4_RNA_steadystate_REP3_250408_CTGGACAC_S15

description:
Library name: Sample 15
mouse leukemia


title: mm202C-sgKat6a-4_RNA_steadystate_REP2_250408_GAGGACAG_S14

description:
Library name: Sample 14
mouse leukemia


title: mm202C-sgKat6a-3_RNA_steadystate_REP3_250408_TATCAGTA_S12

description:
Library name: Sample 12
mouse leukemia


title: mm202C-sgKat6a-3_RNA_steadystate_REP2_250408_GTTGCCTT_S11

description:
Library name: Sample 11
mouse leukemia


title: mm202C-sgKat6a-4_RNA_steadystate_REP1_250408_TTAAGCAG_S13

description:
Library name: Sample 13
mouse leukemia


title: mm202C-sgKat6a-1_RNA_steadystate_REP3_250408_AGTACAAG_S9

description:
Library name: Sample 9
mouse leukemia


title: mm202C-sgKat6a-1_RNA_steadystate_REP2_250408_AGTCTGCT_S8

description:
Library name: Sample 8
mouse leukemia


title: mm202C-sgKat6a-1_RNA_steadystate_REP1_250408_AGTCCCGG_S7

description:
Library name: Sample 7
mouse leukemia


title: mm202C-sgBrpf1-5_RNA_steadystate_REP2_250408_AAAGATCG_S5

description:
Library name: Sample 5
mouse leukemia


title: mm202C-sgBrpf1-5_RNA_steadystate_REP3_250408_AGTAGTAA_S6

description:
Library name: Sample 6
mouse leukemia


title: mm202C-sgKat6a-3_RNA_steadystate_REP1_250408_AGTTGGAT_S10

description:
Library name: Sample 10
mouse leukemia


title: mm202C-sgBrpf1-3_RNA_steadystate_REP3_250408_GCAATGGG_S3

description:
Library name: Sample 3
mouse leukemia


title: mm202C-sgBrpf1-5_RNA_steadystate_REP1_250408_GACATTAA_S4

description:
Library name: Sample 4
mouse leukemia


title: mm202C-sgBrpf1-3_RNA_steadystate_REP2_250408_AGCCTGGA_S2

description:
Library name: Sample 2
mouse leukemia


title: mm202C_RNA_SNDX_2uM_PF9363_500nM_72h_REP3_240805_GGTAGC_S12

description:
Library name: Sample 12
mouse leukemia

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the mouse (Gencode M24/mm10) reference genome using STAR (v2.7.5a, sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl).
Assembly: Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
Supplementary files format and content: M24/mm10
Supplementary files format and content: DESeq2 differential expression summary data (Excel .xlsx format)

extract_protocol:
For RNA isolation from cell lines, 1x10^6 cells were lysed in 350 µl of RLT buffer and RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions for cell line experiments.
1 ug RNA was used as the input quantity for library construction. Poly-A tail selection and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA).

treatment_protocol: Prior to harvesting RNA, cells were treated with DMSO, 500 nM PF9363, 2 uM SNDX-5613, or a combination of both (500 nM PF9363 + 2 uM SNDX-5613) for 72 hours.

tag: timepoint

value: 72 hours


title: mm202C_RNA_SNDX_2uM_PF9363_500nM_72h_REP1_240805_CGTACG_S10

description:
Library name: Sample 10
mouse leukemia


title: mm202C_RNA_SNDX_2uM_72h_REP2_240805_GTAGAG_S5

description:
Library name: Sample 8
mouse leukemia

value: 2 uM SNDX-5613


title: mm202C_RNA_SNDX_2uM_72h_REP1_240805_CCGTCC_S4

description:
Library name: Sample 7
mouse leukemia


title: mm202C-sgBrpf1-3_RNA_steadystate_REP1_250408_ACTTCTGC_S1

description:
Library name: Sample 1
mouse leukemia


title: mm202C_RNA_SNDX_2uM_PF9363_500nM_72h_REP2_240805_GAGTGG_S11

description:
Library name: Sample 11
mouse leukemia


title: mm202C_RNA_SNDX_2uM_72h_REP3_240805_GTCCGC_S6

description:
Library name: Sample 9
mouse leukemia


title: mm202C_RNA_PF9363_500nM_72h_REP3_240805_GTTTCG_S9

description:
Library name: Sample 6
mouse leukemia


title: mm202C_RNA_PF9363_500nM_72h_REP1_240805_GTGAAA_S7

description:
Library name: Sample 4
mouse leukemia


title: mm202C_RNA_DMSO_72h_REP3_240805_ATGTCA_S3

description:
Library name: Sample 3
mouse leukemia

value: DMSO


title: mm202C_RNA_PF9363_500nM_72h_REP2_240805_GTGGCC_S8

description:
Library name: Sample 5
mouse leukemia


title: mm202C_RNA_DMSO_72h_REP1_240805_AGTCAA_S1

description:
Library name: Sample 1
mouse leukemia


title: mm202C_ChIP_MLL1_SNDX_2uM_72h_REP1_240904_AGTTCC_S14

description:
Library name: Sample 16
mouse leukemia

library_source: genomic

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the mouse (Gencode M24/mm10) genome using STAR (v2.7.5a; params --alignIntronMax 1 --alignEndsType EndToEnd --alignM atesGapMax 2000 for ChIPseq analysis), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
ChIP-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75) and deeptools (pileup heatmaps). ChIPseq peaks were called using MACS2 with appropriate input samples used as controls.
TSS- and other interval-associated signals were assessed using bedtools coverage (v2.28.0).
Assembly: Gencode M24/mm10
Supplementary files format and content: Genome-wide signal pileup files for visualization in IGV in TDF format
Supplementary files format and content: Bedtools coverage output for signal at TSS-associated intervals (-1kb to +3kb for each annotated protein-coding transcription start site), summarized in Excel spreadsheet format

molecule: genomic DNA

extract_protocol:
Cells were crosslinked using 1% methanol-free paraformaldehyde for 10 min at room temperature. Glycine (25 mM) was used to quench the reaction. Nuclei were extracted and chromatin was subjected to sonication using an E220 focused ultrasonicator (Covaris).
1-5 µg of DNA was used in preparation of Illumina-compatible libraries using a ThruPLEX DNA-Seq Kit (Takara) followed by sequencing using NextSeq550 (Illumina) to obtain 20-30e6 unique sequencing paired-end reads.

treatment_protocol: Prior to crosslinking, cells were treated with DMSO, 500 nM PF9363, 2 uM SNDX-5613, or a combination of both (500 nM PF9363 + 2 uM SNDX-5613) for 72 hours.

tag: chip antibody

tag: antibody vendor

value: Bethyl

tag: antibody catalog_number

tag: genetic background


title: mm202C_ChIP_input_PF9363_500nM_72h_REP1_240904_GTGGCC_S19

description:
Library name: Sample 11
mouse leukemia


title: mm202C_ChIP_MLL1_PF9363_500nM_72h_REP1_240904_ATGTCA_S15

description:
Library name: Sample 15
mouse leukemia


title: mm202C_ChIP_HA_SNDX_2uM_72h_REP1_240904_GCCAAT_S6

description:
Library name: Sample 8
mouse leukemia

value: HA

value: Diagenode


title: mm202C_ChIP_MLL1_DMSO_72h_REP1_240904_AGTCAA_S13

description:
Library name: Sample 14
mouse leukemia


title: mm202C_ChIP_HA_DMSO_72h_REP1_240904_ACAGTG_S5

description:
Library name: Sample 6
mouse leukemia


title: mm202C_ChIP_input_SNDX_2uM_72h_REP1_240904_GTGAAA_S18

description:
Library name: Sample 12
mouse leukemia


title: mm202C_ChIP_Brpf1_SNDX_2uM_72h_REP1_240904_CGATGT_S2

description:
Library name: Sample 4
mouse leukemia

value: ThermoFisher


title: mm202C_ChIP_Brpf1_Combo_72h_REP1_240904_TGACCA_S4

description:
Library name: Sample 1
mouse leukemia


title: mm75_hsNUP98r_RNA_PF9363_3mpk-1mo_54d_REP1_231031_AGTTCC_S11

description:
Library name: Sample 23
patient-derived xenograft

source_name: patient-derived xenograft

value: 3 mg/kg PF-9363 chow

value: 48 hours

value: patient-derived xenograft


title: mm73_hsNUP98r_RNA_PF9363_3mpk-1mo_54d_REP1_231031_TAGCTT_S7

description:
Library name: Sample 19
patient-derived xenograft


title: mm61_hsNUP98r_RNA_vehicle_54d_REP2_231031_CAGATC_S4

description:
Library name: Sample 16
patient-derived xenograft


title: TET2-05

status: Public on May 21 2025

city: New York

first: Maria

last: Sirenko

state: NY

address: 550 1st Avenue

institute: NYU Langone

description:
Library name: TET2-05
peripheral blood TET2 donor 05

data_processing:
cellranger v5.0.1
R v4.2.2 and Seurat v4.3
Assembly: grch38
Supplementary files format and content: cellranger output files - filtered feature barcode matrix and bam

molecule: polyA RNA

source_name: peripheral blood

extract_protocol:
viably frozen MNCs thawed and processed with 10X GEX
10X genomics 5' v2 next-gem single cell RNAseq

value: peripheral blood

value: PBMCs


title: mm202C_ChIP_input_Combo_72h_REP1_240904_GTTTCG_S20

description:
Library name: Sample 9
mouse leukemia


title: mm202C_ChIP_input_DMSO_72h_REP1_240904_GTCCGC_S17

description:
Library name: Sample 10
mouse leukemia


title: TET2-04

description:
Library name: TET2-04
peripheral blood TET2 donor 04


title: mm202C_ChIP_HA_PF9363_500nM_72h_REP1_240904_CAGATC_S7

description:
Library name: Sample 7
mouse leukemia


title: mm202C_ChIP_HA_Combo_72h_REP1_240904_ACTTGA_S8

description:
Library name: Sample 5
mouse leukemia


title: mm202C_RNA_DMSO_72h_REP2_240805_AGTTCC_S2

description:
Library name: Sample 2
mouse leukemia


title: mm202C_ChIP_Brpf1_PF9363_500nM_72h_REP1_240904_TTAGGC_S3

description:
Library name: Sample 3
mouse leukemia


title: mm202C_ChIP_Brpf1_DMSO_72h_REP1_240904_ATCACG_S1

description:
Library name: Sample 2
mouse leukemia


title: mm75_hsNUP98r_RNA_PF9363_3mpk-1mo_54d_REP2_231031_ATGTCA_S12

description:
Library name: Sample 24
patient-derived xenograft


title: mm74_hsNUP98r_RNA_PF9363_3mpk-1mo_54d_REP2_231031_CTTGTA_S10

description:
Library name: Sample 22
patient-derived xenograft


title: AML-20-CR

description:
Library name: AML-20-CR
remission sample from AML-20

source_name: bone marrow

value: bone marrow

value: BMMCs


title: mm74_hsNUP98r_RNA_PF9363_3mpk-1mo_54d_REP1_231031_AGTCAA_S9

description:
Library name: Sample 21
patient-derived xenograft


title: mm73_hsNUP98r_RNA_PF9363_3mpk-1mo_54d_REP2_231031_GGCTAC_S8

description:
Library name: Sample 20
patient-derived xenograft


title: AML-19-Dx

description:
Library name: AML-19-Dx
diagnosis sample from AML-19


title: AML-18-Rel-2

description:
Library name: AML-18-Rel-2
relapse sample from AML-18 replicate 2


title: AML-18-Rel-1

description:
Library name: AML-18-Rel-1
relapse sample from AML-18 replicate 1


title: AML-20-Rel

description:
Library name: AML-20-Rel
relapse sample from AML-20


title: mm59_hsNUP98r_RNA_vehicle_54d_REP2_231031_ACAGTG_S2

description:
Library name: Sample 14
patient-derived xenograft


title: AML-18-CR-1

description:
Library name: AML-18-CR-1
remission sample from AML-18 replicate 1


title: mm59_hsNUP98r_RNA_vehicle_54d_REP1_231031_TGACCA_S1

description:
Library name: Sample 13
patient-derived xenograft


title: mm64_hsNUP98r_RNA_vehicle_54d_REP2_231031_GATCAG_S6

description:
Library name: Sample 18
patient-derived xenograft


title: mm61_hsNUP98r_RNA_vehicle_54d_REP1_231031_GCCAAT_S3

description:
Library name: Sample 15
patient-derived xenograft


title: mm202C_ChIP_MLL1_Combo_72h_REP1_240904_CCGTCC_S16

description:
Library name: Sample 13
mouse leukemia


title: AML-20-Dx

description:
Library name: AML-20-Dx
diagnosis sample from AML-20


title: AML-19-Rel

description:
Library name: AML-19-Rel
relapse sample from AML-19


title: AML-19-CR1

description:
Library name: AML-19-CR
remission sample from AML-19


title: AML-17-CR-1

description:
Library name: AML-17-CR-1
remission sample from AML-17 replicate 1


title: AML-17-Dx-2

description:
Library name: AML-17-Dx-2
diagnosis sample from AML-17 replicate 2


title: mm64_hsNUP98r_RNA_vehicle_54d_REP1_231031_ACTTGA_S5

description:
Library name: Sample 17
patient-derived xenograft


title: AML-18-Dx-1

description:
Library name: AML-18-Dx-1
diagnosis sample from AML-18 replicate 1

source_name: apheresis

value: apheresis

value: MNCs


title: AML-18-Dx-2

description:
Library name: AML-18-Dx-2
diagnosis sample from AML-18 replicate 2


title: AML15_AML17_2

description:
antibodies/tags: CITEseq_panels.xlsx
CITE-seq

data_processing:
Raw data provided as BAM files. These Bam files contain ADT/HTO data with the feature barcode tag as the cellranger output.
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v.5) and aligning to the GRCh38 genome.
Further processing was done with Seurat v4 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz are provided for each library. The final seurat object after quality control described as in the paper is also provided.

source_name: mRNA/HTO/ADT

extract_protocol:
Frozen bone marrow samples were thawed and transferred into 50ml conical tubes containing 1x PBS +2% fetal bovine serum(FBS). Cell suspensions were centrifuged at 300 x g for 5 minutes at 4℃, and supernatant was removed. Samples were then enriched for >90% alive cells by using a dead cell removal kit, or stained with DAPI before sorted for alive cells using SY3200 Cell Sorter (SONY). For cell sorting, DAPI low cells are collected into 15ml conical tubes containing 3ml FBS on ice. Samples were then centrifuged at 300 x g for 5 mins at 4℃. Enriched alive cells were first stained with cell-hashing oligo-tagged antibodies(Biolegend)  according to manufacturer’s instructions. Then samples were counted and pooled together and stained with a CITE-seq antibody cocktail (Biolegend) according to the manufacturer’s instructions. After staining, samples were processed using 10X Genomics Chromium controller with the Single Cell Gene Expression 3’ Reagent Kits
Library was prepared using Chromium Single Cell 3ʹ v3.1 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v2 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ v2 protocol (10x Genomics). For antibody-derived tagged library, we used the KAPA HiFI HotStart Library Amplification Kit (Roche) with the following primers and amplification program:
CITE-seq library: amplification was performed at 95°C for 3’ followed by ten cycles at 95°C for 20’’; 60°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’.
HASH-seq library: amplification was performed at 95°C for 3’ followed by ten cycles 95°C for 20’’; 64°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’.
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 15% ADT library and 5% HTO library before sequencing.

value: Bone Marrow

value: Bone Marrow Mononuclear cells

tag: disease state

value: AML

tag: library type

value: mRNA/HTO/ADT


title: AML-17-Rel-2

description:
Library name: AML-17-Rel-2
relapse sample from AML-17 replicate 2


title: AML14


title: AML-17-CR-2

description:
Library name: AML-17-CR-2
remission sample from AML-17 replicate 2


title: AML-17-Rel-1

description:
Library name: AML-17-Rel-1
relapse sample from AML-17 replicate 1


title: AML-17-Dx-1

description:
Library name: AML-17-Dx-1
diagnosis sample from AML-17 replicate 1


title: AML15_AML17_3


title: AML12_AML13_1


title: AML-16-Dx

description:
Library name: AML-16-Dx
diagnosis sample from AML-16


title: AML-18-CR-2

description:
Library name: AML-18-CR-2
remission sample from AML-18 replicate 2


title: AML15_AML17_1


title: AML12_AML13_2

value: Bone Marrow/Peripheral Blood

value: Bone Marrow Mononuclear cells / Peripheral Blood Mononuclear cells


title: AML11_AML09_2


title: AML08_4_AML16_2


title: AML08_3_AML16_1


title: AML08_5_AML16_3


title: AML08_2


title: AML08_1


title: AML07_2


title: AML10


title: FFPE_ATAC_Human_melanoma_50um

status: Public on May 19 2025

city: philadelphia

first: Pengfei

last: Guo

state: PA

address: 422 Curie Boulevard, Stellar Chance Labs, 711-712 (lab), philadelphia

institute: University of Pennsylvania

description:
Library name: Sample 18
ATAC-seq

data_processing:
Linkers 1 and 2 are used for targeted filtering of read 2, aligning utilizing BWA followed by sorting and indexing via Samtools to facilitate efficient data handling and retrieval. This reformatting process assigned genome sequences to the first read and incorporated barcodes A and B into the second read. We aligned these fastq files against mouse (GRCm38) or human (GRCh38) reference genomes. The conversion produced tsv-like fragments files, enriched with spatial and genomic information through the integration of barcode pairs, facilitating comprehensive downstream analysis.
Assembly: GRCm38, GRCh38
Supplementary files format and content: TSV files for downstream analysis. The tsv file contains tissue location info (barcode A x barcode B) and fragments info on the genome.
Supplementary files format and content: tif file: The adjacent tissue section was used for H&E staining.
Library strategy: Spatial ATAC-seq

source_name: Human tumor

extract_protocol:
The workflow is summarized in Fig. 1a and Extended Data Fig. 1. Initially, FFPE tissues underwent antigen retrieval (AR) to break crosslinks, followed by in situ Tn5 transposition, where adapters were inserted into accessible genomic regions. Next, spatial barcodes (A1-50 and B1-50) were ligated onto the genomic DNA through two rounds of ligation, facilitated by microfluidic channels. Tissue slides were then imaged to link the spatial barcodes to tissue morphology. After tissue lysis, the barcoded DNA fragments were amplified for library preparation.
After antigen retrieval, tissue was washed twice with 1 ml of 1× DPBS and cleaned with ddH2O. The sequential order for spatial ATAC profiling is as follows: 1. ATAC-seq; 2. Ligation of barcode A; 3. Ligation of barcode B; 4. Reverse crosslink; 5. Library construction; 6. Library QC and sequencing.

value: Human tumor


title: AML07_1


title: FFPE_ATAC_Human_thymus_50um_replicate_1

description:
Library name: Sample 15
ATAC-seq

source_name: Human thymus

value: Human thymus


title: Blood_patient_21

status: Public on Apr 30 2025

city: Biberach a.d. Riss

first: Eric

last: Simon

address: Birkendorfer Str. 65

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co KG

data_processing:
The bulk RNA-Seq analysis pipeline has been described before (Simon et al., 2023). In brief, reads passing quality control filter were mapped against GRCh38 using STAR (v2.5.2b) aligner.
Gene expression levels were quantified using RSEM (v1.3.0) and featureCounts (v1.5.1).
For quality control FastQC (v0.11.5), picardmetrics (v0.2.4) and dupRadar (v1.2.2) were employed.
Assembly: GRCh38
Supplementary files format and content: counts_RNASeq_WBC_bulk.txt: raw counts of all samples as txt file
Supplementary files format and content: tpm_RNASeq_WBC_bulk.txt: transcripts per million of all samples as txt file

source_name: White blood cells

extract_protocol:
White Blood cells were isolated by centrifugation of K3-EDTA blood samples and treated with erythrocyte lysis buffer. After white blood cell (WBC) isolation from blood, RNA has been isolated using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina #E7760, together with the NEBNext Poly(A) mRNA Magnetic Isolation Module #E7490 and NEBNext Multiplex Oligos for Illumina #E7600 (New England Biolabs) as per manufacturer’s instructions

value: White blood cells

tag: Sex

value: female

tag: disease

value: MAFLD/MASH

tag: nas

tag: assaytype

value: bulk

tag: celltype

value: wbc

tag: batch

value: patient

tag: condition


title: Blood_control_14

tag: tissue

value: male

value: Control

value: control


title: Blood_patient_20


title: FFPE_ATAC_Human_cerebellum_50um

description:
Library name: Sample 14
ATAC-seq

source_name: Human cerebellum

value: Human cerebellum


title: Blood_patient_19


title: Blood_patient_18


title: AML11_AML09_3

value: Bone Marrow

tag: cell type

value: Bone Marrow Mononuclear cells


title: Blood_patient_17


title: Blood_control_13


title: Blood_control_11


title: AML11_AML09_1

value: AML

value: mRNA/HTO/ADT


title: Blood_control_12


title: Blood_control_10


title: Blood_patient_14


title: Blood_control_7


title: Blood_patient_13


title: Blood_control_5


title: Blood_control_4


title: Blood_control_3


title: Blood_patient_12


title: Blood_control_2


title: Blood_control_1


title: Blood_control_8


title: Blood_patient_15


title: Blood_patient_16


title: Blood_patient_11


title: Blood_patient_10


title: Blood_patient_8


title: Blood_patient_7


title: Blood_patient_9


title: Blood_patient_3


title: Blood_patient_5


title: Blood_patient_6


title: Blood_patient_4


title: Blood_patient_2


title: Blood_patient_1


title: Blood_control_9


title: MCF7_ATAC_PF9363_50nM_SNDX_200nM_2d_REP2_250129_CAGAGAGG_S8

description: Library name: Sample8

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads were aligned to the human genome (Gencode GRCh38/hg38 v33) using STAR (v2.7.5a; params --alignIntronMax 1 --alignEndsType EndToEnd --alignMatesGapMax 2000), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4). Final “deduped” .BAM files were indexed using SAMtools (v1.95).
MACS2 (v2.1.4) was used to call peaks.
Data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75) and deeptools (tornado plots; v3.1.3; regions around combined peak loci from all ATAC samples plotted using referencePoint option and k=1).
Motif enrichment analysis was performed using HOMER (v4.11) motif analysis tools66. Loss of accessibility was defined as rpk drug/DMSO FC <0.5.
Assembly: GRCh38/hg38
Supplementary files format and content: Tabular results in Excel .xlsx format

growth_protocol: MCF7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 1xL-glutamine, 10% Fetal Bovine Serum, and 1xPenStrep

extract_protocol:
Cell pellets were resuspended in 1mL ATAC-resuspension buffer (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl2) and centrifuged at 1,000 g for 10 min at 4°C. Cell pellets were resuspended in 50μL cold lysis buffer (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% NP40; 0.1% Tween-20 (Roche), 0.01% Digitonin (Promega)) and incubated on ice for 3 minutes. 1mL wash buffer was added (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% Tween-20) and cells were spun down immediately at 1,000 g for 10 min at 4°C. Following this, the pellet was resuspended in a transposase reaction mixture (2X TD buffer, 20X transposase (100nM final, Illumina), 0.01% Digitonin (Promega), 0.1% Tween-20 (Roche)) at 37 °C for 30 minutes in a thermomixer with 1,000 rpm mixing. DNA was purified using a DNA Clean and Concentrator-5 kit (Zymo) as per the manufacturer’s instructions.
The DNA fragments were amplified in a PCR reaction with 2X NEBNext High-Fidelity PCR Master Mix (New England Biolabs) and purified using AMPure XP beads (Beckman Coulter). DNA fragments were quantified by TapeStation 4200 (Agilent) using HSD5000 Tape and Reagent (Agilent) and Qubit (ThermoFisher).
ATAC-sequencing was done using the Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) to obrain 50 million 37bp, paired-end reads.

treatment_protocol: MCF7 cells were plated in duplicate in 6 well plates at 5x105 cells/mL in the appropriate culture medium and were treated with DMSO, PF-9363 (50nM), SNDX-5613 (200nM), or PF-9363 (50nM)+SNDX-5613 (200nM) for 48h.

tag: cell line

value: cell line

tag: time

value: 2 days

tag: treatment


title: MCF7_ATAC_PF9363_50nM_SNDX_200nM_2d_REP1_250129_CTCTCTAC_S7

description: Library name: Sample7


title: MCF7_ATAC_SNDX_200nM_2d_REP1_250129_GGACTCCT_S5

description: Library name: Sample5


title: Blood_control_6


title: MCF7_ATAC_DMSO_2d_REP1_250129_TAAGGCGA_S1

description: Library name: Sample1

value: DMSO


title: MCF7_ATAC_DMSO_2d_REP2_250129_CGTACTAG_S2

description: Library name: Sample2


title: T47DsgMEN1-sgKAT6B_RNA_steadystate_REP3_241016_GTCCGC_S18

description: Library name: Sample36

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers or single 75-mer reads) were aligned to the human genome (Gencode GRCh38/hg38 v33) using STAR (v2.7.5a), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4). Final “deduped” .BAM files were indexed using SAMtools (v1.95).
Raw per-gene counts were calculated with HTSeq (htseq-count, v0.6.1pl) and differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
All heatmaps were generated using the Broad Institute Morpheus tool.
Assembly: GRCh38/hg38
Supplementary files format and content: IGVtools .tdf files (for visualization in Broad IGV)
Supplementary files format and content: Tabular results for selected samples in Excel .xlsx format

growth_protocol: MCF7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 1xL-glutamine, 10% Fetal Bovine Serum, and 1xPenStrep. T47D cells were cultured in Roswell Park Memorial Institute (RPMI) supplemented with 1xL-glutamine, 10% Fetal Bovine Serum, and 1xPenStrep.

extract_protocol:
1 million cells were trypsinized, washed with cold PBS, and lysed in 350μL RLT buffer. RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions and DNase treatment was performed on the column
RNA quality for RNA sequencing was checked on the Agilent TapeStation (Agilent) and quantified by Qubit (ThermoFisher). RNA (1µg) was used to make Illumina compatible libraries by doing Poly-A tail selection (New England Biolabs) and library preparation using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions.
RNA-sequencing was done using the Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) to obrain 20-30 million 37bp, paired-end of 75bp single-end reads.

treatment_protocol: Stable Cas9-expressing MCF7 and T47D cell lines were generated and were infected with sgRNA targeting a non-targeting control (sgLuc), KAT6A, KAT6B, and/or Menin. Cells were selected with puromycin (Sigma-Aldrich) for three days. Selected cells were seeded in in triplicate per well of a 6 well plate (Day 0). Cells were split every 3-4 days and were maintained in full media, supplemented with blasticidin (Gibco) and puromycin. On Day 7 cells were harvested and processed for RNA-sequencing.

tag: guiderna


title: MCF7_ATAC_PF9363_50nM_2d_REP2_250129_TCCTGAGC_S4

description: Library name: Sample4


title: T47DsgMEN1-sgKAT6B_RNA_steadystate_REP1_241016_CCGTCC_S16

description: Library name: Sample34


title: T47DsgMEN1-sgKAT6A_RNA_steadystate_REP3_241016_ATGTCA_S15

description: Library name: Sample33


title: T47DsgMEN1-sgKAT6A_RNA_steadystate_REP1_241016_AGTCAA_S13

description: Library name: Sample31


title: T47D-sgMEN1_RNA_steadystate_REP3_241016_GCCAAT_S6

description: Library name: Sample30


title: MCF7_ATAC_PF9363_50nM_2d_REP1_250129_AGGCAGAA_S3

description: Library name: Sample3


title: T47D-sgMEN1_RNA_steadystate_REP2_241016_ACAGTG_S5

description: Library name: Sample29


title: T47DsgMEN1-sgKAT6B_RNA_steadystate_REP2_241016_GTAGAG_S17

description: Library name: Sample35


title: T47DsgMEN1-sgKAT6A_RNA_steadystate_REP2_241016_AGTTCC_S14

description: Library name: Sample32


title: T47D-sgLuc_RNA_steadystate_REP3_241016_TTAGGC_S3

description: Library name: Sample27

value: sgLuciferase


title: T47D-sgLuc_RNA_steadystate_REP1_241016_ATCACG_S1

description: Library name: Sample25


title: T47D-sgLuc_RNA_steadystate_REP2_241016_CGATGT_S2

description: Library name: Sample26


title: T47D-sgKAT6B_RNA_steadystate_REP3_241016_CTTGTA_S12

description: Library name: Sample24


title: T47D-sgMEN1_RNA_steadystate_REP1_241016_TGACCA_S4

description: Library name: Sample28


title: T47D-sgKAT6B_RNA_steadystate_REP1_241016_TAGCTT_S10

description: Library name: Sample22


title: MCF7-sgMEN1-sgKAT6B_RNA_steadystate_REP3_240812_CGTACG_S18

description: Library name: Sample18


title: MCF7_ATAC_SNDX_200nM_2d_REP2_250129_TAGGCATG_S6

description: Library name: Sample6


title: T47D-sgKAT6A_RNA_steadystate_REP3_241016_GATCAG_S9

description: Library name: Sample21


title: MCF7-sgMEN1-sgKAT6A_RNA_steadystate_REP3_240812_GTGAAA_S15

description: Library name: Sample15


title: MCF7-sgMEN1-sgKAT6B_RNA_steadystate_REP1_240812_GTGGCC_S16

description: Library name: Sample16


title: T47D-sgKAT6A_RNA_steadystate_REP1_241016_CAGATC_S7

description: Library name: Sample19


title: MCF7-sgMEN1-sgKAT6B_RNA_steadystate_REP2_240812_GTTTCG_S17

description: Library name: Sample17


title: T47D-sgKAT6B_RNA_steadystate_REP2_241016_GGCTAC_S11

description: Library name: Sample23


title: MCF7-sgMEN1-sgKAT6A_RNA_steadystate_REP1_240812_CCGTCC_S13

description: Library name: Sample13


title: MCF7-sgMEN1-sgKAT6A_RNA_steadystate_REP2_240812_GTAGAG_S14

description: Library name: Sample14


title: MCF7-sgMEN1_RNA_steadystate_REP3_240812_GATCAG_S6

description: Library name: Sample12


title: MCF7-sgMEN1_RNA_steadystate_REP2_240812_ACTTGA_S5

description: Library name: Sample11


title: MCF7-sgMEN1_RNA_steadystate_REP1_240812_CAGATC_S4

description: Library name: Sample10


title: T47D-sgKAT6A_RNA_steadystate_REP2_241016_ACTTGA_S8

description: Library name: Sample20


title: MCF7-sgLuc_RNA_steadystate_REP3_240812_ACAGTG_S3

description: Library name: Sample9


title: MCF7-sgKAT6B_RNA_steadystate_REP3_240812_ATGTCA_S12

description: Library name: Sample6


title: MCF7-sgKAT6B_RNA_steadystate_REP1_240812_AGTCAA_S10

description: Library name: Sample4


title: MCF7-sgKAT6B_RNA_steadystate_REP2_240812_AGTTCC_S11

description: Library name: Sample5


title: MCF7-sgKAT6A_RNA_steadystate_REP3_240812_CTTGTA_S9

description: Library name: Sample3


title: MCF7-sgKAT6A_RNA_steadystate_REP2_240812_GGCTAC_S8

description: Library name: Sample2


title: MCF7_ChIP_input_steadystate_REP1_240813_GTCCGC_S17

description: Library name: Sample19

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers or single 75-mer reads) were aligned to the human genome (Gencode GRCh38/hg38 v33) using STAR (v2.7.5a; params --alignIntronMax 1 --alignEndsType EndToEnd --alignMatesGapMax 2000), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4). Final “deduped” .BAM files were indexed using SAMtools (v1.95).
MACS2 (v2.1.4) was used to call peaks with appropriate input samples as controls for peak calling. Peaks were called with q-value cut-off of 0.01 and broad peak mode.
Promoter-associated signal was determined using bedtools “coverage” (v2.28.0), using annotated gene body genomic intervals and TSS region intervals (-1kb to +3kb for each protein-coding transcript TSS, using gene orientation).
ChIP-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75) and deeptools (tornado plots; v3.1.3; regions around TSS/promoter intervals plotted using referencePoint or scaledRegion option and k=1).
Read counts were normalized were normalized using ratios of total read counts between treated and control sample pairs
Assembly: GRCh38/hg38
Supplementary files format and content: IGVtools .tdf files (for visualization in Broad IGV)

growth_protocol: MCF7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 1xL-glutamine, 10% Fetal Bovine Serum, and 1xPenStrep. For estrogen starvation, cells were seeded in complete culture medium. The next day (Day 0), cells were washed with PBS 3 times and phenol red-free DMEM (Gibco), supplemented with 10% charcoal-stripped FBS (Gibco), was added. On Day 3 (72 hours upon estrogen starvation), cells were treated with vehicle (DMSO) or estradiol (Selleck Chemicals) for 6 hours prior to harvesting.

extract_protocol:
The cells were collected and washed twice in ice-cold PBS followed by crosslinking in 1% formaldehide (methanol free) for 10 minutes. Excess of formaldehyde was quenched by addition of Tris pH 8.0 to 100nM final and Glycine 125 mM final. Chromatin was sheared using Covaris E220 for 30 min with power 140; duty 5; bursts 200/sec. We then used a 5ul aliquot of sherared chromatin to decrosslink in order to test completeness of shearing. Chromatin passed QC if fragments between 100-700bp were >90%. For immunoprecipitation we used chromatin from 5-20x10^6 cells, antibody and Protein-A/G magnetic beads. Following roatation at 4 degrees overnight, beads were wased in Mixed Micelle Buffer, buffer 500, LiCl/detergent solution and TE buffers. DNA was eluted from the beads using 100mM NaHCO3 100mM NaCl 1% SDS and purified using AmpureXP beads.
1-10 ng of DNA was used for the library preparation using the ThruPLEX DNA-Seq Kit (Takara)
ChIP-sequencing was done using the Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) to obrain 25-30 million 37bp, paired-end reads.

treatment_protocol: Cells were treated with drugs as indicated for 24h.

value: 24 hours


title: MCF7_ChIP_input_SNDX_200nM_24h_REP1_240813_TTAGGC_S3

description: Library name: Sample18


title: MCF7_ChIP_input_PF9363_50nM_SNDX_200nM_24h_REP1_240813_TGACCA_S4

description: Library name: Sample17


title: MCF7_ChIP_input_PF9363_50nM_24h_REP1_240813_CGATGT_S2

description: Library name: Sample16


title: CTSS_cloneC12_rep2_L

status: Public on Jun 17 2025

city: San Diego

first: David

middle: M

last: Gilbert

state: California

address: 3525 John Hopkins Ct Ste 200

institute: San Diego Biomedical Research Institute

description:
Library name: CTSS_cloneC12_rep2_L
Dppadel_CTSS_cloneC12_rep2_L

data_processing:
Sequence reads were trimmed using Trim_Galore/cutadapt and aligned to a custom N-masked mm10 reference genome where N replaces 129 or Castaneus SNPs relative to the standard mm10 reference genome.
Aligned reads were haplotype phased using SNP-split and split into 129- or Cas-specific files
Phased reads were counted in 50kb genomic bins using bedtools intersect
Log2 ratio of Early and Late read counts from corresponding sample and genome files is taken to calculate raw replication timing in each bin
Raw replication timing data is then quantile normalized across all datasets and loess-smoothed in 300kb genomic windows
Assembly: mm10
Supplementary files format and content: bedgraph file containing all datasets, where columns 1-3 are the genomic coordinates of each bin and columns 4-n contain the normalized and smoothed replication timing values. Each column contains a header, with columns 1-3 containing the chromosome, coordinate of bin start, and coordinate of bin end. Columns 4-n contain headers indentifying the cell line, clone, replicate, and parental genome of the dataset (the Zenododata can be found at DOI 10.5281/zenodo.15678081). Additionally, code to repeat our processing and analysis can be found at the following github repositories: https://github.com/jlt3/ERCEs_2023, https://github.com/ay-lab/SignifRT

growth_protocol: F121-9 Hybrid mESCs were grown in 2i + LIF

extract_protocol:
DNA from ~20k cells was extracted using the Quick-gDNA Microprep kit (Zymo)
Sequencing libraries were prepared according to Marchal et al 2018 Nat Protoc (PMID: 29599440). Briefly, DNA was sheared to an average size of 200bp using ultrasonication. Fragmented DNA was end repaired and adaptor-ligated using the NEBNext Ultra II DNA Library prep kit (NEB) following manufacturer instructions. BrdU-labeled DNA was immunoprecipitated using an anti-BrdU antibody and then purified. Purified BrdU-labeled DNA was then amplified using NEBNext Multiplex Oligos for Illumina (NEB). Libraries were pooled and sequenced on a Novaseq6000 machine.

treatment_protocol: Cells were engineered with various CRISPR-mediated deletions. Cells were labeled with BrdU for 2 hours, fixed in ethanol, and sorted for DNA content using flow cytometry into Early and Late S phase fractions.

value: Embryonic stem cell

tag: genotype

value: CRISPR-mediated deletion(s)


title: MCF7_ChIP_input_E2_SNDX_200nM_24h_REP1_240813_CAGATC_S7

description: Library name: Sample15


title: MCF7_ChIP_input_E2_DMSO_24h_REP1_240813_ACAGTG_S5

description: Library name: Sample12


title: MCF7_ChIP_input_E2_PF9363_50nM_SNDX_200nM_24h_REP1_240813_ACTTGA_S8

description: Library name: Sample14


title: MCF7_ChIP_GFP_steadystate_REP1_240813_GTGGCC_S19

description: Library name: Sample10

tag: chip target

value: GFP


title: MCF7_ChIP_input_DMSO_24h_REP1_240813_ATCACG_S1

description: Library name: Sample11


title: MCF7_ChIP_ESR1_steadystate_REP1_240813_GTGAAA_S18

description: Library name: Sample9


title: MCF7_ChIP_ESR1_SNDX_200nM_24h_REP1_240813_GGCTAC_S11

description: Library name: Sample8


title: MCF7_ChIP_ESR1_PF9363_50nM_SNDX_200nM_24h_REP1_240813_CTTGTA_S12

description: Library name: Sample7


title: MCF7-sgLuc_RNA_steadystate_REP2_240812_CGATGT_S2

description: Library name: Sample8


title: MCF7-sgLuc_RNA_steadystate_REP1_240812_ATCACG_S1

description: Library name: Sample7


title: MCF7_ChIP_ESR1_PF9363_50nM_24h_REP1_240813_TAGCTT_S10

description: Library name: Sample6


title: MCF7_ChIP_ESR1_E2_SNDX_200nM_24h_REP1_240813_ATGTCA_S15

description: Library name: Sample5


title: MCF7_ChIP_ESR1_E2_PF9363_50nM_24h_REP1_240813_AGTTCC_S14

description: Library name: Sample3


title: MCF7_ChIP_ESR1_DMSO_24h_REP1_240813_GATCAG_S9

description: Library name: Sample1


title: MCF7_ChIP_ESR1_E2_DMSO_24h_REP1_240813_AGTCAA_S13

description: Library name: Sample2


title: MCF7_ChIP_RNAPol2_SNDX_200nM_24h_REP1_240307_CAGATC_S7

value: RNA Polymerase 2


title: MCF7-sgKAT6A_RNA_steadystate_REP1_240812_TAGCTT_S7

description: Library name: Sample1


title: MCF7_ChIP_RNAPol2_PF9363_50nM_SNDX_200nM_24h_REP1_240307_ACTTGA_S8


title: MCF7_ChIP_RNAPol2_DMSO_24h_REP1_240617_GCCAAT_S20


title: MCF7_ChIP_RNAPol2_DMSO_24h_REP1_240307_ACAGTG_S5


title: MCF7_ChIP_input_PF9363_50nM_SNDX_200nM_24h_REP1_240307_TGACCA_S4


title: MCF7_ChIP_RNAPol2_PF9363_50nM_24h_REP1_240617_CAGATC_S22


title: MCF7_ChIP_input_DMSO_24h_REP1_240617_ATCACG_S15


title: MCF7_ChIP_input_DMSO_24h_REP1_240307_ATCACG_S1


title: MCF7_ChIP_input_E2_PF9363_50nM_24h_REP1_240813_GCCAAT_S6

description: Library name: Sample13


title: T47D_RNA_untreated_REP3_230524_GTAGAG_S3

growth_protocol: MCF7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 1xL-glutamine, 10% Fetal Bovine Serum, and 1xPenStrep. For estrogen starvation, cells were grown in DMEM without phenol red, supplemented with 10% charcoal stripped FBS, 1xPenStrep, and 1xL-glutamine. Organoids were maintained in 200μL Matrigel domes and were passaged by dissociation using TrypLE (Gibco). ER+ HCl-003 and HCl-018 organoids were cultured in Advanced DMEM/F12, supplemented with 5% Fetal Bovine Serum, 10 mM HEPES, 1xGlutamax, 1 μg/ml hydrocortisone, 50 μg/ml gentamicin, 10 ng/ml hEGF, 100 ng/ml FGF2, 1 mM NAC and 10 μM Y-27632. The ER+/HER2+ HCl-040 estrogen independent (EI) organoid was cultured in Advanced DMEM/F12, supplemented with 5% Fetal Bovine Serum, 10 mM HEPES, 1xGlutamax, 1 μg/ml hydrocortisone, 50 μg/ml gentamicin, 10 ng/ml hEGF, 100 ng/ml FGF2, 1 mM NAC, 10 nM heregulin-β1 and 10 μM Y-27632.

extract_protocol:
For cell lines, 1 million cells were trypsinized, washed with cold PBS, and lysed in 350μL RLT buffer. RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions and DNase treatment was performed on the column. For PDxOs, domes were mechanically disrupted using plain Advanced DMEM/F12. Cells were centrifuged at 4°C, 600 g for 5 minutes and washed once in cold PBS. Pellets were lysed in RLT buffer, supplemented with 1% beta-mercaptoethanol and stored at -80°C. Once thawed, samples were transferred to QiaShredder columns (Qiagen) and centrifuged. RNA was isolated from the flow through using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions and DNase treatment was performed on the column.
RNA quality for RNA sequencing was checked on the Agilent TapeStation (Agilent) and quantified by Qubit (ThermoFisher). RNA (1µg) was used to make Illumina compatible libraries by doing Poly-A tail selection (New England Biolabs) and library preparation using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions.
RNA-sequencing was done using the Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) to obrain 20-30 million 37bp, paired-end of 75bp single-end reads.

treatment_protocol: Cells/Organoids were grown in media as indicated and were treated with 50nM PF-9363 and/or 200nM SNDX-5613. For estrogen depletion experiments, 250,000 cells were seeded in complete culture medium in triplicate per well of a 6 well plate. The next day (Day 0), cells were washed with PBS 3 times and phenol red-free DMEM (Gibco), supplemented with 10% charcoal-stripped FBS (Gibco), was added. On Day 3, cells were acutely stimulated with estradiol (100nM) for 6h.


title: MCF7_ChIP_input_PF9363_50nM_24h_REP1_240617_CGATGT_S17


title: MCF7_ChIP_input_SNDX_200nM_24h_REP1_240307_TTAGGC_S3


title: T47D_RNA_untreated_REP2_230524_CCGTCC_S2


title: T47D_RNA_PF9363_50nM_96h_REP3_230524_CACTCA_S12

value: 96 hours


title: T47D_RNA_PF9363_50nM_96h_REP2_230524_CACGAT_S11


title: T47D_RNA_untreated_REP1_230524_ATGTCA_S1


title: T47D_RNA_PF9363_50nM_8h_REP1_230524_GTCCGC_S4

value: 8 hours


title: T47D_RNA_PF9363_50nM_96h_REP1_230524_CACCGG_S10


title: T47D_RNA_PF9363_50nM_8h_REP2_230524_GTGAAA_S5


title: T47D_RNA_PF9363_50nM_8h_REP3_230524_GTGGCC_S6


title: MCF7_ChIP_ESR1_E2_PF9363_50nM_SNDX_200nM_24h_REP1_240813_CCGTCC_S16

description: Library name: Sample4


title: T47D_RNA_PF9363_50nM_48h_REP2_230524_ACTGAT_S8

value: 48 hours


title: T47D_RNA_PF9363_50nM_48h_REP3_230524_ATGAGC_S9


title: T47D_RNA_PF9363_50nM_48h_REP1_230524_GGTAGC_S7


title: MCF7_RNA_untreated_REP3_230525_GTAGAG_S3


title: MCF7_RNA_untreated_REP2_230525_CCGTCC_S2


title: MCF7_RNA_untreated_REP1_230525_ATGTCA_S1


title: MCF7_RNA_SNDX_200nM_4d_REP3_2311x2_GATCAG_S9

value: 4 days

value: Estrogen starvation, 200nM SNDX-5613, DMSO


title: MCF7_RNA_SNDX_200nM_4d_REP3_231117_GATCAG_S9


title: MCF7_RNA_SNDX_200nM_4d_REP2_231117_ACTTGA_S8


title: MCF7_RNA_SNDX_200nM_4d_REP1_2311x2_CAGATC_S7


title: MCF7_RNA_SNDX_200nM_4d_REP2_2311x2_ACTTGA_S8


title: MCF7_RNA_SNDX_200nM_4d_REP1_231117_CAGATC_S7


title: MCF7_RNA_SNDX_200nM_4d_E2_REP1_2311x2_GTGAAA_S19

value: Estrogen starvation, 200nM SNDX-5613,E2


title: MCF7_RNA_SNDX_200nM_4d_E2_REP2_2311x2_GTGGCC_S20


title: MCF7_RNA_PF9363_50nM_SNDX_200nM_4d_REP2_231117_GGCTAC_S11


title: MCF7_RNA_PF9363_50nM_SNDX_200nM_4d_REP2_2311x2_GGCTAC_S11

value: Estrogen starvation, 50 nM PF-9363,200nM SNDX-5613, DMSO


title: MCF7_RNA_PF9363_50nM_SNDX_200nM_4d_E2_REP3_2311x2_GGTAGC_S24

value: Estrogen starvation, 50 nM PF-9363,200nM SNDX-5613, E2


title: MCF7_RNA_PF9363_50nM_SNDX_200nM_4d_E2_REP1_2311x2_CGTACG_S22

value: cell line


title: MCF7_RNA_PF9363_50nM_SNDX_200nM_4d_E2_REP2_2311x2_GAGTGG_S23


title: MCF7_RNA_PF9363_50nM_96h_REP2_230525_CACGAT_S11


title: MCF7_RNA_PF9363_50nM_8h_REP2_230525_GTGAAA_S5


title: MCF7_RNA_PF9363_50nM_96h_REP1_230525_CACCGG_S10


title: MCF7_RNA_PF9363_50nM_8h_REP1_230525_GTCCGC_S4


title: MCF7_RNA_PF9363_50nM_4d_REP3_2311x2_GCCAAT_S6

value: Estrogen starvation, 50 nM PF-9363, DMSO


title: MCF7_RNA_PF9363_50nM_4d_REP3_231117_GCCAAT_S6


title: MCF7_RNA_PF9363_50nM_4d_REP2_2311x2_ACAGTG_S5


title: MCF7_RNA_PF9363_50nM_4d_REP2_231117_ACAGTG_S5


title: MCF7_RNA_PF9363_50nM_4d_REP1_2311x2_TGACCA_S4


title: MCF7_RNA_SNDX_200nM_4d_E2_REP3_2311x2_GTTTCG_S21


title: MCF7_RNA_PF9363_50nM_4d_REP1_231117_TGACCA_S4


title: MCF7_RNA_PF9363_50nM_SNDX_200nM_4d_REP3_2311x2_CTTGTA_S12


title: MCF7_RNA_PF9363_50nM_SNDX_200nM_4d_REP3_231117_CTTGTA_S12


title: MCF7_RNA_PF9363_50nM_4d_E2_REP1_2311x2_CCGTCC_S16

value: Estrogen starvation, 50 nM PF-9363, E2


title: MCF7_RNA_PF9363_50nM_48h_REP3_230525_ATGAGC_S9


title: MCF7_RNA_PF9363_50nM_48h_REP2_230525_ACTGAT_S8


title: MCF7_RNA_PF9363_50nM_SNDX_200nM_4d_REP1_2311x2_TAGCTT_S10


title: MCF7_RNA_PF9363_50nM_4d_E2_REP3_2311x2_GTCCGC_S18


title: MCF7_RNA_DMSO_4d_REP3_2311x2_TTAGGC_S3

value: Estrogen starvation, DMSO, DMSO


title: MCF7_RNA_PF9363_50nM_48h_REP1_230525_GGTAGC_S7


title: MCF7_RNA_PF9363_50nM_SNDX_200nM_4d_REP1_231117_TAGCTT_S10


title: MCF7_RNA_DMSO_4d_REP3_231117_TTAGGC_S3

value: DMSO


title: MCF7_RNA_DMSO_4d_REP2_231117_CGATGT_S2


title: MCF7_RNA_PF9363_50nM_96h_REP3_230525_CACTCA_S12


title: MCF7_RNA_DMSO_4d_REP1_2311x2_ATCACG_S1


title: MCF7_RNA_DMSO_4d_E2_REP3_2311x2_ATGTCA_S15

value: Estrogen starvation, DMSO, E2


title: MCF7_RNA_DMSO_4d_REP2_2311x2_CGATGT_S2


title: MCF7_RNA_DMSO_4d_E2_REP1_2311x2_AGTCAA_S13


title: MCF7_RNA_DMSO_4d_E2_REP2_2311x2_AGTTCC_S14


title: MCF7-N-ESR1_RNA_SNDX_200nM_4d_REP3_2311x2_CAGGCG_S33

description: N-GFP-ESR1 overexpression


title: MCF7-N-ESR1_RNA_SNDX_200nM_4d_REP2_2311x2_CACTCA_S32

description: N-GFP-ESR1 overexpression


title: MCF7_RNA_PF9363_50nM_8h_REP3_230525_GTGGCC_S6


title: MCF7-N-ESR1_RNA_SNDX_200nM_4d_REP1_2311x2_CACGAT_S31

description: N-GFP-ESR1 overexpression


title: MCF7-N-ESR1_RNA_SNDX_200nM_4d_E2_REP3_2311x2_TCATTC_S45

description: N-GFP-ESR1 overexpression


title: MCF7-N-ESR1_RNA_SNDX_200nM_4d_E2_REP1_2311x2_TACAGC_S43

description: N-GFP-ESR1 overexpression


title: MCF7-N-ESR1_RNA_SNDX_200nM_4d_E2_REP2_2311x2_TATAAT_S44

description: N-GFP-ESR1 overexpression


title: MCF7-N-ESR1_RNA_PF9363_50nM_SNDX_200nM_4d_REP2_2311x2_CATTTT_S35

description: N-GFP-ESR1 overexpression


title: MCF7-N-ESR1_RNA_PF9363_50nM_SNDX_200nM_4d_REP3_2311x2_CCAACA_S36

description: N-GFP-ESR1 overexpression


title: MCF7_RNA_PF9363_50nM_4d_E2_REP2_2311x2_GTAGAG_S17


title: MCF7-N-ESR1_RNA_PF9363_50nM_SNDX_200nM_4d_E2_REP1_2311x2_TCCCGA_S46

description: N-GFP-ESR1 overexpression


title: MCF7-N-ESR1_RNA_PF9363_50nM_4d_REP3_2311x2_CACCGG_S30

description: N-GFP-ESR1 overexpression


title: MCF7-N-ESR1_RNA_PF9363_50nM_SNDX_200nM_4d_E2_REP3_2311x2_TCGGCA_S48

description: N-GFP-ESR1 overexpression


title: MCF7-N-ESR1_RNA_PF9363_50nM_SNDX_200nM_4d_E2_REP2_2311x2_TCGAAG_S47

description: N-GFP-ESR1 overexpression


title: MCF7-N-ESR1_RNA_PF9363_50nM_4d_E2_REP3_2311x2_TAATCG_S42

description: N-GFP-ESR1 overexpression


title: MCF7-N-ESR1_RNA_PF9363_50nM_4d_REP1_2311x2_CAAAAG_S28

description: N-GFP-ESR1 overexpression


title: MCF7-N-ESR1_RNA_PF9363_50nM_4d_REP2_2311x2_CAACTA_S29

description: N-GFP-ESR1 overexpression


title: MCF7-N-ESR1_RNA_DMSO_4d_REP3_2311x2_ATTCCT_S27

description: N-GFP-ESR1 overexpression


title: MCF7_RNA_DMSO_4d_REP1_231117_ATCACG_S1


title: MCF7-N-ESR1_RNA_DMSO_4d_REP1_2311x2_ACTGAT_S25

description: N-GFP-ESR1 overexpression


title: MCF7-N-ESR1_RNA_DMSO_4d_REP2_2311x2_ATGAGC_S26

description: N-GFP-ESR1 overexpression


title: MCF7-N-ESR1_RNA_DMSO_4d_E2_REP2_2311x2_CTAGCT_S38

description: N-GFP-ESR1 overexpression


title: MCF7-N-ESR1_RNA_DMSO_4d_E2_REP3_2311x2_CTATAC_S39

description: N-GFP-ESR1 overexpression


title: MCF7-N-ESR1_RNA_DMSO_4d_E2_REP1_2311x2_CGGAAT_S37

description: N-GFP-ESR1 overexpression


title: HCI018_RNA_SNDX_200nM_10d_REP3_240307_TCCCGA_S11

description: from Guillen et al. Nature Cancer 2022

value: organoid

value: 10 days


title: HCI018_RNA_PF9363_50nM_SNDX_200nM_10d_REP3_240307_TCGAAG_S12

description: from Guillen et al. Nature Cancer 2022


title: HCI018_RNA_PF9363_50nM_SNDX_200nM_10d_REP2_240307_TACAGC_S8

description: from Guillen et al. Nature Cancer 2022


title: HCI018_RNA_PF9363_50nM_10d_REP3_240307_TCATTC_S10

description: from Guillen et al. Nature Cancer 2022


title: MCF7-N-ESR1_RNA_PF9363_50nM_SNDX_200nM_4d_REP1_2311x2_CATGGC_S34

description: N-GFP-ESR1 overexpression


title: HCI018_RNA_PF9363_50nM_SNDX_200nM_10d_REP1_240307_CTATAC_S4

description: from Guillen et al. Nature Cancer 2022


title: HCI018_RNA_SNDX_200nM_10d_REP2_240307_TAATCG_S7

description: from Guillen et al. Nature Cancer 2022


title: HCI018_RNA_PF9363_50nM_10d_REP2_240307_GACGAC_S6

description: from Guillen et al. Nature Cancer 2022


title: HCI018_RNA_PF9363_50nM_10d_REP1_240307_CGGAAT_S2

description: from Guillen et al. Nature Cancer 2022


title: MCF7-N-ESR1_RNA_PF9363_50nM_4d_E2_REP2_2311x2_GACGAC_S41

description: N-GFP-ESR1 overexpression


title: HCI018_RNA_DMSO_10d_REP1_240307_CCAACA_S1

description: from Guillen et al. Nature Cancer 2022


title: HCI003_RNA_SNDX_200nM_7d_REP3_240119_GATCAG_S9

description: from Guillen et al. Nature Cancer 2022

value: 7 days


title: MCF7-N-ESR1_RNA_PF9363_50nM_4d_E2_REP1_2311x2_GTGATC_S40

description: N-GFP-ESR1 overexpression


title: HCI018_RNA_DMSO_10d_REP2_240307_GTGATC_S5

description: from Guillen et al. Nature Cancer 2022


title: HCI003_RNA_SNDX_200nM_7d_REP1_240119_CAGATC_S7

description: from Guillen et al. Nature Cancer 2022


title: HCI003_RNA_PF9363_50nM_SNDX_200nM_7d_REP3_240119_CTTGTA_S12

description: from Guillen et al. Nature Cancer 2022


title: HCI003_RNA_PF9363_50nM_7d_REP2_240119_ACAGTG_S5

description: from Guillen et al. Nature Cancer 2022


title: HCI003_RNA_PF9363_50nM_SNDX_200nM_7d_REP2_240119_GGCTAC_S11

description: from Guillen et al. Nature Cancer 2022


title: HCI003_RNA_SNDX_200nM_7d_REP2_240119_ACTTGA_S8

description: from Guillen et al. Nature Cancer 2022


title: HCI003_RNA_PF9363_50nM_7d_REP3_240119_GCCAAT_S6

description: from Guillen et al. Nature Cancer 2022


title: HCI003_RNA_DMSO_7d_REP3_240119_TTAGGC_S3

description: from Guillen et al. Nature Cancer 2022


title: HCI003_RNA_DMSO_7d_REP2_240119_CGATGT_S2

description: from Guillen et al. Nature Cancer 2022


title: HCI003_RNA_PF9363_50nM_7d_REP1_240119_TGACCA_S4

description: from Guillen et al. Nature Cancer 2022


title: HCI018_RNA_SNDX_200nM_10d_REP1_240307_CTAGCT_S3

description: from Guillen et al. Nature Cancer 2022


title: MCF7_sgRNA_hEpi_PF9363_25nM_31d_REP3_220622_AGCCGTGT_S15_R1_merged.fastq.gz

data_processing:
FASTQ files were converted to read-count tables using the MAGeCK ‘count’ command.
Each genetic screen was carried out in n = 3 replicates. The maximum likelihood estimation (MLE) algorithm of MAGeCK-vispr was used to generate count summaries and beta scores.
Assembly: GRCh38/hg38
Supplementary files format and content: Tabular results in Excel .xlsx format

growth_protocol: MCF7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 1xL-glutamine, 10% Fetal Bovine Serum, and 1xPenStrep.

extract_protocol:
Cells were lysed in 1.3 ml lysis buffer per sample (NaCl, 300 mM; SDS, 0.2%; EDTA, 1 mM; Tris-HCl, pH 8.0, 10 mM). Samples were then incubated with RNase A (100 μg/ml) for 1 h at 65°C and then incubated overnight with proteinase K (100 μg/ml) at 55°C with constant rotation. Genomic DNA was then purified by phenol–chloroform extraction.
Amplicon sequencing libraries were  produced using 35 µg genomic DNA from each experimental replicate as follows: a first-round PCR reaction was carried out in 5 separate 100µl reactions, using Q5 High-Fidelity DNA Polymerase (NEB) to amplify the region of the sgRNA corresponding to that between U6 and EF-1α using primers (forward F1, AATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCG and reverse R1, TCTACTATTCTTTCCCCTGCACTGTACCTGTGGGCGATGTGCGCTCTG); the product was pooled from the primary PCR reaction. A second PCR was carried out to incorporate Illumina adaptors and a 6-bp barcode for identification of samples (F2 and R2, see key resource table). A third PCR reaction was carried out to enrich for the full-length amplicon using primers (forward F3, AATGATACGGCGACCACCGAGATC and reverse R3, CAAGCAGAAGACGGCATACGAGAT). Final amplicon libraries were purified by AMPure XP bead (Beckman Coulter) purification.
Sequencing was done using the Illumina Next Gen Sequencing NextSeq platform (Illumina) with >6 million 75 bp single-end reads per sample

treatment_protocol: MCF7 Cas9 expressing cells were infected with an epigentic-focused CRISPR guide library at an MOI of approximately 0.3. Cells were selected in puromycin (2.5μg/ml) and were cultured in triplicate in DMSO or 50nM PF-9363 for 30 days. Cells were split every 3-5 days and at each split 6 million cells per replicate were plated back to maintain >1,000x library coverage.

value: 31 days

tag: crispr library

value: human Epigenetic sgRNA library


title: HCI003_RNA_DMSO_7d_REP1_240119_ATCACG_S1

description: from Guillen et al. Nature Cancer 2022


title: MCF7_sgRNA_hEpi_DMSO_31d_REP3_220622_AACGCGTA_S3_R1_merged.fastq.gz


title: MCF7_sgRNA_hEpi_PF9363_25nM_31d_REP1_220622_GAATCCCG_S13_R1_merged.fastq.gz


title: MCF7_sgRNA_hEpi_PF9363_25nM_31d_REP2_220622_TTCGGCTG_S14_R1_merged.fastq.gz


title: MCF7_sgRNA_hEpi_DMSO_31d_REP2_220622_CGTACGTA_S2_R1_merged.fastq.gz


title: MCF7_sgRNA_hEpi_0d_REP1_220622_AATTCAGC_S16_R1_merged.fastq.gz

value: 0 days


title: MCF7_sgRNA_hEpi_DMSO_31d_REP1_220622_AATCAGAG_S1_R1_merged.fastq.gz


title: T47D_ChIP_MLL1_steadystate_REP1_220531_CAGATC_S7_R1_merged.fastq.gz

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers or single 75-mer reads) were aligned to the human genome (Gencode GRCh38/hg38 v33) using STAR (v2.7.5a; params --alignIntronMax 1 --alignEndsType EndToEnd --alignMatesGapMax 2000), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4). Final “deduped” .BAM files were indexed using SAMtools (v1.95).
MACS2 (v2.1.4) was used to call peaks with appropriate input samples as controls for peak calling. Peaks were called with q-value cut-off of 0.01 and broad peak mode.
Promoter-associated signal was determined using bedtools “coverage” (v2.28.0), using annotated gene body genomic intervals and TSS region intervals (-1kb to +3kb for each protein-coding transcript TSS, using gene orientation).
ChIP-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75) and deeptools (tornado plots; v3.1.3; regions around TSS/promoter intervals plotted using referencePoint or scaledRegion option and k=1).
For RNA Pol II interval counts were normalized using a ratio of TSS signal values among a set of selected housekeeping genes. For KMT2A and KAT6A reads were normalized using ratios of total read counts between treated and control sample pairs. For histone marks, reads were normalized using drosphila-spike in as previously published.
Assembly: GRCh38/hg38
Supplementary files format and content: IGVtools .tdf files (for visualization in Broad IGV)


title: T47D_ChIP_MEN1_steadystate_REP1_220531_GCCAAT_S6_R1_merged.fastq.gz


title: T47D_ChIP_input_steadystate_REP1_230601_CGATGT_S4_R1_merged.fastq.gz


title: T47D_ChIP_input_steadystate_REP1_220531_ACTTGA_S8_R1_merged.fastq.gz


title: T47D_ChIP_KAT6A_steadystate_REP1_230601_GCCAAT_S7_R1_merged.fastq.gz


title: T47D_ChIP_BRPF1_steadystate_REP1_230601_GATCAG_S10_R1_merged.fastq.gz


title: HCI003_RNA_PF9363_50nM_SNDX_200nM_7d_REP1_240119_TAGCTT_S10

description: from Guillen et al. Nature Cancer 2022


title: MCF7_ChIP_MLL1_SNDX_200nM_24h_REP1_231211_GGCTAC_S11_R1_merged.fastq.gz

value: 24 hours


title: MCF7_ChIP_MLL1_PF9363_50nM_SNDX_200nM_24h_REP1_231211_CTTGTA_S12_R1_merged.fastq.gz


title: MCF7_ChIP_MLL1_steadystate_REP1_220531_TTAGGC_S3_R1_merged.fastq.gz


title: MCF7_ChIP_MLL1_DMSO_24h_REP1_231211_GATCAG_S9_R1_merged.fastq.gz


title: MCF7_ChIP_MLL1_PF9363_50nM_24h_REP1_231211_TAGCTT_S10_R1_merged.fastq.gz


title: MCF7_ChIP_MEN1_VTP_200nM_5d_REP1_221012_CTTGTA_S10_R1_merged.fastq.gz

value: 5 days


title: MCF7_ChIP_MEN1_DMSO_5d_REP1_221012_GGCTAC_S9_R1_merged.fastq.gz


title: MCF7_ChIP_KAT6A_steadystate_REP1_230601_ACAGTG_S6_R1_merged.fastq.gz


title: MCF7_ChIP_KAT6A_PF9363_50nM_SNDX_200nM_24h_REP1_231211_CCGTCC_S16_R1_merged.fastq.gz


title: MCF7_ChIP_KAT6A_PF9363_50nM_24h_REP1_231211_AGTTCC_S14_R1_merged.fastq.gz


title: MCF7_ChIP_MEN1_steadystate_REP1_220531_CGATGT_S2_R1_merged.fastq.gz


title: MCF7_ChIP_KAT6A_SNDX_200nM_24h_REP1_231211_ATGTCA_S15_R1_merged.fastq.gz


title: MCF7_ChIP_input_VTP_200nM_5d_REP1_221012_ACTGAT_S12_R1_merged.fastq.gz


title: MCF7_ChIP_input_steadystate_REP1_220531_TGACCA_S4_R1_merged.fastq.gz


title: MCF7_ChIP_input_SNDX_200nM_24h_REP1_231211_TTAGGC_S3_R1_merged.fastq.gz


title: MCF7_ChIP_input_steadystate_REP1_230601_ATCACG_S3_R1_merged.fastq.gz


title: MCF7_ChIP_input_SNDX_200nM_REP1_231110_TTAGGC_S3_R1_merged.fastq.gz


title: MCF7_ChIP_KAT6A_DMSO_24h_REP1_231211_AGTCAA_S13_R1_merged.fastq.gz


title: MCF7_ChIP_input_PF9363_50nM_SNDX_200nM_REP1_231110_TGACCA_S4_R1_merged.fastq.gz


title: MCF7_ChIP_input_DMSO_REP1_231110_ATCACG_S1_R1_merged.fastq.gz


title: MCF7_ChIP_input_DMSO_5d_REP1_221012_GAGTGG_S11_R1_merged.fastq.gz


title: MCF7_ChIP_input_PF9363_50nM_SNDX_200nM_24h_REP1_231211_TGACCA_S4_R1_merged.fastq.gz


title: MCF7_ChIP_input_DMSO_24h_REP1_231211_ATCACG_S1_R1_merged.fastq.gz


title: MCF7_ChIP_input_PF9363_50nM_REP1_231110_CGATGT_S2_R1_merged.fastq.gz


title: MCF7_ChIP_H3K9ac_SNDX_200nM_REP1_231110_AGTTCC_S11_R1_merged.fastq.gz


title: MCF7_ChIP_input_PF9363_50nM_24h_REP1_231211_CGATGT_S2_R1_merged.fastq.gz


title: MCF7_ChIP_H3K4me3_PF9363_50nM_SNDX_200nM_REP1_231110_GTTTCG_S16_R1_merged.fastq.gz


title: MCF7_ChIP_H3K4me3_SNDX_200nM_REP1_231110_GTGGCC_S15_R1_merged.fastq.gz


title: MCF7_ChIP_H3K4me3_PF9363_50nM_REP1_231110_GTGAAA_S14_R1_merged.fastq.gz


title: MCF7_ChIP_H3K9ac_PF9363_50nM_REP1_231110_AGTCAA_S10_R1_merged.fastq.gz


title: MCF7_ChIP_H3K9ac_DMSO_REP1_231110_CTTGTA_S9_R1_merged.fastq.gz


title: MCF7_ChIP_H3K4me3_DMSO_REP1_231110_GTCCGC_S13_R1_merged.fastq.gz


title: MCF7_ChIP_BRPF1_steadystate_REP1_230601_ACTTGA_S9_R1_merged.fastq.gz


title: BR2026 Y2 Flu Day 80-100

status: Public on Apr 24 2025

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
The FASTQs were aligned to the Genome Reference Consortium Human (GRCh) version 38.91, using STAR v.2.4.2a and gene counts were generated using HTSeq-count (v0.4.1) (57, 58). Quality metrics were compiled from PICARD (v1.134FASTQC (v0.11.3) Samtools (v1.2)8, and HTSeq-count. Samples with high median covariance of coverage coverage (>0.6), low total read count (<1 million), and low percent alignment (<92%) were considered low quality and removed from further analysis. Read counts were TMM-normalized (59).
Assembly: GRCh38.91
Supplementary files format and content: gene count matrix

growth_protocol: At each visit, peripheral blood was collected into Tempus Blood RNA tubes (Thermo Fisher Scientific).

extract_protocol:
We extracted RNA using the MagMAX RNA Isolation Kit (Thermo Fisher Scientific) then performed globin reduction with the GLOBINclear-Human Kit (Thermo Fisher Scientific).
We generated full-length cDNA from total RNA (0.5 ng). We amplified cDNA using the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) and constructed sequencing libraries using the NexteraXT DNA Library prep kit (Illumina).
We pooled libraries, quantified concentration with a Qubit Fluorometer (Life Technologies), then sequenced on a NextSeq 2000 sequencer (Illumina) with 59-base paired-end reads on a NextSeq P2 flow cell (Illumina). We targeted a depth of 5 million reads per sample.

value: peripheral blood

tag: donor

tag: timepoint

value: Y2 Flu Day 80-100

value: male

tag: age cohort

tag: cmv status

value: Negative


title: BR2022 Non-Flu Day 7-9

value: Non-Flu Day 7-9

tag: Sex


title: BR1037 Y2 Flu Day 0

value: Y2 Flu Day 0

value: female

value: Positive


title: BR2029 Y1 Flu Day 80-100

value: Y1 Flu Day 80-100


title: BR1031 Non-Flu Day 7-9


title: BR1032 Non-Flu Day 80-100

value: Non-Flu Day 80-100


title: BR1028 Y1 Flu Day 0

value: Y1 Flu Day 0


title: BR1045 Y1 Flu Day 0


title: BR1051 Non-Flu Day 0

value: Non-Flu Day 0


title: BR1013 Y1 Flu Day 0 Replicate 2

description:
sample was run twice
lib82118


title: BR2046 Non-Flu Day 7-9


title: BR1059 Non-Flu Day 7-9


title: BR1014 Non-Flu Day 0


title: BR1014 Standalone Baseline Visit

value: Standalone Baseline Visit


title: BR1014 Y2 Flu Day 80-100


title: MCF7_ChIP_H3K9ac_PF9363_50nM_SNDX_200nM_REP1_231110_ATGTCA_S12_R1_merged.fastq.gz

value: cell line


title: BR1013 Y1 Flu Day 0 Replicate 1

description:
sample was run twice
lib81391


title: BR1030 Y1 Flu Day 7-9 Replicate 1

description:
sample was run twice
lib81395

value: Y1 Flu Day 7-9


title: BR1014 Non-Flu Day 7-9


title: BR1014 Y2 Flu Day 0


title: BR1014 Y1 Flu Day 7-9


title: BR1014 Y2 Flu Day 7-9

value: Y2 Flu Day 7-9


title: BR1014 Y1 Flu Day 0


title: BR2049 Y2 Flu Day 80-100


title: BR1030 Y1 Flu Day 7-9 Replicate 2

description:
sample was run twice
lib82122


title: BR1011 Y2 Flu Day 80-100


title: BR1014 Y1 Flu Day 80-100


title: BR2049 Y2 Flu Day 7-9


title: BR2049 Non-Flu Day 7-9


title: BR2049 Non-Flu Day 0


title: BR2049 Non-Flu Day 80-100


title: BR2049 Y1 Flu Day 0


title: BR2049 Y1 Flu Day 7-9


title: BR2049 Y1 Flu Day 80-100


title: BR1041 Y2 Flu Day 80-100


title: BR1041 Y2 Flu Day 0


title: BR1041 Non-Flu Day 80-100


title: BR1041 Non-Flu Day 7-9


title: BR1041 Y2 Flu Day 7-9


title: BR1041 Y1 Flu Day 7-9


title: BR1041 Y1 Flu Day 0


title: BR2049 Y2 Flu Day 0


title: BR2053 Y2 Flu Day 7-9


title: BR2053 Y2 Flu Day 80-100


title: BR2049 Standalone Baseline Visit


title: BR2053 Y2 Flu Day 0


title: BR2053 Non-Flu Day 80-100


title: BR2053 Non-Flu Day 0


title: BR2053 Non-Flu Day 7-9


title: BR2053 Y1 Flu Day 80-100


title: BR2053 Y1 Flu Day 7-9


title: BR2053 Y1 Flu Day 0


title: BR2048 Y2 Flu Day 80-100


title: BR2048 Non-Flu Day 80-100


title: BR1041 Non-Flu Day 0


title: BR2048 Y2 Flu Day 0


title: BR2048 Y1 Flu Day 7-9


title: BR2048 Non-Flu Day 0


title: BR2048 Non-Flu Day 7-9


title: BR2048 Standalone Baseline Visit


title: BR2048 Y1 Flu Day 80-100


title: BR2040 Standalone Baseline Visit


title: BR2048 Y2 Flu Day 7-9


title: BR2040 Y2 Flu Day 7-9


title: BR2040 Y2 Flu Day 80-100


title: BR2040 Y2 Flu Day 0


title: BR2053 Standalone Baseline Visit


title: BR2040 Non-Flu Day 7-9


title: BR2048 Y1 Flu Day 0


title: BR2040 Y1 Flu Day 80-100


title: BR2040 Y1 Flu Day 7-9


title: BR2040 Non-Flu Day 80-100


title: BR2040 Y1 Flu Day 0


title: BR2038 Standalone Baseline Visit


title: BR2038 Y2 Flu Day 80-100


title: BR2038 Y2 Flu Day 7-9


title: BR2038 Non-Flu Day 80-100


title: BR2038 Y2 Flu Day 0


title: BR2038 Non-Flu Day 7-9


title: BR2038 Y1 Flu Day 80-100


title: BR2038 Y1 Flu Day 7-9


title: BR2038 Y1 Flu Day 0


title: BR2042 Non-Flu Day 80-100


title: BR2042 Y2 Flu Day 80-100


title: BR2042 Non-Flu Day 0


title: BR2042 Y1 Flu Day 80-100


title: BR2038 Non-Flu Day 0


title: BR2042 Standalone Baseline Visit


title: BR2042 Y1 Flu Day 7-9


title: BR2040 Non-Flu Day 0


title: BR2037 Standalone Baseline Visit


title: BR2042 Non-Flu Day 7-9


title: BR2042 Y1 Flu Day 0


title: BR2037 Non-Flu Day 7-9


title: BR2037 Y1 Flu Day 7-9


title: BR2037 Non-Flu Day 0


title: BR2037 Y2 Flu Day 0


title: BR2037 Y2 Flu Day 80-100


title: BR2037 Y1 Flu Day 80-100


title: BR2037 Y1 Flu Day 0


title: BR2032 Standalone Baseline Visit


title: HCI018_RNA_DMSO_10d_REP3_240307_TATAAT_S9

description: from Guillen et al. Nature Cancer 2022

value: organoid

value: 10 days

value: DMSO


title: BR2037 Non-Flu Day 80-100

value: peripheral blood

value: male


title: BR2037 Y2 Flu Day 7-9


title: BR2044 Standalone Baseline Visit


title: BR2032 Y2 Flu Day 80-100

value: Y2 Flu Day 80-100

value: Negative


title: BR2042 Y2 Flu Day 0

value: Y2 Flu Day 0

value: female


title: BR2042 Y2 Flu Day 7-9


title: BR2032 Y2 Flu Day 7-9


title: BR2032 Y2 Flu Day 0


title: BR2032 Non-Flu Day 80-100


title: BR2032 Y1 Flu Day 80-100

value: Y1 Flu Day 80-100


title: BR2036 Standalone Baseline Visit


title: BR2032 Y1 Flu Day 7-9


title: BR2036 Y2 Flu Day 0


title: BR2032 Y1 Flu Day 0


title: BR2036 Y2 Flu Day 7-9


title: BR2032 Non-Flu Day 0


title: BR2036 Non-Flu Day 0


title: BR2036 Non-Flu Day 7-9

value: Non-Flu Day 7-9


title: BR2036 Non-Flu Day 80-100

value: Non-Flu Day 80-100


title: BR2033 Y2 Flu Day 7-9

value: Positive


title: BR2033 Y2 Flu Day 0


title: BR2033 Standalone Baseline Visit

value: Standalone Baseline Visit


title: BR2033 Non-Flu Day 0

value: Non-Flu Day 0


title: BR2036 Y1 Flu Day 80-100


title: BR2033 Y2 Flu Day 80-100


title: BR2036 Y1 Flu Day 0

value: Y1 Flu Day 0


title: BR2033 Non-Flu Day 7-9


title: BR2033 Non-Flu Day 80-100


title: BR2036 Y1 Flu Day 7-9

value: Y1 Flu Day 7-9


title: BR2034 Standalone Baseline Visit


title: BR2033 Y1 Flu Day 80-100


title: BR2032 Non-Flu Day 7-9


title: BR2034 Y2 Flu Day 7-9

value: Y2 Flu Day 7-9


title: BR2033 Y1 Flu Day 0


title: BR2033 Y1 Flu Day 7-9


title: BR2034 Y2 Flu Day 0


title: BR1031 Y2 Flu Day 80-100


title: BR2036 Y2 Flu Day 80-100


title: BR2034 Non-Flu Day 0


title: BR2034 Non-Flu Day 80-100


title: BR2034 Y1 Flu Day 0


title: BR2034 Y1 Flu Day 7-9


title: BR2044 Y2 Flu Day 80-100


title: BR2034 Non-Flu Day 7-9


title: BR2034 Y1 Flu Day 80-100


title: BR2044 Non-Flu Day 80-100


title: BR2044 Non-Flu Day 7-9


title: BR2044 Non-Flu Day 0


title: BR2044 Y1 Flu Day 7-9


title: BR2029 Y2 Flu Day 7-9


title: BR2029 Y2 Flu Day 80-100


title: BR2029 Non-Flu Day 7-9


title: BR2029 Y2 Flu Day 0


title: BR2044 Y2 Flu Day 7-9


title: BR2029 Non-Flu Day 0


title: BR2034 Y2 Flu Day 80-100


title: BR2029 Y1 Flu Day 7-9


title: BR2029 Y1 Flu Day 0


title: BR2029 Non-Flu Day 80-100


title: BR2029 Standalone Baseline Visit


title: BR2030 Y2 Flu Day 80-100


title: BR2030 Non-Flu Day 80-100


title: BR2030 Y2 Flu Day 0


title: BR2030 Y2 Flu Day 7-9


title: BR2030 Non-Flu Day 0


title: BR2030 Non-Flu Day 7-9


title: BR2044 Y2 Flu Day 0


title: BR2030 Y1 Flu Day 80-100


title: BR2030 Y1 Flu Day 7-9


title: BR2030 Standalone Baseline Visit


title: BR2028 Y2 Flu Day 7-9


title: BR2028 Y2 Flu Day 80-100


title: BR2044 Y1 Flu Day 80-100


title: BR2030 Y1 Flu Day 0


title: BR2028 Y2 Flu Day 0


title: BR2028 Non-Flu Day 7-9


title: BR2028 Y1 Flu Day 7-9


title: BR2028 Non-Flu Day 80-100


title: BR2028 Y1 Flu Day 0


title: BR2028 Y1 Flu Day 80-100


title: BR2028 Standalone Baseline Visit


title: BR2031 Y2 Flu Day 80-100


title: BR2031 Y2 Flu Day 7-9


title: BR2031 Non-Flu Day 80-100


title: BR2031 Non-Flu Day 0


title: BR2031 Y1 Flu Day 80-100


title: BR2031 Non-Flu Day 7-9


title: BR2031 Y1 Flu Day 7-9


title: BR2031 Y2 Flu Day 0


title: BR2031 Y1 Flu Day 0


title: BR2023 Y2 Flu Day 7-9


title: BR2023 Y2 Flu Day 80-100


title: BR2023 Y2 Flu Day 0


title: BR2023 Non-Flu Day 80-100


title: BR2023 Non-Flu Day 7-9


title: BR2023 Y1 Flu Day 0


title: BR2023 Standalone Baseline Visit


title: BR2043 Standalone Baseline Visit


title: BR2044 Y1 Flu Day 0


title: BR2043 Y2 Flu Day 80-100


title: BR2028 Non-Flu Day 0


title: BR2043 Y2 Flu Day 7-9


title: BR2043 Non-Flu Day 80-100


title: BR2043 Non-Flu Day 7-9


title: BR2043 Y2 Flu Day 0


title: BR2024 Y2 Flu Day 0


title: BR2024 Non-Flu Day 0


title: BR2024 Y1 Flu Day 0


title: BR2024 Y1 Flu Day 80-100


title: BR2031 Standalone Baseline Visit


title: BR2024 Y1 Flu Day 7-9


title: BR2026 Y2 Flu Day 7-9


title: BR2024 Y2 Flu Day 80-100


title: BR2024 Non-Flu Day 80-100


title: BR2026 Y2 Flu Day 0


title: BR2026 Non-Flu Day 80-100


title: BR2023 Non-Flu Day 0


title: BR2023 Y1 Flu Day 80-100


title: BR2023 Y1 Flu Day 7-9


title: BR2022 Y2 Flu Day 0


title: BR2026 Standalone Baseline Visit


title: BR2022 Y2 Flu Day 7-9


title: BR2022 Y2 Flu Day 80-100


title: BR2026 Y1 Flu Day 80-100


title: BR2043 Non-Flu Day 0


title: BR2026 Y1 Flu Day 7-9


title: BR2026 Non-Flu Day 0


title: BR2022 Non-Flu Day 0


title: BR2024 Y2 Flu Day 7-9


title: BR2018 Y2 Flu Day 80-100


title: BR2024 Standalone Baseline Visit


title: BR2018 Non-Flu Day 80-100


title: BR2018 Y1 Flu Day 7-9


title: BR2018 Non-Flu Day 7-9


title: BR2018 Non-Flu Day 0


title: BR2018 Y1 Flu Day 80-100


title: BR2018 Y1 Flu Day 0


title: BR2018 Y2 Flu Day 0


title: BR2018 Standalone Baseline Visit


title: BR2043 Y1 Flu Day 7-9


title: BR2026 Y1 Flu Day 0


title: BR2019 Y2 Flu Day 80-100


title: BR2043 Y1 Flu Day 0


title: BR2043 Y1 Flu Day 80-100


title: BR2019 Y2 Flu Day 7-9


title: BR2019 Y2 Flu Day 0


title: BR2019 Y1 Flu Day 80-100


title: BR2019 Non-Flu Day 0


title: BR2019 Y1 Flu Day 7-9


title: BR2019 Non-Flu Day 80-100


title: BR2019 Y1 Flu Day 0


title: BR2022 Standalone Baseline Visit


title: BR2047 Y2 Flu Day 7-9


title: BR2022 Y1 Flu Day 0


title: BR2047 Standalone Baseline Visit


title: BR2047 Non-Flu Day 80-100


title: BR2047 Y2 Flu Day 80-100


title: BR2019 Standalone Baseline Visit


title: BR2018 Y2 Flu Day 7-9


title: BR2015 Y2 Flu Day 80-100


title: BR2015 Standalone Baseline Visit


title: BR2015 Non-Flu Day 80-100


title: BR2015 Y2 Flu Day 7-9


title: BR2015 Y2 Flu Day 0


title: BR2015 Non-Flu Day 7-9


title: BR2015 Non-Flu Day 0


title: BR2015 Y1 Flu Day 80-100


title: BR2015 Y1 Flu Day 7-9


title: BR2015 Y1 Flu Day 0


title: BR2021 Y2 Flu Day 80-100


title: BR2021 Y2 Flu Day 7-9


title: BR2021 Y2 Flu Day 0


title: BR2021 Non-Flu Day 80-100


title: BR2021 Non-Flu Day 7-9


title: BR2019 Non-Flu Day 7-9


title: BR2047 Y2 Flu Day 0


title: BR2021 Standalone Baseline Visit


title: BR2021 Y1 Flu Day 0


title: BR2021 Non-Flu Day 0


title: BR2012 Standalone Baseline Visit


title: BR2021 Y1 Flu Day 7-9


title: BR2012 Y2 Flu Day 80-100


title: BR2021 Y1 Flu Day 80-100


title: BR2012 Y2 Flu Day 0


title: BR2012 Non-Flu Day 7-9


title: BR2012 Non-Flu Day 80-100


title: BR2012 Y2 Flu Day 7-9


title: BR2012 Non-Flu Day 0


title: BR2012 Y1 Flu Day 80-100


title: BR2012 Y1 Flu Day 7-9


title: BR2012 Y1 Flu Day 0


title: BR2013 Y2 Flu Day 0


title: BR2013 Y1 Flu Day 0


title: BR2013 Standalone Baseline Visit


title: BR2013 Non-Flu Day 7-9


title: BR2013 Non-Flu Day 0


title: BR2013 Y1 Flu Day 80-100


title: BR2013 Y1 Flu Day 7-9


title: BR2010 Standalone Baseline Visit


title: BR2010 Y2 Flu Day 7-9


title: BR2010 Y1 Flu Day 7-9


title: BR2010 Y2 Flu Day 80-100


title: BR2010 Y2 Flu Day 0


title: BR2010 Y1 Flu Day 0


title: BR2010 Y1 Flu Day 80-100


title: BR2010 Non-Flu Day 7-9


title: BR2010 Non-Flu Day 80-100


title: BR2010 Non-Flu Day 0


title: BR2014 Non-Flu Day 80-100


title: BR2014 Non-Flu Day 0


title: BR2014 Y1 Flu Day 80-100


title: BR2014 Y1 Flu Day 0


title: BR2014 Y2 Flu Day 80-100


title: BR2014 Non-Flu Day 7-9


title: BR2014 Y2 Flu Day 7-9


title: BR2014 Y2 Flu Day 0


title: BR2014 Y1 Flu Day 7-9


title: BR2013 Non-Flu Day 80-100


title: BR2014 Standalone Baseline Visit


title: BR2047 Non-Flu Day 7-9


title: BR2047 Y1 Flu Day 80-100


title: BR2045 Standalone Baseline Visit


title: BR2047 Y1 Flu Day 0


title: BR2045 Y2 Flu Day 80-100


title: BR2045 Y2 Flu Day 7-9


title: BR2005 Y2 Flu Day 7-9


title: BR2005 Y2 Flu Day 80-100


title: BR2005 Standalone Baseline Visit


title: BR2005 Y1 Flu Day 0


title: BR2005 Y1 Flu Day 80-100


title: BR2005 Non-Flu Day 7-9


title: BR2005 Non-Flu Day 80-100


title: BR2008 Y2 Flu Day 80-100


title: BR2005 Non-Flu Day 0


title: BR2008 Y2 Flu Day 7-9


title: BR2008 Y2 Flu Day 0


title: BR2008 Standalone Baseline Visit


title: BR2008 Y1 Flu Day 7-9


title: BR2008 Y1 Flu Day 80-100


title: BR2008 Non-Flu Day 7-9


title: BR2008 Non-Flu Day 0


title: BR2008 Non-Flu Day 80-100


title: BR2008 Y1 Flu Day 0


title: BR2016 Standalone Baseline Visit


title: BR2016 Y2 Flu Day 80-100


title: BR2016 Y2 Flu Day 0


title: BR2016 Y2 Flu Day 7-9


title: BR2047 Non-Flu Day 0


title: BR2016 Non-Flu Day 80-100


title: BR2016 Non-Flu Day 7-9


title: BR2016 Non-Flu Day 0


title: BR2016 Y1 Flu Day 0


title: BR2005 Y2 Flu Day 0


title: BR2047 Y1 Flu Day 7-9


title: BR2016 Y1 Flu Day 80-100


title: BR2009 Y2 Flu Day 80-100


title: BR2009 Standalone Baseline Visit


title: BR2009 Y2 Flu Day 0


title: BR2009 Y1 Flu Day 80-100


title: BR2009 Y1 Flu Day 7-9


title: BR2009 Y2 Flu Day 7-9


title: BR2045 Y2 Flu Day 0


title: BR2009 Non-Flu Day 0


title: BR2045 Non-Flu Day 80-100


title: BR2009 Non-Flu Day 80-100


title: BR2045 Non-Flu Day 7-9


title: BR2045 Y1 Flu Day 80-100


title: BR2045 Non-Flu Day 0


title: BR2009 Non-Flu Day 7-9


title: BR2045 Y1 Flu Day 7-9


title: BR2045 Y1 Flu Day 0


title: BR2002 Non-Flu Day 80-100


title: BR2002 Non-Flu Day 7-9


title: BR2002 Standalone Baseline Visit


title: BR2016 Y1 Flu Day 7-9


title: BR1056 Y2 Flu Day 80-100


title: BR2002 Non-Flu Day 0


title: BR2002 Y2 Flu Day 7-9


title: BR2002 Y2 Flu Day 80-100


title: BR2002 Y2 Flu Day 0


title: BR2002 Y1 Flu Day 80-100


title: BR2002 Y1 Flu Day 7-9


title: BR2009 Y1 Flu Day 0


title: BR2002 Y1 Flu Day 0


title: BR1056 Y2 Flu Day 7-9


title: BR1056 Non-Flu Day 7-9


title: BR1056 Y2 Flu Day 0


title: BR1056 Y1 Flu Day 80-100


title: BR1056 Non-Flu Day 0


title: BR1056 Non-Flu Day 80-100


title: BR1056 Y1 Flu Day 7-9


title: BR1056 Y1 Flu Day 0


title: BR1051 Y2 Flu Day 0


title: BR1051 Y1 Flu Day 80-100


title: BR1051 Non-Flu Day 7-9


title: BR1051 Non-Flu Day 80-100


title: BR1051 Standalone Baseline Visit


title: BR1051 Y2 Flu Day 80-100


title: BR2003 Non-Flu Day 7-9


title: BR1051 Y1 Flu Day 7-9


title: BR2003 Non-Flu Day 0


title: BR2003 Y2 Flu Day 80-100


title: BR2003 Y2 Flu Day 7-9


title: BR1051 Y1 Flu Day 0


title: BR2003 Y1 Flu Day 80-100


title: BR2003 Y1 Flu Day 7-9


title: BR2003 Y1 Flu Day 0


title: BR1049 Standalone Baseline Visit


title: BR1049 Y2 Flu Day 80-100


title: BR1049 Y2 Flu Day 0


title: BR1051 Y2 Flu Day 7-9


title: BR1049 Non-Flu Day 0


title: BR1049 Non-Flu Day 80-100


title: BR1049 Non-Flu Day 7-9


title: BR1049 Y1 Flu Day 7-9


title: BR1049 Y1 Flu Day 80-100


title: BR1049 Y1 Flu Day 0


title: BR1035 Non-Flu Day 7-9


title: BR1035 Non-Flu Day 0


title: BR1040 Y2 Flu Day 80-100


title: BR2003 Y2 Flu Day 0


title: BR2003 Non-Flu Day 80-100


title: BR1040 Non-Flu Day 80-100


title: BR2003 Standalone Baseline Visit


title: BR1040 Y1 Flu Day 7-9


title: BR1040 Non-Flu Day 0


title: BR1040 Standalone Baseline Visit


title: BR1047 Standalone Baseline Visit


title: BR1040 Non-Flu Day 7-9


title: BR1040 Y2 Flu Day 0


title: BR1040 Y2 Flu Day 7-9


title: BR1047 Y2 Flu Day 7-9


title: BR1040 Y1 Flu Day 0


title: BR1047 Y2 Flu Day 80-100


title: BR1040 Y1 Flu Day 80-100


title: BR1047 Non-Flu Day 7-9


title: BR1047 Non-Flu Day 80-100


title: BR1047 Non-Flu Day 0


title: BR1047 Y1 Flu Day 80-100


title: BR1047 Y1 Flu Day 7-9


title: BR1043 Y2 Flu Day 80-100


title: BR1033 Y1 Flu Day 0


title: BR1033 Y1 Flu Day 7-9


title: BR1047 Y1 Flu Day 0


title: BR1043 Standalone Baseline Visit


title: BR1043 Y2 Flu Day 0


title: BR1043 Y2 Flu Day 7-9


title: BR1043 Y1 Flu Day 80-100


title: BR1043 Non-Flu Day 80-100


title: BR1043 Y1 Flu Day 7-9


title: BR2004 Non-Flu Day 80-100


title: BR1043 Non-Flu Day 0


title: BR1043 Y1 Flu Day 0


title: BR1037 Y2 Flu Day 80-100


title: BR2027 Standalone Baseline Visit


title: BR1043 Non-Flu Day 7-9


title: BR2004 Non-Flu Day 7-9


title: BR1037 Standalone Baseline Visit


title: BR1047 Y2 Flu Day 0


title: BR1037 Y1 Flu Day 80-100


title: BR1037 Y1 Flu Day 7-9


title: BR1037 Y1 Flu Day 0


title: BR1037 Non-Flu Day 7-9


title: BR1031 Y2 Flu Day 7-9


title: BR1037 Non-Flu Day 0


title: BR1031 Y2 Flu Day 0


title: BR1037 Non-Flu Day 80-100


title: BR1031 Standalone Baseline Visit


title: BR1031 Y1 Flu Day 80-100


title: BR1031 Non-Flu Day 80-100


title: BR1031 Y1 Flu Day 0


title: BR1037 Y2 Flu Day 7-9


title: BR1031 Non-Flu Day 0


title: BR1031 Y1 Flu Day 7-9


title: BR1028 Y2 Flu Day 7-9


title: BR2004 Non-Flu Day 0


title: BR1028 Non-Flu Day 80-100


title: BR1030 Y1 Flu Day 0


title: BR1028 Y1 Flu Day 7-9


title: BR1030 Y1 Flu Day 80-100


title: BR1030 Y2 Flu Day 0


title: BR1028 Non-Flu Day 0


title: BR1028 Y2 Flu Day 0


title: BR1028 Y1 Flu Day 80-100


title: BR1030 Y2 Flu Day 80-100


title: BR1030 Non-Flu Day 80-100


title: BR1028 Non-Flu Day 7-9


title: BR1030 Non-Flu Day 7-9


title: BR1030 Standalone Baseline Visit


title: BR1045 Y1 Flu Day 7-9


title: BR1045 Y1 Flu Day 80-100


title: BR1032 Y2 Flu Day 80-100


title: BR1030 Non-Flu Day 0


title: BR1032 Y2 Flu Day 7-9


title: BR1032 Y2 Flu Day 0


title: BR1028 Y2 Flu Day 80-100


title: BR1028 Standalone Baseline Visit


title: BR1032 Standalone Baseline Visit


title: BR1032 Y1 Flu Day 7-9


title: BR1032 Non-Flu Day 7-9


title: BR1032 Non-Flu Day 0


title: BR1032 Y1 Flu Day 0


title: BR1030 Y2 Flu Day 7-9


title: BR1032 Y1 Flu Day 80-100


title: BR1052 Standalone Baseline Visit


title: BR1052 Y1 Flu Day 7-9


title: BR1023 Y2 Flu Day 80-100


title: BR1052 Y1 Flu Day 80-100


title: BR1023 Y2 Flu Day 7-9


title: BR1023 Y1 Flu Day 0


title: BR1023 Non-Flu Day 0


title: BR1023 Y1 Flu Day 80-100


title: BR1023 Non-Flu Day 7-9


title: BR1042 Y1 Flu Day 0


title: BR1042 Y1 Flu Day 80-100


title: BR1023 Non-Flu Day 80-100


title: BR1023 Standalone Baseline Visit


title: BR1034 Y1 Flu Day 7-9


title: BR1034 Non-Flu Day 80-100


title: BR1034 Non-Flu Day 7-9


title: BR1023 Y2 Flu Day 0


title: BR1024 Y2 Flu Day 80-100


title: BR1034 Y1 Flu Day 0


title: BR1024 Y2 Flu Day 0


title: BR1024 Standalone Baseline Visit


title: BR1024 Y1 Flu Day 7-9


title: BR1024 Y1 Flu Day 0


title: BR1024 Non-Flu Day 80-100


title: BR1023 Y1 Flu Day 7-9


title: BR1052 Y1 Flu Day 0


title: BR1042 Y1 Flu Day 7-9


title: BR1024 Non-Flu Day 0


title: BR1026 Y2 Flu Day 80-100


title: BR1026 Y2 Flu Day 7-9


title: BR1034 Non-Flu Day 0


title: BR1026 Y1 Flu Day 0


title: BR1026 Y2 Flu Day 0


title: BR1026 Y1 Flu Day 80-100


title: BR1025 Y2 Flu Day 0


title: BR1026 Non-Flu Day 0


title: BR1026 Standalone Baseline Visit


title: BR1026 Non-Flu Day 80-100


title: BR1025 Y1 Flu Day 7-9


title: BR1025 Y1 Flu Day 80-100


title: BR1025 Y1 Flu Day 0


title: BR1025 Standalone Baseline Visit


title: BR1024 Y2 Flu Day 7-9


title: BR1026 Y1 Flu Day 7-9


title: BR1025 Non-Flu Day 80-100


title: BR1024 Non-Flu Day 7-9


title: BR1025 Non-Flu Day 0


title: BR1024 Y1 Flu Day 80-100


title: BR1015 Y1 Flu Day 80-100


title: BR1015 Y1 Flu Day 7-9


title: BR1015 Non-Flu Day 0


title: BR1015 Y1 Flu Day 0


title: BR1015 Non-Flu Day 7-9


title: BR1017 Y2 Flu Day 80-100


title: BR1017 Y2 Flu Day 7-9


title: BR1026 Non-Flu Day 7-9


title: BR1017 Y1 Flu Day 80-100


title: BR1017 Y2 Flu Day 0


title: BR1017 Standalone Baseline Visit


title: BR1025 Y2 Flu Day 7-9


title: BR1017 Y1 Flu Day 7-9


title: BR1017 Non-Flu Day 0


title: BR1017 Non-Flu Day 7-9


title: BR1018 Non-Flu Day 80-100


title: BR1017 Y1 Flu Day 0


title: BR1018 Standalone Baseline Visit


title: BR1018 Y2 Flu Day 0


title: BR1025 Non-Flu Day 7-9


title: BR1018 Non-Flu Day 0


title: BR1018 Y2 Flu Day 80-100


title: BR1018 Y1 Flu Day 80-100


title: BR1018 Y1 Flu Day 0


title: BR1018 Y1 Flu Day 7-9


title: BR1021 Y2 Flu Day 80-100


title: BR1001 Y1 Flu Day 7-9


title: BR1021 Y2 Flu Day 7-9


title: BR1021 Standalone Baseline Visit


title: BR1001 Y1 Flu Day 0


title: BR1021 Y1 Flu Day 80-100


title: BR1016 Y1 Flu Day 0


title: BR1016 Non-Flu Day 7-9


title: BR1010 Non-Flu Day 80-100


title: BR1010 Non-Flu Day 0


title: BR1010 Non-Flu Day 7-9


title: BR1017 Non-Flu Day 80-100


title: BR1010 Standalone Baseline Visit


title: BR1010 Y2 Flu Day 80-100


title: BR1010 Y2 Flu Day 0


title: BR1010 Y1 Flu Day 80-100


title: BR1010 Y1 Flu Day 7-9


title: BR1018 Non-Flu Day 7-9


title: BR1001 Y1 Flu Day 80-100


title: BR1018 Y2 Flu Day 7-9


title: BR1010 Y2 Flu Day 7-9


title: BR1012 Non-Flu Day 7-9


title: BR1012 Standalone Baseline Visit


title: BR1012 Y2 Flu Day 80-100


title: BR1010 Y1 Flu Day 0


title: BR1021 Y2 Flu Day 0


title: BR1012 Non-Flu Day 0


title: BR1012 Non-Flu Day 80-100


title: BR1012 Y2 Flu Day 7-9


title: BR1012 Y2 Flu Day 0


title: BR1012 Y1 Flu Day 0


title: BR1012 Y1 Flu Day 7-9


title: BR1011 Standalone Baseline Visit


title: BR1011 Non-Flu Day 80-100


title: BR1012 Y1 Flu Day 80-100


title: BR1011 Non-Flu Day 0


title: BR1011 Non-Flu Day 7-9


title: BR1011 Y2 Flu Day 7-9


title: BR1011 Y1 Flu Day 7-9


title: BR1013 Standalone Baseline Visit


title: BR1011 Y1 Flu Day 0


title: BR1013 Non-Flu Day 80-100


title: BR1013 Non-Flu Day 7-9


title: BR1013 Y2 Flu Day 80-100


title: BR1013 Y2 Flu Day 7-9


title: BR1013 Y2 Flu Day 0


title: BR1013 Non-Flu Day 0


title: BR1013 Y1 Flu Day 80-100


title: BR1013 Y1 Flu Day 7-9


title: BR2020 Y1 Flu Day 7-9


title: BR2020 Non-Flu Day 7-9


title: BR2020 Y1 Flu Day 0


title: BR2020 Non-Flu Day 0


title: BR2020 Y1 Flu Day 80-100


title: BR1029 Non-Flu Day 7-9


title: BR1029 Non-Flu Day 0


title: BR2020 Standalone Baseline Visit


title: BR1009 Non-Flu Day 80-100


title: BR1009 Standalone Baseline Visit


title: BR1009 Non-Flu Day 7-9


title: BR1009 Y2 Flu Day 80-100


title: BR1009 Non-Flu Day 0


title: BR1009 Y2 Flu Day 7-9


title: BR1009 Y2 Flu Day 0


title: BR1009 Y1 Flu Day 80-100


title: BR1011 Y1 Flu Day 80-100


title: BR1009 Y1 Flu Day 7-9


title: BR1009 Y1 Flu Day 0


title: BR1005 Standalone Baseline Visit


title: BR1005 Non-Flu Day 7-9


title: BR1005 Non-Flu Day 80-100


title: BR1005 Non-Flu Day 0


title: BR1005 Y2 Flu Day 80-100


title: BR1005 Y2 Flu Day 7-9


title: BR1005 Y2 Flu Day 0


title: BR1005 Y1 Flu Day 80-100


title: BR1005 Y1 Flu Day 0


title: BR1020 Non-Flu Day 7-9


title: BR1020 Non-Flu Day 0


title: BR1044 Non-Flu Day 80-100


title: BR1044 Non-Flu Day 0


title: BR1044 Non-Flu Day 7-9


title: BR1044 Y1 Flu Day 7-9


title: BR1044 Y1 Flu Day 80-100


title: BR1044 Y1 Flu Day 0


title: BR1006 Standalone Baseline Visit


title: BR1006 Y2 Flu Day 7-9


title: BR1006 Y2 Flu Day 0


title: BR1006 Non-Flu Day 7-9


title: BR1006 Y2 Flu Day 80-100


title: BR1007 Standalone Baseline Visit


title: BR1006 Y1 Flu Day 80-100


title: BR1006 Y1 Flu Day 0


title: BR1006 Non-Flu Day 0


title: BR1007 Non-Flu Day 80-100


title: BR1007 Non-Flu Day 7-9


title: BR1005 Y1 Flu Day 7-9


title: BR1007 Non-Flu Day 0


title: BR1007 Y2 Flu Day 7-9


title: BR1007 Y2 Flu Day 0


title: BR1007 Y2 Flu Day 80-100


title: BR1007 Y1 Flu Day 7-9


title: BR1007 Y1 Flu Day 0


title: BR2052 Standalone Baseline Visit


title: BR2052 Y2 Flu Day 80-100


title: BR1006 Non-Flu Day 80-100


title: BR2052 Y2 Flu Day 7-9


title: BR2052 Non-Flu Day 80-100


title: BR2052 Non-Flu Day 0


title: BR2052 Y1 Flu Day 7-9


title: BR2052 Y1 Flu Day 0


title: BR2052 Y1 Flu Day 80-100


title: BR1003 Non-Flu Day 7-9


title: BR1003 Non-Flu Day 80-100


title: BR1003 Y2 Flu Day 0


title: BR1003 Non-Flu Day 0


title: BR1003 Y2 Flu Day 7-9


title: BR1003 Y1 Flu Day 80-100


title: BR1006 Y1 Flu Day 7-9


title: BR1007 Y1 Flu Day 80-100


title: BR1003 Y2 Flu Day 80-100


title: BR1003 Y1 Flu Day 0


title: BR1003 Y1 Flu Day 7-9


title: BR1002 Non-Flu Day 80-100


title: BR1002 Non-Flu Day 7-9


title: BR1002 Y2 Flu Day 7-9


title: BR1002 Non-Flu Day 0


title: BR1002 Y2 Flu Day 0


title: BR2052 Y2 Flu Day 0


title: BR2052 Non-Flu Day 7-9


title: BR1002 Standalone Baseline Visit


title: BR1003 Standalone Baseline Visit


title: BR1002 Y1 Flu Day 80-100


title: BR1002 Y2 Flu Day 80-100


title: BR1002 Y1 Flu Day 7-9


title: BR2007 Y2 Flu Day 80-100


title: BR2007 Y2 Flu Day 0


title: BR2007 Standalone Baseline Visit


title: BR2007 Y1 Flu Day 80-100


title: BR1002 Y1 Flu Day 0


title: BR2007 Non-Flu Day 80-100


title: BR2007 Non-Flu Day 7-9


title: BR2007 Non-Flu Day 0


title: BR1004 Non-Flu Day 80-100


title: BR1004 Non-Flu Day 7-9


title: BR1004 Non-Flu Day 0


title: BR1004 Y2 Flu Day 80-100


title: BR1004 Standalone Baseline Visit


title: BR1004 Y2 Flu Day 7-9


title: BR1004 Y2 Flu Day 0


title: BR2007 Y2 Flu Day 7-9


title: BR1004 Y1 Flu Day 80-100


title: BR2050 Y1 Flu Day 80-100


title: BR2046 Y2 Flu Day 80-100


title: BR2050 Non-Flu Day 80-100


title: BR2046 Y2 Flu Day 0


title: BR1004 Y1 Flu Day 0


title: BR2050 Y2 Flu Day 7-9


title: BR2050 Y2 Flu Day 0


title: BR2050 Non-Flu Day 0


title: BR2050 Non-Flu Day 7-9


title: BR2050 Y1 Flu Day 0


title: BR2050 Standalone Baseline Visit


title: BR2050 Y1 Flu Day 7-9


title: BR2046 Non-Flu Day 80-100


title: BR2046 Y1 Flu Day 80-100


title: BR2051 Y2 Flu Day 80-100


title: BR2051 Non-Flu Day 80-100


title: BR2050 Y2 Flu Day 80-100


title: BR2051 Standalone Baseline Visit


title: BR2046 Y1 Flu Day 7-9


title: BR2046 Y1 Flu Day 0


title: BR2046 Non-Flu Day 0


title: BR2051 Non-Flu Day 0


title: BR2051 Y1 Flu Day 80-100


title: BR2051 Non-Flu Day 7-9


title: BR2051 Y2 Flu Day 7-9


title: BR2051 Y2 Flu Day 0


title: BR2046 Standalone Baseline Visit


title: BR2046 Y2 Flu Day 7-9


title: BR2051 Y1 Flu Day 7-9


title: BR2051 Y1 Flu Day 0


title: BR1048 Non-Flu Day 7-9


title: BR2041 Standalone Baseline Visit


title: BR2041 Non-Flu Day 7-9


title: BR1048 Y1 Flu Day 7-9


title: BR2041 Non-Flu Day 80-100


title: BR1048 Y1 Flu Day 0


title: BR1048 Non-Flu Day 0


title: BR2041 Y2 Flu Day 0


title: BR2041 Non-Flu Day 0


title: BR1019 Y2 Flu Day 0


title: BR1019 Standalone Baseline Visit


title: BR1019 Y1 Flu Day 0


title: BR1019 Y2 Flu Day 7-9


title: BR1019 Y1 Flu Day 7-9


title: BR2041 Y1 Flu Day 7-9


title: BR1058 Y2 Flu Day 7-9


title: BR1058 Non-Flu Day 80-100


title: BR2041 Y1 Flu Day 0


title: BR1058 Y2 Flu Day 0


title: BR1058 Non-Flu Day 7-9


title: BR2041 Y1 Flu Day 80-100


title: BR1058 Y2 Flu Day 80-100


title: BR1058 Non-Flu Day 0


title: BR1058 Y1 Flu Day 80-100


title: BR1058 Standalone Baseline Visit


title: BR1048 Y1 Flu Day 80-100


title: BR1019 Non-Flu Day 80-100


title: BR1058 Y1 Flu Day 0


title: BR1019 Non-Flu Day 0


title: BR1058 Y1 Flu Day 7-9


title: BR1059 Y2 Flu Day 80-100


title: BR1059 Standalone Baseline Visit


title: BR1059 Y2 Flu Day 7-9


title: BR1059 Non-Flu Day 0


title: BR1059 Non-Flu Day 80-100


title: BR1059 Y1 Flu Day 7-9


title: BR1059 Y1 Flu Day 0


title: BR1059 Y1 Flu Day 80-100


title: BR2039 Y2 Flu Day 7-9


title: BR2039 Non-Flu Day 7-9


title: BR2039 Standalone Baseline Visit


title: BR2039 Non-Flu Day 0


title: BR2039 Y1 Flu Day 7-9


title: BR2039 Y2 Flu Day 80-100


title: BR2025 Standalone Baseline Visit


title: BR2039 Y1 Flu Day 80-100


title: BR2039 Y2 Flu Day 0


title: BR2025 Non-Flu Day 80-100


title: BR2025 Non-Flu Day 7-9


title: BR2025 Y2 Flu Day 7-9


title: BR2025 Y1 Flu Day 80-100


title: BR2025 Y2 Flu Day 0


title: BR2025 Non-Flu Day 0


title: BR2025 Y1 Flu Day 7-9


title: BR2025 Y2 Flu Day 80-100


title: BR2025 Y1 Flu Day 0


title: BR1054 Standalone Baseline Visit


title: BR1054 Y2 Flu Day 7-9


title: BR2039 Non-Flu Day 80-100


title: BR1054 Y2 Flu Day 0


title: BR1054 Y2 Flu Day 80-100


title: BR2039 Y1 Flu Day 0


title: BR1054 Non-Flu Day 80-100


title: BR1059 Y2 Flu Day 0


title: BR1054 Non-Flu Day 7-9


title: BR1054 Y1 Flu Day 80-100


title: BR1054 Y1 Flu Day 7-9


title: BR1054 Y1 Flu Day 0


title: BR1050 Standalone Baseline Visit


title: BR1050 Y2 Flu Day 80-100


title: BR1050 Non-Flu Day 80-100


title: BR1050 Y1 Flu Day 80-100


title: BR1050 Y2 Flu Day 0


title: BR1050 Y1 Flu Day 0


title: BR1050 Y1 Flu Day 7-9


title: BR1008 Y2 Flu Day 7-9


title: BR1008 Y2 Flu Day 80-100


title: BR1008 Y1 Flu Day 80-100