title: WT_Pro_2

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description:
B126T8
Wild-type cells in proline-containing medium

data_processing:
Reads were mapped to the S. cerevisiae  reference genome using the version 2.0.6 of TopHat, with no mismatch in seed alignment (of size 22) anda tolerance of 3 mismatches in read length, a minimum and a maximum size for introns of 5 bp and 5kb, respectively.
Tags densities were normalized on the total number of reads uniquely mapped on ORFs.
Genome_build: Yeast saccharomyces_cerevisiae R64-1-1
Supplementary_files_format_and_content: A single tab-delimited text file including normalized tag densities (tag/nt) for all annotated genes, in each sample.

organism: Saccharomyces cerevisiae

source_name: Yeast cells

extract_protocol:
Total RNA was extracted using standard hot-phenol procedure
Ribosomal RNAs were depleted from total RNA using the RiboMinus Eukaryote v2 Kit (Life Technologies). Strand-specific total RNA-Seq libraries were prepared from 125 ng of rRNA-depleted RNA using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina). Paired-end sequencing (2 x 50 nt) of the libraries was performed on a HiSeq 2500 sequencer.

tag: genotype/variation

value: Wild-type

tag: growth protocol

value: grown in  proline-containing medium

tag: biological replicate


title: dal80_Pro_2

status: Public on Feb 06 2019

type: SRA

description:
B126T12
dal80-delta cells in proline-containing medium

library_source: transcriptomic

molecule: total RNA


title: dal80_Pro_1

description:
B126T6
dal80-delta cells in proline-containing medium


title: DZQV_Neutrophils_rep4

city: Freiburg

first: Gianni

last: Monaco

address: Breisacher Straße

country: Germany

institute: Freiburg Medical Center

description:
cell_number (facs): 147334
total_rna_yield (ng): 5.076
DZQV_Neutrophils

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
Genome_build: GENCODE 26
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Low-density neutrophils

extract_protocol:
RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.

tag: cell type

value: Low-density neutrophils

tag: disease status

value: healthy

tag: gender

value: M


title: DZQV_Treg_rep4

description:
cell_number (facs): 170358
total_rna_yield (ng): 11.58
DZQV_Treg

source_name: T regulatory cells

value: T regulatory cells


title: DZQV_pDC_rep4

description:
cell_number (facs): 200079
total_rna_yield (ng): 237.228
DZQV_pDC

source_name: Plasmacytoid dendritic cells

value: Plasmacytoid dendritic cells


title: DZQV_Th1/Th17_rep4

description:
cell_number (facs): 156343
total_rna_yield (ng): 23.592
DZQV_Th1/Th17

source_name: Th1/Th17 cells

value: Th1/Th17 cells


title: WT_Pro_1

description:
B126T2
Wild-type cells in proline-containing medium


title: DZQV_TFH_rep4

description:
cell_number (facs): 360352
total_rna_yield (ng): 61.668
DZQV_TFH

source_name: Follicular helper T cells

value: Follicular helper T cells


title: DZQV_Th1_rep4

description:
cell_number (facs): 450000
total_rna_yield (ng): 70.956
DZQV_Th1

source_name: Th1 cells

value: Th1 cells


title: Gat1_Myc_Pro_IN_2

description:
Gat1-Myc strain grown in proline-containing medium
Gat1.Myc_IN.2

library_source: genomic

data_processing:
Reads were uniquely mapped to the S. cerevisiae S288C reference genome using Bowtie2 v2.1.0, with a tolerance of 1 mismatch in seed alignment.
Tags densities were normalized on the total number of uniquely reads mapped.
Dal80- and Gat1-bound regions were identified through a peak-calling procedure using version 2.0.9 of MACS, with a minimum false discovery rate (FRD) of 0.001.
Genome_build: S. cerevisiae S288C
Supplementary_files_format_and_content: Normalized coverage for each sample (bigWig format)

molecule: genomic DNA

growth_protocol: WT (untagged), Dal80-Myc13 and Gat1-Myc13 cells were grown to mid-log phase in proline-containing medium.

extract_protocol:
ChIP-Seq analysis was performed from two biological replicates of each strain.
Libraries were prepared from 10 ng of "input" or "IP" DNA using the TruSeq ChIP Sample Preparation Kit (Illumina). Single-end sequencing (50 nt) of the libraries was performed on a HiSeq 2500 sequencer.

tag: strain

value: Gat1-Myc strain

tag: chip antibody

value: Input

value: grown in proline-containing medium


title: WT_Pro_IN_2

description:
Untagged WT strain grown in proline-containing medium
No_Tag_IN.2

value: Untagged WT strain


title: Dal80_Myc_Pro_IN_2

description:
Dal80-Myc strain grown in proline-containing medium
Dal80_IN.2

value: Dal80-Myc strain


title: DZQV_VD2+_rep4

description:
cell_number (facs): 900000
total_rna_yield (ng): 350.424
DZQV_VD2+

source_name: Vd2 gd T cells

value: Vd2 gd T cells


title: Dal80_Myc_Pro_IP_2

description:
Dal80-Myc strain grown in proline-containing medium
Dal80.Myc.2

value: c-Myc Antibody (9E10) (Santa Cruz Biotechnology, catalog# sc-40)


title: DZQV_MAIT_rep4

description:
cell_number (facs): 900000
total_rna_yield (ng): 449.82
DZQV_MAIT

source_name: MAIT cells

value: MAIT cells


title: DZQV_VD2-_rep4

description:
cell_number (facs): 1003272
total_rna_yield (ng): 240.156
DZQV_VD2-

source_name: Non-Vd2 gd T cells

value: Non-Vd2 gd T cells


title: WT_Pro_IP_2

description:
Untagged WT strain grown in proline-containing medium
No_Tag.2


title: Gat1_Myc_Pro_IP_2

description:
Gat1-Myc strain grown in proline-containing medium
Gat1.Myc.2


title: Dal80_Myc_Pro_IP_1

description:
Dal80-Myc strain grown in proline-containing medium
Dal80.Myc.1


title: Dal80_Myc_Pro_IN_1

description:
Dal80-Myc strain grown in proline-containing medium
Dal80_IN.1


title: Gat1_Myc_Pro_IP_1

description:
Gat1-Myc strain grown in proline-containing medium
Gat1.Myc.1


title: DZQV_B_naive_rep4

description:
cell_number (facs): 702312
total_rna_yield (ng): 149.232
DZQV_B_naive

source_name: Naive B cells

value: Naive B cells


title: WT_Pro_IN_1

description:
Untagged WT strain grown in proline-containing medium
No_Tag_IN.1


title: DZQV_CD8_EM_rep4

description:
cell_number (facs): 1181147
total_rna_yield (ng): 488.508
DZQV_CD8_EM

source_name: Effector memory CD8 T cells

value: Effector memory CD8 T cells

value: healthy


title: DZQV_Th17_rep4

description:
cell_number (facs): 205024
total_rna_yield (ng): 33.696
DZQV_Th17

source_name: Th17 cells

value: Th17 cells

value: M


title: DZQV_CD8_CM_rep4

description:
cell_number (facs): 324600
total_rna_yield (ng): 102.468
DZQV_CD8_CM

source_name: Central memory CD8 T cell

value: Central memory CD8 T cell


title: DZQV_CD8_naive_rep4

description:
cell_number (facs): 900000
total_rna_yield (ng): 321.78
DZQV_CD8_naive

source_name: Naive CD8 T cells

value: Naive CD8 T cells


title: WT+FU_100min_1

data_processing:
Reads were mapped to the S. cerevisiae S288C reference genome using the version 2.0.6 of TopHat, with a tolerance of 3 mismatches and a maximum size for introns of 2 Kb.
All bioinformatics analyses used reads uniquely mapped on the reference genome.
Tag densities for genes, dubious ORFs, sn(o)RNAs, tRNAs and several classes of lncRNAs (including CUTs, SUTs, XUTs and MUTs) were obtained after normalization on the total number of reads that uniquely mapped on ORFs.
Genome_build: S. cerevisiae S288C

extract_protocol:
Total RNA was extracted using the hot phenol procedure
Strand-specific total RNA-Seq libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina), starting from 125 ng of rRNA-depleted RNA. Paired-end sequencing (2x50 nt) of the libraries was performed on a HiSeq 2500 sequencer.

value: wild type

tag: time point

value: 100 min after synchronization

tag: replicate

value: Biological replicate 1

tag: molecule subtype

value: rRNA-depleted RNA


title: rrp6_100min_1

value: 100 minutes after synchronization


title: WT+FU_100min_2

value: Biological replicate 2


title: rrp6_40min_1

value: 40 minutes after synchronization


title: WT+FU_40min_2

value: 40 min after synchronization


title: WT_40min_2


title: rrp6_40min_2


title: WT_100min_1


title: DZQV_CD8_TE_rep4

description:
cell_number (facs): 1000000
total_rna_yield (ng): 274.26
DZQV_CD8_TE

source_name: Terminal effector CD8 T cells

value: Terminal effector CD8 T cells


title: WT+FU_40min_1


title: WT_40min_1


title: WT_Pro_IP_1

description:
Untagged WT strain grown in proline-containing medium
No_Tag.1

value: Untagged WT strain

value: c-Myc Antibody (9E10) (Santa Cruz Biotechnology, catalog# sc-40)

value: grown in proline-containing medium


title: RNA-seq_mal replicate 2

city: Badalona

first: Jeannine

last: Diesch

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

department: Research

country: Spain

institute: Josep Carreras Leukaemia Research Institute

description: malignant

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to the mm9 genome assembly using bowtie with default parameters
Reads were counted using HTSeq
Differential expressed genes were identified using DEseq
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited read counts from Htseq; Table with differential expression determined by Deseq

organism: Mus musculus

source_name: primary preB cells_malignant

growth_protocol: Eμ-Myc mice were maintained as heterozygote on a C57BL/6 background

extract_protocol:
Primary pre-B cells were purified from bone marrow of wt, prem and mal mice on the basis of high B220, low IgM and low IgD surface marker expression by flow cytometry.
Libraries were prepared using TruSeq RNA Sample Prep Kit v2 (Illumina)

treatment_protocol: Wt and prem mice were sacrificed at age 4-6 weeks and mal mice as soon as they established spontaneous lymphoma (age 10-20 weeks)

tag: tissue

value: bone marrow

tag: age

value: 10-20 weeks

value: primary preB cells from bone-marrow

tag: genotype

value: E{mu}Myc/+


title: 4C-seq_LMP replicate 2

description: malignant

data_processing:
Library strategy: 4C-seq
Basecalls performed using CASAVA version 1.8.2
Reads were demultiplexed using the bait sequences and bait sequences removed
Reads were aligned to the mm9 genome assembly using bowtie with default parameters
Reads were split in non-overlapping 5000bp windows
Read coverage was determined using Bed tools package
Genome_build: mm9
Supplementary_files_format_and_content: Genome-wide read coverage

source_name: primary preB cells_tissue-culture adapted extracted from malignant Eμ-Myc mice

extract_protocol:
Primary pre-B cells were purified from bone marrow of wt, prem and mal mice on the basis of high B220, low IgM and low IgD surface marker expression by flow cytometry.
Libraries were prepared using ThruPLEX-FD Prep Kit (Rubicon Genomics Inc.)

value: tissue culture adapted preB cells extracted from malignant E{mu}Myc mice


title: RNA-seq_wt replicate 2

description: wild type

source_name: primary preB cells_wildtype

value: 4-6 weeks

value: wild type


title: 4C-seq_LMP replicate 1

description: malignant


title: 4C-seq_shUBTF replicate 2

description: malignant

source_name: primary preB cells_tissue-culture adapted extracted from malignant Eμ-Myc mice_shUBTF


title: RNA-seq_wt replicate 1

description: wild type


title: RNA-seq_prem replicate 2

description: premalignant

source_name: primary preB cells_premalignant


title: 4C-seq_shUBTF replicate 1

description: malignant


title: RNA-seq_prem replicate 1

description: premalignant


title: Gat1_Myc_Pro_IN_1

description:
Gat1-Myc strain grown in proline-containing medium
Gat1.Myc_IN.1

source_name: Yeast cells

value: Gat1-Myc strain

value: Input


title: 4C-seq_mal replicate 2

description: malignant


title: 4C-seq_prem replicate 2

description: premalignant


title: 4C-seq_prem replicate 1

description: premalignant


title: 4C-seq_mal replicate 1

description: malignant


title: WT_100min_2

value: 100 min after synchronization

value: rRNA-depleted RNA


title: 4C-seq_wt replicate 2

description: wild type


title: Blood-derived immune-cell mixture from donor 2

city: Innsbruck

first: Francesca

last: Finotello

address: Innrain 80-82

department: Division of Bioinformatics

country: Austria

institute: Biocenter, Medical University of Innsbruck

data_processing:
Base calling was performed with Casava software.
FASTQ files of RNA-seq reads were pre-processed with Trimmomatic (Bolger, A. et al., Bioinforma. Oxf. Engl., 2014) to remove adapter sequences and read ends with Phred quality scores lower than 20, to discard reads shorter than 36 bp, and to trim long reads to a maximum length of 50 bp.
Pre-processed RNA-seq reads were analyzed with Kallisto (Bray, N. et al., Nat. Biotechnol., 2016), with options “--single -l 50 -s 20” options, to generate gene counts and transcripts per millions (TPM) using the “hg19_M_rCRS” human reference.
Genome_build: hg19
Supplementary_files_format_and_content: Files with gene raw counts and transcripts per millions (TPM)

source_name: PBMC/PMN cell mixture derived from blood sample

extract_protocol:
The PBMC fraction was collected and washed three times with Dulbecco’s phosphate buffered saline. To isolate polymorphonuclear (PMN) cells, the cells on top of the erythrocytes were collected and contaminating red blood cells were removed by two rounds of lysis with 0.2% NaCl solution at 4°C. PMN were added to the PBMC fractions in low abundance (3-6% of total cells) and aliquots were taken for RNA extraction and flow cytometry analysis. Total RNA was extracted with the Qiagen RNeasy mini kit (Qiagen GmbH, Hilden, Austria), including on-column DNAse I treatment, and subjected to INVIEW polyA RNA library preparation.
Library preparation incorporated adaptor sequences and indexing compatible for Illumina sequencing technology, using proprietary methods of GATC Biotech (https://www.gatc-biotech.com).

tag: subject status

value: healthy donor

tag: subject id

value: donor 2

value: blood

value: PBMC/PMN cell mixture

tag: natural killer cells

tag: b cells

tag: myeloid dendritic cells

tag: tregs

tag: monocytes

tag: neutrophils

tag: cd8+ t cells

tag: cd4+ t cells


title: Blood-derived immune-cell mixture from donor 4

value: donor 4

tag: cell type


title: Blood-derived immune-cell mixture from donor 5

value: donor 5


title: 4C-seq_wt replicate 1

description: wild type

tag: strain

value: bone marrow


title: RNAseq-Th2-WT-rep3

status: Public on Feb 05 2019

city: Toulouse

first: Veronique

last: Adoue

address: CHU Purpan

institute: CNRS

description: RNAseq_htseqcount_allsamples_normalized.txt

data_processing:
Trimming of adaptor sequences and removal of low-quality bases (−q value, <15) (Cutadapt 1.3)
High-quality reads were aligned to the mouse reference genome mm10 using TopHat version 2.0.5 (RNA-seq) or BWA v.0.7.10 (ChIP-seq).
H3K4me1 peaks were detected by using the ‘broad’ option of MACS2 v.2.1.0
H3K9me3 peaks were detected using CSAW v.1.4.1.
Differential expression analysis was performed by using the DESeq package
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include normalized raw reads count for each RNA-seq sample or ChIP-seq peaks coordinates for each histone marks.

source_name: Spleen CD4+ T cells

growth_protocol: Naïve CD4 T cells were cultured for three days in 96-well flat bottom plates coated with 10 ug/mL anti-CD3epsilon antibody (145-2C11, InVivoMabTM, BioXcell) in RPMI 1640 GlutamaxTM supplemented with 1 mM sodium pyruvate, non-essential amino acids, 10 mM HEPES, 100 units/mL penicillin, 100 ug/mL streptomycin, 50 mM 2beta-mercaptoethanol, 10% fetal calf serum (all from Thermo Fischer Scientific) and 1 ug/mL anti-CD28 antibody (37.51, InVivoMabTM, BioXcell). Th2 medium contained 50 ng/mL recombinant mouse IL-4 (R&D systems) and 10 ug/mL anti-IFNgamma neutralizing antibody (XMG1.2, InVivoMabTM, BioXcell). At day 3, the cells were re-plated in the same conditioning medium but without the anti-CD3epsilon and anti-CD28 antibodies and with 30 IU/mL recombinant IL-2 (Proleukin). To test for Th2 cell lineage commitment, cells were harvested at day 6, extensively washed in complete medium, and re-plated in Th1-polarizing conditions: Th1 medium contained 10 ng/mL recombinant mouse IL-12 (R&D Systems) and 10 ug/mL anti-IL-4 neutralizing antibody (11B11, InVivoMabTM, BioXcell).

extract_protocol:
For RNA-seq: Total RNA was extracted by using the RNeasy Micro Kit (Qiagen). For ChIP-seq: DNA purification was performed by column (MiniElute PCR purification kit, Qiagen).
Libraries were prepared for sequencing using standard TruSeq Illumina protocols

value: Th2 T lymphocytes

tag: number of culture days

value: C57BL/6 Setdb1+/+


title: Blood-derived immune-cell mixture from donor 12

value: donor 12


title: Blood-derived immune-cell mixture from donor 6

value: donor 6


title: Blood-derived immune-cell mixture from donor 9

value: donor 9


title: Blood-derived immune-cell mixture from donor 10

value: donor 10


title: RNAseq-Th2-WT-rep2


title: RNAseq-Th2-Th1-Setdb1-KO-rep2

value: Th2 T lymphocytes cultured with pro-Th1 differentiation signals

value: C57BL/6 Setdb1-/-


title: RNAseq-Th2-Th1-Setdb1-KO-rep3


title: RNAseq-Th2-Th1-WT-rep1


title: RNAseq-Th2-Th1-WT-rep2


title: RNAseq-Th2-Th1-Setdb1-KO-rep1


title: ChIPseq-Th2-WT-H3K9me3-rep2

tag: antibody

value: H3K9me3 (ab8898 from Abcam; lot GR114265-2)


title: RNAseq-Th2-Setdb1-KO-rep2


title: RNAseq-Th2-Setdb1-KO-rep3


title: ChIPseq-Th2-WT-H3K9me3-rep1


title: ChIPseq-Th2-WT-H3K4me1-rep1

value: H3K4me1 (ab8895 from Abcam; lot GR186864-1)


title: ChIPseq-Th2-WT-H3K4me1-rep2


title: ChIPseq-Th2-Suv39h1-KO-H3K9me3-rep2

description: ChIPseq-Th2-Suv39h1-KO-H3K9me3-peaks.bed


title: ChIPseq-Th2-Suv39h1-KO-H3K9me3-rep1


title: ChIPseq-Th2-Setdb1-KO-H3K9me3-rep2


title: Blood-derived immune-cell mixture from donor 1

value: healthy donor

value: donor 1

tag: tissue


title: rrp6_100min_2

tag: genotype/variation

tag: time point

value: 100 minutes after synchronization

tag: replicate

value: Biological replicate 2

tag: molecule subtype

value: rRNA-depleted RNA


title: ChIPseq-Th2-Setdb1-KO-H3K9me3-rep1


title: ChIPseq-Naives-WT-H3K4me1-rep2

description: ChIPseq-Naives-WT-H3K4me1-peaks.broadPeak

value: Naives T lymphocytes


title: ChIPseq-Naives-WT-H3K9me3-rep1


title: RNAseq-Th2-WT-rep1


title: ChIPseq-Naives-WT-H3K4me1-rep1


title: ChIPseq-Naives-Setdb1-KO-H3K9me3-rep1

description: ChIPseq-Naives-Setdb1-KO-H3K9me3-peaks.bed


title: RNAseq-Th2-Setdb1-KO-rep1


title: csrA mLPM T15 B

city: Gainesville

first: Anastasia

middle: Haley

last: Potts

state: FL

address: 1355 Museum Drive, Bldg. 981

department: Department of Microbiology and Cell Science

country: USA

institute: University of Florida

data_processing:
Basecalls were made with Casava
Reads were aligned to the Salmonella Typhimurium genome and plasmid sequences with bowtie2 using default parameters.
Read counts per gene were determined with Htseq Count
Reads within each time series were normalized to 4 independently collected qRT-PCR decay data for 11 genes
Genome_build: NC_016855.1
Genome_build: NC_016856.1
Supplementary_files_format_and_content: Normalized count matrix

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: bacterial cells

growth_protocol: Strains were grown in LB (0.5% yeast extract, 1% NaCl, and 1% tryptone) or mLPM (0.5 uM ferric citrate, 5 mM KCl, 7.5 mM (NH4)2SO4, 0.5 mM K2SO4, 0.3% glycerol, 0.00001% thiamine, 337 uM KPO4, 80  mM MES pH 5.8, and 8 uM MgCl2) medium to mid-exponential phase (OD600 = 0.5 for LB and 0.3 for mLPM)

extract_protocol:
Samples were extracted with hot phenol chloroform, treated with Turbo Dnase (Ambion), and cleaned with the RNeasy kit (Qiagen). RNA was normalized using fluorometric methods then an ERCC RNA spike-in was added to all samples (Ambion) to represent 5% of the total sample.
Standard Illumina protocols

treatment_protocol: Samples were treated with 500ug/ml rifampicin and aliquoted collected at the indicated time points and added directly to a stop solution (5% phenol in ethanol). Samples were centrifuged and the stabilized RNA samples frozen at -80C until extraction.

tag: genotype

value: csrA:: (markerless deletion of CDS after 51st codon)

tag: medium

value: mLPM

value: 15 min post-rifampicin addition


title: Blood-derived immune-cell mixture from donor 7

tag: subject status

tag: subject id

value: donor 7

value: blood

value: PBMC/PMN cell mixture

tag: natural killer cells

tag: b cells

tag: myeloid dendritic cells


title: csrA mLPM T5 B

value: 5 min post-rifampicin addition


title: csrA mLPM T5 A


title: csrA mLPM T10 A

value: 10 min post-rifampicin addition


title: csrA mLPM T15 A


title: csrA mLPM T10 B


title: csrA mLPM T2.5 A

value: 2.5 min post-rifampicin addition


title: WT mLPM T10 B

value: wild  type


title: csrA mLPM T0 A

value: 0 min post-rifampicin addition


title: WT mLPM T0 B


title: WT mLPM T15 B


title: WT mLPM T5 B


title: WT mLPM T10 A


title: WT mLPM T0 A


title: ChIPseq-Naives-WT-H3K9me3-rep2

value: C57BL/6 Setdb1+/+

value: H3K9me3 (ab8898 from Abcam; lot GR114265-2)


title: csrA mLPM T0 B


title: WT mLPM T2.5 A


title: WT mLPM T15 A


title: WT mLPM T5 A


title: ChIPseq-Input-DNA-Naives


title: csrA LB T15 B

value: LB


title: csrA LB T10 B


title: csrA LB T2.5 B


title: csrA LB T10 A


title: csrA LB T0 B


title: csrA LB T15 A


title: csrA LB T5 A


title: csrA LB T2.5 A


title: csrA LB T0 A


title: WT mLPM T2.5 B


title: WT LB T0 B


title: WT LB T5 B


title: WT LB T10 A


title: WT LB T15 A


title: WT LB T2.5 A


title: ST_31: RNA csrA:: 3 mLPM

data_processing:
Library strategy: ribosome profiling
Basecalls were made with Casava…
Reads were trimmed to remove adaptor sequences and reads shorter than 12 bases were discarded. Reads were aligned to the E. coli rRNA sequences with bowtie with default parameters and unaligned reads were retained
Reads were aligned to the Salmonella Typhimurium genome and plasmid sequences with bowtie using default parameters.
Read counts per gene were calculated with Htseq Count
Genome_build: NC_016855.1
Genome_build: NC_016856.1
Supplementary_files_format_and_content: Raw count matrix

extract_protocol:
Cell pellets were thawed and lysed with bead beating. Total RNA was extracted with miRNeasy RNA Extraction Kit (Qiagen). rRNA was subtracted with the Ribozero Gram Negative Kit (Illumina). RNA was then fragmented with heat and alkalinity and size selected between 20 and 40 bases with denaturing PAGE.
RNA samples were ligated to a 3' adaptor and reverse transcribed. The cDNA was circularized to add a 5' adaptor then PCR amplified to add sample specific barcodes.

treatment_protocol: Samples were treated with 100ug/ml choramphenicol for 2 minutes, quick chilled on ice, washed, and frozen with liquid nitrogen


title: ST_29: RNA csrA:: 1 mLPM


title: WT LB T0 A


title: ST_32: RNA csrA:: 4 mLPM


title: WT LB T5 A


title: WT LB T15 B


title: ST_30: RNA csrA:: 2 mLPM


title: ST_27: RNA WT 3 mLPM


title: ST_28: RNA WT 4 mLPM


title: csrA LB T5 B


title: ST_26: RNA WT 2 mLPM


title: ST_25: RNA WT 1 mLPM


title: ST_24: RPF csrA:: 4 mLPM

extract_protocol:
Cell pellets were thawed, lysed with bead beating, and treated with micrococcal nuclease to release single monosomes. Ribosomes were isolated by ultracentrifuging lysate over a sucrose cushion. Ribosome protected fragments  (RPF) were extracted from the pelleted ribosomes with miRNeasy RNA Extraction Kit (Qiagen) and size selected between 20 and 35 bases with denaturing PAGE.
RNA samples were ligated to a 3' adaptor and reverse transcribed. The cDNA was circularized to add a 5' adaptor then PCR amplified to add sample specific barcodes.

value: csrA:: markerless deletion of CDS after 51st codon)


title: ST_23: RPF csrA:: 3 mLPM


title: ST_21: RPF csrA:: 1 mLPM


title: ST_22: RPF csrA:: 2 mLPM


title: WT LB T10 B


title: ST_18: RPF WT  2 mLPM


title: ST_19: RPF WT 3 mLPM


title: ST_16: RNA csrA:: 4 LB


title: ST_17: RPF WT LB 1 mLPM


title: ST_15: RNA csrA:: 3 LB


title: RNA-seq_mal replicate 1

description: malignant

value: bone marrow

tag: age

value: 10-20 weeks

value: primary preB cells from bone-marrow

value: E{mu}Myc/+


title: ST_14: RNA csrA:: 2 LB

value: csrA:: (markerless deletion of CDS after 51st codon)


title: ST_12: RNA WT 1 LB


title: ST_11: RNA WT 1 LB


title: ST_13: RNA csrA:: 1 LB


title: ST_6: RPF csrA:: 2 LB


title: ST_7: RPF csrA:: 3 LB


title: ST_9: RNA WT 1 LB


title: ST_5: RPF csrA:: 1 LB


title: ST_3: RPF WT 3 LB


title: ST_8: RPF csrA:: 4 LB


title: WT LB T2.5 B


title: ST_4: RPF WT 4 LB


title: ST_10: RNA WT 1 LB


title: ST_2: RPF WT  2 LB


title: ST_20: RPF WT 4 mLPM

value: mLPM


title: ST_1: RPF WT 1 LB


title: RNAseq-Naives-WT-rep3

tag: cell type

value: Naives T lymphocytes


title: RNAseq-Naives-WT-rep2

tag: strain


title: RNAseq-Naives-WT-rep1

tag: number of culture days


title: RNAseq-Naives-Setdb1-KO-rep3

value: C57BL/6 Setdb1-/-


title: WT ovary 1121

city: Bundoora

first: Luba

last: Sominsky

state: VIC

address: RMIT University, Plenty road

country: Australia

institute: RMIT University

data_processing:
The samples were sequenced on Illumina HiSeq 2000 platform (Illumina, San Diego, CA) generating 50 bp single-reads per lane.
The primary bioinformatics analysis involved de-multiplexing and quality control. The per base sequence quality indicated that the Phred quality score was above 30 for > 96% of bases across all samples
The reads were also screened for the presence of any Illumina adaptor/overrepresented sequences and cross-species contamination.
The cleaned sequence reads were then aligned against the Mus musculus genome (Build version mm10). The Tophat aligner (v2.0.14) was used to map reads to the genomic sequences. The counts of reads mapping to each known gene were summarised.
The transcripts were assembled with the Stringtie tool v1.0.4 (http://ccb.jhu.edu/software/stringtie/) utilising the reads alignment with reference annotation based assembly option (RABT). The GENCODE annotation containing both coding and non-coding annotations for mouse genome version GRcm38 (Ensemble release 81) was used as a guide.
Genome_build: mm 10
Supplementary_files_format_and_content: Differential expression analysis table and bioinformatics analysis in excel (CAGRF11628_GOATKOvsWT_NoOutliers.XSLS)
Summary of mapping statistics with genome and exons (features_summary.csv)
Raw gene counts matrix against known gene annotation (gene_counts.txt)

source_name: ovary

extract_protocol:
Ovaries were excised, snap-frozen in liquid nitrogen and total RNA was isolated using QIAzol reagent and RNeasy mini kits. Total RNA (1 µg) samples were submitted to Australian Gene Research Facility for processing. Samples were sequenced on Illumina HiSeq 2000 platform generating 50 bp single-reads per lane.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary

value: 3 weeks

value: WT


title: GOAT KO ovary 1146

value: GOAT KO


title: GOAT KO ovary 1139


title: WT ovary 1119


title: GOAT KO ovary 1140


title: GOAT KO ovary 1141


title: WT ovary 1118


title: RNAseq-Naives-Setdb1-KO-rep2


title: RNAseq-Naives-Setdb1-KO-rep1


title: PAs-C2-12h

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

description: 12h DMSO exposure

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (GATCGGAAGAGC) trimmed with fastx_clipper
mapped using tophat2 --microexon-search --no-coverage-search --b2-N 1
detecting different expression gene using edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene RPKM values for each Sample

source_name: PANC-1_DMSO for 12h

growth_protocol: PANC-1 cells were cultured as monolayers in Dulbecco's Modified Eagle Medium (Gibco, USA) containing 10% fetal bovine serum (Hyclone, USA).Cells were incubated and maintained in a chamber with 95% air and 5% CO2 at 37℃.

extract_protocol:
Following treatment of PANC-1 cells with or without Proanthocyanidins the cells were harvested, washed with cold PBS, and lysed with ice-cold Trizol reagent.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to illumina NextSeq 500 system for 151 nt pair-end sequencing by ABlife. Inc (Wuhan, China).

treatment_protocol: PANC-1 cells were harvested at the indicated time post Proanthocyanidins (20μg/ml) or DMSO exposure.

tag: cell line

value: pancreatic cancer cells

tag: passage

tag: exposed to

value: DMSO for 12h


title: PAs-S2-12h

description: 12h PAs exposure

source_name: PANC-1_PA for 12hrs

value: 20 μg/ml Proanthocyanidins (PA) for 12hrs


title: WT ovary 1120

tag: tissue


title: PAs-C1-24h

description: 24h DMSO exposure

source_name: PANC-1_DMSO for 24h

value: DMSO for 24h


title: PAs-C2-24h

description: 24h DMSO exposure


title: PAs-S2-24h

description: 24h PAs exposure

source_name: PANC-1_PA for 24hrs

value: 20 μg/ml Proanthocyanidins (PA) for 24hrs


title: PAs-C2-3h

description: 3h DMSO exposure

source_name: PANC-1_DMSO for 3h

value: DMSO for 3h


title: PAs-S1-12h

description: 12h PAs exposure


title: RNAseq-Naives-WT-rep4

value: C57BL/6 Setdb1+/+


title: PAs-S1-3h

description: 3h PAs exposure

source_name: PANC-1_PA for 3hrs

value: 20 μg/ml Proanthocyanidins (PA) for 3hrs


title: PAs-C2-0h

description: Treatment with DMSO for 0h

source_name: PANC-1_DMSO for 0h

value: DMSO for 0h


title: PAs-C1-3h

description: 3h DMSO exposure


title: PAs-C1-0h

description: Treatment with DMSO for 0h


title: PAs-C1-12h

description: 12h DMSO exposure


title: HepetOM-HW-Input

city: Ithaca

first: James

middle: Joseph

last: Lewis

state: NY

address: 215 TOWER ROAD

department: Ecology & Evolutionary Biology

institute: Cornell University

data_processing:
Alignment to H. e. lativitta genome using bowtie 2.
Data were filtered to include only uniquely mapping reads with a quality score greater than 20
Peak call were performed using MACS2
Genome_build: Heliconius erato lativitta genome version 1 (http://ensembl.lepbase.org/Heliconius_erato_lativitta_v1/Info/Index)
Supplementary_files_format_and_content: RPKM normalizaed and input subtracted signal files were produced using Deeptools

organism: Heliconius erato petiverana

source_name: Input DNA, Whole wing tissue

growth_protocol: Caterpillars and pupae were raised at ~27C until 3 days post pupation or ommochrome pigment deposition before sampling.

extract_protocol:
Nuclei from whole wing tissue were digested with MNase and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to NEB instructions accompanying the NEBNext Ultra DNA Library Prep Kit

tag: developmental stage

value: Ommochrome pupal stage

value: Whole wing tissue

tag: chip antibody


title: HelatOM-HW-Input

organism: Heliconius erato lativitta


title: HelatOM-FW-Input


title: HelatD3-HW-Input

value: Day 3 Post-Pupation


title: HepetD3-HW-Input


title: HepetD3-FW-Input


title: PAs-S2-3h

description: 3h PAs exposure


title: HelatD3-FW-Input


title: 2-HelatOM-HW-H3K4me3

source_name: H3K4me3_ChIP-Seq, Whole wing tissue

value: H3K4me3 (Abcam, catalog# ab8580)


title: 2-HepetOM-HW-H3K27ac

source_name: H3K27ac_ChIP-Seq, Whole wing tissue

value: H3K27ac (Abcam, catalog# ab4729)


title: 2-HepetOM-HW-H3K4me3


title: 2-HepetD3-HW-H3K4me3


title: 2-HepetOM-FW-H3K4me3


title: HepetOM-FW-Input


title: 2-HepetD3-HW-H3K27ac


title: PAs-S1-24h

description: 24h PAs exposure


title: 2-HepetD3-FW-H3K4me3


title: 2-HepetD3-FW-H3K27ac


title: 2-HelatOM-FW-H3K27ac


title: 2-HelatD3-HW-H3K27ac


title: 2-HelatD3-FW-H3K4me3


title: 2-HelatD3-HW-H3K4me3


title: 2-HelatD3-FW-H3K27ac


title: 1-HepetOM-HW-H3K4me3


title: 1-HelatOM-HW-H3K4me3


title: 1-HelatOM-HW-H3K27ac


title: 1-HelatOM-FW-H3K4me3


title: 1-HepetOM-FW-H3K4me3


title: 1-HelatOM-FW-H3K27ac


title: 1-HepetOM-FW-H3K27ac


title: 1-HepetD3-HW-H3K4me3


title: 2-HepetOM-FW-H3K27ac


title: 1-HepetD3-FW-H3K4me3


title: 1-HepetD3-HW-H3K27ac


title: 1-HepetD3-FW-H3K27ac


title: 1-HelatD3-FW-H3K4me3


title: 2-HelatOM-FW-H3K4me3


title: 1-HelatD3-FW-H3K27ac


title: F3_Female_Control_Replicate_2

city: Toronto

first: Stephen

last: Matthews

state: Ontario

address: 1 King's College Circle

country: Canada

institute: University of Toronto

data_processing:
Sequenced reads were aligned to cavPor3 genome assembly using TOPHAT2 and default settings
Gene read counts were generated using Genomic Alignemnts (version 1.6.3) and outliers removed using Cook's distance with default cutoffs.
Count data were normalized by residuals using RUVSeq (version 3.12.1)
Differential gene expression was assessed using EdgeR's (version 3.12.1) genral linear model likelihood ratio test and FDR-corrected p< 0.05 was considered significant.
Genome_build: cavPor3
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample- EdgeR output

organism: Cavia porcellus

source_name: prefrontal cortex

extract_protocol:
Brains were removed, flash frozen on dry ice. Paranvetricular nucleus was extracted via micro-punch. RNA was harvested using AllPrep RNA/DNA/microRNA Universal Extraction Kit (Qiagen Cat#80224).TruSeq RNA Library Preparation Kit V2 (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: generation

tag: treatment

value: Control

value: post natal day 40

tag: Sex

value: Female


title: F3_Female_Beta_Replicate_4

value: Beta


title: F3_Female_Control_Replicate_1


title: F3_Female_Beta_Replicate_3


title: F3_Female_Beta_Replicate_2


title: 1-HepetOM-HW-H3K27ac


title: F3_Female_Beta_Replicate_1


title: F2_Female_Control_Replicate_4


title: F2_Female_Control_Replicate_3


title: F2_Female_Control_Replicate_2


title: F2_Female_Beta_Replicate_3


title: F2_Female_Control_Replicate_1


title: HehimOM-HW-Input

organism: Heliconius himera


title: 1-HelatD3-HW-H3K4me3


title: F2_Female_Beta_Replicate_1


title: HehimOM-FW-Input


title: F1_Female_Control_Replicate_4


title: HehimD3-HW-Input


title: F3_Female_Control_Replicate_4


title: F3_Female_Control_Replicate_3


title: HehimD3-FW-Input


title: F1_Female_Control_Replicate_3


title: F1_Female_Control_Replicate_2


title: F1_Female_Control_Replicate_1


title: 2-HehimOM-HW-H3K27ac


title: 1-HelatD3-HW-H3K27ac


title: 2-HehimOM-HW-H3K4me3


title: F1_Female_Beta_Replicate_1


title: 2-HehimOM-FW-H3K4me3


title: F2_Female_Beta_Replicate_4


title: F1_Female_Beta_Replicate_2


title: 2-HehimOM-FW-H3K27ac


title: F1_Female_Beta_Replicate_3


title: F2_Female_Beta_Replicate_2


title: F1_Female_Beta_Replicate_4


title: 2-HehimD3-HW-H3K4me3


title: F1_Male_Control_Replicate_4

value: Male


title: 2-HehimD3-FW-H3K4me3


title: F1_Male_Control_Replicate_3


title: F1_Male_Beta_Replicate_5


title: 1-HehimOM-HW-H3K4me3


title: 1-HehimOM-HW-H3K27ac


title: F1_Male_Beta_Replicate_4


title: F1_Male_Control_Replicate_2


title: 1-HehimOM-FW-H3K27ac


title: F1_Male_Beta_Replicate_3


title: 1-HehimOM-FW-H3K4me3


title: F1_Male_Control_Replicate_1


title: 1-HehimD3-HW-H3K4me3


title: F1_Male_Beta_Replicate_2


title: F1_Male_Beta_Replicate_6


title: F1_Male_Control_Replicate_5


title: F1_Male_Beta_Replicate_1


title: 1-HehimD3-FW-H3K27ac


title: 2-HehimD3-HW-H3K27ac


title: 1-HehimD3-FW-H3K4me3


title: 2-HehimD3-FW-H3K27ac


title: Single Cell 406

status: Public on Feb 04 2019

city: Cambridge

first: Longzhi

last: Tan

state: MA

address: 12 Oxford St

department: Chemistry and Chemical Biology

institute: Harvard University

data_processing:
please see 00README.md
Genome_build: mm10
Supplementary_files_format_and_content: please see 00README.md

source_name: retina

extract_protocol: Dip-C

value: retina


title: Single Cell 409


title: Single Cell 407


title: Single Cell 408


title: Single Cell 401


title: Single Cell 403


title: Single Cell 405


title: Single Cell 400


title: Single Cell 402


title: Single Cell 399


title: Single Cell 404


title: 1-HehimD3-HW-H3K27ac


title: Single Cell 396


title: Single Cell 398


title: Single Cell 397


title: 2-HelatOM-HW-H3K27ac


title: Single Cell 395


title: Single Cell 394


title: Single Cell 390


title: Single Cell 391


title: Single Cell 393


title: Single Cell 388


title: Single Cell 389


title: Single Cell 392


title: Single Cell 387


title: Single Cell 382


title: Single Cell 383


title: Single Cell 384


title: Single Cell 379


title: Single Cell 386


title: Single Cell 380


title: Single Cell 372


title: Single Cell 373


title: Single Cell 377


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title: Single Cell 376


title: Single Cell 370


title: Single Cell 385


title: Single Cell 367


title: Single Cell 366


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title: Single Cell 363


title: Single Cell 362


title: Single Cell 364


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title: Single Cell 358


title: Single Cell 357


title: Single Cell 371


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title: Single Cell 346


title: Single Cell 342


title: Single Cell 341


title: Single Cell 339


title: Single Cell 338


title: Single Cell 353


title: Single Cell 340


title: Single Cell 332

source_name: main olfactory epithelium

value: main olfactory epithelium


title: Single Cell 333


title: Single Cell 336


title: Single Cell 334


title: Single Cell 337


title: Single Cell 335


title: Single Cell 327


title: Single Cell 324


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title: Single Cell 125


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title: Single Cell 060


title: Single Cell 036


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title: Single Cell 032


title: Single Cell 180


title: Single Cell 037


title: Single Cell 050


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title: Single Cell 031


title: Single Cell 056


title: Single Cell 029


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title: Single Cell 028


title: Single Cell 022


title: Single Cell 023


title: Single Cell 025


title: Single Cell 027


title: Tyrosine 1 mNET-Seq OH+ rep2

city: Oxford

first: Monika

last: Gullerova

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

data_processing:
mNET-Seq:
adapter trimming with Cutadapt v. 1.8.3 in paired end mode
data mapping with Tophat v. 2.0.13 to hg38
extraction of properly mapped, properly paired reads
mNET:Seq: Extraction of most 3' nucleotide of Read 2, strandedness of Read 1
creation of bigwig files through the UCSC bedGraphToBigWig tool
Genome_build: hg38
Supplementary_files_format_and_content: bigwig; genomic profiles

source_name: U2OS AsiSI

growth_protocol: cells were cultured in Dulbecco's modified Eagle complete medium (DMEM, Sigma) with 10% fetal bovine serum (Life Technologies) at 37°C and 5% CO2

extract_protocol:
Nascent RNA was isolated using immunopurification of mammalian nascent elongating transcripts (mNET-IP) as described in Nojima 2016. For ChIP-seq: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with Tyrosine 1-p antibody.
Libraries were prepared as described in Nojima 2016; small RNA-seq library

treatment_protocol: DNA double-strand breaks were induced with 4-Hydroxytamoxifen (4OHT, 300 nM, Cayman) for 2 to 4 hours

value: U2OS AsiSI

value: osteosarcoma


title: Single Cell 019


title: Single Cell 020


title: Tyrosine 1 ChIP-Seq, OH+

data_processing:
ChIP-Seq: Reads were trimmed using th Kraken set of tools (SequenceImp v15-075) and renamed
ChIP-Seq: Reads were aligned with Bowtie2 v2.2.6 and filtered to remove low quality and duplicate alignments with samtools and Picard tools (v2.2.1)
ChIP-Seq: Bigwig files were created for relative coverage with deepTools bamCompare (v2.2.1)
Genome_build: hg38

source_name: OS

extract_protocol: Nascent RNA was isolated using immunopurification of mammalian nascent elongating transcripts (mNET-IP) as described in Nojima 2016. For ChIP-seq: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with Tyrosine 1-p antibody.

value: U20S AsiSI


title: Single Cell 024


title: Total (8WG16) mNET-Seq WT

source_name: WT U2OS

value: WT U2OS


title: Total (8WG16) mNET-Seq OH+ rep2


title: Tyrosine 1 mNET-Seq WT


title: Single Cell 026


title: Tyrosine 1 ChIP-Seq, OH-


title: Single Cell 034


title: Total (8WG16) mNET-Seq OH+

data_processing:
Library strategy: mNET-Seq
mNET-Seq: adapter trimming with Cutadapt v. 1.8.3 in paired end mode
mNET-Seq: data mapping with Tophat v. 2.0.13 to hg38
mNET-Seq: extraction of properly mapped, properly paired reads
mNET:Seq: Extraction of most 3' nucleotide of Read 2, strandedness of Read 1
mNET-Seq: creation of bigwig files through the UCSC bedGraphToBigWig tool
Genome_build: hg38

extract_protocol:
Nascent RNA was isolated using immunopurification of mammalian nascent elongating transcripts (mNET-IP) as described in Nojima 2016. For ChIP-seq: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with Tyrosine 1-p antibody.
mNET-seq: Libraries were prepared as described in Nojima 2016; small RNA-seq library


title: Tyrosine 1 mNET-Seq OH+


title: Single Cell 140


title: Single Cell 139


title: Single Cell 136


title: Single Cell 138


title: Single Cell 021


title: Single Cell 135


title: Single Cell 134


title: Single Cell 133


title: Single Cell 137


title: Single Cell 132


title: Single Cell 131


title: Single Cell 016


title: Single Cell 015


title: Single Cell 018


title: Single Cell 014


title: Single Cell 012


title: Single Cell 013


title: Single Cell 009


title: Single Cell 010


title: Single Cell 008


title: Single Cell 007


title: Single Cell 011


title: Single Cell 003


title: Single Cell 005


title: Single Cell 004


title: Single Cell 006


title: Single Cell 002


title: Single Cell 001


title: Single Cell 130


title: WT_Sample 4

city: Sendai

first: Kazuhiko

last: Igarashi

address: Seiryo 2-1

country: Japan

institute: Tohoku University

data_processing:
Trimming; FASTX Toolkit 0.0.14, fastx_trimmer -f 5
Mapping; bowtie 1.1.2, bowtie -p 2 -aS -X 800 --offrate 1
Expression quantitative detarmination; eXpress 1.5.1, express
Production of matrix data file for express output data (only fpkm)
Genome_build: RefSeq (downloaded in 20150626)
Supplementary_files_format_and_content: csv

source_name: WT

extract_protocol:
Total RNA was extracted with RNeasy micro kit (Qiagen).
cDNA were prepared from 100 pg of total RNA per sample using SMARTer Ultra Low Input RNA Kit for Sequencing-v3 (Clontech Laboratories) following the standard protocol with slight modification (18 PCR cycles). The cDNA was fragmented using Covaris S2 Focused-ultrasonicator (Covaris) and RNA-seq libraries were prepared from the fragmented cDNA with Ovation Ultralow DR Multiplex system V2 (Nugen).

tag: strain background

tag: gender

value: female

tag: genotype/variation

value: wild type

value: Alveolar macrophage


title: Bach2-floxed CD4cre_control_Sample 6

source_name: Bach2-floxed CD4cre_control

value: Bach2-floxed CD4cre_control


title: Bach2_germline_KO_Sample 5


title: Single Cell 017


title: Bach2-floxed CD4cre_KO_abnormal_Sample 3

source_name: Bach2-floxed CD4cre_KO_abnormal

value: Bach2-floxed CD4cre_KO_abnormal


title: Bach2-floxed CD4cre_control_Sample 1


title: WT_Sample 9


title: Bach2-floxed CD4cre_KO_normal_Sample 7

source_name: Bach2-floxed CD4cre_KO_normal

value: Bach2-floxed CD4cre_KO_normal


title: Bach2-floxed CD4cre_KO_normal_Sample 2


title: Bach2-floxed CD4cre_KO_abnormal_Sample 8


title: Bach2_germline_KO_Sample 10


title: Env sCD4 Sorted Library C; Replicate 2

status: Public on Feb 03 2019

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

description:
Deep mutational scan of Env for binding to soluble CD4
enrichment_ratios_BaL.xlsx

data_processing:
Data was analyzed using Enrich: http://depts.washington.edu/sfields/software/enrich/
Fuser script: FragmentA1 read 1: python Paired_read_fuser.py --path CD4_fragA1_R1/ --read1 BaLgp160_CD4sort1_A_R1.fastq --read2 BaLgp160_CD4sort1_A_R1.fastq --wtseq GAGGAAAAGCTCTGGGTGACTGTGTATTACGGGGTCCCAGTTTGGAAGGAGGCTACTACCACGCTCTTCTGCGCCTCCGACCGGAAGGCATACGACACCGAGGTGCATAATGTGTGGGCCACACACGCCTGTGTGCCTACC --read1_overlap_start 98 --read1_overlap_end 239 --mode R1
Fuser script: Fragment A1 read 2: python Paired_read_fuser.py --path CD4_fragA1_R2/ --read1 BaLgp160_CD4sort1_A_R2.fastq --read2 BaLgp160_CD4sort1_A_R2.fastq --wtseq TGTACTGACCTCCGGAATGCCACGAACGGAAACGACACAAATACCACGTCAAGCTCCCGAGGGATGGTGGGAGGGGGAGAAATGAAGAACTGCTCATTCAATATAACGACGAATATCCGAGGGAAGGTTCAGAAAGAGTATGCCCTGTTTTACAAACTGGACATCGCTCCTATCGACAACAACAGCAATAACAGGTACCGCCTGATTAGCTGC --read2_overlap_start 15 --read2_overlap_end 228 --mode R2
Fuser script: Fragment A2 read 1: python Paired_read_fuser.py --path CD4_fragA2_R1/ --read1 BaLgp160_CD4sort1_A_R1.fastq --read2 BaLgp160_CD4sort1_A_R1.fastq --wtseq TGGGCCACACACGCCTGTGTGCCTACCGACCCCAACCCACAGGAAGTGGAACTGAAGAACGTGACTGAGAATTTCAATATGTGGAAAAATAATATGGTGGAGCAGATGCACGAGGACATTATTAGCCTCTGGGATCAGTCCCTTAAACCCTGCGTGAAACTGACACCGCTGTGCGTAACGCTGAATTGTACTGACCTCCGGAATGCCACGAACGGAAAC --read1_overlap_start 20 --read1_overlap_end 239 --mode R1
Fuser script: Fragment A2 read 2: python Paired_read_fuser.py --path CD4_fragA2_R2/ --read1 BaLgp160_CD4sort1_A_R2.fastq --read2 BaLgp160_CD4sort1_A_R2.fastq --wtseq TGCAACACTTCTGTGATTACCCAGGCCTGCCCCAAGGTGAGCTTCGAGCCTATCCCAATCCACTACTGCGCCCCAGCAGGCTTTGCCATCCTGAAATGCAAGGACAAGAAGTTCAACGGCAAAGGCCCATGTACAAATGTCAGTACAGTACAGTGCACACACGGTATCCGCCCAGTTGTCTCTACACAACTGCTGCTGAATGGATCCTTG --read2_overlap_start 19 --read2_overlap_end 229 --mode R2
Fuser script: Fragment B1 read 1: python Paired_read_fuser.py --path CD4_fragB1_R1/ --read1 BaLgp160_CD4sort1_B_R1.fastq --read2 BaLgp160_CD4sort1_B_R1.fastq --wtseq GCAGAGGAAGAGGTGGTGATCAGATCTGCTAACTTCGCCGATAATGCTAAAGTCATCATTGTTCAGCTGAACGAGTCTGTCGAAATCAATTGTACTCGCCCAAACAACAACACGCGCAAGAGCATTCATATCGGACCGGGCAGGGCCTTTTACACAACAGGGGAGATTATTGGTGATATTAGACAAGCCCACTGCAACCTCAGTCGAGCAAAGTGGAAT --read1_overlap_start 19 --read1_overlap_end 238 --mode R1
Fuser script: Fragment B1 read 2: python Paired_read_fuser.py --path CD4_fragB1_R2/ --read1 BaLgp160_CD4sort1_B_R2.fastq --read2 BaLgp160_CD4sort1_B_R2.fastq --wtseq ACCCAGCTGTTCAACAGTACGTGGAACGTGACAGAGGAGTCTAACAACACCGTGGAGAATAATACGATCACCCTTCCATGTCGGATTAAGCAGATCATCAATATGTGGCAGGAGGTGGGAAGAGCAATGTACGCGCCGCCCATTAGGGGCCAGATCAGATGCAGTTCAAATATCACAGGCCTGCTCCTGACACGCGACGGAGGCCCAGAGGAC --read2_overlap_start 15 --read2_overlap_end 228 --mode R2
Fuser script: Fragment B2 read 1: python Paired_read_fuser.py --path CD4_fragB2_R1/ --read1 BaLgp160_CD4sort1_B_R1.fastq --read2 BaLgp160_CD4sort1_B_R1.fastq --wtseq CTCAGTCGAGCAAAGTGGAATGATACTCTCAACAAAATTGTTATCAAATTGCGGGAACAGTTTGGGAACAAGACAATCGTATTTAAGCACTCATCCGGAGGCGATCCAGAAATCGTGACACACTCTTTTAACTGCGGTGGAGAATTTTTCTACTGCAACTCCACCCAGCTGTTCAACAGTACGTGGAACGTGACAGAGGAGTCTAACAACACCGTGGAG --read1_overlap_start 19 --read1_overlap_end 238 --mode R1
Fuser script: Fragment B2 read 2: python Paired_read_fuser.py --path CD4_fragB2_R2/ --read1 BaLgp160_CD4sort1_B_R2.fastq --read2 BaLgp160_CD4sort1_B_R2.fastq --wtseq GACAACAAGACAGAGGTGTTTAGGCCCGGCGGCGGCGACATGCGAGATAATTGGAGGTCTGAATTGTACAAGTACAAGGTGGTGAAAATCGAACCCCTGGGAGTGGCGCCTACTAAGGCAAAGCGCCGCGTTGTGCAGAGAGAGAAGAGGGCAGTGGGAATTGGGGCGGTTTTTCTTGGGTTCCTGGGGGCTGCAGGTAGCACC --read2_overlap_start 15 --read2_overlap_end 219 --mode R2
Fuser script: Fragment C1 read 1: python Paired_read_fuser.py --path CD4_fragC1_R1/ --read1 BaLgp160_CD4sort1_C_R1.fastq --read2 BaLgp160_CD4sort1_C_R1.fastq --wtseq ATGGGAGCGGCCGCTATGACACTGACAGTGCAAGCCAGACTCCTGCTGTCTGGTATTGTCCAACAGCAAAACAATTTGCTCCGCGCAATAGAAGCCCAGCAGCACCTGCTCCAACTGACTGTGTGGGGCATTAAACAATTGCAGGCTCGCGTGCTGGCAGTCGAA --read1_overlap_start 75 --read1_overlap_end 240 --mode R1
Fuser script: Fragment C1 read 2: python Paired_read_fuser.py --path CD4_fragC1_R2/ --read1 BaLgp160_CD4sort1_C_R2.fastq --read2 BaLgp160_CD4sort1_C_R2.fastq --wtseq ATAATGATCGTCGGCGGACTCATCGGGCTCCGAATTGTGTTCTCAGTCCTCAGCATTGTGAATAGGGTGCGCCAGGGCTATTCTCCCCTGAGCTTCCAGACCCATCTGCCCTCTAGCCGAGGACCAGATAGGCCTGGTGGGATCGAGGAAGAAGGCGGGGAACGGGACAGGGATAGGAGTGGTCCTCTTGTTAACGGGTTCCTGGCACTTATATGG --read2_overlap_start 14 --read2_overlap_end 230 --mode R2
Fuser script: Fragment C2 read 1: python Paired_read_fuser.py --path CD4_fragC2_R1/ --read1 BaLgp160_CD4sort1_C_R1.fastq --read2 BaLgp160_CD4sort1_C_R1.fastq --wtseq CTGGCAGTCGAACGGTACCTGAGGGATCAACAGCTCCTGGGCATCTGGGGCTGCTCCGGGAAACTCATCTGTACGACAGCGGTCCCTTGGAATGCCAGCTGGTCCAACAAAAGCCTCAACAAGATTTGGGACAATATGACGTGGATTGAGTGGGACAGGGAAATTAACAATTATACCTCAATCATATATTCTCTGATTGAAGAGTCCCAGAATCAG --read1_overlap_start 21 --read1_overlap_end 237 --mode R1
Fuser script: Fragment C2 read 2: python Paired_read_fuser.py --path CD4_fragC2_R2/ --read1 BaLgp160_CD4sort1_C_R2.fastq --read2 BaLgp160_CD4sort1_C_R2.fastq --wtseq GATAGGAGTGGTCCTCTTGTTAACGGGTTCCTGGCACTTATATGGGTGGACTTGAGAAGCCTGTTCCTGTTCTCCTATCATAGGCTCCGGGATCTTCTCCTGATAGTCATGCGGATCGTCGAGCTGTTGGGGCTTGCTGGCGGCTGGGAAGTACTGAAATATTGGTGGAATCTGTTGCAGTATTGGAGCCAGGAACTTAAGAACTCTGCTGTGAGT --read2_overlap_start 14 --read2_overlap_end 230 --mode R2
Fuser script: Fragment C3 read 1: python Paired_read_fuser.py --path CD4_fragC3_R1/ --read1 BaLgp160_CD4sort1_C_R1.fastq --read2 BaLgp160_CD4sort1_C_R1.fastq --wtseq AGGGAAATTAACAATTATACCTCAATCATATATTCTCTGATTGAAGAGTCCCAGAATCAGCAAGAGAAGAATGAGCAGGAATTGTTGGAACTTGATAAATGGGCAAGCCTGTGGAACTGGTTTGACATAACCAAATGGTTGTGGTATATCAAAATCTTCATAATGATCGTCGGCGGACTCATCGGGCTCCGAATTGTGTTCTCAGTCCTCAGCATTGTG --read1_overlap_start 21 --read1_overlap_end 240 --mode R1
Fuser script: Fragment C3 read 2: python Paired_read_fuser.py --path CD4_fragC3_R2/ --read1 BaLgp160_CD4sort1_C_R2.fastq --read2 BaLgp160_CD4sort1_C_R2.fastq --wtseq CTGAAATATTGGTGGAATCTGTTGCAGTATTGGAGCCAGGAACTTAAGAACTCTGCTGTGAGTCTCCTTAATGCCACAGCTGTTGCTGTGGCCGAAGGAACCGATCGAGTTATTGAAGTACTGCAACGAGCAGTTCGCGCTATTCTGCATATCCCACGACGCATTCGGCAGGGGCTGGAGAGAGCTCTCCTG --read2_overlap_start 18 --read2_overlap_end 210 --mode R2
Aligner script: Fragment A1 read 1: python Fused_read_aligner.py --path CD4_fragA1_R1/ --infile BaLgp160_CD4sort1_A_R1.fast_R1_qc1 --referenceDNA GAGGAAAAGCTCTGGGTGACTGTGTATTACGGGGTCCCAGTTTGGAAGGAGGCTACTACCACGCTCTTCTGCGCCTCCGACCGGAAGGCATACGACACCGAGGTGCATAATGTGTGGGCCACACACGCCTGTGTGCCTACC --referenceAA EEKLWVTVYYGVPVWKEATTTLFCASDRKAYDTEVHNVWATHACVPT --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: Fragment A1 read 2: python Fused_read_aligner.py --path CD4_fragA1_R2/ --infile BaLgp160_CD4sort1_A_R2.fast_R2_qc1 --referenceDNA TGTACTGACCTCCGGAATGCCACGAACGGAAACGACACAAATACCACGTCAAGCTCCCGAGGGATGGTGGGAGGGGGAGAAATGAAGAACTGCTCATTCAATATAACGACGAATATCCGAGGGAAGGTTCAGAAAGAGTATGCCCTGTTTTACAAACTGGACATCGCTCCTATCGACAACAACAGCAATAACAGGTACCGCCTGATTAGCTGC --referenceAA CTDLRNATNGNDTNTTSSSRGMVGGGEMKNCSFNITTNIRGKVQKEYALFYKLDIAPIDNNSNNRYRLISC --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: Fragment A2 read 1: python Fused_read_aligner.py --path CD4_fragA2_R1/ --infile BaLgp160_CD4sort1_A_R1.fast_R1_qc1 --referenceDNA TGGGCCACACACGCCTGTGTGCCTACCGACCCCAACCCACAGGAAGTGGAACTGAAGAACGTGACTGAGAATTTCAATATGTGGAAAAATAATATGGTGGAGCAGATGCACGAGGACATTATTAGCCTCTGGGATCAGTCCCTTAAACCCTGCGTGAAACTGACACCGCTGTGCGTAACGCTGAATTGTACTGACCTCCGGAATGCCACGAACGGAAAC --referenceAA WATHACVPTDPNPQEVELKNVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDLRNATNGN --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: Fragment A2 read 2: python Fused_read_aligner.py --path CD4_fragA2_R2/ --infile BaLgp160_CD4sort1_A_R2.fast_R2_qc1 --referenceDNA TGCAACACTTCTGTGATTACCCAGGCCTGCCCCAAGGTGAGCTTCGAGCCTATCCCAATCCACTACTGCGCCCCAGCAGGCTTTGCCATCCTGAAATGCAAGGACAAGAAGTTCAACGGCAAAGGCCCATGTACAAATGTCAGTACAGTACAGTGCACACACGGTATCCGCCCAGTTGTCTCTACACAACTGCTGCTGAATGGATCCTTG --referenceAA CNTSVITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGKGPCTNVSTVQCTHGIRPVVSTQLLLNGSL --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: Fragment B1 read 1: python Fused_read_aligner.py --path CD4_fragB1_R1/ --infile BaLgp160_CD4sort1_B_R1.fast_R1_qc1 --referenceDNA GCAGAGGAAGAGGTGGTGATCAGATCTGCTAACTTCGCCGATAATGCTAAAGTCATCATTGTTCAGCTGAACGAGTCTGTCGAAATCAATTGTACTCGCCCAAACAACAACACGCGCAAGAGCATTCATATCGGACCGGGCAGGGCCTTTTACACAACAGGGGAGATTATTGGTGATATTAGACAAGCCCACTGCAACCTCAGTCGAGCAAAGTGGAAT --referenceAA AEEEVVIRSANFADNAKVIIVQLNESVEINCTRPNNNTRKSIHIGPGRAFYTTGEIIGDIRQAHCNLSRAKWN --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: Fragment B1 read 2: python Fused_read_aligner.py --path CD4_fragB1_R2/ --infile BaLgp160_CD4sort1_B_R2.fast_R2_qc1 --referenceDNA ACCCAGCTGTTCAACAGTACGTGGAACGTGACAGAGGAGTCTAACAACACCGTGGAGAATAATACGATCACCCTTCCATGTCGGATTAAGCAGATCATCAATATGTGGCAGGAGGTGGGAAGAGCAATGTACGCGCCGCCCATTAGGGGCCAGATCAGATGCAGTTCAAATATCACAGGCCTGCTCCTGACACGCGACGGAGGCCCAGAGGAC --referenceAA TQLFNSTWNVTEESNNTVENNTITLPCRIKQIINMWQEVGRAMYAPPIRGQIRCSSNITGLLLTRDGGPED --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: Fragment B2 read 1: python Fused_read_aligner.py --path CD4_fragB2_R1/ --infile BaLgp160_CD4sort1_B_R1.fast_R1_qc1 --referenceDNA CTCAGTCGAGCAAAGTGGAATGATACTCTCAACAAAATTGTTATCAAATTGCGGGAACAGTTTGGGAACAAGACAATCGTATTTAAGCACTCATCCGGAGGCGATCCAGAAATCGTGACACACTCTTTTAACTGCGGTGGAGAATTTTTCTACTGCAACTCCACCCAGCTGTTCAACAGTACGTGGAACGTGACAGAGGAGTCTAACAACACCGTGGAG --referenceAA LSRAKWNDTLNKIVIKLREQFGNKTIVFKHSSGGDPEIVTHSFNCGGEFFYCNSTQLFNSTWNVTEESNNTVE --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: Fragment B2 read 2: python Fused_read_aligner.py --path CD4_fragB2_R2/ --infile BaLgp160_CD4sort1_B_R2.fast_R2_qc1 --referenceDNA GACAACAAGACAGAGGTGTTTAGGCCCGGCGGCGGCGACATGCGAGATAATTGGAGGTCTGAATTGTACAAGTACAAGGTGGTGAAAATCGAACCCCTGGGAGTGGCGCCTACTAAGGCAAAGCGCCGCGTTGTGCAGAGAGAGAAGAGGGCAGTGGGAATTGGGGCGGTTTTTCTTGGGTTCCTGGGGGCTGCAGGTAGCACC --referenceAA DNKTEVFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQREKRAVGIGAVFLGFLGAAGST --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: Fragment C1 read 1: python Fused_read_aligner.py --path CD4_fragC1_R1/ --infile BaLgp160_CD4sort1_C_R1.fast_R1_qc1 --referenceDNA ATGGGAGCGGCCGCTATGACACTGACAGTGCAAGCCAGACTCCTGCTGTCTGGTATTGTCCAACAGCAAAACAATTTGCTCCGCGCAATAGAAGCCCAGCAGCACCTGCTCCAACTGACTGTGTGGGGCATTAAACAATTGCAGGCTCGCGTGCTGGCAGTCGAA --referenceAA MGAAAMTLTVQARLLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARVLAVE --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: Fragment C1 read 2: python Fused_read_aligner.py --path CD4_fragC1_R2/ --infile BaLgp160_CD4sort1_C_R2.fast_R2_qc1 --referenceDNA ATAATGATCGTCGGCGGACTCATCGGGCTCCGAATTGTGTTCTCAGTCCTCAGCATTGTGAATAGGGTGCGCCAGGGCTATTCTCCCCTGAGCTTCCAGACCCATCTGCCCTCTAGCCGAGGACCAGATAGGCCTGGTGGGATCGAGGAAGAAGGCGGGGAACGGGACAGGGATAGGAGTGGTCCTCTTGTTAACGGGTTCCTGGCACTTATATGG --referenceAA IMIVGGLIGLRIVFSVLSIVNRVRQGYSPLSFQTHLPSSRGPDRPGGIEEEGGERDRDRSGPLVNGFLALIW --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: Fragment C2 read 1: python Fused_read_aligner.py --path CD4_fragC2_R1/ --infile BaLgp160_CD4sort1_C_R1.fast_R1_qc1 --referenceDNA CTGGCAGTCGAACGGTACCTGAGGGATCAACAGCTCCTGGGCATCTGGGGCTGCTCCGGGAAACTCATCTGTACGACAGCGGTCCCTTGGAATGCCAGCTGGTCCAACAAAAGCCTCAACAAGATTTGGGACAATATGACGTGGATTGAGTGGGACAGGGAAATTAACAATTATACCTCAATCATATATTCTCTGATTGAAGAGTCCCAGAATCAG --referenceAA LAVERYLRDQQLLGIWGCSGKLICTTAVPWNASWSNKSLNKIWDNMTWIEWDREINNYTSIIYSLIEESQNQ --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: Fragment C2 read 2: python Fused_read_aligner.py --path CD4_fragC2_R2/ --infile BaLgp160_CD4sort1_C_R2.fast_R2_qc1 --referenceDNA GATAGGAGTGGTCCTCTTGTTAACGGGTTCCTGGCACTTATATGGGTGGACTTGAGAAGCCTGTTCCTGTTCTCCTATCATAGGCTCCGGGATCTTCTCCTGATAGTCATGCGGATCGTCGAGCTGTTGGGGCTTGCTGGCGGCTGGGAAGTACTGAAATATTGGTGGAATCTGTTGCAGTATTGGAGCCAGGAACTTAAGAACTCTGCTGTGAGT --referenceAA DRSGPLVNGFLALIWVDLRSLFLFSYHRLRDLLLIVMRIVELLGLAGGWEVLKYWWNLLQYWSQELKNSAVS --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: Fragment C3 read 1: python Fused_read_aligner.py --path CD4_fragC3_R1/ --infile BaLgp160_CD4sort1_C_R1.fast_R1_qc1 --referenceDNA AGGGAAATTAACAATTATACCTCAATCATATATTCTCTGATTGAAGAGTCCCAGAATCAGCAAGAGAAGAATGAGCAGGAATTGTTGGAACTTGATAAATGGGCAAGCCTGTGGAACTGGTTTGACATAACCAAATGGTTGTGGTATATCAAAATCTTCATAATGATCGTCGGCGGACTCATCGGGCTCCGAATTGTGTTCTCAGTCCTCAGCATTGTG --referenceAA REINNYTSIIYSLIEESQNQQEKNEQELLELDKWASLWNWFDITKWLWYIKIFIMIVGGLIGLRIVFSVLSIV --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: Fragment C3 read 2: python Fused_read_aligner.py --path CD4_fragC3_R2/ --infile BaLgp160_CD4sort1_C_R2.fast_R2_qc1 --referenceDNA CTGAAATATTGGTGGAATCTGTTGCAGTATTGGAGCCAGGAACTTAAGAACTCTGCTGTGAGTCTCCTTAATGCCACAGCTGTTGCTGTGGCCGAAGGAACCGATCGAGTTATTGAAGTACTGCAACGAGCAGTTCGCGCTATTCTGCATATCCCACGACGCATTCGGCAGGGGCTGGAGAGAGCTCTCCTG --referenceAA LKYWWNLLQYWSQELKNSAVSLLNATAVAVAEGTDRVIEVLQRAVRAILHIPRRIRQGLERALL --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
MapCounts script: Example: python mapCounts.py --path directory_fragA1_R1/ --infile BaLgp160_libraryA_R1.fast_R1_qc1_PRO_qc2
MapRatios script: Example: python mapRatios.py --path ratios_directory/ --templatepath /deepseq_scripts/r_deepseq_scripts/ --infile2 mapcounts_library --infile1 mapcounts_sorted
MapParts script: Example: python mapParts.py --path ratios_directory/ --infile mapratios_sorted_library --mode mutations:1
Unlink script: Example: python mapUnlink.py --path ratios/ --infile mapratios_sorted_library.m1 --type protein --mode ratios --size ##
In Excel, the log(base2) enrichment ratio of the wildtype sequence was subtracted from the log(2) enrichment ratios for all single mutations.
Data was then assembled from the different fragments/reads to span the full sequence in Excel.  Where there was overlap, real enrichment ratios were averaged and converted back to log(base2). Maximum depletion was set to log(base2) enrichment ratio = -4.
Genome_build: Not applicable
Supplementary_files_format_and_content: Excel spreadsheet of log(base2) enrichment ratios for each single amino acid substitution.  Also includes the frequency of each mutation in the naïve plasmid library.

organism: Human immunodeficiency virus 1

source_name: Synthetic coding sequences

growth_protocol: Expi293F cells cultured in Expi293 Expression Medium (Life Technologies)

extract_protocol:
Total RNA was harvested from sorted cells using GeneJet RNA Purification Kit (Thermo Scientific) and cDNA prepared using Accuscript Hi-Fi (Agilent Genomics) primed with a gene-specific primer: BALgp160_libA_RT_rev (CGTTCAGCTGAACAATGATG, Library A), BALgp160_libB_RT_rev (TGTTGGACAATACCAGACAG, Library B), and EBV_reverse (GTGGTTTGTCCAAACTCATC, Library C).
In the first round of PCR (18 cycles), the Env coding sequences were amplified as overlapping fragments of ~800 bp each.
Primer pair (Library A Fragment 1): MiSeq_pCEP4intron_F2 (TCTTTCCCTACACGACGCTCTTCCGATCTACGACTCACTATAGGCTAGC) and MiSeq_BaLgp160_588_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCCTGGGTAATCACAGAAGTG)
Primer pair (Library A Fragment 2): MiSeq_BaLgp160_167_F (TCTTTCCCTACACGACGCTCTTCCGATCTACACCGAGGTGCATAATGTG) and MiSeq_BaLgp160_799_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGATCACCACCTCTTC)
Primer pair (Library B Fragment 1): MiSeq_BaLgp160_773_F (TCTTTCCCTACACGACGCTCTTCCGATCTGCTGCTGAATGGATCCTTG) and MiSeq_BaLgp160_1368_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCCTAAACACCTCTGTCTTG)
Primer pair (Library B Fragment 2): MiSeq_BaLgp160_971_F (TCTTTCCCTACACGACGCTCTTCCGATCTTAGACAAGCCCACTGCAAC) and MiSeq_BaLgp160_1579_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCACTGTCAGTGTCATAGC)
Primer pair (Library C Fragment 1): MiSeq_BaLgp160_1492_F (TCTTTCCCTACACGACGCTCTTCCGATCTGTTGTGCAGAGAGAGAAGAG) and MiSeq_BaLgp160_2251_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAACAGGCTTCTCAAGTCCAC)
Primer pair (Library C Fragment 2): MiSeq_BaLgp160_1699_F (TCTTTCCCTACACGACGCTCTTCCGATCTAAACAATTGCAGGCTCGCGT) and MiSeq_BaLgp160_2422_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTACAGCTGTGGCATTAAGGAG)
Primer pair (Library C Fragment 3): MiSeq_BaLgp160_1855_F (TCTTTCCCTACACGACGCTCTTCCGATCTATGACGTGGATTGAGTGGGA) and MiSeq_pCEP4_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTATCATGTCTGGATCCGG)
In a second round of PCR (14 cycles), Illumina adaptors and experiment-specific barcodes were added.
Primer pair for adding I5 and I7 Illumina adaptors: MiSeq_Start_Adaptamer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and MiSeq_Index_Adaptamer (CAAGCAGAAGACGGCATACGAGAT-6nt-barcode-GTGACTGGAGTTCAGACGTGTGCTCTTC)
Amplicons were deep sequenced with MiSeq v3 and HiSeq 2500 instruments using a 2x250 nt paired end protocol, though data is analyzed as single reads.

treatment_protocol: Cells expressing DNA libraries of HIV-1(BaL) Env mutants (cloned into a modified version of pCEP4, Invitrogen, with an upstream chimeric intron) were FACS sorted for binding to different protein/antibody ligands.  Three single site-saturation mutagenesis libraries were created, spanning residues 31-265 (Library A; numbering based on the HXB2 reference strain), 266-529 (Library B), and 530-856 (Library C).

tag: protein

value: Env

tag: sort gate

value: Top 1.0% of population for binding signal (200 nM sCD4(D1-D2))

tag: # collected cells


title: Env VRC01 Sorted Library A; Replicate 1

description:
Deep mutational scan of Env for binding to broadly-neutralizing antibody VRC01
enrichment_ratios_BaL.xlsx

value: Top 0.5% of population for binding signal (5 nM VRC01)


title: Env VRC01 Sorted Library B; Replicate 1


title: Env PG16 Sorted Library A; Replicate 2

description:
Deep mutational scan of Env for binding to broadly-neutralizing antibody PG16
enrichment_ratios_BaL.xlsx

value: Top 0.6% of population for binding signal (2 nM PG16)


title: Env PG16 Sorted Library C; Replicate 1

value: Top 0.9% of population for binding signal (2 nM PG16)


title: Env PG16 Sorted Library B; Replicate 2


title: Env PG16 Sorted Library C; Replicate 2


title: Env PG16 Sorted Library B; Replicate 1


title: Env sCD4 Sorted Library B; Replicate 1

value: Top 0.5% of population for binding signal (200 nM sCD4(D1-D2))


title: Env sCD4 Sorted Library A; Replicate 1


title: Env Naive Library C

description:
Naïve HIV-1 (BaL strain) Env SSM library C (a.a. 530-856)
enrichment_ratios_BaL.xlsx

molecule: other


title: Env Naive Library B

description:
Naïve HIV-1 (BaL strain) Env SSM library B (a.a.266-529)
enrichment_ratios_BaL.xlsx


title: Env VRC01 Sorted Library B; Replicate 2


title: Env VRC01 Sorted Library C; Replicate 2

value: Top 1.0% of population for binding signal (5 nM VRC01)


title: Env VRC01 Sorted Library A; Replicate 2


title: Env PG16 Sorted Library A; Replicate 1


title: Env sCD4 Sorted Library B; Replicate 2


title: Env sCD4 Sorted Library A; Replicate 2


title: Env Naive Library A

description:
Naïve HIV-1 (BaL strain) Env SSM library A (a.a. 31-265)
enrichment_ratios_BaL.xlsx


title: Control micoRNA2, 3

status: Public on Feb 02 2019

city: Shanghai

first: Haoyan

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

description:
HCT116_microRNA_mixure_genes.fpkm_tracking
N3

data_processing:
Reads were mapped to the human genome (hg19) using TopHat v2.0.11 (http://tophat.cbcb.umd.edu) with the following default options with a TopHat transcript index built from Ensembl_GRCh37. Transcript expression was estimated with an improved version of Cuffdiff2 (http://cufflinks.cbcb.umd.edu). Cuffdiff was run with the default options against the UCSC iGenomes GTF file from Illumina (available at http://cufflinks.cbcb.umd.edu/igenomes.html).
Genome_build: Ensembl_GRCh37(hg19)
Supplementary_files_format_and_content: HCT116_microRNA_mixure_genes.fpkm_tracking
Supplementary_files_format_and_content: miR-508_genes.fpkm_tracking

source_name: Control micoRNA2

growth_protocol: The human colorectal cancer cells HCT116 were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
total RNA of HCT116 cells with different treatment was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The adenovirus against human miR-508/508/509/514 mimics and miR-508 mimics were introduced into the HCT116 colorectal cells, while nonspecific microRNA virus was used as negative controls.

tag: cell type

value: human colorectal cancer cells


title: Control micoRNA2, 4

description:
HCT116_microRNA_mixure_genes.fpkm_tracking
N4


title: Control micoRNA2, 1

description:
HCT116_microRNA_mixure_genes.fpkm_tracking
N1


title: Env sCD4 Sorted Library C; Replicate 1


title: miR-508/508/509/514 mimics mixure, 2

description:
HCT116_microRNA_mixure_genes.fpkm_tracking
M2


title: Control micoRNA2, 2

description:
HCT116_microRNA_mixure_genes.fpkm_tracking
N2


title: miR-508/508/509/514 mimics mixure, 1

description:
HCT116_microRNA_mixure_genes.fpkm_tracking
M1


title: Control micoRNA1, 3

description:
miR-508_genes.fpkm_tracking
NC3

source_name: Control micoRNA1


title: miR-508 mimics, 3

description:
miR-508_genes.fpkm_tracking
M3

source_name: miR-508 mimics


title: miR-508 mimics, 2

description:
miR-508_genes.fpkm_tracking
M2


title: miR-508 mimics, 1

description:
miR-508_genes.fpkm_tracking
M1


title: GSC2-3

city: London

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

institute: MRC London Institute of Medical Sciences

data_processing:
Illumina Casava1.8.2  software used for basecalling.
Sequenced reads were mapped to dm3 whole genome using tophat v2.0.11 with parameters -p 8 -r 100.
Gene Based read counts were obtained with HTSeq counts module v0.5.3p9
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: Subventricular Zone

growth_protocol: Cells were cultured in NSC standard culture conditions for 10-15 passages prior to orthotopic implantation into nude mice. 5x104 cells were injected in each mouse

extract_protocol:
RNA was isolated by using RNAeasy Plus Mini Kit (Qiagen).
RNA sequencing libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB)

value: NSC-derived tumour cells

tag: mutation


title: GSC2-1


title: GSC1-4

value: lgT/Ras


title: GSC1-3


title: miR-508/508/509/514 mimics mixure, 4

description:
HCT116_microRNA_mixure_genes.fpkm_tracking
M4

tag: cell line


title: miR-508/508/509/514 mimics mixure, 3

description:
HCT116_microRNA_mixure_genes.fpkm_tracking
M3


title: CoMo_2

city: Nijmegen

first: Saartje

last: Hontelez

address: Geert Grooteplein 28

department: Molecular developmental biology

country: Netherlands

institute: Radboud University

data_processing:
Reads were mapped to the reference Xenopus tropicalis genome JGI7.1, using the BWA allowing one mismatch
Genome_build: JGI7.1
Supplementary_files_format_and_content: wig files were generated using bam2bw (https://bitbucket.org/simonvh/bam2bw/src); Scores are scaled with scaling factor 1000000/[total #reads]

organism: Xenopus tropicalis

source_name: Control Morpholino injected

growth_protocol: Embryos were obtained by in vitro fertilisation and grown at 22 celcius untill the approptate developmental stage.

extract_protocol:
Protein-DNA complexes were isolated with antibody from whole embryo lysates that were fixed, sonicated and yolk depleted.
Libraries were prepared with the Kapa Hyper Prep kit (Kapa Biosystems), and sequencing was done on the Illumina HiSeq2000 platform.

treatment_protocol: 1-cell stage embryos were injected with 70 ng CDK9.S morpholino ( 5’-ATGGCCAAGAACTACGACTCGGTGG-3’) or control morpholino (CoMo, 5’-CCTCTTACCTCAGTTACAATTTATA-3’) and developed until the control embryos reached stage 16

tag: developmental stage (nf)

tag: injected with

value: control morpholino

value: anti-RNAPII (Diagenode C15200004)


title: GSC1-1


title: SCR-SIRNA-30-11_S6_L004

status: Public on Feb 01 2019

city: Birmingham

first: Wiebke

last: Arlt

address: Edgbaston

department: Institute of Metabolism and Systems Research  (IMSR)

institute: University of Birmingham

description: Scrambled Control siRNA

data_processing:
RNA-seq reads were mapped to the human genome (hg19, UCSC annotation) using STAR software v2.4.2a
Counts per gene were calculated using the htseq-count tool from the HTSeq v0.6.1p1 package with the following parameters: --format=bam --minaqual=10 --stranded=reverse –mode=union
Normalized counts per gene were generated using DESeq2 v1.14.1
Genome_build: hg19
Supplementary_files_format_and_content: Tab delineated text files containing counts for each sample

source_name: Adrenocortical Carcinoma Cell line

extract_protocol:
RNA samples from KD siRNA, SCR SiRNA (72 hours post-transfection), KD shRNA and SCR shRNA cells (in triplicates) were prepared using the RNeasy Mini kit (Qiagen).
Libraries were generated using the TruSeq Stranded mRNA Library Prep Kit (Illumina). RNA was quantified using Qubit® RNA BR Assay Kit and if necessary diluted to 25-100 ng in 12.5 ul.  This was followed by RNA quality check to establish the RIN (RNA Integrity Number) using the Agilent RNA ScreenTape system. RNA was then processed on the automated Illumina Neoprep system following the Library prep TruSeq Stranded mRNA Library Prep Kit for NeoPrep. Libraries were normalized to 10 nM by the Neoprep. Each library quantity was checked again using Qubit DNA HS Assay Kit and 2 ul of each library were pooled together into a single tube.  This pool of 16 samples was checked on the Agilent High Sensitivity D1000 ScreenTape to ensure the libraries were the correct size at 300 bp. The pooled sample was diluted to 4 nM.

value: siRNA

tag: condition

value: Control


title: SCR-SIRNA-30-11_S6_L003

description: Scrambled Control siRNA


title: SCR-SIRNA-30-11_S6_L002

description: Scrambled Control siRNA


title: SCR-SIRNA-30-11_S6_L001

description: Scrambled Control siRNA


title: SCR-SIRNA-23-5_S2_L004

description: Scrambled Control siRNA


title: SCR-SIRNA-23-5_S2_L003

description: Scrambled Control siRNA


title: Control micoRNA1, 1

description:
miR-508_genes.fpkm_tracking
NC1


title: SCR-SIRNA-23-5_S2_L002

description: Scrambled Control siRNA


title: Control micoRNA1, 2

description:
miR-508_genes.fpkm_tracking
NC2


title: SCR-SIRNA-23-5_S2_L001

description: Scrambled Control siRNA


title: SCR-SIRNA-16-1_S5_L003

description: Scrambled Control siRNA


title: SCR-SIRNA-16-1_S5_L002

description: Scrambled Control siRNA


title: SCR-SIRNA-16-1_S5_L004

description: Scrambled Control siRNA


title: SCR-SHRNA-24-2_S3_L002

description: Scrambled Control shRNA

value: shRNA


title: GSC2-2


title: SCR-SHRNA-24-2_S3_L003

description: Scrambled Control shRNA


title: Env VRC01 Sorted Library C; Replicate 1


title: Cdk9_1

source_name: Cdk9 morpholino injected

value: CDK9.S morpholino


title: SCR-SHRNA-24-2_S3_L004

description: Scrambled Control shRNA


title: SCR-SHRNA-19-2_S4_L002

description: Scrambled Control shRNA


title: SCR-SHRNA-19-2_S4_L004

description: Scrambled Control shRNA


title: SCR-SHRNA-19-2_S4_L003

description: Scrambled Control shRNA


title: SCR-SHRNA-24-2_S3_L001

description: Scrambled Control shRNA


title: GSC1-2


title: SCR-SHRNA-18-3_S8_L003

description: Scrambled Control shRNA


title: SCR-SHRNA-18-3_S8_L004

description: Scrambled Control shRNA


title: SCR-SHRNA-18-3_S8_L002

description: Scrambled Control shRNA


title: KD-SIRNA--3-30-11_S14_L004

description: NNT Knockdown siRNA-3

value: NNT Knockdown


title: KD-SIRNA--3-30-11_S14_L003

description: NNT Knockdown siRNA-3


title: SCR-SHRNA-18-3_S8_L001

description: Scrambled Control shRNA


title: SCR-SIRNA-16-1_S5_L001

description: Scrambled Control siRNA


title: KD-SIRNA--3-30-11_S14_L001

description: NNT Knockdown siRNA-3


title: KD-SiRNA-3-23-5_S7_L004

description: NNT Knockdown siRNA-3


title: KD-SIRNA--3-30-11_S14_L002

description: NNT Knockdown siRNA-3


title: KD-SiRNA-3-23-5_S7_L003

description: NNT Knockdown siRNA-3


title: KD-SiRNA-3-23-5_S7_L002

description: NNT Knockdown siRNA-3


title: KD-SiRNA-3-11-1_S16_L004

description: NNT Knockdown siRNA-3


title: KD-SiRNA-3-23-5_S7_L001

description: NNT Knockdown siRNA-3


title: KD-SiRNA-2-16-1_S15_L004

description: NNT Knockdown siRNA-2


title: KD-SiRNA-3-11-1_S16_L003

description: NNT Knockdown siRNA-3


title: KD-SiRNA-2-16-1_S15_L002

description: NNT Knockdown siRNA-2


title: KD-SiRNA-3-11-1_S16_L001

description: NNT Knockdown siRNA-3


title: KD-SiRNA-3-11-1_S16_L002

description: NNT Knockdown siRNA-3


title: KD-SiRNA-2-11-1_S11_L004

description: NNT Knockdown siRNA-2


title: KD-SiRNA-2-16-1_S15_L001

description: NNT Knockdown siRNA-2


title: KD-SiRNA-2-11-12_S10_L002

description: NNT Knockdown siRNA-2


title: KD-SiRNA-2-11-12_S10_L003

description: NNT Knockdown siRNA-2


title: KD-SiRNA-2-11-12_S10_L001

description: NNT Knockdown siRNA-2


title: SCR-SHRNA-19-2_S4_L001

description: Scrambled Control shRNA


title: KD-SiRNA-2-11-1_S11_L003

description: NNT Knockdown siRNA-2


title: KD-SiRNA-2-11-12_S10_L004

description: NNT Knockdown siRNA-2


title: KD-SiRNA-2-11-1_S11_L002

description: NNT Knockdown siRNA-2


title: KD-SiRNA-2-11-1_S11_L001

description: NNT Knockdown siRNA-2


title: KD-SHRNA-24-2_S1_L004

description: NNT Knockdown shRNA


title: KD-SHRNA-24-2_S1_L002

description: NNT Knockdown shRNA


title: KD-SHRNA-24-2_S1_L003

description: NNT Knockdown shRNA


title: KD-SHRNA-24-2_S1_L001

description: NNT Knockdown shRNA


title: KD-SHRNA--2-3_S9_L003

description: NNT Knockdown shRNA


title: KD-SHRNA--2-3_S9_L004

description: NNT Knockdown shRNA


title: KD-SHRNA--2-3_S9_L002

description: NNT Knockdown shRNA


title: KD-SHRNA--2-3_S9_L001

description: NNT Knockdown shRNA


title: KD-SHRNA--19-2_S13_L003

description: NNT Knockdown shRNA


title: KD-SiRNA-2-16-1_S15_L003

description: NNT Knockdown siRNA-2


title: KD-SHRNA--19-2_S13_L004

description: NNT Knockdown shRNA


title: KD-SHRNA--19-2_S13_L002

description: NNT Knockdown shRNA


title: KD-SHRNA-18-3_S12_L004

description: NNT Knockdown shRNA


title: KD-SHRNA--19-2_S13_L001

description: NNT Knockdown shRNA


title: KD-SHRNA-18-3_S12_L003

description: NNT Knockdown shRNA


title: KD-SHRNA-18-3_S12_L001

description: NNT Knockdown shRNA


title: D316A-Tg HFD [WAT-Activating_m12_s24]

first: David

last: Carling

address: Imperial College London, Hammersmith Hospital Campus, DuCane Road

institute: MRC London Institute of Medical Sciences (LMS)

description:
WAT-Activating_m12_s24
bclfastq 2.16.0.10

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq
The quality of the reads was assessed thanks to FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The reads were then processed and mapped to the human genome mm10 using the Bcbio-nextgen framework version 0.9.0 (https://github.com/chapmanb/bcbio-nextgen). The aligner used was STAR 2.4.1.
The identification of the differentially expressed genes between D316A and WT samples was performed using DESeq2 in R.
Genome_build: mm10
Supplementary_files_format_and_content: Each processed data files is tab separated. It reports the raw counts obtained for each samples. CHOW and HFD diet are reported separately.

source_name: subcutaneous white adipose tissue

extract_protocol:
Animals were euthanized under Schedule 1 of the Animals (Scientific Procedures) Act 1986. Subcutaneous white adipose was retrieved from the inguinal region near the flank, the lymph node removed and the tissue flash-frozen in liquid nitrogen. RNA extraction was performed using Trizol Reagent and isolated using Qiagen RNeasy Mini Kits as per manufacturers instructions. Total RNA quantification was performed using a NanoDrop spectrophotometer. RNA integrity was assessed, with a minimum RIN of 7 permitted for sequencing (Maryam Clausen, contributer).
Illumina TruSeq stranded mRNA-seq protocol

tag: strain

tag: tissue

value: subcutaneous white adipose tissue

tag: age

value: 24 weeks

tag: diet

value: HFD

tag: genotype

value: D316A Transgenic (gain-of-function D316A-Tg)


title: KD-SHRNA-18-3_S12_L002

description: NNT Knockdown shRNA

tag: treatment


title: D316A-Tg HFD [WAT-Activating_m9_s21]

description:
WAT-Activating_m9_s21
bclfastq 2.16.0.10


title: D316A-Tg HFD [WAT-Activating_m8_s20]

description:
WAT-Activating_m8_s20
bclfastq 2.16.0.10


title: D316A-Tg HFD [WAT-Activating_m7_s19]

description:
WAT-Activating_m7_s19
bclfastq 2.16.0.10


title: WT-Tg HFD [WAT-TgWt_m6_s18]

description:
WAT-TgWt_m6_s18
bclfastq 2.16.0.10

value: Wild type Transgenic (AMPKg1-WT)


title: D316A-Tg HFD [WAT-Activating_m10_s22]

description:
WAT-Activating_m10_s22
bclfastq 2.16.0.10


title: WT-Tg HFD [WAT-TgWt_m2_s14]

description:
WAT-TgWt_m2_s14
bclfastq 2.16.0.10


title: WT-Tg HFD [WAT-TgWt_m4_s16]

description:
WAT-TgWt_m4_s16
bclfastq 2.16.0.10


title: WT-Tg HFD [WAT-TgWt_m3_s15]

description:
WAT-TgWt_m3_s15
bclfastq 2.16.0.10


title: WT-Tg HFD [WAT-TgWt_m5_s17]

description:
WAT-TgWt_m5_s17
bclfastq 2.16.0.10


title: D316A-Tg CHOW [12_WATsc_D316A-Tg_S24]

description:
12_WATsc_D316A-Tg_S24
bcl2fastq 2.20.0.422

value: 16 weeks

value: CHOW


title: D316A-Tg CHOW [11_WATsc_D316A-Tg_S23]

description:
11_WATsc_D316A-Tg_S23
bcl2fastq 2.20.0.422


title: D316A-Tg CHOW [9_WATsc_D316A-Tg_S21]

description:
9_WATsc_D316A-Tg_S21
bcl2fastq 2.20.0.422


title: WT-Tg HFD [WAT-TgWt_m1_s13]

description:
WAT-TgWt_m1_s13
bclfastq 2.16.0.10


title: D316A-Tg CHOW [8_WATsc_D316A-Tg_S20]

description:
8_WATsc_D316A-Tg_S20
bcl2fastq 2.20.0.422


title: WT-Tg CHOW [6_WATsc_WT-Tg_S18]

description:
6_WATsc_WT-Tg_S18
bcl2fastq 2.20.0.422


title: WT-Tg CHOW [5_WATsc_WT-Tg_S17]

description:
5_WATsc_WT-Tg_S17
bcl2fastq 2.20.0.422


title: WT-Tg CHOW [4_WATsc_WT-Tg_S16]

description:
4_WATsc_WT-Tg_S16
bcl2fastq 2.20.0.422


title: D316A-Tg CHOW [7_WATsc_D316A-Tg_S19]

description:
7_WATsc_D316A-Tg_S19
bcl2fastq 2.20.0.422


title: WT-Tg CHOW [3_WATsc_WT-Tg_S15]

description:
3_WATsc_WT-Tg_S15
bcl2fastq 2.20.0.422


title: BMMacs_WT_Mock_-_4_L6.LB21_1

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description: mRNA isolated from Macrophages

data_processing:
Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
Quality control of the primary sequencing data was performed using FastQC (version 0.11.3) and included adapter trimming using cutadapt (version 1.8.3).
Reads were aligned using STAR (version 2.4.2)
Genome_build: Mus_musculus UCSC build mm10
Supplementary_files_format_and_content: We mapped reads to the mouse reference genome ( Mus_musculus, UCSC , mm10) from Illumina's igenomes using STAR. After mapping, we assigned aligned read counts from BAM files to exons and genes using the python package HT-Seq.  HT-Seq provided the most accurate way of aligning read counts to overlapping exons. Reads that mapped to multiple positions were removed.

source_name: Bone marrow derived Macrophages from C57BI/6 mice with nothing knocked out and Mock infected at 48 hours

growth_protocol: Primary human astrocytes were maintained on collagen-coated tissue culture plates in a complete astrocyte medium (ScienCell Laboratories) in 2% FBS.

extract_protocol:
mRNA was isolated using the QIAGEN miRNeasy Kit.
Illumina Truseq
Library quality was evaluated using the Qubit® 3.0 Fluorometer and the Agilent 2100 Bioanalyzer instrument. Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).

treatment_protocol: Primary human astrocytes were treated for 4 hours with 10U/ml recombinant human IFN-β or a PBS vehicle. Cells were then lysed in buffer RLT (Qiagen).

value: Bone marrow derived macrophages

tag: gene knockout

tag: infection

value: Mock

tag: timepoint


title: WT-Tg CHOW [1_WATsc_WT-Tg_S13]

description:
1_WATsc_WT-Tg_S13
bcl2fastq 2.20.0.422


title: WT-Tg CHOW [2_WATsc_WT-Tg_S14]

description:
2_WATsc_WT-Tg_S14
bcl2fastq 2.20.0.422


title: D316A-Tg HFD [WAT-Activating_m11_s23]

description:
WAT-Activating_m11_s23
bclfastq 2.16.0.10


title: BMMacs_WT_Mock_-_3_L2.LB10_1

description: mRNA isolated from Macrophages


title: BMMacs_WT_48h_-_2_L4.LB5_1

description: mRNA isolated from Macrophages

source_name: Bone marrow derived Macrophages from C57BI/6 mice with nothing knocked out and WNV infected at 48 hours

value: WNV


title: BMMacs_WT_48h_-_3_L4.LB8_1

description: mRNA isolated from Macrophages


title: BMMacs_WT_Mock_-_2_L6.LB23_1

description: mRNA isolated from Macrophages


title: BMMacs_WT_Mock_-_1_L5.LB11_1

description: mRNA isolated from Macrophages


title: BMMacs_WT_48h_-_1_L2.LB12_1

description: mRNA isolated from Macrophages


title: BMMacs_WT_24h_-_4_L4.LB10_1

description: mRNA isolated from Macrophages

source_name: Bone marrow derived Macrophages from C57BI/6 mice with nothing knocked out and WNV infected at 24 hours


title: BMMacs_RIG-I_WT_Mock_-_3_L6.LB23_1

description: mRNA isolated from Macrophages

source_name: Bone marrow derived Macrophages from C57BI/6_A129 mice with RIG-I knocked out and Mock infected at 48 hours

value: RIG-I


title: BMMacs_WT_24h_-_2_L1.LB5_1

description: mRNA isolated from Macrophages


title: BMMacs_WT_24h_-1_L1.LB1_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_WT_Mock_-_2_L4.LB4_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_WT_Mock_-_1_L8.LB16_1

description: mRNA isolated from Macrophages


title: BMMacs_WT_24h_-1_L4.LB5_1

description: mRNA isolated from Macrophages


title: BMMacs_WT_24h_-_3_L1.LB7_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_WT_24h_-_3_L7.LB8_1

description: mRNA isolated from Macrophages

source_name: Bone marrow derived Macrophages from C57BI/6_A129 mice with RIG-I knocked out and WNV infected at 24 hours


title: BMMacs_RIG-I_WT_48h_-_3_L5.LB15_1

description: mRNA isolated from Macrophages

source_name: Bone marrow derived Macrophages from C57BI/6_A129 mice with RIG-I knocked out and WNV infected at 48 hours


title: BMMacs_RIG-I_WT_24h_-_2_L6.LB4_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_KO_Mock_-_4_L4_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_WT_24h_-_4_L5.LB20_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_WT_48h_-_1_L3.LB25_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_WT_48h_-_2_L1_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_WT_24h_-_1_L3.LB19_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_KO_Mock_-_2_L8.LB27_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_KO_Mock_-_3_L8.LB23_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_KO_48h_-_2_L3.LB22_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_KO_Mock_-_2_L3.LB22_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_KO_48h_-_3_L4.LB9_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_KO_48h_-_1_L2_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_KO_48h_-_4_L2_1

description: mRNA isolated from Macrophages


title: BMMacs_MDA-5_KO_Mock_-_2_L4.LB2_1

description: mRNA isolated from Macrophages

source_name: Bone marrow derived Macrophages from C57BI/6 mice with MDA-5 knocked out and Mock infected at 48 hours


title: BMMacs_RIG-I_KO_24h_-_3_L7.LB14_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_KO_24h_-_4_L4.LB3_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_KO_24h_-_2_L8.LB21_1

description: mRNA isolated from Macrophages


title: BMMacs_RIG-I_KO_24h_-_1_L1.LB2_1

description: mRNA isolated from Macrophages


title: BMMacs_MDA-5_KO_Mock_-_1_L6.LB27_1

description: mRNA isolated from Macrophages


title: BMMacs_MDA-5_KO_48h_-_1_L4.LB5_1

description: mRNA isolated from Macrophages

source_name: Bone marrow derived Macrophages from C57BI/6 mice with MDA-5 knocked out and WNV infected at 48 hours


title: BMMacs_MDA-5_KO_48h_-_2_L8.LB25_1

description: mRNA isolated from Macrophages


title: BMMacs_MDA-5_KO_24h_-_3_L5.LB12_1

description: mRNA isolated from Macrophages

source_name: Bone marrow derived Macrophages from C57BI/6 mice with MDA-5 knocked out and WNV infected at 24 hours


title: BMMacs_MDA-5_KO_24h_-_2_L5.LB11_1

description: mRNA isolated from Macrophages


title: BMMacs_MDA-5_KO_24h_-_1_L7.LB11_1

description: mRNA isolated from Macrophages


title: BMMacs_MDA-5_KO_24h_-_1_L2.LB14_1

description: mRNA isolated from Macrophages


title: BMMacs_DKO_Mock_-_1_L4.LB7_1

description: mRNA isolated from Macrophages

source_name: Bone marrow derived Macrophages from C57BI/6_A129 mice with RIGI and MDA5 knocked out and Mock infected at 48 hours

value: RIGI and MDA5


title: BMMacs_DKO_24h_-_3_L6.LB25_1

description: mRNA isolated from Macrophages

source_name: Bone marrow derived Macrophages from C57BI/6_A129 mice with RIGI and MDA5 knocked out and WNV infected at 24 hours


title: BMMacs_DKO_Mock_-_3_L7.LB6_1

description: mRNA isolated from Macrophages


title: BMMacs_DKO_24h_-_4_L5.LB18_1

description: mRNA isolated from Macrophages


title: BMMacs_DKO_48h_-1_L3.LB27_1

description: mRNA isolated from Macrophages

source_name: Bone marrow derived Macrophages from C57BI/6_A129 mice with RIGI and MDA5 knocked out and WNV infected at 48 hours


title: BMMacs_DKO_Mock_-_2_L7.LB7_1

description: mRNA isolated from Macrophages


title: BMMacs_DKO_24h_-_1_L2.LB9_1

description: mRNA isolated from Macrophages


title: BMMacs_DHX58_KO_Mock_-_2_L6.LB25_1

description: mRNA isolated from Macrophages

source_name: Bone marrow derived Macrophages from C57BI/6 mice with DHX58 knocked out and Mock infected at 48 hours


title: BMMacs_DHX58_KO_Mock_-_4_L5.LB19_1

description: mRNA isolated from Macrophages


title: BMMacs_MDA-5_KO_Mock_-_3_L3_1

description: mRNA isolated from Macrophages


title: BMMacs_DHX58_KO_Mock_-_2_L4.LB8_1

description: mRNA isolated from Macrophages


title: BMMacs_DHX58_KO_48h_-_1_L3.LB20_1

description: mRNA isolated from Macrophages

source_name: Bone marrow derived Macrophages from C57BI/6 mice with DHX58 knocked out and WNV infected at 48 hours


title: BMMacs_DHX58_KO_Mock_-_1_L6.LB20_1

description: mRNA isolated from Macrophages


title: BMMacs_DHX58_KO_24h_-_1_L3_1

description: mRNA isolated from Macrophages

source_name: Bone marrow derived Macrophages from C57BI/6 mice with DHX58 knocked out and WNV infected at 24 hours


title: BMMacs_DHX58_KO_24h_-_1_L5.LB14_1

description: mRNA isolated from Macrophages


title: BMMacs_MDA-5_KO_48h_-_3_L6.LB1_1

description: mRNA isolated from Macrophages


title: BMMacs_DHX58_KO_48h_-_2_L3.LB19_1

description: mRNA isolated from Macrophages


title: BMMacs_DHX58_KO_24h_-_3_L6.LB22_1

description: mRNA isolated from Macrophages


title: CRABP1-2

city: Los Angeles

first: Meng

last: Li

state: CA

address: 2003 Zonal Avenue

institute: University of Southern California

data_processing:
Raw data files in FASTQ format was analyzed with Partek Flow v6
Raw reads were trimmed with Quality Score method (from Both End; Quality score cutoff 20; trimmed reads shorter than 25nt were excluded)
Trimmed reads were mapped with Star 2.4.1 to human hg38 genome build with Genecode v25 as guidance
Mapped reads were quantified to Gencode v25 using Partek E/M method
Read counts were filtered (maximum <= 10), normalized (offset 1 then upper quartile normalization), and analzyed for differential expression using Partek's Gene Specific Analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes raw read counts for each sample

source_name: CRABP1, hepatoma cell line

growth_protocol: Huh7 cells were maintained in DMEM with 10% FBS and subcultured every 3 days.

extract_protocol:
Total RNA was extracted with Quick-RNA mini kit (Zymo Research)
PolyA mRNA libraries were prepared from total RNA using the KAPA mRNA HyperPrep Kit (Kapa Biosystems). Final libraries were quantified using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc.), and the fragment size distribution was determined with the Bioanalyzer. The libraries were then pooled equimolarly, and the final pool was quantified via qPCR using the Kapa Biosystems Library Quantification Kit, according to manufacturer’s instructions.

treatment_protocol: Not applicable

value: Hepatoma cells

tag: genotype/variation

value: overexpressing CRABP1


title: BMMacs_DHX58_KO_24h_-_2_L5.LB16_1

description: mRNA isolated from Macrophages


title: CRABP2-2

source_name: CRABP2, hepatoma cell line

value: overexpressing CRABP2


title: CRABP1-1


title: Empty vector-2

source_name: Empty vector, hepatoma cell line

value: Empty vector


title: CRABP2-1


title: BMMacs_DKO_24h_-_2_L7.LB10_1

description: mRNA isolated from Macrophages


title: Empty vector-1


title: in vitro HBC_3

city: Boston

first: Brian

last: Lin

address: 136 Harrison Avenue

department: DMCB

institute: Tufts University

data_processing:
STAR mapper version 2.5.2b
cuffquant, part of cufflinks 2.2.1
cuffnorm, part of cufflinks 2.2.1
Genome_build: MM9
Supplementary_files_format_and_content: csv of FPKM values from output of cuffnorm

source_name: Olfactory epithelium horizontal basal cells

extract_protocol:
Zymo quick-RNA microprep, cat# R1050 was used for both in vitro samples, and microdissected respiratory basal cells
RNA was prepped using standard Illumina library construction methods

tag: passages

tag: facs

tag: mouse strain

value: wildtype


title: in vitro HBC_1