title: Homozygous atx1/atx3/atx4 Triple Mutant 1 (TM1) rep4

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM1 FPKM
FPKMafterfilter
T1A6R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 1 (TM1) rep8

status: Public on Jul 12 2019

type: SRA

city: Lakewood

first: Will

middle: E

last: Hinckley

state: CA

address: 4440 Gondar Ave

department: Biology

country: USA

institute: CSULB

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM1 FPKM
FPKMafterfilter
T1B6R1

library_source: transcriptomic

data_processing:
Rsubread aligned reads to the TAIR10 Genome
Rsubread converted aligned reads to count data
Noiseq normalized count data to read length to generate an FPKM dataset
Noiseq normalized to library size
HTSfilter removed genes with consistently low expression (zero at every time-point)
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKMafterfilter contains the FPKM values for every detectable transcipt in each of 36 libraries. The first part of the library name is the sample ,(W=WT, T1=TM1, T2=TM2), The letter refers to the replicate (A,B, or C), and the number at the end refers to the time-point (0 ,2, 4, or 6). If you average WA0, WB0, and WC0 you will have the average expression value for a given transcript in WT tissue at timepoint zero.
Supplementary_files_format_and_content: The other three files contain the averaged values of the 3 replicates for each detectable transcript. The 4 columns are the 4 time-points, in order.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: 6th true leaf

growth_protocol: All plants were grown in Sunshine® Mix #1 Fafard®-1P RSi (Sungro Horticulture). The soil was treated with Gnatrol WDG (Valent Professional Products) (0.3 g/500 ml H2O) to inhibit the growth of fungus gnat larvae, and plants were sub-irrigated with Gro-Power 4-8-2 (Gro-Power, Inc.) (10 ml per gallon). Plants were grown at 24°C in Percival AR66L2X growth chambers under a 20:4 light:dark diurnal cycle with a light intensity of 26-28 umoles photons m-2 sec-1. The low light intensity prevents light stress in older leaves, which was evident as anthocyanin accumulation at higher light intensities. To compensate for the reduced light intensity, the day length was extended. The 6th leaf to emerge was marked by tying threads around the petioles soon after emergence from the meristem. Plants were rotated daily and randomized in the chamber to prevent chamber position affects.

extract_protocol:
(n=54 per genotype) WT, atx Triple Mutant 1 (TM1), and atx Triple Mutant 2 (TM2) were grown simultaneously. Bolting (1 cm inflorescence) was measured and plants that bolted at the peak of TM bolting (days 24 and 25) were recorded and added to a list. At each time-point, 10 TM1 and 10 TM2 plants were randomly selected from this list and harvested. This strategy was used to ensure that harvested TM plants were developmentally similar. 10 random vegetative WT plants (same age) were selected for harvesting at the each time-point. Harvesting began at the peak of triple mutant bolting and continued three more times in two day increments. Leaf 6 was harvested (N=10 per line, per time point), ground, and homogenized in liquid nitrogen via mortar and pestle, and stored at -80C. The ground powder was divided into three for the production of three RNA-seq libraries (A-C) for each genotype.
BrAD-seq, (Townsley et. al.) https://doi.org/10.3389/fpls.2015.00366

treatment_protocol: no treatments

tag: development

value: bolting at T0, leaf senescence detected via separate phenotype analysis 2 days after T6


title: Homozygous atx1/atx3/atx4 Triple Mutant 1 (TM1) rep5

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM1 FPKM
FPKMafterfilter
T1B0R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 1 (TM1) rep1

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM1 FPKM
FPKMafterfilter
T1A0R1


title: Wildtype Columbia-0 Ecotype rep7

description:
Wildtype Columbia Type 0
190627 WT FPKM
FPKMafterfilter
WB4R1

value: vegetative throughout timecourse


title: Wildtype Columbia-0 Ecotype rep6

description:
Wildtype Columbia Type 0
190627 WT FPKM
FPKMafterfilter
WB2R1


title: Wildtype Columbia-0 Ecotype rep10

description:
Wildtype Columbia Type 0
190627 WT FPKM
FPKMafterfilter
WC2R1


title: Wildtype Columbia-0 Ecotype rep8

description:
Wildtype Columbia Type 0
190627 WT FPKM
FPKMafterfilter
WB6R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 1 (TM1) rep9

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM1 FPKM
FPKMafterfilter
T1C0R1


title: hac1-2 (SALK_136314)-RNA-seq rep3

description:
Delayed leaf senescence phenotype
FPKMafterfilter.csv (no zeros)
mycounts.csv (All genes, even if not expressed)

data_processing:
RNA-seq raw data reads were aligned to the Arabidopsis TAIR 10 genome using Rsubread
They were then subjected to quality control of count data and differential expression using NOISeq
The FPKM values were normalized using Tmisc
HTSFilter removed genes with low expression levels
A 2-fold cutooff for RNA-seq was used to determine DEGs
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM associated with an AT number. Replicates are clustered together. Values are organized under sample names.

source_name: full leaves

growth_protocol: Arabidopsis thaliana Col-0 ecotype plants were grow in Sunshine® Mix #1 Fafard®-1P RSi (Sungro Horticulture). The soil was treated with Gnatrol WDG (Valent Professional Products) (0.3 g/500 ml H2O) to inhibit the growth of fungus gnat larvae, and plants were sub-irrigated with Gro-Power 4-8-2 (Gro-Power, Inc.) (10 ml per gallon). Plants were grown in Percival AR66L2X growth chambers under a 20:4 light:dark diurnal cycle with a light intensity of 28 umoles photons m-2 sec-1. The low light intensity prevents light stress in older leaves, which was evident as anthocyanin accumulation at higher light intensities. To compensate for the reduced light intensity, the day length was extended. Leaves were marked by tying threads around the petioles soon after emergence from the meristem.

extract_protocol:
described by sample types below
RNA-seq: The breath adapter directional sequencing (BrAD-seq) method (Townsley et al., 2015) https://doi.org/10.3389/fpls.2015.00366

tag: developmental stage

value: non-senescent leaves

tag: leaf number/age

value: leaves 12-14, 49 DAS

tag: genetic background


title: hac1-2 (SALK_136314)-RNA-seq rep1


title: hac1-1 (SALK_080380)-RNA-seq rep3


title: Homozygous atx1/atx3/atx4 Triple Mutant 1 (TM1) rep6

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM1 FPKM
FPKMafterfilter
T1B2R1


title: hac1-1 (SALK_080380)-RNA-seq rep2


title: Wildtype Columbia-0 Ecotype rep3

description:
Wildtype Columbia Type 0
190627 WT FPKM
FPKMafterfilter
WA4R1


title: Wildtype Columbia-0 Ecotype rep1

description:
Wildtype Columbia Type 0
190627 WT FPKM
FPKMafterfilter
WA0R1


title: Wildtype Columbia-0 Ecotype rep2

description:
Wildtype Columbia Type 0
190627 WT FPKM
FPKMafterfilter
WA2R1


title: WT (Col-0) - RNA-seq rep3

description:
WT leaves were undergoing leaf senescence by Day 49
FPKMafterfilter.csv (no zeros)
mycounts.csv (All genes, even if not expressed)

value: senescent leaves


title: Wildtype Columbia-0 Ecotype rep9

description:
Wildtype Columbia Type 0
190627 WT FPKM
FPKMafterfilter
WC0R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 1 (TM1) rep2

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM1 FPKM
FPKMafterfilter
T1A2R1


title: WT (Col-0) - RNA-seq rep1


title: Wildtype Columbia-0 Ecotype rep5

description:
Wildtype Columbia Type 0
190627 WT FPKM
FPKMafterfilter
WB0R1


title: hac1-2 (SALK_136314)-RNA-seq rep2


title: Wildtype Columbia-0 Ecotype rep12

description:
Wildtype Columbia Type 0
190627 WT FPKM
FPKMafterfilter
WC6R1


title: WT (Col-0) - RNA-seq rep2


title: hac1-1 (SALK_080380)-RNA-seq rep1


title: Wild-type + PLX5622 Hip 2

city: Irvine

first: Kim

last: Green

address: 3208 Biological Sciences 3

department: Neurobiology and Behavior

institute: University of California, Irvine

data_processing:
Illumina HiSeq4000 was used to produce 50bp single-end reads.
Sequenced reads mapped to mm10 whole genome using STAR aligner.
featureCounts were calculated using function of the Rsubread package in R.
After filtering out low-count genes, count distributions were scaled using the calcNormFactors function of the edgeR package.
plotMDS function of the limma package in R was used to perform principal component analysis. Reads Per Kilobase of exon per Megabase of library size (RPKM)  were prepared and fitted to linear models using the voom and lmfit functions.
Genome_build: mm10
Supplementary_files_format_and_content: Excel Workbook file includes RPKM values for all Samples.

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Brains were removed, microdissected into cortex, hippocampus, and thalamus/striatum, and flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: treatment

tag: genotype

value: Wild-Type

tag: tissue

value: Brain

tag: tissue region

value: Hippocampus


title: Wild-type + PLX5622 Hip 4


title: Wild-type Thal 4

source_name: Thalamus

value: Vehicle

value: Thalamus


title: Wild-type + PLX5622 Hip 3


title: Wild-type + PLX5622 Cortex 1

source_name: Cortex

value: Cortex


title: Wild-type + PLX5622 Cortex 4


title: Wild-type Hip 4


title: Wild-type + PLX5622 Hip 1


title: Wild-type + PLX5622 Thal 4


title: Wild-type + PLX5622 Thal 3


title: Wild-type + PLX5622 Cortex 2


title: Wild-type + PLX5622 Thal 1


title: Wild-type Hip 1


title: Homozygous atx1/atx3/atx4 Triple Mutant 2 (TM2) rep9

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM2 FPKM
FPKMafterfilter
T2C0R1


title: Wild-type + PLX5622 Cortex 3


title: Wild-type Thal 3


title: serum_Pre_whole_virion_vaccine 178_Pre

status: Public on Jul 13 2019

type: RNA

city: Oxford

first: ruth

middle: Elizabeth

last: Drury

state: Oxforshire

address: Centre for Tropical Medicine and Vaccinology, Churchill Drive

department: Paediatrics

country: United Kingdom

institute: University of Oxford

description:
serum_Pre_whole_virion_vaccine
Pre vaccination miRNA expression in serum

hyb_protocol: Samples were hybridised for 40 hours to increase specific signal against background.

scan_protocol: Serum miRNA levels were assessed using the Human miRNA Microarray 60k (Agilentà Technologies). Slides were scanned immediately after washing on the Agilent Technologies Scanner G2505C US84300231 using one color scan setting for 1x44k array slides.

data_processing:
The scanned images were analyzed using protocol  miRNA_107_Sep09 and Grid: 031181_D_F_20110707).  Processed normalised data was obtained by filtering out miRNAs detected in less than 50% of sample. Where a miRNA was not detected in a sample, its fluorescence value was set to half the value of the minimum detected fluorescence value across all samples for that miRNA. Data were then normalised in R using variance stabilised normalisation (from the R package vsn version 3.40).
vsn normalized signal intensity

organism: Homo sapiens

source_name: serum, baseline, participant 178

label_protocol: The concentration of the RNA was measured using a NanoDropà ND-8000 UV-Vis spec- trophotometer (Thermo Scientific, Massachusetts, USA). For each sample 100ng total RNA (at 50 ng/μl) was taken and used in the miRNA microarray labelling procedure (Agilent Tech- nologies, Santa Clara, USA; Cat: 5190-0456). This procedure followed the Agilent miRNA pro- tocol (Version 2.4 September 2011, http://www.chem.agilent.com/library/usermanuals/ public/g4170-90011_mirna_complete_2.4.pdf); with the exception that after the labelling with Cy3-pCp molecule samples were dried and ‘Step 2’ was omitted.

extract_protocol: Total RNA was extracted from 200 microlitres of previously frozen sera using the Total RNA Extraction Kit (Norgen cat# 17200) as specified by the protocol.

treatment_protocol: Serum samples were collected immediately before vaccination and 21 days (minus 7 days to plus 14 days) after second vaccination with either a

value: serum

tag: gender

value: female

tag: age

tag: vaccination group

value: whole virion non-adjuvanted H1N1 vaccine


title: Wild-type Thal 1


title: Wild-type Thal 2


title: Wild-type Cortex 3


title: Spleen_KO1

city: Kyoto

first: Wooseok

last: Seo

address: Yoshida-Konoe-cho, Sakyo-ku

country: Japan

institute: Kyoto University Graduate School of Medicine

description:
mRNA
Mouse MM10 mRNA
Unidirectional RNA-seq

data_processing:
RNA-seq sequence reads were aligned to mouse reference genome release mm10 using HISAT2 (v2.1.0) with default parameters and produced bam files as outputs. Bam Files were used to count reads for genes by using HTSeq (v0.11.1) and produced tab-delimited text files as outputs.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *txt: Tab-delimited text files of counted reads for genes (mm10).

source_name: NK cell

growth_protocol: Freshly sorted mouse NK cells.

extract_protocol:
Sorted cells were purified by using Trizol (Invitrogen) and Direct-zol RNA kit (Zymo Research) according to the manufacturer’s protocols.
Library construction was conducted by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol. Libraries were sequenced to 50 bp read length on a HiSeq2500 (Illumina).

treatment_protocol: Mouse NK cells were purified from lung and spleen.

tag: strain/background

tag: genotype/variation

value: KO

tag: cell type

value: Spleen NK cells

tag: sorting markers

value: CD45+ TCRb- NK1.1+


title: Spleen_KO2


title: Wild-type Hip 3


title: Wild-type Hip 2


title: Wild-type Cortex 2


title: Spleen_WT2

value: WT


title: Wild-type + PLX5622 Thal 2


title: Wild-type Cortex 1


title: Spleen_WT1


title: 5xfAD + PLX5622 Thal 1


title: Lung_WT1

value: Lung NK cells


title: Lung_WT2


title: 5xfAD + PLX5622 Hip 2


title: 5xfAD + PLX5622 Thal 3


title: Lung_KO2


title: 5xfAD + PLX5622 Hip 1


title: 5xfAD + PLX5622 Cortex 4


title: Wildtype Columbia-0 Ecotype rep4

description:
Wildtype Columbia Type 0
190627 WT FPKM
FPKMafterfilter
WA6R1

value: vegetative throughout timecourse


title: 5xfAD + PLX5622 Hip 4


title: 5xfAD + PLX5622 Hip 3


title: 5xfAD + PLX5622 Cortex 2


title: 5xfAD + PLX5622 Cortex 3


title: 5xfAD + PLX5622 Cortex 1


title: Lung_KO1


title: pm_flu_f_3

city: Philadelphia

first: Shaon

last: Sengupta

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Raw RNA-Seq reads were aligned to the mm10.GRCm38.p5  build of the mouse genome using STAR v2.5.3a. STAR was provided with gene models from the Ensembl v90 genome annotation.
The Pipeline of RNA-Seq Transformations (PORT) v0.8.2a-beta was used to perform gene-level quantification of the aligned data. PORT is an implementation of the re-sampling approach for normalization proposed by Li and Tibshirani. Briefly, PORT accounts for potential confounding factors like reads mapping to rRNA and mitochondrial DNA. Next, PORT determines the input samples with the fewest number of gene-mapping reads and re-samples all datasets to the same number of reads. Lastly, PORT quantifies the normalized gene-level reads counts for each sample.
Genome_build: mm10.GRCm38.p5
Supplementary_files_format_and_content: txt files contain PORT-normalized and quantified read counts for each gene in each sample

extract_protocol:
Whole lung preparations were lysed using Tissuelyzer and RNA extracted using a trizol based method followed by clean up using Mini-Elute kit (qiagen) using manufacturer's protocols.
Library  preparation  was  performed  on  400  ng  DNAse-treated  RNA  using  the  Illumina  Truseq  kit.

tag: Sex

tag: infected with

value: Influenza

tag: time of infection

value: pm

tag: day post-infection

value: day 6

value: lung


title: 5xfAD + PLX5622 Thal 4

value: Brain


title: pm_ctrl_f_3

value: PBS(mock)


title: pm_ctrl_f_2


title: pm_flu_f_2


title: pm_ctrl_f_1


title: pm_ctrl_m_3

value: male


title: 5xfAD Thal 4

value: Vehicle

value: Thalamus


title: pm_ctrl_m_1


title: pm_ctrl_m_2


title: pm_flu_m_4


title: 5xfAD Hip 2

value: Hippocampus


title: pm_flu_m_1


title: pm_flu_m_3


title: 5xfAD + PLX5622 Thal 2


title: am_flu_f_3

value: female

value: am


title: 5xfAD Thal 3


title: pm_flu_m_2


title: 5xfAD Cortex 3

value: Cortex


title: am_flu_f_1


title: pm_flu_f_1


title: 5xfAD Thal 1


title: 5xfAD Hip 4


title: 5xfAD Cortex 1


title: 5xfAD Hip 1


title: am_flu_m_3


title: 5xfAD Cortex 4


title: 5xfAD Hip 3


title: 5xfAD Cortex 2


title: 5xfAD Thal 2


title: am_ctrl_f_2


title: am_ctrl_m_2


title: NUW198wt

city: Madrid

first: Enrique

last: Lara-Pezzi

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

description: Myocardial tissue from left ventricle isolated from 4 months old mice

data_processing:
Illumina RTA software v 1.13.48.0
Fastq files extracted with CASAVA 1.8
Reads were pre-processed with Cutadapt 1.6.1, To remove TruSeq adaptor.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build GRCm38 v76) using RSEM v1.2.3 and Bowtie2 v2.0.6.
Data were normalized using TMM with the Bioconductor package EdgeR v3.0.8
Differential expression were tested using GLM with the Bioconductor package EdgeR
Genome_build: GRCm38.v76
Supplementary_files_format_and_content: NormCounts.txt. Table with ensembl gene ID, gene Name and TMM Normalised counts per million reads sequenced per sample

molecule: polyA RNA

source_name: left ventricle of hearts from WT mice

growth_protocol: Standard protocols were used to maintain the mice

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) and then purified on Rneasy spin columns (Qiagen). RNA integrity (RNA Integrity Score ≥ 7.9) And quantity were determined on the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard TrueSeq Illumina protocols

treatment_protocol: No treatment applied

value: Heart

tag: delevopmental stage

value: Adult (4 months old)


title: NUW193TMEM43wt

source_name: left ventricle of hearts from mice overexpressing the human form of TMEM43 (TMEM43wt)

tag: strain


title: am_flu_m_1


title: NUW181TMEM43wt


title: am_flu_m_2


title: am_ctrl_f_1


title: am_ctrl_m_3


title: am_ctrl_m_1


title: NUW194wt

value: WT


title: HuMEC cells, TGFB driven EMT Outer Colony

city: New York

first: José

middle: L

last: McFaline-Figueroa

email: jm5200@columbia.edu, joselmc@uw.edu

state: NY

department: Biomedical Engineering

institute: Columbia University

description:
Data collected from the outer colony fraction of HuMEC cells seeded as a high density patch in the center of a well of a tissue cultured dish and allowed to undergo a spatially-determined and TGF-B1 driven EMT. Single-cell RNA-seq sample and final sequencing library preparation was performed as outlined in documentation from 10X genomics for version 1 of their single-cell solutions kit.
HuMEC_matrix.mtx
HuMEC_genes.tsv
HuMEC_barcodes.tsv
HuMEC_Pseudospace_aggregated_cds.rds
HuMEC_pseudospace_metadata.tsv

data_processing:
Expression matrix files and BAM files were generated using cellranger (10X genomics) version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. HuMEZC pseudospace samples were aggregated using the aggregate option in cellranges to normalize mean number of reads per cell across 10X libraries.
Genome_build: hg19
Supplementary_files_format_and_content: Expression matrix files and BAM files were generated using cellranger (10X genomics) version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.

source_name: HuMEC cells

growth_protocol: HuMEC cells were cultured in HuMEC ready medium (Thermo Fisher Scientific)

extract_protocol: 10X genomics V1 protocol following manufacturer recommendations.

treatment_protocol: The cloning area of a 3.2 mm diameter cloning ring was traced under the center of wells in 6 well dishes. HuMEC cells were seeded within cloning rings at the marked position and allowed to adhere. On the next day, rings were removed, unattached cells removed by washing with PBS and HuMEC media with or without 4 ng/mL TGF-B1. For TGF-B treated samples, cytokine was replenished every 48 hours. 7 days post removal of cloning rings, inner and outer cell fractions were collected by scraping away outer and inner cells, respectively, using a cell lifter and remaining cells were dissociated using TrypLE (ThermoFisher Scientific) with tthe area to scrape determined by the outer diameter of marked clomning ring area.

value: Primary human mammary epithelial cells

tag: treatment

value: Exposed to 4 ng/mL TGF-B1


title: am_flu_f_2

value: Influenza


title: HuMEC cells, TGFB driven EMT Inner Colony

description:
Data collected from the inner colony fraction of HuMEC cells seeded as a high density patch in the center of a well of a tissue cultured dish and allowed to undergo a spatially-determined and TGF-B1 driven EMT. Single-cell RNA-seq sample and final sequencing library preparation was performed as outlined in documentation from 10X genomics for version 1 of their single-cell solutions kit.
HuMEC_matrix.mtx
HuMEC_genes.tsv
HuMEC_barcodes.tsv
HuMEC_Pseudospace_aggregated_cds.rds
HuMEC_pseudospace_metadata.tsv


title: HuMEC cells, Spontaneous EMT Outer Colony

description:
Data collected from the outer colony fraction of HuMEC cells seeded as a high density patch in the center of a well of a tissue cultured dish and allowed to undergo a spatially-determined spontaneous EMT. Single-cell RNA-seq sample and final sequencing library preparation was performed as outlined in documentation from 10X genomics for version 1 of their single-cell solutions kit.
HuMEC_matrix.mtx
HuMEC_genes.tsv
HuMEC_barcodes.tsv
HuMEC_Pseudospace_aggregated_cds.rds
HuMEC_pseudospace_metadata.tsv

value: Untreated


title: NUT279TMEM43mut

source_name: left ventricle of hearts from mice expressing the human p.S358L mutant form of TMEM43 (TMEM43mut)


title: NUW204TMEM43wt


title: HuMEC cells, Spontaneous EMT Inner Colony

description:
Data collected from the inner colony fraction of HuMEC cells seeded as a high density patch in the center of a well of a tissue cultured dish and allowed to undergo a spatially-determined spontaneous EMT. Single-cell RNA-seq sample and final sequencing library preparation was performed as outlined in documentation from 10X genomics for version 1 of their single-cell solutions kit.
HuMEC_matrix.mtx
HuMEC_genes.tsv
HuMEC_barcodes.tsv
HuMEC_Pseudospace_aggregated_cds.rds
HuMEC_pseudospace_metadata.tsv


title: NUT260TMEM43mut


title: am_ctrl_f_3

value: day 6

value: lung


title: D2

city: Newcastle upon Tyne

first: Kenneth

middle: Frank

last: Baker

address: Framlington Place

department: Translational and Clinical Research Institute

institute: Newcastle University

data_processing:
Transcript abundance was estimated from the raw FASTQ files using Kallisto software (v0.43.0) ran in single-end mode, and using an index based on Gencode v24 transcript sequences.
Read counts were imported to R (v3.4.1) using the ‘tximport’ package (v1.4.0), removing genes with a mean read count of <60.
Gene annotation using the Ensembl GRCh38 assembly was performed using the ‘biomaRt’ package (v2.32.1)
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: tab-delimited tsv file including estimated counts for each sequenced transcript

source_name: CD4+ T cell

extract_protocol:
Total RNA was extracted from CD4+ T cells lysates using the Qiagen Allprep DNA/RNA/miRNA Universal Kit (Catalogue number 80224). 1.5ug total RNA (or entire sample if less) was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease

value: Rheumatoid Arthritis

tag: cd4+ t cell purity (percent)

tag: extraction batch

tag: sequencing batch

tag: flare event

value: no flare

tag: censor time (days)


title: D9


title: D8

value: flare


title: NUW192wt

tag: tissue


title: D5


title: DCAF15_A_repl_IFNG

city: South San Francisco

first: Linda

last: Fong

state: California

address: 1170 Veterans Blvd

department: Oncology

institute: Calico Labs

data_processing:
Sequencing quality control performed using FastQC v0.11.5
Transcript abundance was quantified using Salmon v0.9.1 in pseudo-alignment mode, without adapter trimming, producing TPM estimates using the GRCh38 transcriptome
Differential expression was performing using Sleuth V0.29.0
Genome_build: GRCh38

source_name: K562 cell line

growth_protocol: K562 cells grown in RPMI + 10% FBS , seeded at  a density of 0.33M/ml.

extract_protocol:
Trizol extraction followed by Qiagen Rneasy column-based purification
Truseq Stranded mRNAlibrary prep kit

treatment_protocol: Cells were either left alone or treated for 24hrs with 10ng/ml IFNg

tag: cell line

value: 24hr IFNg

tag: genotype


title: DCAF15_B_IFNG


title: DCAF15_C_IFNG


title: DCAF15_B_repl_IFNG


title: DCAF15_C_repl_IFNG


title: C22


title: D1


title: PTPN2_B_IFNG


title: PTPN2_A_IFNG


title: DCAF15_A_IFNG


title: control_B_IFNG


title: PTPN2_B_repl_IFNG


title: C16


title: C21


title: C4


title: C14


title: C11


title: C8


title: control_B_repl_IFNG


title: control_A_IFNG


title: Wild-type Cortex 4

value: Vehicle

value: Wild-Type

value: Brain

tag: tissue region


title: B35


title: controlA_repl_IFNG


title: B38


title: PTPN2_A_repl_IFNG


title: DCAF15_B_repl

value: untreated


title: B32


title: DCAF15_C_repl


title: DCAF15_C


title: B30


title: DCAF15_B


title: B31


title: B28


title: DCAF15_A


title: DCAF15_A_repl


title: B22


title: B20


title: B16


title: B12


title: PTPN2_B


title: PTPN2_A_repl


title: B11


title: C2


title: control_B_repl


title: B9


title: controlA_repl


title: B8


title: control_B


title: B5


title: B24


title: PTPN2_B_repl


title: A33


title: A36


title: A23


title: control_A


title: A37


title: A18


title: A26


title: A35


title: A20


title: A14


title: A17


title: PTPN2_A


title: A13


title: A10


title: A8


title: A4


title: A7


title: Female IH LPS 2

city: Madison

first: Jyoti

last: Watters

state: WI

address: 2015 Linden Drive

department: CBS

institute: University of Wisconsin-Madison

description: female intermittent hypoxia LPS sample 2

data_processing:
Base calls made using Illumina 1.9 Software
Alignment made using Tophat v2.1
Raw counts generated using htseq-count --stranded reverse option
Filtered and normalized using EdgeR
GLM applied to count data and tagwise LRT performed using EdgeR
Differential expression calculated using decideTestDGE(lrt) in EdgeR
Genome_build: rn6
Supplementary_files_format_and_content: tab delimited txt files with raw counts
Supplementary_files_format_and_content: csv files with normalized counts

organism: Rattus norvegicus

source_name: P9 microglia

growth_protocol: Neonates were exposed with dams in home cages to 8 days of normoxia or intermittent hypoxia starting at P1

extract_protocol:
Microglia were immunomagentically isolated using Miltenyi anti-cd11b antibody. Microglia were lysed in trizol.
RNA stranded libraries were prepared according Illumina protocols

treatment_protocol: Normoxia exposure consisted of 8 hours of room air (21% O2), intermittent hypoxia exposure consisted of expsosure to 2 min cycles of either 10.5% O2 or 21% for 8 hrs a day. At P9, 16 hours following the last IH exposure, pups were injected with either saline or 0.1 mg/mL LPS (i.p.)

value: female intermittent hypoxia LPS

value: whole brain microglia

tag: age

value: Postnatal day 9


title: Female IH LPS 1

description: female intermittent hypoxia LPS sample 1


title: Female IH LPS 3

description: female intermittent hypoxia LPS sample 3


title: Female IH 3

description: female intermittent hypoxia sample 3

value: female intermittent hypoxia


title: A1


title: Female Nx LPS 2

description: female normoxia LPS sample sample 2

value: female normoxia LPS


title: Female IH 2

description: female intermittent hypoxia sample 2


title: Female IH 1

description: female intermittent hypoxia sample 1


title: NUT259TMEM43mut

value: Heart

value: Adult (4 months old)


title: Female Nx LPS 3

description: female normoxia LPS sample sample 3


title: LLC_STING KO_4

city: Seongnam-si

first: Hannah

last: Yang

address: CHA Bundang Medical Center

country: South Korea

institute: CHA Bundang Medical Center

data_processing: See manufacturer's website (http://www.nanostring.com)

source_name: TMEM173gt, lung

growth_protocol: We implanted 5 × 10^5 LLC cells into the right flank of C57BL/6 and TMEM173(gt/gt) mice.

extract_protocol: Total RNA from the whole tumor tissues using TRIzol.

treatment_protocol: When the tumors reached > 4–5 mm in diameter, we performed intratumoral injections of PBS (Sham) or STING agonist.

tag: gender

value: Male

value: Knockout (TMEM173gt)

value: Lung

value: PBS (Sham) treated


title: LLC_STING KO_3


title: CROP-Seq TGFB driven EMT Inner Colony

description:
Data collected from the inner colony fraction of Cas9 expressing MCF10A cells transduced with a CROP-seq CRISPR KO library targeting EMT associated cell surface receptors and transcription factors, seeded as a high density patch in the center of a well of a tissue cultured dish and allowed to undergo a spatially-determined and TGF-B1 driven EMT. Single-cell RNA-seq sample and final sequencing library preparation was performed as outlined in documentation from 10X genomics for version 1 of their single-cell solutions kit.
CROPSeq_pseudospace_matrix.mtx
CROPSeq_pseudospace_genes.tsv
CROPSeq_pseudospace_barcodes.tsv
CROPSeq_pseudospace_cds.rds
CROPSeq_pseudospace_cell_metadata.tsv

data_processing:
Library strategy: CROP-seq
Expression matrix files and BAM files were generated using cellranger (10X genomics) version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Pseudospace and CROPSeq pseudospace samples were aggregated using the aggregate option in cellranges to normalize mean number of reads per cell across 10X libraries.
Guide sequences were extracted from samples corresponding to barcode enrichment libraries as described in the methods section of our manuscript.
Genome_build: hg19
Supplementary_files_format_and_content: Expression matrix files and BAM files were generated using cellranger (10X genomics) version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.

source_name: MCF10A cells

growth_protocol: MCF10A cells were cultured in media composed of DMEM/F12 (ThermoFisher Scientific) containing 10% fetal bovine serum (ThermoFisher Scientific), 1% penn-strep (ThermoFisher Scientific), 10 ng/mL EGF (LC Labs), 5 µg/mL insulin (ThermoFisher Scientific), 10 ng/mL cholera toxin (List Labs) and 1 µg/mL hydrocortisone (Sigma)

extract_protocol:
10X genomics V1 protocol following manufacturer recommendations.
10X genomics V1 protocol following manufacturer recommendations.

treatment_protocol: The cloning area of a 3.2 mm diameter cloning ring was traced under the center of wells in 6 well dishes. MCF10A or CROP-Seq transduced MCF10A-Cas9 cells were seeded within cloning rings at the marked position and allowed to adhere. On the next day, rings were removed, unattached cells removed by washing with PBS and MCF10A media with or without 4 ng/mL TGF-B1. For TGF-B treated samples, cytokine was replenished every 48 hours. 7 days post removal of cloning rings, inner and outer cell fractions were collected by scraping away outer and inner cells, respectively, using a cell lifter and remaining cells were dissociated using TrypLE (ThermoFisher Scientific) with tthe area to scrape determined by the outer diameter of marked clomning ring area.

tag: cell type

value: Spontaneously immortalized human breast epithelial cells

value: Exposed to 4 ng/mL TGF-B1


title: CROP-Seq TGFB driven EMT Outer Colony

description:
Data collected from the outer colony fraction of Cas9 expressing MCF10A cells transduced with a CROP-seq CRISPR KO library targeting EMT associated cell surface receptors and transcription factors, seeded as a high density patch in the center of a well of a tissue cultured dish and allowed to undergo a spatially-determined and TGF-B1 driven EMT. Single-cell RNA-seq sample and final sequencing library preparation was performed as outlined in documentation from 10X genomics for version 1 of their single-cell solutions kit.
CROPSeq_pseudospace_matrix.mtx
CROPSeq_pseudospace_genes.tsv
CROPSeq_pseudospace_barcodes.tsv
CROPSeq_pseudospace_cds.rds
CROPSeq_pseudospace_cell_metadata.tsv


title: LLC_STING_8

source_name: Wild-type, lung

value: Wild-type

value: STING agonist treated


title: LLC_STING KO_2


title: Female Nx 2

description: female normoxia sample 2

value: female normoxia


title: CROP-Seq Spontaneous EMT Outer Colony

description:
Data collected from the outer colony fraction of Cas9 expressing MCF10A cells transduced with a CROP-seq CRISPR KO library targeting EMT associated cell surface receptors and transcription factors, seeded as a high density patch in the center of a well of a tissue cultured dish and allowed to undergo a spatially-determined spontaneous EMT. Single-cell RNA-seq sample and final sequencing library preparation was performed as outlined in documentation from 10X genomics for version 1 of their single-cell solutions kit.
CROPSeq_pseudospace_matrix.mtx
CROPSeq_pseudospace_genes.tsv
CROPSeq_pseudospace_barcodes.tsv
CROPSeq_pseudospace_cds.rds
CROPSeq_pseudospace_cell_metadata.tsv

value: Untreated


title: Female Nx 1

description: female normoxia sample 1


title: Female Nx LPS 1

description: female normoxia LPS sample sample 1


title: CROP-Seq Spontaneous EMT Inner Colony

description:
Data collected from the inner colony fraction of Cas9 expressing MCF10A cells transduced with a CROP-seq CRISPR KO library targeting EMT associated cell surface receptors and transcription factors, seeded as a high density patch in the center of a well of a tissue cultured dish and allowed to undergo a spatially-determined spontaneous EMT. Single-cell RNA-seq sample and final sequencing library preparation was performed as outlined in documentation from 10X genomics for version 1 of their single-cell solutions kit.
CROPSeq_pseudospace_matrix.mtx
CROPSeq_pseudospace_genes.tsv
CROPSeq_pseudospace_barcodes.tsv
CROPSeq_pseudospace_cds.rds
CROPSeq_pseudospace_cell_metadata.tsv


title: LLC_STING KO_1


title: TGFB driven EMT Outer Colony

description:
Data collected from the outer colony fraction of MCF10A cells seeded as a high density patch in the center of a well of a tissue cultured dish and allowed to undergo a spatially-determined and TGF-B1 driven EMT. Single-cell RNA-seq sample and final sequencing library preparation was performed as outlined in documentation from 10X genomics for version 1 of their single-cell solutions kit.
pseudospace_matrix.mtx
pseudospace_genes.tsv
pseudospace_barcodes.tsv
pseudospace_cds.rds
pseudospace_cell_metadata.tsv

data_processing:
Expression matrix files and BAM files were generated using cellranger (10X genomics) version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Pseudospace and CROPSeq pseudospace samples were aggregated using the aggregate option in cellranges to normalize mean number of reads per cell across 10X libraries.
Guide sequences were extracted from samples corresponding to barcode enrichment libraries as described in the methods section of our manuscript.
Genome_build: hg19
Supplementary_files_format_and_content: Expression matrix files and BAM files were generated using cellranger (10X genomics) version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.


title: TGFB driven EMT Inner Colony

description:
Data collected from the inner colony fraction of MCF10A cells seeded as a high density patch in the center of a well of a tissue cultured dish and allowed to undergo a spatially-determined and TGF-B1 driven EMT. Single-cell RNA-seq sample and final sequencing library preparation was performed as outlined in documentation from 10X genomics for version 1 of their single-cell solutions kit.
pseudospace_matrix.mtx
pseudospace_genes.tsv
pseudospace_barcodes.tsv
pseudospace_cds.rds
pseudospace_cell_metadata.tsv


title: Female Nx 3

description: female normoxia sample 3


title: LLC_STING_4


title: LLC_STING_6


title: Day 7 shDpy30 spheroids

city: Vancouver

first: Brad

last: Hoffman

state: BC

country: Canada

institute: University of British Columbia

data_processing:
Sequence reads were aligned to the mouse GRC38/mm10 genome using Salmon (Patro et al., 2017) and DESeq2 (Love et al., 2014) was used to determine differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file includes gene symbols and log2 fold change values for shDpy30/shScramble

source_name: Pancreas

growth_protocol: Dorsal pancreatic buds were dissected from E13.5 embryos using fine-tipped forceps under a dissecting microscope, pooled into a single tube and digested in 250 uL TrypLE Express media (Gibco) for 5 minutes at 37C. The reaction was neutralized by dilution with complete RPMI media (HyClone) and pancreata were further mechanically dispersed by pipetting. Single cells were then spun at 750xg for 4 minutes, the pellet was resuspended in Pancreas Growth Media (Sugiyama et al., 2013) +/- lentivirus, and an 8 uL suspension was plated at one pancreas per well into a 96-well plate. Spin-infection of lentivirus was performed at 1,020xg at 34C for 90 minutes, during which the plate was covered with an adhesive seal to prevent evaporation. To the cell suspension at the bottom rim of the well, 12 uL of Matrigel (Corning) was overlayed and solidified at 37C for 60 minutes on a 45 degree angle. 100 uL of Pancreas Growth Media was added per well and infected cells were selected with 1 ug/mL puromycin ~5 hours post-infection. Media was changed every other day and 0.33 uM retinoic acid (RA, Sigma) was added every day for 3 days to induce sphere proliferation. Pancreas Differentiation Media (Sugiyama et al., 2013) was added on Days 4 and 6 to induce differentiation of the spheres.

extract_protocol:
Pancreas progenitor spheres were released from Matrigel on Day 7 using 100 uL per well of Dispase II (Sigma-Aldrich) dissolved at 1 mg/mL in PrEBM media (Lonza) for 2 hours at 37C. An additional 100 uL per well of RPMI with FBS was overlayed to stop the reaction by dilution, and spheres were subsequently mechanically released from Matrigel by pipetting and collected into a single Eppendorf tube. Spheres were pelleted at 750xg for 4 minutes, supernatant was removed, and 200 uL of TRIzol reagent (Thermo Fisher Scientific) was added for RNA extraction.
Samples from Day 7 shScramble, shWdr5 and shDpy30 spheres were pooled from > 4 replicates into TRIzol to obtain > 500 ng RNA. cDNA libraries were prepared from Illumina TruSeq kits (RNA Sample Preparation Low Throughput (LT) and Stranded mRNA) using Ampure XP beads and validated on an Agilent Bioanalyzer High Sensitivity DNA chip before sequencing on Illumina sequencing platforms (HiSeq or NextSeq). Sequence reads were aligned to the mouse GRC38/mm10 genome using Salmon (Patro et al., 2017) and DESeq2 (Love et al., 2014) was used to determine differential gene expression.

value: Pancreas

tag: Stage

value: Embryonic Day 13.5


title: 202229250033_R01C01

type: genomic

city: New Haven

first: Ranjit

last: Bindra

state: CT

address: 15 York Street Hunter Building (HRT) 313C

department: Therapeutic Radiology

institute: Yale University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to the Illumina Human EPIC Bead Array (850k) using the standard Illumina protocol

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

data_processing: Genome Studio v1.9

label: Cy3, Cy5

molecule: genomic DNA

source_name: Parental Astrocytes

label_protocol: Standard Illumina Protocol

growth_protocol: standard cell passaging conditions, grown to 80% confluence (for adherent cell lines).

extract_protocol: Genomic DNA was extracted and purified from cell lines using the Zymo Quick-DNA Miniprep kit according to standard instructions

treatment_protocol: no treatment

value: Parental Astrocytes

tag: ppm1d status

value: wild type


title: Male IH LPS 1

description: male intermittent hypoxia LPS sample 1

value: male intermittent hypoxia LPS

value: whole brain microglia

value: Postnatal day 9


title: 202875000102_R06C01

value: mutant


title: LLC_STING_7

tag: strain

value: Male


title: Male IH LPS 3

description: male intermittent hypoxia LPS sample 3

tag: treatment


title: LLC_STING_5

value: Lung


title: 202229250033_R04C01

source_name: PPM1D mut OE

value: PPM1D mut OE


title: Spontaneous EMT Outer Colony

description:
Data collected from the outer colony fraction of MCF10A cells seeded as a high density patch in the center of a well of a tissue cultured dish and allowed to undergo a spatially-determined spontaneous EMT. Single-cell RNA-seq sample and final sequencing library preparation was performed as outlined in documentation from 10X genomics for version 1 of their single-cell solutions kit.
pseudospace_matrix.mtx
pseudospace_genes.tsv
pseudospace_barcodes.tsv
pseudospace_cds.rds
pseudospace_cell_metadata.tsv

value: Spontaneously immortalized human breast epithelial cells


title: Spontaneous EMT Inner Colony

description:
Data collected from the inner colony fraction of MCF10A cells seeded as a high density patch in the center of a well of a tissue cultured dish and allowed to undergo a spatially-determined spontaneous EMT. Single-cell RNA-seq sample and final sequencing library preparation was performed as outlined in documentation from 10X genomics for version 1 of their single-cell solutions kit.
pseudospace_matrix.mtx
pseudospace_genes.tsv
pseudospace_barcodes.tsv
pseudospace_cds.rds
pseudospace_cell_metadata.tsv


title: 202229250033_R05C01


title: Male IH LPS 2

description: male intermittent hypoxia LPS sample 2


title: Knockout Embryonic Day 18.5

data_processing:
CellRanger (10x Genomics) was used to generate FastQ files, to map reads to the mouse GRCm38/mm10 genome, and to quantify transcript abundance. Cells that expressed fewer than 750 transcripts were excluded and cells with UMI’s greater than 40,000 were filtered out to remove possible doublets. For the analysis of the E13.5 cells, Seurat v2 (Butler et al., 2018) was used to filter the cells, to scale and normalize the data, and to cluster the cells using tSNE to reduce the dimensionality of the data. Control and Dpy30P epithelial cells were identified and canonical correlation analysis was used to integrate them (Butler et al., 2018). Monocole (Trapnell et al., 2014) was then used to perform semi-supervised clustering of the integrated cells, and to perform pseudotemporal analysis of the cells. For the analysis of the E18.5 cells, Seurat v3 alpha was used (Stuart et al., 2018). In this case cells were first filtered then the data sets integrated by finding integration anchors and using the IntegrateData function of Seurat v3 alpha (Stuart et al., 2018). The integrated data was clustered and visualized using UMAP for dimension reduction (McInnes et al., 2018). Epithelial cells were identified and re-clustered again using UMAP for dimension reduction. GO term analysis was generated using the GOplot package (Walter et al., 2015) and data was displayed using ggplot2 (Wickham, 2016) in R.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file includes log2 fold change values for control vs. knockout

extract_protocol:
At noon, embryos were harvested by hysterectomy and the pancreas was dissected under a microscope in ice-cold phosphate buffered saline (PBS) and transferred into 2 mL of prewarmed 0.25% Trypsin-EDTA (TE) in a 15 mL Falcon tube. Falcon tubes were placed in a 37°C bead bath for 20 minutes of digestion, followed by addition of 1 mL of FBS and 2 mL of PBS to stop the digestion. The cell solution was passed through a 40 µM cell strainer into a new 15 mL Falcon tube. Single cells were spun at 300xg for 5 minutes and cell pellets were resuspended in 500 µL (control) or 250 µL (Dpy30∆P) PBS and cell concentration was adjusted to 1,000 cells/µL.
Using a cell concentration of 1,000 cells/µL, 17.4 µL of cells were loaded for a targeted recovery of 10,000 cells according to the Chromium Single Cell 3’ Reagent Kits v2 User Guide (10X Genomics, Inc.), which was followed as described.
Single Cell RNA-seq

value: Embryonic Day 18.5


title: Day 7 shScramble spheroids


title: 202229250033_R07C01


title: Primary fibroblast established from noncancerous tissue of Pt45

city: Chuo-ku, Tokyo

first: Masahiro

last: Maeda

address: 5-1-1, Tsukiji

department: Division of Epigenomics

institute: National Cancer Center Research Institute

description: biopsy, gastric mucosae

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: Genome Studio software (V2011.1 Methylation module 1.9.0) was used.  Beta values were obtained after background correction and normalization to internal controls.

label: Cy5 and Cy11

source_name: Primary fibroblast  24

extract_protocol: Genomic DNA samples were isolated using Phenol-chloroform extraction protocol.

value: Female

tag: tumor histology (lauren)

value: Diffuse


title: LLC_STING_1

value: Wild-type

value: STING agonist treated


title: 202229250033_R08C01


title: 202229250033_R06C01


title: LLC_STING_2


title: Male IH 2

description: male intermittent hypoxia sample 2

value: male intermittent hypoxia


title: 202229250033_R02C01

source_name: WT iso

value: WT iso


title: Control Embryonic Day 18.5

value: Pancreas


title: Primary fibroblast established from noncancerous tissue of Pt40

description: biopsy, gastric mucosae

label: Cy5 and Cy9

source_name: Primary fibroblast  22

value: Mixed


title: 202229250033_R03C01

source_name: PPM1D trnc.

value: PPM1D trnc.


title: LLC_STING_3


title: Knockout Embryonic Day 18.5 rep3

data_processing:
The resulting FastQ files were combined, filtered (phred33) and trimmed to remove adapters with Trimmomatic (Bolger et al., 2014). Salmon (Patro et al., 2017) was used to quasi-map, assemble and quantify transcripts using the mouse GRCm38/mm10 genome. Differential gene expression analysis was performed using Salmon and DEseq2 (Love et al., 2014) in R, with the apeglm algorithm used to shrink log fold changes (Zhu et al., 2018).
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file includes log2 fold change values for control vs. knockout samples

extract_protocol:
The dorsal pancreas was dissected from 3 control and 3 Dpy30∆P E18.5 embryos directly into 1 mL of TRIzol.
RNA was extracted with 200 uL of chloroform, followed by a combination of 500 uL of 100% isopropanol and 2 uL of glycogen (20 mg/mL). RNA samples were centrifuged at 12,000xg for 5 minutes at 4C and washed with 80% ethanol. The final RNA pellet was air-dried and resuspended in 12 uL of water. RNA was treated with TURBO DNase I (Thermo Fisher Scientific) for 20 minutes at 37C to remove genomic DNA. For each sample, 100 ng of RNA was ribodepleted with the RiboGone kit (Takara Bio). cDNA libraries were prepared from <10 ng RNA using the SMARTer Stranded RNA-seq kit (Clontech Laboratories, Inc.) and SPRIselect beads (Beckman Coulter).


title: LLC_control_9

value: PBS (Sham) treated


title: 202875000102_R07C01


title: Male Nx LPS 3

description: male normoxia LPS sample sample 3

value: male normoxia LPS

value: whole brain microglia

value: Postnatal day 9


title: Male Nx LPS 2

description: male normoxia LPS sample sample 2


title: Knockout Embryonic Day 18.5 rep2


title: Control Embryonic Day 18.5 rep3


title: Male Nx 3

description: male normoxia sample 3

value: male normoxia


title: Knockout Embryonic Day 18.5 rep1


title: Control Embryonic Day 18.5 rep2


title: 202875000147_R06C01

value: mutant


title: LLC_control_6

value: Male

value: Lung


title: Male Nx LPS 1

description: male normoxia LPS sample sample 1


title: Primary fibroblast established from cancerous tissue of Pt33

description: biopsy, gastric mucosae

label: Cy5 and Cy4

source_name: Primary fibroblast  17

value: Female

value: Intestinal


title: Primary fibroblast established from noncancerous tissue of Pt30

description: biopsy, gastric mucosae

label: Cy5 and Cy3

source_name: Primary fibroblast  16


title: Male Nx 1

description: male normoxia sample 1


title: Male IH 3

description: male intermittent hypoxia sample 3


title: Primary fibroblast established from noncancerous tissue of Pt38

description: biopsy, gastric mucosae

label: Cy5 and Cy7

source_name: Primary fibroblast  20

value: Diffuse


title: Primary fibroblast established from cancerous tissue of Pt38

description: biopsy, gastric mucosae

label: Cy5 and Cy6

source_name: Primary fibroblast  19


title: Primary fibroblast established from cancerous tissue of Pt40

description: biopsy, gastric mucosae

label: Cy5 and Cy8

source_name: Primary fibroblast  21


title: Knockout Embryonic Day 13.5

extract_protocol:
At noon, embryos were harvested by hysterectomy and the pancreas was dissected under a microscope in ice-cold phosphate buffered saline (PBS) and transferred into 2 mL of prewarmed 0.25% Trypsin-EDTA (TE) in a 15 mL Falcon tube. Falcon tubes were placed in a 37°C bead bath for 8 minutes of digestion, followed by addition of 1 mL of FBS and 2 mL of PBS to stop the digestion. The cell solution was passed through a 40 µM cell strainer into a new 15 mL Falcon tube. Single cells were spun at 300xg for 5 minutes and all but ~50 µL of supernatant was removed. For FACS sorting, 300 µL of 10% FBS in PBS was added to the cells, transferred to a FACS tube where 7-AAD was added to stain dead cells, and ~30,000 live single cells from each embryo were sorted into 1 mL of 10% FBS in PBS. Cell counts and viability were confirmed under the microscope on a hemocytometer using Trypan Blue and cell numbers were estimated to be ~300 cells/µL.
Using a cell concentration of 300 cells/µL, 29 µL of cells were loaded for a targeted recovery of 5,000 cells according to the Chromium Single Cell 3’ Reagent Kits v2 User Guide (10X Genomics, Inc.), which was followed as described.
Single Cell RNA-seq

value: Embryonic Day 13.5


title: LLC_control_2

value: Wild-type


title: LLC_control_5


title: LLC_control_7


title: LLC_control_8


title: Primary fibroblast established from cancerous tissue of Pt45

description: biopsy, gastric mucosae

label: Cy5 and Cy10

source_name: Primary fibroblast  23


title: Male Nx 2

description: male normoxia sample 2

source_name: P9 microglia


title: Control Embryonic Day 18.5 rep1

value: Embryonic Day 18.5


title: Primary fibroblast established from noncancerous tissue of Pt33

description: biopsy, gastric mucosae

label: Cy5 and Cy5

source_name: Primary fibroblast  18


title: LLC_control_1


title: LLC_control_3


title: LLC_control_4


title: Control Embryonic Day 13.5

value: Pancreas


title: Male IH 1

description: male intermittent hypoxia sample 1

value: male intermittent hypoxia


title: ctrl_CD8_LCMV

city: Boston

first: Brian

middle: Christopher

last: Miller

state: MA

address: 77 Avenue Louis Pasteur

department: Immunology

institute: Harvard Medical School

description: isolation of cd8+ t cells: CD8+ MACS positive selection (Miltenyi) followed by FACS

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of multiple sequencing runs were performed using the Cell Ranger analysis pipeline (v1.2)
Data normalization, dimension reduction, and differential expression analysis were performed using the Seurat R package (v2.3.4)
Single cell signatures scoring was performed using the FastProject software (v1.1.4)
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx file is count matrix in sparse matrix format; barcodes.tsv is list of barcodes for each sample; genes.tsv is list of genes detected in samples

source_name: Transferred control-guide P14+ CD8+ T cells isolated from spleens of mice 30 days after infection with LCMV Clone 13

growth_protocol: C57BL/6 mice were infected with 4 x 10^6 pfu LCMV Clone 13 via IV injection. On day 30 after infection, mice were sacrificed and spleens removed for CD8+ T cell isolation

extract_protocol:
CD8+ MACS positive selection was performed on single-cell suspensions of splenocytes from chronically infected mice, followed by FACS. Purifed cells were loaded onto the 10x device (10x Genomics)
Library construction was performed as per standard 10x protocol (Manual CG00052 Rev B)
10X single-cell 3' RNA-seq v2

treatment_protocol: Mice were treated with 200 microgram CD4 depleting antibody (clone GK1.5) on days -1 and 1

value: CD8+ T-cells

tag: genotype/variation

value: control-guide P14+


title: Ptpn2_CD8_LCMV

source_name: Transferred Ptpn2-guide P14+ CD8+ T cells isolated from spleens of mice 30 days after infection with LCMV Clone 13

value: Ptpn2-guide P14+


title: Day 7 shWdr5 spheroids

data_processing:
Sequence reads were aligned to the mouse GRC38/mm10 genome using Salmon (Patro et al., 2017) and DESeq2 (Love et al., 2014) was used to determine differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file includes gene symbols and log2 fold change values for shWdr5/shScramble

source_name: Pancreas


title: BHK

city: CHANGCHUN CITY

first: Tu

middle: zhong

last: zhong

address: LIUYING XILU 666

country: China

institute: CVRI

data_processing:
the raw reads were subjected to the Illumina pipeline filter (Solexa 0.3)
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment.

organism: Mesocricetus auratus

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq™ Small RNA Sample Prep Kits(Illumina, San Diego, USA) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: infection


title: Day 7 shScramble spheroids (shWdr5 control)


title: Liver from HF-fed FR30 rats

city: Villeneuve d'Ascq

first: christophe

last: breton

address: Cité Scientifique

country: France

institute: University of Lille 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cubic spline normalisation with GenomeStudio (Illumina)

label: biotin

source_name: Rat liver

label_protocol: Biotinylated cRNA were prepared with the TargetAmp Nano-g Biotin-aRNA Labeling for Illumina System

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the manufacturer's instructions

value: Wistar

value: 4 months

value: Liver

tag: Sex

value: male


title: C11F4


title: Primary fibroblast established from noncancerous tissue of Pt29

description: biopsy, gastric mucosae

source_name: Primary fibroblast  14


title: Liver from FR30 rats


title: Farber_65

status: Public on Jul 11 2019

city: Charlottesville

first: Charles

middle: R

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

description:
total RNA Seq from cultured, mineralizing osteoblasts
cc_ob_counts_full.csv

data_processing:
Reads were mapped to the eight collaborative cross founder transcriptomes, based on mm9, using Bowtie, as perscribed by the EMASE tool, "bowtie -q -a --best --strata --sam -v"
Quantification was conducted using EMASE, a tool for quantifying alignments to multi-parental transcriptomes, https://emase.readthedocs.io/en/latest/readme.html
Genome_build: mm9
Supplementary_files_format_and_content: cc_ob_counts_full.csv contains the estimated count data for each sample that is produced by the EMASE program

source_name: isolated osteoblasts

extract_protocol:
Total RNA was extracted from the mineralized cultures using mirVana RNA isolation kit (ThermoFisher Scientific).
RNA-Seq libraries were constructed from 200 ng of total RNA using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kits (Illumina, Carlsbad, CA). Constructed libraries contained RNAs >200 nt (both unpolyadenylated and polyadenylated) and were depleted of cytoplasmic and mitochondrial rRNAs.

treatment_protocol: Neonatal collaborative cross heads were received from the University of North Carolina. At UNC, neonatal (3-5 days) collaborative cross mice were euthanized by CO2, decapitated onto paper towels soaked in 70% ethanol, and placed in cold PBS on ice for overnight shipping. Once received, calvaria were dissected, paying special attention to brain and interparietal bone removal. Isolated calvaria were placed in 24 well plates containing 0.5 mL of digest solution (0.05% trypsin and 1.5 U/ml collagenase P) and incubated on a rocking platform at 37 degrees during six, fifteen-minute digestions in 0.5 mL of digestion solution. Fraction 1 is discarded and fractions 2-6 are collected. Fractions 2-6 are added to an equal volume of cold plating media (89 mL DMEM, 1 mL 100x Pen/Strep solution, and 10 mL Lot tested FBS). The resulting cells are filtered using a 70-100 mm cell strainer to remove clots, centrifuged at 1000 rpm for 5 minutes and re-suspended in 0.5 ml plating media. The resulting cells are plated in a T25 flask. 24 hours later, cells are washed with PBS, treated with trypsin, counted, and plated at a density of 1.5x105 cells per well in a 12-well plate, and allowed to grow to confluence for 48 hours. After 48 hours of growth, cells are switched to differentiation media (10 mL lot tested FCS, 1 mL 100x Pen/Strep solution, 283.8 uL ascorbic acid (0.1 M), 400 uL B-glycerol phosphate (1 M), and 88.3 mL alpha-MEM per 100 mL) and allowed to differentiate for 10 days. On day 10, total RNA was extracted from the mineralized cultures using mirVana RNA isolation kit (ThermoFisher Scientific).

value: osteoblast


title: Farber_75


title: Farber_71


title: Farber_61


title: Farber_79


title: Farber_67


title: Farber_68


title: Farber_73


title: Farber_74


title: Primary fibroblast established from noncancerous tissue of Pt23

description: biopsy, gastric mucosae

source_name: Primary fibroblast  12


title: Liver from HF-fed control rats


title: Liver from control rats


title: Farber_70


title: Primary fibroblast established from cancerous tissue of Pt30

description: biopsy, gastric mucosae

source_name: Primary fibroblast  15

value: Male


title: Farber_557


title: Primary fibroblast established from cancerous tissue of Pt29

description: biopsy, gastric mucosae

source_name: Primary fibroblast  13

value: Female


title: Farber_57


title: Farber_558


title: Farber_482


title: Farber_528


title: Farber_48


title: Farber_523


title: Farber_504


title: Farber_522


title: Farber_502


title: Farber_497


title: Farber_483


title: Farber_46


title: Farber_454


title: Farber_440


title: Farber_442


title: Farber_39


title: Farber_452


title: Farber_358


title: Farber_44


title: Farber_365


title: Farber_446


title: Farber_360


title: Farber_361


title: Farber_364


title: Farber_369


title: Farber_357


title: Primary fibroblast established from noncancerous tissue of Pt19

description: biopsy, gastric mucosae

source_name: Primary fibroblast  10


title: Farber_453


title: Farber_353


title: Farber_332


title: Primary fibroblast established from noncancerous tissue of Pt17

description: biopsy, gastric mucosae

source_name: Primary fibroblast  08


title: Primary fibroblast established from cancerous tissue of Pt17

description: biopsy, gastric mucosae

source_name: Primary fibroblast  07


title: Farber_309


title: Farber_232


title: Farber_235


title: Farber_211


title: Farber_233


title: Primary fibroblast established from cancerous tissue of Pt23

description: biopsy, gastric mucosae

source_name: Primary fibroblast  11

value: Intestinal


title: Primary fibroblast established from cancerous tissue of Pt3

description: biopsy, gastric mucosae

source_name: Primary fibroblast  03


title: Primary fibroblast established from noncancerous tissue of Pt5

description: biopsy, gastric mucosae

source_name: Primary fibroblast  06


title: Farber_209


title: Farber_366


title: Primary fibroblast established from cancerous tissue of Pt5

description: biopsy, gastric mucosae

source_name: Primary fibroblast  05


title: Farber_207


title: Farber_451


title: Farber_447


title: Farber_205


title: Farber_202


title: Farber_203


title: Farber_201


title: Primary fibroblast established from noncancerous tissue of Pt3

description: biopsy, gastric mucosae

source_name: Primary fibroblast  04


title: Farber_200


title: Farber_198


title: Farber_20


title: Farber_212


title: Primary fibroblast established from cancerous tissue of Pt2

description: biopsy, gastric mucosae

source_name: Primary fibroblast  01

value: Diffuse


title: Primary fibroblast established from cancerous tissue of Pt19

description: biopsy, gastric mucosae

source_name: Primary fibroblast  09


title: Farber_310


title: Primary fibroblast established from noncancerous tissue of Pt2

description: biopsy, gastric mucosae

source_name: Primary fibroblast  02


title: Farber_186


title: Farber_188


title: Farber_187


title: Farber_19


title: Farber_183


title: Farber_190


title: Farber_192


title: Farber_169


title: Farber_177


title: Farber_167


title: Farber_193


title: Farber_173


title: Farber_197


title: Farber_179


title: Farber_153


title: Farber_143


title: Farber_152


title: Farber_150


title: Farber_135


title: Farber_139


title: Farber_132


title: Farber_129-2


title: Farber_125


title: Farber_134


title: Farber_165


title: EXOSC4_PAR_iCLIP

city: Frederick

first: Sandra

last: Wolin

state: Maryland

address: 1050 Boyles Street, BLDG 560 Room 11-39

department: NCI

institute: NIH

data_processing:
Base-calling with RTA v2
Data were preprocessed using Cutadapt (Martin, 2011) and FASTX-Toolkit to remove adaptors and low quality reads, collapsed to remove duplicates and split by barcodes.
Reads were then aligned to the hg19 genome using Novoalign. Since CLIP experiments can generate multiple mismatches and deletions within reads, the mapping stringency was lowered (-t 15,3 -l 20 -x 4 -g 20).
Bedgraph files were produced using Bedtools v 2.26.0
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph

source_name: human embryonic stem cells

growth_protocol: Cells were cultured on Matrigel (BD Pharmingen)-coated plates under feeder-free conditions at 37°C in 5% CO2, 5% O2 and 90% humidity. Media consisted of Dulbecco’s modified Eagle medium (DMEM)/F12 (Invitrogen) supplemented with 1% MEM-nonessential amino acids (Invitrogen), 2 mM L-glutamine, 0.12 mM monothioglycerol, 0.5 mg/ml bovine serum albumin, 50 ng/mL basic fibroblast growth factor (Millipore), N2 supplements (1X), and B27 supplements (1X) (Invitrogen). Media were changed every other day.

extract_protocol: PAR-iCLIP was performed as described (Huppertz et al., 2014). Briefly, after incubating hESCs with 100 μM 4-thiouridine for 7 hr, cells were irradiated with 800 mJ/cm2 UV light (365 nm). After sonication in 50 mM Tris-HCl pH 7.4, 100 mM NaCl, 0.1% SDS, 0.5% deoxycholate, 1% NP-40 and 1 mM EDTA, lysates were incubated with 20 U of Turbo DNase (Invitrogen) and 100 U RNase I (Invitrogen) at 37 oC for 10 min, followed by immunoprecipitation with anti-Exosc4 antibody (Bethyl A303-775A) conjugated to Dynabeads Protein G (Invitrogen). Beads were washed with high salt wash buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 0.1% SDS, 0.5% deoxycholate, 1% NP-40, 1 mM EDTA), incubated with T4 PNK (NEB) followed by 3’ linker ligation. After labeling RNA with 32P, the protein-RNA complex was fractionated in a 10% NuPAGE Bis-Tris gel (Invitrogen) and transferred to nitrocellulose. After autoradiography, protein-RNA complexes were excised and RNAs eluted from the membrane. After reverse transcription using Superscript III (Invitrogen) and primers containing 9 nucleotide barcodes (4 nucleotides for sample discrimination and 5 nucleotides to identify PCR duplicates), cDNAs were gel-purified, circularized with Circligase II (Epicentre) and cut using BamHI and a BamH1site-containing complementary oligonucleotide. Linearized cDNA was amplified using Phusion High-Fidelity PCR Master Mix (NEB) and sequenced on Illumina NEXTSeq.

value: H1 cell line

tag: passages

tag: clip antibody

value: EXOSC4 (Bethyl Laboratories, A303-775A


title: IgG_PAR_iCLIP

value: Purified Rabbit IgG (Bethyl Laboratories, P120-101)


title: Farber_126

tag: tissue


title: shEXOSC3 w/ dox 5 days

data_processing:
Base-calling by CASAVA v 1.8
Reads were processed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) to remove low-quality, short (< 16 nt) reads and adapters.
After removing reads mapping to rRNAs, >98% of reads aligned to the human genome (hg19/GRCh37) using TopHat (Kim et al., 2013). Differential expression analyses were performed using Cufflinks (Trapnell et al., 2010).
Genome_build: hg19

growth_protocol: Cells were cultured on Matrigel (BD Pharmingen)-coated plates under feeder-free conditions at 37°C in 5% CO2, 5% O2 and 90% humidity. Media consisted of Dulbecco’s modified Eagle medium (DMEM)/F12 (Invitrogen) supplemented with 1% MEM-nonessential amino acids (Invitrogen), 2 mM L-glutamine, 0.12 mM monothioglycerol, 0.5 mg/ml bovine serum albumin, 50 ng/mL basic fibroblast growth factor (Millipore), N2 supplements (1X), and B27 supplements (1X) (Invitrogen), 0.8 mg/ml puromycin. Media were changed every other day.

extract_protocol:
Total RNAs were extracted using Trizol Reagent. RNA integrity was verified on a 2100 Bioanalyzer (Agilent Technologies).
Libraries were prepared using ScriptSeq v2 RNA-Seq Library Preparation kits (Epicentre) and multiplexed with ScriptSeq Index PCR primers (Epicentre).  ERCC ExFold RNA Spike-In mix (Life Technologies) was added and rRNAs removed using Ribo-Zero (Epicentre).

treatment_protocol: shRNA transcription was induced with 2 mg/ml doxycycline for 5 or 7 days

tag: cell line


title: shEXOSC3 w/o dox 7 days


title: shNS control w/o dox 5 days


title: shEXOSC3 w/ dox 7 days


title: shNS control w/o dox 7 days


title: shNS control w/ dox 5 days


title: Farber_32


title: IgG_CLIP

data_processing:
base-calling with CASAVA v1.8
HITS-CLIP were preprocessed using Cutadapt (Martin, 2011) and FASTX-Toolkit to remove adaptors and low quality reads, collapsed to remove duplicates and split by barcodes.
Reads were then aligned to the hg19 genome using Novoalign. Since CLIP experiments can generate multiple mismatches and deletions within reads, the mapping stringency was lowered (-t 15,3 -l 20 -x 4 -g 20).
Bedgraph files were produced using Bedtools v 2.26.0
Genome_build: hg19

extract_protocol: HITS-CLIP was performed largely as described (Darnell, 2012), except that H1 cells were irradiated with 600 mJ/cm2 UV light (254 nm), 1 mM EDTA was added to PXL (PXL+E) to decrease exosome-mediated RNA degradation during the procedure, beads were washed 3 times with PXL + E, 3 times with 50 mM Tris-HCl pH 7.5, 400 mM NaCl, 1% NP-40, 1% deoxycholate, 0.1% SDS, 1 mM EDTA, 0.2 M urea, and 3 times with PNK buffer prior to using micrococcal nuclease to trim RNA tags.


title: Farber_128


title: EXOSC3_CLIP

value: EXOSC3 (Bethyl Laboratories, A303-909A


title: Adult mouse brain cortex, rep 12, ATAC-seq

city: La Jolla

first: Song

last: Chen

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

description:
2-month-old adult mouse
processed data file: Ad_BrainCortex_SNAREseq_chromatin.counts.mtx
processed data file: Ad_BrainCortex_SNAREseq_chromatin.peaks.tsv
processed data file: Ad_BrainCortex_SNAREseq_chromatin.barcodes.tsv

library_source: genomic

data_processing:
Basecalls performed using bcl2fastq v2.17
Reads with less than five T bases in the last nine bases of read 1 or a poor quality score (<10) were filtered out
Cell barcode and UMI information were inferred from the first 20 bases of read 1.
STAR v2.5 was used to align cDNA reads with reference genome.
Encode ATAC-seq pipeline (https://github.com/kundajelab/atac_dnase_pipelines) was used to trim and call peaks with paired-end chromatin reads as input.
Peak files were converted to Picard style interval_list file and overlapped with each mapped reads to assign reads with peak region.
Digital accessibility matrix or expression matrix was then generated with peak region or gene name as rows and cell barcodes as columns.
Genome_build: mm10
Supplementary_files_format_and_content: Sparse matrix with expression and accessibility counts values and tab-delimited text files showing barcodes and gene/peak names files for mouse brain cortex experiment.

source_name: mouse brain

extract_protocol:
Nuclei were extracted from adult mouse brain cortex by Nuclei EZ Prep kit.
RNA libraries were prepared for sequencing using standard Dropseq protocol. ATAC-seq libraries were prepared by amplifying beads captured chromatin fragments with dropseq P5_Tso and nextera index1 primers and gel size-selected for bands in the range of 225 bp and 1000 bp.

value: brain

tag: developmental stage

value: Adult (2 months)

tag: type

value: Nuclei


title: shNS control w/ dox 7 days


title: Adult mouse brain cortex, rep 11, ATAC-seq


title: Adult mouse brain cortex, rep 9, ATAC-seq


title: Adult mouse brain cortex, rep 10, ATAC-seq


title: Adult mouse brain cortex, rep 7, ATAC-seq


title: Adult mouse brain cortex, rep 6, ATAC-seq


title: Adult mouse brain cortex, rep 5, ATAC-seq


title: EXOSC4_CLIP

value: EXOSC4 (Bethyl Laboratories, A303-774A


title: Farber_230

source_name: isolated osteoblasts


title: Adult mouse brain cortex, rep 4, ATAC-seq


title: Adult mouse brain cortex, rep 3, ATAC-seq


title: Adult mouse brain cortex, rep 1, ATAC-seq


title: mEpiSCs

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

hyb_protocol: Following fragmentation, hybridization to the Mouse Gene 2.0 ST array (Affymetrix) were performed according to Affymetrix protocols.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: The data were summarized with RMA algorithm implemented in GeneSpring GX 12.6.1 software (Agilent Technologies).

source_name: mEpiSCs induced from EB3 mESCs

label_protocol: GeneChip WT PLUS Reagent kit was used according to Affymetrix protocol.

growth_protocol: mESCs were cultured in N2B27 containing 20 ng/ml ActivinA and 2μM PD0325901 (Activin+PD) or 2μM CHIR99021 and 2μM PD0325901 (2i) . mEpiSCs were cultured in N2B27 supplemented with 20 ng/ml ActivinA and 12 ng/ml bFGF

extract_protocol: Total RNAs were extracted using Qiagen RNeasy kit according to the manufacturer’s protocol. On-column DNase digestion was performed.

value: Mouse Embryonic Stem Cells (mESCs)


title: mESCs_Activin+PD

source_name: EB3 mESCs cultured in Activin+PD for 64 days


title: Ctrl_P3

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Cerebellum

extract_protocol:
Cerebellum was dissected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cerebellum

tag: development stage

tag: genotype


title: Prdm16 cKO_P3


title: mESCs_2i

source_name: EB3 mESCs cultured in 2i for 34 days


title: Adult mouse brain cortex, rep 8, ATAC-seq


title: H3K4me3_500_it_input_ESC

first: Chen

last: Li

address: Yihe Yuan Road No.5

department: Institute of Molecular Medicine

institute: Peking University

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Sequenced reads were trimmed and filtered by cutadapt (v 1.11) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "-N 1".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Peaks were called by MACS2 (v 2.1.1), with parameter of "--broad"
Bigwig files were generated from bam files using deeptools (v 2.2.3) bamCoverage. All samples were normalized to 10 million reads with binsize as 50 bp by “--scaleFactor, --binSize 50” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bigwig files. Bigwig files of replicates data could show the stability. Similarity among data of different cell magnitude reflected the applicability of itChIP-seq. H3K27me3-data and H3K4me4-data showed that signals could be detected in both active regions and repressed regions by itChIP.

source_name: cultured mESC (V6.5)

growth_protocol: Mouse embryonic stem cells were cultured in DMEM/F12 and neurobasal with 2i or 15% fetal bovine serum

extract_protocol:
Crosslinked cells were treated with 0.3% SDS at 37°C and followed by gentle sonication. Transposition was set up by incubation at 37°C for 1 h, followed by addition of stopping buffer. Soluble chromatin was used for following ChIP experiments.  DNA was eluted from beads, reverse crosslinked and treated with proteinase K. Finally, DNA was extracted by pheno-chloroform.
After PCR enrichment using NEBNext Q5 Ultra II master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

tag: cell type

value: cultured mESC (V6.5)

tag: fixed by

value: formaldehyde

tag: molecule subtype

value: input-DNA

tag: chip antibody


title: H3K4me3_10K_it_rep2_ESC

tag: strain

value: ChIP-DNA


title: H3K4me3_100_it_input_rep2_ESC


title: H3K4me3_500_it_rep2_ESC


title: H3K4me3_10K_it_EpiLC

source_name: cultured EpiLC

value: cultured EpiLC


title: H3K4me3_500_it_rep1_ESC


title: Adult mouse brain cortex, rep 2, ATAC-seq


title: H3K4me3_100_it_input_rep1_ESC


title: H3K4me3_1M_it_rep2_ESC


title: H3K4me3_1M_it_rep1_ESC


title: H3K4me3_10K_it_rep1_ESC


title: ESC_EpiLC_exp2_cell1152

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Sequenced reads were trimmed and filtered by cutadapt (v 1.11) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "-N 1".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Peaks were called by MACS2 (v 2.1.1), with parameter of "--broad"
Bigwig files were generated from bam files using deeptools (v 2.2.3) bamCoverage. All samples were normalized to 10 million reads with binsize as 50 bp by “--scaleFactor, --binSize 50” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bed files of non-duplicated reads.

source_name: cultured mESC_EpiLC

value: cultured mESC_EpiLC


title: ESC_EpiLC_exp2_cell1151


title: ESC_EpiLC_exp2_cell1150


title: ESC_EpiLC_exp2_cell1148


title: ESC_EpiLC_exp2_cell1149


title: ESC_EpiLC_exp2_cell1147


title: ESC_EpiLC_exp2_cell1146


title: Farber_66

value: osteoblast


title: ESC_EpiLC_exp2_cell1145


title: ESC_EpiLC_exp2_cell1143


title: ESC_EpiLC_exp2_cell1141


title: ESC_EpiLC_exp2_cell1140


title: Farber_129


title: ESC_EpiLC_exp2_cell1138


title: ESC_EpiLC_exp2_cell1137


title: ESC_EpiLC_exp2_cell1139


title: ESC_EpiLC_exp2_cell1133


title: ESC_EpiLC_exp2_cell1132


title: ESC_EpiLC_exp2_cell1135


title: ESC_EpiLC_exp2_cell1134


title: ESC_EpiLC_exp2_cell1136


title: ESC_EpiLC_exp2_cell1131


title: ESC_EpiLC_exp2_cell1130


title: ESC_EpiLC_exp2_cell1129


title: ESC_EpiLC_exp2_cell1142


title: ESC_EpiLC_exp2_cell1144


title: ESC_EpiLC_exp2_cell1127


title: Farber_264


title: Farber_354


title: ESC_EpiLC_exp2_cell1125


title: ESC_EpiLC_exp2_cell1123


title: ESC_EpiLC_exp2_cell1126


title: ESC_EpiLC_exp2_cell1122


title: ESC_EpiLC_exp2_cell1120


title: ESC_EpiLC_exp2_cell1118


title: ESC_EpiLC_exp2_cell1119


title: ESC_EpiLC_exp2_cell1117


title: Farber_368


title: ESC_EpiLC_exp2_cell1115


title: ESC_EpiLC_exp2_cell1114


title: ESC_EpiLC_exp2_cell1116


title: ESC_EpiLC_exp2_cell1113


title: ESC_EpiLC_exp2_cell1128


title: ESC_EpiLC_exp2_cell1108


title: ESC_EpiLC_exp2_cell1109


title: ESC_EpiLC_exp2_cell1112


title: ESC_EpiLC_exp2_cell1111


title: ESC_EpiLC_exp2_cell1110


title: ESC_EpiLC_exp2_cell1107


title: ESC_EpiLC_exp2_cell1106


title: ESC_EpiLC_exp2_cell1105


title: ESC_EpiLC_exp2_cell1124


title: ESC_EpiLC_exp2_cell1104


title: ESC_EpiLC_exp2_cell1101


title: ESC_EpiLC_exp2_cell1121


title: ESC_EpiLC_exp2_cell1103


title: ESC_EpiLC_exp2_cell1099


title: ESC_EpiLC_exp2_cell1097


title: Farber_12


title: ESC_EpiLC_exp2_cell1094


title: ESC_EpiLC_exp2_cell1092


title: ESC_EpiLC_exp2_cell1091


title: ESC_EpiLC_exp2_cell1093


title: ESC_EpiLC_exp2_cell1089


title: ESC_EpiLC_exp2_cell1090


title: ESC_EpiLC_exp2_cell1098


title: ESC_EpiLC_exp2_cell1088


title: ESC_EpiLC_exp2_cell1087


title: ESC_EpiLC_exp2_cell1096


title: ESC_EpiLC_exp2_cell1084


title: ESC_EpiLC_exp2_cell1085


title: ESC_EpiLC_exp2_cell1086


title: ESC_EpiLC_exp2_cell1082


title: ESC_EpiLC_exp2_cell1081


title: ESC_EpiLC_exp2_cell1083


title: ESC_EpiLC_exp2_cell1100


title: ESC_EpiLC_exp2_cell1078


title: ESC_EpiLC_exp2_cell1079


title: ESC_EpiLC_exp2_cell1077


title: ESC_EpiLC_exp2_cell1080


title: ESC_EpiLC_exp2_cell1095


title: ESC_EpiLC_exp2_cell1076


title: ESC_EpiLC_exp2_cell1068


title: ESC_EpiLC_exp2_cell1071


title: ESC_EpiLC_exp2_cell1075


title: ESC_EpiLC_exp2_cell1069


title: ESC_EpiLC_exp2_cell1067


title: ESC_EpiLC_exp2_cell1066


title: ESC_EpiLC_exp2_cell1073


title: ESC_EpiLC_exp2_cell1059


title: ESC_EpiLC_exp2_cell1065


title: ESC_EpiLC_exp2_cell1074


title: ESC_EpiLC_exp2_cell1061


title: ESC_EpiLC_exp2_cell1057


title: ESC_EpiLC_exp2_cell1056


title: ESC_EpiLC_exp2_cell1051


title: ESC_EpiLC_exp2_cell1053


title: ESC_EpiLC_exp2_cell1052


title: ESC_EpiLC_exp2_cell1058


title: ESC_EpiLC_exp2_cell1055


title: ESC_EpiLC_exp2_cell1072


title: ESC_EpiLC_exp2_cell1054


title: ESC_EpiLC_exp2_cell1063


title: Farber_226


title: ESC_EpiLC_exp2_cell1070


title: ESC_EpiLC_exp2_cell1060


title: ESC_EpiLC_exp2_cell1062


title: Farber_304


title: ESC_EpiLC_exp2_cell1050


title: ESC_EpiLC_exp2_cell1047


title: ESC_EpiLC_exp2_cell1049


title: ESC_EpiLC_exp2_cell1039


title: ESC_EpiLC_exp2_cell1046


title: ESC_EpiLC_exp2_cell1040


title: ESC_EpiLC_exp2_cell1042


title: ESC_EpiLC_exp2_cell1043


title: ESC_EpiLC_exp2_cell1037


title: ESC_EpiLC_exp2_cell1044


title: ESC_EpiLC_exp2_cell1038


title: ESC_EpiLC_exp2_cell1041


title: ESC_EpiLC_exp2_cell1064


title: ESC_EpiLC_exp2_cell1029


title: ESC_EpiLC_exp2_cell1028


title: ESC_EpiLC_exp2_cell1036


title: ESC_EpiLC_exp2_cell1030


title: ESC_EpiLC_exp2_cell1035


title: ESC_EpiLC_exp2_cell1027


title: ESC_EpiLC_exp2_cell1025


title: ESC_EpiLC_exp2_cell1031


title: ESC_EpiLC_exp2_cell1024


title: ESC_EpiLC_exp2_cell1026


title: ESC_EpiLC_exp2_cell1048


title: ESC_EpiLC_exp2_cell1045


title: ESC_EpiLC_exp2_cell1032


title: ESC_EpiLC_exp2_cell1023


title: ESC_EpiLC_exp2_cell1021


title: ESC_EpiLC_exp2_cell1033


title: ESC_EpiLC_exp2_cell1020


title: ESC_EpiLC_exp2_cell1017


title: ESC_EpiLC_exp2_cell1019


title: ESC_EpiLC_exp2_cell1012


title: ESC_EpiLC_exp2_cell1016


title: ESC_EpiLC_exp2_cell1013


title: ESC_EpiLC_exp2_cell1014


title: ESC_EpiLC_exp2_cell1018


title: ESC_EpiLC_exp2_cell1011


title: ESC_EpiLC_exp2_cell1102


title: ESC_EpiLC_exp2_cell1008


title: ESC_EpiLC_exp2_cell1007


title: ESC_EpiLC_exp2_cell1010


title: ESC_EpiLC_exp2_cell1015


title: ESC_EpiLC_exp2_cell1003


title: ESC_EpiLC_exp2_cell1004


title: ESC_EpiLC_exp2_cell1002


title: ESC_EpiLC_exp2_cell1001


title: ESC_EpiLC_exp2_cell1006


title: ESC_EpiLC_exp2_cell1000


title: ESC_EpiLC_exp2_cell998


title: ESC_EpiLC_exp2_cell997


title: ESC_EpiLC_exp2_cell995


title: ESC_EpiLC_exp2_cell996


title: ESC_EpiLC_exp2_cell994


title: ESC_EpiLC_exp2_cell1009


title: ESC_EpiLC_exp2_cell988


title: ESC_EpiLC_exp2_cell991


title: ESC_EpiLC_exp2_cell989


title: ESC_EpiLC_exp2_cell986


title: ESC_EpiLC_exp2_cell990


title: ESC_EpiLC_exp2_cell985


title: ESC_EpiLC_exp2_cell983


title: ESC_EpiLC_exp2_cell982


title: ESC_EpiLC_exp2_cell984


title: ESC_EpiLC_exp2_cell999


title: ESC_EpiLC_exp2_cell977


title: ESC_EpiLC_exp2_cell981


title: ESC_EpiLC_exp2_cell978


title: ESC_EpiLC_exp2_cell976


title: ESC_EpiLC_exp2_cell975


title: ESC_EpiLC_exp2_cell974


title: ESC_EpiLC_exp2_cell973


title: ESC_EpiLC_exp2_cell992


title: ESC_EpiLC_exp2_cell979


title: ESC_EpiLC_exp2_cell993


title: ESC_EpiLC_exp2_cell970


title: ESC_EpiLC_exp2_cell987


title: ESC_EpiLC_exp2_cell980


title: ESC_EpiLC_exp2_cell971


title: ESC_EpiLC_exp2_cell968


title: ESC_EpiLC_exp2_cell969


title: ESC_EpiLC_exp2_cell966


title: ESC_EpiLC_exp2_cell964


title: ESC_EpiLC_exp2_cell963


title: ESC_EpiLC_exp2_cell960


title: ESC_EpiLC_exp2_cell957


title: ESC_EpiLC_exp2_cell958


title: ESC_EpiLC_exp2_cell959


title: ESC_EpiLC_exp2_cell961


title: ESC_EpiLC_exp2_cell956


title: ESC_EpiLC_exp2_cell955


title: ESC_EpiLC_exp2_cell953


title: ESC_EpiLC_exp2_cell965


title: ESC_EpiLC_exp2_cell950


title: ESC_EpiLC_exp2_cell949


title: ESC_EpiLC_exp2_cell951


title: ESC_EpiLC_exp2_cell952


title: ESC_EpiLC_exp2_cell945


title: ESC_EpiLC_exp2_cell948


title: ESC_EpiLC_exp2_cell943


title: ESC_EpiLC_exp2_cell967


title: ESC_EpiLC_exp2_cell941


title: ESC_EpiLC_exp2_cell946


title: ESC_EpiLC_exp2_cell942


title: ESC_EpiLC_exp2_cell940


title: shEXOSC3 w/o dox 5 days

value: H1 cell line


title: ESC_EpiLC_exp2_cell939


title: ESC_EpiLC_exp2_cell938


title: ESC_EpiLC_exp2_cell937


title: ESC_EpiLC_exp2_cell947


title: ESC_EpiLC_exp2_cell936


title: ESC_EpiLC_exp2_cell933


title: ESC_EpiLC_exp2_cell944


title: ESC_EpiLC_exp2_cell928


title: ESC_EpiLC_exp2_cell929


title: ESC_EpiLC_exp2_cell931


title: ESC_EpiLC_exp2_cell930


title: ESC_EpiLC_exp2_cell932


title: ESC_EpiLC_exp2_cell935


title: ESC_EpiLC_exp2_cell927


title: ESC_EpiLC_exp2_cell934


title: ESC_EpiLC_exp2_cell926


title: ESC_EpiLC_exp2_cell921


title: ESC_EpiLC_exp2_cell925


title: ESC_EpiLC_exp2_cell924


title: ESC_EpiLC_exp2_cell923


title: ESC_EpiLC_exp2_cell922


title: ESC_EpiLC_exp2_cell919


title: ESC_EpiLC_exp2_cell918


title: ESC_EpiLC_exp2_cell917


title: ESC_EpiLC_exp2_cell913


title: ESC_EpiLC_exp2_cell914


title: ESC_EpiLC_exp2_cell915


title: ESC_EpiLC_exp2_cell912


title: ESC_EpiLC_exp2_cell916


title: ESC_EpiLC_exp2_cell911


title: ESC_EpiLC_exp2_cell909


title: ESC_EpiLC_exp2_cell920


title: ESC_EpiLC_exp2_cell907


title: ESC_EpiLC_exp2_cell908


title: ESC_EpiLC_exp2_cell906


title: ESC_EpiLC_exp2_cell905


title: ESC_EpiLC_exp2_cell903


title: ESC_EpiLC_exp2_cell1022


title: ESC_EpiLC_exp2_cell902


title: ESC_EpiLC_exp2_cell901


title: ESC_EpiLC_exp2_cell896


title: ESC_EpiLC_exp2_cell898


title: ESC_EpiLC_exp2_cell897


title: ESC_EpiLC_exp2_cell899


title: ESC_EpiLC_exp2_cell895


title: ESC_EpiLC_exp2_cell894


title: ESC_EpiLC_exp2_cell893


title: ESC_EpiLC_exp2_cell889


title: ESC_EpiLC_exp2_cell890


title: ESC_EpiLC_exp2_cell910


title: ESC_EpiLC_exp2_cell892


title: ESC_EpiLC_exp2_cell888


title: ESC_EpiLC_exp2_cell900


title: ESC_EpiLC_exp2_cell882


title: ESC_EpiLC_exp2_cell883


title: ESC_EpiLC_exp2_cell885


title: ESC_EpiLC_exp2_cell878


title: ESC_EpiLC_exp2_cell880


title: ESC_EpiLC_exp2_cell881


title: ESC_EpiLC_exp2_cell877


title: ESC_EpiLC_exp2_cell884


title: ESC_EpiLC_exp2_cell874


title: ESC_EpiLC_exp2_cell875


title: ESC_EpiLC_exp2_cell873


title: ESC_EpiLC_exp2_cell904


title: ESC_EpiLC_exp2_cell872


title: ESC_EpiLC_exp2_cell891


title: ESC_EpiLC_exp2_cell876


title: ESC_EpiLC_exp2_cell868


title: ESC_EpiLC_exp2_cell870


title: ESC_EpiLC_exp2_cell869


title: ESC_EpiLC_exp2_cell867


title: ESC_EpiLC_exp2_cell865


title: ESC_EpiLC_exp2_cell866


title: ESC_EpiLC_exp2_cell871


title: ESC_EpiLC_exp2_cell860


title: ESC_EpiLC_exp2_cell863


title: ESC_EpiLC_exp2_cell859


title: ESC_EpiLC_exp2_cell862


title: ESC_EpiLC_exp2_cell857


title: ESC_EpiLC_exp2_cell861


title: ESC_EpiLC_exp2_cell856


title: ESC_EpiLC_exp2_cell854


title: ESC_EpiLC_exp2_cell851


title: ESC_EpiLC_exp2_cell855


title: ESC_EpiLC_exp2_cell852


title: ESC_EpiLC_exp2_cell850


title: ESC_EpiLC_exp2_cell853


title: ESC_EpiLC_exp2_cell849


title: ESC_EpiLC_exp2_cell848


title: ESC_EpiLC_exp2_cell962


title: ESC_EpiLC_exp2_cell954


title: ESC_EpiLC_exp2_cell843


title: ESC_EpiLC_exp2_cell845


title: ESC_EpiLC_exp2_cell846


title: ESC_EpiLC_exp2_cell844


title: ESC_EpiLC_exp2_cell864


title: ESC_EpiLC_exp2_cell858


title: ESC_EpiLC_exp2_cell841


title: ESC_EpiLC_exp2_cell842


title: ESC_EpiLC_exp2_cell840


title: ESC_EpiLC_exp2_cell839


title: ESC_EpiLC_exp2_cell837


title: ESC_EpiLC_exp2_cell836


title: ESC_EpiLC_exp2_cell847


title: ESC_EpiLC_exp2_cell834


title: ESC_EpiLC_exp2_cell830


title: ESC_EpiLC_exp2_cell835


title: ESC_EpiLC_exp2_cell838


title: ESC_EpiLC_exp2_cell831


title: ESC_EpiLC_exp2_cell827


title: ESC_EpiLC_exp2_cell829


title: ESC_EpiLC_exp2_cell972


title: ESC_EpiLC_exp2_cell826


title: ESC_EpiLC_exp2_cell823


title: ESC_EpiLC_exp2_cell824


title: ESC_EpiLC_exp2_cell825


title: ESC_EpiLC_exp2_cell822


title: ESC_EpiLC_exp2_cell820


title: ESC_EpiLC_exp2_cell1034


title: ESC_EpiLC_exp2_cell821


title: ESC_EpiLC_exp2_cell817


title: ESC_EpiLC_exp2_cell818


title: ESC_EpiLC_exp2_cell833


title: ESC_EpiLC_exp2_cell832


title: ESC_EpiLC_exp2_cell819


title: ESC_EpiLC_exp2_cell816


title: ESC_EpiLC_exp2_cell815


title: ESC_EpiLC_exp2_cell828


title: ESC_EpiLC_exp2_cell813


title: ESC_EpiLC_exp2_cell811


title: ESC_EpiLC_exp2_cell814


title: ESC_EpiLC_exp2_cell812


title: ESC_EpiLC_exp2_cell810


title: ESC_EpiLC_exp2_cell809


title: ESC_EpiLC_exp2_cell808


title: ESC_EpiLC_exp2_cell1005


title: ESC_EpiLC_exp2_cell803


title: ESC_EpiLC_exp2_cell804


title: ESC_EpiLC_exp2_cell806


title: ESC_EpiLC_exp2_cell807


title: ESC_EpiLC_exp2_cell805


title: ESC_EpiLC_exp2_cell798


title: ESC_EpiLC_exp2_cell802


title: ESC_EpiLC_exp2_cell800


title: ESC_EpiLC_exp2_cell797


title: ESC_EpiLC_exp2_cell801


title: ESC_EpiLC_exp2_cell799


title: ESC_EpiLC_exp2_cell794


title: ESC_EpiLC_exp2_cell792


title: ESC_EpiLC_exp2_cell793


title: ESC_EpiLC_exp2_cell788


title: ESC_EpiLC_exp2_cell789


title: ESC_EpiLC_exp2_cell786


title: ESC_EpiLC_exp2_cell787


title: ESC_EpiLC_exp2_cell784


title: ESC_EpiLC_exp2_cell782


title: ESC_EpiLC_exp2_cell783


title: ESC_EpiLC_exp2_cell781


title: ESC_EpiLC_exp2_cell796


title: ESC_EpiLC_exp2_cell779


title: ESC_EpiLC_exp2_cell780


title: ESC_EpiLC_exp2_cell778


title: ESC_EpiLC_exp2_cell775


title: ESC_EpiLC_exp2_cell776


title: ESC_EpiLC_exp2_cell773


title: ESC_EpiLC_exp2_cell774


title: ESC_EpiLC_exp2_cell795


title: ESC_EpiLC_exp2_cell771


title: ESC_EpiLC_exp2_cell772


title: ESC_EpiLC_exp2_cell791


title: ESC_EpiLC_exp2_cell770


title: ESC_EpiLC_exp2_cell790


title: ESC_EpiLC_exp2_cell769


title: ESC_EpiLC_exp2_cell785


title: ESC_EpiLC_exp2_cell767


title: ESC_EpiLC_exp2_cell764


title: ESC_EpiLC_exp2_cell765


title: ESC_EpiLC_exp2_cell766


title: ESC_EpiLC_exp2_cell763


title: ESC_EpiLC_exp2_cell760


title: ESC_EpiLC_exp2_cell761


title: ESC_EpiLC_exp2_cell777


title: ESC_EpiLC_exp2_cell759


title: ESC_EpiLC_exp2_cell758


title: ESC_EpiLC_exp2_cell757


title: ESC_EpiLC_exp2_cell755


title: ESC_EpiLC_exp2_cell754


title: ESC_EpiLC_exp2_cell756


title: ESC_EpiLC_exp2_cell768


title: ESC_EpiLC_exp2_cell751


title: ESC_EpiLC_exp2_cell748


title: ESC_EpiLC_exp2_cell747


title: ESC_EpiLC_exp2_cell750


title: ESC_EpiLC_exp2_cell752


title: ESC_EpiLC_exp2_cell753


title: ESC_EpiLC_exp2_cell746


title: ESC_EpiLC_exp2_cell745


title: ESC_EpiLC_exp2_cell744


title: ESC_EpiLC_exp2_cell742


title: ESC_EpiLC_exp2_cell743


title: ESC_EpiLC_exp2_cell762


title: ESC_EpiLC_exp2_cell739


title: ESC_EpiLC_exp2_cell740


title: ESC_EpiLC_exp2_cell738


title: ESC_EpiLC_exp2_cell737


title: ESC_EpiLC_exp2_cell736


title: ESC_EpiLC_exp2_cell735


title: ESC_EpiLC_exp2_cell734


title: ESC_EpiLC_exp2_cell749


title: ESC_EpiLC_exp2_cell879


title: ESC_EpiLC_exp2_cell733


title: ESC_EpiLC_exp2_cell731


title: ESC_EpiLC_exp2_cell729


title: ESC_EpiLC_exp2_cell730


title: ESC_EpiLC_exp2_cell886


title: ESC_EpiLC_exp2_cell727


title: ESC_EpiLC_exp2_cell728


title: ESC_EpiLC_exp2_cell741


title: ESC_EpiLC_exp2_cell732


title: ESC_EpiLC_exp2_cell725


title: ESC_EpiLC_exp2_cell887


title: ESC_EpiLC_exp2_cell726


title: ESC_EpiLC_exp2_cell723


title: ESC_EpiLC_exp2_cell724


title: ESC_EpiLC_exp2_cell721


title: ESC_EpiLC_exp2_cell717


title: ESC_EpiLC_exp2_cell718


title: ESC_EpiLC_exp2_cell722


title: ESC_EpiLC_exp2_cell716


title: ESC_EpiLC_exp2_cell715


title: ESC_EpiLC_exp2_cell719


title: ESC_EpiLC_exp2_cell712


title: ESC_EpiLC_exp2_cell714


title: ESC_EpiLC_exp2_cell711


title: ESC_EpiLC_exp2_cell710


title: ESC_EpiLC_exp2_cell720


title: ESC_EpiLC_exp2_cell708


title: ESC_EpiLC_exp2_cell706


title: ESC_EpiLC_exp2_cell713


title: ESC_EpiLC_exp2_cell705


title: ESC_EpiLC_exp2_cell709


title: ESC_EpiLC_exp2_cell703


title: ESC_EpiLC_exp2_cell702


title: ESC_EpiLC_exp2_cell701


title: ESC_EpiLC_exp2_cell698


title: ESC_EpiLC_exp2_cell697


title: ESC_EpiLC_exp2_cell700


title: ESC_EpiLC_exp2_cell704


title: ESC_EpiLC_exp2_cell699


title: ESC_EpiLC_exp2_cell687


title: ESC_EpiLC_exp2_cell691


title: ESC_EpiLC_exp2_cell692


title: ESC_EpiLC_exp2_cell690


title: ESC_EpiLC_exp2_cell695


title: ESC_EpiLC_exp2_cell693


title: ESC_EpiLC_exp2_cell694


title: ESC_EpiLC_exp2_cell707


title: ESC_EpiLC_exp2_cell686


title: ESC_EpiLC_exp2_cell684


title: ESC_EpiLC_exp2_cell689


title: ESC_EpiLC_exp2_cell682


title: ESC_EpiLC_exp2_cell680


title: ESC_EpiLC_exp2_cell681


title: ESC_EpiLC_exp2_cell688


title: ESC_EpiLC_exp2_cell679


title: ESC_EpiLC_exp2_cell678


title: ESC_EpiLC_exp2_cell677


title: ESC_EpiLC_exp2_cell696


title: ESC_EpiLC_exp2_cell674


title: ESC_EpiLC_exp2_cell673


title: ESC_EpiLC_exp2_cell671


title: ESC_EpiLC_exp2_cell675


title: ESC_EpiLC_exp2_cell676


title: ESC_EpiLC_exp2_cell672


title: ESC_EpiLC_exp2_cell685


title: ESC_EpiLC_exp2_cell683


title: ESC_EpiLC_exp2_cell668


title: ESC_EpiLC_exp2_cell670


title: ESC_EpiLC_exp2_cell663


title: ESC_EpiLC_exp2_cell662


title: ESC_EpiLC_exp2_cell660


title: ESC_EpiLC_exp2_cell665


title: ESC_EpiLC_exp2_cell658


title: ESC_EpiLC_exp2_cell654


title: ESC_EpiLC_exp2_cell659


title: ESC_EpiLC_exp2_cell666


title: ESC_EpiLC_exp2_cell653


title: ESC_EpiLC_exp2_cell657


title: ESC_EpiLC_exp2_cell667


title: ESC_EpiLC_exp2_cell664


title: ESC_EpiLC_exp2_cell656


title: ESC_EpiLC_exp2_cell651


title: ESC_EpiLC_exp2_cell655


title: ESC_EpiLC_exp2_cell652


title: ESC_EpiLC_exp2_cell650


title: ESC_EpiLC_exp2_cell649


title: ESC_EpiLC_exp2_cell645


title: ESC_EpiLC_exp2_cell669


title: ESC_EpiLC_exp2_cell642


title: ESC_EpiLC_exp2_cell648


title: ESC_EpiLC_exp2_cell646


title: ESC_EpiLC_exp2_cell644


title: ESC_EpiLC_exp2_cell661


title: ESC_EpiLC_exp2_cell640


title: ESC_EpiLC_exp2_cell641


title: ESC_EpiLC_exp2_cell639


title: ESC_EpiLC_exp2_cell630


title: ESC_EpiLC_exp2_cell637


title: ESC_EpiLC_exp2_cell636


title: ESC_EpiLC_exp2_cell635


title: ESC_EpiLC_exp2_cell633


title: ESC_EpiLC_exp2_cell638


title: ESC_EpiLC_exp2_cell626


title: ESC_EpiLC_exp2_cell627


title: ESC_EpiLC_exp2_cell643


title: ESC_EpiLC_exp2_cell623


title: ESC_EpiLC_exp2_cell628


title: ESC_EpiLC_exp2_cell624


title: ESC_EpiLC_exp2_cell619


title: ESC_EpiLC_exp2_cell621


title: ESC_EpiLC_exp2_cell634


title: ESC_EpiLC_exp2_cell617


title: ESC_EpiLC_exp2_cell616


title: ESC_EpiLC_exp2_cell625


title: ESC_EpiLC_exp2_cell629


title: ESC_EpiLC_exp2_cell615


title: ESC_EpiLC_exp2_cell618


title: ESC_EpiLC_exp2_cell614


title: ESC_EpiLC_exp2_cell612


title: ESC_EpiLC_exp2_cell613


title: ESC_EpiLC_exp2_cell631


title: ESC_EpiLC_exp2_cell622


title: ESC_EpiLC_exp2_cell611


title: ESC_EpiLC_exp2_cell610


title: ESC_EpiLC_exp2_cell604


title: ESC_EpiLC_exp2_cell605


title: ESC_EpiLC_exp2_cell603


title: ESC_EpiLC_exp2_cell608


title: ESC_EpiLC_exp2_cell620


title: ESC_EpiLC_exp2_cell607


title: ESC_EpiLC_exp2_cell609


title: ESC_EpiLC_exp2_cell599


title: ESC_EpiLC_exp2_cell602


title: ESC_EpiLC_exp2_cell601


title: ESC_EpiLC_exp2_cell597


title: ESC_EpiLC_exp2_cell600


title: ESC_EpiLC_exp2_cell595


title: ESC_EpiLC_exp2_cell591


title: ESC_EpiLC_exp2_cell590


title: ESC_EpiLC_exp2_cell594


title: ESC_EpiLC_exp2_cell596


title: ESC_EpiLC_exp2_cell592


title: ESC_EpiLC_exp2_cell588


title: ESC_EpiLC_exp2_cell587


title: ESC_EpiLC_exp2_cell589


title: ESC_EpiLC_exp2_cell586


title: ESC_EpiLC_exp2_cell585


title: ESC_EpiLC_exp2_cell598


title: ESC_EpiLC_exp2_cell584


title: ESC_EpiLC_exp2_cell577


title: ESC_EpiLC_exp2_cell581


title: ESC_EpiLC_exp2_cell579


title: ESC_EpiLC_exp2_cell580


title: ESC_EpiLC_exp2_cell582


title: ESC_EpiLC_exp2_cell593


title: ESC_EpiLC_exp2_cell575


title: ESC_EpiLC_exp2_cell574


title: ESC_EpiLC_exp2_cell576


title: ESC_EpiLC_exp2_cell583


title: ESC_EpiLC_exp2_cell578


title: ESC_EpiLC_exp2_cell572


title: ESC_EpiLC_exp2_cell573


title: ESC_EpiLC_exp2_cell570


title: ESC_EpiLC_exp2_cell567


title: ESC_EpiLC_exp2_cell571


title: ESC_EpiLC_exp2_cell647


title: ESC_EpiLC_exp2_cell564


title: ESC_EpiLC_exp2_cell566


title: ESC_EpiLC_exp2_cell562