title: Drop-Seq analysis of Pooled Arc-ME single-cell suspension_24 hour fast_3

first: Linus

middle: Tzu-Yen

last: Tsai

address: 330 Brookline Avenue

department: Medicine, Division of Endocrinology, Diabetes, and Metabolism

institute: Beth Israel Deaconess Medical Center

description:
F_Fasted
Cell Barcodes are in read 1, gene sequence in read 2,

data_processing:
Base calls performed with bcl2fastq2.15.0.4
Read 2 was aligned with Star v2.4.0.
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name.
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes. The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample.
Cells expressing >800 genes from Samples 1-11 were merged together into a single matrix. Merged DGE file from all 11 samples generated. log(1+10,000*(DGE normalized to total transcripts per cell)) calculated on DGE. This is the Merged_all_020816_DGE.txt.gz file containing 21,421 cell barcodes
Genes showing expression in <50 cells were removed and batch effect correction was performed using the removeBatchEffect function of edgeR
Data was Natural log transformed and cells were clustered using Seurat software (PCA followed by t-SNE and density clustering)
Cell clusters containing markers for more than one other cluster were considered doublets and were removed. Remaining cells are presented in manuscript  and contained in Merged_all_020816_BatchCorrected_LNtransformed_doubletsremoved_Data.txt file
Genome_build: Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Digital expression matrices. Compressed, flat text files with tab delimiters.
Supplementary_files_format_and_content: Merged_all_020816_DGE.txt: Digital Gene Expression Matrix of raw data
Supplementary_files_format_and_content: Merged_all_020816_BatchCorrected_LNtransformed_doubletsremoved_Data.txt: Digital Gene Expression Matrix, Batch corrected,natural log transformed, cell doublets removed
Supplementary_files_format_and_content: cell_metadata.txt: Metadata for individual cells based on final cluster assignments

source_name: Arcuate Nucleus/Median Eminence

extract_protocol: Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads. Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.

value: Arcuate-Median Eminence

value: F

tag: average age

tag: number of mice pooled

tag: experimental condition

value: 24 hour fast

tag: batch

value: Batch 6


title: Drop-Seq analysis of Pooled Arc-ME single-cell suspension_ad lib Chow_5

status: Public on Jan 31 2017

type: SRA

city: Boston

state: MA

country: USA

description:
F_Fed
Cell Barcodes are in read 1, gene sequence in read 2,

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: Sex

value: Ad lib fed chow diet


title: LCMV Clone13 D28 CD8 T cell  rep 3

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

library_source: genomic

data_processing:
Library strategy: ATAC-seq
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Bowtie-1.1.1
For each sample peaks of accessibility were identified and annotated using the HOMER package v4.8.2.
Peak files from each sample were merged using the HOMER mergePeaks function into a single file.  Next, for each peak the raw read counts and reads per million normalized counts were annotated for all samples.
Genome_build: mm9
Supplementary_files_format_and_content: HOMER annotation file containing raw read counts and log2rpm values for all peaks.

molecule: genomic DNA

source_name: Late chronic infection CD8 T cell

extract_protocol:
At the indicated time points naïve or antigen-specific CD8 T cells were isolated by FACS using the sorting markers described.
Cells were centrifuged for 10 minutes at 500xg, resuspended in 50 ul of Lysis Buffer (contents), and immediately centrifuged for 30 minutes at 500xg. Tagmentation was performed using the Illumina Nextera Kit by resuspending cells in 25 ul of Tagmentation mix (1x TD Buffer, 2.5 ul Tn5 Transpoase) and incubating for 60 minutes at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

treatment_protocol: Wt mice were infected with either LCMV Armstrong (2x105 PFU IP) or LCMV Clone-13 (2x106 PFU IV).

value: female

tag: sorting markers

value: CD8+ CD44+ CD62L-  gp33/gp276/np396 tetramer+

tag: infection

value: LCMV Clone-13 2x106 PFU IV

tag: time post-infection (days)

tag: tissue source

value: spleen

tag: cell type

value: virus-specific CD8 T cell


title: LCMV Armstrong D8 CD8 T cell rep 1

source_name: Peak acute infection CD8 T cell

value: male

value: LCMV Armstrong 2x105 PFU IP


title: Drop-Seq analysis of Pooled Arc-ME single-cell suspension_ad lib 60% high fat diet fed_1

description:
HFD
Cell Barcodes are in read 1, gene sequence in read 2,

value: M

value: Ad lib fed 60% High fat diet

value: Batch 4


title: Drop-Seq analysis of Pooled Arc-ME single-cell suspension_ad lib 10% low fat diet_1

description:
Chow10
Cell Barcodes are in read 1, gene sequence in read 2,

value: Ad lib fed 10% Low fat diet


title: Drop-Seq analysis of Pooled Arc-ME single-cell suspension_ad lib Chow_2

description:
Arc2
Cell Barcodes are in read 1, gene sequence in read 2,

value: Batch 2


title: Drop-Seq analysis of Pooled Arc-ME single-cell suspension_24 hour fast_refed_1

description:
Refed
Cell Barcodes are in read 1, gene sequence in read 2,

value: Arcuate-Median Eminence

value: M and F

value: 7 (4 male, 3 female)

value: 24 hour fast + 2 hour refeeding

value: Batch 5


title: LCMV Clone13 D8 CD8 T cell  rep 2

source_name: Early chronic infection CD8 T cell

value: female


title: LCMV Clone13 D8 CD8 T cell  rep 3

value: CD8+ CD44+ CD62L-  gp33/gp276/np396 tetramer+


title: Drop-Seq analysis of Pooled Arc-ME single-cell suspension_ad lib Chow_1

description:
Arc1
Cell Barcodes are in read 1, gene sequence in read 2,

value: Ad lib fed chow diet

value: Batch 1


title: 8NFMC7d4hCo_S8

city: Münster

first: Shirin

last: Glander

state: Deutschland (DEU)

address: Domagkstraße 3

country: Germany

institute: University Münster

data_processing:
RTA2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Mapping to mm10 using HISAT version 0.1.7-beta
Read counts calculated with SummerizeOverlaps() function from Rsamtools, GenomicFeatures and GenomicAlignments using mm10 UCSC gtf file
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of raw read counts (1 sample per column), tab delimited

growth_protocol: Bone marrow cells (BMCs) were isolated from murine femur and tibia. Ferromagnetic cells (FMCs) and nonferromagnetic cells (NFMCs) were separated using MACS technology. Briefly, the cells without prior staining were directly loaded on the equilibrated MACS column. FMCs (delineated as resident BM macrophages) were retained within the column. NFMCs were collected in flow through fraction. NFMCs were differentiated to macrophages for 6 days in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin-L-glutamine and 20% L929 cell supernatant in 5% CO2 at 37°C (delineated as BM derived macrophages).

extract_protocol:
Total RNA was isolated using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany).
NEBNext Ultra RNA

treatment_protocol: Macrophages were stimulated for 4h with 1µg/ml LPS or left untreated (Co.)

value: bone marrow

value: BM derived macrophages

tag: cell marker

tag: age

value: postnatal 12 weeks


title: 10NFMC7d4hLPS_S10


title: 9NFMC7d4hLPS_S9


title: 7NFMC7d4hCo_S7


title: LCMV Armstrong D30 CD8 T cell rep 3

source_name: Acute infection memory CD8 T cell

value: LCMV Armstrong 2x105 PFU IP

value: spleen

value: virus-specific CD8 T cell


title: 1FMC0h4hCo_S1

value: resident BM macrophages


title: LCMV Armstrong D30 CD8 T cell rep 2


title: ATR WT 3

city: Irvine

first: Anand

last: Ganesan

state: CA

address: 836 Health Science Rd

department: Dermatology

institute: University of California, Irvine

description: ATR +/+ is equivalent to ATR WT. This sample is referred to as "c2_r3" in the procesessed data file.

data_processing:
Paired-end sequencing reads were analyzed for quality using the Fastqc program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and aligned to the mouse reference genome version mm10 using the Tophat alignment software (version 2.0.12). Tophat2 parameters include -T –G mm10.gtf -o [SampleName]_thout
The edgeR library of the R statistical environment was used for differential gene expression analysis of mapped read counts.
Genome_build: mm10
Supplementary_files_format_and_content: comma separated values files include log fold change (logFC), log counts per million (logCPM), p-value (Pvalue), FDR, counts for all samples. Values for all genes are included.

source_name: ATR wild type

extract_protocol:
Skin samples were homogenized using the Precellys24 high-throughput tissue homogenizer in hard tissue homogenizing reinforced tubes that contain 2.8 mm ceramic beads. RNA was extracted using the Rneasy Firous Tissue Mini Kit according to the manufacturer's instructions.
Library construction was performed according to the Illumina TruSeq RNA v2 protocol. Briefly, the input quantity for total RNA was 1g and mRNA was enriched using oligo dT magnetic beads. The enriched mRNA was chemically fragmented for four minutes. First strand synthesis used random primers and reverse transcriptase to make cDNA. After second strand synthesis the ds cDNA was cleaned using AMPure XP beads and the cDNA was end repaired and then the 3’ ends were adenylated. Illumina barcoded adapters were ligated on the ends and the adapter ligated fragments were enriched by nine cycles of PCR. The resulting libraries were validated by qPCR and sized by Agilent Bioanalyzer DNA high sensitivity chip.

tag: strain background

tag: genotype/variation

value: ATR +/+; Braf CA/+; Cre +

value: skin


title: MAQCA_2

city: Ghent

first: Celine

last: Everaert

address: De Pintelaan 185

country: Belgium

institute: University Ghent

data_processing:
Tophat-Cufflinks (Bowtie2 v2.1.0 Tophat v2.0.10 Cufflinks v2.1.1) all standard parameters
Tophat-HTSeq v0.5.4 all standard parameters
Kallisto v0.42.1 all standard parameters
Salmon v0.6.0 all standard parameters
Genome_build: Ensembl GRCh37, release 75
Supplementary_files_format_and_content: txt files

organism: Homo sapiens

source_name: Universal Human Reference RNA, Agilent Technologies

extract_protocol:
Extracted by respectively Agilent Technologies and Thermo Fisher Scientific
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: Universal Human Reference RNA from Agilent Technologies


title: Drop-Seq analysis of Pooled Arc-ME single-cell suspension_ad lib Chow_3

description:
Arc3
Cell Barcodes are in read 1, gene sequence in read 2,

value: Arcuate-Median Eminence

value: M

tag: average age

value: Batch 3


title: Naïve CD8 T cell rep 2

source_name: Naïve CD8 T cell

value: male

value: CD8 T cells


title: TBE wt 48hChiron

city: Utrecht

first: Jacqueline

last: Deschamps

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: 4C-seq viewpoint from TAD boundary element (TBE) in EpiSCs induced with Chiron, 48 hours

data_processing:
The initial step in the 4C-seq analysis is the alignment of the sequencing reads to a reduced genome of sequences that flank DpnII sites (4C fragment ends), using custom Perl scripts. Due to their ambiguous nature in reporting contacts, repetitive fragment ends were excluded from subsequent analysis. The reduced genome was based on mouse genome mm9.
Wiggle tracks contain uniquely mapped reads at 4C fragment ends on the cis chromosome, i.e. the chromosome on which the bait/viewpoint fragment is located.  Scores represent the number of reads mapping to a DpnII restriction fragment end.
Genome_build: mm9

source_name: EpiSCs

growth_protocol: Pre-streak embryos (E6.0) were isolated in M2 medium; extraembryonic tissue and surrounding primitive endoderm was removed. Explants were put on MEFs and cultured in presence of Wnt inhibitor IWP2 (2 µM, Sigma Aldrich, dissolved in DMSO) in medium containing 20% KOSR, 77% DMEM/F12, 1x penicillin/streptomycin (100 units/mL, Thermo Fisher Scientific), 2 mM L-glutamine, 1x non-essential amino acids, 0.01% β-mercaptoethanol, Fgf-basic (12 ng/mL, ThermoFisher Scientific ), Activin A (20 ng/mL, R&D Systems).  MEF-free culture took place on surface coated by fibronectin (ThermoFisher Scientific) in medium containing 48% DMEM/F12, 48% Neurobasal Medium 1% B27 Supplement, 0.5% N2 Supplement B (all Thermo Fisher Scientific), 1x penicillin/streptomycin, Fgf-basic (12 ng/mL), Activin A (20 ng/mL), IWP2 (2 µM), 0.01% β-mercaptoethanol. Medium was refreshed on daily basis.

extract_protocol:
The initial steps of the 4C procedure, as published before (Simonis et al., 2006, Nature Genetics (PMID 17033623)), remain unchanged. Cells are cross-linked using 2% formaldehyde for 10 min at room temperature in PBS 10% FCS and nuclei are isolated, after which chromatin is digested with DpnII and subsequently ligated. After reversal of the cross-links, the DNA is purified and treated with the second restriction enzyme treatment (Csp6I). After a second re-ligation step, the sample is purified and a 4C PCR is performed.
4C PCR

treatment_protocol: Wnt stimulation was done after at least two passages feeder-free culturing by withdrawal of IWP2 and addition of Wnt3a (Cell Guidance Systems, 125 ng/mL) or Chiron (3 µM).

value: EpiSCs

tag: experiment type

tag: antibody

tag: wnt stimulation


title: TBE wt 12hChiron

description: 4C-seq viewpoint from TAD boundary element (TBE) in EpiSCs, induced with Chiron for 12h.


title: MSC_21

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
adapter trimming with trimmomatic (ILLUMINACLIP ":2:40:7 SLIDINGWINDOW:4:15 MAXINFO:20:0.50 MINLEN:18")
alignment with bsmap (RRBS mode; equal_best_hits=100;mismatch rate=.08; report_repeat=1; seed_size=12; random_number=0; filter=5; quality_threshold=0)
methylation calling with biseqmethcalling (minFragmentLength=20; maxFragmentLength=1000;pfStatus=All;maxMismatches=0.1;baseQualityScoreC=20;baseQualityScoreNextToC=10;genomeFraction=50;smartWindows=250000)
Genome_build: hg38
Supplementary_files_format_and_content: bed file format containing for each CpG the number of methylated reads and the total number of reads

extract_protocol:
DNA was isolated from 10 to 25 mg of snap-frozen tumors, cell lines, and MSCs by standard proteinase K digestion and phenol/chloroform extraction. DNA was quantified using a Qubit 2.0 Fluorometer (ThermoFisher Scientific, Q32866) and the Qubit dsDNA BR Assay Kit (ThermoFisher Scientific, Q32850).
For RRBS, 100 ng of genomic DNA was digested for 12 hours at 37°C with 20 units of MspI (New England Biolabs, R0106L) in 30 μl of 1x NEB buffer 2. To retain even the smallest fragments and to minimize the loss of material, end preparation and adaptor ligation were performed in a single-tube setup. End fill-in and A-tailing were performed by addition of Klenow Fragment 3’ > 5’ exo- (New England Biolabs, M0212L) and dNTP mix (10 mM dATP, 1 mM dCTP, 1 mM dGTP). After ligation to methylated Illumina TruSeq LT v2 adaptors using Quick Ligase (New England Biolabs, M2200L), the libraries were size selected by performing a 0.75x clean-up with AMPure XP beads (Beckman Coulter, A63881). The libraries were pooled in combinations of six based on qPCR data and subjected to bisulfite conversion using the EZ DNA Methylation Direct Kit (Zymo Research, D5020) with the following changes to the manufacturer’s protocol: conversion reagent was used at 0.9x concentration, incubation performed for 20 cycles of 1 min at 95°C, 10 min at 60°C and the desulphonation time was extended to 30 min. These changes increase the number of CpG dinucleotides covered, by reducing double-strand break formation in larger library fragments. Bisulfite-converted libraries were enriched using PfuTurbo Cx Hotstart DNA Polymerase (Agilent, 600412). The minimum number of enrichment cycles was estimated based on a qPCR experiment. After a 2x AMPure XP clean-up, quality control was performed by a Qubit dsDNA HS (Life Technologies, Q32854) and Experion DNA 1k assay (BioRad, 700-7107). The RRBS libraries were sequenced on the Illumina HiSeq 2000 platform in 50 bp single read mode.

value: mesenchymal stem cell


title: MSC_30


title: MSC_28


title: 4FMC0h4hLPS_S4

tag: strain

value: bone marrow


title: Drop-Seq analysis of Pooled Arc-ME single-cell suspension_24 hour fast_2

description:
M_Fasted
Cell Barcodes are in read 1, gene sequence in read 2,

tag: tissue

tag: number of mice pooled

tag: experimental condition

value: 24 hour fast

tag: batch

value: Batch 6


title: MSC_22


title: MSC_19


title: Drop-Seq analysis of Pooled Arc-ME single-cell suspension_ad lib Chow_4

description:
M_Fed
Cell Barcodes are in read 1, gene sequence in read 2,

tag: Sex

value: Ad lib fed chow diet


title: MSC_18


title: Drop-Seq analysis of Pooled Arc-ME single-cell suspension_24 hour fast_1

description:
Fasted
Cell Barcodes are in read 1, gene sequence in read 2,

value: M and F

value: 8 ( 4 male, 4 female)

value: Batch 5


title: TBE wt 0h

description: 4C-seq viewpoint from TAD boundary element (TBE) in EpiSCs


title: 6FMC0h4hLPS_S6

value: resident BM macrophages

value: postnatal 12 weeks


title: MSC_17


title: 5FMC0h4hLPS_S5


title: 2FMC0h4hCo_S2


title: 3FMC0h4hCo_S3


title: HP1a_CtrlRNAi_1

city: Planegg-Martinsried

first: Axel

last: Imhof

address: Großhadernerstr. 9

institute: Ludwig-Maximilians-University of Munich

data_processing:
ChIP-Seq reads were aligned to the dm3 genome assembly using Bowtie version 2.2.6 excluding Uextra. Only unique mapping reads were kept with samtools version 1.2.
Raw read quality was accessed using FASTQC version 11.5 and reads filtered using FastX version 0.0.13.
Peak calling was performed using HOMER version 4.8 with parameter sets -style factor -size 200 -fragLength 200 -inputFragLength 200.
Genome_build: dm3
Supplementary_files_format_and_content: BigWig files were generated using MACS version 2.1.1. Bed files were generated using HOMER version 4.8.

organism: Drosophila melanogaster

source_name: Drosophila S2 cells

growth_protocol: S2-DRSC cells were grown at 26 °C in Schneider's Drosophila medium (Invitrogen) supplemented with 10 % fetal calf serum and antibiotics (100 units/mL penicillin and 100 µg/mL streptomycin)

extract_protocol:
For chromatin immunoprecipitation (ChIP) cells were crosslinked with 1 % formaldehyde for 5 min at room temperature. Upon cell lysis, protease inhibitors and proteasome inhibitor MG-132 (Enzo Life Sciences) were applied. The chromatin was isolated and sheared with adaptive focused acoustics (Covaris) to an average size of 200 base pair (bp). For each ChIP reaction, chromatin isolated from 1-2 x 10e6 cells was incubated with antibodies precoupled to Protein A/G Sepharose.
All libraries were prepared using MicroPlex (Diagenode) or NEBNext (NEB) Library Preparation kit.

treatment_protocol: For RNAi experiments cells were incubated in serum-free medium containing 10 mg/mL dsRNA. After 1 hr of incubation, the serum-containing medium was supplied. Samples were taken after 7 days. The dsRNA was prepared using the MEGAScript T7 Transcription Kit (Thermo Fisher Scientific) following the manufacturers instructions.

tag: cell line

tag: treatment

value: Ctrl RNAi

tag: chip antibody

value: mouse anti-HP1a C1A9 (RRID:AB528276)


title: MSC_32


title: MSC_14


title: MSC_13


title: MSC_31


title: MSC_27


title: Input_CtrlRNAi_2

source_name: Input_CtrlRNAi, Drosophila S2 cells


title: HMR_HMRRNAi_2

source_name: HMR_HMRRNAi, Drosophila S2 cells

value: HMR RNAi

value: rat anti-HMR 2C10 (RRID:AB2569849)


title: MSC_25


title: MSC_26


title: MSC_10


title: H3_CP190RNAi_1

source_name: H3_CP190RNAi, Drosophila S2 cells

value: CP190 RNAi

value: rabbit anti-H3 (Abcam Cat# ab1791 RRID:AB302613)


title: MSC_24


title: MSC_9


title: MSC_16


title: MSC_23


title: Input_HMRRNAi_1

source_name: Input_HMRRNAi, Drosophila S2 cells


title: HP1a_HMRRNAi_1


title: Input_HMRRNAi_2


title: MSC_7


title: MSC_20


title: H3K9me3_HMRRNAi_1

value: rabbit anti-H3K9me3 (Active Motif Cat# 39161 RRID:AB2532132)


title: MSC_6

value: mesenchymal stem cell


title: MSC_29


title: MSC_15


title: Input_CtrlRNAi_1


title: HMR_HMRRNAi_1


title: HMR_CP190RNAi_1

source_name: HMR_CP190RNAi, Drosophila S2 cells


title: MSC_2


title: MSC_3


title: MSC_1


title: H3K9me3_CtrlRNAi_1


title: MSC_11


title: MSC_12


title: Input_CP190RNAi_1

source_name: Input_CP190RNAi, Drosophila S2 cells


title: HMR_CtrlRNAi_2

source_name: HMR_CtrlRNAi, Drosophila S2 cells


title: MSC_8


title: HP1a_2

source_name: HP1a, Drosophila S2 cells

value: untreated


title: IgG_2

source_name: IgG, Drosophila S2 cells

value: mouse anti-FLAG (Sigma-Aldrich Cat# F1804 RRID:AB262044)


title: EWS_L13

value: cell line


title: H3_HMRRNAi_1

source_name: H3_HMRRNAi, Drosophila S2 cells


title: MSC_5


title: HMR_2

source_name: HMR, Drosophila S2 cells


title: MSC_4


title: Input_4

source_name: Input, Drosophila S2 cells


title: EWS_L10


title: HMR_CtrlRNAi_1


title: H3_CtrlRNAi_1

source_name: H3_CtrlRNAi, Drosophila S2 cells


title: Input_1


title: EWS_L8


title: HP1a_1


title: EWS_L7


title: HP1a_4


title: Sample 95 ES Cells

city: Tarrytown

first: Yurong

last: Xin

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals, Inc.

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were decoded based on their barcodes. Read quality was evaluated using FastQC.
Reads were mapped to the reference genome (human: GRCh37) using ArrayStudio® software (OmicSoft®, Cary, NC) allowing two mismatches.
Genome_build: NCBI build 37.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Nkx2.1 GFP/W-hESC

extract_protocol: Illumina NGS library was constructed with Nextera XT DNA Sample Prep kit (Illumina), according to the manufacturer’s recommendations (Protocol #100-7168 E1).

value: ES cells

tag: donor id

tag: condition

value: WT

tag: gender

value: F

tag: cell type

value: Undifferentited ES cells


title: EWS_L16


title: Input_3


title: EWS_L15


title: HMR_3


title: EWS_L14


title: EWS_L5


title: Sample 94 ES Cells


title: EWS_L4


title: Sample 93 ES Cells


title: EWS_L3


title: Sample 92 Day12 neuron progenitor

value: Neuron progenitors

value: neuron progenitors


title: EWS_L2


title: Input_2


title: EWS_L12


title: EWS_L17


title: EWS_L9


title: Sample 88 Day27 neurons

value: Hypothalamic ARC-type neurons

value: hypothalamic neurons


title: IgG_1


title: EWS_T139

value: tumor


title: EWS_L11


title: EWS_T140


title: HMR_1

value: rat anti-HMR 2C10 (RRID:AB2569849)


title: Sample 91 Day12 neuron progenitor


title: Sample 87 Day27 neurons


title: EWS_T136


title: Sample 86 Day27 neurons


title: Sample 85 Day27 neurons


title: EWS_T141


title: EWS_L6


title: EWS_T137


title: Sample 84 Day27 neurons


title: EWS_T135


title: Sample 83 Day27 neurons


title: EWS_T134


title: Sample 90 Day12 neuron progenitor


title: EWS_T132


title: EWS_T131


title: EWS_T133


title: Sample 80 Day27 neurons


title: Sample 81 Day27 neurons


title: Sample 89 Day12 neuron progenitor


title: EWS_T129


title: EWS_T130


title: EWS_T138


title: Sample 79 Day27 neurons


title: EWS_T127


title: Sample 77 Day27 neurons


title: Sample 78 Day27 neurons


title: EWS_T126


title: Sample 76 Day27 neurons


title: Sample 74 Day27 neurons


title: Sample 75 Day27 neurons


title: EWS_T122


title: EWS_T125


title: EWS_T124


title: Sample 82 Day27 neurons


title: Sample 71 Day27 neurons


title: Sample 73 Day27 neurons


title: EWS_T121


title: Sample 72 Day27 neurons


title: EWS_T123


title: EWS_T118


title: Sample 68 Day27 neurons


title: EWS_T120


title: Sample 70 Day27 neurons


title: Sample 69 Day27 neurons


title: EWS_T119


title: EWS_T115


title: Sample 67 Day27 neurons


title: Sample 65 Day27 neurons


title: EWS_T114


title: Sample 64 Day27 neurons


title: EWS_T116


title: EWS_T113


title: Sample 63 Day27 neurons


title: Sample 62 Day27 neurons


title: EWS_T112


title: Sample 61 Day27 neurons


title: Sample 66 Day27 neurons


title: Sample 60 Day27 neurons


title: EWS_T109


title: Sample 59 Day27 neurons


title: EWS_T110


title: EWS_T108


title: EWS_T117


title: EWS_T106


title: EWS_T107


title: Sample 58 Day27 neurons


title: Sample 56 Day27 neurons


title: Sample 55 Day27 neurons


title: EWS_T105


title: EWS_T103


title: Sample 53 Day27 neurons


title: EWS_T102


title: Sample 52 Day27 neurons


title: Sample 51 Day27 neurons


title: EWS_T101


title: Sample 50 Day27 neurons


title: EWS_T100


title: Sample 49 Day27 neurons


title: EWS_T111


title: EWS_T99


title: EWS_T98


title: Sample 48 Day27 neurons


title: EWS_T97


title: EWS_T96


title: EWS_T94


title: Sample 46 Day27 neurons


title: Sample 57 Day27 neurons


title: Sample 45 Day27 neurons


title: Sample 47 Day27 neurons


title: EWS_T95


title: Sample 44 Day27 neurons


title: EWS_T93


title: Sample 41 Day27 neurons


title: Sample 42 Day27 neurons


title: Sample 54 Day27 neurons


title: EWS_T104


title: Sample 43 Day27 neurons


title: EWS_T90


title: Sample 40 Day27 neurons


title: EWS_T92


title: Sample 39 Day27 neurons


title: EWS_T89


title: Sample 38 Day27 neurons


title: EWS_T88


title: Sample 36 Day27 neurons


title: EWS_T87


title: EWS_T85


title: Sample 37 Day27 neurons


title: EWS_T86


title: Sample 35 Day27 neurons


title: Sample 34 Day27 neurons


title: Sample 32 Day27 neurons


title: EWS_T82


title: EWS_T81


title: EWS_T80


title: Sample 31 Day27 neurons


title: EWS_T91


title: Sample 33 Day27 neurons


title: EWS_T83


title: Sample 29 Day27 neurons


title: EWS_T78


title: Sample 28 Day27 neurons


title: Sample 30 Day27 neurons


title: EWS_T79


title: EWS_T77


title: EWS_T75


title: EWS_T76


title: EWS_T73


title: Sample 24 Day27 neurons


title: Sample 23 Day27 neurons


title: Sample 25 Day27 neurons


title: EWS_T71


title: Sample 22 Day27 neurons


title: EWS_T70


title: EWS_T84


title: EWS_T74


title: EWS_T69


title: Sample 18 Day27 neurons


title: Sample 19 Day27 neurons


title: Sample 20 Day27 neurons


title: Sample 27 Day27 neurons


title: Sample 17 Day27 neurons


title: Sample 16 Day27 neurons


title: EWS_T67


title: Sample 26 Day27 neurons


title: Sample 15 Day27 neurons


title: EWS_T68


title: EWS_T65


title: EWS_T64


title: EWS_T63


title: EWS_T66


title: Sample 14 Day27 neurons


title: EWS_T72


title: Sample 13 Day27 neurons


title: EWS_T62


title: Sample 11 Day27 neurons


title: EWS_T60


title: Sample 10 Day27 neurons


title: EWS_T59


title: EWS_T58


title: Sample 8 Day27 neurons


title: Sample 12 Day27 neurons


title: EWS_T57


title: EWS_T61


title: Sample 21 Day27 neurons


title: Sample 7 Day27 neurons


title: EWS_T56


title: Sample 6 Day27 neurons


title: Sample 5 Day27 neurons


title: Sample 4 Day27 neurons


title: EWS_T54


title: Sample 2 Day27 neurons


title: EWS_T55


title: Syncytio2 mRNASeq

city: Cincinnati

first: Mihaela

last: Pavlicev

state: OH

address: 3333 Burnet ave

department: Pediatrics

institute: Cincinnati Children`s

description:
Syncytio_2
mRNA
Ribo-SPIA technology
Processed data file: Pavlicev_Syncytio.txt

data_processing:
Reads from fastq files were aligned to human genome using Bowtie (v. 1.1.1).
Quantification of abundances of reads from single genes was performed using eXpress Ver. 1.5.1 (Roberts and Pachter 2012, Nature Methods).
TPM (transcript per million) values were extracted from the output for use.
Genome_build: GRCh38
Supplementary_files_format_and_content: Pavlicev_Syncytio.txt: Tab-delimited text file with TPM values for both samples.

source_name: microdissected placental tissue, >39 weeks pregnancy

growth_protocol: One cubic cm cubes of placental tissue were dissected from fresh, term human placenta and incubated in 30% sucrose overnight at 4°C and then embedded in OCT and frozen at -80°C.

extract_protocol:
Syncytial trophoblast was collected directly at dissection in the lysis buffer (Buffer RLT plus) from Qiagen RNeasy Plus Micro kit and RNA was extracted.
From total RNA we generated the amplified cDNA using Ovation RNA Amplification System (Ribo-SPIA technology, NuGen).

treatment_protocol: Blocks of frozen tissue were sectioned on a cryostat at 15μ thickness and placed on RNase-free PEN membrane coated slides (Leica #11505189). These slides were lightly stained with Haematoxylin and Eosin to enable visualization of cells for laser microdissection (Leica LMD 7000 Laser Microdissection system) of syncytiotrophoblast.

value: placenta

tag: timing

value: term (>39 weeks) pregnancy

tag: health status

value: healthy

tag: birth

value: C-section


title: Sample 1 Day27 neurons


title: EWS_T52


title: Syncytio1 mRNASeq

description:
Syncytio_1
mRNA
Ribo-SPIA technology
Processed data file: Pavlicev_Syncytio.txt


title: EWS_T50


title: EWS_T48


title: EWS_T53


title: EWS_T47


title: EWS_T51


title: EWS_T49


title: Single cell mRNASeq, batch 2, cell 33

description:
B2_Cell_33
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt

data_processing:
Reads from fastq files were aligned to human genome using Bowtie (v. 1.1.1).
Quantification of abundances of reads from single genes was performed using eXpress Ver. 1.5.1 (Roberts and Pachter 2012, Nature Methods).
TPM (transcript per million) values were extracted from the output for use.
Genome_build: GRCh38
Supplementary_files_format_and_content: Placenta_singlecell_Batch1_tpm.txt: Tab-delimited text file with TPM values for all 54 cells of batch 1 (B1_1-B1_54).
Supplementary_files_format_and_content: Placenta_singlecell_Batch2_tpm.txt: Tab-delimited text file with TPM values for all 33 cells of batch 2 (B2_1-B2_33).

source_name: placental tissue, >39 weeks pregnancy

extract_protocol:
C1 Single-Cell Auto Prep Integrated Fluidic Chip for mRNA-seq (17-25 micron cell size selection).
Nextera XT DNA Library Preparation Kit - manufacturer's recommendation.
A total of 125 pg cDNA was tagmented at 55 °C for 20 min. Libraries were pooled and purified on AMPure bead-based magnetic separation before a final quality control using Qubit dsDNA HS Assay Kit (Life Technologies) and Agilent High Sensitivity DNA Kit.

treatment_protocol: Tissue underwent serial trypsin and collagenase digests and the resulting cell suspension was layered on a continuous Percoll gradient. Cells were collected from the 20-60% fractions. Collected cells were filtered through a 40um cell filter and underwent Trypan blue exclusion to assess viability. Cell suspension at 3x10^5 cell/ml was submitted to Cincinnati Children's gene expression core for single cell capture using Fluidigm integrated fluidic circuit.


title: Sample 3 Day27 neurons


title: EWS_T45


title: Single cell mRNASeq, batch 2, cell 31

description:
B2_Cell_31
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: Single cell mRNASeq, batch 2, cell 30

description:
B2_Cell_30
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: Single cell mRNASeq, batch 2, cell 32

description:
B2_Cell_32
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: Sample 9 Day27 neurons


title: EWS_T43


title: EWS_T46


title: EWS_T44


title: Single cell mRNASeq, batch 2, cell 28

description:
B2_Cell_28
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: EWS_T42


title: EWS_T41


title: Single cell mRNASeq, batch 2, cell 27

description:
B2_Cell_27
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: Single cell mRNASeq, batch 2, cell 26

description:
B2_Cell_26
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: EWS_T40


title: Single cell mRNASeq, batch 2, cell 25

description:
B2_Cell_25
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: EWS_T38


title: EWS_T35


title: Single cell mRNASeq, batch 2, cell 29

description:
B2_Cell_29
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: Single cell mRNASeq, batch 2, cell 23

description:
B2_Cell_23
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: Single cell mRNASeq, batch 2, cell 22

description:
B2_Cell_22
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: EWS_T36


title: Single cell mRNASeq, batch 2, cell 19

description:
B2_Cell_19
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: Single cell mRNASeq, batch 2, cell 21

description:
B2_Cell_21
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: Single cell mRNASeq, batch 2, cell 18

description:
B2_Cell_18
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: Single cell mRNASeq, batch 2, cell 20

description:
B2_Cell_20
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: EWS_T31


title: Single cell mRNASeq, batch 2, cell 16

description:
B2_Cell_16
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: EWS_T29


title: Single cell mRNASeq, batch 2, cell 17

description:
B2_Cell_17
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: EWS_T32


title: Single cell mRNASeq, batch 2, cell 15

description:
B2_Cell_15
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: Single cell mRNASeq, batch 2, cell 12

description:
B2_Cell_12
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: EWS_T30


title: Single cell mRNASeq, batch 2, cell 11

description:
B2_Cell_11
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: EWS_T26


title: Single cell mRNASeq, batch 2, cell 14

description:
B2_Cell_14
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: EWS_T27


title: EWS_T39


title: EWS_T37


title: EWS_T25


title: Single cell mRNASeq, batch 2, cell 24

description:
B2_Cell_24
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: EWS_T34


title: Single cell mRNASeq, batch 2, cell 10

description:
B2_Cell_10
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: EWS_T33


title: EWS_T23


title: EWS_T24


title: EWS_T20


title: Single cell mRNASeq, batch 2, cell 8

description:
B2_Cell_8
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: Single cell mRNASeq, batch 2, cell 7

description:
B2_Cell_7
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: Single cell mRNASeq, batch 2, cell 9

description:
B2_Cell_9
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: EWS_T19


title: EWS_T22


title: EWS_T28


title: EWS_T21


title: Single cell mRNASeq, batch 2, cell 6

description:
B2_Cell_6
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: Single cell mRNASeq, batch 2, cell 5

description:
B2_Cell_5
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: Single cell mRNASeq, batch 2, cell 4

description:
B2_Cell_4
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: EWS_T18


title: Single cell mRNASeq, batch 2, cell 13

description:
B2_Cell_13
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: Single cell mRNASeq, batch 2, cell 3

description:
B2_Cell_3
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: EWS_T15


title: EWS_T16


title: EWS_T17


title: Single cell mRNASeq, batch 1, cell 53

description:
B1_Cell_53
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: Single cell mRNASeq, batch 1, cell 54

description:
B1_Cell_54
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: EWS_T13


title: Single cell mRNASeq, batch 1, cell 52

description:
B1_Cell_52
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: EWS_T12


title: EWS_T10


title: EWS_T8


title: EWS_T11


title: Single cell mRNASeq, batch 1, cell 48

description:
B1_Cell_48
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: Single cell mRNASeq, batch 1, cell 50

description:
B1_Cell_50
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: Single cell mRNASeq, batch 1, cell 47

description:
B1_Cell_47
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: Single cell mRNASeq, batch 1, cell 46

description:
B1_Cell_46
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: EWS_T6


title: Single cell mRNASeq, batch 1, cell 45

description:
B1_Cell_45
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: EWS_T7


title: Single cell mRNASeq, batch 1, cell 49

description:
B1_Cell_49
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: Single cell mRNASeq, batch 1, cell 51

description:
B1_Cell_51
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: Single cell mRNASeq, batch 1, cell 44

description:
B1_Cell_44
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: EWS_T5


title: Single cell mRNASeq, batch 2, cell 2

description:
B2_Cell_2
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: Single cell mRNASeq, batch 1, cell 43

description:
B1_Cell_43
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: EWS_T3


title: Single cell mRNASeq, batch 2, cell 1

description:
B2_Cell_1
mRNA
Processed data file: Placenta_singlecell_Batch2_tpm.txt


title: Single cell mRNASeq, batch 1, cell 42

description:
B1_Cell_42
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: EWS_T14


title: EWS_T2


title: SA P9 3

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description:
fresh human lung
SA_P9_3

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v1.4.8 and Real Time Analysis (RTA) v1.18.61, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina CASAVA 1.8.2 pipeline was used to generate the sequence data.
Reads were aligned to the human genome by Rsubread version 1.22.1
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

molecule: polyA RNA

source_name: normal lung tissue (wild-type)

extract_protocol:
FACS sorted cells were lysed for RNA preparation using QIAGEN RNAeasy micro-kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: patient

value: lung

value: Small airway P9


title: Single cell mRNASeq, batch 1, cell 40

description:
B1_Cell_40
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: EWS_T1


title: Single cell mRNASeq, batch 1, cell 41

description:
B1_Cell_41
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: EWS_T9


title: Single cell mRNASeq, batch 1, cell 38

description:
B1_Cell_38
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: Single cell mRNASeq, batch 1, cell 39

description:
B1_Cell_39
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SA P9 2

description:
fresh human lung
SA_P9_2


title: SA P9 1

description:
fresh human lung
SA_P9_1


title: Single cell mRNASeq, batch 1, cell 37

description:
B1_Cell_37
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SA luminal 3

description:
fresh human lung
SA_P6_3

value: Small airway luminal cells


title: Single cell mRNASeq, batch 1, cell 36

description:
B1_Cell_36
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SA luminal 1

description:
fresh human lung
SA_P6_1


title: SA luminal 2

description:
fresh human lung
SA_P6_2


title: SA AT2 3

description:
fresh human lung
SA_P10_3

value: Small airway alveolar type 2 cells


title: Single cell mRNASeq, batch 1, cell 35

description:
B1_Cell_35
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SA AT2 1

description:
fresh human lung
SA_P10_1


title: EWS_T4


title: Single cell mRNASeq, batch 1, cell 34

description:
B1_Cell_34
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SA AT2 2

description:
fresh human lung
SA_P10_2


title: Single cell mRNASeq, batch 1, cell 32

description:
B1_Cell_32
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: Single cell mRNASeq, batch 1, cell 31

description:
B1_Cell_31
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: LA luminal 3

description:
fresh human lung
LA_P6_3

value: Large airway luminal cells


title: Single cell mRNASeq, batch 1, cell 29

description:
B1_Cell_29
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: LA luminal 2

description:
fresh human lung
LA_P6_2


title: LA AT2 3

description:
fresh human lung
LA_P10_3

value: Large Airway alveolar type 2 cells


title: Single cell mRNASeq, batch 1, cell 33

description:
B1_Cell_33
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: Single cell mRNASeq, batch 1, cell 28

description:
B1_Cell_28
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: Single cell mRNASeq, batch 1, cell 27

description:
B1_Cell_27
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: LA AT2 2

description:
fresh human lung
LA_P10_2


title: LA AT2 1

description:
fresh human lung
LA_P10_1


title: LA basal 3

description:
fresh human lung
LA_P5_3

value: Basal cells


title: Single cell mRNASeq, batch 1, cell 26

description:
B1_Cell_26
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: Single cell mRNASeq, batch 1, cell 25

description:
B1_Cell_25
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: LA basal 2

description:
fresh human lung
LA_P5_2


title: Single cell mRNASeq, batch 1, cell 24

description:
B1_Cell_24
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SSL508-28_inoculated powdery mildew_48h_rep_1

city: Yangzhou

first: Xuewen

last: Xu

state: Jiangsu

address: 48 wenhui east road

country: China

institute: Yangzhou University

data_processing:
An index of the reference genome was built using Bowtie v0.12.8
single-end clean reads were aligned to the reference genome using TopHat v2.0.9
Cufflinks v2.1.1 was used to count the read numbers mapped to each gene
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: cucumber 9930 V2 database (http://www.icugi.org/cgi-bin/ICuGI/index.cgi)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Cucumis sativus

source_name: SSL508-28_inoculated powdery mildew_48h

growth_protocol: Normal growth

extract_protocol:
Total RNA was extracted using RNAiso Plus Total RNA extraction reagent  (Cat#9109, TAKARA)和RNeasy Mini Kit(Cat#74106，Qiagen）following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Powdery mildew conidia were collected from naturally-infected cucumber plants in the greenhouse. A spore suspension at 10e6 spores per ml was made by soaking heavily infected leaves in tap water (containing 0.01% Tween-20 as surfactant). Inoculation was performed at the 3rd true-leaf stage by spraying the spore suspension evenly on the surface of the seedlings. After inoculation, the plants were maintained in a controlled growth chamber at 25 °C day/20 °C night with a 16-/8-h (light/dark) photoperiod.

tag: line

value: inoculated with powdery mildew

tag: time

value: leaves


title: SSL508-28_inoculated powdery mildew_48h_rep_2

tag: tissue


title: SSL508-28_control_0h_3

value: control

value: 0 h


title: LA basal 1

description:
fresh human lung
LA_P5_1


title: Single cell mRNASeq, batch 1, cell 22

description:
B1_Cell_22
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SSL508-28_control_0h_2


title: LA luminal 1

description:
fresh human lung
LA_P6_1


title: D8_inoculated powdery mildew_48h_rep_2

source_name: D8_inoculated powdery mildew_48h


title: Single cell mRNASeq, batch 1, cell 30

description:
B1_Cell_30
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: Single cell mRNASeq, batch 1, cell 21

description:
B1_Cell_21
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SSL508-28_control_0h_1


title: SSL508-28_inoculated powdery mildew_48h_rep_3


title: D8_inoculated powdery mildew_48h_rep_1


title: D8_control_0h_rep 2


title: D8_control_0h_rep 3


title: D8_control_0h_rep 1


title: D8_inoculated powdery mildew_48h_rep_3


title: H3K9me2_2

city: Philadelphia

first: Takahiro

last: Sato

state: PA

address: 3307 North Broad Street

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

description:
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression. Each sample was run on two separate lanes on the HiSeq2500 generating two fastq files. The two files were merged for final analysis.
H3K9me2-SICER_W200-G600-FDR0.01.xlsx

data_processing:
Illumina HiSeq2500 single end sequencing
bowtie2 --very sensitive alignment of the reads in two fastq files from each sample to hg19, generating one SAM file per sample
convert SAM file to BAM file using samtools
merge duplicate samples using samtools to create one BAM file for each antibody condition
call peaks for H3K4me2 by comparing to input and using MACS2 --nomodel, q<0.01
call peaks for H3K9me2 and H3K27me3 by comparing to input and using SICER window=200, gap=600, q<0.01
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are in excel format. They contain chromatin start and end sites for all peaks with q<0.01, fold change compared to input, p-value, and FDR(q-value)

source_name: YB5 colon cancer cell line

growth_protocol: YB5 cell line was cultured in L-15 medium with 10% fetal bovine serum

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed using antibodies for rabbit anti-IgG (Abcam, ab46540), anti-histone H3K4 dimethylation (Millipore, 07-030), anti-histone H3K9 dimethylation (Abcam, ab1220), and anti-histone H3K27 trimethylation (Active Motif, 39155).
Indexed libraries were prepared using NEB Next ChIP-Seq Library Prep (Illumina)

value: Dukes' type C, grade IV, colorectal adenocarcinoma

value: female


title: H3K27me3_1

description:
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression. Each sample was run on two separate lanes on the HiSeq2500 generating two fastq files. The two files were merged for final analysis.
H3K27me3-SICER_W200-G600-FDR0.01.xlsx


title: Single cell mRNASeq, batch 1, cell 20

description:
B1_Cell_20
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt

value: placenta


title: H3K27me3_2


title: H3K9me2_1


title: SHM_Patient10_Ibrutinib_pre

first: Roberto

last: Chiarle

state: Massachusetts

address: 300 Longwood Avenue

department: Department of Pathology

institute: Children’s Hospital Boston and Harvard Medical School

data_processing:
For SHM data, sequences with mean quality score < 20 and length < 50 were removed. The remained sequences were used to calculate mutation rate. Sequences obtained from each designed region were aligned to the reference sequence using BLASTN with alignment length > 200. Mutations to be considered valid were calculated after filtering steps, as previously described(Liu, M. et al.,Nature 2008). Briefly, mutations first had to pass a Neighbourhood Quality Standard (NQS) criteria requiring a minimum Phred score of 30 for the mutation itself, and 20 for the five adjacent bases on either side. Mutations that were within five bases of more than two additional mutations were excluded. Mutations within two bases of a deletion or insertion were also excluded. In addition, bases with mutation rate > 0.01 were excluded as a result of overwhelming influence of sequence error or SNP, of which bases with mutation rate > 0.2 were further regarded as SNP and were excluded. Finally, the average base mutation rate of 1-200 bp passing the above criteria were calculated from forward sequence, as well as reverse sequences if applicable. For average base mutation rates of C-to-T or G-to-A transitions, only C or G bp sites we counted.
processed data files format and content: Tab-delimited text file gives average C>T|G>A transitions/mut frequency for each re-sequenced genomic region. Regions with reads less than 100 were excluded and shown as 'NA'.

source_name: Peripheral blood

extract_protocol:
Cells were lysed in lysis buffer (NaCl 200 mM, Tris.HCl 100 mM, EDTA 5mM, SDS 0.2%)  containing 10 μg/ml Proteinase K  at 56°C overnight. Genomic DNA was precipitated with isopropanol at room temperature, washed in ethanol 70% and resuspended in TE buffer (10mM Tris-HCl plus 1mM EDTA)
PCR amplicons

treatment_protocol: pre-ibrutinib treatment

value: peripheral blood, Human Chronic Lymphocytic Leukemia

value: human chronic lymphocytic leukemia B cells

value: ibruitinib


title: Single cell mRNASeq, batch 1, cell 23

description:
B1_Cell_23
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt

value: term (>39 weeks) pregnancy

value: healthy

value: C-section


title: SHM_Patient9_Ibrutinib_pre


title: Single cell mRNASeq, batch 1, cell 17

description:
B1_Cell_17
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SHM_Patient8_Ibrutinib_pre

data_processing:
For SHM data, sequences with mean quality score < 20 and length < 50 were removed. The remained sequences were used to calculate mutation rate. Sequences obtained from each designed region were aligned to the reference sequence using BLASTN with alignment length > 200. Mutations to be considered valid were calculated after filtering steps, as previously described(Liu, M. et al.,Nature 2008). Briefly, mutations first had to pass a Neighbourhood Quality Standard (NQS) criteria requiring a minimum Phred score of 30 for the mutation itself, and 20 for the five adjacent bases on either side. Mutations that were within five bases of more than two additional mutations were excluded. Mutations within two bases of a deletion or insertion were also excluded. In addition, bases with mutation rate > 0.01 were excluded as a result of overwhelming influence of sequence error or SNP, of which bases with mutation rate > 0.2 were further regarded as SNP and were excluded. Finally, the average base mutation rate of 1-200 bp passing the above criteria were calculated from forward sequence, as well as reverse sequences if applicable. For average base mutation rates of C-to-T or G-to-A transitions, only C or G bp sites we counted.
processed data files format and content: Tab-delimited text file gives average C>T|G>A transitions/mut frequency for each re-sequenced genomic region. Regions with reads less than 100 were excluded and shown as 'NA' .


title: SHM_Patient9_Ibrutinib_post

treatment_protocol: post-ibrutinib treatment


title: Single cell mRNASeq, batch 1, cell 16

description:
B1_Cell_16
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: H3K4me2_1

description:
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression. Each sample was run on two separate lanes on the HiSeq2500 generating two fastq files. The two files were merged for final analysis.
H3K4me2_MACS2_peaks.xlsx


title: SHM_Patient7_Ibrutinib_post

data_processing:
For SHM data, sequences with mean quality score < 20 and length < 50 were removed. The remained sequences were used to calculate mutation rate. Sequences obtained from each designed region were aligned to the reference sequence using BLASTN with alignment length > 200. Mutations to be considered valid were calculated after filtering steps, as previously described(Liu, M. et al.,Nature 2008). Briefly, mutations first had to pass a Neighbourhood Quality Standard (NQS) criteria requiring a minimum Phred score of 30 for the mutation itself, and 20 for the five adjacent bases on either side. Mutations that were within five bases of more than two additional mutations were excluded. Mutations within two bases of a deletion or insertion were also excluded. In addition, bases with mutation rate > 0.01 were excluded as a result of overwhelming influence of sequence error or SNP, of which bases with mutation rate > 0.2 were further regarded as SNP and were excluded. Finally, the average base mutation rate of 1-200 bp passing the above criteria were calculated from forward sequence, as well as reverse sequences if applicable. For average base mutation rates of C-to-T or G-to-A transitions, only C or G bp sites we counted.
processed data files format and content: tab-delimited text file gives average C>T|G>A transitions/mut frequency for each re-sequenced genomic region. Regions with reads less than 100 were excluded and shown as 'NA' .


title: Single cell mRNASeq, batch 1, cell 15

description:
B1_Cell_15
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SHM_Patient8_Ibrutinib_post


title: Input_2

description: YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression. Each sample was run on two separate lanes on the HiSeq2500 generating two fastq files. The two files were merged for final analysis.

value: Input


title: SHM_Patient6_Ibrutinib_post

data_processing:
For SHM data, sequences with mean quality score < 20 and length < 50 were removed. The remained sequences were used to calculate mutation rate. Sequences obtained from each designed region were aligned to the reference sequence using BLASTN with alignment length > 200. Mutations to be considered valid were calculated after filtering steps, as previously described(Liu, M. et al.,Nature 2008). Briefly, mutations first had to pass a Neighbourhood Quality Standard (NQS) criteria requiring a minimum Phred score of 30 for the mutation itself, and 20 for the five adjacent bases on either side. Mutations that were within five bases of more than two additional mutations were excluded. Mutations within two bases of a deletion or insertion were also excluded. In addition, bases with mutation rate > 0.01 were excluded as a result of overwhelming influence of sequence error or SNP, of which bases with mutation rate > 0.2 were further regarded as SNP and were excluded. Finally, the average base mutation rate of 1-200 bp passing the above criteria were calculated from forward sequence, as well as reverse sequences if applicable. For average base mutation rates of C-to-T or G-to-A transitions, only C or G bp sites we counted.
processed data files format and content: tab-delimited text file gives average C>T|G>A transitions/mut frequency for each re-sequenced genomic region. Regions with reads less than 100 were excluded and shown as 'NA'.


title: Single cell mRNASeq, batch 1, cell 19

description:
B1_Cell_19
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SHM_Patient5_Ibrutinib_post


title: SHM_Patient6_Ibrutinib_pre


title: Single cell mRNASeq, batch 1, cell 14

description:
B1_Cell_14
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SHM_Patient5_Ibrutinib_pre


title: Single cell mRNASeq, batch 1, cell 18

description:
B1_Cell_18
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: Single cell mRNASeq, batch 1, cell 12

description:
B1_Cell_12
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SHM_Patient4_Ibrutinib_pre


title: Input_1


title: SHM_Patient4_Ibrutinib_post


title: Single cell mRNASeq, batch 1, cell 11

description:
B1_Cell_11
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: H3K4me2_2


title: SHM_Patient3_Ibrutinib_pre


title: SHM_Patient2_Ibrutinib_pre


title: SHM_Patient2_Ibrutinib_post


title: SHM_Patient7_Ibrutinib_pre


title: Single cell mRNASeq, batch 1, cell 10

description:
B1_Cell_10
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SHM_Patient1_Ibrutinib_pre


title: SHM_Patient10_Idelalisib_post

treatment_protocol: post-idelalisib treatment

value: idelalisib


title: Single cell mRNASeq, batch 1, cell 9

description:
B1_Cell_9
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: Single cell mRNASeq, batch 1, cell 13

description:
B1_Cell_13
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: Single cell mRNASeq, batch 1, cell 8

description:
B1_Cell_8
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SHM_Patient9_Idelalisib_post


title: SHM_Patient10_Idelalisib_pre

treatment_protocol: pre-idelalisib treatment


title: SHM_Patient9_Idelalisib_pre


title: Single cell mRNASeq, batch 1, cell 6

description:
B1_Cell_6
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SHM_Patient10_Ibrutinib_post


title: SHM_Patient8_Idelalisib_pre


title: SHM_Patient8_Idelalisib_post


title: SHM_Patient7_Idelalisib_post


title: SHM_Patient7_Idelalisib_pre


title: Single cell mRNASeq, batch 1, cell 5

description:
B1_Cell_5
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SHM_Patient3_Ibrutinib_post


title: Single cell mRNASeq, batch 1, cell 7

description:
B1_Cell_7
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SHM_Patient6_Idelalisib_post


title: SHM_Patient4_Idelalisib_post


title: Single cell mRNASeq, batch 1, cell 3

description:
B1_Cell_3
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SHM_Patient6_Idelalisib_pre


title: SHM_Patient5_Idelalisib_post


title: SHM_Patient5_Idelalisib_pre


title: SHM_Patient4_Idelalisib_pre


title: Single cell mRNASeq, batch 1, cell 2

description:
B1_Cell_2
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SHM_Patient3_Idelalisib_post


title: SHM_Patient3_Idelalisib_pre


title: SHM_Patient1_Ibrutinib_post


title: SHM_Patient1_Idelalisib_post


title: SHM_Patient2_Idelalisib_pre


title: Bulk placenta mRNASeq, rep1

description:
mRNA
Processed data file: humanplacenta_cufflinks.txt

data_processing:
Reads were aligned using TopHat.
Transcript assembly & quantification using Cufflinks.
FPKM value extracted from Cufflinks.
Genome_build: GRCh38
Supplementary_files_format_and_content: humanplacenta_cufflinks.txt: Tab-delimited text file with FPKM values for both samples.

extract_protocol:
Total RNA was isolated using TRIzol. All samples passed initial quality testing using Bioanalyzer 2100 (Agilent), assuring RIN values > 9.
Libraries were prepared from one microgram of total RNA with TRUseq Stranded mRNA HT kit (Illumina Inc.).
The libraries were subjected to paired-end 50 bp RNA-sequencing on a HiSeq 2500 (Illumina Inc.), at the depth of 30 Million reads per sample.

treatment_protocol: Two human placentas were collected at term cesarean section without labor, at 39 weeks and 1 day, respectively 39 weeks and 2 days gestational age (IRB protocol: CCHMC IRB 2013–2243). Collected tissue was flash frozen and kept at -80˚C until RNA extraction.


title: SHM_Patient1_Idelalisib_pre


title: Bulk placenta mRNASeq, rep2


title: SHM_Patient8_Ctrl_pre

treatment_protocol: no treatment

value: no treatment


title: SHM_Patient8_Ctrl_post


title: 1013140_2

description: Adjacent normal breast tissue was isolated from breast cancer patients, then epithelial cells were isolated and grown in culture for a few passages before DNA isolation

data_processing:
Illumina HiSeq2500 single end sequencing
tophat2 --sensitive alignment of the reads in two fastq files from each sample to hg19, generating one BAM file per sample
ht-seq-count  with default settings to generate counts of each gene
edgeR to generate RPKM values for each sample
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are in excel format that contain RPKMs all genes

source_name: normal breast epithelial cells

growth_protocol: Normal breast epithelial cells were grown in 1:1 DMEM/F12 medium with 2.4 g/L sodium bicarbonate, 5% chelated horse serum, 20 ng/ml EGF (BD Biosciences), 100 ng/ml cholera toxin (Sigma-Aldrich), 10 mg/L insulin (Sigma-Aldrich), 0.5 mg/L hydrocortisone (Sigma-Aldrich), and 0.04 mM calcium chloride (Sigma-Aldrich)

extract_protocol:
RNA was isolated using Rneasy Mini Kit (Qiagen)
Strand-specific RNA libraries were generated from 1μg of RNA using TruSeq stranded total RNA with Ribo-Zero Gold (Illumina)

value: adjacent normal tissue from patient with lobular carcinoma in situ

tag: age

value: 69 year old


title: SHM_Patient6_Ctrl_pre


title: SHM_Patient7_Ctrl_post


title: SHM_Patient6_Ctrl_post


title: SHM_Patient5_Ctrl_post


title: Single cell mRNASeq, batch 1, cell 4

description:
B1_Cell_4
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt

tag: batch


title: 1013140_1

tag: Sex


title: SHM_Patient7_Ctrl_pre


title: 1013140_3


title: SHM_Patient5_Ctrl_pre


title: SHM_Patient4_Ctrl_post


title: SHM_Patient4_Ctrl_pre


title: Single cell mRNASeq, batch 1, cell 1

description:
B1_Cell_1
mRNA
Processed data file: Placenta_singlecell_Batch1_tpm.txt


title: SHM_Patient3_Ctrl_post


title: YB5_Cntrl_3

description: YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression.

data_processing:
Illumina HiSeq2500 single end sequencing
tophat2 --sensitive alignment of the reads in two fastq files from each sample to hg19, generating one BAM file per sample
ht-seq-count  with default settings to generate counts of each gene
edgeR to generate RPKM and fold change of each condition compared to control samples from GSE73966 for YB5 and GSE74036 for MCF7, only keep genes with at least one read in one of the samples
export fold change of each inhibitor vs. control into a text file, then import all the fold changes into one excel file
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are in excel format. The first sheet is the YB5 data. First 3 columns are the RPKM values from the control samples from GSE73966 and the next 3 columns are from the RPKM values from 1µM DAC. The following columns are the fold change and FDR of the triplicates of each condition compared against the triplicates of control sample. The second sheet contains the MCF7 data in the same setup using control samples from GSE74036 and MCF7 cells treated with 100nM DAC.

growth_protocol: MCF7 cell line was cultured in DMEM medium with 10% fetal bovine serum, YB5 cell line was cultured in L-15 medium with 10% fetal bovine serum

treatment_protocol: Cells were treated daily with either 1μM or 100nM decitabine (5-aza-CdR, Sigma) for 96 hours

tag: cell line

value: colon cancer cell line

value: colorectal adenocarcinoma

tag: duke's type

value: C, grade IV


title: YB5_Cntrl_1


title: SHM_Patient2_Ctrl_post

tag: treatment


title: SHM_Patient3_Ctrl_pre


title: YB5_Cntrl_2


title: YB5_1μM_DAC_3

description:
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression.
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression. Each sample was run on two separate lanes on the HiSeq2500 generating two fastq files. The two files were merged for final analysis.


title: SHM_Patient2_Ctrl_pre


title: SHM_Patient2_Idelalisib_post


title: SHM_Patient1_Ctrl_post


title: SHM_Patient1_Ctrl_pre


title: HTGTS_MEC1.KO-Duvelisib rep2

data_processing:
Library strategy: High-Throughput Genomic Translocation Sequencing approach, HTGTS
For HTGTS data, we applied prinseq 0.2 to remove sequences with exact PCR duplicates, mean quality score <  20 and length <  50. Next, effect reads for each sample were recognized by designed barcode, primer and bait portion. Lastly,the barcode, primer and bait portion of the remained sequences were masked for alignment analysis to determine translocation junctions as previously described(Chiarle et al.,Cell 2011). Briefly, we aligned sequences to the mouse reference genome (GRCm37/mm9) or human genome (GRCh38/hg38) using BLAT, and then filtered artificial junctions by removing PCR repeats (reads with same junction position in alignment to the reference genome and a start position in the read less than 3 bp apart), invalid alignments (including alignment scores < 30, reads with multiple alignments having a score difference < 4 and alignments having 10-nucleotide gaps) and ligation artifacts (for example, random HaeIII restriction sites ligated to bait breaksite). Translocation junction position was determined based on the genomic position of the 5’ end of the aligned read.
genome build: hg38
processed data files format and content: BED files of HTGTS data contain all obtained translocation junctions information including chromosome,corrdinate,read name,align score and strand.

source_name: DSMZ ACC 497

growth_protocol: RPMI 1640+10% FBS,Human chronic lymphocytic leukemia B cells  transduced with c-MYC CRISPR #1 /Cas9 lentivirus 8 h post treatment with duvelisib.

extract_protocol:
Cells were lysed in lysis buffer (NaCl 200 mM, Tris.HCl 100 mM, EDTA 5mM, SDS 0.2%)  containing 10 μg/ml Proteinase K  at 56°C overnight. Genomic DNA was precipitated with isopropanol at room temperature, washed in ethanol 70% and resuspended in TE buffer (10mM Tris-HCl plus 1mM EDTA)
See Supplemental Experimental procedures from Chiarle et al.  Cell 2011, paragraph Generation of HTGTS libraries by adapter-PCR.

treatment_protocol: 1 micromolar Duvelisib

value: MEC1 AID KO

value: Duvelisib


title: HTGTS_MEC1.KO-Duvelisib rep3

growth_protocol: RPMI 1640+10% FBS,Human chronic lymphocytic leukemia B cells  transduced with c-MYC CRISPR #2 /Cas9 lentivirus 8 h post treatment with duvelisib.


title: YB5_1μM_DAC_1

description:
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression.
Each sample was run on two separate lanes on the HiSeq2500 generating two fastq files. The two files were merged for final analysis.

value: female


title: HTGTS_MEC1.KO-Idelalisib rep3

growth_protocol: RPMI 1640+10% FBS, Human chronic lymphocytic leukemia B cells  transduced with c-MYC CRISPR #2 /Cas9 lentivirus 8 h post treatment with duvelisib.

treatment_protocol: 1 micromolar Idelalisib

value: peripheral blood, Human Chronic Lymphocytic Leukemia

value: Idelalisib


title: MCF7_Cntrl_3

description:
derived from metastatic site: pleural effusion
Each sample was run on two separate lanes on the HiSeq2500 generating two fastq files. The two files were merged for final analysis.

source_name: MCF7 breast cancer cell line

value: breast cancer cell line

value: mammary gland, breast

tag: er status

value: positive


title: HTGTS_MEC1.KO-Idelalisib rep2

value: human chronic lymphocytic leukemia B cells


title: HTGTS_MEC1.KO-DMSO rep2

growth_protocol: RPMI 1640+10% FBS, Human chronic lymphocytic leukemia B cells  transduced with c-MYC CRISPR #1 /Cas9 lentivirus 8 h post treatment with duvelisib.

treatment_protocol: 1 micromolar DMSO

value: DMSO


title: MCF7_Cntrl_1


title: MCF7_Cntrl_2


title: HTGTS_MEC1.KO-Idelalisib rep1


title: HTGTS_MEC1.KO-DMSO rep1


title: MCF7_100nM_DAC_3


title: HTGTS_MEC1.Duvelisib rep5


title: MCF7_100nM_DAC_1


title: CL1-5_S100A7A-

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

data_processing:
Illumina Miseq reporter software 2.1 used for basecalling.
The Strand NGS software (version 2.1) was performed using default parameters for pre-alignment and post-alignment quality control analysis.
Differentially expressed genes (DEGs) from 4 groups of cultured samples were calculated from the raw reads using the DESeq method.
The significance was determined by MannWhitney un-paired test or 2-way ANOVA and a Benjamini and Hochberg false discovery rate (FDR) multiple gene correction was applied.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each sample

source_name: Lung

extract_protocol:
Total RNA will be isolated from liver tissues using TRIzol® reagent (Invitrogen). Total RNA (15 μg) for each sample will be used for purifying the poly(A)-containing mRNA molecules, RNA ampliﬁcation, and synthesis of double stranded cDNAs that will be ligated to adapters, following the Illumina (San Diego, California, USA) TruSeq RNA Sample Prep guidelines.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: S100A7A shRNA (knockdown)


title: CL1-5_C

value: non-silensing shRNA


title: YB5_1μM_DAC_2

tag: gender


title: MCF7_100nM_DAC_2

tag: cell type


title: HTGTS_MEC1.KO-Duvelisib rep1


title: CL1-0_C

value: control vector


title: HTGTS_JeKo-1.Duvelisib rep5

data_processing:
For HTGTS data, we applied prinseq 0.2 to remove sequences with exact PCR duplicates, mean quality score < 20 and length < 50. Next, effect reads for each sample were recognized by designed barcode, primer and bait portion. Lastly,the barcode, primer and bait portion of the remained sequences were masked for alignment analysis to determine translocation junctions as previously described(Chiarle et al.,Cell 2011). Briefly, we aligned sequences to the mouse reference genome (GRCm37/mm9) or human genome (GRCh38/hg38) using BLAT, and then filtered artificial junctions by removing PCR repeats (reads with same junction position in alignment to the reference genome and a start position in the read less than 3 bp apart), invalid alignments (including alignment scores < 30, reads with multiple alignments having a score difference < 4 and alignments having 10-nucleotide gaps) and ligation artifacts (for example, random HaeIII restriction sites ligated to bait breaksite). Translocation junction position was determined based on the genomic position of the 5’ end of the aligned read.
Genome_build: hg38
Supplementary_files_format_and_content: For HTGTS data, BED files contain all obtained translocation junctions information including chromosome,corrdinate,read name,align score and strand.

source_name: ATCC CRL-3006

growth_protocol: RPMI 1640+10% FBS, Human mantle cell lymphoma B cells  transduced with c-MYC CRISPR #2/Cas9 lentivirus 8 h post treatment with duvelisib.

treatment_protocol: 1 micromolar duvelisib

value: peripheral blood, Mantle Cell Lymphoma

value: human mantle cell lymphoma B cells


title: HTGTS_JeKo-1.Duvelisib rep3


title: HTGTS_JeKo-1.Duvelisib rep4


title: HTGTS_JeKo-1.Ibrutinib rep3

growth_protocol: RPMI 1640+10% FBS, Human mantle cell lymphoma B cells  transduced with c-MYC CRISPR #2/Cas9 lentivirus 8 h post treatment with ibrutinib.

treatment_protocol: 1 micromolar ibrutinib

value: Ibrutinib


title: HTGTS_JeKo-1.Duvelisib rep1

growth_protocol: RPMI 1640+10% FBS, Human mantle cell lymphoma B cells  transduced with c-MYC CRISPR #1/Cas9 lentivirus 8 h post treatment with duvelisib.


title: HTGTS_JeKo-1.Ibrutinib rep2

growth_protocol: RPMI 1640+10% FBS, Human mantle cell lymphoma B cells  transduced with c-MYC CRISPR #1/Cas9 lentivirus 8 h post treatment with ibrutinib.


title: HTGTS_JeKo-1.Duvelisib rep2

growth_protocol: RPMI 1640+10% FBS, Human mantle cell lymphoma B cells  transduced with c-MYC CRISPR #1/Cas9 lentivirus 8 h post treatment with duvelisib

extract_protocol:
Cells were lysed in lysis buffer (NaCl 200 mM, Tris.HCl 100 mM, EDTA 5mM, SDS 0.2%)  containing 10 μg/ml Proteinase K  at 56°C overnight. Genomic DNA was precipitated with isopropanol at room temperature, washed in ethanol 70% and resuspended in TE buffer (10mM Tris-HCl plus 1mM EDTA)
See Supplemental Experimental procedures from Chiarle et al.  Cell 2011, paragraph Generation of HTGTS libraries by adapter-PCR


title: HTGTS_JeKo-1.Idelalisib rep5

growth_protocol: RPMI 1640+10% FBS, Human mantle cell lymphoma B cells  transduced with c-MYC CRISPR #2/Cas9 lentivirus 8 h post treatment with idelalisib


title: HTGTS_JeKo-1.Idelalisib rep6

growth_protocol: RPMI 1640+10% FBS, Human mantle cell lymphoma B cells  transduced with c-MYC CRISPR #2/Cas9 lentivirus 8 h post treatment with idelalisib.


title: HTGTS_MEC1.KO-DMSO rep3

tag: strain

value: not applicable


title: HTGTS_JeKo-1.Idelalisib rep3


title: HTGTS_MEC1.Duvelisib rep6


title: HTGTS_JeKo-1.Idelalisib rep1

growth_protocol: RPMI 1640+10% FBS, Human mantle cell lymphoma B cells  transduced with c-MYC CRISPR #1 /Cas9 lentivirus 8 h post treatment with idelalisib


title: HTGTS_MEC1.Ibrutinib rep4

growth_protocol: RPMI 1640+10% FBS, Human chronic lymphocytic leukemia B cells  transduced with c-MYC CRISPR #2 /Cas9 lentivirus 8 h post treatment with ibrutinib


title: HTGTS_JeKo-1.DMSO rep2

growth_protocol: RPMI 1640+10% FBS, Human mantle cell lymphoma B cells  transduced with c-MYC CRISPR #1 and #2/Cas9 lentiviruses 8 h post treatment with control DMSO.


title: HTGTS_JeKo-1.DMSO rep3

growth_protocol: RPMI 1640+10% FBS, Human mantle cell lymphoma B cells  transduced with c-MYC CRISPR #2/Cas9 lentivirus 8 h post treatment with control DMSO.


title: HTGTS_JeKo-1.DMSO rep4


title: HTGTS_JeKo-1.DMSO rep1

growth_protocol: RPMI 1640+10% FBS, Human mantle cell lymphoma B cells  transduced with c-MYC CRISPR #1 /Cas9 lentivirus 8 h post treatment with control DMSO.


title: HTGTS_MEC1.Ibrutinib rep3


title: HTGTS_MEC1.Ibrutinib rep2

growth_protocol: RPMI 1640+10% FBS, Human chronic lymphocytic leukemia B cells  transduced with c-MYC CRISPR #1 /Cas9 lentivirus 8 h post treatment with ibrutinib.


title: CL1-0_S100A7A+

value: S100A7A knock-in


title: HTGTS_MEC1.Duvelisib rep4

value: Duvelisib


title: HTGTS_MEC1.Ibrutinib rep1

growth_protocol: RPMI 1640+10% FBS, Human chronic lymphocytic leukemia B cells  transduced with c-MYC CRISPR #1 /Cas9 lentivirus 8 h post treatment with ibrutinib


title: HTGTS_MEC1.Duvelisib rep2


title: HTGTS_MEC1.Duvelisib rep1

growth_protocol: RPMI 1640+10% FBS, Human chronic lymphocytic leukemia B cells  transduced with c-MYC CRISPR #1 /Cas9 lentivirus 8 h post treatment with duvelisib


title: HTGTS_MEC1.Duvelisib rep3

growth_protocol: RPMI 1640+10% FBS, Human chronic lymphocytic leukemia B cells  transduced with c-MYC CRISPR #2 /Cas9 lentivirus 8 h post treatment with duvelisib.


title: HTGTS_JeKo-1.Idelalisib rep4


title: HTGTS_MEC1.Idelalisib rep4

growth_protocol: RPMI 1640+10% FBS, Human chronic lymphocytic leukemia B cells  transduced with c-MYC CRISPR #2 /Cas9 lentivirus 8 h post treatment with idelalisib.


title: HTGTS_MEC1.Idelalisib rep1

growth_protocol: RPMI 1640+10% FBS, Human chronic lymphocytic leukemia B cells transduced with c-MYC CRISPR #1 /Cas9 lentivirus 8 h post treatment with idelalisib.


title: HTGTS_MEC1.Idelalisib rep3


title: HTGTS_MEC1.DMSO rep1

growth_protocol: RPMI 1640+10% FBS, Human chronic lymphocytic leukemia B cells  transduced with c-MYC CRISPR #1 /Cas9 lentivirus 8 h post treatment with control DMSO.


title: HTGTS_MEC1.DMSO rep2

growth_protocol: RPMI 1640+10% FBS, Human mantle cell lymphoma B cells  transduced with c-MYC CRISPR #2 /Cas9 lentivirus 8 h post treatment with control DMSO.


title: HTGTS_JeKo-1.Idelalisib rep2

growth_protocol: RPMI 1640+10% FBS, Human mantle cell lymphoma B cells  transduced with c-MYC CRISPR #1 /Cas9 lentivirus 8 h post treatment with idelalisib.


title: HTGTS_JeKo-1.Ibrutinib rep1

growth_protocol: RPMI 1640+10% FBS, Human mantle cell lymphoma B cells  transduced with c-MYC CRISPR #1/Cas9 lentivirus 8 h post treatment with ibrutinib.


title: AG553 (unevolved Quad) No formate-3

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

description:
Clostridium thermocellum_1313 culture
Ct 23

data_processing:
Demultiplexing and file conversion performed by bcl2fastq version bcl2fastq-1.8.3
RNAseq reads were aligned to the C. thermocellum DSM1313 (NC_017304.1) genome assembly using Fastq files imported into the CLCBio RNA-sequencing pipeline. Default settings were used for mismatch, insertion, and deletion costs.
Total gene counts from the CLCBio mapping were used for DESeq2 analysis to normalize and determine significant gene expression differences
Genome_build: ASM18492v1
Supplementary_files_format_and_content: Tab deliminated file includes read counts for each gene across the 24 ( 6 conditions with 4 reps each condition) samples used in this study

organism: Acetivibrio thermocellus DSM 1313

source_name: Q0 NO formate

growth_protocol: strains of Clostridium thermocellum 1313  grown in MTC5 defined media with 5 g/L cellobiose as the carbon source.   Del-hpt (parental strain), AG553 (unevolved Quad) and AG601 (“best” evolved strain)

extract_protocol:
Cells  pelleted from a 50 mL sample resuspended in 1 mL of TRIzol (Invitrogen, CA), throughly mixed and then refrozen.  The frozen TRIzol cell suspension was used for cell lysis by bead beating with 0.8 g of 0.1mm glass beads (Biospec Products) with 3 X 20 s bead beating treatments at 6,500 rpm in a Precellys 24 high-throughput tissue homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France). The RNA from each cell lysate was purified and DNaseI treated using the Qiagen RNeasy kit. The RNA quantity and quality assessed by Nanodrop and Bioanalyzer respectively. Purified RNA was depleted of rRNA using the Ribo-Zero rRNA Removal kit for Gram Positive Bacteria (Epicentre/Illumina). The sample was then concentrated with RNA Clean & Concentrate-5 (Zymo Research, CA) following the manufacturer’s protocol.
Depleted RNA was used as the starting material for the Epicentre ScriptSeq™ v2 RNA-Seq Library Preparation kit (Illumina compatible) utilising Epicentres Fail Safe PCR Enzyme mix (Epicentre, WI) and following the manufacturer’s protocol. cDNA, tagged with ScriptSeq adaptors (1-12), was eluted with 20 µl of Buffer EB provided in the Min-Elute PCR purification kit (Qiagen) according to the ScriptSeq™ RNA-Seq Library preparation kit protocol. Twelve PCR cycles were used during library amplification and samples were purified using Agencourt AmPureXP magnetic beads (Beckman Coulter, IN )  and eluted with 20 µl of buffer EB. The final mRNA Seq library was quantified with a Qubit Fluorometer (Invitrogen, CA) and library quality was assessed with an Agilent Bioanalyzer DNA Chip (Agilent, CA). Samples were pooled and the concentration determined.  Pools of barcoded samples were sent to Hudson Alpha for SR50 sequencing run on an Illumina Hiseq 2500 platform.

treatment_protocol: samples were grown with and without 2 mM formate

value: No formate


title: AG553 (unevolved Quad) No formate-1

description:
Clostridium thermocellum_1313 culture
Ct 21


title: AG553 (unevolved Quad) No formate-2

description:
Clostridium thermocellum_1313 culture
Ct 22


title: AG553 (unevolved Quad) No formate-4

description:
Clostridium thermocellum_1313 culture
Ct 24


title: Del-hpt (parental strain)  with 2 mM formate-4

description:
Clostridium thermocellum_1313 culture
Ct 20

source_name: ∆hpt trans 2 mM formate

value: {delta}hpt

value: 2 mM Formate


title: Del-hpt (parental strain)  with 2 mM formate-2

description:
Clostridium thermocellum_1313 culture
Ct 18


title: Del-hpt (parental strain)  with 2 mM formate-1

description:
Clostridium thermocellum_1313 culture
Ct 17


title: Del-hpt (parental strain)  with 2 mM formate-3

description:
Clostridium thermocellum_1313 culture
Ct 19


title: AG553 (unevolved Quad) + 2 mM formate-4

description:
Clostridium thermocellum_1313 culture
Ct 12

source_name: Q0 2 mM formate


title: Del-hpt (parental strain)  No formate-2

description:
Clostridium thermocellum_1313 culture
Ct 14

source_name: ∆hpt trans NO formate


title: AG553 (unevolved Quad) + 2 mM formate-2

description:
Clostridium thermocellum_1313 culture
Ct 10


title: Del-hpt (parental strain)  No formate-3

description:
Clostridium thermocellum_1313 culture
Ct 15


title: AG553 (unevolved Quad) + 2 mM formate-1

description:
Clostridium thermocellum_1313 culture
Ct 9


title: Del-hpt (parental strain)  No formate-4

description:
Clostridium thermocellum_1313 culture
Ct 16


title: Del-hpt (parental strain)  No formate-1

description:
Clostridium thermocellum_1313 culture
Ct 13


title: AG601 (“best” evolved strain) No Formate-4

description:
Clostridium thermocellum_1313 culture
Ct 8

source_name: Q1-150 SC 24  NO formate


title: AG553 (unevolved Quad) + 2 mM formate-3

description:
Clostridium thermocellum_1313 culture
Ct 11


title: AG601 (“best” evolved strain) No Formate-2

description:
Clostridium thermocellum_1313 culture
Ct 6


title: AG601 (“best” evolved strain) No Formate-1

description:
Clostridium thermocellum_1313 culture
Ct 5


title: AG601 (“best” evolved strain) + 2 mM formate-4

description:
Clostridium thermocellum_1313 culture
Ct 4

source_name: Q1-150 SC 24 + formate


title: AG601 (“best” evolved strain) + 2 mM formate-3

description:
Clostridium thermocellum_1313 culture
Ct 3


title: AG601 (“best” evolved strain) + 2 mM formate-2

description:
Clostridium thermocellum_1313 culture
Ct 2


title: AG601 (“best” evolved strain) + 2 mM formate-1

description:
Clostridium thermocellum_1313 culture
Ct 1


title: LSi3

city: Qingdao

first: Hualong

last: Wang

address: Songling road

institute: Ocean University of China

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Skeletonema marinoi

source_name: phytoplankton cell

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels.   RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA).   RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA).   RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment/phase

value: low silicate

tag: location

value: Jiaozhou Bay


title: LSi1


title: LSi2


title: LT3

value: low temperature


title: MtbRvTopoI_CS

city: Bangalore

first: Valakunja

last: Nagaraja

state: Karnataka

address: C V Raman Avenue

department: Department of Microbiology and Cell Biology

country: India

institute: Indian Institute of Science (IISc)

description: Chromatin immunoprecipitation against Topoisomerase I

data_processing:
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to M.tb H37Rv genome (NCBI accession NC_000962.2)
Mapping done using the Bowtie2 program (Version = 2.0.5) with default parameters
Coverage calculated using Bedtools (Version : 2.17.0)
Genome_build: M.tb H37Rv genome (NCBI accession NC_000962.2)
Supplementary_files_format_and_content: .bed file coverage calculated using Bedtools (Version : 2.17.0). Columns: Chromosome, Start, End, Name, Score, Strand, Interval, Read depth

organism: Mycobacterium tuberculosis H37Rv

source_name: Log/exponential phase Mtb H37Rv cells

growth_protocol: Mycobacterium tuberculosis H37Rv was grown at 37°C in 7H9 broth (Difco) supplemented with 0.2% glycerol, 0.05% Tween 80 and 10% albumin-dextrose-catalase (ADC, Middlebrook) or on 7H10 plates supplemented with 0.5% glycerol and 10% oleic acid-albumin-dextrose-catalase (OADC, Middlebrook). Logarithmic-phase cultures (exponential phase) were harvested at an optical density (OD600) of 0.4-0.6.

extract_protocol:
Crosslinked bacteria cells were sonicated and protein-DNA complexes were isolated with either anti-TopoI or anti-gyrA antibodies.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: M. tuberculosis cultures, either in exponential or stationary phase, were cross-linked with 1% formaldehyde for ten minutes at 37°C.

tag: chip antibody

value: anti-TopoI, monoclonal (generated in-house, lot# VNMNL2012)

tag: growth phase

value: Exponential


title: HT

value: high temperature


title: MtbRvGyr_CS

description: Chromatin immunoprecipitation against Gyrase A subunit

value: anti-gyrA (generated in-house, lot# VNMUH1996)


title: LT2


title: LT1


title: EP3

value: exponential phase


title: SP1

value: Stationary phase


title: SHM_Ubc_Duvelisib rep3

city: Boston

data_processing:
For SHM data, sequences with mean quality score < 20 and length < 50 were removed. The remained sequences were used to calculate mutation rate. Sequences obtained from each designed region were aligned to the reference sequence using BLASTN with alignment length > 200. Mutations to be considered valid were calculated after filtering steps, as previously described(Liu, M. et al.,Nature 2008). Briefly, mutations first had to pass a Neighbourhood Quality Standard (NQS) criteria requiring a minimum Phred score of 30 for the mutation itself, and 20 for the five adjacent bases on either side. Mutations that were within five bases of more than two additional mutations were excluded. Mutations within two bases of a deletion or insertion were also excluded. In addition, bases with mutation rate > 0.01 were excluded as a result of overwhelming influence of sequence error or SNP, of which bases with mutation rate > 0.2 were further regarded as SNP and were excluded. Finally, the average base mutation rate of 1-200 bp passing the above criteria were calculated from forward sequence, as well as reverse sequences. For average base mutation rates of C-to-T or G-to-A transitions, only C or G bp sites we counted.
Supplementary_files_format_and_content: For SHM data, tab-delimited text files give mutation information for each base pair incuding mut frequency for all mut, particular C>T|G>A and others. Bases to fail to pass filter criteria were showen as 'NA'.

source_name: CSR activated B cells

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were cultured in RPMI 1640 medium supplemented with 10% FBS and activated with anti-CD40 plus IL-4 for 4 days to generate CSR-activated B cells, and treated with duvelisib.

extract_protocol:
Cells were lysed in lysis buffer (NaCl 200 mM, Tris.HCl 100 mM, EDTA 5mM, SDS 0.2%)  containing 10 μg/ml Proteinase K  at 56°C overnight. Genomic DNA was precipitated with isopropanol at room temperature, washed in ethanol 70% and resuspended in TE buffer (10mM Tris-HCl plus 1mM EDTA)
Phusion High Fidelity DNA polymerase was used to amplify selected regions from template genomic DNA. Amplification products were purified using PCR purification kit and GEL extraction kit and sequenced bi-directionally in a Mi-Seq Illumina sequencing platform.

value: spleen

value: 8-12 weeks

tag: genotype

value: WT

value: splenic B cells activated with anti-CD40 plus IL-4 for 4 days

value: duvelisib


title: EP1


title: SHM_Ubc_Duvelisib rep1

extract_protocol:
Cells were lysed in lysis buffer (NaCl 200 mM, Tris.HCl 100 mM, EDTA 5mM, SDS 0.2%)  containing 10 μg/ml Proteinase K  at 56°C overnight. Genomic DNA was precipitated with isopropanol at room temperature, washed in ethanol 70% and resuspended in TE buffer (10mM Tris-HCl plus 1mM EDTA)
Phusion High Fidelity DNA polymerase was used to amplify selected regions from template genomic DNA. Amplification products were purified using PCR purification kit and GEL extraction kit and sequenced bi-directionally in a Mi-Seq Illumina sequencing platform

tag: tissue


title: AG601 (“best” evolved strain) No Formate-3

description:
Clostridium thermocellum_1313 culture
Ct 7

value: No formate


title: DP3

value: declining phase


title: SHM_Ubc_Idelalisib rep2

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were cultured in RPMI 1640 medium supplemented with 10% FBS and activated with anti-CD40 plus IL-4 for 4 days to generate CSR-activated B cells, and treated with idelalisib.

tag: age

value: idelalisib


title: SHM_Ubc_Idelalisib rep1


title: DP2


title: SHM_Ubc_Idelalisib rep3


title: SP3


title: SHM_Ubc_DMSO rep3

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were cultured in RPMI 1640 medium supplemented with 10% FBS and activated with anti-CD40 plus IL-4 for 4 days to generate CSR-activated B cells, and treated with control DMSO.

value: DMSO


title: SHM_Ubc_DMSO rep2


title: SHM_Ubc_DMSO rep1


title: SHM_KO_Smu_Duvelisib rep3

value: AID -/-


title: SHM_KO_Smu_Duvelisib rep2


title: SHM_KO_Smu_Idelalisib rep3


title: SHM_KO_Smu_Idelalisib rep1

value: not applicable


title: SHM_KO_Smu_DMSO rep2


title: SHM_Smu_Duvelisib rep3


title: SHM_Smu_Duvelisib rep2


title: SHM_KO_Smu_DMSO rep1


title: SHM_Smu_Idelalisib rep3

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were cultured in RPMI 1640 medium supplimented with 10% FBS and activated with anti-CD40 plus IL-4 for 4 days to generate CSR-activated B cells, and treated with idelalisib.


title: Alveolar EpCAM pos 2

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 1.8.4 pipeline was used to generate the sequence data.
Reads were aligned to the mouse genome by Rsubread version 1.22.2
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: normal lung tissue

tag: mouse

value: Alveolar cells

tag: facs gate

value: EpCAM pos CD104 lo 2


title: EpCAM neg (non epithelial) 2

value: Non-epithelial cells

value: EpCAM neg 2


title: SP2

value: Jiaozhou Bay


title: EpCAM neg (non epithelial) 1

value: EpCAM neg 1


title: EpCAM neg (non epithelial) 3

value: EpCAM neg 3


title: SHM_Smu_Idelalisib rep1

value: spleen

value: 8-12 weeks


title: SHM_Ubc_Duvelisib rep2

value: WT

value: splenic B cells activated with anti-CD40 plus IL-4 for 4 days


title: SHM_Smu_DMSO rep3

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were cultured in RPMI 1640 medium supplimented with 10% FBS and activated with anti-CD40 plus IL-4 for 4 days to generate CSR-activated B cells,  and treated with DMSO as control.

value: splenic B cells activated with anti-CD40 plus IL-4  for 4 days


title: Airway CD24L 2

value: Airway luminal cells (enriched in club cells)

value: EpCAM pos CD104 pos CD24lo 2


title: Airway CD24L 1

value: EpCAM pos CD104 pos CD24lo 1


title: SHM_KO_Smu_Duvelisib rep1

value: AID -/-

value: duvelisib


title: SHM_KO_Smu_Idelalisib rep2

value: idelalisib


title: Airway CD24H 3

value: Airway luminal cells (enriched in ciliated cells)

value: EpCAM pos CD104 pos CD24hi 3


title: Airway CD24H 2

value: EpCAM pos CD104 pos CD24hi 2


title: Airway CD24H 1

value: EpCAM pos CD104 pos CD24hi 1


title: SHM_Smu_DMSO rep1

data_processing:
For SHM data, sequences with mean quality score < 20 and length < 50 were removed. The remained sequences were used to calculate mutation rate. Sequences obtained from each designed region were aligned to the reference sequence using BLASTN with alignment length > 200. Mutations to be considered valid were calculated after filtering steps, as previously described(Liu, M. et al.,Nature 2008). Briefly, mutations first had to pass a Neighbourhood Quality Standard (NQS) criteria requiring a minimum Phred score of 30 for the mutation itself, and 20 for the five adjacent bases on either side. Mutations that were within five bases of more than two additional mutations were excluded. Mutations within two bases of a deletion or insertion were also excluded. In addition, bases with mutation rate > 0.01 were excluded as a result of overwhelming influence of sequence error or SNP, of which bases with mutation rate > 0.2 were further regarded as SNP and were excluded. Finally, the average base mutation rate of 1-200 bp passing the above criteria were calculated from forward sequence, as well as reverse sequences. For average base mutation rates of C-to-T or G-to-A transitions, only C or G bp sites we counted.
Supplementary_files_format_and_content: For SHM data, tab-delimited text files give mutation information for each base pair incuding mut frequency for all mut, particular  C>T|G>A and others. Bases to fail to pass filter criteria were showen as 'NA'.

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were cultured in RPMI 1640 medium supplemented with 10% FBS and activated with anti-CD40 plus IL-4 for 4 days to generate CSR-activated B cells, and treated with DMSO as control.

value: DMSO


title: SHM_Smu_DMSO rep2


title: SHM_Smu_Idelalisib rep2


title: Non-Basal 2

source_name: normal trachea tissue

value: Non basal cells

value: NGFR neg 2


title: HTGTS_PI3K-Mut rep3

data_processing:
For HTGTS data, we applied prinseq 0.2 to remove sequences with exact PCR duplicates, mean quality score < 20 and length < 50. Next, effect reads for each sample were recognized by designed barcode, primer and bait portion. Lastly,the barcode, primer and bait portion of the remained sequences were masked for alignment analysis to determine translocation junctions as previously described(Chiarle et al.,Cell 2011). Briefly, we aligned sequences to the mouse reference genome (GRCm37/mm9) or human genome (GRCh38/hg38) using BLAT, and then filtered artificial junctions by removing PCR repeats (reads with same junction position in alignment to the reference genome and a start position in the read less than 3 bp apart), invalid alignments (including alignment scores < 30, reads with multiple alignments having a score difference < 4 and alignments having 10-nucleotide gaps) and ligation artifacts (for example, random HaeIII restriction sites ligated to bait breaksite). Translocation junction position was determined based on the genomic position of the 5’ end of the aligned read.
Genome_build: mm9
Supplementary_files_format_and_content: For HTGTS data, BED files contain all obtained translocation junctions information including chromosome,corrdinate,read name,align score and strand.

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were cultured in RPMI 1640 medium supplemented with 10% FBS and activated with anti-CD40 plus IL-4 for 4 days to generate CSR-activated B cells. 24 h post activation cells were co-transduced with pMX-I-SceI retrovirus to induce double strand breaks and PI3K p110delta E1021K mutant retrovirus.

treatment_protocol: not applicable

value: spleen

value: 8-12 weeks

value: c-myc 25xI-SceI / PI3K p110delta E1021K mutant

value: splenic  B cells activated with anti-CD40 plus IL-4 for 4 days


title: Non-Basal 1

value: NGFR neg 1


title: SHM_Smu_Duvelisib rep1

growth_protocol: Splenic naïve B cells were purified via an anti-CD43 negative selection approach. The purified naïve B cells were cultured in RPMI 1640 medium supplimented with 10% FBS and activated with anti-CD40 plus IL-4 for 4 days to generate CSR-activated B cells, and treated with duvelisib.

value: WT

value: splenic B cells activated with anti-CD40 plus IL-4 for 4 days


title: Non-Basal 3

value: NGFR neg 3


title: Alveolar EpCAM pos 3

value: Alveolar cells

value: EpCAM pos CD104 lo 3


title: Airway CD24L 3

value: Airway luminal cells (enriched in club cells)

value: EpCAM pos CD104 pos CD24lo 3


title: HTGTS_PI3K-Mut rep1


title: Basal 1

value: Basal cells

value: NGFR pos 1


title: HTGTS_PI3K-Mut rep2