title: Mouse E13.5 Control Alk5 Mandible Distal Replicate 1

description: Gene Expression


title: Mouse E12.5 Tgfbr2_Knockout Tgfbr2 Maxilla Proximal Replicate 2

status: Public on Oct 13 2018

type: RNA

city: Los Angeles

first: Michael

last: Kesling

address: 2250 Alcazar Street

country: USA

institute: University of Southern California

description: Gene Expression

hyb_protocol: Following fragmentation, 12 µg of cRNA was hybridized for 16hr on Affymetrix Mouse 430_2 (gene version) as recommended by the manufacturer.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The probe level data was summarized to gene level and was analyzed with PGS 6.6. RMA (Robust Multi array average) normalization was used.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse embryo stage E12.5

label_protocol: Starting from 5 µg total RNA, labeled cRNA was prepared using the Qiagen Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturer's instructions.

extract_protocol: RNA was extracted from tissues using RNeasy kit (Qiagen Valenica, CA).

tag: strain/background

tag: tissue

value: Maxilla

tag: tissue compartment

value: Proximal

tag: genotype/variation

value: Tgfbr2 Knockout

tag: developmental stage


title: Mouse E12.5 Tgfbr2_Knockout Tgfbr2 Maxilla Distal Replicate 2

description: Gene Expression

value: Distal


title: Mouse E12.5 Control Tgfbr2 Maxilla Proximal Replicate 3

description: Gene Expression

value: Control


title: 257236317062_2_2 0257

city: Leicester

first: Nicolas

last: Sylvius

address: University Road

department: CBS-Genetics

country: United Kingdom

institute: University of Leicester

hyb_protocol: Labelled cRNA was then hybridized over night at 65 ˚C onto the SurePrint G3 Human Gene Expression v3 8x60K Microarray (Agilent, Santa Clara, CA, USA).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters

organism: Homo sapiens

source_name: DLBCL cell lines

label_protocol: A total of 100ng of total RNA was reverse transcribed, converted into complementary RNA (cRNA) and labelled with Cy3 using the LowInput QuickAmp Labeling Kit One-Color according to manufacturer’s protocol (Agilent, Santa Clara, CA, USA).

extract_protocol: Cells were harvested and stored at -80 ˚C. RNA was then isolated from cell pellets by means of Trizol/chloroform phase separation followed by PureLink® RNA Mini Kit (ThermoFisher Scientific, Waltham, MA, USA). RNA quality was checked on a Bioanalyzer 2100 (Agilent, Stockport, UK). All RNA samples had a RNA Integration Number (RIN) > 7.

treatment_protocol: Single cell suspensions of tumour tissue (obtained from Crown Bioscience, Santa Clara, CA, USA) was incubated overnight at 37 ˚C with 5% CO2. The following day drug (1 µM) or DMSO vehicle control was added and cells were incubated for a further 24 hours.

tag: agent

value: DMSO

tag: cell line

value: DLBCL


title: 257236317062_2_1 2214

value: IKKepsilon/TBK1 inhibitors


title: 257236317061_1_1 2318


title: APP_WT_O_01 [miRNA-Seq]

type: SRA

city: Leuven

first: Bart

last: De Strooper

address: O&N4 Herestraat 49

department: Centre for Brain and Disease research

country: Belgium

institute: VIB - KU Leuven

description: nm.miRNA.mmu.txt

library_source: transcriptomic

data_processing:
Raw reads were trimmed with Flexbar (version 2.5.35, (22)) and filtered to remove unwanted adaptors, low-quality reads and reads with ambiguous nucleotides. Reads with ≥15 nucleotides were mapped to the mm10/GRCm38 Mus musculus assembly using Bowtie2 (version 2.2.1, (23)) allowing 1 mismatch. Stranded miRNA read counts were produced by FeatureCounts from the Subread package (version 1.4.4, (24)) using the miRBase gff3 annotation file (version 20, (25)).
We found in 2 of the 12 mice in the APPtg-O group a 46% lower expression levels of hsa-APPswe, a 26% lower expression of hsa-Psen1L166p and a 24% reduction in mmu-Thy1 gene, whose promoter drives the expression of the transgenes, compared to the other APPtg-O mice. In the absence of an explanation, these two mice were excluded from all further analyses (data not shown).
miRNAs with an average of raw read counts <5 were discarded, leaving 644 miRNAs for differential expression (DE) analysis. Non-biological variation was removed by the removeBatchEffect function from limma package 3.22.7 Bioconductor/R, preserving biological variation of genotype, age and their interactions in a generalized linear model for the APPtg and TAUtg dataset combined, as well as separately, while removing technical effects such as batch effect, RNA extraction group effects, RNA concentration effects. DE analysis was conducted using a 2-way interaction model (age, genotype, age*genotype) and performing Benjamini-Hochberg p-value adjustment for multiple testing.
Genome_build: mm10/GRCm38 Mus musculus reference genome
Supplementary_files_format_and_content: tab-delimited text file containing read counts after Limma Voom normalisation for all Samples

source_name: hippocampus

growth_protocol: Mice were co-housed and had ad libitum access to food and water.

extract_protocol:
Total RNA was extracted by homogenizing the left hippocampus in TRIzol (Invitrogen, Carlsbad, CA, USA) using 1ml syringes and 22G/26G needles and purified on mirVana spin columns according to the manufacturer’s instructions (Ambion, Austin, TX, USA). RNA purity (260/280 and 260/230 ratios) and integrity was assessed using  Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer with High Sensitivity chips (Agilent Technologies, Inc., Santa Clara, CA, USA) and Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, USA), respectively.
The miRNA library was prepared by the Genomics Core (UZ Leuven) using Illumina TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, CA, USA), adding 2µl of 50% PEG8000 in the 3’ ligation and with 13 cycles of cDNA amplification. Library construction of 96 samples was performed in 4 different batches of 24 samples, with 1-5 samples per experimental group within each batch. Three libraries were pooled and all RNAs between 5 and 40 bps in length were selected using the BluePippin (Sage Science, Beverly, MA, USA). Equimolar concentrations of 8 pools of 3 samples were loaded per lane and 4 lanes in total were used to sequence 50 bps single-end reads using the Illumina HiSeq 2500 (Illumina, San Diego, CA, USA).

treatment_protocol: Mice were sacrificed by cervical dislocation and the hippocampus was microdissected. Brain samples were snap frozen in liquid nitrogen and stored in -80°C until use.

value: hippocampus

tag: strain

tag: age (months)

tag: genotype

value: Wildtype


title: 257236317061_2_3 2345


title: Mouse E12.5 Tgfbr2_Knockout Tgfbr2 Mandible Proximal Replicate 2

description: Gene Expression

value: Mandible


title: Mouse E12.5 Tgfbr2_Knockout Tgfbr2 Mandible Distal Replicate 2

description: Gene Expression


title: 257236317062_1_3 0257


title: Mouse E12.5 Control Tgfbr2 Maxilla Distal Replicate 2

description: Gene Expression


title: Human_kidney_rep2

city: St. Louis

first: Haojia

last: Wu

state: Missouri

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

description:
single nucleus RNA-seq
processed data file: Human_kidney_snRNA.dge.txt.gz

data_processing:
DropSeq: Paired-end sequencing reads were processed as previously described using the Drop-Seq Tools v1.12 software available in McCarroll’s lab (http://mccarrolllab.com/dropseq/). Briefly, each cDNA read (read2) was tagged with the cell barcode (the first 12 bases in read 1) and unique molecular identifier (UMI, the next 8 bases in read 1), trimmed of sequencing adaptors and poly-A sequences, and aligned to the human (GRCh38) or a concatenation of the mouse and human (for the species-mixing experiment) reference genome assembly using STAR v 2.5.3a. Cell barcodes were corrected for possible bead synthesis errors using the DetectBeadSynthesisErrors program, and then collapsed to core barcodes if they were within an edit distance of 1. Digital gene expression (DEG) matrix was compiled by counting the number of unique UMIs for a given gene (as row) in a given cell (as column).
sNuc-10X Chromium: We used a newly developed pipeline, zUMIs (Parekh et al., 2018), to process the single nucleus sequencing data from human adult kidney. In brief, we first filtered out the low-quality barcodes or UMIs based on sequence with the internal read filtering algorithm built in zUMIs. We then used zUMIs to map the filtered reads to human reference genome (GRCh38) using STAR 2.5.3a (two-pass mapping mode). Next, zUMIs quantified the reads uniquely mapped to exonic or intronic reads and inferred the true barcodes that mark cells by fitting a k-dimensional multivariate normal distribution with mclust package. Finally, a UMI count table utilizing both exonic and intronic reads were generated for downstream analysis. The whole data processing was executed by running the script on a HPC cluster with the following example script: bash zUMIs-master.sh -f R1.fastq.gz -r R2.fastq.gz -c 1-16 -m 17-26 -l 98 -n Human_kidney -g GRCh38_ref_genome -a GRCh38_ref_genes.gtf -p 30
Genome_build: hg19

extract_protocol:
Nuclei extraction protocol: Nuclei were isolated with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with protease inhibitor (Roche #5892791001) and RNase inhibitor (Promega #N2615, Life Technologies #AM2696). Samples were cut into <2 mm pieces and homogenized using a Dounce homogenizer (Kimble Chase #885302-0002) in 2ml of ice-cold Nuclei EZ Lysis buffer and incubated on ice for 5 min with an additional 2ml of lysis buffer. The homogenate was filtered through a 40-µm cell strainer (pluriSelect #43-50040-51) and then centrifuged at 500 x for 5 min at 4 ºC. The pellet was resuspended and washed with 4 ml of the buffer and incubated on ice for 5 min. After another centrifugation, the pellet was resuspended with Nuclei Suspension Buffer (1x PBS, 0.07% BSA, 0.1% RNase inhibitor), filtered through a 20-µm cell strainer (pluriSelect 43-50020-50) and counted.
RNA libraries were prepared for sequencing using standard Dropseq and 10X Chromium procedure

treatment_protocol:
Organoid differentiation protocol: We used the protocols established by Takasato et al (Takasato protocol) and Morizane et al (Morizane protocol) to differentiate iPS and hES cells into kidney organoids.
Organoid dissociation and Dropseq protocol: Organoids were dissociated into single cell using TrypLE for 5-10 min at 37C with shaking. We used the DropSeq protocol described by Mackosco et al to generate the single cell transcriptomes

tag: tissue/cell type

value: Human kidney

tag: age

value: Age 62

tag: platform

value: 10X Chromium


title: 257236317061_2_1 2318


title: APP_TG_Y_12 [miRNA-Seq]

description: nm.miRNA.mmu.txt

value: Transgenic


title: APP_TG_Y_11 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: 257236317061_1_2 2214


title: Takasato_iPS_day34

description:
single cell RNA-seq
processed data file: Takasato_iPS_day34.dge.txt.gz

value: Organoid

tag: differentiation protocol

value: Takasato

tag: time point

value: DropSeq


title: APP_TG_Y_10 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E12.5 Control Tgfbr2 Maxilla Proximal Replicate 2

description: Gene Expression

value: Maxilla

value: Proximal


title: Takasato_iPS_day26

description:
single cell RNA-seq
processed data file: Takasato.iPS.timecourse.txt.gz


title: APP_TG_Y_09 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E12.5 Control Tgfbr2 Mandible Proximal Replicate 2

description: Gene Expression


title: Takasato_iPS_day19


title: Mouse E12.5 Control Tgfbr2 Mandible Distal Replicate 2

description: Gene Expression

value: Distal


title: Takasato_iPS_day12


title: APP_TG_Y_08 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: APP_TG_Y_07 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Takasato_iPS_day0


title: Takasato_iPS_day7


title: APP_TG_Y_05 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Morizane_iPS_Batch2

description:
single cell RNA-seq
processed data file: Morizane_iPS_Batch1_2.dge.txt.gz

value: Morizane


title: Morizane_iPS_Batch1


title: BDNF_inhibitor_batch2_rep2

description:
single cell RNA-seq
processed data file: BDNF_inhibitor.dge.txt.gz


title: APP_TG_Y_04 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: APP_TG_Y_03 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: APP_TG_Y_02 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: BDNF_inhibitor_batch2_rep1


title: Mouse E12.5 Tgfbr2_Knockout Tgfbr2 Maxilla Distal Replicate 1

description: Gene Expression

value: Tgfbr2 Knockout


title: Mouse E12.5 Tgfbr2_Knockout Tgfbr2 Mandible Proximal Replicate 1

description: Gene Expression


title: Mouse E12.5 Tgfbr2_Knockout Tgfbr2 Maxilla Proximal Replicate 1

description: Gene Expression


title: Mouse E12.5 Tgfbr2_Knockout Tgfbr2 Mandible Distal Replicate 1

description: Gene Expression


title: 297Adrosophila_PUS7Rep3_Input

city: Rehovot

first: Schraga

last: Schwartz

state: Choose a State or Province

address: Herzl 234, Department of Molecular Genetics

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

data_processing:
Reads were aligned against a database comprising a single copy of the drosophila rRNA, snRNA and tRNA sequences obtained from FlyBase. Unbiased pseudouridylation analyses were performed as above, with Ψ-ratio and Ψ-fc calculated for each position across each of the samples. t-test-based and chi-squared p-values were calculated for each site, comparing the four wild-type samples to Pus7 knockout. Sites were considered as differentially pseudouridylated, if they met the following criteria: (1) Chi-squared p-value <0.05, (2) t-test p-value <0.1, (3) Ψ-ratio in deletion samples <4%, and (4) difference between aggregated Ψ-ratio in wild-type versus knock-out >3%.
Supplementary_files_format_and_content: Set of putative pseudouridylation sites detected as differenetially pseudouridylation between Pus7 KO and WT drosophila.

organism: Drosophila melanogaster

source_name: heads

extract_protocol: Paired end libraries were generated as described in Schwartz et al, Cell, 2014.

treatment_protocol: Ψ-seq, essentially as described in Schwartz et al, Cell, 2014, was applied to 200 ng of RNA extracted from adult drosophila heads with four replicates per wild-type and Pus7 knockout samples.

value: Pus7 mutant

value: heads

value: adult

value: Canton-S

tag: treatment

value: input


title: Mouse E12.5 Control Tgfbr2 Mandible Proximal Replicate 1

description: Gene Expression

value: Mandible

value: Control


title: Mouse E12.5 Control Tgfbr2 Mandible Distal Replicate 1

description: Gene Expression


title: Mouse E12.5 Control Tgfbr2 Maxilla Distal Replicate 1

description: Gene Expression


title: Mouse E12.5 Control Tgfbr2 Maxilla Proximal Replicate 1

description: Gene Expression


title: APP_TG_Y_01 [miRNA-Seq]

description: nm.miRNA.mmu.txt

value: hippocampus


title: BDNF_inhibitor_batch1


title: APP_TG_Y_06 [miRNA-Seq]

description: nm.miRNA.mmu.txt

value: Transgenic


title: 297Adrosophila_PUS7Rep2_Input


title: 297Adrosophila_PUS7Rep1_Input


title: APP_TG_O_12 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Takasato_iPS_Batch2

description:
single cell RNA-seq
processed data file: Takasato_iPS_Batch1_2.dge.txt.gz

value: Organoid


title: APP_TG_O_11 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: 297Adrosophila_PUS7Rep4_Input


title: Takasato_iPS_Batch1

value: Takasato


title: APP_TG_O_10 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: 297Adrosophila_WTRep4_Input

value: wild type


title: 297Adrosophila_WTRep3_Input


title: APP_TG_O_09 [miRNA-Seq]

description: N.A.


title: Mouse E12.5 Alk5_Knockout Alk5 Maxilla Proximal Replicate 4

description: Gene Expression

value: Maxilla

value: Alk5 Knockout


title: Mouse E12.5 Alk5_Knockout Alk5 Maxilla Distal Replicate 4

description: Gene Expression

value: Distal


title: APP_TG_O_08 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: 297Adrosophila_WTRep1_Input


title: 297Adrosophila_WTRep2_Input


title: APP_TG_O_07 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: 297Adrosophila_PUS7Rep4_Treat

value: treated


title: APP_TG_O_06 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E12.5 Alk5_Knockout Alk5 Mandible Distal Replicate 4

description: Gene Expression


title: Mouse E12.5 Alk5_Knockout Alk5 Mandible Proximal Replicate 4

description: Gene Expression

value: Proximal


title: Mouse E12.5 Alk5_Knockout Alk5 Maxilla Proximal Replicate 3

description: Gene Expression


title: APP_TG_O_05 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: 297Adrosophila_PUS7Rep2_Treat

value: Pus7 mutant


title: 297Adrosophila_PUS7Rep1_Treat

value: heads


title: APP_TG_O_04 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E12.5 Alk5_Knockout Alk5 Maxilla Distal Replicate 3

description: Gene Expression


title: TAU_WT_O_10 [miRNA-Seq]

description: nm.miRNA.mmu.txt

value: Wildtype


title: 297Adrosophila_WTRep4_Treat

value: adult

value: Canton-S


title: APP_TG_O_02 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: APP_TG_O_03 [miRNA-Seq]

description: N.A.


title: 297Adrosophila_PUS7Rep3_Treat


title: 297Adrosophila_WTRep3_Treat


title: APP_TG_O_01 [miRNA-Seq]

description: nm.miRNA.mmu.txt


title: Mouse E12.5 Alk5_Knockout Alk5 Mandible Distal Replicate 3

description: Gene Expression

value: Mandible


title: Mouse E12.5 Alk5_Knockout Alk5 Mandible Proximal Replicate 3

description: Gene Expression


title: 297Adrosophila_WTRep2_Treat


title: DII_PSSPCEvPSSTCE_1

city: Ithaca

first: Cresten

last: Mansfeldt

state: NY

address: 220 Hollister Hall

institute: Cornell University

hyb_protocol: For each experiment, Cy5 labeled cDNA from the mixed community mRNA pool was hybridized against an aliquot of common control of Cy3 labeled cDNA from 3-day starved culture. The hybridization, washing, and scanning of the microarray samples was performed by the Cornell University Microarray Core Facility (http://cores.lifesciences.cornell.edu/brcinfo/) and followed the methods outlined by the manufacturer (Agilent Technologies). The general procedure mixed 25 μl (~400 ng) of the labeled cDNA sample with 25 μl 2x Gene Expression (GEx) Hybridization Buffer HI-RPM (5), hybridized the sample to the microarray slide at 65° C for 17 hours, and washed with GEx Wash Buffer 1 and 2 at room and elevated (37° C) temperatures.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505C with a 5 μm resolution.

data_processing: Microarray image analysis was conducted using Agilent Feature Extraction 10.5 Image Analysis Software. The Feature Extraction Software was also utilized to perform a within array modified LOESS normalization between the Cy5 and Cy3 signals, to calculate a log ratio between the Cy5 and Cy3 channels, and to calculate a modified Student t-test p-value between the Cy5 and Cy3 signal distributions.

organism: Dehalococcoides mccartyi

source_name: DET containing DII, Continous Fed PCE 10.6 μmol/(L/hr)

label_protocol: The Superscript I © DNAse RNA cleanup, amino-allyl cDNA formation, cDNA cleanup, and cDNA labeling with Cy3 or Cy5 followed the method outlined (Waller 2010). The quality and quantity of the RNA was determined using the RNA 6000 Nano assay on an Agilent 2100 bioanalyzer (Agilent Technologies). The quantity of resulting cDNA was determined by using the Quant-IT™ OliGreen® ssDNA Assay Kit (Invitrogen). A common control RNA pool sampled from the main Donna II reactor after 3 days of starvation was labeled with Cy3.

growth_protocol: All subcultures studied in this experiment were 100 mL samples from a maintained 6L mixed community culture (Donna II) previously described (Rahm and Richardson 2006; Rahm and Richardson 2008; Rowe et al. 2009) The culture contains a DET population (near 5×108 cells/mL; 60% of total population on per cell basis) mixed with methanogens and organisms that ferment organic substrates.

extract_protocol: 50 mL of liquid culture samples were centrifuged-at 14190×g. The centrifuged sample was split into 8 individual RNA extractions with each sample following the RNeasy© Mini Kit (Qiagen) extraction previously outlined (Rahm and Richardson 2008). The 8 distinct RNA extractions were recombined on the spin filter before the first RW1 buffer wash.

treatment_protocol: In brief, 160 mL glass serum bottles were filled with 100 mL of 3-day starved mixed community culture sampled from the main reactor (Donna II). Varying combination of Pressure Lok syringe volumes (10 mL, 5 mL, 2.5 mL, 500 μL, and 100 μL; VICI Precision Sampling) and concentrations of electron acceptor and donor in media were loaded on a Cole Palmer 74900 Syringe Pump to deliver an expected continuous rate.  Rates of respiration and electron donor feed are given as conditions.

value: strain 195 in the Donna II Mixed Community

tag: feed type

value: Continous

tag: electron acceptor

value: PCE

tag: electron donor

value: Butyrate+Yeast Extract

tag: electron acceptor respiration rate (µeeq/(l-hr))

tag: batch acceptor feed concentration (µeeq/l)

tag: electron donor/electron acceptor ratio on eeq basis

tag: length of experiment (hours)

source_name: DET containing DII, Continous Fed TCE 13.7 μmol/(L/hr)

value: TCE


title: Mouse E12.5 Alk5_Knockout Alk5 Mandible Proximal Replicate 2

description: Gene Expression

tag: strain/background

tag: tissue

tag: tissue compartment

tag: genotype/variation

tag: developmental stage


title: DII_BatchPCEvPSSTCE_2

source_name: DET containing DII, Batch Fed PCE 110 μmol/L

tag: strain

value: Batch


title: Mouse E12.5 Alk5_Knockout Alk5 Maxilla Distal Replicate 2

description: Gene Expression

value: Maxilla


title: Morizane_ES_lane2

description:
single cell RNA-seq
processed data file: Morizane_ES.dge.txt.gz

tag: tissue/cell type

value: Organoid

value: Morizane

tag: platform

value: DropSeq


title: 297Adrosophila_WTRep1_Treat

tag: genotype

value: wild type

value: treated


title: DII_BatchPCEvPSSTCE_1

source_name: DET containing DII, Continous Fed TCE 14.2 μmol/(L/hr)


title: DII_BatchPCEvBatchPCE_1


title: DII_PSSPCEvBatchPCE_2

source_name: DET containing DII, Continous Fed PCE 7.3 μmol/(L/hr)


title: Mouse E12.5 Control Alk5 Maxilla Proximal Replicate 2

description: Gene Expression

value: Proximal

value: Control


title: Mouse E12.5 Alk5_Knockout Alk5 Mandible Distal Replicate 2

description: Gene Expression

value: Distal

value: Alk5 Knockout


title: Morizane_ES_lane1

tag: differentiation protocol

tag: time point


title: DII Tetrachlorobenzene Batch Feed 2 Day Sample [DII_2TCBvBatchPCE_2]

description: Biological replicate 2 of 3

data_processing:
Microarray image analysis was conducted using Agilent Feature Extraction 10.5 Image Analysis Software. The Feature Extraction Software was utilized to perform a background correction and a within array modified LOESS normalization between the Cy5 and Cy3 signals, to calculate a log ratio between the Cy5 and Cy3 channels, and to calculate a modified Student t-test p-value between the Cy5 and Cy3 signal distributions.
Geometrically averaged normalized log10 ratio (Cy5/Cy3) representing test/reference and an absolute intensity of the Cy5 channel data generated.

organism: Dehalococcoides mccartyi 195

source_name: Mixed community treated with 1,2,3,4 tetrachlorobenzene

label_protocol: The Superscript II © DNAse RNA cleanup, amino-allyl cDNA formation, cDNA cleanup, and cDNA labeling with Cy3 or Cy5 followed the method outlined (Waller 2010). The quality and quantity of the RNA was determined using the RNA 6000 Nano assay on an Agilent 2100 bioanalyzer (Agilent Technologies). The quantity of resulting cDNA was determined by using the Quant-IT™ OliGreen® ssDNA Assay Kit (Invitrogen). A common control RNA pool sampled from the main Donna II reactor after 3 days of starvation was labeled with Cy3.

treatment_protocol: In brief, 160 mL glass serum bottles were filled with 100 mL of 3-day starved mixed community culture sampled from the main reactor (Donna II) and were fed with 1 µL neat PCE, 40 µL of 100 mM 1,2,3,4-TeCB (Acros Organics) in hexadecane (Sigma Aldrich), 40 µL of 99% pure butyrate (Sigma Aldrich), 100 µL of 50 g/L YE, and 100 µL of vitamin solution. Triplicate samples were taken at 2 and 3 days after feeding.

tag: community

value: Donna II

tag: community composition

value: Mixed; DMC population with fermenters and methanogens

tag: sampled time

value: 3 days

source_name: Pooled batch PCE fed mixed community sampled three days after starvation


title: Control Dye Swap [DII_BatchvBatchPCE_2]

description: Technical replicate 2 of 2


title: Control Dye Swap [DII_BatchvBatchPCE_1]

description: Technical replicate 1 of 2


title: DII Tetrachlorobenzene Batch Feed 2 Day Sample [DII_2TCBvBatchPCE_1]

description: Biological replicate 1 of 3


title: lacZ_KD_Ctr_3

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology, Mainz

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4
Fastq files were mapped with STAR_2.5.1b to the BDGP6 reference genome
Secondary alignments were filtered with samtools 1.2
Counts for every gene were calculated with FeatureCounts (Subread v1.4.6-p2) using the gene model provided with Ensembl version 90 for BDGP6
Genome_build: dm6
Supplementary_files_format_and_content: tab separated file containing counts per gene

molecule: polyA RNA

growth_protocol: Drosophila S2R+ cells were cultured at 25°C in Schneider's Drosophila Medium (GIBCO, Cat-No 21720) supplemented with 10 % FBS and 2 % Penicillin/Streptomycin.

extract_protocol:
RNA was extracted with the RNeasy Mini Kit (Qiagen) and RNA integrity checked by Bioanalyzer.
NGS library prep was performed with Illumina’s TruSeq stranded mRNA LT Sample Prep Kit following Illumina’s standard protocol (Part #15031047 Rev. E). Libraries were prepared with a starting amount of 500 ng and amplified in 11 PCR cycles. All 68 embryo samples were pooled in equimolar ratio and sequenced on  NextSeq 500, PE for 2x 81 cycles plus 7 cycles for the index read.

treatment_protocol: dsRNA was transfected in S2R+ cells by serum starvation for 6h. The treatment was repeated twice and cells were harvested 5 days after the first treatment.

value: Oregon R

tag: cell line

tag: tissue source

value: embryo

value: late embryonic state

value: lacZ control


title: Morizane_iPS_Batch3_lane2

description:
single cell RNA-seq
processed data file: Morizane_iPS_Batch3.dge.txt.gz


title: DII_PSSPCEvBatchPCE_1

value: strain 195 in the Donna II Mixed Community

tag: feed type

value: Continous

tag: electron acceptor

value: PCE

tag: electron donor

value: Butyrate+Yeast Extract

tag: electron acceptor respiration rate (µeeq/(l-hr))

tag: batch acceptor feed concentration (µeeq/l)

tag: electron donor/electron acceptor ratio on eeq basis

tag: length of experiment (hours)

value: Batch


title: Mouse E12.5 Alk5_Knockout Alk5 Maxilla Proximal Replicate 2

description: Gene Expression

tag: strain/background

tag: tissue

value: Maxilla

tag: tissue compartment

tag: genotype/variation

tag: developmental stage


title: DII Tetrachlorobenzene Batch Feed 1 Day Sample [DII_TCBvBatchPCE_3]

description: Biological replicate 3 of 3

tag: community

value: 2 days


title: Mouse E12.5 Control Alk5 Maxilla Distal Replicate 2

description: Gene Expression

value: Control


title: Mouse E12.5 Control Alk5 Mandible Proximal Replicate 2

description: Gene Expression

value: Mandible

value: Proximal


title: Mouse E12.5 Control Alk5 Mandible Distal Replicate 2

description: Gene Expression

value: Distal


title: DII Tetrachlorobenzene Batch Feed 1 Day Sample [DII_TCBvBatchPCE_2]

description: Biological replicate 2 of 3

value: Donna II

tag: community composition

value: Mixed; DMC population with fermenters and methanogens


title: DII Tetrachlorobenzene Batch Feed 2 Day Sample [DII_2TCBvBatchPCE_3]

description: Biological replicate 3 of 3

tag: sampled time

value: 3 days


title: lacZ_KD_Ctr_1

tag: strain

value: Oregon R

tag: cell line

value: embryo


title: Takasato_ES_Batch2_lane2

description:
single cell RNA-seq
processed data file: Takasato_ES.dge.txt.gz

tag: tissue/cell type

value: Organoid

tag: differentiation protocol

value: Takasato

tag: time point

tag: platform

value: DropSeq


title: Hrb98DE_KD2_4

tag: tissue source

value: late embryonic state

value: Hrb98de knock down


title: Hrb98DE_KD2_2


title: Takasato_ES_Batch2_lane1


title: Hrb98DE_KD2_1


title: Takasato_ES_Batch1_lane2


title: Takasato_ES_Batch1_lane1


title: Hrb98DE_KD1_4


title: breast cancer, ER-negative, rep3

city: Kamogawa City, Chiba

first: Yuko

last: Tsunoda

address: 929 Higashi-cho

country: Japan

institute: Kameda Medical Center

description: breast cancer, ER-negative, rep3

data_processing: see manufacturers instructions (CT, ⊿CT, ⊿⊿CT, 2^⊿⊿CT)

label: SYBR Green

source_name: S (Triple negative)

label_protocol: The miRNA MiScript SYBR Green human breast cancer miRNA PCR kit (Qiagen, Tokyo, Japan) was used in combination with an ABI PRISM 7000 Sequence System (Applied Biosystems Inc., CA).

growth_protocol: Tumor specimens were fixed in 10% formalin, and samples embedded in paraffin were used for miRNA PCR array.

extract_protocol: The degree of RNA cross-linking and RNA degradation was analyzed by electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies). miRNA was isolated from total RNA using an RT2 qPCR-Grade miRNA Isolation Kit (SABiosciences, Frederic, MD).

treatment_protocol: Paraffin in 10-um slices of FFPE tissue was removed by xylene treatment and tissues were washed with ethanol twice to remove xylene. Tissues were then treated with proteinase K at 37°C overnight. Following centrifugation, the supernatant was processed with a silica-based spin column (Toray Industries Inc., Kanagawa, Japan) in order to obtain purified total RNA.

value: breast cancer, ER-negative

tag: gender

value: female

tag: nationality

value: Japanese

tag: diagnosis

value: breast cancer, stage I


title: DII Tetrachlorobenzene Batch Feed 1 Day Sample [DII_TCBvBatchPCE_1]

description: Biological replicate 1 of 3

value: 2 days


title: breast cancer, ER-positive, rep3

description: breast cancer, ER-positive, rep3

source_name: M (Luminal A)

tag: tissue

value: breast cancer, ER-positive


title: Mouse E12.5 Alk5_Knockout Alk5 Mandible Proximal Replicate 1

description: Gene Expression

tag: strain/background

value: Mandible

tag: tissue compartment

value: Proximal

value: Alk5 Knockout


title: breast cancer, ER-negative, rep2

description: breast cancer, ER-negative, rep2


title: breast cancer, ER-positive, rep2

description: breast cancer, ER-positive, rep2


title: Morizane_iPS_Batch3_lane1

value: Morizane


title: Hrb98DE_KD1_3

value: Oregon R

tag: developmental stage

tag: genotype/variation


title: Takasato_iPS_Batch3_lane2

description:
single cell RNA-seq
processed data file: Takasato_iPS_Batch3.dge.txt.gz


title: Mouse E12.5 Alk5_Knockout Alk5 Maxilla Distal Replicate 1

description: Gene Expression

value: Maxilla

value: Distal


title: Takasato_iPS_Batch3_lane1

value: Organoid

value: Takasato


title: Mouse E12.5 Control Alk5 Maxilla Proximal Replicate 1

description: Gene Expression

value: Control


title: Mouse E12.5 Alk5_Knockout Alk5 Maxilla Proximal Replicate 1

description: Gene Expression


title: breast cancer, ER-negative, rep1

description: breast cancer, ER-negative, rep1


title: Mouse E12.5 Control Alk5 Maxilla Distal Replicate 1

description: Gene Expression


title: breast cancer, ER-positive, rep1

description: breast cancer, ER-positive, rep1


title: Mouse E12.5 Control Alk5 Mandible Distal Replicate 1

description: Gene Expression


title: Mouse E12.5 Control Alk5 Mandible Proximal Replicate 1

description: Gene Expression


title: Mouse E12.5 Alk5_Knockout Alk5 Mandible Distal Replicate 1

description: Gene Expression


title: Human_kidney_rep1

value: Human kidney

tag: age

value: Age 62

value: 10X Chromium


title: IWR-1-rep3

status: Public on Oct 12 2018

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

description: CtA endothelial cells from IWR-1 treated embryos

data_processing:
Raw reads were assessed for quality, adapter content and duplication rates with FastQC (available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 (GRCz10.87) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Genome_build: DanRer10
Supplementary_files_format_and_content: tab-delimited text files include library size normlized counts per gene

organism: Danio rerio

source_name: brain endothelial cells

extract_protocol:
Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser (100% laser, 5 iterations, 50s). After several washes in HBSS (Hank’s Balanced Salt Solution, Gibco) without Ca2+/Mg2+, zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin-LE select (Gibco). Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged, frozen by liquid nitrogen and stored at -80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen)
250-500 pg total RNA was used as input for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Clontech) for cDNA pre-amplification. Obtained full-length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine (Covaris). Final Library Preparation was performed by Low Input Library Prep Kit v2 (Takara Clontech).

tag: lines

value: hindbrain endothelium


title: IWR-1-rep2


title: IWR-1-rep1


title: DMSO-rep2

description: CtA endothelial cells from DMSO treated embryos


title: DMSO-rep1


title: Hrb98DE_KD1_1

tag: strain

value: embryo

value: late embryonic state

value: Hrb98de knock down


title: Single cell 5

city: Dalian

first: Meng ying

last: Tong

state: Liaoning

address: Longtou Street

country: China

institute: Dalian Medical University

description:
N5
RNA sequencing
mRNA
processed data file: All_FPKM_table.txt

data_processing:
Sequencing was performed on Illumina HiseqXten with paired-end reads of 150bp.
The quality of sequencing data was assessed by the software FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Mapping to the reference of hg19 Human Genome was conducted by TopHat2 (http://ccb.jhu.edu/software/tophat/index.shtml).
Gene-level expression abundance were obtained from the Cufflinks package (http://cole-trapnell-lab.github.io/cufflinks/).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: All_FPKM_table.txt: Tab-delimited text file including gene-level expression abundance (fragments per kilobase of exon per million fragments mapped) for all samples.

source_name: Breast cancer cell line

growth_protocol: The single-cell (MDA-MB-231, obtained from the American Type Culture Collection) suspension was obtained by trypsinization. Cells were seeded in an ultra-low attachment 96-well plate (Corning, one cell per well). The cells were maintained in serum-free Dulbecco's Modified Eagle Medium/Nutrient Mixture F12 (DMEM /F12) (Gibco) supplemented with B27 (Invitrogen), 20 ng/mL epidermal growth factor (EGF) (Sigma), 20 ng/mL basic fibroblast growth factor (bFGF) (BD Biosciences). Only wells that contained a single cell initially were used for subsequent studies. For spheroid passage, the single-cell-derived spheroid was sucked up by a micro-pipette and dissociated with a small amount of trypsin-Ethylene Diamine Tetraacetic Acid (EDTA) and mechanically dispersed. The resulting single cells were then re-suspended in serum-free medium. The spheroids were passed every 7-10 days, and only spheroids bigger than 50μm in size were included in the analyses.

extract_protocol:
Discover-sc WTA Kit (Vazyme, Cat. N711-01).
TruePrep DNA library Prep Kit V2 for Illumina (Vazyme cat. TD-503).

tag: cell line

tag: sample type

value: Single cell


title: Multiple cell 9

description:
N9
RNA sequencing
mRNA
processed data file: All_FPKM_table.txt

value: Multiple cell


title: Single-cell-derived spheroid 8

description:
C8
RNA sequencing
mRNA
processed data file: All_FPKM_table.txt

value: Single-cell-derived spheroid


title: Multiple single-cell-derived spheroids 10

description:
C10
RNA sequencing
mRNA
processed data file: All_FPKM_table.txt

value: Multiple single-cell-derived spheroid


title: Single cell 4

description:
N4
RNA sequencing
mRNA
processed data file: All_FPKM_table.txt


title: Multiple single-cell-derived spheroids 11

description:
C11
RNA sequencing
mRNA
processed data file: All_FPKM_table.txt


title: Single-cell-derived spheroid 6

description:
C6
RNA sequencing
mRNA
processed data file: All_FPKM_table.txt


title: Single-cell-derived spheroid 7

description:
C7
RNA sequencing
mRNA
processed data file: All_FPKM_table.txt


title: Single-cell-derived spheroid 4

description:
C4
RNA sequencing
mRNA
processed data file: All_FPKM_table.txt


title: Single-cell-derived spheroid 5

description:
C5
RNA sequencing
mRNA
processed data file: All_FPKM_table.txt


title: Single cell 6

description:
N6
RNA sequencing
mRNA
processed data file: All_FPKM_table.txt


title: Multiple single-cell-derived spheroids 9

description:
C9
RNA sequencing
mRNA
processed data file: All_FPKM_table.txt


title: 30_AGTTCC

city: Houston

first: Wenyi

last: Wang

state: TX

address: Unit 1410 1400 Pressler

institute: The University of Texas MD Anderson Cancer Center

description: Lane: 3 & 4

data_processing:
We mapped raw reads generated from pair-end Illumina sequencing to the human reference genome build 37.2 from NCBI through Tophat (default parameters and supplying the -G option with GTF annotation file downloaded from NCBI genome browser).
The mapped reads obtained from Tophat output were cleaned by Samtools to remove improperly mapped and duplicated reads.
We then used Picard tools to sort those cleaned sam files according to their reference sequence names and create an index for the reads.
The gene level expression was quantified by applying the R packages GenomicFeatures and GenomicRanges. We generated a reference table from the human reference genome hg19 and then used the function findOverlaps to count the number of reads mapped to each exon for all the samples.
Genome_build: NCBI genome build 37.2 (GRCh37, hg19)
Supplementary_files_format_and_content: *.cleaned.deduped_ENSG.allCoverage.txt: Tab-delimited text files include count values for each Sample.

source_name: cell line

growth_protocol: Lung adenocarcinoma cell line NCI-H192 was obtained from ATCC. CAF (cancer-associated fibroblasts) and TIL (tumor infiltrated lymphocytes) were gifted by Drs. Chantale Bernatchez and Kazuhiko Shien, respectively, and were grown in RPMI 1640 Glutamax medium (Gibco #61870) supplemented with 100 units/ml Penicillin-Streptomycin (Gibco # 15140) and 10% Fetal Bovine Serum (Gibco # 10437) under ambient oxygen conditions at 37°C.

extract_protocol:
At the end of incubation, TILs growing in suspension were directly collected into a tube; NCI-1792 and CAF cells were collected by trypsinisation. Cells were suspended in PBS and adjusted concentration at 7500 cells/ul. Total RNA was extracted and isolated from the above cell mixture samples using a total AllPrep DNA/RNA Micro purification Kit (Cat#80284, Qiagen, Valencia, CA 91355).
Next-generation sequencing libraries were prepared from approximately 1 μg of RNA using TruSeq RNA v2 Preparation kits (Illumina).Libraries were clustered on a cBot with Illumina HiSeq SR Cluster Kit (v4) and sequenced on an Illumina HiSeq 2000 with an Illumina HiSeq SBS Kit (v4) as pair-end 76 base pair reads at the MD Anderson sequencing facility.

value: Mixed

tag: cell type

tag: mixing proportions


title: 31_ATGTCA

description: Lane: 3 & 4


title: 32_CCGTCC

description: Lane: 3 & 4


title: 29_AGTCAA

description: Lane: 3 & 4


title: DMSO-rep3


title: 26_TAGCTT

description: Lane: 3 & 4


title: 28_CTTGTA

description: Lane: 3 & 4


title: 27_GGCTAC

description: Lane: 3 & 4


title: MammaryTu_negCD_rep2

city: Barretos

first: Lucas

middle: Tadeu

last: Bidinotto

state: SP

address: Antenor Duarte Vilela, 1331

country: Brazil

institute: Barretos Cancer Hospital

description:
251487921669 - GE1_1105_Oct12_1_4. s7
Gene expression array of mammary gland tumor in post-natal day 110.
Mammary gland tumor, negative control, replicate 2.

hyb_protocol: 1.65 ug of labeled cRNA was hybridized to microarray slides (Whole rat genome-4X44K oligo microarrays-G4112F, Agilent Technologies) at 65°C for 17 hours. Slides were then washed and scanned following Agilent's recommendations.

scan_protocol: The hybridization signals were captured using the Agilent G4900DA SureScan Microarray Scanner System (Agilent Technologies, Inc. Life Sciences and Chemical Analysis Group, Santa Clara, CA, USA).

data_processing: The scanned images were analyzed with Feature Extraction Software v.15.5 using the default protocol (GE1_1105_Oct12 and Grid:014879_D_F_20110531) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Mammary gland tumor, maternal control diet

label_protocol: 200 ng of total RNA were hybridized onto whole rat genome 4x44K oligo microarrays (G4131F, Agilent Technologies) using one color (Cy3) Low input Quick Amp labeling kit (Agilent Technologies, Inc. Life Sciences and Chemical Analysis Group, Santa Clara, CA, USA), according to manufacturer instructions. Briefly, total RNA plus spike-in controls were reverse transcribed into double-stranded cDNA. The primers used for this reaction contained consecutive thymine bases attached to a T7 promoter that paired at the 5' end of the first strand of cDNAs. Next, the T7 polymerase was added along with nucleotides labeled with fluorescent Cyanine-3 (Cy3) dye, which amplified the anti-sense complementary RNAs (cRNA).

extract_protocol: Total RNA was extracted from the tubular/papillary mammary tumors using the miRNeasy kit (QIAGEN Inc. USA Valencia, CA - USA) according to the manufacturer’s instructions. The extracted RNA was stored at -80°C. RNA was quantified in a spectrophotometer NanoVue (GE Healthcare UK Limited, UK) and the integrity was evaluated using the equipment Agilent 2100 Bioanalyzer (Agilent Technologies, Inc. Life Sciences and Chemical Analysis Group, Santa Clara, CA, USA) under standard conditions.

treatment_protocol: Pregnant Sprague-Dawley (SD) rats received control diet (CD) or Western-style diet (WD) from gestational days (GD) 12-20 and post-natal days (PND) 1-21. At weaning, the female offspring received CD until the end of the tumor bioassay. Female offspring 3 weeks old from both CD and WD groups received a single intraperitoneal dose of 50 mg/kg of N-Methyl-N-Nitrosourea (MNU) dissolved in phosphate-buffered saline acidified with acetic acid.  At the end of study, the animals were euthanized and mammary tumors were removed and kept at -80°C for molecular analysis.

value: Sprague-Dawley

value: Mammary gland tumor

tag: Sex

value: Female

value: 110 days

tag: dam diet


title: 25_GATCAG

description: Lane: 3 & 4


title: MammaryTu_negCD_rep1

description:
251487921671 - GE1_1105_Oct12_1_4 s6
Gene expression array of mammary gland tumor in post-natal day 110.
Mammary gland tumor, negative control, replicate 1.

value: Control


title: MammaryTu_negCD_rep4

description:
251487921671 - GE1_1105_Oct12_1_2 s9
Gene expression array of mammary gland tumor in post-natal day 110.
Mammary gland tumor, negative control, replicate 4.


title: 24_ACTTGA

description: Lane: 3 & 4


title: MammaryTu_WD_rep1

description:
251487921669 - GE1_1105_Oct12_1_1 s1
Gene expression array of mammary gland tumor in post-natal day 110.
Mammary gland tumor, WD - treated, replicate 1.

source_name: Mammary gland tumor, maternal Western-style diet

value: Western-style (high-fat and low-fiber and oligoelements)


title: 23_CAGATC

description: Lane: 3 & 4


title: MammaryTu_WD_rep3

description:
251487921670 - GE1_1105_Oct12_1_2 s3
Gene expression array of mammary gland tumor in post-natal day 110.
Mammary gland tumor, WD - treated, replicate 3.


title: MammaryTu_WD_rep2

description:
251487921669 - GE1_1105_Oct12_1_3 s2
Gene expression array of mammary gland tumor in post-natal day 110.
Mammary gland tumor, WD - treated, replicate 2.


title: MammaryTu_negCD_rep3

description:
251487921670 - GE1_1105_Oct12_1_1 s8
Gene expression array of mammary gland tumor in post-natal day 110.
Mammary gland tumor, negative control, replicate 3.


title: 20_TGACCA

description: Lane: 3 & 4


title: MammaryTu_WD_rep4

description:
251487921670 - GE1_1105_Oct12_1_4 s4
Gene expression array of mammary gland tumor in post-natal day 110.
Mammary gland tumor, WD - treated, replicate 4.


title: MammaryTu_WD_rep5

description:
251487921671 - GE1_1105_Oct12_1_1 s5
Gene expression array of mammary gland tumor in post-natal day 110.
Mammary gland tumor, WD - treated, replicate 5.


title: MammaryTu_negCD_rep5

description:
251487921670 - GE1_1105_Oct12_1_3 s10
Gene expression array of mammary gland tumor in post-natal day 110.
Mammary gland tumor, negative control, replicate 5.


title: 17_ATCACG

description: Lane: 3 & 4


title: 19_TTAGGC

description: Lane: 3 & 4


title: 18_CGATGT

description: Lane: 3 & 4


title: 16_CCGTCC

description: Lane: 1 & 2


title: 15_ATGTCA

description: Lane: 1 & 2


title: 21_ACAGTG

description: Lane: 3 & 4


title: 22_GCCAAT

description: Lane: 3 & 4


title: 14_AGTTCC

description: Lane: 1 & 2


title: 12_CTTGTA

description: Lane: 1 & 2


title: 9_GATCAG

description: Lane: 1 & 2

value: TIL

value: Tumor infiltrating lymphocytes

value: Pure


title: 11_GGCTAC

description: Lane: 1 & 2


title: 13_AGTCAA

description: Lane: 1 & 2


title: 10_TAGCTT

description: Lane: 1 & 2


title: 8_ACTTGA

description: Lane: 1 & 2


title: 7_CAGATC

description: Lane: 1 & 2


title: 5_ACAGTG

description: Lane: 1 & 2

value: CAF

value: Cancer-associated fibroblasts


title: 2_CGATGT

description: Lane: 1 & 2

value: Lung adenocarcinoma cell line


title: 3_TTAGGC

description: Lane: 1 & 2


title: Control MN 2 Replicate 2

city: Bosisio Parini

first: Uberto

last: Pozzoli

state: LC

address: Via Don L. Monza, 20

department: Neurobiology, Computational Biology and Pharmacology

country: Italy

institute: Scientific Institute IRCCS E.Medea

data_processing:
Each sample was aligned using STAR2 with following parameters:
runMode alignReads
readFilesCommand zcat
outFilterIntronMotifs RemoveNoncanonical
outSAMstrandField intronMotif
outSAMtype BAM SortedByCoordinate
Each sample alignment was quantified by using cuffquant (v2.2.1) with parameters: -u -p 10
Using ENSEMBL release 75 as reference annotation
Differential expression was evaluated by applying cuffdiff (v2.2.1) with parameters: -p 12 -L SMA,CTL --min-reps-for-js-test 4
Differential cassette exons inclusion was evaluated by using rMATS (v 3.2.2) with parameters -t paired -len 101 -a 4
Using ENSEMBL release 75 as reference annotation
Genome_build: hg19
Supplementary_files_format_and_content: gene_exp.diff. This file (part of the cuffdiff output) contains FPKM estimates of genes abundances and statistics for SMA vs CTL sample goups.
Supplementary_files_format_and_content: SE.MATS.ReadsOnTargetAndJunctionCounts.txt. This file (part of the RMATS putput) contains Cassette exons positions as well as estimates and statistics of SMA and CTL sample groups inclusion levels.

source_name: human MN 2

growth_protocol: SMA and control iPSC line were routinely cultured on Matrigel-coated dishes in E8 media (Life Technologies). MNs were differentiated as previously described (Corti et al., 2012)

extract_protocol:
Selected cells were treated with Proteinase K for 1hr at 50°C before addition of Trizol LS (Life technologies) for RNA extraction. DNase treatment using Turbo DNA-free (Ambion) was performed to remove contaminating genomic DNA. RNA analysis was processed by DNA vision as follows: sample quality control was performed on Bioanalyzer 2100 Agilent and quantity checked by Nanodrop.
TrueSeq mRNA library construction was performed followed by Library Quality Control by Bioanalyzer 2100 Agilent. Sequencing on HiSeq 2000: 2 samples per lane with a 2x100 cycles strategy.

treatment_protocol: To differentiate iPSCs into spinal MNs, we followed a multistep protocol developed for human ESCs and iPSCs (Corti et al., 2012, B. Y. Hu, S. C. Zhang, 2009). Cells were plated with neuronal medium (Dulbecco’s modified Eagle’s medium (MEM)/F12 (Life Technologies), supplemented with MEM nonessential amino acids solution (Life Technologies), N2 (Life Technologies), and heparin (2 mg/ml; Sigma- Aldrich), to which retinoic acid (RA, 0.1 µM; Sigma-Aldrich) was added after 10 days for neural caudalization. Posteriorized neuroectodermal cells were collected at day 17 and suspended for a week in the same medium with RAretinoic acid (0.1 µM) and Sonic Hhedgehog (SHH) (100–200 ng/ml; R&D Systems), followed by the addition of BDNF and GDNF on day 24 (10 ng/ml; PeproTech). A centrifugation gradient was used to maximize MN enrichment as described previously (Corti et al, 2012; Gingras et al, 2007; Wada et al. 2009). Cells were fixed and immunostained for quantification following seeding in culture for at least 24 h.

tag: disease state

value: control

value: iPSC-derived motor neuros


title: SMA MN 2 Replicate 2

source_name: SMA patient2-specific MN

value: SMA


title: SMA MN 1 Replicate 2

source_name: SMA patient1-specific MN


title: SMA MN 2 Replicate 1


title: Control MN 1 Replicate 1

source_name: human MN 1


title: Control MN 2 Replicate 1


title: Control MN 1 Replicate 2


title: 6_GCCAAT

description: Lane: 1 & 2


title: SMA MN 1 Replicate 1


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Srrm4+siSrrm3 knockdown (T024), replicate 2

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

description: Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: TCGAGTAC

data_processing:
Library strategy: SPAR-seq
Fastq files contain demultiplexed reads which were assigned to the appropriate treatment by matching to expected forward and reverse barcodes (sequenced in dedicated reads; not supplied).
Forward and reverse event reads were mapped to custom junction libraries representing all expected splice variants (supplied as processed files), using bowtie with settings --best -v 3 -k 1 --trim3 47 --trim5 5. Trimming was done to remove lower-quality, uninformative ends. Junction libraries were constructed from NCBIm37/mm9 gene annotations complemented by additional splice junctions curated from RNA-seq in the same cell type. Mapped reads were counted per junction.
Alternative splicing analysis was performed chiefly as reported in Han et al., Mol. Cell (2016): Percent-spliced-in (PSI) values were calculated for each alternative exon, or part thereof in the case of alternative 5'-/3'-splice sites ('event'), from read tallies as follows: PSI was calculated independently from forward and reverse reads as the percentage of reads supporting inclusion divided by the total number of reads for the event. For alternative 5'/3'-ss events that were part of an alternative exon (Foxm1.A2, Mta1.A1, Uspl1.A3), the PSI was instead calculated with reference to the total reads supporting inclusion of that exon in order to assess independent regulation of alternative splice site usage. Only the read direction in which all reads unambiguously supported either inclusion or exclusion of an event was used, and the average if that applied to both. Junctions used for each event are provided in the file ScreenEvents_junctions.tab. Batch effects due to 96-well plate differences were moderated by subtracting a weighted plate median in which negative controls (siNT) were given 5x more weight than other samples. To derive variances, and because PSI values are not nearly normally distributed but roughly follow a beta distribution, a beta distribution was fit to each pair of replicate treatments, as well as to all negative controls from both replicates (siNT, untreated), using maximum-likelihood fitting as implemented in the fitdistr() function from the R package MASS {Venables & Ripley, Modern Applied Statistics with S (2002)}. Iterative optimization of shape parameters was initiated with settings x=PSI, shape1=1, shape2=1, method=”L-BFGS-B”, lower=0.01, and upper=mean number of reads supporting each PSI value. A modified Strictly Standardized Mean Difference (SSMD {Zhang, Genomics (2007)}) was then calculated based on the formula: SSMD = (μt – μc)/SQRT(vart + varc) where μt and μc are the means (corresponding to the PSI), and vart and varc the variances of the beta distributions fitted to the treatment replicates and negative controls, respectively. Events for which not all reads from at least one direction were informative were excluded from further analysis, as were events in individual treatments with less than 20 reads in one or both replicates.
Genome_build: NCBIm37/mm9
Supplementary_files_format_and_content: Processed files are either tab-delimited  tables (.tab) or FASTA files (.fa). KnockdownAnnotation.tab contains treatment annotations and well/plate positions. Junctions108_11-101_fwd.fa and Junctions108_11-101_rev.fa contain the custom junction upstream and downstram junction libraries, respectively, and ScreenEvents_junctions.tab contains the information which junctions were used to calculate PSI for each event. InclExclCounts.tab contains read pseudocounts (format: inclusion=exclusion) constructed from the PSI and read counts (both averged from fwd and rev junction counts, if applicable). PSI.SSMD.tab contains raw PSI of each replicate and final SSMD.

source_name: Neuroblastoma cells

growth_protocol: Mouse neuroblastoma (N2A) cells were grown in DMEM supplemented with 10% FBS, sodium pyruvate, MEM non-essential amino acids, and penicillin/streptomycin. All cell lines were maintained at 37°C with 5% CO2.

extract_protocol:
Forty-eight hours post-transfection, total RNA were purified from cultured cells using RNeasy Mini Kit (Qiagen), as per the manufacturer’s instructions.
For each sample, a multiplex RT-PCR assay was first applied to simultaneously amplify multi-exonic regions within 108 genes in a single reaction. The multiplex RT-PCR reaction was carried out in 96-well plates using the OneStep RT-PCR kit (Qiagen) as recommended by the manufacturer, with the following changes: reactions were performed in a volume of 20 uL with 2 uL of the purified total RNA as input, and a mixture of 50 pairs of primers was added to each reaction with a final concentration of 0.25 uM for each individual forward and reverse primer. Thermocycler settings were: 50°C for 30 minutes, 95°C for 15 minute, 30 cycles of 94°C for 40 seconds, 58°C for 1 minute (slow ramp rate), 72°C for 3 minutes, and a final extension step at 72°C for 10 minutes. Two sets of barcodes were incorporated into forward and reverse primers, respectively, after the universal adaptors and added to the amplicons in the second PCR reaction to allow demultiplexing all reads that were derived from a particular treatment. Primers sequences were: forward primer, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT (N denotes i5 barcode); reverse primer, CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT (N denotes i7 primer). The second PCR was performed using Phusion High-Fidelity DNA Polymerase (Thermo Scientific), as per the manufacturer’s instructions. For each 20 uL of reaction, 1 uL of the multiplex RT-PCR reaction products was used as templates. The thermal cycling conditions were as follows: 98°C for 30 seconds, 15 cycles of 98°C for 10 seconds, 65°C for 30 seconds, 72°C for 30 seconds, and a final extension step at 72°C for 5 minutes. The resulting libraries were pooled and sequenced.

treatment_protocol: N2A cells were seeded in 6-well plates (500,000 cells per well) and immediately transfected with the SMARTpool siRNAs at 25 nM final concentration using RNAiMax (Invitrogen), as recommended by the manufacturer.

value: Neuroblastoma

value: Srrm4+siSrrm3 knockdown (T024)


title: 4_TGACCA

description: Lane: 1 & 2


title: 1_ATCACG

description: Lane: 1 & 2


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Rbm17 knockdown (T022), replicate 2

description: Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: AGCTAGCT

value: Rbm17 knockdown (T022)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Srsf6 knockdown (T023), replicate 2

description: Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: AGCAGTTC

value: Srsf6 knockdown (T023)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Ncbp1 knockdown (T021), replicate 2

description: Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: GGATGGAT

value: Ncbp1 knockdown (T021)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Ippk knockdown (T020), replicate 2

description: Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: TTGGCCTT

value: Ippk knockdown (T020)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Qk knockdown (T018), replicate 2

description: Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: CTTGACCT

value: Qk knockdown (T018)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Fbxw11 knockdown (T019), replicate 2

description: Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: CAACGAAG

value: Fbxw11 knockdown (T019)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, control non-targeting knockdown (T016), replicate 2

description: Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: GTTCGTAG

value: control non-targeting knockdown (T016)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Ptbp1 knockdown (T017), replicate 2

description: Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: CTGACTCT

value: Ptbp1 knockdown (T017)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Fam133b knockdown (T015), replicate 2

description: Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: AGGATGGT

value: Fam133b knockdown (T015)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Fxr1 knockdown (T011), replicate 2

description: Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: CTAGCTTC

value: Fxr1 knockdown (T011)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Ep300 knockdown (T012), replicate 2

description: Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: ATGCGCAT

value: Ep300 knockdown (T012)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Strbp knockdown (T010), replicate 2

description: Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: CATCAGCA

value: Strbp knockdown (T010)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, CBP knockdown (T013), replicate 2

description: Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: ATCGAAGG

value: CBP knockdown (T013)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Gpatch8 knockdown (T007), replicate 2

description: Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: ATTACGCG

value: Gpatch8 knockdown (T007)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Srrm3 knockdown (T003), replicate 2

description: Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: ACACTCAG

value: Srrm3 knockdown (T003)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Srrm4+siSrrm3 knockdown (T024), replicate 1

description: Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: CAGTAGTC

value: Neuroblastoma


title: SPAR-Seq of multi-exon regions of selected genes in N2A, untreated (T001), replicate 2

description: Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: GTAGTCGT

value: untreated (T001)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Rnps1 knockdown (T008), replicate 2

description: Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: AGAGACAC

value: Rnps1 knockdown (T008)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Cdc5l knockdown (T009), replicate 2

description: Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: GTCAGAGA

value: Cdc5l knockdown (T009)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, hnRNP K knockdown (T006), replicate 2

description: Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: GGTTATGC

value: hnRNP K knockdown (T006)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Rbfox2 knockdown (T004), replicate 2

description: Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: GTACGATC

value: Rbfox2 knockdown (T004)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Rbm17 knockdown (T022), replicate 1

description: Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: CGATCCAA

value: Rbm17 knockdown (T022)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Srrm4 knockdown (T002), replicate 2

description: Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: ACTCCTGT

value: Srrm4 knockdown (T002)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Ptbp1 knockdown (T017), replicate 1

description: Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: TCCACTTG


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Qk knockdown (T018), replicate 1

description: Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: TATAGCGC

value: Qk knockdown (T018)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, control non-targeting knockdown (T016), replicate 1

description: Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GTGAAGTG

value: control non-targeting knockdown (T016)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Srsf6 knockdown (T023), replicate 1

description: Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: TCTCGACT

value: Srsf6 knockdown (T023)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Fam133b knockdown (T015), replicate 1

description: Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GACAGACA

value: Fam133b knockdown (T015)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Fbxw11 knockdown (T019), replicate 1

description: Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GACATGTC

value: Fbxw11 knockdown (T019)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Hira knockdown (T014), replicate 2

description: Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: TTATGGCG

value: Hira knockdown (T014)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Ippk knockdown (T020), replicate 1

description: Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GCAATACC

value: Ippk knockdown (T020)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, CBP knockdown (T013), replicate 1

description: Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GACTCTGA

value: CBP knockdown (T013)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Fxr1 knockdown (T011), replicate 1

description: Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: GCATCGAT

value: Fxr1 knockdown (T011)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Strbp knockdown (T010), replicate 1

description: Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: TCCTCTAG

value: Neuroblastoma

value: Strbp knockdown (T010)


title: lacZ_KD_Ctr_2

value: Oregon R

tag: tissue source

value: embryo

value: late embryonic state

value: lacZ control


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Hira knockdown (T014), replicate 1

description: Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: ATGCGCTA


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Cdc5l knockdown (T009), replicate 1

description: Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: GTTGGTAC

value: Cdc5l knockdown (T009)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, hnRNP K knockdown (T006), replicate 1

description: Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: ATCCTTGC

value: hnRNP K knockdown (T006)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Rnps1 knockdown (T008), replicate 1

description: Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: TCGAGTTG

value: Rnps1 knockdown (T008)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Elavl2 knockdown (T005), replicate 2

description: Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: AGCTGTAC

value: Elavl2 knockdown (T005)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Gpatch8 knockdown (T007), replicate 1

description: Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: ATTAGGCC

value: Gpatch8 knockdown (T007)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Ncbp1 knockdown (T021), replicate 1

description: Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: ACCACAAC

value: Ncbp1 knockdown (T021)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Elavl2 knockdown (T005), replicate 1

description: Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: TTGGTAGC


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Rbfox2 knockdown (T004), replicate 1

description: Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: TTGCAACG

value: Rbfox2 knockdown (T004)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Srrm3 knockdown (T003), replicate 1

description: Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: AACCATCG

value: Srrm3 knockdown (T003)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Ep300 knockdown (T012), replicate 1

description: Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: AGTGCTCA

value: Ep300 knockdown (T012)


title: AB5406

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

data_processing:
Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: 384 cells

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
Mice were perfused by injection of cold PBS via the right ventricle prior to lung dissection. Lung tissue was dissected from mice and half tissues were homogenized using lung dissociation kit (Miltenyi Biotec), while the second half of the lung was dissociated with Eastase. Single cell suspension was stained with Flow cytometry antibodies.
Murine thymi were treated with enzymes cocktail (Collagenase, Dispase and Dnase) at 37C. Cells were separated by Percoll gradient density centrifugation, filtered and stained with Flow cytometry antibodies.
Murine spleens  were treated with acccutase, filtered and stained with Flow cytometry antibodies.
Murine livers  were treated with liberase, filtered and stained with Flow cytometry antibodies.
Murine tumors  were treated with colagenase, filtered and stained with Flow cytometry antibodies.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation

treatment_protocol: Mice were sacrified by CO2

tag: organ

value: tumor

tag: selection marker

tag: treatment

tag: dissociation protocol

value: Colagenase

tag: replicate id

tag: mouse age


title: AB5408

value: lung

value: Milteny + Elastase


title: AB5403


title: AB5360

value: in vitro

value: IL3 + IL33 + GM-CSF


title: AB5359


title: AB5405


title: AB5357


title: AB5356

value: IL3 + IL33 + GM-CSF + coculture with basophils


title: AB5353


title: AB5355


title: AB5407


title: AB5358


title: AB5351

value: IL3 + coculture with basophils


title: AB5297

value: liver

value: Liberase


title: AB5350


title: AB5296


title: AB5293

value: spleen

value: Accutase


title: AB5294


title: SPAR-Seq of multi-exon regions of selected genes in N2A, Srrm4 knockdown (T002), replicate 1

description: Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: GAGAGACT

value: Neuroblastoma

tag: genotype/variation

value: Srrm4 knockdown (T002)


title: SPAR-Seq of multi-exon regions of selected genes in N2A, untreated (T001), replicate 1

description: Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: TATTCCGC

value: untreated (T001)


title: AB5295


title: AB5292


title: AB4887


title: AB5404


title: AB4886


title: AB4884


title: AB5354


title: AB4857


title: AB4855

value: M-CSF+IL3+IL33+GM-CSF + coculture with basophils


title: AB4856


title: AB5352


title: AB4883


title: AB4882


title: AB4854


title: AB4853


title: AB4852


title: AB4849

value: M-CSF+IL3 + coculture with basophils


title: AB4850


title: AB4851


title: AB4847


title: AB4846


title: AB4845


title: AB4302


title: AB4300

value: IL3+M-CSF + coculture with basophils


title: AB4301


title: AB4296

value: M-CSF


title: AB4885


title: AB4299


title: AB4298


title: AB4295


title: AB4294


title: AB4293


title: AB4292


title: AB4291


title: AB4848


title: AB4267

value: C57BL/6-ST2 KO

value: lung


title: AB4269

value: Milteny + Elastase


title: AB4264


title: AB4268


title: AB4266


title: AB4270


title: AB4844

value: in vitro


title: AB4265


title: AB3776

value: IL3 + IL33 + GM-CSF


title: AB3774

value: IL3 + GM-CSF


title: AB3775


title: AB3773


title: AB3772

value: IL3 + IL33


title: AB3769


title: AB3770


title: AB3441

value: IgG injection


title: AB3442


title: AB3440


title: AB4297


title: AB3435

value: MAR1 injection


title: AB3436


title: AB3438


title: AB3439


title: AB3048

value: blood


title: AB3037


title: AB3036


title: AB3032


title: AB3437


title: AB2765


title: AB2758


title: AB3768


title: AB2757


title: AB2755


title: AB3033


title: AB2754


title: AB2756


title: AB2600


title: AB2599


title: AB2602


title: AB2766


title: AB3771


title: AB2299


title: AB2601


title: AB2204


title: AB2203


title: AB2202


title: AB3049


title: AB2201


title: AB2198


title: AB2196


title: AB2191


title: AB2195


title: AB2190


title: AB2189


title: AB2192


title: AB2007


title: AB2006


title: AB2005


title: AB2000


title: AB2003


title: AB2002


title: AB2008


title: AB1911


title: AB2197


title: AB1910


title: AB1999


title: AB2001


title: AB1997


title: AB1912


title: AB1909


title: AB1908


title: AB1858


title: AB1859


title: AB1907


title: AB1906


title: AB2004


title: AB2297


title: AB1998


title: AB1857


title: AB1854


title: AB1856


title: AB1855


title: AB1830


title: AB1829


title: AB1852


title: AB1538


title: AB1853


title: AB1488


title: AB1537


title: AB1491


title: AB1489


title: AB1486


title: AB1534


title: AB1535


title: AB1490


title: AB1484


title: AB1536


title: AB1487


title: AB1439


title: AB1436


title: AB1434


title: AB1435


title: AB1433


title: AB1412


title: AB1410


title: AB1411


title: AB1250


title: AB1248


title: AB1249


title: AB1251


title: AB1409


title: AB1186


title: AB1026

value: Milteny


title: AB1185


title: AB898

value: Liberase


title: AB963

source_name: 192 cells


title: AB897

value: Elastase


title: AB895


title: AB1025


title: AB1183


title: AB896


title: AB894


title: AB1485


title: mutant rep3

city: Dallas

first: Uthra

last: Balaji

state: Texas

address: 3434 Live Oak St

department: Biostatistics Core

institute: Baylor Scott & White Research Institute

data_processing:
bcl2fastq was used for basecalling
Sequenced reads were trimmed for adapters and mapped to GRCm38 genome using hisat2. Gene-level counts were obtained from aligned bam files using featureCounts.
DESeq2 was used to perform normalization and differential expression analysis
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text file with DESeq2 normalized counts for all samples

source_name: mutant_Th17 cells

extract_protocol: RNA libraries were prepared using TueSeq RNA library kit according to manufacturer's protocol

tag: cell type background

value: ROR-gt-/- mouse-derived Th17 cells

value: reconstituted with SUMOylation-defective ROR-gt


title: AB893

tag: strain


title: mutant rep4


title: mutant rep1


title: mutant rep2


title: WT rep4

source_name: WT_Th17 cells

value: reconstituted with WT-ROR-gt


title: WT rep3


title: AB1247


title: AB1245


title: AB1246


title: WT rep1


title: Srrm4 expression reporter, sorted cells with 2% lowest EGFP, replicate3 (T18)

description:
Counts_Srrm4.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_47

library_source: genomic

data_processing:
Library strategy: CRISPR screen
Base calls were processed with bcl2fastq2 (Illumina) version 2.18.
sgRNA sequences were extracted from raw reads based on matches to the tracrRNA and U6 promoter using custom Perl scripts, and perfect matches to expected sgRNAs were tallied.
To score sgRNAs that impact reporter fluorescence, raw counts from sorted and unsorted populations were analyzed with the count module of MAGeCK version 0.5.6 (Li et al., 2014) with default settings where 1,000 non-targeting control sgRNAs present in the Brie library were specified with parameter –control-sgrna.
Genome_build: Brie mouse sgRNA library (Addgene #73633)
Supplementary_files_format_and_content: Tab delimited files with counts per sgRNA sequence in each sample; MAGeCK.scores.xlsx is a speadsheet containing the results of MAGeCK analyses, i.e. the enrichment of genes in the sorted cell polulations.

molecule: genomic DNA

growth_protocol: Mouse neuroblastoma (N2A) and 293T cells were grown in DMEM (high glucose; Sigma-Aldrich) supplemented with 10% FBS, sodium pyruvate, non-essential amino acids, and penicillin/streptomycin, at 37°C with 5% CO2.

extract_protocol:
cell engineering protocol: Srrm4 was endogenously EGFP-tagged at its N-terminus in N2A cells using CRISPR-directed targeted genomic insertion, as described previously (Mali et al., 2013; Ran et al., 2013). In brief, N2A cells were co-transfected with pX459 plasmid expressing Cas9 and an sgRNA targeting Srrm4 near the translation initiation site, as well as with a repair template, using Lipofectamine 2000 (Invitrogen). The repair template containing the EGFP sequence, flanked by 800-900 bp homology arms corresponding to the up- and down-stream sequences of the Srrm4 translation initiation site, was cloned into a pBluescript vector (with the hPGK driven Blasticidin resistance gene inserted). The homology arms were flanked with DNA sequences corresponding to the sgRNA target sequence so that the vector would be linearized in cells. The PAM sequence of the sgRNA sequence upstream of the ATG was mutated in the repair template so as not to be targeted by Cas9. For generating the knock-in lines the following sgRNA target sequence was used: 5´-GTTTCACGCGGACAGCGCCC(CGG)-3´.  Cells were selected for 3 days with Puromycin (2.5 μg/ml) and Blasticidin S (10 μg/ml) for pX459 and pBluescript transfection, respectively, and cultured for seven more days before single cell sorting for EGFP+ cells with a BD Influx FACS sorter (BD Biosciences). The insertion sequence in each sorted clone was confirmed at the genomic level using Sanger sequencing, and clones were tested for EGFP-Srrm4 expression using fluorescent microscopy, western blotting, and 3´ RACE PCR (Scotto–Lavino et al., 2007).
Genomic DNA was extracted from the cell pellets of unsorted samples using the QIAamp Blood Maxi Kit (Qiagen) while gDNA from sorted populations was purified with the Midi Kit as per the manufacturer’s recommendations. Genomic DNA was precipitated using ethanol and sodium chloride, and resuspended in Buffer EB (10 mM Tris-HCl, pH 7.5).
gRNA inserts were amplified via PCR using primers harboring Illumina TruSeq adapters with i5 and i7 barcodes, following a two-step PCR approach.   In the first step, a total of 50 μg of gDNA was subjected to PCR (25 cycles, temperature of annealing (Ta) = 65°C) for enrichment of sgRNA cassettes using NEBNext Ultra II Q5 polymerase and staggered primers annealing to the end of the U6 promoter and the beginning of the tracrRNA. For the 2% highest or lowest expressing sorted cell populations 10 μg of gDNA was used. Subsequently, the individual PCR reactions were pooled and 50 μl of the first step PCR product was loaded onto a 2% agarose gel (Cat # 1613101, BioRad) and run for 1.5 hour at 100V. PCR products of 200-230 bp were selected and the excised gel fragments were purified using the Qiagen MinElute Gel Extraction kit (Cat # 28604, Qiagen). 1/6th of the purified PCR products were subjected to 2nd step PCR (10 cycles, Ta= 62°C) using NEBNext Ultra II Q5 polymerase and primers harboring Illumina TruSeq adapters with i5 and i7 indices to generate barcoded sequencing libraries ready for Illumina sequencing (Table S8). The PCR amplicons were loaded onto a 2% agarose gel (Cat # 1613101, BioRad) and run for 1 hour at 100V. The libraries were size-selected at 270 bp and 300 bp, and the excised gel fragments were purified using Qiagen MinElute Gel Extraction kit (Cat # 28604, Qiagen).  The purified libraries were analyzed for quality control, pooling and sequencing. Size confirmation analysis for each sample was performed on an Agilent Bioanalyzer dsDNA High Sensitivity chip. Amplicons were quantified using Kapa Universal qPCR Master Mix (Cat # KK4923, Roche) and Qubit dsDNA HS Assay Kit (Cat # Q32854, Thermo Fisher Scientific) and pooled at varied ratios by molarity after size-adjustment. To mitigate the effects of index hopping, pooling was performed just prior to sequencing. The final pool was run on an Agilent Bioanalyzer dsDNA High Sensitivity chip and quantified using NEBNext Library Quant Kit for Illumina (Cat # E7630L, NEB).

treatment_protocol: 80 million N2a cells with endogenously tagged EGFP-Srrm4 were infected with the lentiviral Brie library (78,637 gRNAs) at an MOI ~0.3, in the presence of 8 μg/ml polybrene, such that every sgRNA was represented in approximately 300 cells. 24 hours after infection, the medium was replaced with fresh medium containing Puromycin (2.5 μg/ml) and cells were incubated for an additional 72 hours. After selection cells were split such that each sgRNA would be represented by an average of 300 cells in the population (i.e. 24 million cells) and passaged every three days. 24 million cells were collected prior to sorting as a reference point and the 2% of the cells (300,000-500,000 cells) with the highest or lowest EGFP expression were sorted.

tag: cell line

value: Neuroblastoma


title: Srrm4 expression reporter, sorted cells with 2% lowest EGFP, replicate2 (T16)

description:
Counts_Srrm4.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_43


title: Srrm4 expression reporter, sorted cells with 2% lowest EGFP, replicate1 (T16)

description:
Counts_Srrm4.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_39


title: mouse_atac_basket_2

city: New York

first: Xiao

last: Xu

address: 1230 York Ave

department: Laboratory of Molecular Biology

institute: The Rockefeller University

data_processing:
Adapter sequences were trimmed and reads were filtered depending on quality using Trim Galore! (trim_galore --stringency 3 --fastqc --paired *_R1_2.fastq.gz *_R2_2.fastq.gz).
Reads that passed the filter were aligned using Bowtie2 (Langmead and Salzberg, 2012) with parameters “-X 2000 --no-mixed --no-discordant” to the Mus musculus reference genome (mm10).
Duplicate reads were removed using SAMtools (Li et al., 2009).
Reads were normalized to 1x depth (reads per genome coverage, RPGC) and input using deepTools (Ramirez et al., 2016) bamCompare module, ignoring chrX, chrY, chrM and filtering reads for minimum mapping quality of 30.
For data visualization, tdf files were generated using igvtools.
Unique fragments under 100 nt were selected as they could not contain a nucleosome. These fragments were used to call peaks with MACS2 with parameters “--nomodel -q 0.01 --call-summits --keep-dup all”. The summits for each peak from the replicates were extended to 500bp using bedtools slop. The peaks were filtered to remove chrY and chrM peaks and peaks that overlap with the mm10 blacklist from ENCODE (Consortium, 2012; Kundaje, 2013).
Genome_build: mm10
Supplementary_files_format_and_content: tdf format for visualization in IGV
Supplementary_files_format_and_content: txt format of called peaks

source_name: ATAC-seq using nuclei from specific cell types

growth_protocol: All procedures involving mice were approved by The Rockefeller University Institutional Animal Care and Use Committee (IACUC) and were in accordance with the National Institutes of Health guidelines. Mice were housed in a specific-pathogen free facility, in groups of four to five per cage under a 12-h light-dark cycle with food and water ad libitum. Animals were sacrificed between 2-4 months of age.

extract_protocol:
Cerebellum was dissected and nuclei were isolated. ATAC-seq libraries were prepared as described previously (Buenrostro et al., 2013; 2015) with the following modifications: nuclei were resuspended in ice-cold lysis buffer, omitting incubation step on ice and centrifuged. Transposition reaction was performed for 30 min at 37°C using Tn5 transposase from Nextera. DNA fragments were purified and size selected using AMPure XP beads to yield 100-700bp fragments.
Libraries were generated using the Nextera DNA Library Preparation Kit. ATAC-seq libraries were sequenced on Illumina NextSeq 500 to obtain 75bp paired-ended reads.

tag: brain region

value: cerebellum


title: mouse_atac_granule_2


title: mouse_atac_granule_1


title: mouse_atac_basket_1


title: Srrm4 expression reporter, sorted cells with 2% highest EGFP, replicate2 (T16)

description:
Counts_Srrm4.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_44

tag: cell type


title: Mef2d splicing reporter, sorted cells with 30% highest EGFP/mCherry, replicate 5 (T18)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_74

extract_protocol:
cell engineering protocol: A Flp-in cassetted was integrated into the Rosa26 locus in N2a cells by first creating cells with an FRT site in that locus, followed by integration of a Flp-In construct from pcDNA5/FRT/TRE modified to include an rtTA3-compatible Tet Response Element (TRE). A bichromatic microexon splicing reporter based on a microexon from either murine Shank2 (ENSMUSE00001006087) or Mef2d (ENSMUSE00000673645) was then constructed by amplifying the microexons (extended by one nucleotide to cause a frame shift), flanking introns, upstream constitutive exon, and 20-50 nt of the downstream constitutive exon 5' of a fluorescence cassette consisting of EGFP and mCherry in different reading frames. This construct was cloned into a customized pcDNA5-based Gateway(R) compatible vector (Life Technologies) that contained 8x TET response elements followed by a miniCMV promoter, Kozak sequence, 3x Flag-tag, and attR sites, followed by integration in a clonal N2A Flp-In cell line.
Genomic DNA was extracted from the cell pellets of unsorted samples using the QIAamp Blood Maxi Kit (Qiagen) while gDNA from sorted populations was purified with the Midi Kit as per the manufacturer’s recommendations. Genomic DNA was precipitated using ethanol and sodium chloride, and resuspended in Buffer EB (10 mM Tris-HCl, pH 7.5).
gRNA inserts were amplified via PCR using primers harboring Illumina TruSeq adapters with i5 and i7 barcodes, following a two-step PCR approach.   In the first step, a total of 50 μg of gDNA was subjected to PCR (25 cycles, temperature of annealing (Ta) = 65°C) for enrichment of sgRNA cassettes using NEBNext Ultra II Q5 polymerase and staggered primers annealing to the end of the U6 promoter and the beginning of the tracrRNA. For the 2% highest or lowest expressing sorted cell populations 10 μg of gDNA was used. Subsequently, the individual PCR reactions were pooled and 50 μl of the first step PCR product was loaded onto a 2% agarose gel (Cat # 1613101, BioRad) and run for 1.5 hour at 100V. PCR products of 200-230 bp were selected and the excised gel fragments were purified using the Qiagen MinElute Gel Extraction kit (Cat # 28604, Qiagen). 1/6th of the purified PCR products were subjected to 2nd step PCR (10 cycles, Ta= 62°C) using NEBNext Ultra II Q5 polymerase and primers harboring Illumina TruSeq adapters with i5 and i7 indices to generate barcoded sequencing libraries ready for Illumina sequencing (Table S8). The PCR amplicons were loaded onto a 2% agarose gel (Cat # 1613101, BioRad) and run for 1 hour at 100V. The libraries were size-selected at 270 bp and 300 bp, and the excised gel fragments were purified using Qiagen MinElute Gel Extraction kit (Cat # 28604, Qiagen).  The purified libraries were analyzed for quality control, pooling and sequencing. Size confirmation analysis for each sample was performed on an Agilent Bioanalyzer dsDNA High Sensitivity chip. Amplicons were quantified using Kapa Universal qPCR Master Mix (Cat # KK4923, Roche) and Qubit dsDNA HS Assay Kit (Cat # Q32854, Thermo Fisher Scientific) and pooled at varied ratios by molarity after size-adjustment. To mitigate the effects of index hopping, pooling was performed just prior to sequencing. The final pool was run on an Agilent Bioanalyzer dsDNA High Sensitivity chip and quantified using NEBNext Library Quant Kit for Illumina (Cat # E7630L, NEB).

treatment_protocol: 80 million N2A Flp-In cells expressing bichromatic splicing reporters were infected with the lentiviral Brie library (78,637 gRNAs) at an MOI ~0.3, in the presence of 8 μg/ml polybrene, such that every sgRNA was represented in approximately 300 cells. 24 hours after infection, the medium was replaced with fresh medium containing Puromycin (2.5 μg/ml) and cells were incubated for an additional 72 hours. After selection cells were split such that each sgRNA would be represented by an average of 300 cells in the population (i.e. 24 million cells) and passaged every three days.   For cell sorting, the 24 million cells were seeded and the next day 1 μg/ml doxycycline was added to induce bichromatic reporter expression. 24 hours later the cells were harvested and resuspended in sorting buffer (Hanks Balanced Salt Solution, 25 mM HEPES pH 7.0, 1 mM EDTA, 1% Albumin) at a concentration of 5 million cells per ml. The cells were passed through a nylon mesh with a pore size of 40 μm to eliminate large aggregates. Filtered cells were sorted based on the relative EGFP:mCherry expression FACS. For each replicate of the lowest/highest 2% sorting scheme, 300,000-500,000 cells were collected. For the 30% sorting scheme, the same procedure was followed except that the 30% of cells with the highest or lowest EGFP:mCherry ratio were sorted. In addition, 24 million cells were also collected prior to sorting as a reference point for comparing enrichment in the sorted populations.


title: WT rep2


title: Srrm4 expression reporter, unsorted cells after infection (T0)

description:
Counts_Srrm4.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_36

extract_protocol:
cell engineering protocol: Srrm4 was endogenously EGFP-tagged at its N-terminus in N2A cells using CRISPR-directed targeted genomic insertion, as described previously (Mali et al., 2013; Ran et al., 2013). In brief, N2A cells were co-transfected with pX459 plasmid expressing Cas9 and an sgRNA targeting Srrm4 near the translation initiation site, as well as with a repair template, using Lipofectamine 2000 (Invitrogen). The repair template containing the EGFP sequence, flanked by 800-900 bp homology arms corresponding to the up- and down-stream sequences of the Srrm4 translation initiation site, was cloned into a pBluescript vector (with the hPGK driven Blasticidin resistance gene inserted). The homology arms were flanked with DNA sequences corresponding to the sgRNA target sequence so that the vector would be linearized in cells. The PAM sequence of the sgRNA sequence cell engineering protocol: upstream of the ATG was mutated in the repair template so as not to be targeted by Cas9. For generating the knock-in lines the following sgRNA target sequence was used: 5´-GTTTCACGCGGACAGCGCCC(CGG)-3´.  Cells were selected for 3 days with Puromycin (2.5 μg/ml) and Blasticidin S (10 μg/ml) for pX459 and pBluescript transfection, respectively, and cultured for seven more days before single cell sorting for EGFP+ cells with a BD Influx FACS sorter (BD Biosciences). The insertion sequence in each sorted clone was confirmed at the genomic level using Sanger sequencing, and clones were tested for EGFP-Srrm4 expression using fluorescent microscopy, western blotting, and 3´ RACE PCR (Scotto–Lavino et al., 2007).
Genomic DNA was extracted from the cell pellets of unsorted samples using the QIAamp Blood Maxi Kit (Qiagen) while gDNA from sorted populations was purified with the Midi Kit as per the manufacturer’s recommendations. Genomic DNA was precipitated using ethanol and sodium chloride, and resuspended in Buffer EB (10 mM Tris-HCl, pH 7.5).
gRNA inserts were amplified via PCR using primers harboring Illumina TruSeq adapters with i5 and i7 barcodes, following a two-step PCR approach.   In the first step, a total of 50 μg of gDNA was subjected to PCR (25 cycles, temperature of annealing (Ta) = 65°C) for enrichment of sgRNA cassettes using NEBNext Ultra II Q5 polymerase and staggered primers annealing to the end of the U6 promoter and the beginning of the tracrRNA. For the 2% highest or lowest expressing sorted cell populations 10 μg of gDNA was used. Subsequently, the individual PCR reactions were pooled and 50 μl of the first step PCR product was loaded onto a 2% agarose gel (Cat # 1613101, BioRad) and run for 1.5 hour at 100V. PCR products of 200-230 bp were selected and the excised gel fragments were purified using the Qiagen MinElute Gel Extraction kit (Cat # 28604, Qiagen). 1/6th of the purified PCR products were subjected to 2nd step PCR (10 cycles, Ta= 62°C) using NEBNext Ultra II Q5 polymerase and primers harboring Illumina TruSeq adapters with i5 and i7 indices to generate barcoded sequencing libraries ready for Illumina sequencing (Table S8). The PCR amplicons were loaded onto a 2% agarose gel (Cat # 1613101, BioRad) and run for 1 hour at 100V. The libraries were size-selected at 270 bp and 300 bp, and the excised gel fragments were purified using Qiagen MinElute Gel Extraction kit (Cat # 28604, Qiagen).  The purified libraries were analyzed for quality control, pooling and sequencing. Size confirmation analysis for each sample was performed on an Agilent Bioanalyzer dsDNA High Sensitivity chip. Amplicons were quantified using Kapa Universal qPCR Master Mix (Cat # KK4923, Roche) and Qubit dsDNA HS Assay Kit (Cat # Q32854, Thermo Fisher Scientific) and pooled at varied ratios by molarity after size-adjustment. To mitigate the effects of index hopping, pooling was performed just prior to sequencing. The final pool was run on an Agilent Bioanalyzer dsDNA High Sensitivity chip and quantified using NEBNext Library Quant Kit for Illumina (Cat # E7630L, NEB).


title: Srrm4 expression reporter, sorted cells with 2% highest EGFP, replicate3 (T18)

description:
Counts_Srrm4.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_48


title: Srrm4 expression reporter, unsorted cells, replicate 1 (T16)

description:
Counts_Srrm4.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_37


title: Mef2d splicing reporter, sorted cells with 30% lowest EGFP/mCherry, replicate 5 (T18)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_75


title: Srrm4 expression reporter, unsorted cells, replicate 3 (T18)

description:
Counts_Srrm4.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_45


title: Mef2d splicing reporter, sorted cells with 30% highest EGFP/mCherry, replicate 4 (T18)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_72


title: Srrm4 expression reporter, unsorted cells, replicate 2 (T16)

description:
Counts_Srrm4.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_41


title: Mef2d splicing reporter, sorted cells with 30% highest EGFP/mCherry, replicate 2 (T11)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_57


title: Mef2d splicing reporter, sorted cells with 30% highest EGFP/mCherry, replicate 3 (T16)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_70


title: Mef2d splicing reporter, sorted cells with 30% highest EGFP/mCherry, replicate 1 (T9)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_55


title: Mef2d splicing reporter, sorted cells with 30% lowest EGFP/mCherry, replicate 2 (T11)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_58


title: Mef2d splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 1 (T9)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_54


title: Mef2d splicing reporter, sorted cells with 2% highest EGFP/mCherry, replicate 4 (T16)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_68


title: Mef2d splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 2 (T16)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_62


title: Mef2d splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 3 (T16)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_65


title: Srrm4 expression reporter, sorted cells with 2% highest EGFP, replicate1 (T16)

description:
Counts_Srrm4.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_40


title: Mef2d splicing reporter, sorted cells with 2% highest EGFP/mCherry, replicate 3 (T16)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_64


title: Mef2d splicing reporter, sorted cells with 30% lowest EGFP/mCherry, replicate 4 (T18)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_73


title: Mef2d splicing reporter, sorted cells with 2% highest EGFP/mCherry, replicate 2 (T16)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_61


title: Mef2d splicing reporter, sorted cells with 30% lowest EGFP/mCherry, replicate 3 (T16)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_71


title: Mef2d splicing reporter, sorted cells with 30% lowest EGFP/mCherry, replicate 1 (T9)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_56


title: Mef2d splicing reporter, unsorted cells, replicate 1 (T9)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_51


title: Mef2d splicing reporter, unsorted cells after infection (T0)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_49


title: Mef2d splicing reporter, sorted cells with 2% highest EGFP/mCherry, replicate 1 (T9)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_53


title: Mef2d splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 4 (T16)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_69


title: Mef2d splicing reporter, unsorted cells, replicate 3 (T16)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_66


title: Mef2d splicing reporter, unsorted cells, replicate 2 (T16)

description:
Counts_Mef2d.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_59


title: Shank2 splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 4 (T22)

description:
Counts_Shank2.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_30


title: Shank2 splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 5 (T24)

description:
Counts_Shank2.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_34


title: Shank2 splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 2 (T17)

description:
Counts_Shank2.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_15


title: Shank2 splicing reporter, sorted cells with 2% highest EGFP/mCherry, replicate 5 (T24)

description:
Counts_Shank2.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_33


title: Shank2 splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 3 (T9)

description:
Counts_Shank2.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_19


title: Shank2 splicing reporter, sorted cells with 2% highest EGFP/mCherry, replicate 3 (T9)

description:
Counts_Shank2.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_17


title: Shank2 splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 1 (T15)

description:
Counts_Shank2.tab
MAGeCK.scores.xlsx
sample name in processed data file: BB_11