title: SA2-2d-S-Rep2

source_name: 2dpa fruit seeds

value: seeds

value: fruits of 2 days post pollination


title: BF-AO-MBR (SS)

status: Public on Aug 14 2019

type: SRA

city: muang

first: Dome

last: Adoonsook

state: ChiangMai

address: Suthep

country: Thailand

institute: Dome

description:
Bacteria
Sample 5
processed data file: Classification.txt
processed data file: BF-AO-MBR_SS_S5.report.pdf

library_source: transcriptomic

data_processing:
Sequencing was carried out by using Illumina MiSeq sequencing on an Illumina MiSeq device (Illumina Inc., San Diego, CA, USA) with 600 cycles (300 cycles for each paired read and 12 cycles for the barcode sequence) according to the manufacturer’s instructions.
Sequence analysis was conducted using the 16S-based metagenomics workflow of MiSeq Reporter version 2.6.2.3 (Illumina).
Samples were gathered into a single library for sequencing on Illumina MiSeq sequencing system which generated paired 300 bp reads.
Sequences were then demultiplexed based on index sequences.
Genome_build: V3 and V4 regions of the 16S rRNA gene.
Supplementary_files_format_and_content: Classification.txt: Tab-delimited text file includes Sample number 4 (BF-AO-MBR (SP)), Sample number 5 (BF-AO-MBR (SS)) and Sample number 6 (C-AO-MBR (SS)).

molecule: total RNA

organism: wastewater metagenome

source_name: Suspended sludge

extract_protocol:
Fast-DNA SPIN kit for soil (MP Biomedicals, Solon, OH, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: sample type

value: Suspended sludge

tag: mbr system

value: Biolfilm


title: C-AO-MBR (SS)

description:
Bacteria
Sample 6
processed data file: Classification.txt
processed data file: C-AO-MBR_SS_S6.report.pdf

value: Conventional


title: scPool: pus1Δ scS100 Rep2 -CMC

city: Cambridge

first: Thomas

middle: M

last: Carlile

state: Massachusetts

address: 77 Massachusetts Ave

department: Biology

country: USA

institute: MIT

data_processing:
Reverse reads were trimmed of 5′ amplicon sequence using cutadapt (-G)
Trimmed paired end reads collapsed using PEAR (default settings)
PCR duplicates collapsed using fastx_collapser
PCR duplicates collapsed using fastx_collapser
Sequences were trimmed of 3′ adapter (both pools) and 10 random Ns (yeast pools only) using cutadapt
Reads were mapped to bowtie indices of the pools with tophat2
Pseudouridylation was assessed using cutom python scripts (see text)
Genome_build: Bowtie indices made from fasta files of pool sequences
Supplementary_files_format_and_content: Tab delimited text files of peak values for pseudouridylation (see text)

organism: Saccharomyces cerevisiae

source_name: Yeast Pool

extract_protocol:
Oligo pools (yeast, Twist Biosciences; human Custom Array) were PCR amplified, and in vitro transcribed into RNA, which was then gel purified, folded, and pseudouridylated with a pseudouridine synthase activity source.
RNA was phenol:chloroform extracted from pseuoduridylation reactions, treated with 0.4 M CMC, followed by reversal of CMC modification in bicarbonate buffer. RT was performed, and truncated cDNAs were size selected, followed by circularization & PCR amplification.
OTHER: Pseduo-seq

tag: pus activity source

value: S100 extract from pus1delta- Yeast

tag: cmc use

tag: bowite fasta


title: Degradation_Col_2h_rep3

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

country: China

institute: Institute of Genetics and Developmental Biology

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 2 hours
C3-2_L5_313X13

data_processing:
CLIP-seq reads were trimed using FASTX toolkit. PCR duplications were excluded. Clean tags were then aligned to the Arabidopsis genome (TAIR10) using NovoAlign. Pyicoclip was used to identify AtPABs binding clusters.
Ribosome profiling reads were trimed using FASTX toolkit. PCR duplications were excluded. Clean tags were then aligned to the Arabidopsis genome (TAIR10) using TopHat2. Read counts of genes were counted using htseq-count.
RNA-seq reads were aligned to the Arabidopsis genome (TAIR10) using TopHat2. Read counts of genes were counted using htseq-count. Differentially expressed genes were detected using R package edgeR.
Poly(A) tail reads were trimmed and aligned to the Arabidopsis genome (TAIR10) using Bowtie2.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files were generated using bedGraphToBigWig program

organism: Arabidopsis thaliana

growth_protocol: The wild-type Col, atpabs mutants and AtPABs complementary lines were grown on Murashige and Skoog plates with 3% Suc for 14 days

extract_protocol:
The seedlings were ground into a fine power in liquid nitrogen and processed using Trizol reagent (Invitrogen).
CLIP-seq libraries generated from Col and AtPABs complementary lines were constructed following the published method in Arabidopsis (Zhang et al., 2015). Ribosome profiling libraries generated from Col and atpabs were constructed following the published method in Arabidopsis (Juntawong et al., 2014). Strand-specific RNA-Seq libraries generated from Col, atpabs were constructed mRNA-Seq library by SMART method (Levin et al., 2010).PolyA-seq library generated from Col was constructed following treated total RNA with RQ1 DNase and RNase T1, purified poly(A)-containing RNA fragments and ligated with adaptors.

treatment_protocol: The seedlings grown at 23°C under 16 h of light followed by 8 h of darkness

tag: ecotype background

value: Col

tag: developmental stage

value: 2-week seedlings

tag: treatment

value: cordycepin for 2 hours


title: Degradation_Col_2h_rep2

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 2 hours
C2-2_L5_307X07


title: BAR-HP_K6

type: RNA

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

description: Gene expression of lean controls

hyb_protocol: For  each cRNA is hybridised on 8x60K microarrays at 65 ◦C for 17 h using Agilent’s recommended hybridisation chamber and oven. Afterwards microarrays are washed once with the Agilent Gene Expression Wash Buﬀer 1 for one minute at ambient temperature followed by a second wash with preheated (37 ◦C) Gene Expression Wash Buﬀer 2 for one minute.

scan_protocol: Fluorescence signals on microarrays are detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron for SurePrint G3 Gene Expression Microarrays and  5 micron for HD Microarray formats, generating a 20 bit TIFF ﬁle.FSlides were scanned using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities. Data was filtered using 0.1 quantile cutoff to eliminate low level signals.

organism: Homo sapiens

source_name: vastus lateralis

label_protocol: Cy3-labeled cRNA. For labelling, the Low Input QuickAmp Labeling Kit (Agilent Technologies) is used to generate ﬂuorescent cRNA (complementary RNA). For 1st strand synthesis, either oligo-dT primer or a random primer / oligo-dT primer mixture (WT primer) is used. After 2nd strand synthesis, an in vitro transcription for synthesis of cRNA labelled with cyanine 3-CTP is performed. Please refer the summary ﬁle for details regarding the used primer, yield of cRNA as well as cy3 incorporation rate

extract_protocol: total RNA extracted following the manufacturer's recommendations, miRNA micro kit ( Qiagen, Hilden, Germany), The protocol includes separation of organic and aqueous layers, and an on-column DNase digestion

treatment_protocol: No treatment RNA extracted from frozen tissu

tag: tissu

value: Skeletal muscle

tag: group

value: Control

tag: time point

value: No metabolic surgery


title: SA2-2d-C-Rep2

city: Athens

first: Biyao

last: Zhang

state: GA

address: CAGT, Rm120, 111 Riverbend RD

department: Horticulture

institute: University of Georgia

data_processing:
Reads were trimed with 5' end 9bp and poly A contaimination using trimmomatic program
Adaptors were cutted with cutadapt
Clean reads mapped to ITAG3.2 Released Tomato Genome using hisat2
Values were normalized into TPM
Genome_build: ITAG3.2 Released Tomato Genome
Supplementary_files_format_and_content: TPM values for each Sample

organism: Solanum pimpinellifolium

source_name: 2dpa fruit columella

growth_protocol: Plants were grown in 10x10x20 cm pots under natural light supplemented with artificial light (16/8 hr light/dark cycle) in the greenhouse in Athens, GA, USA, 2017. The daytime temperature 80-85F and the night time temperature  60-65F, humidity 60%. Approximately 5~8 fruits were collected for each samples from 2 months plants.

extract_protocol:
During the collection, all fruits were cut inton halfs and immediately immersed in ice-cold RNAlater (QIAGEN) solution at five times the volume of the sample in order to prevent RNA degradation. After sample collection, vacuum infiltration was applied until tissues sunk to the bottom of RNAlater solution. The tissues were then stored in RNAlater at -80℃.  Dissection were done by forceps under a dissection microscope and immediately put into a 1.5 ml eppendorf tube in 1 ml of fresh RNAlater that was kept on ice. Columella and septa were isolated as columella part; seeds and placenta as seed part; remaining as pericarp part. The samples were stored at -80 ℃ prior to the RNA extraction.RNA extraction was conducted using Trizol® (Invitrogen Inc. USA) following manufacture’s recommendation.
3'Tag mRNA library were constructed by following paper "Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure" of Meyer et al., 2011.

tag: tissue

value: columella

tag: ecotype

value: accession LA1589

tag: genotype

value: SUN NIL

tag: Stage


title: Degradation_Col_8h_rep1

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 8 hours
C1-8_L5_303X03

value: cordycepin for 8 hours


title: BAR-DK_K15

description: Gene expression of lean controls


title: scPool: pus1Δ scS100 Rep2 +CMC

value: 0.4M CMC


title: SA2-2d-P-Rep2

source_name: 2dpa fruit pericarp

value: pericarp


title: Degradation_Col_2h_rep1

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 2 hours
C1-2_L5_301X01


title: scPool: pus1Δ scS100 Rep1 -CMC

value: S100 extract from pus1delta-Yeast


title: Degradation_Col_1h_rep3

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 1 hour
C3-1_L5_312X12

value: cordycepin for 1 hour


title: BF-AO-MBR (SP)

description:
Bacteria
Sample 4
processed data file: Classification.txt
processed data file: BF-AO-MBR_SP_S4.report.pdf

source_name: Sponge biomass

value: Sponge biomass

value: Biolfilm


title: SA1-2d-S-Rep2

value: seeds

value: wildtype

value: fruits of 2 days post pollination


title: SA1-2d-C-Rep2


title: Degradation_Col_1h_rep2

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 1 hour
C2-1_L5_306X06

value: Col

value: 2-week seedlings


title: scPool: pus1Δ scS100 Rep1 +CMC

value: S100 extract from pus1delta- Yeast


title: scPool: wt scS100 Rep2 -CMC

value: S100 extract from Wild Type Yeast


title: SA1-2d-P-Rep2


title: scPool: wt scS100 Rep2 +CMC


title: scPool: wt scS100 Rep1 -CMC


title: Degradation_Col_1h_rep1

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 1 hour
C1-1_L5_396X96


title: Degradation_Col_0.5h_rep3

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 0.5 hour
C3-0-5_L5_311X11

value: cordycepin for 0.5 hour


title: scPool: wt scS100 Rep1 +CMC


title: Degradation_Col_0.5h_rep2

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 0.5 hour
C2-0-5_L5_305X05


title: Degradation_Col_0.5h_rep1

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 0.5 hour
C1-0-5_L5_395X95


title: scPool1: pus7Δ scS100 -CMC

data_processing:
Library strategy: Pseduo-seq
Reverse reads were trimmed of 5′ amplicon sequence using cutadapt (-G)
Trimmed paired end reads collapsed using PEAR (default settings)
PCR duplicates collapsed using fastx_collapser
PCR duplicates collapsed using fastx_collapser
Sequences were trimmed of 3′ adapter (both pools) and 10 random Ns (yeast pools only) using cutadapt
Reads were mapped to bowtie indices of the pools with tophat2
Pseudouridylation was assessed using cutom python scripts (see text)
Genome_build: Bowtie indices made from fasta files of pool sequences
Supplementary_files_format_and_content: Tab delimited text files of peak values for pseudouridylation (see text)

source_name: Yeast Pool 1

extract_protocol:
Oligo pools (yeast, Twist Biosciences; human Custom Array) were PCR amplified, and in vitro transcribed into RNA, which was then gel purified, folded, and pseudouridylated with a pseudouridine synthase activity source.
RNA was phenol:chloroform extracted from pseuoduridylation reactions, treated with 0.4 M CMC, followed by reversal of CMC modification in bicarbonate buffer. RT was performed, and truncated cDNAs were size selected, followed by circularization & PCR amplification.

value: S100 extract from pus7Δ Yeast


title: scPool1: pus7Δ scS100 +CMC


title: Degradation_Col_0h_rep3

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 0 hour
C3-0_L5_310X10

value: cordycepin for 0 hour


title: SA1-2d-C-Rep1

value: columella

value: accession LA1589


title: SA2-2d-C-Rep1

value: SUN NIL


title: SA2-2d-P-Rep1

value: pericarp


title: Degradation_Col_0h_rep1

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 0 hour
C1-0_L5_394X94


title: scPool1: wt scS100 -CMC


title: SA2-2d-S-Rep1


title: SA1-2d-P-Rep1


title: SA1-2d-S-Rep1


title: Degradation_Col_0h_rep2

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 0 hour
C2-0_L5_304X04


title: ret965

status: Public on Aug 13 2019

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

description: RetinaExpressionmatrix.txt

data_processing:
StrandNGS Software was used to align, adaptor trim, and call differential expression.
Aligned Against:Transcriptome and genome together (with novel splices;) Transcriptome used:RefSeq Genes and Transcripts (2013.04.01); Maximum number of Novel Splices allowed : 1; Minimum percent identity : 90; Maximum percent gaps : 5; Minimum aligned read length : 25;Number of matches to output per read : 1; Ignore reads with matches more than : 5 ;Fixed trim on 5' end : 5 ;Fixed trim on 3' end : 2
DeSeq quantitation, normalized to male vehicle control.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Abundance measurements- Expression matrix

organism: Mus musculus

source_name: Retina

extract_protocol:
AllPrep DNA/RNA Mini kits (Qiagen, Germantown, MD)
TruSeq RNA Library Prep Kit v2

tag: Sex

value: Male

value: Vehicle (Sunflower Oil)

tag: age

value: 3 Months


title: ret966

description: RetinaExpressionmatrix.txt


title: scPool1: wt scS100 +CMC

value: 0.4M CMC


title: ret964

description: RetinaExpressionmatrix.txt


title: ret954

description: RetinaExpressionmatrix.txt

value: Female

value: Tamoxifen


title: ret958

description: RetinaExpressionmatrix.txt


title: ret959

description: RetinaExpressionmatrix.txt


title: ctx966

description: CortexExpressionmatrix.txt

source_name: Cortex


title: ret963

description: RetinaExpressionmatrix.txt


title: ret951

description: RetinaExpressionmatrix.txt


title: ret955

description: RetinaExpressionmatrix.txt


title: ret952

description: RetinaExpressionmatrix.txt


title: ret960

description: RetinaExpressionmatrix.txt


title: ret953

description: RetinaExpressionmatrix.txt


title: ret957

description: RetinaExpressionmatrix.txt


title: ctx965

description: CortexExpressionmatrix.txt


title: ret961

description: RetinaExpressionmatrix.txt


title: ctx963

description: CortexExpressionmatrix.txt


title: ctx964

description: CortexExpressionmatrix.txt


title: ctx962

description: CortexExpressionmatrix.txt


title: ctx959

description: CortexExpressionmatrix.txt


title: ctx960

description: CortexExpressionmatrix.txt


title: ctx961

description: CortexExpressionmatrix.txt


title: ctx958

description: CortexExpressionmatrix.txt


title: ctx955

description: CortexExpressionmatrix.txt


title: ctx957

description: CortexExpressionmatrix.txt


title: ctx953

description: CortexExpressionmatrix.txt


title: 499_2762

city: Philadelphia

first: Lexus

last: Johnson

state: Pennsylvania

address: 421 Curie Blvd, 532

department: Radiation Oncology

institute: University of Pennsylvania

library_source: genomic

data_processing:
Library strategy: whole exome sequencing
Orginal intensity file (.bcl) was transferred to fastq with tool bcl2fastq2, which also trimmed adaptor sequence. Individual with multiple lines were further merged with "cat" command.
Fastq files were further mapped to mm10 whole genome using bwa-0.7.15 with parameters "mem -M -t 16". Duplicates were marked using MarkDuplicates from Picard tools
Duplicates were marked using MarkDuplicates from Picard tools version 2.10.1. Systematic errors in base quality scores were detected and recalibrated using GATK’s BaseRecalibrator and ApplyBQSR. Known variants for recalibration were downloaded from the Mouse Genome Project SNP and Indel release version 5.
Mutation calling was done according to Canopy manual using UnifiedGenotyper.
Genome_build: mm10
Supplementary_files_format_and_content: vcf file of all samples

molecule: genomic DNA

source_name: in vivo sorted tumor cells

growth_protocol: Respective cells were injected subcutaneously into mice and sorted on Day 16 for whole exome sequencing

extract_protocol:
DNA was extracted using quick-DNA kit by Zymo Research
Libraries were prepared using SureSelectXT HS and Sureselect XT Mouse All exon kits from Agilent

tag: cell type

value: melanoma

tag: strain

tag: cell line


title: 499 GRKO 1

data_processing:
Basecalls performed and aligned using cellranger mkfastq function (bcl2fastq wrapper) and mm10 reference genome
Demultiplexed counts generated by cellranger count function, represented by final .mtx function
Genome_build: mm10
Supplementary_files_format_and_content: .mtx file, gene matrix, barcodes.tsv and genes.tsv in processed_all folder

molecule: polyA RNA

source_name: Melanocyte

growth_protocol: Subcutaneous tumor injection into B6 WT mice, tumors were harvested at d17 and CD45+ cells were isolated by FACS

extract_protocol: 10x 3' kit v2

treatment_protocol: No treatment

value: Melanocyte

tag: genotype/variation

value: IFNgR KO


title: B16_2751


title: B16_2752


title: 499 GRKO 2


title: ctx952

description: CortexExpressionmatrix.txt


title: ctx951

description: CortexExpressionmatrix.txt


title: 499 WT 1

value: WT


title: 499 WT 2


title: SRSF2_MUT7_MS023_GSK591_D7

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Basecalls performed using CASAVA
Sequenced reads were mapped to mm9 genome using STAR version 2.4.2a with default parameters
FPKM and differential expression were calculated using the htseq package and edgeR
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file with gene level abundance counts generated with htseq/edger

source_name: Primary MLL-AF9 mouse leukemia

growth_protocol: Generation and genotyping of the Srsf2P95H/+ conditional knock-in mice as well as MLL-AF9/Vav-cre Srsf2WT/WT and MLL-AF9/Vav-cre Srsf2P95H/WT (all on C57BL/6 backgrounds) are as previously described [Cancer cell 27, 617-630 (2015)]. MLL-AF9 bone marrow transplantation assays were performed as described previously [Nat Med 22, 672-678 (2016)]

extract_protocol:
RNA was isolated from cells using the Purelink RNA Mini Kit (Thermo Fisher Scientific; 12183018A)following the manufacturer’s protocol.
Directional RNA library was prepared according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.

treatment_protocol: Primary murine MLL-AF9 leukemia cell lines were generated from bone marrow cells of leukemia-bearing mice and maintained in IMDM/15% FCS supplemented with L-glutamine, mSCF (25ng/mL), mIL3 (10ng/mL) and mIL6 (10ng/mL)

value: Bone marrow cells

value: Primary MLL-AF9 mouse leukemia


title: SRSF2_MUT7_MS023-100nM_D7


title: SRSF2_MUT7_CTRL_D7


title: 499_2755


title: SRSF2_MUT6_MS023_GSK591_D7


title: SRSF2_MUT6_MS023-100nM_D7


title: ctx954

description: CortexExpressionmatrix.txt


title: genomic DNA from cervical scrapes 6 [Sample9_x572]

type: genomic

city: Henan

first: wang

middle: rui

last: jie

state: zhengzhou

address: No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, Henan, China

institute: The Third Affiliated Hospital of Zhengzhou University, Zhengzhou University

description: squamous cervical carcinoma sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: ChAMP package v2.9.9; the non_normalized.txt contains unmethylated and methylated signal intensities

label: biotin

source_name: squamous cervical carcinoma sample

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: squamous cervical carcinoma sample

tag: sample id

value: cervical scrapes 6


title: genomic DNA from cervical scrapes 9 [Sample10_x250]

description: squamous cervical carcinoma sample

value: cervical scrapes 9


title: genomic DNA from cervical scrapes 3 [Sample8_x461]

description: squamous cervical carcinoma sample

value: cervical scrapes 3


title: SRSF2_MUT6_GSK591-25nM_D7


title: SRSF2_MUT7_GSK591-25nM_D7


title: SRSF2_MUT5_MS023_GSK591_D7


title: SRSF2_MUT6_CTRL_D7


title: 499_2761


title: SRSF2_MUT5_GSK591-25nM_D7


title: SRSF2_MUT5_MS023-100nM_D7


title: SRSF2_MUT5_CTRL_D7


title: WT_N_CTRL_D7


title: WT_N_MS023-100nM_D7


title: WT_N_MS023_GSK591_D7


title: genomic DNA from cervical scrapes 8 [Sample6_x660]

description: cervical intraepithelial neoplasia grade 3 sample

value: cervical scrapes 8


title: WT_L_GSK591-100nM_D7


title: WT_L_MS023_GSK591_D7


title: WT_N_GSK591-100nM_D7


title: genomic DNA from cervical scrapes 7 [Sample3_x158]

description: normal cervical sample

source_name: normal cervical sample

value: normal cervical sample

value: cervical scrapes 7


title: WT_M_MS023_GSK591_D7


title: WT_M_GSK591-100nM_D7


title: WT_M_MS023-100nM_D7


title: WT_M_CTRL_D7


title: WT_L_MS023-100nM_D7


title: genomic DNA from cervical scrapes 1 [Sample1_x893]

description: normal cervical sample

value: cervical scrapes 1


title: genomic DNA from cervical scrapes 4 [Sample2_x130]

description: normal cervical sample

value: cervical scrapes 4


title: Som138

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

description:
ENS_counts.tsv
gene_counts.tsv
normalized_gene_counts.tsv

data_processing:
Illumina RTA v1.12 was used for base calling, and Illumina bc12fastq v2.20 for demultiplexing and fastq file generation
Sequenced reads were pre-processed using Trimmomatic and Flexbar. Reads were aligned to GRCm38 genome using STAR aligner with parameters trimLeft=10, minTailQuality=15, minAverageQuality=20, and minReadLength=30.
Aligned reads were converted to gene counts using featureCounts. Outputs for different cells were merged into a single file (ENS_counts.tsv) using custom Python code
Ensembl names were converted to gene names using Ensembl's Mus_musculus.GRC38.86.gtf file (gene_counts.tsv)
Reads were normalized using scran, and normalized values are stored in normalized_gene_counts.tsv
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited text files. ENS_counts.tsv contains raw counts, with genes labeled by their Ensembl ENS numbers. gene_counts.tsv contains raw counts, with genes labeled by their gene names. normalized_gene_counts.tsv contains normalized (scran) counts of cells that passed quality control

source_name: Neural mature cell

extract_protocol:
cytosol aspiration via patch-clamp pipettes
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Neural mature cell

tag: driver line

value: Sst Cre driver line

value: OLM

tag: quality control

value: Passed


title: genomic DNA from cervical scrapes 5 [Sample5_x906]

description: cervical intraepithelial neoplasia grade 2 sample

value: Female

value: cervical scrapes 5


title: Som131


title: Som134


title: WT_L_CTRL_D7

value: Bone marrow cells


title: Som137


title: Som127


title: Som124


title: Som109


title: Som126


title: genomic DNA from cervical scrapes 2 [Sample4_x472]

description: cervical intraepithelial neoplasia grade 1 sample

value: cervical scrapes 2


title: Som128


title: genomic DNA from cervical scrapes 10 [Sample7_x311]

source_name: cervical intraepithelial neoplasia grade 1 sample

value: cervical scrapes 10


title: Som116


title: Som115


title: Som47


title: Som48


title: Som14


title: Som45


title: Som11


title: Som17


title: H60

value: Htr3a Cre driver line


title: Som7


title: Som6


title: Som5


title: Som9


title: H53


title: H52


title: H48


title: H46


title: Som105


title: H38


title: H42


title: H39


title: H33


title: H26


title: H22


title: H20


title: H32


title: Som43


title: H31


title: H30


title: H12


title: H16


title: H57


title: H11


title: H9


title: H6


title: H2


title: H35


title: ATH575 dataset 2

city: Newark

first: Pamela

middle: J

last: Green

state: DE

address: 15 Innovation Way

department: Plant and Soil Sciences

institute: Delaware Biotechnology Institute

description:
PolyA- RNA / rRNA-depleted
5'p PARE

data_processing:
Basecalling is done using bcl2fastq_1.8.3
Illumina HiSeq 2500
Sequences were trimmed of adapter reads; and quality assessed using FastQC program
Reads mapped to Arabidopsis TAIR10 genome using Bowtie v0.12.8
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: RNA-seq: tab-limited txt files with FPKM counts; PARE: _20s txt file

source_name: two-week-old seedling

growth_protocol: Seedlings grown on 1X MS, 1% (w/v) sucrose, 1% (w/v) agar for two-weeks in growth chamber (21C; 16h day: 8h night)

extract_protocol:
RNA-seq libraries: 50 ug polyA+ (2x enriched) or polyA- (rRNA-depleted by Ribo-zero Epicenter) prepared as per ScriptSeq v2.0 instructions; PARE libraries prepared as per German et al., (2008) and polyA- libraries additionally required >200nt selection and polyA-polymerase treatments
RNA-seq (50nt single-end)  and PARE sequenced on Illumina HiSeq 2500

tag: replicate


title: ATH237

description:
PolyA+ RNA
5'p PARE

extract_protocol: RNA-seq libraries: 50 ug polyA+ (2x enriched) or polyA- (rRNA-depleted by Ribo-zero Epicenter) prepared as per ScriptSeq v2.0 instructions; PARE libraries prepared as per German et al., (2008) and polyA- libraries additionally required >200nt selection and polyA-polymerase treatments

value: WT


title: ATH467 dataset 2

description:
PolyA- RNA / rRNA-depleted
5'p PARE


title: ATH362 dataset 2

description:
PolyA+ RNA
5'p PARE


title: ATH295 dataset 2

description:
PolyA+ RNA
5'p PARE


title: ATH293 dataset 2

description:
PolyA+ RNA
Cap-PARE


title: ATH568 dataset 2

description:
PolyA- RNA / rRNA-depleted
Strand-specific RNA-seq
genes.count_tracking, genes.fpkm_tracking


title: ATH567 dataset 2


title: ATH678 dataset 2

description:
PolyA+ RNA
Strand-specific RNA-seq
genes.count_tracking, genes.fpkm_tracking


title: ATH292 dataset 2

description:
PolyA+ RNA
Cap-PARE


title: ATH677 dataset 2


title: ATH676 dataset 2


title: ATH363 dataset 2

description:
PolyA+ RNA
5'p PARE


title: ATH589 dataset 2


title: ATH566 dataset 2


title: ATH601 dataset 2


title: ATH600 dataset 2


title: ATH591 dataset 2


title: ATH590 dataset 2


title: ATH599 dataset 2


title: ATH576 dataset 2

description:
PolyA- RNA / rRNA-depleted
5'p PARE


title: HD5 NT

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

data_processing:
Reads were mapped on the hg19 Homo sapiens reference assembly using TopHat v2.0.6. Raw counts were computed using the featureCounts package and the latest RefSeq annotation downloaded from the UCSC server (https://genome.ucsc.edu/cgi-bin/hgTables). Differential expression analysis was performed using R and the DESeq2 package. Genes with abs (log2(Fold Change)) >0.5, and p<0.05 were retained for downstream analysis considered.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files generated from BAM alignments

source_name: Human macrophages

growth_protocol: RPMI-1640 without serum, 1% PenStrep

extract_protocol:
Total RNA was isolated using TRIzol Reagent, following manufacturer's instructions
Library preparation was performed using the TruSeq v2 Unstrated RNA-seq kit (Illumina)

treatment_protocol: Transcriptome analysis of human macrophages treated (6 hours) with rNAPRT, rNAMPT (1µg/ml) or LPS (2 µg/ml; Sigma-Aldrich)

value: Human macrophages


title: HD4 NAMPT


title: HD5 LPS


title: HD5 NAMPT


title: HD5 NAPRT


title: HD4 NAPRT


title: HD4 NT


title: HD4 LPS


title: HD2 NT


title: HD2 NAPRT


title: HD2 LPS


title: HD2 NAMPT


title: 10-PHH-J

city: Jerusalem

first: Avner

last: Ehrlich

address: Silberman 3-512, Edmond J. Safra Campus (Givat Ram)

department: Bioengineering

country: Israel

institute: The Hebrew University of Jerusalem

description: in vivo primary reference

data_processing:
Sequenced on Illumina NextSeq500 with single-end, 86 bp reads using the High Output V2 Kit.
Sequencing reads were mapped to the UCSC human transcriptome (genome build hg19) using Bowtie 2 and expression levels of all genes were quantified using RSEM
RSEM yielded an expression matrix of inferred gene counts. Differential expression analysis was performed using R package DESeq2 using default parameters.
Reported are p-values from a negative binomial Wald-test.
Overall, we found 1609 genes that showed significant differential mRNA expression between Control and 9CLA matured cells cell populations with a BH-FDR<0.01.
Genome_build: hg19
Supplementary_files_format_and_content: counts; TMP (transcripts per million) done directly from the RSEM expression matrix

source_name: Isolated primary human hepatocytes

growth_protocol: Cryopreserved human hepatocytes (Gibco, USA) were thawed and plated on growth factor reduced Matrigel™ in Hepatocyte Maintenance Medium (HMM; Lonza, Germany) according to manufacturer instructions.

extract_protocol:
RNA extraction was performed using RNeasy Micro kit (Qiagen, USA) according to manufacturer’s direction. Library preparation and RNA sequencing were performed by the Hebrew University Center for Genomic Technologies.
Library construction was conducted using Illumina TruSeq RNA Library Prep V2 Kit (Illumina, USA) according to manufacturer's protocol and sequenced on Illumina NextSeq500 with single-end, 86 bp reads using the High Output V2 Kit.

value: Cryopreserved human hepatocytes

tag: treatment

value: Matrigel GFR

tag: growth condition

value: 4 days in HMM media (lonza)


title: 09-PHH1

description: in vivo primary reference

tag: tissue


title: 18-9CLA3

description: microbial derived lipids matured hepatocytes

source_name: hPSC-derived heptocytes

growth_protocol: Cells were seeded on Matrigel™ in mTeSR-1 medium and allowed to reach 50% confluence.   On days 1-3, cells were cultured in RPMI-1640, supplemented with 100U penicillin, 100µg/ml streptomycin, 1X B27 (Gibco, USA), 100ng/ml activin A (R&D Systems, USA), 50ng/ml Wnt3A (R&D Systems, USA) and 10ng/ml HGF (PeproTech, UK). On days 4-8, cells were cultured in KnockOut DMEM (Gibco) supplemented with 100U penicillin (Biological Industries, Israel), 100µg/ml streptomycin(Biological Industries, Israel), 20% KnockOut serum replacement (Gibco, USA), 1% non-essential amino acids (Biological Industries, Israel), 2mM L-Alanyl-L-Glutamine (Biological Industries, Israel), 0.1mM 2-mercaptoethanol (Sigma-Aldrich, USA) and 1% DMSO (Sigma Aldrich, USA). On days 9-14, cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM; Biological Industries, Israel) supplemented with 100U penicillin (Biological Industries, Israel), 100µg streptomycin (Biological Industries, Israel), 20ng/ml Oncostatin M (R&D Systems, USA), 4ng/ml FGF2 (PeproTech, UK), 1% Insulin-Transferrin-Selenium (ITS) supplement (Gibco, USA) and 0.5μM Dexamethasone (Sigma Aldrich, USA). On days 15-18, cells were cultured in Williams’ medium E (Sigma Aldrich, USA) supplemented with 100U penicillin (Biological Industries, Israel), 100µg streptomycin (Biological Industries, Israel), 2mM L-Alanyl-L-Glutamin (Biological Industries, Israel), 0.5μM Dexamethasone (Sigma-Aldrich, USA), 10ng/ml HGF (PeproTech, UK)  and 1X ITS supplement (Gibco, USA). days 15-18 were alternatively carried out with different concentrations of Oleic Acid-Albumin from bovine serum (Sigma Aldrich, USA) and Linoleic Acid-Albumin from bovine serum (Sigma Aldrich, USA) or 9-cis, 11-trans Conjugated linoleic acid (9CLA; Sigma Aldrich, USA) and 50uM BSA (Sigma Aldrich, USA),

value: HUES8 hESC-derived hepatocytes

value: 4 days in control media and 100 uM oleic and conjugated linoleic acid


title: 17-9CLA2


title: 13-BSA-ctrl2

description: BSA treated control

value: 4 days in control media (BSA)


title: 15-OA-LA2

description: Mother's milk lipid matured hepatocytes

value: 4 days in control media and 100 uM oleic and linoleic acid


title: 14-OA-LA1

description: Mother's milk lipid matured hepatocytes


title: 11-FHH

description: in vivo fetal reference

source_name: Isolated fetal human hepatocytes

growth_protocol: Deidentified human fetal livers (16-20 weeks gestation) were obtained through Advanced Bioscience Resources. Livers were received on ice and were washed with wash media consisting of Williams' E Medium supplemented with 10 mM HEPES, 50μg/mL gentamicin, 100 U/mL penicillin, and 100 μg/mL streptomycin (Invitrogen, Carlsbad, CA). Tissue was minced and re-suspended in 20-40 mL prewarmed buffer consisting of HBSS supplemented with 40 mM HEPES, 3.26 mM CaCl2, 2 U/mL DNase I Grade II (Roche Life Sciences, Switzerland), and 0.2% Collagenase type IV (Sigma Aldrich). Tissue was allowed to digest for 30 minutes at 37°C, then diluted 1:1 with wash media and gently pushed through 70 μm filters (Small Parts Inc.). The suspension was centrifuged at 100xg for 5 minutes and the cell pellet was collected and washed twice by resuspension in 50 mL wash buffer and centrifuged at 100xg for 5 minutes. Hepatocytes were plated at 100,000 cells/cm2 on 24 or 48-well collagen I-coated plates (BD Biosciences) in William’s E media containing 10% fetal bovine serum (Invitrogen), 2 mM L-glutamine (Invitrogen), ITS (BD Biosciences) and antibiotics. Twelve hours later the cells were washed with Williams E basal media and subsequently maintained in HMM as described above.

value: heptocytes isolated from deidentified human fetal livers (16-20 weeks gestation)


title: 16-9CLA1


title: 01-mtser1

description: undifferentiated reference

source_name: Undifferentiated pluripotent stem cells

growth_protocol: HUES8 hESC were grown in a feeder-independent system. Prior to differentiation, HUES8 hESC were cultured on growth factor reduced Matrigel™ (BD Biosciences, USA) in mTeSR-1 media (Stemcell technologies, Canada)

value: HUES8 hESC

value: in mTeSR


title: 02-mtser2

description: undifferentiated reference


title: 12-BSA-ctrl1

description: BSA treated control


title: CHD128 [2017_007_034]

city: Leuven

first: Paul

last: HOLVOET

address: Herestraat 49

department: Cardiovascular Sciences

country: Belgium

institute: KULeuven

data_processing:
The starting material (100 ng) of total RNA was mRNA enriched using the oligodT bead system (Illumina).
The isolated mRNA was subsequently fragmented using enzymatic fragmentation. Then first strand synthesis and second strand synthesis were performed, and the double stranded cDNA was purified (Agencourt AMPure XP, Beckman Coulter).
The cDNA was end repaired, 3’ adenylated and Illumina sequencing adaptors ligated onto the fragments ends, and the library was purified (Agencourt AMPure XP).
The polyA+ RNA stranded libraries were pre-amplified with PCR and purified (Agencourt AMPure XP).
The libraries size distribution was validated, and quality inspected on the 2100 Bioanalyzer (high sensitivity DNA chip, Agilent).
High quality libraries were quantified using the Qubit fluorometer (Life Technologies), the concentration was normalized, and the samples were pooled according to the project specification.
Single-end sequencing (75 bp) was performed on NextSeq 500 instrument (Illumina) according to the manufacturer’s instructions (Illumina).
Raw reads were evaluated using FastQC (v0.11.3). Adapter content was removed using Trimmomatic (v0.35; Bolger, Bioinformatics). Only reads with very low quality (Phred quality < 5) or very short reads (length < 25 nt) were trimmed before mapping using Trimmomatic as well.
Top Hat (v2.1.0; Kim, Genome Biol) was used to align trimmed RNA-Seq reads to the reference genome and for the identification of splice junctions. Quality control after mapping was performed with QoRTs (v1.0.1; Hartley, BMC Bioinformatics).
HTSeq (v0.6.1; Anders, Bioinformatics) was used to assemble the aligned sequences into genes, constructing a snapshot of the transcriptome.
Genome_build: Annotation of the obtained sequences was performed using the Human Reference genome: GRCh38, UCSC Genome Browser Reference transcriptome: Ensembl 84, LNCipedia 4.0.
Supplementary_files_format_and_content: Gene Level FPKM matrix processed data, DESeq2 normalized counts

source_name: Group 1_monocyte

extract_protocol:
Total RNA from monocytes was extracted with TRIzol reagent (Invitrogen) and purified on (mi)RNeasy Mini Kit columns (Qiagen) at KU Leuven. RNA concentration was determined using the Qubit 2.0 fluorometer (Thermo Fisher Scientific). Average RNA concentration was 122 ng/μl; ranging from 78-382 ng/μl. RNA quality was controlled using the Fragment Analyzer automated capillary electrophoresis system (Advanced Analytical Technologies). Average RQN value was 9.9, indicating very high RNA quality.
Libraries for mRNA sequencing were prepared using the TruSeq stranded mRNA sample prep kit (Illumina).

tag: sample no clinic

tag: group

value: Group 1

value: Circulating CD14+ monocytes

tag: ng/microliter

tag: rna quality score

tag: mrna sequencing raw read counts

tag: detected genes with fpkm >=1


title: CHD157 [2017_007_033]

tag: cell type


title: CHD159 [2017_007_036]


title: CHD122 [2017_007_030]

source_name: Group 2_monocyte

value: Group 2


title: CHD156 [2017_007_032]


title: CHD48 [2017_007_028]


title: CHD112 [2017_007_029]


title: CHD62 [2017_007_031]


title: CHD100 [2017_007_027]


title: CHD47 [2017_007_025]


title: CHD89 [2017_007_026]


title: CHD85 [2017_007_023]


title: CHD119 [2017_007_022]


title: CHD02 [2017_007_018]


title: CHD35 [2017_007_019]


title: CHD81 [2017_007_017]


title: 1233 [2017_007_012]

source_name: Group 3_monocyte

value: Group 3


title: 1191 [2017_007_010]


title: 1196 [2017_007_011]


title: CHD113 [2017_007_013]


title: ATH574

description:
PolyA- RNA / rRNA-depleted
5'p PARE

tag: ecotype

tag: genotype


title: CHD129 [2017_007_035]


title: 1195 [2017_007_007]


title: 1201 [2017_007_008]


title: 1240 [2017_007_006]


title: 1242 [2017_007_009]


title: CHD27 [2017_007_024]


title: 1190 [2017_007_005]


title: 1251 [2017_007_004]


title: 1239 [2017_007_001]


title: 1241 [2017_007_002]


title: CHD56 [2017_007_021]


title: CHD36 [2017_007_020]


title: 1249 [2017_007_003]


title: CHD52 [2017_007_016]


title: CHD20 [2017_007_014]


title: CHD34 [2017_007_015]


title: BCR35__S0233_S233

first: Maya

last: Sangesland

state: MA

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT, and Harvard

description: processed data file: Consensus_Alignments.txt

data_processing:
For single cells, paired end reads were merged into full length heavy and light chain reads using PANDAseq (v2.7).
Full length reads were aligned/constructed from human heavy and light chains using MigMAP (v.1.0.2).
Consensus heavy and light chains for each single cell were then determined by collapsing all reads by CDR3 sequence and calling the top hit for heavy and light, respectively. Any sequence without at least 25 reads or frequency 2x greater than the next sequence of the same chain was denoted without consensus.
For bulk heavy chain analysis, reads were aligned to human using mixcr (v.2.1.8) with the following parameter for alignment: OvParameters.geneFeatureToAlign = {FR3Begin:Vend}.
Downstream bulk analysis was preformed in R (v.3.4.3) using the tcR package (v2.2.3) and custom scripts.
Genome_build: IMGT (compiled Dec. 2017)
Supplementary_files_format_and_content: tab delimited txt file

source_name: IGHV1-69_VH_Adoptive Transfer_Splenic B cells

extract_protocol:
Mouse spleens were removed and single cell suspensions were obtained using 70 um cell strainer. Cells were stained using Aqua Live/Dead dye, followed by a cocktail of the following antibodies with the relevant probes: CD4 Alexa Fluor 700 (Cat# 557956, BD Biosciences); and CD3e PE-Cy7 (100320, Biolegend), CD19 BV421 (Cat# 115549, BioLegend), IgM BV605 (Cat# 406523, BioLegend), IgG PerCPCy5.5 (Cat#405314, Biolegend). Naïve B cells (CD3-/CD19+/IgG-/IgM+) were bulk sorted into RLT/1% beta-mercaptoethanol (BME). SS-np induced single B cells, including post boost 1, post boost 2 and post boost 3 (CD3-/CD19+/IgG+/IgM-/H1+ probe/H5+ probe), were sorted into 96 well plates containing RLT lysis buffer/1% BME. SS-np on-target single B cells were defined as CD3-/CD19+/IgM+/IgG-/SS-np Alexa 488+ probe/SS-np Alexa 594+ probe/SS-npDstem Alexa 647- probe/SS-npDstem Alexa 546- probe. Adoptive transfer single B cells are defined as CD3-/CD4-/B220+/GL7+/CD45.1-/CD45.2+/G6+.
RNA seq BCR libraries from single cells were generated by whole transcriptome amplification (WTA) using the Smart-Seq2 protocol (Trombetta et al., 2014). Single cell BCR amplicons for heavy and light chains (FR1 to CDR3) were generated separately using a pool of partially degenerate V region gene primers against all possible IGHV (human) or IGLV (mouse) and IGKV (mouse) segments in the FR1 region and reverse primers against the heavy or light constant regions containing the Illumina P7 and P5 sequences. Barcodes and Illumina sequencing adaptors (based on Nextera XT Index Adapters, Illumina Inc.) were then added to each amplified heavy and light chain using a step-out PCR.  Single-cell BCR libraries were sequenced using paired end 250x250 reads and 8x8 index reads on an Illumina MiSeq System (MiSeq Reagent Kit v2 500-cycle; Illumina, San Diego, US). Bulk BCR amplicons were generated following the same WTA step and two subsequent PCR steps as above, except that in the first PCR, the cocktail of V gene primers was replaced with a forward primer specific for the FR3 region within the VH gene of interest (IGHV1-69 or IGHV1-2). The resulting product (FR3 to CDRH3) was sequenced on Illumina MiSeq as above except without index reads.

tag: antibody chain

value: VH

tag: experiment

value: Adoptive Transfer

value: Splenic B cells

tag: molecule subtype

value: BCR Amplicon from RNA


title: BCR35__S0235_S235


title: BCR35__S0240_S240


title: BCR35__S0231_S231


title: BCR13_Bulk_IGHV1-2

source_name: IGHV1-2_VH_Naïve Bulk_Splenic B cells

value: Naïve Bulk


title: BCR7_Bulk_IGHV1-69

source_name: IGHV1-69_VH_Naïve Bulk_Splenic B cells


title: BCR35__S0223_S223


title: BCR35__S0230_S230


title: BCR35__S0225_S225


title: BCR35__S0228_S228


title: BCR35__S0226_S226


title: BCR35__S0222_S222


title: BCR35__S0220_S220


title: BCR35__S0221_S221


title: BCR35__S0219_S219


title: BCR35__S0216_S216


title: BCR35__S0215_S215


title: BCR35__S0214_S214


title: BCR35__S0211_S211


title: BCR35__S0209_S209


title: BCR35__S0207_S207


title: BCR35__S0206_S206


title: BCR35__S0204_S204


title: BCR35__S0198_S198


title: BCR35__S0236_S236


title: BCR35__S0195_S195


title: BCR35__S0197_S197


title: BCR35__S0190_S190


title: BCR35__S0188_S188


title: BCR35__S0224_S224


title: BCR35__S0178_S178


title: BCR35__S0187_S187


title: BCR35__S0175_S175


title: BCR35__S0176_S176


title: BCR35__S0183_S183


title: BCR35__S0173_S173


title: BCR35__S0171_S171


title: BCR35__S0174_S174


title: BCR35__S0163_S163


title: BCR35__S0162_S162


title: BCR35__S0165_S165


title: BCR35__S0160_S160


title: BCR35__S0161_S161


title: BCR35__S0159_S159


title: BCR35__S0154_S154


title: BCR35__S0158_S158


title: BCR35__S0149_S149


title: BCR35__S0148_S148


title: BCR35__S0147_S147


title: BCR35__S0136_S136


title: BCR35__S0141_S141


title: BCR35__S0131_S131


title: BCR35__S0132_S132


title: BCR35__S0182_S182


title: BCR35__S0130_S130


title: BCR35__S0128_S128


title: BCR35__S0126_S126


title: BCR35__S0124_S124


title: BCR35__S0170_S170


title: BCR35__S0122_S122


title: BCR35__S0123_S123


title: BCR35__S0119_S119


title: BCR35__S0111_S111


title: BCR35__S0120_S120


title: BCR35__S0105_S105


title: BCR35__S0101_S101


title: BCR35__S0098_S98


title: BCR35__S0100_S100


title: BCR35__S0093_S93


title: BCR35__S0089_S89


title: BCR35__S0086_S86


title: BCR35__S0088_S88


title: BCR35__S0084_S84


title: BCR35__S0087_S87


title: BCR35__S0081_S81


title: BCR35__S0075_S75


title: BCR35__S0077_S77


title: BCR35__S0083_S83


title: BCR35__S0070_S70


title: BCR35__S0069_S69


title: BCR35__S0072_S72


title: BCR35__S0071_S71


title: BCR35__S0062_S62


title: BCR35__S0061_S61


title: BCR35__S0065_S65


title: BCR35__S0108_S108


title: BCR35__S0050_S50


title: BCR35__S0044_S44


title: BCR35__S0047_S47


title: BCR35__S0085_S85


title: BCR35__S0040_S40


title: BCR35__S0039_S39


title: BCR35__S0038_S38


title: BCR35__S0036_S36


title: BCR35__S0025_S25


title: BCR35__S0028_S28


title: BCR35__S0064_S64


title: BCR35__S0020_S20


title: BCR35__S0019_S19


title: BCR35__S0049_S49


title: BCR35__S0013_S13


title: BCR35__S0011_S11


title: BCR35__S0048_S48


title: BCR35__S0023_S23


title: BCR35__S0002_S2


title: BCR35__S0008_S8


title: BCR35__S0006_S6


title: BCR34__S0230_S230


title: BCR35__S0001_S1


title: BCR34__S0236_S236


title: BCR35__S0041_S41


title: BCR35__S0057_S57


title: BCR34__S0228_S228


title: BCR34__S0227_S227


title: BCR34__S0231_S231


title: BCR34__S0222_S222


title: BCR35__S0033_S33


title: BCR35__S0032_S32


title: BCR34__S0221_S221


title: BCR34__S0217_S217


title: BCR34__S0215_S215


title: BCR35__S0017_S17


title: BCR34__S0207_S207


title: BCR34__S0208_S208


title: BCR34__S0204_S204


title: BCR34__S0202_S202


title: BCR34__S0200_S200


title: BCR34__S0197_S197


title: BCR34__S0191_S191


title: BCR34__S0199_S199


title: BCR34__S0171_S171


title: BCR34__S0172_S172


title: BCR34__S0194_S194


title: BCR34__S0169_S169


title: BCR34__S0180_S180


title: BCR34__S0160_S160


title: BCR34__S0158_S158


title: BCR34__S0157_S157


title: BCR34__S0165_S165


title: BCR34__S0219_S219


title: BCR34__S0152_S152


title: BCR34__S0143_S143


title: BCR34__S0142_S142


title: BCR34__S0136_S136


title: BCR34__S0137_S137


title: BCR34__S0134_S134


title: BCR34__S0131_S131


title: BCR34__S0121_S121


title: BCR34__S0111_S111


title: BCR34__S0109_S109


title: BCR34__S0105_S105


title: BCR34__S0096_S96


title: BCR34__S0166_S166


title: BCR34__S0093_S93


title: BCR34__S0094_S94


title: BCR34__S0087_S87


title: BCR34__S0089_S89


title: BCR34__S0147_S147


title: BCR34__S0086_S86


title: BCR34__S0085_S85


title: BCR34__S0091_S91


title: BCR34__S0077_S77


title: BCR34__S0076_S76


title: BCR34__S0088_S88


title: BCR34__S0084_S84


title: BCR34__S0073_S73


title: BCR34__S0075_S75


title: BCR34__S0065_S65


title: BCR34__S0064_S64


title: BCR34__S0066_S66


title: BCR34__S0047_S47


title: BCR34__S0074_S74


title: BCR34__S0048_S48


title: BCR34__S0046_S46


title: BCR34__S0044_S44


title: BCR34__S0062_S62


title: BCR34__S0031_S31


title: BCR34__S0019_S19


title: BCR34__S0038_S38


title: BCR34__S0029_S29


title: BCR34__S0022_S22


title: BCR34__S0011_S11


title: BCR34__S0016_S16


title: BCR34__S0007_S7


title: BCR34__S0010_S10


title: BCR34__S0008_S8


title: BCR34__S0004_S4


title: BCR34__S0012_S12


title: BCR34__S0006_S6


title: BCR27__S0189_S189

source_name: IGHV1-69_VL_H1N1 Pre-Immunity_Splenic B cells

value: VL

value: H1N1 Pre-Immunity


title: BCR27__S0192_S192


title: BCR27__S0190_S190


title: BCR27__S0188_S188


title: BCR27__S0182_S182


title: BCR27__S0178_S178


title: BCR27__S0180_S180


title: BCR27__S0179_S179


title: BCR27__S0191_S191


title: BCR27__S0173_S173


title: BCR27__S0174_S174


title: BCR27__S0177_S177


title: BCR27__S0176_S176


title: BCR27__S0175_S175


title: BCR27__S0172_S172


title: BCR27__S0187_S187


title: BCR27__S0171_S171


title: BCR27__S0168_S168


title: BCR27__S0166_S166


title: BCR27__S0163_S163


title: BCR27__S0165_S165


title: BCR27__S0164_S164


title: BCR27__S0159_S159


title: BCR27__S0162_S162


title: BCR27__S0167_S167


title: BCR27__S0181_S181


title: BCR27__S0158_S158


title: BCR27__S0156_S156


title: BCR27__S0157_S157


title: BCR27__S0155_S155


title: BCR27__S0154_S154


title: BCR27__S0153_S153


title: BCR27__S0169_S169


title: BCR27__S0151_S151


title: BCR27__S0149_S149


title: BCR27__S0150_S150


title: BCR27__S0145_S145


title: BCR27__S0144_S144


title: BCR27__S0142_S142


title: BCR27__S0147_S147


title: BCR27__S0146_S146


title: BCR27__S0170_S170


title: BCR27__S0141_S141


title: BCR27__S0140_S140


title: BCR27__S0139_S139


title: BCR27__S0160_S160


title: BCR27__S0138_S138


title: BCR27__S0135_S135


title: BCR27__S0136_S136


title: BCR27__S0137_S137


title: BCR27__S0134_S134


title: BCR27__S0133_S133


title: BCR27__S0131_S131


title: BCR27__S0129_S129


title: BCR27__S0130_S130


title: BCR27__S0132_S132


title: BCR27__S0128_S128


title: BCR27__S0143_S143


title: BCR27__S0126_S126


title: BCR27__S0125_S125


title: BCR27__S0123_S123


title: BCR27__S0124_S124


title: BCR27__S0127_S127


title: BCR27__S0121_S121


title: BCR27__S0122_S122


title: BCR27__S0117_S117


title: BCR27__S0119_S119


title: BCR27__S0118_S118


title: BCR27__S0115_S115


title: BCR27__S0113_S113


title: BCR27__S0116_S116


title: BCR27__S0114_S114


title: BCR27__S0111_S111


title: BCR27__S0112_S112


title: BCR27__S0110_S110


title: BCR27__S0120_S120


title: ret962

description: RetinaExpressionmatrix.txt

source_name: Retina

tag: Sex

value: Male

value: Tamoxifen

tag: age

value: 3 Months


title: BCR27__S0109_S109


title: BCR27__S0108_S108


title: BCR27__S0107_S107


title: BCR27__S0105_S105


title: BCR27__S0106_S106


title: BCR27__S0104_S104


title: BCR27__S0102_S102


title: BCR27__S0103_S103


title: BCR27__S0101_S101


title: BCR27__S0100_S100


title: BCR27__S0098_S98


title: BCR27__S0099_S99


title: BCR27__S0097_S97


title: BCR27__S0095_S95

source_name: IGHV1-69_VH_H1N1 Pre-Immunity_Splenic B cells


title: BCR27__S0096_S96


title: BCR27__S0093_S93


title: BCR27__S0086_S86


title: BCR27__S0084_S84


title: BCR27__S0083_S83


title: BCR27__S0081_S81


title: BCR27__S0082_S82


title: BCR27__S0077_S77


title: BCR27__S0087_S87


title: BCR27__S0091_S91


title: BCR27__S0076_S76


title: BCR27__S0072_S72


title: BCR27__S0071_S71


title: BCR27__S0067_S67


title: BCR27__S0066_S66


title: BCR27__S0070_S70


title: BCR27__S0063_S63


title: BCR27__S0061_S61


title: BCR27__S0062_S62


title: BCR27__S0052_S52


title: BCR27__S0080_S80


title: BCR27__S0050_S50


title: BCR27__S0051_S51


title: BCR27__S0054_S54


title: BCR27__S0044_S44


title: BCR27__S0045_S45


title: BCR27__S0047_S47


title: BCR27__S0046_S46


title: BCR27__S0049_S49


title: BCR27__S0042_S42


title: BCR27__S0041_S41


title: BCR27__S0075_S75


title: BCR27__S0039_S39


title: BCR27__S0037_S37


title: BCR27__S0035_S35


title: BCR27__S0034_S34


title: BCR27__S0069_S69


title: BCR27__S0065_S65


title: BCR27__S0033_S33


title: BCR27__S0055_S55


title: BCR27__S0043_S43


title: BCR27__S0029_S29


title: BCR27__S0031_S31


title: BCR27__S0032_S32


title: BCR27__S0057_S57


title: BCR27__S0025_S25


title: BCR27__S0021_S21


title: BCR27__S0020_S20


title: BCR27__S0017_S17


title: BCR27__S0016_S16


title: BCR27__S0038_S38


title: BCR27__S0019_S19


title: BCR27__S0015_S15


title: BCR27__S0014_S14


title: BCR27__S0013_S13


title: BCR27__S0008_S8


title: BCR27__S0007_S7


title: BCR27__S0002_S2


title: BCR27__S0012_S12


title: BCR27__S0001_S1


title: BCR27__S0004_S4


title: BCR27__S0003_S3


title: BCR27__S0005_S5


title: BCR24__S0192_S192

source_name: IGHV1-69_VH_on-target_Splenic B cells

value: on-target


title: BCR24__S0191_S191


title: BCR27__S0026_S26


title: BCR24__S0189_S189


title: BCR24__S0190_S190


title: BCR24__S0184_S184


title: BCR24__S0182_S182


title: BCR24__S0186_S186


title: BCR24__S0187_S187


title: BCR24__S0181_S181


title: BCR24__S0179_S179


title: BCR27__S0009_S9


title: BCR24__S0178_S178


title: BCR24__S0188_S188


title: BCR24__S0176_S176


title: BCR24__S0180_S180


title: BCR24__S0175_S175


title: BCR24__S0173_S173


title: BCR24__S0177_S177


title: BCR24__S0172_S172


title: BCR24__S0170_S170


title: BCR24__S0171_S171


title: BCR24__S0169_S169


title: BCR24__S0167_S167


title: BCR24__S0168_S168


title: BCR24__S0166_S166


title: BCR24__S0163_S163


title: BCR24__S0160_S160


title: BCR24__S0161_S161


title: BCR24__S0162_S162


title: BCR24__S0159_S159


title: BCR24__S0158_S158


title: BCR24__S0183_S183


title: BCR24__S0157_S157


title: BCR24__S0156_S156


title: BCR24__S0155_S155


title: BCR24__S0154_S154


title: BCR24__S0153_S153


title: BCR24__S0174_S174


title: BCR24__S0150_S150


title: BCR24__S0149_S149


title: BCR24__S0148_S148


title: BCR24__S0147_S147


title: BCR24__S0145_S145


title: BCR24__S0144_S144


title: BCR24__S0146_S146


title: BCR24__S0151_S151


title: BCR24__S0164_S164


title: BCR24__S0143_S143


title: BCR24__S0140_S140


title: BCR24__S0139_S139


title: BCR24__S0138_S138


title: BCR24__S0136_S136


title: BCR24__S0134_S134


title: BCR24__S0132_S132


title: BCR24__S0131_S131


title: BCR24__S0133_S133


title: BCR24__S0129_S129


title: BCR24__S0127_S127


title: BCR24__S0126_S126


title: BCR24__S0123_S123


title: BCR24__S0121_S121


title: BCR24__S0122_S122


title: BCR24__S0119_S119


title: BCR24__S0116_S116


title: BCR24__S0112_S112


title: BCR24__S0113_S113


title: BCR24__S0109_S109


title: BCR24__S0111_S111


title: BCR24__S0142_S142


title: BCR24__S0107_S107


title: BCR24__S0105_S105


title: BCR24__S0141_S141


title: BCR24__S0137_S137


title: BCR24__S0104_S104


title: BCR24__S0103_S103


title: BCR24__S0125_S125


title: BCR24__S0102_S102


title: BCR24__S0101_S101


title: BCR24__S0099_S99


title: BCR24__S0098_S98


title: BCR24__S0096_S96


title: BCR24__S0120_S120


title: BCR24__S0097_S97


title: BCR24__S0115_S115


title: BCR24__S0093_S93


title: BCR24__S0092_S92


title: BCR24__S0110_S110


title: BCR24__S0094_S94


title: BCR24__S0090_S90


title: BCR24__S0108_S108


title: BCR24__S0089_S89


title: BCR24__S0087_S87


title: BCR24__S0085_S85


title: BCR24__S0095_S95


title: BCR24__S0084_S84


title: BCR24__S0083_S83


title: BCR24__S0082_S82


title: BCR24__S0091_S91


title: BCR24__S0079_S79


title: BCR24__S0077_S77


title: BCR24__S0076_S76


title: BCR24__S0078_S78


title: BCR24__S0075_S75


title: BCR24__S0073_S73


title: BCR24__S0072_S72


title: BCR24__S0080_S80


title: BCR24__S0071_S71


title: BCR24__S0070_S70


title: BCR24__S0066_S66


title: BCR24__S0069_S69


title: BCR24__S0061_S61


title: BCR24__S0064_S64


title: BCR24__S0068_S68


title: BCR24__S0063_S63


title: BCR24__S0059_S59


title: BCR24__S0060_S60


title: BCR24__S0058_S58


title: BCR24__S0057_S57


title: BCR24__S0062_S62


title: BCR24__S0056_S56


title: BCR24__S0053_S53


title: BCR24__S0054_S54


title: BCR24__S0055_S55


title: BCR24__S0051_S51


title: BCR24__S0050_S50


title: BCR24__S0048_S48


title: BCR24__S0052_S52


title: BCR24__S0074_S74


title: BCR24__S0046_S46


title: BCR24__S0049_S49


title: BCR24__S0065_S65


title: BCR24__S0041_S41


title: BCR24__S0047_S47


title: BCR24__S0044_S44


title: BCR24__S0039_S39


title: BCR24__S0043_S43


title: BCR24__S0042_S42


title: BCR24__S0037_S37


title: BCR24__S0040_S40


title: BCR24__S0035_S35


title: BCR24__S0034_S34


title: BCR24__S0032_S32


title: BCR24__S0033_S33


title: BCR24__S0028_S28


title: BCR24__S0029_S29


title: BCR24__S0025_S25


title: BCR24__S0027_S27


title: BCR24__S0030_S30


title: BCR24__S0024_S24


title: BCR24__S0023_S23


title: BCR24__S0022_S22


title: BCR24__S0021_S21


title: BCR24__S0020_S20


title: BCR24__S0019_S19


title: BCR24__S0018_S18


title: BCR24__S0016_S16


title: BCR24__S0017_S17


title: BCR24__S0015_S15


title: BCR24__S0014_S14


title: BCR24__S0013_S13


title: BCR24__S0011_S11


title: BCR24__S0010_S10


title: BCR24__S0006_S6


title: BCR24__S0007_S7


title: BCR24__S0012_S12


title: BCR24__S0005_S5


title: BCR24__S0004_S4


title: BCR24__S0008_S8


title: BCR24__S0003_S3


title: BCR24__S0031_S31


title: BCR24__S0002_S2


title: BCR24__S0001_S1


title: BCR23__S0189_S189

source_name: IGHV1-2_VH_Naïve_Splenic B cells

value: Naïve


title: BCR23__S0183_S183


title: BCR23__S0191_S191


title: BCR23__S0184_S184


title: BCR23__S0187_S187


title: BCR23__S0190_S190


title: BCR23__S0186_S186


title: BCR23__S0188_S188


title: BCR23__S0182_S182


title: BCR23__S0181_S181


title: BCR23__S0180_S180


title: BCR23__S0179_S179


title: BCR23__S0176_S176


title: BCR23__S0173_S173


title: BCR23__S0178_S178


title: BCR23__S0174_S174


title: BCR23__S0163_S163


title: BCR23__S0169_S169


title: BCR23__S0170_S170


title: BCR23__S0160_S160


title: BCR23__S0162_S162


title: BCR23__S0154_S154


title: BCR23__S0153_S153


title: BCR23__S0152_S152


title: BCR23__S0157_S157


title: BCR23__S0156_S156


title: BCR23__S0148_S148


title: BCR23__S0150_S150


title: BCR23__S0149_S149


title: BCR23__S0175_S175


title: BCR23__S0159_S159


title: BCR23__S0146_S146


title: BCR23__S0145_S145


title: BCR23__S0151_S151


title: BCR23__S0144_S144


title: BCR23__S0166_S166


title: BCR23__S0132_S132


title: BCR23__S0161_S161


title: BCR23__S0137_S137


title: BCR23__S0143_S143


title: BCR23__S0167_S167


title: BCR23__S0130_S130


title: BCR23__S0138_S138


title: BCR23__S0147_S147


title: BCR23__S0142_S142


title: BCR23__S0127_S127


title: BCR23__S0139_S139


title: BCR23__S0131_S131


title: BCR23__S0135_S135


title: BCR23__S0129_S129


title: BCR23__S0126_S126


title: BCR23__S0125_S125


title: BCR23__S0134_S134


title: BCR23__S0124_S124


title: BCR23__S0120_S120


title: BCR23__S0119_S119


title: BCR23__S0116_S116


title: BCR23__S0122_S122


title: BCR23__S0118_S118


title: BCR23__S0112_S112


title: BCR23__S0113_S113


title: BCR23__S0117_S117


title: BCR23__S0111_S111


title: BCR23__S0115_S115


title: BCR23__S0110_S110


title: BCR23__S0107_S107


title: BCR23__S0104_S104


title: BCR23__S0108_S108


title: BCR23__S0106_S106


title: BCR23__S0109_S109


title: BCR23__S0097_S97


title: BCR23__S0102_S102


title: BCR23__S0103_S103


title: BCR23__S0101_S101


title: BCR23__S0100_S100


title: BCR23__S0096_S96


title: BCR23__S0095_S95


title: BCR23__S0092_S92


title: BCR23__S0099_S99


title: BCR23__S0094_S94


title: BCR23__S0114_S114


title: BCR23__S0091_S91


title: BCR23__S0090_S90


title: BCR23__S0088_S88


title: BCR23__S0087_S87


title: BCR23__S0084_S84


title: BCR23__S0081_S81


title: BCR23__S0080_S80


title: BCR23__S0082_S82


title: BCR23__S0078_S78


title: BCR23__S0075_S75


title: BCR23__S0068_S68


title: BCR23__S0071_S71


title: BCR23__S0067_S67


title: BCR23__S0074_S74


title: BCR23__S0072_S72


title: BCR23__S0079_S79


title: BCR23__S0073_S73


title: BCR23__S0062_S62


title: BCR23__S0065_S65


title: BCR23__S0070_S70


title: BCR23__S0061_S61


title: BCR23__S0059_S59


title: BCR23__S0057_S57


title: BCR23__S0054_S54


title: BCR23__S0051_S51


title: BCR23__S0052_S52


title: BCR23__S0055_S55


title: BCR23__S0045_S45


title: BCR23__S0046_S46


title: BCR23__S0043_S43


title: BCR23__S0041_S41


title: BCR23__S0040_S40


title: BCR23__S0035_S35


title: BCR23__S0036_S36


title: BCR23__S0056_S56


title: BCR23__S0030_S30


title: BCR23__S0027_S27


title: BCR23__S0017_S17


title: BCR23__S0013_S13


title: BCR23__S0021_S21


title: BCR23__S0047_S47


title: BCR23__S0022_S22


title: BCR23__S0029_S29


title: BCR23__S0012_S12


title: BCR23__S0015_S15


title: BCR23__S0016_S16


title: BCR23__S0010_S10


title: BCR23__S0009_S9


title: BCR23__S0008_S8


title: BCR23__S0005_S5


title: BCR22__S0192_S192

source_name: IGHV1-69_VH_Naïve_Splenic B cells


title: BCR23__S0042_S42


title: BCR23__S0038_S38


title: BCR22__S0188_S188


title: BCR22__S0187_S187


title: BCR23__S0034_S34


title: BCR22__S0186_S186


title: BCR23__S0018_S18


title: BCR23__S0026_S26


title: BCR22__S0185_S185


title: BCR23__S0011_S11


title: BCR22__S0184_S184


title: BCR22__S0183_S183


title: BCR22__S0180_S180


title: BCR22__S0189_S189


title: BCR22__S0177_S177


title: BCR22__S0179_S179


title: BCR22__S0174_S174


title: BCR22__S0178_S178


title: BCR22__S0176_S176


title: BCR22__S0175_S175


title: BCR22__S0172_S172


title: BCR22__S0171_S171


title: BCR22__S0190_S190


title: BCR22__S0165_S165


title: BCR22__S0164_S164


title: BCR22__S0167_S167


title: BCR22__S0160_S160


title: BCR22__S0163_S163


title: BCR22__S0166_S166


title: BCR22__S0170_S170


title: BCR22__S0157_S157


title: BCR22__S0154_S154


title: BCR22__S0158_S158


title: BCR22__S0181_S181


title: BCR22__S0155_S155


title: BCR22__S0151_S151


title: BCR22__S0146_S146


title: BCR22__S0150_S150


title: BCR22__S0149_S149


title: BCR22__S0152_S152


title: BCR22__S0145_S145


title: BCR22__S0143_S143


title: BCR22__S0142_S142


title: BCR22__S0141_S141


title: BCR22__S0136_S136


title: BCR22__S0138_S138


title: BCR22__S0139_S139


title: BCR22__S0135_S135


title: BCR22__S0133_S133


title: BCR22__S0137_S137


title: BCR22__S0132_S132


title: BCR22__S0130_S130


title: BCR22__S0126_S126


title: BCR22__S0127_S127


title: BCR22__S0129_S129


title: BCR22__S0128_S128


title: BCR22__S0153_S153


title: BCR22__S0125_S125


title: BCR22__S0131_S131


title: BCR22__S0124_S124


title: BCR22__S0123_S123


title: BCR22__S0122_S122


title: BCR22__S0121_S121


title: BCR22__S0120_S120


title: BCR22__S0118_S118


title: BCR22__S0119_S119


title: BCR22__S0116_S116


title: BCR22__S0144_S144


title: BCR22__S0117_S117


title: BCR22__S0115_S115


title: BCR22__S0114_S114


title: BCR22__S0113_S113


title: BCR22__S0112_S112


title: BCR22__S0111_S111


title: BCR22__S0107_S107


title: BCR22__S0108_S108


title: BCR22__S0105_S105


title: BCR22__S0103_S103


title: BCR22__S0109_S109


title: BCR22__S0110_S110


title: BCR22__S0099_S99


title: BCR22__S0098_S98


title: BCR22__S0097_S97


title: BCR22__S0095_S95


title: BCR22__S0089_S89


title: BCR22__S0091_S91


title: BCR22__S0088_S88


title: BCR22__S0087_S87


title: BCR22__S0086_S86


title: BCR22__S0083_S83


title: BCR22__S0082_S82


title: BCR22__S0084_S84


title: BCR22__S0081_S81


title: BCR22__S0080_S80


title: BCR22__S0106_S106


title: BCR22__S0079_S79


title: BCR22__S0078_S78


title: BCR22__S0077_S77


title: BCR22__S0076_S76


title: BCR22__S0075_S75


title: BCR22__S0102_S102


title: BCR22__S0100_S100


title: BCR22__S0071_S71


title: BCR22__S0101_S101


title: BCR22__S0070_S70


title: BCR22__S0094_S94


title: BCR22__S0072_S72


title: BCR22__S0066_S66


title: BCR22__S0067_S67


title: BCR22__S0085_S85


title: BCR22__S0058_S58


title: BCR22__S0061_S61


title: BCR22__S0053_S53


title: BCR22__S0057_S57


title: BCR22__S0051_S51


title: BCR22__S0049_S49


title: BCR22__S0055_S55


title: BCR22__S0047_S47


title: BCR22__S0074_S74


title: BCR22__S0042_S42


title: BCR22__S0046_S46


title: BCR22__S0043_S43


title: BCR22__S0038_S38


title: BCR22__S0040_S40


title: BCR22__S0063_S63


title: BCR22__S0069_S69


title: BCR22__S0033_S33


title: BCR22__S0068_S68


title: BCR22__S0031_S31


title: BCR22__S0032_S32


title: BCR22__S0029_S29


title: BCR22__S0030_S30


title: BCR22__S0034_S34


title: BCR22__S0026_S26


title: BCR22__S0027_S27


title: BCR22__S0028_S28


title: BCR22__S0022_S22


title: BCR22__S0021_S21


title: BCR22__S0020_S20


title: BCR22__S0017_S17


title: BCR22__S0025_S25


title: BCR22__S0019_S19


title: BCR22__S0015_S15


title: BCR22__S0035_S35


title: BCR22__S0011_S11


title: BCR22__S0016_S16


title: BCR22__S0009_S9


title: BCR22__S0007_S7


title: BCR22__S0014_S14


title: BCR22__S0006_S6


title: BCR22__S0010_S10


title: BCR21__S0189_S189

source_name: IGHV1-69_VL_Post Boost 1_Splenic B cells

value: Post Boost 1


title: BCR21__S0190_S190


title: BCR22__S0001_S1


title: BCR22__S0002_S2


title: BCR21__S0179_S179


title: BCR22__S0039_S39


title: BCR21__S0182_S182


title: BCR22__S0037_S37


title: BCR21__S0178_S178


title: BCR21__S0187_S187


title: BCR21__S0177_S177


title: BCR21__S0175_S175


title: BCR22__S0004_S4


title: BCR22__S0018_S18


title: BCR21__S0174_S174


title: BCR21__S0173_S173


title: BCR21__S0186_S186


title: BCR21__S0170_S170


title: BCR21__S0169_S169


title: BCR21__S0167_S167


title: BCR21__S0165_S165


title: BCR21__S0166_S166


title: BCR21__S0164_S164


title: BCR21__S0163_S163


title: BCR21__S0160_S160


title: BCR21__S0159_S159


title: BCR21__S0153_S153


title: BCR21__S0152_S152


title: BCR21__S0158_S158


title: BCR21__S0146_S146


title: BCR21__S0144_S144


title: BCR21__S0148_S148


title: BCR21__S0138_S138


title: BCR21__S0141_S141


title: BCR21__S0134_S134


title: BCR21__S0151_S151


title: BCR21__S0142_S142


title: BCR21__S0132_S132


title: BCR21__S0172_S172


title: BCR21__S0120_S120


title: BCR21__S0117_S117


title: BCR21__S0131_S131


title: BCR21__S0125_S125


title: BCR21__S0123_S123


title: BCR21__S0116_S116


title: BCR21__S0129_S129


title: BCR21__S0115_S115


title: BCR21__S0133_S133


title: BCR21__S0114_S114


title: BCR21__S0112_S112


title: BCR21__S0108_S108


title: BCR21__S0107_S107


title: BCR21__S0106_S106


title: BCR21__S0110_S110


title: BCR21__S0113_S113


title: BCR21__S0098_S98


title: BCR18__S0107_S107


title: BCR18__S0105_S105


title: BCR18__S0104_S104


title: BCR18__S0098_S98


title: BCR18__S0099_S99


title: BCR18__S0095_S95


title: BCR18__S0092_S92


title: BCR18__S0106_S106


title: BCR18__S0081_S81


title: BCR18__S0080_S80


title: BCR18__S0089_S89


title: BCR18__S0061_S61


title: BCR18__S0071_S71


title: BCR18__S0064_S64


title: BCR18__S0077_S77


title: BCR18__S0086_S86


title: BCR18__S0056_S56


title: BCR18__S0055_S55


title: BCR18__S0053_S53


title: BCR18__S0052_S52


title: BCR18__S0049_S49


title: BCR18__S0060_S60


title: BCR21__S0105_S105


title: BCR18__S0108_S108


title: BCR18__S0045_S45


title: BCR18__S0048_S48


title: BCR18__S0047_S47


title: BCR18__S0043_S43


title: BCR18__S0102_S102


title: BCR18__S0041_S41


title: BCR18__S0036_S36


title: BCR18__S0031_S31


title: BCR18__S0029_S29


title: BCR18__S0028_S28


title: BCR18__S0085_S85


title: BCR18__S0025_S25


title: BCR18__S0024_S24


title: BCR18__S0019_S19


title: BCR18__S0014_S14


title: BCR18__S0023_S23


title: BCR18__S0007_S7


title: BCR18__S0003_S3


title: BCR18__S0018_S18


title: BCR18__S0011_S11


title: BCR17__S0269_S197


title: BCR18__S0002_S2


title: BCR17__S0257_S185


title: BCR17__S0268_S196


title: BCR17__S0249_S177


title: BCR17__S0244_S172


title: BCR17__S0215_S143


title: BCR17__S0206_S134


title: BCR17__S0250_S178


title: BCR17__S0253_S181


title: BCR17__S0205_S133


title: BCR17__S0188_S116


title: BCR17__S0210_S138


title: BCR17__S0190_S118


title: BCR17__S0191_S119


title: BCR17__S0194_S122


title: BCR17__S0187_S115


title: BCR17__S0183_S111


title: BCR17__S0142_S70


title: BCR17__S0139_S67


title: BCR18__S0030_S30


title: BCR17__S0143_S71


title: BCR17__S0135_S63


title: BCR17__S0132_S60


title: BCR17__S0130_S58


title: BCR17__S0129_S57


title: BCR17__S0127_S55


title: BCR17__S0126_S54


title: BCR17__S0125_S53


title: BCR17__S0128_S56


title: BCR17__S0124_S52


title: BCR17__S0123_S51


title: BCR17__S0122_S50


title: BCR17__S0116_S44


title: BCR17__S0110_S38


title: BCR17__S0114_S42


title: BCR17__S0109_S37


title: BCR17__S0107_S35


title: BCR17__S0106_S34


title: BCR17__S0117_S45


title: BCR17__S0104_S32


title: BCR17__S0103_S31


title: BCR17__S0118_S46


title: BCR17__S0101_S29


title: BCR17__S0092_S20


title: BCR17__S0094_S22


title: BCR17__S0119_S47


title: BCR17__S0091_S19


title: BCR17__S0093_S21


title: BCR17__S0108_S36


title: BCR17__S0080_S8


title: BCR17__S0087_S15


title: BCR17__S0082_S10


title: BCR17__S0078_S6


title: BCR17__S0077_S5


title: BCR17__S0075_S3


title: BCR12__S0180_S180

source_name: IGHV1-69_VH_Post Boost 1_Splenic B cells


title: BCR17__S0086_S14


title: BCR17__S0102_S30


title: BCR12__S0177_S177


title: BCR12__S0178_S178


title: BCR17__S0099_S27


title: BCR12__S0173_S173


title: BCR12__S0174_S174


title: BCR12__S0169_S169


title: BCR12__S0170_S170


title: BCR12__S0171_S171


title: BCR12__S0167_S167


title: BCR12__S0166_S166


title: BCR12__S0165_S165


title: BCR12__S0162_S162


title: BCR17__S0085_S13


title: BCR17__S0083_S11


title: BCR12__S0168_S168


title: BCR12__S0161_S161


title: BCR17__S0076_S4


title: BCR12__S0176_S176


title: BCR12__S0149_S149


title: BCR12__S0172_S172


title: BCR12__S0151_S151


title: BCR12__S0159_S159


title: BCR12__S0156_S156


title: BCR12__S0153_S153


title: BCR12__S0155_S155


title: BCR12__S0150_S150


title: BCR12__S0147_S147


title: BCR12__S0146_S146


title: BCR12__S0071_S71


title: BCR12__S0070_S70


title: BCR12__S0069_S69


title: BCR12__S0066_S66


title: BCR12__S0068_S68


title: BCR12__S0062_S62


title: BCR12__S0063_S63


title: BCR12__S0065_S65


title: BCR12__S0067_S67


title: BCR12__S0059_S59


title: BCR12__S0058_S58


title: BCR12__S0158_S158


title: BCR12__S0057_S57


title: BCR12__S0056_S56


title: BCR12__S0060_S60


title: BCR12__S0053_S53


title: BCR12__S0052_S52


title: BCR12__S0157_S157


title: BCR12__S0051_S51


title: BCR12__S0145_S145


title: BCR12__S0050_S50


title: BCR12__S0047_S47


title: BCR12__S0049_S49


title: BCR12__S0048_S48


title: BCR12__S0043_S43


title: BCR12__S0041_S41


title: BCR12__S0040_S40


title: BCR12__S0037_S37


title: BCR12__S0045_S45


title: BCR12__S0036_S36


title: BCR12__S0035_S35


title: BCR12__S0028_S28


title: BCR12__S0022_S22


title: BCR12__S0029_S29


title: BCR12__S0025_S25


title: BCR12__S0033_S33


title: BCR12__S0027_S27


title: BCR12__S0026_S26


title: BCR12__S0015_S15


title: BCR12__S0018_S18


title: BCR12__S0017_S17


title: BCR12__S0034_S34


title: BCR12__S0014_S14


title: BCR12__S0013_S13


title: BCR12__S0012_S12


title: BCR12__S0024_S24


title: BCR12__S0039_S39


title: BCR12__S0010_S10


title: BCR12__S0011_S11


title: BCR12__S0009_S9


title: BCR12__S0007_S7


title: BCR12__S0008_S8


title: BCR12__S0006_S6


title: BCR12__S0005_S5


title: BCR11__S0195_S195

source_name: IGHV1-69_VH_Post Boost 2_Splenic B cells

value: Post Boost 2


title: BCR11__S0194_S194


title: BCR11__S0191_S191


title: BCR12__S0016_S16


title: BCR11__S0192_S192


title: BCR11__S0193_S193


title: BCR11__S0189_S189


title: BCR11__S0188_S188


title: BCR11__S0183_S183


title: BCR11__S0182_S182


title: BCR11__S0184_S184


title: BCR11__S0186_S186


title: BCR11__S0190_S190


title: BCR11__S0173_S173


title: BCR11__S0179_S179


title: BCR11__S0174_S174


title: BCR11__S0181_S181


title: BCR11__S0169_S169


title: BCR11__S0073_S73


title: BCR11__S0079_S79


title: BCR11__S0081_S81


title: BCR11__S0070_S70


title: BCR11__S0068_S68


title: BCR11__S0069_S69


title: BCR11__S0067_S67


title: BCR11__S0062_S62


title: BCR11__S0063_S63


title: BCR11__S0187_S187


title: BCR11__S0061_S61


title: BCR11__S0059_S59


title: BCR11__S0055_S55


title: BCR11__S0057_S57


title: BCR11__S0170_S170


title: BCR11__S0054_S54


title: BCR11__S0053_S53


title: BCR11__S0048_S48


title: BCR11__S0045_S45


title: BCR11__S0041_S41


title: BCR11__S0051_S51


title: BCR11__S0039_S39


title: BCR11__S0040_S40


title: BCR11__S0038_S38


title: BCR11__S0037_S37


title: BCR11__S0035_S35


title: BCR11__S0064_S64


title: BCR11__S0031_S31


title: BCR11__S0034_S34


title: BCR11__S0065_S65


title: BCR11__S0030_S30


title: BCR11__S0027_S27


title: BCR11__S0026_S26


title: BCR11__S0052_S52


title: BCR11__S0025_S25


title: BCR11__S0023_S23


title: BCR11__S0049_S49


title: BCR11__S0021_S21


title: BCR11__S0022_S22


title: BCR11__S0056_S56


title: BCR11__S0019_S19


title: BCR11__S0043_S43


title: BCR11__S0018_S18


title: BCR11__S0016_S16


title: BCR11__S0020_S20


title: BCR11__S0011_S11


title: BCR11__S0014_S14


title: BCR11__S0012_S12


title: BCR11__S0015_S15


title: BCR11__S0013_S13


title: BCR11__S0010_S10


title: BCR11__S0033_S33


title: BCR11__S0036_S36


title: BCR11__S0029_S29


title: BCR6__S0199_S199

source_name: IGHV1-69_VL_Post Boost 3_Splenic B cells

value: Post Boost 3


title: BCR6__S0201_S201


title: BCR6__S0215_S215


title: BCR11__S0003_S3


title: BCR6__S0198_S198


title: BCR6__S0208_S208


title: BCR6__S0210_S210


title: BCR11__S0005_S5


title: BCR6__S0209_S209


title: BCR11__S0007_S7


title: BCR6__S0214_S214


title: BCR6__S0212_S212


title: BCR6__S0206_S206


title: BCR6__S0211_S211


title: BCR6__S0207_S207


title: BCR11__S0009_S9


title: BCR11__S0008_S8


title: BCR6__S0197_S197


title: BCR6__S0202_S202


title: BCR6__S0216_S216


title: BCR11__S0001_S1


title: BCR6__S0204_S204


title: BCR6__S0205_S205


title: BCR11__S0006_S6


title: BCR11__S0004_S4


title: BCR6__S0213_S213


title: BCR6__S0195_S195


title: BCR6__S0203_S203


title: BCR6__S0200_S200


title: BCR11__S0002_S2


title: BCR6__S0193_S193


title: BCR6__S0194_S194


title: BCR6__S0190_S190


title: BCR6__S0189_S189


title: BCR6__S0188_S188


title: BCR6__S0191_S191


title: BCR6__S0182_S182


title: BCR6__S0184_S184


title: BCR6__S0185_S185


title: BCR6__S0183_S183


title: BCR6__S0186_S186


title: BCR6__S0187_S187


title: BCR6__S0166_S166


title: BCR6__S0174_S174


title: BCR6__S0163_S163


title: BCR6__S0165_S165


title: BCR6__S0177_S177


title: BCR6__S0169_S169


title: BCR6__S0179_S179


title: BCR6__S0181_S181


title: BCR6__S0159_S159


title: BCR6__S0160_S160


title: BCR6__S0161_S161


title: BCR6__S0158_S158


title: BCR6__S0171_S171


title: BCR6__S0176_S176


title: BCR6__S0178_S178


title: BCR6__S0170_S170


title: BCR6__S0180_S180


title: BCR6__S0167_S167


title: BCR6__S0173_S173


title: BCR6__S0157_S157


title: BCR6__S0162_S162


title: BCR6__S0168_S168


title: BCR6__S0175_S175


title: BCR6__S0156_S156


title: BCR6__S0153_S153


title: BCR6__S0155_S155


title: BCR6__S0154_S154


title: BCR6__S0151_S151


title: BCR6__S0150_S150


title: BCR6__S0143_S143


title: BCR6__S0140_S140


title: BCR6__S0148_S148


title: BCR6__S0139_S139


title: BCR6__S0130_S130


title: BCR6__S0132_S132


title: BCR6__S0133_S133


title: BCR6__S0145_S145


title: BCR6__S0144_S144


title: BCR6__S0146_S146


title: BCR6__S0138_S138


title: BCR6__S0128_S128


title: BCR6__S0136_S136


title: BCR6__S0149_S149


title: BCR6__S0152_S152


title: BCR6__S0129_S129


title: BCR6__S0137_S137


title: BCR6__S0134_S134


title: BCR6__S0135_S135


title: BCR6__S0141_S141


title: BCR6__S0125_S125


title: BCR6__S0131_S131


title: BCR6__S0123_S123


title: BCR6__S0121_S121


title: BCR6__S0120_S120


title: BCR6__S0122_S122


title: BCR6__S0147_S147


title: BCR6__S0142_S142


title: BCR6__S0127_S127


title: BCR6__S0119_S119


title: BCR6__S0118_S118


title: BCR6__S0117_S117


title: BCR6__S0115_S115


title: BCR6__S0116_S116


title: BCR6__S0110_S110


title: BCR6__S0111_S111


title: BCR6__S0112_S112


title: BCR6__S0109_S109


title: BCR3__S0120_S120


title: BCR3__S0117_S117


title: BCR3__S0116_S116


title: BCR3__S0114_S114


title: BCR6__S0113_S113


title: BCR3__S0113_S113


title: BCR3__S0119_S119


title: BCR3__S0102_S102


title: BCR3__S0101_S101


title: BCR6__S0124_S124


title: BCR3__S0115_S115


title: BCR3__S0111_S111


title: BCR3__S0107_S107


title: BCR3__S0108_S108


title: BCR3__S0103_S103


title: BCR3__S0109_S109


title: BCR3__S0100_S100


title: BCR3__S0099_S99


title: BCR3__S0096_S96

source_name: IGHV1-69_VH:VL_Post Boost 2_Splenic B cells


title: BCR3__S0112_S112


title: BCR3__S0105_S105


title: BCR3__S0090_S90

source_name: IGHV1-69_VL_Post Boost 2_Splenic B cells


title: BCR3__S0089_S89


title: BCR3__S0085_S85


title: BCR3__S0097_S97


title: BCR3__S0087_S87


title: BCR3__S0088_S88


title: BCR3__S0081_S81


title: BCR3__S0094_S94


title: BCR3__S0082_S82


title: BCR3__S0084_S84


title: BCR3__S0078_S78


title: BCR3__S0077_S77


title: BCR3__S0093_S93


title: BCR3__S0080_S80


title: BCR3__S0086_S86


title: BCR3__S0091_S91


title: BCR3__S0076_S76

description:
S76 Monoclonal HC:LC
processed data file: Consensus_Alignments.txt


title: BCR3__S0075_S75


title: BCR3__S0079_S79


title: BCR3__S0072_S72


title: BCR3__S0073_S73


title: BCR3__S0095_S95


title: BCR3__S0068_S68

description:
S68 Monoclonal HC:LC
processed data file: Consensus_Alignments.txt


title: BCR3__S0071_S71


title: BCR3__S0070_S70


title: BCR3__S0069_S69


title: BCR3__S0092_S92


title: BCR3__S0066_S66


title: BCR3__S0065_S65


title: BCR3__S0064_S64


title: BCR3__S0062_S62


title: BCR3__S0059_S59


title: BCR3__S0061_S61


title: BCR3__S0060_S60


title: BCR3__S0056_S56


title: BCR3__S0054_S54


title: BCR3__S0057_S57


title: BCR3__S0051_S51


title: BCR3__S0052_S52


title: BCR3__S0053_S53

description:
S53 Monoclonal HC:LC
processed data file: Consensus_Alignments.txt


title: BCR3__S0055_S55


title: BCR3__S0049_S49

description:
S49 Monoclonal HC:LC
processed data file: Consensus_Alignments.txt


title: BCR3__S0050_S50


title: BCR3__S0045_S45


title: BCR3__S0067_S67


title: BCR3__S0021_S21


title: BCR3__S0027_S27


title: BCR3__S0024_S24


title: BCR3__S0029_S29


title: BCR3__S0036_S36


title: BCR3__S0058_S58


title: BCR3__S0020_S20


title: BCR3__S0018_S18


title: BCR3__S0044_S44


title: BCR3__S0011_S11


title: BCR3__S0016_S16


title: BCR3__S0015_S15


title: BCR3__S0063_S63


title: BCR3__S0009_S9


title: BCR2__S0211_S211


title: BCR2__S0212_S212


title: BCR3__S0004_S4


title: BCR2__S0214_S214


title: BCR2__S0210_S210


title: BCR2__S0208_S208


title: BCR2__S0203_S203


title: BCR2__S0206_S206


title: BCR2__S0201_S201


title: BCR2__S0204_S204


title: BCR2__S0200_S200


title: BCR2__S0197_S197


title: BCR2__S0207_S207


title: BCR3__S0019_S19


title: BCR2__S0196_S196


title: BCR2__S0194_S194


title: BCR2__S0189_S189


title: BCR2__S0188_S188


title: BCR2__S0192_S192


title: BCR2__S0195_S195


title: BCR2__S0215_S215


title: BCR2__S0185_S185


title: BCR2__S0184_S184


title: BCR2__S0178_S178


title: BCR2__S0202_S202


title: BCR2__S0179_S179


title: BCR2__S0175_S175


title: BCR2__S0174_S174

description:
S102 Monoclonal LC
processed data file: Consensus_Alignments.txt


title: BCR2__S0181_S181


title: BCR2__S0183_S183


title: BCR2__S0176_S176


title: BCR2__S0173_S173


title: BCR2__S0171_S171


title: BCR2__S0172_S172


title: BCR2__S0170_S170


title: BCR2__S0169_S169


title: BCR2__S0165_S165


title: BCR2__S0168_S168


title: BCR2__S0167_S167


title: BCR2__S0166_S166


title: BCR2__S0163_S163


title: BCR2__S0161_S161

description:
S89 Monoclonal LC
processed data file: Consensus_Alignments.txt


title: BCR2__S0159_S159


title: BCR2__S0186_S186


title: BCR2__S0158_S158


title: BCR2__S0157_S157


title: BCR2__S0149_S149


title: BCR2__S0177_S177


title: BCR2__S0151_S151


title: BCR2__S0148_S148


title: BCR2__S0155_S155


title: BCR2__S0153_S153


title: BCR2__S0156_S156


title: BCR2__S0147_S147


title: BCR2__S0144_S144


title: BCR2__S0143_S143


title: BCR2__S0146_S146


title: BCR2__S0145_S145


title: BCR2__S0135_S135


title: BCR2__S0137_S137


title: BCR2__S0141_S141


title: BCR2__S0131_S131


title: BCR2__S0138_S138


title: BCR2__S0134_S134


title: BCR2__S0133_S133


title: BCR2__S0128_S128


title: BCR2__S0130_S130


title: BCR2__S0132_S132


title: BCR2__S0127_S127


title: BCR2__S0121_S121


title: BCR2__S0120_S120


title: BCR2__S0118_S118


title: BCR2__S0122_S122


title: BCR2__S0119_S119


title: BCR2__S0116_S116


title: BCR2__S0126_S126


title: BCR2__S0115_S115


title: BCR2__S0114_S114


title: BCR2__S0108_S108


title: BCR2__S0111_S111


title: BCR2__S0107_S107


title: BCR2__S0140_S140


title: BCR2__S0105_S105


title: BCR2__S0103_S103


title: BCR2__S0109_S109


title: BCR2__S0100_S100


title: BCR2__S0097_S97


title: BCR2__S0101_S101


title: BCR2__S0102_S102

description:
S102 Monoclonal HC
processed data file: Consensus_Alignments.txt


title: BCR2__S0094_S94


title: BCR2__S0096_S96


title: BCR2__S0087_S87


title: BCR2__S0089_S89

description:
S89 Monoloncal HC
processed data file: Consensus_Alignments.txt


title: BCR2__S0091_S91


title: BCR2__S0092_S92


title: BCR2__S0085_S85


title: BCR2__S0080_S80


title: BCR2__S0077_S77


title: BCR2__S0073_S73


title: BCR2__S0074_S74


title: BCR2__S0036_S36


title: BCR2__S0076_S76


title: BCR2__S0035_S35


title: BCR2__S0106_S106


title: BCR2__S0113_S113


title: BCR2__S0093_S93


title: BCR2__S0088_S88


title: BCR2__S0028_S28


title: BCR2__S0032_S32


title: BCR2__S0026_S26


title: BCR2__S0033_S33


title: BCR2__S0030_S30


title: BCR2__S0034_S34


title: BCR2__S0021_S21


title: BCR2__S0020_S20


title: BCR2__S0018_S18


title: BCR2__S0078_S78


title: BCR2__S0017_S17


title: BCR2__S0016_S16


title: BCR2__S0015_S15


title: BCR2__S0014_S14


title: BCR2__S0011_S11


title: BCR2__S0012_S12


title: BCR2__S0010_S10


title: BCR2__S0009_S9


title: BCR2__S0029_S29


title: BCR2__S0027_S27


title: BCR2__S0008_S8


title: BCR2__S0023_S23


title: BCR2__S0024_S24


title: BCR2__S0006_S6


title: BCR2__S0022_S22


title: BCR2__S0007_S7


title: BCR2__S0005_S5


title: BCR2__S0002_S2


title: BCR2__S0004_S4


title: BCR2__S0019_S19


title: BCR1__VH6901-C11_S131


title: BCR2__S0003_S3


title: BCR1__VH6901-C12_S132


title: BCR1__VH6901-C10_S130


title: BCR2__S0001_S1


title: BCR1__VH6901-C06_S126


title: BCR1__VH6901-C07_S127


title: BCR1__VH6901-C04_S124


title: BCR1__VH6901-C08_S128


title: BCR2__S0013_S13


title: BCR1__VH6901-C02_S122


title: BCR1__VH6901-C01_S121


title: BCR1__VH6901-C03_S123


title: BCR1__VH6901-B10_S118


title: BCR1__VH6901-B11_S119


title: BCR1__VH6901-B09_S117


title: BCR1__VH6901-B07_S115


title: BCR1__VH6901-B06_S114


title: BCR1__VH6901-B08_S116


title: BCR1__VH6901-B05_S113


title: BCR1__VH6901-B04_S112


title: BCR1__VH6901-B12_S120


title: BCR1__VH6901-A12_S108


title: BCR1__VH6901-B02_S110


title: BCR1__VH6901-A11_S107


title: BCR1__VH6901-A09_S105


title: BCR1__VH6901-C05_S125


title: BCR1__VH6901-A10_S106


title: BCR1__VH6901-A08_S104


title: BCR1__VH6901-A07_S103


title: BCR1__VH6901-A05_S101


title: BCR1__VH6901-A06_S102


title: BCR1__VH6901-B03_S111


title: BCR2__S0025_S25


title: Capture_H3K27me3_UNC_3866_rep2

city: Los Angeles

first: Oliver

last: Bell

state: CALIFORNIA

address: 1450 Biggy Street

department: Biochemistry and Molecular Medicine

institute: Keck School of Medicine of the University of Southern California

description:
4h treatment with 20uM UNC3866
processed data file: Capture_H3K27me3_UNC3866_merged.bw

data_processing:
Processing and mapping of raw reads: The raw reads of ChIP-seq and capture-seq were mapped to the customized genome using bowtie2 (Langmead and Salzberg, 2012). In addition, the unique mapped reads were retained and duplicated reads were discarded using SAMtools (Li et al., 2009).
Peak calling: After merging biological replicates, peaks were called using MACS2 (Zhang et al., 2008) with -broad option and default q-value cutoff of 0.1 for both ChIP-seq and Capture-seq samples. In particular, only peaks within baits were retained for Capture-seq samples.
Data visualization: For visualization, the coverage tracks (bigWig files) were generated with R package rtracklayer (Lawrence et al., 2009) and heatmaps were done with deepTools (Ramirez et al., 2016).
Differential binding analysis: Read counts within peaks were first quantified with featureCounts function in R package Rsubread (Liao et al., 2013). The differential binding analysis were done with DESeq2 package (Love et al., 2014) in which the ChIP-seq samples were normalized by library sizes and capture-ChIP-seq samples were normalized by total read counts in the baits but excluding the Polycomb proteins binding regions.
Genome_build: ChIP-seq: mm10, Capture ChIP-seq: mm9
Supplementary_files_format_and_content: bigwig were generated using DeepTools.

source_name: mouse embryonic stem cell

growth_protocol: mESCs were cultivated without feeders in high-glucose-DMEM (Sigma, D6429) supplemented with 13.5% fetal bovine serum (Gibco), 10 mM HEPES pH 7.4 (Corning, 25-060-CI), 2 mM GlutaMAX (Gibco, 35050-061), 1 mM Sodium Pyruvate (Gibco, 11360-070), 1% Penicillin/Streptomycin (Sigma, P0781), 1X non-essential amino acids (Gibco, 11140-050), 50 mM β-mercaptoethanol (Gibco, 21985-023) and recombinant LIF, and incubated at 37°C and 5% CO2.

extract_protocol:
ChIP samples were prepared as previously reported (Moussa et al., Nature Communications 2019, doi:10.1038/s41467-019-09628-6). For Capture ChIP-seq, 120nt-long MYbaits sequence capture probes (Arbor Biosciences) were custom designed for 24 genomic loci based on mm9 genome build. Designed probes were tiled at an approximate density of 1.26 (=starting approx. every 95bp) to cover a total of 1,960,734 bp. After repeat masking, candidate probes were filtered for stringent specificity. Sequence capture from genomic DNA recovered in ChIP was carried out according to manufacturer’s instructions.
Libraries were prepared using the NEXTflex ChIP-Seq kit (Bio Scientific) following the “No size-selection cleanup” protocol and doubling the incubation times for all enzymatic steps. Each sample of ChIPed DNA was end-repaired and ligated to unique barcoded adaptors to produce individual libraries. Libraries corresponding to samples to be directly compared to each other (e.g. +IAA vs -IAA) were pooled together and purified using 1 volume of Agencourt AMPure XP (Beckman Coulter). The pooled libraries were eluted with 25 µL of elution buffer (NEXTflex ChIP-Seq kit) and amplified using the KAPA Real-Time Library Amplification Kit (peqlab) following the kit instructions. Finally, the amplified libraries were size-selected to fragments of 200-800 bp by running them on 1.5% agarose gel, and staining with 1x SYBR Gold (Thermo Fisher) to visualize the DNA on a blue light LED screen and cut the appropriate fragments. The size selected libraries were gel purified with the Monarch DNA Gel extraction kit (NEB).

treatment_protocol: 20uM of compound for 4 hours.

value: Embryonic stem cells

tag: treatment

tag: chip antibody

value: anti-H3K27me3 (Diagenode, C15410195)


title: Capture_H3K27me3_UNC_4976_rep1

description:
4h treatment with 20uM UNC4976
processed data file: Capture_H3K27me3_UNC4976_merged.bw


title: Capture_H3K27me3_UNC_4976_rep2


title: Capture_H3K27me3_UNC_4219_rep2

description:
4h treatment with 20uM UNC4219 (control compound)
processed data file: Capture_H3K27me3_UNC4219_merged.bw

value: UNC4219 (control compound)


title: Capture_H3K27me3_UNC_3866_rep1


title: Capture_H3K27me3_UNC_4219_rep1


title: Capture_Suz12_UNC_3866_rep2

description:
4h treatment with 20uM UNC3866
processed data file: Capture_Suz12_UNC3866_merged.bw

value: anti-Suz12 (Cell Signaling, D39F6)


title: Capture_Suz12_UNC_4976_rep1

description:
4h treatment with 20uM UNC4976
processed data file: Capture_Suz12_UNC4976_merged.bw


title: Capture_Suz12_UNC_4976_rep2


title: Capture_Suz12_UNC_3866_rep1


title: Capture_Suz12_UNC_4219_rep1

description:
4h treatment with 20uM UNC4219 (control compound)
processed data file: Capture_Suz12_UNC4219_merged.bw


title: Capture_Ring1B_UNC_3866_rep1

description:
4h treatment with 20uM UNC3866
processed data file: Capture_Ring1B_UNC3866_merged.bw

value: anti-Ring1B (Cell Signaling, D22F2)


title: Capture_Ring1B_UNC_4976_rep2

description:
4h treatment with 20uM UNC4976
processed data file: Capture_Ring1B_UNC4976_merged.bw


title: Capture_Suz12_UNC_4219_rep2


title: Capture_Ring1B_UNC_3866_rep2


title: Capture_Ring1B_UNC_4219_rep1

description:
4h treatment with 20uM UNC4219 (control compound)
processed data file: Capture_Ring1B_UNC4219_merged.bw


title: Capture_Cbx7Cbx7_UNC_4976_rep2

description:
4h treatment with 20uM UNC4976
processed data file: Capture_Cbx7_UNC4976_merged.bw

value: anti-Cbx7 (Abcam, ab21873)


title: Capture_Cbx7Cbx7_UNC_3866_rep2

description:
4h treatment with 20uM UNC3866
processed data file: Capture_Cbx7_UNC3866_merged.bw


title: Capture_Cbx7Cbx7_UNC_3866_rep1


title: BCR1__VH6901-A02_S98

description: processed data file: Consensus_Alignments.txt

value: VH

value: Splenic B cells

value: BCR Amplicon from RNA


title: BCR1__VH6901-A04_S100


title: BCR1__VH6901-A03_S99


title: Capture_Cbx7Cbx7_UNC_4219_rep2

description:
4h treatment with 20uM UNC4219 (control compound)
processed data file: Capture_Cbx7_UNC4219_merged.bw


title: Capture_Cbx7Cbx7_UNC_4219_rep1


title: knockout female mouse [KF21]

city: Farmington

first: Richard

middle: E

last: Mains

state: CT

address: 263 Farmington Ave, Neuroscience Dept., Neuroscience Dept.

department: Neuroscience

institute: University of Connecticut Health Center

description:
CGI-6_S6
KF21

data_processing:
Read trimming: sickle parameters: -l 45 -q 25
alignment: HiSat2 parameters: default
abundance estimation: htseq-count parameters: default
FPKM
Differential expression analyzed using DESeq2 in R
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

source_name: PAM knockout female mus atrium

growth_protocol: adult mice, aged 60-90 days

extract_protocol:
Individual atria were extracted in Trizol and processed as per manufacturer's instructions
Illumina TruSeq Stranded mRNA per manufacturer's instructions
RNASeq samples were barcoded and all run in a single NextSeq run with 20 million total paired end 75bp reads per sample.

value: female

tag: tissue

value: atrium

tag: genotype/variation

value: PAM knockout


title: Capture_Cbx7Cbx7_UNC_4976_rep1


title: Capture_Ring1B_UNC_4976_rep1


title: BCR1__VH6901-A01_S97


title: Capture_Ring1B_UNC_4219_rep2


title: Capture_Input_UNC_4976_rep2

description:
4h treatment with 20uM UNC4976
processed data file: Capture_Input_UNC4976_merged.bw


title: knockout female mouse [KF20]

description:
CGI-5_S5
KF20


title: knockout female mouse [KF19]

description:
CGI-4_S4
KF19


title: Capture_Input_UNC_3866_rep2

description:
4h treatment with 20uM UNC3866
processed data file: Capture_Input_UNC3866_merged.bw


title: knockout female mouse [KF16]

description:
LA11_S10
KF16


title: Capture_Input_UNC_4219_rep2

description:
4h treatment with 20uM UNC4219 (control compound)
processed data file: Capture_Input_UNC4219_merged.bw


title: Capture_Input_UNC_3866_rep1


title: knockout female mouse [KF17]

description:
LA12_S11
KF17


title: knockout female mouse [KF18]

description:
RA10_S12
KF18


title: knockout female mouse [KF15]

description:
RA11_S8
KF15


title: Capture_Input_UNC_4219_rep1


title: knockout female mouse [KF14]

description:
LA5_S4
KF14


title: Cbx7_wt_rep2

description:
Untreated
processed data file: Cbx7wt_merged.bw

value: Untreated


title: Ring1B_wt_rep2

description:
Untreated
processed data file: Ring1Bwt_merged.bw


title: Ring1B_wt_rep1


title: H3K27me3_wt_rep1

description:
Untreated
processed data file: H3K27me3wt_merged.bw


title: knockout male mouse [KM01]

description:
MaleKOAtrium-1_S1
KM01

source_name: PAM knockout male mouse atrium

value: male


title: Suz12_wt_rep2

description:
Untreated
processed data file: Suz12wt_merged.bw


title: knockout male mouse [KM05]

description:
MaleKOAtrium-5_S3
KM05


title: knockout male mouse [KM03]

description:
MaleKOAtrium-3_S2
KM03


title: Ring1B_UNC_4976_rep1

description:
4h treatment with 20uM UNC4976
processed data file: Ring1B_UNC4976_merged.bw


title: wildtype female mouse [WF11]

description:
CGI-8_S8
WF11

source_name: wildtype female mouse atrium

value: wildtype


title: knockout male mouse [KM07]

description:
MaleKOAtrium-7_S4
KM07


title: wildtype female mouse [WF12]

description:
CGI-9_S9
WF12


title: Ring1B_UNC_3866_rep1

description:
4h treatment with 20uM UNC3866
processed data file: Ring1B_UNC3866_merged.bw


title: H3K27me3_wt_rep2


title: wildtype male mouse [WM5]

description:
CGI-1_S1
WM5

source_name: wildtype male mouse atrium


title: Ring1B_UNC_4219_rep2

description:
4h treatment with 20uM UNC4219 (control compound)
processed data file: Ring1B_UNC4219_merged.bw


title: Ring1B_UNC_4219_rep1


title: wildtype female mouse [WF8]

description:
RA8_S6
WF8


title: wildtype male mouse [WM7]

description:
CGI-3_S3
WM7


title: Suz12_wt_rep1


title: knockout male mouse [KM13]

description:
RA12_S9
KM13


title: Ring1B_UNC_3866_rep2


title: Capture_Input_UNC_4976_rep1


title: wildtype male mouse [WM4]

description:
RA7_S5
WM4


title: wildtype male mouse [WM6]

description:
CGI-2_S2
WM6


title: Cbx7_wt_rep1


title: Cbx7_UNC_4219_rep2

description:
4h treatment with 20uM UNC4219 (control compound)
processed data file: Cbx7_UNC4219_merged.bw


title: wildtype female mouse [WF10]

description:
CGI-7_S7
WF10


title: wildtype male mouse [WM2]

description:
LA2_S2
WM2


title: Cbx7_UNC_4219_rep1


title: GC B cells - naive mother rep2

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: GRCm38.80

source_name: draining inguinal lymph nodes

extract_protocol:
inguinal draining lymph nodes were removed at day 18 post HA/CAF01 immunization of neonatal mice born with or without maternal antibodies. Samples from each group were pooled and B cells were enriched by using the EasySep™ Mouse B Cell Isolation Kit. Enriched B cells were then stained with the following antibodies: Alexa Fluor 488 anti- GL7, BV510 anti- B220 , PE-Cy7 anti- CD19, PE anti-Fas, and APC anti- TCR β. DAPI was used to discriminate live from dead cells.  B220+CD19+GL7+CD95+ GC B cells and B220+CD19+GL7negCD95neg non-GC B cells were simultaneously isolated from the enriched B cells by flow-cytometry cell sorting using a MoFlo® Astrios™ flow cytometer.
RNA libraries were prepared for sequencing using standard Illumina protocols; RNA was harvested using the RNeasy Mini Kit (Qiagen), 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina. Library molarity and quality was assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled and loaded at 2 nM for clustering on a Single-read Illumina Flow cell. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer.

tag: group

value: naive mother

tag: strain

value: inguinal lymph nodes

tag: time

value: Day 18 post-immunization

value: 25 days

value: CD19+B220+GL7+FAS+ GC B cells sorted by flow cytometry


title: GC B cells - immune mother rep3

value: immune mother


title: Cbx7_UNC_4976_rep1

description:
4h treatment with 20uM UNC4976
processed data file: Cbx7_UNC4976_merged.bw

value: Embryonic stem cells


title: wildtype female mouse [WF9]

description:
RA9_S7
WF9


title: Cbx7_UNC_4976_rep2

value: anti-Cbx7 (Abcam, ab21873)


title: Ring1B_UNC_4976_rep2

value: anti-Ring1B (Cell Signaling, D22F2)


title: wildtype male mouse [WM3]

description:
LA3_S3
WM3


title: non-GC B cells - immune mother rep2

value: CD19+B220+GL7negFASneg non-GC B cells sorted by flow cytometry


title: non-GC B cells - naive mother rep3


title: GC B cells - naive mother rep3


title: Cbx7_UNC_3866_rep1

description:
4h treatment with 20uM UNC3866
processed data file: Cbx7_UNC3866_merged.bw


title: GC B cells - naive mother rep1


title: Cbx7_UNC_3866_rep2


title: GC B cells - immune mother rep1


title: 966

description: HippExpressionmatrix.txt

source_name: Hippocampus

value: Male

value: Vehicle (Sunflower Oil)

value: 3 Months


title: non-GC B cells - naive mother rep2


title: non-GC B cells - immune mother rep3


title: non-GC B cells - immune mother rep1


title: non-GC B cells - naive mother rep1