title: S27 Parhyale embryo ATAC-Seq, replicate B

description:
S27B_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S27B_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S27AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S27AB_nucleoatac.ins.bw
S27AB_nucleoatac.nucleoatac_signal.bw
S27AB_nucleoatac.nucleoatac_signal.smooth.bw
S27AB_nucleoatac.nfrpos.bed.gz
S27AB_nucleoatac.nucmap_combined.bed.gz
S27_hintatac_specific_bc.bw
S27_hintatac_specific_fixed_mpbs.bed
S27_fulltest_statistics.txt
S27_mpbs_ev.bed
S27_hintatac_specific_fixed.bed

data_processing:
Reads were trimmed using trim_galore (v0.4.4) to run FASTQC (v0.11.7) and cutadapt (v2.4) using these options: --fastqc --paired --nextera --stringency 5 --gzip --retain_unpaired
Reads were aligned to phaw_5.0.fa genome using bowtie2 --local --very-sensitive-local --threads 40 --time -x (bowtie2 v2.3.0)
Reads for each lane were merged and sorted using samtools -view -bS -q 10 piped into samtools sort -T (samtools v1.8)
Reads were deduplicated using PicardTools (v2.9.0, REMOVE_DUPLICATES=TRUE)
Peaks were called and bedgraph files were generated using Genrich (v0.6, -rvq 0.05); the final peaks are the files ending in .narrowPeak
Bedgraph-like files generated by Genrich were split and converted into bigwig files (files ending in .final.bw) using a custom Python script and UCSCtools bedGraphToBigWig (see GitHub repository)
Peaks were merged using bedtools and then sorted using igvtools to create a file for visualization and downstream analyses (Visualization_Files/OmniATAC_bothruns_q005_allpeaks.igv_new.bed)
NucleoATAC v0.2.1 was run on OmniATAC_bothruns_q005_coordinatesonly.bed for each stage to produce all NucleoATAC downstream files (nucleoatac run --bed OmniATAC_bothruns_q005_coordinatesonly.bed)
rgt-motifanalysis matching and rgt-motifanalysis enrichment were run for stage-specific peaks of each developmental stage (RGT-HINT v0.13.1)
bedtools multicov was run on all merged .bam files to generate a matrix of accessibility values across merged peaks (OmniATAC_bothruns_multicov_forDESeq.tsv)
DESeq2 (v1.34.0) was run to compare accessibilty between S19 vs S13, S21 vs S19, and S23 vs S21 accessibility values
ImpulseDE2 (v0.99.10) was run to generate accessibilty trajectories, differential expression quantification, and model fits for all peaks (all files in ImpulseDE2/OmniATAC-Seq_bothruns_ImpulseDE2…)
Mfuzz was run to cluster peaks based on accessibilty values using a slightly modified OmniATAC_bothrun_multicov_forDESeq.tsv file to agree with Mfuzz expected file type (OmniATAC_bothruns_multicov_mfuzz_mikado.tsv)
Using Mfuzz clusters, rgt-motifanalysis transcription factor footprint peaks were re-grouped based on which cluster the peaks fell into (files in match_specific_9acoresplit)
Re-grouped peaks were filtered to remove duplicate footprints, then rgt-motifanalysis enrichment was run to find enriched footprints (files in enrichment_specific_9acoresplit)
Identity of peaks as intronic, exon, etc. was assigned using a custom Python script and bedtools comparisons to the mikado transcriptome (Visualization_Files/Sall_peaktypes_new.sorted.gff)
Genome_build: phaw_5.0.fa
Supplementary_files_format_and_content: see README.md for full descriptions

growth_protocol: Embryos were collected using previously described protocols (Rehm et al., 2009), staged using the Browne et al. 2003 staging guide, and raised at 27°C in a humidity-controlled incubator in filter-sterilized ASW (FASW).

extract_protocol:
Tagmentation was performed using the reagents described in the Corces et al. 2017 Omni-ATAC-Seq paper, with the following modifications. Instead of the Illumina Nextera TD buffer, 2x Tagmentation Buffer from Wang et al. 2013 was used (Corces et al., 2017; Wang et al., 2013). Homemade Tn5 enzymes were purified and received as a gift from Jase Gehring and assembled into Tn5 transposomes as per Picelli et al 2014, using adapters purchased from IDT with 5’ phosphorylation (Picelli et al., 2014). Prior to adding RSB+D, embryos were washed 3x using 1X PBS. Embryos were mashed into a near-uniform solution using the tip of a low-retention p10 pipette, and the pipette was visually inspected for any remaining debris.
Barcodes were added to samples using primers supplied by QB3-Berkeley using PCR as described in the Corces et al. 2017 Omni-ATAC-Seq paper. A Pippin Prep was used to remove fragments larger than 1.5kb.

tag: developmental stage


title: ISPY2_241998

status: Public on May 25 2022

type: RNA

city: San Francisco

first: Denise

middle: M

last: Wolf

state: CA

address: 2340 Sutter st

country: USA

institute: University of California, San Francisco

hyb_protocol: Hybridization was performed by Agendia Inc (Irvine, CA). This company is referenced by the platforms used: GPL20078 and GPL30494 (updated version of GPL16233).

scan_protocol: Scanning was performed by Agendia Inc (Irvine, CA).

data_processing:
For each array, gnormalized signal (log2) data, as provided in the raw files on each patient, was extracted and aligned to its 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity, as indicated by the 'gIsFeatNonUnifOL' column in the raw files, are NA'd out; and a fixed value of 9.5 was added to avoid negative values. Probeset level data per array were mean-collapsed to the gene level, and genes common to the two platforms identified. Expression data from the first ~900 I-SPY2 patients distributed over the two platforms GPL30494 (updated version of GPL16233; n=334) and GPL20078 (n=545) were combined into a single gene-level dataset after batch-adjusting using ComBat [PMID:16632515]. Linear adjustment factors were derived from the ComBat transformation, per platform, which can be used to batch correct raw files. The subsequent ~100 samples, assayed on GPL20078, were batch corrected using these factors and added to the original set, yielding a normalized expression dataset comprising 988 samples (987 unique patients) x 19,134 (common) genes. The linear adjustment factors and updated probe annotation files per platform are provided, as is the ComBat-normalized data we used in our analysis (supplemental file "ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt").
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt: Normalized, gene-level, batch-/platform- adjusted pre-treatment Agilent 44K expression data for patients from 10 arms of the neoadjuvant I-SPY 2 platform trial for early stage, aggressive breast cancer (n=988 samples for 987 patients). This is the dataset we used in our pan-arm analysis, and constitutes part of the I-SPY2-990 mRNA/RPPA Data Resource. To derive this matrix, probeset level expression data from the first ~900 I-SPY2 patients distributed over the two platforms GPL30494 (updated version of GPL16233; n=334) and GPL20078 (n=545) were mean-collapsed by gene and combined into a single gene-level dataset after batch-adjusting using ComBat [PMID:16632515]. Linear adjustment factors were derived from the ComBat transformation, per platform, which can be used to batch correct new files. The subsequent ~100 samples, assayed on GPL20078, were batch corrected using these factors and added to the original set, yielding the resulting normalized expression dataset comprising 988 samples (987 unique patients) x 19,134 (common) genes.
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL20078_ProbeLevel_n654.txt: Normalized probeset level pre-treatment gene expression data from Agilent 44K expression arrays Agendia32627_DPv1.14_SCFGplus [with annotation GPL20078 (n=654)] from the I-SPY 2 platform trial for early stage, aggressive breast cancer. Each column represents a patient sample. Per column, green-channel (Cy3) normalized signal intensity (log2) data, as provided in the raw files on each patient, was extracted and aligned to its (within-array) 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity are NA'd out; and a fixed value of 9.5 was added to avoid negative values.
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL30493.wasGPL16233_ProbeLevel_n334.txt: Normalized probeset level pre-treatment gene expression data from Agilent 44K expression arrays Agilent_human_DiscoverPrint_15746 [with annotation GPL30493 (update of GPL16233; n=334)] from the I-SPY 2 platform trial for early stage, aggressive breast cancer. Each column represents a patient sample. Per column, green-channel (Cy3) normalized signal intensity (log2) data, as provided in the raw files on each patient, was extracted and aligned to its (within-array) 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity are NA'd out; and a fixed value of 9.5 was added to avoid negative values.
ISPY2_LinearFit_forCombiningExp_20078.txt: This file contains linear adjustment factors (intercept and linear coefficient) derived from the ComBat transformation combining data (~900 samples) from GPL20078 and GPL30493 that can be used to batch-/platform- correct new Agilent 44K expression arrays of the type Agendia32627_DPv1.14_SCFGplus [gene-collapsed using annotation GPL20078] for inclusion in the larger normalized dataset. Application of this transformation to columns from ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL20078_ProbeLevel_n654.txt, once mean-collapsed to gene level using GPL20078, results in values nearly identical to those in ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt, the normalized expression matrix in the I-SPY2-990 data resource.
ISPY2_LinearFit_forCombiningExp_GPL30493_wasGPL16233.txt: This file contains linear adjustment factors (intercept and linear coefficient) derived from the ComBat transformation combining data (~900 samples) from GPL20078 and GPL30493 that can be used to batch-/platform- correct new Agilent 44K expression arrays of the type Agilent_human_DiscoverPrint_15746 [with annotation GPL30493 (update of GPL16233)] for inclusion in the larger normalized dataset. Application of this transformation to columns from ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL30493.wasGPL16233_ProbeLevel_n334.txt, once mean-collapsed to gene level using GPL20078, results in values nearly identical to those in ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt.
ProbeAnnotation_ISPY2Edit_GPL30493_wasGPL16233.txt: This is the probeset annotation file for GPL30493, a minor update of GPL16233. For each probeset ID (row), the associated gene name, systematic name and DNA sequence is described (columns).

molecule: total RNA

organism: Homo sapiens

source_name: Breast cancer biopsy (pre-treatment)

label_protocol: Labeling was performed by Agendia Inc (Irvine, CA).

extract_protocol: Extraction was performed by Agendia Inc (Irvine, CA).

tag: patient id

tag: tissue

value: Breast cancer biopsy (pre-treatment)

tag: hr

tag: mp

tag: pcr

tag: arm

value: Paclitaxel

tag: adjustment method

value: ComBat Adjust


title: 309830

type: protein

description: same as GSM4552638

data_processing: These samples were assayed on three different RPPA arrays (RPPA.1, RPPA.2 and RPPA.3) under GPL28470.  Each individual array (containing hundreds of samples) was standardized as follows: (1) sample w/out replacement 5000 times, maintaining a receptor subtype balance equal to that of the first ~1000 patients (HR+HER2-: 0.384, TN:0.368, HR+HER2+:0.158, HR-HER2+:0.09); (2) calculate the mean(mean) and mean(sd) for each RPPA endpoint over the samples; (3) standardize each endpoint of the array, as y=(x-mean(mean))/mean(sd).  Standardized data from the different arrays was then combined.  This procedure resulted in removal of batch effects, without 'warping' due to mismatches in subtype prevalence.

molecule: protein

source_name: breast cancer biopsy

extract_protocol: Reverse phase protein array (RPPA)

value: Paclitaxel + MK-2206

tag: arm (short name)

tag: rppa array (normalization key)


title: ISPY2_240957

value: Paclitaxel + AMG 386


title: ISPY2_766301


title: 861745

description: same as GSM4552589


title: ISPY2_771443

value: Paclitaxel + MK-2206 + Trastuzumab


title: ISPY2_765671


title: S26 Parhyale embryo ATAC-Seq, replicate A

type: SRA

city: Woods Hole

first: Nipam

middle: H

last: Patel

state: MA

address: 7 Mbl Street

institute: Marine Biological Laboratory

description:
S26A_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S26A_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S26AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S26AB_nucleoatac.ins.bw
S26AB_nucleoatac.nucleoatac_signal.bw
S26AB_nucleoatac.nucleoatac_signal.smooth.bw
S26AB_nucleoatac.nfrpos.bed.gz
S26AB_nucleoatac.nucmap_combined.bed.gz
S26_hintatac_specific_bc.bw
S26_hintatac_specific_fixed_mpbs.bed
S26_fulltest_statistics.txt
S26_mpbs_ev.bed
S26_hintatac_specific_fixed.bed

library_source: genomic

molecule: genomic DNA

organism: Parhyale hawaiensis

source_name: whole embryo


title: S27 Parhyale embryo ATAC-Seq, replicate A

description:
S27A_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S27A_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S27AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S27AB_nucleoatac.ins.bw
S27AB_nucleoatac.nucleoatac_signal.bw
S27AB_nucleoatac.nucleoatac_signal.smooth.bw
S27AB_nucleoatac.nfrpos.bed.gz
S27AB_nucleoatac.nucmap_combined.bed.gz
S27_hintatac_specific_bc.bw
S27_hintatac_specific_fixed_mpbs.bed
S27_fulltest_statistics.txt
S27_mpbs_ev.bed
S27_hintatac_specific_fixed.bed


title: ISPY2_240432


title: ISPY2_239910

value: Paclitaxel + Ganitumab


title: ISPY2_766967


title: 294739

description: same as GSM4552596

value: Control

value: RPPA.2 & RPPA.3 (ave)


title: S25 Parhyale embryo ATAC-Seq, replicate A

description:
S25A_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S25A_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S25AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S25AB_nucleoatac.ins.bw
S25AB_nucleoatac.nucleoatac_signal.bw
S25AB_nucleoatac.nucleoatac_signal.smooth.bw
S25AB_nucleoatac.nfrpos.bed.gz
S25AB_nucleoatac.nucmap_combined.bed.gz
S25_hintatac_specific_bc.bw
S25_hintatac_specific_fixed_mpbs.bed
S25_fulltest_statistics.txt
S25_mpbs_ev.bed
S25_hintatac_specific_fixed.bed


title: 289107

value: Paclitaxel + Pembrolizumab

value: Pembro


title: ISPY2_241705


title: ISPY2_240035

value: Paclitaxel + Ganetespib


title: ISPY2_746731

value: Paclitaxel + ABT 888 + Carboplatin


title: 219545

description: same as GSM4552584


title: ISPY2_756412


title: S25 Parhyale embryo ATAC-Seq, replicate B

description:
S25B_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S25B_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S25AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S25AB_nucleoatac.ins.bw
S25AB_nucleoatac.nucleoatac_signal.bw
S25AB_nucleoatac.nucleoatac_signal.smooth.bw
S25AB_nucleoatac.nfrpos.bed.gz
S25AB_nucleoatac.nucmap_combined.bed.gz
S25_hintatac_specific_bc.bw
S25_hintatac_specific_fixed_mpbs.bed
S25_fulltest_statistics.txt
S25_mpbs_ev.bed
S25_hintatac_specific_fixed.bed


title: ISPY2_749097


title: 753109

description: same as GSM4552605


title: ISPY2_237158


title: S24 Parhyale embryo ATAC-Seq, replicate A

description:
S24A_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S24A_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S24AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S24AB_nucleoatac.ins.bw
S24AB_nucleoatac.nucleoatac_signal.bw
S24AB_nucleoatac.nucleoatac_signal.smooth.bw
S24AB_nucleoatac.nfrpos.bed.gz
S24AB_nucleoatac.nucmap_combined.bed.gz
S24_hintatac_specific_bc.bw
S24_hintatac_specific_fixed_mpbs.bed
S24_fulltest_statistics.txt
S24_mpbs_ev.bed
S24_hintatac_specific_fixed.bed


title: S26 Parhyale embryo ATAC-Seq, replicate B

description:
S26B_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S26B_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S26AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S26AB_nucleoatac.ins.bw
S26AB_nucleoatac.nucleoatac_signal.bw
S26AB_nucleoatac.nucleoatac_signal.smooth.bw
S26AB_nucleoatac.nfrpos.bed.gz
S26AB_nucleoatac.nucmap_combined.bed.gz
S26_hintatac_specific_bc.bw
S26_hintatac_specific_fixed_mpbs.bed
S26_fulltest_statistics.txt
S26_mpbs_ev.bed
S26_hintatac_specific_fixed.bed


title: 729732

description: same as GSM4552640


title: 689076

description: same as GSM4552608


title: 427321

value: VC


title: ISPY2_733962

value: Paclitaxel + Neratinib


title: ISPY2_231633

value: Linear Adjustment Factor


title: 742477

value: Paclitaxel + Trastuzumab

value: RPPA.1 & RPPA.2 (ave)


title: S24 Parhyale embryo ATAC-Seq, replicate B

description:
S24B_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S24B_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S24AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S24AB_nucleoatac.ins.bw
S24AB_nucleoatac.nucleoatac_signal.bw
S24AB_nucleoatac.nucleoatac_signal.smooth.bw
S24AB_nucleoatac.nfrpos.bed.gz
S24AB_nucleoatac.nucmap_combined.bed.gz
S24_hintatac_specific_bc.bw
S24_hintatac_specific_fixed_mpbs.bed
S24_fulltest_statistics.txt
S24_mpbs_ev.bed
S24_hintatac_specific_fixed.bed


title: ISPY2_742477

value: Breast cancer biopsy (pre-treatment)


title: S23 Parhyale embryo ATAC-Seq, replicate A

description:
S23A_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S23A_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S23AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S23AB_nucleoatac.ins.bw
S23AB_nucleoatac.nucleoatac_signal.bw
S23AB_nucleoatac.nucleoatac_signal.smooth.bw
S23AB_nucleoatac.nfrpos.bed.gz
S23AB_nucleoatac.nucmap_combined.bed.gz
S23_hintatac_specific_bc.bw
S23_hintatac_specific_fixed_mpbs.bed
S23_fulltest_statistics.txt
S23_mpbs_ev.bed
S23_hintatac_specific_fixed.bed


title: ISPY2_236470

value: ComBat Adjust


title: ISPY2_235995

value: Paclitaxel + Pertuzumab + Trastuzumab


title: ISPY2_746265


title: S22 Parhyale embryo ATAC-Seq, replicate A

description:
S22A_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S22A_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S22AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S22AB_nucleoatac.ins.bw
S22AB_nucleoatac.nucleoatac_signal.bw
S22AB_nucleoatac.nucleoatac_signal.smooth.bw
S22AB_nucleoatac.nfrpos.bed.gz
S22AB_nucleoatac.nucmap_combined.bed.gz
S22_hintatac_specific_bc.bw
S22_hintatac_specific_fixed_mpbs.bed
S22_fulltest_statistics.txt
S22_mpbs_ev.bed
S22_hintatac_specific_fixed.bed


title: S23 Parhyale embryo ATAC-Seq, replicate B

description:
S23B_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S23B_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S23AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S23AB_nucleoatac.ins.bw
S23AB_nucleoatac.nucleoatac_signal.bw
S23AB_nucleoatac.nucleoatac_signal.smooth.bw
S23AB_nucleoatac.nfrpos.bed.gz
S23AB_nucleoatac.nucmap_combined.bed.gz
S23_hintatac_specific_bc.bw
S23_hintatac_specific_fixed_mpbs.bed
S23_fulltest_statistics.txt
S23_mpbs_ev.bed
S23_hintatac_specific_fixed.bed


title: ISPY2_228192

value: Paclitaxel + AMG-386


title: ISPY2_229328


title: ISPY2_729270


title: S22 Parhyale embryo ATAC-Seq, replicate B

description:
S22B_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S22B_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S22AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S22AB_nucleoatac.ins.bw
S22AB_nucleoatac.nucleoatac_signal.bw
S22AB_nucleoatac.nucleoatac_signal.smooth.bw
S22AB_nucleoatac.nfrpos.bed.gz
S22AB_nucleoatac.nucmap_combined.bed.gz
S22_hintatac_specific_bc.bw
S22_hintatac_specific_fixed_mpbs.bed
S22_fulltest_statistics.txt
S22_mpbs_ev.bed
S22_hintatac_specific_fixed.bed


title: 935460

value: Paclitaxel


title: ISPY2_728714


title: S21 Parhyale embryo ATAC-Seq, replicate B

description:
S21B_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S21B_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S21AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S21AB_nucleoatac.ins.bw
S21AB_nucleoatac.nucleoatac_signal.bw
S21AB_nucleoatac.nucleoatac_signal.smooth.bw
S21AB_nucleoatac.nfrpos.bed.gz
S21AB_nucleoatac.nucmap_combined.bed.gz
S21_hintatac_specific_bc.bw
S21_hintatac_specific_fixed_mpbs.bed
S21_fulltest_statistics.txt
S21_mpbs_ev.bed
S21_hintatac_specific_fixed.bed


title: ISPY2_728182

value: Paclitaxel + AMG 386


title: 252748

description: same as GSM4552591

value: Control


title: ISPY2_227055

value: Paclitaxel + AMG 386 + Trastuzumab


title: ISPY2_233191


title: 873686

value: Paclitaxel + Pembrolizumab


title: S21 Parhyale embryo ATAC-Seq, replicate A

description:
S21A_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S21A_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S21AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S21AB_nucleoatac.ins.bw
S21AB_nucleoatac.nucleoatac_signal.bw
S21AB_nucleoatac.nucleoatac_signal.smooth.bw
S21AB_nucleoatac.nfrpos.bed.gz
S21AB_nucleoatac.nucmap_combined.bed.gz
S21_hintatac_specific_bc.bw
S21_hintatac_specific_fixed_mpbs.bed
S21_fulltest_statistics.txt
S21_mpbs_ev.bed
S21_hintatac_specific_fixed.bed


title: ISPY2_726381


title: 421829


title: ISPY2_725455


title: ISPY2_723918


title: S19plus Parhyale embryo ATAC-Seq, replicate B

description:
S19plusB_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S19plusB_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S19plusAB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S19plusAB_nucleoatac.ins.bw
S19plusAB_nucleoatac.nucleoatac_signal.bw
S19plusAB_nucleoatac.nucleoatac_signal.smooth.bw
S19plusAB_nucleoatac.nfrpos.bed.gz
S19plusAB_nucleoatac.nucmap_combined.bed.gz
S19plus_hintatac_specific_bc.bw
S19plus_hintatac_specific_fixed_mpbs.bed
S19plus_fulltest_statistics.txt
S19plus_mpbs_ev.bed
S19plus_hintatac_specific_fixed.bed


title: S20 Parhyale embryo ATAC-Seq, replicate B

description:
S20B_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S20B_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S20AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S20AB_nucleoatac.ins.bw
S20AB_nucleoatac.nucleoatac_signal.bw
S20AB_nucleoatac.nucleoatac_signal.smooth.bw
S20AB_nucleoatac.nfrpos.bed.gz
S20AB_nucleoatac.nucmap_combined.bed.gz
S20_hintatac_specific_bc.bw
S20_hintatac_specific_fixed_mpbs.bed
S20_fulltest_statistics.txt
S20_mpbs_ev.bed
S20_hintatac_specific_fixed.bed


title: ISPY2_223030


title: ISPY2_221686

value: Paclitaxel + Ganitumab


title: ISPY2_726091


title: S19plus Parhyale embryo ATAC-Seq, replicate A

description:
S19plusA_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S19plusA_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S19plusAB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S19plusAB_nucleoatac.ins.bw
S19plusAB_nucleoatac.nucleoatac_signal.bw
S19plusAB_nucleoatac.nucleoatac_signal.smooth.bw
S19plusAB_nucleoatac.nfrpos.bed.gz
S19plusAB_nucleoatac.nucmap_combined.bed.gz
S19plus_hintatac_specific_bc.bw
S19plus_hintatac_specific_fixed_mpbs.bed
S19plus_fulltest_statistics.txt
S19plus_mpbs_ev.bed
S19plus_hintatac_specific_fixed.bed


title: ISPY2_221375

value: Paclitaxel + Ganetespib


title: S19 Parhyale embryo ATAC-Seq, replicate B

description:
S19B_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S19B_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S19AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S19AB_nucleoatac.ins.bw
S19AB_nucleoatac.nucleoatac_signal.bw
S19AB_nucleoatac.nucleoatac_signal.smooth.bw
S19AB_nucleoatac.nfrpos.bed.gz
S19AB_nucleoatac.nucmap_combined.bed.gz
S19_hintatac_specific_bc.bw
S19_hintatac_specific_fixed_mpbs.bed
S19_fulltest_statistics.txt
S19_mpbs_ev.bed
S19_hintatac_specific_fixed.bed


title: ISPY2_220471


title: S20 Parhyale embryo ATAC-Seq, replicate A

description:
S20A_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S20A_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S20AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S20AB_nucleoatac.ins.bw
S20AB_nucleoatac.nucleoatac_signal.bw
S20AB_nucleoatac.nucleoatac_signal.smooth.bw
S20AB_nucleoatac.nfrpos.bed.gz
S20AB_nucleoatac.nucmap_combined.bed.gz
S20_hintatac_specific_bc.bw
S20_hintatac_specific_fixed_mpbs.bed
S20_fulltest_statistics.txt
S20_mpbs_ev.bed
S20_hintatac_specific_fixed.bed


title: S19 Parhyale embryo ATAC-Seq, replicate A

description:
S19A_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S19A_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S19AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S19AB_nucleoatac.ins.bw
S19AB_nucleoatac.nucleoatac_signal.bw
S19AB_nucleoatac.nucleoatac_signal.smooth.bw
S19AB_nucleoatac.nfrpos.bed.gz
S19AB_nucleoatac.nucmap_combined.bed.gz
S19_hintatac_specific_bc.bw
S19_hintatac_specific_fixed_mpbs.bed
S19_fulltest_statistics.txt
S19_mpbs_ev.bed
S19_hintatac_specific_fixed.bed


title: 332655

description: same as GSM4552556

value: Paclitaxel + MK-2206


title: 530095


title: 136536

description: same as GSM4552537


title: 637752


title: ISPY2_708387

value: Paclitaxel + ABT 888 + Carboplatin


title: ISPY2_720065


title: 254060


title: 706639

description: same as GSM4552559

value: RPPA.2 & RPPA.3 (ave)


title: ISPY2_218249

value: Linear Adjustment Factor


title: ISPY2_709559


title: ISPY2_220925

value: T-DM1 + Pertuzumab


title: ISPY2_714205


title: ISPY2_215932


title: ISPY2_219545


title: ISPY2_706943

value: Paclitaxel + Neratinib


title: S18 Parhyale embryo ATAC-Seq, replicate A

description:
S18A_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S18A_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S18AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S18AB_nucleoatac.ins.bw
S18AB_nucleoatac.nucleoatac_signal.bw
S18AB_nucleoatac.nucleoatac_signal.smooth.bw
S18AB_nucleoatac.nfrpos.bed.gz
S18AB_nucleoatac.nucmap_combined.bed.gz
S18_hintatac_specific_bc.bw
S18_hintatac_specific_fixed_mpbs.bed
S18_fulltest_statistics.txt
S18_mpbs_ev.bed
S18_hintatac_specific_fixed.bed


title: S17 Parhyale embryo ATAC-Seq, replicate B

description:
S17B_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S17B_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S17AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S17AB_nucleoatac.ins.bw
S17AB_nucleoatac.nucleoatac_signal.bw
S17AB_nucleoatac.nucleoatac_signal.smooth.bw
S17AB_nucleoatac.nfrpos.bed.gz
S17AB_nucleoatac.nucmap_combined.bed.gz
S17_hintatac_specific_bc.bw
S17_hintatac_specific_fixed_mpbs.bed
S17_fulltest_statistics.txt
S17_mpbs_ev.bed
S17_hintatac_specific_fixed.bed


title: ISPY2_698094

value: Breast cancer biopsy (pre-treatment)


title: ISPY2_213913

value: ComBat Adjust


title: S18 Parhyale embryo ATAC-Seq, replicate B

description:
S18B_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S18B_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S18AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S18AB_nucleoatac.ins.bw
S18AB_nucleoatac.nucleoatac_signal.bw
S18AB_nucleoatac.nucleoatac_signal.smooth.bw
S18AB_nucleoatac.nfrpos.bed.gz
S18AB_nucleoatac.nucmap_combined.bed.gz
S18_hintatac_specific_bc.bw
S18_hintatac_specific_fixed_mpbs.bed
S18_fulltest_statistics.txt
S18_mpbs_ev.bed
S18_hintatac_specific_fixed.bed


title: S17 Parhyale embryo ATAC-Seq, replicate A

description:
S17A_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S17A_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S17AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S17AB_nucleoatac.ins.bw
S17AB_nucleoatac.nucleoatac_signal.bw
S17AB_nucleoatac.nucleoatac_signal.smooth.bw
S17AB_nucleoatac.nfrpos.bed.gz
S17AB_nucleoatac.nucmap_combined.bed.gz
S17_hintatac_specific_bc.bw
S17_hintatac_specific_fixed_mpbs.bed
S17_fulltest_statistics.txt
S17_mpbs_ev.bed
S17_hintatac_specific_fixed.bed


title: 910706

value: VC


title: ISPY2_697871


title: ISPY2_213672


title: ISPY2_697098


title: 928815

value: Paclitaxel + AMG-386


title: 536253


title: 535569


title: ISPY2_213328

value: Paclitaxel


title: ISPY2_212307


title: S15 Parhyale embryo ATAC-Seq, replicate A

description:
S15A_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S15A_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S15AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S15AB_nucleoatac.ins.bw
S15AB_nucleoatac.nucleoatac_signal.bw
S15AB_nucleoatac.nucleoatac_signal.smooth.bw
S15AB_nucleoatac.nfrpos.bed.gz
S15AB_nucleoatac.nucmap_combined.bed.gz
S15_hintatac_specific_bc.bw
S15_hintatac_specific_fixed_mpbs.bed
S15_fulltest_statistics.txt
S15_mpbs_ev.bed
S15_hintatac_specific_fixed.bed


title: ISPY2_685753

value: Paclitaxel + AMG 386


title: S14 Parhyale embryo ATAC-Seq, replicate B

description:
S14B_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S14B_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S14AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S14AB_nucleoatac.ins.bw
S14AB_nucleoatac.nucleoatac_signal.bw
S14AB_nucleoatac.nucleoatac_signal.smooth.bw
S14AB_nucleoatac.nfrpos.bed.gz
S14AB_nucleoatac.nucmap_combined.bed.gz
S14_hintatac_specific_bc.bw
S14_hintatac_specific_fixed_mpbs.bed
S14_fulltest_statistics.txt
S14_mpbs_ev.bed
S14_hintatac_specific_fixed.bed


title: 885871

description: same as GSM4552592

value: Control


title: 411008


title: ISPY2_683374


title: ISPY2_209967


title: S13 Parhyale embryo ATAC-Seq, replicate B

description:
S13B_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S13B_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S13AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S13AB_nucleoatac.ins.bw
S13AB_nucleoatac.nucleoatac_signal.bw
S13AB_nucleoatac.nucleoatac_signal.smooth.bw
S13AB_nucleoatac.nfrpos.bed.gz
S13AB_nucleoatac.nucmap_combined.bed.gz
S13_hintatac_specific_bc.bw
S13_hintatac_specific_fixed_mpbs.bed
S13_fulltest_statistics.txt
S13_mpbs_ev.bed
S13_hintatac_specific_fixed.bed


title: 532183

description: same as GSM4552582


title: ISPY2_680881


title: ISPY2_209397


title: S15 Parhyale embryo ATAC-Seq, replicate B

description:
S15B_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S15B_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S15AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S15AB_nucleoatac.ins.bw
S15AB_nucleoatac.nucleoatac_signal.bw
S15AB_nucleoatac.nucleoatac_signal.smooth.bw
S15AB_nucleoatac.nfrpos.bed.gz
S15AB_nucleoatac.nucmap_combined.bed.gz
S15_hintatac_specific_bc.bw
S15_hintatac_specific_fixed_mpbs.bed
S15_fulltest_statistics.txt
S15_mpbs_ev.bed
S15_hintatac_specific_fixed.bed


title: ISPY2_677915


title: ISPY2_208650


title: ISPY2_676048


title: S13 Parhyale embryo ATAC-Seq, replicate A

description:
S13A_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S13A_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S13AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S13AB_nucleoatac.ins.bw
S13AB_nucleoatac.nucleoatac_signal.bw
S13AB_nucleoatac.nucleoatac_signal.smooth.bw
S13AB_nucleoatac.nfrpos.bed.gz
S13AB_nucleoatac.nucmap_combined.bed.gz
S13_hintatac_specific_bc.bw
S13_hintatac_specific_fixed_mpbs.bed
S13_fulltest_statistics.txt
S13_mpbs_ev.bed
S13_hintatac_specific_fixed.bed


title: 849605

value: N


title: 783771


title: 934906


title: ISPY2_672734


title: ISPY2_208303


title: ISPY2_204939

value: Paclitaxel + Pertuzumab + Trastuzumab


title: ISPY2_203060


title: 845783


title: ISPY2_666450


title: ChIPseq IP D56E Rep C

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

description: ChIP-seq analysis

data_processing:
For RNA-seq analysis, the paired-end FASTQ files were split into R1 and R2 files and R1 files were retained for further analysis as previous data contained only single-end reads. Reads were trimmed using Trimmomatic version 0.3 with the default settings except for a HEADCROP of 5, LEADING of 3, TRAILING of 3,  SLIDINGWINDOW of 3:30, and MINLEN of 36. After trimming the reads were aligned to the R. sphaeroides 2.4.1 genome sequence (GenBank accession GCA_000012905.2) using Bowtie2 version 2.2.2 with default settings except the number of mismatches was set to 1. Aligned reads were mapped to gene locations using HTSeq version 0.6.0 using default settings except for the “reverse” strandedness argument was used. edgeR version 3.26.8 was used to identify significantly differentially expressed genes from pairwise analyses, using Benjamini and Hochberg false discovery rate (FDR) less than 0.05 as a significance threshold. Raw sequencing reads were normalized using the reads per kilobase per million mapped reads (RPKM).
For ChIP-seq analysis, the paired-end FASTQ files were trimmed with Trimmomatic version 0.3 with default settings except for LEADING:3, TRAILING:3, SLIDINGWINDOW:3:30, and MINLEN:36. The trimmed paired-end reads were aligned to the R. sphaeroides 2.4.1 genome sequence (GenBank accession GCA_000012905.2) using Bowtie2 version 2.2.2 with default settings except the number of mismatches was set to 1. Picard-tools version 1.98 and Samtools version 1.2 were used to clean, sort, and index the alignment file using default settings. Areas of enrichment of IP over INPUT (peaks) were identified using MOSAiCS version 2.28 using two factor analysis and an analysisType of “IO”. Conversion of BAM to ELAND format for MOSAiCS was performed using Pyicos version 2.0.6 and default settings. WIG files were generated for each sample using QuEST version 2.4 and default settings.
Genome_build: GCF_000012905.2
Supplementary_files_format_and_content: Normalized RPKM read counts for RNA-seq. Raw read counts from HTSeq for RNA-seq. WIG files for ChIP-seq

organism: Cereibacter sphaeroides 2.4.1

source_name: whole cell lysate and immunoprecipitated DNA

growth_protocol: 500mL of Sistrom's minimal media, sparged with 69% N2, 30% O2, 1% CO2 for aerobic growth to an OD ~ 0.5 mid-log

extract_protocol:
Cells lysed and DNA sheared with sonication, DNA-protein fragments trimmed with micrococal nuclease and Rnase treated, Antibody coimmunoprecipitation, sepharose bead pull down, 250mM LiCl wash, 600mM NaCl wash, 300mM NaCl wash, TE buffer wash, protein-DNA complexes eluted from beads, crosslinking revered by heating, DNA purified with QIAquick PCR purification Kit
ChIP-seq library preparation and sequencing was performed at GeneWiz. Libraries for sequencing were created using the Illumina TruSeq ChIP library preparation kit (Illumina) following the standard protocol. ChIP-seq libraries were sequenced on an Illumina HiSeq 3000 2x150bp reads using the standard protocol.

treatment_protocol: cells fixed and crosslinking was performed with 10mM sodium phosphate buffer, 1% formaldehyde on ice for 5 minutes before stopping with 100mM glycine.

tag: genotype

tag: oxygen

value: aerobic

tag: growth phase

value: mid-log growth phase


title: ChIPseq IP D56E Rep D

description: ChIP-seq analysis


title: ChIPseq noAB D56E Rep D

description: ChIP-seq analysis

extract_protocol:
Cells lysed and DNA sheared with sonication, DNA-protein fragments trimmed with micrococal nuclease and Rnase treated, no antibody was added before proceeding as before
ChIP-seq library preparation and sequencing was performed at GeneWiz. Libraries for sequencing were created using the Illumina TruSeq ChIP library preparation kit (Illumina) following the standard protocol. ChIP-seq libraries were sequenced on an Illumina HiSeq 3000 2x150bp reads using the standard protocol.


title: ISPY2_218503

value: Paclitaxel + MK-2206


title: 651401

value: Paclitaxel + Pembrolizumab

value: Pembro


title: ISPY2_202535

value: Paclitaxel + AMG 386 + Trastuzumab


title: ISPY2_663467

value: Paclitaxel + ABT 888 + Carboplatin


title: ChIPseq IP D56E Rep B

description: ChIP-seq analysis


title: S14 Parhyale embryo ATAC-Seq, replicate A

description:
S14A_bothruns_q10.Genrich_sorted.ATAC.q005.final.bw
S14A_bothruns_q10.Genrich_sorted.fraglengthcount.txt
S14AB_bothruns_q10.Genrich_sorted.ATAC.q005.narrowPeak
S14AB_nucleoatac.ins.bw
S14AB_nucleoatac.nucleoatac_signal.bw
S14AB_nucleoatac.nucleoatac_signal.smooth.bw
S14AB_nucleoatac.nfrpos.bed.gz
S14AB_nucleoatac.nucmap_combined.bed.gz
S14_hintatac_specific_bc.bw
S14_hintatac_specific_fixed_mpbs.bed
S14_fulltest_statistics.txt
S14_mpbs_ev.bed
S14_hintatac_specific_fixed.bed


title: 787415


title: ISPY2_655703


title: ISPY2_660915

value: Paclitaxel + Neratinib


title: ISPY2_201831

value: Breast cancer biopsy (pre-treatment)


title: ChIPseq IP D56E Rep A

description: ChIP-seq analysis


title: ChIPseq INPUT D56E Rep D

description: ChIP-seq analysis

extract_protocol:
Cells lysed and DNA sheared with sonication, DNA-protein fragments trimmed with micrococal nuclease and Rnase treated, no immunoprecipition was performed on Input, crosslinking reversed with heating, and DNA purified with QIAquick PCR purification kit
ChIP-seq library preparation and sequencing was performed at GeneWiz. Libraries for sequencing were created using the Illumina TruSeq ChIP library preparation kit (Illumina) following the standard protocol. ChIP-seq libraries were sequenced on an Illumina HiSeq 3000 2x150bp reads using the standard protocol.


title: ISPY2_651541

value: ComBat Adjust


title: ISPY2_650589


title: 414971

description: same as GSM4552561


title: ISPY2_654956


title: ChIPseq INPUT D56E Rep B

description: ChIP-seq analysis


title: ISPY2_196064


title: ISPY2_646233


title: 661730


title: 949444


title: ISPY2_199115


title: ISPY2_199960


title: ChIPseq INPUT D56E Rep A

description: ChIP-seq analysis


title: ChIPseq noAB D56A Rep D

description: ChIP-seq analysis


title: 726091


title: ISPY2_196024

value: Paclitaxel + Ganetespib


title: 286984

description: same as GSM4552524


title: 421917

description: same as GSM4552593

value: RPPA.2 & RPPA.3 (ave)


title: 180027

value: Paclitaxel + AMG-386


title: ISPY2_641246


title: ChIPseq IP D56A Rep D

description: ChIP-seq analysis


title: ISPY2_640463


title: 668752


title: ISPY2_640927


title: ISPY2_200222


title: ISPY2_182346

value: Paclitaxel + Ganitumab


title: ISPY2_194024

value: Linear Adjustment Factor


title: ISPY2_181442

value: Paclitaxel


title: ISPY2_637752

value: Paclitaxel + AMG 386


title: ChIPseq INPUT D56E Rep C

description: ChIP-seq analysis

value: aerobic


title: 479417

value: VC


title: ISPY2_188700


title: ChIPseq IP D56A Rep C

description: ChIP-seq analysis

value: mid-log growth phase


title: 435313


title: 367682

value: Control

value: RPPA.1 & RPPA.2 (ave)


title: ChIPseq IP D56A Rep A

description: ChIP-seq analysis


title: ChIPseq IP D56A Rep B

description: ChIP-seq analysis


title: ISPY2_635862


title: ISPY2_630758


title: ISPY2_180663

value: Paclitaxel + MK-2206


title: ISPY2_179568


title: ISPY2_632408


title: ChIPseq INPUT D56A Rep C

description: ChIP-seq analysis


title: 245655

value: N


title: ChIPseq INPUT D56A Rep B

description: ChIP-seq analysis


title: ISPY2_179369


title: ChIPseq INPUT D56A Rep A

description: ChIP-seq analysis


title: 581180


title: ISPY2_174904


title: ISPY2_629606-GPL16233


title: ISPY2_177795

value: Paclitaxel + Pembrolizumab


title: ChIPseq INPUT D56A Rep D

description: ChIP-seq analysis


title: ISPY2_172366

value: Breast cancer biopsy (pre-treatment)


title: ISPY2_629210

value: Paclitaxel + Neratinib

value: ComBat Adjust


title: ISPY2_627981


title: 960490

value: Pembro


title: ISPY2_628692


title: ChIPseq noAB WT Rep D

description: ChIP-seq analysis

value: wild-type


title: 550157


title: ChIPseq IP WT Rep D

description: ChIP-seq analysis


title: ChIPseq IP WT Rep C

description: ChIP-seq analysis


title: ISPY2_627118

value: Paclitaxel + Trastuzumab


title: ISPY2_169918


title: ChIPseq IP WT Rep B

description: ChIP-seq analysis


title: ISPY2_172168


title: 609642

description: same as GSM4552616

value: Paclitaxel + MK-2206 + Trastuzumab


title: ISPY2_623086


title: 497010


title: ISPY2_622078


title: ISPY2_168044

value: Linear Adjustment Factor


title: ChIPseq INPUT WT Rep C

description: ChIP-seq analysis


title: 194024


title: ChIPseq INPUT WT Rep D

description: ChIP-seq analysis


title: 443708


title: 489504

value: Paclitaxel


title: 294265

description: same as GSM4552646


title: ISPY2_165925

value: Paclitaxel + Ganitumab


title: ISPY2_625800


title: ISPY2_167271

value: T-DM1 + Pertuzumab


title: ChIPseq INPUT WT Rep B

description: ChIP-seq analysis

value: aerobic

value: mid-log growth phase


title: ISPY2_162562


title: ChIPseq IP WT Rep A

description: ChIP-seq analysis


title: ISPY2_615873


title: 559263

value: Control


title: ISPY2_159284


title: ChIPseq INPUT WT Rep A

description: ChIP-seq analysis


title: ChIPseq IP 1056∆ Rep D

description: ChIP-seq analysis


title: 623086


title: ISPY2_613188

value: Paclitaxel + AMG 386


title: ChIPseq noAB 1056∆ Rep D

description: ChIP-seq analysis


title: 925691

value: N


title: ISPY2_157270

value: Paclitaxel + AMG 386 + Trastuzumab


title: ISPY2_611662

value: Breast cancer biopsy (pre-treatment)


title: ISPY2_605713

value: Paclitaxel + ABT 888 + Carboplatin


title: ISPY2_156163

value: ComBat Adjust


title: 570380

value: Paclitaxel + Neratinib


title: ChIPseq IP 1056∆ Rep C

description: ChIP-seq analysis


title: ISPY2_164468

value: Paclitaxel + Ganetespib


title: ISPY2_614044


title: ISPY2_604380


title: 380769

value: VC


title: ISPY2_153327

value: Paclitaxel + Pembrolizumab


title: 374121


title: ISPY2_152197

value: Linear Adjustment Factor


title: 778020


title: ISPY2_602943

value: Paclitaxel


title: ISPY2_600536


title: ChIPseq INPUT 1056∆ Rep D

description: ChIP-seq analysis


title: ISPY2_152090


title: ChIPseq INPUT 1056∆ Rep C

description: ChIP-seq analysis


title: 663467


title: ISPY2_151980


title: 299364


title: ISPY2_598798


title: ChIPseq INPUT 1056∆ Rep B

description: ChIP-seq analysis


title: ChIPseq IP 1056∆ Rep B

description: ChIP-seq analysis


title: 783427

description: same as GSM4552568

value: RPPA.2 & RPPA.3 (ave)


title: ChIPseq IP 1056∆ Rep A

description: ChIP-seq analysis


title: ISPY2_607047


title: ISPY2_597253


title: ISPY2_596079

value: Paclitaxel + Trastuzumab


title: ChIPseq INPUT 1056∆ Rep A

description: ChIP-seq analysis

value: aerobic


title: ISPY2_149654


title: ISPY2_147139


title: ISPY2_596458


title: ISPY2_148357

value: Paclitaxel + Ganitumab


title: RNAseq 1056∆ Rep C

description:
RNA-seq analysis
Lakey_RNAseq_Log2RPKM_Values.txt
Lakey_RNAseq_HTseq_RawCountValues.txt

library_source: transcriptomic

source_name: whole cell lysate and total RNA

extract_protocol:
Hot acid phenol:chloroform extraction, NaOAc/isopropanol precipitation, ethanol wash, Dnase treatment, Qiagen Rneasy kit clean-up and concentration
RNA-seq library preparation and sequencing was performed at the Joint Genome Institute. Libraries for sequencing were created using the Illumina TruSeq Stranded Total RNA kit (Illumina) following the standard protocol. RNA-seq libraries were sequenced on an Illumina NextSeq in 2x151 reads using the standard protocol.

treatment_protocol: cells fixed with 95% EtOH and 5% acidic phenol:chloroform

value: mid-log growth phase


title: 564234


title: 727804

description: same as GSM4552553

value: Paclitaxel + MK-2206


title: RNAseq 1056∆ Rep B


title: 809649

value: Control


title: RNAseq 1056∆ Rep A


title: 172283

value: N


title: ISPY2_146987

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + AMG 386


title: RNAseq D56E Rep D


title: ISPY2_146033

value: Paclitaxel + Pertuzumab + Trastuzumab

value: ComBat Adjust


title: ISPY2_150547

value: Paclitaxel + Ganetespib


title: ISPY2_592535

value: Paclitaxel + ABT 888 + Carboplatin


title: ISPY2_591180

value: Paclitaxel + Neratinib


title: RNAseq D56E Rep C


title: 331192

value: VC


title: ISPY2_587388


title: ISPY2_145777


title: ISPY2_590220


title: 515141

value: Paclitaxel + AMG-386


title: ISPY2_144302


title: ISPY2_581648

value: Paclitaxel


title: 120001


title: 736721


title: ISPY2_142688

value: Linear Adjustment Factor


title: ISPY2_580632


title: 876511


title: ISPY2_579881


title: ISPY2_139973


title: ISPY2_575372


title: RNAseq D56A Rep B

value: aerobic


title: RNAseq D56A Rep C


title: ISPY2_573919

value: Paclitaxel + MK-2206 + Trastuzumab


title: RNAseq D56A Rep A

value: mid-log growth phase


title: ISPY2_136536


title: RNAseq D56E Rep B


title: ISPY2_133650


title: 586091

value: Paclitaxel + Pembrolizumab

value: Pembro


title: 313243

value: Control


title: ISPY2_573881

value: Breast cancer biopsy (pre-treatment)


title: RNAseq D56E Rep A


title: ISPY2_138027

value: Paclitaxel + Ganitumab


title: 843554


title: 622315


title: ISPY2_132463


title: RNAseq WT Rep E

value: wild-type


title: RNAseq WT Rep F


title: ISPY2_573586

value: Paclitaxel + Trastuzumab

value: ComBat Adjust


title: RNAseq D56A Rep D


title: RNAseq WT Rep D


title: ISPY2_138425

value: T-DM1 + Pertuzumab


title: ISPY2_131961


title: ISPY2_578975

value: Paclitaxel + MK-2206


title: 959366

value: Paclitaxel + ABT 888 + Carboplatin

value: VC


title: 426106

description: same as GSM4552536


title: ISPY2_131595

value: Paclitaxel + AMG 386


title: RNAseq WT Rep C


title: ISPY2_572731


title: 934459


title: ISPY2_130892


title: RNAseq WT Rep B


title: ISPY2_130580


title: ISPY2_572444

value: Paclitaxel + Neratinib


title: ISPY2_572235


title: RNAseq WT Rep A

value: aerobic


title: ISPY2_570380


title: ISPY2_570148


title: ISPY2_128675

value: Paclitaxel

value: Linear Adjustment Factor


title: 139137


title: ISPY2_128051


title: ISPY2_568331


title: 234723

value: Paclitaxel + AMG-386


title: RFA020: smchd1 mz sphere 2

city: Singapore

first: Shifeng

last: Xue

address: 14 Science Drive 4

country: Singapore

institute: National University of Singapore

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to danRer10 genome with Bowtie
TPM were calculated by RSEM
Genome_build: danRer10
Supplementary_files_format_and_content: RPKM and TPM values for each sample

molecule: polyA RNA

organism: Danio rerio

source_name: zebrafish embryos

extract_protocol:
RNA from 30-50 zebrafish embryos at the designated stages was extracted using RNeasy Mini Kit (Qiagen) with DNase digestion on column.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: sphere

tag: strain

value: AB

value: smchd1 mz lof1


title: ISPY2_125418

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + Ganetespib


title: 771151


title: ISPY2_127791

value: Paclitaxel + Pertuzumab + Trastuzumab


title: 590299


title: RFA019: smchd1 mz sphere 1


title: RFA018: smchd1 mz 4 cell 3

value: 4 to 8-cell


title: ISPY2_566011

value: ComBat Adjust


title: RFA017: smchd1 mz 4 cell 2


title: ISPY2_125130

value: T-DM1 + Pertuzumab


title: ISPY2_563856


title: ISPY2_564234

value: Paclitaxel + ABT 888 + Carboplatin


title: 283070


title: 414286

description: same as GSM4552527

value: Paclitaxel + MK-2206


title: RFA016: smchd1 mz 4 cell 1


title: ISPY2_123660

value: Paclitaxel + Trastuzumab


title: 836114


title: ISPY2_553141


title: RFA021: smchd1 mz sphere 3


title: ISPY2_122579


title: RFA012: wt sphere 3

value: wt


title: ISPY2_552313

value: Paclitaxel + Neratinib


title: 804233

value: Paclitaxel + Pembrolizumab

value: Pembro


title: RFA011: wt sphere 2


title: ISPY2_122287


title: RFA010: wt sphere 1


title: ISPY2_120422

value: Paclitaxel + Ganitumab


title: ISPY2_549172

value: Paclitaxel


title: ISPY2_541165


title: 301968

value: Paclitaxel + AMG-386


title: RFA009: wt 4 cell 3

value: AB


title: ISPY2_119928

value: Breast cancer biopsy (pre-treatment)


title: ISPY2_540539


title: 326202


title: 262131

value: VC


title: ISPY2_118307

value: Paclitaxel + AMG 386


title: RFA008: wt 4 cell 2

value: 4 to 8-cell


title: 727255


title: ISPY2_539291

value: ComBat Adjust


title: 640463


title: RFA007: wt 4 cell 1


title: ISPY2_117707

value: Paclitaxel + Ganetespib


title: ISPY2_116603


title: ISPY2_531672


title: 233962

value: N


title: H-T2A

city: shijiazhuang

first: jian

last: Dou

address: No.139 Ziqiang Road

department: Department of Hepatobiliary Surgery

country: China

institute: The Third Hospital of Hebei Medical University

data_processing:
seqenced reads were inmmed for adptor sequnce and masked for low-complexily sequence
mapped to human reference genome
Obtain mapped data(reads, etc., for subsequent transcription assembly and expression count
The distribution of reads compared to the genome in different regions of the reference genome was statistically analyzed, and the target regions were divided into CDS(coding region) Intron(Intron) Intergenic region and UTR(5' and 3 untranslated region).
The FPKM value of each gene/transcript in the sample was calculated, and the value was taken as the expression amount of gene/transcript in the sample
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Gene/transcript COUNT expression matrix

source_name: liver

extract_protocol:
BGIseq-500 platform
RNA libraries were prepared for sequencing using standard illumina protacal

tag: cell type

value: liver cancer cells

tag: group

value: control group

tag: cell line


title: 326433


title: H-T2

value: autophagy group


title: ISPY2_527320


title: ISPY2_520471


title: ISPY2_116165

value: Linear Adjustment Factor


title: S-T1A


title: ISPY2_115987


title: ISPY2_115638


title: ISPY2_520258


title: ISPY2_114087

value: Paclitaxel + Pembrolizumab


title: ISPY2_111646


title: ISPY2_519738

value: Paclitaxel + Neratinib


title: S-T1


title: LX-2


title: ISPY2_517446


title: ISPY2_515565


title: ISPY2_515141


title: 131595


title: ISPY2_111344


title: 571995


title: 971492


title: 792181


title: 335536


title: 566011


title: 797639

description: same as GSM4552547

value: Paclitaxel + MK-2206


title: ISPY2_109623


title: LX-2A


title: ISPY2_507198

value: Paclitaxel


title: siKmt2e_ExE.3

city: shanghai

first: Jin

last: Sun

department: life science and technology

institute: Tongji University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm9 genome_tran using hisat2 (version 2.1.0) with default parameters. Only Reads with high quality (MAPQ>=60) were retained for futher analysis.
The reads count for every gene was counted by featureCounts (Version 1.6.1), and the normalized abundance was calculated as log2(reads per million +1 ) using R edgeR package.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files with normalized abundance for every gene and every sample.
Supplementary_files_format_and_content: tab-delimited text files with raw counts for every gene and every sample

organism: Mus musculus

source_name: ExE

growth_protocol: IVF embryos injected with Kmt2e siRNA were defined as the siKmt2e group, IVF embryos injected with water were defined as the IVF control group

extract_protocol:
The prepared cells were transferred to lysis buffer by a mouth pipette. Reverse transcription was performed directly using Oligo (dT) primer in the lysate containg completely cytoplasm. The second-strand cDNAs were synthesised depending on the poly(A) tail attached to template switching by TSO.
Fragment cDNA was prepared using Covaris sonicator (Covaris S220, Woburn, MA, USA) for sequence library construction. Kapa Hyper Prep Kit（KAPA , KK8504, Switzerland）was used to complete the sequence libraries.

treatment_protocol: Single cell of pre-implatation embryos was collected without polar body by removing zone pellucida with 20mg/ml PE (Pronase E, Sigma), incubating in CZB without Ca2+ and gently pipetting with a firepolished glass tube. Single cell of E7.5 embryos (EXE, Epi) was collected by separating from decidua and digestng with 0.05% TE (Trypsin-EDTA, Gibco, 25300062). All the cells were washed at least three times with 0.5% BSA-PBS (MP Biomedicals ,USA) solution before used.

tag: treatment

value: injected with Kmt2e siRNA

tag: developmental stage

value: embryonic day 7.5 (E7.5)

tag: fertilization

value: IVF


title: ISPY2_105513

tag: patient id

tag: tissue

value: Breast cancer biopsy (pre-treatment)

tag: hr


title: 431061

tag: pcr

tag: arm

value: Pembro


title: ISPY2_496205

tag: mp

value: Paclitaxel + AMG 386

tag: adjustment method


title: ISPY2_511851

value: Paclitaxel + Ganitumab

value: ComBat Adjust


title: 746265

tag: arm (short name)

value: N

tag: rppa array (normalization key)


title: 685795

value: Paclitaxel + AMG-386 + Trastuzumab


title: ISPY2_495440


title: ISPY2_105286


title: siKmt2e_ExE.1


title: ISPY2_104384


title: 796558

description: same as GSM4552619

value: Control


title: 157270


title: ISPY2_515105


title: ISPY2_109874


title: ISPY2_111004


title: ISPY2_491526


title: IVF_control_ExE.3

value: injected with water


title: ISPY2_103939


title: ISPY2_104268


title: ISPY2_489973


title: IVF_control_ExE.2


title: ISPY2_489504


title: ISPY2_484867


title: IVF_control_ExE.1


title: 714205

value: Paclitaxel + ABT 888 + Carboplatin

value: VC


title: 621179

value: Paclitaxel + AMG-386


title: ISPY2_103693

value: Paclitaxel + Pembrolizumab

value: Linear Adjustment Factor


title: 992609


title: siKmt2e_ExE.2

value: injected with Kmt2e siRNA


title: ISPY2_479417


title: ISPY2_102011

value: Paclitaxel + Ganetespib


title: HCCLM3-Control-3

city: Changsha

first: Yiming

last: Li

state: Hunan

address: 78 Xiangya road

department: Department of Surgery

institute: Xiangya Hospital, Central South University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: HCCLM3 HCC cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: HCCLM3 cells were seperated into two groups and respectively transfected with lentivirus-delivered Sema3d and control.

value: Hepatocellular carsinoma cell

tag: genotype


title: ISPY2_102212

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + MK-2206


title: 109874


title: HCCLM3-Control-2


title: ISPY2_478484

value: Paclitaxel + Neratinib


title: HCCLM3-Control-1


title: ISPY2_100899

value: Paclitaxel + Ganitumab


title: HCCLM3-Sema3d-3

value: Sema3d overexpression


title: ISPY2_477816

value: Paclitaxel

value: ComBat Adjust


title: ISPY2_461824


title: 413961

description: same as GSM4552599


title: 587604

value: Control


title: 847272


title: HCCLM3-Sema3d-2


title: 962664


title: ISPY2_460776


title: HCCLM3-Sema3d-1


title: ISPY2_451482

value: Paclitaxel + AMG 386


title: ISPY2_451816

value: Paclitaxel + ABT 888 + Carboplatin


title: ISPY2_443708


title: Macrophage-wild-type-R2

city: Greenfield

first: Bijit

middle: Kumar

last: Bhowmik

state: IN

address: 2500 Innovation Way

department: Discovery Bacteriology & Microbiome

institute: Elanco Animal Health

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned, quantified and analyzed using CLC Genomics Workbench (Qiagen).
Differential gene expression among samples was determined using the DESeq2 package for R in Rstudio (v. 1.0.136). Data were normalized with DESeq2 algorithms.
Transcripts with less than one raw count were excluded, and the default DESeq2 algorithms were used to remove outlier transcripts based on Cook’s distances. The Benjamini and Hochberg algorithm was used to control the false discovery rate (FDR) and transcripts were considered differentially expressed if the expression between two treatments differed by at least 2-fold with FDR < 0.1 (Li et al., 2012).
Genome_build: GRCg6a (GCA_000002315.5)
Supplementary_files_format_and_content: Tab delimited text files of pairwise transcriptome including FDR valus, fold change.

organism: Gallus gallus

source_name: Primary macrophage cells

growth_protocol: Chicken PBMCs were isolated and cultured according to a previous protocol (Feng et al., 2017, Wigley et al., 2002, Peng et al., 2020). Briefly, blood was collected from healthy chickens and heparinized blood was mixed with an equal volume of DPBS. Ten mL of this suspension was then carefully layered on top of 10 mL Histopaque®-1077 (Sigma) in a 50 mL conical tube. Tubes were then centrifuged at 400 × g for 30 minutes at room temperature with the lowest acceleration and no braking. After centrifugation, the top plasma layer was removed and the interface was collected in a fresh tube. The collected lymphocytes were then mixed gently with 5 volumes of DPBS and centrifuged at 250 × g for 10 minutes at room temperature. The supernatant was discarded, and the pellet was washed twice with DPBS at room temperature. The pellet was then finally resuspended in RPMI 1640 Medium, supplemented with GlutaMAX™ (ThermoFisher Sc.), 10% FBS (Gibco), Anti-anti (ThermoFisher Sc.) and 50 µg/mL chicken granulocyte-macrophage colony-stimulating factor (GMCSF, Abcam). The viability of the cells was determined by Trypan Blue exclusion and approximately 1 × 107 cells were transferred to a 24 well plate and incubated at 41°C with 5% CO2. The spent medium was replaced with a fresh medium supplemented with GMCSF every 2 days and the morphology of the adherent cells was monitored using an inverted microscope. After 7 days of incubation, the cells were dislodged from the surface and analyzed using flow cytometry. Macrophages were identified by staining the cells with chicken macrophage marker KUL01 (ThermoFisher Scientific) and analyzing using a flow cytometer (BD FACSAria). as described previously (Mast et al., 1998).

extract_protocol:
The samples were processed by Cofactor Genomics as described previously (do Amaral et al., 2020). Briefly, total RNA was isolated using Qiagen RNAeasy Mini Kit (Qiagen) following the manufacturer’s instructions. The isolated RNA was then treated with DNase I (Thermo Fisher Scientific) to remove potential DNA contamination. RNA was then precipitated using lithium chloride (Sigma). The concentration and quality of RNA were determined using nanophotometer.
RNA samples with RNA integrity number (RIN) > 8.0, A260/A280 > 1.9 and A260/A230 > 2 were selected for mRNA library preparation and Next Generation Sequencing. Briefly, the total RNA was incubated with mRNA capture beads to remove contaminating ribosomal RNA from the sample using the Kapa Stranded mRNA-Seq kit (Kapa Biosystems) following manufacturer’s instructions. The resulting poly(A)-captured mRNA was then fragmented. First-strand cDNA synthesis was performed using reverse transcriptase and random primers in the presence of Actinomycin D, followed by second-strand cDNA synthesis with DNA polymerase I and RNase H. Double-stranded cDNA was end-repaired and A-tailed for subsequent adaptor ligation. Indexed adaptors were ligated to the A-tailed cDNA. Enrichment by PCR was performed to generate the final cDNA sequencing library. Libraries were sequenced as paired-end 150 base reads on an Illumina NextSeq 500 following the manufacturer's protocols.

treatment_protocol: Transcriptome analyses were performed using seven-day old, macrophages differentiated as described above (Huang et al., 2019). Approximately 5 × 104 macrophages were seeded in a 24-well plate and incubated overnight at 41°C with 5% CO2. Overnight grown S. Typhimurium cells were concentrated and washed twice with DPBS. Approximately 1 × 106 bacteria were then resuspended in 1 mL of 10% chicken serum in DPBS and incubated for 30 minutes at 37°C. Bacterial cells were then washed twice in DPBS and resuspended in 1 mL RPMI 1640 medium with 10% heat-inactivated FBS. The primary macrophages were infected with the S. Typhimurium mutants with an MOI of 10 for 30 minutes. After 30 minutes, extracellular bacterial were killed by adding 100 µg/mL of gentamicin for an hour and the medium was then replaced with fresh RPMI-1640 medium supplemented with 30 µg/mL gentamicin and incubated for another hour. Cells were then washed twice with DPBS, lysed by using the RLT buffer (Qiagen) and shipped on dry ice to Cofactor Genomics for RNA-seq

value: PBMC derived macrophages

tag: infection

value: Infected with UK1


title: Macrophage-wild-type-R1

tag: cell type


title: Macrophage-sopF-R2

value: Infected with UK1- sopF


title: ISPY2_442637

value: Paclitaxel + Trastuzumab


title: ISPY2_443444


title: 118307

value: Paclitaxel + AMG-386


title: 677910


title: Macrophage-sifA-R2

value: Infected with UK1- sifA


title: 734997


title: 540539

value: VC


title: Macrophage-sifA-R1


title: 586207


title: 860901


title: ISPY2_437968

value: Breast cancer biopsy (pre-treatment)


title: 805136

value: Paclitaxel + AMG-386 + Trastuzumab


title: ISPY2_435313


title: Macrophage-phoPQ-R2

value: Infected with UK1- phoPQ


title: 374106

value: Paclitaxel + Neratinib

value: N


title: H-T2A, control group

data_processing:
sequenced reads were trimmed for adaptor sequence and masked for low-complexity sequence
mapped to human reference genome
Obtain mapped data reads, etc., for subsequent transcription assembly and expression count
The distribution of reads compared to the genome in different regions of the reference genome was statistically analyzed, and the target regions were divided into CDS(coding region) Intron(Intron) Intergenic region and UTR(5' and 3 untranslated region).
The FPKM value of each gene/transcript in the sample was calculated, and the value was taken as the expression amount of gene/transcript in the sample
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Gene/transcript COUNT expression matrix

extract_protocol: RNA libraries were prepared for sequencing using standard illumina protacal

value: liver cancer cells

tag: group

value: control group


title: H-T2, autophagy group

tag: cell line

value: autophagy group


title: ISPY2_433144

value: Paclitaxel

value: ComBat Adjust


title: Macrophage-phoPQ-R1

value: PBMC derived macrophages


title: Macrophage-sopF-R1


title: Macrophage-MeganVac1-R2

value: Infected with UK1-cya crp


title: ISPY2_426106

value: Paclitaxel + MK-2206


title: 284355

value: Paclitaxel + ABT 888 + Carboplatin


title: S-T1A, control group


title: 943633

value: Paclitaxel + AMG-386


title: Macrophage-only-R1

value: Uninfected


title: LX-2, autophagy group


title: ISPY2_422450


title: 28

city: Rennes

first: Bastien

last: Sadoul

address: 65 rue de Saint Brieuc

country: France

institute: Institut Agro

data_processing:
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina). Demultiplexing and trimming were performed using Illumina's conversion software (bcl2fastq 2.20). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
A splice junction mapper, TopHat 2.1.1 (using Bowtie 2.2.9), was used to align the RNA-Seq reads to the Dicentrarchus labrax genome (NCBI, reference GCA_000689215.1) with a set of gene model annotations (Tine et al., 2014)
Final read alignments having more than 3 mismatches were discarded. Samtools (v1.5) was used to sort the alignment files. Then, the counting was performed with Featurecounts 1.6.2. As the data is from a strand-specific assay, the read has to be mapped to the opposite strand of the gene (-s 2 option).
Genome_build: Dicentrarchus labrax seabass V1
Supplementary_files_format_and_content: tab-delimited text file include raw gene counts for every gene (ID|Symbol) and every sample

organism: Dicentrarchus labrax

source_name: head kidney

growth_protocol: Eggs were reared at 13±3 °C degrees in 9 different tanks until hatching. Temperature was then set at 15 degrees. From 121 days post fertilization (dpf) onwards fish were reared at 21°C. Individuals used for RNA-sequencing were sexed and sampled at 478 dpf.

extract_protocol:
All samples were mechanically disrupted (45 seconds at 30 rpm) in a 2 mL tube filled with 500 µL MR1 and 1 μL of TCEP from NucleoMag® RNA extraction kit (Macherey-Nagel) and 2 stainless steel beads. After a two minutes centrifugation at 13000 rpm, a sub-sample of 200 μL was transferred in a 96 deep-wells plate filled with 150 µL MR1. Automatic extraction was then performed using a KingFisher robot following manufacturer’s instructions for the NucleoMag® RNA kits.
Libraries were constructed using the Truseq stranded mRNA sample prep kit (Illumina, San Diego, CA,USA) according to the manufacturer instructions ; Libraries were pooled in equimolar amounts, denatured with NaOH, and diluted to 20 pM before clustering on a cBot system (Illumina, San Diego, CA, USA). Sequencing was performed on an HiSeq 2500 (Illumina, San Diego, CA, USA) using the single-end 1*50 nt protocol on 3 lanes of a flow cell V4

treatment_protocol: Bold individuals were selected for their constant risk-taking behavior measured by a low latency to exit a sheltered side of a tank. Shy individuals on the contrary either never went out or showed an extremely high latency to exit.

value: head kidney

tag: Sex

value: M

tag: behavior

value: bold behavior


title: LX-2A, control group


title: ISPY2_423619

value: Breast cancer biopsy (pre-treatment)


title: 26

value: F

value: shy behavior


title: P. falciparum drug-resistant line — MRA_1241 (RNA Replicate 2)

city: Pune

first: Krishanpal

last: Karmodiya

state: Maharashtra

address: Dr. Homi Bhabha Road

department: Center of Excellence in Epigenetics

country: India

institute: Indian Institute of Science Education and Research

data_processing:
Alignment to reference genome using STAR aligner in basic 2-pass mode
Variant-calling using REDItools 2.0 (https://github.com/tizianoflati/reditools2.0) on aligned (BAM) files
Annotation with corresponding variant data from whole-genome sequencing followed by variant filtering
Deduplication of BAM files at filtered variant positions using samtools
Second round of variant-calling using REDItools 2.0
Genome_build: Plasmodium falciparum 3D7 v.41 (ASM276v2)
Supplementary_files_format_and_content: .res files (tab-separated text file containing variants from second round of variant calling) and .sf files (output files of gene abundance estimation using Salmon)

organism: Plasmodium falciparum

source_name: P. falciparum blood-stage cultures

growth_protocol: Parasites were cultured in RPMI1640 medium supplemented with 25 mM HEPES, 0.5 % AlbuMAX I, 1.77 mM sodium bicarbonate, 100 μM hypoxanthine and 12.5 μg ml−1 gentamicin sulfate at 37 °C; subculture every two days; parasitemia maintained at ~5%

extract_protocol:
Total RNA was isolated using TRIzol reagent according to the protocol. DNAse treated RNA was used for cDNA synthesis
The cDNA libraries were prepared for samples using Illumina TruSeq RNA library preparation kit

tag: strain

tag: type

value: drug-resistant

tag: Stage

value: Early trophozoite


title: Macrophage-only-R2


title: ISPY2_427321

tag: patient id

tag: tissue

tag: hr


title: 27


title: ISPY2_422013

tag: mp

tag: pcr

tag: arm

value: Paclitaxel + Neratinib


title: 180663

description: same as GSM4552620

tag: arm (short name)

tag: rppa array (normalization key)


title: S-T1, autophagy group

value: liver cancer cells

value: autophagy group


title: ISPY2_420523

tag: adjustment method

value: ComBat Adjust


title: Individual_14

city: Boston

first: Joan

middle: S.

last: Brugge

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

description:
PM-J
Single-cell RNA-Seq

data_processing:
Paired-end reads from Illumina HiSeq were processed and mapped using Cell Ranger v3.0.2.
The following filters were used to eliminate cells with (1) UMI counts < 1,000; (2) gene counts < 500 or > 8,000; and (3) mitochondrial gene ratio > 10%.
Removed genes detected in <20 cells.
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: Li_Brugge_10XscRNAseq_GeneCellMatrix_RNAcounts_human.csv: Gene-cell matrix table containing transcript counts for every gene in every cell for each cell.
Supplementary_files_format_and_content: Li_Brugge_10XscRNAseq_Metadata_human.csv: Metadata table containing information for each cell, including sample of origin and designated cell types.

source_name: mammary tissue

extract_protocol:
Each tissue was minced using razor blades and digested in a solution containing DMEM/F12 (Gibco 11330), 2 mM GlutaMax (Gibco 35050), 10 mM HEPES Gibco (15630), 50 U/mL Penicillin-Streptomycin (Gibco 15070), and 1 mg/ml collagenase XI (Sigma C9407). Cell digestion was incubated at 37°C with constant shaking at 150 rpm for 2 hours. Cells were then pelleted by centrifugation, further dissociated by sequentially pipetting with 10, 5, and 1-ml pipette tips, and recentrifuged. The resulting cell pellet was further dissociated into single cells. Cells were treated for 5 minutes with TrypLE (Gibco 12605010), filtered through a 40 µm strainer, resuspended in PBS containing 0.04% BSA, counted manually under the microscope, and loaded onto the 10X Chromium platform immediately.
Single cell capturing and cDNA library generation were performed using the 10X Chromium 3’ library construction kit v2 following the manufacturer’s instruction.

value: Mammary tissue

tag: surgery

value: Prophylactic

tag: genotype

value: BRCA2 (c.8575delC (p.Gln2859Lysfs*4))

tag: age

tag: menopause

value: Surgical menopause

tag: pregnancies

tag: births

tag: race or ethnicity

value: White

tag: breast cancer history

value: No

tag: chemotherapy


title: P. falciparum drug-resistant line — MRA_1240 (RNA Replicate 3)

tag: strain

tag: type

tag: Stage


title: Individual_16

description:
PM-L
Single-cell RNA-Seq

tag: tissue

value: BRCA2 (n/a)


title: 518000

description: same as GSM4552632

tag: hr

tag: pcr

tag: arm

value: Paclitaxel + MK-2206


title: ISPY2_415039

tag: patient id

value: Breast cancer biopsy (pre-treatment)

tag: mp

tag: adjustment method


title: P. falciparum drug-resistant line — MRA_1241 (RNA Replicate 1)


title: Individual_15

description:
PM-K
Single-cell RNA-Seq

tag: surgery

tag: genotype

tag: age

value: Yes


title: P. falciparum drug-resistant line — MRA_1240 (RNA Replicate 2)


title: Macrophage-MeganVac1-R1

tag: cell type

value: PBMC derived macrophages

tag: infection

value: Infected with UK1-cya crp


title: ISPY2_417654


title: 23

value: head kidney

tag: Sex

value: F

tag: behavior

value: bold behavior


title: 25

value: M


title: 24

value: shy behavior


title: ISPY2_406190

value: Paclitaxel + Neratinib

value: ComBat Adjust


title: ISPY2_414286


title: 21


title: P. falciparum drug-resistant line — MRA_1236 (RNA Replicate 2)

tag: strain

value: drug-resistant

value: Early trophozoite


title: P. falciparum drug-resistant line — MRA_1240 (RNA Replicate 1)

tag: type


title: Individual_12

description:
PM-H
Single-cell RNA-Seq

value: Mammary tissue

value: Prophylactic

tag: menopause

value: Surgical menopause

tag: pregnancies

tag: births

tag: race or ethnicity

value: White

tag: breast cancer history

tag: chemotherapy


title: P. falciparum drug-resistant line — MRA_1236 (RNA Replicate 3)

tag: Stage


title: ISPY2_405717

tag: patient id

tag: tissue

value: Breast cancer biopsy (pre-treatment)

tag: hr

tag: mp

tag: pcr

tag: arm

value: Paclitaxel

tag: adjustment method


title: Individual_13

description:
PM-I
Single-cell RNA-Seq

tag: surgery

tag: genotype

value: BRCA2 (c.715delA (p.Ser239Valfs*2))

tag: age

value: Premenopausal

value: Yes


title: Individual_08

description:
PM-D
Single-cell RNA-Seq

value: BRCA1 (c.4035delA)

tag: menopause


title: ISPY2_402265

value: Paclitaxel + Trastuzumab


title: 18

source_name: brain

value: brain

tag: Sex

value: M

tag: behavior

value: bold behavior


title: Individual_09

description:
PM-E
Single-cell RNA-Seq

value: BRCA1 (IVS10-2A>T)

tag: pregnancies

tag: births

tag: race or ethnicity

value: No


title: ISPY2_395379

value: ComBat Adjust


title: Individual_10

description:
PM-F
Single-cell RNA-Seq

value: Mammary tissue

value: BRCA1 (n/a_

tag: breast cancer history

tag: chemotherapy


title: P. falciparum drug-resistant line — MRA_1236 (RNA Replicate 1)

tag: strain

tag: type

value: drug-resistant

tag: Stage

value: Early trophozoite


title: P. falciparum 3D7 lab-adapted line — Temperature stress (RNA Replicate 2)

description: Temperature stress at 40 degrees Celsius for 6 hrs

value: lab-adapted


title: 17

tag: tissue

value: F

value: shy behavior


title: Individual_06

description:
PM-B
Single-cell RNA-Seq

value: Prophylactic

value: BRCA1 (del exons 21-24)

value: Premenopausal

value: White


title: 22

value: head kidney


title: 19

value: brain


title: P. falciparum 3D7 lab-adapted line — Drug stress (RNA Replicate 2)

description: Drug stress at 30nM for 6 hrs


title: ISPY2_411684

tag: patient id

value: Breast cancer biopsy (pre-treatment)

tag: hr

tag: mp

tag: pcr

tag: arm

value: Paclitaxel + ABT 888 + Carboplatin


title: P. falciparum 3D7 lab-adapted line — Drug stress (RNA Replicate 1)

description: Drug stress at 30nM for 6 hrs


title: Individual_05

description:
PM-A
Single-cell RNA-Seq

tag: surgery

tag: genotype

tag: age

tag: menopause

value: Black

value: No


title: Individual_07

description:
PM-C
Single-cell RNA-Seq

value: Mammary tissue

value: BRCA1 (c.5266dupC (p.GLn1756Profs*74))

value: Surgical menopause

tag: pregnancies

tag: births

value: Jewish

value: Yes


title: ISPY2_386664

value: Paclitaxel + AMG 386

tag: adjustment method

value: ComBat Adjust


title: Individual_04

description:
RM-D
Single-cell RNA-Seq

value: Reductive

tag: race or ethnicity

tag: breast cancer history

tag: chemotherapy


title: Individual_02

description:
RM-B
Single-cell RNA-Seq

value: WT


title: Individual_11

description:
PM-G
Single-cell RNA-Seq

value: Prophylactic

value: Premenopausal


title: ISPY2_395076

value: Paclitaxel


title: ISPY2_388581

value: Paclitaxel + Neratinib


title: 12

value: brain

tag: Sex

value: M

tag: behavior

value: shy behavior


title: 16

tag: tissue

value: F


title: 20

value: bold behavior


title: 11


title: 15


title: whole larvae total RNA- st73 mut10

city: Chapel Hill

first: Celia

middle: E

last: Shiau

state: NC

address: 4344 Genome Sciences Building

institute: UNC Chapel Hill

description:
Sample 2- sequenced on 2 different lanes (MONK and LYNLEY)
140108_MONK_0333_AC3CYDACXX_L4_CAGATC_*_st73mut10pf
140114_LYNLEY_0384_AC3BD6ACXX_L6_CAGATC_*_st73mut10pf

data_processing:
Alignment of reads to the UCSC GRCz10/danRer10 genome build using BBmap v37.99 (assigning ambiguous reads randomly)
Calculating gene counts using the featureCounts tool in the Subread suite v1.5.2 with UCSC annotations
Analysis of differential gene expressions with DESeq2 (R v3.3.1)
Genome_build: GRCz10/danRer10
Supplementary_files_format_and_content: DeSeq2 output text file, all genes list using DeSeq2; genes short list from analysis using DeSeq2 filter 1.5 fold-change

source_name: whole larvae

growth_protocol: for details see Shiau et al., 2013 Cell Reports

extract_protocol:
Toal RNA extracted by using the RNAqueous-Micro Total RNA Isolation Kit (Ambion).
Total RNA was used to create cDNA libraries with adapters using the KAPA stranded mRNA-seq kit. Magnetic oligo-dT beads were used to capture mRNAs. Amplification of libraries was conducted using high fidelity, low bias PCR.

treatment_protocol: no treatment

value: larvae at 4dpf

tag: genotype/variation

value: nlrc3l st73 homozygous mutant


title: Individual_03

description:
RM-C
Single-cell RNA-Seq

value: Mammary tissue

value: White

value: No


title: ISPY2_380769

tag: patient id

value: Breast cancer biopsy (pre-treatment)

tag: hr

tag: mp

value: Paclitaxel + ABT 888 + Carboplatin

value: ComBat Adjust


title: P. falciparum 3D7 lab-adapted line — no stress (RNA Replicate 1)

tag: strain

tag: type

value: lab-adapted

tag: Stage

value: Early trophozoite


title: 13


title: ISPY2_380239

tag: pcr

tag: arm


title: 14


title: ISPY2_374121


title: whole larvae total RNA- st73 mut12

description:
Sample 4- sequenced on 2 different lanes (MONK and LYNLEY)
140108_MONK_0333_AC3CYDACXX_L4_AGTTCC_*_st73mut12pf
140114_LYNLEY_0384_AC3BD6ACXX_L6_AGTTCC_*_st73mut12pf

tag: age


title: Individual_01

description:
RM-A
Single-cell RNA-Seq

tag: surgery

value: Reductive

tag: genotype

value: WT

tag: menopause

value: Premenopausal

tag: pregnancies

tag: births

value: Black


title: ISPY2_378401

value: Paclitaxel + AMG 386

tag: adjustment method


title: whole larvae total RNA- st73 sib12

description:
Sample 3- sequenced on 2 different lanes (MONK and LYNLEY)
140108_MONK_0333_AC3CYDACXX_L4_AGTCAA_*_st73sib12pf
140114_LYNLEY_0384_AC3BD6ACXX_L6_AGTCAA_*_st73sib12pf

value: nlrc3l st73 heterozyous/wt


title: P. falciparum 3D7 lab-adapted line — Temperature stress (RNA Replicate 1)


title: Input

city: Shenyang

first: Wanhua

last: Xie

address: Huanghe North Street 146

institute: Shenyang Medical college

data_processing:
The paired-end raw reads were trimed for adaptor seqence and low-quality seqences (-q 30) using Trim Galore 0.4.1. The filtered ChIP-seq reads were aligned to the hg19 genome using bowtie2 (Version 2.4.1) with   default parameters. PCR duplicates in bam files were moved by using Picard tool.
MACS2 (Version 2.2.7.1 43) was used to call narrow peaks for PHF13 with the parameters (-q 0.001) or broad peaks for EZH2 with the parameters (-q 0.1 --broad). The input sequencing data was set as a control.
The ChIP signal was normalized by using bamCoverage function in deeptools 3.5.0 with the parameters ( --normalizeUsing CPM,  --ignoreDuplicates,  --minMappingQuality 30,  --minFragmentLength 50)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files of the ChIP signal for each sample
Supplementary_files_format_and_content: Peak bed files of each sample include the significant enriched regions of the detected proteins

source_name: Pancreas

growth_protocol: PANC-1 cells were cultured in  high-glucose DMEM/F12 (Invitrogen) supplemented with 10% FBS (Invitrogen) and 1% penicillin-streptomycin (Invitrogen) at 37 °C, 5% CO2.

extract_protocol:
Panc-1 cells in one 15 cm plate were crosslinked sequentially as the followings: for 40 minutes in 5 mM EGS (Thermo Fisher Scientific) at room temperature, for 40 minutes in 1% paraformaldehyde (Sigma) at 4 ℃, then for 10 min in 1% formaldehyde (Sigma). The chromosome was fragmented to the fragment range of 200-400 bp in the Bioruptor® Pico via sonicating 5 cycles. Then, according to the manufacturer's protocol, ChIP was further processed using the ChIP-IT High Sensitivity Chromatin Immunoprecipitation kit.
The VAHTS Universal DNA Library Prep Kit for Illumina V3 (ND607)  was used with 5 ng of ChIP DNA of each sample for the construction of sequencing libraries.

tag: tissue

value: Pancreas

tag: cell line

value: wildtype

tag: chip antibody


title: EZH2


title: 10

source_name: pituitary

value: pituitary

tag: Sex

value: M

tag: behavior

value: bold behavior


title: ISPY2_374106

extract_protocol: Extraction was performed by Agendia Inc (Irvine, CA).

tag: patient id

tag: hr

tag: mp

value: Paclitaxel + Neratinib


title: P. falciparum 3D7 lab-adapted line — no stress (RNA Replicate 2)

tag: strain

tag: type

tag: Stage


title: ISPY2_375455

value: Breast cancer biopsy (pre-treatment)

tag: pcr

tag: arm

value: Paclitaxel + Trastuzumab


title: MC3T3-E1 cells, FR3

city: Hangzhou

first: Yi

last: Zhang

state: Zhejiang

address: 166 North Qiutao Rd

department: Department of Endodontics

institute: Zhejiang University

description: 30ppm F- resistant MC3T3-E1 cells exposed to a gradient of 30 ppm F-

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes count values for each Sample

source_name: cell line

growth_protocol: The mouse osteoblast-like cell line MC3T3-E1 (ATCC: CRL-2594) was cultured in Dulbecco's modified Eagle medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomyc at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 5μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina).  Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 200–300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq 4000 (2 × 150bp read length).

treatment_protocol: Wild-type MC3T3-E1 (WT MC3T3-E1) cells were continuously exposed to a gradient of 10 ppm F- to induced them survive in fluorinated medium. During cell adaptation, the cell proliferation was continuously monitored using Cell Counting Kit-8 (CCK-8) kit until a normal cell proliferation rate was confirmed. The above procedure was repeated for all other MC3T3-E1 clones to develop desired fluorine resistance. Finally, the 30ppm F- resistant MC3T3-E1 (FR MC3T3-E1) cells were obtained.

value: cell line

tag: cell type

value: Osteoblasts

tag: phenotype

value: 30ppm F- resistant

tag: treatment

value: gradient of 30 ppm F-


title: ISPY2_373672

source_name: Breast cancer biopsy (pre-treatment)

value: Paclitaxel

tag: adjustment method

value: ComBat Adjust


title: MC3T3-E1 cells, FR2

tag: tissue


title: 9

value: F


title: Input_siPHF13_TGFb_rep2

data_processing:
The paired-end raw reads were trimed for adaptor seqence and low-quality seqences (-q 30) using Trim Galore 0.4.1. The filtered ChIP-seq reads were aligned to the hg19 genome using bowtie2 (Version 2.4.1) with   default parameters. PCR duplicates in bam files were moved by using Picard tool.
MACS2 (Version 2.2.7.1 43) was used to call narrow peaks for H3K4me3 and H3K27ac with the parameters (-q 0.001) or broad peaks for H3K27me3 with the parameters (-q 0.1 --broad). The input sequencing data was set as a control.
The ChIP signal was normalized by using bamCoverage function in deeptools 3.5.0 with the parameters ( --normalizeUsing CPM,  --ignoreDuplicates,  --minMappingQuality 30,  --minFragmentLength 50)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files of the ChIP signal for each sample
Peak bed files of each sample include the significant enriched regions of the detected hitone modifications

extract_protocol:
106 cells were crosslinked in 1% formaldehyde for 10 minutes and quenched using 125mM of Glycine for 5 minutes. The chromosome was fragmented to the fragment range of 200-400 bp in the Bioruptor® Pico via sonicating 5 cycles. The fragmented histone-DNA complexes were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose.
The VAHTS Universal DNA Library Prep Kit for Illumina V3 (ND607)  was used with 5 ng of ChIP DNA of each sample for the construction of sequencing libraries.

treatment_protocol: siRNA transfections were performed using RNAiMAX (Invitrogen) according to the manufacturer’s instructions. The following day, cells were cultured in 10 ng/ml of TGFb (R&D systems) supplemented growth medium for 48 hours to induce epithelial-mesenchymal transition (EMT)

tag: cell line

value: treated with TGFb for 48 hours


title: Uninfected V1 Cortical Nuclei

city: LA JOLLA

first: Edward

middle: M.

last: Callaway

address: 10010 N Torrey Pines Rd

department: SNL-C

institute: Salk Institute

library_source: transcriptomic single cell

data_processing:
3' polyA RNA-Seq (10X Genomics, chemistry v3)
CellRanger (reference genome: mm10)
The gene count matrices were loaded into Seurat v4. Nuclei with more than 0.5% mitochondrial transcript reads, less than 500 genes, or more than 8000 genes were filtered out. Doublets were removed using DoubletFinder.
Assembly: mm10
Supplementary files format and content: Processed data files are gene count matrices as output by CellRanger.

source_name: mouse primary visual cortex V1 neurons

growth_protocol:
All procedures were carried out in accordance with Institutional Animal Care and Use Committee protocols at the Allen Institute for Brain Science. Animals were provided food and water ad libitum and were maintained on a regular 12-h day/night cycle at no more than five adult animals per cage. Tlx-Cre_PL56/wt in C57BL/6J background were used.
All experimental procedures were approved by the Salk Institute Animal Care and Use Committee. C57BL/6J mice were used as wild-type. Homozygous Gad2-Cre and R26-LSL-TVA-LacZ (Seidler et al., 2008) mice were bred to produce Gad2-Cre; R26-LSL-TVA-LacZ. Mice were housed with a 12-hour light and 12-hour dark cycle and ad libitum access to food and water. Both male and female mice were used for RNA sequencing experiments.

extract_protocol:
Single nuclei preparations were performed from V1 dissected regions and nuclei sorted for NeuN-positive nuclei.
Single nuclei preparations were performed as follows: the frozen brain tissues were transferred to pre-chilled dounce homogenizers with 1ml NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10ul of protease inhibitor (Sigma P8340), 1.5ul of RNasin Plus RNase inhibitor (Promega, N2611)), 0.1% Triton X-100, and 10 uM DAPI, and gently homogenized on ice with ice-cold pestles 10 - 15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 3000 rpm for 8 min at 4°C to pellet the nuclei. The supernatant was aspirated, the pellet gently resuspended in ice-cold 1ml NIM buffer, and again centrifuged at 3000 rpm for 8 min at 4°C. The pellet was then resuspended in 450ul of nuclei storage buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through a 40μM cell strainer. The sample was incubated with 50ul of nuclease-free BSA to prevent nuclei clumping. Fluorescence-activated nuclei sorting of single nuclei was performed using a BD Influx sorter with a 70 μM nozzle at 22.5 PSI sheath pressure. DAPI+/mCherry+ rabies-infected nuclei were sorted into 1.5ml Eppendorf tubes and immediately loaded onto the 10X Genomics Chromium Controller. For 10x processing, we used Chromium Next GEM single-cell 3’ Kit v3.1 (10x Genomics, PN-1000128). We followed the manufacturer’s instructions for single-cell capture, barcoding, reverse transcription, cDNA amplification, and library construction. We targeted sequencing depth of 100,000 reads per cell. Libraries were sequenced on both Illumina NextSeq550 and NovaSeq6000 and raw read (fastq) files from both sequencing platforms were combined and aligned to the mouse pre-mRNA reference transcriptome (mm10) using the 10x Genomics CellRanger pipeline (version 5.0.). Intronic reads were included in expression quantification using the include-introns parameter
snRNA-Seq

treatment_protocol:
Mice were anesthetized with 5% isoflurane and intracardially perfused with ice-cold, oxygenated artificial cerebral spinal fluid (ACSF). The brain was then rapidly dissected and mounted for coronal slice preparation on the chuck of a Compresstome VF-300 vibrating microtome (Precisionary Instruments). Sections were sliced at 350 μm intervals. To guide anatomical targeting for dissection, boundaries were identified by trained anatomists, comparing the blockface image and the slice image to a matched plane of the Allen Reference Atlas.
To collect large numbers of rabies-infected neurons for transcriptomic experiments, 150 nl of unpseudotyped G+RVdG-H2BmCherry (9.59E+09 IU/ml) was injected into the center of V1 of P60-P75 C57BL/6 mice 0.5–0.7 mm ventral from the pia. To bias infection to inhibitory neurons 150 nl of EnvA+RVdG-H2BmCherry (1.09E+08 IU/ml) was injected into P65-P85 Gad2-Cre; R26-LSL-TVA mice. For HCR experiments 100 nl of diluted AAV8-nef-AO-66/71-TVA950 (5.25E+11 GC/mL) was injected into V1 of Sst-Cre; INTACT mice. Two weeks after AAV helper virus injection, 200 nl of EnvA+RVdG-H2BmCherry (7.43E+07 IU/ml) was injected into the same site in V1. Ten days after rabies injection, brains were extracted and immediately submerged in ice-cold slicing solution. Coronal brain slices (400um thick) were cut using VF-300 CompresstomeTM (Precisionary Instruments, Greenville,NC) and submerged in ice-cold slicing solution. Subregions of V1 containing mCherry+ nuclei in brain slices were micro-dissected out under a fluorescent dissection microscope (Olympus SZX6).

value: Tlx-Cre_PL56/wt in C57BL/6J background

value: primary visual cortex V1 neurons


title: whole larvae total RNA- st73 sib10

description:
Sample 1- sequenced on 2 different lanes (MONK and LYNLEY)
140108_MONK_0333_AC3CYDACXX_L4_ACAGTG_*_st73sib10pf
140114_LYNLEY_0384_AC3BD6ACXX_L6_ACAGTG_*_st73sib10pf

tag: age

value: larvae at 4dpf

tag: genotype/variation

value: nlrc3l st73 heterozyous/wt


title: Input_siPHF13_TGFb_rep1

tag: chip antibody


title: 7

value: pituitary

tag: Sex

tag: behavior

value: shy behavior


title: 8

value: M

value: bold behavior


title: 5


title: 6


title: PHF13

value: Pancreas

tag: genotype

value: wildtype


title: Input_siControl_TGFb_rep2

value: siControl


title: Input_siControl_TGFb_rep1


title: 4


title: MC3T3-E1 cells, WT3

description: wildtype MC3T3-E1cells in DMEM medium.

value: cell line

value: Osteoblasts

value: control


title: MC3T3-E1 cells, WT2

description: wildtype MC3T3-E1cells in DMEM medium.


title: ISPY2_367682

data_processing:
For each array, gnormalized signal (log2) data, as provided in the raw files on each patient, was extracted and aligned to its 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity, as indicated by the 'gIsFeatNonUnifOL' column in the raw files, are NA'd out; and a fixed value of 9.5 was added to avoid negative values. Probeset level data per array were mean-collapsed to the gene level, and genes common to the two platforms identified. Expression data from the first ~900 I-SPY2 patients distributed over the two platforms GPL30494 (updated version of GPL16233; n=334) and GPL20078 (n=545) were combined into a single gene-level dataset after batch-adjusting using ComBat [PMID:16632515]. Linear adjustment factors were derived from the ComBat transformation, per platform, which can be used to batch correct raw files. The subsequent ~100 samples, assayed on GPL20078, were batch corrected using these factors and added to the original set, yielding a normalized expression dataset comprising 988 samples (987 unique patients) x 19,134 (common) genes. The linear adjustment factors and updated probe annotation files per platform are provided, as is the ComBat-normalized data we used in our analysis (supplemental file "ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt").
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt: Normalized, gene-level, batch-/platform- adjusted pre-treatment Agilent 44K expression data for patients from 10 arms of the neoadjuvant I-SPY 2 platform trial for early stage, aggressive breast cancer (n=988 samples for 987 patients). This is the dataset we used in our pan-arm analysis, and constitutes part of the I-SPY2-990 mRNA/RPPA Data Resource. To derive this matrix, probeset level expression data from the first ~900 I-SPY2 patients distributed over the two platforms GPL30494 (updated version of GPL16233; n=334) and GPL20078 (n=545) were mean-collapsed by gene and combined into a single gene-level dataset after batch-adjusting using ComBat [PMID:16632515]. Linear adjustment factors were derived from the ComBat transformation, per platform, which can be used to batch correct new files. The subsequent ~100 samples, assayed on GPL20078, were batch corrected using these factors and added to the original set, yielding the resulting normalized expression dataset comprising 988 samples (987 unique patients) x 19,134 (common) genes.
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL20078_ProbeLevel_n654.txt: Normalized probeset level pre-treatment gene expression data from Agilent 44K expression arrays Agendia32627_DPv1.14_SCFGplus [with annotation GPL20078 (n=654)] from the I-SPY 2 platform trial for early stage, aggressive breast cancer. Each column represents a patient sample. Per column, green-channel (Cy3) normalized signal intensity (log2) data, as provided in the raw files on each patient, was extracted and aligned to its (within-array) 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity are NA'd out; and a fixed value of 9.5 was added to avoid negative values.
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL30493.wasGPL16233_ProbeLevel_n334.txt: Normalized probeset level pre-treatment gene expression data from Agilent 44K expression arrays Agilent_human_DiscoverPrint_15746 [with annotation GPL30493 (update of GPL16233; n=334)] from the I-SPY 2 platform trial for early stage, aggressive breast cancer. Each column represents a patient sample. Per column, green-channel (Cy3) normalized signal intensity (log2) data, as provided in the raw files on each patient, was extracted and aligned to its (within-array) 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity are NA'd out; and a fixed value of 9.5 was added to avoid negative values.
ISPY2_LinearFit_forCombiningExp_20078.txt: This file contains linear adjustment factors (intercept and linear coefficient) derived from the ComBat transformation combining data (~900 samples) from GPL20078 and GPL30493 that can be used to batch-/platform- correct new Agilent 44K expression arrays of the type Agendia32627_DPv1.14_SCFGplus [gene-collapsed using annotation GPL20078] for inclusion in the larger normalized dataset. Application of this transformation to columns from ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL20078_ProbeLevel_n654.txt, once mean-collapsed to gene level using GPL20078, results in values nearly identical to those in ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt, the normalized expression matrix in the I-SPY2-990 data resource.
ISPY2_LinearFit_forCombiningExp_GPL30493_wasGPL16233.txt: This file contains linear adjustment factors (intercept and linear coefficient) derived from the ComBat transformation combining data (~900 samples) from GPL20078 and GPL30493 that can be used to batch-/platform- correct new Agilent 44K expression arrays of the type Agilent_human_DiscoverPrint_15746 [with annotation GPL30493 (update of GPL16233)] for inclusion in the larger normalized dataset. Application of this transformation to columns from ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL30493.wasGPL16233_ProbeLevel_n334.txt, once mean-collapsed to gene level using GPL20078, results in values nearly identical to those in ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt.
ProbeAnnotation_ISPY2Edit_GPL30493_wasGPL16233.txt: This is the probeset annotation file for GPL30493, a minor update of GPL16233. For each probeset ID (row), the associated gene name, systematic name and DNA sequence is described (columns).

tag: patient id

value: Breast cancer biopsy (pre-treatment)

tag: hr

tag: mp

value: Paclitaxel

value: ComBat Adjust


title: Input_siControl_rep2

value: untreated


title: ISPY2_373346

tag: pcr

value: Paclitaxel + AMG 386


title: ISPY2_360937

tag: arm

value: Paclitaxel + ABT 888 + Carboplatin


title: 3

value: F


title: ISPY2_362993


title: 2

value: pituitary


title: ISPY2_357017


title: MC3T3-E1 cells, WT1

description: wildtype MC3T3-E1cells in DMEM medium.

tag: cell type


title: Input_siControl_rep1


title: ISPY2_382853

value: Paclitaxel + Trastuzumab


title: 1

value: M

value: shy behavior


title: ISPY2_349639

value: Paclitaxel + Neratinib