title: Alternaria brassicicola treated Col-0 rep 3

description:
index primer: GATCAG
processed data files: DESeq_srna_alter_alterAGO1.csv, DESeq_srna_alter_alterAGO1_sig.csv, DESeq_srna_alter_mockAGO1.csv, DESeq_srna_alter_mockAGO1_sig.csv, DESeq_srna_alter_unAGO1.csv, DESeq_srna_alter_unAGO1_sig.csv, DESeq_srna_mock_alter.csv, DESeq_srna_mock_alter_sig.csv, DESeq_srna_un_alter.csv, DESeq_srna_un_alter_sig.csv

source_name: Alternaria brassicicola treated Col-0

value: Alternaria brassicicola treated


title: HS1-11 N2 RNA rep3 (5' assay)

status: Public on Jun 17 2019

type: SRA

city: Luebeck

first: Martin

last: Kircher

state: SH

address: Ratzeburger Allee 160

department: Humangenetics

country: Germany

institute: University of Luebeck

description: telencephalon

library_source: transcriptomic

data_processing:
Library strategy: lentivirus-based massively parallel reporter assay (lentiMPRA)
Libraries were sequenced on MiSeq or NextSeq 500 instruments (Illumina) and base called using the instruments' Real Time Analysis softwarre. Multiplexed paired end (PE) Illumina sequencing data was split based on sample barcodes allowing up to one substitution in the barcode sequence.
Paired-end reads shorter or equal to read length were consensus called and adapter trimmed. For assignment of barcodes, insert consensus sequences were aligned to all designed oligo sequences using BWA MEM (Li and Durbin 2009) with parameters penalizing soft-clipping of alignment ends (-L 80). A minimum of three barcode observation was required for the assignment, further 90% of the barcode observations had to be with the specific insert.
To normalize RNA and DNA for different sequencing depths in each sample, we divided reads by the sum of observed counts and reported them as counts per million. Only barcodes observed in RNA and DNA of the same sample were considered.
Barcodes (consensus called paired-end reads) and UMI sequences containing unresolved bases (N) or not matching the designed length of 15bp were excluded. Each barcode x UMI pair was counted only once and only barcodes matching perfectly to those included the oligo design considered. To determine RNA/DNA ratios per insert, we summed up the counts of all barcodes belonging to the same insert and determined the ratio of the average of normalized counts.
ChIP-seq peaks were called using the ENCODE pipeline with default parameters (https://github.com/ENCODE-DCC/chip-seq-pipeline2).
Genome_build: GRCh37
Supplementary_files_format_and_content: All processed data files are in gzip-compressed tab-separated text file format. DNA.tsv.gz and RNA.tsv.gz files contain assigned RNA and DNA barcode counts. *_design.tsv.gz contain all designed oligo sequences for HAR and HAR-permutation, respectively. HAR5p_assigment.tsv.gz is the barcode-to-insert assignment obtained from sequencing data.

molecule: polyA RNA

organism: Homo sapiens

source_name: Human neural progenitor cells

growth_protocol:
http://www.pnas.org/content/107/11/5254.short
Human iPSC-derived neural progenitor cells were maintained in N2B27 media supplemented with 20ng/mL bFGF and EGF on matrigel-coated dishes. HepG2 cells were maintained in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
The cells were washed with PBS three times, and genomic DNA and total RNA was extracted using AllPrep DNA/RNA mini kit (Qiagen). Messenger RNA (mRNA) was purified from the total RNA using Oligotex mRNA mini kit (Qiagen) and treated with Turbo DNase to remove contaminating DNA.
mRNA was reverse transcribed with SuperScript II (Invitrogen) using a primer downstream from the barcode. Resulting cDNA was split into multiple reactions to reduce PCR jack-potting effects and cDNA amplification performed with Kapa Robust polymerase for three cycles, incorporating unique molecular identifiers (UMIs) of 10 bp length. PCR products were cleaned with AMPure XP beads (Beckman Coulter) to remove primers and concentrate samples. These products underwent a second round of amplification in 8 reactions per replicate for 15 cycles, with a reverse primer containing only P7. All reactions were pooled and run on agarose gels for size selection and submitted for sequencing. For DNA, each replicate was amplified for 3 cycles with UMI-incorporating primers, just as the RNA. First round products were cleaned up with AMPure XP beads, and amplified in split reactions, each for 20 cycles. Again, reactions were pooled and gel-purified and sequenced.

treatment_protocol: For the lentiMPRA, 6 million human iPSC-derived neural progenitor cells were plated on a 15 cm dish and cultured for 24 hours. The cells were infected with integrating lentivirus libraries and incubated for 4 days, when they have an estimated 50-100 viral particles/cell. Three independent replicate cultures were infected.

tag: cell type

value: neural progenitors

tag: developmental stage


title: N2_empty vector_cadmium_rep3

city: Saskatoon

first: Cheng-Wei

last: Wu

state: SK

address: 52 Campus Drive

country: Canada

institute: University of Saskatchewan

description:
emptyvector_control&cadmium
EC_4

data_processing:
HISAT2 2.1.0-beta used for mapping to the C. elegans reference genome
HTSeq V0.6.1 used for Quantification
rMATS 3.0.8 used for Alternative Splicing analysis
cufflinks 2.1.1 used for novel gene prediction.
DEGSeq 1.12.0 used for differential expression analysis
Genome_build: WS220
Supplementary_files_format_and_content: Processed data files (in Excel format) include readcounts, differential gene expression and alternative splicing for each file.
The data are exported with the standard rMATS format:
IC refers to number of reads mapped to the exon inclusion isoform.
SC refers to number of reads mapped to the exon skipping isoform.
Sample_1 always refers to the experimental group on the name of the processed data file (e.g. cadmium, ints-4 RNAi, ints-4 RNAi + cadmium, etc.)
Sample_2 always refers to the control value (empty vector + control) that is used for all processed files.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: N2_empty vector_cadmium, whole animal

extract_protocol:
Total RNA extracted using the RNAqueous Total RNA Isolation Kit
Standard Illumina protocols with oligo-dT beads

tag: strain

tag: treatment

value: 300um Cadmium (12h)

tag: genotype

value: wildtype

tag: tissue

value: whole animal


title: Tabula Muris Senis (bulk RNA-seq) [A18_384Bulk_Plate1_S18]

city: San Francisco

first: Angela

last: Oliveira Pisco

state: CA

address: 499 Illinois St

department: Data Science

country: USA

institute: Chan Zuckerberg Biohub

description: processed data file: 190214_A00111_0269_AHH3J3DSXX__190214_A00111_0270_BHHMFWDSXX.csv

data_processing:
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316.
Reads were aligned to the mm10plus genome using STAR version 2.5.2b with parameters TK.
Gene counts were produced using HTSEQ version 0.6.1p1 with default parameters, except ‘stranded’ was set to ‘false’, and ‘mode’ was set to ‘intersection-nonempty’.
Genome_build: GRCm38
Supplementary_files_format_and_content: 190214_A00111_0269_AHH3J3DSXX__190214_A00111_0270_BHHMFWDSXX.csv: Comma-separated text file includes gene count table for all organs and ages.
Supplementary_files_format_and_content: MACA_Bulk_metadata.csv: Comma-separated text file includes experiment metadata.

organism: Mus musculus

extract_protocol:
RNeasy (mini and micro) Qiagen RNA isolation from homogenized tissue.
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT.
Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2.

tag: strain/background

value: Brain

tag: age

value: 21 months postnatal

tag: Sex

value: Female


title: HS1-11 N2 RNA rep2 (5' assay)

description: telencephalon


title: Tabula Muris Senis (bulk RNA-seq) [A5_384Bulk_Plate2_S5]

value: Kidney

value: 9 months postnatal


title: HS1-11 N2 RNA rep1 (5' assay)

description: telencephalon


title: Alternaria brassicicola treated Col-0 rep 1

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

institute: University of Oldenburg

description:
index primer: CAGATC
processed data files: DESeq_srna_alter_alterAGO1.csv, DESeq_srna_alter_alterAGO1_sig.csv, DESeq_srna_alter_mockAGO1.csv, DESeq_srna_alter_mockAGO1_sig.csv, DESeq_srna_alter_unAGO1.csv, DESeq_srna_alter_unAGO1_sig.csv, DESeq_srna_mock_alter.csv, DESeq_srna_mock_alter_sig.csv, DESeq_srna_un_alter.csv, DESeq_srna_un_alter_sig.csv

data_processing:
Quality filtering: FASTQC(version v0.10.1), default parameters
Adapter removal and filtering low quality and/or too long or short reads, parameters:cutadapt -e 0.2 -a TGGAAT -m 16 -M 28
Quality filtering: FASTQC(version v0.10.1), default parameters
rRNA/tRNA filtering: UEA sRNA Workbench (version 3.2) Filtering tool, parameters: min.length 16, max. length 28, min. abundance 0, max. abundance not defined, don't filter low complexity reads, don't filter invalid sequences, output redundant files
Identify known miRNA profiles, collecting raw expression data: UEA sRNA Workbench (version 3.2) miRProf tool, parameters: genome: TAIR10, miRNA database:miRBase (version 21),mismatches=0, overhangs=true, group_mismatches=true, group_organisms=true, group_variant=true, group_mature_and_star=false, only_keep_best=true, min_length=18, max_length=25, min_abundance=15, mirbase_version=21, group_options_string=ignore mismatches, combine organisms, combine variants
Differential expression analysis: DESeq (version 1.2), default parameters
Genome_build: TAIR 10, MirBase version 21
Supplementary_files_format_and_content: [DESeq*.csv] DESeq2 differential expression analysis – differential expression data, total or significant data sets.  First column contains the number of hits, second column contains  MirBase version 21 reference microRNA IDs, third column "baseMean" contains the mean of normalized read counts averaged over all samples from both conditions, fourth column "baseMeanA" contains mean normalized counts from condition A, fifth column "baseMeanB" contains mean normalized counts from condition B, sixth column "foldChange" contains fold change from condition A to B, seventh column "log2FoldChange" contains the logarithm (to basis 2) of the fold change, eighth column  "pval" contains p-values for the statistical  significance of this change, ninth column "padj" contains p-values adjusted for multiple testing with the Benjamini-Hochberg procedure, which controls false discovery rate (FDR).  In case of baseMeanA and baseMeanB, comparisons always following the sequence of samples in the file name (For example, for DESeq_srna_alter_alterAGO1.csv, baseMeanA = total alternaria samples, baseMeanB = AGO1-IP alternaria samples).
Supplementary_files_format_and_content: [mirprof_abundance_miRNA.csv] abundance measurement file

organism: Arabidopsis thaliana

growth_protocol: Plants were grown under short day conditions (8 h light, 22°C) with a high humidity on soil for around 5 - 6 weeks.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA MiniPrep Kit (ZymoResearch) and concentrated with RNA Clean and ConcentratorTM-5 (ZymoResearch). For AGO1 immunoprecipitation, around 2.5 mg of plant material was ground in liquid nitrogen, resuspended in extraction buffer (50 mM Tris-HCl pH 7.5; 150 mM NaCl; 10 % glycerol; 0.05 % Nonidet P-40; Proteinase-Inhibitor Roche cOmplete (EDTA-free); 1 mM PMSF), incubated at 4 °C for 20-30 min. on a rotator and centrifuged at 4 °C at 3200 g for 30 min. The protein extract was filtered (2x Miracloth and 1x syringe driven filter unit) and pre‑cleared with 100 ml protein A agarose beads for 30 min. on a rotator. After removal of the beads, supernatant was split in two fractions and incubated with/without 5 µl of AGO1 antibody (Agrisera; AS09 527) at 4°C for 2h on a rotator and an additional hour with 50 µl protein A agarose beads. Beads were collected by centrifugation and washed several times with extraction buffer. AGO1 complex was eluted with AGO1 peptide (Agrisera; AS09 527P) as described in Qi and Mi (2010) with minor modifications. AGO1 complex was eluted in 100 µl peptide elution solution (50 µg/ml). RNA and protein from the complex was extracted by adding TRIzol® reagent and incubation at 50 °C for 5 min. With chloroform, aqueous and organic phase were separated. The RNA containing, aqueous phase was further cleaned with chloroform and precipitated over night with one vol. isopropanol at ‑20 °C followed by centrifugation and washed with 80% ethanol. The organic phase was precipitated with 3 vol. acetone at -20 °C followed by centrifugation and washed with 80 % acetone. The extracted RNA was concentrated with RNA Clean and ConcentratorTM-5 (ZymoResearch).
For total RNA libraries, small RNAs were isolated from 8 µg total RNA as described in Gilbert et al. (2014) and sRNA libraries were done with NEXTflexTM Small RNA Sequencing Kit (Bioo Scientific). sRNA libraries from the AGO1‑immunoprecipitated sRNAs were done according to the TruSeq® Small RNA Library Prep Kit (Illumina). All three biological replicates of each treatment of the total RNA sRNA libraries and the AGO1-immunoprecipitated sRNA libraries, respectively, were pooled and sequenced each on two different lanes.

treatment_protocol: Plants were sprayed with Alternaria brassicicola (strain MUCL 20297) spore solution (1 x 10^6 spores/ml) with 0.01 % Silwet L 77. Rosette leaves were harvested 3 days after inoculation.

tag: ecotype

value: rosette leaves


title: Tabula Muris Senis (bulk RNA-seq) [A17_384Bulk_Plate2_S17]

value: Small Intestine

value: 12 months postnatal

value: Male


description:
Sample 9 - biological replicate 3
index primer: GATCAG
processed data files: DESeq2_mrna_mock_alternaria_05.csv, DESeq2_mrna_mock_alternaria.csv, DESeq2_mrna_untreated_alternaria_05.csv, DESeq2_mrna_untreated_alternaria.csv

data_processing:
Quality filtering: FASTQC(version v0.10.1), default parameters
rRNA and tRNA filtering: TopHat(version 2.0.12), parameters: tophat --library-type fr-secondstrand –no-novel-juncs
Aligning to TAIR10 to collect  TopHat(version 2.0.12), with default parameters
Differential expression analysis: DESeq2 (version1.8.2), with default parameters
Genome_build: TAIR10, Alternaria brassicicola genome (http://genome.jgi.doe.gov/Altbr1/Altbr1.download.ftp.html)  for rRNA/tRNA filering: tRNA collections (http://gtrnadb2009.ucsc.edu/download/tRNAs/GtRNAdb-all-tRNAs.fa.gz),  Arabidopsis thaliana genes for 5.8S rRNA and 25S rRNA with 18S rRNA fragment (geneBank ID: X52320.1);  sequences from arabidopsis.org: AT2G01010.1 – 18SrRNA, AT2G01020 – 5.8sRNA, ATCG00920 – 16SrRNA, ATCG00950 – 23SrRNA, ATCG00960 – 4.5SrRNA, ATCG01160.1 – 5SrRNA, ATMG00020.1 – 26SrRNA
Supplementary_files_format_and_content: [.txt] HTSeq counts
Supplementary_files_format_and_content: [.csv] DESeq2 differential expression analysis – differential expression data, filtered values to padj < 0.1 or padj < 0.05.  First column contains  TAIR10 reference file gene IDs, second column "baseMean" contains the mean of normalized read counts averaged over all samples from both conditions, third column "log2FoldChange" contains the logarithm (to base 2) of the fold change, fourth column "lfcSE" contains standard error, fifth column ""stat" contains Wald statistic values, sixth  column "pval" contains Wald test p-values for the statistical  significance of this change, seventh column "padj" means p-value adjusted for multiple testing with the Benjamini-Hochberg procedure, which controls false discovery rate (FDR).

growth_protocol: Plants were grown under short day conditions (8 h light, 22°C) with a high humidity on soil for around 5-6 weeks.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA MiniPrep Kit (ZymoResearch) and concentrated with RNA Clean and ConcentratorTM-5 (ZymoResearch).
Polyadenylated RNA were isolated from 3 µg total RNA with NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB) and used as input for the ScriptSeq™  v2 RNA-Seq Library Preparation Kit (Epicentre). Size selection (250 - 650 bp) was performed on the pooled libraries using BluePippin (Sage Science).


title: Tabula Muris Senis (bulk RNA-seq) [A17_384Bulk_Plate1_S17]

value: 18 months postnatal


title: N2_empty vector_cadmium_rep1

description:
emptyvector_control&cadmium
EC_1


title: mock treated Col-0 rep 3

description:
index primer: GCCAAT
processed data files: DESeq_srna_mock_alterAGO1.csv ,DESeq_srna_mock_alterAGO1_sig.csv, DESeq_srna_mock_alter.csv, DESeq_srna_mock_alter_sig.csv, DESeq_srna_mock_mockAGO1.csv, DESeq_srna_mock_mockAGO1_sig.csv, DESeq_srna_mock_unAGO1.csv, DESeq_srna_mock_unAGO1_sig.csv, DESeq_srna_un_mock.csv, DESeq_srna_un_mock_sig.csv

source_name: mock treated Col-0

value: mock treated


title: Tabula Muris Senis (bulk RNA-seq) [A16_384Bulk_Plate1_S16]

value: Lung

value: 1 months postnatal


description:
Sample 7 - biological replicate 1
index primer: CAGATC
processed data files: DESeq2_mrna_mock_alternaria_05.csv, DESeq2_mrna_mock_alternaria.csv, DESeq2_mrna_untreated_alternaria_05.csv, DESeq2_mrna_untreated_alternaria.csv

value: Alternaria brassicicola treated


title: mock treated Col-0 rep 1

description:
index primer: TGACCA
processed data files: DESeq_srna_mock_alterAGO1.csv ,DESeq_srna_mock_alterAGO1_sig.csv, DESeq_srna_mock_alter.csv, DESeq_srna_mock_alter_sig.csv, DESeq_srna_mock_mockAGO1.csv, DESeq_srna_mock_mockAGO1_sig.csv, DESeq_srna_mock_unAGO1.csv, DESeq_srna_mock_unAGO1_sig.csv, DESeq_srna_un_mock.csv, DESeq_srna_un_mock_sig.csv


title: mock treated Col-0 rep 2

description:
index primer: ACAGTG
processed data files: DESeq_srna_mock_alterAGO1.csv ,DESeq_srna_mock_alterAGO1_sig.csv, DESeq_srna_mock_alter.csv, DESeq_srna_mock_alter_sig.csv, DESeq_srna_mock_mockAGO1.csv, DESeq_srna_mock_mockAGO1_sig.csv, DESeq_srna_mock_unAGO1.csv, DESeq_srna_mock_unAGO1_sig.csv, DESeq_srna_un_mock.csv, DESeq_srna_un_mock_sig.csv


title: Tabula Muris Senis (bulk RNA-seq) [A16_384Bulk_Plate2_S16]

value: Pancreas


title: N2_empty vector_control_rep1

description:
emptyvector_control&cadmium
E_1

source_name: N2_empty vector_control, whole animal

value: control

value: wildtype


title: untreated Col-0 rep 3

description:
index primer: TTAGGC
processed data files: DESeq_srna_un_alterAGO1.csv, DESeq_srna_un_alterAGO1_sig.csv, DESeq_srna_un_alter.csv, DESeq_srna_un_alter_sig.csv, DESeq_srna_un_mockAGO1.csv, DESeq_srna_un_mockAGO1_sig.csv, DESeq_srna_un_mock.csv, DESeq_srna_un_mock_sig.csv, DESeq_srna_un_unAGO1.csv, DESeq_srna_un_unAGO1_sig.csv

source_name: untreated Col-0

value: untreated


title: TCPOBOP-treated pool 3 (mice euthanized 3 hr after injection, at 11 AM)_G86_M6

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description:
nuclear RNA pooled from 4 mouse livers
poly-A selected, unstranded library
lncRNA_rpkms_G81_G86_G95.xlsx

data_processing:
Sequence reads were mapped to mm9 using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
Reads were counted along exons of lncRNA for each sample and were converted into RPKM values
Genome_build: mm9
Supplementary_files_format_and_content: A Microsoft Excel sheet containing expression levels (in RPKMs) for each lncRNA across datasets. LncRNA genomic locations were discovered as described in PMID: 28903501 and PMID: 26459762

molecule: nuclear RNA

source_name: liver tissue

growth_protocol: Male or female CD-1 mice (Charles River Laboratories), 8 weeks old, were treated with either TCPOBOP or PCN for 3  or 6 hours, and were euthanized. Livers were then harvested.

extract_protocol:
RNA was purified from frozen liver ('otal liver RNA') or from purified nuclei ('nuclear RNA'), as indicated. Nuclei were extracted from mouse liver tissue by homogenization and sucrose purification. RNA was extracted from total liver or from purified nuclei using Trizol following standard protocol.
Poly-A-enriched total RNA or nuclear RNA was prepared for Illumina sequencing using either strand-specific or non strand-specific sample preparation protocol

treatment_protocol: Injection of either PCN or TCPOBOP.

value: TCPOBOP

value: CD-1 (Charles River)

tag: gender

value: female

value: 8 weeks old


title: mock treated Col-0 rep 2

description:
Sample 5 - biological replicate 2
index primer: ACAGTG
processed data files: DESeq2_mrna_mock_alternaria_05.csv, DESeq2_mrna_mock_alternaria.csv,   DESeq2_mrna_untreated_mock_05.csv, DESeq2_mrna_untreated_mock.csv

value: rosette leaves


title: Tabula Muris Senis (bulk RNA-seq) [A15_384Bulk_Plate1_S15]

value: GAT

value: 6 months postnatal


title: mock treated Col-0 rep 1

description:
Sample 4 - biological replicate 1
index primer: TGACCA
processed data files: DESeq2_mrna_mock_alternaria_05.csv, DESeq2_mrna_mock_alternaria.csv,   DESeq2_mrna_untreated_mock_05.csv, DESeq2_mrna_untreated_mock.csv


title: Alternaria brassicicola treated Col-0 rep 2

description:
index primer: ACTTGA
processed data files: DESeq_srna_alter_alterAGO1.csv, DESeq_srna_alter_alterAGO1_sig.csv, DESeq_srna_alter_mockAGO1.csv, DESeq_srna_alter_mockAGO1_sig.csv, DESeq_srna_alter_unAGO1.csv, DESeq_srna_alter_unAGO1_sig.csv, DESeq_srna_mock_alter.csv, DESeq_srna_mock_alter_sig.csv, DESeq_srna_un_alter.csv, DESeq_srna_un_alter_sig.csv


title: Tabula Muris Senis (bulk RNA-seq) [A14_384Bulk_Plate3_S14]

value: Small Intestine

value: 3 months postnatal

value: Male


title: N2_empty vector_cadmium_rep2

description:
emptyvector_control&cadmium
EC_3

value: 300um Cadmium (12h)

value: whole animal


title: TCPOBOP-treated pool 1 (mice euthanized 3 hr after injection, at 11 AM)_G86_M4

description:
nuclear RNA pooled from 3 mouse livers
poly-A selected, unstranded library
lncRNA_rpkms_G81_G86_G95.xlsx


title: untreated Col-0 rep 3

description:
Sample 3 - biological replicate 3
index primer: TTAGGC
processed data files: DESeq2_mrna_untreated_alternaria_05.csv, DESeq2_mrna_untreated_alternaria.csv, DESeq2_mrna_untreated_mock.csv, DESeq2_mrna_untreated_mock_05.csv


title: PCN-treated (mice euthanized 3 hr after injection, at 11 AM)_G81_M10

description:
nuclear RNA pooled from 2 mouse livers
poly-A selected, unstranded library
lncRNA_rpkms_G81_G86_G95.xlsx

value: PCN

value: male


title: untreated Col-0 rep 2

description:
Sample 2 - biological replicate 2
index primer: CGATGT
processed data files: DESeq2_mrna_untreated_alternaria_05.csv, DESeq2_mrna_untreated_alternaria.csv, DESeq2_mrna_untreated_mock.csv, DESeq2_mrna_untreated_mock_05.csv


title: Tabula Muris Senis (bulk RNA-seq) [A14_384Bulk_Plate1_S14]

value: Bone

value: 15 months postnatal


title: mock treated Col-0 rep 3

description:
Sample 6 - biological replicate 3
index primer: GCCAAT
processed data files: DESeq2_mrna_mock_alternaria_05.csv, DESeq2_mrna_mock_alternaria.csv,   DESeq2_mrna_untreated_mock_05.csv, DESeq2_mrna_untreated_mock.csv

value: mock treated


title: Tabula Muris Senis (bulk RNA-seq) [A15_384Bulk_Plate2_S15]

description: processed data file: 190214_A00111_0269_AHH3J3DSXX__190214_A00111_0270_BHHMFWDSXX.csv

value: MAT

value: 18 months postnatal


title: N2_empty vector_control_rep2

description:
emptyvector_control&cadmium
E_2

value: control

value: wildtype


title: N2_empty vector_control_rep3

description:
emptyvector_control&cadmium
E_4


description:
Sample 8 - biological replicate 2
index primer: ACTTGA
processed data files: DESeq2_mrna_mock_alternaria_05.csv, DESeq2_mrna_mock_alternaria.csv, DESeq2_mrna_untreated_alternaria_05.csv, DESeq2_mrna_untreated_alternaria.csv

value: Alternaria brassicicola treated

value: rosette leaves


title: untreated Col-0 rep 2

description:
index primer: CGATGT
processed data files: DESeq_srna_un_alterAGO1.csv, DESeq_srna_un_alterAGO1_sig.csv, DESeq_srna_un_alter.csv, DESeq_srna_un_alter_sig.csv, DESeq_srna_un_mockAGO1.csv, DESeq_srna_un_mockAGO1_sig.csv, DESeq_srna_un_mock.csv, DESeq_srna_un_mock_sig.csv, DESeq_srna_un_unAGO1.csv, DESeq_srna_un_unAGO1_sig.csv

value: untreated


title: TCPOBOP-treated pool 2 (mice euthanized 3 hr after injection, at 11 AM)_G86_M5

value: TCPOBOP

value: CD-1 (Charles River)

value: female

value: 8 weeks old


title: TCPOBOP-treated (mice euthanized 3 hr after injection, at 11 AM)_G81_M9

description:
total RNA pooled from 6 mouse livers
poly-A selected, unstranded library
lncRNA_rpkms_G81_G86_G95.xlsx


title: Tabula Muris Senis (bulk RNA-seq) [A13_384Bulk_Plate3_S13]

value: Brain

value: Female


title: CLC50

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

country: China

institute: CEMCS, CAS

data_processing:
The reads were mapped to the human reference genome (HG38) using TopHat2
Cufflinks algorithm was used to calculate gene expressions. Then the expression profiles of all samples were normalized by the fragments per kilobase of exon per million fragments mapped (FPKM) method.
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: cell line

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

tag: library barcodes

value: TTAGGC


title: Tabula Muris Senis (bulk RNA-seq) [A13_384Bulk_Plate2_S13]

value: Pancreas

value: Male


title: untreated Col-0 rep 1

description:
Sample 1 - biological replicate 1
index primer: ATCACG
processed data files: DESeq2_mrna_untreated_alternaria_05.csv, DESeq2_mrna_untreated_alternaria.csv, DESeq2_mrna_untreated_mock.csv, DESeq2_mrna_untreated_mock_05.csv


title: CLC49

value: CGATGT


title: untreated Col-0 rep 1

description:
index primer: ATCACG
processed data files: DESeq_srna_un_alterAGO1.csv, DESeq_srna_un_alterAGO1_sig.csv, DESeq_srna_un_alter.csv, DESeq_srna_un_alter_sig.csv, DESeq_srna_un_mockAGO1.csv, DESeq_srna_un_mockAGO1_sig.csv, DESeq_srna_un_mock.csv, DESeq_srna_un_mock_sig.csv, DESeq_srna_un_unAGO1.csv, DESeq_srna_un_unAGO1_sig.csv


title: PCN-treated (mice euthanized 6 hr after injection, at 2 PM)_G81_M6

description:
total RNA pooled from 6 mouse livers
poly-A selected RNA, strand-specific library
lncRNA_rpkms_G81_G86_G95.xlsx

value: PCN

value: male


title: PCN-treated (mice euthanized 3 hr after injection, at 11 AM)_G81_M5


title: CLC48

value: ATCACG


title: TCPOBOP-treated (mice euthanized 6 hr after injection, at 2 PM)_G81_M4


title: CLC47

value: TGACCA


title: Tabula Muris Senis (bulk RNA-seq) [A12_384Bulk_Plate2_S12]

value: Liver

value: 6 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [A12_384Bulk_Plate3_S12]

value: Lung

value: 12 months postnatal


title: TCPOBOP-treated (mice euthanized 3 hr after injection, at 11 AM)_G81_M3

value: TCPOBOP

value: CD-1 (Charles River)


title: CLC46

value: ACTTGA


title: P8 rep4

city: Indianapolis

first: Jonathan

middle: Matthew

last: Wilson

state: INDIANA

address: 723 W. Michigan St.

department: Biology

institute: IUPUI

data_processing:
Reads were analyzed with quality recalibration software (Illumina Inc., San Diego, CA) for each sequence read.
A 5-base sliding window was used when assigning quality scores (Q-scores). To eliminate low-quality reads while retaining high-quality regions, a position with an average Q-score of less than 20 was truncated and any read length less than 35 bases was discarded.
Sequence reads were aligned to the mouse genome (mm9) using TopHat.
After aligning the sequence reads to a filtering index, including ribosomal RNAs and other repeat sequences of no interest, three levels of sequence alignment was conducted: genome, known junctions and novel junctions based on enriched regions identified during genomic alignment. Uniquely aligned sequences with no more than two mismatches were allowed.
Fragments per kilobase of transcript per million (FPKM) was calculated based on the number of reads aligned to a gene.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file includes raw counts, CPM and RPKM values for each sample

source_name: GLAST-postive brain cells

extract_protocol:
Using the PicoPure RNA isolation kit (Applied Biosystems, Foster City, CA), RNA was harvested from GLAST-postive cells, which were isolated from whole brains at P0 or P8 by enzymatic and mechanical dissociation prior to magnetic separation using anti-GLAST (ASCA-1) microbead kit (Miltenyi Biotec, Auburn, CA).
Libraries were constructed using the TruSeq RNA Sample Preparation Kit v2 set A and protocol companion (Illumina Inc., San Diego, CA).

value: Post-natal day 8

value: brain

value: Astrocyte Precursors


title: Tabula Muris Senis (bulk RNA-seq) [A13_384Bulk_Plate1_S13]

value: Spleen

value: Female


title: P8 rep3


title: P8 rep2


title: pIX_Halo_empty_ampDAPseq

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

description:
ampDAPseq_CopiaMBD1_peaks.txt
ampDAPseq_CopiaMBD2_peaks.txt
ampDAPseq_CopiaMBD3_peaks.txt

library_source: genomic

data_processing:
Library strategy: ampDAP-seq
CASAVA v1.8.2
For Bisulfite-seq, adapters were trimmed using fastp as default, then aligned to the reference genome using Bowtie2 and BSseeker2 with the option --bt2--end-to-end. PCR duplicates were removed using Sambamba v.0.6.6 before methylation quantification with BSseeker2. For DAP-seq and ampDAP-seq, reads where trimmed with fastp and mapped to the genome using bowtie with the parameters "-m 1 -v 1", then peaks where called using macs2 using pIX Halo empty bam as background and parameters "-q 0.05 --down-sample -g 173599458".
Genome_build: Strigamia maritima genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/strigamia_maritima/dna/Strigamia_maritima.Smar1.dna.toplevel.fa.gz
Supplementary_files_format_and_content: Bisulfite-seq files (CGmap files) are the direct output from BSseeker2 (https://github.com/BSSeeker/BSseeker2), they contain chromosome position, (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C / (#_of_C + #_of_T). (7) #_of_C (methylated C, the count of reads showing C here) (8) = #_of_C + #_of_T (all Cytosines, the sum of reads showing C or T in that position).  Macs2 .txt files are described in https://github.com/taoliu/MACS/blob/master/README.rst.

molecule: genomic DNA

organism: Strigamia maritima

source_name: adult tissue

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters and amplified 11 cycles, next it was incubated with in-vitro translated HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.

value: same as the genome sequence

tag: incubated with

value: in-vitro translated HaloTag


title: Tabula Muris Senis (bulk RNA-seq) [A11_384Bulk_Plate3_S11]

value: Small Intestine

value: Male


title: CopiaMBD3_ampDAPseq

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters and amplified 11 cycles, next it was incubated with in-vitro translated CopiaMBD domain fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.


title: CLC44

value: ATTCCT


title: Tabula Muris Senis (bulk RNA-seq) [A11_384Bulk_Plate2_S11]

value: WBC

value: 9 months postnatal


title: CLC45

value: GATCAG


title: CLC43

value: ACTGAT


title: P0 rep4

value: Post-natal day 0

value: Radial Glia


title: CLC42

value: GCCAAT


title: Tabula Muris Senis (bulk RNA-seq) [A10_384Bulk_Plate3_S10]

value: Lung

value: 12 months postnatal


title: CopiaMBD2_ampDAPseq

value: in-vitro translated CopiaMBD domain fused to HaloTag


title: CopiaMBD1_ampDAPseq


title: CLC41

value: ACAGTG


title: P0 rep3

value: brain


title: P0 rep2


title: pIX_Halo_empty_DAPseq

description:
DAPseq_CopiaMBD1_peaks.txt
DAPseq_CopiaMBD2_peaks.txt
DAPseq_CopiaMBD3_peaks.txt

data_processing:
Library strategy: DAP-seq
CASAVA v1.8.2
For Bisulfite-seq, adapters were trimmed using fastp as default, then aligned to the reference genome using Bowtie2 and BSseeker2 with the option --bt2--end-to-end. PCR duplicates were removed using Sambamba v.0.6.6 before methylation quantification with BSseeker2. For DAP-seq and ampDAP-seq, reads where trimmed with fastp and mapped to the genome using bowtie with the parameters "-m 1 -v 1", then peaks where called using macs2 using pIX Halo empty bam as background and parameters "-q 0.05 --down-sample -g 173599458".
Genome_build: Strigamia maritima genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/strigamia_maritima/dna/Strigamia_maritima.Smar1.dna.toplevel.fa.gz
Supplementary_files_format_and_content: Bisulfite-seq files (CGmap files) are the direct output from BSseeker2 (https://github.com/BSSeeker/BSseeker2), they contain chromosome position, (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C / (#_of_C + #_of_T). (7) #_of_C (methylated C, the count of reads showing C here) (8) = #_of_C + #_of_T (all Cytosines, the sum of reads showing C or T in that position).  Macs2 .txt files are described in https://github.com/taoliu/MACS/blob/master/README.rst.

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters, incubated with in-vitro translated HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.

value: same as the genome sequence


title: CLC40

value: ATGTCA


title: CopiaMBD3_DAPseq

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to Illumina TruSeq adapters, incubated with in-vitro translated CopiaMBD domain fused to HaloTag and affinity purified. The resulting DNA was amplified 20 cycles.


title: Tabula Muris Senis (bulk RNA-seq) [A10_384Bulk_Plate1_S10]

value: Brain

value: 18 months postnatal


title: P0 rep1


title: CLC39

value: TAGCTT


title: Tabula Muris Senis (bulk RNA-seq) [A12_384Bulk_Plate1_S12]

value: Limb Muscle

value: Male


title: Tabula Muris Senis (bulk RNA-seq) [A1_384Bulk_Plate3_S1]

value: SCAT

value: 3 months postnatal


title: CopiaMBD2_DAPseq


title: P8 rep1

value: Post-natal day 8

value: Astrocyte Precursors


title: CLC38

value: CTTGTA


title: Tabula Muris Senis (bulk RNA-seq) [A1_384Bulk_Plate1_S1]

value: BAT

value: 6 months postnatal


title: CopiaMBD1_DAPseq

value: in-vitro translated CopiaMBD domain fused to HaloTag


title: Tabula Muris Senis (bulk RNA-seq) [A11_384Bulk_Plate1_S11]


title: Pt2A N3 ChIP-seq H3K27ac rep2

description: telencephalon

data_processing:
Libraries were sequenced on MiSeq or NextSeq 500 instruments (Illumina) and base called using the instruments' Real Time Analysis softwarre. Multiplexed paired end (PE) Illumina sequencing data was split based on sample barcodes allowing up to one substitution in the barcode sequence.
Paired-end reads shorter or equal to read length were consensus called and adapter trimmed.
To normalize RNA and DNA for different sequencing depths in each sample, we divided reads by the sum of observed counts and reported them as counts per million. Only barcodes observed in RNA and DNA of the same sample were considered.
Barcodes (consensus called paired-end reads) and UMI sequences containing unresolved bases (N) or not matching the designed length of 15bp were excluded. For the HAR control experiments, the control design was combined with the regular HAR design (see human submission). Each barcode x UMI pair was counted only once and only barcodes matching perfectly to those included the oligo design considered. To determine RNA/DNA ratios per insert, we summed up the counts of all barcodes belonging to the same insert and determined the ratio of the average of normalized counts.
ChIP-seq peaks were called using the ENCODE pipeline with default parameters (https://github.com/ENCODE-DCC/chip-seq-pipeline2), aligned to panTro5 and lifted over to GRCh37.
Genome_build: GRCh37
Supplementary_files_format_and_content: All processed data files are in gzip-compressed tab-separated text file format. DNA.tsv.gz and RNA.tsv.gz files contain assigned RNA and DNA barcode counts. HARcontrol_design.tsv.gz contains all additional designed control oligo sequences.

organism: Pan troglodytes

source_name: Chimpanzee glial progenitor cells

growth_protocol:
http://www.pnas.org/content/107/11/5254.short
Chimpanzee iPSC-derived neural progenitor cells were maintained in N2B27 media supplemented with 20ng/mL bFGF and EGF on matrigel-coated dishes.

treatment_protocol: For the lentiMPRA, 6 million chimpanzee iPSC-derived neural progenitor cells were plated on a 15 cm dish and cultured for 24 hours. The cells were infected with integrating lentivirus libraries and incubated for 4 days, when they have an estimated 50-100 viral particles/cell. Three independent replicate cultures were infected.

tag: iPSc line name

value: iPSC-derived neural progenitors


title: CLC36

value: AGTCAA


title: E. coli K-12 MG1655_fastφPA8_R3 [PA8_3]

city: Münster

first: Petya

last: Berger

address: Robert-Koch Straße 41

department: Institute of Hygiene

institute: University of Münster

description:
gDNA free, rRNA-depleted total RNA
MGPA8_3_S6

data_processing:
quality trimming (cut-off of 20) and adapter removal using cutadapt 1.15
generattion of reverse complement reads using FASTX 0.0.14
poly A-tail removal using READemption 0.4.3
mapping of reads to E. coli MG1655, φO104 and φPA8 genomes using READemption 0.4.3 and segemehl 0.2.0
gene wise quantification (quantification of the number of reads overlapping with the locations of the annotation entries) using READemption 0.4.3
differential gene expression analysis based on the gene wise qunatification for  E. coli MG1655 annotation using READemption 0.4.3 and DESeq2 1.16.1
Genome_build: E. coli MG1655 (U00096.3), φPA8 (KP682374.1) and φO104 (3256115 to 3317011 from NC_018658.1)
Supplementary_files_format_and_content: csv file of the gene wise quantification data used for DESeq2 analysis

organism: Escherichia coli K-12

growth_protocol: Overnight cultures were diluted till OD600 of 0.005 in LB medium (10 g/L tryptone, 5 g/L yeast extract, 5 g/L NaCl) and cells were grown at 37oC, 180 rpm to an OD600 of 0.4 - 0.6.

extract_protocol:
Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of RiboLock RNase Inhibitor (Thermo Fisher Scientific) for 60 min at 37°C. Following organic extraction (1x 25:24:1 v/v phenol/chloroform/ isoamyalcohol, 1x chloroform), RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate (pH 5.2). The RNA preparations were further treated with RiboZero (Illumina) and the concentration of the samples was determined with Qubit.
cDNA libraries for the Illumina sequencing platform were constructed using NEBNext Ultra Directional RNA Library Kit following the manufacturer's instructions.

treatment_protocol: After the treatment with stop solution (5 % phenol/95 % ethanol), cells pellets were immediately lysed with cell lysis buffer (85 mg/mL lysozyme in TE buffer, pH 8). One ml of Trizol reagent was added and samples were stored at -20C till the RNA isolation protocol was resumed.

tag: strain background

tag: genotype/variation

value: phagePA8 in the argW gene

tag: growth phase

value: exponentially growing cells


title: CLC37

value: GGCTAC


title: E. coli K-12 MG1655_φPA8_R2 [PA8_2]

description:
gDNA free, rRNA-depleted total RNA
MGPA8_2_S5


title: Pt2A N3 ChIP-seq H3K27ac rep1

description: telencephalon

tag: cell type

tag: developmental stage


title: Tabula Muris Senis (bulk RNA-seq) [A10_384Bulk_Plate2_S10]

value: GAT

value: 1 months postnatal

value: Female


title: CLC35

value: AGTTCC


title: E. coli K-12 MG1655_φPA8_R1 [PA8_1]

description:
gDNA free, rRNA-depleted total RNA
MGPA8_1_S4


title: Pt2A N3 ChIP-seq input rep1

description: telencephalon


title: 2C: EHEC dicF1-4 deletion strain

city: Charlottesville

first: Melissa

last: Kendall

state: VA

address: 1340 Jefferson Park Avenue

department: Microbiology, Immunology, and Cancer Biology

institute: University of Virginia

description: RNA-seq data from a dicF1-4 deletion strain of EHEC

data_processing:
Paired-end, strand specific Illumina libraries mapped using Bowtie v0.12.7
Read counts calculated with HTseq
DESeq Bioconductor package (v1.5.24) to estimate dispersion, normalize read counts by library size, and determine differentially expressed genes between sample groups
Genome_build: Escherichia coli O157:H7 str. EDL933; European Nucleotide Archive Genome assembly: ASM666v1
Supplementary_files_format_and_content: .txt files with RPKM values per sample

organism: Escherichia coli O157:H7 str. EDL933

source_name: enterohemorrhagic Escherichia coli O157:H7

growth_protocol: Strains were grown in DMEM tissue culture medium, statically at 37 degrees under a 5% CO2 atmosphere for 6 h.

extract_protocol:
RNA was extracted using the PureLink RNA mini kit (Invitrogen) following manufacturer's instructions.
rRNA depletion using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Illumina) followed by NEBNext Ultra Directional RNA Library Prep Kit for library preparation following manufacturer's instructions

tag: strain

value: dicF1-4 deletion


title: E. coli K-12 MG1655::φO104_R3 [O104_3]

description:
gDNA free, rRNA-depleted total RNA
MGO104_3_S12

value: phageO104 in the wrbA gene


title: Pt2A N2 ChIP-seq H3K27ac rep2

description: telencephalon

source_name: Chimpanzee neural progenitor cells


title: long association neurons, layer 5

type: RNA

city: Suita

first: Yuichiro

last: Oka

state: Osaka

address: 2-2 Yamada-oka

country: Japan

institute: Osaka University

description: Gene expression data from about 1000 long association neuorns in layer 5 in S1

hyb_protocol: labeled cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: long association neurons, layer 5

label_protocol: cDNAs were synthesized, amplified, Biotin-labeled and fragmented using Ovation Pico WTA System, WT-ovation Exon Module, and Encore Biotin Module (NuGEN).

growth_protocol: Mice were maintained on 12 hour light/dark cycle

extract_protocol: Total RNA was prepared with NucleoSpin RNA XS kit (Macherey-Nagel).

treatment_protocol: Long association neurons and callosal neurons in S1 were labeled by injecting Green RetroBeads into M1 and cotralateral S1, respectively. Labled neurons were collected one by one with laser microdissection.

value: long association neurons, layer 5

value: ICR

value: cerebral cortex

value: postnatal day 24


title: 2B: EHEC dicF1-4 deletion strain


title: Pt2A N3 ChIP-seq input rep2

description: telencephalon


title: E. coli K-12 MG1655::φO104_R2 [O104_2]

description:
gDNA free, rRNA-depleted total RNA
MGO104_2_S11


title: long association neurons, layer 6b

description: Gene expression data from about 1000 long association neuorns in layer 6b in S1

source_name: long association neurons, layer 6b

value: long association neurons, layer 6b


title: 2A: EHEC dicF1-4 deletion strain


title: Scale dermis ventral  Es22

city: Los Angeles

first: Ping

address: 2011 Zonal Ave HMR313A

department: Pathology

institute: University of Southern California

data_processing:
Read alignment was performed using Partek Flow version 3
We used Tophat2 2.1.0 to perform alignment
HTSeq-count was used for quantification.
TMM in edgeR was used for normalization
Genome_build: American alligator genome allMis1
Supplementary_files_format_and_content: Excel files include CPM value for each sample (Alligator skin samples-CPM)

organism: Alligator mississippiensis

source_name: ventral skin

growth_protocol: fertilized eggs

extract_protocol:
Dissected tissue was extracted in Trizol reagent
Libraries were prepared using Illumina TruSeq RNA Sample Preparation V2

treatment_protocol: untreated

value: ventral skin


title: Scale dermis dorsal Es22

source_name: dorsal skin

value: dorsal skin


title: Pt2A N2 ChIP-seq H3K27ac rep1

description: telencephalon

value: iPSC-derived neural progenitors


title: E. coli K-12 MG1655::φO104_R1 [O104_1]

description:
gDNA free, rRNA-depleted total RNA
MGO104_1_S10


title: long association neurons, layer 2/3

description: Gene expression data from about 1000 long association neuorns in layer 2/3 in S1

source_name: long association neurons, layer 2/3

value: long association neurons, layer 2/3


title: 1C: WT EHEC

description: RNA-seq data from wild-type EHEC

value: wild-type


title: callosal neurons, layer 5

description: Gene expression data from about 1000 callosal neuorns in layer 5 in S1

source_name: callosal neurons, layer 5

value: callosal neurons, layer 5


title: Pt2A N2 ChIP-seq input rep2

description: telencephalon


title: Scale dermis ventral  Es19


title: 1B: WT EHEC

description: RNA-seq data from wild-type EHEC


title: Pt2A N2 ChIP-seq input rep1

description: telencephalon


title: E. coli K-12 MG1655_R3 [MG_3]

description:
gDNA free, rRNA-depleted total RNA
MG_3_S9

value: naive (wild type)

value: exponentially growing cells


title: E. coli K-12 MG1655_R2 [MG_2]

description:
gDNA free, rRNA-depleted total RNA
MG_2_S8


title: Scale dermis dorsal Es19


title: callosal neurons, layer 2/3

description: Gene expression data from about 1000 callosal neuorns in layer 2/3 in S1

source_name: callosal neurons, layer 2/3

value: callosal neurons, layer 2/3


title: E. coli K-12 MG1655_R1 [MG_1]

description:
gDNA free, rRNA-depleted total RNA
MG_1_S7


title: 1A: WT EHEC

description: RNA-seq data from wild-type EHEC


title: Cd_72h_1.csv

status: Public on Jun 16 2019

city: Duarte

first: Rama

last: Natarajan

state: California

address: 1500 E Duarte Rd

department: Department of Diabetes Complications and Metabolism

institute: Beckman Research Institute, City of Hope

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-Seq data analysis was performed using Biowardrobe experimental management system. Breifly Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37/hg19 whole genome using STAR version 2.4.oj using default parameters; multi hits removed
Gene expression levels were quantified as reads per kilobase of exon per million fragments mapped (RPKM) using Biowardrobe algorithm
Differential gene expression was calculated using DESeq2
More information on Biowardrobe suite can be found at https://www.biowardrobe.com/
Genome_build: Feb. 2009 (GRCh37/hg19)
Supplementary_files_format_and_content: csv file include RPKM values for each Sample and DESeq Differential expression analysis between control and test samples

source_name: Expt 2: BEAS2B cells treated with Cd-5µM for 72h

growth_protocol: BEAS-2B cells were cultured in Dulbecco’s Modified Eagle’s Medium (Cellgro).

extract_protocol:
Total RNA was isolated from treated cells  using RNeasy kit (Qiagen)
RNASeq libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit (RS-122-2002), according to the manufacturer’s instructions.

treatment_protocol: For Cd exposure 5 µM CdCl2 was added to the media and the cells were cultured for 72 h.

value: Bronchial epithelial cell

tag: treatment

value: treated with Cd-5µM for 72h


title: Control_72h_2.csv

source_name: Expt 1: BEAS2B cells control grown for 72h

value: control


title: Cd_72h_2.csv


title: Control_72h_1.csv


title: Strigamia_maritima_MethylCseq

data_processing:
CASAVA v1.8.2
For Bisulfite-seq, adapters were trimmed using fastp as default, then aligned to the reference genome using Bowtie2 and BSseeker2 with the option --bt2--end-to-end. PCR duplicates were removed using Sambamba v.0.6.6 before methylation quantification with BSseeker2. For DAP-seq and ampDAP-seq, reads where trimmed with fastp and mapped to the genome using bowtie with the parameters "-m 1 -v 1", then peaks where called using macs2 using pIX Halo empty bam as background and parameters "-q 0.05 --down-sample -g 173599458".
Genome_build: Strigamia maritima genome assembly was downloaded from ftp://ftp.ensemblgenomes.org/pub/metazoa/release-40/fasta/strigamia_maritima/dna/Strigamia_maritima.Smar1.dna.toplevel.fa.gz
Supplementary_files_format_and_content: Bisulfite-seq files (CGmap files) are the direct output from BSseeker2 (https://github.com/BSSeeker/BSseeker2), they contain chromosome position, (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C / (#_of_C + #_of_T). (7) #_of_C (methylated C, the count of reads showing C here) (8) = #_of_C + #_of_T (all Cytosines, the sum of reads showing C or T in that position).  Macs2 .txt files are described in https://github.com/taoliu/MACS/blob/master/README.rst.

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, and subjected to 6 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).

value: same as the genome sequence


title: FXXB_1

city: GUANGZHOU

first: zhiyong

last: shen

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-Sen Road/Street Yuexiu District

department: Department of Microbiology

institute: Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Using TopHat to analysis the RNA-seq data and HTSeq v0.6.0 was adopted to generate the count matrix, with default parameters. RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates. The P-value could be assigned to each gene and adjusted by the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with q≤0.05 and |log2_ratio|≥1.5 are identified as differentially expressed genes (DEGs). Heatmaps were produced with the gplots package and heatmap.2 programs in R.
Genome_build: hg38
Supplementary_files_format_and_content: For the  'RPKM' data described in the data processing field, pls see the process file of rpkm.anno.new.xls and rpkm.xls.   The six excel with 'FPKM' here is generate from the software of ASprofile which we used to quantify and compare   alternative splicing (AS) events from RNA-seq data.  we calculates the FPKM value of each event from those of transcripts  harboring the event in a given sample.

source_name: whole blood cells

extract_protocol:
Peripheral blood were collected from three patients during the onset period and also from three healthy donors by using the anticoagulant vacuum blood collection tubes (BD Franklin Lakes, NJ), and subsequently whole blood cells were collected by centrifugation at 800 x g for 20 min at room temperature.  Total RNA was extracted from the collected blood cells with the TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease

value: patients acutely infected by ZIKV

tag: tissue

value: whole blood cells


title: GXXB_1


title: BXXB_1


title: XXD

value: Health


title: scrambled control, Batch 1 repeated in Batch2 sequencing (015339_Sult2b1b-control-repeat)

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

description: Column in CountMatrix: Not Included

data_processing:
FastQC v.0.11.3 was used to observe read quality
FastX v. 0.0.14 was used to trim data
Tophat2 v 2.1.0 was used to align reads to the genome with max-intron-length set to 560, min-intron-length set to 60,  and strandedness set to "fr-firststrand".
HTSeq Count v. 0.6.1  was used to count reads aligning to genes, feature was set to "exon" and attribute was set to "gene id", stranded was set to "reverse" and intersection-nonempty was used
EdgeR v. 3.2.2 was used to normalize and perform DE analysis. The number of reads for the control and experimental groups were then compared to identify differentially expressed genes
Some samples had to be repeated due to sequencing issues.  These bad samples were not included in the gene count matrix (there were two such samples: 013940_G12, 013941_H12).  Additionally, we did not end up including the tube controls in our gene count matrix (there were 7 of these: 015258_3B-tube-control, 015339_Sult2b1b-control-repeat, 015196_3A-tube-control, 015128_2b-Tube-control, 015059_2a-tube-control, 014019_ctrl, 013942_ctrl-S).
Genome_build: Ensembl Genome Reference Consortium Human Build 38 (GRCh38.p3)
Supplementary_files_format_and_content: raw abundance measurements

source_name: whole cell

growth_protocol: LNCaP cells were purchased from the American Tissue Culture Collection (ATCC; Manassas, VA) and maintained in media conditions identical to those recommended by ATCC.

extract_protocol:
Priming of the 17-25µm (large) IFC plate (Fluidigm, 100-5761) was completed according to the manufacturer’s instructions.  Following priming, 15µL of cell mix was added to the IFC plate along with LIVE/DEAD cell staining solution containing 4µM ethidium homodimer-1 and calcein AM (Life Technologies, L-3224).  Cells were isolated and stained within the C1 system and then manually observed on an inverted fluorescence microscope with FITC and Texas Red filters (Olympus IX51).
Capture sites containing 0 or >1 cell were excluded, and cells with positive ethidium homodimer-1 staining were also excluded.  Cell lysis, reverse transcription, and cDNA amplification of single cells were conducted following the protocol for mRNA sequencing (Fluidigm).
RNA sequencing by Illumina HiSeq2500 next generation sequencer

treatment_protocol: To prepare for single-cell analysis, 2x105 LNCaP cells were plated in a 12-well plate coated with poly-L-lysine and allowed to adhere for 24 hours.  LNCaP cells were transfected with non-targeting (control) siRNA (Dharmacon) or SULT2B1 siRNA (IDT, HSC.RNAI.N004605.12.2), previously validated to knockdown SULT2B1b expression and function in prostate cancer cells

value: LNCaP

value: epithelial cell line derived from a human prostate carcinoma

tag: genotype


title: CLL


title: Sult2B1b knockdown, Batch 1 repeated in Batch2 sequencing (015337_Sult2b1b-G12-repeat)

description: Column in CountMatrix: S1G12

value: Sult2B1b knockdown


title: Sult2B1b knock-down, Batch3 (015255_E12)

description: Column in CountMatrix: S3E12


title: Sult2B1b knockdown, Batch 1 repeated in Batch2 sequencing (015338_Sult2b1b-H12-repeat)

description: Column in CountMatrix: S1H12


title: Sult2B1b knock-down, Batch3 (015257_H12)

description: Column in CountMatrix: S3H12


title: Sult2B1b knock-down, Batch3 (015256_G12)

description: Column in CountMatrix: S3G12


title: Sult2B1b knock-down, Batch3 (015254_D12)

description: Column in CountMatrix: S3D12


title: YY


title: Sult2B1b knock-down, Batch3 (015253_C12)

description: Column in CountMatrix: S3C12


title: scrambled control, Batch3, multiple cell control (015258_3B-tube-control)

description: Column in CountMatrix: Not Included


title: Sult2B1b knock-down, Batch3 (015252_B12)

description: Column in CountMatrix: S3B12


title: Sult2B1b knock-down, Batch3 (015249_G11)

description: Column in CountMatrix: S3G11


title: Sult2B1b knock-down, Batch3 (015250_H11)

description: Column in CountMatrix: S3H11


title: Sult2B1b knock-down, Batch3 (015251_A12)

description: Column in CountMatrix: S3A12


title: Sult2B1b knock-down, Batch3 (015247_D11)

description: Column in CountMatrix: S3D11


title: Sult2B1b knock-down, Batch3 (015248_F11)

description: Column in CountMatrix: S3F11


title: Sult2B1b knock-down, Batch3 (015243_F10)

description: Column in CountMatrix: S3F10


title: Sult2B1b knock-down, Batch3 (015245_H10)

description: Column in CountMatrix: S3H10


title: Sult2B1b knock-down, Batch3 (015244_G10)

description: Column in CountMatrix: S3G10


title: Sult2B1b knock-down, Batch3 (015242_E10)

description: Column in CountMatrix: S3E10


title: Sult2B1b knock-down, Batch3 (015246_A11)

description: Column in CountMatrix: S3A11


title: Sult2B1b knock-down, Batch3 (015240_C10)

description: Column in CountMatrix: S3C10


title: Sult2B1b knock-down, Batch3 (015239_B10)

description: Column in CountMatrix: S3B10


title: Sult2B1b knock-down, Batch3 (015238_G9)

description: Column in CountMatrix: S3G9


title: Sult2B1b knock-down, Batch3 (015237_C9)

description: Column in CountMatrix: S3C9


title: Sult2B1b knock-down, Batch3 (015236_B9)

description: Column in CountMatrix: S3B9


title: Sult2B1b knock-down, Batch3 (015235_A9)

description: Column in CountMatrix: S3A9


title: Sult2B1b knock-down, Batch3 (015234_G8)

description: Column in CountMatrix: S3G8


title: Sult2B1b knock-down, Batch3 (015233_D8)

description: Column in CountMatrix: S3D8


title: Sult2B1b knock-down, Batch3 (015229_C7)

description: Column in CountMatrix: S3C7


title: Sult2B1b knock-down, Batch3 (015232_B8)

description: Column in CountMatrix: S3B8


title: Sult2B1b knock-down, Batch3 (015225_H5)

description: Column in CountMatrix: S3H5


title: Sult2B1b knock-down, Batch3 (015230_E7)

description: Column in CountMatrix: S3E7


title: Sult2B1b knock-down, Batch3 (015224_G5)

description: Column in CountMatrix: S3G5


title: Sult2B1b knock-down, Batch3 (015228_A7)

description: Column in CountMatrix: S3A7


title: Sult2B1b knock-down, Batch3 (015227_G6)

description: Column in CountMatrix: S3G6


title: Sult2B1b knock-down, Batch3 (015226_A6)

description: Column in CountMatrix: S3A6


title: Sult2B1b knock-down, Batch3 (015222_D5)

description: Column in CountMatrix: S3D5


title: Sult2B1b knock-down, Batch3 (015223_E5)

description: Column in CountMatrix: S3E5


title: Sult2B1b knock-down, Batch3 (015219_A5)

description: Column in CountMatrix: S3A5


title: Sult2B1b knock-down, Batch3 (015241_D10)

description: Column in CountMatrix: S3D10


title: Sult2B1b knock-down, Batch3 (015220_B5)

description: Column in CountMatrix: S3B5


title: Sult2B1b knock-down, Batch3 (015221_C5)

description: Column in CountMatrix: S3C5


title: Sult2B1b knock-down, Batch3 (015217_E4)

description: Column in CountMatrix: S3E4


title: Sult2B1b knock-down, Batch3 (015216_D4)

description: Column in CountMatrix: S3D4


title: Sult2B1b knock-down, Batch3 (015218_F4)

description: Column in CountMatrix: S3F4


title: Sult2B1b knock-down, Batch3 (015215_C4)

description: Column in CountMatrix: S3C4


title: Sult2B1b knock-down, Batch3 (015214_B4)

description: Column in CountMatrix: S3B4


title: Sult2B1b knock-down, Batch3 (015212_G3)

description: Column in CountMatrix: S3G3


title: Sult2B1b knock-down, Batch3 (015211_D3)

description: Column in CountMatrix: S3D3


title: Sult2B1b knock-down, Batch3 (015210_C3)

description: Column in CountMatrix: S3C3


title: Sult2B1b knock-down, Batch3 (015209_B3)

description: Column in CountMatrix: S3B3


title: Sult2B1b knock-down, Batch3 (015231_F7)

description: Column in CountMatrix: S3F7


title: Sult2B1b knock-down, Batch3 (015208_A3)

description: Column in CountMatrix: S3A3


title: Sult2B1b knock-down, Batch3 (015206_F2)

description: Column in CountMatrix: S3F2


title: Sult2B1b knock-down, Batch3 (015207_H2)

description: Column in CountMatrix: S3H2


title: Sult2B1b knock-down, Batch3 (015205_D2)

description: Column in CountMatrix: S3D2


title: Sult2B1b knock-down, Batch3 (015204_C2)

description: Column in CountMatrix: S3C2


title: Sult2B1b knock-down, Batch3 (015201_F1)

description: Column in CountMatrix: S3F1


title: Sult2B1b knock-down, Batch3 (015200_E1)

description: Column in CountMatrix: S3E1


title: Sult2B1b knock-down, Batch3 (015197_B1)

description: Column in CountMatrix: S3B1


title: Sult2B1b knock-down, Batch3 (015202_H1)

description: Column in CountMatrix: S3H1


title: Sult2B1b knock-down, Batch3 (015198_C1)

description: Column in CountMatrix: S3C1


title: scrambled control, Batch3 (015195_F12)

description: Column in CountMatrix: C3F12


title: Sult2B1b knock-down, Batch3 (015203_B2)

description: Column in CountMatrix: S3B2


title: scrambled control, Batch3, multiple cell control (015196_3A-tube-control)

description: Column in CountMatrix: Not Included


title: Sult2B1b knock-down, Batch3 (015199_D1)

description: Column in CountMatrix: S3D1


title: scrambled control, Batch3 (015193_D12)

description: Column in CountMatrix: C3D12


title: scrambled control, Batch3 (015192_C12)

description: Column in CountMatrix: C3C12


title: scrambled control, Batch3 (015189_G11)

description: Column in CountMatrix: C3G11


title: scrambled control, Batch3 (015188_E11)

description: Column in CountMatrix: C3E11


title: scrambled control, Batch3 (015191_B12)

description: Column in CountMatrix: C3B12


title: scrambled control, Batch3 (015187_D11)

description: Column in CountMatrix: C3D11


title: scrambled control, Batch3 (015183_H10)

description: Column in CountMatrix: C3H10


title: scrambled control, Batch3 (015180_C10)

description: Column in CountMatrix: C3C10


title: scrambled control, Batch3 (015181_F10)

description: Column in CountMatrix: C3F10


title: scrambled control, Batch3 (015194_E12)

description: Column in CountMatrix: C3E12


title: Sult2B1b knock-down, Batch3 (015213_A4)

description: Column in CountMatrix: S3A4


title: scrambled control, Batch3 (015179_A10)

description: Column in CountMatrix: C3A10


title: Tabula Muris Senis (bulk RNA-seq) [A14_384Bulk_Plate2_S14]

description: processed data file: 190214_A00111_0269_AHH3J3DSXX__190214_A00111_0270_BHHMFWDSXX.csv

data_processing:
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316.
Reads were aligned to the mm10plus genome using STAR version 2.5.2b with parameters TK.
Gene counts were produced using HTSEQ version 0.6.1p1 with default parameters, except ‘stranded’ was set to ‘false’, and ‘mode’ was set to ‘intersection-nonempty’.
Genome_build: GRCm38
Supplementary_files_format_and_content: 190214_A00111_0269_AHH3J3DSXX__190214_A00111_0270_BHHMFWDSXX.csv: Comma-separated text file includes gene count table for all organs and ages.
Supplementary_files_format_and_content: MACA_Bulk_metadata.csv: Comma-separated text file includes experiment metadata.

extract_protocol:
RNeasy (mini and micro) Qiagen RNA isolation from homogenized tissue.
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT.
Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2.

tag: strain/background

value: SCAT

tag: age

value: 9 months postnatal

tag: Sex

value: Female


title: scrambled control, Batch3 (015177_D9)

description: Column in CountMatrix: C3D9

tag: cell line


title: scrambled control, Batch3 (015176_B9)

description: Column in CountMatrix: C3B9


title: scrambled control, Batch3 (015178_G9)

description: Column in CountMatrix: C3G9


title: scrambled control, Batch3 (015175_A9)

description: Column in CountMatrix: C3A9


title: scrambled control, Batch3 (015170_G7)

description: Column in CountMatrix: C3G7


title: scrambled control, Batch3 (015172_A8)

description: Column in CountMatrix: C3A8


title: scrambled control, Batch3 (015173_D8)

description: Column in CountMatrix: C3D8


title: scrambled control, Batch3 (015169_D7)

description: Column in CountMatrix: C3D7


title: scrambled control, Batch3 (015168_C7)

description: Column in CountMatrix: C3C7


title: scrambled control, Batch3 (015190_A12)

description: Column in CountMatrix: C3A12


title: scrambled control, Batch3 (015165_G6)

description: Column in CountMatrix: C3G6


title: scrambled control, Batch3 (015174_F8)

description: Column in CountMatrix: C3F8


title: scrambled control, Batch3 (015166_H6)

description: Column in CountMatrix: C3H6


title: scrambled control, Batch3 (015164_F6)

description: Column in CountMatrix: C3F6


title: scrambled control, Batch3 (015186_C11)

description: Column in CountMatrix: C3C11


title: scrambled control, Batch3 (015163_E6)

description: Column in CountMatrix: C3E6


title: scrambled control, Batch3 (015162_D6)

description: Column in CountMatrix: C3D6


title: scrambled control, Batch3 (015182_G10)

description: Column in CountMatrix: C3G10


title: scrambled control, Batch3 (015161_C6)

description: Column in CountMatrix: C3C6


title: scrambled control, Batch3 (015160_A6)

description: Column in CountMatrix: C3A6


title: scrambled control, Batch3 (015159_H5)

description: Column in CountMatrix: C3H5


title: scrambled control, Batch3 (015156_D5)

description: Column in CountMatrix: C3D5


title: scrambled control, Batch3 (015155_C5)

description: Column in CountMatrix: C3C5


title: scrambled control, Batch3 (015171_H7)

description: Column in CountMatrix: C3H7


title: scrambled control, Batch3 (015167_A7)

description: Column in CountMatrix: C3A7


title: scrambled control, Batch3 (015150_F4)

description: Column in CountMatrix: C3F4


title: scrambled control, Batch3 (015152_H4)

description: Column in CountMatrix: C3H4


title: scrambled control, Batch3 (015153_A5)

description: Column in CountMatrix: C3A5


title: scrambled control, Batch3 (015151_G4)

description: Column in CountMatrix: C3G4


title: scrambled control, Batch3 (015144_F3)

description: Column in CountMatrix: C3F3


title: scrambled control, Batch3 (015145_G3)

description: Column in CountMatrix: C3G3


title: scrambled control, Batch3 (015146_H3)

description: Column in CountMatrix: C3H3


title: scrambled control, Batch3 (015141_C3)

description: Column in CountMatrix: C3C3


title: scrambled control, Batch3 (015154_B5)

description: Column in CountMatrix: C3B5


title: scrambled control, Batch3 (015142_D3)

description: Column in CountMatrix: C3D3


title: scrambled control, Batch3 (015147_C4)

description: Column in CountMatrix: C3C4


title: scrambled control, Batch3 (015148_D4)

description: Column in CountMatrix: C3D4


title: scrambled control, Batch3 (015139_A3)

description: Column in CountMatrix: C3A3


title: scrambled control, Batch3 (015138_H2)

description: Column in CountMatrix: C3H2


title: scrambled control, Batch3 (015136_D2)

description: Column in CountMatrix: C3D2


title: scrambled control, Batch3 (015143_E3)

description: Column in CountMatrix: C3E3


title: scrambled control, Batch3 (015158_G5)

description: Column in CountMatrix: C3G5


title: scrambled control, Batch3 (015184_A11)

description: Column in CountMatrix: C3A11


title: scrambled control, Batch3 (015157_F5)

description: Column in CountMatrix: C3F5


title: scrambled control, Batch3 (015134_B2)

description: Column in CountMatrix: C3B2


title: scrambled control, Batch3 (015135_C2)

description: Column in CountMatrix: C3C2


title: scrambled control, Batch3 (015132_G1)

description: Column in CountMatrix: C3G1


title: scrambled control, Batch3 (015130_D1)

description: Column in CountMatrix: C3D1


title: scrambled control, Batch3 (015129_A1)

description: Column in CountMatrix: C3A1


title: Sult2B1b knockdown, Batch2 (015125_F12)

description: Column in CountMatrix: S2F12


title: Sult2B1b knockdown, Batch2, multiple cells control (015128_2b-Tube-control)

description: Column in CountMatrix: Not Included


title: scrambled control, Batch3 (015149_E4)

description: Column in CountMatrix: C3E4


title: Sult2B1b knockdown, Batch2 (015123_D12)

description: Column in CountMatrix: S2D12


title: scrambled control, Batch3 (015137_E2)

description: Column in CountMatrix: C3E2


title: Sult2B1b knockdown, Batch2 (015127_H12)

description: Column in CountMatrix: S2H12


title: Sult2B1b knockdown, Batch2 (015122_C12)

description: Column in CountMatrix: S2C12


title: Sult2B1b knockdown, Batch2 (015121_A12)

description: Column in CountMatrix: S2A12


title: Sult2B1b knockdown, Batch2 (015124_E12)

description: Column in CountMatrix: S2E12


title: scrambled control, Batch3 (015140_B3)

description: Column in CountMatrix: C3B3


title: Sult2B1b knockdown, Batch2 (015115_A11)

description: Column in CountMatrix: S2A11


title: Sult2B1b knockdown, Batch2 (015118_D11)

description: Column in CountMatrix: S2D11


title: Sult2B1b knockdown, Batch2 (015114_G10)

description: Column in CountMatrix: S2G10


title: Sult2B1b knockdown, Batch2 (015116_B11)

description: Column in CountMatrix: S2B11


title: Sult2B1b knockdown, Batch2 (015113_F10)

description: Column in CountMatrix: S2F10


title: Sult2B1b knockdown, Batch2 (015120_G11)

description: Column in CountMatrix: S2G11


title: Sult2B1b knockdown, Batch2 (015110_C10)

description: Column in CountMatrix: S2C10


title: Sult2B1b knockdown, Batch2 (015111_D10)

description: Column in CountMatrix: S2D10


title: Sult2B1b knockdown, Batch2 (015119_F11)

description: Column in CountMatrix: S2F11


title: scrambled control, Batch3 (015131_F1)

description: Column in CountMatrix: C3F1


title: Sult2B1b knockdown, Batch2 (015108_A10)

description: Column in CountMatrix: S2A10


title: Sult2B1b knockdown, Batch2 (015106_B9)

description: Column in CountMatrix: S2B9


title: Sult2B1b knockdown, Batch2 (015126_G12)

description: Column in CountMatrix: S2G12


title: Sult2B1b knockdown, Batch2 (015107_D9)

description: Column in CountMatrix: S2D9


title: scrambled control, Batch3 (015133_A2)

description: Column in CountMatrix: C3A2


title: Sult2B1b knockdown, Batch2 (015109_B10)

description: Column in CountMatrix: S2B10


title: Sult2B1b knockdown, Batch2 (015105_A9)

description: Column in CountMatrix: S2A9


title: Sult2B1b knockdown, Batch2 (015112_E10)

description: Column in CountMatrix: S2E10


title: Sult2B1b knockdown, Batch2 (015102_D8)

description: Column in CountMatrix: S2D8


title: Sult2B1b knockdown, Batch2 (015103_E8)

description: Column in CountMatrix: S2E8


title: Sult2B1b knockdown, Batch2 (015099_A8)

description: Column in CountMatrix: S2A8


title: Sult2B1b knockdown, Batch2 (015101_C8)

description: Column in CountMatrix: S2C8


title: Sult2B1b knockdown, Batch2 (015117_C11)

description: Column in CountMatrix: S2C11


title: Sult2B1b knockdown, Batch2 (015096_B7)

description: Column in CountMatrix: S2B7


title: Sult2B1b knockdown, Batch2 (015097_C7)

description: Column in CountMatrix: S2C7


title: Sult2B1b knockdown, Batch2 (015095_A7)

description: Column in CountMatrix: S2A7


title: Sult2B1b knockdown, Batch2 (015094_H6)

description: Column in CountMatrix: S2H6


title: Sult2B1b knockdown, Batch2 (015092_F6)

description: Column in CountMatrix: S2F6


title: Sult2B1b knockdown, Batch2 (015091_E6)

description: Column in CountMatrix: S2E6


title: Sult2B1b knockdown, Batch2 (015089_B6)

description: Column in CountMatrix: S2B6


title: Sult2B1b knockdown, Batch2 (015088_A6)

description: Column in CountMatrix: S2A6


title: Sult2B1b knockdown, Batch2 (015090_D6)

description: Column in CountMatrix: S2D6


title: Sult2B1b knockdown, Batch2 (015081_A5)

description: Column in CountMatrix: S2A5


title: Sult2B1b knockdown, Batch2 (015093_G6)

description: Column in CountMatrix: S2G6


title: Sult2B1b knockdown, Batch2 (015082_B5)

description: Column in CountMatrix: S2B5


title: Sult2B1b knockdown, Batch2 (015104_F8)

description: Column in CountMatrix: S2F8


title: Sult2B1b knockdown, Batch2 (015083_C5)

description: Column in CountMatrix: S2C5


title: Sult2B1b knockdown, Batch2 (015079_G4)

description: Column in CountMatrix: S2G4


title: Sult2B1b knockdown, Batch2 (015080_H4)

description: Column in CountMatrix: S2H4


title: Sult2B1b knockdown, Batch2 (015085_E5)

description: Column in CountMatrix: S2E5


title: Sult2B1b knockdown, Batch2 (015078_E4)

description: Column in CountMatrix: S2E4


title: Sult2B1b knockdown, Batch2 (015077_D4)

description: Column in CountMatrix: S2D4


title: Sult2B1b knockdown, Batch2 (015076_C4)

description: Column in CountMatrix: S2C4


title: Sult2B1b knockdown, Batch2 (015098_D7)

description: Column in CountMatrix: S2D7


title: Sult2B1b knockdown, Batch2 (015087_G5)

description: Column in CountMatrix: S2G5


title: Sult2B1b knockdown, Batch2 (015071_C3)

description: Column in CountMatrix: S2C3


title: Sult2B1b knockdown, Batch2 (015070_B3)

description: Column in CountMatrix: S2B3


title: Sult2B1b knockdown, Batch2 (015073_F3)

description: Column in CountMatrix: S2F3


title: Sult2B1b knockdown, Batch2 (015072_E3)

description: Column in CountMatrix: S2E3


title: Sult2B1b knockdown, Batch2 (015086_F5)

description: Column in CountMatrix: S2F5


title: Sult2B1b knockdown, Batch2 (015069_A3)

description: Column in CountMatrix: S2A3


title: Sult2B1b knockdown, Batch2 (015074_A4)

description: Column in CountMatrix: S2A4


title: Sult2B1b knockdown, Batch2 (015067_D2)

description: Column in CountMatrix: S2D2


title: Sult2B1b knockdown, Batch2 (015065_H1)

description: Column in CountMatrix: S2H1


title: Sult2B1b knockdown, Batch2 (015066_C2)

description: Column in CountMatrix: S2C2


title: Sult2B1b knockdown, Batch2 (015062_C1)

description: Column in CountMatrix: S2C1


title: Sult2B1b knockdown, Batch2 (015064_E1)

description: Column in CountMatrix: S2E1


title: Sult2B1b knockdown, Batch2 (015100_B8)

description: Column in CountMatrix: S2B8


title: Sult2B1b knockdown, Batch2 (015061_B1)

description: Column in CountMatrix: S2B1


title: Sult2B1b knockdown, Batch2 (015060_A1)

description: Column in CountMatrix: S2A1


title: scrambled control, Batch2 (015058_G12)

description: Column in CountMatrix: C2G12


title: scrambled control, Batch2 (015057_F12)

description: Column in CountMatrix: C2F12


title: scrambled control, Batch2, multiple cells (015059_2a-tube-control)

description: Column in CountMatrix: Not Included


title: Sult2B1b knockdown, Batch2 (015075_B4)

description: Column in CountMatrix: S2B4


title: scrambled control, Batch2 (015055_D12)

description: Column in CountMatrix: C2D12


title: scrambled control, Batch2 (015054_C12)

description: Column in CountMatrix: C2C12


title: scrambled control, Batch2 (015056_E12)

description: Column in CountMatrix: C2E12


title: scrambled control, Batch2 (015053_B12)

description: Column in CountMatrix: C2B12


title: scrambled control, Batch2 (015052_A12)

description: Column in CountMatrix: C2A12


title: scrambled control, Batch2 (015050_G11)

description: Column in CountMatrix: C2G11


title: scrambled control, Batch2 (015051_H11)

description: Column in CountMatrix: C2H11


title: Sult2B1b knockdown, Batch2 (015068_E2)

description: Column in CountMatrix: S2E2


title: scrambled control, Batch2 (015049_F11)

description: Column in CountMatrix: C2F11


title: scrambled control, Batch2 (015048_B11)

description: Column in CountMatrix: C2B11


title: scrambled control, Batch2 (015043_E10)

description: Column in CountMatrix: C2E10


title: scrambled control, Batch2 (015044_F10)

description: Column in CountMatrix: C2F10


title: scrambled control, Batch2 (015046_H10)

description: Column in CountMatrix: C2H10


title: scrambled control, Batch2 (015047_A11)

description: Column in CountMatrix: C2A11


title: scrambled control, Batch2 (015045_G10)

description: Column in CountMatrix: C2G10


title: Sult2B1b knockdown, Batch2 (015063_D1)

description: Column in CountMatrix: S2D1


title: scrambled control, Batch2 (015042_D10)

description: Column in CountMatrix: C2D10


title: scrambled control, Batch2 (015040_B10)

description: Column in CountMatrix: C2B10


title: scrambled control, Batch2 (015038_F9)

description: Column in CountMatrix: C2F9


title: scrambled control, Batch2 (015037_E9)

description: Column in CountMatrix: C2E9


title: scrambled control, Batch2 (015034_E8)

description: Column in CountMatrix: C2E8


title: scrambled control, Batch2 (015035_B9)

description: Column in CountMatrix: C2B9


title: scrambled control, Batch2 (015039_A10)

description: Column in CountMatrix: C2A10


title: scrambled control, Batch2 (015030_F7)

description: Column in CountMatrix: C2F7


title: scrambled control, Batch2 (015032_A8)

description: Column in CountMatrix: C2A8


title: scrambled control, Batch2 (015031_H7)

description: Column in CountMatrix: C2H7


title: scrambled control, Batch2 (015029_D7)

description: Column in CountMatrix: C2D7


title: scrambled control, Batch2 (015026_H6)

description: Column in CountMatrix: C2H6


title: Sult2B1b knockdown, Batch2 (015084_D5)

description: Column in CountMatrix: S2D5


title: scrambled control, Batch2 (015024_F6)

description: Column in CountMatrix: C2F6


title: scrambled control, Batch2 (015025_G6)

description: Column in CountMatrix: C2G6


title: scrambled control, Batch2 (015027_A7)

description: Column in CountMatrix: C2A7


title: scrambled control, Batch2 (015023_E6)

description: Column in CountMatrix: C2E6


title: scrambled control, Batch2 (015021_C6)

description: Column in CountMatrix: C2C6


title: scrambled control, Batch2 (015041_C10)

description: Column in CountMatrix: C2C10


title: scrambled control, Batch2 (015018_H5)

description: Column in CountMatrix: C2H5


title: scrambled control, Batch2 (015019_A6)

description: Column in CountMatrix: C2A6


title: scrambled control, Batch2 (015022_D6)

description: Column in CountMatrix: C2D6


title: scrambled control, Batch2 (015016_D5)

description: Column in CountMatrix: C2D5


title: scrambled control, Batch2 (015015_C5)

description: Column in CountMatrix: C2C5


title: scrambled control, Batch2 (015013_A5)

description: Column in CountMatrix: C2A5


title: scrambled control, Batch2 (015014_B5)

description: Column in CountMatrix: C2B5


title: scrambled control, Batch2 (015033_C8)

description: Column in CountMatrix: C2C8


title: scrambled control, Batch2 (015036_C9)

description: Column in CountMatrix: C2C9


title: scrambled control, Batch2 (015010_F4)

description: Column in CountMatrix: C2F4


title: scrambled control, Batch2 (015012_H4)

description: Column in CountMatrix: C2H4


title: scrambled control, Batch2 (015011_G4)

description: Column in CountMatrix: C2G4


title: scrambled control, Batch2 (015028_C7)

description: Column in CountMatrix: C2C7


title: scrambled control, Batch3 (015185_B11)

description: Column in CountMatrix: C3B11


title: scrambled control, Batch2 (015007_C4)

description: Column in CountMatrix: C2C4


title: scrambled control, Batch2 (015008_D4)

description: Column in CountMatrix: C2D4


title: scrambled control, Batch2 (015006_B4)

description: Column in CountMatrix: C2B4


title: scrambled control, Batch2 (015004_F3)

description: Column in CountMatrix: C2F3


title: scrambled control, Batch2 (015005_A4)

description: Column in CountMatrix: C2A4


title: scrambled control, Batch2 (015009_E4)

description: Column in CountMatrix: C2E4


title: scrambled control, Batch2 (015002_B3)

description: Column in CountMatrix: C2B3


title: scrambled control, Batch2 (015003_E3)

description: Column in CountMatrix: C2E3


title: scrambled control, Batch2 (015017_E5)

description: Column in CountMatrix: C2E5


title: scrambled control, Batch2 (015001_A3)

description: Column in CountMatrix: C2A3


title: scrambled control, Batch2 (015020_B6)

description: Column in CountMatrix: C2B6


title: scrambled control, Batch2 (014999_D2)

description: Column in CountMatrix: C2D2


title: scrambled control, Batch2 (014995_E1)

description: Column in CountMatrix: C2E1


title: scrambled control, Batch2 (014997_G1)

description: Column in CountMatrix: C2G1


title: scrambled control, Batch2 (014998_B2)

description: Column in CountMatrix: C2B2


title: scrambled control, Batch2 (014994_D1)

description: Column in CountMatrix: C2D1


title: scrambled control, Batch2 (015000_E2)

description: Column in CountMatrix: C2E2


title: scrambled control, Batch2 (014996_F1)

description: Column in CountMatrix: C2F1


title: scrambled control, Batch1 (014018_H12)

description: Column in CountMatrix: C1H12


title: scrambled control, Batch1 (014017_G12)

description: Column in CountMatrix: C1G12


title: scrambled control, Batch2 (014993_B1)

description: Column in CountMatrix: C2B1


title: scrambled control, Batch1 (014016_F12)

description: Column in CountMatrix: C1F12


title: scrambled control, Batch1, multiple cells (014019_ctrl)

description: Column in CountMatrix: Not Included


title: scrambled control, Batch2 (014992_A1)

description: Column in CountMatrix: C2A1


title: scrambled control, Batch1 (014013_B12)

description: Column in CountMatrix: C1B12


title: scrambled control, Batch1 (014012_H11)

description: Column in CountMatrix: C1H11


title: scrambled control, Batch1 (014014_C12)

description: Column in CountMatrix: C1C12


title: scrambled control, Batch1 (014015_E12)

description: Column in CountMatrix: C1E12


title: scrambled control, Batch1 (014010_F11)

description: Column in CountMatrix: C1F11


title: scrambled control, Batch1 (014008_D11)

description: Column in CountMatrix: C1D11


title: scrambled control, Batch1 (014009_E11)

description: Column in CountMatrix: C1E11


title: scrambled control, Batch1 (014011_G11)

description: Column in CountMatrix: C1G11


title: scrambled control, Batch1 (014007_C11)

description: Column in CountMatrix: C1C11


title: scrambled control, Batch1 (014006_B11)

description: Column in CountMatrix: C1B11


title: scrambled control, Batch1 (014005_A11)

description: Column in CountMatrix: C1A11


title: scrambled control, Batch1 (014004_G10)

description: Column in CountMatrix: C1G10


title: scrambled control, Batch1 (014003_F10)

description: Column in CountMatrix: C1F10


title: scrambled control, Batch1 (014002_E10)

description: Column in CountMatrix: C1E10


title: scrambled control, Batch1 (014001_D10)

description: Column in CountMatrix: C1D10


title: scrambled control, Batch1 (014000_C10)

description: Column in CountMatrix: C1C10


title: scrambled control, Batch1 (013998_A10)

description: Column in CountMatrix: C1A10


title: scrambled control, Batch1 (013994_D9)

description: Column in CountMatrix: C1D9


title: scrambled control, Batch1 (013997_G9)

description: Column in CountMatrix: C1G9


title: scrambled control, Batch1 (013996_F9)

description: Column in CountMatrix: C1F9


title: scrambled control, Batch1 (013999_B10)

description: Column in CountMatrix: C1B10


title: scrambled control, Batch1 (013995_E9)

description: Column in CountMatrix: C1E9


title: scrambled control, Batch1 (013993_A9)

description: Column in CountMatrix: C1A9


title: scrambled control, Batch1 (013991_G8)

description: Column in CountMatrix: C1G8


title: scrambled control, Batch1 (013987_C8)

description: Column in CountMatrix: C1C8


title: scrambled control, Batch1 (013992_H8)

description: Column in CountMatrix: C1H8


title: scrambled control, Batch1 (013990_F8)

description: Column in CountMatrix: C1F8


title: scrambled control, Batch1 (013989_E8)

description: Column in CountMatrix: C1E8


title: scrambled control, Batch1 (013985_A8)

description: Column in CountMatrix: C1A8


title: scrambled control, Batch1 (013983_F7)

description: Column in CountMatrix: C1F7


title: scrambled control, Batch1 (013986_B8)

description: Column in CountMatrix: C1B8


title: scrambled control, Batch1 (013988_D8)

description: Column in CountMatrix: C1D8


title: scrambled control, Batch1 (013984_H7)

description: Column in CountMatrix: C1H7


title: scrambled control, Batch1 (013982_C7)

description: Column in CountMatrix: C1C7


title: scrambled control, Batch1 (013979_G6)

description: Column in CountMatrix: C1G6


title: scrambled control, Batch1 (013978_F6)

description: Column in CountMatrix: C1F6


title: scrambled control, Batch1 (013977_E6)

description: Column in CountMatrix: C1E6


title: scrambled control, Batch1 (013975_C6)

description: Column in CountMatrix: C1C6


title: scrambled control, Batch1 (013972_H5)

description: Column in CountMatrix: C1H5


title: scrambled control, Batch1 (013981_B7)

description: Column in CountMatrix: C1B7


title: scrambled control, Batch1 (013980_H6)

description: Column in CountMatrix: C1H6


title: scrambled control, Batch1 (013976_D6)

description: Column in CountMatrix: C1D6


title: scrambled control, Batch1 (013971_G5)

description: Column in CountMatrix: C1G5


title: scrambled control, Batch1 (013970_F5)

description: Column in CountMatrix: C1F5


title: scrambled control, Batch1 (013969_E5)

description: Column in CountMatrix: C1E5


title: scrambled control, Batch1 (013974_B6)

description: Column in CountMatrix: C1B6


title: scrambled control, Batch1 (013967_C5)

description: Column in CountMatrix: C1C5


title: scrambled control, Batch1 (013964_H4)

description: Column in CountMatrix: C1H4


title: scrambled control, Batch1 (013965_A5)

description: Column in CountMatrix: C1A5


title: scrambled control, Batch1 (013968_D5)

description: Column in CountMatrix: C1D5


title: scrambled control, Batch1 (013963_G4)

description: Column in CountMatrix: C1G4


title: scrambled control, Batch1 (013962_F4)

description: Column in CountMatrix: C1F4


title: scrambled control, Batch1 (013958_B4)

description: Column in CountMatrix: C1B4


title: scrambled control, Batch1 (013961_E4)

description: Column in CountMatrix: C1E4


title: scrambled control, Batch1 (013960_D4)

description: Column in CountMatrix: C1D4


title: scrambled control, Batch1 (013959_C4)

description: Column in CountMatrix: C1C4


title: scrambled control, Batch1 (013957_A4)

description: Column in CountMatrix: C1A4


title: scrambled control, Batch1 (013973_A6)

description: Column in CountMatrix: C1A6


title: scrambled control, Batch1 (013955_C3)

description: Column in CountMatrix: C1C3


title: scrambled control, Batch1 (013956_F3)

description: Column in CountMatrix: C1F3


title: scrambled control, Batch1 (013954_A3)

description: Column in CountMatrix: C1A3


title: scrambled control, Batch1 (013952_G2)

description: Column in CountMatrix: C1G2


title: scrambled control, Batch1 (013953_H2)

description: Column in CountMatrix: C1H2


title: scrambled control, Batch1 (013950_D2)

description: Column in CountMatrix: C1D2


title: scrambled control, Batch1 (013951_F2)

description: Column in CountMatrix: C1F2


title: scrambled control, Batch1 (013966_B5)

description: Column in CountMatrix: C1B5


title: scrambled control, Batch1 (013946_F1)

description: Column in CountMatrix: C1F1


title: scrambled control, Batch1 (013948_H1)

description: Column in CountMatrix: C1H1


title: scrambled control, Batch1 (013944_C1)

description: Column in CountMatrix: C1C1


title: scrambled control, Batch1 (013947_G1)

description: Column in CountMatrix: C1G1


title: Sult2B1b knockdown, Batch1 tube control with multiple cells (013942_ctrl-S)

description: Column in CountMatrix: Not Included


title: scrambled control, Batch1 (013949_C2)

description: Column in CountMatrix: C1C2


title: scrambled control, Batch1 (013943_B1)

description: Column in CountMatrix: C1B1


title: Sult2B1b knockdown, Batch1 (013941_H12)

description: Column in CountMatrix: Not Included


title: scrambled control, Batch1 (013945_E1)

description: Column in CountMatrix: C1E1


title: Sult2B1b knockdown, Batch1 (013938_D12)

description: Column in CountMatrix: S1D12


title: Sult2B1b knockdown, Batch1 (013937_C12)

description: Column in CountMatrix: S1C12


title: Sult2B1b knockdown, Batch1 (013939_E12)

description: Column in CountMatrix: S1E12


title: Sult2B1b knockdown, Batch1 (013940_G12)

description: Column in CountMatrix: Not Included


title: Sult2B1b knockdown, Batch1 (013932_F11)

description: Column in CountMatrix: S1F11


title: Sult2B1b knockdown, Batch1 (013934_H11)

description: Column in CountMatrix: S1H11


title: Sult2B1b knockdown, Batch1 (013936_B12)

description: Column in CountMatrix: S1B12


title: Sult2B1b knockdown, Batch1 (013933_G11)

description: Column in CountMatrix: S1G11


title: Sult2B1b knockdown, Batch1 (013930_C11)

description: Column in CountMatrix: S1C11


title: Sult2B1b knockdown, Batch1 (013929_B11)

description: Column in CountMatrix: S1B11


title: Sult2B1b knockdown, Batch1 (013931_E11)

description: Column in CountMatrix: S1E11


title: Sult2B1b knockdown, Batch1 (013927_G10)

description: Column in CountMatrix: S1G10


title: Sult2B1b knockdown, Batch1 (013924_C10)

description: Column in CountMatrix: S1C10


title: Sult2B1b knockdown, Batch1 (013926_F10)

description: Column in CountMatrix: S1F10


title: Sult2B1b knockdown, Batch1 (013928_A11)

description: Column in CountMatrix: S1A11


title: Sult2B1b knockdown, Batch1 (013925_E10)

description: Column in CountMatrix: S1E10


title: Sult2B1b knockdown, Batch1 (013922_E9)

description: Column in CountMatrix: S1E9


title: Sult2B1b knockdown, Batch1 (013923_B10)

description: Column in CountMatrix: S1B10


title: Sult2B1b knockdown, Batch1 (013918_G8)

description: Column in CountMatrix: S1G8


title: Sult2B1b knockdown, Batch1 (013920_B9)

description: Column in CountMatrix: S1B9


title: Sult2B1b knockdown, Batch1 (013917_E8)

description: Column in CountMatrix: S1E8


title: Sult2B1b knockdown, Batch1 (013921_C9)

description: Column in CountMatrix: S1C9


title: Sult2B1b knockdown, Batch1 (013916_D8)

description: Column in CountMatrix: S1D8


title: Sult2B1b knockdown, Batch1 (013914_H7)

description: Column in CountMatrix: S1H7


title: Sult2B1b knockdown, Batch1 (013935_A12)

description: Column in CountMatrix: S1A12


title: Sult2B1b knockdown, Batch1 (013913_G7)

description: Column in CountMatrix: S1G7


title: Sult2B1b knockdown, Batch1 (013915_C8)

description: Column in CountMatrix: S1C8


title: Sult2B1b knockdown, Batch1 (013909_C7)

description: Column in CountMatrix: S1C7


title: Sult2B1b knockdown, Batch1 (013908_B7)

description: Column in CountMatrix: S1B7


title: Sult2B1b knockdown, Batch1 (013910_D7)

description: Column in CountMatrix: S1D7


title: Sult2B1b knockdown, Batch1 (013904_D6)

description: Column in CountMatrix: S1D6


title: Sult2B1b knockdown, Batch1 (013907_A7)

description: Column in CountMatrix: S1A7


title: Sult2B1b knockdown, Batch1 (013906_G6)

description: Column in CountMatrix: S1G6


title: Sult2B1b knockdown, Batch1 (013899_C5)

description: Column in CountMatrix: S1C5


title: Sult2B1b knockdown, Batch1 (013901_E5)

description: Column in CountMatrix: S1E5


title: Sult2B1b knockdown, Batch1 (013900_D5)

description: Column in CountMatrix: S1D5


title: Sult2B1b knockdown, Batch1 (013898_B5)

description: Column in CountMatrix: S1B5


title: Sult2B1b knockdown, Batch1 (013895_F4)

description: Column in CountMatrix: S1F4


title: Sult2B1b knockdown, Batch1 (013894_E4)

description: Column in CountMatrix: S1E4


title: Sult2B1b knockdown, Batch1 (013919_H8)

description: Column in CountMatrix: S1H8


title: Sult2B1b knockdown, Batch1 (013911_E7)

description: Column in CountMatrix: S1E7


title: Sult2B1b knockdown, Batch1 (013896_G4)

description: Column in CountMatrix: S1G4


title: Sult2B1b knockdown, Batch1 (013912_F7)

description: Column in CountMatrix: S1F7


title: Sult2B1b knockdown, Batch1 (013889_F3)

description: Column in CountMatrix: S1F3


title: Sult2B1b knockdown, Batch1 (013888_D3)

description: Column in CountMatrix: S1D3


title: Sult2B1b knockdown, Batch1 (013887_C3)

description: Column in CountMatrix: S1C3


title: Sult2B1b knockdown, Batch1 (013893_D4)

description: Column in CountMatrix: S1D4


title: Sult2B1b knockdown, Batch1 (013892_C4)

description: Column in CountMatrix: S1C4


title: Sult2B1b knockdown, Batch1 (013891_B4)

description: Column in CountMatrix: S1B4


title: Sult2B1b knockdown, Batch1 (013905_E6)

description: Column in CountMatrix: S1E6


title: Sult2B1b knockdown, Batch1 (013902_F5)

description: Column in CountMatrix: S1F5


title: Sult2B1b knockdown, Batch1 (013903_G5)

description: Column in CountMatrix: S1G5


title: Sult2B1b knockdown, Batch1 (013882_C2)

description: Column in CountMatrix: S1C2


title: Sult2B1b knockdown, Batch1 (013884_G2)

description: Column in CountMatrix: S1G2


title: Sult2B1b knockdown, Batch1 (013885_H2)

description: Column in CountMatrix: S1H2


title: Sult2B1b knockdown, Batch1 (013886_B3)

description: Column in CountMatrix: S1B3


title: Sult2B1b knockdown, Batch1 (013883_D2)

description: Column in CountMatrix: S1D2


title: Sult2B1b knockdown, Batch1 (013881_B2)

description: Column in CountMatrix: S1B2


title: Sult2B1b knockdown, Batch1 (013880_A2)

description: Column in CountMatrix: S1A2


title: Sult2B1b knockdown, Batch1 (013879_H1)

description: Column in CountMatrix: S1H1


title: Sult2B1b knockdown, Batch1 (013878_E1)

description: Column in CountMatrix: S1E1


title: Sult2B1b knockdown, Batch1 (013897_A5)

description: Column in CountMatrix: S1A5


title: 25-CB1691-1127M

city: Cin

first: Leah

last: Kottyan

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Data analysis was performed in BioWardrobe [PMID:26248465]
RNA-Seq data:  Fastq files from Illumina pipeline were aligned by STAR (version STAR_2.4.2a PMCID: PMC3530905) with ”--outFilterMultimapNmax 1 --outFilterMismatchNmax 2” (for the full manual see https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf?raw=true). RefSeq annotation from UCSC genome browser (11/2012 PMID: 23155063) for hg19 genome was used. The --outFilterMultimapNmax parameter is used to allow uniq alignment only and --outFilterMismatchNmax parameter is used to allow at max 2 errors. All reads from produced .bam files were split for related isoform with respect to RefSeq annotation. Then EM algorithm was used to estimate appropriate number of reads for each isoform (details). To estimate difference between experiments DESeq (PMID: 20979621) or DESeq2 package were used (for experiments without replicates DESeq and blind method was forced).
FPKM values were calculated by BioWardrobe
Genome_build: hg19
Supplementary_files_format_and_content: The columns are RefSeqIDs, Read numbers, FPKM values

source_name: esophageal biopsy

extract_protocol:
Esophageal biopsy RNA was isolated from distal esophageal biopsy RNA from EoE patients with active disease and from unaffected controls using a Qiagen kit.
Libraries were prepared for sequencign using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero.
RiboZero RNA-Seq dUTP

value: female

tag: eoe diagnosis

tag: eosinophils per high powered field

tag: biowardrobe id


title: 14-CB2506-11826


title: Sult2B1b knockdown, Batch1 (013890_H3)

description: Column in CountMatrix: S1H3


title: 12-CB2392-1150H


title: 19_CB2586_11C62

value: male


title: 11-CB2336-114PL


title: 18-CB2584-1171A


title: Sult2B1b knockdown, Batch1 (013877_C1)

description: Column in CountMatrix: S1C1


title: 17-CB2394-11510


title: 24-CB1142-09T75


title: 3-CB2479-117RY

value: EoE


title: 4-CB2518-11C00


title: 16-CB2391-11508


title: 1-CB2455-116GL


title: 2-CB2416-117H6


title: 27-CB3089-124WR


title: 7-CB2758-11CYT


title: 28-CB3104-11MN9


title: 6-CB3085-124TM


title: 30-CB2020-113T1


title: 5-CB1678-10RR1


title: Sult2B1b knockdown, Batch1 (013876_A1)

description: Column in CountMatrix: S1A1


title: rpt4-1leo1D H3K9me2 ChIP-seq 1

city: Daejeon

first: Hogyu David

last: Seo

address: 291 Daehak-ro

country: South Korea

institute: KAIST

data_processing:
Prepared libraries were sequenced on a HiSeq2500 with single-end method (50-bp reads).
ChIP-seq reads were aligned to the S.pombe genome (ASM294v2) using NovoAlign (Novocraft technologies, Malaysia).
Significantly enriched peaks were identified using Homer and mapped reads were quantified using DeepTools and bwtool.
Genome_build: S. pombe EF2 genome assembly; ASM294v2
Supplementary_files_format_and_content: bigWig files of the processed raw files

organism: Schizosaccharomyces pombe

source_name: cells

growth_protocol: Grow cells in  YES medium at 30°C

extract_protocol: ChIP-seq libraries for genome-wide sequencing were prepared using 10 ng of input DNA or 1 to 10 ng of eluted ChIP DNA using NEXTflex ChIP-Seq kit, Bioo Scientific (cat.5143).

tag: antibody

value: anti-H3K9me2 (ab1220, Abcam)

value: Rpt4 point-mutation


title: rpt4-1leo1D H3K9me2 ChIP-seq 2

tag: genotype/variation


title: rpt4-1leo1D input 2


title: rpt4-1 input 2


title: rpt4-1leo1D input 1


title: rpt4-1 No-tag control Flag ChIP-seq

value: FLAG M2 (F1804, Sigma)


title: rpt4-1 H3K9me2 ChIP-seq 2


title: rpt4-1 input 1


title: 15-CB2314-114H8

value: control


title: leo1D input 2

value: lacking Leo1


title: Rpt4-1 Epe1 ChIP-seq 2


title: Rpt4-1 Epe1 ChIP-seq 1


title: leo1D input 1


title: rpt4-1 H3K9me2 ChIP-seq 1


title: leo1D H3K9me2 ChIP-seq 1


title: clr4D H3K9me2 ChIP-seq 2

value: lacking Clr4